Author: [log in to unmask]
Date: Wed Apr 27 11:11:32 2016
New Revision: 4346

Log:
Merge in trunk to ecal geom dev branch so it is up to date.

Added:
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/MollerMonitoring.java
      - copied unchanged from r4345, java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/MollerMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/MuonCandidateMonitoring.java
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    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/VertexAnalysis.java
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    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/plots/
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    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/ClusterDiagnosticModule.java
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    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/DiagnosticsManagementDriver.java
      - copied unchanged from r4345, java/trunk/analysis/src/main/java/org/hps/analysis/trigger/DiagnosticsManagementDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/PairTriggerDiagnosticModule.java
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    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SinglesTriggerDiagnosticModule.java
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    java/branches/HPSJAVA-409/analysis/src/test/
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    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/beam/
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    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/AbstractConditionsObjectConverter.java
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    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalTimeWalk.java
      - copied unchanged from r4345, java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalTimeWalk.java
    java/branches/HPSJAVA-409/conditions/src/test/java/org/hps/conditions/beam/
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerFileVisitor.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DataType.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatAddFile.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatHelper.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileFormat.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileUtilities.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/LcioReconMetadataReader.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/MetadataWriter.java
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    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/PathFilter.java
      - copied unchanged from r4345, java/trunk/crawler/src/main/java/org/hps/crawler/PathFilter.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/Site.java
      - copied unchanged from r4345, java/trunk/crawler/src/main/java/org/hps/crawler/Site.java
    java/branches/HPSJAVA-409/crawler/src/main/python/
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    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-1_5mm-v3-4-fieldmap/HPS-EngRun2015-1_5mm-v3-4-fieldmap.lcdd
      - copied unchanged from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-1_5mm-v3-4-fieldmap/HPS-EngRun2015-1_5mm-v3-4-fieldmap.lcdd
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-0-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-0-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-1-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-1-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-2-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-2-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-3-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v3-5-3-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v4-4-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v4-4-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v5-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-EngRun2015-Nominal-v5-fieldmap/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-1_5mm-v4-4/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-1_5mm-v4-4/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-2mm-v4-4/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-2mm-v4-4/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-3mm-v4-4/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-3mm-v4-4/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-4mm-v4-4/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-4mm-v4-4/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-6pt6-v0/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-6pt6-v0/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-Nominal-v4-4/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-Nominal-v4-4/
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-PhysicsRun2016-Nominal-v4-4-fieldmap/
      - copied from r4345, java/trunk/detector-data/detectors/HPS-PhysicsRun2016-Nominal-v4-4-fieldmap/
    java/branches/HPSJAVA-409/job/src/main/java/org/hps/job/DatabaseConditionsManagerSetup.java
      - copied unchanged from r4345, java/trunk/job/src/main/java/org/hps/job/DatabaseConditionsManagerSetup.java
    java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTPulseFitPlots.java
      - copied unchanged from r4345, java/trunk/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTPulseFitPlots.java
    java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalFeeMonitor.java
      - copied unchanged from r4345, java/trunk/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalFeeMonitor.java
    java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/CosmicPMTFilter.java
      - copied unchanged from r4345, java/trunk/recon/src/main/java/org/hps/recon/filtering/CosmicPMTFilter.java
    java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/PulserSingle0Pair0TriggerFilterDriver.java
      - copied unchanged from r4345, java/trunk/recon/src/main/java/org/hps/recon/filtering/PulserSingle0Pair0TriggerFilterDriver.java
    java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/SvtHitMultiplicityFilter.java
      - copied unchanged from r4345, java/trunk/recon/src/main/java/org/hps/recon/filtering/SvtHitMultiplicityFilter.java
    java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/SvtRawHitMultiplicityFilter.java
      - copied unchanged from r4345, java/trunk/recon/src/main/java/org/hps/recon/filtering/SvtRawHitMultiplicityFilter.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractLoopAdapter.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/AbstractLoopAdapter.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordLoop.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/AbstractRecordLoop.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/TriggerConfigEvioProcessor.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/daqconfig/TriggerConfigEvioProcessor.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsUtilities.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/epics/EpicsUtilities.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventTagMask.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/evio/EventTagMask.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/svt/SvtConfigData.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/svt/SvtConfigData.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/svt/SvtConfigEvioProcessor.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/svt/SvtConfigEvioProcessor.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TiTimeOffsetCalculator.java
      - copied unchanged from r4345, java/trunk/record-util/src/main/java/org/hps/record/triggerbank/TiTimeOffsetCalculator.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TriggerConfigData.java
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    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TriggerType.java
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    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/util/
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/AbstractRunBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/DaoProvider.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/DatacatBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/DatacatUtilities.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EvioDataBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/LivetimeBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunDatabaseBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/SpreadsheetBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/SvtConfigDao.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/SvtConfigDaoImpl.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/TriggerConfigBuilder.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/TriggerConfigDao.java
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    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/TriggerConfigDaoImpl.java
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    java/branches/HPSJAVA-409/run-database/src/test/java/org/hps/run/database/RunBuilderTest.java
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/DataQualityRecon.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/FilterHitsPerSensor.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPair0.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015STRecon.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/baltzell/Cosmic.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/baltzell/EngineeringRun2015FullRecon.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/celentan/LedOnlineOfflineComparison.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EcalFeeViewer.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EngRun2015FullReconMC_FEE.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EngineeringRun2015EcalRecon_noTwalk.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/PhysicsRun2016_FEEIter_Filter.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/HPSReconNoReadout.lcsim
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    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/spaul/MollerBeamtilt.lcsim
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    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HpsHelicalTrackFit.java
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    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/SvtPlotUtils.java
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    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/straight/
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    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/byale/
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    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/LedOnlineDataDumpDriver.java
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    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/LedOnlineOfflineComparisonDriver.java
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    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/SVTPhaseOffsetReader.java
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      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/GblResidualDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/PrintEventInfoDriver.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/PrintEventInfoDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/alignment/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/alignment/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/apps/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/apps/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/daq/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/daq/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/gbl/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/gbl/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/testrun/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/testrun/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/tools/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/phansson/tools/
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/FindBiasOnRange.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/FindBiasOnRange.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ExtractFormFactors.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/ExtractFormFactors.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/FEESpectrumGenerator.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/FEESpectrumGenerator.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/FormFactor.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/FormFactor.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MottIntegral.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/MottIntegral.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MultipleScattering.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/MultipleScattering.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/RemoveDuplicateParticles.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/RemoveDuplicateParticles.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinningXY.java
      - copied unchanged from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinningXY.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/moller/
      - copied from r4345, java/trunk/users/src/main/java/org/hps/users/spaul/moller/
Removed:
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/AbstractConditionsObjectConverter.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerFileUtilities.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatUtilities.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileSet.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/LcioMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RunSummaryMap.java
    java/branches/HPSJAVA-409/datacat-client/
    java/branches/HPSJAVA-409/detector-model/target/classes/org/
    java/branches/HPSJAVA-409/detector-model/target/test-classes/org/
    java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtPlotUtils.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/job/
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfigEvioProcessor.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventCountProcessor.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventTagBitMask.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileMetadata.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataAdapter.java
    java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileMetadataProcessor.java
    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunDatabaseDaoFactory.java
    java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunProcessor.java
    java/branches/HPSJAVA-409/run-database/src/test/java/org/hps/run/database/TiTriggerOffsetTest.java
    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/DataQualityRecon_Pass2.lcsim
    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullReconMC_Pass2.lcsim
    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullRecon_Pass2.lcsim
    java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/HitRecon.lcsim
    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HPSTrack.java
    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLDriver.java
    java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HpsGblFitter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/AlignmentUtils.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/BeamCurrentData.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/Count.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DAQDeadTimeData.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DumpAIDATextFiles.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ECalExtrapolationDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/EcalHitMapPlots.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/GlobalParameter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/GlobalParameters.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/MPAlignmentInputCalculator.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ModuleMPAlignmentInput.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/PolarCount.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ROOTFlatTupleDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ReadSurveyRotations.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/RegExpMatcherTester.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ResLimit.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/RunMPAlignment.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/STUtils.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SimpleHPSConditions.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/StraightThroughAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/StripMPAlignmentInput.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SvtHeaderAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SvtHeaderMetaDataReaderDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SvtOldHeaderAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SvtOldHeaderDataInfo.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TestSort.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrackingGeometryChecker.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrigRateAna.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrigRateDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/WTrack.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/dataMCPlots.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ecalPlots.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/mergeSimpleAIDA.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/trigRate.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/analysis/
Modified:
    java/branches/HPSJAVA-409/   (props changed)
    java/branches/HPSJAVA-409/analysis/pom.xml
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalCellIDPrintDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalClusterPlots.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalHitPlots.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/FEEClusterPlotter.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalFADCPlotsDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalTriggerPlotsDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSMCParticlePlotsDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/DualThresholdSignalFitDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeHitSelectionDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeSignalFitDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/PrintGeometryDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripGoldenEventsDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripMollerEventsDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/DataTriggerSimDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerData.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerModule.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerDiagnosticDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerTurnOnDriver.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterEvent.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterMatchedPair.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterStatModule.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DetailedClusterEvent.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DiagnosticSnapshot.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/GeneralStatModule.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/RunDiagStats.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerDiagStats.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerEvent.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerStatModule.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/event/TriggerPlotsModule.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/ComponentUtils.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/OutputLogger.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Pair.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/PairTrigger.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/SinglesTrigger.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Trigger.java
    java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/TriggerDiagnosticUtil.java
    java/branches/HPSJAVA-409/conditions/   (props changed)
    java/branches/HPSJAVA-409/conditions/pom.xml
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObject.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObjectCollection.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectCollection.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectException.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsRecord.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/package-info.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AbstractCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AddCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/PrintCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/RunSummaryCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/TagCommand.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsRecordConverter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsTagConverter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConnectionParameters.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/Converter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConverterRegistry.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/DatabaseConditionsManager.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/package-info.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/dummy/DummyConditionsObjectConverter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/TestRunEcalConditionsConverter.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/package-info.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/run/RunSpreadsheet.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/DaqMapHandler.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/MotorPositionLoader.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/OpeningAngleLoader.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtBiasConditionsLoader.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsLoader.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java
    java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java
    java/branches/HPSJAVA-409/crawler/pom.xml
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/AidaMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatCrawler.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/EvioMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileFormatFilter.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDqmMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDstMetadataReader.java
    java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RunFilter.java
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-3/compact.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L2-3-4_tu_rw.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-2/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-HPS-EngRun2015-Nominal-v1-4-1-100k-L456_L123_L234_L345_L123_L456_tu_rwIter0Iter1Iter2Iter3Iter4Iter5.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-Proposal2014-v3-2pt2-0zOffset/compact.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v5/compact.xml
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    java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8/compact.xml
    java/branches/HPSJAVA-409/detector-data/detectors/HPSTestRunTracker2014-v0/compact.xml
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    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsSiSensor.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java
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    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java
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    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.java
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    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java
    java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.java
    java/branches/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java
    java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java
    java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java
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    java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java
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    java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java
    java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTest.xml
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    java/branches/HPSJAVA-409/detector-model/target/antrun/build-main.xml
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    java/branches/HPSJAVA-409/distribution/pom.xml
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    java/branches/HPSJAVA-409/ecal-event-display/pom.xml
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Association.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Cluster.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/EcalHit.java
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    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/EventDisplayOutputDriver.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/LCIOBridgeDriver.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/ActiveViewer.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/CalorimeterPanel.java
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    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/FileViewer.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PDataEventViewer.java
    java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PassiveViewer.java
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    java/branches/HPSJAVA-409/ecal-readout-sim/pom.xml
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    java/branches/HPSJAVA-409/ecal-recon/pom.xml
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    java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverter.java
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    java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalPedestalCalculator.java
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    java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/SimpleCosmicClusterer.java
    java/branches/HPSJAVA-409/evio/pom.xml
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    java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/DataQualityTest.lcsim
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    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitterDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfHit.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/RawPedestalComputator.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/StripChartTest.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/ClusterDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClusterICPosition.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClustererCosmics.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalRawConverter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/HPSEcalClusterIC.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/jeremym/EvioFileScanner.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ClusterAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/CountTriggersDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/EvioAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/FADCAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/HPSEcalDataPlotsDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/InvariantMassPairDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTEAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTETriggerPlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ParticleMCAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/PlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/RafoAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TridentTrackDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerPlotsModule.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerProcessAnalysisDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/AddPlots.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot1D.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot2D.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotFormatModule.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/InvariantMassPlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTEPlotFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTETriggerPlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/ParticleMCAnalysisPlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/RafoTridentFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/SingleTriggerPlotsFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TridentTrackFormatter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TriggerPlotsFormat.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FADCVariableTriggerFEEDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger2.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/LCIOReadScript.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/rate.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/ratesim.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/FilterMCBunches.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalAnalogPrintDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalDigitalPrintDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalRawTrackerHitPrintDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSGenericRawTrackerHitPrintDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/LCIOTrackAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/MergeMCBunches.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/SvtChargeIntegrator.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/TridentMCFilter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/ExamplePlotter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HPSTrackerHit.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HelicalTrackHitResidualsDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/SVTRawTrackerHitThresholdDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TrackExtrapolationAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TwoTrackAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/EcalScoringPlaneDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ExtrapolationAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/LheToStdhep.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/PlotUtils.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ReconstructedParticleChecker.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SharedHitAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtClusterAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtDataRates.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtHitCorrelations.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtQA.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackRecoEfficiency.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/TestRunTrackReconEfficiency.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/CmpGenToFittedTracksDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DataTrackerFakeHitDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/FastTrackResidualDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ParticleHelixProducer.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SimpleResiduals.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrackingReconstructionPlots.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TriggerTurnOnAnalysis.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TruthMomentumResolutionDriver.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/rafo/test1.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/GetChargeFromScalersMultirun.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/HitrateHistograms.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/PulserFilter.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/StyleUtil.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/SumEverything.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/BinGenerator.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/CustomBinning.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/DisplayHistograms.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/EcalUtil.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MakeHistograms.java
    java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinning.java
    java/branches/HPSJAVA-409/util/pom.xml
    java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/CalculateAcceptanceFromMadGraph.java
    java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/ConvertToStdhep.java
    java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/DumpLHEEventsToASCII.java
    java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/LCIOFilterDriver.java
    java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/MergeBunches.java

Modified: java/branches/HPSJAVA-409/analysis/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/pom.xml	(original)
+++ java/branches/HPSJAVA-409/analysis/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/analysis/</url>
@@ -21,4 +21,17 @@
             <artifactId>hps-recon</artifactId>
         </dependency>
     </dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <configuration>
+                    <excludes>
+                        <exclude>**/VertexAnalysisTest.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
 </project>

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java	Wed Apr 27 11:11:32 2016
@@ -7,10 +7,7 @@
 import java.sql.Statement;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Formatter;
 import java.util.logging.Level;
-import java.util.logging.LogRecord;
 import java.util.logging.Logger;
 
 import org.hps.conditions.api.TableMetaData;

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,7 @@
 package org.hps.analysis.dataquality;
 
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.HashMap;
@@ -7,7 +9,7 @@
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-
+import org.apache.commons.lang3.StringUtils;
 import org.hps.record.triggerbank.AbstractIntData;
 import org.hps.record.triggerbank.TIData;
 import org.lcsim.event.EventHeader;
@@ -23,8 +25,8 @@
  * calculateEndOfRunQuantities & printDQMData i.e. useful methods
  */
 public class DataQualityMonitor extends Driver {
-    
-    private static Logger LOGGER = Logger.getLogger(DataQualityMonitor.class.getPackage().getName());
+
+    private static final Logger LOGGER = Logger.getLogger(DataQualityMonitor.class.getPackage().getName());
 
     protected AIDA aida = AIDA.defaultInstance();
     protected DQMDatabaseManager manager;
@@ -38,6 +40,11 @@
     protected boolean outputPlots = false;
     protected String outputPlotDir = "DQMOutputPlots/";
 
+    protected PrintWriter tupleWriter = null;
+    protected String[] tupleVariables = {};
+    protected final Map<String, Double> tupleMap = new HashMap<String, Double>();
+    protected boolean cutTuple = false;
+
     String triggerType = "all";//allowed types are "" (blank) or "all", singles0, singles1, pairs0,pairs1
     public boolean isGBL = false;
 
@@ -58,7 +65,7 @@
     }
 
     public void setRunNumber(int run) {
-        this.runNumber = run;
+        DataQualityMonitor.runNumber = run;
     }
 
     public void setOverwriteDB(boolean overwrite) {
@@ -81,17 +88,15 @@
         this.outputPlotDir = dir;
     }
 
-    public void DataQualityMonitor() {
-
-    }
-
+    @Override
     public void endOfData() {
         calculateEndOfRunQuantities();
         fillEndOfRunPlots();
         printDQMData();
-        if (printDQMStrings)
+        if (printDQMStrings) {
             printDQMStrings();
-        LOGGER.info("Should I write to the database?  " + connectToDB);
+        }
+        LOGGER.info("Write to database =  " + connectToDB);
         if (connectToDB) {
             LOGGER.info("Connecting To Database...getting DQMDBManager");
             manager = DQMDatabaseManager.getInstance();
@@ -99,17 +104,21 @@
             boolean entryExists = false;
             try {
                 entryExists = checkRowExists();
-                if (entryExists)
+                if (entryExists) {
                     LOGGER.info("Found an existing run/reco entry in the dqm database; overwrite = " + overwriteDB);
+                }
             } catch (SQLException ex) {
                 Logger.getLogger(DataQualityMonitor.class.getName()).log(Level.SEVERE, null, ex);
             }
 
-            if (!entryExists)
+            if (!entryExists) {
                 makeNewRow();
+            }
             dumpDQMData();
         }
-
+        if (tupleWriter != null) {
+            tupleWriter.close();
+        }
     }
 
     private void makeNewRow() {
@@ -127,9 +136,7 @@
     private boolean checkRowExists() throws SQLException {
         String ins = "select * from dqm where " + getRunRecoString();
         ResultSet res = manager.selectQuery(ins);
-        if (res.next()) //this is a funny way of determining if the ResultSet has any entries
-            return true;
-        return false;
+        return res.next(); //this is a funny way of determining if the ResultSet has any entries
     }
 
     public boolean checkSelectionIsNULL(String var) throws SQLException {
@@ -137,8 +144,9 @@
         ResultSet res = manager.selectQuery(ins);
         res.next();
         double result = res.getDouble(var);
-        if (res.wasNull())
-            return true;
+        if (res.wasNull()) {
+            return true;
+        }
         LOGGER.info("checkSelectionIsNULL::" + var + " = " + result);
         return false;
     }
@@ -183,16 +191,21 @@
     }
 
     public boolean matchTriggerType(TIData triggerData) {
-        if (triggerType.contentEquals("") || triggerType.contentEquals("all"))
-            return true;
-        if (triggerData.isSingle0Trigger() && triggerType.contentEquals("singles0"))
-            return true;
-        if (triggerData.isSingle1Trigger() && triggerType.contentEquals("singles1"))
-            return true;
-        if (triggerData.isPair0Trigger() && triggerType.contentEquals("pairs0"))
-            return true;
-        if (triggerData.isPair1Trigger() && triggerType.contentEquals("pairs1"))
-            return true;
+        if (triggerType.contentEquals("") || triggerType.contentEquals("all")) {
+            return true;
+        }
+        if (triggerData.isSingle0Trigger() && triggerType.contentEquals("singles0")) {
+            return true;
+        }
+        if (triggerData.isSingle1Trigger() && triggerType.contentEquals("singles1")) {
+            return true;
+        }
+        if (triggerData.isPair0Trigger() && triggerType.contentEquals("pairs0")) {
+            return true;
+        }
+        if (triggerData.isPair1Trigger() && triggerType.contentEquals("pairs1")) {
+            return true;
+        }
         return false;
 
     }
@@ -201,14 +214,18 @@
         boolean match = true;
         if (event.hasCollection(GenericObject.class, "TriggerBank")) {
             List<GenericObject> triggerList = event.get(GenericObject.class, "TriggerBank");
-            for (GenericObject data : triggerList)
+            for (GenericObject data : triggerList) {
                 if (AbstractIntData.getTag(data) == TIData.BANK_TAG) {
                     TIData triggerData = new TIData(data);
                     if (!matchTriggerType(triggerData))//only process singles0 triggers...
+                    {
                         match = false;
+                    }
                 }
-        } else if (debug)
+            }
+        } else if (debug) {
             LOGGER.info(this.getClass().getSimpleName() + ":  No trigger bank found...running over all trigger types");
+        }
         return match;
     }
 
@@ -223,4 +240,42 @@
     public void printDQMStrings() {
     }
 
+    protected void writeTuple() {
+        for (String variable : tupleVariables) {
+            Double value = tupleMap.get(variable);
+            if (value == null) {
+                value = -9999.0;
+            }
+            if (variable.endsWith("/I") || variable.endsWith("/B")) {
+                tupleWriter.format("%d\t", Math.round(value));
+            } else {
+                tupleWriter.format("%f\t", value);
+            }
+        }
+        tupleWriter.println();
+        tupleMap.clear();
+    }
+
+    public void setTupleFile(String tupleFile) {
+        try {
+            tupleWriter = new PrintWriter(tupleFile);
+        } catch (FileNotFoundException e) {
+            tupleWriter = null;
+        }
+        tupleWriter.println(StringUtils.join(tupleVariables, ":"));
+//        for (String variable : tupleVariables) {
+//            tupleWriter.format("%s:", variable);
+//        }
+//        tupleWriter.println();
+    }
+
+    /**
+     * apply loose cuts to the tuple (cuts to be defined in the specific DQM
+     * driver)
+     *
+     * @param cutTuple
+     */
+    public void setCutTuple(boolean cutTuple) {
+        this.cutTuple = cutTuple;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java	Wed Apr 27 11:11:32 2016
@@ -8,6 +8,7 @@
 import java.util.logging.Logger;
 
 import org.apache.commons.math.stat.StatUtils;
+import org.hps.conditions.beam.BeamEnergy.BeamEnergyCollection;
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.Cluster;
@@ -73,7 +74,11 @@
     boolean fillHitPlots = true;
     String[] ecalQuantNames = {"avg_N_hits", "avg_Hit_Energy",
         "avg_N_clusters", "avg_N_hitsPerCluster", "avg_Cluster_Energy", "avg_ClusterTime"};
-    double maxE = 1.1;
+    
+    double maxFactor = 1.5;
+    
+   
+    
     private final String plotHitsDir = "EcalHits/";
     private final String plotClustersDir = "EcalClusters/";
     private final String plotFidCutDir = "FiducialCut/";
@@ -90,44 +95,49 @@
         this.clusterCollectionName = clusterCollectionName;
     }
 
+    
     public void setFillHitPlots(boolean fill) {
         this.fillHitPlots = fill;
     }
 
     @Override
     protected void detectorChanged(Detector detector) {
+        BeamEnergyCollection beamEnergyCollection = 
+            this.getConditionsManager().getCachedConditions(BeamEnergyCollection.class, "beam_energies").getCachedData();        
+        double beamEnergy = beamEnergyCollection.get(0).getBeamEnergy();
+        //this.getConditionsManager().getCachedConditions(org.hps.conditions.EcalChannelCollection.class, "ecal_channels").
         LOGGER.info("EcalMonitoring::detectorChanged  Setting up the plotter");
         aida.tree().cd("/");
         if (fillHitPlots) {
             // Setup hit plots.
             hitCountPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+ calibratedHitCollectionName + " Hit Count In Event", 40, -0.5, 39.5);
             hitTimePlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Time", 50, 0 * 4.0, 50 * 4.0);
-            hitEnergyPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Energy", 100, -0.1, maxE);
+            hitEnergyPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Energy", 100, -0.1, beamEnergy*maxFactor);
             fiducialHitCountPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Count with Fiducial Cut", 10, -0.5, 9.5);
-            fiducialEnergyPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Energy with Fiducial Cut", 100, -0.1, maxE);
+            fiducialEnergyPlot = aida.histogram1D(plotHitsDir + triggerType + "/"+calibratedHitCollectionName + " Hit Energy with Fiducial Cut", 100, -0.1, beamEnergy*maxFactor);
         }
         // Setup cluster plots
         clusterCountPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Count per Event", 10, -0.5, 9.5);
         clusterSizePlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Size", 10, -0.5, 9.5);
-        clusterEnergyPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Energy", 100, -0.1, maxE);
+        clusterEnergyPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Energy", 100, -0.1, beamEnergy*maxFactor);
         clusterTimes = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Seed Times", 400, 0, 4.0 * 50);
         clusterTimeMean = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Time Mean", 400, 0, 4.0 * 50);
         clusterTimeSigma = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Cluster Time Sigma", 100, 0, 10);
-        twoclusterTotEnergy = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Two Cluster Energy Sum", 100, 0, maxE);
-        twoclusterEnergyAsymmetry = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Two Cluster Energy Asymmetry", 100, 0, 1.0);
-        energyVsT = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs time", 400, 0.0, 200.0, 100, -0.1, maxE);
+        twoclusterTotEnergy = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Two Cluster Energy Sum", 100, 0, beamEnergy*maxFactor);
+        twoclusterEnergyAsymmetry = aida.histogram1D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Two Cluster Energy Asymmetry", 100, 0, beamEnergy*maxFactor);
+        energyVsT = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs time", 400, 0.0, 200.0, 100, -0.1, beamEnergy*maxFactor);
         xVsY = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " X vs Y (NHits >1)", 200, -200.0, 200.0, 85, -85.0, 85.0);
-        energyVsX = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs X", 50, 0, 1.6, 50, .0, 200.0);
-        energyVsY = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs Y", 50, 0, 1.6, 50, 20.0, 85.0);
-        pairsE1vsE2 = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + "Pair E1 vs E2", 50, 0, 2, 50, 0, 2);
+        energyVsX = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs X", 50, 0, maxFactor*beamEnergy, 50, .0, 200.0);
+        energyVsY = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + " Energy vs Y", 50, 0, maxFactor*beamEnergy, 50, 20.0, 85.0);
+        pairsE1vsE2 = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + "Pair E1 vs E2", 50, 0, beamEnergy*maxFactor, 50, 0, beamEnergy*maxFactor);
         pairsT1vsT2 = aida.histogram2D(plotClustersDir +  triggerType + "/"+clusterCollectionName + "Pair T1 vs T2", 200, 0, 100, 200, 0, 100);
         pairsDeltaT = aida.histogram1D(plotClustersDir + triggerType + "/" + clusterCollectionName + " Pair Time Difference", 100, -20.0, 20.0);
 
         fiducialClusterCountPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+plotFidCutDir + clusterCollectionName + " Cluster Count with Fiducal Cut", 10, -0.5, 9.5);
         fiducialClusterSizePlot = aida.histogram1D(plotClustersDir+  triggerType + "/" +plotFidCutDir + clusterCollectionName + " Cluster Size with Fiducal Cut", 10, -0.5, 9.5);
-        fiducialClusterEnergyPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+plotFidCutDir  + clusterCollectionName + " Cluster Energy with Fiducal Cut", 100, -0.1, maxE);
-        fiducialenergyVsY = aida.histogram2D(plotClustersDir +  triggerType + "/"+plotFidCutDir + clusterCollectionName + " Energy vs Y with Fiducial Cuts", 50, 0, 1.6, 50, 45.0, 85.0);
-        fiducialenergyVsX = aida.histogram2D(plotClustersDir+  triggerType + "/" +plotFidCutDir + clusterCollectionName + " Energy vs X with Fiducial Cuts", 50, 0, 1.6, 50, 0.0, 200.0);
+        fiducialClusterEnergyPlot = aida.histogram1D(plotClustersDir +  triggerType + "/"+plotFidCutDir  + clusterCollectionName + " Cluster Energy with Fiducal Cut", 100, -0.1, beamEnergy*maxFactor);
+        fiducialenergyVsY = aida.histogram2D(plotClustersDir +  triggerType + "/"+plotFidCutDir + clusterCollectionName + " Energy vs Y with Fiducial Cuts", 50, 0, beamEnergy*maxFactor, 50, 45.0, 85.0);
+        fiducialenergyVsX = aida.histogram2D(plotClustersDir+  triggerType + "/" +plotFidCutDir + clusterCollectionName + " Energy vs X with Fiducial Cuts", 50, 0, beamEnergy*maxFactor, 50, 0.0, 200.0);
 
     }
 
@@ -265,5 +275,5 @@
     public void printDQMStrings() {
 
     }
-
+    
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java	Wed Apr 27 11:11:32 2016
@@ -17,6 +17,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import org.hps.conditions.beam.BeamEnergy.BeamEnergyCollection;
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
@@ -60,9 +61,9 @@
     double sumdelY = 0.0;
     double sumEoverP = 0.0;
     private final String plotDir = "FinalStateParticles/";
-    double beamEnergy = 1.05; //GeV
+   // double beamEnergy = 1.05; //GeV
     double maxFactor = 1.5;
-    double feeMomentumCut = 0.8; //GeV
+    double feeMomentumCut = 0.75; //this number, multiplied by the beam energy, is the actual cut
 
     IHistogram1D elePx;
     IHistogram1D elePy;
@@ -97,12 +98,19 @@
     /* number of unassocaited tracks/event */
     IHistogram1D nUnAssTracksHisto;
     
+    
+   
     public void setFinalStateParticlesColName(String fsp) {
         this.finalStateParticlesColName = fsp;
     }
 
     @Override
     protected void detectorChanged(Detector detector) {
+        BeamEnergyCollection beamEnergyCollection = 
+            this.getConditionsManager().getCachedConditions(BeamEnergyCollection.class, "beam_energies").getCachedData();        
+        double beamEnergy = beamEnergyCollection.get(0).getBeamEnergy();
+        
+        
         LOGGER.info("Setting up the plotter");
         aida.tree().cd("/");
           String trkType="SeedTrack/";
@@ -111,24 +119,24 @@
        
         /*  Final State Particle Quantities   */
         /*  plot electron & positron momentum separately  */
-        elePx = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Px (GeV)", 100, -0.1, 0.200);
-        elePy = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Py (GeV)", 100, -0.1, 0.1);
+        elePx = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Px (GeV)", 100, -0.1*beamEnergy, 0.200*beamEnergy);
+        elePy = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Py (GeV)", 100, -0.1*beamEnergy, 0.1*beamEnergy);
         elePz = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Pz (GeV)", 100, 0, beamEnergy * maxFactor);
-        elePzBeam = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV)", 100, feeMomentumCut, beamEnergy * maxFactor);
-        elePzBeamTop = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV):  Top", 100, feeMomentumCut, beamEnergy * maxFactor);
-        elePzBeamBottom = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV):  Bottom", 100, feeMomentumCut, beamEnergy * maxFactor);
+        elePzBeam = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV)", 100, feeMomentumCut*beamEnergy, beamEnergy * maxFactor);
+        elePzBeamTop = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV):  Top", 100, feeMomentumCut*beamEnergy, beamEnergy * maxFactor);
+        elePzBeamBottom = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Beam Electrons Total P (GeV):  Bottom", 100, feeMomentumCut*beamEnergy, beamEnergy * maxFactor);
         elePTop = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Total P (GeV):  Top", 100, 0, beamEnergy * maxFactor);
         elePBottom = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Electron Total P (GeV):  Bottom", 100, 0, beamEnergy * maxFactor);
 
-        posPx = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Px (GeV)", 50, -0.1, 0.200);
-        posPy = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Py (GeV)", 50, -0.1, 0.1);
+        posPx = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Px (GeV)", 50, -0.1*beamEnergy, 0.200*beamEnergy);
+        posPy = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Py (GeV)", 50, -0.1*beamEnergy, 0.1*beamEnergy);
         posPz = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Pz (GeV)", 50, 0, beamEnergy * maxFactor);
         posPTop = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Total P (GeV):  Top", 100, 0, beamEnergy * maxFactor);
         posPBottom = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Positron Total P (GeV):  Bottom", 100, 0, beamEnergy * maxFactor);
 
         /*  photon quanties (...right now, just unassociated clusters) */
         nPhotonsHisto = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Number of photons per event", 15, 0, 15);
-        enePhoton = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Photon Energy (GeV)", 50, 0, 2.4);
+        enePhoton = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Photon Energy (GeV)", 50, 0, 2.4*beamEnergy);
         xPhoton = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Photon X position (mm)", 50, -200, 200);
         yPhoton = aida.histogram1D(plotDir +trkType+ triggerType + "/" + "Photon Y position (mm)", 50, -100, 100);
 

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java	Wed Apr 27 11:11:32 2016
@@ -19,6 +19,7 @@
 
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 
 import org.lcsim.util.aida.AIDA;
 
@@ -29,7 +30,7 @@
 public class PlotAndFitUtilities {
 
     private static Logger LOGGER = Logger.getLogger(PlotAndFitUtilities.class.getPackage().getName());
-    
+
     static private AIDA aida = AIDA.defaultInstance();
 
     /*
@@ -37,13 +38,15 @@
      *  copied from org.hps.monitoring.drivers.ecal.EcalMonitoringUtilities.java
      */
     static IPlotter plot(IPlotterFactory plotterFactory, IBaseHistogram histogram, IPlotterStyle style, boolean show) {
-        if (style == null)
+        if (style == null) {
             style = getPlotterStyle(histogram);
+        }
         IPlotter plotter = plotterFactory.create(histogram.title());
         plotter.createRegion();
         plotter.region(0).plot(histogram, style);
-        if (show)
+        if (show) {
             plotter.show();
+        }
         return plotter;
     }
 
@@ -52,8 +55,9 @@
      *  copied from org.hps.monitoring.drivers.ecal.EcalMonitoringUtilities.java
      */
     static void plot(IPlotter plotter, IBaseHistogram histogram, IPlotterStyle style, int region) {
-        if (style == null)
+        if (style == null) {
             style = getPlotterStyle(histogram);
+        }
         LOGGER.info("Putting plot in region " + region);
         plotter.region(region).plot(histogram, style);
 
@@ -64,8 +68,9 @@
      */
 
     static void plot(IPlotter plotter, IFunction function, IPlotterStyle style, int region) {
-        if (style == null)
+        if (style == null) {
             style = getPlotterStyle(function);
+        }
         LOGGER.info("Putting function in region " + region);
         plotter.region(region).plot(function, style);
     }
@@ -78,16 +83,17 @@
         StyleRegistry styleRegistry = StyleRegistry.getStyleRegistry();
         IStyleStore store = styleRegistry.getStore("DefaultStyleStore");
         IPlotterStyle style = null;
-        if ((histogram instanceof IHistogram1D) || (histogram instanceof ICloud1D) || (histogram instanceof IProfile1D))
+        if ((histogram instanceof IHistogram1D) || (histogram instanceof ICloud1D) || (histogram instanceof IProfile1D)) {
             style = store.getStyle("DefaultHistogram1DStyle");
-        else if ((histogram instanceof IHistogram2D) || (histogram instanceof IProfile2D)) {
+        } else if ((histogram instanceof IHistogram2D) || (histogram instanceof IProfile2D)) {
             style = store.getStyle("DefaultColorMapStyle");
             style.statisticsBoxStyle().setVisible(false);
             style.setParameter("hist2DStyle", "colorMap");
             style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
         }
-        if (style == null)
+        if (style == null) {
             throw new RuntimeException("A default style could not be found for " + histogram.title());
+        }
 
         //custom stuff...mg
         style.dataStyle().errorBarStyle().setVisible(false);
@@ -106,8 +112,9 @@
         IStyleStore store = styleRegistry.getStore("DefaultStyleStore");
         IPlotterStyle style = null;
         style = store.getStyle("DefaultFunctionStyle");
-        if (style == null)
+        if (style == null) {
             throw new RuntimeException("A default style could not be found for " + func.title());
+        }
         return style;
     }
 
@@ -122,10 +129,10 @@
         parameters[2] = histogram.rms();
         function.setParameters(parameters);
         IFitResult fitResult = null;
-         Logger minuitLogger = Logger.getLogger("org.freehep.math.minuit");
+        Logger minuitLogger = Logger.getLogger("org.freehep.math.minuit");
         minuitLogger.setLevel(Level.OFF);
         minuitLogger.info("minuit logger test");
-        
+
         try {
             fitResult = fitter.fit(histogram, function);
         } catch (RuntimeException e) {
@@ -142,4 +149,44 @@
         }
     }
 
+    private static final String nameStrip = "Tracker_TestRunModule_";
+
+    private static String getNiceSensorName(HpsSiSensor sensor) {
+        return sensor.getName().replaceAll(nameStrip, "")
+                .replace("module", "mod")
+                .replace("layer", "lyr")
+                .replace("sensor", "sens");
+    }
+
+    public static IHistogram1D getSensorPlot(String prefix, HpsSiSensor sensor) {
+        String hname = prefix + getNiceSensorName(sensor);
+        return aida.histogram1D(hname);
+    }
+
+//    private static IHistogram1D getSensorPlot(String prefix, String sensorName) {
+//        return aida.histogram1D(prefix + sensorName);
+//    }
+    public static IHistogram1D createSensorPlot(String prefix, HpsSiSensor sensor, int nchan, double min, double max) {
+        String hname = prefix + getNiceSensorName(sensor);
+        IHistogram1D hist = aida.histogram1D(hname, nchan, min, max);
+        hist.setTitle(getNiceSensorName(sensor));
+
+        return hist;
+    }
+
+    public static IHistogram2D getSensorPlot2D(String prefix, HpsSiSensor sensor) {
+        String hname = prefix + getNiceSensorName(sensor);
+        return aida.histogram2D(hname);
+    }
+
+    public static IHistogram2D createSensorPlot2D(String prefix, HpsSiSensor sensor, int nchanX, double minX, double maxX, int nchanY, double minY, double maxY) {
+        String hname = prefix + getNiceSensorName(sensor);
+        IHistogram2D hist = aida.histogram2D(hname, nchanX, minX, maxX, nchanY, minY, maxY);
+        hist.setTitle(sensor.getName().replaceAll(nameStrip, "")
+                .replace("module", "mod")
+                .replace("layer", "lyr")
+                .replace("sensor", "sens"));
+
+        return hist;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	Wed Apr 27 11:11:32 2016
@@ -38,7 +38,7 @@
  */
 //TODO:  add some more quantities to DQM database:  <t0> or <sigma>_t0 for intime events;  <chi^2>, <amplitude> etc
 public class SvtMonitoring extends DataQualityMonitor {
-    
+
     private static Logger LOGGER = Logger.getLogger(SvtMonitoring.class.getPackage().getName());
 
     private String rawTrackerHitCollectionName = "SVTRawTrackerHits";
@@ -90,22 +90,22 @@
         aida.tree().cd("/");
         for (HpsSiSensor sensor : sensors) {
             //IHistogram1D occupancyPlot = aida.histogram1D(sensor.getName().replaceAll("Tracker_TestRunModule_", ""), 640, 0, 639);
-            IHistogram1D occupancyPlot = createSensorPlot(plotDir + triggerType + "/"+"occupancy_", sensor, maxChannels, 0, maxChannels - 1);
-            IHistogram1D t0Plot = createSensorPlot(plotDir + triggerType + "/"+"t0Hit_", sensor, 400, -100., 100.);
-            IHistogram1D nHits = createSensorPlot(plotDir + triggerType + "/"+"nHitsPerEvent_", sensor, 100, -0.5, 99.5);
-            IHistogram1D pileup = createSensorPlot(plotDir + triggerType + "/"+"nFitsPerHit_", sensor, 3, 0.5, 3.5);
-
-            IHistogram1D amplitudePlot = createSensorPlot(plotDir + triggerType + "/"+"amplitude_", sensor, 50, 0, 4000.0);
-            IHistogram2D t0AmpPlot = createSensorPlot2D(plotDir + triggerType + "/"+"t0AmpHit_", sensor, 200, -100., 100., 50, 0, 4000.0);
-            IHistogram2D t0ChanPlot = createSensorPlot2D(plotDir + triggerType + "/"+"t0ChanBigHit_", sensor, 640, -0.5, 639.5, 200, -100., 100.);
-            IHistogram2D ampChanPlot = createSensorPlot2D(plotDir + triggerType + "/"+"ampChanHit_", sensor, 640, -0.5, 639.5, 50, 0, 4000);
-            IHistogram2D chiprobChanPlot = createSensorPlot2D(plotDir + triggerType + "/"+"chiprobChanBigHit_", sensor, 640, -0.5, 639.5, 50, 0, 1.0);
-            IHistogram2D t0TrigTimeHitPlot = createSensorPlot2D(plotDir + triggerType + "/"+"t0BigHitTrigTime_", sensor, 400, -100., 100., 6, 0, 24);
-
-            IHistogram1D chiProbPlot = createSensorPlot(plotDir + triggerType + "/"+"chiProb_", sensor, 50, 0, 1.0);
-            IHistogram1D t0ClusterPlot = createSensorPlot(plotDir + triggerType + "/"+"t0Cluster_", sensor, 400, -100., 100.);
-            IHistogram2D t0TrigTimePlot = createSensorPlot2D(plotDir + triggerType + "/"+"t0ClusterTrigTime_", sensor, 400, -100., 100., 6, 0, 24);
-            IHistogram1D dedxClusterPlot = createSensorPlot(plotDir + triggerType + "/"+"electrons_", sensor, 50, 0., 10.);
+            IHistogram1D occupancyPlot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "occupancy_", sensor, maxChannels, 0, maxChannels - 1);
+            IHistogram1D t0Plot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "t0Hit_", sensor, 400, -100., 100.);
+            IHistogram1D nHits = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "nHitsPerEvent_", sensor, 100, -0.5, 99.5);
+            IHistogram1D pileup = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "nFitsPerHit_", sensor, 3, 0.5, 3.5);
+
+            IHistogram1D amplitudePlot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "amplitude_", sensor, 50, 0, 4000.0);
+            IHistogram2D t0AmpPlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "t0AmpHit_", sensor, 200, -100., 100., 50, 0, 4000.0);
+            IHistogram2D t0ChanPlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "t0ChanBigHit_", sensor, 640, -0.5, 639.5, 200, -100., 100.);
+            IHistogram2D ampChanPlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "ampChanHit_", sensor, 640, -0.5, 639.5, 50, 0, 4000);
+            IHistogram2D chiprobChanPlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "chiprobChanBigHit_", sensor, 640, -0.5, 639.5, 50, 0, 1.0);
+            IHistogram2D t0TrigTimeHitPlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "t0BigHitTrigTime_", sensor, 400, -100., 100., 6, 0, 24);
+
+            IHistogram1D chiProbPlot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "chiProb_", sensor, 50, 0, 1.0);
+            IHistogram1D t0ClusterPlot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "t0Cluster_", sensor, 400, -100., 100.);
+            IHistogram2D t0TrigTimePlot = PlotAndFitUtilities.createSensorPlot2D(plotDir + triggerType + "/" + "t0ClusterTrigTime_", sensor, 400, -100., 100., 6, 0, 24);
+            IHistogram1D dedxClusterPlot = PlotAndFitUtilities.createSensorPlot(plotDir + triggerType + "/" + "electrons_", sensor, 50, 0., 10.);
             occupancyPlot.reset();
         }
 
@@ -116,10 +116,11 @@
 
     public void process(EventHeader event) {
 
-          //check to see if this event is from the correct trigger (or "all");
-        if (!matchTrigger(event))
+        //check to see if this event is from the correct trigger (or "all");
+        if (!matchTrigger(event)) {
             return;
-        
+        }
+
         /*  increment the strip occupancy arrays */
         Map<String, Integer> hitsPerSensor = new HashMap<String, Integer>();
 
@@ -140,7 +141,7 @@
             ++eventCountRaw;
         }
         for (HpsSiSensor sensor : sensors) {
-            IHistogram1D sensorHist = getSensorPlot(plotDir + triggerType + "/"+"nHitsPerEvent_", sensor);
+            IHistogram1D sensorHist = PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "nHitsPerEvent_", sensor);
             Integer nHits = hitsPerSensor.get(sensor.getName());
             if (nHits == null) {
                 sensorHist.fill(0);
@@ -161,22 +162,22 @@
                 RawTrackerHit rth = (RawTrackerHit) hit.getFrom();
                 GenericObject pars = (GenericObject) hit.getTo();
 
-                String sensorName = getNiceSensorName((HpsSiSensor) rth.getDetectorElement());
+                HpsSiSensor sensor = ((HpsSiSensor) rth.getDetectorElement());
                 //this is a clever way to get the parameters we want from the generic object
                 double t0 = ShapeFitParameters.getT0(pars);
                 double amp = ShapeFitParameters.getAmp(pars);
                 double chiProb = ShapeFitParameters.getChiProb(pars);
                 int channel = rth.getIdentifierFieldValue("strip");
-                getSensorPlot(plotDir + triggerType + "/"+"nFitsPerHit_", sensorName).fill(rthtofit.allFrom(rth).size());
-                getSensorPlot(plotDir + triggerType + "/"+"t0Hit_", sensorName).fill(t0);
-                getSensorPlot(plotDir + triggerType + "/"+"amplitude_", sensorName).fill(amp);
-                getSensorPlot2D(plotDir + triggerType + "/"+"t0AmpHit_", sensorName).fill(t0, amp);
-                getSensorPlot(plotDir + triggerType + "/"+"chiProb_", sensorName).fill(chiProb);
-                getSensorPlot2D(plotDir + triggerType + "/"+"ampChanHit_", sensorName).fill(channel, amp);
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "nFitsPerHit_", sensor).fill(rthtofit.allFrom(rth).size());
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "t0Hit_", sensor).fill(t0);
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "amplitude_", sensor).fill(amp);
+                PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "t0AmpHit_", sensor).fill(t0, amp);
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "chiProb_", sensor).fill(chiProb);
+                PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "ampChanHit_", sensor).fill(channel, amp);
                 if (amp > 1000.0) {
-                    getSensorPlot2D(plotDir + triggerType + "/"+"t0ChanBigHit_", sensorName).fill(channel, t0);
-                    getSensorPlot2D(plotDir + triggerType + "/"+"chiprobChanBigHit_", sensorName).fill(channel, chiProb);
-                    getSensorPlot2D(plotDir + triggerType + "/"+"t0BigHitTrigTime_", sensorName).fill(t0, event.getTimeStamp() % 24);
+                    PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "t0ChanBigHit_", sensor).fill(channel, t0);
+                    PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "chiprobChanBigHit_", sensor).fill(channel, chiProb);
+                    PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "t0BigHitTrigTime_", sensor).fill(t0, event.getTimeStamp() % 24);
                 }
             }
             ++eventCountFit;
@@ -186,55 +187,15 @@
 //            LOGGER.info("Found a Si cluster collection");
             List<TrackerHit> siClusters = (List<TrackerHit>) event.get(trackerHitCollectionName);
             for (TrackerHit cluster : siClusters) {
-                String sensorName = getNiceSensorName((HpsSiSensor) ((RawTrackerHit) cluster.getRawHits().get(0)).getDetectorElement());
+                HpsSiSensor sensor = (HpsSiSensor) ((RawTrackerHit) cluster.getRawHits().get(0)).getDetectorElement();
                 double t0 = cluster.getTime();
                 double dedx = cluster.getdEdx() * 1e6;
 //                LOGGER.info("dedx = "+dedx);
-                getSensorPlot(plotDir + triggerType + "/"+"t0Cluster_", sensorName).fill(t0);
-                getSensorPlot2D(plotDir + triggerType + "/"+"t0ClusterTrigTime_", sensorName).fill(t0, event.getTimeStamp() % 24);
-                getSensorPlot(plotDir + triggerType + "/"+"electrons_", sensorName).fill(dedx);
-            }
-        }
-    }
-
-    private IHistogram1D getSensorPlot(String prefix, HpsSiSensor sensor) {
-        String hname = prefix + getNiceSensorName(sensor);
-        return aida.histogram1D(hname);
-    }
-
-    private IHistogram1D getSensorPlot(String prefix, String sensorName) {
-        return aida.histogram1D(prefix + sensorName);
-    }
-
-    private IHistogram1D createSensorPlot(String prefix, HpsSiSensor sensor, int nchan, double min, double max) {
-        String hname = prefix + getNiceSensorName(sensor);
-        IHistogram1D hist = aida.histogram1D(hname, nchan, min, max);
-        hist.setTitle(sensor.getName().replaceAll(nameStrip, "")
-                .replace("module", "mod")
-                .replace("layer", "lyr")
-                .replace("sensor", "sens"));
-
-        return hist;
-    }
-
-    private IHistogram2D getSensorPlot2D(String prefix, HpsSiSensor sensor) {
-        String hname = prefix + getNiceSensorName(sensor);
-        return aida.histogram2D(hname);
-    }
-
-    private IHistogram2D getSensorPlot2D(String prefix, String sensorName) {
-        return aida.histogram2D(prefix + sensorName);
-    }
-
-    private IHistogram2D createSensorPlot2D(String prefix, HpsSiSensor sensor, int nchanX, double minX, double maxX, int nchanY, double minY, double maxY) {
-        String hname = prefix + getNiceSensorName(sensor);
-        IHistogram2D hist = aida.histogram2D(hname, nchanX, minX, maxX, nchanY, minY, maxY);
-        hist.setTitle(sensor.getName().replaceAll(nameStrip, "")
-                .replace("module", "mod")
-                .replace("layer", "lyr")
-                .replace("sensor", "sens"));
-
-        return hist;
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "t0Cluster_", sensor).fill(t0);
+                PlotAndFitUtilities.getSensorPlot2D(plotDir + triggerType + "/" + "t0ClusterTrigTime_", sensor).fill(t0, event.getTimeStamp() % 24);
+                PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "electrons_", sensor).fill(dedx);
+            }
+        }
     }
 
     private void resetOccupancyMap() {
@@ -279,7 +240,7 @@
         for (HpsSiSensor sensor : sensors) {
             Double avg = 0.0;
             //IHistogram1D sensorHist = aida.histogram1D(sensor.getName());
-            IHistogram1D sensorHist = getSensorPlot(plotDir + triggerType + "/"+"occupancy_", sensor);
+            IHistogram1D sensorHist = PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "occupancy_", sensor);
             sensorHist.reset();
             int[] strips = occupancyMap.get(sensor.getName());
             for (int i = 0; i < strips.length; i++) {
@@ -314,7 +275,7 @@
         int irTop = 0;
         int irBot = 0;
         for (HpsSiSensor sensor : sensors) {
-            IHistogram1D sensPlot = getSensorPlot(plotDir + triggerType + "/"+"t0Hit_", sensor);
+            IHistogram1D sensPlot = PlotAndFitUtilities.getSensorPlot(plotDir + triggerType + "/" + "t0Hit_", sensor);
             IFitResult result = fitGaussian(sensPlot, fitter, "range=\"(-8.0,8.0)\"");
 
             boolean isTop = sensor.isTopLayer();
@@ -362,9 +323,9 @@
     @Override
     public void printDQMData() {
         for (HpsSiSensor sensor : sensors) {
-            LOGGER.info(avgOccupancyNames.get(sensor.getName()) + "  " +triggerType+" " + avgOccupancyMap.get(sensor.getName()));
-            LOGGER.info(avgt0Names.get(sensor.getName()) + "  " +triggerType+" " + avgt0Map.get(sensor.getName()));
-            LOGGER.info(sigt0Names.get(sensor.getName()) + "  " +triggerType+" " + sigt0Map.get(sensor.getName()));
+            LOGGER.info(avgOccupancyNames.get(sensor.getName()) + "  " + triggerType + " " + avgOccupancyMap.get(sensor.getName()));
+            LOGGER.info(avgt0Names.get(sensor.getName()) + "  " + triggerType + " " + avgt0Map.get(sensor.getName()));
+            LOGGER.info(sigt0Names.get(sensor.getName()) + "  " + triggerType + " " + sigt0Map.get(sensor.getName()));
         }
     }
 

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	Wed Apr 27 11:11:32 2016
@@ -8,16 +8,17 @@
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
-
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 import java.util.logging.Logger;
-
 import org.hps.recon.tracking.CoordinateTransformations;
 import org.hps.recon.tracking.TrackUtils;
+import org.hps.recon.tracking.gbl.GBLKinkData;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
+import org.lcsim.event.GenericObject;
 import org.lcsim.event.LCRelation;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.event.RelationalTable;
@@ -37,7 +38,7 @@
 public class TrackingMonitoring extends DataQualityMonitor {
 
     private static Logger LOGGER = Logger.getLogger(SvtMonitoring.class.getPackage().getName());
-    
+
     private String helicalTrackHitCollectionName = "HelicalTrackHits";
     private final String rotatedTrackHitCollectionName = "RotatedHelicalTrackHits";
     private final String helicalTrackHitRelationsCollectionName = "HelicalTrackHitRelations";
@@ -64,6 +65,7 @@
     private final String botDir = "Bottom/";
     private final String hthplotDir = "HelicalTrackHits/";
     private final String timeresidDir = "HitTimeResiduals/";
+    private final String kinkDir = "Kinks/";
     String[] trackingQuantNames = {"avg_N_tracks", "avg_N_hitsPerTrack", "avg_d0", "avg_z0", "avg_absslope", "avg_chi2"};
     int nmodules = 6;
     IHistogram1D[] hthTop = new IHistogram1D[nmodules];
@@ -163,7 +165,8 @@
     IHistogram2D chi2VsLambda;
     IHistogram2D chi2VsZ0;
 
-    IHistogram2D beamAngle2D;
+    IHistogram2D beamAngleXY;
+    IHistogram2D beamAngleThetaPhi;
 
     IHistogram1D L1Iso;
     IHistogram1D L12Iso;
@@ -286,7 +289,8 @@
         chi2VsLambda = aida.histogram2D(plotDir + trackCollectionName + "/" + triggerType + "/" + "chi2 vs lambda", 50, -lambdaCut, lambdaCut, 50, 0.0, 50.0);
         chi2VsZ0 = aida.histogram2D(plotDir + trackCollectionName + "/" + triggerType + "/" + "chi2 vs z0", 50, -z0Cut, z0Cut, 50, 0.0, 50.0);
 
-        beamAngle2D = aida.histogram2D(plotDir + trackCollectionName + "/" + triggerType + "/" + "angles around beam axis: theta vs phi", 100, -Math.PI, Math.PI, 100, 0, 0.25);
+        beamAngleXY = aida.histogram2D(plotDir + trackCollectionName + "/" + triggerType + "/" + "angles around beam axis: theta_y vs theta_x", 100, -0.1, 0.1, 100, -0.1, 0.1);
+        beamAngleThetaPhi = aida.histogram2D(plotDir + trackCollectionName + "/" + triggerType + "/" + "angles around beam axis: theta vs phi", 100, -Math.PI, Math.PI, 100, 0, 0.25);
 
         L1Iso = aida.histogram1D(plotDir + trackCollectionName + "/" + triggerType + "/" + "L1 isolation", 100, -5.0, 5.0);
         L12Iso = aida.histogram1D(plotDir + trackCollectionName + "/" + triggerType + "/" + "L1-2 isolation", 100, -5.0, 5.0);
@@ -300,9 +304,12 @@
         aida.tree().cd("/");
         for (HpsSiSensor sensor : sensors) {
             //IHistogram1D occupancyPlot = aida.histogram1D(sensor.getName().replaceAll("Tracker_TestRunModule_", ""), 640, 0, 639);
-            IHistogram1D hitTimeResidual = createSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", sensor, 100, -20, 20);
-        }
-
+            IHistogram1D hitTimeResidual = PlotAndFitUtilities.createSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", sensor, 100, -20, 20);
+            IHistogram1D lambdaKink = PlotAndFitUtilities.createSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "lambdaKink_", sensor, 100, -5e-3, 5e-3);
+            IHistogram1D phiKink = PlotAndFitUtilities.createSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "phiKink_", sensor, 100, -5e-3, 5e-3);
+            IHistogram2D lambdaKink2D = PlotAndFitUtilities.createSensorPlot2D(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "lambdaKinkVsOmega_", sensor, 100, -omegaCut, omegaCut, 100, -5e-3, 5e-3);
+            IHistogram2D phiKink2D = PlotAndFitUtilities.createSensorPlot2D(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "phiKinkVsOmega_", sensor, 100, -omegaCut, omegaCut, 100, -5e-3, 5e-3);
+        }
     }
 
     @Override
@@ -366,9 +373,8 @@
         int cntPos = 0;
         int cntTop = 0;
         int cntBot = 0;
-        double ecalFace = 1393.0;//mm
         for (Track trk : tracks) {
-            Hep3Vector trackPosAtEcalFace = TrackUtils.extrapolateTrack(trk, ecalFace);
+            Hep3Vector trackPosAtEcalFace = TrackUtils.getTrackPositionAtEcal(trk);
             double xAtECal = trackPosAtEcalFace.x();
             double yAtECal = trackPosAtEcalFace.y();
             if (yAtECal > 0) {
@@ -385,7 +391,7 @@
             double sinphi0 = Math.sin(trk.getTrackStates().get(0).getPhi());
             double omega = trk.getTrackStates().get(0).getOmega();
             double lambda = trk.getTrackStates().get(0).getTanLambda();
-            double z0 = trk.getTrackStates().get(0).getZ0();            
+            double z0 = trk.getTrackStates().get(0).getZ0();
             trkChi2.fill(trk.getChi2());
             nHits.fill(trk.getTrackerHits().size());
             trackNhitsVsChi2.fill(trk.getChi2(), trk.getTrackerHits().size());
@@ -418,7 +424,8 @@
             double beamPhi = Math.atan2(dirRotated.y(), dirRotated.x());
             double beamTheta = Math.acos(dirRotated.z());
 
-            beamAngle2D.fill(beamPhi, beamTheta);
+            beamAngleXY.fill(dirRotated.x(), dirRotated.y());
+            beamAngleThetaPhi.fill(beamPhi, beamTheta);
 
             Double[] isolations = TrackUtils.getIsolations(trk, hitToStrips, hitToRotated);
             double l1Iso = Double.MAX_VALUE;
@@ -447,8 +454,12 @@
             int nSeedStrips = 0;
             double meanTime = 0;
             double meanSeedTime = 0;
+
+            List<TrackerHit> stripHits = new ArrayList<TrackerHit>();
+
             for (TrackerHit hit : trk.getTrackerHits()) {
                 Collection<TrackerHit> htsList = hitToStrips.allFrom(hitToRotated.from(hit));
+                stripHits.addAll(htsList);
                 double hitTimes[] = new double[2];
                 for (TrackerHit hts : htsList) {
                     int stripLayer = ((HpsSiSensor) ((RawTrackerHit) hts.getRawHits().get(0)).getDetectorElement()).getLayerNumber();
@@ -479,18 +490,16 @@
 
             double rmsTime = 0;
             double rmsSeedTime = 0;
-            for (TrackerHit hit : trk.getTrackerHits()) {
-                Collection<TrackerHit> htsList = hitToStrips.allFrom(hitToRotated.from(hit));
-                for (TrackerHit hts : htsList) {
-                    rmsTime += Math.pow(hts.getTime() - meanTime, 2);
-                    HpsSiSensor sensor = (HpsSiSensor) ((RawTrackerHit) hts.getRawHits().get(0)).getDetectorElement();
-                    int layer = sensor.getLayerNumber();
-                    if (layer <= 6) {
-                        rmsSeedTime += Math.pow(hts.getTime() - meanSeedTime, 2);
-                    }
-                    String sensorName = getNiceSensorName(sensor);
-                    getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", sensorName).fill((hts.getTime() - meanTime) * nStrips / (nStrips - 1)); //correct residual for bias
+
+            stripHits = TrackUtils.sortHits(stripHits);
+            for (TrackerHit hts : stripHits) {
+                rmsTime += Math.pow(hts.getTime() - meanTime, 2);
+                HpsSiSensor sensor = (HpsSiSensor) ((RawTrackerHit) hts.getRawHits().get(0)).getDetectorElement();
+                int layer = sensor.getLayerNumber();
+                if (layer <= 6) {
+                    rmsSeedTime += Math.pow(hts.getTime() - meanSeedTime, 2);
                 }
+                PlotAndFitUtilities.getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", sensor).fill((hts.getTime() - meanTime) * nStrips / (nStrips - 1)); //correct residual for bias
             }
             rmsTime = Math.sqrt(rmsTime / nStrips);
             trackMeanTime.fill(meanTime);
@@ -501,6 +510,23 @@
 
             rmsSeedTime = Math.sqrt(rmsSeedTime / nSeedStrips);
             seedRMSTime.fill(rmsSeedTime);
+
+            GenericObject kinkData = GBLKinkData.getKinkData(event, trk);
+            if (kinkData != null) {
+                for (int i = 0; i < stripHits.size(); i++) {
+                    TrackerHit hts = stripHits.get(i);
+                    HpsSiSensor sensor = (HpsSiSensor) ((RawTrackerHit) hts.getRawHits().get(0)).getDetectorElement();
+//                    int layer = sensor.getLayerNumber();
+                    double lambdaKink = GBLKinkData.getLambdaKink(kinkData, i);
+                    double phiKink = GBLKinkData.getPhiKink(kinkData, i);
+//                    System.out.format("%d %d %f %f\n", i, layer, lambdaKink, phiKink);
+
+                    PlotAndFitUtilities.getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "lambdaKink_", sensor).fill(lambdaKink);
+                    PlotAndFitUtilities.getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "phiKink_", sensor).fill(phiKink);
+                    PlotAndFitUtilities.getSensorPlot2D(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "lambdaKinkVsOmega_", sensor).fill(trk.getTrackStates().get(0).getOmega(), lambdaKink);
+                    PlotAndFitUtilities.getSensorPlot2D(plotDir + trackCollectionName + "/" + triggerType + "/" + kinkDir + "phiKinkVsOmega_", sensor).fill(trk.getTrackStates().get(0).getOmega(), phiKink);
+                }
+            }
 
             if (trk.getTrackStates().get(0).getOmega() < 0) {//positrons
                 trkChi2Pos.fill(trk.getChi2());
@@ -568,10 +594,10 @@
 
         for (HpsSiSensor sensor : sensors) {
             //IHistogram1D occupancyPlot = aida.histogram1D(sensor.getName().replaceAll("Tracker_TestRunModule_", ""), 640, 0, 639);
-            IHistogram1D hitTimeResidual = getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", getNiceSensorName(sensor));
+            IHistogram1D hitTimeResidual = PlotAndFitUtilities.getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", sensor);
             IFitResult result = fitGaussian(hitTimeResidual, fitter, "range=\"(-20.0,20.0)\"");
             if (result != null) {
-                LOGGER.info(String.format("%s\t%f\t%f\t%d\t%d", getNiceSensorName(sensor), result.fittedParameters()[1], result.fittedParameters()[2], sensor.getFebID(), sensor.getFebHybridID()));
+                System.out.format("%s\t%f\t%f\t%d\t%d\t%f\n", getNiceSensorName(sensor), result.fittedParameters()[1], result.fittedParameters()[2], sensor.getFebID(), sensor.getFebHybridID(), sensor.getT0Shift());
             }
         }
 
@@ -611,26 +637,6 @@
         }
     }
 
-    private IHistogram1D getSensorPlot(String prefix, HpsSiSensor sensor) {
-        String hname = prefix + getNiceSensorName(sensor);
-        return aida.histogram1D(hname);
-    }
-
-    private IHistogram1D getSensorPlot(String prefix, String sensorName) {
-        return aida.histogram1D(prefix + sensorName);
-    }
-
-    private IHistogram1D createSensorPlot(String prefix, HpsSiSensor sensor, int nchan, double min, double max) {
-        String hname = prefix + getNiceSensorName(sensor);
-        IHistogram1D hist = aida.histogram1D(hname, nchan, min, max);
-        hist.setTitle(sensor.getName().replaceAll(nameStrip, "")
-                .replace("module", "mod")
-                .replace("layer", "lyr")
-                .replace("sensor", "sens"));
-
-        return hist;
-    }
-
     private String getNiceSensorName(HpsSiSensor sensor) {
         return sensor.getName().replaceAll(nameStrip, "")
                 .replace("module", "mod")

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	Wed Apr 27 11:11:32 2016
@@ -28,8 +28,8 @@
 // TODO:  Add some quantities for DQM monitoring: 
 public class TrackingResiduals extends DataQualityMonitor {
 
-    private static Logger LOGGER = Logger.getLogger(TrackingResiduals.class.getPackage().getName());
-    
+    private static final Logger LOGGER = Logger.getLogger(TrackingResiduals.class.getPackage().getName());
+
     // Collection Names
     String trackTimeDataCollectionName = "TrackTimeData";
     String trackResidualsCollectionName = "TrackResiduals";
@@ -82,8 +82,9 @@
             yresidbot[i - 1] = aida.histogram1D(plotDir + triggerType + "/" + posresDir + "Module " + i + " Bot y Residual", 50, -getRange(i, false), getRange(i, false));
         }
 
-        for (int i = 1; i <= nmodules * 2; i++)
+        for (int i = 1; i <= nmodules * 2; i++) {
             tresid[i - 1] = aida.histogram1D(plotDir + triggerType + "/" + timeresDir + "HalfModule " + i + " t Residual", 50, -20, 20);
+        }
         for (int i = 1; i <= nsensors; i++) {
 //            IHistogram1D utopresid = aida.histogram1D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Top u Residual", 50, -getRange((i + 1) / 2, false), getRange((i + 1) / 2, false));
 //            IHistogram1D ubotresid = aida.histogram1D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Bot u Residual", 50, -getRange((i + 1) / 2, false), getRange((i + 1) / 2, false));
@@ -106,17 +107,19 @@
     @Override
     public void process(EventHeader event) {
         aida.tree().cd("/");
-        if (!event.hasCollection(GenericObject.class, trackResidualsCollectionName))
+        if (!event.hasCollection(GenericObject.class, trackResidualsCollectionName)) {
             return;
+        }
         //check to see if this event is from the correct trigger (or "all");
-        if (!matchTrigger(event))
+        if (!matchTrigger(event)) {
             return;
+        }
         nEvents++;
         List<GenericObject> trdList = event.get(GenericObject.class, trackResidualsCollectionName);
         for (GenericObject trd : trdList) {
             int nResid = trd.getNDouble();
             int isBot = trd.getIntVal(trd.getNInt() - 1);//last Int is the top/bottom flag
-            for (int i = 1; i <= nResid; i++)
+            for (int i = 1; i <= nResid; i++) {
                 if (isBot == 1) {
                     xresidbot[i - 1].fill(trd.getDoubleVal(i - 1));//x is the double value in the generic object
                     yresidbot[i - 1].fill(trd.getFloatVal(i - 1));//y is the float value in the generic object
@@ -124,19 +127,22 @@
                     xresidtop[i - 1].fill(trd.getDoubleVal(i - 1));//x is the double value in the generic object
                     yresidtop[i - 1].fill(trd.getFloatVal(i - 1));//y is the float value in the generic object                    
                 }
-        }
-
+            }
+        }
+        
         if (event.hasCollection(GenericObject.class, trackTimeDataCollectionName)) {
             List<GenericObject> ttdList = event.get(GenericObject.class, trackTimeDataCollectionName);
             for (GenericObject ttd : ttdList) {
                 int nResid = ttd.getNDouble();
-                for (int i = 1; i <= nResid; i++)
+                for (int i = 1; i <= nResid; i++) {
                     tresid[i - 1].fill(ttd.getDoubleVal(i - 1));//x is the double value in the generic object               
-            }
-        }
-
-        if (!event.hasCollection(GenericObject.class, gblStripClusterDataCollectionName))
+                }
+            }
+        }
+
+        if (!event.hasCollection(GenericObject.class, gblStripClusterDataCollectionName)) {
             return;
+        }
         List<GenericObject> gblSCDList = event.get(GenericObject.class, gblStripClusterDataCollectionName);
         for (GenericObject gblSCD : gblSCDList) {
             double umeas = gblSCD.getDoubleVal(GBLStripClusterData.GBLDOUBLE.UMEAS);//TODO:  implement generic methods into GBLStripClusterData so this isn't hard coded
@@ -146,23 +152,25 @@
             double tanlambda = gblSCD.getDoubleVal(GBLStripClusterData.GBLDOUBLE.TLAMBDA);//use the slope as a proxy for the top/bottom half of tracker
 
             int i = gblSCD.getIntVal(GBLStripClusterData.GBLINT.ID);//implement generic methods into GBLStripClusterData so this isn't hard coded
-            if (i == 666)
-                if (tanlambda > 0)
+            if (i == 666) {
+                if (tanlambda > 0) {
                     xtopresidBS.fill(resid);
-                else
+                } else {
                     xbotresidBS.fill(resid);
-            else if (i == 667)
-                if (tanlambda > 0)
+                }
+            } else if (i == 667) {
+                if (tanlambda > 0) {
                     ytopresidBS.fill(resid);
-                else
+                } else {
                     ybotresidBS.fill(resid);
-            else if (tanlambda > 0)
+                }
+            } else if (tanlambda > 0) {
                 utopresid[i - 1].fill(resid);//x is the double value in the generic object                 
-            //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Top u Residual vs. u").fill(utrk,resid);//x is the double value in the generic object                 
+            } //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Top u Residual vs. u").fill(utrk,resid);//x is the double value in the generic object                 
             //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Top u Residual vs. v").fill(vtrk,resid);//x is the double value in the generic object                 
-            else
+            else {
                 ubotresid[i - 1].fill(resid);//x is the double value in the generic object                 
-            //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Bot u Residual vs. u").fill(utrk,resid);//x is the double value in the generic object                 
+            }            //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Bot u Residual vs. u").fill(utrk,resid);//x is the double value in the generic object                 
             //                aida.histogram2D(plotDir + triggerType + "/"+uresDir + "HalfModule " + i + " Bot u Residual vs. v").fill(vtrk,resid);//x is the double value in the generic object                 
         }
     }
@@ -287,20 +295,25 @@
     private String getQuantityName(int itype, int iquant, int top, int nlayer) {
         String typeString = "position_resid";
         String quantString = "mean_";
-        if (itype == 1)
+        if (itype == 1) {
             typeString = "time_resid";
-        if (iquant == 1)
+        }
+        if (iquant == 1) {
             quantString = "sigma_";
+        }
 
         String botString = "bot_";
-        if (top == 1)
+        if (top == 1) {
             botString = "top_";
-        if (top == 2)
+        }
+        if (top == 2) {
             botString = "";
+        }
 
         String layerString = "module" + nlayer;
-        if (itype == 1)
+        if (itype == 1) {
             layerString = "halfmodule" + nlayer;
+        }
 
         return typeString + quantString + botString + layerString;
     }
@@ -308,51 +321,71 @@
     @Override
     public void printDQMData() {
         LOGGER.info("TrackingResiduals::printDQMData");
-        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
         LOGGER.info("*******************************");
     }
 
     @Override
     public void printDQMStrings() {
-        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
-        for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet())
-            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
+        for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet()) {
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+        }
     }
 
     private void resetOccupancyMap() {
@@ -399,31 +432,35 @@
     private double getRange(int layer, boolean isX) {
         double range = 2.5;
         if (isX) {
-            if (layer == 1)
-                return 0.2;
-            if (layer == 2)
-                return 0.5;
-            if (layer == 3)
-                return 0.5;
-            if (layer == 4)
-                return 1.0;
-            if (layer == 5)
-                return 1.0;
-            if (layer == 6)
-                return 1.0;
+            switch (layer) {
+                case 1:
+                    return 0.2;
+                case 2:
+                    return 0.5;
+                case 3:
+                    return 0.5;
+                case 4:
+                    return 1.0;
+                case 5:
+                    return 1.0;
+                case 6:
+                    return 1.0;
+            }
         } else {
-            if (layer == 1)
-                return 0.005;
-            if (layer == 2)
-                return 0.5;
-            if (layer == 3)
-                return 0.5;
-            if (layer == 4)
-                return 1.0;
-            if (layer == 5)
-                return 1.0;
-            if (layer == 6)
-                return 1.5;
+            switch (layer) {
+                case 1:
+                    return 0.005;
+                case 2:
+                    return 0.5;
+                case 3:
+                    return 0.5;
+                case 4:
+                    return 1.0;
+                case 5:
+                    return 1.0;
+                case 6:
+                    return 1.5;
+            }
         }
         return range;
 

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java	Wed Apr 27 11:11:32 2016
@@ -9,17 +9,21 @@
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
-
 import java.util.ArrayList;
 import java.util.EnumSet;
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.logging.Logger;
-
+import org.hps.conditions.beam.BeamEnergy.BeamEnergyCollection;
 import org.hps.recon.ecal.cluster.ClusterUtilities;
+import org.hps.recon.particle.HpsReconParticleDriver;
 import org.hps.recon.particle.ReconParticleDriver;
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
+import org.hps.recon.vertexing.BilliorTrack;
+import org.hps.recon.vertexing.BilliorVertex;
+import org.hps.recon.vertexing.BilliorVertexer;
+import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.ReconstructedParticle;
 import org.lcsim.event.RelationalTable;
@@ -72,7 +76,6 @@
 
     private final static Logger LOGGER = Logger.getLogger(TridentMonitoring.class.getPackage().getName());
 
-    private double ebeam = 1.05;
     private final BasicHep3Matrix beamAxisRotation = new BasicHep3Matrix();
 //    private static final int nCuts = 9;
 //    private final String[] cutNames = {"Trk Quality",
@@ -97,8 +100,8 @@
 
     private final String plotDir = "TridentMonitoring/";
 
-    private IHistogram2D triTrackTime2D;
-    private IHistogram1D triTrackTimeDiff;
+//    private IHistogram2D triTrackTime2D;
+//    private IHistogram1D triTrackTimeDiff;
     private IHistogram2D triMassMomentum;
     private IHistogram2D triZVsMomentum;
     private IHistogram2D triTrackMomentum2D;
@@ -108,22 +111,22 @@
     private IHistogram1D triSumP;
     private IHistogram1D triMass;
     private IHistogram2D triZVsMass;
-    private IHistogram1D triX;
-    private IHistogram1D triY;
-    private IHistogram1D triZ;
-    private IHistogram2D triZY;
-    private IHistogram2D triXY;
-    private IHistogram1D triPx;
-    private IHistogram1D triPy;
-    private IHistogram1D triPz;
-    private IHistogram2D triPxPy;
-    private IHistogram1D triU;
-    private IHistogram1D triV;
+//    private IHistogram1D triX;
+//    private IHistogram1D triY;
+//    private IHistogram1D triZ;
+//    private IHistogram2D triZY;
+//    private IHistogram2D triXY;
+//    private IHistogram1D triPx;
+//    private IHistogram1D triPy;
+//    private IHistogram1D triPz;
+//    private IHistogram2D triPxPy;
+//    private IHistogram1D triU;
+//    private IHistogram1D triV;
 
     private IHistogram2D triRadTrackTime2D;
     private IHistogram1D triRadTrackTimeDiff;
-    private IHistogram2D triRadMassMomentum;
-    private IHistogram2D triRadZVsMomentum;
+//    private IHistogram2D triRadMassMomentum;
+//    private IHistogram2D triRadZVsMomentum;
     private IHistogram2D triRadTrackMomentum2D;
     private IHistogram2D triRadPyEleVsPyPos;
     private IHistogram2D triRadPxEleVsPxPos;
@@ -131,11 +134,11 @@
     private IHistogram1D triRadSumP;
     private IHistogram1D triRadMass;
     private IHistogram2D triRadZVsMass;
-    private IHistogram1D triRadX;
-    private IHistogram1D triRadY;
-    private IHistogram1D triRadZ;
-    private IHistogram2D triRadZY;
-    private IHistogram2D triRadXY;
+//    private IHistogram1D triRadX;
+//    private IHistogram1D triRadY;
+//    private IHistogram1D triRadZ;
+//    private IHistogram2D triRadZY;
+//    private IHistogram2D triRadXY;
     private IHistogram1D triRadPx;
     private IHistogram1D triRadPy;
     private IHistogram1D triRadPz;
@@ -143,8 +146,8 @@
     private IHistogram1D triRadU;
     private IHistogram1D triRadV;
 
-    private IHistogram2D vertTrackTime2D;
-    private IHistogram1D vertTrackTimeDiff;
+//    private IHistogram2D vertTrackTime2D;
+//    private IHistogram1D vertTrackTimeDiff;
     private IHistogram2D vertMassMomentum;
     private IHistogram2D vertZVsMomentum;
     private IHistogram2D vertTrackMomentum2D;
@@ -154,17 +157,17 @@
     private IHistogram1D vertSumP;
     private IHistogram1D vertMass;
     private IHistogram2D vertZVsMass;
-    private IHistogram1D vertX;
+//    private IHistogram1D vertX;
     private IHistogram1D vertY;
-    private IHistogram1D vertZ;
+//    private IHistogram1D vertZ;
     private IHistogram2D vertZY;
     private IHistogram2D vertXY;
-    private IHistogram1D vertPx;
-    private IHistogram1D vertPy;
-    private IHistogram1D vertPz;
-    private IHistogram2D vertPxPy;
-    private IHistogram1D vertU;
-    private IHistogram1D vertV;
+//    private IHistogram1D vertPx;
+//    private IHistogram1D vertPy;
+//    private IHistogram1D vertPz;
+//    private IHistogram2D vertPxPy;
+//    private IHistogram1D vertU;
+//    private IHistogram1D vertV;
 
     private IHistogram2D vertRadTrackTime2D;
     private IHistogram1D vertRadTrackTimeDiff;
@@ -189,6 +192,8 @@
     private IHistogram1D vertRadU;
     private IHistogram1D vertRadV;
 
+    private IHistogram2D vertRadUnconBsconChi2;
+
     private IHistogram1D nTriCand;
     private IHistogram1D nVtxCand;
 //    IHistogram1D vertexW;
@@ -197,7 +202,11 @@
     private IHistogram1D maxTrkChi2;
     private IHistogram2D zVsMaxTrkChi2;
     private IHistogram1D v0Chi2;
+    private IHistogram1D bsconV0Chi2;
     private IHistogram2D zVsV0Chi2;
+    private IHistogram2D zVsBsconV0Chi2;
+    private IHistogram1D v0Chi2Diff;
+    private IHistogram2D zVsV0Chi2Diff;
     private IHistogram1D trackTimeDiff;
     private IHistogram2D zVsTrackTimeDiff;
     private IHistogram1D hitTimeStdDev;
@@ -213,55 +222,149 @@
     private final IHistogram1D[][] cutVertexZ = new IHistogram1D[Cut.nCuts][2];
     private final IHistogram2D[][] cutVertexZVsMass = new IHistogram2D[Cut.nCuts][2];
 
-    private final double plotsMinMass = 0.03 * ebeam;
-    private final double plotsMaxMass = 0.04 * ebeam;
+    private final double plotsMinMass = 0.03;
+    private final double plotsMaxMass = 0.04;
 
     //clean up event first
     private final int nTrkMax = 5;
     private final int nPosMax = 1;
 
     private final double maxChi2SeedTrack = 7.0;
-    private final double maxChi2GBLTrack = 15.0;
-    private final double maxVertChi2 = 7.0;
-
-    //v0 cuts   
-    private final double v0PzMax = 1.25 * ebeam;//GeV 
+    private double maxChi2GBLTrack = 15.0;
+    private double maxUnconVertChi2 = 7.0;
+    private double maxBsconVertChi2 = 1000.0; //disable by default
+
+    //v0 plot ranges
+    private final double v0PzMax = 1.25;//GeV 
     private final double v0PzMin = 0.1;// GeV
     private final double v0PyMax = 0.04;//GeV absolute value
     private final double v0PxMax = 0.04;//GeV absolute value
     private final double v0VzMax = 50.0;// mm from target...someday make mass dependent
-    private final double v0VyMax = 1.0;// mm from target...someday make mass dependent
+    private final double v0VyMax = 2.0;// mm from target...someday make mass dependent
     private final double v0VxMax = 2.0;// mm from target...someday make mass dependent
-    //  track quality cuts
+
+    //v0 cuts
+    private final double v0PzMaxCut = 1.25;//GeV 
+    private final double v0PzMinCut = 0.1;// GeV
+    private final double v0PyCut = 0.04;//GeV absolute value
+    private final double v0PxCut = 0.04;//GeV absolute value
+    private final double v0UnconVzCut = 50.0;// mm from target...someday make mass dependent
+    private double v0UnconVyCut = 2.0;// mm from target...someday make mass dependent
+    private double v0UnconVxCut = 2.0;// mm from target...someday make mass dependent
+    private double v0BsconVyCut = 10.0; //disable by default
+    private double v0BsconVxCut = 10.0; //disable by default
+
+//  track quality cuts
     private final double beamPCut = 0.85;
     private final double minPCut = 0.05;
 //    private double trkPyMax = 0.2;
 //    private double trkPxMax = 0.2;
-    private final double radCut = 0.8 * ebeam;
+    private final double radCut = 0.8;
     private final double trkTimeDiff = 5.0;
     private final double clusterTimeDiffCut = 2.5;
 
-    private final double l1IsoMin = 1.0;
+    private double l1IsoMin = 0.5;
+
+    private final double tupleTrkPCut = 0.9;
+    private final double tupleMaxSumCut = 1.3;
+
+    private final double[] beamSize = {0.001, 0.130, 0.050}; //rough estimate from harp scans during engineering run production running
+    private final double[] beamPos = {0.0, 0.0, 0.0};
+    private final double[] vzcBeamSize = {0.001, 100, 100};
+
 //cluster matching
 //    private boolean reqCluster = false;
 //    private int nClustMax = 3;
 //    private double eneLossFactor = 0.7; //average E/p roughly
 //    private double eneOverPCut = 0.3; //|(E/p)_meas - (E/p)_mean|<eneOverPCut
-
 //counters
     private float nEvents = 0;
     private float nRecoV0 = 0;
     private final float[] nPassCut = new float[Cut.nCuts];
 
-    public void setEbeam(double ebeam) {
-        this.ebeam = ebeam;
-    }
+    public TridentMonitoring() {
+        this.tupleVariables = new String[]{"run/I", "event/I",
+            "nTrk/I", "nPos/I",
+            "uncPX/D", "uncPY/D", "uncPZ/D", "uncP/D",
+            "uncVX/D", "uncVY/D", "uncVZ/D", "uncChisq/D", "uncM/D",
+            "bscPX/D", "bscPY/D", "bscPZ/D", "bscP/D",
+            "bscVX/D", "bscVY/D", "bscVZ/D", "bscChisq/D", "bscM/D",
+            "tarPX/D", "tarPY/D", "tarPZ/D", "tarP/D",
+            "tarVX/D", "tarVY/D", "tarVZ/D", "tarChisq/D", "tarM/D",
+            "vzcPX/D", "vzcPY/D", "vzcPZ/D", "vzcP/D",
+            "vzcVX/D", "vzcVY/D", "vzcVZ/D", "vzcChisq/D", "vzcM/D",
+            "elePX/D", "elePY/D", "elePZ/D", "eleP/D",
+            "eleTrkChisq/D", "eleTrkHits/I", "eleTrkType/I", "eleTrkT/D",
+            "eleTrkD0/D", "eleTrkZ0/D", "eleTrkEcalX/D", "eleTrkEcalY/D",
+            "eleHasL1/B", "eleHasL2/B",
+            "eleMatchChisq/D", "eleClT/D", "eleClE/D", "eleClHits/I",
+            "posPX/D", "posPY/D", "posPZ/D", "posP/D",
+            "posTrkChisq/D", "posTrkHits/I", "posTrkType/I", "posTrkT/D",
+            "posTrkD0/D", "posTrkZ0/D", "posTrkEcalX/D", "posTrkEcalY/D",
+            "posHasL1/B", "posHasL2/B",
+            "posMatchChisq/D", "posClT/D", "posClE/D", "posClHits/I",
+            "minL1Iso/D"
+        };
+    }
+
+    public void setMaxChi2GBLTrack(double maxChi2GBLTrack) {
+        this.maxChi2GBLTrack = maxChi2GBLTrack;
+    }
+
+    public void setMaxUnconVertChi2(double maxUnconVertChi2) {
+        this.maxUnconVertChi2 = maxUnconVertChi2;
+    }
+
+    public void setMaxBsconVertChi2(double maxBsconVertChi2) {
+        this.maxBsconVertChi2 = maxBsconVertChi2;
+    }
+
+    public void setV0UnconVyCut(double v0UnconVyCut) {
+        this.v0UnconVyCut = v0UnconVyCut;
+    }
+
+    public void setV0UnconVxCut(double v0UnconVxCut) {
+        this.v0UnconVxCut = v0UnconVxCut;
+    }
+
+    public void setV0BsconVyCut(double v0BsconVyCut) {
+        this.v0BsconVyCut = v0BsconVyCut;
+    }
+
+    public void setV0BsconVxCut(double v0BsconVxCut) {
+        this.v0BsconVxCut = v0BsconVxCut;
+    }
+
+    public void setL1IsoMin(double l1IsoMin) {
+        this.l1IsoMin = l1IsoMin;
+    }
+
+    public void setBeamSizeX(double beamSizeX) {
+        this.beamSize[1] = beamSizeX;
+    }
+
+    public void setBeamSizeY(double beamSizeY) {
+        this.beamSize[2] = beamSizeY;
+    }
+
+    public void setBeamPosX(double beamPosX) {
+        this.beamPos[1] = beamPosX;
+    }
+
+    public void setBeamPosY(double beamPosY) {
+        this.beamPos[2] = beamPosY;
+    }
+
+    double ebeam;
 
     @Override
     protected void detectorChanged(Detector detector) {
         LOGGER.info("TridendMonitoring::detectorChanged  Setting up the plotter");
         beamAxisRotation.setActiveEuler(Math.PI / 2, -0.0305, -Math.PI / 2);
 
+        BeamEnergyCollection beamEnergyCollection
+                = this.getConditionsManager().getCachedConditions(BeamEnergyCollection.class, "beam_energies").getCachedData();
+        ebeam = beamEnergyCollection.get(0).getBeamEnergy();
         aida.tree().cd("/");
         String trkType = "SeedTrack/";
         if (isGBL) {
@@ -284,106 +387,106 @@
 //        IHistogram1D tarconChi2 = aida.histogram1D(plotDir +  triggerType + "/"+ triggerType + "/"+"Target Constrained Chi2", 25, 0, 25);
         nTriCand = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Number of Trident Candidates", 5, 0, 4);
 
-        triTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Track time difference", 100, -10, 10);
-        triTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Track time vs. track time", 100, -10, 10, 100, -10, 10);
-
-        triTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Positron vs. electron momentum", 100, 0, v0PzMax, 100, 0, v0PzMax);
-        triDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Positron - electron momentum", 100, -1., 1.0);
-        triSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Positron + electron momentum", 100, v0PzMin, v0PzMax);
-        triPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Py(e) vs Py(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        triPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Px(e) vs Px(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-
-        triMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex mass vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, 0, 0.1);
-        triZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, -v0VzMax, v0VzMax);
-        triMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex mass", 100, 0, 0.11);
-        triZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. mass", 100, 0, 0.11, 100, -v0VzMax, v0VzMax);
-        triX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex X", 100, -v0VxMax, v0VxMax);
-        triY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Y", 100, -v0VyMax, v0VyMax);
-        triZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z", 100, -v0VzMax, v0VzMax);
-        triXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
-        triZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
-        triPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Px", 100, -v0PxMax, v0PxMax);
-        triPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py", 100, -v0PyMax, v0PyMax);
-        triPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Pz", 100, v0PzMin, v0PzMax);
-        triPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
-        triU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Px over Ptot", 100, -0.1, 0.1);
-        triV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py over Ptot", 100, -0.1, 0.1);
+//        triTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Track time difference", 100, -10, 10);
+//        triTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Track time vs. track time", 100, -10, 10, 100, -10, 10);
+        triTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Positron vs. electron momentum", 100, 0, v0PzMax * ebeam, 100, 0, v0PzMax * ebeam);
+        triDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Positron - electron momentum", 100, -ebeam, ebeam);
+        triSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Positron + electron momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        triPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Py(e) vs Py(p)", 50, -v0PyMax * ebeam, v0PyMax * ebeam, 50, -v0PyMax * ebeam, v0PyMax * ebeam);
+        triPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Px(e) vs Px(p)", 50, -v0PxMax * ebeam, v0PxMax * ebeam, 50, -v0PxMax * ebeam, v0PxMax * ebeam);
+
+        triMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex mass vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, 0, 0.1 * ebeam);
+        triZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, -v0VzMax, v0VzMax);
+        triMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex mass", 100, 0, 0.1 * ebeam);
+        triZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. mass", 100, 0, 0.1 * ebeam, 100, -v0VzMax, v0VzMax);
+//        triX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex X", 100, -v0VxMax, v0VxMax);
+//        triY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Y", 100, -v0VyMax, v0VyMax);
+//        triZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z", 100, -v0VzMax, v0VzMax);
+//        triXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
+//        triZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
+//        triPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Px", 100, -v0PxMax, v0PxMax);
+//        triPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py", 100, -v0PyMax, v0PyMax);
+//        triPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Pz", 100, v0PzMin, v0PzMax);
+//        triPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
+//        triU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Px over Ptot", 100, -0.1, 0.1);
+//        triV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Trident: Vertex Py over Ptot", 100, -0.1, 0.1);
 
         triRadTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Track time difference", 100, -10, 10);
         triRadTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Track time vs. track time", 100, -10, 10, 100, -10, 10);
 
-        triRadTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron vs. electron momentum", 100, 0, v0PzMax, 100, 0, v0PzMax);
-        triRadDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron - electron momentum", 100, -1., 1.0);
-        triRadSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron + electron momentum", 100, v0PzMin, v0PzMax);
-        triRadPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Py(e) vs Py(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        triRadPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Px(e) vs Px(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-
-        triRadMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex mass vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, 0, 0.1);
-        triRadZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, -v0VzMax, v0VzMax);
-        triRadMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex mass", 100, 0, 0.11);
-        triRadZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. mass", 100, 0, 0.11, 100, -v0VzMax, v0VzMax);
-        triRadX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex X", 100, -v0VxMax, v0VxMax);
-        triRadY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Y", 100, -v0VyMax, v0VyMax);
-        triRadZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z", 100, -v0VzMax, v0VzMax);
-        triRadXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
-        triRadZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
-        triRadPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Px", 100, -v0PxMax, v0PxMax);
-        triRadPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Py", 100, -v0PyMax, v0PyMax);
-        triRadPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Pz", 100, v0PzMin, v0PzMax);
-        triRadPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
+        triRadTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron vs. electron momentum", 100, 0, v0PzMax * ebeam, 100, 0, v0PzMax * ebeam);
+        triRadDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron - electron momentum", 100, -ebeam, ebeam);
+        triRadSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Positron + electron momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        triRadPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Py(e) vs Py(p)", 50, -v0PyMax * ebeam, v0PyMax * ebeam, 50, -v0PyMax * ebeam, v0PyMax * ebeam);
+        triRadPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Px(e) vs Px(p)", 50, -v0PxMax * ebeam, v0PxMax * ebeam, 50, -v0PxMax * ebeam, v0PxMax * ebeam);
+
+//        triRadMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex mass vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, 0, 0.1);
+//        triRadZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, -v0VzMax, v0VzMax);
+        triRadMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex mass", 100, 0, 0.1 * ebeam);
+        triRadZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. mass", 100, 0, 0.1 * ebeam, 100, -v0VzMax, v0VzMax);
+//        triRadX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex X", 100, -v0VxMax, v0VxMax);
+//        triRadY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Y", 100, -v0VyMax, v0VyMax);
+//        triRadZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z", 100, -v0VzMax, v0VzMax);
+//        triRadXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
+//        triRadZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
+        triRadPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Px", 100, -v0PxMax * ebeam, v0PxMax * ebeam);
+        triRadPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Py", 100, -v0PyMax * ebeam, v0PyMax * ebeam);
+        triRadPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Pz", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        triRadPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Py vs. Px", 100, -v0PxMax * ebeam, v0PxMax * ebeam, 100, -v0PyMax * ebeam, v0PyMax * ebeam);
         triRadU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Px over Ptot", 100, -0.1, 0.1);
         triRadV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative trident: Vertex Py over Ptot", 100, -0.1, 0.1);
 
-        vertTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Track time difference", 100, -10, 10);
-        vertTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Track time vs. track time", 100, -10, 10, 100, -10, 10);
-
-        vertTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Positron vs. electron momentum", 100, 0, v0PzMax, 100, 0, v0PzMax);
-        vertDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Positron - electron momentum", 100, -1., 1.0);
-        vertSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Positron + electron momentum", 100, v0PzMin, v0PzMax);
-        vertPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Py(e) vs Py(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        vertPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Px(e) vs Px(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-
-        vertMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex mass vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, 0, 0.1);
-        vertZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, -v0VzMax, v0VzMax);
-        vertMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex mass", 100, 0, 0.11);
-        vertZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z vs. mass", 100, 0, 0.11, 100, -v0VzMax, v0VzMax);
-        vertX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex X", 100, -v0VxMax, v0VxMax);
+//        vertTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Track time difference", 100, -10, 10);
+//        vertTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Track time vs. track time", 100, -10, 10, 100, -10, 10);
+        vertTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Positron vs. electron momentum", 100, 0, v0PzMax * ebeam, 100, 0, v0PzMax * ebeam);
+        vertDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Positron - electron momentum", 100, -ebeam, ebeam);
+        vertSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Positron + electron momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        vertPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Py(e) vs Py(p)", 50, -v0PyMax * ebeam, v0PyMax * ebeam, 50, -v0PyMax * ebeam, v0PyMax * ebeam);
+        vertPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Px(e) vs Px(p)", 50, -v0PxMax * ebeam, v0PxMax * ebeam, 50, -v0PxMax * ebeam, v0PxMax * ebeam);
+
+        vertMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex mass vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, 0, 0.1 * ebeam);
+        vertZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, -v0VzMax, v0VzMax);
+        vertMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex mass", 100, 0, 0.1 * ebeam);
+        vertZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z vs. mass", 100, 0, 0.1 * ebeam, 100, -v0VzMax, v0VzMax);
+//        vertX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex X", 100, -v0VxMax, v0VxMax);
         vertY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Y", 100, -v0VyMax, v0VyMax);
-        vertZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z", 100, -v0VzMax, v0VzMax);
+//        vertZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z", 100, -v0VzMax, v0VzMax);
         vertXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
         vertZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
-        vertPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Px", 100, -v0PxMax, v0PxMax);
-        vertPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py", 100, -v0PyMax, v0PyMax);
-        vertPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Pz", 100, v0PzMin, v0PzMax);
-        vertPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
-        vertU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Px over Ptot", 100, -0.1, 0.1);
-        vertV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py over Ptot", 100, -0.1, 0.1);
+//        vertPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Px", 100, -v0PxMax, v0PxMax);
+//        vertPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py", 100, -v0PyMax, v0PyMax);
+//        vertPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Pz", 100, v0PzMin, v0PzMax);
+//        vertPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
+//        vertU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Px over Ptot", 100, -0.1, 0.1);
+//        vertV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Vertex: Vertex Py over Ptot", 100, -0.1, 0.1);
 
         vertRadTrackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Track time difference", 100, -10, 10);
         vertRadTrackTime2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Track time vs. track time", 100, -10, 10, 100, -10, 10);
 
-        vertRadTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron vs. electron momentum", 100, 0, v0PzMax, 100, 0, v0PzMax);
-        vertRadDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron - electron momentum", 100, -1., 1.0);
-        vertRadSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron + electron momentum", 100, v0PzMin, v0PzMax);
-        vertRadPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Py(e) vs Py(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        vertRadPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Px(e) vs Px(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-
-        vertRadMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex mass vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, 0, 0.1);
-        vertRadZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z vs. vertex momentum", 100, v0PzMin, v0PzMax, 100, -v0VzMax, v0VzMax);
-        vertRadMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex mass", 100, 0, 0.11);
-        vertRadZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z vs. mass", 100, 0, 0.11, 100, -v0VzMax, v0VzMax);
+        vertRadTrackMomentum2D = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron vs. electron momentum", 100, 0, v0PzMax * ebeam, 100, 0, v0PzMax * ebeam);
+        vertRadDeltaP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron - electron momentum", 100, -ebeam, ebeam);
+        vertRadSumP = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Positron + electron momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        vertRadPyEleVsPyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Py(e) vs Py(p)", 50, -v0PyMax * ebeam, v0PyMax * ebeam, 50, -v0PyMax * ebeam, v0PyMax * ebeam);
+        vertRadPxEleVsPxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Px(e) vs Px(p)", 50, -v0PxMax * ebeam, v0PxMax * ebeam, 50, -v0PxMax * ebeam, v0PxMax * ebeam);
+
+        vertRadMassMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex mass vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, 0, 0.1 * ebeam);
+        vertRadZVsMomentum = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z vs. vertex momentum", 100, v0PzMin * ebeam, v0PzMax * ebeam, 100, -v0VzMax, v0VzMax);
+        vertRadMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex mass", 100, 0, 0.1 * ebeam);
+        vertRadZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z vs. mass", 100, 0, 0.1 * ebeam, 100, -v0VzMax, v0VzMax);
         vertRadX = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex X", 100, -v0VxMax, v0VxMax);
         vertRadY = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Y", 100, -v0VyMax, v0VyMax);
         vertRadZ = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z", 100, -v0VzMax, v0VzMax);
         vertRadXY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Y vs. X", 100, -v0VxMax, v0VxMax, 100, -v0VyMax, v0VyMax);
         vertRadZY = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Z vs. Y", 100, -v0VyMax, v0VyMax, 100, -v0VzMax, v0VzMax);
-        vertRadPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Px", 100, -v0PxMax, v0PxMax);
-        vertRadPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Py", 100, -v0PyMax, v0PyMax);
-        vertRadPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Pz", 100, v0PzMin, v0PzMax);
-        vertRadPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Py vs. Px", 100, -v0PxMax, v0PxMax, 100, -v0PyMax, v0PyMax);
+        vertRadPx = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Px", 100, -v0PxMax * ebeam, v0PxMax * ebeam);
+        vertRadPy = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Py", 100, -v0PyMax * ebeam, v0PyMax * ebeam);
+        vertRadPz = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Pz", 100, v0PzMin * ebeam, v0PzMax * ebeam);
+        vertRadPxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Py vs. Px", 100, -v0PxMax * ebeam, v0PxMax * ebeam, 100, -v0PyMax * ebeam, v0PyMax * ebeam);
         vertRadU = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Px over Ptot", 100, -0.1, 0.1);
         vertRadV = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Radiative vertex: Vertex Py over Ptot", 100, -0.1, 0.1);
 
+        vertRadUnconBsconChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Radiative vertex: beamspot chi2 vs. uncon chi2", 100, 0, 25.0, 100, 0, 25.0);
+
         nVtxCand = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Number of Vertexing Candidates", 5, 0, 4);
 
         maxTrkChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: Trk Chi2", 50, 0.0, 50.0);
@@ -391,6 +494,10 @@
 
         v0Chi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: V0 Chi2", 50, 0.0, 25.0);
         zVsV0Chi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs V0 Chi2", 50, 0.0, 25.0, 50, -v0VzMax, v0VzMax);
+        bsconV0Chi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: Bscon V0 Chi2", 50, 0.0, 25.0);
+        zVsBsconV0Chi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs Bscon V0 Chi2", 50, 0.0, 25.0, 50, -v0VzMax, v0VzMax);
+        v0Chi2Diff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: Bscon-Uncon V0 Chi2 Diff", 50, 0.0, 25.0);
+        zVsV0Chi2Diff = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs Bscon-Uncon V0 Chi2 Diff", 50, 0.0, 25.0, 50, -v0VzMax, v0VzMax);
 
         trackTimeDiff = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: Trk Time Diff", 50, 0.0, 10.0);
         hitTimeStdDev = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: Hit Time Std Dev", 50, 0.0, 10.0);
@@ -402,16 +509,16 @@
         zVsEventTrkCount = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs Num Tracks", 10, 0.5, 10.5, 50, -v0VzMax, v0VzMax);
         zVsEventPosCount = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs Num Positrons", 5, 0.5, 5.5, 50, -v0VzMax, v0VzMax);
 
-        l1Iso = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: L1 Isolation", 50, 0.0, 5.0);
-        zVsL1Iso = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs L1 Isolation", 50, 0.0, 5.0, 50, -v0VzMax, v0VzMax);
+        l1Iso = aida.histogram1D(plotDir + trkType + triggerType + "/" + "Cut: L1 Isolation", 100, 0.0, 5.0);
+        zVsL1Iso = aida.histogram2D(plotDir + trkType + triggerType + "/" + "Cut: Vz vs L1 Isolation", 100, 0.0, 5.0, 50, -v0VzMax, v0VzMax);
 
         for (Cut cut : Cut.values()) {
             for (int i = 0; i < 2; i++) {
-                cutVertexZ[cut.ordinal()][i] = aida.histogram1D(String.format("%s%s%s/failed cut: %s/%s: Vertex Z position (mm)", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
+                cutVertexZ[cut.ordinal()][i] = aida.histogram1D(String.format("%s%s%s/failed cut %d: %s/%s: Vertex Z position (mm)", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
                         100, -v0VzMax, v0VzMax);
-                cutVertexMass[cut.ordinal()][i] = aida.histogram1D(String.format("%s%s%s/failed cut: %s/%s: Vertex mass (GeV)", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
+                cutVertexMass[cut.ordinal()][i] = aida.histogram1D(String.format("%s%s%s/failed cut %d: %s/%s: Vertex mass (GeV)", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
                         100, 0, 0.1 * ebeam);
-                cutVertexZVsMass[cut.ordinal()][i] = aida.histogram2D(String.format("%s%s%s/failed cut: %s/%s: Vertex Z vs. mass", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
+                cutVertexZVsMass[cut.ordinal()][i] = aida.histogram2D(String.format("%s%s%s/failed cut %d: %s/%s: Vertex Z vs. mass", plotDir, trkType, triggerType, cut.ordinal(), cut.name, i == VERTEX ? "vertex" : "trident"),
                         100, 0, 0.1 * ebeam, 100, -v0VzMax, v0VzMax);
             }
         }
@@ -489,11 +596,9 @@
             if (tracks.size() != 2) {
                 throw new RuntimeException("expected two tracks in vertex, got " + tracks.size());
             }
-            List<Double> trackTimes = new ArrayList<Double>();
             List<Double> hitTimes = new ArrayList<Double>();
             double mean = 0;
             for (Track track : tracks) {
-                trackTimes.add(TrackUtils.getTrackTime(track, hitToStrips, hitToRotated));
                 for (TrackerHit hit : TrackUtils.getStripHits(track, hitToStrips, hitToRotated)) {
                     mean += hit.getTime();
                     hitTimes.add(hit.getTime());
@@ -516,57 +621,180 @@
                 minL1Iso = Math.min(eleL1Iso, posL1Iso);
             }
 
+            double tEle = TrackUtils.getTrackTime(electron.getTracks().get(0), hitToStrips, hitToRotated);
+            double tPos = TrackUtils.getTrackTime(positron.getTracks().get(0), hitToStrips, hitToRotated);
+            Hep3Vector pEleRot = VecOp.mult(beamAxisRotation, electron.getMomentum());
+            Hep3Vector pPosRot = VecOp.mult(beamAxisRotation, positron.getMomentum());
+
+            Hep3Vector eleAtEcal = TrackUtils.getTrackPositionAtEcal(electron.getTracks().get(0));
+            Hep3Vector posAtEcal = TrackUtils.getTrackPositionAtEcal(positron.getTracks().get(0));
+
+            BilliorVertexer vtxFitter = new BilliorVertexer(TrackUtils.getBField(event.getDetector()).y());
+            vtxFitter.setBeamSize(beamSize);
+            vtxFitter.setBeamPosition(beamPos);
+            List<BilliorTrack> billiorTracks = new ArrayList<BilliorTrack>();
+            billiorTracks.add(new BilliorTrack(electron.getTracks().get(0)));
+            billiorTracks.add(new BilliorTrack(positron.getTracks().get(0)));
+
+            vtxFitter.doBeamSpotConstraint(true);
+            BilliorVertex bsconVertex = vtxFitter.fitVertex(billiorTracks);
+            ReconstructedParticle bscV0 = HpsReconParticleDriver.makeReconstructedParticle(electron, positron, bsconVertex);
+            Hep3Vector bscMomRot = VecOp.mult(beamAxisRotation, bscV0.getMomentum());
+            Hep3Vector bscVtx = VecOp.mult(beamAxisRotation, bscV0.getStartVertex().getPosition());
+
+            vtxFitter.doTargetConstraint(true);
+            BilliorVertex tarVertex = vtxFitter.fitVertex(billiorTracks);
+            ReconstructedParticle tarV0 = HpsReconParticleDriver.makeReconstructedParticle(electron, positron, tarVertex);
+            Hep3Vector tarMomRot = VecOp.mult(beamAxisRotation, tarV0.getMomentum());
+            Hep3Vector tarVtx = VecOp.mult(beamAxisRotation, tarV0.getStartVertex().getPosition());
+
+            vtxFitter.setBeamSize(vzcBeamSize);
+            vtxFitter.doTargetConstraint(true);
+            BilliorVertex vzcVertex = vtxFitter.fitVertex(billiorTracks);
+            ReconstructedParticle vzcV0 = HpsReconParticleDriver.makeReconstructedParticle(electron, positron, vzcVertex);
+            Hep3Vector vzcMomRot = VecOp.mult(beamAxisRotation, vzcV0.getMomentum());
+            Hep3Vector vzcVtx = VecOp.mult(beamAxisRotation, vzcV0.getStartVertex().getPosition());
+
+            if (tupleWriter != null) {
+                boolean trkCut = electron.getMomentum().magnitude() < tupleTrkPCut * ebeam && positron.getMomentum().magnitude() < tupleTrkPCut * ebeam;
+                boolean sumCut = electron.getMomentum().magnitude() + positron.getMomentum().magnitude() < tupleMaxSumCut * ebeam;
+                if (!cutTuple || (trkCut && sumCut)) {
+
+                    tupleMap.put("run/I", (double) event.getRunNumber());
+                    tupleMap.put("event/I", (double) event.getEventNumber());
+
+                    tupleMap.put("uncPX/D", v0MomRot.x());
+                    tupleMap.put("uncPY/D", v0MomRot.y());
+                    tupleMap.put("uncPZ/D", v0MomRot.z());
+                    tupleMap.put("uncP/D", v0MomRot.magnitude());
+                    tupleMap.put("uncVX/D", v0Vtx.x());
+                    tupleMap.put("uncVY/D", v0Vtx.y());
+                    tupleMap.put("uncVZ/D", v0Vtx.z());
+                    tupleMap.put("uncChisq/D", uncV0.getStartVertex().getChi2());
+                    tupleMap.put("uncM/D", uncV0.getMass());
+
+                    tupleMap.put("bscPX/D", bscMomRot.x());
+                    tupleMap.put("bscPY/D", bscMomRot.y());
+                    tupleMap.put("bscPZ/D", bscMomRot.z());
+                    tupleMap.put("bscP/D", bscMomRot.magnitude());
+                    tupleMap.put("bscVX/D", bscVtx.x());
+                    tupleMap.put("bscVY/D", bscVtx.y());
+                    tupleMap.put("bscVZ/D", bscVtx.z());
+                    tupleMap.put("bscChisq/D", bscV0.getStartVertex().getChi2());
+                    tupleMap.put("bscM/D", bscV0.getMass());
+
+                    tupleMap.put("tarPX/D", tarMomRot.x());
+                    tupleMap.put("tarPY/D", tarMomRot.y());
+                    tupleMap.put("tarPZ/D", tarMomRot.z());
+                    tupleMap.put("tarP/D", tarMomRot.magnitude());
+                    tupleMap.put("tarVX/D", tarVtx.x());
+                    tupleMap.put("tarVY/D", tarVtx.y());
+                    tupleMap.put("tarVZ/D", tarVtx.z());
+                    tupleMap.put("tarChisq/D", tarV0.getStartVertex().getChi2());
+                    tupleMap.put("tarM/D", tarV0.getMass());
+
+                    tupleMap.put("vzcPX/D", vzcMomRot.x());
+                    tupleMap.put("vzcPY/D", vzcMomRot.y());
+                    tupleMap.put("vzcPZ/D", vzcMomRot.z());
+                    tupleMap.put("vzcP/D", vzcMomRot.magnitude());
+                    tupleMap.put("vzcVX/D", vzcVtx.x());
+                    tupleMap.put("vzcVY/D", vzcVtx.y());
+                    tupleMap.put("vzcVZ/D", vzcVtx.z());
+                    tupleMap.put("vzcChisq/D", vzcV0.getStartVertex().getChi2());
+                    tupleMap.put("vzcM/D", vzcV0.getMass());
+
+                    tupleMap.put("elePX/D", pEleRot.x());
+                    tupleMap.put("elePY/D", pEleRot.y());
+                    tupleMap.put("elePZ/D", pEleRot.z());
+                    tupleMap.put("eleP/D", pEleRot.magnitude());
+                    tupleMap.put("eleTrkD0/D", electron.getTracks().get(0).getTrackStates().get(0).getD0());
+                    tupleMap.put("eleTrkZ0/D", electron.getTracks().get(0).getTrackStates().get(0).getZ0());
+                    tupleMap.put("eleTrkEcalX/D", eleAtEcal.x());
+                    tupleMap.put("eleTrkEcalY/D", eleAtEcal.y());
+                    tupleMap.put("eleTrkChisq/D", electron.getTracks().get(0).getChi2());
+                    tupleMap.put("eleTrkHits/I", (double) electron.getTracks().get(0).getTrackerHits().size());
+                    tupleMap.put("eleTrkType/I", (double) electron.getType());
+                    tupleMap.put("eleTrkT/D", tEle);
+                    tupleMap.put("eleHasL1/B", eleIso[0] != null ? 1.0 : 0.0);
+                    tupleMap.put("eleHasL2/B", eleIso[2] != null ? 1.0 : 0.0);
+                    tupleMap.put("eleMatchChisq/D", electron.getGoodnessOfPID());
+                    if (!electron.getClusters().isEmpty()) {
+                        Cluster eleC = electron.getClusters().get(0);
+                        tupleMap.put("eleClT/D", ClusterUtilities.getSeedHitTime(eleC));
+                        tupleMap.put("eleClE/D", eleC.getEnergy());
+                        tupleMap.put("eleClHits/I", (double) eleC.getCalorimeterHits().size());
+                    }
+
+                    tupleMap.put("posPX/D", pPosRot.x());
+                    tupleMap.put("posPY/D", pPosRot.y());
+                    tupleMap.put("posPZ/D", pPosRot.z());
+                    tupleMap.put("posP/D", pPosRot.magnitude());
+                    tupleMap.put("posTrkD0/D", positron.getTracks().get(0).getTrackStates().get(0).getD0());
+                    tupleMap.put("posTrkZ0/D", positron.getTracks().get(0).getTrackStates().get(0).getZ0());
+                    tupleMap.put("posTrkEcalX/D", posAtEcal.x());
+                    tupleMap.put("posTrkEcalY/D", posAtEcal.y());
+                    tupleMap.put("posTrkChisq/D", positron.getTracks().get(0).getChi2());
+                    tupleMap.put("posTrkHits/I", (double) positron.getTracks().get(0).getTrackerHits().size());
+                    tupleMap.put("posTrkType/I", (double) positron.getType());
+                    tupleMap.put("posTrkT/D", tPos);
+                    tupleMap.put("posHasL1/B", posIso[0] != null ? 1.0 : 0.0);
+                    tupleMap.put("posHasL2/B", posIso[2] != null ? 1.0 : 0.0);
+                    tupleMap.put("posMatchChisq/D", positron.getGoodnessOfPID());
+                    if (!positron.getClusters().isEmpty()) {
+                        Cluster posC = positron.getClusters().get(0);
+                        tupleMap.put("posClT/D", ClusterUtilities.getSeedHitTime(posC));
+                        tupleMap.put("posClE/D", posC.getEnergy());
+                        tupleMap.put("posClHits/I", (double) posC.getCalorimeterHits().size());
+                    }
+
+                    tupleMap.put("minL1Iso/D", minL1Iso);
+
+                    tupleMap.put("nTrk/I", (double) ntrk);
+                    tupleMap.put("nPos/I", (double) npos);
+                    writeTuple();
+                }
+            }
+
             //start applying cuts
             EnumSet<Cut> bits = EnumSet.noneOf(Cut.class);
 
-            boolean trackQualityCut = Math.max(tracks.get(0).getChi2(), tracks.get(1).getChi2()) < (isGBL ? maxChi2GBLTrack : maxChi2SeedTrack);
-            maxTrkChi2.fill(Math.max(tracks.get(0).getChi2(), tracks.get(1).getChi2()));
-            zVsMaxTrkChi2.fill(Math.max(tracks.get(0).getChi2(), tracks.get(1).getChi2()), v0Vtx.z());
+            boolean trackQualityCut = Math.max(electron.getTracks().get(0).getChi2(), positron.getTracks().get(0).getChi2()) < (isGBL ? maxChi2GBLTrack : maxChi2SeedTrack);
             if (trackQualityCut) {
                 bits.add(Cut.TRK_QUALITY);
             }
 
-            boolean v0QualityCut = uncVert.getChi2() < maxVertChi2;
-            v0Chi2.fill(uncVert.getChi2());
-            zVsV0Chi2.fill(uncVert.getChi2(), v0Vtx.z());
+            boolean v0QualityCut = uncVert.getChi2() < maxUnconVertChi2 && bsconVertex.getChi2() < maxBsconVertChi2;
             if (v0QualityCut) {
                 bits.add(Cut.VTX_QUALITY);
             }
 
-            boolean vertexMomentumCut = v0MomRot.z() < v0PzMax && v0MomRot.z() > v0PzMin && Math.abs(v0MomRot.x()) < v0PxMax && Math.abs(v0MomRot.y()) < v0PyMax;
-            boolean vertexPositionCut = Math.abs(v0Vtx.x()) < v0VxMax && Math.abs(v0Vtx.y()) < v0VyMax && Math.abs(v0Vtx.z()) < v0VzMax;
+            boolean vertexMomentumCut = v0MomRot.z() < v0PzMaxCut * ebeam && v0MomRot.z() > v0PzMinCut * ebeam && Math.abs(v0MomRot.x()) < v0PxCut * ebeam && Math.abs(v0MomRot.y()) < v0PyCut * ebeam;
+            boolean vertexPositionCut = Math.abs(v0Vtx.x()) < v0UnconVxCut && Math.abs(v0Vtx.y()) < v0UnconVyCut && Math.abs(v0Vtx.z()) < v0UnconVzCut && Math.abs(bscVtx.x()) < v0BsconVxCut && Math.abs(bscVtx.y()) < v0BsconVyCut;
             if (vertexMomentumCut && vertexPositionCut) {
                 bits.add(Cut.VERTEX_CUTS);
             }
 
-            boolean trackTimeDiffCut = Math.abs(trackTimes.get(0) - trackTimes.get(1)) < trkTimeDiff;
-            trackTimeDiff.fill(Math.abs(trackTimes.get(0) - trackTimes.get(1)));
-            hitTimeStdDev.fill(stdDev);
-            zVsTrackTimeDiff.fill(Math.abs(trackTimes.get(0) - trackTimes.get(1)), v0Vtx.z());
-            zVsHitTimeStdDev.fill(stdDev, v0Vtx.z());
+            boolean trackTimeDiffCut = Math.abs(tEle - tPos) < trkTimeDiff;
             if (trackTimeDiffCut) {
                 bits.add(Cut.TIMING);
             }
 
             boolean topBottomCut = electron.getMomentum().y() * positron.getMomentum().y() < 0;
-            boolean pMinCut = electron.getMomentum().magnitude() > minPCut && positron.getMomentum().magnitude() > minPCut;
-            boolean pMaxCut = electron.getMomentum().magnitude() < beamPCut && positron.getMomentum().magnitude() < beamPCut;
+            boolean pMinCut = electron.getMomentum().magnitude() > minPCut * ebeam && positron.getMomentum().magnitude() > minPCut * ebeam;
+            boolean pMaxCut = electron.getMomentum().magnitude() < beamPCut * ebeam && positron.getMomentum().magnitude() < beamPCut * ebeam;
             if (topBottomCut && pMaxCut && pMinCut) {
                 bits.add(Cut.TRACK_CUTS);
             }
 
             boolean clusterMatchCut = !electron.getClusters().isEmpty() && !positron.getClusters().isEmpty();
             boolean clusterTimeCut = clusterMatchCut && Math.abs(ClusterUtilities.getSeedHitTime(electron.getClusters().get(0)) - ClusterUtilities.getSeedHitTime(positron.getClusters().get(0))) < clusterTimeDiffCut;
-            if (clusterMatchCut && clusterTimeCut) {
-                bits.add(Cut.CLUSTER_CUTS);
-            }
+//disable cut for now
+//            if (clusterMatchCut && clusterTimeCut) {
+            bits.add(Cut.CLUSTER_CUTS);
+//            }
 
             boolean eventTrkCountCut = ntrk >= 2 && ntrk <= nTrkMax;
             boolean eventPosCountCut = npos >= 1 && npos <= nPosMax;
-            eventTrkCount.fill(ntrk);
-            eventPosCount.fill(npos);
-            zVsEventTrkCount.fill(ntrk, v0Vtx.z());
-            zVsEventPosCount.fill(npos, v0Vtx.z());
             if (eventTrkCountCut && eventPosCountCut) {
                 bits.add(Cut.EVENT_QUALITY);
             }
@@ -576,10 +804,8 @@
                 bits.add(Cut.FRONT_HITS);
             }
 
-            l1Iso.fill(minL1Iso);
-            zVsL1Iso.fill(minL1Iso, v0Vtx.z());
             boolean isoCut = minL1Iso > l1IsoMin;
-            if (isoCut) {
+            if (!frontHitsCut || isoCut) { //diagnostic plots look better if failing the front hits cut makes you pass this one
                 bits.add(Cut.ISOLATION);
             }
 
@@ -597,22 +823,58 @@
             for (Cut cut : Cut.values()) {
                 EnumSet<Cut> allButThisCut = EnumSet.allOf(Cut.class);
                 allButThisCut.remove(cut);
-                if (bits.equals(allButThisCut)) {
-                    if (uncV0.getMass() > plotsMinMass && uncV0.getMass() < plotsMaxMass) {
-                        cutVertexZ[cut.ordinal()][VERTEX].fill(v0Vtx.z());
+                if (bits.containsAll(allButThisCut)) {
+                    if (uncV0.getMass() > plotsMinMass * ebeam && uncV0.getMass() < plotsMaxMass * ebeam && uncV0.getMomentum().magnitude() > radCut * ebeam) {
+                        switch (cut) {
+                            case ISOLATION:
+                                l1Iso.fill(minL1Iso);
+                                zVsL1Iso.fill(minL1Iso, v0Vtx.z());
+                                break;
+                            case EVENT_QUALITY:
+                                eventTrkCount.fill(ntrk);
+                                eventPosCount.fill(npos);
+                                zVsEventTrkCount.fill(ntrk, v0Vtx.z());
+                                zVsEventPosCount.fill(npos, v0Vtx.z());
+                                break;
+                            case TIMING:
+                                trackTimeDiff.fill(Math.abs(tEle - tPos));
+                                hitTimeStdDev.fill(stdDev);
+                                zVsTrackTimeDiff.fill(Math.abs(tEle - tPos), v0Vtx.z());
+                                zVsHitTimeStdDev.fill(stdDev, v0Vtx.z());
+                                break;
+                            case VTX_QUALITY:
+                                v0Chi2.fill(uncVert.getChi2());
+                                zVsV0Chi2.fill(uncVert.getChi2(), v0Vtx.z());
+                                bsconV0Chi2.fill(bsconVertex.getChi2());
+                                zVsBsconV0Chi2.fill(bsconVertex.getChi2(), v0Vtx.z());
+                                v0Chi2Diff.fill(bsconVertex.getChi2() - uncVert.getChi2());
+                                zVsV0Chi2Diff.fill(bsconVertex.getChi2() - uncVert.getChi2(), v0Vtx.z());
+                                break;
+                            case TRK_QUALITY:
+                                maxTrkChi2.fill(Math.max(tracks.get(0).getChi2(), tracks.get(1).getChi2()));
+                                zVsMaxTrkChi2.fill(Math.max(tracks.get(0).getChi2(), tracks.get(1).getChi2()), v0Vtx.z());
+                                break;
+                        }
                     }
-                    cutVertexMass[cut.ordinal()][VERTEX].fill(uncV0.getMass());
-                    cutVertexZVsMass[cut.ordinal()][VERTEX].fill(uncV0.getMass(), v0Vtx.z());
+                    if (!bits.contains(cut)) {
+                        if (uncV0.getMass() > plotsMinMass * ebeam && uncV0.getMass() < plotsMaxMass * ebeam) {
+                            cutVertexZ[cut.ordinal()][VERTEX].fill(v0Vtx.z());
+                        }
+                        cutVertexMass[cut.ordinal()][VERTEX].fill(uncV0.getMass());
+                        cutVertexZVsMass[cut.ordinal()][VERTEX].fill(uncV0.getMass(), v0Vtx.z());
+                    }
                 }
 
                 EnumSet<Cut> allTriCutsButThisCut = EnumSet.range(Cut.values()[0], Cut.values()[Cut.firstVertexingCut - 1]);
                 allTriCutsButThisCut.remove(cut);
-                if (bits.containsAll(allTriCutsButThisCut) && !bits.contains(cut)) {
-                    if (uncV0.getMass() > plotsMinMass && uncV0.getMass() < plotsMaxMass) {
-                        cutVertexZ[cut.ordinal()][TRIDENT].fill(v0Vtx.z());
+                if (bits.containsAll(allTriCutsButThisCut)) {
+                    if (!bits.contains(cut)) {
+                        if (uncV0.getMass() > plotsMinMass * ebeam && uncV0.getMass() < plotsMaxMass * ebeam) {
+                            cutVertexZ[cut.ordinal()][TRIDENT].fill(v0Vtx.z());
+                        }
+                        cutVertexMass[cut.ordinal()][TRIDENT].fill(uncV0.getMass());
+                        cutVertexZVsMass[cut.ordinal()][TRIDENT].fill(uncV0.getMass(), v0Vtx.z());
                     }
-                    cutVertexMass[cut.ordinal()][TRIDENT].fill(uncV0.getMass());
-                    cutVertexZVsMass[cut.ordinal()][TRIDENT].fill(uncV0.getMass(), v0Vtx.z());
                 }
             }
 
@@ -645,8 +907,8 @@
             Hep3Vector pPosRot = VecOp.mult(beamAxisRotation, positron.getMomentum());
             Hep3Vector v0Vtx = VecOp.mult(beamAxisRotation, bestCandidate.getStartVertex().getPosition());
 
-            triTrackTime2D.fill(tEle, tPos);
-            triTrackTimeDiff.fill(tEle - tPos);
+//            triTrackTime2D.fill(tEle, tPos);
+//            triTrackTimeDiff.fill(tEle - tPos);
             triZVsMomentum.fill(bestCandidate.getMomentum().magnitude(), v0Vtx.z());
             triMassMomentum.fill(bestCandidate.getMomentum().magnitude(), bestCandidate.getMass());
             triTrackMomentum2D.fill(electron.getMomentum().magnitude(), positron.getMomentum().magnitude());
@@ -655,24 +917,24 @@
             triSumP.fill(bestCandidate.getMomentum().magnitude());
             triDeltaP.fill(positron.getMomentum().magnitude() - electron.getMomentum().magnitude());
 
-            triPxPy.fill(pBestV0Rot.x(), pBestV0Rot.y());
+//            triPxPy.fill(pBestV0Rot.x(), pBestV0Rot.y());
             triMass.fill(bestCandidate.getMass());
             triZVsMass.fill(bestCandidate.getMass(), v0Vtx.z());
-            triX.fill(v0Vtx.x());
-            triY.fill(v0Vtx.y());
-            triZ.fill(v0Vtx.z());
-            triPx.fill(pBestV0Rot.x());
-            triPy.fill(pBestV0Rot.y());
-            triPz.fill(pBestV0Rot.z());
-            triU.fill(pBestV0Rot.x() / pBestV0Rot.magnitude());
-            triV.fill(pBestV0Rot.y() / pBestV0Rot.magnitude());
-            triXY.fill(v0Vtx.x(), v0Vtx.y());
-            triZY.fill(v0Vtx.y(), v0Vtx.z());
-            if (bestCandidate.getMomentum().magnitude() > radCut) {
+//            triX.fill(v0Vtx.x());
+//            triY.fill(v0Vtx.y());
+//            triZ.fill(v0Vtx.z());
+//            triPx.fill(pBestV0Rot.x());
+//            triPy.fill(pBestV0Rot.y());
+//            triPz.fill(pBestV0Rot.z());
+//            triU.fill(pBestV0Rot.x() / pBestV0Rot.magnitude());
+//            triV.fill(pBestV0Rot.y() / pBestV0Rot.magnitude());
+//            triXY.fill(v0Vtx.x(), v0Vtx.y());
+//            triZY.fill(v0Vtx.y(), v0Vtx.z());
+            if (bestCandidate.getMomentum().magnitude() > radCut * ebeam) {
                 triRadTrackTime2D.fill(tEle, tPos);
                 triRadTrackTimeDiff.fill(tEle - tPos);
-                triRadZVsMomentum.fill(bestCandidate.getMomentum().magnitude(), v0Vtx.z());
-                triRadMassMomentum.fill(bestCandidate.getMomentum().magnitude(), bestCandidate.getMass());
+//                triRadZVsMomentum.fill(bestCandidate.getMomentum().magnitude(), v0Vtx.z());
+//                triRadMassMomentum.fill(bestCandidate.getMomentum().magnitude(), bestCandidate.getMass());
                 triRadTrackMomentum2D.fill(electron.getMomentum().magnitude(), positron.getMomentum().magnitude());
                 triRadPyEleVsPyPos.fill(pEleRot.y(), pPosRot.y());
                 triRadPxEleVsPxPos.fill(pEleRot.x(), pPosRot.x());
@@ -682,22 +944,23 @@
                 triRadPxPy.fill(pBestV0Rot.x(), pBestV0Rot.y());
                 triRadMass.fill(bestCandidate.getMass());
                 triRadZVsMass.fill(bestCandidate.getMass(), v0Vtx.z());
-                triRadX.fill(v0Vtx.x());
-                triRadY.fill(v0Vtx.y());
-                triRadZ.fill(v0Vtx.z());
+//                triRadX.fill(v0Vtx.x());
+//                triRadY.fill(v0Vtx.y());
+//                triRadZ.fill(v0Vtx.z());
                 triRadPx.fill(pBestV0Rot.x());
                 triRadPy.fill(pBestV0Rot.y());
                 triRadPz.fill(pBestV0Rot.z());
                 triRadU.fill(pBestV0Rot.x() / pBestV0Rot.magnitude());
                 triRadV.fill(pBestV0Rot.y() / pBestV0Rot.magnitude());
-                triRadXY.fill(v0Vtx.x(), v0Vtx.y());
-                triRadZY.fill(v0Vtx.y(), v0Vtx.z());
+//                triRadXY.fill(v0Vtx.x(), v0Vtx.y());
+//                triRadZY.fill(v0Vtx.y(), v0Vtx.z());
             }
         }
 
         if (!vertCandidateList.isEmpty()) {
             // pick the best candidate...for now just pick a random one. 
             ReconstructedParticle bestCandidate = vertCandidateList.get((int) (Math.random() * vertCandidateList.size()));
+            Vertex unconVertex = bestCandidate.getStartVertex();
 
             //fill some stuff: 
             ReconstructedParticle electron = bestCandidate.getParticles().get(ReconParticleDriver.ELECTRON);
@@ -711,10 +974,10 @@
             Hep3Vector pBestV0Rot = VecOp.mult(beamAxisRotation, bestCandidate.getMomentum());
             Hep3Vector pEleRot = VecOp.mult(beamAxisRotation, electron.getMomentum());
             Hep3Vector pPosRot = VecOp.mult(beamAxisRotation, positron.getMomentum());
-            Hep3Vector v0Vtx = VecOp.mult(beamAxisRotation, bestCandidate.getStartVertex().getPosition());
-
-            vertTrackTime2D.fill(tEle, tPos);
-            vertTrackTimeDiff.fill(tEle - tPos);
+            Hep3Vector v0Vtx = VecOp.mult(beamAxisRotation, unconVertex.getPosition());
+
+//            vertTrackTime2D.fill(tEle, tPos);
+//            vertTrackTimeDiff.fill(tEle - tPos);
             vertZVsMomentum.fill(bestCandidate.getMomentum().magnitude(), v0Vtx.z());
             vertMassMomentum.fill(bestCandidate.getMomentum().magnitude(), bestCandidate.getMass());
             vertTrackMomentum2D.fill(electron.getMomentum().magnitude(), positron.getMomentum().magnitude());
@@ -723,20 +986,34 @@
             vertSumP.fill(bestCandidate.getMomentum().magnitude());
             vertDeltaP.fill(positron.getMomentum().magnitude() - electron.getMomentum().magnitude());
 
-            vertPxPy.fill(pBestV0Rot.x(), pBestV0Rot.y());
+//            vertPxPy.fill(pBestV0Rot.x(), pBestV0Rot.y());
             vertMass.fill(bestCandidate.getMass());
             vertZVsMass.fill(bestCandidate.getMass(), v0Vtx.z());
-            vertX.fill(v0Vtx.x());
+//            vertX.fill(v0Vtx.x());
             vertY.fill(v0Vtx.y());
-            vertZ.fill(v0Vtx.z());
-            vertPx.fill(pBestV0Rot.x());
-            vertPy.fill(pBestV0Rot.y());
-            vertPz.fill(pBestV0Rot.z());
-            vertU.fill(pBestV0Rot.x() / pBestV0Rot.magnitude());
-            vertV.fill(pBestV0Rot.y() / pBestV0Rot.magnitude());
+//            vertZ.fill(v0Vtx.z());
+//            vertPx.fill(pBestV0Rot.x());
+//            vertPy.fill(pBestV0Rot.y());
+//            vertPz.fill(pBestV0Rot.z());
+//            vertU.fill(pBestV0Rot.x() / pBestV0Rot.magnitude());
+//            vertV.fill(pBestV0Rot.y() / pBestV0Rot.magnitude());
             vertXY.fill(v0Vtx.x(), v0Vtx.y());
             vertZY.fill(v0Vtx.y(), v0Vtx.z());
-            if (bestCandidate.getMomentum().magnitude() > radCut) {
+            if (bestCandidate.getMomentum().magnitude() > radCut * ebeam) {
+
+                BilliorVertexer vtxFitter = new BilliorVertexer(TrackUtils.getBField(event.getDetector()).y());
+                vtxFitter.setBeamSize(beamSize);
+                vtxFitter.setBeamPosition(beamPos);
+//                vtxFitter.setDebug(false);
+                List<BilliorTrack> billiorTracks = new ArrayList<BilliorTrack>();
+                billiorTracks.add(new BilliorTrack(electron.getTracks().get(0)));
+                billiorTracks.add(new BilliorTrack(positron.getTracks().get(0)));
+                vtxFitter.doBeamSpotConstraint(true);
+                BilliorVertex bsconVertex = vtxFitter.fitVertex(billiorTracks);
+                vtxFitter.doTargetConstraint(true);
+                BilliorVertex tarconVertex = vtxFitter.fitVertex(billiorTracks);
+                vertRadUnconBsconChi2.fill(unconVertex.getChi2(), bsconVertex.getChi2());
+
                 vertRadTrackTime2D.fill(tEle, tPos);
                 vertRadTrackTimeDiff.fill(tEle - tPos);
                 vertRadZVsMomentum.fill(bestCandidate.getMomentum().magnitude(), v0Vtx.z());

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java	Wed Apr 27 11:11:32 2016
@@ -8,8 +8,8 @@
 import hep.aida.IHistogram2D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
+import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Vector;
-import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.VecOp;
 
 import java.io.IOException;
@@ -19,6 +19,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import org.hps.conditions.beam.BeamEnergy.BeamEnergyCollection;
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
 import org.hps.recon.vertexing.BilliorTrack;
@@ -33,252 +34,493 @@
 import org.lcsim.recon.tracking.seedtracker.SeedTrack;
 
 /**
- * DQM driver V0 particles (i.e. e+e- pars) plots things like number of vertex
- * position an mass
+ * DQM driver V0 particles (i.e. e+e- pars) plots things like number of vertex position an mass
  *
  * @author mgraham on May 14, 2014
- *
  */
 public class V0Monitoring extends DataQualityMonitor {
 
     private static Logger LOGGER = Logger.getLogger(V0Monitoring.class.getPackage().getName());
-    
-    String finalStateParticlesColName = "FinalStateParticles";
-    String unconstrainedV0CandidatesColName = "UnconstrainedV0Candidates";
-    String beamConV0CandidatesColName = "BeamspotConstrainedV0Candidates";
-    String targetV0ConCandidatesColName = "TargetConstrainedV0Candidates";
-    String[] fpQuantNames = {"nV0_per_Event", "avg_BSCon_mass", "avg_BSCon_Vx", "avg_BSCon_Vy", "avg_BSCon_Vz", "sig_BSCon_Vx", "sig_BSCon_Vy", "sig_BSCon_Vz", "avg_BSCon_Chi2"};
-    //some counters
-    int nRecoEvents = 0;
-    int nTotV0 = 0;
-    int nTot2Ele = 0;
-    //some summers
-    double sumMass = 0.0;
-    double sumVx = 0.0;
-    double sumVy = 0.0;
-    double sumVz = 0.0;
-    double sumChi2 = 0.0;
-
-    /*  V0 Quantities   */
-    /*  Mass, vertex, chi^2 of fit */
-    /*  unconstrained */
-    IHistogram1D unconMass;
-    IHistogram1D unconVx;
-    IHistogram1D unconVy;
-    IHistogram1D unconVz;
-    IHistogram1D unconChi2;
-    IHistogram2D unconVzVsChi2;
-    IHistogram2D unconChi2VsTrkChi2;
+
+    private static boolean hasSharedStrips(final ReconstructedParticle fs1, final ReconstructedParticle fs2,
+            final RelationalTable hittostrip, final RelationalTable hittorotated) {
+        return TrackUtils.hasSharedStrips(fs1.getTracks().get(0), fs2.getTracks().get(0), hittostrip, hittorotated);
+    }
+
+    private final BasicHep3Matrix beamAxisRotation = new BasicHep3Matrix();
+    private final String beamConV0CandidatesColName = "BeamspotConstrainedV0Candidates";
+    private IHistogram1D bsconChi2;
+    private IHistogram2D bsconChi2VsTrkChi2;
+    private IHistogram1D bsconMass;
+    private IHistogram1D bsconVx;
+    private IHistogram1D bsconVy;
+    private IHistogram1D bsconVz;
+    private IHistogram2D bsconVzVsChi2;
+    private final String finalStateParticlesColName = "FinalStateParticles";
+    private final String[] fpQuantNames = {"nV0_per_Event", "avg_BSCon_mass", "avg_BSCon_Vx", "avg_BSCon_Vy",
+            "avg_BSCon_Vz", "sig_BSCon_Vx", "sig_BSCon_Vy", "sig_BSCon_Vz", "avg_BSCon_Chi2"};
+
+    private final double maxFactor = 1.25;
+    private IHistogram1D mollerHiP, mollerLoP, mollerEitherP, mollerPsum;
+    private IHistogram1D mollerMass;
+    private IHistogram1D mollerMassVtxCut;
+    private IHistogram1D mollerUx;
+    private IHistogram1D mollerUy;
+    private IHistogram1D mollerVx;
+
+    private IHistogram1D mollerVy;
+
+    private IHistogram1D mollerVz;
+    private IHistogram1D mollerVzVtxCut;
+    private IHistogram2D mollerXVsVtxY;
+    private IHistogram2D mollerXVsVtxZ;
+
+    private IHistogram2D mollerYVsVtxZ;
+    // some counters
+    private int nRecoEvents = 0;
+    private int nTotV0 = 0;
+    private IHistogram1D numChargeHisto;
+    private IHistogram1D nV0;
+    private IHistogram1D pEle;
+    private IHistogram2D pEleVspEle;
+    private IHistogram2D pEleVspEleBeamBeam;
+    private IHistogram2D pEleVspEleMoller;
+    private IHistogram2D pEleVspEleNoBeam;
+    private IHistogram2D pEleVspPos;
+    private IHistogram2D pEleVspPosWithCut;
+    private IHistogram2D pEleVsthetaBeamBeam;
+    private IHistogram2D pEleVsthetaMoller;
+
+    private IHistogram2D phiEleVsphiEle;
+    private final String plotDir = "V0Monitoring/";
+    private IHistogram1D pPos;
+
+    private IHistogram2D pxEleVspxEle;
+    private IHistogram2D pxEleVspxEleNoBeam;
+    private IHistogram2D pxEleVspxPos;
+
+    private IHistogram2D pyEleVspyEle;
+    private IHistogram2D pyEleVspyEleNoBeam;
+    private IHistogram2D pyEleVspyPos;
+    private IHistogram1D sumChargeHisto;
+    private double sumChi2 = 0.0;
+    // some summers
+    private double sumMass = 0.0;
+    private double sumVx = 0.0;
+    private double sumVy = 0.0;
+    private double sumVz = 0.0;
+
+    private IHistogram1D tarconChi2;
+    private IHistogram2D tarconChi2VsTrkChi2;
+
+    /* target constrained */
+    private IHistogram1D tarconMass;
+    private IHistogram1D tarconVx;
+    private IHistogram1D tarconVy;
+    private IHistogram1D tarconVz;
+    private IHistogram2D tarconVzVsChi2;
+    private final String targetV0ConCandidatesColName = "TargetConstrainedV0Candidates";
+    private IHistogram2D thetaEleVsthetaBeamBeam;
+    private IHistogram2D thetaEleVsthetaMoller;
+    private final double thetaMax = 0.06;
+    private final double thetaMin = 0.015;
+    private IHistogram1D trigTime;
+    private IHistogram2D trigTimeV0Time;
+    private IHistogram1D unconChi2;
+
+    private IHistogram2D unconChi2VsTrkChi2;
     /* beamspot constrained */
-
-    IHistogram1D nV0;
-
-    IHistogram1D v0Time;
-    IHistogram1D v0Dt;
-    IHistogram2D trigTimeV0Time;
-    IHistogram1D trigTime;
-
-    IHistogram1D bsconMass;
-    IHistogram1D bsconVx;
-    IHistogram1D bsconVy;
-    IHistogram1D bsconVz;
-    IHistogram1D bsconChi2;
-    IHistogram2D bsconVzVsChi2;
-    IHistogram2D bsconChi2VsTrkChi2;
-    /* target constrained */
-    IHistogram1D tarconMass;
-    IHistogram1D tarconVx;
-    IHistogram1D tarconVy;
-    IHistogram1D tarconVz;
-    IHistogram1D tarconChi2;
-    IHistogram2D tarconVzVsChi2;
-    IHistogram2D tarconChi2VsTrkChi2;
-
-    IHistogram2D pEleVspPos;
-    IHistogram2D pEleVspPosWithCut;
-    IHistogram2D pyEleVspyPos;
-    IHistogram2D pxEleVspxPos;
-
-    IHistogram2D VtxZVsMass;
-    IHistogram2D VtxYVsVtxZ;
-    IHistogram2D VtxXVsVtxZ;
-    IHistogram2D VtxXVsVtxY;
-    IHistogram2D VtxXVsVtxPx;
-    IHistogram2D VtxYVsVtxPy;
-    IHistogram2D VtxZVsVtxPx;
-    IHistogram2D VtxZVsVtxPy;
-    IHistogram2D VtxZVsVtxPz;
-
-    IHistogram2D VtxZVsL1Iso;
-    IHistogram2D VtxZVsTrkChi2;
-
-    IHistogram2D pEleVspEle;
-    IHistogram2D phiEleVsphiEle;
-    IHistogram2D pyEleVspyEle;
-    IHistogram2D pxEleVspxEle;
-    IHistogram2D pEleVspEleNoBeam;
-    IHistogram2D pyEleVspyEleNoBeam;
-    IHistogram2D pxEleVspxEleNoBeam;
-    IHistogram2D pEleVspEleMoller;
-    IHistogram2D pEleVsthetaMoller;
-    IHistogram2D thetaEleVsthetaMoller;
-    IHistogram2D pEleVspEleBeamBeam;
-    IHistogram2D pEleVsthetaBeamBeam;
-    IHistogram2D thetaEleVsthetaBeamBeam;
-
-    IHistogram1D mollerMass;
-    IHistogram1D mollerMassVtxCut;
-    IHistogram1D mollerVx;
-    IHistogram1D mollerVy;
-    IHistogram1D mollerVz;
-    IHistogram1D mollerVzVtxCut;
-    IHistogram2D mollerXVsVtxZ;
-    IHistogram2D mollerYVsVtxZ;
-    IHistogram2D mollerXVsVtxY;
-
-    IHistogram1D sumChargeHisto;
-    IHistogram1D numChargeHisto;
-
-    private final String plotDir = "V0Monitoring/";
-
-    double beamEnergy = 1.05; //GeV
-    private final BasicHep3Matrix beamAxisRotation = new BasicHep3Matrix();
-
-    double maxFactor = 1.25;
-    double feeMomentumCut = 0.8; //GeV
-
-    double v0ESumMinCut = 0.8 * beamEnergy;
-    double v0ESumMaxCut = 1.25 * beamEnergy;
-    double v0MaxPCut = 1.1;//GeV
-    double molPSumMin = 0.85;
-    double molPSumMax = 1.3;
-    double beambeamCut = 0.85;
-    double thetaMax = 0.06;
-    double thetaMin = 0.015;
-
+    /* V0 Quantities */
+    /* Mass, vertex, chi^2 of fit */
+    /* unconstrained */
+    private IHistogram1D unconMass;
+    private final String unconstrainedV0CandidatesColName = "UnconstrainedV0Candidates";
+    private IHistogram1D unconVx;
+    private IHistogram1D unconVy;
+    private IHistogram1D unconVz;
+    private IHistogram2D unconVzVsChi2;
+    private IHistogram1D v0Dt;
+    private double v0ESumMinCut, v0MaxPCut, v0ESumMaxCut, molPSumMin, molPSumMax, beambeamCut;
+
+    private IHistogram1D v0Time;
+    private IHistogram2D VtxXVsVtxPx;
+
+    private IHistogram2D VtxXVsVtxY;
+    private IHistogram2D VtxXVsVtxZ;
+
+    private IHistogram2D VtxYVsVtxPy;
+
+    private IHistogram2D VtxYVsVtxZ;
+
+    private IHistogram2D VtxZVsL1Iso;
+
+    private IHistogram2D VtxZVsMass;
+    private IHistogram2D VtxZVsTrkChi2;
+
+    private IHistogram2D VtxZVsVtxPx;
+
+    private IHistogram2D VtxZVsVtxPy;
+
+    private IHistogram2D VtxZVsVtxPz;
+
+    /**
+     * Calculate the averages here and fill the map
+     */
     @Override
-    protected void detectorChanged(Detector detector) {
+    public void calculateEndOfRunQuantities() {
+
+        final IAnalysisFactory analysisFactory = IAnalysisFactory.create();
+        final IFitFactory fitFactory = analysisFactory.createFitFactory();
+        final IFitter fitter = fitFactory.createFitter("chi2");
+        final double[] init = {50.0, 0.0, 0.2, 1.0, 0.0};
+        final IFitResult resVx = this.fitVertexPosition(bsconVx, fitter, init, "range=\"(-0.5,0.5)\"");
+        final double[] init2 = {50.0, 0.0, 0.04, 1.0, 0.0};
+        final IFitResult resVy = this.fitVertexPosition(bsconVy, fitter, init2, "range=\"(-0.2,0.2)\"");
+        final double[] init3 = {50.0, 0.0, 3.0, 1.0, 0.0};
+        final IFitResult resVz = this.fitVertexPosition(bsconVz, fitter, init3, "range=\"(-6,6)\"");
+
+        if (resVx != null && resVy != null & resVz != null) {
+            final double[] parsVx = resVx.fittedParameters();
+            final double[] parsVy = resVy.fittedParameters();
+            final double[] parsVz = resVz.fittedParameters();
+
+            for (int i = 0; i < 5; i++) {
+                LOGGER.info("Vertex Fit Parameters:  " + resVx.fittedParameterNames()[i] + " = " + parsVx[i] + "; "
+                        + parsVy[i] + "; " + parsVz[i]);
+            }
+
+            final IPlotter plotter = analysisFactory.createPlotterFactory().create("Vertex Position");
+            plotter.createRegions(1, 3);
+            final IPlotterStyle pstyle = plotter.style();
+            pstyle.legendBoxStyle().setVisible(false);
+            pstyle.dataStyle().fillStyle().setColor("green");
+            pstyle.dataStyle().lineStyle().setColor("black");
+            plotter.region(0).plot(bsconVx);
+            plotter.region(0).plot(resVx.fittedFunction());
+            plotter.region(1).plot(bsconVy);
+            plotter.region(1).plot(resVy.fittedFunction());
+            plotter.region(2).plot(bsconVz);
+            plotter.region(2).plot(resVz.fittedFunction());
+            if (outputPlots) {
+                try {
+                    plotter.writeToFile(outputPlotDir + "vertex.png");
+                } catch (final IOException ex) {
+                    Logger.getLogger(V0Monitoring.class.getName()).log(Level.SEVERE, null, ex);
+                }
+            }
+
+            // monitoredQuantityMap.put(fpQuantNames[2], sumVx / nTotV0);
+            // monitoredQuantityMap.put(fpQuantNames[3], sumVy / nTotV0);
+            // monitoredQuantityMap.put(fpQuantNames[4], sumVz / nTotV0);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[2], parsVx[1]);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[3], parsVy[1]);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[4], parsVz[1]);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[5], parsVx[2]);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[6], parsVy[2]);
+            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[7], parsVz[2]);
+        }
+        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[0],
+                (double) nTotV0 / nRecoEvents);
+        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[1], sumMass
+                / nTotV0);
+        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[8], sumChi2
+                / nTotV0);
+
+    }
+
+    @Override
+    protected void detectorChanged(final Detector detector) {
+
+        final BeamEnergyCollection beamEnergyCollection = this.getConditionsManager()
+                .getCachedConditions(BeamEnergyCollection.class, "beam_energies").getCachedData();
+        final double beamEnergy = beamEnergyCollection.get(0).getBeamEnergy();
+        v0ESumMinCut = 0.8 * beamEnergy;
+        v0ESumMaxCut = 1.25 * beamEnergy;
+
+        v0MaxPCut = 1.05 * beamEnergy;// GeV
+        molPSumMin = 0.80 * beamEnergy;
+        molPSumMax = 1.25 * beamEnergy;
+        beambeamCut = 0.80 * beamEnergy;
+
         beamAxisRotation.setActiveEuler(Math.PI / 2, -0.0305, -Math.PI / 2);
 
-        LOGGER.info("Setting up the plotter");
+        // LOGGER.info("Setting up the plotter");
         aida.tree().cd("/");
-        String xtra = "Extras";
+        final String xtra = "Extras";
         String trkType = "SeedTrack/";
-        if (isGBL)
+        if (isGBL) {
             trkType = "GBLTrack/";
-        /*  V0 Quantities   */
-        /*  Mass, vertex, chi^2 of fit */
-        /*  unconstrained */
-        unconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Invariant Mass (GeV)", 100, 0, 0.200);
-        unconVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Vx (mm)", 50, -10, 10);
-        unconVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Vy (mm)", 50, -10, 10);
-        unconVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Vz (mm)", 50, -50, 50);
-        unconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Chi2", 25, 0, 25);
-        unconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
-        unconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/" + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
+        }
+
+        final double maxMass = .2 * beamEnergy;
+        final double maxMassMoller = .1 * Math.sqrt(beamEnergy);
+        /* V0 Quantities */
+        /* Mass, vertex, chi^2 of fit */
+        /* unconstrained */
+        unconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Invariant Mass (GeV)", 100, 0, maxMass);
+        unconVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Vx (mm)", 50, -10, 10);
+        unconVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Vy (mm)", 50, -10, 10);
+        unconVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Vz (mm)", 50, -50, 50);
+        unconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Chi2", 25, 0, 25);
+        unconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName + "/"
+                + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
+        unconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + unconstrainedV0CandidatesColName
+                + "/" + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
         /* beamspot constrained */
-        bsconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Mass (GeV)", 100, 0, 0.200);
-        bsconVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vx (mm)", 50, -10, 10);
-        bsconVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vy (mm)", 50, -10, 10);
-        bsconVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vz (mm)", 50, -50, 50);
-        bsconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Chi2", 25, 0, 25);
-        bsconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
-        bsconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
+        bsconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/"
+                + "Mass (GeV)", 100, 0, maxMass);
+        bsconVx = aida.histogram1D(
+                plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vx (mm)", 50, -10, 10);
+        bsconVy = aida.histogram1D(
+                plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vy (mm)", 50, -10, 10);
+        bsconVz = aida.histogram1D(
+                plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Vz (mm)", 50, -50, 50);
+        bsconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/" + "Chi2",
+                25, 0, 25);
+        bsconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/"
+                + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
+        bsconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + beamConV0CandidatesColName + "/"
+                + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
         /* target constrained */
-        tarconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Mass (GeV)", 100, 0, 0.200);
-        tarconVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Vx (mm)", 50, -1, 1);
-        tarconVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Vy (mm)", 50, -1, 1);
-        tarconVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Vz (mm)", 50, -10, 10);
-        tarconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Chi2", 25, 0, 25);
-        tarconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
-        tarconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/" + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
-
-        nV0 = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Number of V0 per event", 10, 0, 10);
+        tarconMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Mass (GeV)", 100, 0, maxMass);
+        tarconVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Vx (mm)", 50, -1, 1);
+        tarconVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Vy (mm)", 50, -1, 1);
+        tarconVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Vz (mm)", 50, -10, 10);
+        tarconChi2 = aida.histogram1D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Chi2", 25, 0, 25);
+        tarconVzVsChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName + "/"
+                + "Vz vs. Chi2", 25, 0, 25, 50, -50, 50);
+        tarconChi2VsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + targetV0ConCandidatesColName
+                + "/" + "Chi2 vs. total track chi2", 50, 0, 50, 50, 0, 25);
+
+        nV0 = aida
+                .histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Number of V0 per event", 10, 0, 10);
         v0Time = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "V0 mean time", 100, -25, 25);
-        v0Dt = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "V0 time difference", 100, -25, 25);
-        trigTimeV0Time = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Trigger phase vs. V0 mean time", 100, -25, 25, 6, 0, 24);
+        v0Dt = aida
+                .histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "V0 time difference", 100, -25, 25);
+        trigTimeV0Time = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "Trigger phase vs. V0 mean time", 100, -25, 25, 6, 0, 24);
         trigTime = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Trigger phase", 6, 0, 24);
 
-        pEleVspPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "P(e) vs P(p)", 50, 0, beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
-        pEleVspPosWithCut = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "P(e) vs P(p): Radiative", 50, 0, beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
-        pyEleVspyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Py(e) vs Py(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        pxEleVspxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Px(e) vs Px(p)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        VtxZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Mass", 50, 0, 0.15, 50, -50, 80);
-        VtxXVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Vz", 100, -10, 10, 100, -50, 80);
-        VtxYVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vy vs Vz", 100, -5, 5, 100, -50, 80);
-        VtxXVsVtxY = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Vy", 100, -10, 10, 100, -5, 5);
-        VtxXVsVtxPx = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Px", 100, -0.1, 0.1, 100, -10, 10);
-        VtxYVsVtxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vy vs Py", 100, -0.1, 0.1, 100, -5, 5);
-        VtxZVsVtxPx = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Px", 100, -0.1, 0.1, 100, -50, 80);
-        VtxZVsVtxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Py", 100, -0.1, 0.1, 100, -50, 80);
-        VtxZVsVtxPz = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Pz", 100, 0.0, beamEnergy * maxFactor, 100, -50, 80);
-        VtxZVsL1Iso = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs L1 Isolation", 100, 0.0, 5.0, 50, -50, 80);
-        VtxZVsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Track Chi2", 50, 0, 50, 50, -50, 80);
-        pEleVspEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs P(e)", 50, 0, beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
-        phiEleVsphiEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/phi(e) vs phi(e)", 50, -Math.PI, Math.PI, 50, -Math.PI, Math.PI);
-        pyEleVspyEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Py(e) vs Py(e)", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        pxEleVspxEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Px(e) vs Px(e)", 50, -0.02, 0.06, 50, -0.02, 0.06);
-        pEleVspEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs P(e) NoBeam", 50, 0, beambeamCut, 50, 0, beambeamCut);
-        pEleVspEleMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs P(e) Moller", 50, 0, beambeamCut, 50, 0, beambeamCut);
-        pEleVspEleBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs P(e) BeamBeam", 50, beambeamCut, beamEnergy * maxFactor, 50, beambeamCut, beamEnergy * maxFactor);
-        pyEleVspyEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Py(e) vs Py(e) NoBeam", 50, -0.04, 0.04, 50, -0.04, 0.04);
-        pxEleVspxEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Px(e) vs Px(e) NoBeam", 50, -0.02, 0.06, 50, -0.02, 0.06);
-        sumChargeHisto = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Total Charge of  Event", 5, -2, 3);
-        numChargeHisto = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Number of Charged Particles", 6, 0, 6);
-
-        pEleVsthetaMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs Theta Moller", 50, 0, beambeamCut, 50, thetaMin, thetaMax);
-        thetaEleVsthetaMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Theta vs Theta Moller", 50, thetaMin, thetaMax, 50, thetaMin, thetaMax);
-        pEleVsthetaBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs Theta BeamBeam", 50, beambeamCut, beamEnergy * maxFactor, 50, thetaMin, thetaMax);
-        thetaEleVsthetaBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Theta vs Theta BeamBeam", 50, thetaMin, thetaMax, 50, thetaMin, thetaMax);
-
-        mollerMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Mass (GeV)", 100, 0, 0.100);
-        mollerMassVtxCut = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Mass (GeV): VtxCut", 100, 0, 0.100);
-        mollerVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vx (mm)", 50, -10, 10);
-        mollerVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vy (mm)", 50, -2, 2);
-        mollerVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vz (mm)", 50, -50, 50);
-        mollerVzVtxCut = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vz (mm): VtxCut", 50, -50, 50);
-        mollerXVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vx vs Vz", 100, -5, 5, 100, -50, 50);
-        mollerYVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vy vs Vz", 100, -2, 2, 100, -50, 50);
-        mollerXVsVtxY = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vx vs Vy", 100, -5, 5, 100, -2, 2);
+        pEleVspPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "P(e) vs P(p)", 50, 0,
+                beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
+
+        pEle = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "P(e)", 50, 0, beamEnergy
+                * maxFactor);
+        pPos = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "P(p)", 50, 0, beamEnergy
+                * maxFactor);
+
+        pEleVspPosWithCut = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "P(e) vs P(p): Radiative", 50, 0, beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
+        pyEleVspyPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Py(e) vs Py(p)", 50,
+                -0.04 * beamEnergy, 0.04 * beamEnergy, 50, -0.04 * beamEnergy, 0.04 * beamEnergy);
+        pxEleVspxPos = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Px(e) vs Px(p)", 50,
+                -0.04 * beamEnergy, 0.04 * beamEnergy, 50, -0.04 * beamEnergy, 0.04 * beamEnergy);
+        VtxZVsMass = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Mass", 50, 0,
+                maxMass, 50, -50, 80);
+        VtxXVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Vz", 100, -10, 10,
+                100, -50, 80);
+        VtxYVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vy vs Vz", 100, -5, 5, 100,
+                -50, 80);
+        VtxXVsVtxY = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Vy", 100, -10, 10,
+                100, -5, 5);
+        VtxXVsVtxPx = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vx vs Px", 100, -0.1, 0.1,
+                100, -10, 10);
+        VtxYVsVtxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vy vs Py", 100, -0.1, 0.1,
+                100, -5, 5);
+        VtxZVsVtxPx = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Px", 100, -0.1, 0.1,
+                100, -50, 80);
+        VtxZVsVtxPy = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Py", 100, -0.1, 0.1,
+                100, -50, 80);
+        VtxZVsVtxPz = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Pz", 100, 0.0,
+                beamEnergy * maxFactor, 100, -50, 80);
+        VtxZVsL1Iso = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs L1 Isolation", 100,
+                0.0, 5.0, 50, -50, 80);
+        VtxZVsTrkChi2 = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "Vz vs Track Chi2", 50,
+                0, 50, 50, -50, 80);
+        phiEleVsphiEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/phi(e) vs phi(e)", 50, -Math.PI, Math.PI, 50, -Math.PI, Math.PI);
+        pyEleVspyEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Py(e) vs Py(e)", 50, -0.04 * beamEnergy, 0.04 * beamEnergy, 50, -0.04 * beamEnergy,
+                0.04 * beamEnergy);
+        pxEleVspxEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Px(e) vs Px(e)", 50, -0.02 * beamEnergy, 0.06 * beamEnergy, 50, -0.02 * beamEnergy,
+                0.06 * beamEnergy);
+
+        // electron vs electron momentum with different cuts
+        // 1) no cut
+        // 2) cut out FEE
+        // 3) cut out FEE and also cut on momentum sum
+        // 4) cut out everything except FEE coincidentals
+        pEleVspEle = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(e) vs P(e)",
+                50, 0, beamEnergy * maxFactor, 50, 0, beamEnergy * maxFactor);
+        pEleVspEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/P(e) vs P(e) NoBeam", 50, 0, beambeamCut, 50, 0, beambeamCut);
+        pEleVspEleMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/P(e) vs P(e) Moller", 50, 0, beambeamCut, 50, 0, beambeamCut);
+        pEleVspEleBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/P(e) vs P(e) BeamBeam", 50, beambeamCut, beamEnergy * maxFactor, 50, beambeamCut,
+                beamEnergy * maxFactor);
+
+        pyEleVspyEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Py(e) vs Py(e) NoBeam", 50, -0.04 * beamEnergy, 0.04 * beamEnergy, 50,
+                -0.04 * beamEnergy, 0.04 * beamEnergy);
+        pxEleVspxEleNoBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Px(e) vs Px(e) NoBeam", 50, -0.02 * beamEnergy, 0.06 * beamEnergy, 50,
+                -0.02 * beamEnergy, 0.06 * beamEnergy);
+        sumChargeHisto = aida.histogram1D(
+                plotDir + trkType + triggerType + "/" + xtra + "/" + "Total Charge of  Event", 5, -2, 3);
+        numChargeHisto = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "Number of Charged Particles", 6, 0, 6);
+
+        pEleVsthetaMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/P(e) vs Theta Moller", 50, 0, beambeamCut, 50, thetaMin, thetaMax);
+        thetaEleVsthetaMoller = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Theta vs Theta Moller", 50, thetaMin, thetaMax, 50, thetaMin, thetaMax);
+        pEleVsthetaBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/P(e) vs Theta BeamBeam", 50, beambeamCut, beamEnergy * maxFactor, 50, thetaMin, thetaMax);
+        thetaEleVsthetaBeamBeam = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Theta vs Theta BeamBeam", 50, thetaMin, thetaMax, 50, thetaMin, thetaMax);
+
+        mollerMass = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Mass (GeV)", 100, 0, maxMassMoller);
+        mollerMassVtxCut = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Mass (GeV): VtxCut", 100, 0, maxMassMoller);
+        mollerVx = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vx (mm)",
+                50, -10, 10);
+        mollerVy = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vy (mm)",
+                50, -2, 2);
+        mollerVz = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Moller Vz (mm)",
+                50, -50, 50);
+        mollerVzVtxCut = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Vz (mm): VtxCut", 50, -50, 50);
+        mollerXVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Vx vs Vz", 100, -5, 5, 100, -50, 50);
+        mollerYVsVtxZ = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Vy vs Vz", 100, -2, 2, 100, -50, 50);
+        mollerXVsVtxY = aida.histogram2D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Vx vs Vy", 100, -5, 5, 100, -2, 2);
+
+        mollerUx = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Pair Momentum Direction Ux", 100, .015, .045);
+        mollerUy = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/"
+                + "2 Electron/Moller Pair Momentum Direction Uy", 100, -.01, .01);
+
+        mollerHiP = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(high)", 100, 0,
+                beamEnergy * maxFactor);
+        mollerLoP = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(low)", 100, 0,
+                beamEnergy * maxFactor);
+
+        mollerEitherP = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/P(either)",
+                100, 0, beamEnergy * maxFactor);
+        mollerPsum = aida.histogram1D(plotDir + trkType + triggerType + "/" + xtra + "/" + "2 Electron/Psum", 100, 0,
+                beamEnergy * maxFactor);
+
     }
 
+    private BilliorVertex fitVertex(final BilliorTrack electron, final BilliorTrack positron, final double bField) {
+        // Create a vertex fitter from the magnetic field.
+        final double[] beamSize = {0.001, 0.2, 0.02};
+        final BilliorVertexer vtxFitter = new BilliorVertexer(bField);
+        // TODO: The beam size should come from the conditions database.
+        vtxFitter.setBeamSize(beamSize);
+
+        // Perform the vertexing based on the specified constraint.
+        vtxFitter.doBeamSpotConstraint(false);
+
+        // Add the electron and positron tracks to a track list for
+        // the vertex fitter.
+        final List<BilliorTrack> billiorTracks = new ArrayList<BilliorTrack>();
+
+        billiorTracks.add(electron);
+
+        billiorTracks.add(positron);
+
+        // Find and return a vertex based on the tracks.
+        return vtxFitter.fitVertex(billiorTracks);
+    }
+
+    IFitResult fitVertexPosition(final IHistogram1D h1d, final IFitter fitter, final double[] init, final String range) {
+        IFitResult ifr = null;
+        try {
+            ifr = fitter.fit(h1d, "g+p1", init, range);
+        } catch (final RuntimeException ex) {
+            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
+        }
+        return ifr;
+    }
+
     @Override
-    public void process(EventHeader event) {
-        /*  make sure everything is there */
-        if (!event.hasCollection(ReconstructedParticle.class, finalStateParticlesColName))
+    public void printDQMData() {
+        LOGGER.info("V0Monitoring::printDQMData");
+        for (final Entry<String, Double> entry : monitoredQuantityMap.entrySet()) {
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        LOGGER.info("*******************************");
+    }
+
+    @Override
+    public void printDQMStrings() {
+        for (int i = 0; i < 9; i++) {
+            LOGGER.info("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
+        }
+    }
+
+    @Override
+    public void process(final EventHeader event) {
+        /* make sure everything is there */
+        if (!event.hasCollection(ReconstructedParticle.class, finalStateParticlesColName)) {
             return;
-        if (!event.hasCollection(ReconstructedParticle.class, unconstrainedV0CandidatesColName))
+        }
+        if (!event.hasCollection(ReconstructedParticle.class, unconstrainedV0CandidatesColName)) {
             return;
-        if (!event.hasCollection(ReconstructedParticle.class, beamConV0CandidatesColName))
+        }
+        if (!event.hasCollection(ReconstructedParticle.class, beamConV0CandidatesColName)) {
             return;
-        if (!event.hasCollection(ReconstructedParticle.class, targetV0ConCandidatesColName))
+        }
+        if (!event.hasCollection(ReconstructedParticle.class, targetV0ConCandidatesColName)) {
             return;
-
-        //check to see if this event is from the correct trigger (or "all");
-        if (!matchTrigger(event))
+        }
+
+        // check to see if this event is from the correct trigger (or "all");
+        if (!this.matchTrigger(event)) {
             return;
+        }
 
         nRecoEvents++;
 
-        RelationalTable hitToStrips = TrackUtils.getHitToStripsTable(event);
-        RelationalTable hitToRotated = TrackUtils.getHitToRotatedTable(event);
-
-        List<ReconstructedParticle> unonstrainedV0List = event.get(ReconstructedParticle.class, unconstrainedV0CandidatesColName);
-        for (ReconstructedParticle uncV0 : unonstrainedV0List) {
-            if (isGBL != TrackType.isGBL(uncV0.getType()))
+        final RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
+        final RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
+
+        final List<ReconstructedParticle> unonstrainedV0List = event.get(ReconstructedParticle.class,
+                unconstrainedV0CandidatesColName);
+        for (final ReconstructedParticle uncV0 : unonstrainedV0List) {
+            if (isGBL != TrackType.isGBL(uncV0.getType())) {
                 continue;
-            Vertex uncVert = uncV0.getStartVertex();
-            Hep3Vector pVtxRot = VecOp.mult(beamAxisRotation, uncV0.getMomentum());
-            Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, uncVert.getPosition());
-            double theta = Math.acos(pVtxRot.z() / pVtxRot.magnitude());
-            double phi = Math.atan2(pVtxRot.y(), pVtxRot.x());
+            }
+            final Vertex uncVert = uncV0.getStartVertex();
+            final Hep3Vector pVtxRot = VecOp.mult(beamAxisRotation, uncV0.getMomentum());
+            final Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, uncVert.getPosition());
+            final double theta = Math.acos(pVtxRot.z() / pVtxRot.magnitude());
+            final double phi = Math.atan2(pVtxRot.y(), pVtxRot.x());
             unconVx.fill(vtxPosRot.x());
             unconVy.fill(vtxPosRot.y());
             unconVz.fill(vtxPosRot.z());
             unconMass.fill(uncV0.getMass());
             unconChi2.fill(uncVert.getChi2());
             unconVzVsChi2.fill(uncVert.getChi2(), vtxPosRot.z());
-            unconChi2VsTrkChi2.fill(Math.max(uncV0.getParticles().get(0).getTracks().get(0).getChi2(), uncV0.getParticles().get(1).getTracks().get(0).getChi2()), uncVert.getChi2());
+            unconChi2VsTrkChi2.fill(
+                    Math.max(uncV0.getParticles().get(0).getTracks().get(0).getChi2(), uncV0.getParticles().get(1)
+                            .getTracks().get(0).getChi2()), uncVert.getChi2());
 
             VtxZVsMass.fill(uncV0.getMass(), vtxPosRot.z());
             VtxXVsVtxZ.fill(vtxPosRot.x(), vtxPosRot.z());
@@ -290,76 +532,90 @@
             VtxZVsVtxPy.fill(pVtxRot.y(), vtxPosRot.z());
             VtxZVsVtxPz.fill(pVtxRot.z(), vtxPosRot.z());
 
-            //this always has 2 tracks. 
-            List<ReconstructedParticle> trks = uncV0.getParticles();
-//            Track ele = trks.get(0).getTracks().get(0);
-//            Track pos = trks.get(1).getTracks().get(0);
-//            //if track #0 has charge>0 it's the electron!  This seems mixed up, but remember the track 
-//            //charge is assigned assuming a positive B-field, while ours is negative
-//            if (trks.get(0).getCharge() > 0) {
-//                pos = trks.get(0).getTracks().get(0);
-//                ele = trks.get(1).getTracks().get(0);
-//            }
-//            aida.histogram2D(plotDir + trkType + triggerType + "/" + "P(e) vs P(p)").fill(getMomentum(ele), getMomentum(pos));
-//            aida.histogram2D(plotDir + trkType + triggerType + "/" + "Px(e) vs Px(p)").fill(ele.getTrackStates().get(0).getMomentum()[1], pos.getTrackStates().get(0).getMomentum()[1]);
-//            aida.histogram2D(plotDir + trkType + triggerType + "/" + "Py(e) vs Py(p)").fill(ele.getTrackStates().get(0).getMomentum()[2], pos.getTrackStates().get(0).getMomentum()[2]);
+            // this always has 2 tracks.
+            final List<ReconstructedParticle> trks = uncV0.getParticles();
+            // Track ele = trks.get(0).getTracks().get(0);
+            // Track pos = trks.get(1).getTracks().get(0);
+            // //if track #0 has charge>0 it's the electron! This seems mixed up, but remember the track
+            // //charge is assigned assuming a positive B-field, while ours is negative
+            // if (trks.get(0).getCharge() > 0) {
+            // pos = trks.get(0).getTracks().get(0);
+            // ele = trks.get(1).getTracks().get(0);
+            // }
+            // aida.histogram2D(plotDir + trkType + triggerType + "/" + "P(e) vs P(p)").fill(getMomentum(ele),
+            // getMomentum(pos));
+            // aida.histogram2D(plotDir + trkType + triggerType + "/" +
+            // "Px(e) vs Px(p)").fill(ele.getTrackStates().get(0).getMomentum()[1],
+            // pos.getTrackStates().get(0).getMomentum()[1]);
+            // aida.histogram2D(plotDir + trkType + triggerType + "/" +
+            // "Py(e) vs Py(p)").fill(ele.getTrackStates().get(0).getMomentum()[2],
+            // pos.getTrackStates().get(0).getMomentum()[2]);
             ReconstructedParticle ele = trks.get(0);
             ReconstructedParticle pos = trks.get(1);
-            //ReconParticles have the charge correct. 
+            // ReconParticles have the charge correct.
             if (trks.get(0).getCharge() > 0) {
                 pos = trks.get(0);
                 ele = trks.get(1);
             }
             if (ele.getCharge() < 0 && pos.getCharge() > 0) {
-                VtxZVsTrkChi2.fill(Math.max(uncV0.getParticles().get(0).getTracks().get(0).getChi2(), uncV0.getParticles().get(1).getTracks().get(0).getChi2()), uncVert.getPosition().z());
-
-                Double[] eleIso = TrackUtils.getIsolations(ele.getTracks().get(0), hitToStrips, hitToRotated);
-                Double[] posIso = TrackUtils.getIsolations(pos.getTracks().get(0), hitToStrips, hitToRotated);
+                VtxZVsTrkChi2.fill(
+                        Math.max(uncV0.getParticles().get(0).getTracks().get(0).getChi2(), uncV0.getParticles().get(1)
+                                .getTracks().get(0).getChi2()), uncVert.getPosition().z());
+
+                final Double[] eleIso = TrackUtils.getIsolations(ele.getTracks().get(0), hitToStrips, hitToRotated);
+                final Double[] posIso = TrackUtils.getIsolations(pos.getTracks().get(0), hitToStrips, hitToRotated);
                 if (eleIso[0] != null && posIso[0] != null) {
-                    double eleL1Iso = Math.min(Math.abs(eleIso[0]), Math.abs(eleIso[1]));
-                    double posL1Iso = Math.min(Math.abs(posIso[0]), Math.abs(posIso[1]));
-                    double minL1Iso = Math.min(eleL1Iso, posL1Iso);
+                    final double eleL1Iso = Math.min(Math.abs(eleIso[0]), Math.abs(eleIso[1]));
+                    final double posL1Iso = Math.min(Math.abs(posIso[0]), Math.abs(posIso[1]));
+                    final double minL1Iso = Math.min(eleL1Iso, posL1Iso);
                     VtxZVsL1Iso.fill(minL1Iso, uncVert.getPosition().z());
                 }
 
-                double pe = ele.getMomentum().magnitude();
-                double pp = pos.getMomentum().magnitude();
-                Hep3Vector pEleRot = VecOp.mult(beamAxisRotation, ele.getMomentum());
-                Hep3Vector pPosRot = VecOp.mult(beamAxisRotation, pos.getMomentum());
+                final double pe = ele.getMomentum().magnitude();
+                final double pp = pos.getMomentum().magnitude();
+                final Hep3Vector pEleRot = VecOp.mult(beamAxisRotation, ele.getMomentum());
+                final Hep3Vector pPosRot = VecOp.mult(beamAxisRotation, pos.getMomentum());
 
                 pEleVspPos.fill(pe, pp);
+                pEle.fill(pe);
+                pPos.fill(pp);
+
                 pxEleVspxPos.fill(pEleRot.x(), pPosRot.x());
                 pyEleVspyPos.fill(pEleRot.y(), pPosRot.y());
-                if (pe < v0MaxPCut && pp < v0MaxPCut && (pe + pp) > v0ESumMinCut && (pe + pp) < v0ESumMaxCut)//enrich radiative-like events
-                
+                if (pe < v0MaxPCut && pp < v0MaxPCut && pe + pp > v0ESumMinCut && pe + pp < v0ESumMaxCut) {
                     pEleVspPosWithCut.fill(pe, pp);
-            }
-
-            double eleT = TrackUtils.getTrackTime(ele.getTracks().get(0), hitToStrips, hitToRotated);
-            double posT = TrackUtils.getTrackTime(pos.getTracks().get(0), hitToStrips, hitToRotated);
-            double meanT = (eleT + posT) / 2.0;
+                }
+            }
+
+            final double eleT = TrackUtils.getTrackTime(ele.getTracks().get(0), hitToStrips, hitToRotated);
+            final double posT = TrackUtils.getTrackTime(pos.getTracks().get(0), hitToStrips, hitToRotated);
+            final double meanT = (eleT + posT) / 2.0;
             v0Time.fill(meanT);
             v0Dt.fill(eleT - posT);
             trigTimeV0Time.fill(meanT, event.getTimeStamp() % 24);
             trigTime.fill(event.getTimeStamp() % 24);
         }
 
-        List<ReconstructedParticle> beamConstrainedV0List = event.get(ReconstructedParticle.class, beamConV0CandidatesColName);
+        final List<ReconstructedParticle> beamConstrainedV0List = event.get(ReconstructedParticle.class,
+                beamConV0CandidatesColName);
         nV0.fill(beamConstrainedV0List.size());
-        for (ReconstructedParticle bsV0 : beamConstrainedV0List) {
-
-            if (isGBL != TrackType.isGBL(bsV0.getType()))
+        for (final ReconstructedParticle bsV0 : beamConstrainedV0List) {
+
+            if (isGBL != TrackType.isGBL(bsV0.getType())) {
                 continue;
+            }
             nTotV0++;
-            Vertex bsVert = bsV0.getStartVertex();
-            Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, bsVert.getPosition());
+            final Vertex bsVert = bsV0.getStartVertex();
+            final Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, bsVert.getPosition());
             bsconVx.fill(vtxPosRot.x());
             bsconVy.fill(vtxPosRot.y());
             bsconVz.fill(vtxPosRot.z());
             bsconMass.fill(bsV0.getMass());
             bsconChi2.fill(bsVert.getChi2());
             bsconVzVsChi2.fill(bsVert.getChi2(), vtxPosRot.z());
-            bsconChi2VsTrkChi2.fill(Math.max(bsV0.getParticles().get(0).getTracks().get(0).getChi2(), bsV0.getParticles().get(1).getTracks().get(0).getChi2()), bsVert.getChi2());
+            bsconChi2VsTrkChi2.fill(
+                    Math.max(bsV0.getParticles().get(0).getTracks().get(0).getChi2(), bsV0.getParticles().get(1)
+                            .getTracks().get(0).getChi2()), bsVert.getChi2());
             sumMass += bsV0.getMass();
             sumVx += vtxPosRot.x();
             sumVy += vtxPosRot.y();
@@ -367,71 +623,82 @@
             sumChi2 += bsVert.getChi2();
         }
 
-        List<ReconstructedParticle> targetConstrainedV0List = event.get(ReconstructedParticle.class, targetV0ConCandidatesColName);
-        for (ReconstructedParticle tarV0 : targetConstrainedV0List) {
-
-            if (isGBL != TrackType.isGBL(tarV0.getType()))
+        final List<ReconstructedParticle> targetConstrainedV0List = event.get(ReconstructedParticle.class,
+                targetV0ConCandidatesColName);
+        for (final ReconstructedParticle tarV0 : targetConstrainedV0List) {
+
+            if (isGBL != TrackType.isGBL(tarV0.getType())) {
                 continue;
-
-            Vertex tarVert = tarV0.getStartVertex();
-            Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, tarVert.getPosition());
+            }
+
+            final Vertex tarVert = tarV0.getStartVertex();
+            final Hep3Vector vtxPosRot = VecOp.mult(beamAxisRotation, tarVert.getPosition());
             tarconVx.fill(vtxPosRot.x());
             tarconVy.fill(vtxPosRot.y());
             tarconVz.fill(vtxPosRot.z());
             tarconMass.fill(tarV0.getMass());
             tarconChi2.fill(tarVert.getChi2());
             tarconVzVsChi2.fill(tarVert.getChi2(), vtxPosRot.z());
-            tarconChi2VsTrkChi2.fill(Math.max(tarV0.getParticles().get(0).getTracks().get(0).getChi2(), tarV0.getParticles().get(1).getTracks().get(0).getChi2()), tarVert.getChi2());
-        }
-        List<ReconstructedParticle> finalStateParticles = event.get(ReconstructedParticle.class, finalStateParticlesColName);
-        if (debug)
+            tarconChi2VsTrkChi2.fill(
+                    Math.max(tarV0.getParticles().get(0).getTracks().get(0).getChi2(), tarV0.getParticles().get(1)
+                            .getTracks().get(0).getChi2()), tarVert.getChi2());
+        }
+        final List<ReconstructedParticle> finalStateParticles = event.get(ReconstructedParticle.class,
+                finalStateParticlesColName);
+        if (debug) {
             LOGGER.info("This events has " + finalStateParticles.size() + " final state particles");
+        }
 
         ReconstructedParticle ele1 = null;
         ReconstructedParticle ele2 = null;
         int sumCharge = 0;
         int numChargedParticles = 0;
-        for (ReconstructedParticle fsPart : finalStateParticles) {
-            if (isGBL != TrackType.isGBL(fsPart.getType()))
+        for (final ReconstructedParticle fsPart : finalStateParticles) {
+            if (isGBL != TrackType.isGBL(fsPart.getType())) {
                 continue;
-            if (debug)
-                LOGGER.info("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = " + fsPart.getMomentum().x());
-            double charge = fsPart.getCharge();
+            }
+            if (debug) {
+                LOGGER.info("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = "
+                        + fsPart.getMomentum().x());
+            }
+            final double charge = fsPart.getCharge();
             sumCharge += charge;
             if (charge != 0) {
                 numChargedParticles++;
-                if (charge < 1)
-                    if (ele1 == null)
+                if (charge < 1) {
+                    if (ele1 == null) {
                         ele1 = fsPart;
-                    else if (!hasSharedStrips(ele1, fsPart, hitToStrips, hitToRotated))
+                    } else if (!hasSharedStrips(ele1, fsPart, hitToStrips, hitToRotated)) {
                         ele2 = fsPart;
+                    }
+                }
             }
         }
         sumChargeHisto.fill(sumCharge);
         numChargeHisto.fill(numChargedParticles);
 
         if (ele1 != null && ele2 != null) {
-            Hep3Vector p1 = VecOp.mult(beamAxisRotation, ele1.getMomentum());
-            Hep3Vector p2 = VecOp.mult(beamAxisRotation, ele2.getMomentum());
-//            Hep3Vector beamAxis = new BasicHep3Vector(Math.sin(0.0305), 0, Math.cos(0.0305));
-//            LOGGER.info(p1);
-//            LOGGER.info(VecOp.mult(rot, p1));
-
-            double theta1 = Math.acos(p1.z() / p1.magnitude());
-            double theta2 = Math.acos(p2.z() / p2.magnitude());
-            double phi1 = Math.atan2(p1.y(), p1.x());
-            double phi2 = Math.atan2(p2.y(), p2.x());
+            final Hep3Vector p1 = VecOp.mult(beamAxisRotation, ele1.getMomentum());
+            final Hep3Vector p2 = VecOp.mult(beamAxisRotation, ele2.getMomentum());
+            // Hep3Vector beamAxis = new BasicHep3Vector(Math.sin(0.0305), 0, Math.cos(0.0305));
+            // LOGGER.info(p1);
+            // LOGGER.info(VecOp.mult(rot, p1));
+
+            final double theta1 = Math.acos(p1.z() / p1.magnitude());
+            final double theta2 = Math.acos(p2.z() / p2.magnitude());
+            final double phi1 = Math.atan2(p1.y(), p1.x());
+            final double phi2 = Math.atan2(p2.y(), p2.x());
             phiEleVsphiEle.fill(phi1, phi2);
             pEleVspEle.fill(ele1.getMomentum().magnitude(), ele2.getMomentum().magnitude());
             pyEleVspyEle.fill(ele1.getMomentum().y(), ele2.getMomentum().y());
             pxEleVspxEle.fill(ele1.getMomentum().x(), ele2.getMomentum().x());
-            //remove beam electrons
+            // remove beam electrons
             if (ele1.getMomentum().magnitude() < beambeamCut && ele2.getMomentum().magnitude() < beambeamCut) {
                 pEleVspEleNoBeam.fill(ele1.getMomentum().magnitude(), ele2.getMomentum().magnitude());
                 pyEleVspyEleNoBeam.fill(ele1.getMomentum().y(), ele2.getMomentum().y());
                 pxEleVspxEleNoBeam.fill(ele1.getMomentum().x(), ele2.getMomentum().x());
             }
-            //look at beam-beam events
+            // look at beam-beam events
             if (ele1.getMomentum().magnitude() > beambeamCut && ele2.getMomentum().magnitude() > beambeamCut) {
                 pEleVspEleBeamBeam.fill(ele1.getMomentum().magnitude(), ele2.getMomentum().magnitude());
                 pEleVsthetaBeamBeam.fill(p1.magnitude(), theta1);
@@ -439,29 +706,51 @@
                 thetaEleVsthetaBeamBeam.fill(theta1, theta2);
             }
 
-            //look at "Moller" events (if that's what they really are
+            // look at "Moller" events (if that's what they really are
             if (ele1.getMomentum().magnitude() + ele2.getMomentum().magnitude() > molPSumMin
                     && ele1.getMomentum().magnitude() + ele2.getMomentum().magnitude() < molPSumMax
-                    && (p1.magnitude() < beambeamCut && p2.magnitude() < beambeamCut)) {
-
-                Track ele1trk = ele1.getTracks().get(0);
-                Track ele2trk = ele2.getTracks().get(0);
-                SeedTrack stEle1 = TrackUtils.makeSeedTrackFromBaseTrack(ele1trk);
-                SeedTrack stEle2 = TrackUtils.makeSeedTrackFromBaseTrack(ele2trk);
-                BilliorTrack btEle1 = new BilliorTrack(stEle1.getSeedCandidate().getHelix());
-                BilliorTrack btEle2 = new BilliorTrack(stEle2.getSeedCandidate().getHelix());
-                BilliorVertex bv = fitVertex(btEle1, btEle2);
-//                LOGGER.info("ee vertex: "+bv.toString());
-                mollerMass.fill(bv.getParameters().get("invMass"));
+                    && p1.magnitude() < beambeamCut && p2.magnitude() < beambeamCut) {
+
+                final Track ele1trk = ele1.getTracks().get(0);
+                final Track ele2trk = ele2.getTracks().get(0);
+                final SeedTrack stEle1 = TrackUtils.makeSeedTrackFromBaseTrack(ele1trk);
+                final SeedTrack stEle2 = TrackUtils.makeSeedTrackFromBaseTrack(ele2trk);
+                final BilliorTrack btEle1 = new BilliorTrack(stEle1.getSeedCandidate().getHelix());
+                final BilliorTrack btEle2 = new BilliorTrack(stEle2.getSeedCandidate().getHelix());
+                final BilliorVertex bv = this.fitVertex(btEle1, btEle2, TrackUtils.getBField(event.getDetector())
+                        .magnitude());
+                // LOGGER.info("ee vertex: "+bv.toString());
+                final double invMass = bv.getParameters().get("invMass");
+                mollerMass.fill(invMass);
                 mollerVx.fill(bv.getPosition().x());
                 mollerVy.fill(bv.getPosition().y());
                 mollerVz.fill(bv.getPosition().z());
                 mollerXVsVtxZ.fill(bv.getPosition().x(), bv.getPosition().z());
                 mollerYVsVtxZ.fill(bv.getPosition().y(), bv.getPosition().z());
                 mollerXVsVtxY.fill(bv.getPosition().x(), bv.getPosition().y());
-                if (Math.abs(bv.getPosition().x()) < 2
-                        && Math.abs(bv.getPosition().y()) < 0.5) {
-                    mollerMassVtxCut.fill(bv.getParameters().get("invMass"));
+
+                final double ux = (ele1.getMomentum().x() + ele2.getMomentum().x())
+                        / (ele1.getMomentum().z() + ele2.getMomentum().z());
+                final double uy = (ele1.getMomentum().y() + ele2.getMomentum().y())
+                        / (ele1.getMomentum().z() + ele2.getMomentum().z());
+                mollerUx.fill(ux);
+                mollerUy.fill(uy);
+
+                // higher and lower energy electrons in moller pair
+                final double pt1 = ele1.getMomentum().magnitude();
+                final double pt2 = ele2.getMomentum().magnitude();
+                final double ph = pt1 > pt2 ? pt1 : pt2;
+                final double pl = pt1 > pt2 ? pt2 : pt1;
+
+                mollerHiP.fill(ph);
+                mollerLoP.fill(pl);
+
+                mollerEitherP.fill(ph);
+                mollerEitherP.fill(pl);
+                mollerPsum.fill(pt1 + pt2);
+
+                if (Math.abs(bv.getPosition().x()) < 2 && Math.abs(bv.getPosition().y()) < 0.5) {
+                    mollerMassVtxCut.fill(invMass);
                     mollerVzVtxCut.fill(bv.getPosition().z());
                 }
                 pEleVspEleMoller.fill(p1.magnitude(), p2.magnitude());
@@ -471,119 +760,4 @@
             }
         }
     }
-
-    @Override
-    public void printDQMData() {
-        LOGGER.info("V0Monitoring::printDQMData");
-        for (Entry<String, Double> entry : monitoredQuantityMap.entrySet())
-            LOGGER.info(entry.getKey() + " = " + entry.getValue());
-        LOGGER.info("*******************************");
-    }
-
-    /**
-     * Calculate the averages here and fill the map
-     */
-    @Override
-    public void calculateEndOfRunQuantities() {
-
-        IAnalysisFactory analysisFactory = IAnalysisFactory.create();
-        IFitFactory fitFactory = analysisFactory.createFitFactory();
-        IFitter fitter = fitFactory.createFitter("chi2");
-        double[] init = {50.0, 0.0, 0.2, 1.0, 0.0};
-        IFitResult resVx = fitVertexPosition(bsconVx, fitter, init, "range=\"(-0.5,0.5)\"");
-        double[] init2 = {50.0, 0.0, 0.04, 1.0, 0.0};
-        IFitResult resVy = fitVertexPosition(bsconVy, fitter, init2, "range=\"(-0.2,0.2)\"");
-        double[] init3 = {50.0, 0.0, 3.0, 1.0, 0.0};
-        IFitResult resVz = fitVertexPosition(bsconVz, fitter, init3, "range=\"(-6,6)\"");
-
-        if (resVx != null && resVy != null & resVz != null) {
-            double[] parsVx = resVx.fittedParameters();
-            double[] parsVy = resVy.fittedParameters();
-            double[] parsVz = resVz.fittedParameters();
-
-            for (int i = 0; i < 5; i++)
-                LOGGER.info("Vertex Fit Parameters:  " + resVx.fittedParameterNames()[i] + " = " + parsVx[i] + "; " + parsVy[i] + "; " + parsVz[i]);
-
-            IPlotter plotter = analysisFactory.createPlotterFactory().create("Vertex Position");
-            plotter.createRegions(1, 3);
-            IPlotterStyle pstyle = plotter.style();
-            pstyle.legendBoxStyle().setVisible(false);
-            pstyle.dataStyle().fillStyle().setColor("green");
-            pstyle.dataStyle().lineStyle().setColor("black");
-            plotter.region(0).plot(bsconVx);
-            plotter.region(0).plot(resVx.fittedFunction());
-            plotter.region(1).plot(bsconVy);
-            plotter.region(1).plot(resVy.fittedFunction());
-            plotter.region(2).plot(bsconVz);
-            plotter.region(2).plot(resVz.fittedFunction());
-            if (outputPlots)
-                try {
-                    plotter.writeToFile(outputPlotDir + "vertex.png");
-                } catch (IOException ex) {
-                    Logger.getLogger(V0Monitoring.class.getName()).log(Level.SEVERE, null, ex);
-                }
-
-//        monitoredQuantityMap.put(fpQuantNames[2], sumVx / nTotV0);
-//        monitoredQuantityMap.put(fpQuantNames[3], sumVy / nTotV0);
-//        monitoredQuantityMap.put(fpQuantNames[4], sumVz / nTotV0);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[2], parsVx[1]);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[3], parsVy[1]);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[4], parsVz[1]);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[5], parsVx[2]);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[6], parsVy[2]);
-            monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[7], parsVz[2]);
-        }
-        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[0], (double) nTotV0 / nRecoEvents);
-        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[1], sumMass / nTotV0);
-        monitoredQuantityMap.put(beamConV0CandidatesColName + " " + triggerType + " " + fpQuantNames[8], sumChi2 / nTotV0);
-
-    }
-
-    @Override
-    public void printDQMStrings() {
-        for (int i = 0; i < 9; i++)//TODO:  do this in a smarter way...loop over the map
-            LOGGER.info("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
-    }
-
-    IFitResult fitVertexPosition(IHistogram1D h1d, IFitter fitter, double[] init, String range
-    ) {
-        IFitResult ifr = null;
-        try {
-            ifr = fitter.fit(h1d, "g+p1", init, range);
-        } catch (RuntimeException ex) {
-            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
-        }
-        return ifr;
-    }
-
-    private BilliorVertex fitVertex(BilliorTrack electron, BilliorTrack positron) {
-        // Create a vertex fitter from the magnetic field.
-        double bField = 0.24;
-        double[] beamSize = {0.001, 0.2, 0.02};
-        BilliorVertexer vtxFitter = new BilliorVertexer(bField);
-        // TODO: The beam size should come from the conditions database.
-        vtxFitter.setBeamSize(beamSize);
-
-        // Perform the vertexing based on the specified constraint.
-        vtxFitter.doBeamSpotConstraint(false);
-
-        // Add the electron and positron tracks to a track list for
-        // the vertex fitter.
-        List<BilliorTrack> billiorTracks = new ArrayList<BilliorTrack>();
-
-        billiorTracks.add(electron);
-
-        billiorTracks.add(positron);
-
-        // Find and return a vertex based on the tracks.
-        return vtxFitter.fitVertex(billiorTracks);
-    }
-
-    private static boolean hasSharedStrips(ReconstructedParticle vertex, RelationalTable hittostrip, RelationalTable hittorotated) {
-        return hasSharedStrips(vertex.getParticles().get(0), vertex.getParticles().get(1), hittostrip, hittorotated);
-    }
-
-    private static boolean hasSharedStrips(ReconstructedParticle fs1, ReconstructedParticle fs2, RelationalTable hittostrip, RelationalTable hittorotated) {
-        return TrackUtils.hasSharedStrips(fs1.getTracks().get(0), fs2.getTracks().get(0), hittostrip, hittorotated);
-    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalCellIDPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalCellIDPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalCellIDPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -19,63 +19,63 @@
  */
 public class EcalCellIDPrintDriver extends Driver {
 
-	Subdetector ecal;
-	IDDecoder dec;
-	String ecalName = "Ecal";
-	String ecalCollectionName = "EcalReadoutHits";
-	String outputFileName;
-	PrintWriter outputStream = null;
+    Subdetector ecal;
+    IDDecoder dec;
+    String ecalName = "Ecal";
+    String ecalCollectionName = "EcalReadoutHits";
+    String outputFileName;
+    PrintWriter outputStream = null;
 
-	public EcalCellIDPrintDriver() {
-	}
+    public EcalCellIDPrintDriver() {
+    }
 
-	public void setEcalCollectionName(String ecalCollectionName) {
-		this.ecalCollectionName = ecalCollectionName;
-	}
+    public void setEcalCollectionName(String ecalCollectionName) {
+        this.ecalCollectionName = ecalCollectionName;
+    }
 
-	public void setEcalName(String ecalName) {
-		this.ecalName = ecalName;
-	}
+    public void setEcalName(String ecalName) {
+        this.ecalName = ecalName;
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	public void startOfData() {
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+    public void startOfData() {
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void detectorChanged(Detector detector) {
-		// Get the Subdetector.
-		ecal = (Subdetector) detector.getSubdetector(ecalName);
-		dec = ecal.getIDDecoder();
-	}
+    public void detectorChanged(Detector detector) {
+        // Get the Subdetector.
+        ecal = (Subdetector) detector.getSubdetector(ecalName);
+        dec = ecal.getIDDecoder();
+    }
 
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(RawCalorimeterHit.class, ecalCollectionName)) {
-			List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, ecalCollectionName);
-			//outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
-			for (RawCalorimeterHit hit : hits) {
-				dec.setID(hit.getCellID());
-				outputStream.printf("x=%d\ty=%d\n", dec.getValue("ix"), dec.getValue("iy"));
-			}
-		}
-		if (event.hasCollection(RawTrackerHit.class, ecalCollectionName)) {
-			List<RawTrackerHit> hits = event.get(RawTrackerHit.class, ecalCollectionName);
-			//outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
-			for (RawTrackerHit hit : hits) {
-				dec.setID(hit.getCellID());
-				outputStream.printf("x=%d\ty=%d\n", dec.getValue("ix"), dec.getValue("iy"));
-			}
-		}
-	}
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(RawCalorimeterHit.class, ecalCollectionName)) {
+            List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, ecalCollectionName);
+            //outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
+            for (RawCalorimeterHit hit : hits) {
+                dec.setID(hit.getCellID());
+                outputStream.printf("x=%d\ty=%d\n", dec.getValue("ix"), dec.getValue("iy"));
+            }
+        }
+        if (event.hasCollection(RawTrackerHit.class, ecalCollectionName)) {
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, ecalCollectionName);
+            //outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
+            for (RawTrackerHit hit : hits) {
+                dec.setID(hit.getCellID());
+                outputStream.printf("x=%d\ty=%d\n", dec.getValue("ix"), dec.getValue("iy"));
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalClusterPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalClusterPlots.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalClusterPlots.java	Wed Apr 27 11:11:32 2016
@@ -17,7 +17,7 @@
 
 public class EcalClusterPlots extends Driver {
 
-	//AIDAFrame plotterFrame;
+    //AIDAFrame plotterFrame;
     String inputCollection = "EcalClusters";
     AIDA aida = AIDA.defaultInstance();
     IPlotter plotter, plotter2, plotter3, plotter4;
@@ -47,7 +47,7 @@
     @Override
     protected void detectorChanged(Detector detector) {
 
-    	//plotterFrame = new AIDAFrame();
+        //plotterFrame = new AIDAFrame();
         //plotterFrame.setTitle("HPS ECal Cluster Plots");
 
         // Setup the plotter.
@@ -172,6 +172,6 @@
 
     @Override
     public void endOfData() {
-    	//plotterFrame.dispose();
+        //plotterFrame.dispose();
     }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalHitPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalHitPlots.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/EcalHitPlots.java	Wed Apr 27 11:11:32 2016
@@ -192,8 +192,8 @@
                 } else if (AbstractIntData.getTag(data) == SSPData.BANK_TAG) {
                     //SSPData triggerData = new SSPData(data);
                     // TODO: TOP, BOTTOM, AND, and OR trigger are test
-                	// run-specific parameters and are not supported by
-                	// SSPData.
+                    // run-specific parameters and are not supported by
+                    // SSPData.
                     int orTrig = 0; //triggerData.getOrTrig();
                     if(orTrig != 0) {
                         for (int i = 0; i < 32; i++) {
@@ -237,7 +237,7 @@
             double botTime = Double.POSITIVE_INFINITY;
             double orTime = Double.POSITIVE_INFINITY;
             for (CalorimeterHit hit : hits) {
-            	/*
+                /*
                 if (hit.getIdentifierFieldValue("iy") > 0) {
                     topX.fill(hit.getIdentifierFieldValue("ix"),hit.getPosition()[0]);
                     topY.fill(hit.getIdentifierFieldValue("iy"),hit.getPosition()[1]);

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/FEEClusterPlotter.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/FEEClusterPlotter.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/FEEClusterPlotter.java	Wed Apr 27 11:11:32 2016
@@ -28,8 +28,8 @@
 */
 
 public class FEEClusterPlotter extends Driver {
-	
-	//private AIDAFrame plotterFrame;
+    
+    //private AIDAFrame plotterFrame;
     private AIDA aida = AIDA.defaultInstance();
     IPlotter plotter;
     IAnalysisFactory fac = aida.analysisFactory();
@@ -43,6 +43,28 @@
     private String histoNameFormat = "%3d";
     
     private String outputPlots = null;
+    
+    //Set min energy in histo
+    private double minHistoE = 0.5;
+    
+    //Set max energy in histo
+    private double maxHistoE = 1.3;
+    
+    /**
+     * Set the minimum histogram energy
+     * @param minHistoE
+     */
+    public void setMinHistoE(double minHistoE) {
+        this.minHistoE = minHistoE;
+    }
+    
+    /**
+     * Set the maximum histogram energy
+     * @param maxHistoE
+     */
+    public void setMaxHistoE(double maxHistoE) {
+        this.maxHistoE = maxHistoE;
+    }
     
     @Override
     protected void detectorChanged(Detector detector) {
@@ -52,7 +74,7 @@
         
         aida.tree().cd("/");
         for (EcalChannel cc : ecalConditions.getChannelCollection()) {
-            aida.histogram1D(getHistoName(cc),200,0.5,1.3);
+            aida.histogram1D(getHistoName(cc),200,minHistoE,maxHistoE);
         }
 
     }
@@ -61,43 +83,121 @@
         return String.format(histoNameFormat,cc.getChannelId());
     }
     
+    
+    //Set min seed energy value, default to 2015 run
+    private double seedCut = 0.4;
+    
+    //set min cluster time in window, default to 2015 run
+    private double minTime = 30;
+    
+    //set max cluster time in window, default to 2015 run
+    private double maxTime = 70;
+    
+  //set min number of hits in a cluster in row 1, default to 2015 run
+    private int hitCut = 5;
+    
+    //hit cut is only used in 2016 data, not 2015
+    private boolean useHitCut = false;
+    
+    
+    /**
+     * Set the cut value for seed energy in GeV
+     * @param seedCut
+     */
+    public void setSeedCut(double seedCut) {
+        this.seedCut = seedCut;
+    }
+    
+    /**
+     * Set the min time in window to look for cluster
+     * @param minTime
+     */
+    public void setMinTime(double minTime) {
+        this.minTime = minTime;
+    }
+    
+    /**
+     * Set the max time in window to look for cluster
+     * @param maxTime
+     */
+    public void setMaxTime(double maxTime) {
+        this.maxTime = maxTime;
+    }
+    
+    /**
+     * Set the hit cut value for hits in cluster
+     * This cut is used in 2016 running (not 2015)
+     * @param hitCut
+     */
+    public void setHitCut(int hitCut) {
+        this.hitCut = hitCut;
+    }
+    
+    /**
+     * Set the hit cut value for hits in cluster
+     * This cut is used in 2016 running (not 2015)
+     * @param hitCut
+     */
+    public void setUseHitCut(boolean useHitCut) {
+        this.useHitCut = useHitCut;
+    }
+    
     public void process(EventHeader event) {
         aida.tree().cd("/");
 
         //only keep singles triggers:
         if (!event.hasCollection(GenericObject.class,"TriggerBank"))
-        	throw new Driver.NextEventException();
+            throw new Driver.NextEventException();
         boolean isSingles=false;
         for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
-        {	
-        	if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
-        	TIData tid = new TIData(gob);
-        	if (tid.isSingle0Trigger()  || tid.isSingle1Trigger())
-        	{
-        		isSingles=true;
-        		break;
-        	}
+        {   
+            if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
+            TIData tid = new TIData(gob);
+            if (tid.isSingle0Trigger()  || tid.isSingle1Trigger())
+            {
+                isSingles=true;
+                break;
+            }
         }
         
         if (isSingles){
-        	List<Cluster> clusters = event.get(Cluster.class, inputCollection);
-        	for (Cluster clus : clusters) {
-        		List<CalorimeterHit> hits = clus.getCalorimeterHits();
-        		CalorimeterHit seed = hits.get(0);
-        	
-        		double seedE = seed.getCorrectedEnergy();
-        		double clusE = clus.getEnergy();
-        		double time = seed.getTime();
-        			
-        		if ((seedE/clusE > 0.6) && seedE >0.45 && time>30 && time <70){
-        	
-        			EcalChannel cc = findChannel(seed);
-        			aida.histogram1D(getHistoName(cc)).fill(clusE);
-        		}
-        	}
-        }
-    }
-	
+            List<Cluster> clusters = event.get(Cluster.class, inputCollection);
+            for (Cluster clus : clusters) {
+                List<CalorimeterHit> hits = clus.getCalorimeterHits();
+                CalorimeterHit seed = hits.get(0);
+            
+                double seedE = seed.getCorrectedEnergy();
+                double clusE = clus.getEnergy();
+                double time = seed.getTime();
+                
+                //in 2015, not hit count cut used at all
+                if (useHitCut){
+                    if (Math.abs(seed.getIdentifierFieldValue("iy"))==1 && (seedE/clusE > 0.6) && seedE >seedCut 
+                        && time>minTime && time <maxTime && hits.size()>(hitCut+2) ){
+            
+                        EcalChannel cc = findChannel(seed);
+                        aida.histogram1D(getHistoName(cc)).fill(clusE);
+                    }
+                    else if (Math.abs(seed.getIdentifierFieldValue("iy"))>1 && (seedE/clusE > 0.6) && seedE >seedCut 
+                        && time>minTime && time <maxTime && hits.size()>(hitCut) ){
+                        
+                        EcalChannel cc = findChannel(seed);
+                        aida.histogram1D(getHistoName(cc)).fill(clusE);
+                    }
+                }
+                else {
+                    if ((seedE/clusE > 0.6) && seedE >seedCut 
+                            && time>minTime && time <maxTime ){
+                
+                            EcalChannel cc = findChannel(seed);
+                            aida.histogram1D(getHistoName(cc)).fill(clusE);
+                         
+                    }   
+                }   
+            }
+        }
+    }
+    
     public void setOutputPlots(String output) {
         this.outputPlots = output;
     }
@@ -119,5 +219,5 @@
                 Logger.getLogger(FEEClusterPlotter.class.getName()).log(Level.SEVERE, null, ex);
             }
         }
-    }	
+    }   
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalFADCPlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalFADCPlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalFADCPlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -20,90 +20,90 @@
  */
 public class HPSEcalFADCPlotsDriver extends Driver {
 
-	String edepCollectionName = "EcalHits";
-	String rawCollectionName = null;
-	String ecalCollectionName = null;
-	String clusterCollectionName = "EcalClusters";
-	AIDA aida = AIDA.defaultInstance();
-	IHistogram1D edepE;
-	IHistogram1D rawE;
-	IHistogram1D ecalE;
-	IHistogram1D clusterE;
-	ICloud2D window_E;
-	double edepThreshold = 0.05;
+    String edepCollectionName = "EcalHits";
+    String rawCollectionName = null;
+    String ecalCollectionName = null;
+    String clusterCollectionName = "EcalClusters";
+    AIDA aida = AIDA.defaultInstance();
+    IHistogram1D edepE;
+    IHistogram1D rawE;
+    IHistogram1D ecalE;
+    IHistogram1D clusterE;
+    ICloud2D window_E;
+    double edepThreshold = 0.05;
 
-	public void setEdepThreshold(double edepThreshold) {
-		this.edepThreshold = edepThreshold;
-	}
+    public void setEdepThreshold(double edepThreshold) {
+        this.edepThreshold = edepThreshold;
+    }
 
-	public void setRawCollectionName(String rawCollectionName) {
-		this.rawCollectionName = rawCollectionName;
-	}
+    public void setRawCollectionName(String rawCollectionName) {
+        this.rawCollectionName = rawCollectionName;
+    }
 
-	public void setEcalCollectionName(String ecalCollectionName) {
-		this.ecalCollectionName = ecalCollectionName;
-	}
+    public void setEcalCollectionName(String ecalCollectionName) {
+        this.ecalCollectionName = ecalCollectionName;
+    }
 
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
 
-	public void startOfData() {
-		edepE = aida.histogram1D(
-				"FADC plots: " + edepCollectionName + " : Hits",
-				500, 0.0, 5.0);
-		if (rawCollectionName != null) {
-			rawE = aida.histogram1D(
-					"FADC plots: " + rawCollectionName + " : Hits",
-					500, 0.0, 500.0);
-			window_E = aida.cloud2D("FADC plots: " + rawCollectionName + " : Window vs. E");
-		}
-		if (ecalCollectionName != null) {
-			ecalE = aida.histogram1D(
-					"FADC plots: " + ecalCollectionName + " : Hits",
-					500, 0.0, 5.0);
-		}
-		clusterE = aida.histogram1D(
-				"FADC plots: " + clusterCollectionName + " : Clusters",
-				500, 0.0, 5.0);
-	}
+    public void startOfData() {
+        edepE = aida.histogram1D(
+                "FADC plots: " + edepCollectionName + " : Hits",
+                500, 0.0, 5.0);
+        if (rawCollectionName != null) {
+            rawE = aida.histogram1D(
+                    "FADC plots: " + rawCollectionName + " : Hits",
+                    500, 0.0, 500.0);
+            window_E = aida.cloud2D("FADC plots: " + rawCollectionName + " : Window vs. E");
+        }
+        if (ecalCollectionName != null) {
+            ecalE = aida.histogram1D(
+                    "FADC plots: " + ecalCollectionName + " : Hits",
+                    500, 0.0, 5.0);
+        }
+        clusterE = aida.histogram1D(
+                "FADC plots: " + clusterCollectionName + " : Clusters",
+                500, 0.0, 5.0);
+    }
 
-	public void process(EventHeader event) {
-		List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
-		if (clusters == null)
-			throw new RuntimeException("Missing cluster collection!");
+    public void process(EventHeader event) {
+        List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
+        if (clusters == null)
+            throw new RuntimeException("Missing cluster collection!");
 
-		List<CalorimeterHit> edepHits = event.get(CalorimeterHit.class, edepCollectionName);
-		if (edepHits == null)
-			throw new RuntimeException("Missing hit collection!");
+        List<CalorimeterHit> edepHits = event.get(CalorimeterHit.class, edepCollectionName);
+        if (edepHits == null)
+            throw new RuntimeException("Missing hit collection!");
 
-		if (rawCollectionName != null) {
-			List<RawCalorimeterHit> rawHits = event.get(RawCalorimeterHit.class, rawCollectionName);
-			if (rawHits == null)
-				throw new RuntimeException("Missing hit collection!");
+        if (rawCollectionName != null) {
+            List<RawCalorimeterHit> rawHits = event.get(RawCalorimeterHit.class, rawCollectionName);
+            if (rawHits == null)
+                throw new RuntimeException("Missing hit collection!");
 
-			for (RawCalorimeterHit hit : rawHits) {
-				rawE.fill(hit.getAmplitude());
-				//window_E.fill(hit.getAmplitude(),hit.getWindowSize());
-			}
-		}
+            for (RawCalorimeterHit hit : rawHits) {
+                rawE.fill(hit.getAmplitude());
+                //window_E.fill(hit.getAmplitude(),hit.getWindowSize());
+            }
+        }
 
-		if (ecalCollectionName != null) {
-			List<CalorimeterHit> ecalHits = event.get(CalorimeterHit.class, ecalCollectionName);
-			if (ecalHits == null)
-				throw new RuntimeException("Missing hit collection!");
+        if (ecalCollectionName != null) {
+            List<CalorimeterHit> ecalHits = event.get(CalorimeterHit.class, ecalCollectionName);
+            if (ecalHits == null)
+                throw new RuntimeException("Missing hit collection!");
 
-			for (CalorimeterHit hit : ecalHits) {
-				ecalE.fill(hit.getRawEnergy());
-			}
-		}
+            for (CalorimeterHit hit : ecalHits) {
+                ecalE.fill(hit.getRawEnergy());
+            }
+        }
 
-		for (CalorimeterHit hit : edepHits) {
-			if (hit.getRawEnergy() > edepThreshold)
-				edepE.fill(hit.getRawEnergy());
-		}
-		for (Cluster cluster : clusters) {
-			clusterE.fill(cluster.getEnergy());
-		}
-	}
+        for (CalorimeterHit hit : edepHits) {
+            if (hit.getRawEnergy() > edepThreshold)
+                edepE.fill(hit.getRawEnergy());
+        }
+        for (Cluster cluster : clusters) {
+            clusterE.fill(cluster.getEnergy());
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalTriggerPlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalTriggerPlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSEcalTriggerPlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
  * Exp $
  */
 public class HPSEcalTriggerPlotsDriver extends Driver {
-	// LCSim collection names.
+    // LCSim collection names.
     String ecalCollectionName = "EcalHits";
     String clusterCollectionName = "EcalClusters";
     
@@ -55,46 +55,46 @@
     }
     
     public void startOfData() {
-    	// Initialize a hit histogram for each declared energy.
-    	for(int e = 0; e < energyCut.length; e++) {
-    		hitXYPlot[e] = aida.histogram2D("Trigger Plots: " + ecalCollectionName +
-    				" : Hits above " + energyCut[e] + " MeV", 46, -23, 23, 11, -5.5, 5.5);
-    	}
-    	// Initialize the remaining plots.
+        // Initialize a hit histogram for each declared energy.
+        for(int e = 0; e < energyCut.length; e++) {
+            hitXYPlot[e] = aida.histogram2D("Trigger Plots: " + ecalCollectionName +
+                    " : Hits above " + energyCut[e] + " MeV", 46, -23, 23, 11, -5.5, 5.5);
+        }
+        // Initialize the remaining plots.
         crystalDeadTime = aida.histogram2D("Trigger Plots: " + ecalCollectionName +
-        		" : Crystal dead time", 46, -23, 23, 11, -5.5, 5.5);
+                " : Crystal dead time", 46, -23, 23, 11, -5.5, 5.5);
         clusterHitXYPlot = aida.histogram2D("Trigger Plots: " + clusterCollectionName +
-        		" : Crystals in clusters", 47, -23.5, 23.5, 11, -5.5, 5.5);
+                " : Crystals in clusters", 47, -23.5, 23.5, 11, -5.5, 5.5);
         seedHitXYPlot = aida.histogram2D("Trigger Plots: " + clusterCollectionName +
-        		" : Seed hits", 47, -23.5, 23.5, 11, -5.5, 5.5);
+                " : Seed hits", 47, -23.5, 23.5, 11, -5.5, 5.5);
         triggerClusterHitXYPlot = aida.histogram2D("Trigger Plots: " + clusterCollectionName +
                 " : Crystals in clusters, with trigger", 47, -23.5, 23.5, 11, -5.5, 5.5);
         triggerSeedHitXYPlot = aida.histogram2D("Trigger Plots: " + clusterCollectionName +
-        		" : Seed hits, with trigger", 47, -23.5, 23.5, 11, -5.5, 5.5);
+                " : Seed hits, with trigger", 47, -23.5, 23.5, 11, -5.5, 5.5);
     }
     
     public void process(EventHeader event) {
-    	// If the current event has the indicated hit collection,
-    	// use it as the hit list.
-    	List<CalorimeterHit> hits;
-    	if(event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
-    		hits = event.get(CalorimeterHit.class, ecalCollectionName);
-    	}
-    	// If it does not, then use an empty list to avoid crashing.
-    	else { hits = new ArrayList<CalorimeterHit>(0); }
-    	
-    	// If the current event has the indicated cluster collection,
-    	// use it as the cluster list.
-    	List<Cluster> clusters;
-    	if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-    		clusters = event.get(Cluster.class, clusterCollectionName);
-    	}
-    	// If it does not, then use an empty list to avoid crashing.
-    	else { clusters = new ArrayList<Cluster>(0); }
+        // If the current event has the indicated hit collection,
+        // use it as the hit list.
+        List<CalorimeterHit> hits;
+        if(event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
+            hits = event.get(CalorimeterHit.class, ecalCollectionName);
+        }
+        // If it does not, then use an empty list to avoid crashing.
+        else { hits = new ArrayList<CalorimeterHit>(0); }
+        
+        // If the current event has the indicated cluster collection,
+        // use it as the cluster list.
+        List<Cluster> clusters;
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            clusters = event.get(Cluster.class, clusterCollectionName);
+        }
+        // If it does not, then use an empty list to avoid crashing.
+        else { clusters = new ArrayList<Cluster>(0); }
         
         // Populate hit plots.
         for (CalorimeterHit hit : hits) {
-        	// Get the hit crystal position.
+            // Get the hit crystal position.
             int ix = hit.getIdentifierFieldValue("ix");
             int iy = hit.getIdentifierFieldValue("iy");
             double energy = hit.getRawEnergy();
@@ -102,9 +102,9 @@
             // Loop through the energy plots and fill them if the hit
             // is over the current energy threshold/
             for(int e = 0; e < energyCut.length; e++) {
-            	if(energy > energyCut[e] * EcalUtils.MeV) {
-            		hitXYPlot[e].fill(ix - 0.5 * Math.signum(ix), iy);
-            	}
+                if(energy > energyCut[e] * EcalUtils.MeV) {
+                    hitXYPlot[e].fill(ix - 0.5 * Math.signum(ix), iy);
+                }
             }
             
             // Generate the dead time plot.
@@ -121,8 +121,8 @@
         
         // Populate cluster based plots.
         for (Cluster cluster : clusters) {
-        	// Get the cluster's seed hit position.
-        	CalorimeterHit seed = cluster.getCalorimeterHits().get(0);
+            // Get the cluster's seed hit position.
+            CalorimeterHit seed = cluster.getCalorimeterHits().get(0);
             int ix = seed.getIdentifierFieldValue("ix");
             int iy = seed.getIdentifierFieldValue("iy");
             
@@ -135,7 +135,7 @@
             
             // Populate the component hit histogram.
             for (CalorimeterHit hit : cluster.getCalorimeterHits()) {
-            	// Get the component hit location.
+                // Get the component hit location.
                 ix = hit.getIdentifierFieldValue("ix");
                 iy = hit.getIdentifierFieldValue("iy");
                 

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSMCParticlePlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSMCParticlePlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/HPSMCParticlePlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -25,138 +25,138 @@
  */
 public class HPSMCParticlePlotsDriver extends Driver {
 
-	AIDA aida = AIDA.defaultInstance();
+    AIDA aida = AIDA.defaultInstance();
         //private AIDAFrame pFrame;
         IAnalysisFactory af = aida.analysisFactory();
         public boolean _hideFrame = false;
         // MCParticle plots.
-	ICloud1D primaryEPlot;
-	ICloud1D fsCountPlot;
-	IHistogram1D fsCountVsEventPlot;
-	ICloud1D fsCountTypePlot;
-	ICloud1D fsCountEventTypePlot;
-	ICloud1D fsCountEventTypePlot2;
-	ICloud1D fsCountTypePlot500;
-	IHistogram1D fsEPlot;
-	IHistogram1D fsGammaEPlot;
-	IHistogram1D fsElectronEPlot;
-	IHistogram1D fsPositronEPlot;
-	IHistogram1D fsThetayPlot;
-	ICloud1D fsGammaThetaPlot;
-	IHistogram1D fsGammaThetayPlot;
-	IHistogram1D fsGammaThetayTrigPlot;
-	ICloud2D fsGammaThetayEPlot;
-	ICloud1D fsElectronThetaPlot;
-	IHistogram1D fsElectronThetayPlot;
-	IHistogram1D fsElectronThetayTrigPlot;
-	ICloud2D fsElectronThetayEPlot;
-	ICloud1D fsPositronThetaPlot;
-	IHistogram1D fsPositronThetayPlot;
-	IHistogram1D fsPositronThetayTrigPlot;
-	ICloud2D fsPositronThetayEPlot;
+    ICloud1D primaryEPlot;
+    ICloud1D fsCountPlot;
+    IHistogram1D fsCountVsEventPlot;
+    ICloud1D fsCountTypePlot;
+    ICloud1D fsCountEventTypePlot;
+    ICloud1D fsCountEventTypePlot2;
+    ICloud1D fsCountTypePlot500;
+    IHistogram1D fsEPlot;
+    IHistogram1D fsGammaEPlot;
+    IHistogram1D fsElectronEPlot;
+    IHistogram1D fsPositronEPlot;
+    IHistogram1D fsThetayPlot;
+    ICloud1D fsGammaThetaPlot;
+    IHistogram1D fsGammaThetayPlot;
+    IHistogram1D fsGammaThetayTrigPlot;
+    ICloud2D fsGammaThetayEPlot;
+    ICloud1D fsElectronThetaPlot;
+    IHistogram1D fsElectronThetayPlot;
+    IHistogram1D fsElectronThetayTrigPlot;
+    ICloud2D fsElectronThetayEPlot;
+    ICloud1D fsPositronThetaPlot;
+    IHistogram1D fsPositronThetayPlot;
+    IHistogram1D fsPositronThetayTrigPlot;
+    ICloud2D fsPositronThetayEPlot;
         ICloud1D eventEPlot;
 
-	class MCParticleEComparator implements Comparator<MCParticle> {
-
-		public int compare(MCParticle p1, MCParticle p2) {
-			double e1 = p1.getEnergy();
-			double e2 = p2.getEnergy();
-			if (e1 < e2) {
-				return -1;
-			} else if (e1 == e2) {
-				return 0;
-			} else {
-				return 1;
-			}
-		}
-	}
+    class MCParticleEComparator implements Comparator<MCParticle> {
+
+        public int compare(MCParticle p1, MCParticle p2) {
+            double e1 = p1.getEnergy();
+            double e2 = p2.getEnergy();
+            if (e1 < e2) {
+                return -1;
+            } else if (e1 == e2) {
+                return 0;
+            } else {
+                return 1;
+            }
+        }
+    }
 
         public void setHideFrame(boolean hideFrame) {
             this._hideFrame = hideFrame;
         }
         
         
-	@Override
-	public void startOfData() {
-		fsCountPlot = aida.cloud1D("MCParticle: Number of Final State Particles");
-		fsCountPlot.annotation().addItem("xAxisLabel", "Number of FS Particles");
+    @Override
+    public void startOfData() {
+        fsCountPlot = aida.cloud1D("MCParticle: Number of Final State Particles");
+        fsCountPlot.annotation().addItem("xAxisLabel", "Number of FS Particles");
                 
                 fsCountVsEventPlot = aida.histogram1D("MCParticle: Number of Final State Particles vs Event Nr", 501, -0.5, 500.5);
-		fsCountVsEventPlot.annotation().addItem("xAxisLabel", "Event Number");
+        fsCountVsEventPlot.annotation().addItem("xAxisLabel", "Event Number");
 
                 fsCountTypePlot = aida.cloud1D("MCParticle: Number of Final State Particles Type");
-		fsCountTypePlot.annotation().addItem("xAxisLabel", "Number of FS Particles of Type");
+        fsCountTypePlot.annotation().addItem("xAxisLabel", "Number of FS Particles of Type");
 
                 fsCountTypePlot500 = aida.cloud1D("MCParticle: Number of Final State Particles Type E>0.5GeV");
-		fsCountTypePlot500.annotation().addItem("xAxisLabel", "Number of FS Particles of Type E>0.5GeV");
+        fsCountTypePlot500.annotation().addItem("xAxisLabel", "Number of FS Particles of Type E>0.5GeV");
 
                 fsCountEventTypePlot = aida.cloud1D("MCParticle: Number of Final State Types");
-		fsCountEventTypePlot.annotation().addItem("xAxisLabel", "Number of FS Types");
+        fsCountEventTypePlot.annotation().addItem("xAxisLabel", "Number of FS Types");
 
                 fsCountEventTypePlot2 = aida.cloud1D("MCParticle: Number of Final State Types Gamma E>500");
-		fsCountEventTypePlot2.annotation().addItem("xAxisLabel", "Number of FS Types Gamma E>500");                
-                
-		fsEPlot = aida.histogram1D("MCParticle: FS Particle E",100,0,3);
-		fsEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
-
-		fsGammaEPlot = aida.histogram1D("MCParticle: FS Gamma E",100,0,3);
-		fsGammaEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
-
-		fsElectronEPlot = aida.histogram1D("MCParticle: FS Electron E",100,0,3);
-		fsElectronEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
-
-		fsPositronEPlot = aida.histogram1D("MCParticle: FS Positron E",100,0,3);
-		fsPositronEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
-
-		fsGammaThetaPlot = aida.cloud1D("MCParticle: FS Gamma Theta");
-		fsGammaThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
+        fsCountEventTypePlot2.annotation().addItem("xAxisLabel", "Number of FS Types Gamma E>500");                
+                
+        fsEPlot = aida.histogram1D("MCParticle: FS Particle E",100,0,3);
+        fsEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
+
+        fsGammaEPlot = aida.histogram1D("MCParticle: FS Gamma E",100,0,3);
+        fsGammaEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
+
+        fsElectronEPlot = aida.histogram1D("MCParticle: FS Electron E",100,0,3);
+        fsElectronEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
+
+        fsPositronEPlot = aida.histogram1D("MCParticle: FS Positron E",100,0,3);
+        fsPositronEPlot.annotation().addItem("xAxisLabel", "Particle E [GeV]");
+
+        fsGammaThetaPlot = aida.cloud1D("MCParticle: FS Gamma Theta");
+        fsGammaThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
 
                 fsThetayPlot = aida.histogram1D("MCParticle: FS Particle Thetay",100,0,0.1);
-		fsThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 
                 fsGammaThetayPlot = aida.histogram1D("MCParticle: FS Gamma Thetay",100,0,0.1);
-		fsGammaThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsGammaThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 fsGammaThetayTrigPlot = aida.histogram1D("MCParticle: FS Gamma Thetay Trig",100,0,0.1);
-		fsGammaThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsGammaThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
              
                 fsGammaThetayEPlot = aida.cloud2D("MCParticle: FS Gamma Thetay vs E");
-		fsGammaThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
-		fsGammaThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
-                
-		fsElectronThetaPlot = aida.cloud1D("MCParticle: FS Electron Theta");
-		fsElectronThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
+        fsGammaThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsGammaThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
+                
+        fsElectronThetaPlot = aida.cloud1D("MCParticle: FS Electron Theta");
+        fsElectronThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
 
                 fsElectronThetayPlot = aida.histogram1D("MCParticle: FS Electron Thetay",100,0,0.1);
-		fsElectronThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsElectronThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 fsElectronThetayTrigPlot = aida.histogram1D("MCParticle: FS Electron Thetay Trig",100,0,0.1);
-		fsElectronThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsElectronThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 fsElectronThetayEPlot = aida.cloud2D("MCParticle: FS Electron Thetay vs E");
-		fsElectronThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
-		fsElectronThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
-
-		fsPositronThetaPlot = aida.cloud1D("MCParticle: FS Positron Theta");
-		fsPositronThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
+        fsElectronThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsElectronThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
+
+        fsPositronThetaPlot = aida.cloud1D("MCParticle: FS Positron Theta");
+        fsPositronThetaPlot.annotation().addItem("xAxisLabel", "Particle angle [rad]");
 
                 fsPositronThetayPlot = aida.histogram1D("MCParticle: FS Positron Thetay",100,0,0.1);
-		fsPositronThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsPositronThetayPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 fsPositronThetayTrigPlot = aida.histogram1D("MCParticle: FS Positron Thetay Trig",100,0,0.1);
-		fsPositronThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsPositronThetayTrigPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
 
                 fsPositronThetayEPlot = aida.cloud2D("MCParticle: FS Positron Thetay vs E");
-		fsPositronThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
-		fsPositronThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
-
-                
-		primaryEPlot = aida.cloud1D("MCParticle: Highest Primary E in Event");
-		primaryEPlot.annotation().addItem("xAxisLabel", "E [GeV]");
-
-		eventEPlot = aida.cloud1D("MCParticle: Total Gen FS Electron E in Event");
-		eventEPlot.annotation().addItem("xAxisLabel", "E [GeV]");
+        fsPositronThetayEPlot.annotation().addItem("xAxisLabel", "Particle Thetay angle [rad]");
+        fsPositronThetayEPlot.annotation().addItem("yAxisLabel", "Particle Energy [GeV]");
+
+                
+        primaryEPlot = aida.cloud1D("MCParticle: Highest Primary E in Event");
+        primaryEPlot.annotation().addItem("xAxisLabel", "E [GeV]");
+
+        eventEPlot = aida.cloud1D("MCParticle: Total Gen FS Electron E in Event");
+        eventEPlot.annotation().addItem("xAxisLabel", "E [GeV]");
 
                 
                 //pFrame = new AIDAFrame();
@@ -205,19 +205,19 @@
                 
                 
                 
-	}
-
-	@Override
-	public void process(EventHeader event) {
-
-		// MCParticles
-		List<MCParticle> mcparticles = event.get(MCParticle.class).get(0);
-
-		// Final State particles.
-		List<MCParticle> fsParticles = makeGenFSParticleList(mcparticles);
-
-		//System.out.println("fsParticles="+fsParticles.size());
-		fsCountPlot.fill(fsParticles.size());
+    }
+
+    @Override
+    public void process(EventHeader event) {
+
+        // MCParticles
+        List<MCParticle> mcparticles = event.get(MCParticle.class).get(0);
+
+        // Final State particles.
+        List<MCParticle> fsParticles = makeGenFSParticleList(mcparticles);
+
+        //System.out.println("fsParticles="+fsParticles.size());
+        fsCountPlot.fill(fsParticles.size());
                 
                 for (int i=0;i<fsParticles.size();++i) fsCountVsEventPlot.fill(event.getEventNumber());
                 
@@ -229,69 +229,69 @@
                 int[] ngammas = {0,0};
                 int count = 0;
                 double trigThr = 0.2;
-		for (MCParticle fs : fsParticles) {
+        for (MCParticle fs : fsParticles) {
                         //System.out.println("Index " + count);
 
-			double fsE = fs.getEnergy();
-			double theta = Math.atan2(Math.sqrt(fs.getPX() * fs.getPX() + fs.getPY() * fs.getPY()), fs.getPZ());
-			double thetay = Math.atan2(fs.getPY(), fs.getPZ());
-			int fsPdg = fs.getPDGID();
-			fsEPlot.fill(fsE);
+            double fsE = fs.getEnergy();
+            double theta = Math.atan2(Math.sqrt(fs.getPX() * fs.getPX() + fs.getPY() * fs.getPY()), fs.getPZ());
+            double thetay = Math.atan2(fs.getPY(), fs.getPZ());
+            int fsPdg = fs.getPDGID();
+            fsEPlot.fill(fsE);
                         this.fsThetayPlot.fill(Math.abs(thetay));
                         fsCountTypePlot.fill(fsPdg);
                         if(fsE>0.5) fsCountTypePlot500.fill(fsPdg);
-			if (ParticleTypeClassifier.isElectron(fsPdg)) {
-				fsElectronEPlot.fill(fsE);
-				fsElectronThetaPlot.fill(theta);
-				fsElectronThetayPlot.fill(Math.abs(thetay));
-				if(fsE>trigThr) fsElectronThetayTrigPlot.fill(Math.abs(thetay));
-				fsElectronThetayEPlot.fill(Math.abs(thetay),fsE);
+            if (ParticleTypeClassifier.isElectron(fsPdg)) {
+                fsElectronEPlot.fill(fsE);
+                fsElectronThetaPlot.fill(theta);
+                fsElectronThetayPlot.fill(Math.abs(thetay));
+                if(fsE>trigThr) fsElectronThetayTrigPlot.fill(Math.abs(thetay));
+                fsElectronThetayEPlot.fill(Math.abs(thetay),fsE);
                                 nelectrons[0]++;
                                 if(fsGammaEmax>0.5) nelectrons[1]++; 
-			} else if (ParticleTypeClassifier.isPositron(fsPdg)) {
-				fsPositronEPlot.fill(fsE);
-				fsPositronThetaPlot.fill(theta);
-				fsPositronThetayPlot.fill(Math.abs(thetay));
-				if(fsE>trigThr) fsPositronThetayTrigPlot.fill(Math.abs(thetay));
-				fsPositronThetayEPlot.fill(Math.abs(thetay),fsE);
+            } else if (ParticleTypeClassifier.isPositron(fsPdg)) {
+                fsPositronEPlot.fill(fsE);
+                fsPositronThetaPlot.fill(theta);
+                fsPositronThetayPlot.fill(Math.abs(thetay));
+                if(fsE>trigThr) fsPositronThetayTrigPlot.fill(Math.abs(thetay));
+                fsPositronThetayEPlot.fill(Math.abs(thetay),fsE);
                                 npositrons[0]++;
                                 if(fsGammaEmax>0.5) npositrons[1]++; 
-			} else if (ParticleTypeClassifier.isPhoton(fsPdg)) {
-				fsGammaEPlot.fill(fsE);
-				fsGammaThetaPlot.fill(theta);
-				fsGammaThetayPlot.fill(Math.abs(thetay));
-				if(fsE>trigThr) fsGammaThetayTrigPlot.fill(Math.abs(thetay));
-				fsGammaThetayEPlot.fill(Math.abs(thetay),fsE);
+            } else if (ParticleTypeClassifier.isPhoton(fsPdg)) {
+                fsGammaEPlot.fill(fsE);
+                fsGammaThetaPlot.fill(theta);
+                fsGammaThetayPlot.fill(Math.abs(thetay));
+                if(fsE>trigThr) fsGammaThetayTrigPlot.fill(Math.abs(thetay));
+                fsGammaThetayEPlot.fill(Math.abs(thetay),fsE);
                                 ngammas[0]++;
                                 if(fsGammaEmax>0.5) {
                                     ngammas[1]++;
                                     //System.out.println("Counting high E gamma at count "+ count);
                                 } 
-			}
-		}
+            }
+        }
 
                 fsCountEventTypePlot.fill(getEventTypeId(nelectrons[0],npositrons[0],ngammas[0]));
                 fsCountEventTypePlot2.fill(getEventTypeId(nelectrons[1],npositrons[1],ngammas[1]));
 
-		// Sort MCParticles on energy.
-		//Collections.sort(fsParticles, new MCParticleEComparator());
-
-		// Energy of top two FS particles.
-		//double e2 = fsParticles.get(0).getEnergy() + fsParticles.get(1).getEnergy();
-
-		// Energy of top three FS particles.
-		//double e3 = e2 + fsParticles.get(2).getEnergy();
-
-		if (!fsParticles.isEmpty()) {
-			// primary particle with most E
-			double primaryE = getPrimary(fsParticles).getEnergy();
-			primaryEPlot.fill(primaryE);
-		}
-
-		// event electron energy
-		double eventE = getPrimaryElectronE(fsParticles);
-		eventEPlot.fill(eventE);
-	}
+        // Sort MCParticles on energy.
+        //Collections.sort(fsParticles, new MCParticleEComparator());
+
+        // Energy of top two FS particles.
+        //double e2 = fsParticles.get(0).getEnergy() + fsParticles.get(1).getEnergy();
+
+        // Energy of top three FS particles.
+        //double e3 = e2 + fsParticles.get(2).getEnergy();
+
+        if (!fsParticles.isEmpty()) {
+            // primary particle with most E
+            double primaryE = getPrimary(fsParticles).getEnergy();
+            primaryEPlot.fill(primaryE);
+        }
+
+        // event electron energy
+        double eventE = getPrimaryElectronE(fsParticles);
+        eventEPlot.fill(eventE);
+    }
 
         
         public int getEventTypeId(int ne, int np, int ng) {
@@ -314,57 +314,57 @@
             return 0;
         }
         
-	public double getHighestPhotonE(List<MCParticle> particles) {
-		double Emax = -1;
+    public double getHighestPhotonE(List<MCParticle> particles) {
+        double Emax = -1;
                 double E=0;
                 int count = 0;
-		for (MCParticle particle : particles) {
-			if (ParticleTypeClassifier.isPhoton(particle.getPDGID())) {
-				E = particle.getEnergy();
+        for (MCParticle particle : particles) {
+            if (ParticleTypeClassifier.isPhoton(particle.getPDGID())) {
+                E = particle.getEnergy();
                                 if(E>Emax) {
                                     Emax = E;
                                     //System.out.println("Emax from photon with index " + count);
                                 }
-			count++;
+            count++;
                         }
-		}
-		return Emax;
-	}
+        }
+        return Emax;
+    }
 
         private double getPrimaryElectronE(List<MCParticle> particles) {
-		double totalE = 0;
-		for (MCParticle particle : particles) {
-			if (Math.abs(particle.getPDGID()) == 11) {
-				totalE += particle.getEnergy();
-			}
-		}
-		return totalE;
-	}
-
-	private MCParticle getPrimary(List<MCParticle> particles) {
-		double maxE = 0;
-		MCParticle primary = null;
-		for (MCParticle particle : particles) {
-			if (particle.getEnergy() > maxE) {
-				maxE = particle.getEnergy();
-				primary = particle;
-			}
-		}
-		return primary;
-	}
-
-	public static List<MCParticle> makeGenFSParticleList(List<MCParticle> mcparticles) {
-		List<MCParticle> fsParticles = new ArrayList<MCParticle>();
-		for (MCParticle mcparticle : mcparticles) {
-			if (mcparticle.getGeneratorStatus() == MCParticle.FINAL_STATE) {
-				double theta = Math.atan2(Math.sqrt(mcparticle.getPX() * mcparticle.getPX() + mcparticle.getPY() * mcparticle.getPY()), mcparticle.getPZ());
-				if (theta > 1e-3) {
-					fsParticles.add(mcparticle);
-				}
-			}
-		}
-		return fsParticles;
-	}
+        double totalE = 0;
+        for (MCParticle particle : particles) {
+            if (Math.abs(particle.getPDGID()) == 11) {
+                totalE += particle.getEnergy();
+            }
+        }
+        return totalE;
+    }
+
+    private MCParticle getPrimary(List<MCParticle> particles) {
+        double maxE = 0;
+        MCParticle primary = null;
+        for (MCParticle particle : particles) {
+            if (particle.getEnergy() > maxE) {
+                maxE = particle.getEnergy();
+                primary = particle;
+            }
+        }
+        return primary;
+    }
+
+    public static List<MCParticle> makeGenFSParticleList(List<MCParticle> mcparticles) {
+        List<MCParticle> fsParticles = new ArrayList<MCParticle>();
+        for (MCParticle mcparticle : mcparticles) {
+            if (mcparticle.getGeneratorStatus() == MCParticle.FINAL_STATE) {
+                double theta = Math.atan2(Math.sqrt(mcparticle.getPX() * mcparticle.getPX() + mcparticle.getPY() * mcparticle.getPY()), mcparticle.getPZ());
+                if (theta > 1e-3) {
+                    fsParticles.add(mcparticle);
+                }
+            }
+        }
+        return fsParticles;
+    }
         
         
         public void endOfData() {

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/DualThresholdSignalFitDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/DualThresholdSignalFitDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/DualThresholdSignalFitDriver.java	Wed Apr 27 11:11:32 2016
@@ -182,7 +182,7 @@
      * Process the event, performing a signal fit for every raw data hit in the input collection.
      * The hits that pass the sigma selection cut are added to a new hits collection, which can be
      * converted to a CalorimeterHit collection and then clustered.
-     * @throw NextEventException if there are not enough hits that pass the selection cut.
+     * @throws NextEventException if there are not enough hits that pass the selection cut.
      */
     public void process(EventHeader event) {
         if (event.hasCollection(RawTrackerHit.class, inputHitsCollectionName)) {

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeHitSelectionDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeHitSelectionDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeHitSelectionDriver.java	Wed Apr 27 11:11:32 2016
@@ -54,7 +54,7 @@
 
     /**
      * Set the number of ADC samples in a row which must be above the threshold.
-     * @param selectedHits The minimum number of samples above threshold.
+     * @param minimumSelectedSamples The minimum number of samples above threshold.
      */
     public void setMinimumSelectedSamples(int minimumSelectedSamples) {
         this.minimumSelectedSamples = minimumSelectedSamples;

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeSignalFitDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeSignalFitDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/ecal/cosmic/RawModeSignalFitDriver.java	Wed Apr 27 11:11:32 2016
@@ -168,7 +168,7 @@
      * Process the event, performing a signal fit for every raw data hit in the input collection.
      * The hits that pass the sigma selection cut are added to a new hits collection, which can be
      * converted to a CalorimeterHit collection and then clustered.
-     * @throw NextEventException if there are not enough hits that pass the selection cut.
+     * @throws NextEventException if there are not enough hits that pass the selection cut.
      */
     public void process(EventHeader event) {
         if (event.hasCollection(RawTrackerHit.class, inputHitsCollectionName)) {

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/PrintGeometryDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/PrintGeometryDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/PrintGeometryDriver.java	Wed Apr 27 11:11:32 2016
@@ -2,8 +2,9 @@
 
 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
-import java.util.ArrayList;
+
 import java.util.List;
+
 import org.lcsim.detector.IDetectorElement;
 import org.lcsim.detector.ITransform3D;
 import org.lcsim.detector.Transform3D;
@@ -13,13 +14,7 @@
 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.detector.tracker.silicon.SiSensorElectrodes;
 import org.lcsim.detector.tracker.silicon.SiTrackerIdentifierHelper;
-import org.lcsim.event.RawTrackerHit;
-import org.lcsim.event.SimTrackerHit;
-import org.lcsim.event.base.BaseRawTrackerHit;
 import org.lcsim.geometry.Detector;
-import org.hps.recon.tracking.MaterialSupervisor;
-import org.hps.recon.tracking.TrackerHitUtils;
-import org.lcsim.recon.tracking.digitization.sisim.TrackerHitType;
 import org.lcsim.util.Driver;
 
 /**

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripGoldenEventsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripGoldenEventsDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripGoldenEventsDriver.java	Wed Apr 27 11:11:32 2016
@@ -1,11 +1,11 @@
 package org.hps.analysis.examples;
 
 import java.util.List;
+
 import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.ReconstructedParticle;
 import org.lcsim.event.Track;
-import org.lcsim.event.Vertex;
 import org.lcsim.util.Driver;
 
 /**
@@ -27,7 +27,7 @@
         boolean skipEvent = false;
         if (event.hasCollection(ReconstructedParticle.class, "UnconstrainedV0Candidates")) {
             List<ReconstructedParticle> vertices = event.get(ReconstructedParticle.class, "UnconstrainedV0Candidates");
-	    //System.out.println("Thete are: "+vertices.size()+" Unconstrained V0 candidates");
+        //System.out.println("Thete are: "+vertices.size()+" Unconstrained V0 candidates");
             if (vertices.size() > 1 || vertices.isEmpty()) {
                 skipEvent = true;
             } else {
@@ -38,14 +38,14 @@
                     List<Track> trks = rp.getTracks();
                     // require each track to have six hits
                     if (trks.get(0).getTrackerHits().size() != 6) {
-			//System.out.println("Thete are: "+trks.get(0).getTrackerHits().size()+" hits on Track");
+            //System.out.println("Thete are: "+trks.get(0).getTrackerHits().size()+" hits on Track");
                         skipEvent = true;
                     }
                 }
                 // require no other tracks in the event
                 if (event.get(Track.class, "MatchedTracks").size() > 2) {
                     skipEvent = true;
-		    //System.out.println("Thete are: "+event.get(Track.class, "MatchedTracks").size()+" Matched tracks");
+            //System.out.println("Thete are: "+event.get(Track.class, "MatchedTracks").size()+" Matched tracks");
                 }
                 // require no other clusters in the event
                 if (event.get(Cluster.class, "EcalClustersGTP").size() > 2) {

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripMollerEventsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripMollerEventsDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/examples/StripMollerEventsDriver.java	Wed Apr 27 11:11:32 2016
@@ -94,7 +94,7 @@
                             skipEvent = false;
                         }
                     }
-		    //System.out.println("Thete are: "+event.get(Track.class, "MatchedTracks").size()+" Matched tracks");
+            //System.out.println("Thete are: "+event.get(Track.class, "MatchedTracks").size()+" Matched tracks");
                 }
             }
         }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/DataTriggerSimDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/DataTriggerSimDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/DataTriggerSimDriver.java	Wed Apr 27 11:11:32 2016
@@ -48,454 +48,454 @@
  * output object is not persisted into LCIO after runtime.
  * 
  * @author Kyle McCarty <[log in to unmask]>
- * @see DAQConfigDriver
- * @see EcalOnlineRawConverterDriver
- * @see GTPOnlineClusterDriver
+ * @see org.hps.record.daqconfig.DAQConfigDriver
+ * @see org.hps.recon.ecal.EcalOnlineRawConverterDriver
+ * @see org.hps.recon.ecal.cluster.GTPOnlineClusterDriver
  * @see SimTriggerData
  */
 public class DataTriggerSimDriver extends Driver {
-	// Store the LCIO collection names for the needed objects.
-	private boolean filterUnverifiable = false;
-	private String bankCollectionName = "TriggerBank";
-	private String clusterCollectionName = "EcalClusters";
-	private String simTriggerCollectionName = "SimTriggers";
-	
-	// Store the SSP bank.
-	private SSPData sspBank = null;
-	
-	// Store cluster verifiability parameters.
-	private int nsa = 0;
-	private int nsb = 0;
-	private int windowWidth = 0;
-	
-	// Define trigger simulation modules.
-	private boolean[] pairTriggerEnabled = new boolean[2];
-	private boolean[] singlesTriggerEnabled = new boolean[2];
-	private boolean[][] pairCutsEnabled = new boolean[2][7];
-	private boolean[][] singlesCutsEnabled = new boolean[2][3];
-	private TriggerModule[] pairsTrigger = new TriggerModule[2];
-	private TriggerModule[] singlesTrigger = new TriggerModule[2];
-	
-	// Reference variables.
-	private static final int ENERGY_MIN   = TriggerDiagnosticUtil.SINGLES_ENERGY_MIN;
-	private static final int ENERGY_MAX   = TriggerDiagnosticUtil.SINGLES_ENERGY_MAX;
-	private static final int HIT_COUNT    = TriggerDiagnosticUtil.SINGLES_HIT_COUNT;
-	private static final int ENERGY_SUM   = TriggerDiagnosticUtil.PAIR_ENERGY_SUM;
-	private static final int ENERGY_DIFF  = TriggerDiagnosticUtil.PAIR_ENERGY_DIFF;
-	private static final int ENERGY_SLOPE = TriggerDiagnosticUtil.PAIR_ENERGY_SLOPE;
-	private static final int COPLANARITY  = TriggerDiagnosticUtil.PAIR_COPLANARITY;
-	
-	/**
-	 * Connects the driver to the the <code>ConfigurationManager</code>
-	 * in order to obtain the correct trigger information. Trigger
-	 * settings are stored in the <code>TriggerModule</code> objects.
-	 */
-	@Override
-	public void startOfData() {
-		// Define the first singles trigger.
-		singlesTrigger[0] = new TriggerModule();
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.500);
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		
-		// Define the second singles trigger.
-		singlesTrigger[1] = new TriggerModule();
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		
-		// Define the first pairs trigger.
-		pairsTrigger[0] = new TriggerModule();
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
-		
-		// Define the second pairs trigger.
-		pairsTrigger[1] = new TriggerModule();
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
-		
-		// Listen for the configuration manager to provide the real
-		// trigger settings.
-		ConfigurationManager.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				// Get the DAQ configuration.
-				DAQConfig daq = ConfigurationManager.getInstance();
-				
-				// Get cluster verifiability parameters.
-				nsa = daq.getFADCConfig().getNSA();
-				nsb = daq.getFADCConfig().getNSB();
-				windowWidth = daq.getFADCConfig().getWindowWidth();
-				
-				// Load the DAQ settings from the configuration manager.
-				singlesTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getSingles1Config());
-				singlesTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getSingles2Config());
-				pairsTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getPair1Config());
-				pairsTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getPair2Config());
-				
-				// Get the trigger configurations from the DAQ.
-				SinglesTriggerConfig[] singles = { daq.getSSPConfig().getSingles1Config(),
-						daq.getSSPConfig().getSingles2Config() };
-				PairTriggerConfig[] pairs = { daq.getSSPConfig().getPair1Config(),
-						daq.getSSPConfig().getPair2Config() };
-				
-				// Update the enabled/disabled statuses.
-				for(int i = 0; i < 2; i++) {
-					// Set the trigger enabled status.
-					pairTriggerEnabled[i] = pairs[i].isEnabled();
-					singlesTriggerEnabled[i] = singles[i].isEnabled();
-					
-					// Set the singles cut statuses.
-					singlesCutsEnabled[i][ENERGY_MIN] = singles[i].getEnergyMinCutConfig().isEnabled();
-					singlesCutsEnabled[i][ENERGY_MAX] = singles[i].getEnergyMaxCutConfig().isEnabled();
-					singlesCutsEnabled[i][HIT_COUNT] = singles[i].getHitCountCutConfig().isEnabled();
-					
-					// Set the pair cut statuses.
-					pairCutsEnabled[i][ENERGY_MIN] = pairs[i].getEnergyMinCutConfig().isEnabled();
-					pairCutsEnabled[i][ENERGY_MAX] = pairs[i].getEnergyMaxCutConfig().isEnabled();
-					pairCutsEnabled[i][HIT_COUNT] = pairs[i].getHitCountCutConfig().isEnabled();
-					pairCutsEnabled[i][3 + ENERGY_SUM] = pairs[i].getEnergySumCutConfig().isEnabled();
-					pairCutsEnabled[i][3 + ENERGY_DIFF] = pairs[i].getEnergyDifferenceCutConfig().isEnabled();
-					pairCutsEnabled[i][3 + ENERGY_SLOPE] = pairs[i].getEnergySlopeCutConfig().isEnabled();
-					pairCutsEnabled[i][3 + COPLANARITY] = pairs[i].getCoplanarityCutConfig().isEnabled();
-				}
-			}
-		});
-	}
-	
-	/**
-	 * Processes an LCIO event and simulates triggers in the same manner
-	 * as the hardware for both <code>SSPCluster</code> objects as well
-	 * as <code>Cluster</code> objects reconstructed from FADC hits.
-	 * Triggers are then output to the data stream.
-	 * @param event - The <code>EventHeader</code> object representing
-	 * the current LCIO event.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		// If the DAQ configuration manager has not been initialized,
-		// then no action can be performed.
-		if(!ConfigurationManager.isInitialized()) {
-			// Put an empty trigger results module into the data stream.
-			SimTriggerData triggerData = new SimTriggerData();
-			List<SimTriggerData> dataList = new ArrayList<SimTriggerData>(1);
-			dataList.add(triggerData);
-			event.put(simTriggerCollectionName, dataList, SimTriggerData.class, 0);
-			
-			// Nothing further can be done, since trigger settings are
-			// not yet defined.
-			return;
-		}
-		
-		// Get the SSP bank.
-		if(event.hasCollection(GenericObject.class, bankCollectionName)) {
-			// Get the bank list.
-			List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-			
-			// Search through the banks and get the SSP and TI banks.
-			for(GenericObject obj : bankList) {
-				// If this is an SSP bank, parse it.
-				if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
-					sspBank = new SSPData(obj);
-				}
-			}
-		}
-		
-		// Get a list of SSPClusters.
-		List<SSPCluster> sspClusters = null;
-		if(sspBank != null) { sspClusters = sspBank.getClusters(); }
-		else { sspClusters = new ArrayList<SSPCluster>(0); }
-		
-		// Get reconstructed clusters.
-		List<Cluster> reconClusters = null;
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			reconClusters = event.get(Cluster.class, clusterCollectionName);
-		}
-		else { reconClusters = new ArrayList<Cluster>(0); }
-		
-		// If only "verifiable" clusters should be used, test all the
-		// reconstructed clusters for verifiability.
-		if(filterUnverifiable) {
-			// Create a list to store the verifiable clusters.
-			List<Cluster> goodClusters = new ArrayList<Cluster>();
-			
-			// Iterate over all the clusters and test them to see if
-			// they are verifiable.
-			for(Cluster cluster : reconClusters) {
-				if(TriggerDiagnosticUtil.isVerifiable(cluster, nsa, nsb, windowWidth)) {
-					goodClusters.add(cluster);
-				}
-			}
-			
-			// Replace the old cluster list with the new one.
-			reconClusters = goodClusters;
-		}
-		
-		// Generate simulated triggers.
-		SimTriggerModule<Cluster> reconModule = constructTriggers(reconClusters, Cluster.class);
-		SimTriggerModule<SSPCluster> sspModule = constructTriggers(sspClusters, SSPCluster.class);
-		
-		// Insert the trigger results in the data stream.
-		SimTriggerData triggerData = new SimTriggerData(reconModule, sspModule);
-		List<SimTriggerData> dataList = new ArrayList<SimTriggerData>(1);
-		dataList.add(triggerData);
-		event.put(simTriggerCollectionName, dataList, SimTriggerData.class, 0);
-	}
-	
-	/**
-	 * Constructs simulated triggers in the same manner as the hardware.
-	 * Method can accept either <code>Cluster</code> objects, any object
-	 * that is a subclass of <code>Cluster</code>, or objects of type
-	 * <code>SSPCluster</code>.
-	 * @param clusters - A <code>List</code> collection of the cluster
-	 * objects from which triggers are to be derived.
-	 * @param clusterType - The class of the cluster objects from which
-	 * triggers are to be derived. This can be <code>Cluster</code>,
-	 * <code>SSPCluster</code>, or a subclass thereof.
-	 * @return Returns a <code>SimTriggerModule</code> object containing
-	 * the simulated trigger results.
-	 * @throws IllegalArgumentException Occurs if the class of the
-	 * cluster objects is not of a supported type.
-	 * 
-	 */
-	private <E> SimTriggerModule<E> constructTriggers(List<E> clusters, Class<E> clusterType) throws IllegalArgumentException {
-		// Verify that the cluster type is supported.
-		if(!clusterType.equals(Cluster.class) && !clusterType.equals(SSPCluster.class)) {
-			throw new IllegalArgumentException("Class \"" + clusterType.getSimpleName() + "\" is not a supported cluster type.");
-		}
-		
-		// Store the singles and pair triggers.
-		List<List<PairTrigger<E[]>>> pairTriggers = new ArrayList<List<PairTrigger<E[]>>>(2);
-		pairTriggers.add(new ArrayList<PairTrigger<E[]>>());
-		pairTriggers.add(new ArrayList<PairTrigger<E[]>>());
-		List<List<SinglesTrigger<E>>> singlesTriggers = new ArrayList<List<SinglesTrigger<E>>>(2);
-		singlesTriggers.add(new ArrayList<SinglesTrigger<E>>());
-		singlesTriggers.add(new ArrayList<SinglesTrigger<E>>());
-		
-		// Run the clusters through the singles trigger to determine
-		// whether or not they pass it.
-		for(E cluster : clusters) {
-			// Simulate each of the cluster singles triggers.
-			triggerLoop:
-			for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-				// Track whether the cluster passed each singles cut.
-				boolean passSeedLow = true;
-				boolean passSeedHigh = true;
-				boolean passClusterLow = false;
-				boolean passClusterHigh = false;
-				boolean passHitCount = false;
-				
-				// Perform the trigger cuts appropriately for the type
-				// of cluster.
-				if(cluster instanceof Cluster) {
-					// Cast the cluster to the appropriate type.
-					Cluster c = (Cluster) cluster;
-					
-					// Perform each trigger cut.
-					passClusterLow = singlesTrigger[triggerNum].clusterTotalEnergyCutLow(c);
-					passClusterHigh = singlesTrigger[triggerNum].clusterTotalEnergyCutHigh(c);
-					passHitCount = singlesTrigger[triggerNum].clusterHitCountCut(c);
-				} else if(cluster instanceof SSPCluster) {
-					// Cast the cluster to the appropriate type.
-					SSPCluster c = (SSPCluster) cluster;
-					
-					// Perform each trigger cut.
-					passClusterLow = singlesTrigger[triggerNum].clusterTotalEnergyCutLow(c);
-					passClusterHigh = singlesTrigger[triggerNum].clusterTotalEnergyCutHigh(c);
-					passHitCount = singlesTrigger[triggerNum].clusterHitCountCut(c);
-				}
-				
-				// Make a trigger to store the results.
-				SinglesTrigger<E> trigger = new SinglesTrigger<E>(cluster, triggerNum);
-				trigger.setStateSeedEnergyLow(passSeedLow);
-				trigger.setStateSeedEnergyHigh(passSeedHigh);
-				trigger.setStateClusterEnergyLow(passClusterLow);
-				trigger.setStateClusterEnergyHigh(passClusterHigh);
-				trigger.setStateHitCount(passHitCount);
-				
-				// A trigger will only be reported by the SSP if it
-				// passes all of the enabled cuts for that trigger.
-				// Check whether this trigger meets these conditions.
-				if(singlesCutsEnabled[triggerNum][ENERGY_MIN] && !trigger.getStateClusterEnergyLow()) {
-					continue triggerLoop;
-				} if(singlesCutsEnabled[triggerNum][ENERGY_MAX] && !trigger.getStateClusterEnergyHigh()) {
-					continue triggerLoop;
-				} if(singlesCutsEnabled[triggerNum][HIT_COUNT] && !trigger.getStateHitCount()) {
-					continue triggerLoop;
-				}
-				
-				// Store the trigger.
-				singlesTriggers.get(triggerNum).add(trigger);
-			}
-		}
-		
-		// Store cluster pairs.
-		List<E[]> pairs = TriggerModule.getTopBottomPairs(clusters, clusterType);
-		
-		// Simulate the pair triggers and record the results.
-		for(E[] pair : pairs) {
-			// Simulate each of the cluster pair triggers.
-			pairTriggerLoop:
-			for(int triggerIndex = 0; triggerIndex < 2; triggerIndex++) {
-				// Track whether the cluster passed each singles cut.
-				boolean passSeedLow = true;
-				boolean passSeedHigh = true;
-				boolean passClusterLow = false;
-				boolean passClusterHigh = false;
-				boolean passHitCount = false;
-				boolean passPairEnergySumLow = false;
-				boolean passPairEnergySumHigh = false;
-				boolean passPairEnergyDifference = false;
-				boolean passPairEnergySlope = false;
-				boolean passPairCoplanarity = false;
-				boolean passTimeCoincidence = false;
-				
-				// Apply the trigger cuts appropriately according to the
-				// cluster type.
-				if(clusterType.equals(Cluster.class)) {
-					// Cast the cluster object.
-					Cluster[] reconPair = { (Cluster) pair[0], (Cluster) pair[1] };
-					
-					// Check that the pair passes the time coincidence cut.
-					// If it does not, it is not a valid pair and should be
-					// destroyed.
-					if(!pairsTrigger[triggerIndex].pairTimeCoincidenceCut(reconPair)) {
-						continue pairTriggerLoop;
-					}
-					
-					passClusterLow = pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(reconPair[0])
-							&& pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(reconPair[1]);
-					passClusterHigh = pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(reconPair[0])
-							&& pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(reconPair[1]);
-					passHitCount = pairsTrigger[triggerIndex].clusterHitCountCut(reconPair[0])
-							&& pairsTrigger[triggerIndex].clusterHitCountCut(reconPair[1]);
-					passPairEnergySumLow = pairsTrigger[triggerIndex].pairEnergySumCutLow(reconPair);
-					passPairEnergySumHigh = pairsTrigger[triggerIndex].pairEnergySumCutHigh(reconPair);
-					passPairEnergyDifference = pairsTrigger[triggerIndex].pairEnergyDifferenceCut(reconPair);
-					passPairEnergySlope = pairsTrigger[triggerIndex].pairEnergySlopeCut(reconPair);
-					passPairCoplanarity = pairsTrigger[triggerIndex].pairCoplanarityCut(reconPair);
-					passTimeCoincidence = pairsTrigger[triggerIndex].pairTimeCoincidenceCut(reconPair);
-				} else if(clusterType.equals(SSPCluster.class)) {
-					// Cast the cluster object.
-					SSPCluster[] sspPair = { (SSPCluster) pair[0], (SSPCluster) pair[1] };
-					
-					// Check that the pair passes the time coincidence cut.
-					// If it does not, it is not a valid pair and should be
-					// destroyed.
-					if(!pairsTrigger[triggerIndex].pairTimeCoincidenceCut(sspPair)) {
-						continue pairTriggerLoop;
-					}
-					
-					// Perform each trigger cut.
-					passClusterLow = pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(sspPair[0])
-							&& pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(sspPair[1]);
-					passClusterHigh = pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(sspPair[0])
-							&& pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(sspPair[1]);
-					passHitCount = pairsTrigger[triggerIndex].clusterHitCountCut(sspPair[0])
-							&& pairsTrigger[triggerIndex].clusterHitCountCut(sspPair[1]);
-					passPairEnergySumLow = pairsTrigger[triggerIndex].pairEnergySumCutLow(sspPair);
-					passPairEnergySumHigh = pairsTrigger[triggerIndex].pairEnergySumCutHigh(sspPair);
-					passPairEnergyDifference = pairsTrigger[triggerIndex].pairEnergyDifferenceCut(sspPair);
-					passPairEnergySlope = pairsTrigger[triggerIndex].pairEnergySlopeCut(sspPair);
-					passPairCoplanarity = pairsTrigger[triggerIndex].pairCoplanarityCut(sspPair);
-					passTimeCoincidence = pairsTrigger[triggerIndex].pairTimeCoincidenceCut(sspPair);
-				}
-				
-				// Create a trigger from the results.
-				PairTrigger<E[]> trigger = new PairTrigger<E[]>(pair, triggerIndex);
-				trigger.setStateSeedEnergyLow(passSeedLow);
-				trigger.setStateSeedEnergyHigh(passSeedHigh);
-				trigger.setStateClusterEnergyLow(passClusterLow);
-				trigger.setStateClusterEnergyHigh(passClusterHigh);
-				trigger.setStateHitCount(passHitCount);
-				trigger.setStateEnergySumLow(passPairEnergySumLow);
-				trigger.setStateEnergySumHigh(passPairEnergySumHigh);
-				trigger.setStateEnergyDifference(passPairEnergyDifference);
-				trigger.setStateEnergySlope(passPairEnergySlope);
-				trigger.setStateCoplanarity(passPairCoplanarity);
-				trigger.setStateTimeCoincidence(passTimeCoincidence);
-				
-				// A trigger will only be reported by the SSP if it
-				// passes all of the enabled cuts for that trigger.
-				// Check whether this trigger meets these conditions.
-				if(pairCutsEnabled[triggerIndex][ENERGY_MIN] && !trigger.getStateClusterEnergyLow()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][ENERGY_MAX] && !trigger.getStateClusterEnergyHigh()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][HIT_COUNT] && !trigger.getStateHitCount()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][3 + ENERGY_SUM] && !trigger.getStateEnergySum()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][3 + ENERGY_DIFF] && !trigger.getStateEnergyDifference()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][3 + ENERGY_SLOPE] && !trigger.getStateEnergySlope()) {
-					continue pairTriggerLoop;
-				} if(pairCutsEnabled[triggerIndex][3 + COPLANARITY] && !trigger.getStateCoplanarity()) {
-					continue pairTriggerLoop;
-				}
-				
-				// Add the trigger to the list.
-				pairTriggers.get(triggerIndex).add(trigger);
-			}
-		}
-		
-		// Create a new simulated trigger module to contain the results.
-		return new SimTriggerModule<E>(singlesTriggers.get(0), singlesTriggers.get(1),
-				pairTriggers.get(0), pairTriggers.get(1));
-	}
-	
-	/**
-	 * Sets the name of the LCIO collection containing the TI and SSP
-	 * banks.
-	 * @param bankCollectionName - The bank collection name.
-	 */
-	public void setBankCollectionName(String bankCollectionName) {
-		this.bankCollectionName = bankCollectionName;
-	}
-	
-	/**
-	 * Sets the name of the LCIO collection containing the simulated
-	 * reconstructed clusters.
-	 * @param clusterCollectionName - The cluster collection name.
-	 */
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
-	
-	/**
-	 * Sets whether or not triggers should be formed using all clusters,
-	 * or only those that where the integration window for the cluster
-	 * is completely within the bounds of the event window.
-	 * @param state - <code>true</code> means that only clusters where
-	 * the entire cluster integration window is within the event time
-	 * window will be used, while <code>false</code> means that all
-	 * clusters will be used.
-	 */
-	public void setFilterUnverifiableClusters(boolean state) {
-		this.filterUnverifiable = state;
-	}
-	
-	/**
-	 * Sets the name of the LCIO collection containing simulated triggers.
-	 * @param triggerCollection - The trigger collection name.
-	 */
-	public void setTriggerCollectionName(String triggerCollection) {
-		this.simTriggerCollectionName = triggerCollection;
-	}
+    // Store the LCIO collection names for the needed objects.
+    private boolean filterUnverifiable = false;
+    private String bankCollectionName = "TriggerBank";
+    private String clusterCollectionName = "EcalClusters";
+    private String simTriggerCollectionName = "SimTriggers";
+    
+    // Store the SSP bank.
+    private SSPData sspBank = null;
+    
+    // Store cluster verifiability parameters.
+    private int nsa = 0;
+    private int nsb = 0;
+    private int windowWidth = 0;
+    
+    // Define trigger simulation modules.
+    private boolean[] pairTriggerEnabled = new boolean[2];
+    private boolean[] singlesTriggerEnabled = new boolean[2];
+    private boolean[][] pairCutsEnabled = new boolean[2][7];
+    private boolean[][] singlesCutsEnabled = new boolean[2][3];
+    private TriggerModule[] pairsTrigger = new TriggerModule[2];
+    private TriggerModule[] singlesTrigger = new TriggerModule[2];
+    
+    // Reference variables.
+    private static final int ENERGY_MIN   = TriggerDiagnosticUtil.SINGLES_ENERGY_MIN;
+    private static final int ENERGY_MAX   = TriggerDiagnosticUtil.SINGLES_ENERGY_MAX;
+    private static final int HIT_COUNT    = TriggerDiagnosticUtil.SINGLES_HIT_COUNT;
+    private static final int ENERGY_SUM   = TriggerDiagnosticUtil.PAIR_ENERGY_SUM;
+    private static final int ENERGY_DIFF  = TriggerDiagnosticUtil.PAIR_ENERGY_DIFF;
+    private static final int ENERGY_SLOPE = TriggerDiagnosticUtil.PAIR_ENERGY_SLOPE;
+    private static final int COPLANARITY  = TriggerDiagnosticUtil.PAIR_COPLANARITY;
+    
+    /**
+     * Connects the driver to the the <code>ConfigurationManager</code>
+     * in order to obtain the correct trigger information. Trigger
+     * settings are stored in the <code>TriggerModule</code> objects.
+     */
+    @Override
+    public void startOfData() {
+        // Define the first singles trigger.
+        singlesTrigger[0] = new TriggerModule();
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.500);
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        
+        // Define the second singles trigger.
+        singlesTrigger[1] = new TriggerModule();
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        
+        // Define the first pairs trigger.
+        pairsTrigger[0] = new TriggerModule();
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
+        
+        // Define the second pairs trigger.
+        pairsTrigger[1] = new TriggerModule();
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
+        
+        // Listen for the configuration manager to provide the real
+        // trigger settings.
+        ConfigurationManager.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // Get the DAQ configuration.
+                DAQConfig daq = ConfigurationManager.getInstance();
+                
+                // Get cluster verifiability parameters.
+                nsa = daq.getFADCConfig().getNSA();
+                nsb = daq.getFADCConfig().getNSB();
+                windowWidth = daq.getFADCConfig().getWindowWidth();
+                
+                // Load the DAQ settings from the configuration manager.
+                singlesTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getSingles1Config());
+                singlesTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getSingles2Config());
+                pairsTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getPair1Config());
+                pairsTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getPair2Config());
+                
+                // Get the trigger configurations from the DAQ.
+                SinglesTriggerConfig[] singles = { daq.getSSPConfig().getSingles1Config(),
+                        daq.getSSPConfig().getSingles2Config() };
+                PairTriggerConfig[] pairs = { daq.getSSPConfig().getPair1Config(),
+                        daq.getSSPConfig().getPair2Config() };
+                
+                // Update the enabled/disabled statuses.
+                for(int i = 0; i < 2; i++) {
+                    // Set the trigger enabled status.
+                    pairTriggerEnabled[i] = pairs[i].isEnabled();
+                    singlesTriggerEnabled[i] = singles[i].isEnabled();
+                    
+                    // Set the singles cut statuses.
+                    singlesCutsEnabled[i][ENERGY_MIN] = singles[i].getEnergyMinCutConfig().isEnabled();
+                    singlesCutsEnabled[i][ENERGY_MAX] = singles[i].getEnergyMaxCutConfig().isEnabled();
+                    singlesCutsEnabled[i][HIT_COUNT] = singles[i].getHitCountCutConfig().isEnabled();
+                    
+                    // Set the pair cut statuses.
+                    pairCutsEnabled[i][ENERGY_MIN] = pairs[i].getEnergyMinCutConfig().isEnabled();
+                    pairCutsEnabled[i][ENERGY_MAX] = pairs[i].getEnergyMaxCutConfig().isEnabled();
+                    pairCutsEnabled[i][HIT_COUNT] = pairs[i].getHitCountCutConfig().isEnabled();
+                    pairCutsEnabled[i][3 + ENERGY_SUM] = pairs[i].getEnergySumCutConfig().isEnabled();
+                    pairCutsEnabled[i][3 + ENERGY_DIFF] = pairs[i].getEnergyDifferenceCutConfig().isEnabled();
+                    pairCutsEnabled[i][3 + ENERGY_SLOPE] = pairs[i].getEnergySlopeCutConfig().isEnabled();
+                    pairCutsEnabled[i][3 + COPLANARITY] = pairs[i].getCoplanarityCutConfig().isEnabled();
+                }
+            }
+        });
+    }
+    
+    /**
+     * Processes an LCIO event and simulates triggers in the same manner
+     * as the hardware for both <code>SSPCluster</code> objects as well
+     * as <code>Cluster</code> objects reconstructed from FADC hits.
+     * Triggers are then output to the data stream.
+     * @param event - The <code>EventHeader</code> object representing
+     * the current LCIO event.
+     */
+    @Override
+    public void process(EventHeader event) {
+        // If the DAQ configuration manager has not been initialized,
+        // then no action can be performed.
+        if(!ConfigurationManager.isInitialized()) {
+            // Put an empty trigger results module into the data stream.
+            SimTriggerData triggerData = new SimTriggerData();
+            List<SimTriggerData> dataList = new ArrayList<SimTriggerData>(1);
+            dataList.add(triggerData);
+            event.put(simTriggerCollectionName, dataList, SimTriggerData.class, 0);
+            
+            // Nothing further can be done, since trigger settings are
+            // not yet defined.
+            return;
+        }
+        
+        // Get the SSP bank.
+        if(event.hasCollection(GenericObject.class, bankCollectionName)) {
+            // Get the bank list.
+            List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+            
+            // Search through the banks and get the SSP and TI banks.
+            for(GenericObject obj : bankList) {
+                // If this is an SSP bank, parse it.
+                if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
+                    sspBank = new SSPData(obj);
+                }
+            }
+        }
+        
+        // Get a list of SSPClusters.
+        List<SSPCluster> sspClusters = null;
+        if(sspBank != null) { sspClusters = sspBank.getClusters(); }
+        else { sspClusters = new ArrayList<SSPCluster>(0); }
+        
+        // Get reconstructed clusters.
+        List<Cluster> reconClusters = null;
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            reconClusters = event.get(Cluster.class, clusterCollectionName);
+        }
+        else { reconClusters = new ArrayList<Cluster>(0); }
+        
+        // If only "verifiable" clusters should be used, test all the
+        // reconstructed clusters for verifiability.
+        if(filterUnverifiable) {
+            // Create a list to store the verifiable clusters.
+            List<Cluster> goodClusters = new ArrayList<Cluster>();
+            
+            // Iterate over all the clusters and test them to see if
+            // they are verifiable.
+            for(Cluster cluster : reconClusters) {
+                if(TriggerDiagnosticUtil.isVerifiable(cluster, nsa, nsb, windowWidth)) {
+                    goodClusters.add(cluster);
+                }
+            }
+            
+            // Replace the old cluster list with the new one.
+            reconClusters = goodClusters;
+        }
+        
+        // Generate simulated triggers.
+        SimTriggerModule<Cluster> reconModule = constructTriggers(reconClusters, Cluster.class);
+        SimTriggerModule<SSPCluster> sspModule = constructTriggers(sspClusters, SSPCluster.class);
+        
+        // Insert the trigger results in the data stream.
+        SimTriggerData triggerData = new SimTriggerData(reconModule, sspModule);
+        List<SimTriggerData> dataList = new ArrayList<SimTriggerData>(1);
+        dataList.add(triggerData);
+        event.put(simTriggerCollectionName, dataList, SimTriggerData.class, 0);
+    }
+    
+    /**
+     * Constructs simulated triggers in the same manner as the hardware.
+     * Method can accept either <code>Cluster</code> objects, any object
+     * that is a subclass of <code>Cluster</code>, or objects of type
+     * <code>SSPCluster</code>.
+     * @param clusters - A <code>List</code> collection of the cluster
+     * objects from which triggers are to be derived.
+     * @param clusterType - The class of the cluster objects from which
+     * triggers are to be derived. This can be <code>Cluster</code>,
+     * <code>SSPCluster</code>, or a subclass thereof.
+     * @return Returns a <code>SimTriggerModule</code> object containing
+     * the simulated trigger results.
+     * @throws IllegalArgumentException Occurs if the class of the
+     * cluster objects is not of a supported type.
+     * 
+     */
+    private <E> SimTriggerModule<E> constructTriggers(List<E> clusters, Class<E> clusterType) throws IllegalArgumentException {
+        // Verify that the cluster type is supported.
+        if(!clusterType.equals(Cluster.class) && !clusterType.equals(SSPCluster.class)) {
+            throw new IllegalArgumentException("Class \"" + clusterType.getSimpleName() + "\" is not a supported cluster type.");
+        }
+        
+        // Store the singles and pair triggers.
+        List<List<PairTrigger<E[]>>> pairTriggers = new ArrayList<List<PairTrigger<E[]>>>(2);
+        pairTriggers.add(new ArrayList<PairTrigger<E[]>>());
+        pairTriggers.add(new ArrayList<PairTrigger<E[]>>());
+        List<List<SinglesTrigger<E>>> singlesTriggers = new ArrayList<List<SinglesTrigger<E>>>(2);
+        singlesTriggers.add(new ArrayList<SinglesTrigger<E>>());
+        singlesTriggers.add(new ArrayList<SinglesTrigger<E>>());
+        
+        // Run the clusters through the singles trigger to determine
+        // whether or not they pass it.
+        for(E cluster : clusters) {
+            // Simulate each of the cluster singles triggers.
+            triggerLoop:
+            for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+                // Track whether the cluster passed each singles cut.
+                boolean passSeedLow = true;
+                boolean passSeedHigh = true;
+                boolean passClusterLow = false;
+                boolean passClusterHigh = false;
+                boolean passHitCount = false;
+                
+                // Perform the trigger cuts appropriately for the type
+                // of cluster.
+                if(cluster instanceof Cluster) {
+                    // Cast the cluster to the appropriate type.
+                    Cluster c = (Cluster) cluster;
+                    
+                    // Perform each trigger cut.
+                    passClusterLow = singlesTrigger[triggerNum].clusterTotalEnergyCutLow(c);
+                    passClusterHigh = singlesTrigger[triggerNum].clusterTotalEnergyCutHigh(c);
+                    passHitCount = singlesTrigger[triggerNum].clusterHitCountCut(c);
+                } else if(cluster instanceof SSPCluster) {
+                    // Cast the cluster to the appropriate type.
+                    SSPCluster c = (SSPCluster) cluster;
+                    
+                    // Perform each trigger cut.
+                    passClusterLow = singlesTrigger[triggerNum].clusterTotalEnergyCutLow(c);
+                    passClusterHigh = singlesTrigger[triggerNum].clusterTotalEnergyCutHigh(c);
+                    passHitCount = singlesTrigger[triggerNum].clusterHitCountCut(c);
+                }
+                
+                // Make a trigger to store the results.
+                SinglesTrigger<E> trigger = new SinglesTrigger<E>(cluster, triggerNum);
+                trigger.setStateSeedEnergyLow(passSeedLow);
+                trigger.setStateSeedEnergyHigh(passSeedHigh);
+                trigger.setStateClusterEnergyLow(passClusterLow);
+                trigger.setStateClusterEnergyHigh(passClusterHigh);
+                trigger.setStateHitCount(passHitCount);
+                
+                // A trigger will only be reported by the SSP if it
+                // passes all of the enabled cuts for that trigger.
+                // Check whether this trigger meets these conditions.
+                if(singlesCutsEnabled[triggerNum][ENERGY_MIN] && !trigger.getStateClusterEnergyLow()) {
+                    continue triggerLoop;
+                } if(singlesCutsEnabled[triggerNum][ENERGY_MAX] && !trigger.getStateClusterEnergyHigh()) {
+                    continue triggerLoop;
+                } if(singlesCutsEnabled[triggerNum][HIT_COUNT] && !trigger.getStateHitCount()) {
+                    continue triggerLoop;
+                }
+                
+                // Store the trigger.
+                singlesTriggers.get(triggerNum).add(trigger);
+            }
+        }
+        
+        // Store cluster pairs.
+        List<E[]> pairs = TriggerModule.getTopBottomPairs(clusters, clusterType);
+        
+        // Simulate the pair triggers and record the results.
+        for(E[] pair : pairs) {
+            // Simulate each of the cluster pair triggers.
+            pairTriggerLoop:
+            for(int triggerIndex = 0; triggerIndex < 2; triggerIndex++) {
+                // Track whether the cluster passed each singles cut.
+                boolean passSeedLow = true;
+                boolean passSeedHigh = true;
+                boolean passClusterLow = false;
+                boolean passClusterHigh = false;
+                boolean passHitCount = false;
+                boolean passPairEnergySumLow = false;
+                boolean passPairEnergySumHigh = false;
+                boolean passPairEnergyDifference = false;
+                boolean passPairEnergySlope = false;
+                boolean passPairCoplanarity = false;
+                boolean passTimeCoincidence = false;
+                
+                // Apply the trigger cuts appropriately according to the
+                // cluster type.
+                if(clusterType.equals(Cluster.class)) {
+                    // Cast the cluster object.
+                    Cluster[] reconPair = { (Cluster) pair[0], (Cluster) pair[1] };
+                    
+                    // Check that the pair passes the time coincidence cut.
+                    // If it does not, it is not a valid pair and should be
+                    // destroyed.
+                    if(!pairsTrigger[triggerIndex].pairTimeCoincidenceCut(reconPair)) {
+                        continue pairTriggerLoop;
+                    }
+                    
+                    passClusterLow = pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(reconPair[0])
+                            && pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(reconPair[1]);
+                    passClusterHigh = pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(reconPair[0])
+                            && pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(reconPair[1]);
+                    passHitCount = pairsTrigger[triggerIndex].clusterHitCountCut(reconPair[0])
+                            && pairsTrigger[triggerIndex].clusterHitCountCut(reconPair[1]);
+                    passPairEnergySumLow = pairsTrigger[triggerIndex].pairEnergySumCutLow(reconPair);
+                    passPairEnergySumHigh = pairsTrigger[triggerIndex].pairEnergySumCutHigh(reconPair);
+                    passPairEnergyDifference = pairsTrigger[triggerIndex].pairEnergyDifferenceCut(reconPair);
+                    passPairEnergySlope = pairsTrigger[triggerIndex].pairEnergySlopeCut(reconPair);
+                    passPairCoplanarity = pairsTrigger[triggerIndex].pairCoplanarityCut(reconPair);
+                    passTimeCoincidence = pairsTrigger[triggerIndex].pairTimeCoincidenceCut(reconPair);
+                } else if(clusterType.equals(SSPCluster.class)) {
+                    // Cast the cluster object.
+                    SSPCluster[] sspPair = { (SSPCluster) pair[0], (SSPCluster) pair[1] };
+                    
+                    // Check that the pair passes the time coincidence cut.
+                    // If it does not, it is not a valid pair and should be
+                    // destroyed.
+                    if(!pairsTrigger[triggerIndex].pairTimeCoincidenceCut(sspPair)) {
+                        continue pairTriggerLoop;
+                    }
+                    
+                    // Perform each trigger cut.
+                    passClusterLow = pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(sspPair[0])
+                            && pairsTrigger[triggerIndex].clusterTotalEnergyCutLow(sspPair[1]);
+                    passClusterHigh = pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(sspPair[0])
+                            && pairsTrigger[triggerIndex].clusterTotalEnergyCutHigh(sspPair[1]);
+                    passHitCount = pairsTrigger[triggerIndex].clusterHitCountCut(sspPair[0])
+                            && pairsTrigger[triggerIndex].clusterHitCountCut(sspPair[1]);
+                    passPairEnergySumLow = pairsTrigger[triggerIndex].pairEnergySumCutLow(sspPair);
+                    passPairEnergySumHigh = pairsTrigger[triggerIndex].pairEnergySumCutHigh(sspPair);
+                    passPairEnergyDifference = pairsTrigger[triggerIndex].pairEnergyDifferenceCut(sspPair);
+                    passPairEnergySlope = pairsTrigger[triggerIndex].pairEnergySlopeCut(sspPair);
+                    passPairCoplanarity = pairsTrigger[triggerIndex].pairCoplanarityCut(sspPair);
+                    passTimeCoincidence = pairsTrigger[triggerIndex].pairTimeCoincidenceCut(sspPair);
+                }
+                
+                // Create a trigger from the results.
+                PairTrigger<E[]> trigger = new PairTrigger<E[]>(pair, triggerIndex);
+                trigger.setStateSeedEnergyLow(passSeedLow);
+                trigger.setStateSeedEnergyHigh(passSeedHigh);
+                trigger.setStateClusterEnergyLow(passClusterLow);
+                trigger.setStateClusterEnergyHigh(passClusterHigh);
+                trigger.setStateHitCount(passHitCount);
+                trigger.setStateEnergySumLow(passPairEnergySumLow);
+                trigger.setStateEnergySumHigh(passPairEnergySumHigh);
+                trigger.setStateEnergyDifference(passPairEnergyDifference);
+                trigger.setStateEnergySlope(passPairEnergySlope);
+                trigger.setStateCoplanarity(passPairCoplanarity);
+                trigger.setStateTimeCoincidence(passTimeCoincidence);
+                
+                // A trigger will only be reported by the SSP if it
+                // passes all of the enabled cuts for that trigger.
+                // Check whether this trigger meets these conditions.
+                if(pairCutsEnabled[triggerIndex][ENERGY_MIN] && !trigger.getStateClusterEnergyLow()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][ENERGY_MAX] && !trigger.getStateClusterEnergyHigh()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][HIT_COUNT] && !trigger.getStateHitCount()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][3 + ENERGY_SUM] && !trigger.getStateEnergySum()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][3 + ENERGY_DIFF] && !trigger.getStateEnergyDifference()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][3 + ENERGY_SLOPE] && !trigger.getStateEnergySlope()) {
+                    continue pairTriggerLoop;
+                } if(pairCutsEnabled[triggerIndex][3 + COPLANARITY] && !trigger.getStateCoplanarity()) {
+                    continue pairTriggerLoop;
+                }
+                
+                // Add the trigger to the list.
+                pairTriggers.get(triggerIndex).add(trigger);
+            }
+        }
+        
+        // Create a new simulated trigger module to contain the results.
+        return new SimTriggerModule<E>(singlesTriggers.get(0), singlesTriggers.get(1),
+                pairTriggers.get(0), pairTriggers.get(1));
+    }
+    
+    /**
+     * Sets the name of the LCIO collection containing the TI and SSP
+     * banks.
+     * @param bankCollectionName - The bank collection name.
+     */
+    public void setBankCollectionName(String bankCollectionName) {
+        this.bankCollectionName = bankCollectionName;
+    }
+    
+    /**
+     * Sets the name of the LCIO collection containing the simulated
+     * reconstructed clusters.
+     * @param clusterCollectionName - The cluster collection name.
+     */
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
+    
+    /**
+     * Sets whether or not triggers should be formed using all clusters,
+     * or only those that where the integration window for the cluster
+     * is completely within the bounds of the event window.
+     * @param state - <code>true</code> means that only clusters where
+     * the entire cluster integration window is within the event time
+     * window will be used, while <code>false</code> means that all
+     * clusters will be used.
+     */
+    public void setFilterUnverifiableClusters(boolean state) {
+        this.filterUnverifiable = state;
+    }
+    
+    /**
+     * Sets the name of the LCIO collection containing simulated triggers.
+     * @param triggerCollection - The trigger collection name.
+     */
+    public void setTriggerCollectionName(String triggerCollection) {
+        this.simTriggerCollectionName = triggerCollection;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerData.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerData.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerData.java	Wed Apr 27 11:11:32 2016
@@ -7,53 +7,76 @@
  * Class <code>SimTriggerData</code> is a container class that holds
  * simulated trigger data modules. It is intended to be placed in the
  * LCIO data stream by the <code>DataTriggerSimDriver</code> to allow
- * other classes to access triggers simulated from SSP and reconstructed
+ * other classes to access triggers simulated from hardware and software
  * cluster data.
  * 
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class SimTriggerData {
-	private final SimTriggerModule<Cluster> reconTriggers;
-	private final SimTriggerModule<SSPCluster> sspTriggers;
-	
-	/**
-	 * Instantiates a new <code>SimTriggerData</code> object with empty
-	 * trigger results modules.
-	 */
-	SimTriggerData() {
-		reconTriggers = new SimTriggerModule<Cluster>();
-		sspTriggers = new SimTriggerModule<SSPCluster>();
-	}
-	
-	/**
-	 * Instantiates a new <code>SimTriggerData</code> object that will
-	 * contain the argument trigger modules.
-	 * @param reconTriggers - The simulated reconstructed cluster
-	 * triggers module.
-	 * @param sspTriggers - The simulated SSP cluster triggers module.
-	 */
-	SimTriggerData(SimTriggerModule<Cluster> reconTriggers, SimTriggerModule<SSPCluster> sspTriggers) {
-		this.reconTriggers = reconTriggers;
-		this.sspTriggers = sspTriggers;
-	}
-	
-	/**
-	 * Gets the module containing all simulated SSP trigger data for
-	 * each of the four primary triggers.
-	 * @return Returns the trigger data in a <code>SimTriggerModule</code>
-	 * object.
-	 */
-	public SimTriggerModule<SSPCluster> getSimSSPTriggers() {
-		return sspTriggers;
-	}
-	
-	/**
-	 * Gets the module containing all simulated LCSim trigger data for
-	 * each of the four primary triggers.
-	 * @return Returns the trigger data in a <code>SimTriggerModule</code>
-	 * object.
-	 */
-	public SimTriggerModule<Cluster> getSimReconTriggers() {
-		return reconTriggers;
-	}
+    private final SimTriggerModule<Cluster> softwareClusterTriggers;
+    private final SimTriggerModule<SSPCluster> hardwareClusterTriggers;
+    
+    /**
+     * Instantiates a new <code>SimTriggerData</code> object with empty
+     * trigger results modules.
+     */
+    SimTriggerData() {
+        softwareClusterTriggers = new SimTriggerModule<Cluster>();
+        hardwareClusterTriggers = new SimTriggerModule<SSPCluster>();
+    }
+    
+    /**
+     * Instantiates a new <code>SimTriggerData</code> object that will
+     * contain the argument trigger modules.
+     * @param softwareClusterTriggers - The module containing triggers
+     * simulated from software simulated clusters.
+     * @param hardwareClusterTriggers - The module containing triggers
+     * simulated from hardware reported clusters.
+     */
+    SimTriggerData(SimTriggerModule<Cluster> softwareClusterTriggers, SimTriggerModule<SSPCluster> hardwareClusterTriggers) {
+        this.softwareClusterTriggers = softwareClusterTriggers;
+        this.hardwareClusterTriggers = hardwareClusterTriggers;
+    }
+    
+    /**
+     * Gets the module containing all simulated SSP trigger data for
+     * each of the four primary triggers.
+     * @return Returns the trigger data in a <code>SimTriggerModule</code>
+     * object.
+     */
+    @Deprecated
+    public SimTriggerModule<SSPCluster> getSimSSPTriggers() {
+        return hardwareClusterTriggers;
+    }
+    
+    /**
+     * Gets the module containing all simulated LCSim trigger data for
+     * each of the four primary triggers.
+     * @return Returns the trigger data in a <code>SimTriggerModule</code>
+     * object.
+     */
+    @Deprecated
+    public SimTriggerModule<Cluster> getSimReconTriggers() {
+        return softwareClusterTriggers;
+    }
+    
+    /**
+     * Gets the module containing all triggers simulated from hardware
+     * reported clusters for each of the four production triggers.
+     * @return Returns the trigger data in a <code>SimTriggerModule</code>
+     * object.
+     */
+    public SimTriggerModule<SSPCluster> getSimHardwareClusterTriggers() {
+        return hardwareClusterTriggers;
+    }
+    
+    /**
+     * Gets the module containing all triggers simulated from software
+     * simulated clusters for each of the four production triggers.
+     * @return Returns the trigger data in a <code>SimTriggerModule</code>
+     * object.
+     */
+    public SimTriggerModule<Cluster> getSimSoftwareClusterTriggers() {
+        return softwareClusterTriggers;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerModule.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/SimTriggerModule.java	Wed Apr 27 11:11:32 2016
@@ -18,71 +18,115 @@
  * @see DataTriggerSimDriver
  */
 public class SimTriggerModule<E> {
-	private final List<SinglesTrigger<E>> singles0;
-	private final List<SinglesTrigger<E>> singles1;
-	private final List<PairTrigger<E[]>> pair0;
-	private final List<PairTrigger<E[]>> pair1;
-	
-	/**
-	 * Constructs a new <code>SimTriggerModule</code> with the no
-	 * triggers results for any triggers.
-	 */
-	SimTriggerModule() {
-		singles0 = new ArrayList<SinglesTrigger<E>>(0);
-		singles1 = new ArrayList<SinglesTrigger<E>>(0);
-		pair0    = new ArrayList<PairTrigger<E[]>>(0);
-		pair1    = new ArrayList<PairTrigger<E[]>>(0);
-	}
-	
-	/**
-	 * Constructs a new <code>SimTriggerModule</code> with the specified
-	 * trigger results for each of the four primary triggers.
-	 * @param singles0Triggers - The results for the singles 0 trigger.
-	 * @param singles1Triggers - The results for the singles 1 trigger.
-	 * @param pair0Triggers - The results for the pair 0 trigger.
-	 * @param pair1Triggers - The results for the pair 1 trigger.
-	 */
-	SimTriggerModule(List<SinglesTrigger<E>> singles0Triggers, List<SinglesTrigger<E>> singles1Triggers,
-			List<PairTrigger<E[]>> pair0Triggers, List<PairTrigger<E[]>> pair1Triggers) {
-		this.singles0 = singles0Triggers;
-		this.singles1 = singles1Triggers;
-		this.pair0    = pair0Triggers;
-		this.pair1    = pair1Triggers;
-	}
-	
-	/**
-	 * Gets the simulated trigger results for the singles 0 trigger.
-	 * @return Returns the trigger results as a <code>List</code> of
-	 * <code>SinglesTrigger</code> objects.
-	 */
-	public List<SinglesTrigger<E>> getSingles0Triggers() {
-		return singles0;
-	}
-	
-	/**
-	 * Gets the simulated trigger results for the singles 1 trigger.
-	 * @return Returns the trigger results as a <code>List</code> of
-	 * <code>SinglesTrigger</code> objects.
-	 */
-	public List<SinglesTrigger<E>> getSingles1Triggers() {
-		return singles1;
-	}
-	
-	/**
-	 * Gets the simulated trigger results for the pair 0 trigger.
-	 * @return Returns the trigger results as a <code>List</code> of
-	 * <code>PairTrigger</code> objects.
-	 */
-	public List<PairTrigger<E[]>> getPair0Triggers() {
-		return pair0;
-	}
-	
-	/**
-	 * Gets the simulated trigger results for the pair 1 trigger.
-	 * @return Returns the trigger results as a <code>List</code> of
-	 * <code>PairTrigger</code> objects.
-	 */
-	public List<PairTrigger<E[]>> getPair1Triggers() {
-		return pair1;
-	}
-}
+    private final List<SinglesTrigger<E>> singles0;
+    private final List<SinglesTrigger<E>> singles1;
+    private final List<PairTrigger<E[]>> pair0;
+    private final List<PairTrigger<E[]>> pair1;
+    
+    /**
+     * Constructs a new <code>SimTriggerModule</code> with the no
+     * triggers results for any triggers.
+     */
+    SimTriggerModule() {
+        singles0 = new ArrayList<SinglesTrigger<E>>(0);
+        singles1 = new ArrayList<SinglesTrigger<E>>(0);
+        pair0    = new ArrayList<PairTrigger<E[]>>(0);
+        pair1    = new ArrayList<PairTrigger<E[]>>(0);
+    }
+    
+    /**
+     * Constructs a new <code>SimTriggerModule</code> with the specified
+     * trigger results for each of the four primary triggers.
+     * @param singles0Triggers - The results for the singles 0 trigger.
+     * @param singles1Triggers - The results for the singles 1 trigger.
+     * @param pair0Triggers - The results for the pair 0 trigger.
+     * @param pair1Triggers - The results for the pair 1 trigger.
+     */
+    SimTriggerModule(List<SinglesTrigger<E>> singles0Triggers, List<SinglesTrigger<E>> singles1Triggers,
+            List<PairTrigger<E[]>> pair0Triggers, List<PairTrigger<E[]>> pair1Triggers) {
+        this.singles0 = singles0Triggers;
+        this.singles1 = singles1Triggers;
+        this.pair0    = pair0Triggers;
+        this.pair1    = pair1Triggers;
+    }
+    
+    /**
+     * Gets the simulated trigger results for the indicated singles
+     * trigger. Note that only inputs of <code>0</code> and <code>1</code>
+     * are allowed.
+     * @param triggerNumber - A value of either <code>0</code>, to
+     * obtain the singles 0 trigger results, or <code>1</code>, to
+     * obtain the singles 1 trigger results.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>SinglesTrigger</code> objects.
+     * @throws IllegalArgumentException Occurs if the input argument
+     * is not either <code>0</code> or <code>1</code>.
+     */
+    public List<SinglesTrigger<E>> getSinglesTriggers(int triggerNumber) {
+        // Return the appropriate trigger list.
+        if(triggerNumber == 0) { return getSingles0Triggers(); }
+        else if(triggerNumber == 1) { return getSingles1Triggers(); }
+        
+        // Any other trigger number is not valid and should produce an
+        // exception.
+        throw new IllegalArgumentException("Trigger number " + triggerNumber + " is not valid.");
+    }
+    
+    /**
+     * Gets the simulated trigger results for the singles 0 trigger.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>SinglesTrigger</code> objects.
+     */
+    public List<SinglesTrigger<E>> getSingles0Triggers() {
+        return singles0;
+    }
+    
+    /**
+     * Gets the simulated trigger results for the singles 1 trigger.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>SinglesTrigger</code> objects.
+     */
+    public List<SinglesTrigger<E>> getSingles1Triggers() {
+        return singles1;
+    }
+    
+    /**
+     * Gets the simulated trigger results for the indicated pair trigger.
+     * Note that only inputs of <code>0</code> and <code>1</code> are
+     * allowed.
+     * @param triggerNumber - A value of either <code>0</code>, to
+     * obtain the pair 0 trigger results, or <code>1</code>, to obtain
+     * the pair 1 trigger results.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>PairTrigger</code> objects.
+     * @throws IllegalArgumentException Occurs if the input argument
+     * is not either <code>0</code> or <code>1</code>.
+     */
+    public List<PairTrigger<E[]>> getPairTriggers(int triggerNumber) {
+        // Return the appropriate trigger list.
+        if(triggerNumber == 0) { return getPair0Triggers(); }
+        else if(triggerNumber == 1) { return getPair1Triggers(); }
+        
+        // Any other trigger number is not valid and should produce an
+        // exception.
+        throw new IllegalArgumentException("Trigger number " + triggerNumber + " is not valid.");
+    }
+    
+    /**
+     * Gets the simulated trigger results for the pair 0 trigger.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>PairTrigger</code> objects.
+     */
+    public List<PairTrigger<E[]>> getPair0Triggers() {
+        return pair0;
+    }
+    
+    /**
+     * Gets the simulated trigger results for the pair 1 trigger.
+     * @return Returns the trigger results as a <code>List</code> of
+     * <code>PairTrigger</code> objects.
+     */
+    public List<PairTrigger<E[]>> getPair1Triggers() {
+        return pair1;
+    }
+}

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerDiagnosticDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerDiagnosticDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerDiagnosticDriver.java	Wed Apr 27 11:11:32 2016
@@ -52,54 +52,54 @@
 import org.lcsim.util.aida.AIDA;
 
 public class TriggerDiagnosticDriver extends Driver {
-	// Store the LCIO collection names for the needed objects.
-	private String hitCollectionName = "EcalCalHits";
-	private String bankCollectionName = "TriggerBank";
-	private String clusterCollectionName = "EcalClusters";
-	private String diagnosticCollectionName = "DiagnosticSnapshot";
-	private static final int clusterCollectionFlag = 1 << LCIOConstants.CLBIT_HITS;
-	private String[] singlesCandidateCollectionName = { "Singles0TriggerCandidates", "Singles1TriggerCandidates" };
-	private String[] pairCandidateCollectionName = { "Pair0TriggerCandidates", "Pair1TriggerCandidates" };
-	
-	// Store the lists of parsed objects.
-	private TIData tiBank;
-	private SSPData sspBank;
-	private List<SSPCluster> sspClusters;
-	private List<Cluster> reconClusters = new ArrayList<Cluster>();
-	private SimTriggerData triggerData = null;
-	
-	// Trigger modules for performing trigger analysis.
-	//private int activeTrigger = -1;
-	private boolean[] tiFlags = new boolean[6];
-	private TriggerModule[] singlesTrigger = new TriggerModule[2];
-	private TriggerModule[] pairsTrigger = new TriggerModule[2];
-	private boolean[][] singlesCutsEnabled = new boolean[2][3];
-	private boolean[][] pairCutsEnabled = new boolean[2][7];
-	private boolean[] singlesTriggerEnabled = new boolean[2];
-	private boolean[] pairTriggerEnabled = new boolean[2];
-	
-	// Verification settings.
-	private int nsa = 100;
-	private int nsb = 20;
-	private int windowWidth = 200;
-	private int hitAcceptance = 1;
-	private int noiseThreshold = 50;
-	private double energyAcceptance = 0.003;
-	private boolean readDAQConfig = false;
-	private int localWindowThreshold = 1000000000;
-	private boolean performClusterVerification = true;
-	private boolean performSinglesTriggerVerification = true;
-	private boolean performPairTriggerVerification = true;
-	private boolean enforceTimeCompliance = false;
-	
-	// Efficiency tracking variables.
-	private RunDiagStats localStats = new RunDiagStats();
-	private RunDiagStats globalStats = new RunDiagStats();
-    
-	// Track which clusters/pairs are trigger candidates.
-	private List<List<Cluster>> singlesCandidates = new ArrayList<List<Cluster>>(2);
-	private List<List<LCRelation>> pairCandidates = new ArrayList<List<LCRelation>>(2);
-	
+    // Store the LCIO collection names for the needed objects.
+    private String hitCollectionName = "EcalCalHits";
+    private String bankCollectionName = "TriggerBank";
+    private String clusterCollectionName = "EcalClusters";
+    private String diagnosticCollectionName = "DiagnosticSnapshot";
+    private static final int clusterCollectionFlag = 1 << LCIOConstants.CLBIT_HITS;
+    private String[] singlesCandidateCollectionName = { "Singles0TriggerCandidates", "Singles1TriggerCandidates" };
+    private String[] pairCandidateCollectionName = { "Pair0TriggerCandidates", "Pair1TriggerCandidates" };
+    
+    // Store the lists of parsed objects.
+    private TIData tiBank;
+    private SSPData sspBank;
+    private List<SSPCluster> sspClusters;
+    private List<Cluster> reconClusters = new ArrayList<Cluster>();
+    private SimTriggerData triggerData = null;
+    
+    // Trigger modules for performing trigger analysis.
+    //private int activeTrigger = -1;
+    private boolean[] tiFlags = new boolean[6];
+    private TriggerModule[] singlesTrigger = new TriggerModule[2];
+    private TriggerModule[] pairsTrigger = new TriggerModule[2];
+    private boolean[][] singlesCutsEnabled = new boolean[2][3];
+    private boolean[][] pairCutsEnabled = new boolean[2][7];
+    private boolean[] singlesTriggerEnabled = new boolean[2];
+    private boolean[] pairTriggerEnabled = new boolean[2];
+    
+    // Verification settings.
+    private int nsa = 100;
+    private int nsb = 20;
+    private int windowWidth = 200;
+    private int hitAcceptance = 1;
+    private int noiseThreshold = 50;
+    private double energyAcceptance = 0.003;
+    private boolean readDAQConfig = false;
+    private int localWindowThreshold = 1000000000;
+    private boolean performClusterVerification = true;
+    private boolean performSinglesTriggerVerification = true;
+    private boolean performPairTriggerVerification = true;
+    private boolean enforceTimeCompliance = false;
+    
+    // Efficiency tracking variables.
+    private RunDiagStats localStats = new RunDiagStats();
+    private RunDiagStats globalStats = new RunDiagStats();
+    
+    // Track which clusters/pairs are trigger candidates.
+    private List<List<Cluster>> singlesCandidates = new ArrayList<List<Cluster>>(2);
+    private List<List<LCRelation>> pairCandidates = new ArrayList<List<LCRelation>>(2);
+    
     // Verbose settings.
     private boolean clusterFail = false;
     private boolean singlesEfficiencyFail = false;
@@ -115,2125 +115,2125 @@
     private int     statPrintInterval = Integer.MAX_VALUE;
 
     // Cut index arrays for trigger verification.
-	private static final int ENERGY_MIN   = TriggerDiagnosticUtil.SINGLES_ENERGY_MIN;
-	private static final int ENERGY_MAX   = TriggerDiagnosticUtil.SINGLES_ENERGY_MAX;
-	private static final int HIT_COUNT    = TriggerDiagnosticUtil.SINGLES_HIT_COUNT;
-	private static final int ENERGY_SUM   = TriggerDiagnosticUtil.PAIR_ENERGY_SUM;
-	private static final int ENERGY_DIFF  = TriggerDiagnosticUtil.PAIR_ENERGY_DIFF;
-	private static final int ENERGY_SLOPE = TriggerDiagnosticUtil.PAIR_ENERGY_SLOPE;
-	private static final int COPLANARITY  = TriggerDiagnosticUtil.PAIR_COPLANARITY;
-    
-	// Track the total run time.
-	private long startTime = -1;
-	private long endTime = -1;
-	
-	// Cut names for logging.
-	private static final String[][] cutNames = {
-			{ "E_min", "E_max", "hit count", "null" },
-			{ "E_sum", "E_diff", "E_slope", "coplanar" }
-	};
-	
-	// Temporary AIDA Plots
-	private TriggerPlotsModule globalTriggerPlots = new TriggerPlotsModule(0, 0);
-	private static final int RECON   = 0;
-	private static final int SSP     = 1;
-	private static final int ALL     = 0;
-	private static final int MATCHED = 1;
-	private static final int FAILED  = 2;
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D[][] clusterHitPlot = {
-			{
-				aida.histogram1D("Clustering/Recon Cluster Hit Count (All)",     9, 0.5, 9.5),
-				aida.histogram1D("Clustering/Recon Cluster Hit Count (Matched)", 9, 0.5, 9.5),
-				aida.histogram1D("Clustering/Recon Cluster Hit Count (Failed)",  9, 0.5, 9.5)
-			},
-			{
-				aida.histogram1D("Clustering/SSP Cluster Hit Count (All)",     9, 0.5, 9.5),
-				aida.histogram1D("Clustering/SSP Cluster Hit Count (Matched)", 9, 0.5, 9.5),
-				aida.histogram1D("Clustering/SSP Cluster Hit Count (Failed)",  9, 0.5, 9.5)
-			}
-	};
-	private IHistogram1D[][] clusterEnergyPlot = {
-			{
-				aida.histogram1D("Clustering/Recon Cluster Energy (All)",     300, 0.0, 3.0),
-				aida.histogram1D("Clustering/Recon Cluster Energy (Matched)", 300, 0.0, 3.0),
-				aida.histogram1D("Clustering/Recon Cluster Energy (Failed)",  300, 0.0, 3.0)
-			},
-			{
-				aida.histogram1D("Clustering/SSP Cluster Energy (All)",     300, 0.0, 3.0),
-				aida.histogram1D("Clustering/SSP Cluster Energy (Matched)", 300, 0.0, 3.0),
-				aida.histogram1D("Clustering/SSP Cluster Energy (Failed)",  300, 0.0, 3.0)
-			}
-	};
-	private IHistogram1D[][] clusterTimePlot = {
-			{
-				aida.histogram1D("Clustering/Recon Cluster Time (All)",     115, 0, 460),
-				aida.histogram1D("Clustering/Recon Cluster Time (Matched)", 115, 0, 460),
-				aida.histogram1D("Clustering/Recon Cluster Time (Failed)",  115, 0, 460)
-			},
-			{
-				aida.histogram1D("Clustering/SSP Cluster Time (All)",     115, 0, 460),
-				aida.histogram1D("Clustering/SSP Cluster Time (Matched)", 115, 0, 460),
-				aida.histogram1D("Clustering/SSP Cluster Time (Failed)",  115, 0, 460)
-			}
-	};
-	private IHistogram2D[][] clusterPositionPlot = {
-			{
-				aida.histogram2D("Clustering/Recon Cluster Position (All)",     47, -23.5, 23.5, 11, -5.5, 5.5),
-				aida.histogram2D("Clustering/Recon Cluster Position (Matched)", 47, -23.5, 23.5, 11, -5.5, 5.5),
-				aida.histogram2D("Clustering/Recon Cluster Position (Failed)",  47, -23.5, 23.5, 11, -5.5, 5.5)
-			},
-			{
-				aida.histogram2D("Clustering/SSP Cluster Position (All)",     47, -23.5, 23.5, 11, -5.5, 5.5),
-				aida.histogram2D("Clustering/SSP Cluster Position (Matched)", 47, -23.5, 23.5, 11, -5.5, 5.5),
-				aida.histogram2D("Clustering/SSP Cluster Position (Failed)",  47, -23.5, 23.5, 11, -5.5, 5.5)
-			}
-	};
-	private IHistogram2D[] energyhitDiffPlot = {
-		aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (All)",     21, -0.010, 0.010, 6, -3, 3),
-		aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (Matched)", 21, -0.010, 0.010, 6, -3, 3),
-		aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (Failed)",  21, -0.010, 0.010, 6, -3, 3)
-	};
-	private ICloud2D[] efficiencyTimeHist = {
-			aida.cloud2D("Clustering/Cluster Efficiency vs. Time"),
-			aida.cloud2D("Singles Trigger 0/Cluster Efficiency vs. Time"),
-			aida.cloud2D("Singles Trigger 1/Cluster Efficiency vs. Time"),
-			aida.cloud2D("Pair Trigger 0/Cluster Efficiency vs. Time"),
-			aida.cloud2D("Pair Trigger 1/Cluster Efficiency vs. Time")
-	};
-	
-	/**
-	 * Define the trigger modules. This should be replaced by parsing
-	 * the DAQ configuration at some point.
-	 */
-	@Override
-	public void startOfData() {
-		// By default, all triggers and cuts are enabled.
-		for(int i = 0; i < 2; i++) {
-			// Enable the triggers.
-			pairTriggerEnabled[i] = true;
-			singlesTriggerEnabled[i] = true;
-			
-			// Enable the singles cuts.
-			for(int j = 0; j < singlesCutsEnabled.length; j++) {
-				singlesCutsEnabled[i][j] = true;
-			}
-			
-			// Enable the pair cuts.
-			for(int j = 0; j < pairCutsEnabled.length; j++) {
-				pairCutsEnabled[i][j] = true;
-			}
-		}
-		
-		// If the DAQ configuration should be read, attach a listener
-		// to track when it updates.
-		if(readDAQConfig) {
-			ConfigurationManager.addActionListener(new ActionListener() {
-				@Override
-				public void actionPerformed(ActionEvent e) {
-					// Get the DAQ configuration.
-					DAQConfig daq = ConfigurationManager.getInstance();
-					
-					// Update the plotting energy slope values.
-					globalTriggerPlots.setEnergySlopeParamF(0, daq.getSSPConfig().getPair1Config().getEnergySlopeCutConfig().getParameterF());
-					globalTriggerPlots.setEnergySlopeParamF(1, daq.getSSPConfig().getPair2Config().getEnergySlopeCutConfig().getParameterF());
-					
-					// Load the DAQ settings from the configuration manager.
-					singlesTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getSingles1Config());
-					singlesTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getSingles2Config());
-					pairsTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getPair1Config());
-					pairsTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getPair2Config());
-					nsa = daq.getFADCConfig().getNSA();
-					nsb = daq.getFADCConfig().getNSB();
-					windowWidth = daq.getFADCConfig().getWindowWidth();
-					
-					// Get the trigger configurations from the DAQ.
-					SinglesTriggerConfig[] singles = { daq.getSSPConfig().getSingles1Config(),
-							daq.getSSPConfig().getSingles2Config() };
-					PairTriggerConfig[] pairs = { daq.getSSPConfig().getPair1Config(),
-							daq.getSSPConfig().getPair2Config() };
-					
-					// Update the enabled/disabled statuses.
-					for(int i = 0; i < 2; i++) {
-						// Set the trigger enabled status.
-						pairTriggerEnabled[i] = pairs[i].isEnabled();
-						singlesTriggerEnabled[i] = singles[i].isEnabled();
-						
-						// Set the singles cut statuses.
-						singlesCutsEnabled[i][ENERGY_MIN] = singles[i].getEnergyMinCutConfig().isEnabled();
-						singlesCutsEnabled[i][ENERGY_MAX] = singles[i].getEnergyMaxCutConfig().isEnabled();
-						singlesCutsEnabled[i][HIT_COUNT] = singles[i].getHitCountCutConfig().isEnabled();
-						
-						// Set the pair cut statuses.
-						pairCutsEnabled[i][ENERGY_MIN] = pairs[i].getEnergyMinCutConfig().isEnabled();
-						pairCutsEnabled[i][ENERGY_MAX] = pairs[i].getEnergyMaxCutConfig().isEnabled();
-						pairCutsEnabled[i][HIT_COUNT] = pairs[i].getHitCountCutConfig().isEnabled();
-						pairCutsEnabled[i][3 + ENERGY_SUM] = pairs[i].getEnergySumCutConfig().isEnabled();
-						pairCutsEnabled[i][3 + ENERGY_DIFF] = pairs[i].getEnergyDifferenceCutConfig().isEnabled();
-						pairCutsEnabled[i][3 + ENERGY_SLOPE] = pairs[i].getEnergySlopeCutConfig().isEnabled();
-						pairCutsEnabled[i][3 + COPLANARITY] = pairs[i].getCoplanarityCutConfig().isEnabled();
-					}
-					
-					// Update the trigger plots values.
-					globalTriggerPlots.setEnergySlopeParamF(0, daq.getSSPConfig().getPair1Config().getEnergySlopeCutConfig().getParameterF());
-					globalTriggerPlots.setEnergySlopeParamF(1, daq.getSSPConfig().getPair2Config().getEnergySlopeCutConfig().getParameterF());
-					
-					// Print a DAQ configuration settings header.
-					System.out.println();
-					System.out.println();
-					System.out.println("======================================================================");
-					System.out.println("=== DAQ Configuration Settings =======================================");
-					System.out.println("======================================================================");
-					logSettings();
-				}
-			});
-		}
-		
-		// Print the cluster verification header.
-		System.out.println();
-		System.out.println();
-		System.out.println("======================================================================");
-		System.out.println("=== Cluster/Trigger Verification Settings ============================");
-		System.out.println("======================================================================");
-		
-		// Define the first singles trigger.
-		singlesTrigger[0] = new TriggerModule();
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.500);
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		
-		// Define the second singles trigger.
-		singlesTrigger[1] = new TriggerModule();
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		
-		// Define the first pairs trigger.
-		pairsTrigger[0] = new TriggerModule();
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
-		pairsTrigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
-		
-		// Define the second pairs trigger.
-		pairsTrigger[1] = new TriggerModule();
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
-		pairsTrigger[1].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
-		
-		// Print the initial settings.
-		logSettings();
-	}
-	
-	/**
-	 * Prints the total run statistics.
-	 */
-	@Override
-	public void endOfData() {
-		// Output the statistics.
-		logStatistics();
-		
-		/*
-		// Calculate the values needed for the efficiency histogram.
-		long totalTime = entryList.get(entryList.size()).time / 1000000000;
-		int entries = (int) (totalTime / (localWindowThreshold / 1000000000)) + 1;
-		
-		// Generate a histogram containing the efficiencies.
-		IHistogram1D[] efficiencyHist = new IHistogram1D[5];
-		for(int i = 0; i < 5; i++) {
-			efficiencyHist[i] = aida.histogram1D("Efficiency " + i, entries, 0.0, totalTime + (localWindowThreshold / 1000000000));
-		}
-		
-		// Input the efficiencies.
-		for(EfficiencyEntry entry : entryList) {
-			for(int i = 0; i < 5; i++) {
-				efficiencyHist[i].fill(entry.time / 1000000000, entry.efficiency[i]);
-			}
-		}
-		*/
-	}
-	
-	/**
-	 * Gets the banks and clusters from the event.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		// ==========================================================
-		// ==== Event Pre-Initialization ============================
-		// ==========================================================
-        
-		// If DAQ settings are to be used, check if they are initialized
-		// yet. If not, skip the event.
-		if(readDAQConfig) {
-			if(!ConfigurationManager.isInitialized()) {
-				return;
-			}
-		}
-		
-		// Reset the candidate cluster lists.
-		singlesCandidates.clear();
-		singlesCandidates.add(new ArrayList<Cluster>());
-		singlesCandidates.add(new ArrayList<Cluster>());
-		pairCandidates.clear();
-		pairCandidates.add(new ArrayList<LCRelation>());
-		pairCandidates.add(new ArrayList<LCRelation>());
-		
-		// Increment the total event count.
-		localStats.sawEvent(event.getTimeStamp());
-		globalStats.sawEvent(event.getTimeStamp());
-		
-		// Print the statistics every so often during a run.
-		if(globalStats.getEventCount() % statPrintInterval == 0) {
-			logStatistics();
-		}
-		
-		// Reset the output buffer and print flags.
-		clusterFail = false;
-		singlesInternalFail = false;
-		singlesEfficiencyFail = false;
-		pairInternalFail = false;
-		pairEfficiencyFail = false;
-		OutputLogger.clearLog();
-		
-		// Track the times.
-		if(startTime == -1) { startTime = event.getTimeStamp(); }
-		else { endTime = event.getTimeStamp(); }
-		
-		
-		
-		// ==========================================================
-		// ==== Output GTP Information ==============================
-		// ==========================================================
-		
+    private static final int ENERGY_MIN   = TriggerDiagnosticUtil.SINGLES_ENERGY_MIN;
+    private static final int ENERGY_MAX   = TriggerDiagnosticUtil.SINGLES_ENERGY_MAX;
+    private static final int HIT_COUNT    = TriggerDiagnosticUtil.SINGLES_HIT_COUNT;
+    private static final int ENERGY_SUM   = TriggerDiagnosticUtil.PAIR_ENERGY_SUM;
+    private static final int ENERGY_DIFF  = TriggerDiagnosticUtil.PAIR_ENERGY_DIFF;
+    private static final int ENERGY_SLOPE = TriggerDiagnosticUtil.PAIR_ENERGY_SLOPE;
+    private static final int COPLANARITY  = TriggerDiagnosticUtil.PAIR_COPLANARITY;
+    
+    // Track the total run time.
+    private long startTime = -1;
+    private long endTime = -1;
+    
+    // Cut names for logging.
+    private static final String[][] cutNames = {
+            { "E_min", "E_max", "hit count", "null" },
+            { "E_sum", "E_diff", "E_slope", "coplanar" }
+    };
+    
+    // Temporary AIDA Plots
+    private TriggerPlotsModule globalTriggerPlots = new TriggerPlotsModule(0, 0);
+    private static final int RECON   = 0;
+    private static final int SSP     = 1;
+    private static final int ALL     = 0;
+    private static final int MATCHED = 1;
+    private static final int FAILED  = 2;
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D[][] clusterHitPlot = {
+            {
+                aida.histogram1D("Clustering/Recon Cluster Hit Count (All)",     9, 0.5, 9.5),
+                aida.histogram1D("Clustering/Recon Cluster Hit Count (Matched)", 9, 0.5, 9.5),
+                aida.histogram1D("Clustering/Recon Cluster Hit Count (Failed)",  9, 0.5, 9.5)
+            },
+            {
+                aida.histogram1D("Clustering/SSP Cluster Hit Count (All)",     9, 0.5, 9.5),
+                aida.histogram1D("Clustering/SSP Cluster Hit Count (Matched)", 9, 0.5, 9.5),
+                aida.histogram1D("Clustering/SSP Cluster Hit Count (Failed)",  9, 0.5, 9.5)
+            }
+    };
+    private IHistogram1D[][] clusterEnergyPlot = {
+            {
+                aida.histogram1D("Clustering/Recon Cluster Energy (All)",     300, 0.0, 3.0),
+                aida.histogram1D("Clustering/Recon Cluster Energy (Matched)", 300, 0.0, 3.0),
+                aida.histogram1D("Clustering/Recon Cluster Energy (Failed)",  300, 0.0, 3.0)
+            },
+            {
+                aida.histogram1D("Clustering/SSP Cluster Energy (All)",     300, 0.0, 3.0),
+                aida.histogram1D("Clustering/SSP Cluster Energy (Matched)", 300, 0.0, 3.0),
+                aida.histogram1D("Clustering/SSP Cluster Energy (Failed)",  300, 0.0, 3.0)
+            }
+    };
+    private IHistogram1D[][] clusterTimePlot = {
+            {
+                aida.histogram1D("Clustering/Recon Cluster Time (All)",     115, 0, 460),
+                aida.histogram1D("Clustering/Recon Cluster Time (Matched)", 115, 0, 460),
+                aida.histogram1D("Clustering/Recon Cluster Time (Failed)",  115, 0, 460)
+            },
+            {
+                aida.histogram1D("Clustering/SSP Cluster Time (All)",     115, 0, 460),
+                aida.histogram1D("Clustering/SSP Cluster Time (Matched)", 115, 0, 460),
+                aida.histogram1D("Clustering/SSP Cluster Time (Failed)",  115, 0, 460)
+            }
+    };
+    private IHistogram2D[][] clusterPositionPlot = {
+            {
+                aida.histogram2D("Clustering/Recon Cluster Position (All)",     47, -23.5, 23.5, 11, -5.5, 5.5),
+                aida.histogram2D("Clustering/Recon Cluster Position (Matched)", 47, -23.5, 23.5, 11, -5.5, 5.5),
+                aida.histogram2D("Clustering/Recon Cluster Position (Failed)",  47, -23.5, 23.5, 11, -5.5, 5.5)
+            },
+            {
+                aida.histogram2D("Clustering/SSP Cluster Position (All)",     47, -23.5, 23.5, 11, -5.5, 5.5),
+                aida.histogram2D("Clustering/SSP Cluster Position (Matched)", 47, -23.5, 23.5, 11, -5.5, 5.5),
+                aida.histogram2D("Clustering/SSP Cluster Position (Failed)",  47, -23.5, 23.5, 11, -5.5, 5.5)
+            }
+    };
+    private IHistogram2D[] energyhitDiffPlot = {
+        aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (All)",     21, -0.010, 0.010, 6, -3, 3),
+        aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (Matched)", 21, -0.010, 0.010, 6, -3, 3),
+        aida.histogram2D("Clustering/Recon-SSP Energy-Hit Difference (Failed)",  21, -0.010, 0.010, 6, -3, 3)
+    };
+    private ICloud2D[] efficiencyTimeHist = {
+            aida.cloud2D("Clustering/Cluster Efficiency vs. Time"),
+            aida.cloud2D("Singles Trigger 0/Cluster Efficiency vs. Time"),
+            aida.cloud2D("Singles Trigger 1/Cluster Efficiency vs. Time"),
+            aida.cloud2D("Pair Trigger 0/Cluster Efficiency vs. Time"),
+            aida.cloud2D("Pair Trigger 1/Cluster Efficiency vs. Time")
+    };
+    
+    /**
+     * Define the trigger modules. This should be replaced by parsing
+     * the DAQ configuration at some point.
+     */
+    @Override
+    public void startOfData() {
+        // By default, all triggers and cuts are enabled.
+        for(int i = 0; i < 2; i++) {
+            // Enable the triggers.
+            pairTriggerEnabled[i] = true;
+            singlesTriggerEnabled[i] = true;
+            
+            // Enable the singles cuts.
+            for(int j = 0; j < singlesCutsEnabled.length; j++) {
+                singlesCutsEnabled[i][j] = true;
+            }
+            
+            // Enable the pair cuts.
+            for(int j = 0; j < pairCutsEnabled.length; j++) {
+                pairCutsEnabled[i][j] = true;
+            }
+        }
+        
+        // If the DAQ configuration should be read, attach a listener
+        // to track when it updates.
+        if(readDAQConfig) {
+            ConfigurationManager.addActionListener(new ActionListener() {
+                @Override
+                public void actionPerformed(ActionEvent e) {
+                    // Get the DAQ configuration.
+                    DAQConfig daq = ConfigurationManager.getInstance();
+                    
+                    // Update the plotting energy slope values.
+                    globalTriggerPlots.setEnergySlopeParamF(0, daq.getSSPConfig().getPair1Config().getEnergySlopeCutConfig().getParameterF());
+                    globalTriggerPlots.setEnergySlopeParamF(1, daq.getSSPConfig().getPair2Config().getEnergySlopeCutConfig().getParameterF());
+                    
+                    // Load the DAQ settings from the configuration manager.
+                    singlesTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getSingles1Config());
+                    singlesTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getSingles2Config());
+                    pairsTrigger[0].loadDAQConfiguration(daq.getSSPConfig().getPair1Config());
+                    pairsTrigger[1].loadDAQConfiguration(daq.getSSPConfig().getPair2Config());
+                    nsa = daq.getFADCConfig().getNSA();
+                    nsb = daq.getFADCConfig().getNSB();
+                    windowWidth = daq.getFADCConfig().getWindowWidth();
+                    
+                    // Get the trigger configurations from the DAQ.
+                    SinglesTriggerConfig[] singles = { daq.getSSPConfig().getSingles1Config(),
+                            daq.getSSPConfig().getSingles2Config() };
+                    PairTriggerConfig[] pairs = { daq.getSSPConfig().getPair1Config(),
+                            daq.getSSPConfig().getPair2Config() };
+                    
+                    // Update the enabled/disabled statuses.
+                    for(int i = 0; i < 2; i++) {
+                        // Set the trigger enabled status.
+                        pairTriggerEnabled[i] = pairs[i].isEnabled();
+                        singlesTriggerEnabled[i] = singles[i].isEnabled();
+                        
+                        // Set the singles cut statuses.
+                        singlesCutsEnabled[i][ENERGY_MIN] = singles[i].getEnergyMinCutConfig().isEnabled();
+                        singlesCutsEnabled[i][ENERGY_MAX] = singles[i].getEnergyMaxCutConfig().isEnabled();
+                        singlesCutsEnabled[i][HIT_COUNT] = singles[i].getHitCountCutConfig().isEnabled();
+                        
+                        // Set the pair cut statuses.
+                        pairCutsEnabled[i][ENERGY_MIN] = pairs[i].getEnergyMinCutConfig().isEnabled();
+                        pairCutsEnabled[i][ENERGY_MAX] = pairs[i].getEnergyMaxCutConfig().isEnabled();
+                        pairCutsEnabled[i][HIT_COUNT] = pairs[i].getHitCountCutConfig().isEnabled();
+                        pairCutsEnabled[i][3 + ENERGY_SUM] = pairs[i].getEnergySumCutConfig().isEnabled();
+                        pairCutsEnabled[i][3 + ENERGY_DIFF] = pairs[i].getEnergyDifferenceCutConfig().isEnabled();
+                        pairCutsEnabled[i][3 + ENERGY_SLOPE] = pairs[i].getEnergySlopeCutConfig().isEnabled();
+                        pairCutsEnabled[i][3 + COPLANARITY] = pairs[i].getCoplanarityCutConfig().isEnabled();
+                    }
+                    
+                    // Update the trigger plots values.
+                    globalTriggerPlots.setEnergySlopeParamF(0, daq.getSSPConfig().getPair1Config().getEnergySlopeCutConfig().getParameterF());
+                    globalTriggerPlots.setEnergySlopeParamF(1, daq.getSSPConfig().getPair2Config().getEnergySlopeCutConfig().getParameterF());
+                    
+                    // Print a DAQ configuration settings header.
+                    System.out.println();
+                    System.out.println();
+                    System.out.println("======================================================================");
+                    System.out.println("=== DAQ Configuration Settings =======================================");
+                    System.out.println("======================================================================");
+                    logSettings();
+                }
+            });
+        }
+        
+        // Print the cluster verification header.
+        System.out.println();
+        System.out.println();
+        System.out.println("======================================================================");
+        System.out.println("=== Cluster/Trigger Verification Settings ============================");
+        System.out.println("======================================================================");
+        
+        // Define the first singles trigger.
+        singlesTrigger[0] = new TriggerModule();
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.500);
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        singlesTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        
+        // Define the second singles trigger.
+        singlesTrigger[1] = new TriggerModule();
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        singlesTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        
+        // Define the first pairs trigger.
+        pairsTrigger[0] = new TriggerModule();
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
+        pairsTrigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
+        
+        // Define the second pairs trigger.
+        pairsTrigger[1] = new TriggerModule();
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, 0);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 8.191);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, 0.000);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, 0.001);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, 180);
+        pairsTrigger[1].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, 8);
+        
+        // Print the initial settings.
+        logSettings();
+    }
+    
+    /**
+     * Prints the total run statistics.
+     */
+    @Override
+    public void endOfData() {
+        // Output the statistics.
+        logStatistics();
+        
+        /*
+        // Calculate the values needed for the efficiency histogram.
+        long totalTime = entryList.get(entryList.size()).time / 1000000000;
+        int entries = (int) (totalTime / (localWindowThreshold / 1000000000)) + 1;
+        
+        // Generate a histogram containing the efficiencies.
+        IHistogram1D[] efficiencyHist = new IHistogram1D[5];
+        for(int i = 0; i < 5; i++) {
+            efficiencyHist[i] = aida.histogram1D("Efficiency " + i, entries, 0.0, totalTime + (localWindowThreshold / 1000000000));
+        }
+        
+        // Input the efficiencies.
+        for(EfficiencyEntry entry : entryList) {
+            for(int i = 0; i < 5; i++) {
+                efficiencyHist[i].fill(entry.time / 1000000000, entry.efficiency[i]);
+            }
+        }
+        */
+    }
+    
+    /**
+     * Gets the banks and clusters from the event.
+     */
+    @Override
+    public void process(EventHeader event) {
+        // ==========================================================
+        // ==== Event Pre-Initialization ============================
+        // ==========================================================
+        
+        // If DAQ settings are to be used, check if they are initialized
+        // yet. If not, skip the event.
+        if(readDAQConfig) {
+            if(!ConfigurationManager.isInitialized()) {
+                return;
+            }
+        }
+        
+        // Reset the candidate cluster lists.
+        singlesCandidates.clear();
+        singlesCandidates.add(new ArrayList<Cluster>());
+        singlesCandidates.add(new ArrayList<Cluster>());
+        pairCandidates.clear();
+        pairCandidates.add(new ArrayList<LCRelation>());
+        pairCandidates.add(new ArrayList<LCRelation>());
+        
+        // Increment the total event count.
+        localStats.sawEvent(event.getTimeStamp());
+        globalStats.sawEvent(event.getTimeStamp());
+        
+        // Print the statistics every so often during a run.
+        if(globalStats.getEventCount() % statPrintInterval == 0) {
+            logStatistics();
+        }
+        
+        // Reset the output buffer and print flags.
+        clusterFail = false;
+        singlesInternalFail = false;
+        singlesEfficiencyFail = false;
+        pairInternalFail = false;
+        pairEfficiencyFail = false;
+        OutputLogger.clearLog();
+        
+        // Track the times.
+        if(startTime == -1) { startTime = event.getTimeStamp(); }
+        else { endTime = event.getTimeStamp(); }
+        
+        
+        
+        // ==========================================================
+        // ==== Output GTP Information ==============================
+        // ==========================================================
+        
         // Print the verification header.
-		OutputLogger.printNewLine(2);
-		OutputLogger.println("======================================================================");
-		OutputLogger.println("==== FADC/GTP Readout ================================================");
-		OutputLogger.println("======================================================================");
-		
-		OutputLogger.println("FADC Hits:");
-		for(CalorimeterHit hit : event.get(CalorimeterHit.class, "EcalCalHits")) {
-			int ix = hit.getIdentifierFieldValue("ix");
-			int iy = hit.getIdentifierFieldValue("iy");
-			OutputLogger.printf("\tHit at (%3d, %3d) with %7.3f GeV at time %3.0f ns%n", ix, iy, hit.getCorrectedEnergy(), hit.getTime());
-		}
-		OutputLogger.printNewLine(2);
-		OutputLogger.println("GTP Clusters:");
-		for(Cluster cluster : event.get(Cluster.class, clusterCollectionName)) {
-			OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(cluster));
-			for(CalorimeterHit hit : cluster.getCalorimeterHits()) {
-				int ix = hit.getIdentifierFieldValue("ix");
-				int iy = hit.getIdentifierFieldValue("iy");
-				OutputLogger.printf("\t\t> (%3d, %3d) :: %7.3f GeV%n", ix, iy, hit.getCorrectedEnergy());
-			}
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Initialize the Event ================================
-		// ==========================================================
-		
+        OutputLogger.printNewLine(2);
+        OutputLogger.println("======================================================================");
+        OutputLogger.println("==== FADC/GTP Readout ================================================");
+        OutputLogger.println("======================================================================");
+        
+        OutputLogger.println("FADC Hits:");
+        for(CalorimeterHit hit : event.get(CalorimeterHit.class, "EcalCalHits")) {
+            int ix = hit.getIdentifierFieldValue("ix");
+            int iy = hit.getIdentifierFieldValue("iy");
+            OutputLogger.printf("\tHit at (%3d, %3d) with %7.3f GeV at time %3.0f ns%n", ix, iy, hit.getCorrectedEnergy(), hit.getTime());
+        }
+        OutputLogger.printNewLine(2);
+        OutputLogger.println("GTP Clusters:");
+        for(Cluster cluster : event.get(Cluster.class, clusterCollectionName)) {
+            OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(cluster));
+            for(CalorimeterHit hit : cluster.getCalorimeterHits()) {
+                int ix = hit.getIdentifierFieldValue("ix");
+                int iy = hit.getIdentifierFieldValue("iy");
+                OutputLogger.printf("\t\t> (%3d, %3d) :: %7.3f GeV%n", ix, iy, hit.getCorrectedEnergy());
+            }
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Initialize the Event ================================
+        // ==========================================================
+        
         // Print the verification header.
-		OutputLogger.printNewLine(2);
-		OutputLogger.println("======================================================================");
-		OutputLogger.println("==== Cluster/Trigger Verification ====================================");
-		OutputLogger.println("======================================================================");
-		
-		
-		
-		// ==========================================================
-		// ==== Obtain SSP and TI Banks =============================
-		// ==========================================================
-		
-		// Get the SSP clusters.
-		if(event.hasCollection(GenericObject.class, bankCollectionName)) {
-			// Get the bank list.
-			List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-			
-			// Search through the banks and get the SSP and TI banks.
-			for(GenericObject obj : bankList) {
-				// If this is an SSP bank, parse it.
-				if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
-					sspBank = new SSPData(obj);
-				}
-				
-				// Otherwise, if this is a TI bank, parse it.
-				else if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
-					tiBank = new TIData(obj);
-					
-					tiFlags = new boolean[6];
-					if(tiBank.isPulserTrigger()) {
-						OutputLogger.println("Trigger type :: Pulser");
-						tiFlags[TriggerDiagStats.PULSER] = true;
-					} else if(tiBank.isSingle0Trigger()) {
-						OutputLogger.println("Trigger type :: Singles 1");
-						tiFlags[TriggerDiagStats.SINGLES0] = true;
-					} else if(tiBank.isSingle1Trigger()) {
-						OutputLogger.println("Trigger type :: Singles 2");
-						tiFlags[TriggerDiagStats.SINGLES1] = true;
-					} else if(tiBank.isPair0Trigger()) {
-						OutputLogger.println("Trigger type :: Pair 1");
-						tiFlags[TriggerDiagStats.PAIR0] = true;
-					} else if(tiBank.isPair1Trigger()) {
-						OutputLogger.println("Trigger type :: Pair 2");
-						tiFlags[TriggerDiagStats.PAIR1] = true;
-					} else if(tiBank.isCalibTrigger()) {
-						OutputLogger.println("Trigger type :: Cosmic");
-						tiFlags[TriggerDiagStats.COSMIC] = true;
-					} else {
-						System.err.println("TriggerDiagnosticDriver: Skipping event; no TI trigger source found.");
-						return;
-					}
-					
-					// Pass the TI triggers to the run statistical data
-					// manager object.
-					localStats.getTriggerStats().sawTITriggers(tiFlags);
-					globalStats.getTriggerStats().sawTITriggers(tiFlags);
-				}
-			}
-			
-			// If there is an SSP bank, get the list of SSP clusters.
-			if(sspBank != null) {
-				sspClusters = sspBank.getClusters();
-				if(sspClusters.size() == 1) {
-					OutputLogger.println("1 SSP cluster found.");
-				} else {
-					OutputLogger.printf("%d SSP clusters found.%n", sspClusters.size());
-				}
-			}
-		}
-		
-		// Make sure that both an SSP bank and a TI bank were found.
-		if(tiBank == null || sspBank == null) {
-			System.err.println("TriggerDiagnosticDriver :: SEVERE WARNING :: TI bank or SSP bank missing from event!");
-			return;
-		}
-		
-		// Output the event number and information.
-		OutputLogger.printf("Event Number %d (%d)%n", sspBank.getEventNumber(), event.getEventNumber());
-		
-		
-		
-		// ==========================================================
-		// ==== Establish Event Integrity ===========================
-		// ==========================================================
-		
-		// Check that all of the required objects are present.
-		if(sspBank == null) {
-			OutputLogger.println("No SSP bank found for this event. No verification will be performed.");
-			if(verbose) { OutputLogger.printLog(); }
-			return;
-		} if(tiBank == null) {
-			OutputLogger.println("No TI bank found for this event. No verification will be performed.");
-			if(verbose) { OutputLogger.printLog(); }
-			return;
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Check the Noise Level ===============================
-		// ==========================================================
-		
-		// Check if there are hits.
-		if(event.hasCollection(CalorimeterHit.class, hitCollectionName)) {
-			// Check if there are more hits than the noise threshold.
-			if(event.get(CalorimeterHit.class, hitCollectionName).size() >= noiseThreshold) {
-				localStats.sawNoiseEvent();
-				globalStats.sawNoiseEvent();
-				OutputLogger.println("Noise event detected. Skipping event...");
-				if(verbose) { OutputLogger.printLog(); }
-				return;
-			}
-		}
-        
-        
-        
-		// ==========================================================
-		// ==== Obtain Reconstructed Clusters =======================
-		// ==========================================================
-		
-		// Get the reconstructed clusters.
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Get the reconstructed clusters.
-			List<Cluster> allClusters = event.get(Cluster.class, clusterCollectionName);
-			
-			// Keep only the clusters that can be verified.
-			OutputLogger.println();
-			OutputLogger.println("Process cluster for verifiability:");
-			reconClusters.clear();
-			for(Cluster reconCluster : allClusters) {
-				// Check that the cluster is within the safe region of the
-				// FADC readout window. If it is not, it will likely have
-				// inaccurate energy or hit values and may not produce the
-				// expected results.
-				OutputLogger.printf("\t%s", TriggerDiagnosticUtil.clusterToString(reconCluster));
-				if(isVerifiable(reconCluster)) {
-					reconClusters.add(reconCluster);
-					OutputLogger.println(" [  verifiable  ]");
-				} else { OutputLogger.println(" [ unverifiable ]"); }
-			}
-			
-			// Output the number of verifiable clusters found.
-			if(reconClusters.size() == 1) { OutputLogger.println("1 verifiable reconstructed cluster found."); }
-			else { OutputLogger.printf("%d verifiable reconstructed clusters found.%n", reconClusters.size()); }
-			
-			// Output the number of unverifiable clusters found.
-			int unverifiableClusters = allClusters.size() - reconClusters.size();
-			if(unverifiableClusters == 1) { OutputLogger.println("1 unverifiable reconstructed cluster found."); }
-			else { OutputLogger.printf("%d unverifiable reconstructed clusters found.%n", unverifiableClusters); }
-		} else {
-			reconClusters = new ArrayList<Cluster>(0);
-			OutputLogger.printf("No reconstructed clusters were found for collection \"%s\" in this event.%n", clusterCollectionName);
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Perform Event Verification ==========================
-		// ==========================================================
-		
-		// Perform the cluster verification step.
-		if(performClusterVerification) { clusterVerification(); }
-		
-		// Get the simulated triggers.
-		if(event.hasCollection(SimTriggerData.class, "SimTriggers")) {
-			List<SimTriggerData> stdList = event.get(SimTriggerData.class, "SimTriggers");
-			triggerData = stdList.get(0);
-		}
-		
-		// Construct lists of triggers for the SSP clusters and the
-		// reconstructed clusters.
-		if(performSinglesTriggerVerification) {
-			singlesTriggerVerification();
-		}
-		if(performPairTriggerVerification) {
-			pairTriggerVerification();
-		}
-		
-		// Track how many events failed due to each type of verification.
-		if(clusterFail) {
-			localStats.failedClusterEvent();
-			globalStats.failedClusterEvent();
-		} if(pairInternalFail || pairEfficiencyFail) {
-			localStats.failedPairEvent();
-			globalStats.failedPairEvent();
-		} if(singlesInternalFail || singlesEfficiencyFail) {
-			localStats.failedSinglesEvent();
-			globalStats.failedSinglesEvent();
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Perform Event Write-Out =============================
-		// ==========================================================
-		
-		if(verbose ||(clusterFail && printClusterFail) ||
-				(singlesInternalFail && printSinglesTriggerInternalFail) ||
-				(singlesEfficiencyFail && printSinglesTriggerEfficiencyFail) ||
-				(pairInternalFail && printPairTriggerInternalFail) ||
-				(pairEfficiencyFail && printPairTriggerEfficiencyFail)) {
-			OutputLogger.printLog();
-		}	
-		
-		
-				
-		// ==========================================================
-		// ==== Process Local Tracked Variables =====================
-		// ==========================================================
-		if(localStats.getDuration() > localWindowThreshold) {
-			// Write a snapshot of the driver to the event stream.
-			List<DiagnosticSnapshot> snapshotList = new ArrayList<DiagnosticSnapshot>(2);
-			snapshotList.add(localStats.getSnapshot());
-			snapshotList.add(globalStats.getSnapshot());
-			
-			// Push the snapshot to the data stream.
-			event.put(diagnosticCollectionName, snapshotList);
-			
-			// Store values needed to calculate efficiency.
-			int[] matched = {
-					localStats.getClusterStats().getMatches(),
-					localStats.getTriggerStats().getSingles0Stats().getMatchedReconSimulatedTriggers(),
-					localStats.getTriggerStats().getSingles1Stats().getMatchedReconSimulatedTriggers(),
-					localStats.getTriggerStats().getPair0Stats().getMatchedReconSimulatedTriggers(),
-					localStats.getTriggerStats().getPair1Stats().getMatchedReconSimulatedTriggers()
-			};
-			int[] total = {
-					localStats.getClusterStats().getReconClusterCount(),
-					localStats.getTriggerStats().getSingles0Stats().getReconSimulatedTriggers(),
-					localStats.getTriggerStats().getSingles1Stats().getReconSimulatedTriggers(),
-					localStats.getTriggerStats().getPair0Stats().getReconSimulatedTriggers(),
-					localStats.getTriggerStats().getPair1Stats().getReconSimulatedTriggers()
-			};
-			
-			// Calculate the efficiencies and upper/lower errors.
-			double[] efficiency = new double[5];
-			for(int i = 0; i < 5; i++) {
-				efficiency[i] = 1.0 * matched[i] / total[i];
-			}
-			
-			// Get the time for the current snapshot. This is the total
-			// run time before the snapshot plus half of the snapshot.
-			long time = globalStats.getDuration() - (localStats.getDuration() / 2);
-			
-			// Add them to the appropriate cloud plot.
-			for(int i = 0; i < 5; i++) { efficiencyTimeHist[i].fill(time, efficiency[i]); }
-			
-			// Clear the local statistical data.
-			localStats.clear();
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Write the Candidate Triggers ========================
-		// ==========================================================
-		
-		// Write the candidates to a collection.
-		event.put(pairCandidateCollectionName[0], pairCandidates.get(0), LCRelation.class, 0);
-		event.put(pairCandidateCollectionName[1], pairCandidates.get(1), LCRelation.class, 0);
-		event.put(singlesCandidateCollectionName[0], singlesCandidates.get(0), Cluster.class, clusterCollectionFlag);
-		event.put(singlesCandidateCollectionName[1], singlesCandidates.get(1), Cluster.class, clusterCollectionFlag);
-	}
+        OutputLogger.printNewLine(2);
+        OutputLogger.println("======================================================================");
+        OutputLogger.println("==== Cluster/Trigger Verification ====================================");
+        OutputLogger.println("======================================================================");
+        
+        
+        
+        // ==========================================================
+        // ==== Obtain SSP and TI Banks =============================
+        // ==========================================================
+        
+        // Get the SSP clusters.
+        if(event.hasCollection(GenericObject.class, bankCollectionName)) {
+            // Get the bank list.
+            List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+            
+            // Search through the banks and get the SSP and TI banks.
+            for(GenericObject obj : bankList) {
+                // If this is an SSP bank, parse it.
+                if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
+                    sspBank = new SSPData(obj);
+                }
+                
+                // Otherwise, if this is a TI bank, parse it.
+                else if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
+                    tiBank = new TIData(obj);
+                    
+                    tiFlags = new boolean[6];
+                    if(tiBank.isPulserTrigger()) {
+                        OutputLogger.println("Trigger type :: Pulser");
+                        tiFlags[TriggerDiagStats.PULSER] = true;
+                    } else if(tiBank.isSingle0Trigger()) {
+                        OutputLogger.println("Trigger type :: Singles 1");
+                        tiFlags[TriggerDiagStats.SINGLES0] = true;
+                    } else if(tiBank.isSingle1Trigger()) {
+                        OutputLogger.println("Trigger type :: Singles 2");
+                        tiFlags[TriggerDiagStats.SINGLES1] = true;
+                    } else if(tiBank.isPair0Trigger()) {
+                        OutputLogger.println("Trigger type :: Pair 1");
+                        tiFlags[TriggerDiagStats.PAIR0] = true;
+                    } else if(tiBank.isPair1Trigger()) {
+                        OutputLogger.println("Trigger type :: Pair 2");
+                        tiFlags[TriggerDiagStats.PAIR1] = true;
+                    } else if(tiBank.isCalibTrigger()) {
+                        OutputLogger.println("Trigger type :: Cosmic");
+                        tiFlags[TriggerDiagStats.COSMIC] = true;
+                    } else {
+                        System.err.println("TriggerDiagnosticDriver: Skipping event; no TI trigger source found.");
+                        return;
+                    }
+                    
+                    // Pass the TI triggers to the run statistical data
+                    // manager object.
+                    localStats.getTriggerStats().sawTITriggers(tiFlags);
+                    globalStats.getTriggerStats().sawTITriggers(tiFlags);
+                }
+            }
+            
+            // If there is an SSP bank, get the list of SSP clusters.
+            if(sspBank != null) {
+                sspClusters = sspBank.getClusters();
+                if(sspClusters.size() == 1) {
+                    OutputLogger.println("1 SSP cluster found.");
+                } else {
+                    OutputLogger.printf("%d SSP clusters found.%n", sspClusters.size());
+                }
+            }
+        }
+        
+        // Make sure that both an SSP bank and a TI bank were found.
+        if(tiBank == null || sspBank == null) {
+            System.err.println("TriggerDiagnosticDriver :: SEVERE WARNING :: TI bank or SSP bank missing from event!");
+            return;
+        }
+        
+        // Output the event number and information.
+        OutputLogger.printf("Event Number %d (%d)%n", sspBank.getEventNumber(), event.getEventNumber());
+        
+        
+        
+        // ==========================================================
+        // ==== Establish Event Integrity ===========================
+        // ==========================================================
+        
+        // Check that all of the required objects are present.
+        if(sspBank == null) {
+            OutputLogger.println("No SSP bank found for this event. No verification will be performed.");
+            if(verbose) { OutputLogger.printLog(); }
+            return;
+        } if(tiBank == null) {
+            OutputLogger.println("No TI bank found for this event. No verification will be performed.");
+            if(verbose) { OutputLogger.printLog(); }
+            return;
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Check the Noise Level ===============================
+        // ==========================================================
+        
+        // Check if there are hits.
+        if(event.hasCollection(CalorimeterHit.class, hitCollectionName)) {
+            // Check if there are more hits than the noise threshold.
+            if(event.get(CalorimeterHit.class, hitCollectionName).size() >= noiseThreshold) {
+                localStats.sawNoiseEvent();
+                globalStats.sawNoiseEvent();
+                OutputLogger.println("Noise event detected. Skipping event...");
+                if(verbose) { OutputLogger.printLog(); }
+                return;
+            }
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Obtain Reconstructed Clusters =======================
+        // ==========================================================
+        
+        // Get the reconstructed clusters.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the reconstructed clusters.
+            List<Cluster> allClusters = event.get(Cluster.class, clusterCollectionName);
+            
+            // Keep only the clusters that can be verified.
+            OutputLogger.println();
+            OutputLogger.println("Process cluster for verifiability:");
+            reconClusters.clear();
+            for(Cluster reconCluster : allClusters) {
+                // Check that the cluster is within the safe region of the
+                // FADC readout window. If it is not, it will likely have
+                // inaccurate energy or hit values and may not produce the
+                // expected results.
+                OutputLogger.printf("\t%s", TriggerDiagnosticUtil.clusterToString(reconCluster));
+                if(isVerifiable(reconCluster)) {
+                    reconClusters.add(reconCluster);
+                    OutputLogger.println(" [  verifiable  ]");
+                } else { OutputLogger.println(" [ unverifiable ]"); }
+            }
+            
+            // Output the number of verifiable clusters found.
+            if(reconClusters.size() == 1) { OutputLogger.println("1 verifiable reconstructed cluster found."); }
+            else { OutputLogger.printf("%d verifiable reconstructed clusters found.%n", reconClusters.size()); }
+            
+            // Output the number of unverifiable clusters found.
+            int unverifiableClusters = allClusters.size() - reconClusters.size();
+            if(unverifiableClusters == 1) { OutputLogger.println("1 unverifiable reconstructed cluster found."); }
+            else { OutputLogger.printf("%d unverifiable reconstructed clusters found.%n", unverifiableClusters); }
+        } else {
+            reconClusters = new ArrayList<Cluster>(0);
+            OutputLogger.printf("No reconstructed clusters were found for collection \"%s\" in this event.%n", clusterCollectionName);
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Perform Event Verification ==========================
+        // ==========================================================
+        
+        // Perform the cluster verification step.
+        if(performClusterVerification) { clusterVerification(); }
+        
+        // Get the simulated triggers.
+        if(event.hasCollection(SimTriggerData.class, "SimTriggers")) {
+            List<SimTriggerData> stdList = event.get(SimTriggerData.class, "SimTriggers");
+            triggerData = stdList.get(0);
+        }
+        
+        // Construct lists of triggers for the SSP clusters and the
+        // reconstructed clusters.
+        if(performSinglesTriggerVerification) {
+            singlesTriggerVerification();
+        }
+        if(performPairTriggerVerification) {
+            pairTriggerVerification();
+        }
+        
+        // Track how many events failed due to each type of verification.
+        if(clusterFail) {
+            localStats.failedClusterEvent();
+            globalStats.failedClusterEvent();
+        } if(pairInternalFail || pairEfficiencyFail) {
+            localStats.failedPairEvent();
+            globalStats.failedPairEvent();
+        } if(singlesInternalFail || singlesEfficiencyFail) {
+            localStats.failedSinglesEvent();
+            globalStats.failedSinglesEvent();
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Perform Event Write-Out =============================
+        // ==========================================================
+        
+        if(verbose ||(clusterFail && printClusterFail) ||
+                (singlesInternalFail && printSinglesTriggerInternalFail) ||
+                (singlesEfficiencyFail && printSinglesTriggerEfficiencyFail) ||
+                (pairInternalFail && printPairTriggerInternalFail) ||
+                (pairEfficiencyFail && printPairTriggerEfficiencyFail)) {
+            OutputLogger.printLog();
+        }   
+        
+        
+                
+        // ==========================================================
+        // ==== Process Local Tracked Variables =====================
+        // ==========================================================
+        if(localStats.getDuration() > localWindowThreshold) {
+            // Write a snapshot of the driver to the event stream.
+            List<DiagnosticSnapshot> snapshotList = new ArrayList<DiagnosticSnapshot>(2);
+            snapshotList.add(localStats.getSnapshot());
+            snapshotList.add(globalStats.getSnapshot());
+            
+            // Push the snapshot to the data stream.
+            event.put(diagnosticCollectionName, snapshotList);
+            
+            // Store values needed to calculate efficiency.
+            int[] matched = {
+                    localStats.getClusterStats().getMatches(),
+                    localStats.getTriggerStats().getSingles0Stats().getMatchedReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getSingles1Stats().getMatchedReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getPair0Stats().getMatchedReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getPair1Stats().getMatchedReconSimulatedTriggers()
+            };
+            int[] total = {
+                    localStats.getClusterStats().getReconClusterCount(),
+                    localStats.getTriggerStats().getSingles0Stats().getReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getSingles1Stats().getReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getPair0Stats().getReconSimulatedTriggers(),
+                    localStats.getTriggerStats().getPair1Stats().getReconSimulatedTriggers()
+            };
+            
+            // Calculate the efficiencies and upper/lower errors.
+            double[] efficiency = new double[5];
+            for(int i = 0; i < 5; i++) {
+                efficiency[i] = 1.0 * matched[i] / total[i];
+            }
+            
+            // Get the time for the current snapshot. This is the total
+            // run time before the snapshot plus half of the snapshot.
+            long time = globalStats.getDuration() - (localStats.getDuration() / 2);
+            
+            // Add them to the appropriate cloud plot.
+            for(int i = 0; i < 5; i++) { efficiencyTimeHist[i].fill(time, efficiency[i]); }
+            
+            // Clear the local statistical data.
+            localStats.clear();
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Write the Candidate Triggers ========================
+        // ==========================================================
+        
+        // Write the candidates to a collection.
+        event.put(pairCandidateCollectionName[0], pairCandidates.get(0), LCRelation.class, 0);
+        event.put(pairCandidateCollectionName[1], pairCandidates.get(1), LCRelation.class, 0);
+        event.put(singlesCandidateCollectionName[0], singlesCandidates.get(0), Cluster.class, clusterCollectionFlag);
+        event.put(singlesCandidateCollectionName[1], singlesCandidates.get(1), Cluster.class, clusterCollectionFlag);
+    }
 
-	public void setPrintResultsEveryNEvents(int n) {
-		statPrintInterval = n;
-	}
-	
-	public void setPrintOnClusterFailure(boolean state) {
-		printClusterFail = state;
-	}
-	
-	public void setPrintOnSinglesEfficiencyFailure(boolean state) {
-		printSinglesTriggerEfficiencyFail = state;
-	}
-	
-	public void setPrintOnSinglesSSPFailure(boolean state) {
-		printSinglesTriggerInternalFail = state;
-	}
-	
-	public void setPrintOnPairEfficiencyFailure(boolean state) {
-		printPairTriggerEfficiencyFail = state;
-	}
-	
-	public void setPrintOnPairSSPFailure(boolean state) {
-		printPairTriggerInternalFail = state;
-	}
-	
-	public void setVerbose(boolean state) {
-		verbose = state;
-	}
-	
-	public void setHitCollectionName(String hitCollectionName) {
-		this.hitCollectionName = hitCollectionName;
-	}
-	
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
-	
-	public void setBankCollectionName(String bankCollectionName) {
-		this.bankCollectionName = bankCollectionName;
-	}
-	
-	public void setNoiseThresholdCount(int noiseHits) {
-		noiseThreshold = noiseHits;
-	}
-	
-	public void setHitAcceptanceWindow(int window) {
-		hitAcceptance = window;
-	}
-	
-	public void setEnergyAcceptanceWindow(double window) {
-		energyAcceptance = window;
-	}
-	
-	public void setEnforceStrictTimeCompliance(boolean state) {
-		enforceTimeCompliance = state;
-	}
-	
-	public void setReadDAQConfig(boolean state) {
-		readDAQConfig = state;
-	}
-	
-	public void setLocalWindowThresholdMilliseconds(int localWindowThreshold) {
-	    this.localWindowThreshold = localWindowThreshold;
-	}
-	
-	/**
-	 * Attempts to match all reconstructed clusters that are safely
-	 * within the integration window with clusters reported by the SSP.
-	 * Method also tracks the ratio of valid reconstructed clusters to
-	 * matches found.<br/>
-	 * <br/>
-	 * Note that unmatched SSP clusters are ignored. Since these may
-	 * or may not correspond to reconstructed clusters that occur in
-	 * the forbidden time region, it is impossible to say whether or
-	 * not these legitimately failed to match or not.
-	 */
-	private void clusterVerification() {
-		// ==========================================================
-		// ==== Initialize Cluster Verification =====================
-		// ==========================================================
-		
-		// Print the cluster verification header.
-		OutputLogger.printNewLine(2);
-		OutputLogger.println("======================================================================");
-		OutputLogger.println("=== Cluster Verification =============================================");
-		OutputLogger.println("======================================================================");
-		
-		
-		
-		// ==========================================================
-		// ==== Perform Cluster Matching ============================
-		// ==========================================================
-		
-		// Track the number of cluster pairs that were matched and that
-		// failed by failure type.
-		DetailedClusterEvent event;
-		
-		if(enforceTimeCompliance) {
-			event = matchClustersTimeCompliant(reconClusters, sspClusters, energyAcceptance, hitAcceptance);
-		} else {
-			event = matchClusters(reconClusters, sspClusters, energyAcceptance, hitAcceptance);
-		}
-		
-		// Add the event results to the global results.
-		localStats.getClusterStats().addEvent(event);
-		globalStats.getClusterStats().addEvent(event);
-		localStats.getClusterStats().sawSSPClusters(sspClusters.size());
-		globalStats.getClusterStats().sawSSPClusters(sspClusters.size());
-		localStats.getClusterStats().sawReconClusters(reconClusters.size());
-		globalStats.getClusterStats().sawReconClusters(reconClusters.size());
-		
-		
-		
-		// ==========================================================
-		// ==== Output Event Summary ================================
-		// ==========================================================
-		
-		// Print the valid reconstructed clusters and populate their
-		// distribution graphs.
-		OutputLogger.println();
-		OutputLogger.println("Verified Reconstructed Clusters:");
-		if(!reconClusters.isEmpty()) {
-			for(Cluster reconCluster : reconClusters) {
-				OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(reconCluster));
-			}
-		} else { OutputLogger.println("\tNone"); }
-		
-		// Print the SSP clusters and populate their distribution graphs.
-		OutputLogger.println("SSP Clusters:");
-		if(!sspClusters.isEmpty()) {
-			for(SSPCluster sspCluster : sspClusters) {
-				OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(sspCluster));
-			}
-		} else { OutputLogger.println("\tNone"); }
-		
-		// Print the matched clusters.
-		OutputLogger.println("Matched Clusters:");
-		if(event.getMatches() != 0) {
-			// Iterate over the matched pairs.
-			for(ClusterMatchedPair pair : event.getClusterPairs()) {
-				// If the pair is a match, print it out.
-				if(pair.isMatch()) {
-					OutputLogger.printf("\t%s --> %s%n",
-							TriggerDiagnosticUtil.clusterToString(pair.getReconstructedCluster()),
-							TriggerDiagnosticUtil.clusterToString(pair.getSSPCluster()));
-				}
-			}
-		}
-		 else { OutputLogger.println("\tNone"); }
-		
-		// Print event statistics.
-		OutputLogger.println();
-		OutputLogger.println("Event Statistics:");
-		OutputLogger.printf("\tRecon Clusters     :: %d%n", reconClusters.size());
-		OutputLogger.printf("\tClusters Matched   :: %d%n", event.getMatches());
-		OutputLogger.printf("\tFailed (Position)  :: %d%n", event.getPositionFailures());
-		OutputLogger.printf("\tFailed (Time)      :: %d%n", event.getTimeFailures());
-		OutputLogger.printf("\tFailed (Energy)    :: %d%n", event.getEnergyFailures());
-		OutputLogger.printf("\tFailed (Hit Count) :: %d%n", event.getHitCountFailures());
-		OutputLogger.printf("\tCluster Efficiency :: %3.0f%%%n", 100.0 * event.getMatches() / reconClusters.size());
-		
-		// Note whether there was a cluster match failure.
-		if(event.isFailState() || event.getMatches() - reconClusters.size() != 0) {
-			clusterFail = true;
-		}
-		
-		
-		
-		// TEMP :: Populate the cluster diagnostic plots.
-		
-		// Populate the ALL cluster plots.
-		for(Cluster cluster : reconClusters) {
-			clusterHitPlot[RECON][ALL].fill(cluster.getCalorimeterHits().size());
-			clusterEnergyPlot[RECON][ALL].fill(cluster.getEnergy());
-			clusterTimePlot[RECON][ALL].fill(cluster.getCalorimeterHits().get(0).getTime());
-			Point position = TriggerDiagnosticUtil.getClusterPosition(cluster);
-			clusterPositionPlot[RECON][ALL].fill(position.x, position.y);
-		}
-		for(SSPCluster cluster : sspClusters) {
-			clusterHitPlot[SSP][ALL].fill(cluster.getHitCount());
-			clusterEnergyPlot[SSP][ALL].fill(cluster.getEnergy());
-			clusterTimePlot[SSP][ALL].fill(cluster.getTime());
-			clusterPositionPlot[SSP][ALL].fill(cluster.getXIndex(), cluster.getYIndex());
-		}
-		
-		// Populate the matched and failed plots.
-		for(ClusterMatchedPair pair : event.getClusterPairs()) {
-			 if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
-				double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
-				int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
-				energyhitDiffPlot[ALL].fill(energyDiff, hitDiff);
-			 }
-			
-			if(pair.isMatch()) {
-				if(pair.getFirstElement() != null) {
-					clusterHitPlot[RECON][MATCHED].fill(pair.getFirstElement().getCalorimeterHits().size());
-					clusterEnergyPlot[RECON][MATCHED].fill(pair.getFirstElement().getEnergy());
-					clusterTimePlot[RECON][MATCHED].fill(pair.getFirstElement().getCalorimeterHits().get(0).getTime());
-					Point position = TriggerDiagnosticUtil.getClusterPosition(pair.getFirstElement());
-					clusterPositionPlot[RECON][MATCHED].fill(position.x, position.y);
-				} if(pair.getSecondElement() != null) {
-					clusterHitPlot[SSP][MATCHED].fill(pair.getSecondElement().getHitCount());
-					clusterEnergyPlot[SSP][MATCHED].fill(pair.getSecondElement().getEnergy());
-					clusterTimePlot[SSP][MATCHED].fill(pair.getSecondElement().getTime());
-					clusterPositionPlot[SSP][MATCHED].fill(pair.getSecondElement().getXIndex(), pair.getSecondElement().getYIndex());
-				} if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
-					double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
-					int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
-					energyhitDiffPlot[MATCHED].fill(energyDiff, hitDiff);
-				}
-			} else {
-				if(pair.getFirstElement() != null) {
-					clusterHitPlot[RECON][FAILED].fill(pair.getFirstElement().getCalorimeterHits().size());
-					clusterEnergyPlot[RECON][FAILED].fill(pair.getFirstElement().getEnergy());
-					clusterTimePlot[RECON][FAILED].fill(pair.getFirstElement().getCalorimeterHits().get(0).getTime());
-					Point position = TriggerDiagnosticUtil.getClusterPosition(pair.getFirstElement());
-					clusterPositionPlot[RECON][FAILED].fill(position.x, position.y);
-				} if(pair.getSecondElement() != null) {
-					clusterHitPlot[SSP][FAILED].fill(pair.getSecondElement().getHitCount());
-					clusterEnergyPlot[SSP][FAILED].fill(pair.getSecondElement().getEnergy());
-					clusterTimePlot[SSP][FAILED].fill(pair.getSecondElement().getTime());
-					clusterPositionPlot[SSP][FAILED].fill(pair.getSecondElement().getXIndex(), pair.getSecondElement().getYIndex());
-				} if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
-					double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
-					int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
-					energyhitDiffPlot[FAILED].fill(energyDiff, hitDiff);
-				}
-			}
-		}
-	}
-	
-	/**
+    public void setPrintResultsEveryNEvents(int n) {
+        statPrintInterval = n;
+    }
+    
+    public void setPrintOnClusterFailure(boolean state) {
+        printClusterFail = state;
+    }
+    
+    public void setPrintOnSinglesEfficiencyFailure(boolean state) {
+        printSinglesTriggerEfficiencyFail = state;
+    }
+    
+    public void setPrintOnSinglesSSPFailure(boolean state) {
+        printSinglesTriggerInternalFail = state;
+    }
+    
+    public void setPrintOnPairEfficiencyFailure(boolean state) {
+        printPairTriggerEfficiencyFail = state;
+    }
+    
+    public void setPrintOnPairSSPFailure(boolean state) {
+        printPairTriggerInternalFail = state;
+    }
+    
+    public void setVerbose(boolean state) {
+        verbose = state;
+    }
+    
+    public void setHitCollectionName(String hitCollectionName) {
+        this.hitCollectionName = hitCollectionName;
+    }
+    
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
+    
+    public void setBankCollectionName(String bankCollectionName) {
+        this.bankCollectionName = bankCollectionName;
+    }
+    
+    public void setNoiseThresholdCount(int noiseHits) {
+        noiseThreshold = noiseHits;
+    }
+    
+    public void setHitAcceptanceWindow(int window) {
+        hitAcceptance = window;
+    }
+    
+    public void setEnergyAcceptanceWindow(double window) {
+        energyAcceptance = window;
+    }
+    
+    public void setEnforceStrictTimeCompliance(boolean state) {
+        enforceTimeCompliance = state;
+    }
+    
+    public void setReadDAQConfig(boolean state) {
+        readDAQConfig = state;
+    }
+    
+    public void setLocalWindowThresholdMilliseconds(int localWindowThreshold) {
+        this.localWindowThreshold = localWindowThreshold;
+    }
+    
+    /**
+     * Attempts to match all reconstructed clusters that are safely
+     * within the integration window with clusters reported by the SSP.
+     * Method also tracks the ratio of valid reconstructed clusters to
+     * matches found.<br/>
+     * <br/>
+     * Note that unmatched SSP clusters are ignored. Since these may
+     * or may not correspond to reconstructed clusters that occur in
+     * the forbidden time region, it is impossible to say whether or
+     * not these legitimately failed to match or not.
+     */
+    private void clusterVerification() {
+        // ==========================================================
+        // ==== Initialize Cluster Verification =====================
+        // ==========================================================
+        
+        // Print the cluster verification header.
+        OutputLogger.printNewLine(2);
+        OutputLogger.println("======================================================================");
+        OutputLogger.println("=== Cluster Verification =============================================");
+        OutputLogger.println("======================================================================");
+        
+        
+        
+        // ==========================================================
+        // ==== Perform Cluster Matching ============================
+        // ==========================================================
+        
+        // Track the number of cluster pairs that were matched and that
+        // failed by failure type.
+        DetailedClusterEvent event;
+        
+        if(enforceTimeCompliance) {
+            event = matchClustersTimeCompliant(reconClusters, sspClusters, energyAcceptance, hitAcceptance);
+        } else {
+            event = matchClusters(reconClusters, sspClusters, energyAcceptance, hitAcceptance);
+        }
+        
+        // Add the event results to the global results.
+        localStats.getClusterStats().addEvent(event);
+        globalStats.getClusterStats().addEvent(event);
+        localStats.getClusterStats().sawSSPClusters(sspClusters.size());
+        globalStats.getClusterStats().sawSSPClusters(sspClusters.size());
+        localStats.getClusterStats().sawReconClusters(reconClusters.size());
+        globalStats.getClusterStats().sawReconClusters(reconClusters.size());
+        
+        
+        
+        // ==========================================================
+        // ==== Output Event Summary ================================
+        // ==========================================================
+        
+        // Print the valid reconstructed clusters and populate their
+        // distribution graphs.
+        OutputLogger.println();
+        OutputLogger.println("Verified Reconstructed Clusters:");
+        if(!reconClusters.isEmpty()) {
+            for(Cluster reconCluster : reconClusters) {
+                OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(reconCluster));
+            }
+        } else { OutputLogger.println("\tNone"); }
+        
+        // Print the SSP clusters and populate their distribution graphs.
+        OutputLogger.println("SSP Clusters:");
+        if(!sspClusters.isEmpty()) {
+            for(SSPCluster sspCluster : sspClusters) {
+                OutputLogger.printf("\t%s%n", TriggerDiagnosticUtil.clusterToString(sspCluster));
+            }
+        } else { OutputLogger.println("\tNone"); }
+        
+        // Print the matched clusters.
+        OutputLogger.println("Matched Clusters:");
+        if(event.getMatches() != 0) {
+            // Iterate over the matched pairs.
+            for(ClusterMatchedPair pair : event.getClusterPairs()) {
+                // If the pair is a match, print it out.
+                if(pair.isMatch()) {
+                    OutputLogger.printf("\t%s --> %s%n",
+                            TriggerDiagnosticUtil.clusterToString(pair.getReconstructedCluster()),
+                            TriggerDiagnosticUtil.clusterToString(pair.getSSPCluster()));
+                }
+            }
+        }
+         else { OutputLogger.println("\tNone"); }
+        
+        // Print event statistics.
+        OutputLogger.println();
+        OutputLogger.println("Event Statistics:");
+        OutputLogger.printf("\tRecon Clusters     :: %d%n", reconClusters.size());
+        OutputLogger.printf("\tClusters Matched   :: %d%n", event.getMatches());
+        OutputLogger.printf("\tFailed (Position)  :: %d%n", event.getPositionFailures());
+        OutputLogger.printf("\tFailed (Time)      :: %d%n", event.getTimeFailures());
+        OutputLogger.printf("\tFailed (Energy)    :: %d%n", event.getEnergyFailures());
+        OutputLogger.printf("\tFailed (Hit Count) :: %d%n", event.getHitCountFailures());
+        OutputLogger.printf("\tCluster Efficiency :: %3.0f%%%n", 100.0 * event.getMatches() / reconClusters.size());
+        
+        // Note whether there was a cluster match failure.
+        if(event.isFailState() || event.getMatches() - reconClusters.size() != 0) {
+            clusterFail = true;
+        }
+        
+        
+        
+        // TEMP :: Populate the cluster diagnostic plots.
+        
+        // Populate the ALL cluster plots.
+        for(Cluster cluster : reconClusters) {
+            clusterHitPlot[RECON][ALL].fill(cluster.getCalorimeterHits().size());
+            clusterEnergyPlot[RECON][ALL].fill(cluster.getEnergy());
+            clusterTimePlot[RECON][ALL].fill(cluster.getCalorimeterHits().get(0).getTime());
+            Point position = TriggerDiagnosticUtil.getClusterPosition(cluster);
+            clusterPositionPlot[RECON][ALL].fill(position.x, position.y);
+        }
+        for(SSPCluster cluster : sspClusters) {
+            clusterHitPlot[SSP][ALL].fill(cluster.getHitCount());
+            clusterEnergyPlot[SSP][ALL].fill(cluster.getEnergy());
+            clusterTimePlot[SSP][ALL].fill(cluster.getTime());
+            clusterPositionPlot[SSP][ALL].fill(cluster.getXIndex(), cluster.getYIndex());
+        }
+        
+        // Populate the matched and failed plots.
+        for(ClusterMatchedPair pair : event.getClusterPairs()) {
+             if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
+                double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
+                int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
+                energyhitDiffPlot[ALL].fill(energyDiff, hitDiff);
+             }
+            
+            if(pair.isMatch()) {
+                if(pair.getFirstElement() != null) {
+                    clusterHitPlot[RECON][MATCHED].fill(pair.getFirstElement().getCalorimeterHits().size());
+                    clusterEnergyPlot[RECON][MATCHED].fill(pair.getFirstElement().getEnergy());
+                    clusterTimePlot[RECON][MATCHED].fill(pair.getFirstElement().getCalorimeterHits().get(0).getTime());
+                    Point position = TriggerDiagnosticUtil.getClusterPosition(pair.getFirstElement());
+                    clusterPositionPlot[RECON][MATCHED].fill(position.x, position.y);
+                } if(pair.getSecondElement() != null) {
+                    clusterHitPlot[SSP][MATCHED].fill(pair.getSecondElement().getHitCount());
+                    clusterEnergyPlot[SSP][MATCHED].fill(pair.getSecondElement().getEnergy());
+                    clusterTimePlot[SSP][MATCHED].fill(pair.getSecondElement().getTime());
+                    clusterPositionPlot[SSP][MATCHED].fill(pair.getSecondElement().getXIndex(), pair.getSecondElement().getYIndex());
+                } if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
+                    double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
+                    int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
+                    energyhitDiffPlot[MATCHED].fill(energyDiff, hitDiff);
+                }
+            } else {
+                if(pair.getFirstElement() != null) {
+                    clusterHitPlot[RECON][FAILED].fill(pair.getFirstElement().getCalorimeterHits().size());
+                    clusterEnergyPlot[RECON][FAILED].fill(pair.getFirstElement().getEnergy());
+                    clusterTimePlot[RECON][FAILED].fill(pair.getFirstElement().getCalorimeterHits().get(0).getTime());
+                    Point position = TriggerDiagnosticUtil.getClusterPosition(pair.getFirstElement());
+                    clusterPositionPlot[RECON][FAILED].fill(position.x, position.y);
+                } if(pair.getSecondElement() != null) {
+                    clusterHitPlot[SSP][FAILED].fill(pair.getSecondElement().getHitCount());
+                    clusterEnergyPlot[SSP][FAILED].fill(pair.getSecondElement().getEnergy());
+                    clusterTimePlot[SSP][FAILED].fill(pair.getSecondElement().getTime());
+                    clusterPositionPlot[SSP][FAILED].fill(pair.getSecondElement().getXIndex(), pair.getSecondElement().getYIndex());
+                } if(pair.getFirstElement() != null && pair.getSecondElement() != null) {
+                    double energyDiff = pair.getSecondElement().getEnergy() - pair.getFirstElement().getEnergy();
+                    int hitDiff = pair.getSecondElement().getHitCount() - pair.getFirstElement().getCalorimeterHits().size();
+                    energyhitDiffPlot[FAILED].fill(energyDiff, hitDiff);
+                }
+            }
+        }
+    }
+    
+    /**
      * Performs cluster matching between a collection of reconstructed
-	 * clusters and a collection of SSP clusters with an algorithm that
-	 * ignores the times reported for each cluster.
-	 * @param reconClusters - A collection of reconstructed clusters.
-	 * @param sspClusters - A collection of SSP clusters.
-	 * @param energyWindow - The window of allowed deviation between
-	 * the reconstructed cluster and SSP cluster energies.
-	 * @param hitWindow - The window of allowed deviation between
-	 * the reconstructed cluster and SSP cluster hit counts.
-	 * @return Returns the cluster matching results stored inside a
-	 * <code>clusterMatchEvent</code> object.
-	 */
-	private static final DetailedClusterEvent matchClusters(Collection<Cluster> reconClusters,
-			Collection<SSPCluster> sspClusters, double energyWindow, int hitWindow) {
-		// Track the number of cluster pairs that were matched and that
-		// failed by failure type.
-		DetailedClusterEvent event = new DetailedClusterEvent();
-		
-		// Create maps to link cluster position to the list of clusters
-		// that were found at that location.
-		Map<Point, List<Cluster>> reconClusterMap = new HashMap<Point, List<Cluster>>(reconClusters.size());
-		Map<Point, List<SSPCluster>> sspClusterMap = new HashMap<Point, List<SSPCluster>>(reconClusters.size());
-		
-		// Populate the reconstructed cluster map.
-		for(Cluster reconCluster : reconClusters) {
-			// Get the cluster position.
-			Point position = new Point(TriggerDiagnosticUtil.getXIndex(reconCluster),
-					TriggerDiagnosticUtil.getYIndex(reconCluster));
-			
-			// Get the list for this cluster position.
-			List<Cluster> reconList = reconClusterMap.get(position);
-			if(reconList == null) {
-				reconList = new ArrayList<Cluster>();
-				reconClusterMap.put(position, reconList);
-			}
-			
-			// Add the cluster to the list.
-			reconList.add(reconCluster);
-		}
-		
-		// Populate the SSP cluster map.
-		for(SSPCluster sspCluster : sspClusters) {
-			// Get the cluster position.
-			Point position = new Point(sspCluster.getXIndex(), sspCluster.getYIndex());
-			
-			// Get the list for this cluster position.
-			List<SSPCluster> sspList = sspClusterMap.get(position);
-			if(sspList == null) {
-				sspList = new ArrayList<SSPCluster>();
-				sspClusterMap.put(position, sspList);
-			}
-			
-			// Add the cluster to the list.
-			sspList.add(sspCluster);
-		}
-		
-		// For each reconstructed cluster, attempt to match the clusters
-		// with SSP clusters at the same position.
-		positionLoop:
-		for(Entry<Point, List<Cluster>> clusterSet : reconClusterMap.entrySet()) {
-			// Get the reconstructed and SSP clusters at this position.
-			List<Cluster> reconList = clusterSet.getValue();
-			List<SSPCluster> sspList = sspClusterMap.get(clusterSet.getKey());
-			
-			// Print the crystal position header.
-			OutputLogger.println();
-			OutputLogger.printf("Considering clusters at (%3d, %3d)%n", clusterSet.getKey().x, clusterSet.getKey().y);
-			
-			// If there are no SSP clusters, then matching fails by
-			// reason of position. The remainder of the loop may be
-			// skipped, since there is nothing to check.
-			if(sspList == null || sspList.isEmpty()) {
-				event.pairFailPosition(reconList.size());
-				continue positionLoop;
-			}
-			
-			// Get all possible permutations of SSP clusters.
-			List<List<Pair<Cluster, SSPCluster>>> permutations = getPermutations(reconList, sspList);
-			
-			// Print the information for this crystal position.
-			OutputLogger.printf("\tRecon Clusters :: %d%n", reconList.size());
-			OutputLogger.printf("\tSSP Clusters   :: %d%n", sspList.size());
-			OutputLogger.printf("\tPermutations   :: %d%n", permutations.size());
-			
-			// Track the plotted values for the current best permutation.
-			DetailedClusterEvent bestPerm = null;
-			
-			// Iterate over the permutations and find the permutation
-			// that produces the best possible result when compared to
-			// the reconstructed clusters.
-			int permIndex = 0;
-			for(List<Pair<Cluster, SSPCluster>> pairs : permutations) {
-				// Update the current permutation number.
-				permIndex++;
-				
-				// Track the plot values for this permutation.
-				DetailedClusterEvent perm = new DetailedClusterEvent();
-				
-				// Try to match each pair.
-				pairLoop:
-				for(Pair<Cluster, SSPCluster> pair : pairs) {
-					// Print the current reconstructed/SSP cluster pair.
-					OutputLogger.printf("\tP%d :: %s --> %s", permIndex,
-							pair.getFirstElement() == null ? "None" : TriggerDiagnosticUtil.clusterToString(pair.getFirstElement()),
-							pair.getSecondElement() == null ? "None" : TriggerDiagnosticUtil.clusterToString(pair.getSecondElement()));
-					
-					// If either cluster in the pair is null, there
-					// are not enough clusters to perform this match.
-					if(pair.getFirstElement() == null || pair.getSecondElement() == null) {
-						// Log the result.
-						OutputLogger.printf(" [ %18s ]%n", "failure: unpaired");
-						
-						// An unpaired SSP cluster does not necessarily
-						// represent a problem. Often, this just means
-						// that the SSP cluster's matching reconstructed
-						// cluster is outside the verification window.
-						if(pair.getSecondElement() == null) {
-							perm.pairFailPosition(pair.getFirstElement(), pair.getSecondElement());
-						}
-						
-						// Skip the rest of the checks.
-						continue pairLoop;
-					}
-					
-					// Check if the reconstructed cluster has an energy
-					// within the allotted threshold of the SSP cluster.
-					if(pair.getSecondElement().getEnergy() >= pair.getFirstElement().getEnergy() - energyWindow &&
-							pair.getSecondElement().getEnergy() <= pair.getFirstElement().getEnergy() + energyWindow) {
-						
-						// Check that the hit count of the reconstructed
-						// is within the allotted threshold of the SSP
-						// cluster.
-						if(pair.getSecondElement().getHitCount() >= pair.getFirstElement().getCalorimeterHits().size() - hitWindow &&
-								pair.getSecondElement().getHitCount() <= pair.getFirstElement().getCalorimeterHits().size() + hitWindow) {
-							// Designate the pair as a match.
-							perm.pairMatch(pair.getFirstElement(), pair.getSecondElement());
-							OutputLogger.printf(" [ %18s ]%n", "success: matched");
-						} else {
-							perm.pairFailHitCount(pair.getFirstElement(), pair.getSecondElement());
-							OutputLogger.printf(" [ %18s ]%n", "failure: hit count");
-						} // End hit count check.
-					} else {
-						perm.pairFailEnergy(pair.getFirstElement(), pair.getSecondElement());
-						OutputLogger.printf(" [ %18s ]%n", "failure: energy");
-					} // End energy check.
-				} // End Pair Loop
-				
-				// Print the results of the permutation.
-				OutputLogger.printf("\t\tPermutation Matched   :: %d%n", perm.getMatches());
-				OutputLogger.printf("\t\tPermutation Energy    :: %d%n", perm.getEnergyFailures());
-				OutputLogger.printf("\t\tPermutation Hit Count :: %d%n", perm.getHitCountFailures());
-				
-				// Check whether the results from this permutation
-				// exceed the quality of the last best results. A
-				// greater number of matches is always better. If the
-				// matches are the same, select the one with fewer
-				// failures due to energy.
-				bestPerm = getBestPermutation(bestPerm, perm);
-			} // End Permutation Loop
-			
-			// Print the final results for the position.
-			OutputLogger.printf("\tPosition Matched   :: %d%n", bestPerm.getMatches());
-			OutputLogger.printf("\tPosition Energy    :: %d%n", bestPerm.getEnergyFailures());
-			OutputLogger.printf("\tPosition Hit Count :: %d%n", bestPerm.getHitCountFailures());
-			
-			// Add the results from the best-matched permutation
-			// to the event efficiency results.
-			event.addEvent(bestPerm);
-		} // End Crystal Position Loop
-		
-		// Return the cluster match summary.
-		return event;
-	}
-	
-	/**
-	 * Performs cluster matching between a collection of reconstructed
-	 * clusters and a collection of SSP clusters using the strictly
-	 * time-compliant algorithm.
-	 * @param reconClusters - A collection of reconstructed clusters.
-	 * @param sspClusters - A collection of SSP clusters.
-	 * @param energyWindow - The window of allowed deviation between
-	 * the reconstructed cluster and SSP cluster energies.
-	 * @param hitWindow - The window of allowed deviation between
-	 * the reconstructed cluster and SSP cluster hit counts.
-	 * @return Returns the cluster matching results stored inside a
-	 * <code>clusterMatchEvent</code> object.
-	 */
-	private static final DetailedClusterEvent matchClustersTimeCompliant(Collection<Cluster> reconClusters,
-			Collection<SSPCluster> sspClusters, double energyWindow, int hitWindow) {
-		// Track the number of cluster pairs that were matched and that
-		// failed by failure type.
-		DetailedClusterEvent event = new DetailedClusterEvent();
-		
-		// Store the clusters which have been successfully paired.
-		Set<SSPCluster> sspMatched = new HashSet<SSPCluster>(sspClusters.size());
-		
-		// Find reconstructed/SSP cluster matched pairs.
-		reconLoop:
-		for(Cluster reconCluster : reconClusters) {
-			// Track whether a position-matched cluster was found.
-			boolean matchedPosition = false;
-			
-			// VERBOSE :: Output the cluster being matched.
-			OutputLogger.printf("Considering %s%n", TriggerDiagnosticUtil.clusterToString(reconCluster));
-			
-			// Search through the SSP clusters for a matching cluster.
-			sspLoop:
-			for(SSPCluster sspCluster : sspClusters) {
-				// VERBOSE :: Output the SSP cluster being considered.
-				OutputLogger.printf("\t%s ", TriggerDiagnosticUtil.clusterToString(sspCluster));
-				
-				// If this cluster has been paired, skip it.
-				if(sspMatched.contains(sspCluster)) {
-					OutputLogger.printf("[ %7s; %9s ]%n", "fail", "matched");
-					continue sspLoop;
-				}
-				
-				// Matched clusters must have the same position.
-				if(TriggerDiagnosticUtil.getXIndex(reconCluster) != sspCluster.getXIndex()
-						|| TriggerDiagnosticUtil.getYIndex(reconCluster) != sspCluster.getYIndex()) {
-					OutputLogger.printf("[ %7s; %9s ]%n", "fail", "position");
-					continue sspLoop;
-				}
-				
-				// Note that a cluster was found at this position.
-				matchedPosition = true;
-				
-				// Matched clusters must have the same time-stamp.
-				if(reconCluster.getCalorimeterHits().get(0).getTime() != sspCluster.getTime()) {
-					OutputLogger.printf("[ %7s; %9s ]%n", "fail", "time");
-					continue sspLoop;
-				}
-				
-				// Clusters that pass all of the above checks are the
-				// same cluster.
-				sspMatched.add(sspCluster);
-				
-				// Check that the clusters are sufficiently close in
-				// energy to one another.
-				if(sspCluster.getEnergy() >= reconCluster.getEnergy() - energyWindow
-						&& sspCluster.getEnergy() <= reconCluster.getEnergy() + energyWindow) {
-					// If a cluster matches in energy, check that it
-					// is also sufficiently close in hit count.
-					if(sspCluster.getHitCount() >= reconCluster.getCalorimeterHits().size() - hitWindow &&
-							sspCluster.getHitCount() <= reconCluster.getCalorimeterHits().size() + hitWindow) {
-						// The cluster is a match.
-						event.pairMatch(reconCluster, sspCluster);
-						OutputLogger.printf("[ %7s; %9s ]%n", "success", "matched");
-						continue reconLoop;
-					} else {
-						event.pairFailHitCount(reconCluster, sspCluster);
-						OutputLogger.printf("[ %7s; %9s ]%n", "fail", "hit count");
-						continue reconLoop;
-					} // End hit count check.
-				} else {
-					event.pairFailEnergy(reconCluster, sspCluster);
-					OutputLogger.printf("[ %7s; %9s ]%n", "fail", "energy");
-					continue reconLoop;
-				} // End energy check.
-			}// End SSP loop.
-			
-			// If the reconstructed cluster has not been matched, check
-			// if a cluster was found at the same position. If not, then
-			// the cluster fails by reason of position.
-			if(!matchedPosition) {
-				event.pairFailPosition(reconCluster, null);
-			}
-			
-			// Otherwise, the cluster had a potential matched, but the
-			// time-stamps were off. The cluster fails by reason of time.
-			else {
-				event.pairFailTime(reconCluster, null);
-			}
-		} // End recon loop.
-		
-		// Return the populated match event.
-		return event;
-	}
-	
-	/**
-	 * Checks triggers simulated on SSP clusters against the SSP bank's
-	 * reported triggers to verify that the trigger is correctly applying
-	 * cuts to the clusters it sees. Additionally compares triggers
-	 * simulated on reconstructed clusters to measure trigger efficiency.
-	 */
-	private void singlesTriggerVerification() {
-		// Create lists of generic triggers.
-		List<List<? extends Trigger<?>>> sspTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
-		List<List<? extends Trigger<?>>> reconTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
-		
-		// Convert the simulated triggers to generic versions and add
-		// them to the generic list.
-		sspTriggerList.add(triggerData.getSimSSPTriggers().getSingles0Triggers());
-		sspTriggerList.add(triggerData.getSimSSPTriggers().getSingles1Triggers());
-		reconTriggerList.add(triggerData.getSimReconTriggers().getSingles0Triggers());
-		reconTriggerList.add(triggerData.getSimReconTriggers().getSingles1Triggers());
-		
-		// Run generic trigger verification.
-		triggerVerification(sspTriggerList, reconTriggerList, true);
-	}
-	
-	/**
-	 * Checks triggers simulated on SSP clusters against the SSP bank's
-	 * reported triggers to verify that the trigger is correctly applying
-	 * cuts to the clusters it sees. Additionally compares triggers
-	 * simulated on reconstructed clusters to measure trigger efficiency.
-	 */
-	private void pairTriggerVerification() {
-		// Create lists of generic triggers.
-		List<List<? extends Trigger<?>>> sspTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
-		List<List<? extends Trigger<?>>> reconTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
-		
-		// Convert the simulated triggers to generic versions and add
-		// them to the generic list.
-		sspTriggerList.add(triggerData.getSimSSPTriggers().getPair0Triggers());
-		sspTriggerList.add(triggerData.getSimSSPTriggers().getPair1Triggers());
-		reconTriggerList.add(triggerData.getSimReconTriggers().getPair0Triggers());
-		reconTriggerList.add(triggerData.getSimReconTriggers().getPair1Triggers());
-		
-		// Run generic trigger verification.
-		triggerVerification(sspTriggerList, reconTriggerList, false);
-	}
-	
-	/**
-	 * Performs trigger verification for both trigger types.
-	 * @param sspTriggerList - The list of SSP triggers.
-	 * @param reconTriggerList - The list of reconstructed triggers.
-	 * @param isSingles - Whether or not this is a singles trigger
-	 * verification.
-	 */
-	private void triggerVerification(List<List<? extends Trigger<?>>> sspTriggerList, 
-			List<List<? extends Trigger<?>>> reconTriggerList, boolean isSingles) {
-		
-		// ==========================================================
-		// ==== Initialize Trigger Verification =====================
-		// ==========================================================
-		
-		// Print the cluster verification header.
-		OutputLogger.println();
-		OutputLogger.println();
-		OutputLogger.println("======================================================================");
-		if(isSingles) { OutputLogger.println("=== Singles Trigger Verification ====================================="); }
-		else { OutputLogger.println("=== Pair Trigger Verification ========================================"); }
-		OutputLogger.println("======================================================================");
-		
-		// Track the number of triggers seen and the number found.
-		TriggerEvent[] triggerEvent = { new TriggerEvent(), new TriggerEvent() };
-		
-		// ==========================================================
-		// ==== Output Event Summary ================================
-		// ==========================================================
-		
-		// Get the list of triggers reported by the SSP.
-		List<? extends SSPNumberedTrigger> sspTriggers;
-		if(isSingles) { sspTriggers = sspBank.getSinglesTriggers(); }
-		else { sspTriggers = sspBank.getPairTriggers(); }
-		
-		// Output the SSP cluster triggers.
-		OutputLogger.println();
-		OutputLogger.println("SSP Cluster " + (isSingles ? "Singles" : "Pair") + " Triggers");
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
-				OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
-						(triggerNum + 1), triggerPositionString(simTrigger),
-						getTriggerTime(simTrigger), simTrigger.toString());
-			}
-		}
-		if(sspTriggerList.get(0).size() + sspTriggerList.get(1).size() == 0) {
-			OutputLogger.println("\tNone");
-		}
-		
-		// Output the reconstructed cluster singles triggers.
-		OutputLogger.println("Reconstructed Cluster " + (isSingles ? "Singles" : "Pair") + " Triggers");
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			for(Trigger<?> simTrigger : reconTriggerList.get(triggerNum)) {
-				OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
-						(triggerNum + 1), triggerPositionString(simTrigger),
-						getTriggerTime(simTrigger), simTrigger.toString());
-			}
-		}
-		if(reconTriggerList.get(0).size() + reconTriggerList.get(1).size() == 0) {
-			OutputLogger.println("\tNone");
-		}
-		
-		// Output the SSP reported triggers.
-		OutputLogger.println("SSP Reported " + (isSingles ? "Singles" : "Pair") + " Triggers");
-		for(SSPTrigger sspTrigger : sspTriggers) {
-			OutputLogger.printf("\t%s%n", sspTrigger.toString());
-		}
-		if(sspTriggers.size() == 0) { OutputLogger.println("\tNone"); }
-		
-		// Update the trigger event with the counts for each type of
-		// simulated trigger. Reported triggers are counted later when
-		// already iterating over them.
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			triggerEvent[triggerNum].sawSSPSimulatedTriggers(tiFlags, sspTriggerList.get(triggerNum).size());
-			triggerEvent[triggerNum].sawReconSimulatedTriggers(tiFlags, reconTriggerList.get(triggerNum).size());
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== SSP Internal Logic Verification =====================
-		// ==========================================================
-		
-		// Track which SSP triggers have been matched to avoid matching
-		// multiple reconstructed SSP cluster triggers to the same SSP
-		// trigger.
-		Set<SSPNumberedTrigger> sspTriggerSet = new HashSet<SSPNumberedTrigger>();
-		Set<Trigger<?>> simTriggerSet = new HashSet<Trigger<?>>();
-		
-		// Track the number of SSP reported triggers that are found in
-		// excess of the SSP simulated triggers.
-		int sspReportedExtras = sspTriggers.size() - (sspTriggerList.get(0).size() + sspTriggerList.get(1).size());
-		if(sspReportedExtras > 0) {
-			if(isSingles) { singlesInternalFail = true; }
-			else { pairInternalFail = true; }
-		} else { sspReportedExtras = 0; }
-		
-		// Iterate over the triggers.
-		OutputLogger.println();
-		OutputLogger.println("Matching SSP Reported Triggers to SSP Simulated Triggers:");
-		for(SSPNumberedTrigger sspTrigger : sspTriggers) {
-			// Get the trigger information.
-			int triggerNum = sspTrigger.isFirstTrigger() ? 0 : 1;
-			OutputLogger.printf("\t%s%n", sspTrigger.toString());
-			
-			// Note that a bank trigger was seen.
-			triggerEvent[triggerNum].sawReportedTrigger();
-			
-			// Iterate over the SSP cluster simulated triggers and
-			// look for a trigger that matches.
-			matchLoop:
-			for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
-				// VERBOSE :: Output the trigger being considered for
-				//            matching.
-				OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s ",
-						(triggerNum + 1), triggerPositionString(simTrigger),
-						getTriggerTime(simTrigger), simTrigger.toString());
-				
-				// If the current SSP trigger has already been matched,
-				// skip it.
-				if(simTriggerSet.contains(simTrigger)) {
-					OutputLogger.printf("[ %-15s ]%n", "failed; matched");
-					continue matchLoop;
-				}
-				
-				// Check that the triggers have the same time. Triggers
-				// generated from SSP bank clusters should always align
-				// in time.
-				if(sspTrigger.getTime() != getTriggerTime(simTrigger)) {
-					OutputLogger.printf("[ %-15s ]%n", "failed; time");
-					continue matchLoop;
-				}
-				
-				// Check whether the trigger cuts match.
-				boolean[] matchedCuts = triggerCutMatch(simTrigger, sspTrigger);
-				for(int i = 0; i < matchedCuts.length; i++) {
-					if(!matchedCuts[i]) {
-						int typeIndex = isSingles ? 0 : 1;
-						OutputLogger.printf("[ %-15s ]%n", String.format("failed; %s", cutNames[typeIndex][i]));
-						continue matchLoop;
-					}
-				}
-				
-				// If all the cuts match, along with the time and the
-				// trigger number, than these triggers are a match.
-				sspTriggerSet.add(sspTrigger);
-				simTriggerSet.add(simTrigger);
-				triggerEvent[triggerNum].matchedSSPTrigger(tiFlags);
-				OutputLogger.printf("[ %-15s ]%n", "success");
-				break matchLoop;
-			}
-		}
-		
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
-				globalTriggerPlots.sawTrigger(simTrigger);
-				if(simTriggerSet.contains(simTrigger)) {
-					globalTriggerPlots.matchedTrigger(simTrigger);
-				} else {
-					globalTriggerPlots.failedTrigger(simTrigger);
-				}
-			}
-		}
-		
-		// Iterate over the unmatched simulated triggers again and the
-		// unmatched SSP reported trigger that most closely matches it.
-		OutputLogger.println();
-		OutputLogger.println("Matching Failed SSP Reported Triggers to Remaining SSP Simulated Triggers:");
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			simLoop:
-			for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
-				OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
-						(triggerNum + 1), triggerPositionString(simTrigger),
-						getTriggerTime(simTrigger), simTrigger.toString());
-				
-				// Check whether this trigger has already been matched
-				// or not. If it has been matched, skip it.
-				if(simTriggerSet.contains(simTrigger)) {
-					OutputLogger.println("\t\tSkipping; already matched successfully");
-					continue simLoop;
-				}
-				
-				// Get the trigger time for the simulated trigger.
-				double simTime = getTriggerTime(simTrigger);
-				
-				// Track the match statistics for each reported trigger
-				// so that the closest match may be found.
-				int numMatched = -1;
-				boolean[] matchedCut = null;
-				SSPNumberedTrigger bestMatch = null;
-				
-				// Store the readout for the best match.
-				String bestMatchText = null;
-				
-				// Iterate over the reported triggers to find a match.
-				reportedLoop:
-				for(SSPNumberedTrigger sspTrigger : sspTriggers) {
-					OutputLogger.printf("\t\t%s ", sspTrigger.toString());
-					
-					// If the two triggers have different times, this
-					// trigger should be skipped.
-					if(sspTrigger.getTime() != simTime) {
-						OutputLogger.printf("[ %-15s ]%n", "failed; time");
-						continue reportedLoop;
-					}
-					
-					// If this reported trigger has been matched then
-					// it should be skipped.
-					if(sspTriggerSet.contains(sspTrigger)) {
-						OutputLogger.printf("[ %-15s ]%n", "failed; matched");
-						continue reportedLoop;
-					}
-					
-					// Check each of the cuts.
-					boolean[] tempMatchedCut = triggerCutMatch(simTrigger, sspTrigger);
-					
-					// Check each cut and see if this is a closer match
-					// than the previous best match.
-					int tempNumMatched = 0;
-					for(boolean passed : tempMatchedCut) { if(passed) { tempNumMatched++; } }
-					OutputLogger.printf("[ %-15s ]%n", String.format("maybe; %d failed", tempNumMatched));
-					
-					// If the number of matched cuts exceeds the old
-					// best result, this becomes the new best result.
-					if(tempNumMatched > numMatched) {
-						numMatched = tempNumMatched;
-						matchedCut = tempMatchedCut;
-						bestMatch = sspTrigger;
-						bestMatchText = String.format("%s%n", sspTrigger.toString());
-					}
-				}
-				
-				// If there was no match found, it means that there were
-				// no triggers that were both unmatched and at the same
-				// time as this simulated trigger.
-				if(bestMatch == null) {
-					if(isSingles) { singlesInternalFail = true; }
-					else { pairInternalFail = true; }
-					triggerEvent[triggerNum].failedSSPTrigger();
-					OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s",
-							(triggerNum + 1), triggerPositionString(simTrigger),
-							getTriggerTime(simTrigger), simTrigger.toString());
-					OutputLogger.println(" --> No Valid Match Found");
-				} else {
-					triggerEvent[triggerNum].matchedSSPTrigger(tiFlags, matchedCut);
-					OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s",
-							(triggerNum + 1), triggerPositionString(simTrigger),
-							getTriggerTime(simTrigger), simTrigger.toString());
-					OutputLogger.println(" --> " + bestMatchText);
-				}
-			}
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Trigger Efficiency ==================================
-		// ==========================================================
-		
-		// Reset the SSP matched trigger set.
-		sspTriggerSet.clear();
-		
-		// Iterate over the reconstructed cluster singles triggers.
-		OutputLogger.println();
-		OutputLogger.println("Recon Cluster Trigger --> SSP Reported Trigger Match Status");
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			for(Trigger<?> simTrigger : reconTriggerList.get(triggerNum)) {
-				OutputLogger.printf("\tTrigger %d :: %s :: %s%n", (triggerNum + 1),
-						triggerPositionString(simTrigger), simTrigger.toString());
-				
-				// TEMP :: Populate the recon ALL pairs plots.
-				globalTriggerPlots.sawTrigger(simTrigger);
-				
-				// Iterate over the SSP reported triggers and compare
-				// them to the reconstructed cluster simulated trigger.
-				boolean matched = false;
-				matchLoop:
-				for(SSPNumberedTrigger sspTrigger : sspTriggers) {
-					OutputLogger.printf("\t\t\t%s", sspTrigger.toString());
-					
-					// Only compare triggers if they are from the
-					// same trigger source.
-					if((triggerNum == 0 && sspTrigger.isSecondTrigger())
-							|| (triggerNum == 1 && sspTrigger.isFirstTrigger())) {
-						OutputLogger.print(" [ fail; source    ]%n");
-						continue matchLoop;
-					}
-					
-					// Only compare the singles trigger if it was
-					// not already matched to another trigger.
-					if(sspTriggerSet.contains(sspTrigger)) {
-						OutputLogger.print(" [ fail; matched   ]%n");
-						continue matchLoop;
-					}
-					
-					// Test each cut.
-					int typeIndex = isSingles ? 0 : 1;
-					boolean[] matchedCuts = triggerCutMatch(simTrigger, sspTrigger);
-					for(int cutIndex = 0; cutIndex < matchedCuts.length; cutIndex++) {
-						if(!matchedCuts[cutIndex]) {
-							OutputLogger.printf(" [ fail; %-9s ]%n", cutNames[typeIndex][cutIndex]);
-							continue matchLoop;
-						}
-					}
-					
-					// If all the trigger flags match, then the
-					// triggers are a match.
-					sspTriggerSet.add(sspTrigger);
-					triggerEvent[triggerNum].matchedReconTrigger(tiFlags);
-					OutputLogger.print(" [ success         ]%n");
-					globalTriggerPlots.matchedTrigger(simTrigger);
-					matched = true;
-					break matchLoop;
-				}
-				
-				if(!matched) { globalTriggerPlots.failedTrigger(simTrigger); }
-			}
-		}
-		
-		
-		
-		// ==========================================================
-		// ==== Output Event Results ================================
-		// ==========================================================
-		
-		// Get the number of SSP and reconstructed cluster simulated
-		// triggers.
-		int sspSimTriggers = sspTriggerList.get(0).size() + sspTriggerList.get(1).size();
-		int reconSimTriggers = reconTriggerList.get(0).size() + reconTriggerList.get(1).size();
-		int[] sspTriggerCount = { sspTriggerList.get(0).size(), sspTriggerList.get(1).size() };
-		
-		// Print event statistics.
-		OutputLogger.println();
-		OutputLogger.println("Event Statistics:");
-		OutputLogger.printf("\tSSP Cluster Sim Triggers   :: %d%n", sspSimTriggers);
-		OutputLogger.printf("\tRecon Cluster Sim Triggers :: %d%n", reconSimTriggers);
-		OutputLogger.printf("\tSSP Reported Triggers      :: %d%n", sspTriggers.size());
-		
-		int matchedSSPTriggers = triggerEvent[0].getMatchedSSPSimulatedTriggers() + triggerEvent[1].getMatchedSSPSimulatedTriggers();
-		OutputLogger.printf("\tInternal Efficiency        :: %d / %d ", matchedSSPTriggers, sspSimTriggers);
-		if(sspSimTriggers == 0) { OutputLogger.printf("(N/A)%n"); }
-		else { OutputLogger.printf("(%3.0f%%)%n", (100.0 * matchedSSPTriggers / sspSimTriggers)); }
-		
-		int matchedReconTriggers = triggerEvent[0].getMatchedReconSimulatedTriggers() + triggerEvent[1].getMatchedReconSimulatedTriggers();
-		OutputLogger.printf("\tTrigger Efficiency         :: %d / %d", matchedReconTriggers, reconSimTriggers);
-		if(reconSimTriggers == 0) { OutputLogger.printf("(N/A)%n"); }
-		else { OutputLogger.printf("(%3.0f%%)%n", (100.0 * matchedReconTriggers / reconSimTriggers)); }
-		
-		// Print the individual cut performances.
-		if(isSingles) {
-			OutputLogger.println();
-			for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-				OutputLogger.printf("Trigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
-				if(sspSimTriggers == 0) {
-					OutputLogger.printf("\tCluster Energy Lower Bound :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN), sspTriggerCount[triggerNum]);
-					OutputLogger.printf("\tCluster Energy Upper Bound :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX), sspTriggerCount[triggerNum]);
-					OutputLogger.printf("\tCluster Hit Count          :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT), sspTriggerCount[triggerNum]);
-				} else {
-					OutputLogger.printf("\tCluster Energy Lower Bound :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN) / sspTriggerCount[triggerNum]));
-					OutputLogger.printf("\tCluster Energy Upper Bound :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX) / sspTriggerCount[triggerNum]));
-					OutputLogger.printf("\tCluster Hit Count          :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT) / sspTriggerCount[triggerNum]));
-				}
-			}
-			
-			// Update the global trigger tracking variables.
-			localStats.getTriggerStats().getSingles0Stats().addEvent(triggerEvent[0]);
-			localStats.getTriggerStats().getSingles1Stats().addEvent(triggerEvent[1]);
-			globalStats.getTriggerStats().getSingles0Stats().addEvent(triggerEvent[0]);
-			globalStats.getTriggerStats().getSingles1Stats().addEvent(triggerEvent[1]);
-		} else {
-			for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-				OutputLogger.println();
-				OutputLogger.printf("Trigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
-				if(sspTriggerCount[triggerNum] == 0) {
-					OutputLogger.printf("\tPair Energy Sum            :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM), sspTriggerCount[triggerNum]);
-					OutputLogger.printf("\tPair Energy Difference     :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF), sspTriggerCount[triggerNum]);
-					OutputLogger.printf("\tPair Energy Slope          :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount[triggerNum]);
-					OutputLogger.printf("\tPair Coplanarity           :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY), sspTriggerCount[triggerNum]);
-				} else {
-					OutputLogger.printf("\tPair Energy Sum            :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM) / sspTriggerCount[triggerNum]));
-					OutputLogger.printf("\tPair Energy Difference     :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF) / sspTriggerCount[triggerNum]));
-					OutputLogger.printf("\tPair Energy Slope          :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE) / sspTriggerCount[triggerNum]));
-					OutputLogger.printf("\tPair Coplanarity           :: %d / %d (%3.0f%%)%n",
-							triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY), sspTriggerCount[triggerNum],
-							(100.0 * triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY) / sspTriggerCount[triggerNum]));
-				}
-			}
-			
-			// Update the global trigger tracking variables.
-			localStats.getTriggerStats().getPair0Stats().addEvent(triggerEvent[0]);
-			localStats.getTriggerStats().getPair1Stats().addEvent(triggerEvent[1]);
-			globalStats.getTriggerStats().getPair0Stats().addEvent(triggerEvent[0]);
-			globalStats.getTriggerStats().getPair1Stats().addEvent(triggerEvent[1]);
-		}
-		
-		// Note whether the was a trigger match failure.
-		if(triggerEvent[0].getFailedReconSimulatedTriggers() != 0 && triggerEvent[1].getFailedReconSimulatedTriggers() != 0) {
-			if(isSingles) { singlesEfficiencyFail = true; }
-			else { pairEfficiencyFail = true; }
-		} if(triggerEvent[0].getFailedSSPSimulatedTriggers() != 0 && triggerEvent[1].getFailedSSPSimulatedTriggers() != 0) {
-			if(isSingles) { singlesInternalFail = true; }
-			else { pairInternalFail = true; }
-		}
-	}
-	
-	/**
-	 * Outputs all of the verification parameters currently in use by
-	 * the software. A warning will be issued if the values for NSA and
-	 * NSB, along with the FADC window, preclude clusters from being
-	 * verified.
-	 */
-	private void logSettings() {
-		// Output general settings.
-		System.out.println("Cluster Verification Settings");
-		System.out.printf("\tHit Threshold          :: %1d hit(s)%n", hitAcceptance);
-		System.out.printf("\tEnergy Threshold       :: %5.3f GeV%n",  energyAcceptance);
-		System.out.println();
-		
-		// Output window settings.
-		System.out.println("FADC Timing Window Settings");
-		System.out.printf("\tNSB                    :: %3d ns%n", nsb);
-		System.out.printf("\tNSA                    :: %3d ns%n", nsa);
-		System.out.printf("\tFADC Window            :: %3d ns%n", windowWidth);
-		
-		// Calculate the valid clustering window.
-		int start = nsb;
-		int end = windowWidth - nsa;
-		if(start < end) {
-			System.out.printf("\tValid Cluster Window   :: [ %3d ns, %3d ns ]%n", start, end);
-			performClusterVerification = true;
-		} else {
-			System.out.println("\tNSB, NSA, and FADC window preclude a valid cluster verification window.");
-			System.out.println("\tCluster verification will not be performed!");
-			performClusterVerification = false;
-		}
-		System.out.println();
-		
-		// Output the singles trigger settings.
-		for(int i = 0; i < 2; i++) {
-			// Print the settings.
-			System.out.printf("Singles Trigger %d Settings%23s[%5b]%n", (i + 1), "", singlesTriggerEnabled[i]);
-			System.out.printf("\tCluster Energy Low     :: %.3f GeV      [%5b]%n",
-					singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), singlesCutsEnabled[i][0]);
-			System.out.printf("\tCluster Energy High    :: %.3f GeV      [%5b]%n",
-					singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH), singlesCutsEnabled[i][1]);
-			System.out.printf("\tCluster Hit Count      :: %.0f hit(s)       [%5b]%n",
-					singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW), singlesCutsEnabled[i][2]);
-			System.out.println();
-		}
-		
-		// Output the pair trigger settings.
-		for(int i = 0; i < 2; i++) {
-			System.out.printf("Pairs Trigger %d Settings%25s[%5b]%n", (i + 1), "", pairTriggerEnabled[i]);
-			System.out.printf("\tCluster Energy Low     :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), pairCutsEnabled[i][0]);
-			System.out.printf("\tCluster Energy High    :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH), pairCutsEnabled[i][1]);
-			System.out.printf("\tCluster Hit Count      :: %.0f hit(s)       [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW), pairCutsEnabled[i][2]);
-			System.out.printf("\tPair Energy Sum Low    :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW), pairCutsEnabled[i][3]);
-			System.out.printf("\tPair Energy Sum High   :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH), pairCutsEnabled[i][3]);
-			System.out.printf("\tPair Energy Difference :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH), pairCutsEnabled[i][4]);
-			System.out.printf("\tPair Energy Slope      :: %.3f GeV      [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW), pairCutsEnabled[i][5]);
-			System.out.printf("\tPair Energy Slope F    :: %.4f GeV / mm%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F));
-			System.out.printf("\tPair Coplanarity       :: %3.0f Degrees    [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_COPLANARITY_HIGH), pairCutsEnabled[i][6]);
-			System.out.printf("\tPair Time Coincidence  :: %2.0f ns          [%5b]%n",
-					pairsTrigger[i].getCutValue(TriggerModule.PAIR_TIME_COINCIDENCE), true);
-			System.out.println();
-		}
-	}
-	
-	/**
-	 * Summarizes the global run statistics in a log to the terminal.
-	 */
-	private void logStatistics() {
-		// Print the cluster/trigger verification header.
-		System.out.println();
-		System.out.println();
-		System.out.println("======================================================================");
-		System.out.println("=== Cluster/Trigger Verification Results =============================");
-		System.out.println("======================================================================");
-		
-		// Print the general event failure rate.
-		int headSpaces = getPrintSpaces(globalStats.getEventCount());
-		System.out.println("General Event Statistics:");
-		System.out.printf("\tEvent Start Time      :: %.3f s%n", (startTime / Math.pow(10, 9)));
-		System.out.printf("\tEvent End Time        :: %.3f%n", (endTime / Math.pow(10, 9)));
-		System.out.printf("\tEvent Run Time        :: %.3f%n", ((endTime - startTime) / Math.pow(10, 9)));
-		System.out.printf("\tNoise Events          :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
-				globalStats.getNoiseEvents(), globalStats.getEventCount(), (100.0 * globalStats.getNoiseEvents() / globalStats.getEventCount()));
-		System.out.printf("\tCluster Events Failed :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
-				globalStats.getFailedClusterEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedClusterEventCount() / globalStats.getEventCount()));
-		System.out.printf("\tSingles Events Failed :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
-				globalStats.getFailedSinglesEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedSinglesEventCount() / globalStats.getEventCount()));
-		System.out.printf("\tPair Events Failed    :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
-				globalStats.getFailedPairEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedPairEventCount() / globalStats.getEventCount()));
-		
-		// Print out how many events reported a given TI type, both in
-		// total and hierarchically.
-		System.out.println();
-		System.out.println("Event Triggering Type Verification:");
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Trigger", "Total", "Hierarchical");
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Pulser", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PULSER, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PULSER, true));
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Cosmic", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.COSMIC, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.COSMIC, true));
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Singles 1", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES0, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES0, true));
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Singles 2", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES1, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES1, true));
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Pair 1", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR0, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR0, true));
-		System.out.printf("\t%15s\t%15s\t%15s%n", "Pair 2", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR1, false),
-				globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR1, true));
-		
-		// Print the cluster verification data.
-		System.out.println();
-		System.out.println("Cluster Verification:");
-		System.out.printf("\tRecon Clusters        :: %d%n", globalStats.getClusterStats().getReconClusterCount());
-		System.out.printf("\tSSP Clusters          :: %d%n", globalStats.getClusterStats().getSSPClusterCount());
-		System.out.printf("\tClusters Matched      :: %d%n", globalStats.getClusterStats().getMatches());
-		System.out.printf("\tFailed (Position)     :: %d%n", globalStats.getClusterStats().getPositionFailures());
-		System.out.printf("\tFailed (Energy)       :: %d%n", globalStats.getClusterStats().getEnergyFailures());
-		System.out.printf("\tFailed (Hit Count)    :: %d%n", globalStats.getClusterStats().getHitCountFailures());
-		if(globalStats.getClusterStats().getReconClusterCount() == 0) {
-			System.out.printf("\tCluster Efficiency    :: N/A%n");
-		} else {
-			System.out.printf("\tCluster Efficiency    :: %7.3f%%%n",
-					100.0 * globalStats.getClusterStats().getMatches() / globalStats.getClusterStats().getReconClusterCount());
-		}
-		
-		// Print the trigger verification data.
-		for(int triggerType = 0; triggerType < 2; triggerType++) {
-			// Get the trigger data. Type 0 represents singles triggers.
-			TriggerEvent[] triggerData = new TriggerEvent[2];
-			if(triggerType == 0) {
-				triggerData[0] = globalStats.getTriggerStats().getSingles0Stats();
-				triggerData[1] = globalStats.getTriggerStats().getSingles1Stats();
-			} else {
-				triggerData[0] = globalStats.getTriggerStats().getPair0Stats();
-				triggerData[1] = globalStats.getTriggerStats().getPair1Stats();
-			}
-			
-			// Get the basic trigger data.
-			int sspSimTriggers = triggerData[0].getSSPSimulatedTriggers() + triggerData[1].getSSPSimulatedTriggers();
-			int reconSimTriggers = triggerData[0].getReconSimulatedTriggers() + triggerData[1].getReconSimulatedTriggers();
-			int sspReportedTriggers = triggerData[0].getReportedTriggers() + triggerData[1].getReportedTriggers();
-			int sspMatchedTriggers = triggerData[0].getMatchedSSPSimulatedTriggers() + triggerData[1].getMatchedSSPSimulatedTriggers();
-			int reconMatchedTriggers = triggerData[0].getMatchedReconSimulatedTriggers() + triggerData[1].getMatchedReconSimulatedTriggers();
-			
-			// Print the basic trigger statistics.
-			int spaces = getPrintSpaces(sspSimTriggers, reconSimTriggers, sspReportedTriggers);
-			System.out.println();
-			if(triggerType == 0) { System.out.println("Singles Trigger Verification:"); }
-			else { System.out.println("Pair Trigger Verification:"); }
-			System.out.printf("\tSSP Cluster Sim Triggers   :: %" + spaces + "d%n", sspSimTriggers);
-			System.out.printf("\tRecon Cluster Sim Triggers :: %" + spaces + "d%n", reconSimTriggers);
-			System.out.printf("\tSSP Reported Triggers      :: %" + spaces + "d%n", sspReportedTriggers);
-			
-			System.out.printf("\tInternal Efficiency        :: %" + spaces + "d / %" + spaces + "d ", sspMatchedTriggers, sspSimTriggers);
-			if(sspSimTriggers == 0) { System.out.printf("(N/A)%n"); }
-			else { System.out.printf("(%7.3f%%)%n", (100.0 * sspMatchedTriggers / sspSimTriggers)); }
-			
-			System.out.printf("\tTrigger Efficiency         :: %" + spaces + "d / %" + spaces + "d ", reconMatchedTriggers, reconSimTriggers);
-			if(reconSimTriggers == 0) { System.out.printf("(N/A)%n"); }
-			else { System.out.printf("(%7.3f%%)%n" , (100.0 * reconMatchedTriggers / reconSimTriggers)); }
-			
-			// Print the individual cut performances.
-			if(triggerType == 0) {
-				for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-					// Get the appropriate trigger statistics module.
-					TriggerEvent triggerStats;
-					if(triggerNum == 0) { triggerStats = globalStats.getTriggerStats().getSingles0Stats(); }
-					else { triggerStats = globalStats.getTriggerStats().getSingles1Stats(); }
-					
-					// Get the number of SSP triggers for this trigger number.
-					int sspTriggerCount = triggerStats.getSSPSimulatedTriggers();
-					//int sspTriggerCount = triggerRunStats[0].getTotalSSPTriggers(triggerNum);
-				
-					System.out.println();
-					System.out.printf("\tTrigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
-					System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerStats.getUnmatchedSSPSimulatedTriggers());
-					//System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerRunStats[0].getUnmatchedTriggers(triggerNum));
-					if(sspTriggerCount == 0) {
-						System.out.printf("\t\tCluster Energy Lower Bound :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(ENERGY_MIN), sspTriggerCount);
-						System.out.printf("\t\tCluster Energy Upper Bound :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(ENERGY_MAX), sspTriggerCount);
-						System.out.printf("\t\tCluster Hit Count          :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(HIT_COUNT), sspTriggerCount);
-					} else {
-						System.out.printf("\t\tCluster Energy Lower Bound :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(ENERGY_MIN), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(ENERGY_MIN) / sspTriggerCount));
-						System.out.printf("\t\tCluster Energy Upper Bound :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(ENERGY_MAX), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(ENERGY_MAX) / sspTriggerCount));
-						System.out.printf("\t\tCluster Hit Count          :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(HIT_COUNT), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(HIT_COUNT) / sspTriggerCount));
-					}
-				}
-			} else {
-				for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-					// Get the appropriate trigger statistics module.
-					TriggerEvent triggerStats;
-					if(triggerNum == 0) { triggerStats = globalStats.getTriggerStats().getPair0Stats(); }
-					else { triggerStats = globalStats.getTriggerStats().getPair1Stats(); }
-					
-					// Get the number of SSP triggers for this trigger number.
-					int sspTriggerCount = triggerStats.getSSPSimulatedTriggers();
-					
-					System.out.println();
-					System.out.printf("\tTrigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
-					System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerStats.getUnmatchedSSPSimulatedTriggers());
-					if(sspTriggerCount == 0) {
-						System.out.printf("\t\tPair Energy Sum            :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(ENERGY_SUM), sspTriggerCount);
-						System.out.printf("\t\tPair Energy Difference     :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(ENERGY_DIFF), sspTriggerCount);
-						System.out.printf("\t\tPair Energy Slope          :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount);
-						System.out.printf("\t\tPair Coplanarity           :: %" + spaces + "d / %" + spaces + "d%n",
-								triggerStats.getSSPCutFailures(COPLANARITY), sspTriggerCount);
-					} else {
-						System.out.printf("\t\tPair Energy Sum            :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(ENERGY_SUM), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(ENERGY_SUM) / sspTriggerCount));
-						System.out.printf("\t\tPair Energy Difference     :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(ENERGY_DIFF), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(ENERGY_DIFF) / sspTriggerCount));
-						System.out.printf("\t\tPair Energy Slope          :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(ENERGY_SLOPE) / sspTriggerCount));
-						System.out.printf("\t\tPair Coplanarity           :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
-								triggerStats.getSSPCutFailures(COPLANARITY), sspTriggerCount,
-								(100.0 * triggerStats.getSSPCutFailures(COPLANARITY) / sspTriggerCount));
-					}
-				}
-			}
-		}
-		
-		// Print out the trigger efficiency table.
-		System.out.println();
-		globalStats.getTriggerStats().printEfficiencyTable();
-	}
-	
-	/**
-	 * Checks whether all of the hits in a cluster are within the safe
-	 * region of the FADC output window.
-	 * @param reconCluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is safe and
-	 * returns <code>false</code> otherwise.
-	 */
-	private final boolean isVerifiable(Cluster reconCluster) {
-		return TriggerDiagnosticUtil.isVerifiable(reconCluster, nsa, nsb, windowWidth);
-	}
-	
-	/**
-	 * Generates a <code>List</code> collection that contains a set
-	 * of <code>ArrayList</code> collections representing a unique
-	 * permutation of the entries in the argument.
-	 * @param values - A collection of the entries to be permuted.
-	 * @return Returns a list of lists representing the permutations.
-	 */
-	private static final List<List<Pair<Cluster, SSPCluster>>> getPermutations(List<Cluster> reconClusters, List<SSPCluster> sspClusters) {
-		// Store the SSP cluster permutations.
-		List<List<SSPCluster>> permList = new ArrayList<List<SSPCluster>>();
-		
-		// Make sure that the two lists are the same size.
-		int reconSize = reconClusters.size();
-		int sspSize = sspClusters.size();
-		while(sspClusters.size() < reconClusters.size()) {
-			sspClusters.add(null);
-		}
-		while(reconClusters.size() < sspClusters.size()) {
-			reconClusters.add(null);
-		}
-		
-		// Get the SSP cluster permutations.
-		permute(new ArrayList<SSPCluster>(0), sspClusters, permList);
-		
-		// Create pairs from the permutations.
-		List<List<Pair<Cluster, SSPCluster>>> pairList = new ArrayList<List<Pair<Cluster, SSPCluster>>>();
-		for(List<SSPCluster> permutation : permList) {
-			List<Pair<Cluster, SSPCluster>> pairs = new ArrayList<Pair<Cluster, SSPCluster>>(reconClusters.size());
-			
-			for(int clusterIndex = 0; (clusterIndex < reconClusters.size() && clusterIndex < permutation.size()); clusterIndex++) {
-				pairs.add(new Pair<Cluster, SSPCluster>(reconClusters.get(clusterIndex), permutation.get(clusterIndex)));
-			}
-			
-			pairList.add(pairs);
-		}
-		
-		// Remove the extra values.
-		for(int i = sspClusters.size() - 1; i >= sspSize; i--) { sspClusters.remove(i); }
-		for(int i = reconClusters.size() - 1; i >= reconSize; i--) { reconClusters.remove(i); }
-		
-		// Return the pairs.
-		return pairList;
-	}
-	
-	/**
-	 * Recursive method for permuting all entries in the argument
-	 * collection <code>remainingValues</code> into the argument
-	 * <code>permutedValues</code> values. Completed permutations are
-	 * placed in the argument <code>permList</code>.
-	 * @param permutedValues - List to store entries that have already
-	 * been permuted.
-	 * @param remainingValues - List to store  entries that need to be
-	 * permuted.
-	 * @param permList - List to store completed permutations.
-	 */
-	private static final void permute(List<SSPCluster> permutedValues, List<SSPCluster> remainingValues, List<List<SSPCluster>> permList) {
-		// If the list of entries that still need to be sorted is empty,
-		// then there is nothing to sort. Just return and empty list.
-		if(remainingValues.isEmpty()) { return; }
-		
-		// If there is only one value left in the list of entries that
-		// still need to be sorted, then just add it to the permutation
-		// list and return it.
-		else if(remainingValues.size() <= 1) {
-			// Add the last entry.
-			permutedValues.add(remainingValues.get(0));
-			
-			// Add the permutation to the list of completed permutations.
-			permList.add(permutedValues);
-		}
-		
-		// Otherwise, continue to get all possible permutations.
-		else {
-			// Iterate over the entries that have not been permuted.
-			for(int i = 0; i < remainingValues.size(); i++) {
-				// Make new lists to contain the permutations.
-				List<SSPCluster> newPermList = new ArrayList<SSPCluster>(permutedValues.size() + 1);
-				List<SSPCluster> newRemainList = new ArrayList<SSPCluster>(remainingValues.size());
-				
-				// Copy the current permuted entries to the new list
-				// and one value from the list of entries that have
-				// not been permuted yet.
-				newPermList.addAll(permutedValues);
-				newPermList.add(remainingValues.get(i));
-				
-				// The new list of entries that have not been permuted
-				// should be identical, except it should now be missing
-				// the entry that was moved.
-				for(int index = 0; index < remainingValues.size(); index++) {
-					if(index != i) { newRemainList.add(remainingValues.get(index)); }
-				}
-				
-				// Repeat the process with the new lists.
-				permute(newPermList, newRemainList, permList);
-			}
-		}
-	}
-	
-	/**
-	 * Compares two cluster matching events and finds the one that has
-	 * the better results. Note that this will only return results that
-	 * make sense if both of the events represent different permutations
-	 * of the same set of clusters. Comparing events with different sets
-	 * of clusters will produce meaningless results.
-	 * @param firstEvent - The first cluster matching event,
-	 * @param secondEvent - The second cluster matching event.
-	 * @return Returns the cluster matching event that is better.
-	 */
-	private static final DetailedClusterEvent getBestPermutation(DetailedClusterEvent firstEvent, DetailedClusterEvent secondEvent) {
-		// If both permutations are null, return that.
-		if(firstEvent == null && secondEvent == null) {
-			return null;
-		}
-		
-		// If one permutation is null, it is not the best.
-		if(firstEvent == null) { return secondEvent; }
-		else if(secondEvent == null) { return firstEvent; }
-		
-		// A permutation is better if it has more matches.
-		if(firstEvent.getMatches() > secondEvent.getMatches()) { return firstEvent; }
-		else if(secondEvent.getMatches() > firstEvent.getMatches()) { return secondEvent; }
-		
-		// Otherwise, the permutation with the least energy failures is
-		// the better permutation.
-		if(firstEvent.getEnergyFailures() < secondEvent.getEnergyFailures()) { return firstEvent; }
-		else if(secondEvent.getEnergyFailures() < firstEvent.getEnergyFailures()) { return secondEvent; }
-		
-		// If both these values are the same, then the events are identical.
-		return firstEvent;
-	}
-	
-	/**
-	 * Determines the number of spaces needed to render the longest of
-	 * a series of integers as a string.
-	 * @param vals - The series of integers.
-	 * @return Returns the number of spaces needed to render the longest
-	 * integer as a base-10 string.
-	 */
-	private static final int getPrintSpaces(int... vals) {
-		// Track the largest value.
-		int largest = 0;
-		
-		// Iterate over the arguments and find the largest.
-		for(int val : vals) {
-			// Get the length of the string.
-			int length = TriggerDiagnosticUtil.getDigits(val);
-			
-			// If it is larger, track it.
-			if(length > largest) { largest = length; }
-		}
-		
-		// Return the longer one.
-		return largest;
-	}
-	
-	/**
-	 * Gets the position of the source of a <code>Trigger</code> object
-	 * as text. This method only supports trigger sources of the types
-	 * <code>SSPCluster</code>, <code>Cluster</code>, and arrays of size
-	 * two of either type.
-	 * @param trigger - The trigger from which to obtain the source.
-	 * @return Returns the source of the trigger as a <code>String</code>
-	 * object.
-	 * @throws IllegalArgumentException Occurs if the source of the
-	 * trigger is not any of the supported types.
-	 */
-	private static final String triggerPositionString(Trigger<?> trigger) throws IllegalArgumentException {
-		// Get the trigger source.
-		Object source = trigger.getTriggerSource();
-		
-		// Handle valid trigger sources.
-		if(source instanceof SSPCluster) {
-			return TriggerDiagnosticUtil.clusterPositionString((SSPCluster) source);
-		} else if(source instanceof Cluster) {
-			return TriggerDiagnosticUtil.clusterPositionString((Cluster) source);
-		} else if(source instanceof SSPCluster[]) {
-			SSPCluster[] sourcePair = (SSPCluster[]) source;
-			if(sourcePair.length == 2) {
-				return String.format("%s, %s", TriggerDiagnosticUtil.clusterPositionString(sourcePair[0]),
-						TriggerDiagnosticUtil.clusterPositionString(sourcePair[1]));
-			}
-		} else if(source instanceof Cluster[]) {
-			Cluster[] sourcePair = (Cluster[]) source;
-			if(sourcePair.length == 2) {
-				return String.format("%s, %s", TriggerDiagnosticUtil.clusterPositionString(sourcePair[0]),
-						TriggerDiagnosticUtil.clusterPositionString(sourcePair[1]));
-			}
-		}
-		
-		// Otherwise, the source type is unrecognized. Throw an error.
-		throw new IllegalArgumentException(String.format("Trigger source type \"%s\" is not supported.",
-				trigger.getTriggerSource().getClass().getSimpleName()));
-	}
-	
-	/**
-	 * Gets the time of a simulated trigger object. Method supports
-	 * triggers with source objects of type <code>SSPCluster</code>,
-	 * <code>Cluster</code>, and arrays of size two composed of either
-	 * object type.
-	 * @param trigger - The trigger.
-	 * @return Returns the time at which the trigger occurred.
-	 * @throws IllegalArgumentException Occurs if the trigger source
-	 * is not a supported type.
-	 */
-	private static final double getTriggerTime(Trigger<?> trigger) throws IllegalArgumentException {
-		// Get the trigger source.
-		Object source = trigger.getTriggerSource();
-		
-		// Get the trigger time for supported trigger types.
-		if(source instanceof SSPCluster) {
-			return ((SSPCluster) source).getTime();
-		} else if(source instanceof Cluster) {
-			return TriggerDiagnosticUtil.getClusterTime((Cluster) source);
-		} else if(source instanceof SSPCluster[]) {
-			// Get the pair.
-			SSPCluster[] sourcePair = (SSPCluster[]) source;
-			
-			// Get the time of the bottom cluster.
-			if(sourcePair.length == 2) {
-				if(sourcePair[0].getYIndex() < 0) { return sourcePair[0].getTime(); }
-				else if(sourcePair[1].getYIndex() < 0) { return sourcePair[1].getTime(); }
-				else { throw new IllegalArgumentException("Cluster pairs must be formed of a top/bottom pair."); }
-			}
-			else { throw new IllegalArgumentException("Cluster pairs must be of size 2."); }
-		} else if(source instanceof Cluster[]) {
-			// Get the pair.
-			Cluster[] sourcePair = (Cluster[]) source;
-			int[] iy = {
-				TriggerDiagnosticUtil.getYIndex(sourcePair[0]),
-				TriggerDiagnosticUtil.getYIndex(sourcePair[1])
-			};
-			
-			// Get the time of the bottom cluster.
-			if(sourcePair.length == 2) {
-				if(iy[0] < 0) { return TriggerDiagnosticUtil.getClusterTime(sourcePair[0]); }
-				else if(iy[1] < 0) { return TriggerDiagnosticUtil.getClusterTime(sourcePair[1]); }
-				else { throw new IllegalArgumentException("Cluster pairs must be formed of a top/bottom pair."); }
-			}
-			else { throw new IllegalArgumentException("Cluster pairs must be of size 2."); }
-		}
-		
-		// If the source type is unrecognized, throw an exception.
-		throw new IllegalArgumentException(String.format("Trigger source type \"%\" is not supported.",
-				source.getClass().getSimpleName()));
-	}
-	
-	/**
-	 * Checks if a simulated trigger and an SSP trigger match. Note
-	 * that only certain types can be compared. These are:
-	 * <ul><li><code>SinglesTrigger<?> --> SSPSinglesTrigger</code></li>
-	 * <li><code>PairTrigger<?> --> SSPPairTrigger</code></li></ul>
-	 * @param simTrigger - The simulated trigger.
-	 * @param sspTrigger - The SSP bank trigger.
-	 * @return Returns an array of <code>boolean</code> primitives that
-	 * indicate which cuts passed and which failed.
-	 */
-	private static final boolean[] triggerCutMatch(Trigger<?> simTrigger, SSPTrigger sspTrigger) {
-		// Check that the cuts match for supported trigger types.
-		if(simTrigger instanceof SinglesTrigger && sspTrigger instanceof SSPSinglesTrigger) {
-			// Create an array to store the cut checks.
-			boolean[] cutMatch = new boolean[3];
-			
-			// Cast the triggers.
-			SinglesTrigger<?> simSingles = (SinglesTrigger<?>) simTrigger;
-			SSPSinglesTrigger sspSingles = (SSPSinglesTrigger) sspTrigger;
-			
-			// Perform the check.
-			cutMatch[ENERGY_MIN] = (simSingles.getStateClusterEnergyLow()  == sspSingles.passCutEnergyMin());
-			cutMatch[ENERGY_MAX] = (simSingles.getStateClusterEnergyHigh() == sspSingles.passCutEnergyMax());
-			cutMatch[HIT_COUNT] = (simSingles.getStateHitCount()          == sspSingles.passCutHitCount());
-			
-			// Return the match array.
-			return cutMatch;
-		} else if(simTrigger instanceof PairTrigger && sspTrigger instanceof SSPPairTrigger) {
-			// Create an array to store the cut checks.
-			boolean[] cutMatch = new boolean[4];
-			
-			// Cast the triggers.
-			PairTrigger<?> simPair = (PairTrigger<?>) simTrigger;
-			SSPPairTrigger sspPair = (SSPPairTrigger) sspTrigger;
-			
-			// Perform the check.
-			cutMatch[ENERGY_SUM] = (simPair.getStateEnergySum()        == sspPair.passCutEnergySum());
-			cutMatch[ENERGY_DIFF] = (simPair.getStateEnergyDifference() == sspPair.passCutEnergyDifference());
-			cutMatch[ENERGY_SLOPE] = (simPair.getStateEnergySlope()      == sspPair.passCutEnergySlope());
-			cutMatch[COPLANARITY] = (simPair.getStateCoplanarity()      == sspPair.passCutCoplanarity());
-			
-			// Return the match array.
-			return cutMatch;
-		}
-		
-		// If this point is reached, the triggers are not of a supported
-		// type for cut comparison. Produce an exception.
-		throw new IllegalArgumentException(String.format("Triggers of type \"%s\" can not be cut-matched with triggers of type \"%s\".",
-				simTrigger.getClass().getSimpleName(), sspTrigger.getClass().getSimpleName()));
-	}
+     * clusters and a collection of SSP clusters with an algorithm that
+     * ignores the times reported for each cluster.
+     * @param reconClusters - A collection of reconstructed clusters.
+     * @param sspClusters - A collection of SSP clusters.
+     * @param energyWindow - The window of allowed deviation between
+     * the reconstructed cluster and SSP cluster energies.
+     * @param hitWindow - The window of allowed deviation between
+     * the reconstructed cluster and SSP cluster hit counts.
+     * @return Returns the cluster matching results stored inside a
+     * <code>clusterMatchEvent</code> object.
+     */
+    private static final DetailedClusterEvent matchClusters(Collection<Cluster> reconClusters,
+            Collection<SSPCluster> sspClusters, double energyWindow, int hitWindow) {
+        // Track the number of cluster pairs that were matched and that
+        // failed by failure type.
+        DetailedClusterEvent event = new DetailedClusterEvent();
+        
+        // Create maps to link cluster position to the list of clusters
+        // that were found at that location.
+        Map<Point, List<Cluster>> reconClusterMap = new HashMap<Point, List<Cluster>>(reconClusters.size());
+        Map<Point, List<SSPCluster>> sspClusterMap = new HashMap<Point, List<SSPCluster>>(reconClusters.size());
+        
+        // Populate the reconstructed cluster map.
+        for(Cluster reconCluster : reconClusters) {
+            // Get the cluster position.
+            Point position = new Point(TriggerDiagnosticUtil.getXIndex(reconCluster),
+                    TriggerDiagnosticUtil.getYIndex(reconCluster));
+            
+            // Get the list for this cluster position.
+            List<Cluster> reconList = reconClusterMap.get(position);
+            if(reconList == null) {
+                reconList = new ArrayList<Cluster>();
+                reconClusterMap.put(position, reconList);
+            }
+            
+            // Add the cluster to the list.
+            reconList.add(reconCluster);
+        }
+        
+        // Populate the SSP cluster map.
+        for(SSPCluster sspCluster : sspClusters) {
+            // Get the cluster position.
+            Point position = new Point(sspCluster.getXIndex(), sspCluster.getYIndex());
+            
+            // Get the list for this cluster position.
+            List<SSPCluster> sspList = sspClusterMap.get(position);
+            if(sspList == null) {
+                sspList = new ArrayList<SSPCluster>();
+                sspClusterMap.put(position, sspList);
+            }
+            
+            // Add the cluster to the list.
+            sspList.add(sspCluster);
+        }
+        
+        // For each reconstructed cluster, attempt to match the clusters
+        // with SSP clusters at the same position.
+        positionLoop:
+        for(Entry<Point, List<Cluster>> clusterSet : reconClusterMap.entrySet()) {
+            // Get the reconstructed and SSP clusters at this position.
+            List<Cluster> reconList = clusterSet.getValue();
+            List<SSPCluster> sspList = sspClusterMap.get(clusterSet.getKey());
+            
+            // Print the crystal position header.
+            OutputLogger.println();
+            OutputLogger.printf("Considering clusters at (%3d, %3d)%n", clusterSet.getKey().x, clusterSet.getKey().y);
+            
+            // If there are no SSP clusters, then matching fails by
+            // reason of position. The remainder of the loop may be
+            // skipped, since there is nothing to check.
+            if(sspList == null || sspList.isEmpty()) {
+                event.pairFailPosition(reconList.size());
+                continue positionLoop;
+            }
+            
+            // Get all possible permutations of SSP clusters.
+            List<List<Pair<Cluster, SSPCluster>>> permutations = getPermutations(reconList, sspList);
+            
+            // Print the information for this crystal position.
+            OutputLogger.printf("\tRecon Clusters :: %d%n", reconList.size());
+            OutputLogger.printf("\tSSP Clusters   :: %d%n", sspList.size());
+            OutputLogger.printf("\tPermutations   :: %d%n", permutations.size());
+            
+            // Track the plotted values for the current best permutation.
+            DetailedClusterEvent bestPerm = null;
+            
+            // Iterate over the permutations and find the permutation
+            // that produces the best possible result when compared to
+            // the reconstructed clusters.
+            int permIndex = 0;
+            for(List<Pair<Cluster, SSPCluster>> pairs : permutations) {
+                // Update the current permutation number.
+                permIndex++;
+                
+                // Track the plot values for this permutation.
+                DetailedClusterEvent perm = new DetailedClusterEvent();
+                
+                // Try to match each pair.
+                pairLoop:
+                for(Pair<Cluster, SSPCluster> pair : pairs) {
+                    // Print the current reconstructed/SSP cluster pair.
+                    OutputLogger.printf("\tP%d :: %s --> %s", permIndex,
+                            pair.getFirstElement() == null ? "None" : TriggerDiagnosticUtil.clusterToString(pair.getFirstElement()),
+                            pair.getSecondElement() == null ? "None" : TriggerDiagnosticUtil.clusterToString(pair.getSecondElement()));
+                    
+                    // If either cluster in the pair is null, there
+                    // are not enough clusters to perform this match.
+                    if(pair.getFirstElement() == null || pair.getSecondElement() == null) {
+                        // Log the result.
+                        OutputLogger.printf(" [ %18s ]%n", "failure: unpaired");
+                        
+                        // An unpaired SSP cluster does not necessarily
+                        // represent a problem. Often, this just means
+                        // that the SSP cluster's matching reconstructed
+                        // cluster is outside the verification window.
+                        if(pair.getSecondElement() == null) {
+                            perm.pairFailPosition(pair.getFirstElement(), pair.getSecondElement());
+                        }
+                        
+                        // Skip the rest of the checks.
+                        continue pairLoop;
+                    }
+                    
+                    // Check if the reconstructed cluster has an energy
+                    // within the allotted threshold of the SSP cluster.
+                    if(pair.getSecondElement().getEnergy() >= pair.getFirstElement().getEnergy() - energyWindow &&
+                            pair.getSecondElement().getEnergy() <= pair.getFirstElement().getEnergy() + energyWindow) {
+                        
+                        // Check that the hit count of the reconstructed
+                        // is within the allotted threshold of the SSP
+                        // cluster.
+                        if(pair.getSecondElement().getHitCount() >= pair.getFirstElement().getCalorimeterHits().size() - hitWindow &&
+                                pair.getSecondElement().getHitCount() <= pair.getFirstElement().getCalorimeterHits().size() + hitWindow) {
+                            // Designate the pair as a match.
+                            perm.pairMatch(pair.getFirstElement(), pair.getSecondElement());
+                            OutputLogger.printf(" [ %18s ]%n", "success: matched");
+                        } else {
+                            perm.pairFailHitCount(pair.getFirstElement(), pair.getSecondElement());
+                            OutputLogger.printf(" [ %18s ]%n", "failure: hit count");
+                        } // End hit count check.
+                    } else {
+                        perm.pairFailEnergy(pair.getFirstElement(), pair.getSecondElement());
+                        OutputLogger.printf(" [ %18s ]%n", "failure: energy");
+                    } // End energy check.
+                } // End Pair Loop
+                
+                // Print the results of the permutation.
+                OutputLogger.printf("\t\tPermutation Matched   :: %d%n", perm.getMatches());
+                OutputLogger.printf("\t\tPermutation Energy    :: %d%n", perm.getEnergyFailures());
+                OutputLogger.printf("\t\tPermutation Hit Count :: %d%n", perm.getHitCountFailures());
+                
+                // Check whether the results from this permutation
+                // exceed the quality of the last best results. A
+                // greater number of matches is always better. If the
+                // matches are the same, select the one with fewer
+                // failures due to energy.
+                bestPerm = getBestPermutation(bestPerm, perm);
+            } // End Permutation Loop
+            
+            // Print the final results for the position.
+            OutputLogger.printf("\tPosition Matched   :: %d%n", bestPerm.getMatches());
+            OutputLogger.printf("\tPosition Energy    :: %d%n", bestPerm.getEnergyFailures());
+            OutputLogger.printf("\tPosition Hit Count :: %d%n", bestPerm.getHitCountFailures());
+            
+            // Add the results from the best-matched permutation
+            // to the event efficiency results.
+            event.addEvent(bestPerm);
+        } // End Crystal Position Loop
+        
+        // Return the cluster match summary.
+        return event;
+    }
+    
+    /**
+     * Performs cluster matching between a collection of reconstructed
+     * clusters and a collection of SSP clusters using the strictly
+     * time-compliant algorithm.
+     * @param reconClusters - A collection of reconstructed clusters.
+     * @param sspClusters - A collection of SSP clusters.
+     * @param energyWindow - The window of allowed deviation between
+     * the reconstructed cluster and SSP cluster energies.
+     * @param hitWindow - The window of allowed deviation between
+     * the reconstructed cluster and SSP cluster hit counts.
+     * @return Returns the cluster matching results stored inside a
+     * <code>clusterMatchEvent</code> object.
+     */
+    private static final DetailedClusterEvent matchClustersTimeCompliant(Collection<Cluster> reconClusters,
+            Collection<SSPCluster> sspClusters, double energyWindow, int hitWindow) {
+        // Track the number of cluster pairs that were matched and that
+        // failed by failure type.
+        DetailedClusterEvent event = new DetailedClusterEvent();
+        
+        // Store the clusters which have been successfully paired.
+        Set<SSPCluster> sspMatched = new HashSet<SSPCluster>(sspClusters.size());
+        
+        // Find reconstructed/SSP cluster matched pairs.
+        reconLoop:
+        for(Cluster reconCluster : reconClusters) {
+            // Track whether a position-matched cluster was found.
+            boolean matchedPosition = false;
+            
+            // VERBOSE :: Output the cluster being matched.
+            OutputLogger.printf("Considering %s%n", TriggerDiagnosticUtil.clusterToString(reconCluster));
+            
+            // Search through the SSP clusters for a matching cluster.
+            sspLoop:
+            for(SSPCluster sspCluster : sspClusters) {
+                // VERBOSE :: Output the SSP cluster being considered.
+                OutputLogger.printf("\t%s ", TriggerDiagnosticUtil.clusterToString(sspCluster));
+                
+                // If this cluster has been paired, skip it.
+                if(sspMatched.contains(sspCluster)) {
+                    OutputLogger.printf("[ %7s; %9s ]%n", "fail", "matched");
+                    continue sspLoop;
+                }
+                
+                // Matched clusters must have the same position.
+                if(TriggerDiagnosticUtil.getXIndex(reconCluster) != sspCluster.getXIndex()
+                        || TriggerDiagnosticUtil.getYIndex(reconCluster) != sspCluster.getYIndex()) {
+                    OutputLogger.printf("[ %7s; %9s ]%n", "fail", "position");
+                    continue sspLoop;
+                }
+                
+                // Note that a cluster was found at this position.
+                matchedPosition = true;
+                
+                // Matched clusters must have the same time-stamp.
+                if(reconCluster.getCalorimeterHits().get(0).getTime() != sspCluster.getTime()) {
+                    OutputLogger.printf("[ %7s; %9s ]%n", "fail", "time");
+                    continue sspLoop;
+                }
+                
+                // Clusters that pass all of the above checks are the
+                // same cluster.
+                sspMatched.add(sspCluster);
+                
+                // Check that the clusters are sufficiently close in
+                // energy to one another.
+                if(sspCluster.getEnergy() >= reconCluster.getEnergy() - energyWindow
+                        && sspCluster.getEnergy() <= reconCluster.getEnergy() + energyWindow) {
+                    // If a cluster matches in energy, check that it
+                    // is also sufficiently close in hit count.
+                    if(sspCluster.getHitCount() >= reconCluster.getCalorimeterHits().size() - hitWindow &&
+                            sspCluster.getHitCount() <= reconCluster.getCalorimeterHits().size() + hitWindow) {
+                        // The cluster is a match.
+                        event.pairMatch(reconCluster, sspCluster);
+                        OutputLogger.printf("[ %7s; %9s ]%n", "success", "matched");
+                        continue reconLoop;
+                    } else {
+                        event.pairFailHitCount(reconCluster, sspCluster);
+                        OutputLogger.printf("[ %7s; %9s ]%n", "fail", "hit count");
+                        continue reconLoop;
+                    } // End hit count check.
+                } else {
+                    event.pairFailEnergy(reconCluster, sspCluster);
+                    OutputLogger.printf("[ %7s; %9s ]%n", "fail", "energy");
+                    continue reconLoop;
+                } // End energy check.
+            }// End SSP loop.
+            
+            // If the reconstructed cluster has not been matched, check
+            // if a cluster was found at the same position. If not, then
+            // the cluster fails by reason of position.
+            if(!matchedPosition) {
+                event.pairFailPosition(reconCluster, null);
+            }
+            
+            // Otherwise, the cluster had a potential matched, but the
+            // time-stamps were off. The cluster fails by reason of time.
+            else {
+                event.pairFailTime(reconCluster, null);
+            }
+        } // End recon loop.
+        
+        // Return the populated match event.
+        return event;
+    }
+    
+    /**
+     * Checks triggers simulated on SSP clusters against the SSP bank's
+     * reported triggers to verify that the trigger is correctly applying
+     * cuts to the clusters it sees. Additionally compares triggers
+     * simulated on reconstructed clusters to measure trigger efficiency.
+     */
+    private void singlesTriggerVerification() {
+        // Create lists of generic triggers.
+        List<List<? extends Trigger<?>>> sspTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
+        List<List<? extends Trigger<?>>> reconTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
+        
+        // Convert the simulated triggers to generic versions and add
+        // them to the generic list.
+        sspTriggerList.add(triggerData.getSimSSPTriggers().getSingles0Triggers());
+        sspTriggerList.add(triggerData.getSimSSPTriggers().getSingles1Triggers());
+        reconTriggerList.add(triggerData.getSimReconTriggers().getSingles0Triggers());
+        reconTriggerList.add(triggerData.getSimReconTriggers().getSingles1Triggers());
+        
+        // Run generic trigger verification.
+        triggerVerification(sspTriggerList, reconTriggerList, true);
+    }
+    
+    /**
+     * Checks triggers simulated on SSP clusters against the SSP bank's
+     * reported triggers to verify that the trigger is correctly applying
+     * cuts to the clusters it sees. Additionally compares triggers
+     * simulated on reconstructed clusters to measure trigger efficiency.
+     */
+    private void pairTriggerVerification() {
+        // Create lists of generic triggers.
+        List<List<? extends Trigger<?>>> sspTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
+        List<List<? extends Trigger<?>>> reconTriggerList = new ArrayList<List<? extends Trigger<?>>>(2);
+        
+        // Convert the simulated triggers to generic versions and add
+        // them to the generic list.
+        sspTriggerList.add(triggerData.getSimSSPTriggers().getPair0Triggers());
+        sspTriggerList.add(triggerData.getSimSSPTriggers().getPair1Triggers());
+        reconTriggerList.add(triggerData.getSimReconTriggers().getPair0Triggers());
+        reconTriggerList.add(triggerData.getSimReconTriggers().getPair1Triggers());
+        
+        // Run generic trigger verification.
+        triggerVerification(sspTriggerList, reconTriggerList, false);
+    }
+    
+    /**
+     * Performs trigger verification for both trigger types.
+     * @param sspTriggerList - The list of SSP triggers.
+     * @param reconTriggerList - The list of reconstructed triggers.
+     * @param isSingles - Whether or not this is a singles trigger
+     * verification.
+     */
+    private void triggerVerification(List<List<? extends Trigger<?>>> sspTriggerList, 
+            List<List<? extends Trigger<?>>> reconTriggerList, boolean isSingles) {
+        
+        // ==========================================================
+        // ==== Initialize Trigger Verification =====================
+        // ==========================================================
+        
+        // Print the cluster verification header.
+        OutputLogger.println();
+        OutputLogger.println();
+        OutputLogger.println("======================================================================");
+        if(isSingles) { OutputLogger.println("=== Singles Trigger Verification ====================================="); }
+        else { OutputLogger.println("=== Pair Trigger Verification ========================================"); }
+        OutputLogger.println("======================================================================");
+        
+        // Track the number of triggers seen and the number found.
+        TriggerEvent[] triggerEvent = { new TriggerEvent(), new TriggerEvent() };
+        
+        // ==========================================================
+        // ==== Output Event Summary ================================
+        // ==========================================================
+        
+        // Get the list of triggers reported by the SSP.
+        List<? extends SSPNumberedTrigger> sspTriggers;
+        if(isSingles) { sspTriggers = sspBank.getSinglesTriggers(); }
+        else { sspTriggers = sspBank.getPairTriggers(); }
+        
+        // Output the SSP cluster triggers.
+        OutputLogger.println();
+        OutputLogger.println("SSP Cluster " + (isSingles ? "Singles" : "Pair") + " Triggers");
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
+                OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
+                        (triggerNum + 1), triggerPositionString(simTrigger),
+                        getTriggerTime(simTrigger), simTrigger.toString());
+            }
+        }
+        if(sspTriggerList.get(0).size() + sspTriggerList.get(1).size() == 0) {
+            OutputLogger.println("\tNone");
+        }
+        
+        // Output the reconstructed cluster singles triggers.
+        OutputLogger.println("Reconstructed Cluster " + (isSingles ? "Singles" : "Pair") + " Triggers");
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            for(Trigger<?> simTrigger : reconTriggerList.get(triggerNum)) {
+                OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
+                        (triggerNum + 1), triggerPositionString(simTrigger),
+                        getTriggerTime(simTrigger), simTrigger.toString());
+            }
+        }
+        if(reconTriggerList.get(0).size() + reconTriggerList.get(1).size() == 0) {
+            OutputLogger.println("\tNone");
+        }
+        
+        // Output the SSP reported triggers.
+        OutputLogger.println("SSP Reported " + (isSingles ? "Singles" : "Pair") + " Triggers");
+        for(SSPTrigger sspTrigger : sspTriggers) {
+            OutputLogger.printf("\t%s%n", sspTrigger.toString());
+        }
+        if(sspTriggers.size() == 0) { OutputLogger.println("\tNone"); }
+        
+        // Update the trigger event with the counts for each type of
+        // simulated trigger. Reported triggers are counted later when
+        // already iterating over them.
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            triggerEvent[triggerNum].sawSSPSimulatedTriggers(tiFlags, sspTriggerList.get(triggerNum).size());
+            triggerEvent[triggerNum].sawReconSimulatedTriggers(tiFlags, reconTriggerList.get(triggerNum).size());
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== SSP Internal Logic Verification =====================
+        // ==========================================================
+        
+        // Track which SSP triggers have been matched to avoid matching
+        // multiple reconstructed SSP cluster triggers to the same SSP
+        // trigger.
+        Set<SSPNumberedTrigger> sspTriggerSet = new HashSet<SSPNumberedTrigger>();
+        Set<Trigger<?>> simTriggerSet = new HashSet<Trigger<?>>();
+        
+        // Track the number of SSP reported triggers that are found in
+        // excess of the SSP simulated triggers.
+        int sspReportedExtras = sspTriggers.size() - (sspTriggerList.get(0).size() + sspTriggerList.get(1).size());
+        if(sspReportedExtras > 0) {
+            if(isSingles) { singlesInternalFail = true; }
+            else { pairInternalFail = true; }
+        } else { sspReportedExtras = 0; }
+        
+        // Iterate over the triggers.
+        OutputLogger.println();
+        OutputLogger.println("Matching SSP Reported Triggers to SSP Simulated Triggers:");
+        for(SSPNumberedTrigger sspTrigger : sspTriggers) {
+            // Get the trigger information.
+            int triggerNum = sspTrigger.isFirstTrigger() ? 0 : 1;
+            OutputLogger.printf("\t%s%n", sspTrigger.toString());
+            
+            // Note that a bank trigger was seen.
+            triggerEvent[triggerNum].sawReportedTrigger();
+            
+            // Iterate over the SSP cluster simulated triggers and
+            // look for a trigger that matches.
+            matchLoop:
+            for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
+                // VERBOSE :: Output the trigger being considered for
+                //            matching.
+                OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s ",
+                        (triggerNum + 1), triggerPositionString(simTrigger),
+                        getTriggerTime(simTrigger), simTrigger.toString());
+                
+                // If the current SSP trigger has already been matched,
+                // skip it.
+                if(simTriggerSet.contains(simTrigger)) {
+                    OutputLogger.printf("[ %-15s ]%n", "failed; matched");
+                    continue matchLoop;
+                }
+                
+                // Check that the triggers have the same time. Triggers
+                // generated from SSP bank clusters should always align
+                // in time.
+                if(sspTrigger.getTime() != getTriggerTime(simTrigger)) {
+                    OutputLogger.printf("[ %-15s ]%n", "failed; time");
+                    continue matchLoop;
+                }
+                
+                // Check whether the trigger cuts match.
+                boolean[] matchedCuts = triggerCutMatch(simTrigger, sspTrigger);
+                for(int i = 0; i < matchedCuts.length; i++) {
+                    if(!matchedCuts[i]) {
+                        int typeIndex = isSingles ? 0 : 1;
+                        OutputLogger.printf("[ %-15s ]%n", String.format("failed; %s", cutNames[typeIndex][i]));
+                        continue matchLoop;
+                    }
+                }
+                
+                // If all the cuts match, along with the time and the
+                // trigger number, than these triggers are a match.
+                sspTriggerSet.add(sspTrigger);
+                simTriggerSet.add(simTrigger);
+                triggerEvent[triggerNum].matchedSSPTrigger(tiFlags);
+                OutputLogger.printf("[ %-15s ]%n", "success");
+                break matchLoop;
+            }
+        }
+        
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
+                globalTriggerPlots.sawTrigger(simTrigger);
+                if(simTriggerSet.contains(simTrigger)) {
+                    globalTriggerPlots.matchedTrigger(simTrigger);
+                } else {
+                    globalTriggerPlots.failedTrigger(simTrigger);
+                }
+            }
+        }
+        
+        // Iterate over the unmatched simulated triggers again and the
+        // unmatched SSP reported trigger that most closely matches it.
+        OutputLogger.println();
+        OutputLogger.println("Matching Failed SSP Reported Triggers to Remaining SSP Simulated Triggers:");
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            simLoop:
+            for(Trigger<?> simTrigger : sspTriggerList.get(triggerNum)) {
+                OutputLogger.printf("\tTrigger %d :: %s :: %3.0f :: %s%n",
+                        (triggerNum + 1), triggerPositionString(simTrigger),
+                        getTriggerTime(simTrigger), simTrigger.toString());
+                
+                // Check whether this trigger has already been matched
+                // or not. If it has been matched, skip it.
+                if(simTriggerSet.contains(simTrigger)) {
+                    OutputLogger.println("\t\tSkipping; already matched successfully");
+                    continue simLoop;
+                }
+                
+                // Get the trigger time for the simulated trigger.
+                double simTime = getTriggerTime(simTrigger);
+                
+                // Track the match statistics for each reported trigger
+                // so that the closest match may be found.
+                int numMatched = -1;
+                boolean[] matchedCut = null;
+                SSPNumberedTrigger bestMatch = null;
+                
+                // Store the readout for the best match.
+                String bestMatchText = null;
+                
+                // Iterate over the reported triggers to find a match.
+                reportedLoop:
+                for(SSPNumberedTrigger sspTrigger : sspTriggers) {
+                    OutputLogger.printf("\t\t%s ", sspTrigger.toString());
+                    
+                    // If the two triggers have different times, this
+                    // trigger should be skipped.
+                    if(sspTrigger.getTime() != simTime) {
+                        OutputLogger.printf("[ %-15s ]%n", "failed; time");
+                        continue reportedLoop;
+                    }
+                    
+                    // If this reported trigger has been matched then
+                    // it should be skipped.
+                    if(sspTriggerSet.contains(sspTrigger)) {
+                        OutputLogger.printf("[ %-15s ]%n", "failed; matched");
+                        continue reportedLoop;
+                    }
+                    
+                    // Check each of the cuts.
+                    boolean[] tempMatchedCut = triggerCutMatch(simTrigger, sspTrigger);
+                    
+                    // Check each cut and see if this is a closer match
+                    // than the previous best match.
+                    int tempNumMatched = 0;
+                    for(boolean passed : tempMatchedCut) { if(passed) { tempNumMatched++; } }
+                    OutputLogger.printf("[ %-15s ]%n", String.format("maybe; %d failed", tempNumMatched));
+                    
+                    // If the number of matched cuts exceeds the old
+                    // best result, this becomes the new best result.
+                    if(tempNumMatched > numMatched) {
+                        numMatched = tempNumMatched;
+                        matchedCut = tempMatchedCut;
+                        bestMatch = sspTrigger;
+                        bestMatchText = String.format("%s%n", sspTrigger.toString());
+                    }
+                }
+                
+                // If there was no match found, it means that there were
+                // no triggers that were both unmatched and at the same
+                // time as this simulated trigger.
+                if(bestMatch == null) {
+                    if(isSingles) { singlesInternalFail = true; }
+                    else { pairInternalFail = true; }
+                    triggerEvent[triggerNum].failedSSPTrigger();
+                    OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s",
+                            (triggerNum + 1), triggerPositionString(simTrigger),
+                            getTriggerTime(simTrigger), simTrigger.toString());
+                    OutputLogger.println(" --> No Valid Match Found");
+                } else {
+                    triggerEvent[triggerNum].matchedSSPTrigger(tiFlags, matchedCut);
+                    OutputLogger.printf("\t\tTrigger %d :: %s :: %3.0f :: %s",
+                            (triggerNum + 1), triggerPositionString(simTrigger),
+                            getTriggerTime(simTrigger), simTrigger.toString());
+                    OutputLogger.println(" --> " + bestMatchText);
+                }
+            }
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Trigger Efficiency ==================================
+        // ==========================================================
+        
+        // Reset the SSP matched trigger set.
+        sspTriggerSet.clear();
+        
+        // Iterate over the reconstructed cluster singles triggers.
+        OutputLogger.println();
+        OutputLogger.println("Recon Cluster Trigger --> SSP Reported Trigger Match Status");
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            for(Trigger<?> simTrigger : reconTriggerList.get(triggerNum)) {
+                OutputLogger.printf("\tTrigger %d :: %s :: %s%n", (triggerNum + 1),
+                        triggerPositionString(simTrigger), simTrigger.toString());
+                
+                // TEMP :: Populate the recon ALL pairs plots.
+                globalTriggerPlots.sawTrigger(simTrigger);
+                
+                // Iterate over the SSP reported triggers and compare
+                // them to the reconstructed cluster simulated trigger.
+                boolean matched = false;
+                matchLoop:
+                for(SSPNumberedTrigger sspTrigger : sspTriggers) {
+                    OutputLogger.printf("\t\t\t%s", sspTrigger.toString());
+                    
+                    // Only compare triggers if they are from the
+                    // same trigger source.
+                    if((triggerNum == 0 && sspTrigger.isSecondTrigger())
+                            || (triggerNum == 1 && sspTrigger.isFirstTrigger())) {
+                        OutputLogger.print(" [ fail; source    ]%n");
+                        continue matchLoop;
+                    }
+                    
+                    // Only compare the singles trigger if it was
+                    // not already matched to another trigger.
+                    if(sspTriggerSet.contains(sspTrigger)) {
+                        OutputLogger.print(" [ fail; matched   ]%n");
+                        continue matchLoop;
+                    }
+                    
+                    // Test each cut.
+                    int typeIndex = isSingles ? 0 : 1;
+                    boolean[] matchedCuts = triggerCutMatch(simTrigger, sspTrigger);
+                    for(int cutIndex = 0; cutIndex < matchedCuts.length; cutIndex++) {
+                        if(!matchedCuts[cutIndex]) {
+                            OutputLogger.printf(" [ fail; %-9s ]%n", cutNames[typeIndex][cutIndex]);
+                            continue matchLoop;
+                        }
+                    }
+                    
+                    // If all the trigger flags match, then the
+                    // triggers are a match.
+                    sspTriggerSet.add(sspTrigger);
+                    triggerEvent[triggerNum].matchedReconTrigger(tiFlags);
+                    OutputLogger.print(" [ success         ]%n");
+                    globalTriggerPlots.matchedTrigger(simTrigger);
+                    matched = true;
+                    break matchLoop;
+                }
+                
+                if(!matched) { globalTriggerPlots.failedTrigger(simTrigger); }
+            }
+        }
+        
+        
+        
+        // ==========================================================
+        // ==== Output Event Results ================================
+        // ==========================================================
+        
+        // Get the number of SSP and reconstructed cluster simulated
+        // triggers.
+        int sspSimTriggers = sspTriggerList.get(0).size() + sspTriggerList.get(1).size();
+        int reconSimTriggers = reconTriggerList.get(0).size() + reconTriggerList.get(1).size();
+        int[] sspTriggerCount = { sspTriggerList.get(0).size(), sspTriggerList.get(1).size() };
+        
+        // Print event statistics.
+        OutputLogger.println();
+        OutputLogger.println("Event Statistics:");
+        OutputLogger.printf("\tSSP Cluster Sim Triggers   :: %d%n", sspSimTriggers);
+        OutputLogger.printf("\tRecon Cluster Sim Triggers :: %d%n", reconSimTriggers);
+        OutputLogger.printf("\tSSP Reported Triggers      :: %d%n", sspTriggers.size());
+        
+        int matchedSSPTriggers = triggerEvent[0].getMatchedSSPSimulatedTriggers() + triggerEvent[1].getMatchedSSPSimulatedTriggers();
+        OutputLogger.printf("\tInternal Efficiency        :: %d / %d ", matchedSSPTriggers, sspSimTriggers);
+        if(sspSimTriggers == 0) { OutputLogger.printf("(N/A)%n"); }
+        else { OutputLogger.printf("(%3.0f%%)%n", (100.0 * matchedSSPTriggers / sspSimTriggers)); }
+        
+        int matchedReconTriggers = triggerEvent[0].getMatchedReconSimulatedTriggers() + triggerEvent[1].getMatchedReconSimulatedTriggers();
+        OutputLogger.printf("\tTrigger Efficiency         :: %d / %d", matchedReconTriggers, reconSimTriggers);
+        if(reconSimTriggers == 0) { OutputLogger.printf("(N/A)%n"); }
+        else { OutputLogger.printf("(%3.0f%%)%n", (100.0 * matchedReconTriggers / reconSimTriggers)); }
+        
+        // Print the individual cut performances.
+        if(isSingles) {
+            OutputLogger.println();
+            for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+                OutputLogger.printf("Trigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
+                if(sspSimTriggers == 0) {
+                    OutputLogger.printf("\tCluster Energy Lower Bound :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN), sspTriggerCount[triggerNum]);
+                    OutputLogger.printf("\tCluster Energy Upper Bound :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX), sspTriggerCount[triggerNum]);
+                    OutputLogger.printf("\tCluster Hit Count          :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT), sspTriggerCount[triggerNum]);
+                } else {
+                    OutputLogger.printf("\tCluster Energy Lower Bound :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MIN) / sspTriggerCount[triggerNum]));
+                    OutputLogger.printf("\tCluster Energy Upper Bound :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_MAX) / sspTriggerCount[triggerNum]));
+                    OutputLogger.printf("\tCluster Hit Count          :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(HIT_COUNT) / sspTriggerCount[triggerNum]));
+                }
+            }
+            
+            // Update the global trigger tracking variables.
+            localStats.getTriggerStats().getSingles0Stats().addEvent(triggerEvent[0]);
+            localStats.getTriggerStats().getSingles1Stats().addEvent(triggerEvent[1]);
+            globalStats.getTriggerStats().getSingles0Stats().addEvent(triggerEvent[0]);
+            globalStats.getTriggerStats().getSingles1Stats().addEvent(triggerEvent[1]);
+        } else {
+            for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+                OutputLogger.println();
+                OutputLogger.printf("Trigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
+                if(sspTriggerCount[triggerNum] == 0) {
+                    OutputLogger.printf("\tPair Energy Sum            :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM), sspTriggerCount[triggerNum]);
+                    OutputLogger.printf("\tPair Energy Difference     :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF), sspTriggerCount[triggerNum]);
+                    OutputLogger.printf("\tPair Energy Slope          :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount[triggerNum]);
+                    OutputLogger.printf("\tPair Coplanarity           :: %d / %d%n", triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY), sspTriggerCount[triggerNum]);
+                } else {
+                    OutputLogger.printf("\tPair Energy Sum            :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SUM) / sspTriggerCount[triggerNum]));
+                    OutputLogger.printf("\tPair Energy Difference     :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_DIFF) / sspTriggerCount[triggerNum]));
+                    OutputLogger.printf("\tPair Energy Slope          :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(ENERGY_SLOPE) / sspTriggerCount[triggerNum]));
+                    OutputLogger.printf("\tPair Coplanarity           :: %d / %d (%3.0f%%)%n",
+                            triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY), sspTriggerCount[triggerNum],
+                            (100.0 * triggerEvent[triggerNum].getSSPCutFailures(COPLANARITY) / sspTriggerCount[triggerNum]));
+                }
+            }
+            
+            // Update the global trigger tracking variables.
+            localStats.getTriggerStats().getPair0Stats().addEvent(triggerEvent[0]);
+            localStats.getTriggerStats().getPair1Stats().addEvent(triggerEvent[1]);
+            globalStats.getTriggerStats().getPair0Stats().addEvent(triggerEvent[0]);
+            globalStats.getTriggerStats().getPair1Stats().addEvent(triggerEvent[1]);
+        }
+        
+        // Note whether the was a trigger match failure.
+        if(triggerEvent[0].getFailedReconSimulatedTriggers() != 0 && triggerEvent[1].getFailedReconSimulatedTriggers() != 0) {
+            if(isSingles) { singlesEfficiencyFail = true; }
+            else { pairEfficiencyFail = true; }
+        } if(triggerEvent[0].getFailedSSPSimulatedTriggers() != 0 && triggerEvent[1].getFailedSSPSimulatedTriggers() != 0) {
+            if(isSingles) { singlesInternalFail = true; }
+            else { pairInternalFail = true; }
+        }
+    }
+    
+    /**
+     * Outputs all of the verification parameters currently in use by
+     * the software. A warning will be issued if the values for NSA and
+     * NSB, along with the FADC window, preclude clusters from being
+     * verified.
+     */
+    private void logSettings() {
+        // Output general settings.
+        System.out.println("Cluster Verification Settings");
+        System.out.printf("\tHit Threshold          :: %1d hit(s)%n", hitAcceptance);
+        System.out.printf("\tEnergy Threshold       :: %5.3f GeV%n",  energyAcceptance);
+        System.out.println();
+        
+        // Output window settings.
+        System.out.println("FADC Timing Window Settings");
+        System.out.printf("\tNSB                    :: %3d ns%n", nsb);
+        System.out.printf("\tNSA                    :: %3d ns%n", nsa);
+        System.out.printf("\tFADC Window            :: %3d ns%n", windowWidth);
+        
+        // Calculate the valid clustering window.
+        int start = nsb;
+        int end = windowWidth - nsa;
+        if(start < end) {
+            System.out.printf("\tValid Cluster Window   :: [ %3d ns, %3d ns ]%n", start, end);
+            performClusterVerification = true;
+        } else {
+            System.out.println("\tNSB, NSA, and FADC window preclude a valid cluster verification window.");
+            System.out.println("\tCluster verification will not be performed!");
+            performClusterVerification = false;
+        }
+        System.out.println();
+        
+        // Output the singles trigger settings.
+        for(int i = 0; i < 2; i++) {
+            // Print the settings.
+            System.out.printf("Singles Trigger %d Settings%23s[%5b]%n", (i + 1), "", singlesTriggerEnabled[i]);
+            System.out.printf("\tCluster Energy Low     :: %.3f GeV      [%5b]%n",
+                    singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), singlesCutsEnabled[i][0]);
+            System.out.printf("\tCluster Energy High    :: %.3f GeV      [%5b]%n",
+                    singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH), singlesCutsEnabled[i][1]);
+            System.out.printf("\tCluster Hit Count      :: %.0f hit(s)       [%5b]%n",
+                    singlesTrigger[i].getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW), singlesCutsEnabled[i][2]);
+            System.out.println();
+        }
+        
+        // Output the pair trigger settings.
+        for(int i = 0; i < 2; i++) {
+            System.out.printf("Pairs Trigger %d Settings%25s[%5b]%n", (i + 1), "", pairTriggerEnabled[i]);
+            System.out.printf("\tCluster Energy Low     :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), pairCutsEnabled[i][0]);
+            System.out.printf("\tCluster Energy High    :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH), pairCutsEnabled[i][1]);
+            System.out.printf("\tCluster Hit Count      :: %.0f hit(s)       [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW), pairCutsEnabled[i][2]);
+            System.out.printf("\tPair Energy Sum Low    :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW), pairCutsEnabled[i][3]);
+            System.out.printf("\tPair Energy Sum High   :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH), pairCutsEnabled[i][3]);
+            System.out.printf("\tPair Energy Difference :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH), pairCutsEnabled[i][4]);
+            System.out.printf("\tPair Energy Slope      :: %.3f GeV      [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW), pairCutsEnabled[i][5]);
+            System.out.printf("\tPair Energy Slope F    :: %.4f GeV / mm%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F));
+            System.out.printf("\tPair Coplanarity       :: %3.0f Degrees    [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_COPLANARITY_HIGH), pairCutsEnabled[i][6]);
+            System.out.printf("\tPair Time Coincidence  :: %2.0f ns          [%5b]%n",
+                    pairsTrigger[i].getCutValue(TriggerModule.PAIR_TIME_COINCIDENCE), true);
+            System.out.println();
+        }
+    }
+    
+    /**
+     * Summarizes the global run statistics in a log to the terminal.
+     */
+    private void logStatistics() {
+        // Print the cluster/trigger verification header.
+        System.out.println();
+        System.out.println();
+        System.out.println("======================================================================");
+        System.out.println("=== Cluster/Trigger Verification Results =============================");
+        System.out.println("======================================================================");
+        
+        // Print the general event failure rate.
+        int headSpaces = getPrintSpaces(globalStats.getEventCount());
+        System.out.println("General Event Statistics:");
+        System.out.printf("\tEvent Start Time      :: %.3f s%n", (startTime / Math.pow(10, 9)));
+        System.out.printf("\tEvent End Time        :: %.3f%n", (endTime / Math.pow(10, 9)));
+        System.out.printf("\tEvent Run Time        :: %.3f%n", ((endTime - startTime) / Math.pow(10, 9)));
+        System.out.printf("\tNoise Events          :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
+                globalStats.getNoiseEvents(), globalStats.getEventCount(), (100.0 * globalStats.getNoiseEvents() / globalStats.getEventCount()));
+        System.out.printf("\tCluster Events Failed :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
+                globalStats.getFailedClusterEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedClusterEventCount() / globalStats.getEventCount()));
+        System.out.printf("\tSingles Events Failed :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
+                globalStats.getFailedSinglesEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedSinglesEventCount() / globalStats.getEventCount()));
+        System.out.printf("\tPair Events Failed    :: %" + headSpaces + "d / %" + headSpaces + "d (%7.3f%%)%n",
+                globalStats.getFailedPairEventCount(), globalStats.getEventCount(), (100.0 * globalStats.getFailedPairEventCount() / globalStats.getEventCount()));
+        
+        // Print out how many events reported a given TI type, both in
+        // total and hierarchically.
+        System.out.println();
+        System.out.println("Event Triggering Type Verification:");
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Trigger", "Total", "Hierarchical");
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Pulser", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PULSER, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PULSER, true));
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Cosmic", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.COSMIC, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.COSMIC, true));
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Singles 1", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES0, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES0, true));
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Singles 2", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES1, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.SINGLES1, true));
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Pair 1", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR0, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR0, true));
+        System.out.printf("\t%15s\t%15s\t%15s%n", "Pair 2", globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR1, false),
+                globalStats.getTriggerStats().getTITriggers(TriggerDiagStats.PAIR1, true));
+        
+        // Print the cluster verification data.
+        System.out.println();
+        System.out.println("Cluster Verification:");
+        System.out.printf("\tRecon Clusters        :: %d%n", globalStats.getClusterStats().getReconClusterCount());
+        System.out.printf("\tSSP Clusters          :: %d%n", globalStats.getClusterStats().getSSPClusterCount());
+        System.out.printf("\tClusters Matched      :: %d%n", globalStats.getClusterStats().getMatches());
+        System.out.printf("\tFailed (Position)     :: %d%n", globalStats.getClusterStats().getPositionFailures());
+        System.out.printf("\tFailed (Energy)       :: %d%n", globalStats.getClusterStats().getEnergyFailures());
+        System.out.printf("\tFailed (Hit Count)    :: %d%n", globalStats.getClusterStats().getHitCountFailures());
+        if(globalStats.getClusterStats().getReconClusterCount() == 0) {
+            System.out.printf("\tCluster Efficiency    :: N/A%n");
+        } else {
+            System.out.printf("\tCluster Efficiency    :: %7.3f%%%n",
+                    100.0 * globalStats.getClusterStats().getMatches() / globalStats.getClusterStats().getReconClusterCount());
+        }
+        
+        // Print the trigger verification data.
+        for(int triggerType = 0; triggerType < 2; triggerType++) {
+            // Get the trigger data. Type 0 represents singles triggers.
+            TriggerEvent[] triggerData = new TriggerEvent[2];
+            if(triggerType == 0) {
+                triggerData[0] = globalStats.getTriggerStats().getSingles0Stats();
+                triggerData[1] = globalStats.getTriggerStats().getSingles1Stats();
+            } else {
+                triggerData[0] = globalStats.getTriggerStats().getPair0Stats();
+                triggerData[1] = globalStats.getTriggerStats().getPair1Stats();
+            }
+            
+            // Get the basic trigger data.
+            int sspSimTriggers = triggerData[0].getSSPSimulatedTriggers() + triggerData[1].getSSPSimulatedTriggers();
+            int reconSimTriggers = triggerData[0].getReconSimulatedTriggers() + triggerData[1].getReconSimulatedTriggers();
+            int sspReportedTriggers = triggerData[0].getReportedTriggers() + triggerData[1].getReportedTriggers();
+            int sspMatchedTriggers = triggerData[0].getMatchedSSPSimulatedTriggers() + triggerData[1].getMatchedSSPSimulatedTriggers();
+            int reconMatchedTriggers = triggerData[0].getMatchedReconSimulatedTriggers() + triggerData[1].getMatchedReconSimulatedTriggers();
+            
+            // Print the basic trigger statistics.
+            int spaces = getPrintSpaces(sspSimTriggers, reconSimTriggers, sspReportedTriggers);
+            System.out.println();
+            if(triggerType == 0) { System.out.println("Singles Trigger Verification:"); }
+            else { System.out.println("Pair Trigger Verification:"); }
+            System.out.printf("\tSSP Cluster Sim Triggers   :: %" + spaces + "d%n", sspSimTriggers);
+            System.out.printf("\tRecon Cluster Sim Triggers :: %" + spaces + "d%n", reconSimTriggers);
+            System.out.printf("\tSSP Reported Triggers      :: %" + spaces + "d%n", sspReportedTriggers);
+            
+            System.out.printf("\tInternal Efficiency        :: %" + spaces + "d / %" + spaces + "d ", sspMatchedTriggers, sspSimTriggers);
+            if(sspSimTriggers == 0) { System.out.printf("(N/A)%n"); }
+            else { System.out.printf("(%7.3f%%)%n", (100.0 * sspMatchedTriggers / sspSimTriggers)); }
+            
+            System.out.printf("\tTrigger Efficiency         :: %" + spaces + "d / %" + spaces + "d ", reconMatchedTriggers, reconSimTriggers);
+            if(reconSimTriggers == 0) { System.out.printf("(N/A)%n"); }
+            else { System.out.printf("(%7.3f%%)%n" , (100.0 * reconMatchedTriggers / reconSimTriggers)); }
+            
+            // Print the individual cut performances.
+            if(triggerType == 0) {
+                for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+                    // Get the appropriate trigger statistics module.
+                    TriggerEvent triggerStats;
+                    if(triggerNum == 0) { triggerStats = globalStats.getTriggerStats().getSingles0Stats(); }
+                    else { triggerStats = globalStats.getTriggerStats().getSingles1Stats(); }
+                    
+                    // Get the number of SSP triggers for this trigger number.
+                    int sspTriggerCount = triggerStats.getSSPSimulatedTriggers();
+                    //int sspTriggerCount = triggerRunStats[0].getTotalSSPTriggers(triggerNum);
+                
+                    System.out.println();
+                    System.out.printf("\tTrigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
+                    System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerStats.getUnmatchedSSPSimulatedTriggers());
+                    //System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerRunStats[0].getUnmatchedTriggers(triggerNum));
+                    if(sspTriggerCount == 0) {
+                        System.out.printf("\t\tCluster Energy Lower Bound :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(ENERGY_MIN), sspTriggerCount);
+                        System.out.printf("\t\tCluster Energy Upper Bound :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(ENERGY_MAX), sspTriggerCount);
+                        System.out.printf("\t\tCluster Hit Count          :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(HIT_COUNT), sspTriggerCount);
+                    } else {
+                        System.out.printf("\t\tCluster Energy Lower Bound :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(ENERGY_MIN), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(ENERGY_MIN) / sspTriggerCount));
+                        System.out.printf("\t\tCluster Energy Upper Bound :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(ENERGY_MAX), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(ENERGY_MAX) / sspTriggerCount));
+                        System.out.printf("\t\tCluster Hit Count          :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(HIT_COUNT), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(HIT_COUNT) / sspTriggerCount));
+                    }
+                }
+            } else {
+                for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+                    // Get the appropriate trigger statistics module.
+                    TriggerEvent triggerStats;
+                    if(triggerNum == 0) { triggerStats = globalStats.getTriggerStats().getPair0Stats(); }
+                    else { triggerStats = globalStats.getTriggerStats().getPair1Stats(); }
+                    
+                    // Get the number of SSP triggers for this trigger number.
+                    int sspTriggerCount = triggerStats.getSSPSimulatedTriggers();
+                    
+                    System.out.println();
+                    System.out.printf("\tTrigger %d Individual Cut Failure Rate:%n", (triggerNum + 1));
+                    System.out.printf("\t\tUmatched Triggers          :: %" + spaces + "d%n", triggerStats.getUnmatchedSSPSimulatedTriggers());
+                    if(sspTriggerCount == 0) {
+                        System.out.printf("\t\tPair Energy Sum            :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(ENERGY_SUM), sspTriggerCount);
+                        System.out.printf("\t\tPair Energy Difference     :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(ENERGY_DIFF), sspTriggerCount);
+                        System.out.printf("\t\tPair Energy Slope          :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount);
+                        System.out.printf("\t\tPair Coplanarity           :: %" + spaces + "d / %" + spaces + "d%n",
+                                triggerStats.getSSPCutFailures(COPLANARITY), sspTriggerCount);
+                    } else {
+                        System.out.printf("\t\tPair Energy Sum            :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(ENERGY_SUM), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(ENERGY_SUM) / sspTriggerCount));
+                        System.out.printf("\t\tPair Energy Difference     :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(ENERGY_DIFF), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(ENERGY_DIFF) / sspTriggerCount));
+                        System.out.printf("\t\tPair Energy Slope          :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(ENERGY_SLOPE), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(ENERGY_SLOPE) / sspTriggerCount));
+                        System.out.printf("\t\tPair Coplanarity           :: %" + spaces + "d / %" + spaces + "d (%7.3f%%)%n",
+                                triggerStats.getSSPCutFailures(COPLANARITY), sspTriggerCount,
+                                (100.0 * triggerStats.getSSPCutFailures(COPLANARITY) / sspTriggerCount));
+                    }
+                }
+            }
+        }
+        
+        // Print out the trigger efficiency table.
+        System.out.println();
+        globalStats.getTriggerStats().printEfficiencyTable();
+    }
+    
+    /**
+     * Checks whether all of the hits in a cluster are within the safe
+     * region of the FADC output window.
+     * @param reconCluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is safe and
+     * returns <code>false</code> otherwise.
+     */
+    private final boolean isVerifiable(Cluster reconCluster) {
+        return TriggerDiagnosticUtil.isVerifiable(reconCluster, nsa, nsb, windowWidth);
+    }
+    
+    /**
+     * Generates a <code>List</code> collection that contains a set
+     * of <code>ArrayList</code> collections representing a unique
+     * permutation of the entries in the argument.
+     * @param values - A collection of the entries to be permuted.
+     * @return Returns a list of lists representing the permutations.
+     */
+    private static final List<List<Pair<Cluster, SSPCluster>>> getPermutations(List<Cluster> reconClusters, List<SSPCluster> sspClusters) {
+        // Store the SSP cluster permutations.
+        List<List<SSPCluster>> permList = new ArrayList<List<SSPCluster>>();
+        
+        // Make sure that the two lists are the same size.
+        int reconSize = reconClusters.size();
+        int sspSize = sspClusters.size();
+        while(sspClusters.size() < reconClusters.size()) {
+            sspClusters.add(null);
+        }
+        while(reconClusters.size() < sspClusters.size()) {
+            reconClusters.add(null);
+        }
+        
+        // Get the SSP cluster permutations.
+        permute(new ArrayList<SSPCluster>(0), sspClusters, permList);
+        
+        // Create pairs from the permutations.
+        List<List<Pair<Cluster, SSPCluster>>> pairList = new ArrayList<List<Pair<Cluster, SSPCluster>>>();
+        for(List<SSPCluster> permutation : permList) {
+            List<Pair<Cluster, SSPCluster>> pairs = new ArrayList<Pair<Cluster, SSPCluster>>(reconClusters.size());
+            
+            for(int clusterIndex = 0; (clusterIndex < reconClusters.size() && clusterIndex < permutation.size()); clusterIndex++) {
+                pairs.add(new Pair<Cluster, SSPCluster>(reconClusters.get(clusterIndex), permutation.get(clusterIndex)));
+            }
+            
+            pairList.add(pairs);
+        }
+        
+        // Remove the extra values.
+        for(int i = sspClusters.size() - 1; i >= sspSize; i--) { sspClusters.remove(i); }
+        for(int i = reconClusters.size() - 1; i >= reconSize; i--) { reconClusters.remove(i); }
+        
+        // Return the pairs.
+        return pairList;
+    }
+    
+    /**
+     * Recursive method for permuting all entries in the argument
+     * collection <code>remainingValues</code> into the argument
+     * <code>permutedValues</code> values. Completed permutations are
+     * placed in the argument <code>permList</code>.
+     * @param permutedValues - List to store entries that have already
+     * been permuted.
+     * @param remainingValues - List to store  entries that need to be
+     * permuted.
+     * @param permList - List to store completed permutations.
+     */
+    private static final void permute(List<SSPCluster> permutedValues, List<SSPCluster> remainingValues, List<List<SSPCluster>> permList) {
+        // If the list of entries that still need to be sorted is empty,
+        // then there is nothing to sort. Just return and empty list.
+        if(remainingValues.isEmpty()) { return; }
+        
+        // If there is only one value left in the list of entries that
+        // still need to be sorted, then just add it to the permutation
+        // list and return it.
+        else if(remainingValues.size() <= 1) {
+            // Add the last entry.
+            permutedValues.add(remainingValues.get(0));
+            
+            // Add the permutation to the list of completed permutations.
+            permList.add(permutedValues);
+        }
+        
+        // Otherwise, continue to get all possible permutations.
+        else {
+            // Iterate over the entries that have not been permuted.
+            for(int i = 0; i < remainingValues.size(); i++) {
+                // Make new lists to contain the permutations.
+                List<SSPCluster> newPermList = new ArrayList<SSPCluster>(permutedValues.size() + 1);
+                List<SSPCluster> newRemainList = new ArrayList<SSPCluster>(remainingValues.size());
+                
+                // Copy the current permuted entries to the new list
+                // and one value from the list of entries that have
+                // not been permuted yet.
+                newPermList.addAll(permutedValues);
+                newPermList.add(remainingValues.get(i));
+                
+                // The new list of entries that have not been permuted
+                // should be identical, except it should now be missing
+                // the entry that was moved.
+                for(int index = 0; index < remainingValues.size(); index++) {
+                    if(index != i) { newRemainList.add(remainingValues.get(index)); }
+                }
+                
+                // Repeat the process with the new lists.
+                permute(newPermList, newRemainList, permList);
+            }
+        }
+    }
+    
+    /**
+     * Compares two cluster matching events and finds the one that has
+     * the better results. Note that this will only return results that
+     * make sense if both of the events represent different permutations
+     * of the same set of clusters. Comparing events with different sets
+     * of clusters will produce meaningless results.
+     * @param firstEvent - The first cluster matching event,
+     * @param secondEvent - The second cluster matching event.
+     * @return Returns the cluster matching event that is better.
+     */
+    private static final DetailedClusterEvent getBestPermutation(DetailedClusterEvent firstEvent, DetailedClusterEvent secondEvent) {
+        // If both permutations are null, return that.
+        if(firstEvent == null && secondEvent == null) {
+            return null;
+        }
+        
+        // If one permutation is null, it is not the best.
+        if(firstEvent == null) { return secondEvent; }
+        else if(secondEvent == null) { return firstEvent; }
+        
+        // A permutation is better if it has more matches.
+        if(firstEvent.getMatches() > secondEvent.getMatches()) { return firstEvent; }
+        else if(secondEvent.getMatches() > firstEvent.getMatches()) { return secondEvent; }
+        
+        // Otherwise, the permutation with the least energy failures is
+        // the better permutation.
+        if(firstEvent.getEnergyFailures() < secondEvent.getEnergyFailures()) { return firstEvent; }
+        else if(secondEvent.getEnergyFailures() < firstEvent.getEnergyFailures()) { return secondEvent; }
+        
+        // If both these values are the same, then the events are identical.
+        return firstEvent;
+    }
+    
+    /**
+     * Determines the number of spaces needed to render the longest of
+     * a series of integers as a string.
+     * @param vals - The series of integers.
+     * @return Returns the number of spaces needed to render the longest
+     * integer as a base-10 string.
+     */
+    private static final int getPrintSpaces(int... vals) {
+        // Track the largest value.
+        int largest = 0;
+        
+        // Iterate over the arguments and find the largest.
+        for(int val : vals) {
+            // Get the length of the string.
+            int length = TriggerDiagnosticUtil.getDigits(val);
+            
+            // If it is larger, track it.
+            if(length > largest) { largest = length; }
+        }
+        
+        // Return the longer one.
+        return largest;
+    }
+    
+    /**
+     * Gets the position of the source of a <code>Trigger</code> object
+     * as text. This method only supports trigger sources of the types
+     * <code>SSPCluster</code>, <code>Cluster</code>, and arrays of size
+     * two of either type.
+     * @param trigger - The trigger from which to obtain the source.
+     * @return Returns the source of the trigger as a <code>String</code>
+     * object.
+     * @throws IllegalArgumentException Occurs if the source of the
+     * trigger is not any of the supported types.
+     */
+    private static final String triggerPositionString(Trigger<?> trigger) throws IllegalArgumentException {
+        // Get the trigger source.
+        Object source = trigger.getTriggerSource();
+        
+        // Handle valid trigger sources.
+        if(source instanceof SSPCluster) {
+            return TriggerDiagnosticUtil.clusterPositionString((SSPCluster) source);
+        } else if(source instanceof Cluster) {
+            return TriggerDiagnosticUtil.clusterPositionString((Cluster) source);
+        } else if(source instanceof SSPCluster[]) {
+            SSPCluster[] sourcePair = (SSPCluster[]) source;
+            if(sourcePair.length == 2) {
+                return String.format("%s, %s", TriggerDiagnosticUtil.clusterPositionString(sourcePair[0]),
+                        TriggerDiagnosticUtil.clusterPositionString(sourcePair[1]));
+            }
+        } else if(source instanceof Cluster[]) {
+            Cluster[] sourcePair = (Cluster[]) source;
+            if(sourcePair.length == 2) {
+                return String.format("%s, %s", TriggerDiagnosticUtil.clusterPositionString(sourcePair[0]),
+                        TriggerDiagnosticUtil.clusterPositionString(sourcePair[1]));
+            }
+        }
+        
+        // Otherwise, the source type is unrecognized. Throw an error.
+        throw new IllegalArgumentException(String.format("Trigger source type \"%s\" is not supported.",
+                trigger.getTriggerSource().getClass().getSimpleName()));
+    }
+    
+    /**
+     * Gets the time of a simulated trigger object. Method supports
+     * triggers with source objects of type <code>SSPCluster</code>,
+     * <code>Cluster</code>, and arrays of size two composed of either
+     * object type.
+     * @param trigger - The trigger.
+     * @return Returns the time at which the trigger occurred.
+     * @throws IllegalArgumentException Occurs if the trigger source
+     * is not a supported type.
+     */
+    private static final double getTriggerTime(Trigger<?> trigger) throws IllegalArgumentException {
+        // Get the trigger source.
+        Object source = trigger.getTriggerSource();
+        
+        // Get the trigger time for supported trigger types.
+        if(source instanceof SSPCluster) {
+            return ((SSPCluster) source).getTime();
+        } else if(source instanceof Cluster) {
+            return TriggerDiagnosticUtil.getClusterTime((Cluster) source);
+        } else if(source instanceof SSPCluster[]) {
+            // Get the pair.
+            SSPCluster[] sourcePair = (SSPCluster[]) source;
+            
+            // Get the time of the bottom cluster.
+            if(sourcePair.length == 2) {
+                if(sourcePair[0].getYIndex() < 0) { return sourcePair[0].getTime(); }
+                else if(sourcePair[1].getYIndex() < 0) { return sourcePair[1].getTime(); }
+                else { throw new IllegalArgumentException("Cluster pairs must be formed of a top/bottom pair."); }
+            }
+            else { throw new IllegalArgumentException("Cluster pairs must be of size 2."); }
+        } else if(source instanceof Cluster[]) {
+            // Get the pair.
+            Cluster[] sourcePair = (Cluster[]) source;
+            int[] iy = {
+                TriggerDiagnosticUtil.getYIndex(sourcePair[0]),
+                TriggerDiagnosticUtil.getYIndex(sourcePair[1])
+            };
+            
+            // Get the time of the bottom cluster.
+            if(sourcePair.length == 2) {
+                if(iy[0] < 0) { return TriggerDiagnosticUtil.getClusterTime(sourcePair[0]); }
+                else if(iy[1] < 0) { return TriggerDiagnosticUtil.getClusterTime(sourcePair[1]); }
+                else { throw new IllegalArgumentException("Cluster pairs must be formed of a top/bottom pair."); }
+            }
+            else { throw new IllegalArgumentException("Cluster pairs must be of size 2."); }
+        }
+        
+        // If the source type is unrecognized, throw an exception.
+        throw new IllegalArgumentException(String.format("Trigger source type \"%\" is not supported.",
+                source.getClass().getSimpleName()));
+    }
+    
+    /**
+     * Checks if a simulated trigger and an SSP trigger match. Note
+     * that only certain types can be compared. These are:
+     * <ul><li><code>SinglesTrigger<?> --> SSPSinglesTrigger</code></li>
+     * <li><code>PairTrigger<?> --> SSPPairTrigger</code></li></ul>
+     * @param simTrigger - The simulated trigger.
+     * @param sspTrigger - The SSP bank trigger.
+     * @return Returns an array of <code>boolean</code> primitives that
+     * indicate which cuts passed and which failed.
+     */
+    private static final boolean[] triggerCutMatch(Trigger<?> simTrigger, SSPTrigger sspTrigger) {
+        // Check that the cuts match for supported trigger types.
+        if(simTrigger instanceof SinglesTrigger && sspTrigger instanceof SSPSinglesTrigger) {
+            // Create an array to store the cut checks.
+            boolean[] cutMatch = new boolean[3];
+            
+            // Cast the triggers.
+            SinglesTrigger<?> simSingles = (SinglesTrigger<?>) simTrigger;
+            SSPSinglesTrigger sspSingles = (SSPSinglesTrigger) sspTrigger;
+            
+            // Perform the check.
+            cutMatch[ENERGY_MIN] = (simSingles.getStateClusterEnergyLow()  == sspSingles.passCutEnergyMin());
+            cutMatch[ENERGY_MAX] = (simSingles.getStateClusterEnergyHigh() == sspSingles.passCutEnergyMax());
+            cutMatch[HIT_COUNT] = (simSingles.getStateHitCount()          == sspSingles.passCutHitCount());
+            
+            // Return the match array.
+            return cutMatch;
+        } else if(simTrigger instanceof PairTrigger && sspTrigger instanceof SSPPairTrigger) {
+            // Create an array to store the cut checks.
+            boolean[] cutMatch = new boolean[4];
+            
+            // Cast the triggers.
+            PairTrigger<?> simPair = (PairTrigger<?>) simTrigger;
+            SSPPairTrigger sspPair = (SSPPairTrigger) sspTrigger;
+            
+            // Perform the check.
+            cutMatch[ENERGY_SUM] = (simPair.getStateEnergySum()        == sspPair.passCutEnergySum());
+            cutMatch[ENERGY_DIFF] = (simPair.getStateEnergyDifference() == sspPair.passCutEnergyDifference());
+            cutMatch[ENERGY_SLOPE] = (simPair.getStateEnergySlope()      == sspPair.passCutEnergySlope());
+            cutMatch[COPLANARITY] = (simPair.getStateCoplanarity()      == sspPair.passCutCoplanarity());
+            
+            // Return the match array.
+            return cutMatch;
+        }
+        
+        // If this point is reached, the triggers are not of a supported
+        // type for cut comparison. Produce an exception.
+        throw new IllegalArgumentException(String.format("Triggers of type \"%s\" can not be cut-matched with triggers of type \"%s\".",
+                simTrigger.getClass().getSimpleName(), sspTrigger.getClass().getSimpleName()));
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerTurnOnDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerTurnOnDriver.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/TriggerTurnOnDriver.java	Wed Apr 27 11:11:32 2016
@@ -70,9 +70,9 @@
     public TriggerTurnOnDriver() {
     }
     
-	public void setShowPlots(boolean showPlots) {
-		this.showPlots = showPlots;
-	}
+    public void setShowPlots(boolean showPlots) {
+        this.showPlots = showPlots;
+    }
 
     @Override
     protected void detectorChanged(Detector detector) {

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterEvent.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterEvent.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterEvent.java	Wed Apr 27 11:11:32 2016
@@ -9,104 +9,104 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ClusterEvent extends ClusterStatModule {
-	/**
-	 * Fuses another <code>ClusterEvent</code> with this object. The
-	 * other event's cluster pairs and states will be added to those
-	 * already in this event.
-	 * @param event - The event to fuse.
-	 */
-	public void addEvent(ClusterEvent event) {
-		// If the event is null, do nothing.
-		if(event == null) { return; }
-		
-		// Add the values stored in the argument event to the counters
-		// in this event.
-		sspClusters   += event.sspClusters;
-		reconClusters += event.reconClusters;
-		matches       += event.matches;
-		failEnergy    += event.failEnergy;
-		failPosition  += event.failPosition;
-		failHitCount  += event.failHitCount;
-	}
-	
-	/**
-	 * Indicates whether at least one cluster pair in the event created
-	 * a fail state.
-	 * @return Returns <code>true</code> if not all clusters matched and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean isFailState() {
-		return (failEnergy > 0) || (failHitCount > 0) || (failTime > 0) || (failPosition > 0);
-	}
-	
-	/**
-	 * Notes that a reconstructed cluster and SSP cluster pair failed
-	 * due to energy.
-	 */
-	public void pairFailEnergy() {
-		failEnergy++;
-	}
-	
-	/**
-	 * Notes that a reconstructed cluster and SSP cluster pair failed
-	 * due to hit count.
-	 */
-	public void pairFailHitCount() {
-		failHitCount++;
-	}
-	
-	/**
-	 * Notes that a reconstructed cluster and SSP cluster pair failed
-	 * due to position.
-	 */
-	public void pairFailPosition() {
-		failPosition++;
-	}
-	
-	/**
-	 * Notes that one or more reconstructed cluster and SSP cluster pair
-	 * failed due to position.
-	 * @param count - The number of events that failed in this manner.
-	 */
-	public void pairFailPosition(int count) {
-		// negative values are non-physical.
-		if(count < 0) {
-			throw new IllegalArgumentException("Cluster failure counts must be non-negative.");
-		}
-		
-		// Increment the count.
-		failPosition += count;
-	}
-	
-	/**
-	 * Notes that a reconstructed cluster and SSP cluster pair failed
-	 * due to time.
-	 */
-	public void pairFailTime() {
-		failTime++;
-	}
-	
-	/**
-	 * Notes that a reconstructed cluster and SSP cluster pair was
-	 * successfully matched.
-	 */
-	public void pairMatch() {
-		matches++;
-	}
-	
-	/**
-	 * Increments the number of reconstructed FADC clusters seen.
-	 * @param count - The number of clusters seen.
-	 */
-	public void sawReconClusters(int count) {
-		reconClusters += count;
-	}
-	
-	/**
-	 * Increments the number of SSP bank clusters seen.
-	 * @param count - The number of clusters seen.
-	 */
-	public void sawSSPClusters(int count) {
-		sspClusters += count;
-	}
+    /**
+     * Fuses another <code>ClusterEvent</code> with this object. The
+     * other event's cluster pairs and states will be added to those
+     * already in this event.
+     * @param event - The event to fuse.
+     */
+    public void addEvent(ClusterEvent event) {
+        // If the event is null, do nothing.
+        if(event == null) { return; }
+        
+        // Add the values stored in the argument event to the counters
+        // in this event.
+        sspClusters   += event.sspClusters;
+        reconClusters += event.reconClusters;
+        matches       += event.matches;
+        failEnergy    += event.failEnergy;
+        failPosition  += event.failPosition;
+        failHitCount  += event.failHitCount;
+    }
+    
+    /**
+     * Indicates whether at least one cluster pair in the event created
+     * a fail state.
+     * @return Returns <code>true</code> if not all clusters matched and
+     * <code>false</code> otherwise.
+     */
+    public boolean isFailState() {
+        return (failEnergy > 0) || (failHitCount > 0) || (failTime > 0) || (failPosition > 0);
+    }
+    
+    /**
+     * Notes that a reconstructed cluster and SSP cluster pair failed
+     * due to energy.
+     */
+    public void pairFailEnergy() {
+        failEnergy++;
+    }
+    
+    /**
+     * Notes that a reconstructed cluster and SSP cluster pair failed
+     * due to hit count.
+     */
+    public void pairFailHitCount() {
+        failHitCount++;
+    }
+    
+    /**
+     * Notes that a reconstructed cluster and SSP cluster pair failed
+     * due to position.
+     */
+    public void pairFailPosition() {
+        failPosition++;
+    }
+    
+    /**
+     * Notes that one or more reconstructed cluster and SSP cluster pair
+     * failed due to position.
+     * @param count - The number of events that failed in this manner.
+     */
+    public void pairFailPosition(int count) {
+        // negative values are non-physical.
+        if(count < 0) {
+            throw new IllegalArgumentException("Cluster failure counts must be non-negative.");
+        }
+        
+        // Increment the count.
+        failPosition += count;
+    }
+    
+    /**
+     * Notes that a reconstructed cluster and SSP cluster pair failed
+     * due to time.
+     */
+    public void pairFailTime() {
+        failTime++;
+    }
+    
+    /**
+     * Notes that a reconstructed cluster and SSP cluster pair was
+     * successfully matched.
+     */
+    public void pairMatch() {
+        matches++;
+    }
+    
+    /**
+     * Increments the number of reconstructed FADC clusters seen.
+     * @param count - The number of clusters seen.
+     */
+    public void sawReconClusters(int count) {
+        reconClusters += count;
+    }
+    
+    /**
+     * Increments the number of SSP bank clusters seen.
+     * @param count - The number of clusters seen.
+     */
+    public void sawSSPClusters(int count) {
+        sspClusters += count;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterMatchedPair.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterMatchedPair.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterMatchedPair.java	Wed Apr 27 11:11:32 2016
@@ -14,114 +14,114 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ClusterMatchedPair extends Pair<Cluster, SSPCluster> {
-	// CLass variables.
-	private final byte state;
-	
-	/**
-	 * Instantiates a new <code>ClusterMatchedPair</code> object from
-	 * the two indicated clusters and marks their match state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 * @param state - The pair match state.
-	 */
-	public ClusterMatchedPair(Cluster reconCluster, SSPCluster sspCluster, byte state) {
-		// Set the cluster pairs.
-		super(reconCluster, sspCluster);
-		
-		// If the state is defined, set it. Otherwise, it is unknown.
-		if(state == TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED
-				|| state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION
-				|| state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY
-				|| state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT) {
-			this.state = state;
-		} else {
-			this.state = TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_UNKNOWN;
-		}
-	}
-	
-	/**
-	 * Gets the reconstructed cluster of the pair.
-	 * @return Returns the reconstructed cluster a <code>Cluster</cod>
-	 * object.
-	 */
-	public Cluster getReconstructedCluster() {
-		return getFirstElement();
-	}
-	
-	/**
-	 * Gets the SSP cluster of the pair.
-	 * @return Returns the SSP cluster as an <code>SSPCluster</code>
-	 * object.
-	 */
-	public SSPCluster getSSPCluster() {
-		return getSecondElement();
-	}
-	
-	/**
-	 * Gets the raw state identifier.
-	 * @return Returns the state identifier as a <code>byte</code>
-	 * primitive. Valid identifiers are defined in the class
-	 * <code>TriggerDiagnosticUtil</code>.
-	 */
-	public byte getState() {
-		return state;
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair failed to not being close
-	 * enough in energy.
-	 * @return Returns <code>true</code> if the pair match state is an
-	 * energy fail state and <code>false</code> otherwise.
-	 */
-	public boolean isEnergyFailState() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY);
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair failed to match due to not
-	 * being close enough in hit count.
-	 * @return Returns <code>true</code> if the pair match state is a
-	 * hit count fail state and <code>false</code> otherwise.
-	 */
-	public boolean isHitCountFailState() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT);
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair matched.
-	 * @return Returns <code>true</code> if the pair match state is a
-	 * match state and <code>false</code> otherwise.
-	 */
-	public boolean isMatch() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED);
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair failed to match due to the
-	 * cluster positions not aligning.
-	 * @return Returns <code>true</code> if the pair match state is a
-	 * position fail state and <code>false</code> otherwise.
-	 */
-	public boolean isPositionFailState() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION);
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair failed to match due to the
-	 * cluster time-stamps not aligning.
-	 * @return Returns <code>true</code> if the pair match state is a
-	 * time fail state and <code>false</code> otherwise.
-	 */
-	public boolean isTimeFailState() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_TIME);
-	}
-	
-	/**
-	 * Indicates whether the recon/SSP pair has no known match state.
-	 * @return Returns <code>true</code> if the pair match state is
-	 * unknown and <code>false</code> otherwise.
-	 */
-	public boolean isUnknownState() {
-		return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_UNKNOWN);
-	}
+    // CLass variables.
+    private final byte state;
+    
+    /**
+     * Instantiates a new <code>ClusterMatchedPair</code> object from
+     * the two indicated clusters and marks their match state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     * @param state - The pair match state.
+     */
+    public ClusterMatchedPair(Cluster reconCluster, SSPCluster sspCluster, byte state) {
+        // Set the cluster pairs.
+        super(reconCluster, sspCluster);
+        
+        // If the state is defined, set it. Otherwise, it is unknown.
+        if(state == TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED
+                || state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION
+                || state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY
+                || state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT) {
+            this.state = state;
+        } else {
+            this.state = TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_UNKNOWN;
+        }
+    }
+    
+    /**
+     * Gets the reconstructed cluster of the pair.
+     * @return Returns the reconstructed cluster a <code>Cluster</cod>
+     * object.
+     */
+    public Cluster getReconstructedCluster() {
+        return getFirstElement();
+    }
+    
+    /**
+     * Gets the SSP cluster of the pair.
+     * @return Returns the SSP cluster as an <code>SSPCluster</code>
+     * object.
+     */
+    public SSPCluster getSSPCluster() {
+        return getSecondElement();
+    }
+    
+    /**
+     * Gets the raw state identifier.
+     * @return Returns the state identifier as a <code>byte</code>
+     * primitive. Valid identifiers are defined in the class
+     * <code>TriggerDiagnosticUtil</code>.
+     */
+    public byte getState() {
+        return state;
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair failed to not being close
+     * enough in energy.
+     * @return Returns <code>true</code> if the pair match state is an
+     * energy fail state and <code>false</code> otherwise.
+     */
+    public boolean isEnergyFailState() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY);
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair failed to match due to not
+     * being close enough in hit count.
+     * @return Returns <code>true</code> if the pair match state is a
+     * hit count fail state and <code>false</code> otherwise.
+     */
+    public boolean isHitCountFailState() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT);
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair matched.
+     * @return Returns <code>true</code> if the pair match state is a
+     * match state and <code>false</code> otherwise.
+     */
+    public boolean isMatch() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED);
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair failed to match due to the
+     * cluster positions not aligning.
+     * @return Returns <code>true</code> if the pair match state is a
+     * position fail state and <code>false</code> otherwise.
+     */
+    public boolean isPositionFailState() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION);
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair failed to match due to the
+     * cluster time-stamps not aligning.
+     * @return Returns <code>true</code> if the pair match state is a
+     * time fail state and <code>false</code> otherwise.
+     */
+    public boolean isTimeFailState() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_TIME);
+    }
+    
+    /**
+     * Indicates whether the recon/SSP pair has no known match state.
+     * @return Returns <code>true</code> if the pair match state is
+     * unknown and <code>false</code> otherwise.
+     */
+    public boolean isUnknownState() {
+        return (state == TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_UNKNOWN);
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterStatModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterStatModule.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/ClusterStatModule.java	Wed Apr 27 11:11:32 2016
@@ -7,100 +7,100 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ClusterStatModule {
-	// Track cluster statistics.
-	protected int sspClusters   = 0;
-	protected int reconClusters = 0;
-	protected int matches       = 0;
-	protected int failEnergy    = 0;
-	protected int failPosition  = 0;
-	protected int failHitCount  = 0;
-	protected int failTime      = 0;
-	
-	/**
-	 * Instantiates a <code>ClusterStatModule</code> with no statistics
-	 * stored.
-	 */
-	ClusterStatModule() {  }
-	
-	/**
-	 * Clears all statistical information and resets the object of its
-	 * default, empty state.
-	 */
-	void clear() {
-		sspClusters   = 0;
-		reconClusters = 0;
-		matches       = 0;
-		failEnergy    = 0;
-		failPosition  = 0;
-		failHitCount  = 0;
-		failTime      = 0;
-	}
-	
-	@Override
-	public ClusterStatModule clone() {
-		// Create a clone.
-		ClusterStatModule clone = new ClusterStatModule();
-		
-		// Copy the statistical values to the clone.
-		clone.sspClusters   = sspClusters;
-		clone.reconClusters = reconClusters;
-		clone.matches       = matches;
-		clone.failEnergy    = failEnergy;
-		clone.failPosition  = failPosition;
-		clone.failHitCount  = failHitCount;
-		clone.failTime      = failTime;
-		
-		// Return the clone.
-		return clone;
-	}
-	
-	/**
-	 * Gets the number of cluster pairs stored in this event that are
-	 * marked with energy fail states.
-	 * @return Returns the number of instances of this state as an
-	 * <code>int</code> primitive.
-	 */
-	public int getEnergyFailures() {
-		return failEnergy;
-	}
-	
-	/**
-	 * Gets the number of cluster pairs stored in this event that are
-	 * marked with hit count fail states.
-	 * @return Returns the number of instances of this state as an
-	 * <code>int</code> primitive.
-	 */
-	public int getHitCountFailures() {
-		return failHitCount;
-	}
-	
-	/**
-	 * Gets the number of cluster pairs stored in this event that are
-	 * marked with position fail states.
-	 * @return Returns the number of instances of this state as an
-	 * <code>int</code> primitive.
-	 */
-	public int getMatches() {
-		return matches;
-	}
-	
-	/**
-	 * Gets the number of cluster pairs stored in this event that are
-	 * marked with position fail states.
-	 * @return Returns the number of instances of this state as an
-	 * <code>int</code> primitive.
-	 */
-	public int getPositionFailures() {
-		return failPosition;
-	}
-	
-	/**
-	 * Gets the total number of verifiable reconstructed clusters seen.
+    // Track cluster statistics.
+    protected int sspClusters   = 0;
+    protected int reconClusters = 0;
+    protected int matches       = 0;
+    protected int failEnergy    = 0;
+    protected int failPosition  = 0;
+    protected int failHitCount  = 0;
+    protected int failTime      = 0;
+    
+    /**
+     * Instantiates a <code>ClusterStatModule</code> with no statistics
+     * stored.
+     */
+    ClusterStatModule() {  }
+    
+    /**
+     * Clears all statistical information and resets the object of its
+     * default, empty state.
+     */
+    void clear() {
+        sspClusters   = 0;
+        reconClusters = 0;
+        matches       = 0;
+        failEnergy    = 0;
+        failPosition  = 0;
+        failHitCount  = 0;
+        failTime      = 0;
+    }
+    
+    @Override
+    public ClusterStatModule clone() {
+        // Create a clone.
+        ClusterStatModule clone = new ClusterStatModule();
+        
+        // Copy the statistical values to the clone.
+        clone.sspClusters   = sspClusters;
+        clone.reconClusters = reconClusters;
+        clone.matches       = matches;
+        clone.failEnergy    = failEnergy;
+        clone.failPosition  = failPosition;
+        clone.failHitCount  = failHitCount;
+        clone.failTime      = failTime;
+        
+        // Return the clone.
+        return clone;
+    }
+    
+    /**
+     * Gets the number of cluster pairs stored in this event that are
+     * marked with energy fail states.
+     * @return Returns the number of instances of this state as an
+     * <code>int</code> primitive.
+     */
+    public int getEnergyFailures() {
+        return failEnergy;
+    }
+    
+    /**
+     * Gets the number of cluster pairs stored in this event that are
+     * marked with hit count fail states.
+     * @return Returns the number of instances of this state as an
+     * <code>int</code> primitive.
+     */
+    public int getHitCountFailures() {
+        return failHitCount;
+    }
+    
+    /**
+     * Gets the number of cluster pairs stored in this event that are
+     * marked with position fail states.
+     * @return Returns the number of instances of this state as an
+     * <code>int</code> primitive.
+     */
+    public int getMatches() {
+        return matches;
+    }
+    
+    /**
+     * Gets the number of cluster pairs stored in this event that are
+     * marked with position fail states.
+     * @return Returns the number of instances of this state as an
+     * <code>int</code> primitive.
+     */
+    public int getPositionFailures() {
+        return failPosition;
+    }
+    
+    /**
+     * Gets the total number of verifiable reconstructed clusters seen.
      * @return Returns the cluster count as an <code>int</code>
      * primitive.
-	 */
+     */
     public int getReconClusterCount() {
-    	return reconClusters;
+        return reconClusters;
     }
     
     /**
@@ -109,16 +109,16 @@
      * primitive.
      */
     public int getSSPClusterCount() {
-    	return sspClusters;
+        return sspClusters;
     }
-	
-	/**
-	 * Gets the number of cluster pairs stored in this event that are
-	 * marked with time fail states.
-	 * @return Returns the number of instances of this state as an
-	 * <code>int</code> primitive.
-	 */
-	public int getTimeFailures() {
-		return failTime;
-	}
+    
+    /**
+     * Gets the number of cluster pairs stored in this event that are
+     * marked with time fail states.
+     * @return Returns the number of instances of this state as an
+     * <code>int</code> primitive.
+     */
+    public int getTimeFailures() {
+        return failTime;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DetailedClusterEvent.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DetailedClusterEvent.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DetailedClusterEvent.java	Wed Apr 27 11:11:32 2016
@@ -8,89 +8,89 @@
 import org.lcsim.event.Cluster;
 
 public class DetailedClusterEvent extends ClusterEvent {
-	// Store all of the pairs.
-	private List<ClusterMatchedPair> pairList = new ArrayList<ClusterMatchedPair>();
-	
-	/**
-	 * Fuses another <code>ClusterEvent</code> with this object. The
-	 * other event's cluster pairs and states will be added to those
-	 * already in this event.
-	 * @param event - The event to fuse.
-	 */
-	public void addEvent(ClusterEvent event) {
-		// Run the superclass method.
-		super.addEvent(event);
-		
-		// If the event is null, do nothing.
-		if(event == null) { return; }
-		
-		// Merge the list of cluster pairs, if applicable.
-		if(event instanceof DetailedClusterEvent) {
-			pairList.addAll(((DetailedClusterEvent) event).pairList);
-		}
-	}
-	
-	/**
-	 * Adds a reconstructed/SSP cluster pair and marks it as having an
-	 * energy fail state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 */
-	public void pairFailEnergy(Cluster reconCluster, SSPCluster sspCluster) {
-		pairFailEnergy();
-		pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY));
-	}
-	
-	/**
-	 * Adds a reconstructed/SSP cluster pair and marks it as having a
-	 * hit count fail state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 */
-	public void pairFailHitCount(Cluster reconCluster, SSPCluster sspCluster) {
-		pairFailHitCount();
-		pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT));
-	}
-	
-	/**
-	 * Adds a reconstructed/SSP cluster pair and marks it as having a
-	 * position fail state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 */
-	public void pairFailPosition(Cluster reconCluster, SSPCluster sspCluster) {
-		pairFailPosition();
-		pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION));
-	}
-	
-	/**
-	 * Adds a reconstructed/SSP cluster pair and marks it as having a
-	 * time fail state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 */
-	public void pairFailTime(Cluster reconCluster, SSPCluster sspCluster) {
-		pairFailTime();
-		pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_TIME));
-	}
-	
-	/**
-	 * Adds a reconstructed/SSP cluster pair and marks it as having a
-	 * match state.
-	 * @param reconCluster - The reconstructed cluster.
-	 * @param sspCluster - The SSP cluster.
-	 */
-	public void pairMatch(Cluster reconCluster, SSPCluster sspCluster) {
-		pairMatch();
-		pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED));
-	}
-	
-	/**
-	 * Gets a list of all matched cluster pairs and their match states.
-	 * @return Returns the matched cluster pairs as a <code>List</code>
-	 * of <code>ClusterMatchedPair</code> objects.
-	 */
-	public List<ClusterMatchedPair> getClusterPairs() {
-		return pairList;
-	}
+    // Store all of the pairs.
+    private List<ClusterMatchedPair> pairList = new ArrayList<ClusterMatchedPair>();
+    
+    /**
+     * Fuses another <code>ClusterEvent</code> with this object. The
+     * other event's cluster pairs and states will be added to those
+     * already in this event.
+     * @param event - The event to fuse.
+     */
+    public void addEvent(ClusterEvent event) {
+        // Run the superclass method.
+        super.addEvent(event);
+        
+        // If the event is null, do nothing.
+        if(event == null) { return; }
+        
+        // Merge the list of cluster pairs, if applicable.
+        if(event instanceof DetailedClusterEvent) {
+            pairList.addAll(((DetailedClusterEvent) event).pairList);
+        }
+    }
+    
+    /**
+     * Adds a reconstructed/SSP cluster pair and marks it as having an
+     * energy fail state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     */
+    public void pairFailEnergy(Cluster reconCluster, SSPCluster sspCluster) {
+        pairFailEnergy();
+        pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_ENERGY));
+    }
+    
+    /**
+     * Adds a reconstructed/SSP cluster pair and marks it as having a
+     * hit count fail state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     */
+    public void pairFailHitCount(Cluster reconCluster, SSPCluster sspCluster) {
+        pairFailHitCount();
+        pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_HIT_COUNT));
+    }
+    
+    /**
+     * Adds a reconstructed/SSP cluster pair and marks it as having a
+     * position fail state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     */
+    public void pairFailPosition(Cluster reconCluster, SSPCluster sspCluster) {
+        pairFailPosition();
+        pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_POSITION));
+    }
+    
+    /**
+     * Adds a reconstructed/SSP cluster pair and marks it as having a
+     * time fail state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     */
+    public void pairFailTime(Cluster reconCluster, SSPCluster sspCluster) {
+        pairFailTime();
+        pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_FAIL_TIME));
+    }
+    
+    /**
+     * Adds a reconstructed/SSP cluster pair and marks it as having a
+     * match state.
+     * @param reconCluster - The reconstructed cluster.
+     * @param sspCluster - The SSP cluster.
+     */
+    public void pairMatch(Cluster reconCluster, SSPCluster sspCluster) {
+        pairMatch();
+        pairList.add(new ClusterMatchedPair(reconCluster, sspCluster, TriggerDiagnosticUtil.CLUSTER_STATE_MATCHED));
+    }
+    
+    /**
+     * Gets a list of all matched cluster pairs and their match states.
+     * @return Returns the matched cluster pairs as a <code>List</code>
+     * of <code>ClusterMatchedPair</code> objects.
+     */
+    public List<ClusterMatchedPair> getClusterPairs() {
+        return pairList;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DiagnosticSnapshot.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DiagnosticSnapshot.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/DiagnosticSnapshot.java	Wed Apr 27 11:11:32 2016
@@ -8,117 +8,117 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class DiagnosticSnapshot {
-	// Store the TI trigger information.
-	private int[] tiSeenAll = new int[6];
-	private int[] tiSeenHierarchical = new int[6];
-	
-	// Store the statistical modules.
-	private final GeneralStatModule generalStats;
-	private final ClusterStatModule clusterStats;
-	private final TriggerStatModule[] triggerStats = new TriggerStatModule[4];
-	
-	/**
-	 * Creates a snapshot of the trigger diagnostic results.
-	 * @param stats - The run statistical object.
-	 */
-	DiagnosticSnapshot(RunDiagStats stats) {
-		// Store the statistical modules.
-		generalStats = stats.clone();
-		clusterStats = stats.getClusterStats().clone();
-		triggerStats[0] = stats.getTriggerStats().getSingles0Stats().clone();
-		triggerStats[1] = stats.getTriggerStats().getSingles1Stats().clone();
-		triggerStats[2] = stats.getTriggerStats().getPair0Stats().clone();
-		triggerStats[3] = stats.getTriggerStats().getPair1Stats().clone();
-		
-		// Copy the TI trigger data.
-		for(int triggerType = 0; triggerType < 6; triggerType++) {
-			tiSeenAll[triggerType] = stats.getTriggerStats().getTITriggers(triggerType, false);
-			tiSeenHierarchical[triggerType] = stats.getTriggerStats().getTITriggers(triggerType, true);
-		}
-	}
-	
-	/**
-	 * Gets the general run statistics.
-	 * @return Returns a <code>GeneralStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public GeneralStatModule getGeneralStats() {
-		return generalStats;
-	}
-	
-	/**
-	 * Gets the cluster statistics.
-	 * @return Returns a <code>ClusterStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public ClusterStatModule getClusterStats() {
-		return clusterStats;
-	}
-	
-	/**
-	 * Gets the singles 0 trigger statistics.
-	 * @return Returns a <code>TriggerStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public TriggerStatModule getSingles0Stats() {
-		return triggerStats[0];
-	}
-	
-	/**
-	 * Gets the singles 1 trigger statistics.
-	 * @return Returns a <code>TriggerStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public TriggerStatModule getSingles1Stats() {
-		return triggerStats[1];
-	}
-	
-	/**
-	 * Gets the pair 0 trigger statistics.
-	 * @return Returns a <code>TriggerStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public TriggerStatModule getPair0Stats() {
-		return triggerStats[2];
-	}
-	
-	/**
-	 * Gets the pair 1 trigger statistics.
-	 * @return Returns a <code>TriggerStatModule</code> object that
-	 * contains the statistics.
-	 */
-	public TriggerStatModule getPair1Stats() {
-		return triggerStats[3];
-	}
-	
-	/**
-	 * Gets the total number of events where the TI reported a trigger
-	 * of the specified type.
-	 * @param triggerID - The identifier for the type of trigger.
-	 * @param unique - <code>true</code> returns only the number of
-	 * events where this trigger type was the <i>only</i> type seen by
-	 * the TI while <code>false</code> returns the number of events
-	 * that saw this trigger type without regards for other trigger
-	 * flags.
-	 * @return Returns the count as an <code>int</code>.
-	 */
-	public int getTITriggers(int triggerID, boolean hierarchical) {
-		// Verify the trigger type.
-		validateTriggerType(triggerID);
-		
-		// Increment the counters.
-		if(hierarchical) { return tiSeenHierarchical[triggerID]; }
-		else { return tiSeenAll[triggerID]; }
-	}
-	
-	/**
-	 * Produces an exception if the argument trigger type is not of a
-	 * supported type.
-	 * @param triggerType - The trigger type to verify.
-	 */
-	private static final void validateTriggerType(int triggerType) {
-		if(triggerType < 0 || triggerType > 5) {
-			throw new IndexOutOfBoundsException(String.format("Trigger type \"%d\" is not supported.", triggerType));
-		}
-	}
+    // Store the TI trigger information.
+    private int[] tiSeenAll = new int[6];
+    private int[] tiSeenHierarchical = new int[6];
+    
+    // Store the statistical modules.
+    private final GeneralStatModule generalStats;
+    private final ClusterStatModule clusterStats;
+    private final TriggerStatModule[] triggerStats = new TriggerStatModule[4];
+    
+    /**
+     * Creates a snapshot of the trigger diagnostic results.
+     * @param stats - The run statistical object.
+     */
+    DiagnosticSnapshot(RunDiagStats stats) {
+        // Store the statistical modules.
+        generalStats = stats.clone();
+        clusterStats = stats.getClusterStats().clone();
+        triggerStats[0] = stats.getTriggerStats().getSingles0Stats().clone();
+        triggerStats[1] = stats.getTriggerStats().getSingles1Stats().clone();
+        triggerStats[2] = stats.getTriggerStats().getPair0Stats().clone();
+        triggerStats[3] = stats.getTriggerStats().getPair1Stats().clone();
+        
+        // Copy the TI trigger data.
+        for(int triggerType = 0; triggerType < 6; triggerType++) {
+            tiSeenAll[triggerType] = stats.getTriggerStats().getTITriggers(triggerType, false);
+            tiSeenHierarchical[triggerType] = stats.getTriggerStats().getTITriggers(triggerType, true);
+        }
+    }
+    
+    /**
+     * Gets the general run statistics.
+     * @return Returns a <code>GeneralStatModule</code> object that
+     * contains the statistics.
+     */
+    public GeneralStatModule getGeneralStats() {
+        return generalStats;
+    }
+    
+    /**
+     * Gets the cluster statistics.
+     * @return Returns a <code>ClusterStatModule</code> object that
+     * contains the statistics.
+     */
+    public ClusterStatModule getClusterStats() {
+        return clusterStats;
+    }
+    
+    /**
+     * Gets the singles 0 trigger statistics.
+     * @return Returns a <code>TriggerStatModule</code> object that
+     * contains the statistics.
+     */
+    public TriggerStatModule getSingles0Stats() {
+        return triggerStats[0];
+    }
+    
+    /**
+     * Gets the singles 1 trigger statistics.
+     * @return Returns a <code>TriggerStatModule</code> object that
+     * contains the statistics.
+     */
+    public TriggerStatModule getSingles1Stats() {
+        return triggerStats[1];
+    }
+    
+    /**
+     * Gets the pair 0 trigger statistics.
+     * @return Returns a <code>TriggerStatModule</code> object that
+     * contains the statistics.
+     */
+    public TriggerStatModule getPair0Stats() {
+        return triggerStats[2];
+    }
+    
+    /**
+     * Gets the pair 1 trigger statistics.
+     * @return Returns a <code>TriggerStatModule</code> object that
+     * contains the statistics.
+     */
+    public TriggerStatModule getPair1Stats() {
+        return triggerStats[3];
+    }
+    
+    /**
+     * Gets the total number of events where the TI reported a trigger
+     * of the specified type.
+     * @param triggerID - The identifier for the type of trigger.
+     * @param hierarchical - <code>true</code> returns only the number of
+     * events where this trigger type was the <i>only</i> type seen by
+     * the TI while <code>false</code> returns the number of events
+     * that saw this trigger type without regards for other trigger
+     * flags.
+     * @return Returns the count as an <code>int</code>.
+     */
+    public int getTITriggers(int triggerID, boolean hierarchical) {
+        // Verify the trigger type.
+        validateTriggerType(triggerID);
+        
+        // Increment the counters.
+        if(hierarchical) { return tiSeenHierarchical[triggerID]; }
+        else { return tiSeenAll[triggerID]; }
+    }
+    
+    /**
+     * Produces an exception if the argument trigger type is not of a
+     * supported type.
+     * @param triggerType - The trigger type to verify.
+     */
+    private static final void validateTriggerType(int triggerType) {
+        if(triggerType < 0 || triggerType > 5) {
+            throw new IndexOutOfBoundsException(String.format("Trigger type \"%d\" is not supported.", triggerType));
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/GeneralStatModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/GeneralStatModule.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/GeneralStatModule.java	Wed Apr 27 11:11:32 2016
@@ -7,97 +7,97 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class GeneralStatModule {
-	// Store general run statistics.
-	protected long endTime = -1;
-	protected long startTime = -1;
-	protected int totalEvents = 0;
-	protected int noiseEvents = 0;
-	protected int failedPairEvents = 0;
-	protected int failedClusterEvents = 0;
-	protected int failedSinglesEvents = 0;
-	
-	/**
-	 * Clears all of the statistical counters in the object.
-	 */
-	void clear() {
-		endTime = -1;
-		startTime = -1;
-		totalEvents = 0;
-		noiseEvents = 0;
-		failedPairEvents = 0;
-		failedClusterEvents = 0;
-		failedSinglesEvents = 0;
-	}
-	
-	@Override
-	public GeneralStatModule clone() {
-		// Create the a cloned object.
-		GeneralStatModule clone = new GeneralStatModule();
-		
-		// Copy the tracked statistical data to the clone.
-		clone.endTime             = endTime;
-		clone.startTime           = startTime;
-		clone.totalEvents         = totalEvents;
-		clone.noiseEvents         = noiseEvents;
-		clone.failedPairEvents    = failedPairEvents;
-		clone.failedClusterEvents = failedClusterEvents;
-		clone.failedSinglesEvents = failedSinglesEvents;
-		
-		// Return the clone.
-		return clone;
-	}
-	
-	/**
-	 * Gets the length of time, in nanoseconds, over which the events
-	 * represented by this object occurred.
-	 * @return Returns the length of time as a <code>long</code>.
-	 */
-	public long getDuration() {
-		return endTime - startTime;
-	}
-	
-	/**
-	 * Gets the number of events seen.
-	 * @return Returns the number of events as an <code>int</code>.
-	 */
-	public int getEventCount() {
-		return totalEvents;
-	}
-	
-	/**
-	 * Gets the number of events in which at least one cluster was
-	 * not matched.
-	 * @return Returns the number of events as an <code>int</code>.
-	 */
-	public int getFailedClusterEventCount() {
-		return failedClusterEvents;
-	}
-	
-	/**
-	 * Gets the number of events in which at least one pair trigger
-	 * was not matched.
-	 * @return Returns the number of events as an <code>int</code>.
-	 */
-	public int getFailedPairEventCount() {
-		return failedPairEvents;
-	}
+    // Store general run statistics.
+    protected long endTime = -1;
+    protected long startTime = -1;
+    protected int totalEvents = 0;
+    protected int noiseEvents = 0;
+    protected int failedPairEvents = 0;
+    protected int failedClusterEvents = 0;
+    protected int failedSinglesEvents = 0;
+    
+    /**
+     * Clears all of the statistical counters in the object.
+     */
+    void clear() {
+        endTime = -1;
+        startTime = -1;
+        totalEvents = 0;
+        noiseEvents = 0;
+        failedPairEvents = 0;
+        failedClusterEvents = 0;
+        failedSinglesEvents = 0;
+    }
+    
+    @Override
+    public GeneralStatModule clone() {
+        // Create the a cloned object.
+        GeneralStatModule clone = new GeneralStatModule();
+        
+        // Copy the tracked statistical data to the clone.
+        clone.endTime             = endTime;
+        clone.startTime           = startTime;
+        clone.totalEvents         = totalEvents;
+        clone.noiseEvents         = noiseEvents;
+        clone.failedPairEvents    = failedPairEvents;
+        clone.failedClusterEvents = failedClusterEvents;
+        clone.failedSinglesEvents = failedSinglesEvents;
+        
+        // Return the clone.
+        return clone;
+    }
+    
+    /**
+     * Gets the length of time, in nanoseconds, over which the events
+     * represented by this object occurred.
+     * @return Returns the length of time as a <code>long</code>.
+     */
+    public long getDuration() {
+        return endTime - startTime;
+    }
+    
+    /**
+     * Gets the number of events seen.
+     * @return Returns the number of events as an <code>int</code>.
+     */
+    public int getEventCount() {
+        return totalEvents;
+    }
+    
+    /**
+     * Gets the number of events in which at least one cluster was
+     * not matched.
+     * @return Returns the number of events as an <code>int</code>.
+     */
+    public int getFailedClusterEventCount() {
+        return failedClusterEvents;
+    }
+    
+    /**
+     * Gets the number of events in which at least one pair trigger
+     * was not matched.
+     * @return Returns the number of events as an <code>int</code>.
+     */
+    public int getFailedPairEventCount() {
+        return failedPairEvents;
+    }
 
-	/**
-	 * Gets the number of events in which at least one singles trigger
-	 * was not matched.
-	 * @return Returns the number of events as an <code>int</code>.
-	 */
-	public int getFailedSinglesEventCount() {
-		return failedSinglesEvents;
-	}
-	
-	/**
-	 * Gets the number of events which were ignored due to having too
-	 * many hits in them.
-	 * @return Returns the number of events as an <code>int</code>.
-	 */
-	public int getNoiseEvents() {
-		return noiseEvents;
-	}
+    /**
+     * Gets the number of events in which at least one singles trigger
+     * was not matched.
+     * @return Returns the number of events as an <code>int</code>.
+     */
+    public int getFailedSinglesEventCount() {
+        return failedSinglesEvents;
+    }
+    
+    /**
+     * Gets the number of events which were ignored due to having too
+     * many hits in them.
+     * @return Returns the number of events as an <code>int</code>.
+     */
+    public int getNoiseEvents() {
+        return noiseEvents;
+    }
 
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/RunDiagStats.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/RunDiagStats.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/RunDiagStats.java	Wed Apr 27 11:11:32 2016
@@ -9,89 +9,89 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class RunDiagStats extends GeneralStatModule {
-	// Store the statistics for trigger matching.
-	private TriggerDiagStats triggerStats = new TriggerDiagStats();
-	
-	// Store the statistics for cluster matching.
-	private ClusterEvent clusterStats = new ClusterEvent();
-	
-	/**
-	 * Clears all of the statistical counters in the object.
-	 */
-	public void clear() {
-		super.clear();
-		clusterStats.clear();
-		triggerStats.clear();
-	}
-	
-	/**
-	 * Notes that an event failed to match all clusters.
-	 */
-	public void failedClusterEvent() {
-		failedClusterEvents++;
-	}
-	
-	/**
-	 * Notes that an event failed to match all pair triggers.
-	 */
-	public void failedPairEvent() {
-		failedPairEvents++;
-	}
+    // Store the statistics for trigger matching.
+    private TriggerDiagStats triggerStats = new TriggerDiagStats();
+    
+    // Store the statistics for cluster matching.
+    private ClusterEvent clusterStats = new ClusterEvent();
+    
+    /**
+     * Clears all of the statistical counters in the object.
+     */
+    public void clear() {
+        super.clear();
+        clusterStats.clear();
+        triggerStats.clear();
+    }
+    
+    /**
+     * Notes that an event failed to match all clusters.
+     */
+    public void failedClusterEvent() {
+        failedClusterEvents++;
+    }
+    
+    /**
+     * Notes that an event failed to match all pair triggers.
+     */
+    public void failedPairEvent() {
+        failedPairEvents++;
+    }
 
-	/**
-	 * Notes that an event failed to match all singles triggers.
-	 */
-	public void failedSinglesEvent() {
-		failedSinglesEvents++;
-	}
-	
-	/**
-	 * Gets the cluster data.
-	 * @return Returns the <code>ClusterEvent</code> object that holds
-	 * the cluster data.
-	 */
-	public ClusterEvent getClusterStats() {
-		return clusterStats;
-	}
-	
-	/**
-	 * Gets a snapshot of the statistical data at the present time. The
-	 * snapshot will remain static and unchanged even if the generating
-	 * object itself is updated.
-	 * @return Returns a snapshot as a <code>DiagnosticSnapshot</code>
-	 * object.
-	 */
-	public DiagnosticSnapshot getSnapshot() {
-		return new DiagnosticSnapshot(this);
-	}
-	
-	/**
-	 * Gets the trigger data.
-	 * @return Returns the <code>TriggerDiagStats</code> object that holds
-	 * the cluster data.
-	 */
-	public TriggerDiagStats getTriggerStats() {
-		return triggerStats;
-	}
-	
-	/**
-	 * Notes that an event occurred.
-	 */
-	public void sawEvent(long eventTime) {
-		// Increment the event count.
-		totalEvents++;
-		
-		// If the start time is not defined, use this as the start time.
-		if(startTime == -1) { startTime = eventTime; }
-		
-		// The end time should always match the most recent event.
-		endTime = eventTime;
-	}
+    /**
+     * Notes that an event failed to match all singles triggers.
+     */
+    public void failedSinglesEvent() {
+        failedSinglesEvents++;
+    }
+    
+    /**
+     * Gets the cluster data.
+     * @return Returns the <code>ClusterEvent</code> object that holds
+     * the cluster data.
+     */
+    public ClusterEvent getClusterStats() {
+        return clusterStats;
+    }
+    
+    /**
+     * Gets a snapshot of the statistical data at the present time. The
+     * snapshot will remain static and unchanged even if the generating
+     * object itself is updated.
+     * @return Returns a snapshot as a <code>DiagnosticSnapshot</code>
+     * object.
+     */
+    public DiagnosticSnapshot getSnapshot() {
+        return new DiagnosticSnapshot(this);
+    }
+    
+    /**
+     * Gets the trigger data.
+     * @return Returns the <code>TriggerDiagStats</code> object that holds
+     * the cluster data.
+     */
+    public TriggerDiagStats getTriggerStats() {
+        return triggerStats;
+    }
+    
+    /**
+     * Notes that an event occurred.
+     */
+    public void sawEvent(long eventTime) {
+        // Increment the event count.
+        totalEvents++;
+        
+        // If the start time is not defined, use this as the start time.
+        if(startTime == -1) { startTime = eventTime; }
+        
+        // The end time should always match the most recent event.
+        endTime = eventTime;
+    }
 
-	/**
-	 * Notes that an event was labeled as noise.
-	 */
-	public void sawNoiseEvent() {
-		noiseEvents++;
-	}
+    /**
+     * Notes that an event was labeled as noise.
+     */
+    public void sawNoiseEvent() {
+        noiseEvents++;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerDiagStats.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerDiagStats.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerDiagStats.java	Wed Apr 27 11:11:32 2016
@@ -4,304 +4,304 @@
 import org.hps.analysis.trigger.util.TriggerDiagnosticUtil;
 
 public class TriggerDiagStats {
-	// Define TI trigger type identifiers.
-	public static final int SINGLES0 = TriggerStatModule.SINGLES_0;
-	public static final int SINGLES1 = TriggerStatModule.SINGLES_1;
-	public static final int PAIR0    = TriggerStatModule.PAIR_0;
-	public static final int PAIR1    = TriggerStatModule.PAIR_1;
-	public static final int PULSER   = TriggerStatModule.PULSER;
-	public static final int COSMIC   = TriggerStatModule.COSMIC;
-	
-	// Tracks the number of TI triggers seen across all events for only
-	// the TI trigger with the highest priority in the event.
-	private int[] tiSeenHierarchical = new int[6];
-	
-	// Tracks the number of TI triggers across all events.
-	private int[] tiSeenAll = new int[6];
-	
-	// Store the statistics modules for each of the regular triggers.
-	private TriggerEvent[] triggerStats = new TriggerEvent[4];
-	
-	/**
-	 * Instantiates a new <code>TriggerDiagStats</code> object.
-	 */
-	public TriggerDiagStats() {
-		// Instantiate a trigger statistics module for each of the
-		// triggers for which statistics are supported.
-		for(int triggerType = 0; triggerType < 4; triggerType++) {
-			triggerStats[triggerType] = new TriggerEvent();
-		}
-	}
-	
-	/**
-	 * Clears all of the statistical counters in the object.
-	 */
-	void clear() {
-		// Clear the tracked TI trigger data.
-		for(int tiType = 0; tiType < 6; tiType++) {
-			tiSeenAll[tiType] = 0;
-			tiSeenHierarchical[tiType] = 0;
-		}
-		
-		// Clear the trigger statistical modules.
-		for(int triggerType = 0; triggerType < 4; triggerType++) {
-			triggerStats[triggerType].clear();
-		}
-	}
-	
-	/**
-	 * Gets the trigger data for the pair 0 trigger.
-	 * @return Returns the <code>TriggerEvent</code> object that holds
-	 * the trigger data for the pair 0 trigger.
-	 */
-	public TriggerEvent getPair0Stats() {
-		return triggerStats[PAIR0];
-	}
-	
-	/**
-	 * Gets the trigger data for the pair 1 trigger.
-	 * @return Returns the <code>TriggerEvent</code> object that holds
-	 * the trigger data for the pair 1 trigger.
-	 */
-	public TriggerEvent getPair1Stats() {
-		return triggerStats[PAIR1];
-	}
-	
-	/**
-	 * Gets the trigger data for the singles 0 trigger.
-	 * @return Returns the <code>TriggerEvent</code> object that holds
-	 * the trigger data for the singles 0 trigger.
-	 */
-	public TriggerEvent getSingles0Stats() {
-		return triggerStats[SINGLES0];
-	}
-	
-	/**
-	 * Gets the trigger data for the singles 1 trigger.
-	 * @return Returns the <code>TriggerEvent</code> object that holds
-	 * the trigger data for the singles 1 trigger.
-	 */
-	public TriggerEvent getSingles1Stats() {
-		return triggerStats[SINGLES1];
-	}
-	
-	/**
-	 * Gets the total number of events where the TI reported a trigger
-	 * of the specified type.
-	 * @param triggerID - The identifier for the type of trigger.
-	 * @param unique - <code>true</code> returns only the number of
-	 * events where this trigger type was the <i>only</i> type seen by
-	 * the TI while <code>false</code> returns the number of events
-	 * that saw this trigger type without regards for other trigger
-	 * flags.
-	 * @return Returns the count as an <code>int</code>.
-	 */
-	public int getTITriggers(int triggerID, boolean hierarchical) {
-		// Verify the trigger type.
-		validateTriggerType(triggerID);
-		
-		// Increment the counters.
-		if(hierarchical) { return tiSeenHierarchical[triggerID]; }
-		else { return tiSeenAll[triggerID]; }
-	}
-	
-	/**
-	 * Increments the counts tracking the number of TI flags seen.
-	 * @param flags - An array of <code>boolean</code> values of size
-	 * six. This represents one flag for each possible TI trigger type.
-	 */
-	public void sawTITriggers(boolean[] flags) {
-		// There must be six trigger flags and the array must not be
-		// null.
-		if(flags == null) {
-			throw new NullPointerException("TI trigger flags can not be null.");
-		} if(flags.length != 6) {
-			throw new IllegalArgumentException("TI trigger flags must be of size six.");
-		}
-		
-		// Check each TI flag in the order of the flag hierarchy. The
-		// first flag in the hierarchy that is true is recorded in the
-		// hierarchical count. All flags are recorded in the all count.
-		boolean foundHierarchical = false;
-		if(flags[PAIR1]) {
-			tiSeenAll[PAIR1]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[PAIR1]++;
-				foundHierarchical = true;
-			}
-		} if(flags[PAIR0]) {
-			tiSeenAll[PAIR0]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[PAIR0]++;
-				foundHierarchical = true;
-			}
-		} if(flags[SINGLES1]) {
-			tiSeenAll[SINGLES1]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[SINGLES1]++;
-				foundHierarchical = true;
-			}
-		} if(flags[SINGLES0]) {
-			tiSeenAll[SINGLES0]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[SINGLES0]++;
-				foundHierarchical = true;
-			}
-		} if(flags[PULSER]) {
-			tiSeenAll[PULSER]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[PULSER]++;
-				foundHierarchical = true;
-			}
-		} if(flags[COSMIC]) {
-			tiSeenAll[COSMIC]++;
-			if(!foundHierarchical) {
-				tiSeenHierarchical[COSMIC]++;
-				foundHierarchical = true;
-			}
-		}
-	}
-	
-	/**
-	 * Prints the trigger statistics to the terminal as a table.
-	 */
-	public void printEfficiencyTable() {
-		// Get the trigger statistics tables.
-		int[][] seenStats = new int[6][4];
-		int[][] matchedStats = new int[6][4];
-		TriggerEvent[] triggerEvents = { getSingles0Stats(), getSingles1Stats(), getPair0Stats(), getPair1Stats() };
-		for(int i = 0; i < 4; i++) {
-			for(int j = 0; j < 6; j++) {
-				seenStats[j][i] = triggerEvents[i].getReconSimulatedTriggers(j);
-				matchedStats[j][i] = triggerEvents[i].getMatchedReconSimulatedTriggers(j);
-			}
-		}
-		
-		// Define constant spacing variables.
-		int columnSpacing = 3;
-		
-		// Define table headers.
-		String sourceName = "Source";
-		String seenName = "Trigger Efficiency";
-		
-		// Get the longest column header name.
-		int longestHeader = -1;
-		String[] headerNames = {
-				TriggerDiagnosticUtil.TRIGGER_NAME[0],
-				TriggerDiagnosticUtil.TRIGGER_NAME[1],
-				TriggerDiagnosticUtil.TRIGGER_NAME[2],
-				TriggerDiagnosticUtil.TRIGGER_NAME[3],
-				"TI Highest Type"
-		};
-		for(String triggerName : headerNames) {
-			longestHeader = ComponentUtils.max(longestHeader, triggerName.length());
-		}
-		longestHeader = ComponentUtils.max(longestHeader, sourceName.length());
-		
-		// Determine the spacing needed to display the largest numerical
-		// cell value.
-		int numWidth = -1;
-		int longestCell = -1;
-		for(int eventTriggerID = 0; eventTriggerID < 6; eventTriggerID++) {
-			for(int seenTriggerID = 0; seenTriggerID < 4; seenTriggerID++) {
-				int valueSize = ComponentUtils.getDigits(seenStats[eventTriggerID][seenTriggerID]);
-				int cellSize = valueSize * 2 + 13;
-				if(cellSize > longestCell) {
-					longestCell = cellSize;
-					numWidth = valueSize;
-				}
-			}
-		}
-		
-		// The total column width can then be calculated from the
-		// longer of the header and cell values.
-		int columnWidth = ComponentUtils.max(longestCell, longestHeader);
-		int sourceWidth = ComponentUtils.max(
-				TriggerDiagnosticUtil.TRIGGER_NAME[0].length(), TriggerDiagnosticUtil.TRIGGER_NAME[1].length(),
-				TriggerDiagnosticUtil.TRIGGER_NAME[2].length(), TriggerDiagnosticUtil.TRIGGER_NAME[3].length(),
-				TriggerDiagnosticUtil.TRIGGER_NAME[4].length(), TriggerDiagnosticUtil.TRIGGER_NAME[5].length(),
-				sourceName.length() );
-		
-		// Calculate the total width of the table value header columns.
-		int headerTotalWidth = (headerNames.length * columnWidth)
-				+ ((headerNames.length - 1) * columnSpacing);
-		
-		// Write the table header.
-		String spacingText = ComponentUtils.getChars(' ', columnSpacing);
-		System.out.println(ComponentUtils.getChars(' ', sourceWidth) + spacingText
-				+ getCenteredString(seenName, headerTotalWidth));
-		
-		// Create the format strings for the cell values.
-		String headerFormat = "%-" + sourceWidth + "s" + spacingText;
-		String cellFormat = "%" + numWidth + "d / %" + numWidth + "d (%7.3f)";
-		String nullText = getCenteredString(ComponentUtils.getChars('-', numWidth) + " / "
-				+ ComponentUtils.getChars('-', numWidth) + " (  N/A  )", columnWidth) + spacingText;
-		
-		// Print the column headers.
-		System.out.printf(headerFormat, sourceName);
-		for(String header : headerNames) {
-			System.out.print(getCenteredString(header, columnWidth) + spacingText);
-		}
-		System.out.println();
-		
-		// Write out the value columns.
-		for(int eventTriggerID = 0; eventTriggerID < 6; eventTriggerID++) {
-			// Print out the row header.
-			System.out.printf(headerFormat, TriggerDiagnosticUtil.TRIGGER_NAME[eventTriggerID]);
-			
-			// Print the cell values.
-			for(int seenTriggerID = 0; seenTriggerID < 4; seenTriggerID++) {
-				if(seenTriggerID == eventTriggerID) { System.out.print(nullText); }
-				else {
-					String cellText = String.format(cellFormat, matchedStats[eventTriggerID][seenTriggerID],
-							seenStats[eventTriggerID][seenTriggerID],
-							(100.0 * matchedStats[eventTriggerID][seenTriggerID] / seenStats[eventTriggerID][seenTriggerID]));
-					System.out.print(getCenteredString(cellText, columnWidth) + spacingText);
-				}
-			}
-			
-			// Output the number of events that had only the trigger
-			// type ID for the current trigger type flagged by the TI.
-			System.out.print(getCenteredString("" + getTITriggers(eventTriggerID, true), columnWidth) + spacingText);
-			
-			// Start a new line.
-			System.out.println();
-		}
-	}
-	
-	/**
-	 * Produces a <code>String</code> of the indicated length with the
-	 * text <code>value</code> centered in the middle. Extra length is
-	 * filled through spaces before and after the text.
-	 * @param value - The text to display.
-	 * @param width - The number of spaces to include.
-	 * @return Returns a <code>String</code> of the specified length,
-	 * or the argument text if it is longer.
-	 */
-	private static final String getCenteredString(String value, int width) {
-		// The method can not perform as intended if the argument text
-		// exceeds the requested string length. Just return the text.
-		if(width <= value.length()) {
-			return value;
-		}
-		
-		// Otherwise, get the amount of buffering needed to center the
-		// text and add it around the text to produce the string.
-		else {
-			int buffer = (width - value.length()) / 2;
-			return ComponentUtils.getChars(' ', buffer) + value
-					+ ComponentUtils.getChars(' ', width - buffer - value.length());
-		}
-	}
-	
-	/**
-	 * Produces an exception if the argument trigger type is not of a
-	 * supported type.
-	 * @param triggerType - The trigger type to verify.
-	 */
-	private static final void validateTriggerType(int triggerType) {
-		if(triggerType < 0 || triggerType > 5) {
-			throw new IndexOutOfBoundsException(String.format("Trigger type \"%d\" is not supported.", triggerType));
-		}
-	}
+    // Define TI trigger type identifiers.
+    public static final int SINGLES0 = TriggerStatModule.SINGLES_0;
+    public static final int SINGLES1 = TriggerStatModule.SINGLES_1;
+    public static final int PAIR0    = TriggerStatModule.PAIR_0;
+    public static final int PAIR1    = TriggerStatModule.PAIR_1;
+    public static final int PULSER   = TriggerStatModule.PULSER;
+    public static final int COSMIC   = TriggerStatModule.COSMIC;
+    
+    // Tracks the number of TI triggers seen across all events for only
+    // the TI trigger with the highest priority in the event.
+    private int[] tiSeenHierarchical = new int[6];
+    
+    // Tracks the number of TI triggers across all events.
+    private int[] tiSeenAll = new int[6];
+    
+    // Store the statistics modules for each of the regular triggers.
+    private TriggerEvent[] triggerStats = new TriggerEvent[4];
+    
+    /**
+     * Instantiates a new <code>TriggerDiagStats</code> object.
+     */
+    public TriggerDiagStats() {
+        // Instantiate a trigger statistics module for each of the
+        // triggers for which statistics are supported.
+        for(int triggerType = 0; triggerType < 4; triggerType++) {
+            triggerStats[triggerType] = new TriggerEvent();
+        }
+    }
+    
+    /**
+     * Clears all of the statistical counters in the object.
+     */
+    void clear() {
+        // Clear the tracked TI trigger data.
+        for(int tiType = 0; tiType < 6; tiType++) {
+            tiSeenAll[tiType] = 0;
+            tiSeenHierarchical[tiType] = 0;
+        }
+        
+        // Clear the trigger statistical modules.
+        for(int triggerType = 0; triggerType < 4; triggerType++) {
+            triggerStats[triggerType].clear();
+        }
+    }
+    
+    /**
+     * Gets the trigger data for the pair 0 trigger.
+     * @return Returns the <code>TriggerEvent</code> object that holds
+     * the trigger data for the pair 0 trigger.
+     */
+    public TriggerEvent getPair0Stats() {
+        return triggerStats[PAIR0];
+    }
+    
+    /**
+     * Gets the trigger data for the pair 1 trigger.
+     * @return Returns the <code>TriggerEvent</code> object that holds
+     * the trigger data for the pair 1 trigger.
+     */
+    public TriggerEvent getPair1Stats() {
+        return triggerStats[PAIR1];
+    }
+    
+    /**
+     * Gets the trigger data for the singles 0 trigger.
+     * @return Returns the <code>TriggerEvent</code> object that holds
+     * the trigger data for the singles 0 trigger.
+     */
+    public TriggerEvent getSingles0Stats() {
+        return triggerStats[SINGLES0];
+    }
+    
+    /**
+     * Gets the trigger data for the singles 1 trigger.
+     * @return Returns the <code>TriggerEvent</code> object that holds
+     * the trigger data for the singles 1 trigger.
+     */
+    public TriggerEvent getSingles1Stats() {
+        return triggerStats[SINGLES1];
+    }
+    
+    /**
+     * Gets the total number of events where the TI reported a trigger
+     * of the specified type.
+     * @param triggerID - The identifier for the type of trigger.
+     * @param hierarchical - <code>true</code> returns only the number of
+     * events where this trigger type was the <i>only</i> type seen by
+     * the TI while <code>false</code> returns the number of events
+     * that saw this trigger type without regards for other trigger
+     * flags.
+     * @return Returns the count as an <code>int</code>.
+     */
+    public int getTITriggers(int triggerID, boolean hierarchical) {
+        // Verify the trigger type.
+        validateTriggerType(triggerID);
+        
+        // Increment the counters.
+        if(hierarchical) { return tiSeenHierarchical[triggerID]; }
+        else { return tiSeenAll[triggerID]; }
+    }
+    
+    /**
+     * Increments the counts tracking the number of TI flags seen.
+     * @param flags - An array of <code>boolean</code> values of size
+     * six. This represents one flag for each possible TI trigger type.
+     */
+    public void sawTITriggers(boolean[] flags) {
+        // There must be six trigger flags and the array must not be
+        // null.
+        if(flags == null) {
+            throw new NullPointerException("TI trigger flags can not be null.");
+        } if(flags.length != 6) {
+            throw new IllegalArgumentException("TI trigger flags must be of size six.");
+        }
+        
+        // Check each TI flag in the order of the flag hierarchy. The
+        // first flag in the hierarchy that is true is recorded in the
+        // hierarchical count. All flags are recorded in the all count.
+        boolean foundHierarchical = false;
+        if(flags[PAIR1]) {
+            tiSeenAll[PAIR1]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[PAIR1]++;
+                foundHierarchical = true;
+            }
+        } if(flags[PAIR0]) {
+            tiSeenAll[PAIR0]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[PAIR0]++;
+                foundHierarchical = true;
+            }
+        } if(flags[SINGLES1]) {
+            tiSeenAll[SINGLES1]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[SINGLES1]++;
+                foundHierarchical = true;
+            }
+        } if(flags[SINGLES0]) {
+            tiSeenAll[SINGLES0]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[SINGLES0]++;
+                foundHierarchical = true;
+            }
+        } if(flags[PULSER]) {
+            tiSeenAll[PULSER]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[PULSER]++;
+                foundHierarchical = true;
+            }
+        } if(flags[COSMIC]) {
+            tiSeenAll[COSMIC]++;
+            if(!foundHierarchical) {
+                tiSeenHierarchical[COSMIC]++;
+                foundHierarchical = true;
+            }
+        }
+    }
+    
+    /**
+     * Prints the trigger statistics to the terminal as a table.
+     */
+    public void printEfficiencyTable() {
+        // Get the trigger statistics tables.
+        int[][] seenStats = new int[6][4];
+        int[][] matchedStats = new int[6][4];
+        TriggerEvent[] triggerEvents = { getSingles0Stats(), getSingles1Stats(), getPair0Stats(), getPair1Stats() };
+        for(int i = 0; i < 4; i++) {
+            for(int j = 0; j < 6; j++) {
+                seenStats[j][i] = triggerEvents[i].getReconSimulatedTriggers(j);
+                matchedStats[j][i] = triggerEvents[i].getMatchedReconSimulatedTriggers(j);
+            }
+        }
+        
+        // Define constant spacing variables.
+        int columnSpacing = 3;
+        
+        // Define table headers.
+        String sourceName = "Source";
+        String seenName = "Trigger Efficiency";
+        
+        // Get the longest column header name.
+        int longestHeader = -1;
+        String[] headerNames = {
+                TriggerDiagnosticUtil.TRIGGER_NAME[0],
+                TriggerDiagnosticUtil.TRIGGER_NAME[1],
+                TriggerDiagnosticUtil.TRIGGER_NAME[2],
+                TriggerDiagnosticUtil.TRIGGER_NAME[3],
+                "TI Highest Type"
+        };
+        for(String triggerName : headerNames) {
+            longestHeader = ComponentUtils.max(longestHeader, triggerName.length());
+        }
+        longestHeader = ComponentUtils.max(longestHeader, sourceName.length());
+        
+        // Determine the spacing needed to display the largest numerical
+        // cell value.
+        int numWidth = -1;
+        int longestCell = -1;
+        for(int eventTriggerID = 0; eventTriggerID < 6; eventTriggerID++) {
+            for(int seenTriggerID = 0; seenTriggerID < 4; seenTriggerID++) {
+                int valueSize = ComponentUtils.getDigits(seenStats[eventTriggerID][seenTriggerID]);
+                int cellSize = valueSize * 2 + 13;
+                if(cellSize > longestCell) {
+                    longestCell = cellSize;
+                    numWidth = valueSize;
+                }
+            }
+        }
+        
+        // The total column width can then be calculated from the
+        // longer of the header and cell values.
+        int columnWidth = ComponentUtils.max(longestCell, longestHeader);
+        int sourceWidth = ComponentUtils.max(
+                TriggerDiagnosticUtil.TRIGGER_NAME[0].length(), TriggerDiagnosticUtil.TRIGGER_NAME[1].length(),
+                TriggerDiagnosticUtil.TRIGGER_NAME[2].length(), TriggerDiagnosticUtil.TRIGGER_NAME[3].length(),
+                TriggerDiagnosticUtil.TRIGGER_NAME[4].length(), TriggerDiagnosticUtil.TRIGGER_NAME[5].length(),
+                sourceName.length() );
+        
+        // Calculate the total width of the table value header columns.
+        int headerTotalWidth = (headerNames.length * columnWidth)
+                + ((headerNames.length - 1) * columnSpacing);
+        
+        // Write the table header.
+        String spacingText = ComponentUtils.getChars(' ', columnSpacing);
+        System.out.println(ComponentUtils.getChars(' ', sourceWidth) + spacingText
+                + getCenteredString(seenName, headerTotalWidth));
+        
+        // Create the format strings for the cell values.
+        String headerFormat = "%-" + sourceWidth + "s" + spacingText;
+        String cellFormat = "%" + numWidth + "d / %" + numWidth + "d (%7.3f)";
+        String nullText = getCenteredString(ComponentUtils.getChars('-', numWidth) + " / "
+                + ComponentUtils.getChars('-', numWidth) + " (  N/A  )", columnWidth) + spacingText;
+        
+        // Print the column headers.
+        System.out.printf(headerFormat, sourceName);
+        for(String header : headerNames) {
+            System.out.print(getCenteredString(header, columnWidth) + spacingText);
+        }
+        System.out.println();
+        
+        // Write out the value columns.
+        for(int eventTriggerID = 0; eventTriggerID < 6; eventTriggerID++) {
+            // Print out the row header.
+            System.out.printf(headerFormat, TriggerDiagnosticUtil.TRIGGER_NAME[eventTriggerID]);
+            
+            // Print the cell values.
+            for(int seenTriggerID = 0; seenTriggerID < 4; seenTriggerID++) {
+                if(seenTriggerID == eventTriggerID) { System.out.print(nullText); }
+                else {
+                    String cellText = String.format(cellFormat, matchedStats[eventTriggerID][seenTriggerID],
+                            seenStats[eventTriggerID][seenTriggerID],
+                            (100.0 * matchedStats[eventTriggerID][seenTriggerID] / seenStats[eventTriggerID][seenTriggerID]));
+                    System.out.print(getCenteredString(cellText, columnWidth) + spacingText);
+                }
+            }
+            
+            // Output the number of events that had only the trigger
+            // type ID for the current trigger type flagged by the TI.
+            System.out.print(getCenteredString("" + getTITriggers(eventTriggerID, true), columnWidth) + spacingText);
+            
+            // Start a new line.
+            System.out.println();
+        }
+    }
+    
+    /**
+     * Produces a <code>String</code> of the indicated length with the
+     * text <code>value</code> centered in the middle. Extra length is
+     * filled through spaces before and after the text.
+     * @param value - The text to display.
+     * @param width - The number of spaces to include.
+     * @return Returns a <code>String</code> of the specified length,
+     * or the argument text if it is longer.
+     */
+    private static final String getCenteredString(String value, int width) {
+        // The method can not perform as intended if the argument text
+        // exceeds the requested string length. Just return the text.
+        if(width <= value.length()) {
+            return value;
+        }
+        
+        // Otherwise, get the amount of buffering needed to center the
+        // text and add it around the text to produce the string.
+        else {
+            int buffer = (width - value.length()) / 2;
+            return ComponentUtils.getChars(' ', buffer) + value
+                    + ComponentUtils.getChars(' ', width - buffer - value.length());
+        }
+    }
+    
+    /**
+     * Produces an exception if the argument trigger type is not of a
+     * supported type.
+     * @param triggerType - The trigger type to verify.
+     */
+    private static final void validateTriggerType(int triggerType) {
+        if(triggerType < 0 || triggerType > 5) {
+            throw new IndexOutOfBoundsException(String.format("Trigger type \"%d\" is not supported.", triggerType));
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerEvent.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerEvent.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerEvent.java	Wed Apr 27 11:11:32 2016
@@ -9,263 +9,255 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class TriggerEvent extends TriggerStatModule {
-	/**
-	 * Adds the statistics from one event object into this one.
-	 * @param event - The event data to add.
-	 */
-	public void addEvent(TriggerStatModule event) {
-		// Merge the values that do not depend on trigger source type.
-		reportedTriggers += event.reportedTriggers;
-		
-		// Merge each value that depends on the trigger source type.
-		for(int sourceType = 0; sourceType < 2; sourceType++) {
-			simTriggers[sourceType] += event.simTriggers[sourceType];
-			matchedTriggers[sourceType] += event.matchedTriggers[sourceType];
-			unmatchedTriggers[sourceType] += event.unmatchedTriggers[sourceType];
-			
-			// Merge the number of times each cut failed.
-			for(int cutID = 0; cutID < 4; cutID++) {
-				failedCuts[sourceType][cutID] += event.failedCuts[sourceType][cutID];
-			}
-			
-			// Copy the values for the TI flag trigger counters.
-			for(int tiType = 0; tiType < 6; tiType++) {
-				tiTriggersSeen[sourceType][tiType] += event.tiTriggersSeen[sourceType][tiType];
-				tiTriggersMatched[sourceType][tiType] += event.tiTriggersMatched[sourceType][tiType];
-			}
-		}
-	}
-	
-	/**
-	 * Indicates that a reconstructed trigger could not be matched, even
-	 * partially, to an SSP bank trigger.
-	 */
-	public void failedReconTrigger() {
-		unmatchedTriggers[RECON]++;
-	}
-	
-	/**
-	 * Indicates that an SSP simulated trigger could not be matched, even
-	 * partially, to an SSP bank trigger.
-	 */
-	public void failedSSPTrigger() {
-		unmatchedTriggers[SSP]++;
-	}
+    /**
+     * Adds the statistics from one event object into this one.
+     * @param event - The event data to add.
+     */
+    public void addEvent(TriggerStatModule event) {
+        // Merge the values that do not depend on trigger source type.
+        reportedTriggers += event.reportedTriggers;
+        
+        // Merge each value that depends on the trigger source type.
+        for(int sourceType = 0; sourceType < 2; sourceType++) {
+            simTriggers[sourceType] += event.simTriggers[sourceType];
+            matchedTriggers[sourceType] += event.matchedTriggers[sourceType];
+            unmatchedTriggers[sourceType] += event.unmatchedTriggers[sourceType];
+            
+            // Merge the number of times each cut failed.
+            for(int cutID = 0; cutID < 4; cutID++) {
+                failedCuts[sourceType][cutID] += event.failedCuts[sourceType][cutID];
+            }
+            
+            // Copy the values for the TI flag trigger counters.
+            for(int tiType = 0; tiType < 6; tiType++) {
+                tiTriggersSeen[sourceType][tiType] += event.tiTriggersSeen[sourceType][tiType];
+                tiTriggersMatched[sourceType][tiType] += event.tiTriggersMatched[sourceType][tiType];
+            }
+        }
+    }
+    
+    /**
+     * Indicates that a reconstructed trigger could not be matched, even
+     * partially, to an SSP bank trigger.
+     */
+    public void failedReconTrigger() {
+        unmatchedTriggers[RECON]++;
+    }
+    
+    /**
+     * Indicates that an SSP simulated trigger could not be matched, even
+     * partially, to an SSP bank trigger.
+     */
+    public void failedSSPTrigger() {
+        unmatchedTriggers[SSP]++;
+    }
 
-	/**
-	 * Indicates that a trigger simulated from a reconstructed cluster
-	 * was successfully matched to a trigger in the SSP bank.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param triggerTypeID - An identifier indicating the type of
-	 * trigger that was matched.
-	 */
-	public void matchedReconTrigger(boolean[] tiFlags) {
-		matchedTriggers(tiFlags, RECON);
-	}
-	
-	/**
-	 * Indicates that a trigger simulated from a reconstructed cluster
-	 * was partially matched to a trigger in the SSP bank, and notes
-	 * which cuts did and did not match.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param triggerTypeID - An identifier indicating the type of
-	 * trigger that was matched.
-	 * @param matchedCuts - An array of size 3 or 4 indicating which
-	 * cuts did and did not align between the triggers.
-	 */
-	public void matchedReconTrigger(boolean[] tiFlags, boolean[] matchedCuts) {
-		matchedTriggers(tiFlags, matchedCuts, RECON);
-	}
-	
-	/**
-	 * Indicates that a trigger simulated from an SSP bank cluster was
-	 * successfully matched to a trigger in the SSP bank.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param triggerTypeID - An identifier indicating the type of
-	 * trigger that was matched.
-	 */
-	public void matchedSSPTrigger(boolean[] tiFlags) {
-		matchedTriggers(tiFlags, SSP);
-	}
-	
-	/**
-	 * Indicates that a trigger simulated from an SSP bank cluster was
-	 * partially matched to a trigger in the SSP bank, and notes which
-	 * cuts did and did not match.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param triggerTypeID - An identifier indicating the type of
-	 * trigger that was matched.
-	 * @param matchedCuts - An array of size 3 or 4 indicating which
-	 * cuts did and did not align between the triggers.
-	 */
-	public void matchedSSPTrigger(boolean[] tiFlags, boolean[] matchedCuts) {
-		matchedTriggers(tiFlags, matchedCuts, SSP);
-	}
-	
-	/**
-	 * Indicates that a trigger simulated from a reconstructed cluster
-	 * was seen and increments the count for this type of trigger by one.
-	 * @param tiFlags - Whether or not each of the TI bank flags is
-	 * active or not.
-	 */
-	public void sawReconSimulatedTrigger(boolean[] tiFlags) {
-		sawReconSimulatedTriggers(tiFlags, 1);
-	}
-	
-	/**
-	 * Indicates that a number triggers simulated from reconstructed
-	 * clusters were seen and increments the count for this type of
-	 * trigger by the indicated number.
-	 * @param tiFlags - Whether or not each of the TI bank flags is
-	 * active or not.
-	 * @param count - The number of simulated triggers seen.
-	 */
-	public void sawReconSimulatedTriggers(boolean[] tiFlags, int count) {
-		// Increment the total count.
-		simTriggers[RECON] += count;
-		
-		// Increment the TI flag counters.
-		for(int tiType = 0; tiType < 6; tiType++) {
-			if(tiFlags[tiType]) {
-				tiTriggersSeen[RECON][tiType] += count;
-			}
-		}
-	}
-	
-	/**
-	 * Indicates that a trigger from the SSP trigger bank was seen and
-	 * increments the count for this type of trigger by one.
-	 */
-	public void sawReportedTrigger() {
-		sawReportedTriggers(1);
-	}
-	
-	/**
-	 * Indicates that a number triggers from the SSP trigger bank were
-	 * seen and increments the count for this type of trigger by the
-	 * indicated number.
-	 * @param count - The number of simulated triggers seen.
-	 */
-	public void sawReportedTriggers(int count) {
-		reportedTriggers += count;
-	}
-	
-	/**
-	 * Indicates that a trigger simulated from an SSP bank cluster was
-	 * seen and increments the count for this type of trigger by one.
-	 * @param tiFlags - Whether or not each of the TI bank flags is
-	 * active or not.
-	 */
-	public void sawSSPSimulatedTrigger(boolean[] tiFlags) {
-		sawSSPSimulatedTriggers(tiFlags, 1);
-	}
-	
-	/**
-	 * Indicates that a number triggers simulated from SSP bank clusters
-	 * were seen and increments the count for this type of trigger by
-	 * the indicated number.
-	 * @param tiFlags - Whether or not each of the TI bank flags is
-	 * active or not.
-	 * @param count - The number of simulated triggers seen.
-	 */
-	public void sawSSPSimulatedTriggers(boolean[] tiFlags, int count) {
-		// Increment the total count.
-		simTriggers[SSP] += count;
-		
-		// Increment the TI flag counters.
-		for(int tiType = 0; tiType < 6; tiType++) {
-			if(tiFlags[tiType]) {
-				tiTriggersSeen[SSP][tiType] += count;
-			}
-		}
-	}
-	
-	/**
-	 * Indicates that a simulated trigger was successfully matched to
-	 * an SSP bank trigger.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param sourceType - Uses <code>SSP</code> for triggers simulated
-	 * from an SSP bank cluster and <code>RECON</code> for triggers that
-	 * were simulated from a reconstructed cluster.
-	 */
-	private final void matchedTriggers(boolean[] tiFlags, int sourceType) {
-		// Increment the total triggers matched.
-		matchedTriggers[sourceType]++;
-		
-		// Increment the triggers matched for this type for each if
-		// the active TI bank flags.
-		for(int tiType = 0; tiType < 6; tiType++) {
-			if(tiFlags[tiType]) {
-				tiTriggersMatched[sourceType][tiType]++;
-			}
-		}
-	}
-	
-	/**
-	 * Indicates that a simulated trigger was partially matched to a
-	 * trigger in the SSP bank, and notes which cuts did and did not
-	 * match.
-	 * @param tiFlags - An array of size 6 indicating which TI bank
-	 * flags are active and which are not.
-	 * @param sourceType - Uses <code>SSP</code> for triggers simulated
-	 * from an SSP bank cluster and <code>RECON</code> for triggers that
-	 * were simulated from a reconstructed cluster.
-	 */
-	private void matchedTriggers(boolean[] tiFlags, boolean[] matchedCuts, int sourceType) {
-		// The matched cuts must be defined.
-		if(matchedCuts == null) {
-			throw new NullPointerException("The matched cuts array must be defined.");
-		}
-		
-		// The matched cuts array must be of either size 3 or 4.
-		if(matchedCuts.length != 3 && matchedCuts.length != 4) {
-			throw new IllegalArgumentException("All triggers must use either three or four cuts.");
-		}
-		
-		// Increment the counters for each cut that was no matched. Also
-		// track whether or not a cut actually failed.
-		boolean cutFailed = false;
-		for(int cutIndex = 0; cutIndex < matchedCuts.length; cutIndex++) {
-			if(!matchedCuts[cutIndex]) {
-				failedCuts[sourceType][cutIndex]++;
-				cutFailed = true;
-			}
-		}
-		
-		// If no cut failed, this is actually a match. Increment the
-		// appropriate counters.
-		if(!cutFailed) {
-			matchedTriggers(tiFlags, sourceType);
-		}
-	}
-	
-	@Deprecated
-	public String getPrintData() {
-		StringBuffer out = new StringBuffer();
+    /**
+     * Indicates that a trigger simulated from a reconstructed cluster
+     * was successfully matched to a trigger in the SSP bank.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     */
+    public void matchedReconTrigger(boolean[] tiFlags) {
+        matchedTriggers(tiFlags, RECON);
+    }
+    
+    /**
+     * Indicates that a trigger simulated from a reconstructed cluster
+     * was partially matched to a trigger in the SSP bank, and notes
+     * which cuts did and did not match.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     * @param matchedCuts - An array of size 3 or 4 indicating which
+     * cuts did and did not align between the triggers.
+     */
+    public void matchedReconTrigger(boolean[] tiFlags, boolean[] matchedCuts) {
+        matchedTriggers(tiFlags, matchedCuts, RECON);
+    }
+    
+    /**
+     * Indicates that a trigger simulated from an SSP bank cluster was
+     * successfully matched to a trigger in the SSP bank.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     */
+    public void matchedSSPTrigger(boolean[] tiFlags) {
+        matchedTriggers(tiFlags, SSP);
+    }
+    
+    /**
+     * Indicates that a trigger simulated from an SSP bank cluster was
+     * partially matched to a trigger in the SSP bank, and notes which
+     * cuts did and did not match.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     * @param matchedCuts - An array of size 3 or 4 indicating which
+     * cuts did and did not align between the triggers.
+     */
+    public void matchedSSPTrigger(boolean[] tiFlags, boolean[] matchedCuts) {
+        matchedTriggers(tiFlags, matchedCuts, SSP);
+    }
+    
+    /**
+     * Indicates that a trigger simulated from a reconstructed cluster
+     * was seen and increments the count for this type of trigger by one.
+     * @param tiFlags - Whether or not each of the TI bank flags is
+     * active or not.
+     */
+    public void sawReconSimulatedTrigger(boolean[] tiFlags) {
+        sawReconSimulatedTriggers(tiFlags, 1);
+    }
+    
+    /**
+     * Indicates that a number triggers simulated from reconstructed
+     * clusters were seen and increments the count for this type of
+     * trigger by the indicated number.
+     * @param tiFlags - Whether or not each of the TI bank flags is
+     * active or not.
+     * @param count - The number of simulated triggers seen.
+     */
+    public void sawReconSimulatedTriggers(boolean[] tiFlags, int count) {
+        // Increment the total count.
+        simTriggers[RECON] += count;
+        
+        // Increment the TI flag counters.
+        for(int tiType = 0; tiType < 6; tiType++) {
+            if(tiFlags[tiType]) {
+                tiTriggersSeen[RECON][tiType] += count;
+            }
+        }
+    }
+    
+    /**
+     * Indicates that a trigger from the SSP trigger bank was seen and
+     * increments the count for this type of trigger by one.
+     */
+    public void sawReportedTrigger() {
+        sawReportedTriggers(1);
+    }
+    
+    /**
+     * Indicates that a number triggers from the SSP trigger bank were
+     * seen and increments the count for this type of trigger by the
+     * indicated number.
+     * @param count - The number of simulated triggers seen.
+     */
+    public void sawReportedTriggers(int count) {
+        reportedTriggers += count;
+    }
+    
+    /**
+     * Indicates that a trigger simulated from an SSP bank cluster was
+     * seen and increments the count for this type of trigger by one.
+     * @param tiFlags - Whether or not each of the TI bank flags is
+     * active or not.
+     */
+    public void sawSSPSimulatedTrigger(boolean[] tiFlags) {
+        sawSSPSimulatedTriggers(tiFlags, 1);
+    }
+    
+    /**
+     * Indicates that a number triggers simulated from SSP bank clusters
+     * were seen and increments the count for this type of trigger by
+     * the indicated number.
+     * @param tiFlags - Whether or not each of the TI bank flags is
+     * active or not.
+     * @param count - The number of simulated triggers seen.
+     */
+    public void sawSSPSimulatedTriggers(boolean[] tiFlags, int count) {
+        // Increment the total count.
+        simTriggers[SSP] += count;
+        
+        // Increment the TI flag counters.
+        for(int tiType = 0; tiType < 6; tiType++) {
+            if(tiFlags[tiType]) {
+                tiTriggersSeen[SSP][tiType] += count;
+            }
+        }
+    }
+    
+    /**
+     * Indicates that a simulated trigger was successfully matched to
+     * an SSP bank trigger.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     * @param sourceType - Uses <code>SSP</code> for triggers simulated
+     * from an SSP bank cluster and <code>RECON</code> for triggers that
+     * were simulated from a reconstructed cluster.
+     */
+    private final void matchedTriggers(boolean[] tiFlags, int sourceType) {
+        // Increment the total triggers matched.
+        matchedTriggers[sourceType]++;
+        
+        // Increment the triggers matched for this type for each if
+        // the active TI bank flags.
+        for(int tiType = 0; tiType < 6; tiType++) {
+            if(tiFlags[tiType]) {
+                tiTriggersMatched[sourceType][tiType]++;
+            }
+        }
+    }
+    
+    /**
+     * Indicates that a simulated trigger was partially matched to a
+     * trigger in the SSP bank, and notes which cuts did and did not
+     * match.
+     * @param tiFlags - An array of size 6 indicating which TI bank
+     * flags are active and which are not.
+     * @param sourceType - Uses <code>SSP</code> for triggers simulated
+     * from an SSP bank cluster and <code>RECON</code> for triggers that
+     * were simulated from a reconstructed cluster.
+     */
+    private void matchedTriggers(boolean[] tiFlags, boolean[] matchedCuts, int sourceType) {
+        // The matched cuts must be defined.
+        if(matchedCuts == null) {
+            throw new NullPointerException("The matched cuts array must be defined.");
+        }
+        
+        // The matched cuts array must be of either size 3 or 4.
+        if(matchedCuts.length != 3 && matchedCuts.length != 4) {
+            throw new IllegalArgumentException("All triggers must use either three or four cuts.");
+        }
+        
+        // Increment the counters for each cut that was no matched. Also
+        // track whether or not a cut actually failed.
+        boolean cutFailed = false;
+        for(int cutIndex = 0; cutIndex < matchedCuts.length; cutIndex++) {
+            if(!matchedCuts[cutIndex]) {
+                failedCuts[sourceType][cutIndex]++;
+                cutFailed = true;
+            }
+        }
+        
+        // If no cut failed, this is actually a match. Increment the
+        // appropriate counters.
+        if(!cutFailed) {
+            matchedTriggers(tiFlags, sourceType);
+        }
+    }
+    
+    @Deprecated
+    public String getPrintData() {
+        StringBuffer out = new StringBuffer();
 
-		out.append("\n");
-		out.append("Trigger Result\n");
-		out.append("SSP Sim Triggers    :: " + simTriggers[SSP] + "\n");
-		out.append("Recon Sim Triggers  :: " + simTriggers[RECON] + "\n");
-		out.append("Reported Triggers   :: " + reportedTriggers + "\n");
-		out.append(String.format("Internal Efficiency :: %d / %d (%7.3f)%n", matchedTriggers[SSP], simTriggers[SSP],
-				(100.0 * matchedTriggers[SSP] / simTriggers[SSP])));
-		out.append(String.format("Trigger Efficiency  :: %d / %d (%7.3f)%n", matchedTriggers[RECON], simTriggers[RECON],
-				(100.0 * matchedTriggers[RECON] / simTriggers[RECON])));
-		
-		out.append("\n");
-		out.append("Individual Cut Failure Rates\n");
-		out.append("Unmatched Triggers   :: " + unmatchedTriggers[SSP] + "\n");
-		for(int i = 0; i < 4; i++) {
-			out.append(String.format("\tCut %d :: %d / %d (%7.3f)%n", i, failedCuts[SSP][i], simTriggers[SSP],
-					(100.0 * failedCuts[SSP][i] / simTriggers[SSP])));
-		}
-		
-		return out.toString();
-	}
+        out.append("\n");
+        out.append("Trigger Result\n");
+        out.append("SSP Sim Triggers    :: " + simTriggers[SSP] + "\n");
+        out.append("Recon Sim Triggers  :: " + simTriggers[RECON] + "\n");
+        out.append("Reported Triggers   :: " + reportedTriggers + "\n");
+        out.append(String.format("Internal Efficiency :: %d / %d (%7.3f)%n", matchedTriggers[SSP], simTriggers[SSP],
+                (100.0 * matchedTriggers[SSP] / simTriggers[SSP])));
+        out.append(String.format("Trigger Efficiency  :: %d / %d (%7.3f)%n", matchedTriggers[RECON], simTriggers[RECON],
+                (100.0 * matchedTriggers[RECON] / simTriggers[RECON])));
+        
+        out.append("\n");
+        out.append("Individual Cut Failure Rates\n");
+        out.append("Unmatched Triggers   :: " + unmatchedTriggers[SSP] + "\n");
+        for(int i = 0; i < 4; i++) {
+            out.append(String.format("\tCut %d :: %d / %d (%7.3f)%n", i, failedCuts[SSP][i], simTriggers[SSP],
+                    (100.0 * failedCuts[SSP][i] / simTriggers[SSP])));
+        }
+        
+        return out.toString();
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerStatModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerStatModule.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/data/TriggerStatModule.java	Wed Apr 27 11:11:32 2016
@@ -10,285 +10,281 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class TriggerStatModule {
-	// Store the reference index for SSP simulated triggers and recon
-	// simulated triggers.
-	protected static final int SSP = 0;
-	protected static final int RECON = 1;
-	
-	// Define TI trigger type identifiers.
-	public static final int SINGLES_0 = 0;
-	public static final int SINGLES_1 = 1;
-	public static final int PAIR_0    = 2;
-	public static final int PAIR_1    = 3;
-	public static final int PULSER    = 4;
-	public static final int COSMIC    = 5;
-	
-	// Track the number of simulated triggers seen for each source type.
-	// SSP simulated triggers from the SSP bank clusters. Reconstructed
-	// simulated triggers come from clusters built from FADC data.
-	protected int[] simTriggers = new int[2];
-	
-	// Also track the number of triggers reported by the SSP bank.
-	protected int reportedTriggers = 0;
-	
-	// Track the number of simulated triggers of each type that were
-	// successfully matched.
-	protected int[] matchedTriggers = new int[2];
-	
-	// Track the number of simulated triggers that could not be matched
-	// at all.
-	protected int[] unmatchedTriggers = new int[2];
-	
-	// Track which cuts succeeded and which cuts failed for each type.
-	// Note that this is currently only tracked for SSP cluster triggers.
-	protected int[][] failedCuts = new int[2][4];
-	
-	// Store the number of trigger matches seen over all events that
-	// contain a given TI flag.
-	protected int[][] tiTriggersSeen = new int[2][6];
-	protected int[][] tiTriggersMatched = new int[2][6];
-	
-	/**
-	 * Clears all of the statistical counters in the object.
-	 */
-	void clear() {
-		// Clear all values.
-		for(int sourceType = 0; sourceType < 2; sourceType++) {
-			// Clear the general statistics.
-			simTriggers[sourceType]       = 0;
-			matchedTriggers[sourceType]   = 0;
-			unmatchedTriggers[sourceType] = 0;
-			
-			// Clear the cut failure statistics.
-			for(int cutID = 0; cutID < 4; cutID++) {
-				failedCuts[sourceType][cutID] = 0;
-			}
-			
-			// Clear the TI flag statistics.
-			for(int tiType = 0; tiType < 6; tiType++) {
-				tiTriggersSeen[sourceType][tiType]    = 0;
-				tiTriggersMatched[sourceType][tiType] = 0;
-			}
-		}
-	}
-	
-	@Override
-	public TriggerStatModule clone() {
-		// Make a new statistics module.
-		TriggerStatModule clone = new TriggerStatModule();
-		
-		// Copy the values that do not depend on trigger source type.
-		clone.reportedTriggers = reportedTriggers;
-		
-		// Set each value that depends on the trigger source type.
-		for(int sourceType = 0; sourceType < 2; sourceType++) {
-			clone.simTriggers[sourceType] = simTriggers[sourceType];
-			clone.matchedTriggers[sourceType] = matchedTriggers[sourceType];
-			clone.unmatchedTriggers[sourceType] = unmatchedTriggers[sourceType];
-			
-			// Set the number of times each cut failed.
-			for(int cutID = 0; cutID < 4; cutID++) {
-				clone.failedCuts[sourceType][cutID] = failedCuts[sourceType][cutID];
-			}
-			
-			// Copy the values for the TI flag trigger counters.
-			for(int tiType = 0; tiType < 6; tiType++) {
-				clone.tiTriggersSeen[sourceType][tiType] = tiTriggersSeen[sourceType][tiType];
-				clone.tiTriggersMatched[sourceType][tiType] = tiTriggersMatched[sourceType][tiType];
-			}
-		}
-		
-		// Return the copied clone.
-		return clone;
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were not matched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getFailedReconSimulatedTriggers() {
-		return simTriggers[RECON] - matchedTriggers[RECON];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were not matched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getFailedSSPSimulatedTriggers() {
-		return simTriggers[SSP] - matchedTriggers[SSP];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were matched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getMatchedReconSimulatedTriggers() {
-		return matchedTriggers[RECON];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were matched for a given type of trigger when a given TI
-	 * bank flag was active.
-	 * @param tiTypeID - The identifier for the type of TI bank trigger
-	 * that should be active.
-	 * @param triggerTypeID - The identifier for the type of trigger.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getMatchedReconSimulatedTriggers(int tiTypeID) {
-		return tiTriggersMatched[RECON][tiTypeID];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were matched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getMatchedSSPSimulatedTriggers() {
-		return matchedTriggers[SSP];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were matched for a given type of trigger when a given TI
-	 * bank flag was active.
-	 * @param tiTypeID - The identifier for the type of TI bank trigger
-	 * that should be active.
-	 * @param triggerTypeID - The identifier for the type of trigger.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getMatchedSSPSimulatedTriggers(int tiTypeID) {
-		return tiTriggersMatched[SSP][tiTypeID];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were matched, but did not see full cut alignment.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getPartiallyMatchedReconSimulatedTriggers() {
-		return simTriggers[RECON] - (matchedTriggers[RECON] + unmatchedTriggers[RECON]);
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were matched, but did not see full cut alignment.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getPartiallyMatchedSSPSimulatedTriggers() {
-		return simTriggers[SSP] - (matchedTriggers[SSP] + unmatchedTriggers[SSP]);
-	}
-	
-	/**
-	 * Gets the number of times the specified cut failed for triggers
-	 * that were partially matched for triggers simulated from FADC
-	 * reconstructed clusters.
-	 * @param cutIndex - The numerical cut identifier.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getReconCutFailures(int cutIndex) {
-		return getCutFailures(RECON, cutIndex);
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were seen.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getReconSimulatedTriggers() {
-		return simTriggers[RECON];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were seen for a given trigger type when a given TI bank
-	 * flag was active.
-	 * @param tiTypeID - The identifier for the type of TI bank trigger
-	 * that should be active.
-	 * @param triggerTypeID - The identifier for the type of trigger.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getReconSimulatedTriggers(int tiTypeID) {
-		return tiTriggersSeen[RECON][tiTypeID];
-	}
-	
-	/**
-	 * Gets the number of triggers reported by the SSP bank.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getReportedTriggers() {
-		return reportedTriggers;
-	}
-	
-	/**
-	 * Gets the number of times the specified cut failed for triggers
-	 * that were partially matched for triggers simulated from SSP
-	 * bank clusters.
-	 * @param cutIndex - The numerical cut identifier.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getSSPCutFailures(int cutIndex) {
-		return getCutFailures(SSP, cutIndex);
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were seen.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getSSPSimulatedTriggers() {
-		return simTriggers[SSP];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were seen for a given trigger type when a given TI bank
-	 * flag was active.
-	 * @param tiTypeID - The identifier for the type of TI bank trigger
-	 * that should be active.
-	 * @param triggerTypeID - The identifier for the type of trigger.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getSSPSimulatedTriggers(int tiTypeID) {
-		return tiTriggersSeen[SSP][tiTypeID];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from reconstructed clusters
-	 * that were completely unmatched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getUnmatchedReconSimulatedTriggers() {
-		return unmatchedTriggers[RECON];
-	}
-	
-	/**
-	 * Gets the number of simulated triggers from SSP bank clusters
-	 * that were completely unmatched.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	public int getUnmatchedSSPSimulatedTriggers() {
-		return unmatchedTriggers[SSP];
-	}
-	
-	/**
-	 * Gets the number of times the specified cut failed for triggers
-	 * that were partially matched for triggers simulated from the type
-	 * of cluster indicated.
-	 * @param type - Either <code>SSP</code> or <code>RECON</code>.
-	 * @param cutIndex - The numerical cut identifier.
-	 * @return Returns the number of triggers as an <code>int</code>.
-	 */
-	private int getCutFailures(int type, int cutIndex) {
-		// Ensure that the cut index is valid.
-		if(cutIndex < 0 || cutIndex >= 4) {
-			throw new IndexOutOfBoundsException(String.format("Cut index \"%d\" is not recognized.", cutIndex));
-		}
-		
-		// Return the cut failures.
-		return failedCuts[type][cutIndex];
-	}
+    // Store the reference index for SSP simulated triggers and recon
+    // simulated triggers.
+    protected static final int SSP = 0;
+    protected static final int RECON = 1;
+    
+    // Define TI trigger type identifiers.
+    public static final int SINGLES_0 = 0;
+    public static final int SINGLES_1 = 1;
+    public static final int PAIR_0    = 2;
+    public static final int PAIR_1    = 3;
+    public static final int PULSER    = 4;
+    public static final int COSMIC    = 5;
+    
+    // Track the number of simulated triggers seen for each source type.
+    // SSP simulated triggers from the SSP bank clusters. Reconstructed
+    // simulated triggers come from clusters built from FADC data.
+    protected int[] simTriggers = new int[2];
+    
+    // Also track the number of triggers reported by the SSP bank.
+    protected int reportedTriggers = 0;
+    
+    // Track the number of simulated triggers of each type that were
+    // successfully matched.
+    protected int[] matchedTriggers = new int[2];
+    
+    // Track the number of simulated triggers that could not be matched
+    // at all.
+    protected int[] unmatchedTriggers = new int[2];
+    
+    // Track which cuts succeeded and which cuts failed for each type.
+    // Note that this is currently only tracked for SSP cluster triggers.
+    protected int[][] failedCuts = new int[2][4];
+    
+    // Store the number of trigger matches seen over all events that
+    // contain a given TI flag.
+    protected int[][] tiTriggersSeen = new int[2][6];
+    protected int[][] tiTriggersMatched = new int[2][6];
+    
+    /**
+     * Clears all of the statistical counters in the object.
+     */
+    void clear() {
+        // Clear all values.
+        for(int sourceType = 0; sourceType < 2; sourceType++) {
+            // Clear the general statistics.
+            simTriggers[sourceType]       = 0;
+            matchedTriggers[sourceType]   = 0;
+            unmatchedTriggers[sourceType] = 0;
+            
+            // Clear the cut failure statistics.
+            for(int cutID = 0; cutID < 4; cutID++) {
+                failedCuts[sourceType][cutID] = 0;
+            }
+            
+            // Clear the TI flag statistics.
+            for(int tiType = 0; tiType < 6; tiType++) {
+                tiTriggersSeen[sourceType][tiType]    = 0;
+                tiTriggersMatched[sourceType][tiType] = 0;
+            }
+        }
+    }
+    
+    @Override
+    public TriggerStatModule clone() {
+        // Make a new statistics module.
+        TriggerStatModule clone = new TriggerStatModule();
+        
+        // Copy the values that do not depend on trigger source type.
+        clone.reportedTriggers = reportedTriggers;
+        
+        // Set each value that depends on the trigger source type.
+        for(int sourceType = 0; sourceType < 2; sourceType++) {
+            clone.simTriggers[sourceType] = simTriggers[sourceType];
+            clone.matchedTriggers[sourceType] = matchedTriggers[sourceType];
+            clone.unmatchedTriggers[sourceType] = unmatchedTriggers[sourceType];
+            
+            // Set the number of times each cut failed.
+            for(int cutID = 0; cutID < 4; cutID++) {
+                clone.failedCuts[sourceType][cutID] = failedCuts[sourceType][cutID];
+            }
+            
+            // Copy the values for the TI flag trigger counters.
+            for(int tiType = 0; tiType < 6; tiType++) {
+                clone.tiTriggersSeen[sourceType][tiType] = tiTriggersSeen[sourceType][tiType];
+                clone.tiTriggersMatched[sourceType][tiType] = tiTriggersMatched[sourceType][tiType];
+            }
+        }
+        
+        // Return the copied clone.
+        return clone;
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were not matched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getFailedReconSimulatedTriggers() {
+        return simTriggers[RECON] - matchedTriggers[RECON];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were not matched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getFailedSSPSimulatedTriggers() {
+        return simTriggers[SSP] - matchedTriggers[SSP];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were matched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getMatchedReconSimulatedTriggers() {
+        return matchedTriggers[RECON];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were matched for a given type of trigger when a given TI
+     * bank flag was active.
+     * @param tiTypeID - The identifier for the type of TI bank trigger
+     * that should be active.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getMatchedReconSimulatedTriggers(int tiTypeID) {
+        return tiTriggersMatched[RECON][tiTypeID];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were matched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getMatchedSSPSimulatedTriggers() {
+        return matchedTriggers[SSP];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were matched for a given type of trigger when a given TI
+     * bank flag was active.
+     * @param tiTypeID - The identifier for the type of TI bank trigger
+     * that should be active.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getMatchedSSPSimulatedTriggers(int tiTypeID) {
+        return tiTriggersMatched[SSP][tiTypeID];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were matched, but did not see full cut alignment.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getPartiallyMatchedReconSimulatedTriggers() {
+        return simTriggers[RECON] - (matchedTriggers[RECON] + unmatchedTriggers[RECON]);
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were matched, but did not see full cut alignment.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getPartiallyMatchedSSPSimulatedTriggers() {
+        return simTriggers[SSP] - (matchedTriggers[SSP] + unmatchedTriggers[SSP]);
+    }
+    
+    /**
+     * Gets the number of times the specified cut failed for triggers
+     * that were partially matched for triggers simulated from FADC
+     * reconstructed clusters.
+     * @param cutIndex - The numerical cut identifier.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getReconCutFailures(int cutIndex) {
+        return getCutFailures(RECON, cutIndex);
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were seen.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getReconSimulatedTriggers() {
+        return simTriggers[RECON];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were seen for a given trigger type when a given TI bank
+     * flag was active.
+     * @param tiTypeID - The identifier for the type of TI bank trigger
+     * that should be active.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getReconSimulatedTriggers(int tiTypeID) {
+        return tiTriggersSeen[RECON][tiTypeID];
+    }
+    
+    /**
+     * Gets the number of triggers reported by the SSP bank.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getReportedTriggers() {
+        return reportedTriggers;
+    }
+    
+    /**
+     * Gets the number of times the specified cut failed for triggers
+     * that were partially matched for triggers simulated from SSP
+     * bank clusters.
+     * @param cutIndex - The numerical cut identifier.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getSSPCutFailures(int cutIndex) {
+        return getCutFailures(SSP, cutIndex);
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were seen.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getSSPSimulatedTriggers() {
+        return simTriggers[SSP];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were seen for a given trigger type when a given TI bank
+     * flag was active.
+     * @param tiTypeID - The identifier for the type of TI bank trigger
+     * that should be active.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getSSPSimulatedTriggers(int tiTypeID) {
+        return tiTriggersSeen[SSP][tiTypeID];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from reconstructed clusters
+     * that were completely unmatched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getUnmatchedReconSimulatedTriggers() {
+        return unmatchedTriggers[RECON];
+    }
+    
+    /**
+     * Gets the number of simulated triggers from SSP bank clusters
+     * that were completely unmatched.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    public int getUnmatchedSSPSimulatedTriggers() {
+        return unmatchedTriggers[SSP];
+    }
+    
+    /**
+     * Gets the number of times the specified cut failed for triggers
+     * that were partially matched for triggers simulated from the type
+     * of cluster indicated.
+     * @param type - Either <code>SSP</code> or <code>RECON</code>.
+     * @param cutIndex - The numerical cut identifier.
+     * @return Returns the number of triggers as an <code>int</code>.
+     */
+    private int getCutFailures(int type, int cutIndex) {
+        // Ensure that the cut index is valid.
+        if(cutIndex < 0 || cutIndex >= 4) {
+            throw new IndexOutOfBoundsException(String.format("Cut index \"%d\" is not recognized.", cutIndex));
+        }
+        
+        // Return the cut failures.
+        return failedCuts[type][cutIndex];
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/event/TriggerPlotsModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/event/TriggerPlotsModule.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/event/TriggerPlotsModule.java	Wed Apr 27 11:11:32 2016
@@ -16,383 +16,383 @@
  * @author Kyle McCarty
  */
 public class TriggerPlotsModule {
-	// Reference variables.
-	private static final int RECON     = 0;
-	private static final int SSP       = 1;
-	private static final int ALL       = 0;
-	private static final int MATCHED   = 1;
-	private static final int FAILED    = 2;
-	private static final int TRIGGERED = 3;
-	private static final int NO_CUTS   = 4;
-	
-	// Class variables.
-	private final double[] energySlopeParamF;
-	private static final double MØLLER_SUM_THRESHOLD = 0.750;
-	
-	// Plots.
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D[][][] singlesClusterEnergyPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] singlesHitCountPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] singlesTriggerTimePlot = new IHistogram1D[2][2][5];
-	
-	private IHistogram1D[][][] pairClusterEnergyPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairHitCountPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairTimePlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairSumPlot = new IHistogram1D[2][2][5];
+    // Reference variables.
+    private static final int RECON     = 0;
+    private static final int SSP       = 1;
+    private static final int ALL       = 0;
+    private static final int MATCHED   = 1;
+    private static final int FAILED    = 2;
+    private static final int TRIGGERED = 3;
+    private static final int NO_CUTS   = 4;
+    
+    // Class variables.
+    private final double[] energySlopeParamF;
+    private static final double MØLLER_SUM_THRESHOLD = 0.750;
+    
+    // Plots.
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D[][][] singlesClusterEnergyPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] singlesHitCountPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] singlesTriggerTimePlot = new IHistogram1D[2][2][5];
+    
+    private IHistogram1D[][][] pairClusterEnergyPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairHitCountPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairTimePlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairSumPlot = new IHistogram1D[2][2][5];
     private IHistogram2D[][][] pairSumEnergiesPlot = new IHistogram2D[2][2][5];
-	private IHistogram1D[][][] pairDiffPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairSlopePlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairCoplanarityPlot = new IHistogram1D[2][2][5];
-	private IHistogram1D[][][] pairTriggerTimePlot = new IHistogram1D[2][2][5];
-	
-	private IHistogram1D[] møllerClusterEnergyPlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerHitCountPlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerTimePlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerSumPlot = new IHistogram1D[2];
+    private IHistogram1D[][][] pairDiffPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairSlopePlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairCoplanarityPlot = new IHistogram1D[2][2][5];
+    private IHistogram1D[][][] pairTriggerTimePlot = new IHistogram1D[2][2][5];
+    
+    private IHistogram1D[] møllerClusterEnergyPlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerHitCountPlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerTimePlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerSumPlot = new IHistogram1D[2];
     private IHistogram2D[] møllerSumEnergiesPlot = new IHistogram2D[2];
-	private IHistogram1D[] møllerDiffPlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerSlopePlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerCoplanarityPlot = new IHistogram1D[2];
-	private IHistogram1D[] møllerTriggerTimePlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerDiffPlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerSlopePlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerCoplanarityPlot = new IHistogram1D[2];
+    private IHistogram1D[] møllerTriggerTimePlot = new IHistogram1D[2];
     private IHistogram2D[] møllerPositionPlot = new IHistogram2D[2];
-	
-	private IHistogram1D[] tridentClusterEnergyPlot = new IHistogram1D[2];
-	private IHistogram1D[] tridentHitCountPlot = new IHistogram1D[2];
+    
+    private IHistogram1D[] tridentClusterEnergyPlot = new IHistogram1D[2];
+    private IHistogram1D[] tridentHitCountPlot = new IHistogram1D[2];
     private IHistogram2D[] tridentPositionPlot = new IHistogram2D[2];
-	
-	/**
-	 * Instantiates a new <code>TriggerPlotsModule</code> that will use
-	 * the indicated values for the energy slope conversion factor when
-	 * plotting energy slope values. Plots will be attached to the
-	 * default AIDA instance.
-	 * @param trigger0F - The energy slope conversion factor for the
-	 * first trigger.
-	 * @param trigger1F - The energy slope conversion factor for the
-	 * second trigger.
-	 */
-	public TriggerPlotsModule(double trigger0F, double trigger1F) {
-		// Store the energy slope parameter.
-		energySlopeParamF = new double[2];
-		energySlopeParamF[0] = trigger0F;
-		energySlopeParamF[1] = trigger1F;
-		
-		// Define type string values.
-		String[] sourceType = { "Recon", "SSP" };
-		String[] resultType = { "All", "Matched", "Failed", "Triggered", "No Cuts" };
-		
-		// Instantiate the trigger result plots for each trigger.
-		for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-			// Get the directory for the current triggers.
-			String pairDir = "Pair Trigger " + triggerNum;
-			String singlesDir = "Singles Trigger " + triggerNum;
-			
-			// Instantiate the trigger result plots for each type of
-			// trigger source object.
-			for(int source = 0; source < 2; source++) {
-				// Instantiate the trigger result plots for each type
-				// of trigger match result.
-				for(int result = 0; result < 5; result++) {
-					// Instantiate the singles trigger plots.
-					singlesClusterEnergyPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Cluster Energy (%s)",
-							singlesDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
-					singlesHitCountPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Hit Count (%s)",
-							singlesDir, sourceType[source], resultType[result]), 9, 0.5, 9.5);
-					singlesTriggerTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Trigger Time (%s)",
-							singlesDir, sourceType[source], resultType[result]), 100, 0, 400);
-					
-					// Instantiate the pair trigger plots.
-					pairHitCountPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Hit Count (%s)",
-							pairDir, sourceType[source], resultType[result]), 9, 0.5, 9.5);
-					pairClusterEnergyPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Cluster Energy (%s)",
-							pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
-					pairTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Time Coincidence (%s)",
-							pairDir, sourceType[source], resultType[result]), 8, 0, 32);
-					pairSumPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Sum (%s)",
-							pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
+    
+    /**
+     * Instantiates a new <code>TriggerPlotsModule</code> that will use
+     * the indicated values for the energy slope conversion factor when
+     * plotting energy slope values. Plots will be attached to the
+     * default AIDA instance.
+     * @param trigger0F - The energy slope conversion factor for the
+     * first trigger.
+     * @param trigger1F - The energy slope conversion factor for the
+     * second trigger.
+     */
+    public TriggerPlotsModule(double trigger0F, double trigger1F) {
+        // Store the energy slope parameter.
+        energySlopeParamF = new double[2];
+        energySlopeParamF[0] = trigger0F;
+        energySlopeParamF[1] = trigger1F;
+        
+        // Define type string values.
+        String[] sourceType = { "Recon", "SSP" };
+        String[] resultType = { "All", "Matched", "Failed", "Triggered", "No Cuts" };
+        
+        // Instantiate the trigger result plots for each trigger.
+        for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
+            // Get the directory for the current triggers.
+            String pairDir = "Pair Trigger " + triggerNum;
+            String singlesDir = "Singles Trigger " + triggerNum;
+            
+            // Instantiate the trigger result plots for each type of
+            // trigger source object.
+            for(int source = 0; source < 2; source++) {
+                // Instantiate the trigger result plots for each type
+                // of trigger match result.
+                for(int result = 0; result < 5; result++) {
+                    // Instantiate the singles trigger plots.
+                    singlesClusterEnergyPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Cluster Energy (%s)",
+                            singlesDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
+                    singlesHitCountPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Hit Count (%s)",
+                            singlesDir, sourceType[source], resultType[result]), 9, 0.5, 9.5);
+                    singlesTriggerTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Singles Trigger Time (%s)",
+                            singlesDir, sourceType[source], resultType[result]), 100, 0, 400);
+                    
+                    // Instantiate the pair trigger plots.
+                    pairHitCountPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Hit Count (%s)",
+                            pairDir, sourceType[source], resultType[result]), 9, 0.5, 9.5);
+                    pairClusterEnergyPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Cluster Energy (%s)",
+                            pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
+                    pairTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Time Coincidence (%s)",
+                            pairDir, sourceType[source], resultType[result]), 8, 0, 32);
+                    pairSumPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Sum (%s)",
+                            pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
                                         pairSumEnergiesPlot[triggerNum][source][result] = aida.histogram2D(String.format("%s/%s/Pair 2D Energy Sum (%s)",
                                                         pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0, 300, 0.0, 3.0);
-					pairDiffPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Difference (%s)",
-							pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
-					pairSlopePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Slope (%s)",
-							pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
-					pairCoplanarityPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Coplanarity (%s)",
-							pairDir, sourceType[source], resultType[result]), 180, 0, 180);
-					pairTriggerTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Trigger Time (%s)",
-							pairDir, sourceType[source], resultType[result]), 100, 0, 400);
-				}
-			}
-			
-			// Instantiate the Møller plots.
-			møllerHitCountPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Hit Count",
-					pairDir), 9, 0.5, 9.5);
-			møllerClusterEnergyPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Cluster Energy",
-					pairDir), 300, 0.0, 3.0);
-			møllerTimePlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Time Coincidence",
-					pairDir), 8, 0, 32);
-			møllerSumPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Energy Sum",
-					pairDir), 300, 0.0, 3.0);
-			møllerSumEnergiesPlot[triggerNum] = aida.histogram2D(String.format("%s/Møller/Møller-like Pair 2D Energy Sum",
+                    pairDiffPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Difference (%s)",
+                            pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
+                    pairSlopePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Energy Slope (%s)",
+                            pairDir, sourceType[source], resultType[result]), 300, 0.0, 3.0);
+                    pairCoplanarityPlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Coplanarity (%s)",
+                            pairDir, sourceType[source], resultType[result]), 180, 0, 180);
+                    pairTriggerTimePlot[triggerNum][source][result] = aida.histogram1D(String.format("%s/%s/Pair Trigger Time (%s)",
+                            pairDir, sourceType[source], resultType[result]), 100, 0, 400);
+                }
+            }
+            
+            // Instantiate the Møller plots.
+            møllerHitCountPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Hit Count",
+                    pairDir), 9, 0.5, 9.5);
+            møllerClusterEnergyPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Cluster Energy",
+                    pairDir), 300, 0.0, 3.0);
+            møllerTimePlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Time Coincidence",
+                    pairDir), 8, 0, 32);
+            møllerSumPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Energy Sum",
+                    pairDir), 300, 0.0, 3.0);
+            møllerSumEnergiesPlot[triggerNum] = aida.histogram2D(String.format("%s/Møller/Møller-like Pair 2D Energy Sum",
                     pairDir), 300, 0.0, 3.0, 300, 0.0, 3.0);
             møllerDiffPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Energy Difference",
-					pairDir), 300, 0.0, 3.0);
+                    pairDir), 300, 0.0, 3.0);
             møllerSlopePlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Energy Slope",
-					pairDir), 300, 0.0, 3.0);
+                    pairDir), 300, 0.0, 3.0);
             møllerCoplanarityPlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Coplanarity",
-					pairDir), 180, 0, 180);
+                    pairDir), 180, 0, 180);
             møllerTriggerTimePlot[triggerNum] = aida.histogram1D(String.format("%s/Møller/Møller-like Pair Trigger Time",
-					pairDir), 100, 0, 400);
+                    pairDir), 100, 0, 400);
             møllerPositionPlot[triggerNum] = aida.histogram2D(String.format("%s/Møller/Møller-like Pair Position",
-					pairDir), 46, -23, 23, 11, -5.5, 5.5);
+                    pairDir), 46, -23, 23, 11, -5.5, 5.5);
             
             // Instantiate the trident plots.
             tridentHitCountPlot[triggerNum] = aida.histogram1D(String.format("%s/Trident/Trident-like Pair Hit Count",
-            		singlesDir), 9, 0.5, 9.5);
-			tridentClusterEnergyPlot[triggerNum] = aida.histogram1D(String.format("%s/Trident/Trident-like Pair Cluster Energy",
-					singlesDir), 300, 0.0, 3.0);
+                    singlesDir), 9, 0.5, 9.5);
+            tridentClusterEnergyPlot[triggerNum] = aida.histogram1D(String.format("%s/Trident/Trident-like Pair Cluster Energy",
+                    singlesDir), 300, 0.0, 3.0);
             tridentPositionPlot[triggerNum] = aida.histogram2D(String.format("%s/Trident/Trident-like Pair Position",
-            		singlesDir), 46, -23, 23, 11, -5.5, 5.5);
-		}
-	}
-	
-	/**
-	 * Populates the "failed" plots of the appropriate type with the
-	 * cut results from the argument trigger.
-	 * @param trigger - The trigger from which to populate the plots.
-	 */
-	public void failedTrigger(Trigger<?> trigger) {
-		processTrigger(trigger, FAILED);
-	}
-	
-	/**
-	 * Populates the "matched" plots of the appropriate type with the
-	 * cut results from the argument trigger.
-	 * @param trigger - The trigger from which to populate the plots.
-	 */
-	public void matchedTrigger(Trigger<?> trigger) {
-		processTrigger(trigger, MATCHED);
-	}
-	
-	/**
-	 * Populates the "triggered" plots of the appropriate type with the
-	 * cut results from the argument trigger.
-	 * @param trigger - The trigger from which to populate the plots.
-	 */
-	public void passedTrigger(Trigger<?> trigger) {
-		processTrigger(trigger, TRIGGERED);
-	}
-	
-	/**
-	 * Indicates that a cluster was seen by a trigger and adds it to
-	 * the "no cuts" plots.
-	 * @param triggerNum - The number of the trigger.
-	 * @param cluster - The cluster that was seen.
-	 */
-	public void sawCluster(int triggerNum, Cluster cluster) {
-		processSingles(triggerNum, NO_CUTS, cluster);
-	}
-	
-	/**
-	 * Indicates that a cluster was seen by a trigger and adds it to
-	 * the "no cuts" plots.
-	 * @param triggerNum - The number of the trigger.
-	 * @param cluster - The cluster that was seen.
-	 */
-	public void sawCluster(int triggerNum, SSPCluster cluster) {
-		processSingles(triggerNum, NO_CUTS, cluster);
-	}
-	
-	/**
-	 * Indicates that a cluster pair was seen by a trigger and adds it
-	 * to the "no cuts" plots.
-	 * @param triggerNum - The number of the trigger.
-	 * @param pair - The cluster pair that was seen.
-	 */
-	public void sawPair(int triggerNum, Cluster[] pair) {
-		processPair(triggerNum, NO_CUTS, pair);
-	}
-	
-	/**
-	 * Indicates that a cluster pair was seen by a trigger and adds it
-	 * to the "no cuts" plots.
-	 * @param triggerNum - The number of the trigger.
-	 * @param pair - The cluster pair that was seen.
-	 */
-	public void sawPair(int triggerNum, SSPCluster[] pair) {
-		processPair(triggerNum, NO_CUTS, pair);
-	}
-	
-	/**
-	 * Populates the "all" plots of the appropriate type with the cut
-	 * results from the argument trigger.
-	 * @param trigger - The trigger from which to populate the plots.
-	 */
-	public void sawTrigger(Trigger<?> trigger) {
-		processTrigger(trigger, ALL);
-	}
-	
-	/**
-	 * Sets the energy slope conversion factor to be used to calculate
-	 * the energy slope value for plots.
-	 * @param triggerNum - The trigger for which the conversion factor
-	 * should be used.
-	 * @param value - The conversion factor in units of GeV/mm.
-	 */
-	public void setEnergySlopeParamF(int triggerNum, double value) {
-		// Make sure that the trigger number is valid.
-		if(triggerNum < 0 || triggerNum > 1) {
-			throw new IllegalArgumentException(String.format("Trigger number %d is not valid.", triggerNum));
-		}
-		
-		// Set the parameter.
-		energySlopeParamF[triggerNum] = value;
-	}
-	
-	/**
-	 * Populates the indicated type of plots of the appropriate type
-	 * for the argument trigger.
-	 * @param trigger - The trigger from which to populate the plots.
-	 * @param plotType - The type of plot to populate. This must be one
-	 * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
-	 */
-	private void processTrigger(Trigger<?> trigger, int plotType) {
-		// Get the trigger number and source.
-		Object source = trigger.getTriggerSource();
-		int triggerNum = trigger.getTriggerNumber();
-		
-		// Populate the plots using the appropriate method.
-		if(source instanceof Cluster) {
-			processSingles(triggerNum, plotType, (Cluster) source);
-		}
-		else if(source instanceof SSPCluster) {
-			processSingles(triggerNum, plotType, (SSPCluster) source);
-		}
-		else if(source instanceof Cluster[]) {
-			processPair(triggerNum, plotType, (Cluster[]) source);
-		}
-		else if(source instanceof SSPCluster[]) {
-			processPair(triggerNum, plotType, (SSPCluster[]) source);
-		}
-		
-		// If the trigger source is unsupported, produce an error.
-		else {
-			throw new IllegalArgumentException(String.format("Trigger source \"%s\" is not supported.", source.getClass().getSimpleName()));
-		}
-	}
-	
-	/**
-	 * Populates the trigger singles plots for the indicated type for
-	 * reconstructed clusters.
-	 * @param triggerNum - The trigger number of the source trigger.
-	 * @param plotType - The type of plot to populate. This must be one
-	 * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
-	 * @param pair - The triggering cluster.
-	 */
-	private void processSingles(int triggerNum, int plotType, Cluster cluster) {
-		// Fill the cluster singles plots.
-		singlesHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(cluster));
-		singlesClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
-		singlesTriggerTimePlot[triggerNum][RECON][plotType].fill(cluster.getCalorimeterHits().get(0).getTime());
-	}
-	
-	/**
-	 * Populates the trigger singles plots for the indicated type for SSP
-	 * clusters.
-	 * @param triggerNum - The trigger number of the source trigger.
-	 * @param plotType - The type of plot to populate. This must be one
-	 * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
-	 * @param pair - The triggering cluster.
-	 */
-	private void processSingles(int triggerNum, int plotType, SSPCluster cluster) {
-		// Fill the cluster singles plots.
-		singlesHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(cluster));
-		singlesClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
-		singlesTriggerTimePlot[triggerNum][SSP][plotType].fill(cluster.getTime());
-		
-		// Check if this cluster is "trident-like."
-		// TODO: Define "trident-like."
-		boolean processTrident = false;
-		
-		// If this is a trident-like event, add it to the trident plots.
-		if(processTrident) {
-			tridentHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(cluster));
-			tridentClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
-			tridentPositionPlot[triggerNum].fill(cluster.getXIndex() > 0 ? cluster.getXIndex() - 1 : cluster.getXIndex(), cluster.getYIndex());
-		}
-	}
-	
-	/**
-	 * Populates the trigger pair plots for the indicated type for
-	 * reconstructed cluster pairs.
-	 * @param triggerNum - The trigger number of the source trigger.
-	 * @param plotType - The type of plot to populate. This must be one
-	 * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
-	 * @param pair - The triggering pair.
-	 */
-	private void processPair(int triggerNum, int plotType, Cluster[] pair) {
-		// Fill the cluster singles plots.
-		pairHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(pair[0]));
-		pairHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(pair[1]));
-		pairClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
-		pairClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
-		pairTriggerTimePlot[triggerNum][RECON][plotType].fill(pair[0].getCalorimeterHits().get(0).getTime());
-		pairTriggerTimePlot[triggerNum][RECON][plotType].fill(pair[1].getCalorimeterHits().get(0).getTime());
-		
-		// Fill the cluster pair plots.
-		pairTimePlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueTimeCoincidence(pair));
-		pairSumPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergySum(pair));
+                    singlesDir), 46, -23, 23, 11, -5.5, 5.5);
+        }
+    }
+    
+    /**
+     * Populates the "failed" plots of the appropriate type with the
+     * cut results from the argument trigger.
+     * @param trigger - The trigger from which to populate the plots.
+     */
+    public void failedTrigger(Trigger<?> trigger) {
+        processTrigger(trigger, FAILED);
+    }
+    
+    /**
+     * Populates the "matched" plots of the appropriate type with the
+     * cut results from the argument trigger.
+     * @param trigger - The trigger from which to populate the plots.
+     */
+    public void matchedTrigger(Trigger<?> trigger) {
+        processTrigger(trigger, MATCHED);
+    }
+    
+    /**
+     * Populates the "triggered" plots of the appropriate type with the
+     * cut results from the argument trigger.
+     * @param trigger - The trigger from which to populate the plots.
+     */
+    public void passedTrigger(Trigger<?> trigger) {
+        processTrigger(trigger, TRIGGERED);
+    }
+    
+    /**
+     * Indicates that a cluster was seen by a trigger and adds it to
+     * the "no cuts" plots.
+     * @param triggerNum - The number of the trigger.
+     * @param cluster - The cluster that was seen.
+     */
+    public void sawCluster(int triggerNum, Cluster cluster) {
+        processSingles(triggerNum, NO_CUTS, cluster);
+    }
+    
+    /**
+     * Indicates that a cluster was seen by a trigger and adds it to
+     * the "no cuts" plots.
+     * @param triggerNum - The number of the trigger.
+     * @param cluster - The cluster that was seen.
+     */
+    public void sawCluster(int triggerNum, SSPCluster cluster) {
+        processSingles(triggerNum, NO_CUTS, cluster);
+    }
+    
+    /**
+     * Indicates that a cluster pair was seen by a trigger and adds it
+     * to the "no cuts" plots.
+     * @param triggerNum - The number of the trigger.
+     * @param pair - The cluster pair that was seen.
+     */
+    public void sawPair(int triggerNum, Cluster[] pair) {
+        processPair(triggerNum, NO_CUTS, pair);
+    }
+    
+    /**
+     * Indicates that a cluster pair was seen by a trigger and adds it
+     * to the "no cuts" plots.
+     * @param triggerNum - The number of the trigger.
+     * @param pair - The cluster pair that was seen.
+     */
+    public void sawPair(int triggerNum, SSPCluster[] pair) {
+        processPair(triggerNum, NO_CUTS, pair);
+    }
+    
+    /**
+     * Populates the "all" plots of the appropriate type with the cut
+     * results from the argument trigger.
+     * @param trigger - The trigger from which to populate the plots.
+     */
+    public void sawTrigger(Trigger<?> trigger) {
+        processTrigger(trigger, ALL);
+    }
+    
+    /**
+     * Sets the energy slope conversion factor to be used to calculate
+     * the energy slope value for plots.
+     * @param triggerNum - The trigger for which the conversion factor
+     * should be used.
+     * @param value - The conversion factor in units of GeV/mm.
+     */
+    public void setEnergySlopeParamF(int triggerNum, double value) {
+        // Make sure that the trigger number is valid.
+        if(triggerNum < 0 || triggerNum > 1) {
+            throw new IllegalArgumentException(String.format("Trigger number %d is not valid.", triggerNum));
+        }
+        
+        // Set the parameter.
+        energySlopeParamF[triggerNum] = value;
+    }
+    
+    /**
+     * Populates the indicated type of plots of the appropriate type
+     * for the argument trigger.
+     * @param trigger - The trigger from which to populate the plots.
+     * @param plotType - The type of plot to populate. This must be one
+     * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
+     */
+    private void processTrigger(Trigger<?> trigger, int plotType) {
+        // Get the trigger number and source.
+        Object source = trigger.getTriggerSource();
+        int triggerNum = trigger.getTriggerNumber();
+        
+        // Populate the plots using the appropriate method.
+        if(source instanceof Cluster) {
+            processSingles(triggerNum, plotType, (Cluster) source);
+        }
+        else if(source instanceof SSPCluster) {
+            processSingles(triggerNum, plotType, (SSPCluster) source);
+        }
+        else if(source instanceof Cluster[]) {
+            processPair(triggerNum, plotType, (Cluster[]) source);
+        }
+        else if(source instanceof SSPCluster[]) {
+            processPair(triggerNum, plotType, (SSPCluster[]) source);
+        }
+        
+        // If the trigger source is unsupported, produce an error.
+        else {
+            throw new IllegalArgumentException(String.format("Trigger source \"%s\" is not supported.", source.getClass().getSimpleName()));
+        }
+    }
+    
+    /**
+     * Populates the trigger singles plots for the indicated type for
+     * reconstructed clusters.
+     * @param triggerNum - The trigger number of the source trigger.
+     * @param plotType - The type of plot to populate. This must be one
+     * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
+     * @param pair - The triggering cluster.
+     */
+    private void processSingles(int triggerNum, int plotType, Cluster cluster) {
+        // Fill the cluster singles plots.
+        singlesHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(cluster));
+        singlesClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
+        singlesTriggerTimePlot[triggerNum][RECON][plotType].fill(cluster.getCalorimeterHits().get(0).getTime());
+    }
+    
+    /**
+     * Populates the trigger singles plots for the indicated type for SSP
+     * clusters.
+     * @param triggerNum - The trigger number of the source trigger.
+     * @param plotType - The type of plot to populate. This must be one
+     * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
+     * @param pair - The triggering cluster.
+     */
+    private void processSingles(int triggerNum, int plotType, SSPCluster cluster) {
+        // Fill the cluster singles plots.
+        singlesHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(cluster));
+        singlesClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
+        singlesTriggerTimePlot[triggerNum][SSP][plotType].fill(cluster.getTime());
+        
+        // Check if this cluster is "trident-like."
+        // TODO: Define "trident-like."
+        boolean processTrident = false;
+        
+        // If this is a trident-like event, add it to the trident plots.
+        if(processTrident) {
+            tridentHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(cluster));
+            tridentClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(cluster));
+            tridentPositionPlot[triggerNum].fill(cluster.getXIndex() > 0 ? cluster.getXIndex() - 1 : cluster.getXIndex(), cluster.getYIndex());
+        }
+    }
+    
+    /**
+     * Populates the trigger pair plots for the indicated type for
+     * reconstructed cluster pairs.
+     * @param triggerNum - The trigger number of the source trigger.
+     * @param plotType - The type of plot to populate. This must be one
+     * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
+     * @param pair - The triggering pair.
+     */
+    private void processPair(int triggerNum, int plotType, Cluster[] pair) {
+        // Fill the cluster singles plots.
+        pairHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(pair[0]));
+        pairHitCountPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterHitCount(pair[1]));
+        pairClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
+        pairClusterEnergyPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
+        pairTriggerTimePlot[triggerNum][RECON][plotType].fill(pair[0].getCalorimeterHits().get(0).getTime());
+        pairTriggerTimePlot[triggerNum][RECON][plotType].fill(pair[1].getCalorimeterHits().get(0).getTime());
+        
+        // Fill the cluster pair plots.
+        pairTimePlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueTimeCoincidence(pair));
+        pairSumPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergySum(pair));
                 pairSumEnergiesPlot[triggerNum][RECON][plotType].fill(pair[0].getEnergy(), pair[1].getEnergy());
-		pairDiffPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergyDifference(pair));
-		pairSlopePlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
-		pairCoplanarityPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueCoplanarity(pair));
-	}
-	
-	/**
-	 * Populates the trigger pair plots for the indicated type for SSP
-	 * cluster pairs.
-	 * @param triggerNum - The trigger number of the source trigger.
-	 * @param plotType - The type of plot to populate. This must be one
-	 * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
-	 * @param pair - The triggering pair.
-	 */
-	private void processPair(int triggerNum, int plotType, SSPCluster[] pair) {
-		// Fill the cluster singles plots.
-		pairHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(pair[0]));
-		pairHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(pair[1]));
-		pairClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
-		pairClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
-		pairTriggerTimePlot[triggerNum][SSP][plotType].fill(pair[0].getTime());
-		pairTriggerTimePlot[triggerNum][SSP][plotType].fill(pair[1].getTime());
-		
-		// Fill the cluster pair plots.
-		pairTimePlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueTimeCoincidence(pair));
-		pairSumPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergySum(pair));
+        pairDiffPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergyDifference(pair));
+        pairSlopePlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
+        pairCoplanarityPlot[triggerNum][RECON][plotType].fill(TriggerModule.getValueCoplanarity(pair));
+    }
+    
+    /**
+     * Populates the trigger pair plots for the indicated type for SSP
+     * cluster pairs.
+     * @param triggerNum - The trigger number of the source trigger.
+     * @param plotType - The type of plot to populate. This must be one
+     * of <code>ALL</code>, <code>MATCHED</code>, or <code>FAILED</code>.
+     * @param pair - The triggering pair.
+     */
+    private void processPair(int triggerNum, int plotType, SSPCluster[] pair) {
+        // Fill the cluster singles plots.
+        pairHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(pair[0]));
+        pairHitCountPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterHitCount(pair[1]));
+        pairClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
+        pairClusterEnergyPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
+        pairTriggerTimePlot[triggerNum][SSP][plotType].fill(pair[0].getTime());
+        pairTriggerTimePlot[triggerNum][SSP][plotType].fill(pair[1].getTime());
+        
+        // Fill the cluster pair plots.
+        pairTimePlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueTimeCoincidence(pair));
+        pairSumPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergySum(pair));
         pairSumEnergiesPlot[triggerNum][SSP][plotType].fill(pair[0].getEnergy(), pair[1].getEnergy());
-		pairDiffPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergyDifference(pair));
-		pairSlopePlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
-		pairCoplanarityPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueCoplanarity(pair));
-		
-		// Check if this pair is "Møller-like."
-		boolean processMøller = TriggerModule.getValueEnergySum(pair) >= MØLLER_SUM_THRESHOLD;
-		
-		// If the pair is Møller-like, populate the Møller plots.
-		if(processMøller) {
-			// Fill the cluster singles plots.
-			møllerHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(pair[0]));
-			møllerHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(pair[1]));
-			møllerClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
-			møllerClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
-			møllerTriggerTimePlot[triggerNum].fill(pair[0].getTime());
-			møllerTriggerTimePlot[triggerNum].fill(pair[1].getTime());
-			møllerPositionPlot[triggerNum].fill(pair[0].getXIndex() > 0 ? pair[0].getXIndex() - 1 : pair[0].getXIndex(), pair[0].getYIndex());
-			møllerPositionPlot[triggerNum].fill(pair[1].getXIndex() > 0 ? pair[1].getXIndex() - 1 : pair[1].getXIndex(), pair[1].getYIndex());
-			
-			// Fill the cluster pair plots.
-			møllerTimePlot[triggerNum].fill(TriggerModule.getValueTimeCoincidence(pair));
-			møllerSumPlot[triggerNum].fill(TriggerModule.getValueEnergySum(pair));
-			møllerSumEnergiesPlot[triggerNum].fill(pair[0].getEnergy(), pair[1].getEnergy());
-	        møllerDiffPlot[triggerNum].fill(TriggerModule.getValueEnergyDifference(pair));
-	        møllerSlopePlot[triggerNum].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
-	        møllerCoplanarityPlot[triggerNum].fill(TriggerModule.getValueCoplanarity(pair));
-		}
-	}
+        pairDiffPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergyDifference(pair));
+        pairSlopePlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
+        pairCoplanarityPlot[triggerNum][SSP][plotType].fill(TriggerModule.getValueCoplanarity(pair));
+        
+        // Check if this pair is "Møller-like."
+        boolean processMøller = TriggerModule.getValueEnergySum(pair) >= MØLLER_SUM_THRESHOLD;
+        
+        // If the pair is Møller-like, populate the Møller plots.
+        if(processMøller) {
+            // Fill the cluster singles plots.
+            møllerHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(pair[0]));
+            møllerHitCountPlot[triggerNum].fill(TriggerModule.getValueClusterHitCount(pair[1]));
+            møllerClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(pair[0]));
+            møllerClusterEnergyPlot[triggerNum].fill(TriggerModule.getValueClusterTotalEnergy(pair[1]));
+            møllerTriggerTimePlot[triggerNum].fill(pair[0].getTime());
+            møllerTriggerTimePlot[triggerNum].fill(pair[1].getTime());
+            møllerPositionPlot[triggerNum].fill(pair[0].getXIndex() > 0 ? pair[0].getXIndex() - 1 : pair[0].getXIndex(), pair[0].getYIndex());
+            møllerPositionPlot[triggerNum].fill(pair[1].getXIndex() > 0 ? pair[1].getXIndex() - 1 : pair[1].getXIndex(), pair[1].getYIndex());
+            
+            // Fill the cluster pair plots.
+            møllerTimePlot[triggerNum].fill(TriggerModule.getValueTimeCoincidence(pair));
+            møllerSumPlot[triggerNum].fill(TriggerModule.getValueEnergySum(pair));
+            møllerSumEnergiesPlot[triggerNum].fill(pair[0].getEnergy(), pair[1].getEnergy());
+            møllerDiffPlot[triggerNum].fill(TriggerModule.getValueEnergyDifference(pair));
+            møllerSlopePlot[triggerNum].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF[triggerNum]));
+            møllerCoplanarityPlot[triggerNum].fill(TriggerModule.getValueCoplanarity(pair));
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/ComponentUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/ComponentUtils.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/ComponentUtils.java	Wed Apr 27 11:11:32 2016
@@ -1,8 +1,6 @@
 package org.hps.analysis.trigger.util;
 
 import java.awt.Component;
-
-import org.hps.analysis.trigger.util.TriggerDiagnosticUtil;
 
 /**
  * Class <code>ComponentUtils</code> is a list of utility methods used
@@ -11,116 +9,116 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ComponentUtils {
-	/** The default spacing used between a horizontal edge of one
-	 * component and the horizontal edge of another. */
-	public static final int hinternal = 10;
-	/** The default spacing used between a vertical edge of one
-	 * component and the vertical edge of another. */
-	public static final int vinternal = 10;
-	/** The default spacing used between a horizontal edge of one
-	 * component and the edge of its parent component. */
-	public static final int hexternal = 0;
-	/** The default spacing used between a vertical edge of one
-	 * component and the edge of its parent component. */
-	public static final int vexternal = 0;
-	
-	/**
-	 * Gets a <code>String</code> composed of a number of instances of
-	 * character <code>c</code> equal to <code>number</code>.
-	 * @param c - The character to repeat.
-	 * @param number - The number of repetitions.
-	 * @return Returns the repeated character as a <code>String</code>.
-	 */
-	public static final String getChars(char c, int number) {
-		// Create a buffer to store the characters in.
-		StringBuffer s = new StringBuffer();
-		
-		// Add the indicated number of instances.
-		for(int i = 0; i < number; i++) {
-			s.append(c);
-		}
-		
-		// Return the string.
-		return s.toString();
-	}
-	
-	/**
-	 * Gets the number of digits in the base-10 String representation
-	 * of an integer primitive. Negative signs are not included in the
-	 * digit count.
-	 * @param value - The value of which to obtain the length.
-	 * @return Returns the number of digits in the String representation
-	 * of the argument value.
-	 */
-	public static final int getDigits(int value) {
-		return TriggerDiagnosticUtil.getDigits(value);
-	}
-	
-	/**
-	 * Gets the maximum value from a list of values.
-	 * @param values - The values to compare.
-	 * @return Returns the largest of the argument values.
-	 * @throws IllegalArgumentException Occurs if no values are given.
-	 */
-	public static final int max(int... values) throws IllegalArgumentException {
-		// Throw an error if no arguments are provided.
-		if(values == null || values.length == 0) {
-			throw new IllegalArgumentException("Can not determine maximum value from a list of 0 values.");
-		}
-		
-		// If there is only one value, return it.
-		if(values.length == 1) { return values[0]; }
-		
-		// Otherwise, get the largest value.
-		int largest = Integer.MIN_VALUE;
-		for(int value : values) {
-			if(value > largest) { largest = value; }
-		}
-		
-		// Return the result.
-		return largest;
-	}
-	
-	/**
-	 * Gets the x-coordinate immediately to the right of the given
-	 * component.
-	 * @param c - The component of which to find the edge.
-	 * @return Returns the x-coordinate as an <code>int</code> value.
-	 */
-	public static final int getNextX(Component c) {
-		return getNextX(c, 0);
-	}
-	
-	/**
-	 * Gets the x-coordinate a given distance to the right edge of the
-	 * argument component.
-	 * @param c - The component of which to find the edge.
-	 * @param spacing - The additional spacing past the edge of the
-	 * component to add.
-	 * @return Returns the x-coordinate as an <code>int</code> value.
-	 */
-	public static final int getNextX(Component c, int spacing) {
-		return c.getX() + c.getWidth() + spacing;
-	}
-	
-	/**
-	 * Gets the y-coordinate immediately below the given component.
-	 * @param c - The component of which to find the edge.
-	 * @return Returns the y-coordinate as an <code>int</code> value.
-	 */
-	public static final int getNextY(Component c) {
-		return getNextY(c, 0);
-	}
-	
-	/**
-	 * Gets the y-coordinate a given distance below the bottom edge
-	 * of the argument component.
-	 * @param c - The component of which to find the edge.
-	 * @param spacing - The additional spacing past the edge of the
-	 * component to add.
-	 * @return Returns the y-coordinate as an <code>int</code> value.
-	 */
-	public static final int getNextY(Component c, int spacing) {
-		return c.getY() + c.getHeight() + spacing;
-	}
+    /** The default spacing used between a horizontal edge of one
+     * component and the horizontal edge of another. */
+    public static final int hinternal = 10;
+    /** The default spacing used between a vertical edge of one
+     * component and the vertical edge of another. */
+    public static final int vinternal = 10;
+    /** The default spacing used between a horizontal edge of one
+     * component and the edge of its parent component. */
+    public static final int hexternal = 0;
+    /** The default spacing used between a vertical edge of one
+     * component and the edge of its parent component. */
+    public static final int vexternal = 0;
+    
+    /**
+     * Gets a <code>String</code> composed of a number of instances of
+     * character <code>c</code> equal to <code>number</code>.
+     * @param c - The character to repeat.
+     * @param number - The number of repetitions.
+     * @return Returns the repeated character as a <code>String</code>.
+     */
+    public static final String getChars(char c, int number) {
+        // Create a buffer to store the characters in.
+        StringBuffer s = new StringBuffer();
+        
+        // Add the indicated number of instances.
+        for(int i = 0; i < number; i++) {
+            s.append(c);
+        }
+        
+        // Return the string.
+        return s.toString();
+    }
+    
+    /**
+     * Gets the number of digits in the base-10 String representation
+     * of an integer primitive. Negative signs are not included in the
+     * digit count.
+     * @param value - The value of which to obtain the length.
+     * @return Returns the number of digits in the String representation
+     * of the argument value.
+     */
+    public static final int getDigits(int value) {
+        return TriggerDiagnosticUtil.getDigits(value);
+    }
+    
+    /**
+     * Gets the maximum value from a list of values.
+     * @param values - The values to compare.
+     * @return Returns the largest of the argument values.
+     * @throws IllegalArgumentException Occurs if no values are given.
+     */
+    public static final int max(int... values) throws IllegalArgumentException {
+        // Throw an error if no arguments are provided.
+        if(values == null || values.length == 0) {
+            throw new IllegalArgumentException("Can not determine maximum value from a list of 0 values.");
+        }
+        
+        // If there is only one value, return it.
+        if(values.length == 1) { return values[0]; }
+        
+        // Otherwise, get the largest value.
+        int largest = Integer.MIN_VALUE;
+        for(int value : values) {
+            if(value > largest) { largest = value; }
+        }
+        
+        // Return the result.
+        return largest;
+    }
+    
+    /**
+     * Gets the x-coordinate immediately to the right of the given
+     * component.
+     * @param c - The component of which to find the edge.
+     * @return Returns the x-coordinate as an <code>int</code> value.
+     */
+    public static final int getNextX(Component c) {
+        return getNextX(c, 0);
+    }
+    
+    /**
+     * Gets the x-coordinate a given distance to the right edge of the
+     * argument component.
+     * @param c - The component of which to find the edge.
+     * @param spacing - The additional spacing past the edge of the
+     * component to add.
+     * @return Returns the x-coordinate as an <code>int</code> value.
+     */
+    public static final int getNextX(Component c, int spacing) {
+        return c.getX() + c.getWidth() + spacing;
+    }
+    
+    /**
+     * Gets the y-coordinate immediately below the given component.
+     * @param c - The component of which to find the edge.
+     * @return Returns the y-coordinate as an <code>int</code> value.
+     */
+    public static final int getNextY(Component c) {
+        return getNextY(c, 0);
+    }
+    
+    /**
+     * Gets the y-coordinate a given distance below the bottom edge
+     * of the argument component.
+     * @param c - The component of which to find the edge.
+     * @param spacing - The additional spacing past the edge of the
+     * component to add.
+     * @return Returns the y-coordinate as an <code>int</code> value.
+     */
+    public static final int getNextY(Component c, int spacing) {
+        return c.getY() + c.getHeight() + spacing;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/OutputLogger.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/OutputLogger.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/OutputLogger.java	Wed Apr 27 11:11:32 2016
@@ -3,28 +3,28 @@
 public class OutputLogger {
     private static StringBuffer outputBuffer = new StringBuffer();
     
-	public static final void printf(String text, Object... args) {
-		outputBuffer.append(String.format(text, args));
-	}
-	
-	public static final void println() { printf(String.format("%n")); }
-	
-	public static final void println(String text) { printf(String.format("%s%n", text)); }
-	
-	public static final void print(String text) { printf(text); }
-	
-	public static final void printLog() {
-		System.out.println(outputBuffer.toString());
-		clearLog();
-	}
-	
-	public static final void printNewLine() { println(); }
-	
-	public static final void printNewLine(int quantity) {
-		for(int i = 0; i < quantity; i++) { println(); }
-	}
-	
-	public static final void clearLog() {
-		outputBuffer = new StringBuffer();
-	}
+    public static final void printf(String text, Object... args) {
+        outputBuffer.append(String.format(text, args));
+    }
+    
+    public static final void println() { printf(String.format("%n")); }
+    
+    public static final void println(String text) { printf(String.format("%s%n", text)); }
+    
+    public static final void print(String text) { printf(text); }
+    
+    public static final void printLog() {
+        System.out.println(outputBuffer.toString());
+        clearLog();
+    }
+    
+    public static final void printNewLine() { println(); }
+    
+    public static final void printNewLine(int quantity) {
+        for(int i = 0; i < quantity; i++) { println(); }
+    }
+    
+    public static final void clearLog() {
+        outputBuffer = new StringBuffer();
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Pair.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Pair.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Pair.java	Wed Apr 27 11:11:32 2016
@@ -8,32 +8,32 @@
  * @param <F> - The object type of the second element in the pair.
  */
 public class Pair<E, F> {
-	private final E firstObject;
-	private final F secondObject;
-	
-	/**
-	 * Creates a pair of the two indicated objects.
-	 * @param firstObject - The first object.
-	 * @param secondObject - The second object.
-	 */
-	public Pair(E firstElement, F secondElement) {
-		this.firstObject = firstElement;
-		this.secondObject = secondElement;
-	}
-	
-	/**
-	 * Gets the first element of the pair.
-	 * @return Returns the first element.
-	 */
-	public E getFirstElement() {
-		return firstObject;
-	}
-	
-	/**
-	 * Gets the second element of the pair.
-	 * @return Returns the second element.
-	 */
-	public F getSecondElement() {
-		return secondObject;
-	}
+    private final E firstObject;
+    private final F secondObject;
+    
+    /**
+     * Creates a pair of the two indicated objects.
+     * @param firstElement - The first object.
+     * @param secondElement - The second object.
+     */
+    public Pair(E firstElement, F secondElement) {
+        this.firstObject = firstElement;
+        this.secondObject = secondElement;
+    }
+    
+    /**
+     * Gets the first element of the pair.
+     * @return Returns the first element.
+     */
+    public E getFirstElement() {
+        return firstObject;
+    }
+    
+    /**
+     * Gets the second element of the pair.
+     * @return Returns the second element.
+     */
+    public F getSecondElement() {
+        return secondObject;
+    }
 }

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/PairTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/PairTrigger.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/PairTrigger.java	Wed Apr 27 11:11:32 2016
@@ -3,164 +3,164 @@
 import org.hps.record.triggerbank.TriggerModule;
 
 public class PairTrigger<E> extends SinglesTrigger<E> {
-	// Define the supported trigger cuts.
-	private static final String PAIR_ENERGY_SUM_LOW = TriggerModule.PAIR_ENERGY_SUM_LOW;
-	private static final String PAIR_ENERGY_SUM_HIGH = TriggerModule.PAIR_ENERGY_SUM_HIGH;
-	private static final String PAIR_ENERGY_DIFFERENCE_HIGH = TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH;
-	private static final String PAIR_ENERGY_SLOPE_LOW = TriggerModule.PAIR_ENERGY_SLOPE_LOW;
-	private static final String PAIR_COPLANARITY_HIGH = TriggerModule.PAIR_COPLANARITY_HIGH;
+    // Define the supported trigger cuts.
+    private static final String PAIR_ENERGY_SUM_LOW = TriggerModule.PAIR_ENERGY_SUM_LOW;
+    private static final String PAIR_ENERGY_SUM_HIGH = TriggerModule.PAIR_ENERGY_SUM_HIGH;
+    private static final String PAIR_ENERGY_DIFFERENCE_HIGH = TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH;
+    private static final String PAIR_ENERGY_SLOPE_LOW = TriggerModule.PAIR_ENERGY_SLOPE_LOW;
+    private static final String PAIR_COPLANARITY_HIGH = TriggerModule.PAIR_COPLANARITY_HIGH;
     private static final String PAIR_TIME_COINCIDENCE = "pairTimeCoincidence";
-	
-	/**
-	 * Instantiates a new <code>PairTrigger</code> with all cut
-	 * states set to <code>false</code> and with the trigger source
-	 * defined according to the specified object.
-	 * @param source - The object from which the trigger cut states
-	 * are derived.
-	 */
-	public PairTrigger(E source, int triggerNum) {
-		// Instantiate the superclass.
-		super(source, triggerNum);
-		
-		// Add the supported cuts types.
-		addValidCut(PAIR_ENERGY_SUM_LOW);
-		addValidCut(PAIR_ENERGY_SUM_HIGH);
-		addValidCut(PAIR_ENERGY_DIFFERENCE_HIGH);
-		addValidCut(PAIR_ENERGY_SLOPE_LOW);
-		addValidCut(PAIR_COPLANARITY_HIGH);
-		addValidCut(PAIR_TIME_COINCIDENCE);
-	}
-	
-	/**
-	 * Gets whether the pair energy sum lower bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateEnergySumLow() {
-		return getCutState(PAIR_ENERGY_SUM_LOW);
-	}
-	
-	/**
-	 * Gets whether the pair energy sum upper bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateEnergySumHigh() {
-		return getCutState(PAIR_ENERGY_SUM_HIGH);
-	}
-	
-	/**
-	 * Gets whether both the pair energy sum upper and lower bound cuts
-	 * were met.
-	 * @return Returns <code>true</code> if the cuts were met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateEnergySum() {
-		return getCutState(PAIR_ENERGY_SUM_HIGH);
-	}
-	
-	/**
-	 * Gets whether the pair energy difference cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateEnergyDifference() {
-		return getCutState(PAIR_ENERGY_DIFFERENCE_HIGH);
-	}
-	
-	/**
-	 * Gets whether the pair energy slope cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateEnergySlope() {
-		return getCutState(PAIR_ENERGY_SLOPE_LOW);
-	}
-	
-	/**
-	 * Gets whether the pair coplanarity cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateCoplanarity() {
-		return getCutState(PAIR_COPLANARITY_HIGH);
-	}
-	
-	/**
-	 * Gets whether the time coincidence cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateTimeCoincidence() {
-		return getCutState(PAIR_TIME_COINCIDENCE);
-	}
-	
-	/**
-	 * Sets whether the conditions for the pair energy sum lower bound
-	 * cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateEnergySumLow(boolean state) {
-		setCutState(PAIR_ENERGY_SUM_LOW, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the pair energy sum upper bound
-	 * cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateEnergySumHigh(boolean state) {
-		setCutState(PAIR_ENERGY_SUM_HIGH, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the pair energy difference cut
-	 * were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateEnergyDifference(boolean state) {
-		setCutState(PAIR_ENERGY_DIFFERENCE_HIGH, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the pair energy slope cut were
-	 * met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateEnergySlope(boolean state) {
-		setCutState(PAIR_ENERGY_SLOPE_LOW, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the pair coplanarity cut were
-	 * met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateCoplanarity(boolean state) {
-		setCutState(PAIR_COPLANARITY_HIGH, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the time coincidence cut were
-	 * met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateTimeCoincidence(boolean state) {
-		setCutState(PAIR_TIME_COINCIDENCE, state);
-	}
-	
-	@Override
-	public String toString() {
-		return String.format("EClusterLow: %d; EClusterHigh %d; HitCount: %d; ESumLow: %d, ESumHigh: %d, EDiff: %d, ESlope: %d, Coplanarity: %d",
-				getStateClusterEnergyLow() ? 1 : 0, getStateClusterEnergyHigh() ? 1 : 0,
-				getStateHitCount() ? 1 : 0, getStateEnergySumLow() ? 1 : 0,
-				getStateEnergySumHigh() ? 1 : 0, getStateEnergyDifference() ? 1 : 0,
-				getStateEnergySlope() ? 1 : 0, getStateCoplanarity() ? 1 : 0);
-	}
-}
+    
+    /**
+     * Instantiates a new <code>PairTrigger</code> with all cut
+     * states set to <code>false</code> and with the trigger source
+     * defined according to the specified object.
+     * @param source - The object from which the trigger cut states
+     * are derived.
+     */
+    public PairTrigger(E source, int triggerNum) {
+        // Instantiate the superclass.
+        super(source, triggerNum);
+        
+        // Add the supported cuts types.
+        addValidCut(PAIR_ENERGY_SUM_LOW);
+        addValidCut(PAIR_ENERGY_SUM_HIGH);
+        addValidCut(PAIR_ENERGY_DIFFERENCE_HIGH);
+        addValidCut(PAIR_ENERGY_SLOPE_LOW);
+        addValidCut(PAIR_COPLANARITY_HIGH);
+        addValidCut(PAIR_TIME_COINCIDENCE);
+    }
+    
+    /**
+     * Gets whether the pair energy sum lower bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateEnergySumLow() {
+        return getCutState(PAIR_ENERGY_SUM_LOW);
+    }
+    
+    /**
+     * Gets whether the pair energy sum upper bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateEnergySumHigh() {
+        return getCutState(PAIR_ENERGY_SUM_HIGH);
+    }
+    
+    /**
+     * Gets whether both the pair energy sum upper and lower bound cuts
+     * were met.
+     * @return Returns <code>true</code> if the cuts were met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateEnergySum() {
+        return getCutState(PAIR_ENERGY_SUM_HIGH);
+    }
+    
+    /**
+     * Gets whether the pair energy difference cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateEnergyDifference() {
+        return getCutState(PAIR_ENERGY_DIFFERENCE_HIGH);
+    }
+    
+    /**
+     * Gets whether the pair energy slope cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateEnergySlope() {
+        return getCutState(PAIR_ENERGY_SLOPE_LOW);
+    }
+    
+    /**
+     * Gets whether the pair coplanarity cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateCoplanarity() {
+        return getCutState(PAIR_COPLANARITY_HIGH);
+    }
+    
+    /**
+     * Gets whether the time coincidence cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateTimeCoincidence() {
+        return getCutState(PAIR_TIME_COINCIDENCE);
+    }
+    
+    /**
+     * Sets whether the conditions for the pair energy sum lower bound
+     * cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateEnergySumLow(boolean state) {
+        setCutState(PAIR_ENERGY_SUM_LOW, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the pair energy sum upper bound
+     * cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateEnergySumHigh(boolean state) {
+        setCutState(PAIR_ENERGY_SUM_HIGH, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the pair energy difference cut
+     * were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateEnergyDifference(boolean state) {
+        setCutState(PAIR_ENERGY_DIFFERENCE_HIGH, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the pair energy slope cut were
+     * met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateEnergySlope(boolean state) {
+        setCutState(PAIR_ENERGY_SLOPE_LOW, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the pair coplanarity cut were
+     * met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateCoplanarity(boolean state) {
+        setCutState(PAIR_COPLANARITY_HIGH, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the time coincidence cut were
+     * met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateTimeCoincidence(boolean state) {
+        setCutState(PAIR_TIME_COINCIDENCE, state);
+    }
+    
+    @Override
+    public String toString() {
+        return String.format("EClusterLow: %d; EClusterHigh %d; HitCount: %d; ESumLow: %d, ESumHigh: %d, EDiff: %d, ESlope: %d, Coplanarity: %d",
+                getStateClusterEnergyLow() ? 1 : 0, getStateClusterEnergyHigh() ? 1 : 0,
+                getStateHitCount() ? 1 : 0, getStateEnergySumLow() ? 1 : 0,
+                getStateEnergySumHigh() ? 1 : 0, getStateEnergyDifference() ? 1 : 0,
+                getStateEnergySlope() ? 1 : 0, getStateCoplanarity() ? 1 : 0);
+    }
+}

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/SinglesTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/SinglesTrigger.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/SinglesTrigger.java	Wed Apr 27 11:11:32 2016
@@ -3,151 +3,151 @@
 import org.hps.record.triggerbank.TriggerModule;
 
 public class SinglesTrigger<E> extends Trigger<E> {
-	// Define the supported trigger cuts.
-	private static final String CLUSTER_HIT_COUNT_LOW = TriggerModule.CLUSTER_HIT_COUNT_LOW;
-	private static final String CLUSTER_SEED_ENERGY_LOW = TriggerModule.CLUSTER_SEED_ENERGY_LOW;
-	private static final String CLUSTER_SEED_ENERGY_HIGH = TriggerModule.CLUSTER_SEED_ENERGY_HIGH;
-	private static final String CLUSTER_TOTAL_ENERGY_LOW = TriggerModule.CLUSTER_TOTAL_ENERGY_LOW;
-	private static final String CLUSTER_TOTAL_ENERGY_HIGH = TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH;
-	
-	/**
-	 * Instantiates a new <code>SinglesTrigger</code> with all cut
-	 * states set to <code>false</code> and with the trigger source
-	 * defined according to the specified object.
-	 * @param source - The object from which the trigger cut states
-	 * are derived.
-	 */
-	public SinglesTrigger(E source, int triggerNum) {
-		// Instantiate the superclass.
-		super(source, triggerNum);
-		
-		// Add the supported cuts types.
-		addValidCut(CLUSTER_HIT_COUNT_LOW);
-		addValidCut(CLUSTER_SEED_ENERGY_LOW);
-		addValidCut(CLUSTER_SEED_ENERGY_HIGH);
-		addValidCut(CLUSTER_TOTAL_ENERGY_LOW);
-		addValidCut(CLUSTER_TOTAL_ENERGY_HIGH);
-	}
-	
-	/**
-	 * Gets whether the cluster hit count cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateHitCount() {
-		return getCutState(CLUSTER_HIT_COUNT_LOW);
-	}
-	
-	/**
-	 * Gets whether the cluster seed energy lower bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateSeedEnergyLow() {
-		return getCutState(CLUSTER_SEED_ENERGY_LOW);
-	}
-	
-	/**
-	 * Gets whether the cluster seed energy upper bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateSeedEnergyHigh() {
-		return getCutState(CLUSTER_SEED_ENERGY_HIGH);
-	}
-	
-	/**
-	 * Gets whether both the cluster seed energy upper and lower bound
-	 * cuts were met.
-	 * @return Returns <code>true</code> if the cuts were met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateSeedEnergy() {
-		return getCutState(CLUSTER_SEED_ENERGY_LOW) && getCutState(CLUSTER_SEED_ENERGY_HIGH);
-	}
-	
-	/**
-	 * Gets whether the cluster total energy lower bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateClusterEnergyLow() {
-		return getCutState(CLUSTER_TOTAL_ENERGY_LOW);
-	}
-	
-	/**
-	 * Gets whether the cluster total energy upper bound cut was met.
-	 * @return Returns <code>true</code> if the cut was met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateClusterEnergyHigh() {
-		return getCutState(CLUSTER_TOTAL_ENERGY_HIGH);
-	}
-	
-	/**
-	 * Gets whether both the cluster total energy upper and lower bound
-	 * cuts were met.
-	 * @return Returns <code>true</code> if the cuts were met and
-	 * <code>false</code> otherwise.
-	 */
-	public boolean getStateClusterEnergy() {
-		return getCutState(CLUSTER_TOTAL_ENERGY_LOW) && getCutState(CLUSTER_TOTAL_ENERGY_HIGH);
-	}
-	
-	/**
-	 * Sets whether the conditions for the cluster hit count cut were
-	 * met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateHitCount(boolean state) {
-		setCutState(CLUSTER_HIT_COUNT_LOW, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the cluster seed energy lower
-	 * bound cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateSeedEnergyLow(boolean state) {
-		setCutState(CLUSTER_SEED_ENERGY_LOW, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the cluster seed energy upper
-	 * bound cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateSeedEnergyHigh(boolean state) {
-		setCutState(CLUSTER_SEED_ENERGY_HIGH, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the cluster total energy lower
-	 * bound cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateClusterEnergyLow(boolean state) {
-		setCutState(CLUSTER_TOTAL_ENERGY_LOW, state);
-	}
-	
-	/**
-	 * Sets whether the conditions for the cluster total energy upper
-	 * bound cut were met.
-	 * @param state - <code>true</code> indicates that the cut conditions
-	 * were met and <code>false</code> that they were not.
-	 */
-	public void setStateClusterEnergyHigh(boolean state) {
-		setCutState(CLUSTER_TOTAL_ENERGY_HIGH, state);
-	}
-	
-	@Override
-	public String toString() {
-		return String.format("EClusterLow: %d; EClusterHigh %d; HitCount: %d",
-				getStateClusterEnergyLow() ? 1 : 0, getStateClusterEnergyHigh() ? 1 : 0,
-				getStateHitCount() ? 1 : 0);
-	}
-}
+    // Define the supported trigger cuts.
+    private static final String CLUSTER_HIT_COUNT_LOW = TriggerModule.CLUSTER_HIT_COUNT_LOW;
+    private static final String CLUSTER_SEED_ENERGY_LOW = TriggerModule.CLUSTER_SEED_ENERGY_LOW;
+    private static final String CLUSTER_SEED_ENERGY_HIGH = TriggerModule.CLUSTER_SEED_ENERGY_HIGH;
+    private static final String CLUSTER_TOTAL_ENERGY_LOW = TriggerModule.CLUSTER_TOTAL_ENERGY_LOW;
+    private static final String CLUSTER_TOTAL_ENERGY_HIGH = TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH;
+    
+    /**
+     * Instantiates a new <code>SinglesTrigger</code> with all cut
+     * states set to <code>false</code> and with the trigger source
+     * defined according to the specified object.
+     * @param source - The object from which the trigger cut states
+     * are derived.
+     */
+    public SinglesTrigger(E source, int triggerNum) {
+        // Instantiate the superclass.
+        super(source, triggerNum);
+        
+        // Add the supported cuts types.
+        addValidCut(CLUSTER_HIT_COUNT_LOW);
+        addValidCut(CLUSTER_SEED_ENERGY_LOW);
+        addValidCut(CLUSTER_SEED_ENERGY_HIGH);
+        addValidCut(CLUSTER_TOTAL_ENERGY_LOW);
+        addValidCut(CLUSTER_TOTAL_ENERGY_HIGH);
+    }
+    
+    /**
+     * Gets whether the cluster hit count cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateHitCount() {
+        return getCutState(CLUSTER_HIT_COUNT_LOW);
+    }
+    
+    /**
+     * Gets whether the cluster seed energy lower bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateSeedEnergyLow() {
+        return getCutState(CLUSTER_SEED_ENERGY_LOW);
+    }
+    
+    /**
+     * Gets whether the cluster seed energy upper bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateSeedEnergyHigh() {
+        return getCutState(CLUSTER_SEED_ENERGY_HIGH);
+    }
+    
+    /**
+     * Gets whether both the cluster seed energy upper and lower bound
+     * cuts were met.
+     * @return Returns <code>true</code> if the cuts were met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateSeedEnergy() {
+        return getCutState(CLUSTER_SEED_ENERGY_LOW) && getCutState(CLUSTER_SEED_ENERGY_HIGH);
+    }
+    
+    /**
+     * Gets whether the cluster total energy lower bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateClusterEnergyLow() {
+        return getCutState(CLUSTER_TOTAL_ENERGY_LOW);
+    }
+    
+    /**
+     * Gets whether the cluster total energy upper bound cut was met.
+     * @return Returns <code>true</code> if the cut was met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateClusterEnergyHigh() {
+        return getCutState(CLUSTER_TOTAL_ENERGY_HIGH);
+    }
+    
+    /**
+     * Gets whether both the cluster total energy upper and lower bound
+     * cuts were met.
+     * @return Returns <code>true</code> if the cuts were met and
+     * <code>false</code> otherwise.
+     */
+    public boolean getStateClusterEnergy() {
+        return getCutState(CLUSTER_TOTAL_ENERGY_LOW) && getCutState(CLUSTER_TOTAL_ENERGY_HIGH);
+    }
+    
+    /**
+     * Sets whether the conditions for the cluster hit count cut were
+     * met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateHitCount(boolean state) {
+        setCutState(CLUSTER_HIT_COUNT_LOW, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the cluster seed energy lower
+     * bound cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateSeedEnergyLow(boolean state) {
+        setCutState(CLUSTER_SEED_ENERGY_LOW, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the cluster seed energy upper
+     * bound cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateSeedEnergyHigh(boolean state) {
+        setCutState(CLUSTER_SEED_ENERGY_HIGH, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the cluster total energy lower
+     * bound cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateClusterEnergyLow(boolean state) {
+        setCutState(CLUSTER_TOTAL_ENERGY_LOW, state);
+    }
+    
+    /**
+     * Sets whether the conditions for the cluster total energy upper
+     * bound cut were met.
+     * @param state - <code>true</code> indicates that the cut conditions
+     * were met and <code>false</code> that they were not.
+     */
+    public void setStateClusterEnergyHigh(boolean state) {
+        setCutState(CLUSTER_TOTAL_ENERGY_HIGH, state);
+    }
+    
+    @Override
+    public String toString() {
+        return String.format("EClusterLow: %d; EClusterHigh %d; HitCount: %d",
+                getStateClusterEnergyLow() ? 1 : 0, getStateClusterEnergyHigh() ? 1 : 0,
+                getStateHitCount() ? 1 : 0);
+    }
+}

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Trigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Trigger.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/Trigger.java	Wed Apr 27 11:11:32 2016
@@ -14,139 +14,139 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public abstract class Trigger<E> {
-	// Track whether the trigger conditions were met.
-	private boolean passTrigger = false;
-	// Store the cut condition states.
-	private Map<String, Boolean> passMap = new HashMap<String, Boolean>();
-	// Store the cluster associated with the trigger.
-	private final E source;
-	// Store the trigger number.
-	private final int triggerNum;
-	
-	/**
-	 * Creates a new <code>Trigger</code> object with the argument
-	 * specifying the object from whence the trigger state is derived.
-	 * @param source - The trigger source object.
-	 */
-	protected Trigger(E source) {
-		this(source, -1);
-	}
-	
-	/**
-	 * Creates a new <code>Trigger</code> object with the argument
-	 * specifying the object from whence the trigger state is derived.
-	 * @param source - The trigger source object.
-	 * @param triggerNum - The number of the trigger.
-	 */
-	protected Trigger(E source, int triggerNum) {
-		this.source = source;
-		this.triggerNum = triggerNum;
-	}
-	
-	/**
-	 * Adds a cut to the set of cuts tracked by this trigger.
-	 * @param cut - The identifier for the cut.
-	 */
-	protected void addValidCut(String cut) {
-		passMap.put(cut, new Boolean(false));
-	}
-	
-	/**
-	 * Gets the state of the specified cut.
-	 * @param cut - The identifier for the cut.
-	 * @return Returns <code>true</code> if the conditions for the
-	 * specified cut were met and <code>false</code> otherwise.
-	 * @throws IllegalArgumentException Occurs if the specified cut
-	 * is not supported by the object.
-	 */
-	protected boolean getCutState(String cut) throws IllegalArgumentException {
-		if(passMap.containsKey(cut)) {
-			return passMap.get(cut);
-		} else {
-			throw new IllegalArgumentException(String.format("Trigger cut \"%s\" is not a supported trigger cut.", cut));
-		}
-	}
-	
-	/**
-	 * Gets the number of the trigger. If the trigger has no number,
-	 * it will return <code>-1</code>.
-	 * @return Returns the trigger number as an <code>int</code>.
-	 */
-	public int getTriggerNumber() {
-		return triggerNum;
-	}
-	
-	/**
-	 * Gets the object to which the trigger cuts are applied.
-	 * @return Returns the trigger source object.
-	 */
-	public E getTriggerSource() { return source; }
-	
-	/**
-	 * Gets whether the conditions for the trigger were met.
-	 * @return Returns <code>true</code> if the conditions for the
-	 * trigger were met and <code>false</code> if they were not.
-	 */
-	public boolean getTriggerState() {
-		return passTrigger;
-	}
-	
-	/**
-	 * Removes a cut from the set of cuts tracked by the trigger.
-	 * @param cut - The identifier for the cut.
-	 */
-	protected void removeValidCut(String cut) {
-		passMap.remove(cut);
-	}
-	
-	/**
-	 * Checks whether the all of the trigger cut conditions were met.
-	 * @return Returns <code>true</code> if all of the cut conditions
-	 * were met and <code>false</code> otherwise.
-	 */
-	private boolean isValidTrigger() {
-		// Iterate over all of the cuts and look for any that have not
-		// been met.
-		for(Entry<String, Boolean> cut : passMap.entrySet()) {
-			if(!cut.getValue()) { return false; }
-		}
-		
-		// If there are no cut conditions that have not been met, then
-		// the trigger is valid.
-		return true;
-	}
-	
-	/**
-	 * Sets whether the conditions for the specified cut were met.
-	 * @param cut - The identifier for the cut.
-	 * @param state - <code>true</code> indicates that the conditions
-	 * for the cut were met and <code>false</code> that they were not.
-	 * @throws IllegalArgumentException Occurs if the specified cut
-	 * is not supported by the object.
-	 */
-	protected void setCutState(String cut, boolean state) throws IllegalArgumentException {
-		if(passMap.containsKey(cut)) {
-			// Set the cut state.
-			passMap.put(cut, state);
-			
-			// If the cut state is true, then all cut conditions may have
-			// been met. Check whether this is true and, if so, set the
-			// trigger state accordingly.
-			if(state && isValidTrigger()) { passTrigger = true; }
-			else { passTrigger = false; }
-		} else {
-			throw new IllegalArgumentException(String.format("Trigger cut \"%s\" is not a supported trigger cut.", cut));
-		}
-	}
-	
-	/**
-	 * Indicates whether the specified cut state is tracked by this
-	 * object or not.
-	 * @param cut - The identifier for the cut.
-	 * @return Returns <code>true</code> if the cut state is tracked
-	 * by this object and <code>false</code> otherwise.
-	 */
-	protected boolean supportsCut(String cut) {
-		return passMap.containsKey(cut);
-	}
-}
+    // Track whether the trigger conditions were met.
+    private boolean passTrigger = false;
+    // Store the cut condition states.
+    private Map<String, Boolean> passMap = new HashMap<String, Boolean>();
+    // Store the cluster associated with the trigger.
+    private final E source;
+    // Store the trigger number.
+    private final int triggerNum;
+    
+    /**
+     * Creates a new <code>Trigger</code> object with the argument
+     * specifying the object from whence the trigger state is derived.
+     * @param source - The trigger source object.
+     */
+    protected Trigger(E source) {
+        this(source, -1);
+    }
+    
+    /**
+     * Creates a new <code>Trigger</code> object with the argument
+     * specifying the object from whence the trigger state is derived.
+     * @param source - The trigger source object.
+     * @param triggerNum - The number of the trigger.
+     */
+    protected Trigger(E source, int triggerNum) {
+        this.source = source;
+        this.triggerNum = triggerNum;
+    }
+    
+    /**
+     * Adds a cut to the set of cuts tracked by this trigger.
+     * @param cut - The identifier for the cut.
+     */
+    protected void addValidCut(String cut) {
+        passMap.put(cut, new Boolean(false));
+    }
+    
+    /**
+     * Gets the state of the specified cut.
+     * @param cut - The identifier for the cut.
+     * @return Returns <code>true</code> if the conditions for the
+     * specified cut were met and <code>false</code> otherwise.
+     * @throws IllegalArgumentException Occurs if the specified cut
+     * is not supported by the object.
+     */
+    protected boolean getCutState(String cut) throws IllegalArgumentException {
+        if(passMap.containsKey(cut)) {
+            return passMap.get(cut);
+        } else {
+            throw new IllegalArgumentException(String.format("Trigger cut \"%s\" is not a supported trigger cut.", cut));
+        }
+    }
+    
+    /**
+     * Gets the number of the trigger. If the trigger has no number,
+     * it will return <code>-1</code>.
+     * @return Returns the trigger number as an <code>int</code>.
+     */
+    public int getTriggerNumber() {
+        return triggerNum;
+    }
+    
+    /**
+     * Gets the object to which the trigger cuts are applied.
+     * @return Returns the trigger source object.
+     */
+    public E getTriggerSource() { return source; }
+    
+    /**
+     * Gets whether the conditions for the trigger were met.
+     * @return Returns <code>true</code> if the conditions for the
+     * trigger were met and <code>false</code> if they were not.
+     */
+    public boolean getTriggerState() {
+        return passTrigger;
+    }
+    
+    /**
+     * Removes a cut from the set of cuts tracked by the trigger.
+     * @param cut - The identifier for the cut.
+     */
+    protected void removeValidCut(String cut) {
+        passMap.remove(cut);
+    }
+    
+    /**
+     * Checks whether the all of the trigger cut conditions were met.
+     * @return Returns <code>true</code> if all of the cut conditions
+     * were met and <code>false</code> otherwise.
+     */
+    private boolean isValidTrigger() {
+        // Iterate over all of the cuts and look for any that have not
+        // been met.
+        for(Entry<String, Boolean> cut : passMap.entrySet()) {
+            if(!cut.getValue()) { return false; }
+        }
+        
+        // If there are no cut conditions that have not been met, then
+        // the trigger is valid.
+        return true;
+    }
+    
+    /**
+     * Sets whether the conditions for the specified cut were met.
+     * @param cut - The identifier for the cut.
+     * @param state - <code>true</code> indicates that the conditions
+     * for the cut were met and <code>false</code> that they were not.
+     * @throws IllegalArgumentException Occurs if the specified cut
+     * is not supported by the object.
+     */
+    protected void setCutState(String cut, boolean state) throws IllegalArgumentException {
+        if(passMap.containsKey(cut)) {
+            // Set the cut state.
+            passMap.put(cut, state);
+            
+            // If the cut state is true, then all cut conditions may have
+            // been met. Check whether this is true and, if so, set the
+            // trigger state accordingly.
+            if(state && isValidTrigger()) { passTrigger = true; }
+            else { passTrigger = false; }
+        } else {
+            throw new IllegalArgumentException(String.format("Trigger cut \"%s\" is not a supported trigger cut.", cut));
+        }
+    }
+    
+    /**
+     * Indicates whether the specified cut state is tracked by this
+     * object or not.
+     * @param cut - The identifier for the cut.
+     * @return Returns <code>true</code> if the cut state is tracked
+     * by this object and <code>false</code> otherwise.
+     */
+    protected boolean supportsCut(String cut) {
+        return passMap.containsKey(cut);
+    }
+}

Modified: java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/TriggerDiagnosticUtil.java
 =============================================================================
--- java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/TriggerDiagnosticUtil.java	(original)
+++ java/branches/HPSJAVA-409/analysis/src/main/java/org/hps/analysis/trigger/util/TriggerDiagnosticUtil.java	Wed Apr 27 11:11:32 2016
@@ -15,208 +15,208 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class TriggerDiagnosticUtil {
-	// Cluster match state variables.
-	public static final byte CLUSTER_STATE_MATCHED        = 0;
-	public static final byte CLUSTER_STATE_FAIL_POSITION  = 1;
-	public static final byte CLUSTER_STATE_FAIL_ENERGY    = 2;
-	public static final byte CLUSTER_STATE_FAIL_HIT_COUNT = 3;
-	public static final byte CLUSTER_STATE_FAIL_TIME      = 4;
-	public static final byte CLUSTER_STATE_FAIL_UNKNOWN   = 5;
-	
-	// Trigger match cut IDs.
-	public static final int SINGLES_ENERGY_MIN = 0;
-	public static final int SINGLES_ENERGY_MAX = 1;
-	public static final int SINGLES_HIT_COUNT = 2;
-	public static final int PAIR_ENERGY_SUM = 0;
-	public static final int PAIR_ENERGY_DIFF = 1;
-	public static final int PAIR_ENERGY_SLOPE = 2;
-	public static final int PAIR_COPLANARITY = 3;
-	
-	// Trigger type variables.
-	public static final int TRIGGER_PULSER    = TriggerStatModule.PULSER;
-	public static final int TRIGGER_COSMIC    = TriggerStatModule.COSMIC;
-	public static final int TRIGGER_SINGLES_0 = TriggerStatModule.SINGLES_0;
-	public static final int TRIGGER_SINGLES_1 = TriggerStatModule.SINGLES_1;
-	public static final int TRIGGER_PAIR_0    = TriggerStatModule.PAIR_0;
-	public static final int TRIGGER_PAIR_1    = TriggerStatModule.PAIR_1;
-	public static final String[] TRIGGER_NAME = { "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Pulser", "Cosmic" };
-	
-	/**
-	 * Convenience method that writes the position of a cluster in the
-	 * form (ix, iy).
-	 * @param cluster - The cluster.
-	 * @return Returns the cluster position as a <code>String</code>.
-	 */
-	public static final String clusterPositionString(Cluster cluster) {
-		return String.format("(%3d, %3d)",
-				cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
-				cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"));
-	}
-	
-	/**
-	 * Convenience method that writes the position of a cluster in the
-	 * form (ix, iy).
-	 * @param cluster - The cluster.
-	 * @return Returns the cluster position as a <code>String</code>.
-	 */
-	public static final String clusterPositionString(SSPCluster cluster) {
-		return String.format("(%3d, %3d)", cluster.getXIndex(), cluster.getYIndex());
-	}
-	
-	/**
-	 * Convenience method that writes the information in a cluster to
-	 * a <code>String</code>.
-	 * @param cluster - The cluster.
-	 * @return Returns the cluster information as a <code>String</code>.
-	 */
-	public static final String clusterToString(Cluster cluster) {
-		return String.format("Cluster at (%3d, %3d) with %.3f GeV and %d hits at %4.0f ns.",
-				cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
-				cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"),
-				cluster.getEnergy(), cluster.getCalorimeterHits().size(),
-				cluster.getCalorimeterHits().get(0).getTime());
-	}
-	
-	/**
-	 * Convenience method that writes the information in a cluster to
-	 * a <code>String</code>.
-	 * @param cluster - The cluster.
-	 * @return Returns the cluster information as a <code>String</code>.
-	 */
-	public static final String clusterToString(SSPCluster cluster) {
-		return String.format("Cluster at (%3d, %3d) with %.3f GeV and %d hits at %4d ns.",
-				cluster.getXIndex(), cluster.getYIndex(), cluster.getEnergy(),
-				cluster.getHitCount(), cluster.getTime());
-	}
-	
-	/**
-	 * Gets the x/y-indices of the cluster.
-	 * @param cluster -  The cluster of which to obtain the indices.
-	 * @return Returns the indices as a <code>Point</code> object.
-	 */
-	public static final Point getClusterPosition(Cluster cluster) {
-		return new Point(getXIndex(cluster), getYIndex(cluster));
-	}
-	
-	/**
-	 * Gets the x/y-indices of the cluster.
-	 * @param cluster -  The cluster of which to obtain the indices.
-	 * @return Returns the indices as a <code>Point</code> object.
-	 */
-	public static final Point getClusterPosition(SSPCluster cluster) {
-		return new Point(cluster.getXIndex(), cluster.getYIndex());
-	}
-	
-	/**
-	 * Gets the time stamp of the cluster in nanoseconds.
-	 * @param cluster - The cluster.
-	 * @return Returns the time-stamp.
-	 */
-	public static final double getClusterTime(Cluster cluster) {
-		return cluster.getCalorimeterHits().get(0).getTime();
-	}
-	
-	/**
-	 * Gets the time stamp of the cluster in nanoseconds.
-	 * @param cluster - The cluster.
-	 * @return Returns the time-stamp.
-	 */
-	public static final int getClusterTime(SSPCluster cluster) {
-		return cluster.getTime();
-	}
-	
-	/**
-	 * Gets the number of digits in the base-10 String representation
-	 * of an integer primitive. Negative signs are not included in the
-	 * digit count.
-	 * @param value - The value of which to obtain the length.
-	 * @return Returns the number of digits in the String representation
-	 * of the argument value.
-	 */
-	public static final int getDigits(int value) {
-		if(value < 0) { return Integer.toString(value).length() - 1; }
-		else { return Integer.toString(value).length(); }
-	}
-	
-	/**
-	 * Gets the number of hits in a cluster.
-	 * @param cluster - The cluster.
-	 * @return Returns the number of hits in the cluster.
-	 */
-	public static final int getHitCount(Cluster cluster) {
-		return cluster.getCalorimeterHits().size();
-	}
-	
-	/**
-	 * Gets the number of hits in a cluster.
-	 * @param cluster - The cluster.
-	 * @return Returns the number of hits in the cluster.
-	 */
-	public static final int getHitCount(SSPCluster cluster) {
-		return cluster.getHitCount();
-	}
-	
-	/**
-	 * Gets the x-index of the cluster's seed hit.
-	 * @param cluster - The cluster.
-	 * @return Returns the x-index.
-	 */
-	public static final int getXIndex(Cluster cluster) {
-		return cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-	}
-	
-	/**
-	 * Gets the x-index of the cluster's seed hit.
-	 * @param cluster - The cluster.
-	 * @return Returns the x-index.
-	 */
-	public static final int getXIndex(SSPCluster cluster) {
-		return cluster.getXIndex();
-	}
-	
-	/**
-	 * Gets the y-index of the cluster's seed hit.
-	 * @param cluster - The cluster.
-	 * @return Returns the y-index.
-	 */
-	public static final int getYIndex(Cluster cluster) {
-		return cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-	}
-	
-	/**
-	 * Gets the y-index of the cluster's seed hit.
-	 * @param cluster - The cluster.
-	 * @return Returns the y-index.
-	 */
-	public static final int getYIndex(SSPCluster cluster) {
-		return cluster.getYIndex();
-	}
-	
-	/**
-	 * Checks whether all of the hits in a cluster are within the safe
-	 * region of the FADC output window.
-	 * @param reconCluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is safe and
-	 * returns <code>false</code> otherwise.
-	 */
-	public static final boolean isVerifiable(Cluster reconCluster, int nsa, int nsb, int windowWidth) {
-		// Iterate over the hits in the cluster.
-		for(CalorimeterHit hit : reconCluster.getCalorimeterHits()) {
-			// Check that none of the hits are within the disallowed
-			// region of the FADC readout window.
-			if(hit.getTime() <= nsb || hit.getTime() >= (windowWidth - nsa)) {
-				return false;
-			}
-			
-			// Also check to make sure that the cluster does not have
-			// any negative energy hits. These are, obviously, wrong.
-			if(hit.getCorrectedEnergy() < 0.0) {
-				return false;
-			}
-		}
-		
-		// If all of the cluster hits pass the time cut, the cluster
-		// is valid.
-		return true;
-	}
+    // Cluster match state variables.
+    public static final byte CLUSTER_STATE_MATCHED        = 0;
+    public static final byte CLUSTER_STATE_FAIL_POSITION  = 1;
+    public static final byte CLUSTER_STATE_FAIL_ENERGY    = 2;
+    public static final byte CLUSTER_STATE_FAIL_HIT_COUNT = 3;
+    public static final byte CLUSTER_STATE_FAIL_TIME      = 4;
+    public static final byte CLUSTER_STATE_FAIL_UNKNOWN   = 5;
+    
+    // Trigger match cut IDs.
+    public static final int SINGLES_ENERGY_MIN = 0;
+    public static final int SINGLES_ENERGY_MAX = 1;
+    public static final int SINGLES_HIT_COUNT = 2;
+    public static final int PAIR_ENERGY_SUM = 0;
+    public static final int PAIR_ENERGY_DIFF = 1;
+    public static final int PAIR_ENERGY_SLOPE = 2;
+    public static final int PAIR_COPLANARITY = 3;
+    
+    // Trigger type variables.
+    public static final int TRIGGER_PULSER    = TriggerStatModule.PULSER;
+    public static final int TRIGGER_COSMIC    = TriggerStatModule.COSMIC;
+    public static final int TRIGGER_SINGLES_0 = TriggerStatModule.SINGLES_0;
+    public static final int TRIGGER_SINGLES_1 = TriggerStatModule.SINGLES_1;
+    public static final int TRIGGER_PAIR_0    = TriggerStatModule.PAIR_0;
+    public static final int TRIGGER_PAIR_1    = TriggerStatModule.PAIR_1;
+    public static final String[] TRIGGER_NAME = { "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Pulser", "Cosmic" };
+    
+    /**
+     * Convenience method that writes the position of a cluster in the
+     * form (ix, iy).
+     * @param cluster - The cluster.
+     * @return Returns the cluster position as a <code>String</code>.
+     */
+    public static final String clusterPositionString(Cluster cluster) {
+        return String.format("(%3d, %3d)",
+                cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
+                cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"));
+    }
+    
+    /**
+     * Convenience method that writes the position of a cluster in the
+     * form (ix, iy).
+     * @param cluster - The cluster.
+     * @return Returns the cluster position as a <code>String</code>.
+     */
+    public static final String clusterPositionString(SSPCluster cluster) {
+        return String.format("(%3d, %3d)", cluster.getXIndex(), cluster.getYIndex());
+    }
+    
+    /**
+     * Convenience method that writes the information in a cluster to
+     * a <code>String</code>.
+     * @param cluster - The cluster.
+     * @return Returns the cluster information as a <code>String</code>.
+     */
+    public static final String clusterToString(Cluster cluster) {
+        return String.format("Cluster at (%3d, %3d) with %.3f GeV and %d hits at %4.0f ns.",
+                cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
+                cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"),
+                cluster.getEnergy(), cluster.getCalorimeterHits().size(),
+                cluster.getCalorimeterHits().get(0).getTime());
+    }
+    
+    /**
+     * Convenience method that writes the information in a cluster to
+     * a <code>String</code>.
+     * @param cluster - The cluster.
+     * @return Returns the cluster information as a <code>String</code>.
+     */
+    public static final String clusterToString(SSPCluster cluster) {
+        return String.format("Cluster at (%3d, %3d) with %.3f GeV and %d hits at %4d ns.",
+                cluster.getXIndex(), cluster.getYIndex(), cluster.getEnergy(),
+                cluster.getHitCount(), cluster.getTime());
+    }
+    
+    /**
+     * Gets the x/y-indices of the cluster.
+     * @param cluster -  The cluster of which to obtain the indices.
+     * @return Returns the indices as a <code>Point</code> object.
+     */
+    public static final Point getClusterPosition(Cluster cluster) {
+        return new Point(getXIndex(cluster), getYIndex(cluster));
+    }
+    
+    /**
+     * Gets the x/y-indices of the cluster.
+     * @param cluster -  The cluster of which to obtain the indices.
+     * @return Returns the indices as a <code>Point</code> object.
+     */
+    public static final Point getClusterPosition(SSPCluster cluster) {
+        return new Point(cluster.getXIndex(), cluster.getYIndex());
+    }
+    
+    /**
+     * Gets the time stamp of the cluster in nanoseconds.
+     * @param cluster - The cluster.
+     * @return Returns the time-stamp.
+     */
+    public static final double getClusterTime(Cluster cluster) {
+        return cluster.getCalorimeterHits().get(0).getTime();
+    }
+    
+    /**
+     * Gets the time stamp of the cluster in nanoseconds.
+     * @param cluster - The cluster.
+     * @return Returns the time-stamp.
+     */
+    public static final int getClusterTime(SSPCluster cluster) {
+        return cluster.getTime();
+    }
+    
+    /**
+     * Gets the number of digits in the base-10 String representation
+     * of an integer primitive. Negative signs are not included in the
+     * digit count.
+     * @param value - The value of which to obtain the length.
+     * @return Returns the number of digits in the String representation
+     * of the argument value.
+     */
+    public static final int getDigits(int value) {
+        if(value < 0) { return Integer.toString(value).length() - 1; }
+        else { return Integer.toString(value).length(); }
+    }
+    
+    /**
+     * Gets the number of hits in a cluster.
+     * @param cluster - The cluster.
+     * @return Returns the number of hits in the cluster.
+     */
+    public static final int getHitCount(Cluster cluster) {
+        return cluster.getCalorimeterHits().size();
+    }
+    
+    /**
+     * Gets the number of hits in a cluster.
+     * @param cluster - The cluster.
+     * @return Returns the number of hits in the cluster.
+     */
+    public static final int getHitCount(SSPCluster cluster) {
+        return cluster.getHitCount();
+    }
+    
+    /**
+     * Gets the x-index of the cluster's seed hit.
+     * @param cluster - The cluster.
+     * @return Returns the x-index.
+     */
+    public static final int getXIndex(Cluster cluster) {
+        return cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+    }
+    
+    /**
+     * Gets the x-index of the cluster's seed hit.
+     * @param cluster - The cluster.
+     * @return Returns the x-index.
+     */
+    public static final int getXIndex(SSPCluster cluster) {
+        return cluster.getXIndex();
+    }
+    
+    /**
+     * Gets the y-index of the cluster's seed hit.
+     * @param cluster - The cluster.
+     * @return Returns the y-index.
+     */
+    public static final int getYIndex(Cluster cluster) {
+        return cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+    }
+    
+    /**
+     * Gets the y-index of the cluster's seed hit.
+     * @param cluster - The cluster.
+     * @return Returns the y-index.
+     */
+    public static final int getYIndex(SSPCluster cluster) {
+        return cluster.getYIndex();
+    }
+    
+    /**
+     * Checks whether all of the hits in a cluster are within the safe
+     * region of the FADC output window.
+     * @param reconCluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is safe and
+     * returns <code>false</code> otherwise.
+     */
+    public static final boolean isVerifiable(Cluster reconCluster, int nsa, int nsb, int windowWidth) {
+        // Iterate over the hits in the cluster.
+        for(CalorimeterHit hit : reconCluster.getCalorimeterHits()) {
+            // Check that none of the hits are within the disallowed
+            // region of the FADC readout window.
+            if(hit.getTime() <= nsb || hit.getTime() >= (windowWidth - nsa)) {
+                return false;
+            }
+            
+            // Also check to make sure that the cluster does not have
+            // any negative energy hits. These are, obviously, wrong.
+            if(hit.getCorrectedEnergy() < 0.0) {
+                return false;
+            }
+        }
+        
+        // If all of the cluster hits pass the time cut, the cluster
+        // is valid.
+        return true;
+    }
 }

Modified: java/branches/HPSJAVA-409/conditions/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/pom.xml	(original)
+++ java/branches/HPSJAVA-409/conditions/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/conditions/</url>
@@ -37,6 +37,7 @@
                         <exclude>org/hps/conditions/api/ConditionsTagTest.java</exclude>
                         <exclude>org/hps/conditions/HPSJAVA_529_Test.java</exclude>
                         <exclude>org/hps/conditions/dummy/**.java</exclude>
+                        <exclude>org/hps/conditions/beam/BeamEnergyTest.java</exclude>
                     </excludes>
                 </configuration>
             </plugin>

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java	Wed Apr 27 11:11:32 2016
@@ -28,12 +28,15 @@
  * This is a "special" Driver which must have its initialization occur at the right time. It has a custom initialization
  * method {@link #initialize()} which should be called after all Driver setup has occurred, but before the job actually
  * begins. This is so the conditions system functions properly, including the activation of registered listeners. The
- * setup is performed by in the class {@link org.hps.job.JobManager}, which is used in the default command line front
- * end of the hps-distribution. If that class is not being used, then the method must be executed manually at the right
+ * setup is performed by the <code>JobManager</code>, which is used in the default command line front end of the 
+ * hps-distribution. If that class is not being used, then the method must be executed manually at the right
  * time to achieve the proper behavior.
  *
  * @author Jeremy McCormick, SLAC
+ * 
+ * @deprecated Use built-in options of job manager.
  */
+@Deprecated
 public class ConditionsDriver extends Driver {
 
     /** The name of the detector model. */
@@ -142,4 +145,12 @@
     public final void setXmlConfigResource(final String xmlConfigResource) {
         this.xmlConfigResource = xmlConfigResource;
     }
+
+    public int getRunNumber() {
+        return this.runNumber;
+    }
+
+    public String getDetectorName() {
+        return this.detectorName;
+    }
 }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObject.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObject.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObject.java	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,7 @@
  *
  * @author Jeremy McCormick, SLAC
  */
-public class BaseConditionsObject implements ConditionsObject {
+public abstract class BaseConditionsObject implements ConditionsObject {
 
     /**
      * Field name for collection ID.
@@ -206,8 +206,8 @@
      * Get a field value.
      *
      * @param name the field name
-     * @param T the field value
-     * @param <T> the implicit return return
+     * @param <T> the implicit return type
+     * @return the value of field cast to given type
      */
     @Override
     public <T> T getFieldValue(final String name) {
@@ -247,7 +247,7 @@
     /**
      * Return <code>true</code> if collection ID is valid.
      *
-     * @param <code>true</code> if collection ID is valid
+     * @return <code>true</code> if collection ID is valid
      */
     @Override
     public boolean hasValidCollectionId() {
@@ -440,4 +440,22 @@
         }
         return rowsUpdated != 0;
     }
+    
+    public boolean equals(Object object) {
+        // Is it the same object?
+        if (object == this) {
+            return true;
+        }
+        // Are these objects the same class?
+        if (object.getClass().equals(this.getClass())) {
+            BaseConditionsObject otherObject = BaseConditionsObject.class.cast(object);
+            // Do the row IDs and database table name match?
+            if (otherObject.getTableMetaData().getTableName().equals(this.getTableMetaData().getTableName()) &&
+                    this.getRowId() == otherObject.getRowId()) {
+                // These are considered the same object (same database table and row ID).
+                return true;
+            }
+        }
+        return false;
+    }
 }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObjectCollection.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObjectCollection.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/BaseConditionsObjectCollection.java	Wed Apr 27 11:11:32 2016
@@ -102,6 +102,15 @@
         if (object == null) {
             throw new IllegalArgumentException("The object argument is null.");
         }
+        //checkCollectionId(object);
+        final boolean added = this.objects.add(object);
+        if (!added) {
+            throw new RuntimeException("Failed to add object.");
+        }
+        return added;
+    }
+
+    private void checkCollectionId(final ObjectType object) {
         // Does this collection have a valid ID yet?
         if (this.getCollectionId() != BaseConditionsObject.UNSET_COLLECTION_ID) {
             // Does the object that is being added have a collection ID?
@@ -122,11 +131,6 @@
                 }
             }
         }
-        final boolean added = this.objects.add(object);
-        if (!added) {
-            throw new RuntimeException("Failed to add object.");
-        }
-        return added;
     }
 
     /**
@@ -344,7 +348,7 @@
         } else {
             // If the collection already exists in the database with this ID then it cannot be inserted.
             if (this.exists()) {
-                throw new DatabaseObjectException("The collection " + this.collectionId
+                throw new DatabaseObjectException("The collection ID " + this.collectionId
                         + " cannot be inserted because it already exists in the " + this.tableMetaData.getTableName()
                         + " table.", this);
             }
@@ -605,7 +609,7 @@
     /**
      * Set the table meta data of the collection.
      *
-     * @param the table meta data of the collection
+     * @param tableMetaData the table meta data of the collection
      * @see TableMetaData
      */
     @Override
@@ -703,7 +707,6 @@
     public void writeCsv(final File file) throws IOException {
         FileWriter fileWriter = null;
         CSVPrinter csvFilePrinter = null;
-
         try {
             fileWriter = new FileWriter(file);
             csvFilePrinter = new CSVPrinter(fileWriter, CSVFormat.DEFAULT);

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectCollection.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectCollection.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectCollection.java	Wed Apr 27 11:11:32 2016
@@ -64,7 +64,6 @@
      * Load collection from a CSV file.
      *
      * @param file the input CSV file
-     * @param delimiter the field delimiter (leave blank for default which is comma-delimited)
      * @throws IOException if there is an error closing the reader
      * @throws FileNotFoundException if the input file does not exist
      * @throws ConditionsObjectException if there is an error creating a conditions object
@@ -104,7 +103,6 @@
      * Write the collection contents to a text file.
      *
      * @param file the output text file
-     * @param delimiter the field delimiter (leave blank for default which is comma-delimited)
      */
     void writeCsv(File file) throws IOException;
 }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectException.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectException.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsObjectException.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
     /**
      * Error with a message.
      *
-     * @param message the error message
+     * @param e the original exception
      */
     public ConditionsObjectException(Exception e) {
         super(e);

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsRecord.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsRecord.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/ConditionsRecord.java	Wed Apr 27 11:11:32 2016
@@ -8,6 +8,7 @@
 import org.hps.conditions.database.ConditionsRecordConverter;
 import org.hps.conditions.database.Converter;
 import org.hps.conditions.database.Field;
+import org.hps.conditions.database.MultipleCollectionsAction;
 import org.hps.conditions.database.Table;
 
 /**
@@ -233,6 +234,33 @@
         public final ConditionsRecordCollection sortedByUpdated() {
             return (ConditionsRecordCollection) this.sorted(new UpdatedComparator());
         }
+        
+        /**
+         * Find a unique record using the selected action for disambiguating conditions with the same key.
+         * @param key the name of the key
+         * @param action the disambiguation action
+         * @return the unique conditions record or <code>null</code> if does not exist
+         */
+        public ConditionsRecord findUniqueRecord(String key, MultipleCollectionsAction action) {
+            ConditionsRecord record = null;
+            ConditionsRecordCollection keyRecords = this.findByKey(key);
+            if (keyRecords.size() > 0) {
+                if (keyRecords.size() == 1) {
+                    record = keyRecords.get(0);
+                } else {
+                    if (action.equals(MultipleCollectionsAction.LAST_UPDATED)) {
+                        record = keyRecords.sortedByUpdated().get(keyRecords.size() - 1);
+                    } else if (action.equals(MultipleCollectionsAction.LAST_CREATED)) {
+                        record = keyRecords.sortedByCreated().get(keyRecords.size() - 1);
+                    } else if (action.equals(MultipleCollectionsAction.LATEST_RUN_START)) {
+                        record = keyRecords.sortedByRunStart().get(keyRecords.size() - 1);
+                    } else if (action.equals(MultipleCollectionsAction.ERROR)) {
+                        throw new RuntimeException("Multiple ConditionsRecord object found for conditions key " + key + ".");
+                    }
+                }
+            }
+            return record;
+        }
     }
 
     /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/package-info.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/package-info.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/api/package-info.java	Wed Apr 27 11:11:32 2016
@@ -1,11 +1,13 @@
 /**
- * User interface to the database conditions system
+ * User API to the database conditions system
  *
  * @author Jeremy McCormick, SLAC
- * @see ConditionsObject
- * @see ConditionsObjectCollection
- * @see ConditionsSeries
- * @see ConditionsRecord
+ * 
+ * @see org.hps.conditions.api.ConditionsObject
+ * @see org.hps.conditions.api.ConditionsObjectCollection
+ * @see org.hps.conditions.api.ConditionsSeries
+ * @see org.hps.conditions.api.ConditionsRecord
+ * @see org.hps.conditions.api.ConditionsTag
  */
 package org.hps.conditions.api;
 

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AbstractCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AbstractCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AbstractCommand.java	Wed Apr 27 11:11:32 2016
@@ -1,7 +1,7 @@
 package org.hps.conditions.cli;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -32,7 +32,7 @@
     /**
      * The parser for the options.
      */
-    private final DefaultParser parser = new DefaultParser();
+    private final PosixParser parser = new PosixParser();
 
     /**
      * Class constructor.

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AddCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AddCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/AddCommand.java	Wed Apr 27 11:11:32 2016
@@ -32,16 +32,13 @@
      */
     private static final Options OPTIONS = new Options();
     static {
-        OPTIONS.addOption(new Option("h", false, "print help for add command"));
-        OPTIONS.addOption("r", true, "starting run number (required)");
-        OPTIONS.getOption("r").setRequired(true);
-        OPTIONS.addOption("e", true, "ending run number (default is starting run number)");
-        OPTIONS.addOption("t", true, "table name (required)");
-        OPTIONS.getOption("t").setRequired(true);
-        OPTIONS.addOption("c", true, "collection ID (required)");
-        OPTIONS.getOption("c").setRequired(true);
-        OPTIONS.addOption("u", true, "user name (optional)");
-        OPTIONS.addOption("m", true, "notes about this conditions set (optional)");
+        OPTIONS.addOption(new Option("h", "help", false, "print help for add command"));
+        OPTIONS.addOption("r", "run-start", true, "starting run number (required)");
+        OPTIONS.addOption("e", "run-end", true, "ending run number (default is starting run number)");
+        OPTIONS.addOption("t", "table", true, "table name (required)");
+        OPTIONS.addOption("c", "collection", true, "collection ID (required)");
+        OPTIONS.addOption("u", "user", true, "user name (optional)");
+        OPTIONS.addOption("m", "notes", true, "notes about this conditions set (optional)");
     }
 
     /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java	Wed Apr 27 11:11:32 2016
@@ -11,7 +11,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.conditions.database.DatabaseConditionsManager;
 import org.lcsim.conditions.ConditionsManager.ConditionsNotFoundException;
 
@@ -34,13 +34,12 @@
     private static Options OPTIONS = new Options();
 
     static {
-        OPTIONS.addOption(new Option("h", false, "print help"));
-        OPTIONS.addOption(new Option("d", true, "detector name"));
-        OPTIONS.addOption(new Option("r", true, "run number"));
-        OPTIONS.addOption(new Option("p", true, "database connection properties file"));
-        OPTIONS.addOption(new Option("x", true, "conditions XML configuration file"));
-        OPTIONS.addOption(new Option("t", true, "conditions tag to use for filtering records"));
-        OPTIONS.addOption(new Option("l", true, "log level of the conditions manager (INFO, FINE, etc.)"));
+        OPTIONS.addOption(new Option("h", "help", false, "print help"));
+        OPTIONS.addOption(new Option("d", "detector", true, "detector name"));
+        OPTIONS.addOption(new Option("r", "run", true, "run number"));
+        OPTIONS.addOption(new Option("p", "connection", true, "database connection properties file"));
+        OPTIONS.addOption(new Option("x", "xml", true, "conditions XML configuration file"));
+        OPTIONS.addOption(new Option("t", "tag", true, "conditions tag to use for filtering records"));
     }
 
     /**
@@ -80,7 +79,7 @@
     /**
      * The options parser.
      */
-    private final DefaultParser parser = new DefaultParser();
+    private final PosixParser parser = new PosixParser();
 
     /**
      * Exit with the given status.
@@ -176,13 +175,6 @@
 
         // Create new manager.
         this.conditionsManager = DatabaseConditionsManager.getInstance();
-
-        // Set the conditions manager log level (does not affect logger of this class or sub-commands).
-        if (commandLine.hasOption("l")) {
-            final Level newLevel = Level.parse(commandLine.getOptionValue("l"));
-            Logger.getLogger(DatabaseConditionsManager.class.getPackage().getName()).setLevel(newLevel);
-            LOGGER.config("conditions manager log level will be set to " + newLevel.toString());
-        }
 
         // Connection properties.
         if (commandLine.hasOption("p")) {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java	Wed Apr 27 11:11:32 2016
@@ -33,12 +33,10 @@
      */
     private static final Options OPTIONS = new Options();
     static {
-        OPTIONS.addOption(new Option("h", false, "print help for load command"));
-        OPTIONS.addOption(new Option("t", true, "name of the target table (required)"));
-        OPTIONS.getOption("t").setRequired(true);
-        OPTIONS.addOption(new Option("f", true, "input data file path (required)"));
-        OPTIONS.getOption("f").setRequired(true);
-        OPTIONS.addOption(new Option("d", true, "description for the collection log"));
+        OPTIONS.addOption(new Option("h", "help", false, "print help for load command"));
+        OPTIONS.addOption(new Option("t", "table", true, "name of the target table (required)"));
+        OPTIONS.addOption(new Option("f", "file", true, "input data file path (required)"));
+        OPTIONS.addOption(new Option("d", "description", true, "description for the collection log"));
     }
 
     /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/PrintCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/PrintCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/PrintCommand.java	Wed Apr 27 11:11:32 2016
@@ -38,18 +38,17 @@
     static Options options = new Options();
 
     static {
-        options.addOption(new Option("h", false, "print help for print command"));
-        options.addOption(new Option("t", true, "table name"));
-        options.addOption(new Option("i", false, "print the ID for the records (off by default)"));
-        options.addOption(new Option("f", true, "write print output to a file (must be used with -t option)"));
-        options.addOption(new Option("H", false, "suppress printing of conditions record and table info"));
-        options.addOption(new Option("d", false, "use tabs for field delimiter instead of spaces"));
+        options.addOption(new Option("h", "help", false, "print help for print command"));
+        options.addOption(new Option("t", "table", true, "table name"));
+        options.addOption(new Option("i", "print-id", false, "include the row IDs in printouts"));
+        options.addOption(new Option("f", "file", true, "write output to a file (requires -t option)"));
+        options.addOption(new Option("H", "no-header", false, "suppress printing of conditions record and table info"));
     }
 
     /**
      * The field delimiter for print output.
      */
-    private char fieldDelimiter = ' ';
+    private static final char DELIMITER = ',';    
 
     /**
      * Output file if printing to a file.
@@ -125,11 +124,6 @@
         // Print header info. Option turns this off.
         if (commandLine.hasOption("h")) {
             this.printHeaders = false;
-        }
-
-        // Use tabs instead of spaces for field delimiter.
-        if (commandLine.hasOption("d")) {
-            this.fieldDelimiter = '\t';
         }
 
         // List of conditions records to print.
@@ -173,7 +167,7 @@
             for (final String columnName : collection.getTableMetaData().getFieldNames()) {
                 if (!"collection_id".equals(columnName)) {
                     buffer.append(((ConditionsObject) object).getFieldValue(columnName));
-                    buffer.append(this.fieldDelimiter);
+                    buffer.append(DELIMITER);
                 }
             }
             buffer.setLength(buffer.length() - 1);
@@ -221,15 +215,17 @@
     private void printColumnNames(final TableMetaData tableMetaData) {
         if (this.printIDs) {
             this.ps.print("id");
-            this.ps.print(this.fieldDelimiter);
-        }
+            this.ps.print(DELIMITER);
+        }
+        StringBuffer sb = new StringBuffer();
         for (final String columnName : tableMetaData.getFieldNames()) {
             if (!"collection_id".equals(columnName)) {
-                this.ps.print(columnName);
-                this.ps.print(this.fieldDelimiter);
-            }
-        }
-        this.ps.println();
+                sb.append(columnName);
+                sb.append(DELIMITER);
+            }
+        }
+        sb.setLength(sb.length() - 1);
+        this.ps.println(sb.toString());
     }
 
     /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/RunSummaryCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/RunSummaryCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/RunSummaryCommand.java	Wed Apr 27 11:11:32 2016
@@ -35,8 +35,8 @@
      */
     static Options options = new Options();
     static {
-        options.addOption(new Option("h", false, "Show help for run-summary command"));
-        options.addOption(new Option("a", false, "Print all collections found for the run"));
+        options.addOption(new Option("h", "help", false, "Show help for run-summary command"));
+        options.addOption(new Option("a", "all", false, "Print all collections found for the run"));
     }
 
     /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/TagCommand.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/TagCommand.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/cli/TagCommand.java	Wed Apr 27 11:11:32 2016
@@ -1,10 +1,9 @@
 package org.hps.conditions.cli;
 
-import java.sql.Connection;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
 import java.sql.SQLException;
-import java.util.logging.Level;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
 import java.util.logging.Logger;
 
 import org.apache.commons.cli.CommandLine;
@@ -16,17 +15,16 @@
 import org.hps.conditions.api.ConditionsTag;
 import org.hps.conditions.api.ConditionsTag.ConditionsTagCollection;
 import org.hps.conditions.api.DatabaseObjectException;
-import org.hps.conditions.api.TableMetaData;
 import org.hps.conditions.api.TableRegistry;
+import org.hps.conditions.database.DatabaseConditionsManager;
 import org.hps.conditions.database.MultipleCollectionsAction;
+import org.lcsim.conditions.ConditionsManager.ConditionsNotFoundException;
 
 /**
  * Create a conditions system tag.
  * <p>
  * The tag groups together conditions records from the <i>conditions</i> database table with a run validity range that 
  * is between a specified starting and ending run.
- * <p>
- * Tagging will not disambiguate overlapping conditions, which is done at run-time based on the current run number.
  *
  * @author Jeremy McCormick, SLAC
  */
@@ -41,20 +39,29 @@
      * Defines command options.
      */
     private static Options OPTIONS = new Options();
+    
+    private MultipleCollectionsAction multipleCollectionsAction = MultipleCollectionsAction.LAST_CREATED; 
+    
+    private static String getMultipleCollectionsActionString() {
+        StringBuffer sb = new StringBuffer();
+        for (MultipleCollectionsAction action : MultipleCollectionsAction.values()) {
+            sb.append(action.name() + " ");
+        }
+        sb.setLength(sb.length() - 1);
+        return sb.toString();
+    }
 
     /**
      * Define all command options.
      */
     static {
-        OPTIONS.addOption(new Option("h", false, "Show help for tag command"));
-        OPTIONS.addOption(new Option("t", true, "Conditions tag name"));
-        OPTIONS.addOption(new Option("s", true, "Starting run number (required)"));
-        OPTIONS.getOption("s").setRequired(true);
-        OPTIONS.addOption(new Option("e", true, "Ending run number (default is unlimited)"));
-        OPTIONS.getOption("t").setRequired(true);
-        OPTIONS.addOption(new Option("m", true,
-                "MultipleCollectionsAction to use for disambiguation (default is LAST_CREATED)"));
-        OPTIONS.addOption(new Option("d", false, "Don't prompt before making tag (be careful!)"));
+        OPTIONS.addOption(new Option("h", "help", false, "Show help for tag command"));
+        OPTIONS.addOption(new Option("t", "tag", true, "Conditions tag name"));
+        OPTIONS.addOption(new Option("s", "run-start", true, "Starting run number (required)"));
+        OPTIONS.addOption(new Option("e", "run-end", true, "Ending run number (required)"));
+        OPTIONS.addOption(new Option("m", "multiple", true, 
+                "set run overlap handling (" + getMultipleCollectionsActionString() + ")"));
+        OPTIONS.addOption(new Option("D", "dont-prompt", false, "Don't prompt before making tag (careful!)"));
     }
 
     /**
@@ -103,6 +110,11 @@
         } else {
             throw new RuntimeException("Missing required -t argument with the tag name.");
         }
+        
+        // Check if tag exists already.
+        if (getManager().getAvailableTags().contains(tagName)) {
+            throw new RuntimeException("The tag '" + tagName + "' already exists in the database.");
+        }
 
         // Starting run number (required).
         int runStart = -1;
@@ -110,19 +122,16 @@
             runStart = Integer.parseInt(commandLine.getOptionValue("s"));
             LOGGER.config("run start set to " + runStart);
         } else {
-            throw new RuntimeException("missing require -s argument with starting run number");
-        }
-
-        // Ending run number (max integer is default).
-        int runEnd = Integer.MAX_VALUE;
+            throw new RuntimeException("Missing required -s argument with starting run number.");
+        }
+
+        // Ending run number (required).
+        int runEnd = -1;
         if (commandLine.hasOption("e")) {
             runEnd = Integer.parseInt(commandLine.getOptionValue("e"));
             LOGGER.config("run end set to " + runEnd);
-        }
-
-        // Run end must be greater than or equal to run start.
-        if (runEnd < runStart) {
-            throw new IllegalArgumentException("runEnd < runStart");
+        } else {
+            throw new RuntimeException("Missing required -e argument with starting run number.");
         }
 
         // Action for disambiguating overlapping collections (default is to use the most recent creation date).
@@ -131,20 +140,24 @@
             multipleCollectionsAction = MultipleCollectionsAction
                     .valueOf(commandLine.getOptionValue("m").toUpperCase());
         }
-        LOGGER.config("multiple collections action set tco " + multipleCollectionsAction);
+        LOGGER.config("run overlaps will be disambiguated using " + multipleCollectionsAction);
 
         // Whether to prompt before tagging (default is yes).
         boolean promptBeforeTagging = true;
         if (commandLine.hasOption("d")) {
             promptBeforeTagging = false;
         }
-        LOGGER.config("prompt before tagging: " + promptBeforeTagging);
+        LOGGER.config("prompt before tagging = " + promptBeforeTagging);
 
         // Conditions system configuration.
         this.getManager().setXmlConfig("/org/hps/conditions/config/conditions_database_no_svt.xml");
 
         // Find all the applicable conditions records by their run number ranges.
         ConditionsRecordCollection tagConditionsRecordCollection = this.findConditionsRecords(runStart, runEnd);
+        
+        if (tagConditionsRecordCollection.size() == 0) {
+            throw new RuntimeException("No records found for tag.");
+        }
 
         LOGGER.info("found " + tagConditionsRecordCollection.size() + " conditions records for the tag");
 
@@ -152,8 +165,8 @@
         final ConditionsTagCollection conditionsTagCollection = this.createConditionsTagCollection(
                 tagConditionsRecordCollection, tagName);
 
-        LOGGER.info("created " + conditionsTagCollection.size() + " tag records ..." + '\n' + conditionsTagCollection);
-
+        printConditionsRecords(tagConditionsRecordCollection);
+        
         // Prompt user to verify tag creation.
         boolean createTag = true;
         if (promptBeforeTagging) {
@@ -178,68 +191,85 @@
 
         LOGGER.info("done!");
     }
-   
-    /**
-     * Find all the conditions records that are applicable for the given run range.
-     * <p>
-     * Overlapping run numbers in conditions with the same key are not disambiguated.
-     * This must be done in the user's job at runtime; usually the most recently created 
-     * conditions record will be used if multiple one's are applicable to the current run.
-     *
-     * @param runStart the start run
-     * @param runEnd the end run (must be greater than or equal to <code>runStart</code>)
-     * @return the conditions records that fall in the run range
+    
+    /**
+     * Print information about conditions records in the tag to the log.
+     * 
+     * @param collection the conditions tag collection
+     */
+    private void printConditionsRecords(ConditionsRecordCollection records) {
+        StringBuffer sb = new StringBuffer();
+        Set<String> keys = new TreeSet<String>(records.getConditionsKeys());
+        for (String key : keys) {
+            ConditionsRecordCollection keyRecords = records.findByKey(key);
+            keyRecords.sortByKey();
+            for (ConditionsRecord record : keyRecords) {
+                sb.append("conditions_id: " + record.getRowId() + ", name: " + record.getName() + ", collection_id: "
+                        + record.getCollectionId() + ", run_start: " + record.getRunStart() 
+                        + ", run_end: " + record.getRunEnd() + ", notes: " + record.getNotes() + '\n');
+                
+            }
+        }        
+        LOGGER.info("including " + records.size() + " records in tag ..." + '\n' + sb.toString());
+    }
+     
+    /**
+     * Scan through a run range to find conditions records for the tag.
+     * 
+     * @param runStart the starting run number
+     * @param runEnd the ending run number
+     * @return the conditions records for the tag
      */
     private ConditionsRecordCollection findConditionsRecords(final int runStart, final int runEnd) {
-        if (runStart > runEnd) {
-            throw new IllegalArgumentException("runStart > runEnd");
-        }
-        if (runStart < 0) {
-            throw new IllegalArgumentException("invalid runStart: " + runStart);
-        }
-        if (runEnd < 0) {
-            throw new IllegalArgumentException("invalid runEnd: " + runEnd);
-        }
-        final Connection connection = this.getManager().getConnection();
-        final ConditionsRecordCollection conditionsRecordCollection = new ConditionsRecordCollection();
-        final TableMetaData tableMetaData = TableRegistry.getTableRegistry().findByTableName("conditions");
-        PreparedStatement statement = null;
-        try {
-            /*
-             * SQL statement handles 3 cases: 
-             * 1) condition's run_start in range 
-             * 2) condition's run_end in range 
-             * 3) condition's run_start and run_end enclose the range
-             */
-            statement = connection
-                    .prepareStatement("SELECT id FROM conditions WHERE (run_start >= ? and run_start <= ?) or (run_end >= ? and run_end <= ?)"
-                            + " or (run_start <= ? and run_end >= ?)");
-            statement.setInt(1, runStart);
-            statement.setInt(2, runEnd);
-            statement.setInt(3, runStart);
-            statement.setInt(4, runEnd);
-            statement.setInt(5, runStart);
-            statement.setInt(6, runEnd);
-
-            final ResultSet resultSet = statement.executeQuery();
-            while (resultSet.next()) {
-                final ConditionsRecord record = new ConditionsRecord();
-                record.setConnection(connection);
-                record.setTableMetaData(tableMetaData);
-                record.select(resultSet.getInt(1));
-                conditionsRecordCollection.add(record);
-            }
-        } catch (DatabaseObjectException | ConditionsObjectException | SQLException e) {
-            throw new RuntimeException(e);
-        } finally {
+        if (runStart < 0 ) {
+            throw new IllegalArgumentException("The run start " + runStart + " is invalid.");
+        }
+        if (runEnd < 0 ) {
+            throw new IllegalArgumentException("The run end " + runEnd + " is invalid.");
+        }
+        if (runStart > runEnd ) {
+            throw new IllegalArgumentException("The run start is greater than the run end.");
+        }
+        DatabaseConditionsManager dbManager = this.getManager();
+        if (dbManager.isFrozen()) {
+            dbManager.unfreeze();
+        }
+        if (!dbManager.getActiveTags().isEmpty()) {
+            dbManager.clearTags();
+        }
+        final String detectorName = "HPS-dummy-detector";
+        ConditionsRecordCollection tagRecords = new ConditionsRecordCollection();
+        Set<Integer> ids = new HashSet<Integer>();
+        for (int run = runStart; run <= runEnd; run++) {
+            LOGGER.info("loading run " + run);
             try {
-                if (statement != null) {
-                    statement.close();
+                dbManager.setDetector(detectorName, run);
+            } catch (ConditionsNotFoundException e) {
+                throw new RuntimeException(e);
+            }
+            ConditionsRecordCollection runRecords = dbManager.getConditionsRecords();
+            Set<String> keys = runRecords.getConditionsKeys();
+            LOGGER.fine("run has " + runRecords.size() + " conditions records");
+            for (String key : keys) {
+                ConditionsRecord record = runRecords.findUniqueRecord(key, this.multipleCollectionsAction);
+                if (record == null) {
+                    throw new RuntimeException("Missing expected unique condition record for " + key + ".");
                 }
-            } catch (final SQLException e) {
-                e.printStackTrace();
-            }
-        }
-        return conditionsRecordCollection;
+                if (!ids.contains(record.getRowId())) {
+                    try {
+                        LOGGER.fine("adding conditions to tag ..." + '\n' + record.toString());
+                        tagRecords.add(record);
+                        ids.add(record.getRowId());
+                    } catch (ConditionsObjectException e) {
+                        throw new RuntimeException(e);
+                    }
+                } else {
+                    LOGGER.fine("Conditions record with row id " + record.getRowId() + " is already in the tag.");
+                }
+            }
+            LOGGER.info("done processing run " + run);
+        }
+        LOGGER.info("Found " + tagRecords.size() + " conditions records for tag.");
+        return tagRecords;
     }
 }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsRecordConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsRecordConverter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsRecordConverter.java	Wed Apr 27 11:11:32 2016
@@ -3,7 +3,6 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 import org.hps.conditions.api.ConditionsObject;
 import org.hps.conditions.api.ConditionsObjectCollection;
 import org.hps.conditions.api.ConditionsObjectException;

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsTagConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsTagConverter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConditionsTagConverter.java	Wed Apr 27 11:11:32 2016
@@ -5,7 +5,6 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 import org.hps.conditions.api.ConditionsObjectException;
 import org.hps.conditions.api.ConditionsTag;
 import org.hps.conditions.api.ConditionsTag.ConditionsTagCollection;
@@ -24,14 +23,13 @@
     private static final String SELECT_SQL = "SELECT conditions_id, tag from conditions_tags where tag = ?";
    
     /**
-     * Get a {@link org.hps.conditions.api.ConditionsTagCollection} which specifies a group of collections
-     * that are tagged in the <i>conditions_tags</i> table in the database.
-     * <p>
-     * The run number is not used, and the <code>name</code> argument specifies the tag name.
+     * Get a {@link org.hps.conditions.api.ConditionsTag.ConditionsTagCollection} which specifies a group of 
+     * collections that are tagged in the <i>conditions_tags</i> table in the database.  The <code>name</code> 
+     * argument is the tag name.
      *
-     * @param manager The current conditions manager.
-     * @param name The name of the conditions set.
-     * @return The matching ConditionsRecords.
+     * @param manager the current conditions manager
+     * @param name the name of the conditions set
+     * @return the matching <code>ConditionsRecord</code> objects
      */
     @Override
     public ConditionsTagCollection getData(final ConditionsManager manager, final String name) {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConnectionParameters.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConnectionParameters.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConnectionParameters.java	Wed Apr 27 11:11:32 2016
@@ -13,7 +13,8 @@
 import java.util.logging.Logger;
 
 /**
- * This class encapsulates the parameters for connecting to a database, including host name, port, user and password.
+ * This class encapsulates the parameters for connecting to a database,
+ * including host name, port, user and password.
  *
  * @author Jeremy McCormick, SLAC
  */
@@ -28,6 +29,12 @@
      * Number of connection retries allowed.
      */
     private static final int MAX_ATTEMPTS = 10;
+    
+    /**
+     * Wait time (in millis) for the first retry. The nth retry waits for
+     * n*RETRY_WAIT millis.
+     */
+    private static final int RETRY_WAIT = 5000;
 
     /**
      * Configure the connection parameters from a properties file.
@@ -46,7 +53,8 @@
     }
 
     /**
-     * Configure the connection parameters from an <code>InputStream</code> of properties.
+     * Configure the connection parameters from an <code>InputStream</code> of
+     * properties.
      *
      * @param in the InputStream of the properties
      * @return the connection parameters
@@ -71,7 +79,8 @@
     }
 
     /**
-     * Configure the connection parameters from an embedded classpath resource which should be a properties file.
+     * Configure the connection parameters from an embedded classpath resource
+     * which should be a properties file.
      *
      * @param resource the resource path
      * @return the connection parameters
@@ -146,8 +155,8 @@
     }
 
     /**
-     * Create a database connection from these parameters. The caller becomes the "owner" and is responsible for closing
-     * it when finished.
+     * Create a database connection from these parameters. The caller becomes
+     * the "owner" and is responsible for closing it when finished.
      *
      * @return the new <code>Connection</code> object
      */
@@ -166,7 +175,7 @@
                     throw new RuntimeException("Failed to connect to database after " + attempt + " attempts: " + this.getConnectionString(), x);
                 }
                 try {
-                    Thread.sleep(attempt * 1000);
+                    Thread.sleep(attempt * RETRY_WAIT);
                 } catch (InterruptedException ex) {
                     Logger.getLogger(ConnectionParameters.class.getName()).log(Level.SEVERE, null, ex);
                 }
@@ -247,13 +256,13 @@
     String getUser() {
         return this.user;
     }
-    
+
     /**
      * Convert to human readable string.
-     * 
+     *
      * @return this object converted to a string
      */
-    public String toString() {                        
+    public String toString() {
         return "ConnectionParameters { database: " + database + ", hostname: " + hostname + ", password: " + password
                 + ", port: " + port + ", user: " + user + " }";
     }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/Converter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/Converter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/Converter.java	Wed Apr 27 11:11:32 2016
@@ -4,8 +4,6 @@
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
-
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 
 /**
  * This is an annotation for providing converter configuration for {@link org.hps.conditions.api.ConditionsObject}

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConverterRegistry.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConverterRegistry.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/ConverterRegistry.java	Wed Apr 27 11:11:32 2016
@@ -6,7 +6,6 @@
 
 import javassist.Modifier;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 import org.hps.conditions.api.BaseConditionsObjectCollection;
 import org.hps.conditions.api.ConditionsObject;
 import org.hps.conditions.api.TableRegistry;

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/DatabaseConditionsManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/DatabaseConditionsManager.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/DatabaseConditionsManager.java	Wed Apr 27 11:11:32 2016
@@ -20,7 +20,6 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 import org.hps.conditions.api.ConditionsObject;
 import org.hps.conditions.api.ConditionsObjectCollection;
 import org.hps.conditions.api.ConditionsRecord.ConditionsRecordCollection;
@@ -338,7 +337,7 @@
     }
 
     /**
-     * Clear the tags used to filter the {@link org.hps.conditons.api.ConditionsRecord}s.
+     * Clear the tags used to filter the {@link org.hps.conditions.api.ConditionsRecord}s.
      */
     public void clearTags() {
         this.tags.clear();
@@ -505,9 +504,8 @@
 
     /**
      * Add a row for a new collection and return the new collection ID assigned to it.
-     *
-     * @param tableName the name of the table
-     * @param comment an optional comment about this new collection
+     * @param collection the conditions object collection
+     * @param description text description for the new collection ID record in the database
      * @return the collection's ID
      * @throws SQLException
      */

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/package-info.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/package-info.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/database/package-info.java	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,10 @@
 /**
- * Implementation of database API to detector conditions
+ * Implementation of database API for detector conditions
+ * <p>
+ * The {@link org.hps.conditions.database.DatabaseConditionsManager} has a set of converters for handling the 
+ * conversion of conditions table data to typed collections.  The converters are created automatically using 
+ * introspection of {@link org.hps.conditions.api.ConditionsObject} classes that have the
+ * {@link org.hps.conditions.database.Table} and {@link org.hps.conditions.database.Field} annotations.
  *
  * @author Jeremy McCormick, SLAC
  */

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/dummy/DummyConditionsObjectConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/dummy/DummyConditionsObjectConverter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/dummy/DummyConditionsObjectConverter.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,6 @@
 package org.hps.conditions.dummy;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
+import org.hps.conditions.database.AbstractConditionsObjectConverter;
 import org.hps.conditions.dummy.DummyConditionsObject.DummyConditionsObjectCollection;
 
 /**

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java	Wed Apr 27 11:11:32 2016
@@ -4,12 +4,12 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import org.hps.conditions.api.AbstractConditionsObjectConverter;
 import org.hps.conditions.api.AbstractIdentifier;
 import org.hps.conditions.api.BaseConditionsObject;
 import org.hps.conditions.api.BaseConditionsObjectCollection;
 import org.hps.conditions.api.ConditionsObjectCollection;
 import org.hps.conditions.api.ConditionsObjectException;
+import org.hps.conditions.database.AbstractConditionsObjectConverter;
 import org.hps.conditions.database.Converter;
 import org.hps.conditions.database.DatabaseConditionsManager;
 import org.hps.conditions.database.Field;
@@ -290,11 +290,16 @@
         public EcalChannelCollection getData(final ConditionsManager conditionsManager, final String name) {
             final EcalChannelCollection collection = super.getData(conditionsManager, name);
             final Subdetector ecal = DatabaseConditionsManager.getInstance().getEcalSubdetector();
-            if (ecal.getDetectorElement() != null) {
-                collection.buildGeometryMap(ecal.getDetectorElement().getIdentifierHelper(), ecal.getSystemID());
+            if (ecal != null) {
+                if (ecal.getDetectorElement() != null) {
+                    collection.buildGeometryMap(ecal.getDetectorElement().getIdentifierHelper(), ecal.getSystemID());
+                } else {
+                    // This can happen when not running with the detector-framework jar in the classpath.
+                    throw new IllegalStateException("The ECal subdetector's detector element is not setup.");
+                }
             } else {
-                // This can happen when not running with the detector-framework jar in the classpath.
-                throw new IllegalStateException("The ECal subdetector's detector element is not setup.");
+                // Bad detector or conditions system not initialized properly.
+                throw new IllegalStateException("The ECal subdetector object is null.");
             }
             return collection;
         }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java	Wed Apr 27 11:11:32 2016
@@ -11,7 +11,7 @@
  * settings, per crystal.
  * <p>
  * Unlike most conditions data types, it does not extend {@link org.hps.conditions.api.ConditionsObject}, because it is
- * a composite object containing data assembled from many other {@link org.hps.conditions.ConditionsObjects} and has a
+ * a composite object containing data assembled from many other {@link org.hps.conditions.api.ConditionsObject} and has a
  * special data converter {@link EcalConditionsConverter}.
  *
  * @author Jeremy McCormick, SLAC

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java	Wed Apr 27 11:11:32 2016
@@ -22,6 +22,7 @@
  *
  * @author Jeremy McCormick, SLAC
  * @author Omar Moreno, UCSC
+ * 
  * @see EcalConditions
  * @see EcalChannel
  * @see EcalGain
@@ -38,8 +39,7 @@
        
     /**
      * Create combined ECAL conditions object containing all data for the current run.
-     *
-     * @param manager the conditions manager
+     * 
      * @param name the conditions set name (unused but must satisfy conditions API)
      */
     @Override
@@ -129,7 +129,6 @@
     /**
      * Get the default collections of {@link EcalBadChannel} objects.
      *
-     * @param manager the conditions manager
      * @return the collections of ECAL bad channel objects
      */
     protected ConditionsSeries<EcalBadChannel, EcalBadChannelCollection> getEcalBadChannelSeries() {
@@ -139,7 +138,6 @@
     /**
      * Get the default {@link EcalCalibration} collection.
      *
-     * @param manager the conditions manager
      * @return the collection of ECAL channel calibration objects
      */
     protected EcalCalibrationCollection getEcalCalibrationCollection() {
@@ -149,7 +147,6 @@
     /**
      * Get the default {@link EcalChannel} collection.
      *
-     * @param manager the conditions manager
      * @return the default ECAL channel object collection
      */
     protected EcalChannelCollection getEcalChannelCollection() {
@@ -159,7 +156,6 @@
     /**
      * Get the default {@link EcalGain} collection.
      *
-     * @param manager the conditions manager
      * @return the ECAL channel gain collection
      */
     protected EcalGainCollection getEcalGainCollection() {
@@ -169,7 +165,6 @@
     /**
      * Get the default {@link EcalTimeShift} collection.
      *
-     * @param manager the conditions manager
      * @return the collection of ECAL time shift objects
      */
     protected EcalTimeShiftCollection getEcalTimeShiftCollection() {
@@ -177,9 +172,8 @@
     }
     
     /**
-     * Get the default {@link EcalPulseWith} collection.
-     *
-     * @param manager the conditions manager
+     * Get the default {@link EcalPulseWidth} collection.
+     *
      * @return the collection of ECAL pulse widths
      */
     protected EcalPulseWidthCollection getEcalPulseWidthCollection() {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/TestRunEcalConditionsConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/TestRunEcalConditionsConverter.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/ecal/TestRunEcalConditionsConverter.java	Wed Apr 27 11:11:32 2016
@@ -20,7 +20,6 @@
     /**
      * Get the collections of {@link EcalBadChannel} objects for Test Run.
      *
-     * @param manager the conditions manager
      * @return the Test Run bad channel collections
      */
     @Override
@@ -31,7 +30,6 @@
     /**
      * Get the {@link EcalCalibration} collection for Test Run.
      *
-     * @param manager the conditions manager
      * @return the Test Run ECAL calibration collection
      */
     @Override
@@ -43,7 +41,6 @@
     /**
      * Get the {@link EcalChannel} collection for Test Run.
      *
-     * @param manager the conditions manager
      * @return the Test Run ECAL channel collection
      */
     @Override
@@ -54,7 +51,6 @@
     /**
      * Get the {@link EcalGain} collection for Test Run.
      *
-     * @param manager the conditions manager
      * @return the Test Run ECAL gain collection
      */
     @Override
@@ -65,7 +61,6 @@
     /**
      * Get the {@link EcalTimeShift} collection for Test Run.
      *
-     * @param manager the conditions manager
      * @return the Test Run ECAL time shift collection
      */
     @Override

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/package-info.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/package-info.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/package-info.java	Wed Apr 27 11:11:32 2016
@@ -2,8 +2,7 @@
  * Database conditions system
  * <p>
  * The HPS conditions module provides facilities for accessing time dependent conditions for a detector at runtime using
- * a framework built on the LCSim conditions system. The {@link DatabaseConditionsReader} has a set of converters for
- * reading data from tables using SQL queries and creating appropriate, typed objects for them.
+ * a framework built on the LCSim conditions system. 
  *
  * @author Jeremy McCormick, SLAC
  * @see org.hps.conditions.api

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/run/RunSpreadsheet.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/run/RunSpreadsheet.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/run/RunSpreadsheet.java	Wed Apr 27 11:11:32 2016
@@ -25,7 +25,7 @@
  * The rows are accessible as raw CSV data through the Apache Commons CSV library, and this data must be manually cleaned up and converted 
  * to the correct data type before being inserted into the conditions database.
  *
- * @author Jeremy McCormick
+ * @author Jeremy McCormick, SLAC
  */
 public final class RunSpreadsheet {
 
@@ -38,23 +38,23 @@
         "start_time", 
         "end_time", 
         "to_tape", 
-        "n_events", 
+        "events",
         "files",
         "trigger_rate", 
         "target", 
         "beam_current",
         "beam_x", 
-        "beam_y", 
-        "trigger_config",
-        /*
-        "ecal_fadc_mode", 
+        "beam_y",
+        "trigger_config", 
+        /* Next 7 are actually hidden in the spreadsheet! */
+        "ecal_fadc_mode",
         "ecal_fadc_thresh", 
         "ecal_fadc_window", 
         "ecal_cluster_thresh_seed", 
         "ecal_cluster_thresh_cluster",
         "ecal_cluster_window_hits", 
-        "ecal_cluster_window_pairs",
-        */ 
+        "ecal_cluster_window_pairs", 
+        /* End hidden fields. */
         "ecal_scalers_fadc", 
         "ecal_scalers_dsc", 
         "svt_y_position", 
@@ -62,8 +62,7 @@
         "svt_offset_time",
         "ecal_temp", 
         "ecal_lv_current", 
-        "notes"
-    };
+        "notes"};
 
     /**
      * Read the CSV file from the command line and print the data to the terminal (just a basic test).
@@ -100,11 +99,14 @@
      * @param file the CSV file
      */
     public RunSpreadsheet(final File file) {
+        if (file == null) {
+            throw new IllegalArgumentException("The file argument is null.");
+        }
         this.file = file;
         try {
             this.fromCsv(this.file);
         } catch (final Exception e) {
-            throw new RuntimeException();
+            throw new RuntimeException("Failed to parse run spreadsheet.", e);
         }
     }
 
@@ -161,14 +163,15 @@
         return records;
     }
     
-    public static final AnotherSimpleDateFormat DATE_FORMAT = new AnotherSimpleDateFormat("MM/dd/yyyy H:mm"); 
+    public static final RunSpreadsheetDateFormat DATE_FORMAT = new RunSpreadsheetDateFormat("MM/dd/yyyy H:mm"); 
     private static final TimeZone TIME_ZONE =  TimeZone.getTimeZone("EST");
     
     
     @SuppressWarnings("serial")
     public
-    static class AnotherSimpleDateFormat extends SimpleDateFormat {
-        public AnotherSimpleDateFormat(String formatstring) {
+    static class RunSpreadsheetDateFormat extends SimpleDateFormat {
+        
+        public RunSpreadsheetDateFormat(String formatstring) {
             super(formatstring);
             //Calendar c = Calendar.getInstance(TIME_ZONE,Locale.US);
             //setTimeZone(TIME_ZONE);
@@ -264,7 +267,7 @@
                 try {
                     addRunData(new RunData(record));
                 } catch (NumberFormatException e) {
-                    e.printStackTrace();
+                    //e.printStackTrace();
                 }
             }
         }

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java	Wed Apr 27 11:11:32 2016
@@ -20,7 +20,7 @@
     @SuppressWarnings("serial")
     public static abstract class AbstractSvtDaqMappingCollection<T extends AbstractSvtDaqMapping> extends
             BaseConditionsObjectCollection<T> {
-      
+
         /**
          * Get the orientation of a sensor.
          *
@@ -65,8 +65,8 @@
     /**
      * Get the orientation of an SVT sensor (AXIAL or STEREO).
      *
-     * @see AXIAL
-     * @see STEREO
+     * @see #AXIAL
+     * @see #STEREO
      * @return the orientation of the SVT sensor
      */
     @Field(names = {"orientation"})
@@ -87,7 +87,7 @@
     /**
      * Set the SVT sensor layer number (1-10 for test run and 1-12 for engineering run).
      *
-     * @param layer : SVT sensor layer number
+     * @param layer SVT sensor layer number
      */
     public final void setLayerNumber(final int layer) {
         this.setFieldValue("layer", layer);
@@ -109,8 +109,8 @@
      * Set the SVT half that the sensor belongs to.
      *
      * @param svtHalf the SVT half (TOP or BOTTOM)
-     * @see TOP_HALF
-     * @see BOTTOM_HALF
+     * @see #TOP_HALF
+     * @see #BOTTOM_HALF
      */
     public final void setSvtHalf(final String svtHalf) {
         if (!svtHalf.equals(AbstractSvtDaqMapping.TOP_HALF) && !svtHalf.equals(AbstractSvtDaqMapping.BOTTOM_HALF)) {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/DaqMapHandler.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/DaqMapHandler.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/DaqMapHandler.java	Wed Apr 27 11:11:32 2016
@@ -96,7 +96,7 @@
      * Method that is triggered when the end of a tag is encountered.
      *
      * @param uri the Namespace URI.
-     * @param locaName the local name (without prefix)
+     * @param localName the local name (without prefix)
      * @param qName the qualified name (with prefix)
      * @throws SAXException if there is an error processing the element
      */

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/MotorPositionLoader.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/MotorPositionLoader.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/MotorPositionLoader.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 
 /**
  * Load SVT motor positions from a MYA dump, figure out time ranges (same position for > 10 seconds), and then convert
@@ -195,7 +195,7 @@
      */
     void run(final String args[]) {
 
-        final DefaultParser parser = new DefaultParser();
+        final PosixParser parser = new PosixParser();
 
         CommandLine cl = null;
         try {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/OpeningAngleLoader.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/OpeningAngleLoader.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/OpeningAngleLoader.java	Wed Apr 27 11:11:32 2016
@@ -30,7 +30,7 @@
      * Check if the run record looks good.
      *
      * @param data
-     * @return
+     * @return whether to accept the run or not
      */
     private static boolean acceptRun(final RunData data) {
         return !data.getRecord().get("to_tape").equals("JUNK")

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtBiasConditionsLoader.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtBiasConditionsLoader.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtBiasConditionsLoader.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.conditions.api.ConditionsRecord;
 import org.hps.conditions.database.DatabaseConditionsManager;
 import org.hps.conditions.run.RunRange;
@@ -176,7 +176,7 @@
 //        options.addOption(new Option("b", true, "beam current file"));
         options.addOption(new Option("s", false, "Show plots"));
 
-        final CommandLineParser parser = new DefaultParser();
+        final CommandLineParser parser = new PosixParser();
         CommandLine cl = null;
         try {
             cl = parser.parse(options, args);

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsLoader.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsLoader.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsLoader.java	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.conditions.api.ConditionsRecord;
 import org.hps.conditions.api.TableMetaData;
 import org.hps.conditions.database.DatabaseConditionsManager;
@@ -60,7 +60,7 @@
         final Options options = setupCommandLineOptions();
 
         // Parse the command line arguments
-        final CommandLineParser parser = new DefaultParser();
+        final CommandLineParser parser = new PosixParser();
         final CommandLine commandLine;
         try {
             commandLine = parser.parse(options, args);

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java	Wed Apr 27 11:11:32 2016
@@ -129,8 +129,8 @@
     /**
      * Get the side of the sensor (ELECTRON or POSITRON).
      *
-     * @see ELECTRON
-     * @see POSITRON
+     * @see #ELECTRON
+     * @see #POSITRON
      * @return sensor side (ELECTRON or POSITRON)
      */
     @Field(names = {"side"})
@@ -160,8 +160,8 @@
      * Set the side of the sensor (ELECTRON or POSITRON).
      *
      * @param side the sensor side (ELECTRON or POSITRON)
-     * @see {@link #ELECTRON}
-     * @see {@link #POSITRON}
+     * @see #ELECTRON
+     * @see #POSITRON
      */
     public final void setSide(final String side) {
         if (!side.equals(SvtDaqMapping.ELECTRON) && !side.equals(SvtDaqMapping.POSITRON)) {

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
         /**
          * Get the {@link SvtT0Shift} associated with a given DAQ pair.
          *
-         * @param DAQ pair for a given sensor
+         * @param pair DAQ pair for a given sensor
          * @return the {@link SvtT0Shift} associated with the DAQ pair or null if does not exist
          */
         @Override

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java	Wed Apr 27 11:11:32 2016
@@ -26,7 +26,7 @@
         /**
          * Find a collection of channels by their DAQ pair assignment.
          *
-         * @param the DAQ pair (FEB ID and FEB Hybrid ID)
+         * @param pair the DAQ pair (FEB ID and FEB Hybrid ID)
          * @return the collection of channels
          */
         @Override

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java	Wed Apr 27 11:11:32 2016
@@ -10,7 +10,7 @@
 
 /**
  * This class contains all test run SVT conditions data by readout channel. {@link TestRunSvtChannel} objects from the
- * SVT channel map should be used to lookup the conditions using the {@link #getChannelConstants(TestRunSvtChannel)}
+ * SVT channel map should be used to lookup the conditions using the {@link #getChannelConstants(AbstractSvtChannel)}
  * method.
  *
  * @author Jeremy McCormick, SLAC

Modified: java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java
 =============================================================================
--- java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java	(original)
+++ java/branches/HPSJAVA-409/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java	Wed Apr 27 11:11:32 2016
@@ -22,7 +22,7 @@
         /**
          * Get the {@link TestRunSvtT0Shift} associated with a given DAQ pair
          *
-         * @param DAQ pair for a given sensor
+         * @param pair DAQ pair for a given sensor
          * @return the {@link TestRunSvtT0Shift} associated with the DAQ pair or null if does not exist
          */
         @Override

Modified: java/branches/HPSJAVA-409/crawler/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/pom.xml	(original)
+++ java/branches/HPSJAVA-409/crawler/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/crawler/</url>
@@ -17,7 +17,11 @@
     <dependencies>
         <dependency>
             <groupId>org.hps</groupId>
-            <artifactId>hps-run-database</artifactId>
+            <artifactId>hps-record-util</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>srs</groupId>
+            <artifactId>org-srs-datacat-client</artifactId>
         </dependency>
     </dependencies>
 </project>

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/AidaMetadataReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/AidaMetadataReader.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/AidaMetadataReader.java	Wed Apr 27 11:11:32 2016
@@ -12,7 +12,7 @@
  *
  * @author Jeremy McCormick, SLAC
  */
-public class AidaMetadataReader implements FileMetadataReader {
+final class AidaMetadataReader implements FileMetadataReader {
 
     /**
      * Get the metadata for a ROOT DQM file.
@@ -22,7 +22,7 @@
     @Override
     public Map<String, Object> getMetadata(final File file) throws IOException {
         final Map<String, Object> metadata = new HashMap<String, Object>();
-        final int run = CrawlerFileUtilities.getRunFromFileName(file);
+        final Long run = FileUtilities.getRunFromFileName(file);
         metadata.put("runMin", run);
         metadata.put("runMax", run);
         return metadata;

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/CrawlerConfig.java	Wed Apr 27 11:11:32 2016
@@ -11,13 +11,9 @@
 import java.util.Set;
 
 import org.hps.conditions.database.ConnectionParameters;
-import org.hps.datacat.client.DatasetFileFormat;
-import org.hps.datacat.client.DatasetSite;
 
 /**
  * Full configuration information for the {@link Crawler} class.
- * <p>
- * Method chaining of setters is supported.
  *
  * @author Jeremy McCormick, SLAC
  */
@@ -41,20 +37,13 @@
 
     /**
      * The name of the folder in the data catalog for inserting data (under "/HPS" root folder).
-     * <p>
-     * Default provided for Eng Run 2015 data.
      */
     private String datacatFolder = null;
 
     /**
-     * Set whether extraction of metadata from files is enabled.
-     */
-    private boolean enableMetadata;
-
-    /**
-     * Set of file formats for filtering files.
-     */
-    Set<DatasetFileFormat> formats = new HashSet<DatasetFileFormat>();
+     * Set of accepted file formats.
+     */
+    private Set<FileFormat> formats = new HashSet<FileFormat>();
 
     /**
      * The maximum depth to crawl.
@@ -69,7 +58,7 @@
     /**
      * The dataset site for the datacat.
      */
-    private DatasetSite site;
+    private Site site = Site.JLAB;
 
     /**
      * A timestamp to use for filtering input files on their creation date.
@@ -80,6 +69,21 @@
      * A file to use for getting the timestamp date.
      */
     private File timestampFile = null;
+    
+    /**
+     * Dry run for not actually executing updates.
+     */
+    private boolean dryRun = false;
+    
+    /**
+     * Base URL of datacat client.
+     */
+    private String baseUrl = DatacatHelper.DATACAT_URL;
+        
+    /**
+     * Set of paths used for filtering files (file's path must match one of these).
+     */
+    private Set<String> paths = new HashSet<String>();
 
     /**
      * Get the set of runs that will be accepted for the job.
@@ -94,7 +98,7 @@
      * Add the default file formats.
      */
     CrawlerConfig addDefaultFileFormats() {
-        final List<DatasetFileFormat> defaultFormats = Arrays.asList(DatasetFileFormat.values());
+        final List<FileFormat> defaultFormats = Arrays.asList(FileFormat.values());
         this.formats.addAll(defaultFormats);
         return this;
     }
@@ -104,9 +108,8 @@
      *
      * @param format the file format
      */
-    CrawlerConfig addFileFormat(final DatasetFileFormat format) {
+    void addFileFormat(final FileFormat format) {
         this.formats.add(format);
-        return this;
     }
 
     /**
@@ -123,7 +126,7 @@
      *
      * @return the data catalog folder
      */
-    String datacatFolder() {
+    String folder() {
         return this.datacatFolder;
     }
 
@@ -132,25 +135,16 @@
      *
      * @return the dataset site
      */
-    DatasetSite datasetSite() {
+    Site site() {
         return this.site;
     }
 
     /**
-     * Return <code>true</code> if metadata extraction from files is enabled.
-     *
-     * @return <code>true</code> if metadata extraction is enabled
-     */
-    boolean enableMetaData() {
-        return this.enableMetadata;
-    }
-
-    /**
      * Get the file formats for filtering.
      *
      * @return the file formats for filtering
      */
-    Set<DatasetFileFormat> getFileFormats() {
+    Set<FileFormat> getFileFormats() {
         return this.formats;
     }
 
@@ -164,7 +158,7 @@
     }
 
     /**
-     * Get the root directory for the file search.
+     * Get the root directory in the file catalog.
      *
      * @return the root directory for the file search
      */
@@ -178,9 +172,8 @@
      * @param acceptRuns the list of acceptable run numbers
      * @return this object
      */
-    CrawlerConfig setAcceptRuns(final Set<Integer> acceptRuns) {
+    void setAcceptRuns(final Set<Integer> acceptRuns) {
         this.acceptRuns = acceptRuns;
-        return this;
     }
 
     /**
@@ -189,9 +182,8 @@
      * @param connectionParameters the database connection parameters
      * @return this object
      */
-    CrawlerConfig setConnection(final ConnectionParameters connectionParameters) {
+    void setConnection(final ConnectionParameters connectionParameters) {
         this.connectionParameters = connectionParameters;
-        return this;
     }
 
     /**
@@ -199,9 +191,8 @@
      *
      * @param datacatFolder the data catalog folder
      */
-    CrawlerConfig setDatacatFolder(final String datacatFolder) {
+    void setDatacatFolder(final String datacatFolder) {
         this.datacatFolder = datacatFolder;
-        return this;
     }
 
     /**
@@ -209,29 +200,28 @@
      *
      * @return this object
      */
-    void setDatasetSite(final DatasetSite site) {
+    void setSite(final Site site) {
         this.site = site;
     }
-
-    /**
-     * Set whether metadata extraction is enabled.
-     *
-     * @param enableMetadata <code>true</code> to enable metadata
-     * @return this object
-     */
-    CrawlerConfig setEnableMetadata(final boolean enableMetadata) {
-        this.enableMetadata = enableMetadata;
-        return this;
-    }
+    
+    /**
+     * Enable dry run.
+     * 
+     * @param dryRun set to <code>true</code> to enable dry run
+     * @return this object
+     */
+    void setDryRun(boolean dryRun) {
+        this.dryRun = dryRun;
+    }
+    
 
     /**
      * Set the max depth.
      *
      * @param maxDepth the max depth
      */
-    CrawlerConfig setMaxDepth(final Integer maxDepth) {
+    void setMaxDepth(final Integer maxDepth) {
         this.maxDepth = maxDepth;
-        return this;
     }
 
     /**
@@ -240,9 +230,8 @@
      * @param rootDir the root directory for the file search
      * @return this object
      */
-    CrawlerConfig setRootDir(final File rootDir) {
+    void setRootDir(final File rootDir) {
         this.rootDir = rootDir;
-        return this;
     }
 
     /**
@@ -253,9 +242,8 @@
      * @param timestamp the date for filtering files
      * @return this object
      */
-    CrawlerConfig setTimestamp(final Date timestamp) {
+    void setTimestamp(final Date timestamp) {
         this.timestamp = timestamp;
-        return this;
     }
 
     /**
@@ -267,9 +255,8 @@
      * @param timestamp the date string for filtering files
      * @return this object
      */
-    CrawlerConfig setTimestamp(final String timestampString) throws ParseException {
+    void setTimestamp(final String timestampString) throws ParseException {
         TIMESTAMP_FORMAT.parse(timestampString);
-        return this;
     }
 
     /**
@@ -278,9 +265,8 @@
      * @param timestampFile the timestamp file for date filtering
      * @return this object
      */
-    CrawlerConfig setTimestampFile(final File timestampFile) {
+    void setTimestampFile(final File timestampFile) {
         this.timestampFile = timestampFile;
-        return this;
     }
 
     /**
@@ -302,4 +288,49 @@
     File timestampFile() {
         return timestampFile;
     }
+    
+    /**
+     * Returns <code>true</code> if dry run which means no updates will occur.
+     * 
+     * @return <code>true</code> if dry run
+     */
+    boolean dryRun() {
+        return this.dryRun;
+    }
+    
+    /**
+     * Set the data catalog URL.
+     * 
+     * @param baseUrl the data catalog URL
+     */
+    void setDatacatUrl(String baseUrl) {
+        this.baseUrl = baseUrl;        
+    }
+    
+    /**
+     * Get the data catalog URL.
+     * 
+     * @return the data catalog URL
+     */
+    String datacatUrl() {
+        return this.baseUrl;
+    }
+        
+    /**
+     * Add a path for filtering files.
+     * 
+     * @param path the path for filtering
+     */
+    void addPath(String path) {
+        this.paths.add(path);
+    }
+    
+    /**
+     * Get the list of paths for filtering. 
+     * 
+     * @return the list of paths for filtering
+     */
+    Set<String> paths() {
+        return this.paths;
+    }
 }

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatCrawler.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatCrawler.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/DatacatCrawler.java	Wed Apr 27 11:11:32 2016
@@ -1,112 +1,30 @@
 package org.hps.crawler;
 
 import java.io.File;
-import java.io.FileFilter;
 import java.io.IOException;
 import java.nio.file.FileVisitOption;
-import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.ArrayList;
 import java.util.Date;
 import java.util.EnumSet;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
-import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
-import org.hps.datacat.client.DatacatClient;
-import org.hps.datacat.client.DatacatClientFactory;
-import org.hps.datacat.client.DatasetFileFormat;
+import org.srs.datacat.model.DatasetModel;
 
 /**
  * Command line file crawler for populating the data catalog.
  *
  * @author Jeremy McCormick, SLAC
  */
-public class DatacatCrawler {
-
-    /**
-     * Visitor which creates a {@link FileSet} from walking a directory tree.
-     * <p>
-     * Any number of {@link java.io.FileFilter} objects can be registered with this visitor to restrict which files are
-     * accepted.
-     *
-     * @author Jeremy McCormick, SLAC
-     */
-    final class DatacatFileVisitor extends SimpleFileVisitor<Path> {
-
-        /**
-         * The run log containing information about files from each run.
-         */
-        private final FileSet fileSet = new FileSet();
-
-        /**
-         * A list of file filters to apply.
-         */
-        private final List<FileFilter> filters = new ArrayList<FileFilter>();
-
-        /**
-         * Run the filters on the file to tell whether it should be accepted or not.
-         *
-         * @param file the EVIO file
-         * @return <code>true</code> if file should be accepted
-         */
-        private boolean accept(final File file) {
-            boolean accept = true;
-            for (final FileFilter filter : this.filters) {
-                accept = filter.accept(file);
-                if (!accept) {
-                    break;
-                }
-            }
-            return accept;
-        }
-
-        /**
-         * Add a file filter.
-         *
-         * @param filter the file filter
-         */
-        void addFilter(final FileFilter filter) {
-            this.filters.add(filter);
-        }
-
-        /**
-         * Get the file set created by visiting the directory tree.
-         *
-         * @return the file set from visiting the directory tree
-         */
-        FileSet getFileSet() {
-            return this.fileSet;
-        }
-
-        /**
-         * Visit a single file.
-         *
-         * @param path the file to visit
-         * @param attrs the file attributes
-         */
-        @Override
-        public FileVisitResult visitFile(final Path path, final BasicFileAttributes attrs) {
-            final File file = path.toFile();
-            if (this.accept(file)) {
-                final DatasetFileFormat format = DatacatUtilities.getFileFormat(file);
-                fileSet.addFile(format, file);
-            }
-            return FileVisitResult.CONTINUE;
-        }
-    }
+public final class DatacatCrawler {
 
     /**
      * Make a list of available file formats for printing help.
@@ -117,14 +35,14 @@
      * Setup the logger.
      */
     private static final Logger LOGGER = Logger.getLogger(DatacatCrawler.class.getPackage().getName());
-
+    
     /**
      * Command line options for the crawler.
      */
     private static final Options OPTIONS = new Options();
     static {
         final StringBuffer buffer = new StringBuffer();
-        for (final DatasetFileFormat format : DatasetFileFormat.values()) {
+        for (final FileFormat format : FileFormat.values()) {
             buffer.append(format.name() + " ");
         }
         buffer.setLength(buffer.length() - 1);
@@ -135,17 +53,17 @@
      * Statically define the command options.
      */
     static {
-        OPTIONS.addOption("L", "log-level", true, "set the log level (INFO, FINE, etc.)");
         OPTIONS.addOption("b", "min-date", true, "min date for a file (example \"2015-03-26 11:28:59\")");
         OPTIONS.addOption("d", "directory", true, "root directory to crawl");
         OPTIONS.addOption("f", "folder", true, "datacat folder");
         OPTIONS.addOption("h", "help", false, "print help and exit (overrides all other arguments)");
         OPTIONS.addOption("o", "format", true, "add a file format for filtering: " + AVAILABLE_FORMATS);
-        OPTIONS.addOption("m", "metadata", false, "create metadata for datasets");
         OPTIONS.addOption("r", "run", true, "add a run number to accept");
         OPTIONS.addOption("s", "site", true, "datacat site");
         OPTIONS.addOption("t", "timestamp-file", true, "existing or new timestamp file name");
         OPTIONS.addOption("x", "max-depth", true, "max depth to crawl");
+        OPTIONS.addOption("D", "dry-run", false, "dry run which will not update the datacat");
+        OPTIONS.addOption("u", "base-url", true, "provide a base URL of the datacat server");
     }
 
     /**
@@ -165,33 +83,16 @@
     /**
      * The options parser.
      */
-    private final DefaultParser parser = new DefaultParser();
-
-    /**
-     * Throw an exception if the path doesn't exist in the data catalog or it is not a folder.
-     *
-     * @param folder the folder in the datacat
-     * @throws RuntimeException if the given path does not exist or it is not a folder
-     */
-    void checkFolder(final String folder) {
-        final DatacatClient datacatClient = new DatacatClientFactory().createClient();
-        if (!datacatClient.exists(folder)) {
-            throw new RuntimeException("The folder " + folder + " does not exist in the data catalog.");
-        }
-        if (!datacatClient.isFolder(folder)) {
-            throw new RuntimeException("The path " + folder + " is not a folder.");
-        }
-    }
-
+    private final PosixParser parser = new PosixParser();
+    
     /**
      * Parse command line options.
      *
      * @param args the command line arguments
      * @return this object (for method chaining)
      */
-    public DatacatCrawler parse(final String[] args) {
-        config = new CrawlerConfig();
-
+    private DatacatCrawler parse(final String[] args) {
+        
         LOGGER.config("parsing command line options");
 
         this.config = new CrawlerConfig();
@@ -202,13 +103,6 @@
             // Print help.
             if (cl.hasOption("h") || args.length == 0) {
                 this.printUsage();
-            }
-
-            // Log level.
-            if (cl.hasOption("L")) {
-                final Level level = Level.parse(cl.getOptionValue("L"));
-                LOGGER.config("setting log level to " + level);
-                LOGGER.setLevel(level);
             }
 
             // Root directory for file crawling.
@@ -221,7 +115,7 @@
                     throw new IllegalArgumentException("The specified path is not a directory.");
                 }
                 config.setRootDir(rootDir);
-                LOGGER.config("root dir set to " + config.rootDir());
+                LOGGER.config("root dir " + config.rootDir());
             }
 
             // Timestamp file for date filtering.
@@ -278,9 +172,9 @@
             // Configure enabled file formats.
             if (cl.hasOption("o")) {
                 for (final String arg : cl.getOptionValues("o")) {
-                    DatasetFileFormat format = null;
+                    FileFormat format = null;
                     try {
-                        format = DatasetFileFormat.valueOf(arg);
+                        format = FileFormat.valueOf(arg);
                     } catch (IllegalArgumentException | NullPointerException e) {
                         throw new IllegalArgumentException("The format " + arg + " is not valid.", e);
                     }
@@ -288,19 +182,22 @@
                     this.config.addFileFormat(format);
                 }
             } else {
-                throw new RuntimeException("The -o argument with data format must be supplied at least once.");
-            }
-
-            // Enable metadata extraction from files.
-            if (cl.hasOption("m")) {
-                config.setEnableMetadata(true);
-                LOGGER.config("metadata extraction enabled");
+                for (FileFormat format : FileFormat.values()) {
+                    this.config.addFileFormat(format);
+                    LOGGER.config("adding default format " + format);
+                }
+            }
+            
+            // Enable the default set of file formats.
+            if (this.config.getFileFormats().isEmpty()) {
+                LOGGER.config("enabling default file formats");
+                this.config.addDefaultFileFormats();
             }
 
             // Datacat folder.
             if (cl.hasOption("f")) {
                 config.setDatacatFolder(cl.getOptionValue("f"));
-                LOGGER.config("set datacat folder to " + config.datacatFolder());
+                LOGGER.config("set datacat folder to " + config.folder());
             } else {
                 throw new RuntimeException("The -f argument with the datacat folder is required.");
             }
@@ -313,20 +210,43 @@
                 }
                 config.setAcceptRuns(acceptRuns);
             }
+                                    
+            // Dry run.
+            if (cl.hasOption("D")) {
+                config.setDryRun(true);
+            }
+                        
+            // List of paths.
+            if (!cl.getArgList().isEmpty()) {
+                for (String arg : cl.getArgList()) {
+                    config.addPath(arg);
+                }
+            }
+            
+            // Dataset site (defaults to JLAB).
+            Site site = Site.JLAB;
+            if (cl.hasOption("s")) {
+                site = Site.valueOf(cl.getOptionValue("s"));
+            }
+            LOGGER.config("dataset site " + site);
+            config.setSite(site);
+            
+            // Data catalog URL.
+            if (cl.hasOption("u")) {
+                config.setDatacatUrl(cl.getOptionValue("u"));
+                LOGGER.config("datacat URL " + config.datacatUrl());
+            }
 
         } catch (final ParseException e) {
             throw new RuntimeException("Error parsing options.", e);
         }
 
-        // Check the datacat folder which must already exist.
-        this.checkFolder(config.datacatFolder());
-
         // Check that there is at least one file format enabled for filtering.
         if (this.config.getFileFormats().isEmpty()) {
-            throw new IllegalStateException("At least one file format must be provided with the -f switch.");
-        }
-
-        LOGGER.info("done parsing command line options");
+            throw new IllegalStateException("At least one file format must be provided with the -o switch.");
+        }
+
+        LOGGER.info("Done parsing command line options.");
 
         return this;
     }
@@ -336,72 +256,65 @@
      */
     private void printUsage() {
         final HelpFormatter help = new HelpFormatter();
-        help.printHelp(70, "DatacatCrawler [options]", "", OPTIONS, "");
+        help.printHelp(70, "DatacatCrawler [options] path ...", "", OPTIONS, "");
         System.exit(0);
     }
 
     /**
      * Run the crawler job.
      */
-    void run() {
-
+    private void run() {
+                
         // Create the file visitor for crawling the root directory with the given date filter.
-        final DatacatFileVisitor visitor = new DatacatFileVisitor();
+        final CrawlerFileVisitor visitor = new CrawlerFileVisitor();
 
         // Add date filter if timestamp is supplied.
         if (config.timestamp() != null) {
             visitor.addFilter(new DateFileFilter(config.timestamp()));
+            LOGGER.config("added timestamp filter " + config.timestamp());
+        }
+        
+        // Add path filter.
+        if (!config.paths().isEmpty()) {
+            visitor.addFilter(new PathFilter(config.paths()));
+            StringBuffer sb = new StringBuffer();
+            for (String path : config.paths()) {
+                sb.append(path + ":");
+            }
+            sb.setLength(sb.length() - 1);
+            LOGGER.config("added paths " + sb.toString());
         }
 
         // Add file format filter.
-        for (final DatasetFileFormat fileFormat : config.getFileFormats()) {
-            LOGGER.info("adding file format filter for " + fileFormat.name());
-        }
         visitor.addFilter(new FileFormatFilter(config.getFileFormats()));
 
-        // Run number filter.
+        // Add run number filter.
         if (!config.acceptRuns().isEmpty()) {
             visitor.addFilter(new RunFilter(config.acceptRuns()));
         }
 
-        // Walk the file tree using the visitor.
+        // Walk the file tree and get list of files.
         this.walk(visitor);
-
-        // Update the data catalog.
-        this.updateDatacat(visitor.getFileSet());
-    }
-
-    /**
-     * Update the data catalog.
-     *
-     * @param runMap the map of run information including the EVIO file list
-     */
-    private void updateDatacat(final FileSet fileSet) {
-        final DatacatClient datacatClient = new DatacatClientFactory().createClient();
-        for (final DatasetFileFormat fileFormat : config.getFileFormats()) {
-            LOGGER.info("adding files to datacat with format " + fileFormat.name());
-            for (final File file : fileSet.get(fileFormat)) {
-
-                LOGGER.info("adding file " + file.getAbsolutePath() + " to datacat");
-
-                // Create metadata if this is enabled (takes awhile).
-                Map<String, Object> metadata = new HashMap<String, Object>();
-                if (config.enableMetaData()) {
-                    metadata = DatacatUtilities.createMetadata(file);
-                }
-
-                // Register file in the catalog.
-                DatacatUtilities.addFile(datacatClient, config.datacatFolder(), file, metadata);
-            }
-        }
-    }
-
-    /**
-     * Walk the directory tree to find EVIO files for the runs that are being processed in the job.
+                
+        // Insert datasets if files were found.
+        if (!visitor.getFiles().isEmpty()) {
+            List<DatasetModel> datasets = DatacatHelper.createDatasets(visitor.getFiles(), config.folder(), config.site().toString());
+            LOGGER.info("built " + datasets.size() + " datasets");
+            DatacatHelper.addDatasets(datasets, config.folder(), config.datacatUrl());
+            LOGGER.info("added datasets to datacat");
+        } else {
+            LOGGER.warning("No files were found by the crawler.");
+        }
+        
+        LOGGER.info("Done!");
+    }
+                         
+    /**
+     * Walk the directory tree to find files for the runs that are being processed in the job.
      *
      * @param visitor the file visitor
      */
-    private void walk(final DatacatFileVisitor visitor) {
+    private void walk(final CrawlerFileVisitor visitor) {
         try {
             // Walk the file tree from the root directory.
             final EnumSet<FileVisitOption> options = EnumSet.noneOf(FileVisitOption.class);

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/EvioMetadataReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/EvioMetadataReader.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/EvioMetadataReader.java	Wed Apr 27 11:11:32 2016
@@ -2,147 +2,330 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.Date;
-import java.util.HashMap;
+import java.math.RoundingMode;
+import java.text.DecimalFormat;
+import java.util.LinkedHashMap;
 import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 
 import org.hps.record.evio.EventTagConstant;
 import org.hps.record.evio.EvioEventUtilities;
 import org.hps.record.evio.EvioFileUtilities;
+import org.hps.record.triggerbank.AbstractIntData.IntBankDefinition;
+import org.hps.record.triggerbank.HeadBankData;
+import org.hps.record.triggerbank.TiTimeOffsetEvioProcessor;
+import org.hps.record.triggerbank.TriggerType;
+import org.jlab.coda.jevio.BaseStructure;
 import org.jlab.coda.jevio.EvioEvent;
 import org.jlab.coda.jevio.EvioException;
 import org.jlab.coda.jevio.EvioReader;
 
 /**
- * Reads metadata from EVIO files.
- *
+ * Creates detailed metadata for the datacat from an EVIO input file.
+ * 
  * @author Jeremy McCormick, SLAC
  */
-public class EvioMetadataReader implements FileMetadataReader {
+final class EvioMetadataReader implements FileMetadataReader {
 
     /**
-     * Initialize the logger.
+     * Initialize the package logger.
      */
     private static Logger LOGGER = Logger.getLogger(EvioMetadataReader.class.getPackage().getName());
 
     /**
+     * Head bank definition.
+     */
+    private static IntBankDefinition HEAD_BANK = new IntBankDefinition(HeadBankData.class, new int[] {0x2e, 0xe10f});
+
+    /**
      * Get the EVIO file metadata.
-     *
+     * 
      * @param file the EVIO file
      * @return the metadata map of key and value pairs
      */
     @Override
     public Map<String, Object> getMetadata(final File file) throws IOException {
-
-        Date startDate = null;
-        Date endDate = null;
-        int badEventCount = 0;
-        int eventCount = 0;
-        int byteCount = 0;
-        boolean hasPrestart = false;
-        boolean hasEnd = false;
-        int[] eventIdData = null;
-        Integer run = null;
-        Integer endEvent = null;
-        Integer startEvent = null;
-        Long lastTimestamp = null;
+        
+        long totalEvents = 0;
+        int physicsEvents = 0;
+        int badEvents = 0;
+        int blinded = 0;
+        Long run = null;
+        Integer firstHeadTimestamp = null;
+        Integer lastHeadTimestamp = null;
+        Integer lastPhysicsEvent = null;
+        Integer firstPhysicsEvent = null;
+        Integer prestartTimestamp = null;
+        Integer endTimestamp = null;
+        Integer goTimestamp = null;
+        Double triggerRate = null;
+        
+        // Processor for calculating TI time offsets.
+        TiTimeOffsetEvioProcessor tiProcessor = new TiTimeOffsetEvioProcessor();
+
+        // Create map for counting trigger types.
+        Map<TriggerType, Integer> triggerCounts = new LinkedHashMap<TriggerType, Integer>();
+        for (TriggerType triggerType : TriggerType.values()) {
+            triggerCounts.put(triggerType, 0);
+        }
+
+        // Get the file number from the name.
+        final int fileNumber = EvioFileUtilities.getSequenceFromName(file);
+
+        // File numbers indivisible by 10 are blinded (Eng Run 2015 scheme).
+        if (!(fileNumber % 10 == 0)) {
+            blinded = 1;
+        }
+        
+        // Get file size.
+        long size = 0;
+        File cacheFile = file;
+        if (FileUtilities.isMssFile(file)) {
+            cacheFile = FileUtilities.getCachedFile(file);
+        }
+        size = cacheFile.length();
+        
+        // Compute MD5 checksum string.
+        String checksum = FileUtilities.createMD5Checksum(cacheFile);
 
         EvioReader evioReader = null;
         try {
-            evioReader = EvioFileUtilities.open(file, false);
+            // Open file in sequential mode.
+            evioReader = EvioFileUtilities.open(file, true);
+            EvioEvent evioEvent = null;
+
+            // Event read loop.
+            eventLoop: while (true) {
+                try {
+                    // Parse next event.
+                    evioEvent = evioReader.parseNextEvent();
+
+                    // End of file.
+                    if (evioEvent == null) {
+                        LOGGER.fine("EOF after " + totalEvents + " events.");
+                        break eventLoop;
+                    }
+                    
+                    // Increment event count (doesn't count events that can't be parsed).
+                    ++totalEvents;
+
+                    // Debug print event number and tag.
+                    LOGGER.finest("Parsed event " + evioEvent.getEventNumber() + " with tag 0x"
+                            + String.format("%08x", evioEvent.getHeader().getTag()));
+
+                    // Get head bank.
+                    BaseStructure headBank = HEAD_BANK.findBank(evioEvent);
+
+                    // Current timestamp.
+                    int thisTimestamp = 0;
+
+                    // Process head bank if not null.
+                    if (headBank != null) {
+                        if (headBank != null) {
+                            final int[] headBankData = headBank.getIntData();
+                            thisTimestamp = headBankData[3];
+                            if (thisTimestamp != 0) {
+                                // First header timestamp.
+                                if (firstHeadTimestamp == null) {
+                                    firstHeadTimestamp = thisTimestamp;
+                                    LOGGER.finer("First head timestamp " + firstHeadTimestamp + " from event "
+                                            + evioEvent.getEventNumber());
+                                }
+
+                                // Last header timestamp.
+                                lastHeadTimestamp = thisTimestamp;
+                            }
+
+                            // Run number.
+                            if (run == null) {
+                                if (headBankData[1] != 0) {
+                                    run = (long) headBankData[1];
+                                    LOGGER.finer("Run number " + run + " from event " + evioEvent.getEventNumber());
+                                }
+                            }
+                        }
+                    }
+                    
+                    if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
+                                                
+                        final int[] eventIdData = EvioEventUtilities.getEventIdData(evioEvent);
+                        
+                        if (eventIdData != null) {
+                        
+                            // Set the last physics event.
+                            lastPhysicsEvent = eventIdData[0];
+
+                            // Set the first physics event.
+                            if (firstPhysicsEvent == null) {
+                                firstPhysicsEvent = eventIdData[0];
+                                LOGGER.finer("Set first physics event " + firstPhysicsEvent);
+                            }
+                        }
+                        
+                        ++physicsEvents;
+                    } else if (EvioEventUtilities.isControlEvent(evioEvent)) {
+                        int[] controlData = EvioEventUtilities.getControlEventData(evioEvent);
+                        if (controlData[0] != 0) {
+                            if (EventTagConstant.PRESTART.isEventTag(evioEvent)) {
+                                prestartTimestamp = controlData[0];
+                            }                        
+                            if (EventTagConstant.GO.isEventTag(evioEvent)) {
+                                goTimestamp = controlData[0];
+                            }
+                            if (EventTagConstant.END.isEventTag(evioEvent)) {
+                                endTimestamp = controlData[0];
+                            }
+                        }
+                    }
+
+                    // Count trigger types for this event.
+                    Set<TriggerType> triggerTypes = TriggerType.getTriggerTypes(evioEvent);
+                    for (TriggerType mask : triggerTypes) {
+                        int count = triggerCounts.get(mask) + 1;
+                        triggerCounts.put(mask, count);
+                        LOGGER.finest("Incremented " + mask.name() + " to " + count);
+                    }
+                    
+                    // Activate TI time offset processor.
+                    tiProcessor.process(evioEvent);
+                    
+                } catch (Exception e) {  
+                    // Trap all event processing errors.
+                    badEvents++;
+                    LOGGER.warning("Error processing EVIO event " + evioEvent.getEventNumber());
+                }
+            }
         } catch (final EvioException e) {
-            throw new IOException(e);
-        }
-
-        final int fileNumber = EvioFileUtilities.getSequenceFromName(file);
-
-        EvioEvent evioEvent = null;
-
-        while (true) {
-            try {
-                evioEvent = evioReader.parseNextEvent();
-            } catch (IOException | EvioException e) {
-                ++badEventCount;
-                continue;
+            // Error reading the EVIO file.
+            throw new IOException("Error reading EVIO file.", e);
+        } finally {
+            // Close the reader.
+            if (evioReader != null) {
+                try {
+                    evioReader.close();
+                } catch (IOException e) {
+                    LOGGER.log(Level.WARNING, "Error closing EVIO reader", e);
+                }
             }
-            if (evioEvent == null) {
-                break;
+        }
+
+        LOGGER.info("Done reading " + totalEvents + " events from " + file.getPath());
+
+        // Rough trigger rate calculation.
+        try {
+            if (firstHeadTimestamp != null && lastHeadTimestamp != null && totalEvents > 0 
+                    && (firstHeadTimestamp - lastHeadTimestamp != 0)) {
+                triggerRate = calculateTriggerRate(firstHeadTimestamp, lastHeadTimestamp, totalEvents);
+            } else {
+                LOGGER.log(Level.WARNING, "Missing information for calculating trigger rate.");
             }
-            byteCount += evioEvent.getTotalBytes();
-            if (EventTagConstant.PRESTART.equals(evioEvent)) {
-                LOGGER.info("found PRESTART");
-                hasPrestart = true;
-                final int[] controlEventData = EvioEventUtilities.getControlEventData(evioEvent);
-                final long timestamp = controlEventData[0] * 1000L;
-                startDate = new Date(timestamp);
-                LOGGER.info("set start date to " + startDate + " from PRESTART");
-                if (run == null) {
-                    run = controlEventData[1];
-                    LOGGER.info("set run to " + run);
-                }
-            } else if (EventTagConstant.END.equals(evioEvent)) {
-                LOGGER.info("found END event");
-                hasEnd = true;
-                final int[] controlEventData = EvioEventUtilities.getControlEventData(evioEvent);
-                final long timestamp = controlEventData[0] * 1000L;
-                endDate = new Date(timestamp);
-                LOGGER.info("set end date to " + endDate);
-                if (run == null) {
-                    run = controlEventData[1];
-                    LOGGER.info("set run to " + run);
-                }
-            } else if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
-                final int[] headBankData = EvioEventUtilities.getHeadBankData(evioEvent);
-                if (startDate == null) {
-                    if (headBankData[3] != 0) {
-                        startDate = new Date(headBankData[3] * 1000L);
-                        LOGGER.info("set start date to " + startDate + " from physics event");
-                    }
-                }
-                if (run == null) {
-                    run = headBankData[1];
-                    LOGGER.info("set run to " + run + " from physics event");
-                }
-                eventIdData = EvioEventUtilities.getEventIdData(evioEvent);
-                if (startEvent == null) {
-                    startEvent = eventIdData[0];
-                    LOGGER.info("set start event " + startEvent);
-                }
-                if (headBankData[3] != 0) {
-                    lastTimestamp = headBankData[3] * 1000L;
-                }
-                ++eventCount;
+        } catch (Exception e) {
+            LOGGER.log(Level.WARNING, "Error calculating the trigger rate.", e);
+        }
+
+        // Create and fill the metadata map.
+        final Map<String, Object> metadataMap = new LinkedHashMap<String, Object>();
+
+        try {
+            if (run == null) {
+                run = new Long(EvioFileUtilities.getRunFromName(file));
             }
-        }
-
-        // Set end date from last valid timestamp.
-        if (endDate == null) {
-            endDate = new Date(lastTimestamp);
-            LOGGER.info("set end date to " + endDate + " from last timestamp " + lastTimestamp);
-        }
-
-        // Set end event number.
-        if (eventIdData != null) {
-            endEvent = eventIdData[0];
-            LOGGER.info("set end event " + endEvent);
-        }
-
-        final Map<String, Object> metaDataMap = new HashMap<String, Object>();
-
-        metaDataMap.put("runMin", run);
-        metaDataMap.put("runMax", run);
-        metaDataMap.put("eventCount", eventCount);
-        metaDataMap.put("size", byteCount);
-        metaDataMap.put("fileNumber", fileNumber);
-        metaDataMap.put("badEventCount", badEventCount);
-        metaDataMap.put("endTimestamp", endDate.getTime());
-        metaDataMap.put("startTimestamp", startDate.getTime());
-        metaDataMap.put("startEvent", startEvent);
-        metaDataMap.put("endEvent", endEvent);
-        metaDataMap.put("hasEnd", hasEnd ? 1 : 0);
-        metaDataMap.put("hasPrestart", hasPrestart ? 1 : 0);
-
-        return metaDataMap;
+        } catch (Exception e) {
+            throw new RuntimeException("Failed to get run number from event data or file name.", e);
+        }
+
+        // Set locationExtras metadata.
+        metadataMap.put("runMin", run);
+        metadataMap.put("runMax", run);
+        metadataMap.put("eventCount", totalEvents);
+        metadataMap.put("size", size);
+        metadataMap.put("checksum", checksum);     
+        
+        // File sequence number.
+        metadataMap.put("FILE", fileNumber);
+
+        // Blinded flag.
+        metadataMap.put("BLINDED", blinded);
+
+        // First and last timestamps which may come from control or physics events.
+        if (firstHeadTimestamp != null) {
+            metadataMap.put("FIRST_HEAD_TIMESTAMP", firstHeadTimestamp);
+        } 
+        
+        if (lastHeadTimestamp != null) {
+            metadataMap.put("LAST_HEAD_TIMESTAMP", lastHeadTimestamp);
+        } 
+
+        // First and last physics event numbers.
+        if (firstPhysicsEvent != null) {
+            metadataMap.put("FIRST_PHYSICS_EVENT", firstPhysicsEvent);
+        } 
+        
+        if (lastPhysicsEvent != null) {
+            metadataMap.put("LAST_PHYSICS_EVENT", lastPhysicsEvent);
+        }
+        
+        // Timestamps which are only set if the corresponding control events were found in the file.
+        if (prestartTimestamp != null) {
+            metadataMap.put("PRESTART_TIMESTAMP", prestartTimestamp);
+        }
+        if (endTimestamp != null) {
+            metadataMap.put("END_TIMESTAMP", endTimestamp);
+        }
+        if (goTimestamp != null) {
+            metadataMap.put("GO_TIMESTAMP", goTimestamp);
+        }
+
+        // TI times and offset.
+        metadataMap.put("TI_TIME_MIN_OFFSET", new Long(tiProcessor.getMinOffset()).toString());
+        metadataMap.put("TI_TIME_MAX_OFFSET", new Long(tiProcessor.getMaxOffset()).toString());
+        metadataMap.put("TI_TIME_N_OUTLIERS", tiProcessor.getNumOutliers());
+        
+        // Event counts.
+        metadataMap.put("BAD_EVENTS", badEvents);
+        
+        // Physics event count.
+        metadataMap.put("PHYSICS_EVENTS", physicsEvents);
+        
+        // Rough trigger rate.
+        if (triggerRate != null && !Double.isInfinite(triggerRate) && !Double.isNaN(triggerRate)) {
+            DecimalFormat df = new DecimalFormat("#.##");
+            df.setRoundingMode(RoundingMode.CEILING);
+            LOGGER.info("Setting trigger rate to " + triggerRate + " Hz.");
+            metadataMap.put("TRIGGER_RATE", Double.parseDouble(df.format(triggerRate)));
+        } else {
+            LOGGER.warning("Failed to calculate trigger rate.");
+        }        
+
+        // Trigger type counts.
+        for (Entry<TriggerType, Integer> entry : triggerCounts.entrySet()) {
+            metadataMap.put(entry.getKey().name(), entry.getValue());
+        }
+
+        // Print the file metadata to log.
+        StringBuffer sb = new StringBuffer();
+        sb.append('\n');
+        for (Entry<String, Object> entry : metadataMap.entrySet()) {
+            sb.append("  " + entry.getKey() + " = " + entry.getValue() + '\n');
+        }
+        LOGGER.info("File metadata ..." + '\n' + sb.toString());
+
+        // Return the completed metadata map.
+        return metadataMap;
+    }
+         
+    /**
+     * Calculate the trigger rate in Hz.
+     * 
+     * @param firstTimestamp the first physics timestamp
+     * @param lastTimestamp the last physics timestamp
+     * @param events the number of physics events
+     * @return the trigger rate calculation in KHz
+     */
+    private double calculateTriggerRate(Integer firstTimestamp, Integer lastTimestamp, long events) {
+        return ((double) events / ((double) lastTimestamp - (double) firstTimestamp));
     }
 }

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileFormatFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileFormatFilter.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileFormatFilter.java	Wed Apr 27 11:11:32 2016
@@ -3,9 +3,6 @@
 import java.io.File;
 import java.io.FileFilter;
 import java.util.Set;
-import java.util.logging.Logger;
-
-import org.hps.datacat.client.DatasetFileFormat;
 
 /**
  * Filter files on their format.
@@ -17,21 +14,16 @@
 public class FileFormatFilter implements FileFilter {
 
     /**
-     * Initialize the logger.
-     */
-    private static final Logger LOGGER = Logger.getLogger(FileFormatFilter.class.getPackage().getName());
-
-    /**
      * The file format.
      */
-    private final Set<DatasetFileFormat> formats;
+    private final Set<FileFormat> formats;
 
     /**
      * Create a new filter with the given format.
      *
      * @param format the file format
      */
-    FileFormatFilter(final Set<DatasetFileFormat> formats) {
+    FileFormatFilter(final Set<FileFormat> formats) {
         if (formats == null) {
             throw new IllegalArgumentException("The formats collection is null.");
         }
@@ -48,13 +40,10 @@
      */
     @Override
     public boolean accept(final File pathname) {
-        LOGGER.info(pathname.getPath());
-        final DatasetFileFormat fileFormat = DatacatUtilities.getFileFormat(pathname);
+        final FileFormat fileFormat = DatacatHelper.getFileFormat(pathname);
         if (fileFormat != null) {
-            LOGGER.info("file " + pathname.getPath() + " has format " + fileFormat.name());
             return formats.contains(fileFormat);
         } else {
-            LOGGER.info("rejected file " + pathname.getPath() + " with unknown format");
             return false;
         }
     }

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileMetadataReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileMetadataReader.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/FileMetadataReader.java	Wed Apr 27 11:11:32 2016
@@ -4,8 +4,19 @@
 import java.io.IOException;
 import java.util.Map;
 
-
+/**
+ * Interface for reading metadata for the datacat from files.
+ * 
+ * @author Jeremy McCormick, SLAC
+ */
 public interface FileMetadataReader {   
     
-    public Map<String, Object> getMetadata(File file) throws IOException;
+    /**
+     * Create a metadata map with keys and values from the contents of a file.
+     * 
+     * @param file the input file from which to extract metadata
+     * @return the metadata map of field names to values
+     * @throws IOException if there is an error reading the file
+     */
+    Map<String, Object> getMetadata(File file) throws IOException;
 }

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDqmMetadataReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDqmMetadataReader.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDqmMetadataReader.java	Wed Apr 27 11:11:32 2016
@@ -22,7 +22,7 @@
     @Override
     public Map<String, Object> getMetadata(final File file) throws IOException {
         final Map<String, Object> metadata = new HashMap<String, Object>();
-        final int run = CrawlerFileUtilities.getRunFromFileName(file);
+        final Long run = FileUtilities.getRunFromFileName(file);
         metadata.put("runMin", run);
         metadata.put("runMax", run);
         return metadata;

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDstMetadataReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDstMetadataReader.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RootDstMetadataReader.java	Wed Apr 27 11:11:32 2016
@@ -1,10 +1,10 @@
 package org.hps.crawler;
 
-import hep.io.root.RootClassNotFound;
-import hep.io.root.RootFileReader;
-import hep.io.root.interfaces.TLeafElement;
-import hep.io.root.interfaces.TObjArray;
-import hep.io.root.interfaces.TTree;
+//import hep.io.root.RootClassNotFound;
+//import hep.io.root.RootFileReader;
+//import hep.io.root.interfaces.TLeafElement;
+//import hep.io.root.interfaces.TObjArray;
+//import hep.io.root.interfaces.TTree;
 
 import java.io.File;
 import java.io.IOException;
@@ -28,6 +28,10 @@
     @Override
     public Map<String, Object> getMetadata(final File file) throws IOException {
         final Map<String, Object> metadata = new HashMap<String, Object>();
+        Long run = FileUtilities.getRunFromFileName(file);
+        metadata.put("runMin", run);
+        metadata.put("runMax", run);
+        /*
         RootFileReader rootReader = null;
         long eventCount = 0;
         int runMin = 0;
@@ -60,6 +64,7 @@
         metadata.put("runMin", runMin);
         metadata.put("runMax", runMax);
         metadata.put("size", size);
+        */
         return metadata;
     }
 }

Modified: java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RunFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RunFilter.java	(original)
+++ java/branches/HPSJAVA-409/crawler/src/main/java/org/hps/crawler/RunFilter.java	Wed Apr 27 11:11:32 2016
@@ -3,8 +3,6 @@
 import java.io.File;
 import java.io.FileFilter;
 import java.util.Set;
-
-import org.hps.record.evio.EvioFileUtilities;
 
 /**
  * A filter which rejects files with run numbers not in a specified set.
@@ -25,7 +23,7 @@
      */
     RunFilter(final Set<Integer> acceptRuns) {
         if (acceptRuns.isEmpty()) {
-            throw new IllegalArgumentException("the acceptRuns collection is empty");
+            throw new IllegalArgumentException("The acceptRuns collection is empty.");
         }
         this.acceptRuns = acceptRuns;
     }
@@ -38,6 +36,11 @@
      */
     @Override
     public boolean accept(final File file) {
-        return this.acceptRuns.contains(EvioFileUtilities.getRunFromName(file));
+        try {
+            int run = Integer.parseInt(file.getName().substring(5, 10));
+            return this.acceptRuns.contains(run);
+        } catch (Exception e) {
+            return false;
+        }
     }
 }

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-3/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-3/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-3/compact.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
         </comment>
     </info>
     

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
            4th: round start with v1-3
            L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw
         </comment>

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
         </comment>
     </info>
     

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
            4th: round start with v1-3
            1) float L2_tu_rw, L3_tu_rw, L4_tu_rw
         </comment>

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L2-3-4_tu_rw.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L2-3-4_tu_rw.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-4/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L2-3-4_tu_rw.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
         </comment>
     </info>
     

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-1/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
         </comment>
     </info>
     

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-2/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-HPS-EngRun2015-Nominal-v1-4-1-100k-L456_L123_L234_L345_L123_L456_tu_rwIter0Iter1Iter2Iter3Iter4Iter5.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-2/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-HPS-EngRun2015-Nominal-v1-4-1-100k-L456_L123_L234_L345_L123_L456_tu_rwIter0Iter1Iter2Iter3Iter4Iter5.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-EngRun2015-Nominal-v1-5-2/compact_millepede-milleBinaryISN_hps_005772.evio.0.gbl-HPS-EngRun2015-Nominal-v1-4-1-100k-L456_L123_L234_L345_L123_L456_tu_rwIter0Iter1Iter2Iter3Iter4Iter5.xml	Wed Apr 27 11:11:32 2016
@@ -9,8 +9,8 @@
                1) float L2_tu, 2) float L2_tu, L4_tu, L5_tu
                2nd: round
                1) float L2_tu, L4_tu, L5_tu
-	       3rd: round
-	       1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
+           3rd: round
+           1) float L2_tu_rw, L4_tu_rw, L5_tu_rw
            4th: round start with v1-3
            L3_L4_L5_tu_rw_THEN_L2_tu_rw_THEN_L2_L3_L4_tu_rw_THEN_L2_L3_L5_tu_rw_THEN_L2_L3_L4_L5_excl_L3ST_tu_L4Sb_tu_THEN_L2_L4_L5_tu_rw
         </comment>

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-Proposal2014-v3-2pt2-0zOffset/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-Proposal2014-v3-2pt2-0zOffset/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-Proposal2014-v3-2pt2-0zOffset/compact.xml	Wed Apr 27 11:11:32 2016
@@ -305,7 +305,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="endOfFieldZ" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
             
            
         </detector>     

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v5/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v5/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v5/compact.xml	Wed Apr 27 11:11:32 2016
@@ -488,7 +488,7 @@
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001"/>
             <fraction n="1.0" ref="Vacuum" />
@@ -578,7 +578,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="endOfFieldZ" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v6/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v6/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v6/compact.xml	Wed Apr 27 11:11:32 2016
@@ -488,7 +488,7 @@
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001"/>
             <fraction n="1.0" ref="Vacuum" />
@@ -578,7 +578,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="endOfFieldZ" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-2/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-2/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-2/compact.xml	Wed Apr 27 11:11:32 2016
@@ -86,127 +86,127 @@
         <constant name="y9b_misalign" value="0.0"/>
         <constant name="y10b_misalign" value="0.0"/>
 
-		<!-- alignment corrections -->
-	<constant name="x1t_align" value="0.000000"/>
-	<constant name="x2t_align" value="0.000000"/>
-	<constant name="x3t_align" value="0.000000"/>
-	<constant name="x4t_align" value="0.000000"/>
-	<constant name="x5t_align" value="0.000000"/>
-	<constant name="x6t_align" value="0.000000"/>
-	<constant name="x7t_align" value="0.000000"/>
-	<constant name="x8t_align" value="0.000000"/>
-	<constant name="x9t_align" value="0.000000"/>
-	<constant name="x10t_align" value="0.000000"/>
-	<constant name="y1t_align" value="0.000000"/>
-	<constant name="y2t_align" value="0.000000"/>
-	<constant name="y3t_align" value="0.0"/>
-	<constant name="y4t_align" value="0.0"/>
-	<constant name="y5t_align" value="0.000000"/>
-	<constant name="y6t_align" value="0.000000"/>
-	<constant name="y7t_align" value="0.000000"/>
-	<constant name="y8t_align" value="0.000000"/>
-	<constant name="y9t_align" value="0.000000"/>
-	<constant name="y10t_align" value="0.000000"/>
-	<constant name="z1t_align" value="0.000000"/>
-	<constant name="z2t_align" value="0.000000"/>
-	<constant name="z3t_align" value="0.000000"/>
-	<constant name="z4t_align" value="0.000000"/>
-	<constant name="z5t_align" value="0.000000"/>
-	<constant name="z6t_align" value="0.000000"/>
-	<constant name="z7t_align" value="0.000000"/>
-	<constant name="z8t_align" value="0.000000"/>
-	<constant name="z9t_align" value="0.000000"/>
-	<constant name="z10t_align" value="0.000000"/>
-	<constant name="rx1t_align" value="0.000000"/>
-	<constant name="rx2t_align" value="0.000000"/>
-	<constant name="rx3t_align" value="0.000000"/>
-	<constant name="rx4t_align" value="0.000000"/>
-	<constant name="rx5t_align" value="0.000000"/>
-	<constant name="rx6t_align" value="0.000000"/>
-	<constant name="rx7t_align" value="0.000000"/>
-	<constant name="rx8t_align" value="0.000000"/>
-	<constant name="rx9t_align" value="0.000000"/>
-	<constant name="rx10t_align" value="0.000000"/>
-	<constant name="ry1t_align" value="0.000000"/>
-	<constant name="ry2t_align" value="0.000000"/>
-	<constant name="ry3t_align" value="0.000000"/>
-	<constant name="ry4t_align" value="0.000000"/>
-	<constant name="ry5t_align" value="0.000000"/>
-	<constant name="ry6t_align" value="0.000000"/>
-	<constant name="ry7t_align" value="0.000000"/>
-	<constant name="ry8t_align" value="0.000000"/>
-	<constant name="ry9t_align" value="0.000000"/>
-	<constant name="ry10t_align" value="0.000000"/>
-	<constant name="rz1t_align" value="0.000000"/>
-	<constant name="rz2t_align" value="0.000000"/>
-	<constant name="rz3t_align" value="0.000000"/>
-	<constant name="rz4t_align" value="0.000000"/>
-	<constant name="rz5t_align" value="0.000000"/>
-	<constant name="rz6t_align" value="0.000000"/>
-	<constant name="rz7t_align" value="0.000000"/>
-	<constant name="rz8t_align" value="0.000000"/>
-	<constant name="rz9t_align" value="0.000000"/>
-	<constant name="rz10t_align" value="0.000000"/>
-	<constant name="x1b_align" value="0.000000"/>
-	<constant name="x2b_align" value="0.000000"/>
-	<constant name="x3b_align" value="0.000000"/>
-	<constant name="x4b_align" value="0.000000"/>
-	<constant name="x5b_align" value="0.000000"/>
-	<constant name="x6b_align" value="0.00000"/>
-	<constant name="x7b_align" value="0.000000"/>
-	<constant name="x8b_align" value="0.000000"/>
-	<constant name="x9b_align" value="0.000000"/>
-	<constant name="x10b_align" value="0.000000"/>
-	<constant name="y1b_align" value="0.000000"/>
-	<constant name="y2b_align" value="0.000000"/>
-	<constant name="y3b_align" value="0.000000"/>
-	<constant name="y4b_align" value="0.000000"/>
-	<constant name="y5b_align" value="0.0"/>
-	<constant name="y6b_align" value="0.0"/>
-	<constant name="y7b_align" value="0.000000"/>
-	<constant name="y8b_align" value="0.000000"/>
-	<constant name="y9b_align" value="0.000000"/>
-	<constant name="y10b_align" value="0.000000"/>
-	<constant name="z1b_align" value="0.000000"/>
-	<constant name="z2b_align" value="0.000000"/>
-	<constant name="z3b_align" value="0.000000"/>
-	<constant name="z4b_align" value="0.000000"/>
-	<constant name="z5b_align" value="0.000000"/>
-	<constant name="z6b_align" value="0.000000"/>
-	<constant name="z7b_align" value="0.000000"/>
-	<constant name="z8b_align" value="0.000000"/>
-	<constant name="z9b_align" value="0.000000"/>
-	<constant name="z10b_align" value="0.000000"/>
-	<constant name="rx1b_align" value="0.000000"/>
-	<constant name="rx2b_align" value="0.000000"/>
-	<constant name="rx3b_align" value="0.000000"/>
-	<constant name="rx4b_align" value="0.000000"/>
-	<constant name="rx5b_align" value="0.000000"/>
-	<constant name="rx6b_align" value="0.000000"/>
-	<constant name="rx7b_align" value="0.000000"/>
-	<constant name="rx8b_align" value="0.000000"/>
-	<constant name="rx9b_align" value="0.000000"/>
-	<constant name="rx10b_align" value="0.000000"/>
-	<constant name="ry1b_align" value="0.000000"/>
-	<constant name="ry2b_align" value="0.000000"/>
-	<constant name="ry3b_align" value="0.000000"/>
-	<constant name="ry4b_align" value="0.000000"/>
-	<constant name="ry5b_align" value="0.000000"/>
-	<constant name="ry6b_align" value="0.000000"/>
-	<constant name="ry7b_align" value="0.000000"/>
-	<constant name="ry8b_align" value="0.000000"/>
-	<constant name="ry9b_align" value="0.000000"/>
-	<constant name="ry10b_align" value="0.000000"/>
-	<constant name="rz1b_align" value="0.000000"/>
-	<constant name="rz2b_align" value="0.000000"/>
-	<constant name="rz3b_align" value="0.000000"/>
-	<constant name="rz4b_align" value="0.000000"/>
-	<constant name="rz5b_align" value="0.000000"/>
-	<constant name="rz6b_align" value="0.000000"/>
-	<constant name="rz7b_align" value="0.000000"/>
-	<constant name="rz8b_align" value="0.000000"/>
-	<constant name="rz9b_align" value="0.000000"/>
-	<constant name="rz10b_align" value="0.000000"/>
+        <!-- alignment corrections -->
+    <constant name="x1t_align" value="0.000000"/>
+    <constant name="x2t_align" value="0.000000"/>
+    <constant name="x3t_align" value="0.000000"/>
+    <constant name="x4t_align" value="0.000000"/>
+    <constant name="x5t_align" value="0.000000"/>
+    <constant name="x6t_align" value="0.000000"/>
+    <constant name="x7t_align" value="0.000000"/>
+    <constant name="x8t_align" value="0.000000"/>
+    <constant name="x9t_align" value="0.000000"/>
+    <constant name="x10t_align" value="0.000000"/>
+    <constant name="y1t_align" value="0.000000"/>
+    <constant name="y2t_align" value="0.000000"/>
+    <constant name="y3t_align" value="0.0"/>
+    <constant name="y4t_align" value="0.0"/>
+    <constant name="y5t_align" value="0.000000"/>
+    <constant name="y6t_align" value="0.000000"/>
+    <constant name="y7t_align" value="0.000000"/>
+    <constant name="y8t_align" value="0.000000"/>
+    <constant name="y9t_align" value="0.000000"/>
+    <constant name="y10t_align" value="0.000000"/>
+    <constant name="z1t_align" value="0.000000"/>
+    <constant name="z2t_align" value="0.000000"/>
+    <constant name="z3t_align" value="0.000000"/>
+    <constant name="z4t_align" value="0.000000"/>
+    <constant name="z5t_align" value="0.000000"/>
+    <constant name="z6t_align" value="0.000000"/>
+    <constant name="z7t_align" value="0.000000"/>
+    <constant name="z8t_align" value="0.000000"/>
+    <constant name="z9t_align" value="0.000000"/>
+    <constant name="z10t_align" value="0.000000"/>
+    <constant name="rx1t_align" value="0.000000"/>
+    <constant name="rx2t_align" value="0.000000"/>
+    <constant name="rx3t_align" value="0.000000"/>
+    <constant name="rx4t_align" value="0.000000"/>
+    <constant name="rx5t_align" value="0.000000"/>
+    <constant name="rx6t_align" value="0.000000"/>
+    <constant name="rx7t_align" value="0.000000"/>
+    <constant name="rx8t_align" value="0.000000"/>
+    <constant name="rx9t_align" value="0.000000"/>
+    <constant name="rx10t_align" value="0.000000"/>
+    <constant name="ry1t_align" value="0.000000"/>
+    <constant name="ry2t_align" value="0.000000"/>
+    <constant name="ry3t_align" value="0.000000"/>
+    <constant name="ry4t_align" value="0.000000"/>
+    <constant name="ry5t_align" value="0.000000"/>
+    <constant name="ry6t_align" value="0.000000"/>
+    <constant name="ry7t_align" value="0.000000"/>
+    <constant name="ry8t_align" value="0.000000"/>
+    <constant name="ry9t_align" value="0.000000"/>
+    <constant name="ry10t_align" value="0.000000"/>
+    <constant name="rz1t_align" value="0.000000"/>
+    <constant name="rz2t_align" value="0.000000"/>
+    <constant name="rz3t_align" value="0.000000"/>
+    <constant name="rz4t_align" value="0.000000"/>
+    <constant name="rz5t_align" value="0.000000"/>
+    <constant name="rz6t_align" value="0.000000"/>
+    <constant name="rz7t_align" value="0.000000"/>
+    <constant name="rz8t_align" value="0.000000"/>
+    <constant name="rz9t_align" value="0.000000"/>
+    <constant name="rz10t_align" value="0.000000"/>
+    <constant name="x1b_align" value="0.000000"/>
+    <constant name="x2b_align" value="0.000000"/>
+    <constant name="x3b_align" value="0.000000"/>
+    <constant name="x4b_align" value="0.000000"/>
+    <constant name="x5b_align" value="0.000000"/>
+    <constant name="x6b_align" value="0.00000"/>
+    <constant name="x7b_align" value="0.000000"/>
+    <constant name="x8b_align" value="0.000000"/>
+    <constant name="x9b_align" value="0.000000"/>
+    <constant name="x10b_align" value="0.000000"/>
+    <constant name="y1b_align" value="0.000000"/>
+    <constant name="y2b_align" value="0.000000"/>
+    <constant name="y3b_align" value="0.000000"/>
+    <constant name="y4b_align" value="0.000000"/>
+    <constant name="y5b_align" value="0.0"/>
+    <constant name="y6b_align" value="0.0"/>
+    <constant name="y7b_align" value="0.000000"/>
+    <constant name="y8b_align" value="0.000000"/>
+    <constant name="y9b_align" value="0.000000"/>
+    <constant name="y10b_align" value="0.000000"/>
+    <constant name="z1b_align" value="0.000000"/>
+    <constant name="z2b_align" value="0.000000"/>
+    <constant name="z3b_align" value="0.000000"/>
+    <constant name="z4b_align" value="0.000000"/>
+    <constant name="z5b_align" value="0.000000"/>
+    <constant name="z6b_align" value="0.000000"/>
+    <constant name="z7b_align" value="0.000000"/>
+    <constant name="z8b_align" value="0.000000"/>
+    <constant name="z9b_align" value="0.000000"/>
+    <constant name="z10b_align" value="0.000000"/>
+    <constant name="rx1b_align" value="0.000000"/>
+    <constant name="rx2b_align" value="0.000000"/>
+    <constant name="rx3b_align" value="0.000000"/>
+    <constant name="rx4b_align" value="0.000000"/>
+    <constant name="rx5b_align" value="0.000000"/>
+    <constant name="rx6b_align" value="0.000000"/>
+    <constant name="rx7b_align" value="0.000000"/>
+    <constant name="rx8b_align" value="0.000000"/>
+    <constant name="rx9b_align" value="0.000000"/>
+    <constant name="rx10b_align" value="0.000000"/>
+    <constant name="ry1b_align" value="0.000000"/>
+    <constant name="ry2b_align" value="0.000000"/>
+    <constant name="ry3b_align" value="0.000000"/>
+    <constant name="ry4b_align" value="0.000000"/>
+    <constant name="ry5b_align" value="0.000000"/>
+    <constant name="ry6b_align" value="0.000000"/>
+    <constant name="ry7b_align" value="0.000000"/>
+    <constant name="ry8b_align" value="0.000000"/>
+    <constant name="ry9b_align" value="0.000000"/>
+    <constant name="ry10b_align" value="0.000000"/>
+    <constant name="rz1b_align" value="0.000000"/>
+    <constant name="rz2b_align" value="0.000000"/>
+    <constant name="rz3b_align" value="0.000000"/>
+    <constant name="rz4b_align" value="0.000000"/>
+    <constant name="rz5b_align" value="0.000000"/>
+    <constant name="rz6b_align" value="0.000000"/>
+    <constant name="rz7b_align" value="0.000000"/>
+    <constant name="rz8b_align" value="0.000000"/>
+    <constant name="rz9b_align" value="0.000000"/>
+    <constant name="rz10b_align" value="0.000000"/>
 
         <!-- Positions of sensor centers above/below nominal beam -->
         <constant name="y1t" value="36.894" />
@@ -606,134 +606,134 @@
         <constant name="mod2_rx10b" value="mod_rx10b"/>
         <constant name="mod2_ry10b" value="mod_ry10b+y_rot_bot_pivot"/>
         <constant name="mod2_rz10b" value="mod_rz10b"/>
-    	
-    	<!-- final constants -->
-	<constant name="final_x1t" value="mod2_x1t+x1t_align"/>
-	<constant name="final_x2t" value="mod2_x2t+x2t_align"/>
-	<constant name="final_x3t" value="mod2_x3t+x3t_align"/>
-	<constant name="final_x4t" value="mod2_x4t+x4t_align"/>
-	<constant name="final_x5t" value="mod2_x5t+x5t_align"/>
-	<constant name="final_x6t" value="mod2_x6t+x6t_align"/>
-	<constant name="final_x7t" value="mod2_x7t+x7t_align"/>
-	<constant name="final_x8t" value="mod2_x8t+x8t_align"/>
-	<constant name="final_x9t" value="mod2_x9t+x9t_align"/>
-	<constant name="final_x10t" value="mod2_x10t+x10t_align"/>
-	<constant name="final_y1t" value="mod2_y1t+y1t_align"/>
-	<constant name="final_y2t" value="mod2_y2t+y2t_align"/>
-	<constant name="final_y3t" value="mod2_y3t+y3t_align"/>
-	<constant name="final_y4t" value="mod2_y4t+y4t_align"/>
-	<constant name="final_y5t" value="mod2_y5t+y5t_align"/>
-	<constant name="final_y6t" value="mod2_y6t+y6t_align"/>
-	<constant name="final_y7t" value="mod2_y7t+y7t_align"/>
-	<constant name="final_y8t" value="mod2_y8t+y8t_align"/>
-	<constant name="final_y9t" value="mod2_y9t+y9t_align"/>
-	<constant name="final_y10t" value="mod2_y10t+y10t_align"/>
-	<constant name="final_z1t" value="mod2_z1t+z1t_align"/>
-	<constant name="final_z2t" value="mod2_z2t+z2t_align"/>
-	<constant name="final_z3t" value="mod2_z3t+z3t_align"/>
-	<constant name="final_z4t" value="mod2_z4t+z4t_align"/>
-	<constant name="final_z5t" value="mod2_z5t+z5t_align"/>
-	<constant name="final_z6t" value="mod2_z6t+z6t_align"/>
-	<constant name="final_z7t" value="mod2_z7t+z7t_align"/>
-	<constant name="final_z8t" value="mod2_z8t+z8t_align"/>
-	<constant name="final_z9t" value="mod2_z9t+z9t_align"/>
-	<constant name="final_z10t" value="mod2_z10t+z10t_align"/>
-	<constant name="final_rx1t" value="mod2_rx1t+rx1t_align"/>
-	<constant name="final_rx2t" value="mod2_rx2t+rx2t_align"/>
-	<constant name="final_rx3t" value="mod2_rx3t+rx3t_align"/>
-	<constant name="final_rx4t" value="mod2_rx4t+rx4t_align"/>
-	<constant name="final_rx5t" value="mod2_rx5t+rx5t_align"/>
-	<constant name="final_rx6t" value="mod2_rx6t+rx6t_align"/>
-	<constant name="final_rx7t" value="mod2_rx7t+rx7t_align"/>
-	<constant name="final_rx8t" value="mod2_rx8t+rx8t_align"/>
-	<constant name="final_rx9t" value="mod2_rx9t+rx9t_align"/>
-	<constant name="final_rx10t" value="mod2_rx10t+rx10t_align"/>
-	<constant name="final_ry1t" value="mod2_ry1t+ry1t_align"/>
-	<constant name="final_ry2t" value="mod2_ry2t+ry2t_align"/>
-	<constant name="final_ry3t" value="mod2_ry3t+ry3t_align"/>
-	<constant name="final_ry4t" value="mod2_ry4t+ry4t_align"/>
-	<constant name="final_ry5t" value="mod2_ry5t+ry5t_align"/>
-	<constant name="final_ry6t" value="mod2_ry6t+ry6t_align"/>
-	<constant name="final_ry7t" value="mod2_ry7t+ry7t_align"/>
-	<constant name="final_ry8t" value="mod2_ry8t+ry8t_align"/>
-	<constant name="final_ry9t" value="mod2_ry9t+ry9t_align"/>
-	<constant name="final_ry10t" value="mod2_ry10t+ry10t_align"/>
-	<constant name="final_rz1t" value="mod2_rz1t+rz1t_align"/>
-	<constant name="final_rz2t" value="mod2_rz2t+rz2t_align"/>
-	<constant name="final_rz3t" value="mod2_rz3t+rz3t_align"/>
-	<constant name="final_rz4t" value="mod2_rz4t+rz4t_align"/>
-	<constant name="final_rz5t" value="mod2_rz5t+rz5t_align"/>
-	<constant name="final_rz6t" value="mod2_rz6t+rz6t_align"/>
-	<constant name="final_rz7t" value="mod2_rz7t+rz7t_align"/>
-	<constant name="final_rz8t" value="mod2_rz8t+rz8t_align"/>
-	<constant name="final_rz9t" value="mod2_rz9t+rz9t_align"/>
-	<constant name="final_rz10t" value="mod2_rz10t+rz10t_align"/>
-	<constant name="final_x1b" value="mod2_x1b+x1b_align"/>
-	<constant name="final_x2b" value="mod2_x2b+x2b_align"/>
-	<constant name="final_x3b" value="mod2_x3b+x3b_align"/>
-	<constant name="final_x4b" value="mod2_x4b+x4b_align"/>
-	<constant name="final_x5b" value="mod2_x5b+x5b_align"/>
-	<constant name="final_x6b" value="mod2_x6b+x6b_align"/>
-	<constant name="final_x7b" value="mod2_x7b+x7b_align"/>
-	<constant name="final_x8b" value="mod2_x8b+x8b_align"/>
-	<constant name="final_x9b" value="mod2_x9b+x9b_align"/>
-	<constant name="final_x10b" value="mod2_x10b+x10b_align"/>
-	<constant name="final_y1b" value="mod2_y1b+y1b_align"/>
-	<constant name="final_y2b" value="mod2_y2b+y2b_align"/>
-	<constant name="final_y3b" value="mod2_y3b+y3b_align"/>
-	<constant name="final_y4b" value="mod2_y4b+y4b_align"/>
-	<constant name="final_y5b" value="mod2_y5b+y5b_align"/>
-	<constant name="final_y6b" value="mod2_y6b+y6b_align"/>
-	<constant name="final_y7b" value="mod2_y7b+y7b_align"/>
-	<constant name="final_y8b" value="mod2_y8b+y8b_align"/>
-	<constant name="final_y9b" value="mod2_y9b+y9b_align"/>
-	<constant name="final_y10b" value="mod2_y10b+y10b_align"/>
-	<constant name="final_z1b" value="mod2_z1b+z1b_align"/>
-	<constant name="final_z2b" value="mod2_z2b+z2b_align"/>
-	<constant name="final_z3b" value="mod2_z3b+z3b_align"/>
-	<constant name="final_z4b" value="mod2_z4b+z4b_align"/>
-	<constant name="final_z5b" value="mod2_z5b+z5b_align"/>
-	<constant name="final_z6b" value="mod2_z6b+z6b_align"/>
-	<constant name="final_z7b" value="mod2_z7b+z7b_align"/>
-	<constant name="final_z8b" value="mod2_z8b+z8b_align"/>
-	<constant name="final_z9b" value="mod2_z9b+z9b_align"/>
-	<constant name="final_z10b" value="mod2_z10b+z10b_align"/>
-	<constant name="final_rx1b" value="mod2_rx1b+rx1b_align"/>
-	<constant name="final_rx2b" value="mod2_rx2b+rx2b_align"/>
-	<constant name="final_rx3b" value="mod2_rx3b+rx3b_align"/>
-	<constant name="final_rx4b" value="mod2_rx4b+rx4b_align"/>
-	<constant name="final_rx5b" value="mod2_rx5b+rx5b_align"/>
-	<constant name="final_rx6b" value="mod2_rx6b+rx6b_align"/>
-	<constant name="final_rx7b" value="mod2_rx7b+rx7b_align"/>
-	<constant name="final_rx8b" value="mod2_rx8b+rx8b_align"/>
-	<constant name="final_rx9b" value="mod2_rx9b+rx9b_align"/>
-	<constant name="final_rx10b" value="mod2_rx10b+rx10b_align"/>
-	<constant name="final_ry1b" value="mod2_ry1b+ry1b_align"/>
-	<constant name="final_ry2b" value="mod2_ry2b+ry2b_align"/>
-	<constant name="final_ry3b" value="mod2_ry3b+ry3b_align"/>
-	<constant name="final_ry4b" value="mod2_ry4b+ry4b_align"/>
-	<constant name="final_ry5b" value="mod2_ry5b+ry5b_align"/>
-	<constant name="final_ry6b" value="mod2_ry6b+ry6b_align"/>
-	<constant name="final_ry7b" value="mod2_ry7b+ry7b_align"/>
-	<constant name="final_ry8b" value="mod2_ry8b+ry8b_align"/>
-	<constant name="final_ry9b" value="mod2_ry9b+ry9b_align"/>
-	<constant name="final_ry10b" value="mod2_ry10b+ry10b_align"/>
-	<constant name="final_rz1b" value="mod2_rz1b+rz1b_align"/>
-	<constant name="final_rz2b" value="mod2_rz2b+rz2b_align"/>
-	<constant name="final_rz3b" value="mod2_rz3b+rz3b_align"/>
-	<constant name="final_rz4b" value="mod2_rz4b+rz4b_align"/>
-	<constant name="final_rz5b" value="mod2_rz5b+rz5b_align"/>
-	<constant name="final_rz6b" value="mod2_rz6b+rz6b_align"/>
-	<constant name="final_rz7b" value="mod2_rz7b+rz7b_align"/>
-	<constant name="final_rz8b" value="mod2_rz8b+rz8b_align"/>
-	<constant name="final_rz9b" value="mod2_rz9b+rz9b_align"/>
-	<constant name="final_rz10b" value="mod2_rz10b+rz10b_align"/>
-    	
-    	
+        
+        <!-- final constants -->
+    <constant name="final_x1t" value="mod2_x1t+x1t_align"/>
+    <constant name="final_x2t" value="mod2_x2t+x2t_align"/>
+    <constant name="final_x3t" value="mod2_x3t+x3t_align"/>
+    <constant name="final_x4t" value="mod2_x4t+x4t_align"/>
+    <constant name="final_x5t" value="mod2_x5t+x5t_align"/>
+    <constant name="final_x6t" value="mod2_x6t+x6t_align"/>
+    <constant name="final_x7t" value="mod2_x7t+x7t_align"/>
+    <constant name="final_x8t" value="mod2_x8t+x8t_align"/>
+    <constant name="final_x9t" value="mod2_x9t+x9t_align"/>
+    <constant name="final_x10t" value="mod2_x10t+x10t_align"/>
+    <constant name="final_y1t" value="mod2_y1t+y1t_align"/>
+    <constant name="final_y2t" value="mod2_y2t+y2t_align"/>
+    <constant name="final_y3t" value="mod2_y3t+y3t_align"/>
+    <constant name="final_y4t" value="mod2_y4t+y4t_align"/>
+    <constant name="final_y5t" value="mod2_y5t+y5t_align"/>
+    <constant name="final_y6t" value="mod2_y6t+y6t_align"/>
+    <constant name="final_y7t" value="mod2_y7t+y7t_align"/>
+    <constant name="final_y8t" value="mod2_y8t+y8t_align"/>
+    <constant name="final_y9t" value="mod2_y9t+y9t_align"/>
+    <constant name="final_y10t" value="mod2_y10t+y10t_align"/>
+    <constant name="final_z1t" value="mod2_z1t+z1t_align"/>
+    <constant name="final_z2t" value="mod2_z2t+z2t_align"/>
+    <constant name="final_z3t" value="mod2_z3t+z3t_align"/>
+    <constant name="final_z4t" value="mod2_z4t+z4t_align"/>
+    <constant name="final_z5t" value="mod2_z5t+z5t_align"/>
+    <constant name="final_z6t" value="mod2_z6t+z6t_align"/>
+    <constant name="final_z7t" value="mod2_z7t+z7t_align"/>
+    <constant name="final_z8t" value="mod2_z8t+z8t_align"/>
+    <constant name="final_z9t" value="mod2_z9t+z9t_align"/>
+    <constant name="final_z10t" value="mod2_z10t+z10t_align"/>
+    <constant name="final_rx1t" value="mod2_rx1t+rx1t_align"/>
+    <constant name="final_rx2t" value="mod2_rx2t+rx2t_align"/>
+    <constant name="final_rx3t" value="mod2_rx3t+rx3t_align"/>
+    <constant name="final_rx4t" value="mod2_rx4t+rx4t_align"/>
+    <constant name="final_rx5t" value="mod2_rx5t+rx5t_align"/>
+    <constant name="final_rx6t" value="mod2_rx6t+rx6t_align"/>
+    <constant name="final_rx7t" value="mod2_rx7t+rx7t_align"/>
+    <constant name="final_rx8t" value="mod2_rx8t+rx8t_align"/>
+    <constant name="final_rx9t" value="mod2_rx9t+rx9t_align"/>
+    <constant name="final_rx10t" value="mod2_rx10t+rx10t_align"/>
+    <constant name="final_ry1t" value="mod2_ry1t+ry1t_align"/>
+    <constant name="final_ry2t" value="mod2_ry2t+ry2t_align"/>
+    <constant name="final_ry3t" value="mod2_ry3t+ry3t_align"/>
+    <constant name="final_ry4t" value="mod2_ry4t+ry4t_align"/>
+    <constant name="final_ry5t" value="mod2_ry5t+ry5t_align"/>
+    <constant name="final_ry6t" value="mod2_ry6t+ry6t_align"/>
+    <constant name="final_ry7t" value="mod2_ry7t+ry7t_align"/>
+    <constant name="final_ry8t" value="mod2_ry8t+ry8t_align"/>
+    <constant name="final_ry9t" value="mod2_ry9t+ry9t_align"/>
+    <constant name="final_ry10t" value="mod2_ry10t+ry10t_align"/>
+    <constant name="final_rz1t" value="mod2_rz1t+rz1t_align"/>
+    <constant name="final_rz2t" value="mod2_rz2t+rz2t_align"/>
+    <constant name="final_rz3t" value="mod2_rz3t+rz3t_align"/>
+    <constant name="final_rz4t" value="mod2_rz4t+rz4t_align"/>
+    <constant name="final_rz5t" value="mod2_rz5t+rz5t_align"/>
+    <constant name="final_rz6t" value="mod2_rz6t+rz6t_align"/>
+    <constant name="final_rz7t" value="mod2_rz7t+rz7t_align"/>
+    <constant name="final_rz8t" value="mod2_rz8t+rz8t_align"/>
+    <constant name="final_rz9t" value="mod2_rz9t+rz9t_align"/>
+    <constant name="final_rz10t" value="mod2_rz10t+rz10t_align"/>
+    <constant name="final_x1b" value="mod2_x1b+x1b_align"/>
+    <constant name="final_x2b" value="mod2_x2b+x2b_align"/>
+    <constant name="final_x3b" value="mod2_x3b+x3b_align"/>
+    <constant name="final_x4b" value="mod2_x4b+x4b_align"/>
+    <constant name="final_x5b" value="mod2_x5b+x5b_align"/>
+    <constant name="final_x6b" value="mod2_x6b+x6b_align"/>
+    <constant name="final_x7b" value="mod2_x7b+x7b_align"/>
+    <constant name="final_x8b" value="mod2_x8b+x8b_align"/>
+    <constant name="final_x9b" value="mod2_x9b+x9b_align"/>
+    <constant name="final_x10b" value="mod2_x10b+x10b_align"/>
+    <constant name="final_y1b" value="mod2_y1b+y1b_align"/>
+    <constant name="final_y2b" value="mod2_y2b+y2b_align"/>
+    <constant name="final_y3b" value="mod2_y3b+y3b_align"/>
+    <constant name="final_y4b" value="mod2_y4b+y4b_align"/>
+    <constant name="final_y5b" value="mod2_y5b+y5b_align"/>
+    <constant name="final_y6b" value="mod2_y6b+y6b_align"/>
+    <constant name="final_y7b" value="mod2_y7b+y7b_align"/>
+    <constant name="final_y8b" value="mod2_y8b+y8b_align"/>
+    <constant name="final_y9b" value="mod2_y9b+y9b_align"/>
+    <constant name="final_y10b" value="mod2_y10b+y10b_align"/>
+    <constant name="final_z1b" value="mod2_z1b+z1b_align"/>
+    <constant name="final_z2b" value="mod2_z2b+z2b_align"/>
+    <constant name="final_z3b" value="mod2_z3b+z3b_align"/>
+    <constant name="final_z4b" value="mod2_z4b+z4b_align"/>
+    <constant name="final_z5b" value="mod2_z5b+z5b_align"/>
+    <constant name="final_z6b" value="mod2_z6b+z6b_align"/>
+    <constant name="final_z7b" value="mod2_z7b+z7b_align"/>
+    <constant name="final_z8b" value="mod2_z8b+z8b_align"/>
+    <constant name="final_z9b" value="mod2_z9b+z9b_align"/>
+    <constant name="final_z10b" value="mod2_z10b+z10b_align"/>
+    <constant name="final_rx1b" value="mod2_rx1b+rx1b_align"/>
+    <constant name="final_rx2b" value="mod2_rx2b+rx2b_align"/>
+    <constant name="final_rx3b" value="mod2_rx3b+rx3b_align"/>
+    <constant name="final_rx4b" value="mod2_rx4b+rx4b_align"/>
+    <constant name="final_rx5b" value="mod2_rx5b+rx5b_align"/>
+    <constant name="final_rx6b" value="mod2_rx6b+rx6b_align"/>
+    <constant name="final_rx7b" value="mod2_rx7b+rx7b_align"/>
+    <constant name="final_rx8b" value="mod2_rx8b+rx8b_align"/>
+    <constant name="final_rx9b" value="mod2_rx9b+rx9b_align"/>
+    <constant name="final_rx10b" value="mod2_rx10b+rx10b_align"/>
+    <constant name="final_ry1b" value="mod2_ry1b+ry1b_align"/>
+    <constant name="final_ry2b" value="mod2_ry2b+ry2b_align"/>
+    <constant name="final_ry3b" value="mod2_ry3b+ry3b_align"/>
+    <constant name="final_ry4b" value="mod2_ry4b+ry4b_align"/>
+    <constant name="final_ry5b" value="mod2_ry5b+ry5b_align"/>
+    <constant name="final_ry6b" value="mod2_ry6b+ry6b_align"/>
+    <constant name="final_ry7b" value="mod2_ry7b+ry7b_align"/>
+    <constant name="final_ry8b" value="mod2_ry8b+ry8b_align"/>
+    <constant name="final_ry9b" value="mod2_ry9b+ry9b_align"/>
+    <constant name="final_ry10b" value="mod2_ry10b+ry10b_align"/>
+    <constant name="final_rz1b" value="mod2_rz1b+rz1b_align"/>
+    <constant name="final_rz2b" value="mod2_rz2b+rz2b_align"/>
+    <constant name="final_rz3b" value="mod2_rz3b+rz3b_align"/>
+    <constant name="final_rz4b" value="mod2_rz4b+rz4b_align"/>
+    <constant name="final_rz5b" value="mod2_rz5b+rz5b_align"/>
+    <constant name="final_rz6b" value="mod2_rz6b+rz6b_align"/>
+    <constant name="final_rz7b" value="mod2_rz7b+rz7b_align"/>
+    <constant name="final_rz8b" value="mod2_rz8b+rz8b_align"/>
+    <constant name="final_rz9b" value="mod2_rz9b+rz9b_align"/>
+    <constant name="final_rz10b" value="mod2_rz10b+rz10b_align"/>
+        
+        
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001"/>
             <fraction n="1.0" ref="Vacuum" />
@@ -822,7 +822,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-3/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-3/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7-3/compact.xml	Wed Apr 27 11:11:32 2016
@@ -84,127 +84,127 @@
         <constant name="y9b_misalign" value="0.0" />
         <constant name="y10b_misalign" value="0.0" />
 
-		<!-- alignment corrections -->
-	<constant name="x1t_align" value="0.000000" />
-	<constant name="x2t_align" value="-0.000000" />
-	<constant name="x3t_align" value="-0.000012" />
-	<constant name="x4t_align" value="-0.017488" />
-	<constant name="x5t_align" value="-0.000064" />
-	<constant name="x6t_align" value="-0.000141" />
-	<constant name="x7t_align" value="0.000002" />
-	<constant name="x8t_align" value="0.000573" />
-	<constant name="x9t_align" value="0.000000" />
-	<constant name="x10t_align" value="-0.000000" />
-	<constant name="y1t_align" value="0.000000" />
-	<constant name="y2t_align" value="0.000000" />
-	<constant name="y3t_align" value="-0.094679" />
-	<constant name="y4t_align" value="-0.174440" />
-	<constant name="y5t_align" value="0.118670" />
-	<constant name="y6t_align" value="-0.001400" />
-	<constant name="y7t_align" value="0.047526" />
-	<constant name="y8t_align" value="0.011511" />
-	<constant name="y9t_align" value="0.000000" />
-	<constant name="y10t_align" value="0.000000" />
-	<constant name="z1t_align" value="0.000000" />
-	<constant name="z2t_align" value="0.000000" />
-	<constant name="z3t_align" value="-0.002463" />
-	<constant name="z4t_align" value="-0.003986" />
-	<constant name="z5t_align" value="0.003089" />
-	<constant name="z6t_align" value="-0.000032" />
-	<constant name="z7t_align" value="0.001236" />
-	<constant name="z8t_align" value="0.000281" />
-	<constant name="z9t_align" value="0.000000" />
-	<constant name="z10t_align" value="0.000000" />
-	<constant name="rx1t_align" value="0.000000" />
-	<constant name="rx2t_align" value="-0.000000" />
-	<constant name="rx3t_align" value="0.000000" />
-	<constant name="rx4t_align" value="-0.000000" />
-	<constant name="rx5t_align" value="0.000000" />
-	<constant name="rx6t_align" value="-0.000000" />
-	<constant name="rx7t_align" value="0.000000" />
-	<constant name="rx8t_align" value="-0.000000" />
-	<constant name="rx9t_align" value="0.000000" />
-	<constant name="rx10t_align" value="-0.000000" />
-	<constant name="ry1t_align" value="0.000000" />
-	<constant name="ry2t_align" value="0.000000" />
-	<constant name="ry3t_align" value="0.000000" />
-	<constant name="ry4t_align" value="0.000000" />
-	<constant name="ry5t_align" value="0.000000" />
-	<constant name="ry6t_align" value="0.000000" />
-	<constant name="ry7t_align" value="0.000000" />
-	<constant name="ry8t_align" value="0.000000" />
-	<constant name="ry9t_align" value="0.000000" />
-	<constant name="ry10t_align" value="0.000000" />
-	<constant name="rz1t_align" value="0.000000" />
-	<constant name="rz2t_align" value="0.000000" />
-	<constant name="rz3t_align" value="0.000000" />
-	<constant name="rz4t_align" value="0.000000" />
-	<constant name="rz5t_align" value="0.000000" />
-	<constant name="rz6t_align" value="0.000000" />
-	<constant name="rz7t_align" value="0.000000" />
-	<constant name="rz8t_align" value="0.000000" />
-	<constant name="rz9t_align" value="0.000000" />
-	<constant name="rz10t_align" value="0.000000" />
-	<constant name="x1b_align" value="0.000000" />
-	<constant name="x2b_align" value="-0.000000" />
-	<constant name="x3b_align" value="-0.068351" />
-	<constant name="x4b_align" value="0.000012" />
-	<constant name="x5b_align" value="-0.100385" />
-	<constant name="x6b_align" value="0.000012" />
-	<constant name="x7b_align" value="-0.025606" />
-	<constant name="x8b_align" value="0.000007" />
-	<constant name="x9b_align" value="0.000000" />
-	<constant name="x10b_align" value="-0.000000" />
-	<constant name="y1b_align" value="0.000000" />
-	<constant name="y2b_align" value="0.000000" />
-	<constant name="y3b_align" value="0.681109" />
-	<constant name="y4b_align" value="0.061551" />
-	<constant name="y5b_align" value="1.004204" />
-	<constant name="y6b_align" value="0.037831" />
-	<constant name="y7b_align" value="0.506463" />
-	<constant name="y8b_align" value="0.015775" />
-	<constant name="y9b_align" value="0.000000" />
-	<constant name="y10b_align" value="0.000000" />
-	<constant name="z1b_align" value="0.000000" />
-	<constant name="z2b_align" value="0.000000" />
-	<constant name="z3b_align" value="-0.013322" />
-	<constant name="z4b_align" value="-0.001371" />
-	<constant name="z5b_align" value="-0.019651" />
-	<constant name="z6b_align" value="-0.000843" />
-	<constant name="z7b_align" value="-0.010587" />
-	<constant name="z8b_align" value="-0.000352" />
-	<constant name="z9b_align" value="0.000000" />
-	<constant name="z10b_align" value="0.000000" />
-	<constant name="rx1b_align" value="0.000000" />
-	<constant name="rx2b_align" value="-0.000000" />
-	<constant name="rx3b_align" value="0.000000" />
-	<constant name="rx4b_align" value="-0.000000" />
-	<constant name="rx5b_align" value="0.000000" />
-	<constant name="rx6b_align" value="-0.000000" />
-	<constant name="rx7b_align" value="0.000000" />
-	<constant name="rx8b_align" value="-0.000000" />
-	<constant name="rx9b_align" value="0.000000" />
-	<constant name="rx10b_align" value="-0.000000" />
-	<constant name="ry1b_align" value="0.000000" />
-	<constant name="ry2b_align" value="0.000000" />
-	<constant name="ry3b_align" value="0.000000" />
-	<constant name="ry4b_align" value="0.000000" />
-	<constant name="ry5b_align" value="0.000000" />
-	<constant name="ry6b_align" value="0.000000" />
-	<constant name="ry7b_align" value="0.000000" />
-	<constant name="ry8b_align" value="0.000000" />
-	<constant name="ry9b_align" value="0.000000" />
-	<constant name="ry10b_align" value="0.000000" />
-	<constant name="rz1b_align" value="0.000000" />
-	<constant name="rz2b_align" value="0.000000" />
-	<constant name="rz3b_align" value="0.000000" />
-	<constant name="rz4b_align" value="0.000000" />
-	<constant name="rz5b_align" value="0.000000" />
-	<constant name="rz6b_align" value="0.000000" />
-	<constant name="rz7b_align" value="0.000000" />
-	<constant name="rz8b_align" value="0.000000" />
-	<constant name="rz9b_align" value="0.000000" />
-	<constant name="rz10b_align" value="0.000000" />
+        <!-- alignment corrections -->
+    <constant name="x1t_align" value="0.000000" />
+    <constant name="x2t_align" value="-0.000000" />
+    <constant name="x3t_align" value="-0.000012" />
+    <constant name="x4t_align" value="-0.017488" />
+    <constant name="x5t_align" value="-0.000064" />
+    <constant name="x6t_align" value="-0.000141" />
+    <constant name="x7t_align" value="0.000002" />
+    <constant name="x8t_align" value="0.000573" />
+    <constant name="x9t_align" value="0.000000" />
+    <constant name="x10t_align" value="-0.000000" />
+    <constant name="y1t_align" value="0.000000" />
+    <constant name="y2t_align" value="0.000000" />
+    <constant name="y3t_align" value="-0.094679" />
+    <constant name="y4t_align" value="-0.174440" />
+    <constant name="y5t_align" value="0.118670" />
+    <constant name="y6t_align" value="-0.001400" />
+    <constant name="y7t_align" value="0.047526" />
+    <constant name="y8t_align" value="0.011511" />
+    <constant name="y9t_align" value="0.000000" />
+    <constant name="y10t_align" value="0.000000" />
+    <constant name="z1t_align" value="0.000000" />
+    <constant name="z2t_align" value="0.000000" />
+    <constant name="z3t_align" value="-0.002463" />
+    <constant name="z4t_align" value="-0.003986" />
+    <constant name="z5t_align" value="0.003089" />
+    <constant name="z6t_align" value="-0.000032" />
+    <constant name="z7t_align" value="0.001236" />
+    <constant name="z8t_align" value="0.000281" />
+    <constant name="z9t_align" value="0.000000" />
+    <constant name="z10t_align" value="0.000000" />
+    <constant name="rx1t_align" value="0.000000" />
+    <constant name="rx2t_align" value="-0.000000" />
+    <constant name="rx3t_align" value="0.000000" />
+    <constant name="rx4t_align" value="-0.000000" />
+    <constant name="rx5t_align" value="0.000000" />
+    <constant name="rx6t_align" value="-0.000000" />
+    <constant name="rx7t_align" value="0.000000" />
+    <constant name="rx8t_align" value="-0.000000" />
+    <constant name="rx9t_align" value="0.000000" />
+    <constant name="rx10t_align" value="-0.000000" />
+    <constant name="ry1t_align" value="0.000000" />
+    <constant name="ry2t_align" value="0.000000" />
+    <constant name="ry3t_align" value="0.000000" />
+    <constant name="ry4t_align" value="0.000000" />
+    <constant name="ry5t_align" value="0.000000" />
+    <constant name="ry6t_align" value="0.000000" />
+    <constant name="ry7t_align" value="0.000000" />
+    <constant name="ry8t_align" value="0.000000" />
+    <constant name="ry9t_align" value="0.000000" />
+    <constant name="ry10t_align" value="0.000000" />
+    <constant name="rz1t_align" value="0.000000" />
+    <constant name="rz2t_align" value="0.000000" />
+    <constant name="rz3t_align" value="0.000000" />
+    <constant name="rz4t_align" value="0.000000" />
+    <constant name="rz5t_align" value="0.000000" />
+    <constant name="rz6t_align" value="0.000000" />
+    <constant name="rz7t_align" value="0.000000" />
+    <constant name="rz8t_align" value="0.000000" />
+    <constant name="rz9t_align" value="0.000000" />
+    <constant name="rz10t_align" value="0.000000" />
+    <constant name="x1b_align" value="0.000000" />
+    <constant name="x2b_align" value="-0.000000" />
+    <constant name="x3b_align" value="-0.068351" />
+    <constant name="x4b_align" value="0.000012" />
+    <constant name="x5b_align" value="-0.100385" />
+    <constant name="x6b_align" value="0.000012" />
+    <constant name="x7b_align" value="-0.025606" />
+    <constant name="x8b_align" value="0.000007" />
+    <constant name="x9b_align" value="0.000000" />
+    <constant name="x10b_align" value="-0.000000" />
+    <constant name="y1b_align" value="0.000000" />
+    <constant name="y2b_align" value="0.000000" />
+    <constant name="y3b_align" value="0.681109" />
+    <constant name="y4b_align" value="0.061551" />
+    <constant name="y5b_align" value="1.004204" />
+    <constant name="y6b_align" value="0.037831" />
+    <constant name="y7b_align" value="0.506463" />
+    <constant name="y8b_align" value="0.015775" />
+    <constant name="y9b_align" value="0.000000" />
+    <constant name="y10b_align" value="0.000000" />
+    <constant name="z1b_align" value="0.000000" />
+    <constant name="z2b_align" value="0.000000" />
+    <constant name="z3b_align" value="-0.013322" />
+    <constant name="z4b_align" value="-0.001371" />
+    <constant name="z5b_align" value="-0.019651" />
+    <constant name="z6b_align" value="-0.000843" />
+    <constant name="z7b_align" value="-0.010587" />
+    <constant name="z8b_align" value="-0.000352" />
+    <constant name="z9b_align" value="0.000000" />
+    <constant name="z10b_align" value="0.000000" />
+    <constant name="rx1b_align" value="0.000000" />
+    <constant name="rx2b_align" value="-0.000000" />
+    <constant name="rx3b_align" value="0.000000" />
+    <constant name="rx4b_align" value="-0.000000" />
+    <constant name="rx5b_align" value="0.000000" />
+    <constant name="rx6b_align" value="-0.000000" />
+    <constant name="rx7b_align" value="0.000000" />
+    <constant name="rx8b_align" value="-0.000000" />
+    <constant name="rx9b_align" value="0.000000" />
+    <constant name="rx10b_align" value="-0.000000" />
+    <constant name="ry1b_align" value="0.000000" />
+    <constant name="ry2b_align" value="0.000000" />
+    <constant name="ry3b_align" value="0.000000" />
+    <constant name="ry4b_align" value="0.000000" />
+    <constant name="ry5b_align" value="0.000000" />
+    <constant name="ry6b_align" value="0.000000" />
+    <constant name="ry7b_align" value="0.000000" />
+    <constant name="ry8b_align" value="0.000000" />
+    <constant name="ry9b_align" value="0.000000" />
+    <constant name="ry10b_align" value="0.000000" />
+    <constant name="rz1b_align" value="0.000000" />
+    <constant name="rz2b_align" value="0.000000" />
+    <constant name="rz3b_align" value="0.000000" />
+    <constant name="rz4b_align" value="0.000000" />
+    <constant name="rz5b_align" value="0.000000" />
+    <constant name="rz6b_align" value="0.000000" />
+    <constant name="rz7b_align" value="0.000000" />
+    <constant name="rz8b_align" value="0.000000" />
+    <constant name="rz9b_align" value="0.000000" />
+    <constant name="rz10b_align" value="0.000000" />
 
         <!-- Positions of sensor centers above/below nominal beam -->
         <constant name="y1t" value="36.894" />
@@ -604,134 +604,134 @@
         <constant name="mod2_rx10b" value="mod_rx10b" />
         <constant name="mod2_ry10b" value="mod_ry10b+y_rot_bot_pivot" />
         <constant name="mod2_rz10b" value="mod_rz10b" />
-    	
-    	<!-- final constants -->
-	<constant name="final_x1t" value="mod2_x1t+x1t_align" />
-	<constant name="final_x2t" value="mod2_x2t+x2t_align" />
-	<constant name="final_x3t" value="mod2_x3t+x3t_align" />
-	<constant name="final_x4t" value="mod2_x4t+x4t_align" />
-	<constant name="final_x5t" value="mod2_x5t+x5t_align" />
-	<constant name="final_x6t" value="mod2_x6t+x6t_align" />
-	<constant name="final_x7t" value="mod2_x7t+x7t_align" />
-	<constant name="final_x8t" value="mod2_x8t+x8t_align" />
-	<constant name="final_x9t" value="mod2_x9t+x9t_align" />
-	<constant name="final_x10t" value="mod2_x10t+x10t_align" />
-	<constant name="final_y1t" value="mod2_y1t+y1t_align" />
-	<constant name="final_y2t" value="mod2_y2t+y2t_align" />
-	<constant name="final_y3t" value="mod2_y3t+y3t_align" />
-	<constant name="final_y4t" value="mod2_y4t+y4t_align" />
-	<constant name="final_y5t" value="mod2_y5t+y5t_align" />
-	<constant name="final_y6t" value="mod2_y6t+y6t_align" />
-	<constant name="final_y7t" value="mod2_y7t+y7t_align" />
-	<constant name="final_y8t" value="mod2_y8t+y8t_align" />
-	<constant name="final_y9t" value="mod2_y9t+y9t_align" />
-	<constant name="final_y10t" value="mod2_y10t+y10t_align" />
-	<constant name="final_z1t" value="mod2_z1t+z1t_align" />
-	<constant name="final_z2t" value="mod2_z2t+z2t_align" />
-	<constant name="final_z3t" value="mod2_z3t+z3t_align" />
-	<constant name="final_z4t" value="mod2_z4t+z4t_align" />
-	<constant name="final_z5t" value="mod2_z5t+z5t_align" />
-	<constant name="final_z6t" value="mod2_z6t+z6t_align" />
-	<constant name="final_z7t" value="mod2_z7t+z7t_align" />
-	<constant name="final_z8t" value="mod2_z8t+z8t_align" />
-	<constant name="final_z9t" value="mod2_z9t+z9t_align" />
-	<constant name="final_z10t" value="mod2_z10t+z10t_align" />
-	<constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
-	<constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
-	<constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
-	<constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
-	<constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
-	<constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
-	<constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
-	<constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
-	<constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
-	<constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
-	<constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
-	<constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
-	<constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
-	<constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
-	<constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
-	<constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
-	<constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
-	<constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
-	<constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
-	<constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
-	<constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
-	<constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
-	<constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
-	<constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
-	<constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
-	<constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
-	<constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
-	<constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
-	<constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
-	<constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
-	<constant name="final_x1b" value="mod2_x1b+x1b_align" />
-	<constant name="final_x2b" value="mod2_x2b+x2b_align" />
-	<constant name="final_x3b" value="mod2_x3b+x3b_align" />
-	<constant name="final_x4b" value="mod2_x4b+x4b_align" />
-	<constant name="final_x5b" value="mod2_x5b+x5b_align" />
-	<constant name="final_x6b" value="mod2_x6b+x6b_align" />
-	<constant name="final_x7b" value="mod2_x7b+x7b_align" />
-	<constant name="final_x8b" value="mod2_x8b+x8b_align" />
-	<constant name="final_x9b" value="mod2_x9b+x9b_align" />
-	<constant name="final_x10b" value="mod2_x10b+x10b_align" />
-	<constant name="final_y1b" value="mod2_y1b+y1b_align" />
-	<constant name="final_y2b" value="mod2_y2b+y2b_align" />
-	<constant name="final_y3b" value="mod2_y3b+y3b_align" />
-	<constant name="final_y4b" value="mod2_y4b+y4b_align" />
-	<constant name="final_y5b" value="mod2_y5b+y5b_align" />
-	<constant name="final_y6b" value="mod2_y6b+y6b_align" />
-	<constant name="final_y7b" value="mod2_y7b+y7b_align" />
-	<constant name="final_y8b" value="mod2_y8b+y8b_align" />
-	<constant name="final_y9b" value="mod2_y9b+y9b_align" />
-	<constant name="final_y10b" value="mod2_y10b+y10b_align" />
-	<constant name="final_z1b" value="mod2_z1b+z1b_align" />
-	<constant name="final_z2b" value="mod2_z2b+z2b_align" />
-	<constant name="final_z3b" value="mod2_z3b+z3b_align" />
-	<constant name="final_z4b" value="mod2_z4b+z4b_align" />
-	<constant name="final_z5b" value="mod2_z5b+z5b_align" />
-	<constant name="final_z6b" value="mod2_z6b+z6b_align" />
-	<constant name="final_z7b" value="mod2_z7b+z7b_align" />
-	<constant name="final_z8b" value="mod2_z8b+z8b_align" />
-	<constant name="final_z9b" value="mod2_z9b+z9b_align" />
-	<constant name="final_z10b" value="mod2_z10b+z10b_align" />
-	<constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
-	<constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
-	<constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
-	<constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
-	<constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
-	<constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
-	<constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
-	<constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
-	<constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
-	<constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
-	<constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
-	<constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
-	<constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
-	<constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
-	<constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
-	<constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
-	<constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
-	<constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
-	<constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
-	<constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
-	<constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
-	<constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
-	<constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
-	<constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
-	<constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
-	<constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
-	<constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
-	<constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
-	<constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
-	<constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
-    	
-    	
+        
+        <!-- final constants -->
+    <constant name="final_x1t" value="mod2_x1t+x1t_align" />
+    <constant name="final_x2t" value="mod2_x2t+x2t_align" />
+    <constant name="final_x3t" value="mod2_x3t+x3t_align" />
+    <constant name="final_x4t" value="mod2_x4t+x4t_align" />
+    <constant name="final_x5t" value="mod2_x5t+x5t_align" />
+    <constant name="final_x6t" value="mod2_x6t+x6t_align" />
+    <constant name="final_x7t" value="mod2_x7t+x7t_align" />
+    <constant name="final_x8t" value="mod2_x8t+x8t_align" />
+    <constant name="final_x9t" value="mod2_x9t+x9t_align" />
+    <constant name="final_x10t" value="mod2_x10t+x10t_align" />
+    <constant name="final_y1t" value="mod2_y1t+y1t_align" />
+    <constant name="final_y2t" value="mod2_y2t+y2t_align" />
+    <constant name="final_y3t" value="mod2_y3t+y3t_align" />
+    <constant name="final_y4t" value="mod2_y4t+y4t_align" />
+    <constant name="final_y5t" value="mod2_y5t+y5t_align" />
+    <constant name="final_y6t" value="mod2_y6t+y6t_align" />
+    <constant name="final_y7t" value="mod2_y7t+y7t_align" />
+    <constant name="final_y8t" value="mod2_y8t+y8t_align" />
+    <constant name="final_y9t" value="mod2_y9t+y9t_align" />
+    <constant name="final_y10t" value="mod2_y10t+y10t_align" />
+    <constant name="final_z1t" value="mod2_z1t+z1t_align" />
+    <constant name="final_z2t" value="mod2_z2t+z2t_align" />
+    <constant name="final_z3t" value="mod2_z3t+z3t_align" />
+    <constant name="final_z4t" value="mod2_z4t+z4t_align" />
+    <constant name="final_z5t" value="mod2_z5t+z5t_align" />
+    <constant name="final_z6t" value="mod2_z6t+z6t_align" />
+    <constant name="final_z7t" value="mod2_z7t+z7t_align" />
+    <constant name="final_z8t" value="mod2_z8t+z8t_align" />
+    <constant name="final_z9t" value="mod2_z9t+z9t_align" />
+    <constant name="final_z10t" value="mod2_z10t+z10t_align" />
+    <constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
+    <constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
+    <constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
+    <constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
+    <constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
+    <constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
+    <constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
+    <constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
+    <constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
+    <constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
+    <constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
+    <constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
+    <constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
+    <constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
+    <constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
+    <constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
+    <constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
+    <constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
+    <constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
+    <constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
+    <constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
+    <constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
+    <constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
+    <constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
+    <constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
+    <constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
+    <constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
+    <constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
+    <constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
+    <constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
+    <constant name="final_x1b" value="mod2_x1b+x1b_align" />
+    <constant name="final_x2b" value="mod2_x2b+x2b_align" />
+    <constant name="final_x3b" value="mod2_x3b+x3b_align" />
+    <constant name="final_x4b" value="mod2_x4b+x4b_align" />
+    <constant name="final_x5b" value="mod2_x5b+x5b_align" />
+    <constant name="final_x6b" value="mod2_x6b+x6b_align" />
+    <constant name="final_x7b" value="mod2_x7b+x7b_align" />
+    <constant name="final_x8b" value="mod2_x8b+x8b_align" />
+    <constant name="final_x9b" value="mod2_x9b+x9b_align" />
+    <constant name="final_x10b" value="mod2_x10b+x10b_align" />
+    <constant name="final_y1b" value="mod2_y1b+y1b_align" />
+    <constant name="final_y2b" value="mod2_y2b+y2b_align" />
+    <constant name="final_y3b" value="mod2_y3b+y3b_align" />
+    <constant name="final_y4b" value="mod2_y4b+y4b_align" />
+    <constant name="final_y5b" value="mod2_y5b+y5b_align" />
+    <constant name="final_y6b" value="mod2_y6b+y6b_align" />
+    <constant name="final_y7b" value="mod2_y7b+y7b_align" />
+    <constant name="final_y8b" value="mod2_y8b+y8b_align" />
+    <constant name="final_y9b" value="mod2_y9b+y9b_align" />
+    <constant name="final_y10b" value="mod2_y10b+y10b_align" />
+    <constant name="final_z1b" value="mod2_z1b+z1b_align" />
+    <constant name="final_z2b" value="mod2_z2b+z2b_align" />
+    <constant name="final_z3b" value="mod2_z3b+z3b_align" />
+    <constant name="final_z4b" value="mod2_z4b+z4b_align" />
+    <constant name="final_z5b" value="mod2_z5b+z5b_align" />
+    <constant name="final_z6b" value="mod2_z6b+z6b_align" />
+    <constant name="final_z7b" value="mod2_z7b+z7b_align" />
+    <constant name="final_z8b" value="mod2_z8b+z8b_align" />
+    <constant name="final_z9b" value="mod2_z9b+z9b_align" />
+    <constant name="final_z10b" value="mod2_z10b+z10b_align" />
+    <constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
+    <constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
+    <constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
+    <constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
+    <constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
+    <constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
+    <constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
+    <constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
+    <constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
+    <constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
+    <constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
+    <constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
+    <constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
+    <constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
+    <constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
+    <constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
+    <constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
+    <constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
+    <constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
+    <constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
+    <constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
+    <constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
+    <constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
+    <constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
+    <constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
+    <constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
+    <constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
+    <constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
+    <constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
+    <constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
+        
+        
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001" />
             <fraction n="1.0" ref="Vacuum" />
@@ -820,7 +820,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2" />
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v7/compact.xml	Wed Apr 27 11:11:32 2016
@@ -488,7 +488,7 @@
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001"/>
             <fraction n="1.0" ref="Vacuum" />
@@ -577,7 +577,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-4/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-4/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-4/compact.xml	Wed Apr 27 11:11:32 2016
@@ -3,9 +3,9 @@
     
     <info name="HPS-TestRun-v8-4">
         <comment>
-		  HPS JLab Test Run detector with dipole field starting at z=0
-		  Alignment based on millepede: compact-u3-6-float-1351-v8-10k.xml
-		</comment>
+          HPS JLab Test Run detector with dipole field starting at z=0
+          Alignment based on millepede: compact-u3-6-float-1351-v8-10k.xml
+        </comment>
     </info>
 
     <define>
@@ -65,127 +65,127 @@
 <!--        <constant name="x_off" value = "-15.0"/> -->
         <constant name="x_off" value="0.0" /> 
 
-		<!-- alignment corrections -->
-	<constant name="x1t_align" value="0.000000" />
-	<constant name="x2t_align" value="0.000000" />
-	<constant name="x3t_align" value="0.000014" />
-	<constant name="x4t_align" value="0.015024" />
-	<constant name="x5t_align" value="0.000045" />
-	<constant name="x6t_align" value="-0.003411" />
-	<constant name="x7t_align" value="0.000000" />
-	<constant name="x8t_align" value="0.000000" />
-	<constant name="x9t_align" value="0.000000" />
-	<constant name="x10t_align" value="0.000000" />
-	<constant name="y1t_align" value="0.000000" />
-	<constant name="y2t_align" value="0.000000" />
-	<constant name="y3t_align" value="0.112932" />
-	<constant name="y4t_align" value="0.149860" />
-	<constant name="y5t_align" value="-0.082467" />
-	<constant name="y6t_align" value="-0.033966" />
-	<constant name="y7t_align" value="0.000000" />
-	<constant name="y8t_align" value="0.000000" />
-	<constant name="y9t_align" value="0.000000" />
-	<constant name="y10t_align" value="0.000000" />
-	<constant name="z1t_align" value="-0.000000" />
-	<constant name="z2t_align" value="0.000000" />
-	<constant name="z3t_align" value="0.002938" />
-	<constant name="z4t_align" value="0.003424" />
-	<constant name="z5t_align" value="-0.002147" />
-	<constant name="z6t_align" value="-0.000776" />
-	<constant name="z7t_align" value="-0.000000" />
-	<constant name="z8t_align" value="0.000000" />
-	<constant name="z9t_align" value="-0.000000" />
-	<constant name="z10t_align" value="0.000000" />
-	<constant name="rx1t_align" value="0.000000" />
-	<constant name="rx2t_align" value="0.000000" />
-	<constant name="rx3t_align" value="0.000000" />
-	<constant name="rx4t_align" value="0.000000" />
-	<constant name="rx5t_align" value="0.000000" />
-	<constant name="rx6t_align" value="0.000000" />
-	<constant name="rx7t_align" value="0.000000" />
-	<constant name="rx8t_align" value="0.000000" />
-	<constant name="rx9t_align" value="0.000000" />
-	<constant name="rx10t_align" value="0.000000" />
-	<constant name="ry1t_align" value="0.000000" />
-	<constant name="ry2t_align" value="0.000000" />
-	<constant name="ry3t_align" value="0.000000" />
-	<constant name="ry4t_align" value="0.000000" />
-	<constant name="ry5t_align" value="0.000000" />
-	<constant name="ry6t_align" value="0.000000" />
-	<constant name="ry7t_align" value="0.000000" />
-	<constant name="ry8t_align" value="0.000000" />
-	<constant name="ry9t_align" value="0.000000" />
-	<constant name="ry10t_align" value="0.000000" />
-	<constant name="rz1t_align" value="-0.000000" />
-	<constant name="rz2t_align" value="0.000000" />
-	<constant name="rz3t_align" value="-0.000000" />
-	<constant name="rz4t_align" value="0.000000" />
-	<constant name="rz5t_align" value="-0.000000" />
-	<constant name="rz6t_align" value="0.000000" />
-	<constant name="rz7t_align" value="-0.000000" />
-	<constant name="rz8t_align" value="0.000000" />
-	<constant name="rz9t_align" value="-0.000000" />
-	<constant name="rz10t_align" value="0.000000" />
-	<constant name="x1b_align" value="0.000000" />
-	<constant name="x2b_align" value="0.000000" />
-	<constant name="x3b_align" value="0.008443" />
-	<constant name="x4b_align" value="-0.000012" />
-	<constant name="x5b_align" value="0.004437" />
-	<constant name="x6b_align" value="-0.000010" />
-	<constant name="x7b_align" value="0.000000" />
-	<constant name="x8b_align" value="0.000000" />
-	<constant name="x9b_align" value="0.000000" />
-	<constant name="x10b_align" value="0.000000" />
-	<constant name="y1b_align" value="0.000000" />
-	<constant name="y2b_align" value="0.000000" />
-	<constant name="y3b_align" value="-0.084138" />
-	<constant name="y4b_align" value="-0.061835" />
-	<constant name="y5b_align" value="-0.044388" />
-	<constant name="y6b_align" value="-0.032317" />
-	<constant name="y7b_align" value="0.000000" />
-	<constant name="y8b_align" value="0.000000" />
-	<constant name="y9b_align" value="0.000000" />
-	<constant name="y10b_align" value="0.000000" />
-	<constant name="z1b_align" value="0.000000" />
-	<constant name="z2b_align" value="0.000000" />
-	<constant name="z3b_align" value="0.001646" />
-	<constant name="z4b_align" value="0.001377" />
-	<constant name="z5b_align" value="0.000869" />
-	<constant name="z6b_align" value="0.000720" />
-	<constant name="z7b_align" value="0.000000" />
-	<constant name="z8b_align" value="0.000000" />
-	<constant name="z9b_align" value="0.000000" />
-	<constant name="z10b_align" value="0.000000" />
-	<constant name="rx1b_align" value="0.000000" />
-	<constant name="rx2b_align" value="0.000000" />
-	<constant name="rx3b_align" value="0.000000" />
-	<constant name="rx4b_align" value="0.000000" />
-	<constant name="rx5b_align" value="0.000000" />
-	<constant name="rx6b_align" value="0.000000" />
-	<constant name="rx7b_align" value="0.000000" />
-	<constant name="rx8b_align" value="0.000000" />
-	<constant name="rx9b_align" value="0.000000" />
-	<constant name="rx10b_align" value="0.000000" />
-	<constant name="ry1b_align" value="0.000000" />
-	<constant name="ry2b_align" value="0.000000" />
-	<constant name="ry3b_align" value="0.000000" />
-	<constant name="ry4b_align" value="0.000000" />
-	<constant name="ry5b_align" value="0.000000" />
-	<constant name="ry6b_align" value="0.000000" />
-	<constant name="ry7b_align" value="0.000000" />
-	<constant name="ry8b_align" value="0.000000" />
-	<constant name="ry9b_align" value="0.000000" />
-	<constant name="ry10b_align" value="0.000000" />
-	<constant name="rz1b_align" value="0.000000" />
-	<constant name="rz2b_align" value="0.000000" />
-	<constant name="rz3b_align" value="0.000000" />
-	<constant name="rz4b_align" value="0.000000" />
-	<constant name="rz5b_align" value="0.000000" />
-	<constant name="rz6b_align" value="0.000000" />
-	<constant name="rz7b_align" value="0.000000" />
-	<constant name="rz8b_align" value="0.000000" />
-	<constant name="rz9b_align" value="0.000000" />
-	<constant name="rz10b_align" value="0.000000" />
+        <!-- alignment corrections -->
+    <constant name="x1t_align" value="0.000000" />
+    <constant name="x2t_align" value="0.000000" />
+    <constant name="x3t_align" value="0.000014" />
+    <constant name="x4t_align" value="0.015024" />
+    <constant name="x5t_align" value="0.000045" />
+    <constant name="x6t_align" value="-0.003411" />
+    <constant name="x7t_align" value="0.000000" />
+    <constant name="x8t_align" value="0.000000" />
+    <constant name="x9t_align" value="0.000000" />
+    <constant name="x10t_align" value="0.000000" />
+    <constant name="y1t_align" value="0.000000" />
+    <constant name="y2t_align" value="0.000000" />
+    <constant name="y3t_align" value="0.112932" />
+    <constant name="y4t_align" value="0.149860" />
+    <constant name="y5t_align" value="-0.082467" />
+    <constant name="y6t_align" value="-0.033966" />
+    <constant name="y7t_align" value="0.000000" />
+    <constant name="y8t_align" value="0.000000" />
+    <constant name="y9t_align" value="0.000000" />
+    <constant name="y10t_align" value="0.000000" />
+    <constant name="z1t_align" value="-0.000000" />
+    <constant name="z2t_align" value="0.000000" />
+    <constant name="z3t_align" value="0.002938" />
+    <constant name="z4t_align" value="0.003424" />
+    <constant name="z5t_align" value="-0.002147" />
+    <constant name="z6t_align" value="-0.000776" />
+    <constant name="z7t_align" value="-0.000000" />
+    <constant name="z8t_align" value="0.000000" />
+    <constant name="z9t_align" value="-0.000000" />
+    <constant name="z10t_align" value="0.000000" />
+    <constant name="rx1t_align" value="0.000000" />
+    <constant name="rx2t_align" value="0.000000" />
+    <constant name="rx3t_align" value="0.000000" />
+    <constant name="rx4t_align" value="0.000000" />
+    <constant name="rx5t_align" value="0.000000" />
+    <constant name="rx6t_align" value="0.000000" />
+    <constant name="rx7t_align" value="0.000000" />
+    <constant name="rx8t_align" value="0.000000" />
+    <constant name="rx9t_align" value="0.000000" />
+    <constant name="rx10t_align" value="0.000000" />
+    <constant name="ry1t_align" value="0.000000" />
+    <constant name="ry2t_align" value="0.000000" />
+    <constant name="ry3t_align" value="0.000000" />
+    <constant name="ry4t_align" value="0.000000" />
+    <constant name="ry5t_align" value="0.000000" />
+    <constant name="ry6t_align" value="0.000000" />
+    <constant name="ry7t_align" value="0.000000" />
+    <constant name="ry8t_align" value="0.000000" />
+    <constant name="ry9t_align" value="0.000000" />
+    <constant name="ry10t_align" value="0.000000" />
+    <constant name="rz1t_align" value="-0.000000" />
+    <constant name="rz2t_align" value="0.000000" />
+    <constant name="rz3t_align" value="-0.000000" />
+    <constant name="rz4t_align" value="0.000000" />
+    <constant name="rz5t_align" value="-0.000000" />
+    <constant name="rz6t_align" value="0.000000" />
+    <constant name="rz7t_align" value="-0.000000" />
+    <constant name="rz8t_align" value="0.000000" />
+    <constant name="rz9t_align" value="-0.000000" />
+    <constant name="rz10t_align" value="0.000000" />
+    <constant name="x1b_align" value="0.000000" />
+    <constant name="x2b_align" value="0.000000" />
+    <constant name="x3b_align" value="0.008443" />
+    <constant name="x4b_align" value="-0.000012" />
+    <constant name="x5b_align" value="0.004437" />
+    <constant name="x6b_align" value="-0.000010" />
+    <constant name="x7b_align" value="0.000000" />
+    <constant name="x8b_align" value="0.000000" />
+    <constant name="x9b_align" value="0.000000" />
+    <constant name="x10b_align" value="0.000000" />
+    <constant name="y1b_align" value="0.000000" />
+    <constant name="y2b_align" value="0.000000" />
+    <constant name="y3b_align" value="-0.084138" />
+    <constant name="y4b_align" value="-0.061835" />
+    <constant name="y5b_align" value="-0.044388" />
+    <constant name="y6b_align" value="-0.032317" />
+    <constant name="y7b_align" value="0.000000" />
+    <constant name="y8b_align" value="0.000000" />
+    <constant name="y9b_align" value="0.000000" />
+    <constant name="y10b_align" value="0.000000" />
+    <constant name="z1b_align" value="0.000000" />
+    <constant name="z2b_align" value="0.000000" />
+    <constant name="z3b_align" value="0.001646" />
+    <constant name="z4b_align" value="0.001377" />
+    <constant name="z5b_align" value="0.000869" />
+    <constant name="z6b_align" value="0.000720" />
+    <constant name="z7b_align" value="0.000000" />
+    <constant name="z8b_align" value="0.000000" />
+    <constant name="z9b_align" value="0.000000" />
+    <constant name="z10b_align" value="0.000000" />
+    <constant name="rx1b_align" value="0.000000" />
+    <constant name="rx2b_align" value="0.000000" />
+    <constant name="rx3b_align" value="0.000000" />
+    <constant name="rx4b_align" value="0.000000" />
+    <constant name="rx5b_align" value="0.000000" />
+    <constant name="rx6b_align" value="0.000000" />
+    <constant name="rx7b_align" value="0.000000" />
+    <constant name="rx8b_align" value="0.000000" />
+    <constant name="rx9b_align" value="0.000000" />
+    <constant name="rx10b_align" value="0.000000" />
+    <constant name="ry1b_align" value="0.000000" />
+    <constant name="ry2b_align" value="0.000000" />
+    <constant name="ry3b_align" value="0.000000" />
+    <constant name="ry4b_align" value="0.000000" />
+    <constant name="ry5b_align" value="0.000000" />
+    <constant name="ry6b_align" value="0.000000" />
+    <constant name="ry7b_align" value="0.000000" />
+    <constant name="ry8b_align" value="0.000000" />
+    <constant name="ry9b_align" value="0.000000" />
+    <constant name="ry10b_align" value="0.000000" />
+    <constant name="rz1b_align" value="0.000000" />
+    <constant name="rz2b_align" value="0.000000" />
+    <constant name="rz3b_align" value="0.000000" />
+    <constant name="rz4b_align" value="0.000000" />
+    <constant name="rz5b_align" value="0.000000" />
+    <constant name="rz6b_align" value="0.000000" />
+    <constant name="rz7b_align" value="0.000000" />
+    <constant name="rz8b_align" value="0.000000" />
+    <constant name="rz9b_align" value="0.000000" />
+    <constant name="rz10b_align" value="0.000000" />
 
         <!-- Positions of sensor centers above/below nominal beam -->
         <constant name="y1t" value="36.894" />
@@ -585,134 +585,134 @@
         <constant name="mod2_rx10b" value="mod_rx10b" />
         <constant name="mod2_ry10b" value="mod_ry10b+y_rot_bot_pivot" />
         <constant name="mod2_rz10b" value="mod_rz10b" />
-    	
-    	<!-- final constants -->
-	<constant name="final_x1t" value="mod2_x1t+x1t_align" />
-	<constant name="final_x2t" value="mod2_x2t+x2t_align" />
-	<constant name="final_x3t" value="mod2_x3t+x3t_align" />
-	<constant name="final_x4t" value="mod2_x4t+x4t_align" />
-	<constant name="final_x5t" value="mod2_x5t+x5t_align" />
-	<constant name="final_x6t" value="mod2_x6t+x6t_align" />
-	<constant name="final_x7t" value="mod2_x7t+x7t_align" />
-	<constant name="final_x8t" value="mod2_x8t+x8t_align" />
-	<constant name="final_x9t" value="mod2_x9t+x9t_align" />
-	<constant name="final_x10t" value="mod2_x10t+x10t_align" />
-	<constant name="final_y1t" value="mod2_y1t+y1t_align" />
-	<constant name="final_y2t" value="mod2_y2t+y2t_align" />
-	<constant name="final_y3t" value="mod2_y3t+y3t_align" />
-	<constant name="final_y4t" value="mod2_y4t+y4t_align" />
-	<constant name="final_y5t" value="mod2_y5t+y5t_align" />
-	<constant name="final_y6t" value="mod2_y6t+y6t_align" />
-	<constant name="final_y7t" value="mod2_y7t+y7t_align" />
-	<constant name="final_y8t" value="mod2_y8t+y8t_align" />
-	<constant name="final_y9t" value="mod2_y9t+y9t_align" />
-	<constant name="final_y10t" value="mod2_y10t+y10t_align" />
-	<constant name="final_z1t" value="mod2_z1t+z1t_align" />
-	<constant name="final_z2t" value="mod2_z2t+z2t_align" />
-	<constant name="final_z3t" value="mod2_z3t+z3t_align" />
-	<constant name="final_z4t" value="mod2_z4t+z4t_align" />
-	<constant name="final_z5t" value="mod2_z5t+z5t_align" />
-	<constant name="final_z6t" value="mod2_z6t+z6t_align" />
-	<constant name="final_z7t" value="mod2_z7t+z7t_align" />
-	<constant name="final_z8t" value="mod2_z8t+z8t_align" />
-	<constant name="final_z9t" value="mod2_z9t+z9t_align" />
-	<constant name="final_z10t" value="mod2_z10t+z10t_align" />
-	<constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
-	<constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
-	<constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
-	<constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
-	<constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
-	<constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
-	<constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
-	<constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
-	<constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
-	<constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
-	<constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
-	<constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
-	<constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
-	<constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
-	<constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
-	<constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
-	<constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
-	<constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
-	<constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
-	<constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
-	<constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
-	<constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
-	<constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
-	<constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
-	<constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
-	<constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
-	<constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
-	<constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
-	<constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
-	<constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
-	<constant name="final_x1b" value="mod2_x1b+x1b_align" />
-	<constant name="final_x2b" value="mod2_x2b+x2b_align" />
-	<constant name="final_x3b" value="mod2_x3b+x3b_align" />
-	<constant name="final_x4b" value="mod2_x4b+x4b_align" />
-	<constant name="final_x5b" value="mod2_x5b+x5b_align" />
-	<constant name="final_x6b" value="mod2_x6b+x6b_align" />
-	<constant name="final_x7b" value="mod2_x7b+x7b_align" />
-	<constant name="final_x8b" value="mod2_x8b+x8b_align" />
-	<constant name="final_x9b" value="mod2_x9b+x9b_align" />
-	<constant name="final_x10b" value="mod2_x10b+x10b_align" />
-	<constant name="final_y1b" value="mod2_y1b+y1b_align" />
-	<constant name="final_y2b" value="mod2_y2b+y2b_align" />
-	<constant name="final_y3b" value="mod2_y3b+y3b_align" />
-	<constant name="final_y4b" value="mod2_y4b+y4b_align" />
-	<constant name="final_y5b" value="mod2_y5b+y5b_align" />
-	<constant name="final_y6b" value="mod2_y6b+y6b_align" />
-	<constant name="final_y7b" value="mod2_y7b+y7b_align" />
-	<constant name="final_y8b" value="mod2_y8b+y8b_align" />
-	<constant name="final_y9b" value="mod2_y9b+y9b_align" />
-	<constant name="final_y10b" value="mod2_y10b+y10b_align" />
-	<constant name="final_z1b" value="mod2_z1b+z1b_align" />
-	<constant name="final_z2b" value="mod2_z2b+z2b_align" />
-	<constant name="final_z3b" value="mod2_z3b+z3b_align" />
-	<constant name="final_z4b" value="mod2_z4b+z4b_align" />
-	<constant name="final_z5b" value="mod2_z5b+z5b_align" />
-	<constant name="final_z6b" value="mod2_z6b+z6b_align" />
-	<constant name="final_z7b" value="mod2_z7b+z7b_align" />
-	<constant name="final_z8b" value="mod2_z8b+z8b_align" />
-	<constant name="final_z9b" value="mod2_z9b+z9b_align" />
-	<constant name="final_z10b" value="mod2_z10b+z10b_align" />
-	<constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
-	<constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
-	<constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
-	<constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
-	<constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
-	<constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
-	<constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
-	<constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
-	<constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
-	<constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
-	<constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
-	<constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
-	<constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
-	<constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
-	<constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
-	<constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
-	<constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
-	<constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
-	<constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
-	<constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
-	<constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
-	<constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
-	<constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
-	<constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
-	<constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
-	<constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
-	<constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
-	<constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
-	<constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
-	<constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
-    	
-    	
+        
+        <!-- final constants -->
+    <constant name="final_x1t" value="mod2_x1t+x1t_align" />
+    <constant name="final_x2t" value="mod2_x2t+x2t_align" />
+    <constant name="final_x3t" value="mod2_x3t+x3t_align" />
+    <constant name="final_x4t" value="mod2_x4t+x4t_align" />
+    <constant name="final_x5t" value="mod2_x5t+x5t_align" />
+    <constant name="final_x6t" value="mod2_x6t+x6t_align" />
+    <constant name="final_x7t" value="mod2_x7t+x7t_align" />
+    <constant name="final_x8t" value="mod2_x8t+x8t_align" />
+    <constant name="final_x9t" value="mod2_x9t+x9t_align" />
+    <constant name="final_x10t" value="mod2_x10t+x10t_align" />
+    <constant name="final_y1t" value="mod2_y1t+y1t_align" />
+    <constant name="final_y2t" value="mod2_y2t+y2t_align" />
+    <constant name="final_y3t" value="mod2_y3t+y3t_align" />
+    <constant name="final_y4t" value="mod2_y4t+y4t_align" />
+    <constant name="final_y5t" value="mod2_y5t+y5t_align" />
+    <constant name="final_y6t" value="mod2_y6t+y6t_align" />
+    <constant name="final_y7t" value="mod2_y7t+y7t_align" />
+    <constant name="final_y8t" value="mod2_y8t+y8t_align" />
+    <constant name="final_y9t" value="mod2_y9t+y9t_align" />
+    <constant name="final_y10t" value="mod2_y10t+y10t_align" />
+    <constant name="final_z1t" value="mod2_z1t+z1t_align" />
+    <constant name="final_z2t" value="mod2_z2t+z2t_align" />
+    <constant name="final_z3t" value="mod2_z3t+z3t_align" />
+    <constant name="final_z4t" value="mod2_z4t+z4t_align" />
+    <constant name="final_z5t" value="mod2_z5t+z5t_align" />
+    <constant name="final_z6t" value="mod2_z6t+z6t_align" />
+    <constant name="final_z7t" value="mod2_z7t+z7t_align" />
+    <constant name="final_z8t" value="mod2_z8t+z8t_align" />
+    <constant name="final_z9t" value="mod2_z9t+z9t_align" />
+    <constant name="final_z10t" value="mod2_z10t+z10t_align" />
+    <constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
+    <constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
+    <constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
+    <constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
+    <constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
+    <constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
+    <constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
+    <constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
+    <constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
+    <constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
+    <constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
+    <constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
+    <constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
+    <constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
+    <constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
+    <constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
+    <constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
+    <constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
+    <constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
+    <constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
+    <constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
+    <constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
+    <constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
+    <constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
+    <constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
+    <constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
+    <constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
+    <constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
+    <constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
+    <constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
+    <constant name="final_x1b" value="mod2_x1b+x1b_align" />
+    <constant name="final_x2b" value="mod2_x2b+x2b_align" />
+    <constant name="final_x3b" value="mod2_x3b+x3b_align" />
+    <constant name="final_x4b" value="mod2_x4b+x4b_align" />
+    <constant name="final_x5b" value="mod2_x5b+x5b_align" />
+    <constant name="final_x6b" value="mod2_x6b+x6b_align" />
+    <constant name="final_x7b" value="mod2_x7b+x7b_align" />
+    <constant name="final_x8b" value="mod2_x8b+x8b_align" />
+    <constant name="final_x9b" value="mod2_x9b+x9b_align" />
+    <constant name="final_x10b" value="mod2_x10b+x10b_align" />
+    <constant name="final_y1b" value="mod2_y1b+y1b_align" />
+    <constant name="final_y2b" value="mod2_y2b+y2b_align" />
+    <constant name="final_y3b" value="mod2_y3b+y3b_align" />
+    <constant name="final_y4b" value="mod2_y4b+y4b_align" />
+    <constant name="final_y5b" value="mod2_y5b+y5b_align" />
+    <constant name="final_y6b" value="mod2_y6b+y6b_align" />
+    <constant name="final_y7b" value="mod2_y7b+y7b_align" />
+    <constant name="final_y8b" value="mod2_y8b+y8b_align" />
+    <constant name="final_y9b" value="mod2_y9b+y9b_align" />
+    <constant name="final_y10b" value="mod2_y10b+y10b_align" />
+    <constant name="final_z1b" value="mod2_z1b+z1b_align" />
+    <constant name="final_z2b" value="mod2_z2b+z2b_align" />
+    <constant name="final_z3b" value="mod2_z3b+z3b_align" />
+    <constant name="final_z4b" value="mod2_z4b+z4b_align" />
+    <constant name="final_z5b" value="mod2_z5b+z5b_align" />
+    <constant name="final_z6b" value="mod2_z6b+z6b_align" />
+    <constant name="final_z7b" value="mod2_z7b+z7b_align" />
+    <constant name="final_z8b" value="mod2_z8b+z8b_align" />
+    <constant name="final_z9b" value="mod2_z9b+z9b_align" />
+    <constant name="final_z10b" value="mod2_z10b+z10b_align" />
+    <constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
+    <constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
+    <constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
+    <constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
+    <constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
+    <constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
+    <constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
+    <constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
+    <constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
+    <constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
+    <constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
+    <constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
+    <constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
+    <constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
+    <constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
+    <constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
+    <constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
+    <constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
+    <constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
+    <constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
+    <constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
+    <constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
+    <constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
+    <constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
+    <constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
+    <constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
+    <constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
+    <constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
+    <constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
+    <constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
+        
+        
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001" />
             <fraction n="1.0" ref="Vacuum" />
@@ -801,7 +801,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2" />
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-5/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-5/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8-5/compact.xml	Wed Apr 27 11:11:32 2016
@@ -3,9 +3,9 @@
     
     <info name="HPS-TestRun-v8-5">
         <comment>
-	  HPS JLab Test Run detector with dipole field starting at z=0
-	  Based on millepede-u3-6-float-then-u7-8float-then-u3-6-float-then-u1-2-float-then-u3-6-float-then-u9-10-float-then-u7-10-float-then-u3-6-float-then-u1-4-float-then-u9-10-float-1351-v8-10k.res.txt
-	</comment>
+      HPS JLab Test Run detector with dipole field starting at z=0
+      Based on millepede-u3-6-float-then-u7-8float-then-u3-6-float-then-u1-2-float-then-u3-6-float-then-u9-10-float-then-u7-10-float-then-u3-6-float-then-u1-4-float-then-u9-10-float-1351-v8-10k.res.txt
+    </comment>
     </info>
 
     <define>
@@ -65,127 +65,127 @@
 <!--        <constant name="x_off" value = "-15.0"/> -->
         <constant name="x_off" value="0.0" /> 
 
-		<!-- alignment corrections -->
-	<constant name="x1t_align" value="0.000000" />
-	<constant name="x2t_align" value="0.000338" />
-	<constant name="x3t_align" value="0.000013" />
-	<constant name="x4t_align" value="0.014360" />
-	<constant name="x5t_align" value="0.000051" />
-	<constant name="x6t_align" value="-0.004610" />
-	<constant name="x7t_align" value="-0.000000" />
-	<constant name="x8t_align" value="-0.000200" />
-	<constant name="x9t_align" value="0.000023" />
-	<constant name="x10t_align" value="0.003314" />
-	<constant name="y1t_align" value="0.003643" />
-	<constant name="y2t_align" value="0.003372" />
-	<constant name="y3t_align" value="0.106214" />
-	<constant name="y4t_align" value="0.143235" />
-	<constant name="y5t_align" value="-0.094779" />
-	<constant name="y6t_align" value="-0.045906" />
-	<constant name="y7t_align" value="-0.004270" />
-	<constant name="y8t_align" value="-0.004014" />
-	<constant name="y9t_align" value="0.069062" />
-	<constant name="y10t_align" value="0.066775" />
-	<constant name="z1t_align" value="0.000095" />
-	<constant name="z2t_align" value="0.000077" />
-	<constant name="z3t_align" value="0.002763" />
-	<constant name="z4t_align" value="0.003273" />
-	<constant name="z5t_align" value="-0.002467" />
-	<constant name="z6t_align" value="-0.001049" />
-	<constant name="z7t_align" value="-0.000111" />
-	<constant name="z8t_align" value="-0.000098" />
-	<constant name="z9t_align" value="0.001796" />
-	<constant name="z10t_align" value="0.001633" />
-	<constant name="rx1t_align" value="0.000000" />
-	<constant name="rx2t_align" value="0.000000" />
-	<constant name="rx3t_align" value="0.000000" />
-	<constant name="rx4t_align" value="0.000000" />
-	<constant name="rx5t_align" value="0.000000" />
-	<constant name="rx6t_align" value="0.000000" />
-	<constant name="rx7t_align" value="0.000000" />
-	<constant name="rx8t_align" value="0.000000" />
-	<constant name="rx9t_align" value="0.000000" />
-	<constant name="rx10t_align" value="0.000000" />
-	<constant name="ry1t_align" value="0.000000" />
-	<constant name="ry2t_align" value="0.000000" />
-	<constant name="ry3t_align" value="0.000000" />
-	<constant name="ry4t_align" value="0.000000" />
-	<constant name="ry5t_align" value="0.000000" />
-	<constant name="ry6t_align" value="0.000000" />
-	<constant name="ry7t_align" value="0.000000" />
-	<constant name="ry8t_align" value="0.000000" />
-	<constant name="ry9t_align" value="0.000000" />
-	<constant name="ry10t_align" value="0.000000" />
-	<constant name="rz1t_align" value="-0.000000" />
-	<constant name="rz2t_align" value="0.000000" />
-	<constant name="rz3t_align" value="-0.000000" />
-	<constant name="rz4t_align" value="0.000000" />
-	<constant name="rz5t_align" value="-0.000000" />
-	<constant name="rz6t_align" value="0.000000" />
-	<constant name="rz7t_align" value="-0.000000" />
-	<constant name="rz8t_align" value="0.000000" />
-	<constant name="rz9t_align" value="-0.000000" />
-	<constant name="rz10t_align" value="0.000000" />
-	<constant name="x1b_align" value="-0.000240" />
-	<constant name="x2b_align" value="0.000001" />
-	<constant name="x3b_align" value="0.008881" />
-	<constant name="x4b_align" value="-0.000013" />
-	<constant name="x5b_align" value="0.005242" />
-	<constant name="x6b_align" value="-0.000013" />
-	<constant name="x7b_align" value="0.000171" />
-	<constant name="x8b_align" value="-0.000002" />
-	<constant name="x9b_align" value="-0.002390" />
-	<constant name="x10b_align" value="0.000002" />
-	<constant name="y1b_align" value="0.002386" />
-	<constant name="y2b_align" value="0.002507" />
-	<constant name="y3b_align" value="-0.088503" />
-	<constant name="y4b_align" value="-0.066488" />
-	<constant name="y5b_align" value="-0.052443" />
-	<constant name="y6b_align" value="-0.040809" />
-	<constant name="y7b_align" value="-0.003389" />
-	<constant name="y8b_align" value="-0.003634" />
-	<constant name="y9b_align" value="0.047254" />
-	<constant name="y10b_align" value="0.047194" />
-	<constant name="z1b_align" value="-0.000047" />
-	<constant name="z2b_align" value="-0.000056" />
-	<constant name="z3b_align" value="0.001731" />
-	<constant name="z4b_align" value="0.001481" />
-	<constant name="z5b_align" value="0.001026" />
-	<constant name="z6b_align" value="0.000909" />
-	<constant name="z7b_align" value="0.000071" />
-	<constant name="z8b_align" value="0.000081" />
-	<constant name="z9b_align" value="-0.000988" />
-	<constant name="z10b_align" value="-0.001051" />
-	<constant name="rx1b_align" value="0.000000" />
-	<constant name="rx2b_align" value="0.000000" />
-	<constant name="rx3b_align" value="0.000000" />
-	<constant name="rx4b_align" value="0.000000" />
-	<constant name="rx5b_align" value="0.000000" />
-	<constant name="rx6b_align" value="0.000000" />
-	<constant name="rx7b_align" value="0.000000" />
-	<constant name="rx8b_align" value="0.000000" />
-	<constant name="rx9b_align" value="0.000000" />
-	<constant name="rx10b_align" value="0.000000" />
-	<constant name="ry1b_align" value="0.000000" />
-	<constant name="ry2b_align" value="0.000000" />
-	<constant name="ry3b_align" value="0.000000" />
-	<constant name="ry4b_align" value="0.000000" />
-	<constant name="ry5b_align" value="0.000000" />
-	<constant name="ry6b_align" value="0.000000" />
-	<constant name="ry7b_align" value="0.000000" />
-	<constant name="ry8b_align" value="0.000000" />
-	<constant name="ry9b_align" value="0.000000" />
-	<constant name="ry10b_align" value="0.000000" />
-	<constant name="rz1b_align" value="0.000000" />
-	<constant name="rz2b_align" value="0.000000" />
-	<constant name="rz3b_align" value="0.000000" />
-	<constant name="rz4b_align" value="0.000000" />
-	<constant name="rz5b_align" value="0.000000" />
-	<constant name="rz6b_align" value="0.000000" />
-	<constant name="rz7b_align" value="0.000000" />
-	<constant name="rz8b_align" value="0.000000" />
-	<constant name="rz9b_align" value="0.000000" />
-	<constant name="rz10b_align" value="0.000000" />
+        <!-- alignment corrections -->
+    <constant name="x1t_align" value="0.000000" />
+    <constant name="x2t_align" value="0.000338" />
+    <constant name="x3t_align" value="0.000013" />
+    <constant name="x4t_align" value="0.014360" />
+    <constant name="x5t_align" value="0.000051" />
+    <constant name="x6t_align" value="-0.004610" />
+    <constant name="x7t_align" value="-0.000000" />
+    <constant name="x8t_align" value="-0.000200" />
+    <constant name="x9t_align" value="0.000023" />
+    <constant name="x10t_align" value="0.003314" />
+    <constant name="y1t_align" value="0.003643" />
+    <constant name="y2t_align" value="0.003372" />
+    <constant name="y3t_align" value="0.106214" />
+    <constant name="y4t_align" value="0.143235" />
+    <constant name="y5t_align" value="-0.094779" />
+    <constant name="y6t_align" value="-0.045906" />
+    <constant name="y7t_align" value="-0.004270" />
+    <constant name="y8t_align" value="-0.004014" />
+    <constant name="y9t_align" value="0.069062" />
+    <constant name="y10t_align" value="0.066775" />
+    <constant name="z1t_align" value="0.000095" />
+    <constant name="z2t_align" value="0.000077" />
+    <constant name="z3t_align" value="0.002763" />
+    <constant name="z4t_align" value="0.003273" />
+    <constant name="z5t_align" value="-0.002467" />
+    <constant name="z6t_align" value="-0.001049" />
+    <constant name="z7t_align" value="-0.000111" />
+    <constant name="z8t_align" value="-0.000098" />
+    <constant name="z9t_align" value="0.001796" />
+    <constant name="z10t_align" value="0.001633" />
+    <constant name="rx1t_align" value="0.000000" />
+    <constant name="rx2t_align" value="0.000000" />
+    <constant name="rx3t_align" value="0.000000" />
+    <constant name="rx4t_align" value="0.000000" />
+    <constant name="rx5t_align" value="0.000000" />
+    <constant name="rx6t_align" value="0.000000" />
+    <constant name="rx7t_align" value="0.000000" />
+    <constant name="rx8t_align" value="0.000000" />
+    <constant name="rx9t_align" value="0.000000" />
+    <constant name="rx10t_align" value="0.000000" />
+    <constant name="ry1t_align" value="0.000000" />
+    <constant name="ry2t_align" value="0.000000" />
+    <constant name="ry3t_align" value="0.000000" />
+    <constant name="ry4t_align" value="0.000000" />
+    <constant name="ry5t_align" value="0.000000" />
+    <constant name="ry6t_align" value="0.000000" />
+    <constant name="ry7t_align" value="0.000000" />
+    <constant name="ry8t_align" value="0.000000" />
+    <constant name="ry9t_align" value="0.000000" />
+    <constant name="ry10t_align" value="0.000000" />
+    <constant name="rz1t_align" value="-0.000000" />
+    <constant name="rz2t_align" value="0.000000" />
+    <constant name="rz3t_align" value="-0.000000" />
+    <constant name="rz4t_align" value="0.000000" />
+    <constant name="rz5t_align" value="-0.000000" />
+    <constant name="rz6t_align" value="0.000000" />
+    <constant name="rz7t_align" value="-0.000000" />
+    <constant name="rz8t_align" value="0.000000" />
+    <constant name="rz9t_align" value="-0.000000" />
+    <constant name="rz10t_align" value="0.000000" />
+    <constant name="x1b_align" value="-0.000240" />
+    <constant name="x2b_align" value="0.000001" />
+    <constant name="x3b_align" value="0.008881" />
+    <constant name="x4b_align" value="-0.000013" />
+    <constant name="x5b_align" value="0.005242" />
+    <constant name="x6b_align" value="-0.000013" />
+    <constant name="x7b_align" value="0.000171" />
+    <constant name="x8b_align" value="-0.000002" />
+    <constant name="x9b_align" value="-0.002390" />
+    <constant name="x10b_align" value="0.000002" />
+    <constant name="y1b_align" value="0.002386" />
+    <constant name="y2b_align" value="0.002507" />
+    <constant name="y3b_align" value="-0.088503" />
+    <constant name="y4b_align" value="-0.066488" />
+    <constant name="y5b_align" value="-0.052443" />
+    <constant name="y6b_align" value="-0.040809" />
+    <constant name="y7b_align" value="-0.003389" />
+    <constant name="y8b_align" value="-0.003634" />
+    <constant name="y9b_align" value="0.047254" />
+    <constant name="y10b_align" value="0.047194" />
+    <constant name="z1b_align" value="-0.000047" />
+    <constant name="z2b_align" value="-0.000056" />
+    <constant name="z3b_align" value="0.001731" />
+    <constant name="z4b_align" value="0.001481" />
+    <constant name="z5b_align" value="0.001026" />
+    <constant name="z6b_align" value="0.000909" />
+    <constant name="z7b_align" value="0.000071" />
+    <constant name="z8b_align" value="0.000081" />
+    <constant name="z9b_align" value="-0.000988" />
+    <constant name="z10b_align" value="-0.001051" />
+    <constant name="rx1b_align" value="0.000000" />
+    <constant name="rx2b_align" value="0.000000" />
+    <constant name="rx3b_align" value="0.000000" />
+    <constant name="rx4b_align" value="0.000000" />
+    <constant name="rx5b_align" value="0.000000" />
+    <constant name="rx6b_align" value="0.000000" />
+    <constant name="rx7b_align" value="0.000000" />
+    <constant name="rx8b_align" value="0.000000" />
+    <constant name="rx9b_align" value="0.000000" />
+    <constant name="rx10b_align" value="0.000000" />
+    <constant name="ry1b_align" value="0.000000" />
+    <constant name="ry2b_align" value="0.000000" />
+    <constant name="ry3b_align" value="0.000000" />
+    <constant name="ry4b_align" value="0.000000" />
+    <constant name="ry5b_align" value="0.000000" />
+    <constant name="ry6b_align" value="0.000000" />
+    <constant name="ry7b_align" value="0.000000" />
+    <constant name="ry8b_align" value="0.000000" />
+    <constant name="ry9b_align" value="0.000000" />
+    <constant name="ry10b_align" value="0.000000" />
+    <constant name="rz1b_align" value="0.000000" />
+    <constant name="rz2b_align" value="0.000000" />
+    <constant name="rz3b_align" value="0.000000" />
+    <constant name="rz4b_align" value="0.000000" />
+    <constant name="rz5b_align" value="0.000000" />
+    <constant name="rz6b_align" value="0.000000" />
+    <constant name="rz7b_align" value="0.000000" />
+    <constant name="rz8b_align" value="0.000000" />
+    <constant name="rz9b_align" value="0.000000" />
+    <constant name="rz10b_align" value="0.000000" />
 
         <!-- Positions of sensor centers above/below nominal beam -->
         <constant name="y1t" value="36.894" />
@@ -585,134 +585,134 @@
         <constant name="mod2_rx10b" value="mod_rx10b" />
         <constant name="mod2_ry10b" value="mod_ry10b+y_rot_bot_pivot" />
         <constant name="mod2_rz10b" value="mod_rz10b" />
-    	
-    	<!-- final constants -->
-	<constant name="final_x1t" value="mod2_x1t+x1t_align" />
-	<constant name="final_x2t" value="mod2_x2t+x2t_align" />
-	<constant name="final_x3t" value="mod2_x3t+x3t_align" />
-	<constant name="final_x4t" value="mod2_x4t+x4t_align" />
-	<constant name="final_x5t" value="mod2_x5t+x5t_align" />
-	<constant name="final_x6t" value="mod2_x6t+x6t_align" />
-	<constant name="final_x7t" value="mod2_x7t+x7t_align" />
-	<constant name="final_x8t" value="mod2_x8t+x8t_align" />
-	<constant name="final_x9t" value="mod2_x9t+x9t_align" />
-	<constant name="final_x10t" value="mod2_x10t+x10t_align" />
-	<constant name="final_y1t" value="mod2_y1t+y1t_align" />
-	<constant name="final_y2t" value="mod2_y2t+y2t_align" />
-	<constant name="final_y3t" value="mod2_y3t+y3t_align" />
-	<constant name="final_y4t" value="mod2_y4t+y4t_align" />
-	<constant name="final_y5t" value="mod2_y5t+y5t_align" />
-	<constant name="final_y6t" value="mod2_y6t+y6t_align" />
-	<constant name="final_y7t" value="mod2_y7t+y7t_align" />
-	<constant name="final_y8t" value="mod2_y8t+y8t_align" />
-	<constant name="final_y9t" value="mod2_y9t+y9t_align" />
-	<constant name="final_y10t" value="mod2_y10t+y10t_align" />
-	<constant name="final_z1t" value="mod2_z1t+z1t_align" />
-	<constant name="final_z2t" value="mod2_z2t+z2t_align" />
-	<constant name="final_z3t" value="mod2_z3t+z3t_align" />
-	<constant name="final_z4t" value="mod2_z4t+z4t_align" />
-	<constant name="final_z5t" value="mod2_z5t+z5t_align" />
-	<constant name="final_z6t" value="mod2_z6t+z6t_align" />
-	<constant name="final_z7t" value="mod2_z7t+z7t_align" />
-	<constant name="final_z8t" value="mod2_z8t+z8t_align" />
-	<constant name="final_z9t" value="mod2_z9t+z9t_align" />
-	<constant name="final_z10t" value="mod2_z10t+z10t_align" />
-	<constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
-	<constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
-	<constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
-	<constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
-	<constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
-	<constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
-	<constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
-	<constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
-	<constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
-	<constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
-	<constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
-	<constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
-	<constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
-	<constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
-	<constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
-	<constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
-	<constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
-	<constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
-	<constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
-	<constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
-	<constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
-	<constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
-	<constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
-	<constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
-	<constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
-	<constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
-	<constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
-	<constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
-	<constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
-	<constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
-	<constant name="final_x1b" value="mod2_x1b+x1b_align" />
-	<constant name="final_x2b" value="mod2_x2b+x2b_align" />
-	<constant name="final_x3b" value="mod2_x3b+x3b_align" />
-	<constant name="final_x4b" value="mod2_x4b+x4b_align" />
-	<constant name="final_x5b" value="mod2_x5b+x5b_align" />
-	<constant name="final_x6b" value="mod2_x6b+x6b_align" />
-	<constant name="final_x7b" value="mod2_x7b+x7b_align" />
-	<constant name="final_x8b" value="mod2_x8b+x8b_align" />
-	<constant name="final_x9b" value="mod2_x9b+x9b_align" />
-	<constant name="final_x10b" value="mod2_x10b+x10b_align" />
-	<constant name="final_y1b" value="mod2_y1b+y1b_align" />
-	<constant name="final_y2b" value="mod2_y2b+y2b_align" />
-	<constant name="final_y3b" value="mod2_y3b+y3b_align" />
-	<constant name="final_y4b" value="mod2_y4b+y4b_align" />
-	<constant name="final_y5b" value="mod2_y5b+y5b_align" />
-	<constant name="final_y6b" value="mod2_y6b+y6b_align" />
-	<constant name="final_y7b" value="mod2_y7b+y7b_align" />
-	<constant name="final_y8b" value="mod2_y8b+y8b_align" />
-	<constant name="final_y9b" value="mod2_y9b+y9b_align" />
-	<constant name="final_y10b" value="mod2_y10b+y10b_align" />
-	<constant name="final_z1b" value="mod2_z1b+z1b_align" />
-	<constant name="final_z2b" value="mod2_z2b+z2b_align" />
-	<constant name="final_z3b" value="mod2_z3b+z3b_align" />
-	<constant name="final_z4b" value="mod2_z4b+z4b_align" />
-	<constant name="final_z5b" value="mod2_z5b+z5b_align" />
-	<constant name="final_z6b" value="mod2_z6b+z6b_align" />
-	<constant name="final_z7b" value="mod2_z7b+z7b_align" />
-	<constant name="final_z8b" value="mod2_z8b+z8b_align" />
-	<constant name="final_z9b" value="mod2_z9b+z9b_align" />
-	<constant name="final_z10b" value="mod2_z10b+z10b_align" />
-	<constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
-	<constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
-	<constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
-	<constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
-	<constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
-	<constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
-	<constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
-	<constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
-	<constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
-	<constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
-	<constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
-	<constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
-	<constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
-	<constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
-	<constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
-	<constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
-	<constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
-	<constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
-	<constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
-	<constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
-	<constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
-	<constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
-	<constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
-	<constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
-	<constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
-	<constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
-	<constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
-	<constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
-	<constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
-	<constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
-    	
-    	
+        
+        <!-- final constants -->
+    <constant name="final_x1t" value="mod2_x1t+x1t_align" />
+    <constant name="final_x2t" value="mod2_x2t+x2t_align" />
+    <constant name="final_x3t" value="mod2_x3t+x3t_align" />
+    <constant name="final_x4t" value="mod2_x4t+x4t_align" />
+    <constant name="final_x5t" value="mod2_x5t+x5t_align" />
+    <constant name="final_x6t" value="mod2_x6t+x6t_align" />
+    <constant name="final_x7t" value="mod2_x7t+x7t_align" />
+    <constant name="final_x8t" value="mod2_x8t+x8t_align" />
+    <constant name="final_x9t" value="mod2_x9t+x9t_align" />
+    <constant name="final_x10t" value="mod2_x10t+x10t_align" />
+    <constant name="final_y1t" value="mod2_y1t+y1t_align" />
+    <constant name="final_y2t" value="mod2_y2t+y2t_align" />
+    <constant name="final_y3t" value="mod2_y3t+y3t_align" />
+    <constant name="final_y4t" value="mod2_y4t+y4t_align" />
+    <constant name="final_y5t" value="mod2_y5t+y5t_align" />
+    <constant name="final_y6t" value="mod2_y6t+y6t_align" />
+    <constant name="final_y7t" value="mod2_y7t+y7t_align" />
+    <constant name="final_y8t" value="mod2_y8t+y8t_align" />
+    <constant name="final_y9t" value="mod2_y9t+y9t_align" />
+    <constant name="final_y10t" value="mod2_y10t+y10t_align" />
+    <constant name="final_z1t" value="mod2_z1t+z1t_align" />
+    <constant name="final_z2t" value="mod2_z2t+z2t_align" />
+    <constant name="final_z3t" value="mod2_z3t+z3t_align" />
+    <constant name="final_z4t" value="mod2_z4t+z4t_align" />
+    <constant name="final_z5t" value="mod2_z5t+z5t_align" />
+    <constant name="final_z6t" value="mod2_z6t+z6t_align" />
+    <constant name="final_z7t" value="mod2_z7t+z7t_align" />
+    <constant name="final_z8t" value="mod2_z8t+z8t_align" />
+    <constant name="final_z9t" value="mod2_z9t+z9t_align" />
+    <constant name="final_z10t" value="mod2_z10t+z10t_align" />
+    <constant name="final_rx1t" value="mod2_rx1t+rx1t_align" />
+    <constant name="final_rx2t" value="mod2_rx2t+rx2t_align" />
+    <constant name="final_rx3t" value="mod2_rx3t+rx3t_align" />
+    <constant name="final_rx4t" value="mod2_rx4t+rx4t_align" />
+    <constant name="final_rx5t" value="mod2_rx5t+rx5t_align" />
+    <constant name="final_rx6t" value="mod2_rx6t+rx6t_align" />
+    <constant name="final_rx7t" value="mod2_rx7t+rx7t_align" />
+    <constant name="final_rx8t" value="mod2_rx8t+rx8t_align" />
+    <constant name="final_rx9t" value="mod2_rx9t+rx9t_align" />
+    <constant name="final_rx10t" value="mod2_rx10t+rx10t_align" />
+    <constant name="final_ry1t" value="mod2_ry1t+ry1t_align" />
+    <constant name="final_ry2t" value="mod2_ry2t+ry2t_align" />
+    <constant name="final_ry3t" value="mod2_ry3t+ry3t_align" />
+    <constant name="final_ry4t" value="mod2_ry4t+ry4t_align" />
+    <constant name="final_ry5t" value="mod2_ry5t+ry5t_align" />
+    <constant name="final_ry6t" value="mod2_ry6t+ry6t_align" />
+    <constant name="final_ry7t" value="mod2_ry7t+ry7t_align" />
+    <constant name="final_ry8t" value="mod2_ry8t+ry8t_align" />
+    <constant name="final_ry9t" value="mod2_ry9t+ry9t_align" />
+    <constant name="final_ry10t" value="mod2_ry10t+ry10t_align" />
+    <constant name="final_rz1t" value="mod2_rz1t+rz1t_align" />
+    <constant name="final_rz2t" value="mod2_rz2t+rz2t_align" />
+    <constant name="final_rz3t" value="mod2_rz3t+rz3t_align" />
+    <constant name="final_rz4t" value="mod2_rz4t+rz4t_align" />
+    <constant name="final_rz5t" value="mod2_rz5t+rz5t_align" />
+    <constant name="final_rz6t" value="mod2_rz6t+rz6t_align" />
+    <constant name="final_rz7t" value="mod2_rz7t+rz7t_align" />
+    <constant name="final_rz8t" value="mod2_rz8t+rz8t_align" />
+    <constant name="final_rz9t" value="mod2_rz9t+rz9t_align" />
+    <constant name="final_rz10t" value="mod2_rz10t+rz10t_align" />
+    <constant name="final_x1b" value="mod2_x1b+x1b_align" />
+    <constant name="final_x2b" value="mod2_x2b+x2b_align" />
+    <constant name="final_x3b" value="mod2_x3b+x3b_align" />
+    <constant name="final_x4b" value="mod2_x4b+x4b_align" />
+    <constant name="final_x5b" value="mod2_x5b+x5b_align" />
+    <constant name="final_x6b" value="mod2_x6b+x6b_align" />
+    <constant name="final_x7b" value="mod2_x7b+x7b_align" />
+    <constant name="final_x8b" value="mod2_x8b+x8b_align" />
+    <constant name="final_x9b" value="mod2_x9b+x9b_align" />
+    <constant name="final_x10b" value="mod2_x10b+x10b_align" />
+    <constant name="final_y1b" value="mod2_y1b+y1b_align" />
+    <constant name="final_y2b" value="mod2_y2b+y2b_align" />
+    <constant name="final_y3b" value="mod2_y3b+y3b_align" />
+    <constant name="final_y4b" value="mod2_y4b+y4b_align" />
+    <constant name="final_y5b" value="mod2_y5b+y5b_align" />
+    <constant name="final_y6b" value="mod2_y6b+y6b_align" />
+    <constant name="final_y7b" value="mod2_y7b+y7b_align" />
+    <constant name="final_y8b" value="mod2_y8b+y8b_align" />
+    <constant name="final_y9b" value="mod2_y9b+y9b_align" />
+    <constant name="final_y10b" value="mod2_y10b+y10b_align" />
+    <constant name="final_z1b" value="mod2_z1b+z1b_align" />
+    <constant name="final_z2b" value="mod2_z2b+z2b_align" />
+    <constant name="final_z3b" value="mod2_z3b+z3b_align" />
+    <constant name="final_z4b" value="mod2_z4b+z4b_align" />
+    <constant name="final_z5b" value="mod2_z5b+z5b_align" />
+    <constant name="final_z6b" value="mod2_z6b+z6b_align" />
+    <constant name="final_z7b" value="mod2_z7b+z7b_align" />
+    <constant name="final_z8b" value="mod2_z8b+z8b_align" />
+    <constant name="final_z9b" value="mod2_z9b+z9b_align" />
+    <constant name="final_z10b" value="mod2_z10b+z10b_align" />
+    <constant name="final_rx1b" value="mod2_rx1b+rx1b_align" />
+    <constant name="final_rx2b" value="mod2_rx2b+rx2b_align" />
+    <constant name="final_rx3b" value="mod2_rx3b+rx3b_align" />
+    <constant name="final_rx4b" value="mod2_rx4b+rx4b_align" />
+    <constant name="final_rx5b" value="mod2_rx5b+rx5b_align" />
+    <constant name="final_rx6b" value="mod2_rx6b+rx6b_align" />
+    <constant name="final_rx7b" value="mod2_rx7b+rx7b_align" />
+    <constant name="final_rx8b" value="mod2_rx8b+rx8b_align" />
+    <constant name="final_rx9b" value="mod2_rx9b+rx9b_align" />
+    <constant name="final_rx10b" value="mod2_rx10b+rx10b_align" />
+    <constant name="final_ry1b" value="mod2_ry1b+ry1b_align" />
+    <constant name="final_ry2b" value="mod2_ry2b+ry2b_align" />
+    <constant name="final_ry3b" value="mod2_ry3b+ry3b_align" />
+    <constant name="final_ry4b" value="mod2_ry4b+ry4b_align" />
+    <constant name="final_ry5b" value="mod2_ry5b+ry5b_align" />
+    <constant name="final_ry6b" value="mod2_ry6b+ry6b_align" />
+    <constant name="final_ry7b" value="mod2_ry7b+ry7b_align" />
+    <constant name="final_ry8b" value="mod2_ry8b+ry8b_align" />
+    <constant name="final_ry9b" value="mod2_ry9b+ry9b_align" />
+    <constant name="final_ry10b" value="mod2_ry10b+ry10b_align" />
+    <constant name="final_rz1b" value="mod2_rz1b+rz1b_align" />
+    <constant name="final_rz2b" value="mod2_rz2b+rz2b_align" />
+    <constant name="final_rz3b" value="mod2_rz3b+rz3b_align" />
+    <constant name="final_rz4b" value="mod2_rz4b+rz4b_align" />
+    <constant name="final_rz5b" value="mod2_rz5b+rz5b_align" />
+    <constant name="final_rz6b" value="mod2_rz6b+rz6b_align" />
+    <constant name="final_rz7b" value="mod2_rz7b+rz7b_align" />
+    <constant name="final_rz8b" value="mod2_rz8b+rz8b_align" />
+    <constant name="final_rz9b" value="mod2_rz9b+rz9b_align" />
+    <constant name="final_rz10b" value="mod2_rz10b+rz10b_align" />
+        
+        
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001" />
             <fraction n="1.0" ref="Vacuum" />
@@ -801,7 +801,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2" />
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPS-TestRun-v8/compact.xml	Wed Apr 27 11:11:32 2016
@@ -64,127 +64,127 @@
 <!--        <constant name="x_off" value = "-15.0"/> -->
         <constant name="x_off" value = "0.0"/> 
 
-		<!-- alignment corrections -->
-	<constant name="x1t_align" value="0.000000"/>
-	<constant name="x2t_align" value="0.000000"/>
-	<constant name="x3t_align" value="0.000000"/>
-	<constant name="x4t_align" value="0.000000"/>
-	<constant name="x5t_align" value="0.000000"/>
-	<constant name="x6t_align" value="0.000000"/>
-	<constant name="x7t_align" value="0.000000"/>
-	<constant name="x8t_align" value="0.000000"/>
-	<constant name="x9t_align" value="0.000000"/>
-	<constant name="x10t_align" value="0.000000"/>
-	<constant name="y1t_align" value="0.000000"/>
-	<constant name="y2t_align" value="0.000000"/>
-	<constant name="y3t_align" value="0.000000"/>
-	<constant name="y4t_align" value="0.000000"/>
-	<constant name="y5t_align" value="0.000000"/>
-	<constant name="y6t_align" value="0.000000"/>
-	<constant name="y7t_align" value="0.000000"/>
-	<constant name="y8t_align" value="0.000000"/>
-	<constant name="y9t_align" value="0.000000"/>
-	<constant name="y10t_align" value="0.000000"/>
-	<constant name="z1t_align" value="0.000000"/>
-	<constant name="z2t_align" value="0.000000"/>
-	<constant name="z3t_align" value="0.000000"/>
-	<constant name="z4t_align" value="0.000000"/>
-	<constant name="z5t_align" value="0.000000"/>
-	<constant name="z6t_align" value="0.000000"/>
-	<constant name="z7t_align" value="0.000000"/>
-	<constant name="z8t_align" value="0.000000"/>
-	<constant name="z9t_align" value="0.000000"/>
-	<constant name="z10t_align" value="0.000000"/>
-	<constant name="rx1t_align" value="0.000000"/>
-	<constant name="rx2t_align" value="0.000000"/>
-	<constant name="rx3t_align" value="0.000000"/>
-	<constant name="rx4t_align" value="0.000000"/>
-	<constant name="rx5t_align" value="0.000000"/>
-	<constant name="rx6t_align" value="0.000000"/>
-	<constant name="rx7t_align" value="0.000000"/>
-	<constant name="rx8t_align" value="0.000000"/>
-	<constant name="rx9t_align" value="0.000000"/>
-	<constant name="rx10t_align" value="0.000000"/>
-	<constant name="ry1t_align" value="0.000000"/>
-	<constant name="ry2t_align" value="0.000000"/>
-	<constant name="ry3t_align" value="0.000000"/>
-	<constant name="ry4t_align" value="0.000000"/>
-	<constant name="ry5t_align" value="0.000000"/>
-	<constant name="ry6t_align" value="0.000000"/>
-	<constant name="ry7t_align" value="0.000000"/>
-	<constant name="ry8t_align" value="0.000000"/>
-	<constant name="ry9t_align" value="0.000000"/>
-	<constant name="ry10t_align" value="0.000000"/>
-	<constant name="rz1t_align" value="0.000000"/>
-	<constant name="rz2t_align" value="0.000000"/>
-	<constant name="rz3t_align" value="0.000000"/>
-	<constant name="rz4t_align" value="0.000000"/>
-	<constant name="rz5t_align" value="0.000000"/>
-	<constant name="rz6t_align" value="0.000000"/>
-	<constant name="rz7t_align" value="0.000000"/>
-	<constant name="rz8t_align" value="0.000000"/>
-	<constant name="rz9t_align" value="0.000000"/>
-	<constant name="rz10t_align" value="0.000000"/>
-	<constant name="x1b_align" value="0.000000"/>
-	<constant name="x2b_align" value="0.000000"/>
-	<constant name="x3b_align" value="0.000000"/>
-	<constant name="x4b_align" value="0.000000"/>
-	<constant name="x5b_align" value="0.000000"/>
-	<constant name="x6b_align" value="0.000000"/>
-	<constant name="x7b_align" value="0.000000"/>
-	<constant name="x8b_align" value="0.000000"/>
-	<constant name="x9b_align" value="0.000000"/>
-	<constant name="x10b_align" value="0.000000"/>
-	<constant name="y1b_align" value="0.000000"/>
-	<constant name="y2b_align" value="0.000000"/>
-	<constant name="y3b_align" value="0.000000"/>
-	<constant name="y4b_align" value="0.000000"/>
-	<constant name="y5b_align" value="0.000000"/>
-	<constant name="y6b_align" value="0.000000"/>
-	<constant name="y7b_align" value="0.000000"/>
-	<constant name="y8b_align" value="0.000000"/>
-	<constant name="y9b_align" value="0.000000"/>
-	<constant name="y10b_align" value="0.000000"/>
-	<constant name="z1b_align" value="0.000000"/>
-	<constant name="z2b_align" value="0.000000"/>
-	<constant name="z3b_align" value="0.000000"/>
-	<constant name="z4b_align" value="0.000000"/>
-	<constant name="z5b_align" value="0.000000"/>
-	<constant name="z6b_align" value="0.000000"/>
-	<constant name="z7b_align" value="0.000000"/>
-	<constant name="z8b_align" value="0.000000"/>
-	<constant name="z9b_align" value="0.000000"/>
-	<constant name="z10b_align" value="0.000000"/>
-	<constant name="rx1b_align" value="0.000000"/>
-	<constant name="rx2b_align" value="0.000000"/>
-	<constant name="rx3b_align" value="0.000000"/>
-	<constant name="rx4b_align" value="0.000000"/>
-	<constant name="rx5b_align" value="0.000000"/>
-	<constant name="rx6b_align" value="0.000000"/>
-	<constant name="rx7b_align" value="0.000000"/>
-	<constant name="rx8b_align" value="0.000000"/>
-	<constant name="rx9b_align" value="0.000000"/>
-	<constant name="rx10b_align" value="0.000000"/>
-	<constant name="ry1b_align" value="0.000000"/>
-	<constant name="ry2b_align" value="0.000000"/>
-	<constant name="ry3b_align" value="0.000000"/>
-	<constant name="ry4b_align" value="0.000000"/>
-	<constant name="ry5b_align" value="0.000000"/>
-	<constant name="ry6b_align" value="0.000000"/>
-	<constant name="ry7b_align" value="0.000000"/>
-	<constant name="ry8b_align" value="0.000000"/>
-	<constant name="ry9b_align" value="0.000000"/>
-	<constant name="ry10b_align" value="0.000000"/>
-	<constant name="rz1b_align" value="0.000000"/>
-	<constant name="rz2b_align" value="0.000000"/>
-	<constant name="rz3b_align" value="0.000000"/>
-	<constant name="rz4b_align" value="0.000000"/>
-	<constant name="rz5b_align" value="0.000000"/>
-	<constant name="rz6b_align" value="0.000000"/>
-	<constant name="rz7b_align" value="0.000000"/>
-	<constant name="rz8b_align" value="0.000000"/>
-	<constant name="rz9b_align" value="0.000000"/>
-	<constant name="rz10b_align" value="0.000000"/>
+        <!-- alignment corrections -->
+    <constant name="x1t_align" value="0.000000"/>
+    <constant name="x2t_align" value="0.000000"/>
+    <constant name="x3t_align" value="0.000000"/>
+    <constant name="x4t_align" value="0.000000"/>
+    <constant name="x5t_align" value="0.000000"/>
+    <constant name="x6t_align" value="0.000000"/>
+    <constant name="x7t_align" value="0.000000"/>
+    <constant name="x8t_align" value="0.000000"/>
+    <constant name="x9t_align" value="0.000000"/>
+    <constant name="x10t_align" value="0.000000"/>
+    <constant name="y1t_align" value="0.000000"/>
+    <constant name="y2t_align" value="0.000000"/>
+    <constant name="y3t_align" value="0.000000"/>
+    <constant name="y4t_align" value="0.000000"/>
+    <constant name="y5t_align" value="0.000000"/>
+    <constant name="y6t_align" value="0.000000"/>
+    <constant name="y7t_align" value="0.000000"/>
+    <constant name="y8t_align" value="0.000000"/>
+    <constant name="y9t_align" value="0.000000"/>
+    <constant name="y10t_align" value="0.000000"/>
+    <constant name="z1t_align" value="0.000000"/>
+    <constant name="z2t_align" value="0.000000"/>
+    <constant name="z3t_align" value="0.000000"/>
+    <constant name="z4t_align" value="0.000000"/>
+    <constant name="z5t_align" value="0.000000"/>
+    <constant name="z6t_align" value="0.000000"/>
+    <constant name="z7t_align" value="0.000000"/>
+    <constant name="z8t_align" value="0.000000"/>
+    <constant name="z9t_align" value="0.000000"/>
+    <constant name="z10t_align" value="0.000000"/>
+    <constant name="rx1t_align" value="0.000000"/>
+    <constant name="rx2t_align" value="0.000000"/>
+    <constant name="rx3t_align" value="0.000000"/>
+    <constant name="rx4t_align" value="0.000000"/>
+    <constant name="rx5t_align" value="0.000000"/>
+    <constant name="rx6t_align" value="0.000000"/>
+    <constant name="rx7t_align" value="0.000000"/>
+    <constant name="rx8t_align" value="0.000000"/>
+    <constant name="rx9t_align" value="0.000000"/>
+    <constant name="rx10t_align" value="0.000000"/>
+    <constant name="ry1t_align" value="0.000000"/>
+    <constant name="ry2t_align" value="0.000000"/>
+    <constant name="ry3t_align" value="0.000000"/>
+    <constant name="ry4t_align" value="0.000000"/>
+    <constant name="ry5t_align" value="0.000000"/>
+    <constant name="ry6t_align" value="0.000000"/>
+    <constant name="ry7t_align" value="0.000000"/>
+    <constant name="ry8t_align" value="0.000000"/>
+    <constant name="ry9t_align" value="0.000000"/>
+    <constant name="ry10t_align" value="0.000000"/>
+    <constant name="rz1t_align" value="0.000000"/>
+    <constant name="rz2t_align" value="0.000000"/>
+    <constant name="rz3t_align" value="0.000000"/>
+    <constant name="rz4t_align" value="0.000000"/>
+    <constant name="rz5t_align" value="0.000000"/>
+    <constant name="rz6t_align" value="0.000000"/>
+    <constant name="rz7t_align" value="0.000000"/>
+    <constant name="rz8t_align" value="0.000000"/>
+    <constant name="rz9t_align" value="0.000000"/>
+    <constant name="rz10t_align" value="0.000000"/>
+    <constant name="x1b_align" value="0.000000"/>
+    <constant name="x2b_align" value="0.000000"/>
+    <constant name="x3b_align" value="0.000000"/>
+    <constant name="x4b_align" value="0.000000"/>
+    <constant name="x5b_align" value="0.000000"/>
+    <constant name="x6b_align" value="0.000000"/>
+    <constant name="x7b_align" value="0.000000"/>
+    <constant name="x8b_align" value="0.000000"/>
+    <constant name="x9b_align" value="0.000000"/>
+    <constant name="x10b_align" value="0.000000"/>
+    <constant name="y1b_align" value="0.000000"/>
+    <constant name="y2b_align" value="0.000000"/>
+    <constant name="y3b_align" value="0.000000"/>
+    <constant name="y4b_align" value="0.000000"/>
+    <constant name="y5b_align" value="0.000000"/>
+    <constant name="y6b_align" value="0.000000"/>
+    <constant name="y7b_align" value="0.000000"/>
+    <constant name="y8b_align" value="0.000000"/>
+    <constant name="y9b_align" value="0.000000"/>
+    <constant name="y10b_align" value="0.000000"/>
+    <constant name="z1b_align" value="0.000000"/>
+    <constant name="z2b_align" value="0.000000"/>
+    <constant name="z3b_align" value="0.000000"/>
+    <constant name="z4b_align" value="0.000000"/>
+    <constant name="z5b_align" value="0.000000"/>
+    <constant name="z6b_align" value="0.000000"/>
+    <constant name="z7b_align" value="0.000000"/>
+    <constant name="z8b_align" value="0.000000"/>
+    <constant name="z9b_align" value="0.000000"/>
+    <constant name="z10b_align" value="0.000000"/>
+    <constant name="rx1b_align" value="0.000000"/>
+    <constant name="rx2b_align" value="0.000000"/>
+    <constant name="rx3b_align" value="0.000000"/>
+    <constant name="rx4b_align" value="0.000000"/>
+    <constant name="rx5b_align" value="0.000000"/>
+    <constant name="rx6b_align" value="0.000000"/>
+    <constant name="rx7b_align" value="0.000000"/>
+    <constant name="rx8b_align" value="0.000000"/>
+    <constant name="rx9b_align" value="0.000000"/>
+    <constant name="rx10b_align" value="0.000000"/>
+    <constant name="ry1b_align" value="0.000000"/>
+    <constant name="ry2b_align" value="0.000000"/>
+    <constant name="ry3b_align" value="0.000000"/>
+    <constant name="ry4b_align" value="0.000000"/>
+    <constant name="ry5b_align" value="0.000000"/>
+    <constant name="ry6b_align" value="0.000000"/>
+    <constant name="ry7b_align" value="0.000000"/>
+    <constant name="ry8b_align" value="0.000000"/>
+    <constant name="ry9b_align" value="0.000000"/>
+    <constant name="ry10b_align" value="0.000000"/>
+    <constant name="rz1b_align" value="0.000000"/>
+    <constant name="rz2b_align" value="0.000000"/>
+    <constant name="rz3b_align" value="0.000000"/>
+    <constant name="rz4b_align" value="0.000000"/>
+    <constant name="rz5b_align" value="0.000000"/>
+    <constant name="rz6b_align" value="0.000000"/>
+    <constant name="rz7b_align" value="0.000000"/>
+    <constant name="rz8b_align" value="0.000000"/>
+    <constant name="rz9b_align" value="0.000000"/>
+    <constant name="rz10b_align" value="0.000000"/>
 
         <!-- Positions of sensor centers above/below nominal beam -->
         <constant name="y1t" value="36.894" />
@@ -584,134 +584,134 @@
         <constant name="mod2_rx10b" value="mod_rx10b"/>
         <constant name="mod2_ry10b" value="mod_ry10b+y_rot_bot_pivot"/>
         <constant name="mod2_rz10b" value="mod_rz10b"/>
-    	
-    	<!-- final constants -->
-	<constant name="final_x1t" value="mod2_x1t+x1t_align"/>
-	<constant name="final_x2t" value="mod2_x2t+x2t_align"/>
-	<constant name="final_x3t" value="mod2_x3t+x3t_align"/>
-	<constant name="final_x4t" value="mod2_x4t+x4t_align"/>
-	<constant name="final_x5t" value="mod2_x5t+x5t_align"/>
-	<constant name="final_x6t" value="mod2_x6t+x6t_align"/>
-	<constant name="final_x7t" value="mod2_x7t+x7t_align"/>
-	<constant name="final_x8t" value="mod2_x8t+x8t_align"/>
-	<constant name="final_x9t" value="mod2_x9t+x9t_align"/>
-	<constant name="final_x10t" value="mod2_x10t+x10t_align"/>
-	<constant name="final_y1t" value="mod2_y1t+y1t_align"/>
-	<constant name="final_y2t" value="mod2_y2t+y2t_align"/>
-	<constant name="final_y3t" value="mod2_y3t+y3t_align"/>
-	<constant name="final_y4t" value="mod2_y4t+y4t_align"/>
-	<constant name="final_y5t" value="mod2_y5t+y5t_align"/>
-	<constant name="final_y6t" value="mod2_y6t+y6t_align"/>
-	<constant name="final_y7t" value="mod2_y7t+y7t_align"/>
-	<constant name="final_y8t" value="mod2_y8t+y8t_align"/>
-	<constant name="final_y9t" value="mod2_y9t+y9t_align"/>
-	<constant name="final_y10t" value="mod2_y10t+y10t_align"/>
-	<constant name="final_z1t" value="mod2_z1t+z1t_align"/>
-	<constant name="final_z2t" value="mod2_z2t+z2t_align"/>
-	<constant name="final_z3t" value="mod2_z3t+z3t_align"/>
-	<constant name="final_z4t" value="mod2_z4t+z4t_align"/>
-	<constant name="final_z5t" value="mod2_z5t+z5t_align"/>
-	<constant name="final_z6t" value="mod2_z6t+z6t_align"/>
-	<constant name="final_z7t" value="mod2_z7t+z7t_align"/>
-	<constant name="final_z8t" value="mod2_z8t+z8t_align"/>
-	<constant name="final_z9t" value="mod2_z9t+z9t_align"/>
-	<constant name="final_z10t" value="mod2_z10t+z10t_align"/>
-	<constant name="final_rx1t" value="mod2_rx1t+rx1t_align"/>
-	<constant name="final_rx2t" value="mod2_rx2t+rx2t_align"/>
-	<constant name="final_rx3t" value="mod2_rx3t+rx3t_align"/>
-	<constant name="final_rx4t" value="mod2_rx4t+rx4t_align"/>
-	<constant name="final_rx5t" value="mod2_rx5t+rx5t_align"/>
-	<constant name="final_rx6t" value="mod2_rx6t+rx6t_align"/>
-	<constant name="final_rx7t" value="mod2_rx7t+rx7t_align"/>
-	<constant name="final_rx8t" value="mod2_rx8t+rx8t_align"/>
-	<constant name="final_rx9t" value="mod2_rx9t+rx9t_align"/>
-	<constant name="final_rx10t" value="mod2_rx10t+rx10t_align"/>
-	<constant name="final_ry1t" value="mod2_ry1t+ry1t_align"/>
-	<constant name="final_ry2t" value="mod2_ry2t+ry2t_align"/>
-	<constant name="final_ry3t" value="mod2_ry3t+ry3t_align"/>
-	<constant name="final_ry4t" value="mod2_ry4t+ry4t_align"/>
-	<constant name="final_ry5t" value="mod2_ry5t+ry5t_align"/>
-	<constant name="final_ry6t" value="mod2_ry6t+ry6t_align"/>
-	<constant name="final_ry7t" value="mod2_ry7t+ry7t_align"/>
-	<constant name="final_ry8t" value="mod2_ry8t+ry8t_align"/>
-	<constant name="final_ry9t" value="mod2_ry9t+ry9t_align"/>
-	<constant name="final_ry10t" value="mod2_ry10t+ry10t_align"/>
-	<constant name="final_rz1t" value="mod2_rz1t+rz1t_align"/>
-	<constant name="final_rz2t" value="mod2_rz2t+rz2t_align"/>
-	<constant name="final_rz3t" value="mod2_rz3t+rz3t_align"/>
-	<constant name="final_rz4t" value="mod2_rz4t+rz4t_align"/>
-	<constant name="final_rz5t" value="mod2_rz5t+rz5t_align"/>
-	<constant name="final_rz6t" value="mod2_rz6t+rz6t_align"/>
-	<constant name="final_rz7t" value="mod2_rz7t+rz7t_align"/>
-	<constant name="final_rz8t" value="mod2_rz8t+rz8t_align"/>
-	<constant name="final_rz9t" value="mod2_rz9t+rz9t_align"/>
-	<constant name="final_rz10t" value="mod2_rz10t+rz10t_align"/>
-	<constant name="final_x1b" value="mod2_x1b+x1b_align"/>
-	<constant name="final_x2b" value="mod2_x2b+x2b_align"/>
-	<constant name="final_x3b" value="mod2_x3b+x3b_align"/>
-	<constant name="final_x4b" value="mod2_x4b+x4b_align"/>
-	<constant name="final_x5b" value="mod2_x5b+x5b_align"/>
-	<constant name="final_x6b" value="mod2_x6b+x6b_align"/>
-	<constant name="final_x7b" value="mod2_x7b+x7b_align"/>
-	<constant name="final_x8b" value="mod2_x8b+x8b_align"/>
-	<constant name="final_x9b" value="mod2_x9b+x9b_align"/>
-	<constant name="final_x10b" value="mod2_x10b+x10b_align"/>
-	<constant name="final_y1b" value="mod2_y1b+y1b_align"/>
-	<constant name="final_y2b" value="mod2_y2b+y2b_align"/>
-	<constant name="final_y3b" value="mod2_y3b+y3b_align"/>
-	<constant name="final_y4b" value="mod2_y4b+y4b_align"/>
-	<constant name="final_y5b" value="mod2_y5b+y5b_align"/>
-	<constant name="final_y6b" value="mod2_y6b+y6b_align"/>
-	<constant name="final_y7b" value="mod2_y7b+y7b_align"/>
-	<constant name="final_y8b" value="mod2_y8b+y8b_align"/>
-	<constant name="final_y9b" value="mod2_y9b+y9b_align"/>
-	<constant name="final_y10b" value="mod2_y10b+y10b_align"/>
-	<constant name="final_z1b" value="mod2_z1b+z1b_align"/>
-	<constant name="final_z2b" value="mod2_z2b+z2b_align"/>
-	<constant name="final_z3b" value="mod2_z3b+z3b_align"/>
-	<constant name="final_z4b" value="mod2_z4b+z4b_align"/>
-	<constant name="final_z5b" value="mod2_z5b+z5b_align"/>
-	<constant name="final_z6b" value="mod2_z6b+z6b_align"/>
-	<constant name="final_z7b" value="mod2_z7b+z7b_align"/>
-	<constant name="final_z8b" value="mod2_z8b+z8b_align"/>
-	<constant name="final_z9b" value="mod2_z9b+z9b_align"/>
-	<constant name="final_z10b" value="mod2_z10b+z10b_align"/>
-	<constant name="final_rx1b" value="mod2_rx1b+rx1b_align"/>
-	<constant name="final_rx2b" value="mod2_rx2b+rx2b_align"/>
-	<constant name="final_rx3b" value="mod2_rx3b+rx3b_align"/>
-	<constant name="final_rx4b" value="mod2_rx4b+rx4b_align"/>
-	<constant name="final_rx5b" value="mod2_rx5b+rx5b_align"/>
-	<constant name="final_rx6b" value="mod2_rx6b+rx6b_align"/>
-	<constant name="final_rx7b" value="mod2_rx7b+rx7b_align"/>
-	<constant name="final_rx8b" value="mod2_rx8b+rx8b_align"/>
-	<constant name="final_rx9b" value="mod2_rx9b+rx9b_align"/>
-	<constant name="final_rx10b" value="mod2_rx10b+rx10b_align"/>
-	<constant name="final_ry1b" value="mod2_ry1b+ry1b_align"/>
-	<constant name="final_ry2b" value="mod2_ry2b+ry2b_align"/>
-	<constant name="final_ry3b" value="mod2_ry3b+ry3b_align"/>
-	<constant name="final_ry4b" value="mod2_ry4b+ry4b_align"/>
-	<constant name="final_ry5b" value="mod2_ry5b+ry5b_align"/>
-	<constant name="final_ry6b" value="mod2_ry6b+ry6b_align"/>
-	<constant name="final_ry7b" value="mod2_ry7b+ry7b_align"/>
-	<constant name="final_ry8b" value="mod2_ry8b+ry8b_align"/>
-	<constant name="final_ry9b" value="mod2_ry9b+ry9b_align"/>
-	<constant name="final_ry10b" value="mod2_ry10b+ry10b_align"/>
-	<constant name="final_rz1b" value="mod2_rz1b+rz1b_align"/>
-	<constant name="final_rz2b" value="mod2_rz2b+rz2b_align"/>
-	<constant name="final_rz3b" value="mod2_rz3b+rz3b_align"/>
-	<constant name="final_rz4b" value="mod2_rz4b+rz4b_align"/>
-	<constant name="final_rz5b" value="mod2_rz5b+rz5b_align"/>
-	<constant name="final_rz6b" value="mod2_rz6b+rz6b_align"/>
-	<constant name="final_rz7b" value="mod2_rz7b+rz7b_align"/>
-	<constant name="final_rz8b" value="mod2_rz8b+rz8b_align"/>
-	<constant name="final_rz9b" value="mod2_rz9b+rz9b_align"/>
-	<constant name="final_rz10b" value="mod2_rz10b+rz10b_align"/>
-    	
-    	
+        
+        <!-- final constants -->
+    <constant name="final_x1t" value="mod2_x1t+x1t_align"/>
+    <constant name="final_x2t" value="mod2_x2t+x2t_align"/>
+    <constant name="final_x3t" value="mod2_x3t+x3t_align"/>
+    <constant name="final_x4t" value="mod2_x4t+x4t_align"/>
+    <constant name="final_x5t" value="mod2_x5t+x5t_align"/>
+    <constant name="final_x6t" value="mod2_x6t+x6t_align"/>
+    <constant name="final_x7t" value="mod2_x7t+x7t_align"/>
+    <constant name="final_x8t" value="mod2_x8t+x8t_align"/>
+    <constant name="final_x9t" value="mod2_x9t+x9t_align"/>
+    <constant name="final_x10t" value="mod2_x10t+x10t_align"/>
+    <constant name="final_y1t" value="mod2_y1t+y1t_align"/>
+    <constant name="final_y2t" value="mod2_y2t+y2t_align"/>
+    <constant name="final_y3t" value="mod2_y3t+y3t_align"/>
+    <constant name="final_y4t" value="mod2_y4t+y4t_align"/>
+    <constant name="final_y5t" value="mod2_y5t+y5t_align"/>
+    <constant name="final_y6t" value="mod2_y6t+y6t_align"/>
+    <constant name="final_y7t" value="mod2_y7t+y7t_align"/>
+    <constant name="final_y8t" value="mod2_y8t+y8t_align"/>
+    <constant name="final_y9t" value="mod2_y9t+y9t_align"/>
+    <constant name="final_y10t" value="mod2_y10t+y10t_align"/>
+    <constant name="final_z1t" value="mod2_z1t+z1t_align"/>
+    <constant name="final_z2t" value="mod2_z2t+z2t_align"/>
+    <constant name="final_z3t" value="mod2_z3t+z3t_align"/>
+    <constant name="final_z4t" value="mod2_z4t+z4t_align"/>
+    <constant name="final_z5t" value="mod2_z5t+z5t_align"/>
+    <constant name="final_z6t" value="mod2_z6t+z6t_align"/>
+    <constant name="final_z7t" value="mod2_z7t+z7t_align"/>
+    <constant name="final_z8t" value="mod2_z8t+z8t_align"/>
+    <constant name="final_z9t" value="mod2_z9t+z9t_align"/>
+    <constant name="final_z10t" value="mod2_z10t+z10t_align"/>
+    <constant name="final_rx1t" value="mod2_rx1t+rx1t_align"/>
+    <constant name="final_rx2t" value="mod2_rx2t+rx2t_align"/>
+    <constant name="final_rx3t" value="mod2_rx3t+rx3t_align"/>
+    <constant name="final_rx4t" value="mod2_rx4t+rx4t_align"/>
+    <constant name="final_rx5t" value="mod2_rx5t+rx5t_align"/>
+    <constant name="final_rx6t" value="mod2_rx6t+rx6t_align"/>
+    <constant name="final_rx7t" value="mod2_rx7t+rx7t_align"/>
+    <constant name="final_rx8t" value="mod2_rx8t+rx8t_align"/>
+    <constant name="final_rx9t" value="mod2_rx9t+rx9t_align"/>
+    <constant name="final_rx10t" value="mod2_rx10t+rx10t_align"/>
+    <constant name="final_ry1t" value="mod2_ry1t+ry1t_align"/>
+    <constant name="final_ry2t" value="mod2_ry2t+ry2t_align"/>
+    <constant name="final_ry3t" value="mod2_ry3t+ry3t_align"/>
+    <constant name="final_ry4t" value="mod2_ry4t+ry4t_align"/>
+    <constant name="final_ry5t" value="mod2_ry5t+ry5t_align"/>
+    <constant name="final_ry6t" value="mod2_ry6t+ry6t_align"/>
+    <constant name="final_ry7t" value="mod2_ry7t+ry7t_align"/>
+    <constant name="final_ry8t" value="mod2_ry8t+ry8t_align"/>
+    <constant name="final_ry9t" value="mod2_ry9t+ry9t_align"/>
+    <constant name="final_ry10t" value="mod2_ry10t+ry10t_align"/>
+    <constant name="final_rz1t" value="mod2_rz1t+rz1t_align"/>
+    <constant name="final_rz2t" value="mod2_rz2t+rz2t_align"/>
+    <constant name="final_rz3t" value="mod2_rz3t+rz3t_align"/>
+    <constant name="final_rz4t" value="mod2_rz4t+rz4t_align"/>
+    <constant name="final_rz5t" value="mod2_rz5t+rz5t_align"/>
+    <constant name="final_rz6t" value="mod2_rz6t+rz6t_align"/>
+    <constant name="final_rz7t" value="mod2_rz7t+rz7t_align"/>
+    <constant name="final_rz8t" value="mod2_rz8t+rz8t_align"/>
+    <constant name="final_rz9t" value="mod2_rz9t+rz9t_align"/>
+    <constant name="final_rz10t" value="mod2_rz10t+rz10t_align"/>
+    <constant name="final_x1b" value="mod2_x1b+x1b_align"/>
+    <constant name="final_x2b" value="mod2_x2b+x2b_align"/>
+    <constant name="final_x3b" value="mod2_x3b+x3b_align"/>
+    <constant name="final_x4b" value="mod2_x4b+x4b_align"/>
+    <constant name="final_x5b" value="mod2_x5b+x5b_align"/>
+    <constant name="final_x6b" value="mod2_x6b+x6b_align"/>
+    <constant name="final_x7b" value="mod2_x7b+x7b_align"/>
+    <constant name="final_x8b" value="mod2_x8b+x8b_align"/>
+    <constant name="final_x9b" value="mod2_x9b+x9b_align"/>
+    <constant name="final_x10b" value="mod2_x10b+x10b_align"/>
+    <constant name="final_y1b" value="mod2_y1b+y1b_align"/>
+    <constant name="final_y2b" value="mod2_y2b+y2b_align"/>
+    <constant name="final_y3b" value="mod2_y3b+y3b_align"/>
+    <constant name="final_y4b" value="mod2_y4b+y4b_align"/>
+    <constant name="final_y5b" value="mod2_y5b+y5b_align"/>
+    <constant name="final_y6b" value="mod2_y6b+y6b_align"/>
+    <constant name="final_y7b" value="mod2_y7b+y7b_align"/>
+    <constant name="final_y8b" value="mod2_y8b+y8b_align"/>
+    <constant name="final_y9b" value="mod2_y9b+y9b_align"/>
+    <constant name="final_y10b" value="mod2_y10b+y10b_align"/>
+    <constant name="final_z1b" value="mod2_z1b+z1b_align"/>
+    <constant name="final_z2b" value="mod2_z2b+z2b_align"/>
+    <constant name="final_z3b" value="mod2_z3b+z3b_align"/>
+    <constant name="final_z4b" value="mod2_z4b+z4b_align"/>
+    <constant name="final_z5b" value="mod2_z5b+z5b_align"/>
+    <constant name="final_z6b" value="mod2_z6b+z6b_align"/>
+    <constant name="final_z7b" value="mod2_z7b+z7b_align"/>
+    <constant name="final_z8b" value="mod2_z8b+z8b_align"/>
+    <constant name="final_z9b" value="mod2_z9b+z9b_align"/>
+    <constant name="final_z10b" value="mod2_z10b+z10b_align"/>
+    <constant name="final_rx1b" value="mod2_rx1b+rx1b_align"/>
+    <constant name="final_rx2b" value="mod2_rx2b+rx2b_align"/>
+    <constant name="final_rx3b" value="mod2_rx3b+rx3b_align"/>
+    <constant name="final_rx4b" value="mod2_rx4b+rx4b_align"/>
+    <constant name="final_rx5b" value="mod2_rx5b+rx5b_align"/>
+    <constant name="final_rx6b" value="mod2_rx6b+rx6b_align"/>
+    <constant name="final_rx7b" value="mod2_rx7b+rx7b_align"/>
+    <constant name="final_rx8b" value="mod2_rx8b+rx8b_align"/>
+    <constant name="final_rx9b" value="mod2_rx9b+rx9b_align"/>
+    <constant name="final_rx10b" value="mod2_rx10b+rx10b_align"/>
+    <constant name="final_ry1b" value="mod2_ry1b+ry1b_align"/>
+    <constant name="final_ry2b" value="mod2_ry2b+ry2b_align"/>
+    <constant name="final_ry3b" value="mod2_ry3b+ry3b_align"/>
+    <constant name="final_ry4b" value="mod2_ry4b+ry4b_align"/>
+    <constant name="final_ry5b" value="mod2_ry5b+ry5b_align"/>
+    <constant name="final_ry6b" value="mod2_ry6b+ry6b_align"/>
+    <constant name="final_ry7b" value="mod2_ry7b+ry7b_align"/>
+    <constant name="final_ry8b" value="mod2_ry8b+ry8b_align"/>
+    <constant name="final_ry9b" value="mod2_ry9b+ry9b_align"/>
+    <constant name="final_ry10b" value="mod2_ry10b+ry10b_align"/>
+    <constant name="final_rz1b" value="mod2_rz1b+rz1b_align"/>
+    <constant name="final_rz2b" value="mod2_rz2b+rz2b_align"/>
+    <constant name="final_rz3b" value="mod2_rz3b+rz3b_align"/>
+    <constant name="final_rz4b" value="mod2_rz4b+rz4b_align"/>
+    <constant name="final_rz5b" value="mod2_rz5b+rz5b_align"/>
+    <constant name="final_rz6b" value="mod2_rz6b+rz6b_align"/>
+    <constant name="final_rz7b" value="mod2_rz7b+rz7b_align"/>
+    <constant name="final_rz8b" value="mod2_rz8b+rz8b_align"/>
+    <constant name="final_rz9b" value="mod2_rz9b+rz9b_align"/>
+    <constant name="final_rz10b" value="mod2_rz10b+rz10b_align"/>
+        
+        
     </define>
     
     <materials>      
-    	<!-- Set the world material to vacuum. -->
+        <!-- Set the world material to vacuum. -->
         <material name="WorldMaterial">
             <D type="density" unit="g/cm3" value="0.0000000000000001"/>
             <fraction n="1.0" ref="Vacuum" />
@@ -800,7 +800,7 @@
             </layer>
             <layer id="2">
                 <module_placement name="TestRunModuleFieldDef" id="0" x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0" ry="0" rz="-PI/2"/>
-			</layer>
+            </layer>
         </detector>     
         
         <detector id="13" name="Ecal" type="HPSEcal3" insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">

Modified: java/branches/HPSJAVA-409/detector-data/detectors/HPSTestRunTracker2014-v0/compact.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/detectors/HPSTestRunTracker2014-v0/compact.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/detectors/HPSTestRunTracker2014-v0/compact.xml	Wed Apr 27 11:11:32 2016
@@ -7,9 +7,9 @@
   </info> 
   
   <define>
-	<!-- units -->
-	<constant name="mm" value="0.1*cm"/>
-	<constant name="inch" value="25.4*mm"/>
+    <!-- units -->
+    <constant name="mm" value="0.1*cm"/>
+    <constant name="inch" value="25.4*mm"/>
 
     <!-- world -->
     <constant name="world_side" value="500.0*cm" />
@@ -17,48 +17,48 @@
     <constant name="world_y" value="world_side" />
     <constant name="world_z" value="world_side" />
   
- 	 <!-- tracking region -->
- 	<constant name="tracking_region_radius" value="200.0*cm"/>
+     <!-- tracking region -->
+    <constant name="tracking_region_radius" value="200.0*cm"/>
     <constant name="tracking_region_min" value="5.0*cm"/>
     <constant name="tracking_region_zmax" value="131.8*cm"/>
     
      <!--  dipole magnet and  B-field -->
-	<constant name="dipoleMagnetPositionZ" value="45.72*cm" />
-	<constant name="dipoleMagnetHeight" value="17.78*cm" />
-	<constant name="dipoleMagnetWidth" value="41.6052*cm" />
-	<constant name="dipoleMagnetLength" value="dipoleMagnetPositionZ*2.0" />
-	<constant name="constBFieldY" value="-0.491" />
+    <constant name="dipoleMagnetPositionZ" value="45.72*cm" />
+    <constant name="dipoleMagnetHeight" value="17.78*cm" />
+    <constant name="dipoleMagnetWidth" value="41.6052*cm" />
+    <constant name="dipoleMagnetLength" value="dipoleMagnetPositionZ*2.0" />
+    <constant name="constBFieldY" value="-0.491" />
  
-	<!-- ECAL -->
+    <!-- ECAL -->
     <constant name="ecal_front" value="13.3/2*mm" />
-	<constant name="ecal_back" value="16/2*mm" />
-	<constant name="ecal_z" value="160/2*mm" />
-   	<constant name="ecal_dx" value="41.27*mm" />
+    <constant name="ecal_back" value="16/2*mm" />
+    <constant name="ecal_z" value="160/2*mm" />
+    <constant name="ecal_dx" value="41.27*mm" />
  
   </define>
   
   <materials>
-  	<!-- Set the world material to vacuum. -->
+    <!-- Set the world material to vacuum. -->
     <material name="WorldMaterial">
-    	<D type="density" unit="g/cm3" value="0.0000000000000001"/>
-    	<fraction n="1.0" ref="Vacuum" />
+        <D type="density" unit="g/cm3" value="0.0000000000000001"/>
+        <fraction n="1.0" ref="Vacuum" />
     </material>
     <!-- Set tracking material to vacuum. -->
     <material name="TrackingMaterial">
       <D type="density" unit="g/cm3" value="0.0000000000000001" />
       <fraction n="1.0" ref="Vacuum" />
     </material>
-	<!-- ECal crystal material. -->
-	<material name="LeadTungstate">
-		<D value="8.28" unit="g/cm3" />
-		<composite n="1" ref="Pb" />
-		<composite n="1" ref="W" />
-		<composite n="4" ref="O" />
-	</material>
+    <!-- ECal crystal material. -->
+    <material name="LeadTungstate">
+        <D value="8.28" unit="g/cm3" />
+        <composite n="1" ref="Pb" />
+        <composite n="1" ref="W" />
+        <composite n="4" ref="O" />
+    </material>
   </materials>
   
   <display>
-	
+    
     <vis name="SensorVis" alpha="1.0" r="1.0" g="0.0" b="0.0" drawingStyle="wireframe" lineStyle="unbroken" showDaughters="true" visible="true"/>
     <vis name="ActiveSensorVis" alpha="1.0" r="1.0" g="0.0" b="0.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="true" visible="true"/>
     <vis name="CarbonFiberVis" alpha="1.0" r="0.88" g="0.88" b="0.88" drawingStyle="solid" lineStyle="unbroken" showDaughters="true" visible="true"/>
@@ -72,14 +72,14 @@
     <vis name="BasePlateVis" alpha="1.0" r="0.35" g="0.35" b="0.35" drawingStyle="solid" lineStyle="dashed" showDaughters="true" visible="true"/>
     <vis name="LayerVis" alpha="0.0" r="0.0" g="0.0" b="1.0" drawingStyle="wireframe" showDaughters="true" visible="false"/>
     <vis name="ComponentVis" alpha="0.0" r="0.0" g="0.2" b="0.4" drawingStyle="solid" showDaughters="false" visible="false"/>
-	<vis name="BeamPlaneVis" alpha="1.0" r="1.0" g="1.0" b="1.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="false" visible="true"/>
+    <vis name="BeamPlaneVis" alpha="1.0" r="1.0" g="1.0" b="1.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="false" visible="true"/>
 
     <vis name="ECALVis" r="0.8" g="0.5" b="0.1" />
   </display>
   
   <detectors>
     <detector id="1" name="Tracker" type="HPSTestRunTracker2014" readout="TrackerHits">
-	   <millepede_constants>
+       <millepede_constants>
             <!-- top translations -->
             <millepede_constant name="11101" value="0.0"/>
             <millepede_constant name="11102" value="0.0"/>
@@ -234,43 +234,43 @@
      
     </detector>
 
-	<detector id="30" name="TrackerFieldDef" type="HPSTracker2"
-		readout="TrackerHitsThin">
-		<comment>The Silicon Vertex Tracker</comment>
-		<module name="TestRunModuleFieldDef">
-			<box x="dipoleMagnetWidth*4+1" y="dipoleMagnetHeight*4+1" />
-			<module_component thickness="0.000000001*cm"
-				material="Vacuum" sensitive="true">
-				<dimensions x="dipoleMagnetWidth*4" y="dipoleMagnetHeight*4" />
-			</module_component>
-		</module>
-		<layer id="1">
-			<module_placement name="TestRunModuleFieldDef" id="0"
-				x="0" y="0" z="dipoleMagnetPositionZ-dipoleMagnetLength/2" rx="0"
-				ry="0" rz="-PI/2" />
-		</layer>
-		<layer id="2">
-			<module_placement name="TestRunModuleFieldDef" id="0"
-				x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0"
-				ry="0" rz="-PI/2" />
-		</layer>
-	</detector>
-
-	<detector id="13" name="Ecal" type="HPSEcal3"
-		insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">
-		<comment>The crystal ECal</comment>
-		<material name="LeadTungstate" />
-		<dimensions x1="ecal_front" y1="ecal_front" x2="ecal_back"
-			y2="ecal_back" z="ecal_z" />
-		<!-- Measurements as found in installation by Stepan -->
-		<!-- Moving ecal halves out by 6.5mm from SVT ecal-track matching - Pelle -->
-		<!-- Moving ecal face to reflect latest survey calculation 2/17/14 - Pelle -->
-		<layout beamgap="43.5*mm" nx="46" ny="5" dface="147.0*cm">
-			<remove ixmin="-10" ixmax="-2" iymin="-1" iymax="1" />
-			<top dx="ecal_dx" dy="0." dz="0." />
-			<bottom dx="ecal_dx" dy="0." dz="0." />
-		</layout>
-	</detector>
+    <detector id="30" name="TrackerFieldDef" type="HPSTracker2"
+        readout="TrackerHitsThin">
+        <comment>The Silicon Vertex Tracker</comment>
+        <module name="TestRunModuleFieldDef">
+            <box x="dipoleMagnetWidth*4+1" y="dipoleMagnetHeight*4+1" />
+            <module_component thickness="0.000000001*cm"
+                material="Vacuum" sensitive="true">
+                <dimensions x="dipoleMagnetWidth*4" y="dipoleMagnetHeight*4" />
+            </module_component>
+        </module>
+        <layer id="1">
+            <module_placement name="TestRunModuleFieldDef" id="0"
+                x="0" y="0" z="dipoleMagnetPositionZ-dipoleMagnetLength/2" rx="0"
+                ry="0" rz="-PI/2" />
+        </layer>
+        <layer id="2">
+            <module_placement name="TestRunModuleFieldDef" id="0"
+                x="0" y="0" z="dipoleMagnetPositionZ+dipoleMagnetLength/2" rx="0"
+                ry="0" rz="-PI/2" />
+        </layer>
+    </detector>
+
+    <detector id="13" name="Ecal" type="HPSEcal3"
+        insideTrackingVolume="false" readout="EcalHits" vis="ECALVis">
+        <comment>The crystal ECal</comment>
+        <material name="LeadTungstate" />
+        <dimensions x1="ecal_front" y1="ecal_front" x2="ecal_back"
+            y2="ecal_back" z="ecal_z" />
+        <!-- Measurements as found in installation by Stepan -->
+        <!-- Moving ecal halves out by 6.5mm from SVT ecal-track matching - Pelle -->
+        <!-- Moving ecal face to reflect latest survey calculation 2/17/14 - Pelle -->
+        <layout beamgap="43.5*mm" nx="46" ny="5" dface="147.0*cm">
+            <remove ixmin="-10" ixmax="-2" iymin="-1" iymax="1" />
+            <top dx="ecal_dx" dy="0." dz="0." />
+            <bottom dx="ecal_dx" dy="0." dz="0." />
+        </layout>
+    </detector>
     
      
     
@@ -279,28 +279,28 @@
     <readout name="TrackerHits">
       <id>system:6,barrel:3,layer:4,module:12,sensor:1,side:32:-2,strip:12</id>
     </readout>
-	<readout name="TrackerHitsThin">
-		<id>system:6,barrel:3,layer:4,module:12,sensor:1,side:32:-2,strip:12</id>
-	</readout>
-
-	<readout name="EcalHits">
-		<segmentation type="GridXYZ" gridSizeX="0.0" gridSizeY="0.0"
-			gridSizeZ="0.0" />
-		<id>system:6,layer:2,ix:-8,iy:-6</id>
-	</readout>
+    <readout name="TrackerHitsThin">
+        <id>system:6,barrel:3,layer:4,module:12,sensor:1,side:32:-2,strip:12</id>
+    </readout>
+
+    <readout name="EcalHits">
+        <segmentation type="GridXYZ" gridSizeX="0.0" gridSizeY="0.0"
+            gridSizeZ="0.0" />
+        <id>system:6,layer:2,ix:-8,iy:-6</id>
+    </readout>
   </readouts>
 
-	<fields>
-		<field type="BoxDipole" name="AnalyzingDipole" x="0*cm" y="0*cm"
-			z="dipoleMagnetPositionZ" dx="dipoleMagnetWidth/2.0" dy="dipoleMagnetHeight/2.0"
-			dz="dipoleMagnetLength/2.0" bx="0.0" by="constBFieldY" bz="0.0" />
-	</fields>
+    <fields>
+        <field type="BoxDipole" name="AnalyzingDipole" x="0*cm" y="0*cm"
+            z="dipoleMagnetPositionZ" dx="dipoleMagnetWidth/2.0" dy="dipoleMagnetHeight/2.0"
+            dz="dipoleMagnetLength/2.0" bx="0.0" by="constBFieldY" bz="0.0" />
+    </fields>
 
 <!-- 
-	<includes>
-		<gdmlFile
-			ref="http://www.lcsim.org/test/gdml/testRunDownstreamVacuumFlange.gdml" />
-	</includes>
+    <includes>
+        <gdmlFile
+            ref="http://www.lcsim.org/test/gdml/testRunDownstreamVacuumFlange.gdml" />
+    </includes>
     -->
  
 </lccdd>

Modified: java/branches/HPSJAVA-409/detector-data/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-data/pom.xml	(original)
+++ java/branches/HPSJAVA-409/detector-data/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/detector-data/</url>

Modified: java/branches/HPSJAVA-409/detector-model/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/pom.xml	(original)
+++ java/branches/HPSJAVA-409/detector-model/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <build>
         <plugins>

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTestRunTracker2014Converter.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTestRunTracker2014Converter.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTestRunTracker2014Converter.java	Wed Apr 27 11:11:32 2016
@@ -11,7 +11,6 @@
 import org.lcsim.geometry.compact.converter.HPSTestRunTracker2014JavaBuilder;
 import org.lcsim.geometry.compact.converter.HPSTrackerBuilder;
 import org.lcsim.geometry.compact.converter.HPSTrackerJavaBuilder;
-import org.lcsim.geometry.compact.converter.JavaSurveyVolume;
 import org.lcsim.geometry.subdetector.HPSTestRunTracker2014;
 
 /**
@@ -21,21 +20,21 @@
  */
 public class HPSTestRunTracker2014Converter extends HPSTracker2014ConverterBase {
 
-	public HPSTestRunTracker2014Converter() {
-		super();
-	}
-	
-	/* (non-Javadoc)
-	 * @see org.lcsim.detector.converter.compact.HPSTracker2014ConverterBase#initializeBuilder(org.jdom.Element)
-	 */
-	protected HPSTrackerJavaBuilder initializeBuilder(Element node) {
-	     return new HPSTestRunTracker2014JavaBuilder(_debug,node);
-	 }
+    public HPSTestRunTracker2014Converter() {
+        super();
+    }
     
-	/* (non-Javadoc)
-	 * @see org.lcsim.detector.converter.compact.AbstractSubdetectorConverter#getSubdetectorType()
-	 */
-	public Class getSubdetectorType() {
+    /* (non-Javadoc)
+     * @see org.lcsim.detector.converter.compact.HPSTracker2014ConverterBase#initializeBuilder(org.jdom.Element)
+     */
+    protected HPSTrackerJavaBuilder initializeBuilder(Element node) {
+         return new HPSTestRunTracker2014JavaBuilder(_debug,node);
+     }
+    
+    /* (non-Javadoc)
+     * @see org.lcsim.detector.converter.compact.AbstractSubdetectorConverter#getSubdetectorType()
+     */
+    public Class getSubdetectorType() {
         return HPSTestRunTracker2014.class;
     }
 
@@ -53,5 +52,5 @@
     protected int getModuleNumber(String surveyVolume) {
         return HPSTrackerBuilder.getHalfFromName(surveyVolume).equals("top") ? 0 : 1;
     }
-	
+    
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014Converter.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014Converter.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014Converter.java	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,6 @@
 import org.lcsim.geometry.compact.converter.HPSTracker2014JavaBuilder;
 import org.lcsim.geometry.compact.converter.HPSTrackerBuilder;
 import org.lcsim.geometry.compact.converter.HPSTrackerJavaBuilder;
-import org.lcsim.geometry.compact.converter.JavaSurveyVolume;
 import org.lcsim.geometry.subdetector.HPSTracker2014;
 
 

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.java	Wed Apr 27 11:11:32 2016
@@ -71,7 +71,7 @@
      * @see org.lcsim.detector.converter.compact.AbstractSubdetectorConverter#makeIdentifierHelper(org.lcsim.geometry.compact.Subdetector, org.lcsim.detector.DetectorIdentifierHelper.SystemMap)
      */
     public IIdentifierHelper makeIdentifierHelper(Subdetector subdetector, SystemMap systemMap) {
-    	return new SiTrackerIdentifierHelper(subdetector.getDetectorElement(), makeIdentifierDictionary(subdetector), systemMap);
+        return new SiTrackerIdentifierHelper(subdetector.getDetectorElement(), makeIdentifierDictionary(subdetector), systemMap);
     }
 
     

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java	Wed Apr 27 11:11:32 2016
@@ -1,8 +1,4 @@
 package org.lcsim.detector.converter.compact;
-
-import hep.physics.matrix.BasicMatrix;
-import hep.physics.vec.BasicHep3Vector;
-import hep.physics.vec.VecOp;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -16,15 +12,11 @@
 import org.lcsim.detector.DetectorIdentifierHelper;
 import org.lcsim.detector.DetectorIdentifierHelper.SystemMap;
 import org.lcsim.detector.IDetectorElement;
-
 import org.lcsim.detector.IPhysicalVolume;
 import org.lcsim.detector.IPhysicalVolumePath;
-import org.lcsim.detector.IRotation3D;
-import org.lcsim.detector.ITranslation3D;
 import org.lcsim.detector.LogicalVolume;
 import org.lcsim.detector.PhysicalVolume;
 import org.lcsim.detector.RotationGeant;
-import org.lcsim.detector.RotationPassiveXYZ;
 import org.lcsim.detector.Transform3D;
 import org.lcsim.detector.Translation3D;
 import org.lcsim.detector.identifier.ExpandedIdentifier;
@@ -35,10 +27,7 @@
 import org.lcsim.detector.material.IMaterial;
 import org.lcsim.detector.material.MaterialStore;
 import org.lcsim.detector.solids.Box;
-import org.lcsim.detector.solids.Polygon3D;
-import org.lcsim.detector.tracker.silicon.ChargeCarrier;
 import org.lcsim.detector.tracker.silicon.SiSensor;
-import org.lcsim.detector.tracker.silicon.SiStrips;
 import org.lcsim.detector.tracker.silicon.SiTrackerIdentifierHelper;
 import org.lcsim.detector.tracker.silicon.SiTrackerModule;
 import org.lcsim.geometry.compact.Detector;
@@ -238,7 +227,7 @@
     {
         //double moduleX = moduleParameters.getDimension(0);
         //double moduleY = moduleParameters.getDimension(1);        
-    	double moduleY = moduleParameters.getDimension(0);
+        double moduleY = moduleParameters.getDimension(0);
         double moduleX = moduleParameters.getDimension(1);
         Box box = (Box)moduleVolume.getSolid();
         double moduleZ = box.getZHalfLength() * 2;                        
@@ -375,7 +364,7 @@
     /*
     private void configSensor(SiSensor sensor)
     {
-    	//
+        //
         Box sensorSolid = (Box) sensor.getGeometry().getLogicalVolume().getSolid();                                                        
         
         Polygon3D pside = sensorSolid.getFacesNormalTo(new BasicHep3Vector(0, 0, 1)).get(0);

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
 import org.lcsim.detector.converter.compact.SubdetectorDetectorElement;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 /**
- * Class describing an {@link HPSTracker2} subdetector. 
+ * Detector element for <code>HPSTracker2</code> type.
  * 
  * @author Omar Moreno <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
@@ -19,89 +19,89 @@
     private boolean debug = false;
     
     // List of stereo layers composing the SVT
-	List<SvtStereoLayer> stereoPairs = new ArrayList<SvtStereoLayer>(); 
-	
-	public HpsTracker2(String name, IDetectorElement parent) {
-		super(name, parent);
-	}
-	
-	/**
-	 * Get a collection of stereo pairs ({@link SvtStereoLayer}) composing the SVT.
-	 * 
-	 * @return List of stereo pairs
-	 */
-	public List<SvtStereoLayer> getStereoPairs(){
-	    return Collections.unmodifiableList(stereoPairs);
-	}
+    List<SvtStereoLayer> stereoPairs = new ArrayList<SvtStereoLayer>(); 
+    
+    public HpsTracker2(String name, IDetectorElement parent) {
+        super(name, parent);
+    }
+    
+    /**
+     * Get a collection of stereo pairs ({@link SvtStereoLayer}) composing the SVT.
+     * 
+     * @return List of stereo pairs
+     */
+    public List<SvtStereoLayer> getStereoPairs(){
+        return Collections.unmodifiableList(stereoPairs);
+    }
 
-	/**
-	 * Get the collection of {@link HpsSiSensor} composing the SVT. 
-	 * 
-	 * @return List of sensors
-	 */
-	public List<HpsSiSensor> getSensors(){
-	    List<HpsSiSensor> list = this.findDescendants(HpsSiSensor.class);
-	    if(debug) {
-	        System.out.printf("%s: found %d HpsSiSensors\n",getClass().getSimpleName(), list.size());
-	        System.out.printf("%s: %45s %5s %5s\n",getClass().getSimpleName(), "<name>", "<layerID>", "<moduleID>");
-	        for(HpsSiSensor sensor : list) {
-	            System.out.printf("%s: %45s %5d %5d\n",getClass().getSimpleName(), sensor.getName(), sensor.getLayerNumber(), sensor.getModuleNumber());
-	        }
-	    }
-	    return list;
-	}
-	
-	/**
-	 * Get a {@link HpsSiSensor} by layer and module number.
-	 * 
-	 * @param layer The SVT layer number
-	 * @param module The SVT module number
-	 * @return Corresponding sensor
-	 */
-	public HpsSiSensor getSensor(int layer, int module){
-	    for(HpsSiSensor sensor : this.getSensors()){
-	        if(sensor.getLayerNumber() == layer && sensor.getModuleNumber() == module) 
-	            return sensor; 
-	    }
-	    return null;
-	}
-	
-	/**
-	 * Get the maximum layer number present in the collection of {@link HpsSiSensor}.
-	 * 
-	 * @return maximum layer number
-	 */
-	private int getMaxLayerNumber(){
-	    int maxLayerNumber = 0;
-	    for(HpsSiSensor sensor : this.getSensors()){
-	       if(sensor.getLayerNumber() > maxLayerNumber) maxLayerNumber = sensor.getLayerNumber();
-	    }
-	    return maxLayerNumber; 
-	}
+    /**
+     * Get the collection of {@link HpsSiSensor} composing the SVT. 
+     * 
+     * @return List of sensors
+     */
+    public List<HpsSiSensor> getSensors(){
+        List<HpsSiSensor> list = this.findDescendants(HpsSiSensor.class);
+        if(debug) {
+            System.out.printf("%s: found %d HpsSiSensors\n",getClass().getSimpleName(), list.size());
+            System.out.printf("%s: %45s %5s %5s\n",getClass().getSimpleName(), "<name>", "<layerID>", "<moduleID>");
+            for(HpsSiSensor sensor : list) {
+                System.out.printf("%s: %45s %5d %5d\n",getClass().getSimpleName(), sensor.getName(), sensor.getLayerNumber(), sensor.getModuleNumber());
+            }
+        }
+        return list;
+    }
+    
+    /**
+     * Get a {@link HpsSiSensor} by layer and module number.
+     * 
+     * @param layer The SVT layer number
+     * @param module The SVT module number
+     * @return Corresponding sensor
+     */
+    public HpsSiSensor getSensor(int layer, int module){
+        for(HpsSiSensor sensor : this.getSensors()){
+            if(sensor.getLayerNumber() == layer && sensor.getModuleNumber() == module) 
+                return sensor; 
+        }
+        return null;
+    }
+    
+    /**
+     * Get the maximum layer number present in the collection of {@link HpsSiSensor}.
+     * 
+     * @return maximum layer number
+     */
+    private int getMaxLayerNumber(){
+        int maxLayerNumber = 0;
+        for(HpsSiSensor sensor : this.getSensors()){
+           if(sensor.getLayerNumber() > maxLayerNumber) maxLayerNumber = sensor.getLayerNumber();
+        }
+        return maxLayerNumber; 
+    }
 
-	/**
-	 * Get the maximum module number present in the collection of {@link HpsSiSensor}.
-	 * 
-	 * @return maximum module number
-	 */
-	private int getMaxModuleNumber(){
-	    int maxModuleID = 0; 
-	    for(HpsSiSensor sensor : this.getSensors()){
-	       if(sensor.getModuleNumber() > maxModuleID) maxModuleID = sensor.getModuleNumber();
-	    }
-	    return maxModuleID; 
-	}
-	
-	/**
-	 * Method that loops through the collection of {@link HpsSiSensor} and creates 
-	 * stereo layers. A stereo layer is composed of two adjacent sensors (stereo and axial)
-	 * with the same module number.
-	 */
-	public void createStereoLayers(){
+    /**
+     * Get the maximum module number present in the collection of {@link HpsSiSensor}.
+     * 
+     * @return maximum module number
+     */
+    private int getMaxModuleNumber(){
+        int maxModuleID = 0; 
+        for(HpsSiSensor sensor : this.getSensors()){
+           if(sensor.getModuleNumber() > maxModuleID) maxModuleID = sensor.getModuleNumber();
+        }
+        return maxModuleID; 
+    }
+    
+    /**
+     * Method that loops through the collection of {@link HpsSiSensor} and creates 
+     * stereo layers. A stereo layer is composed of two adjacent sensors (stereo and axial)
+     * with the same module number.
+     */
+    public void createStereoLayers(){
 
-	    //System.out.printf("%s: create stereo layers\n",getClass().getSimpleName());
+        //System.out.printf("%s: create stereo layers\n",getClass().getSimpleName());
         
-	    HpsSiSensor firstSensor = null;
+        HpsSiSensor firstSensor = null;
         HpsSiSensor secondSensor = null;
 
         //System.out.printf("%s: %10s %10s %42s %42s\n",getClass().getSimpleName(), "layerID/moduleID", "layerID/moduleID", "sensor1", "sensor2");

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java	Wed Apr 27 11:11:32 2016
@@ -9,76 +9,76 @@
  */
 public class SvtStereoLayer {
 
-	
-	// Layer number to which the stereo pair belongs to
-	private int stereoLayerNumber = 0; 
-	
-	// The axial and stereo sensors
-	private HpsSiSensor axialSensor = null; 
-	private HpsSiSensor stereoSensor = null;
-	
-	
-	/**
-	 * Ctor
-	 * 
-	 * @param layerNumber  Layer number to which the stereo pair belongs to
-	 * @param firstSensor  The first sensor in the stereo layer 
-	 * @param secondSensor The second sensor in the stereo layer
-	 */
-	public SvtStereoLayer(int stereoLayerNumber, HpsSiSensor firstSensor, HpsSiSensor secondSensor){
-		this.stereoLayerNumber = stereoLayerNumber;
-		if(firstSensor.isAxial()){
-		    this.axialSensor = firstSensor; 
-		    this.stereoSensor = secondSensor; 
-		} else { 
-		    this.axialSensor = secondSensor; 
-		    this.stereoSensor = firstSensor; 
-		}
-	}
-	
-	
-	/**
-	 * Get the axial sensor of the stereo pair
-	 * 
-	 * @return Axial sensor. Returns null if it hasn't been set yet.
-	 */
-	public HpsSiSensor getAxialSensor(){
-		return axialSensor; 
-	}
-	
-	/**
-	 * Get the stereo sensor of the stereo pair
-	 * 
-	 * @return Stereo sensor. Returns null if it hasn't been set yet.
-	 */
-	public HpsSiSensor getStereoSensor(){
-		return stereoSensor; 
-	}
+    
+    // Layer number to which the stereo pair belongs to
+    private int stereoLayerNumber = 0; 
+    
+    // The axial and stereo sensors
+    private HpsSiSensor axialSensor = null; 
+    private HpsSiSensor stereoSensor = null;
+    
+    
+    /**
+     * Ctor
+     * 
+     * @param stereoLayerNumber  Layer number to which the stereo pair belongs
+     * @param firstSensor  The first sensor in the stereo layer 
+     * @param secondSensor The second sensor in the stereo layer
+     */
+    public SvtStereoLayer(int stereoLayerNumber, HpsSiSensor firstSensor, HpsSiSensor secondSensor){
+        this.stereoLayerNumber = stereoLayerNumber;
+        if(firstSensor.isAxial()){
+            this.axialSensor = firstSensor; 
+            this.stereoSensor = secondSensor; 
+        } else { 
+            this.axialSensor = secondSensor; 
+            this.stereoSensor = firstSensor; 
+        }
+    }
+    
+    
+    /**
+     * Get the axial sensor of the stereo pair
+     * 
+     * @return Axial sensor. Returns null if it hasn't been set yet.
+     */
+    public HpsSiSensor getAxialSensor(){
+        return axialSensor; 
+    }
+    
+    /**
+     * Get the stereo sensor of the stereo pair
+     * 
+     * @return Stereo sensor. Returns null if it hasn't been set yet.
+     */
+    public HpsSiSensor getStereoSensor(){
+        return stereoSensor; 
+    }
 
-	/**
-	 * Get the layer number to which the stereo pair belongs to.
-	 * 
-	 * @return stereo layer number
-	 */
-	public int getLayerNumber(){
-		return stereoLayerNumber; 
-	}
-	
-	/**
-	 * Return a string describing the stereo pair
-	 * 
-	 * @return stereo pair description
-	 */
-	@Override
-	public String toString(){
-	    StringBuffer buffer = new StringBuffer();
-	    buffer.append("[ Stereo Pair ]: Layer number: " + this.getLayerNumber() + "\n");
-	    buffer.append("\t\tAxial Sensor: ");
-	    buffer.append(axialSensor == null ? "None" : axialSensor.getName());
-	    buffer.append("\tStereo Sensor: ");
-		buffer.append(stereoSensor == null ? "None" : stereoSensor.getName());
-		return buffer.toString(); 
-	}
+    /**
+     * Get the layer number to which the stereo pair belongs to.
+     * 
+     * @return stereo layer number
+     */
+    public int getLayerNumber(){
+        return stereoLayerNumber; 
+    }
+    
+    /**
+     * Return a string describing the stereo pair
+     * 
+     * @return stereo pair description
+     */
+    @Override
+    public String toString(){
+        StringBuffer buffer = new StringBuffer();
+        buffer.append("[ Stereo Pair ]: Layer number: " + this.getLayerNumber() + "\n");
+        buffer.append("\t\tAxial Sensor: ");
+        buffer.append(axialSensor == null ? "None" : axialSensor.getName());
+        buffer.append("\tStereo Sensor: ");
+        buffer.append(stereoSensor == null ? "None" : stereoSensor.getName());
+        return buffer.toString(); 
+    }
 
 }
 

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsSiSensor.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsSiSensor.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsSiSensor.java	Wed Apr 27 11:11:32 2016
@@ -303,9 +303,8 @@
     /**
      * Generate an ID for a channel (strip) on a sensor.
      *
-     * @param sensor
      * @param channel : Physical channel number
-     * @return ID
+     * @return the channel ID
      */
     public long makeChannelID(final int channel) {
         final int sideNumber = this.hasElectrodesOnSide(ChargeCarrier.HOLE) ? ChargeCarrier.HOLE.charge()
@@ -385,7 +384,7 @@
     /**
      * Set the front end board (FEB) ID of the sensor.
      * 
-     * @param FEB ID The FEB ID of the sensor.
+     * @param febID FEB ID The FEB ID of the sensor.
      */
     public void setFebID(final int febID) {
         this.febID = febID;
@@ -394,7 +393,7 @@
     /**
      * Set the FEB hybrid ID of the sensor.
      * 
-     * @param FEB hybrid ID The FEB hybrid ID.
+     * @param febHybridID FEB hybrid ID The FEB hybrid ID.
      */
     public void setFebHybridID(final int febHybridID) {
         this.febHybridID = febHybridID;
@@ -412,7 +411,7 @@
     /**
      * Flag the sensor as being axial.
      * 
-     * @param true if the sensor is Axial, false otherwise
+     * @param isAxial true if the sensor is Axial, false otherwise
      */
     public void setAxial(final boolean isAxial) {
         this.isAxial = isAxial;
@@ -421,7 +420,7 @@
     /**
      * Flag the sensor as being stereo
      * 
-     * @param true is the sensor is stereo, false otherwise
+     * @param isStereo true is the sensor is stereo, false otherwise
      */
     public void setStereo(final boolean isStereo) {
         this.isStereo = isStereo;
@@ -449,6 +448,8 @@
         buffer.append("\n");
         buffer.append("----------------------------------");
         buffer.append("\n");
+        buffer.append("Feb ID: " + this.getFebID() + "\n");
+        buffer.append("Feb Hybrid ID: " + this.getFebHybridID() + "\n");
         buffer.append("Layer: " + this.getLayerNumber() + "\n");
         buffer.append("Module: " + this.getModuleNumber() + "\n");
         buffer.append("Number of readout strips: " + this.getReadoutElectrodes(ChargeCarrier.HOLE).getNCells() + "\n");

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.java	Wed Apr 27 11:11:32 2016
@@ -14,85 +14,85 @@
  * @author Omar Moreno <[log in to unmask]>
  */
 public class HpsTestRunSiSensor extends HpsSiSensor {
-	
-	
-	protected int fpgaID;
-	protected int hybridID;
-			
-	
-	/**
-	 * This class constructor matches the signature of <code>SiSensor</code>.
-	 * @param sensorid The sensor ID.
-	 * @param name The name of the sensor.
-	 * @param parent The parent DetectorElement.
-	 * @param support The physical support path.
-	 * @param id The identifier of the sensor.
-	 */
-	public HpsTestRunSiSensor(
+    
+    
+    protected int fpgaID;
+    protected int hybridID;
+            
+    
+    /**
+     * This class constructor matches the signature of <code>SiSensor</code>.
+     * @param sensorid The sensor ID.
+     * @param name The name of the sensor.
+     * @param parent The parent DetectorElement.
+     * @param support The physical support path.
+     * @param id The identifier of the sensor.
+     */
+    public HpsTestRunSiSensor(
             int sensorid,
             String name,
             IDetectorElement parent,
             String support,
             IIdentifier id)
     {
-		super(sensorid, name, parent, support, id);
+        super(sensorid, name, parent, support, id);
     }
-	
-	
+    
+    
 
-	/**
-	 * Get the FPGA ID associated with this sensor.
-	 * 
-	 * @return The FPGA ID
-	 */
-	public int getFpgaID() {
-		return fpgaID;
-	}
+    /**
+     * Get the FPGA ID associated with this sensor.
+     * 
+     * @return The FPGA ID
+     */
+    public int getFpgaID() {
+        return fpgaID;
+    }
 
-	/**
-	 * Get the hybrid ID associated with this sensor.
-	 * 
-	 * @return The hybrid ID
-	 */
-	public int getHybridID() {
-		return hybridID;
-	}
+    /**
+     * Get the hybrid ID associated with this sensor.
+     * 
+     * @return The hybrid ID
+     */
+    public int getHybridID() {
+        return hybridID;
+    }
 
-	@Override
-	public int getFebID(){
-	    throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
-	}
-	
-	@Override
-	public int getFebHybridID(){
-	    throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
-	}
+    @Override
+    public int getFebID(){
+        throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
+    }
+    
+    @Override
+    public int getFebHybridID(){
+        throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
+    }
 
-	/**
-	 * Set the FPGA ID associated with this sensor.
-	 * 
-	 * @param The FPGA ID
-	 */
-	public void setFpgaID(int fpgaID) {
-		this.fpgaID = fpgaID;
-	}
+    /**
+     * Set the FPGA ID associated with this sensor.
+     * 
+     * @param fpgaID The FPGA ID
+     */
+    public void setFpgaID(int fpgaID) {
+        this.fpgaID = fpgaID;
+    }
 
-	/**
-	 * Set the hybrid ID associated with this sensor.
-	 * 
-	 * @param The hybrid ID.
-	 */
-	public void setHybridID(int hybridID) {
-		this.hybridID = hybridID;
-	}
-	
-	@Override
-	public void setFebID(int febID) {
-	    throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
-	}
-	
-	@Override
-	public void setFebHybridID(int febHybridID) {
-	    throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
-	}
+    /**
+     * Set the hybrid ID associated with this sensor.
+     * 
+     * @param hybridID The hybrid ID.
+     */
+    public void setHybridID(int hybridID) {
+        this.hybridID = hybridID;
+    }
+    
+    @Override
+    public void setFebID(int febID) {
+        throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
+    }
+    
+    @Override
+    public void setFebHybridID(int febHybridID) {
+        throw new RuntimeException("This method is not supported for the HpsTestRunSiSensor.");
+    }
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java	Wed Apr 27 11:11:32 2016
@@ -29,7 +29,7 @@
     protected static final boolean use30mradRotation = true;
     protected static final boolean useFakeHalfModuleAxialPos = false;
 
-    // Global position references	
+    // Global position references   
     protected static final double target_pos_wrt_base_plate_x = 162.3; //from Marco's 3D model
     protected static final double target_pos_wrt_base_plate_y = 80.55; //from Tim's sketchup //68.75; //from Marco's 3D model
     protected static final double target_pos_wrt_base_plate_z = 926.59; //from Marco's 3D model
@@ -208,7 +208,7 @@
         protected void setPos() {
             final double ball_pos_base_x = -1.0*target_pos_wrt_base_plate_x;
             final double ball_pos_base_y = -1.0*target_pos_wrt_base_plate_y;
-            final double ball_pos_base_z = target_pos_wrt_base_plate_z;		
+            final double ball_pos_base_z = target_pos_wrt_base_plate_z;     
             final double vee_pos_base_x = ball_pos_base_x + BasePlate.base_plate_width;
             final double vee_pos_base_y = ball_pos_base_y;
             final double vee_pos_base_z = ball_pos_base_z;
@@ -230,7 +230,7 @@
 
 
     public static class BasePlate extends SurveyVolume {
-        // Base plate references	
+        // Base plate references    
         public static final double base_plate_thickness = 0.25*inch;
         public static final double base_plate_width = 385.00;
         public static final double base_plate_length = 1216.00;
@@ -281,7 +281,7 @@
         public CSupport(String name, SurveyVolume mother) {
             super(name,mother, null);
             init();
-        }			
+        }           
         private void calcAndSetFlatPos() {
             if(use30mradRotation) {
                 // find the rotation to place the flat point
@@ -462,7 +462,7 @@
         // this is referenced to the pin position of the c-support
         private static final double ball_pos_csup_bearings_bottom_x = 240.0 - 265.0 + 14.0;
         private static final double ball_pos_csup_bearings_bottom_y = (-6.0 + 22.0);
-        private static final double ball_pos_csup_bearings_bottom_z = 14.7;		
+        private static final double ball_pos_csup_bearings_bottom_z = 14.7;     
         private static final double vee_pos_csup_bearings_bottom_x = 240.0- 129.0;
         private static final double vee_pos_csup_bearings_bottom_y = (-6.0 + 22.0);
         private static final double vee_pos_csup_bearings_bottom_z = 14.7;
@@ -499,12 +499,12 @@
 
             // make vectors
             setBallPos(ball_pos_csup_bearings_bottom_x,ball_pos_csup_bearings_bottom_y,ball_pos_csup_bearings_bottom_z);
-            setVeePos(vee_pos_csup_bearings_bottom_x,vee_pos_csup_bearings_bottom_y,vee_pos_csup_bearings_bottom_z);	
+            setVeePos(vee_pos_csup_bearings_bottom_x,vee_pos_csup_bearings_bottom_y,vee_pos_csup_bearings_bottom_z);    
             setFlatPos(flat_pos_csup_bearings_bottom_x,flat_pos_csup_bearings_bottom_y,flat_pos_csup_bearings_bottom_z);
 
 
             // create the coordinate system of the c-support bearings
-            //HPSTestRunTracker2014GeomDef.Coord csup_bearings_bottom_coord = new HPSTestRunTracker2014GeomDef.Coord(ball_pos_csup_bearings_bottom, vee_pos_csup_bearings_bottom, flat_pos_csup_bearings_bottom);		
+            //HPSTestRunTracker2014GeomDef.Coord csup_bearings_bottom_coord = new HPSTestRunTracker2014GeomDef.Coord(ball_pos_csup_bearings_bottom, vee_pos_csup_bearings_bottom, flat_pos_csup_bearings_bottom);       
 
             // since we don't care (no volume is built) about the local position of the bearings in the pin coord system we'll get rid of it
             // and find the bearings position in the base coordinate system directly
@@ -579,11 +579,11 @@
 
         public SupportPlateBottom(String name, SurveyVolume mother, SurveyVolume referenceGeom, String material) {
             super(mother, referenceGeom, name, material);
-            init();				
+            init();             
         }
         public SupportPlateBottom(String name, SurveyVolume mother, List<SurveyVolume> referenceGeom, String material) {
             super(mother, referenceGeom, name, material);
-            init();				
+            init();             
         }
         protected void setPos() {
             if(debug) System.out.printf("%s: setPos for %s\n",this.getClass().getSimpleName(),getName());
@@ -755,11 +755,11 @@
         public TestRunModule(String name, SurveyVolume mother, int layer, String half) {
             super(name, mother,null,layer, half);
             init();
-        }			
+        }           
         public TestRunModule(String name, SurveyVolume mother, SurveyVolume ref, int layer, String half) {
             super(name, mother,null,ref,layer, half);
             init();
-        }			
+        }           
         protected abstract double getColdBlockThickness();
         protected abstract double getModuleBoxLength();
         protected abstract double getModuleBoxWidth();
@@ -771,7 +771,7 @@
         }
         protected void setCenter() {
             setCenter(getModuleBoxLength()/2.0-5.0, 0.0, getModuleBoxWidth()/2.0-box_extra_width/5.0); 
-        }			
+        }           
         protected void setPos() {
 
             if(debug) System.out.printf("%s: setPos for %s\n",this.getClass().getSimpleName(),getName());
@@ -787,7 +787,7 @@
                 case 2:
                     ballPos = new BasicHep3Vector(25.0, 561.1, SupportPlateBottom.pedestal_height_L2-SupportPlateBottom.support_plate_pocket_depth);
                     veePos = new BasicHep3Vector(95.0, 561.1, SupportPlateBottom.pedestal_height_L2-SupportPlateBottom.support_plate_pocket_depth);
-                    flatPos = new BasicHep3Vector(60.0, 567.10, SupportPlateBottom.pedestal_height_L2-SupportPlateBottom.support_plate_pocket_depth);	
+                    flatPos = new BasicHep3Vector(60.0, 567.10, SupportPlateBottom.pedestal_height_L2-SupportPlateBottom.support_plate_pocket_depth);   
                     break;
                 case 3:
                     ballPos = new BasicHep3Vector(25.0, 461.1, SupportPlateBottom.pedestal_height_L3-SupportPlateBottom.support_plate_pocket_depth);
@@ -938,7 +938,7 @@
         // Distance from CF edge to screw hole: 30mm
         // Distance from screw hole to edge of cold block: 33.75mm
         // Distance from edge of cold block to hole/ball position: 5mm
-        protected static final double dist_sensor_center_to_coldblock_hole_vdir = (180.0 - 30.0 + (33.75 - 5.0)) - Sensor.length/2.0;	
+        protected static final double dist_sensor_center_to_coldblock_hole_vdir = (180.0 - 30.0 + (33.75 - 5.0)) - Sensor.length/2.0;   
         protected static final double half_module_thickness = TestRunHalfModule.getHybridThickness() + TestRunHalfModule.getCFThickness() + HalfModuleLamination.thickness;
         protected static final double half_module_length = TestRunHalfModule.getCFLength();
         protected static final double half_module_width = 6.83 + Sensor.width;
@@ -1038,7 +1038,7 @@
             if(useFakeHalfModuleAxialPos) {
                 ball_pos_halfmod_local_x = ball_pos_halfmod_local_x*2.0;
                 ball_pos_halfmod_local_y = -2.0*ball_pos_halfmod_local_y;
-            }				
+            }               
             final double ball_pos_halfmod_local_z =  dist_lower_sensor_edge_to_cold_block_mounting_surface + Sensor.width/2.0;
             
             
@@ -1118,7 +1118,7 @@
 //            final double vee_pos_halfmod_local_z =  ball_pos_halfmod_local_z;
 //            final double flat_pos_halfmod_local_x =  ball_pos_halfmod_local_x;
 //            final double flat_pos_halfmod_local_y =  ball_pos_halfmod_local_y + Sensor.getSensorThickness()/2.0;
-//            final double flat_pos_halfmod_local_z =  ball_pos_halfmod_local_z;		
+//            final double flat_pos_halfmod_local_z =  ball_pos_halfmod_local_z;        
 //            ballPos = new BasicHep3Vector(ball_pos_halfmod_local_x, ball_pos_halfmod_local_y, ball_pos_halfmod_local_z);
 //            veePos = new BasicHep3Vector(vee_pos_halfmod_local_x, vee_pos_halfmod_local_y,vee_pos_halfmod_local_z);
 //            flatPos = new BasicHep3Vector(flat_pos_halfmod_local_x, flat_pos_halfmod_local_y,flat_pos_halfmod_local_z);
@@ -1235,7 +1235,7 @@
 
     }
 
-    public static abstract class TestRunColdBlock extends SurveyVolume {		
+    public static abstract class TestRunColdBlock extends SurveyVolume {        
         private int layer;
         public TestRunColdBlock(String name, SurveyVolume mother, int layer) {
             super(name, mother, null);
@@ -1284,7 +1284,7 @@
         }
     }
 
-    public static class TestRunColdBlockL13 extends TestRunColdBlock {			
+    public static class TestRunColdBlockL13 extends TestRunColdBlock {          
         protected static final double coldblock_L13_length = 82.00;
         protected static final double coldblock_L13_width = 52.50;
         protected static final double coldblock_L13_thickness = 6.00;
@@ -1306,7 +1306,7 @@
         }
     }
 
-    public static class TestRunColdBlockL45 extends TestRunColdBlock {			
+    public static class TestRunColdBlockL45 extends TestRunColdBlock {          
         protected static final double coldblock_L45_length = 82.00;
         protected static final double coldblock_L45_width = 51.00;
         protected static final double coldblock_L45_thickness = 6.00;
@@ -1358,7 +1358,7 @@
 //            if(useSiStripsConvention) {
 //                setBallPos(0,0,0);
 //                setVeePos(ballPos.x(), ballPos.y(), ballPos.z() + getSensorWidth()/2.0);
-//                setFlatPos(ballPos.x() + getSensorLength()/2.0,ballPos.y(), ballPos.z());					
+//                setFlatPos(ballPos.x() + getSensorLength()/2.0,ballPos.y(), ballPos.z());                 
 //            } else {
 //                setBallPos(0,0,0);
 //                setVeePos(ballPos.x() + getSensorLength()/2.0, ballPos.y(), ballPos.z());
@@ -1392,7 +1392,7 @@
         }
         protected double getLength() {
             return length;
-        }			
+        }           
     }
 
     /**

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.java	Wed Apr 27 11:11:32 2016
@@ -28,175 +28,175 @@
  */
 public class HPSTestRunTracker2014JavaBuilder extends HPSTrackerJavaBuilder {
 
-	
-	
-	/**
-	 * Default constructor
-	 * @param node 
-	 */
-	public HPSTestRunTracker2014JavaBuilder(boolean debugFlag, Element node) {
-		super(debugFlag, node);
-	}
-	
-	
-	
-	/**
-	 * Build the JAVA geometry objects from the geometry definition.
-	 * @param trackingVolume - the reference volume.
-	 */
-	public void build(ILogicalVolume trackingVolume) {
-
-		// build geometry
+    
+    
+    /**
+     * Default constructor
+     * @param node 
+     */
+    public HPSTestRunTracker2014JavaBuilder(boolean debugFlag, Element node) {
+        super(debugFlag, node);
+    }
+    
+    
+    
+    /**
+     * Build the JAVA geometry objects from the geometry definition.
+     * @param trackingVolume - the reference volume.
+     */
+    public void build(ILogicalVolume trackingVolume) {
+
+        // build geometry
         setBuilder(createGeometryDefinition(_debug, node));
-		
-		if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
-
-		if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
-		
-		_builder.build();
-
-		if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
-
-		if(isDebug()) System.out.printf("%s: build the JAVA geometry objects\n", getClass().getSimpleName());
-		
-		// initialize the list to store a reference to each object
-		javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
-
-		// Go through the list of volumes to build that is created in the generic builder class
-		JavaSurveyVolume trackingGeometry = new JavaSurveyVolume(_builder.getSurveyVolume(org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition.TrackingVolume.class), trackingVolume);
-		add(trackingGeometry);
-		//setBaseTrackerGeometry(new GhostJavaBaseGeom(_builder.getBaseGeometry(Base.class), trackingGeometry));
+        
+        if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
+
+        if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
+        
+        _builder.build();
+
+        if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
+
+        if(isDebug()) System.out.printf("%s: build the JAVA geometry objects\n", getClass().getSimpleName());
+        
+        // initialize the list to store a reference to each object
+        javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
+
+        // Go through the list of volumes to build that is created in the generic builder class
+        JavaSurveyVolume trackingGeometry = new JavaSurveyVolume(_builder.getSurveyVolume(org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition.TrackingVolume.class), trackingVolume);
+        add(trackingGeometry);
+        //setBaseTrackerGeometry(new GhostJavaBaseGeom(_builder.getBaseGeometry(Base.class), trackingGeometry));
         setBaseTrackerGeometry(new JavaSurveyVolume(_builder.getSurveyVolume(TrackerEnvelope.class), trackingGeometry,1));
         add(getBaseTrackerGeometry());
-		JavaSurveyVolume basePlateGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(BasePlate.class), getBaseTrackerGeometry());
-		add(basePlateGeometry);
-		// skip the c-support, this is purely a reference volume in the builder so should have no use here!?
-		//JavaBaseGeometry cSupportGeometry = new GhostJavaBaseGeom(_builder.getBaseGeometry(CSupport.class), baseTrackerGeometry);
-		//add(cSupportGeometry);
-		JavaSurveyVolume supportBottomGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportBottom.class), getBaseTrackerGeometry());
-		add(supportBottomGeometry);
-		JavaSurveyVolume supportPlateBottomGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportPlateBottom.class), getBaseTrackerGeometry());
-		add(supportPlateBottomGeometry);
-		JavaSurveyVolume supportTopGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportTop.class), getBaseTrackerGeometry());
-		add(supportTopGeometry);
-		JavaSurveyVolume supportPlateTopGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportPlateTop.class), getBaseTrackerGeometry());
-		add(supportPlateTopGeometry);
-
-		// build modules	
-		
-		if(isDebug()) System.out.printf("%s: build JAVA modules\n", getClass().getSimpleName());
-
-		// Loop over all modules created
-		for(BaseModuleBundle mod : _builder.modules) {
-			TestRunModuleBundle m = (TestRunModuleBundle) mod;
-		    if(isDebug()) { 
-				System.out.printf("%s: build module %s (layer %d half %s)\n", getClass().getSimpleName(),m.module.getName(),m.getLayer(),m.getHalf());
-				m.print();
-			}
-
-			// Find the mother among the objects using its name, should probably have a better way...
-			String name_mother = m.getMother().getName();
-			JavaSurveyVolume mother = null;
-			for(JavaSurveyVolume g : javaSurveyVolumes) {
-				if(g.getName().equals(name_mother)) {
-					mother = g;
-					break;
-				}
-			}
-			// Check that it had a mother
-			if(mother==null) throw new RuntimeException("Cound't find mother to module " + m.module.getName());
-
-			if(isDebug()) System.out.printf("%s: found mother %s to module %s\n", getClass().getSimpleName(),mother.getName(),m.module.getName());
-			
-			// put the module in the list of objects that will be added to LCDD
-			addTestRunModule(m, mother);
-			
-			if(isDebug()) System.out.printf("%s: DONE build module %s\n", getClass().getSimpleName(), m.module.getName());
-
-			
-		}
-		
-		if(isDebug()) System.out.printf("%s: DONE build JAVA modules\n", getClass().getSimpleName());
-
-		
-		if(isDebug()) System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
-		if(isDebug()) {
-		    System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
-		    System.out.printf("%s: List of all the JAVA geometry objects built\n", this.getClass().getSimpleName());
-		    for(JavaSurveyVolume bg : javaSurveyVolumes) {
-		        System.out.printf("-------\n%s\n", bg.toString());
-		    }
-		}
-
-
-		// Set visualization features
-		//setVis();
-
-
-	}
-
-	/**
-	 * Rules for adding the JAVA module geometry.
-	 * @param bundle - module to be added
-	 * @param mother - mother JAVA geometry object
-	 */
-	protected void addTestRunModule(TestRunModuleBundle bundle, JavaSurveyVolume mother) {
-		
-		if(isDebug()) {
-			System.out.printf("%s: addModule %s containing:\n",this.getClass().getSimpleName(), bundle.module.getName());
-			bundle.print();
-		}
-		
-		// Create the module
-		JavaSurveyVolume lcddM = new JavaGhostSurveyVolume(bundle.module, mother);
-		add(lcddM);
-		
-		// add half modules
-		if(bundle.halfModuleAxial!=null)  addHalfModule((TestRunHalfModuleBundle)bundle.halfModuleAxial,lcddM);     
+        JavaSurveyVolume basePlateGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(BasePlate.class), getBaseTrackerGeometry());
+        add(basePlateGeometry);
+        // skip the c-support, this is purely a reference volume in the builder so should have no use here!?
+        //JavaBaseGeometry cSupportGeometry = new GhostJavaBaseGeom(_builder.getBaseGeometry(CSupport.class), baseTrackerGeometry);
+        //add(cSupportGeometry);
+        JavaSurveyVolume supportBottomGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportBottom.class), getBaseTrackerGeometry());
+        add(supportBottomGeometry);
+        JavaSurveyVolume supportPlateBottomGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportPlateBottom.class), getBaseTrackerGeometry());
+        add(supportPlateBottomGeometry);
+        JavaSurveyVolume supportTopGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportTop.class), getBaseTrackerGeometry());
+        add(supportTopGeometry);
+        JavaSurveyVolume supportPlateTopGeometry = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SupportPlateTop.class), getBaseTrackerGeometry());
+        add(supportPlateTopGeometry);
+
+        // build modules    
+        
+        if(isDebug()) System.out.printf("%s: build JAVA modules\n", getClass().getSimpleName());
+
+        // Loop over all modules created
+        for(BaseModuleBundle mod : _builder.modules) {
+            TestRunModuleBundle m = (TestRunModuleBundle) mod;
+            if(isDebug()) { 
+                System.out.printf("%s: build module %s (layer %d half %s)\n", getClass().getSimpleName(),m.module.getName(),m.getLayer(),m.getHalf());
+                m.print();
+            }
+
+            // Find the mother among the objects using its name, should probably have a better way...
+            String name_mother = m.getMother().getName();
+            JavaSurveyVolume mother = null;
+            for(JavaSurveyVolume g : javaSurveyVolumes) {
+                if(g.getName().equals(name_mother)) {
+                    mother = g;
+                    break;
+                }
+            }
+            // Check that it had a mother
+            if(mother==null) throw new RuntimeException("Cound't find mother to module " + m.module.getName());
+
+            if(isDebug()) System.out.printf("%s: found mother %s to module %s\n", getClass().getSimpleName(),mother.getName(),m.module.getName());
+            
+            // put the module in the list of objects that will be added to LCDD
+            addTestRunModule(m, mother);
+            
+            if(isDebug()) System.out.printf("%s: DONE build module %s\n", getClass().getSimpleName(), m.module.getName());
+
+            
+        }
+        
+        if(isDebug()) System.out.printf("%s: DONE build JAVA modules\n", getClass().getSimpleName());
+
+        
+        if(isDebug()) System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
+        if(isDebug()) {
+            System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
+            System.out.printf("%s: List of all the JAVA geometry objects built\n", this.getClass().getSimpleName());
+            for(JavaSurveyVolume bg : javaSurveyVolumes) {
+                System.out.printf("-------\n%s\n", bg.toString());
+            }
+        }
+
+
+        // Set visualization features
+        //setVis();
+
+
+    }
+
+    /**
+     * Rules for adding the JAVA module geometry.
+     * @param bundle - module to be added
+     * @param mother - mother JAVA geometry object
+     */
+    protected void addTestRunModule(TestRunModuleBundle bundle, JavaSurveyVolume mother) {
+        
+        if(isDebug()) {
+            System.out.printf("%s: addModule %s containing:\n",this.getClass().getSimpleName(), bundle.module.getName());
+            bundle.print();
+        }
+        
+        // Create the module
+        JavaSurveyVolume lcddM = new JavaGhostSurveyVolume(bundle.module, mother);
+        add(lcddM);
+        
+        // add half modules
+        if(bundle.halfModuleAxial!=null)  addHalfModule((TestRunHalfModuleBundle)bundle.halfModuleAxial,lcddM);     
         if(bundle.halfModuleStereo!=null) addHalfModule((TestRunHalfModuleBundle)bundle.halfModuleStereo,lcddM);
-		
-		
-		if(isDebug()) {
-			System.out.printf("%s: DONE addModule %s \n",this.getClass().getSimpleName(), bundle.module.getName());
-		}
-		
-	}
-	
-	
-	/**
-	 * Rules for adding the JAVA half module geometry.
-	 * @param bundle - module to be added
-	 * @param mother - mother JAVA geometry object
-	 */
-	private void addHalfModule(TestRunHalfModuleBundle bundle, JavaSurveyVolume mother) {
-		// Create the half-module
-		// This is not a ghost element but reflects the module 
-		// concept in the old compact description
-		// TODO fix the layer IDs
-		int oldCompactModuleId = 0;
-		JavaSurveyVolume lcddHM = new JavaSurveyVolume(bundle.halfModule, mother,oldCompactModuleId);
-		add(lcddHM);
-		
-		// ComponentNumber is taken from old geometry where it is simply a counter when adding the xml daughters to the TestRunModule.
-		// It is simply 0 for sensor and 1 for carbon fiber in the old geometry 
-		int componentNumber = ((Sensor)bundle.sensor).getId();
-
-		// create the sensor
-		JavaSurveyVolume lcddS = new JavaSurveyVolume(bundle.sensor, lcddHM, componentNumber);
-		add(lcddS);
-
-		// create the active sensor
-		JavaSurveyVolume lcddAS = new JavaSurveyVolume(bundle.activeSensor, lcddS, componentNumber);
-		add(lcddAS);
-		
-//		if(isDebug()) {
-//			System.out.printf("%s: added sensor %s \n",this.getClass().getSimpleName(), lcddS.getName());
-//			System.out.printf("%s: local coordinate system\n%s\n",this.getClass().getSimpleName(), bundle.sensor.getCoord().toString());
-//			dsd
-//		}
-		
-		
-	}
+        
+        
+        if(isDebug()) {
+            System.out.printf("%s: DONE addModule %s \n",this.getClass().getSimpleName(), bundle.module.getName());
+        }
+        
+    }
+    
+    
+    /**
+     * Rules for adding the JAVA half module geometry.
+     * @param bundle - module to be added
+     * @param mother - mother JAVA geometry object
+     */
+    private void addHalfModule(TestRunHalfModuleBundle bundle, JavaSurveyVolume mother) {
+        // Create the half-module
+        // This is not a ghost element but reflects the module 
+        // concept in the old compact description
+        // TODO fix the layer IDs
+        int oldCompactModuleId = 0;
+        JavaSurveyVolume lcddHM = new JavaSurveyVolume(bundle.halfModule, mother,oldCompactModuleId);
+        add(lcddHM);
+        
+        // ComponentNumber is taken from old geometry where it is simply a counter when adding the xml daughters to the TestRunModule.
+        // It is simply 0 for sensor and 1 for carbon fiber in the old geometry 
+        int componentNumber = ((Sensor)bundle.sensor).getId();
+
+        // create the sensor
+        JavaSurveyVolume lcddS = new JavaSurveyVolume(bundle.sensor, lcddHM, componentNumber);
+        add(lcddS);
+
+        // create the active sensor
+        JavaSurveyVolume lcddAS = new JavaSurveyVolume(bundle.activeSensor, lcddS, componentNumber);
+        add(lcddAS);
+        
+//      if(isDebug()) {
+//          System.out.printf("%s: added sensor %s \n",this.getClass().getSimpleName(), lcddS.getName());
+//          System.out.printf("%s: local coordinate system\n%s\n",this.getClass().getSimpleName(), bundle.sensor.getCoord().toString());
+//          dsd
+//      }
+        
+        
+    }
 
 
 
@@ -206,8 +206,8 @@
     }
 
 
-	
-	
-	
+    
+    
+    
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.java	Wed Apr 27 11:11:32 2016
@@ -26,157 +26,157 @@
 public class HPSTestRunTracker2014LCDDBuilder extends HPSTrackerLCDDBuilder {
 
 
-	public HPSTestRunTracker2014LCDDBuilder(boolean debugFlag, Element node, LCDD lcdd, SensitiveDetector sens) {
-		super(debugFlag, node, lcdd, sens);
-	}
+    public HPSTestRunTracker2014LCDDBuilder(boolean debugFlag, Element node, LCDD lcdd, SensitiveDetector sens) {
+        super(debugFlag, node, lcdd, sens);
+    }
 
-	
-	public void setBuilder() {
-	    setBuilder();
-	}
-	
-	public void build(Volume worldVolume) {
-		
-		// set and build geometry
+    
+    public void setBuilder() {
+        setBuilder();
+    }
+    
+    public void build(Volume worldVolume) {
+        
+        // set and build geometry
         setBuilder(createGeometryDefinition(_debug, node));
         
-		if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
+        if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
 
-		if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
+        if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
 
-		_builder.build();
+        _builder.build();
 
-		if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
+        if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
 
 
-		if(isDebug()) System.out.printf("%s: build the LCDD geometry objects\n", getClass().getSimpleName());
+        if(isDebug()) System.out.printf("%s: build the LCDD geometry objects\n", getClass().getSimpleName());
 
-		
-		// Go through the list of volumes to build that is created in the generic builder class
-		// TODO this is manual now since I don't have a way of knowing in the generic builder class what is a ghost volume at this point.
-		LCDDSurveyVolume trackingGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition.TrackingVolume.class), worldVolume);
-		add(trackingGeometry);
-		baseSurveyVolume = new LCDDSurveyVolume(_builder.getSurveyVolume(TrackerEnvelope.class), lcdd, trackingGeometry);
-		add(baseSurveyVolume);
-		LCDDSurveyVolume basePlateGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(BasePlate.class), lcdd, baseSurveyVolume);
-		add(basePlateGeometry);
-		// TODO I don't think this c-support has any use at all since the coordinates of it has been already used in the builder. Should remove?
-		LCDDSurveyVolume cSupportGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(CSupport.class), baseSurveyVolume);
-		add(cSupportGeometry);
-		LCDDSurveyVolume supportBottomGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(SupportBottom.class), baseSurveyVolume);
-		add(supportBottomGeometry);
-		LCDDSurveyVolume supportPlateBottomGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(SupportPlateBottom.class), lcdd, baseSurveyVolume);
-		add(supportPlateBottomGeometry);
-		LCDDSurveyVolume supportTopGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(SupportTop.class), baseSurveyVolume);
-		add(supportTopGeometry);
-		LCDDSurveyVolume supportPlateTopGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(SupportPlateTop.class), lcdd, baseSurveyVolume);
-		add(supportPlateTopGeometry);
+        
+        // Go through the list of volumes to build that is created in the generic builder class
+        // TODO this is manual now since I don't have a way of knowing in the generic builder class what is a ghost volume at this point.
+        LCDDSurveyVolume trackingGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition.TrackingVolume.class), worldVolume);
+        add(trackingGeometry);
+        baseSurveyVolume = new LCDDSurveyVolume(_builder.getSurveyVolume(TrackerEnvelope.class), lcdd, trackingGeometry);
+        add(baseSurveyVolume);
+        LCDDSurveyVolume basePlateGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(BasePlate.class), lcdd, baseSurveyVolume);
+        add(basePlateGeometry);
+        // TODO I don't think this c-support has any use at all since the coordinates of it has been already used in the builder. Should remove?
+        LCDDSurveyVolume cSupportGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(CSupport.class), baseSurveyVolume);
+        add(cSupportGeometry);
+        LCDDSurveyVolume supportBottomGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(SupportBottom.class), baseSurveyVolume);
+        add(supportBottomGeometry);
+        LCDDSurveyVolume supportPlateBottomGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(SupportPlateBottom.class), lcdd, baseSurveyVolume);
+        add(supportPlateBottomGeometry);
+        LCDDSurveyVolume supportTopGeometry = new LCDDGhostSurveyVolume(_builder.getSurveyVolume(SupportTop.class), baseSurveyVolume);
+        add(supportTopGeometry);
+        LCDDSurveyVolume supportPlateTopGeometry = new LCDDSurveyVolume(_builder.getSurveyVolume(SupportPlateTop.class), lcdd, baseSurveyVolume);
+        add(supportPlateTopGeometry);
 
-		// build modules	
+        // build modules    
 
-		if(isDebug()) System.out.printf("%s: build modules\n", getClass().getSimpleName());
+        if(isDebug()) System.out.printf("%s: build modules\n", getClass().getSimpleName());
 
-		// Loop over all modules created
-		for(BaseModuleBundle mod : _builder.modules) {
-		    TestRunModuleBundle m = (TestRunModuleBundle) mod;
-			if(isDebug()) { 
-				System.out.printf("%s: module layer %d half %s\n", getClass().getSimpleName(),m.getLayer(),m.getHalf());
-				m.print();
-			}
+        // Loop over all modules created
+        for(BaseModuleBundle mod : _builder.modules) {
+            TestRunModuleBundle m = (TestRunModuleBundle) mod;
+            if(isDebug()) { 
+                System.out.printf("%s: module layer %d half %s\n", getClass().getSimpleName(),m.getLayer(),m.getHalf());
+                m.print();
+            }
 
-			// Find the mother among the LCDD objects using its name, should probably have a better way...
-			String name_mother = m.getMother().getName();
-			LCDDSurveyVolume mother = null;
-			for(LCDDSurveyVolume g : lcddSurveyVolumes) {
-				if(g.getName().equals(name_mother)) {
-					mother = g;
-					break;
-				}
-			}
-			// Check that it had a mother
-			if(mother==null) throw new RuntimeException("Cound't find mother to module layer " + m.getLayer() + " half "+ m.getHalf());
+            // Find the mother among the LCDD objects using its name, should probably have a better way...
+            String name_mother = m.getMother().getName();
+            LCDDSurveyVolume mother = null;
+            for(LCDDSurveyVolume g : lcddSurveyVolumes) {
+                if(g.getName().equals(name_mother)) {
+                    mother = g;
+                    break;
+                }
+            }
+            // Check that it had a mother
+            if(mother==null) throw new RuntimeException("Cound't find mother to module layer " + m.getLayer() + " half "+ m.getHalf());
 
-			if(isDebug()) System.out.printf("%s: found mother %s for module layer %d half %s\n", getClass().getSimpleName(),mother.getName(),m.getLayer(),m.getHalf());
+            if(isDebug()) System.out.printf("%s: found mother %s for module layer %d half %s\n", getClass().getSimpleName(),mother.getName(),m.getLayer(),m.getHalf());
 
-			// add the module to the list of objects that will be added to LCDD
-			addTestRunModule(m, mother);
+            // add the module to the list of objects that will be added to LCDD
+            addTestRunModule(m, mother);
 
-		}
+        }
 
 
 
-		if(isDebug()) {
-		    System.out.printf("%s: DONE building the LCDD geometry objects\n", getClass().getSimpleName());
-		    System.out.printf("%s: List of all %d LCDD geometry objects built\n", this.getClass().getSimpleName(), lcddSurveyVolumes.size());
-		    for(SurveyVolumeImpl bg : lcddSurveyVolumes) {
-		        System.out.printf("-------\n%s\n", bg.toString());
-		    }
-		}
+        if(isDebug()) {
+            System.out.printf("%s: DONE building the LCDD geometry objects\n", getClass().getSimpleName());
+            System.out.printf("%s: List of all %d LCDD geometry objects built\n", this.getClass().getSimpleName(), lcddSurveyVolumes.size());
+            for(SurveyVolumeImpl bg : lcddSurveyVolumes) {
+                System.out.printf("-------\n%s\n", bg.toString());
+            }
+        }
 
 
 
-		// Set visualization features
-		setVisualization();
+        // Set visualization features
+        setVisualization();
 
 
-	}
+    }
 
 
-	/**
-	 * Rules for adding the LCDD module geometry.
-	 * @param bundle - module to be added
-	 * @param mother - mother LCDD geometry object
-	 */
-	protected void addTestRunModule(TestRunModuleBundle bundle, LCDDSurveyVolume mother) {
-		// This could perhaps be fixed if there is a relation with daughters in geometry definition?
-		// create the module
-		LCDDSurveyVolume lcddM = new LCDDSurveyVolume(bundle.module, lcdd, mother);
-		add(lcddM);
-		if(bundle.halfModuleAxial!=null)  addTestRunHalfModule(bundle.halfModuleAxial,lcddM);
-		if(bundle.coldBlock!=null)        add(new LCDDSurveyVolume(bundle.coldBlock, lcdd, lcddM));		
-		if(bundle.halfModuleStereo!=null) addTestRunHalfModule((TestRunHalfModuleBundle)bundle.halfModuleStereo,lcddM);
+    /**
+     * Rules for adding the LCDD module geometry.
+     * @param bundle - module to be added
+     * @param mother - mother LCDD geometry object
+     */
+    protected void addTestRunModule(TestRunModuleBundle bundle, LCDDSurveyVolume mother) {
+        // This could perhaps be fixed if there is a relation with daughters in geometry definition?
+        // create the module
+        LCDDSurveyVolume lcddM = new LCDDSurveyVolume(bundle.module, lcdd, mother);
+        add(lcddM);
+        if(bundle.halfModuleAxial!=null)  addTestRunHalfModule(bundle.halfModuleAxial,lcddM);
+        if(bundle.coldBlock!=null)        add(new LCDDSurveyVolume(bundle.coldBlock, lcdd, lcddM));     
+        if(bundle.halfModuleStereo!=null) addTestRunHalfModule((TestRunHalfModuleBundle)bundle.halfModuleStereo,lcddM);
 //        if(bundle.halfModuleAxial!=null)  addHalfModule((TestRunHalfModuleBundle)bundle.halfModuleAxial,lcddM);
 //        if(bundle.coldBlock!=null)        add(new LCDDSurveyVolume(bundle.coldBlock, lcdd, lcddM));     
 //        if(bundle.halfModuleStereo!=null) addHalfModule((TestRunHalfModuleBundle)bundle.halfModuleStereo,lcddM);
 
-	}
+    }
 
-	/**
-	 * Rules for adding the LCDD half module geometry.
-	 * @param bundle - module to be added
-	 * @param mother - mother LCDD geometry object
-	 */
-	protected void addTestRunHalfModule(HalfModuleBundle bundle2, LCDDSurveyVolume mother) {
-		// This could perhaps be fixed if there is a relation with daughters in geometry definition?
-	    TestRunHalfModuleBundle bundle = (TestRunHalfModuleBundle) bundle2;
-	    
-	    // create the half-module
-		LCDDSurveyVolume lcddHM = new LCDDSurveyVolume(bundle.halfModule, lcdd, mother);
-		add(lcddHM);
-		// create the sensor
-		LCDDSurveyVolume lcddS = new LCDDSurveyVolume(bundle.sensor, lcdd, lcddHM);
-		add(lcddS);
-		// create the active sensor
-		LCDDSurveyVolume lcddAS = new LCDDSurveyVolume(bundle.activeSensor, lcdd, lcddS);
-		add(lcddAS);
-		// create the lamination
-		LCDDSurveyVolume lcddL = new LCDDSurveyVolume(bundle.lamination, lcdd, lcddHM);
-		add(lcddL);
-		// create the carbon fiber frame
-		LCDDSurveyVolume lcddCF = new LCDDSurveyVolume(bundle.carbonFiber, lcdd, lcddHM);
-		add(lcddCF);
-		// create the hybrid frame
-		LCDDSurveyVolume lcddH = new LCDDSurveyVolume(bundle.hybrid, lcdd, lcddHM);
-		add(lcddH);
+    /**
+     * Rules for adding the LCDD half module geometry.
+     * @param bundle2 - module to be added
+     * @param mother - mother LCDD geometry object
+     */
+    protected void addTestRunHalfModule(HalfModuleBundle bundle2, LCDDSurveyVolume mother) {
+        // This could perhaps be fixed if there is a relation with daughters in geometry definition?
+        TestRunHalfModuleBundle bundle = (TestRunHalfModuleBundle) bundle2;
+        
+        // create the half-module
+        LCDDSurveyVolume lcddHM = new LCDDSurveyVolume(bundle.halfModule, lcdd, mother);
+        add(lcddHM);
+        // create the sensor
+        LCDDSurveyVolume lcddS = new LCDDSurveyVolume(bundle.sensor, lcdd, lcddHM);
+        add(lcddS);
+        // create the active sensor
+        LCDDSurveyVolume lcddAS = new LCDDSurveyVolume(bundle.activeSensor, lcdd, lcddS);
+        add(lcddAS);
+        // create the lamination
+        LCDDSurveyVolume lcddL = new LCDDSurveyVolume(bundle.lamination, lcdd, lcddHM);
+        add(lcddL);
+        // create the carbon fiber frame
+        LCDDSurveyVolume lcddCF = new LCDDSurveyVolume(bundle.carbonFiber, lcdd, lcddHM);
+        add(lcddCF);
+        // create the hybrid frame
+        LCDDSurveyVolume lcddH = new LCDDSurveyVolume(bundle.hybrid, lcdd, lcddHM);
+        add(lcddH);
 
-	}
+    }
 
 
     @Override
     public HPSTrackerGeometryDefinition createGeometryDefinition(boolean debug,
             Element node) {
         return new HPSTestRunTracker2014GeometryDefinition(_debug, node);
-    }	
+    }   
 
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.java	Wed Apr 27 11:11:32 2016
@@ -27,8 +27,8 @@
  *
  */
  public class HPSTracker2014GeometryDefinition extends HPSTrackerGeometryDefinition {
-
-     private static final Logger LOGGER = Logger.getLogger(HPSTracker2014GeometryDefinition.class.getPackage().getName());
+    
+    private static final Logger LOGGER = Logger.getLogger(HPSTracker2014GeometryDefinition.class.getPackage().getName());
 
     public HPSTracker2014GeometryDefinition(boolean debug, Element node) {
         super(debug, node);
@@ -38,8 +38,7 @@
         doBottom = true;
         doTop = true;
         layerBitMask = 0x3F;
-    }
-
+     }
 
     /* (non-Javadoc)
      * @see org.lcsim.geometry.compact.converter.HPSTrackerBuilder#build()
@@ -47,12 +46,11 @@
     public void build() {
 
         if(isDebug()) System.out.printf("%s: constructing the geometry objects\n", this.getClass().getSimpleName());
-
         
         // Create alignment correction objects
         // THis is really a ugly approach with MP corrections initialized before and 
         // the survey corrections based on the XML node
-        // FIX THIS! //TODO
+        // TODO: FIX THIS!
         AlignmentCorrection alignmentCorrections = new AlignmentCorrection();
         alignmentCorrections.setNode(node);
         AlignmentCorrection supBotCorr = getL13UChannelAlignmentCorrection(false);
@@ -74,25 +72,19 @@
 
         SvtBoxBasePlate svtBoxBasePlate = new SvtBoxBasePlate("base_plate",svtBox,null);
         surveyVolumes.add(svtBoxBasePlate);
-                
-        
-        
+                             
         SupportRingL13BottomKinMount supportRingKinL13Bottom = new SupportRingL13BottomKinMount("c_support_kin_L13b", svtBox, supBotCorr); 
-        surveyVolumes.add(supportRingKinL13Bottom);
-        
+        surveyVolumes.add(supportRingKinL13Bottom);        
         
         UChannelL13 uChannelL13Bottom = new UChannelL13Bottom("support_bottom_L13", svtBox, alignmentCorrections, supportRingKinL13Bottom); 
         surveyVolumes.add(uChannelL13Bottom);
         
         UChannelL13Plate uChannelL13BottomPlate = new UChannelL13BottomPlate("support_plate_bottom_L13", svtBox, null, uChannelL13Bottom); 
         surveyVolumes.add(uChannelL13BottomPlate);
-
         
         SupportRingL13TopKinMount supportRingKinL13Top = new SupportRingL13TopKinMount("c_support_kin_L13t", svtBox, supTopCorr); 
         surveyVolumes.add(supportRingKinL13Top);
-
-        
-        
+                
         UChannelL13Top uChannelL13Top = new UChannelL13Top("support_top_L13", svtBox, alignmentCorrections, supportRingKinL13Top); 
         surveyVolumes.add(uChannelL13Top);
         
@@ -110,7 +102,6 @@
         
         UChannelL46Plate uChannelL46TopPlate = new UChannelL46TopPlate("support_plate_top_L46", svtBox, null, uChannelL46Top);
         surveyVolumes.add(uChannelL46TopPlate);
-
         
         for(int l=1; l<=6;++l) {
             if(doLayer(l)) {
@@ -135,30 +126,20 @@
                 bundle.print();
             }
         }
-        
-        
-        
-        
-
-    }
-
+    }
     
     /**
      * {@link SurveyVolume} volume defining the pair spectrometer (PS) vacuum chamber
      * Reference: tracking volume coordinate system
      * Origin: same as reference
      * Orientation:  u - points in x direction (towards positron side), v - points upstream
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class PSVacuumChamber extends SurveyVolume {
+        
         public static final double height = PS_vac_box_inner_height; 
         public static final double width = PS_vac_box_inner_width;
         public static final double length = PS_vac_box_inner_length;
-        
-        
-        
+                       
         public PSVacuumChamber(String name, SurveyVolume mother, AlignmentCorrection alignmentCorrection) {
             super(name, mother, alignmentCorrection);
             init();
@@ -184,9 +165,6 @@
      * Reference: PS vacuum chamber coordinate system. Note that the PS vacuum chamber box is placed w.r.t. this box and the target positions.
      * Origin: intersection of midplanes vertically and horizontally
      * Orientation: same as reference
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class SvtBox extends SurveyVolume {
         public static final double height = 6.740*inch;
@@ -198,10 +176,7 @@
         public static final double center_to_target_z = 13.777*inch;
         public static final double center_to_target_x = 0.84*inch;
         public static final double center_to_target_y = 0.0;
-        
-        
-        
-        
+                               
         public SvtBox(String name, SurveyVolume mother, AlignmentCorrection alignmentCorrection) {
             super(name, mother, alignmentCorrection);
             init();
@@ -217,8 +192,7 @@
             
             ballPos = new BasicHep3Vector(0, 0, 0);
             veePos = new BasicHep3Vector(ballPos.x()+1, ballPos.y(), ballPos.z());
-            flatPos = new BasicHep3Vector(ballPos.x(), ballPos.y()+1, ballPos.z());
-            
+            flatPos = new BasicHep3Vector(ballPos.x(), ballPos.y()+1, ballPos.z());            
         }
     }
     
@@ -228,9 +202,6 @@
      * Reference: {@link SvtBox}  coordinate system.
      * Origin: surface of base plate intersection with center of hole for adjustment screw on positron side
      * Orientation: same as reference
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class SvtBoxBasePlate extends SurveyVolume {
         public static final double length = 50.5*inch;
@@ -268,16 +239,11 @@
         
     }
     
-    
-    
-    
     /**
      * {@link SurveyVolume} volume defining the coordinate system of the support ring
      *  Reference: @SvtBoxBasePlate
      *  Origin: pin position of support ring (electron side)
      *  Orientation: slot position is vee position (positron side) i.e u points towards the positron side and v in the upstream beam direction
-     *  
-     * @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     public static class SupportRing extends SurveyVolume {
@@ -315,14 +281,9 @@
             flatPos = VecOp.add(ballPos, vPrime);
         }
     }
-   
-    
-    
+        
     /**
      * Abstract {@link SurveyVolume} volume defining a coordinate system from the kinematic mount positions for support channels
-     *  
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public abstract static class SupportRingL13KinMount extends SurveyVolume {
 
@@ -360,9 +321,6 @@
      *  Reference: {@link SvtBox} coordinate system
      *  Origin: cone mount (it's on the electron side)
      *  Orientation: ball is cone mount, slot mount is vee position and flat is along beam line pointing upstream
-     *  
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class SupportRingL13BottomKinMount extends SupportRingL13KinMount {
 
@@ -385,9 +343,6 @@
      *  Reference: @SupportRing coordinate system
      *  Origin: cone mount (it's on the electron side)
      *  Orientation: ball is cone mount, slot mount is vee position and flat is along beamline pointing upstream
-     *  
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class SupportRingL13TopKinMount extends SupportRingL13KinMount {
         //public static final double mount_surface_wrt_baseplate_vertically = 5.388*inch;
@@ -420,12 +375,9 @@
 //            flatPos = new BasicHep3Vector(flat_pos_x,flat_pos_y,flat_pos_z);
 //        }
     }
-    
-    
-    /**
-     * Abstract {@link SurveyVolume} volume defining the coordinate system of the L1-3 u-channels 
-     *  
-     *  @author Per Hansson Adrian <[log in to unmask]>
+        
+    /**
+     * Abstract {@link SurveyVolume} volume defining the coordinate system of the L1-3 u-channels
      */
     public abstract static class UChannelL13 extends SurveyVolume {
         public final static double length = UChannelL13Plate.length;
@@ -457,9 +409,6 @@
      *  Reference: {@link SupportRingL13BottomKinMount} coordinate system
      *  Origin: midpoint between upstream survey cones
      *  Orientation: u - width pointing towards electron side, v - pointing along the U-channel in the beam direction
-     *  
-     *  @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class UChannelL13Bottom extends UChannelL13 {
         private final static double cone_to_edge_of_plate_y = 12.25*inch; 
@@ -489,14 +438,9 @@
         }
     }
     
-    
-    
     /**
      * Position of the center of the survey balls when engaging the cones in the side plates of the U-channel. 
      * This is at nominal position.
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     private static class UChannelL13BottomSurveyBalls  {
         
@@ -523,18 +467,12 @@
         }
     }
     
-    
-  
-    
     /**
      * {@link SurveyVolume} volume defining the coordinate system of the top L1-3 u-channel 
      *  Reference: SupportRingL13TopKinMount coordinate system
      *  Origin: midpoint between upstream survey cones
      *  Orientation: u - width pointing towards positron side, v - pointing along the U-channel in the beam direction
      *  Note that this is flipped w.r.t. bottom support.
-     *  
-     *  @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class UChannelL13Top extends UChannelL13 {
         private final static Hep3Vector ball_kinMount = new BasicHep3Vector(SupportRingL13TopKinMount.kin_mount_pos_x,SupportRingL13TopKinMount.kin_mount_pos_y,SupportRingL13TopKinMount.kin_mount_pos_z);
@@ -567,15 +505,10 @@
            return length;
         }
     }
-
-    
-    
+       
     /**
      * Position of the center of the survey balls when engaging the cones in the side plates of the U-channel. 
      * This is at nominal position.
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     private static class UChannelL13TopSurveyBalls  {
         
@@ -602,16 +535,8 @@
         }
     }
     
-    
-    
-    
-    
-
     /**
      * Abstract {@link SurveyVolume} volume defining the coordinate system of the u-channel plate
-
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public abstract static class UChannelPlate extends SurveyVolume {
         public UChannelPlate(String name, SurveyVolume m,
@@ -626,9 +551,6 @@
 
     /**
      * Abstract {@link SurveyVolume} volume defining the coordinate system of the u-channel plate
-
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public abstract static class UChannelL13Plate extends UChannelPlate {
         private final static double pocket_depth_L1 = 0.025;
@@ -689,9 +611,6 @@
      * Reference:  @UChannelL13Bottom coordinate system
      * Origin:  same as reference
      * Orientation: same as reference
-     *
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
      */
     public static class UChannelL13BottomPlate extends UChannelL13Plate {
         protected final static double L1_module_pin_to_edge_of_plate = (16.0-4.126)*inch;
@@ -715,10 +634,7 @@
      * {@link SurveyVolume} volume defining the coordinate system of the bottom u-channel plate
      * Reference:  @UChannelL13Bottom coordinate system
      * Origin:  same as reference
-     * Orientation: same as reference
-     *
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
+     * Orientation: same as reference     
      */
     public static class UChannelL13TopPlate extends UChannelL13Plate {
         protected final static double L1_module_pin_to_edge_of_plate = (16.0-2.75)*inch;
@@ -737,12 +653,9 @@
         }
        
     }
-    
-    
+        
     /**
      * Abstract {@link SurveyVolume} volume defining the L4-6 u-channel volume
-     * 
-     *  @author Per Hansson Adrian <[log in to unmask]>
      */
     public abstract static class UChannelL46 extends SurveyVolume {
 
@@ -760,26 +673,18 @@
 
         protected void setBoxDim() {
             setBoxDim(width,length,height);
-        }
-        
-    }
-    
-    
-   
-   
-    
+        }        
+    }
+                 
     /**
      * {@link SurveyVolume} volume defining the coordinate system of the u-channel 
      *  Reference: SVTBox coordinate system
      *  Origin: midpoint between upstream survey cones
      *  Orientation: u - width pointing towards electron side, v - pointing along the U-channel in the beam direction
-     *  
-     *  @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     public static class UChannelL46Bottom extends UChannelL46 {
-        
-        
+                
         protected static final double cone_to_edge_of_plate_y = 2.75*inch;
 
         public UChannelL46Bottom(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection) {
@@ -803,15 +708,12 @@
     
     /**
      * Position of the center of the survey balls when engaging the cones in the side plates of the U-channel.
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     private static class UChannelL46BottomSurveyBalls  {
         
-     // Shawn's calculated point at midpoint between two forward survey balls
+        // Shawn's calculated point at midpoint between two forward survey balls
         protected final static Hep3Vector ball_pos = new BasicHep3Vector(-5.857, -157.776, -8.423);
-
         
         private static final double cone_fwd_right_x = -7.019*inch;
         private static final double cone_fwd_right_y = -6.419*inch;
@@ -841,22 +743,14 @@
             return VecOp.sub(bwd_left, fwd_left);
         }
     }
-    
-    
-    
   
-    
     /**
      * {@link SurveyVolume} volume defining the coordinate system of the u-channel 
-     *  Reference: {@link SVTBox} coordinate system
-     *  Origin: midpoint between upstream survey cones
-     *  Orientation: u - width pointing towards electron side, v - pointing along the U-channel in the beam direction
-     *  
-     *  @author Per Hansson Adrian <[log in to unmask]>
-     *
+     * Reference: {@link HPSTracker2014GeometryDefinition.SVTBox} coordinate system
+     * Origin: midpoint between upstream survey cones
+     * Orientation: u - width pointing towards electron side, v - pointing along the U-channel in the beam direction
      */
     public static class UChannelL46Top extends UChannelL46 {
-
         
         private static final double cone_to_side_plate_pin_y = (0.875-0.25)*inch;
         private static final double side_plate_pin_to_edge_of_plate_y = 1.5*inch;
@@ -886,8 +780,7 @@
             //flatPos = new BasicHep3Vector(ballPos.x(), ballPos.y()-1, ballPos.z()); // random offset
         }
     }
-    
-    
+        
     /**
      * Position of the center of the survey balls when engaging the cones in the side plates of the U-channel.
      * 
@@ -899,7 +792,6 @@
         // Shawn's calculated point at midpoint between two forward survey balls
         protected final static Hep3Vector ball_pos = new BasicHep3Vector(-6.341, -141.909, 8.423);
 
-
         protected static final double cone_fwd_right_x = -7.038*inch;
         protected static final double cone_fwd_right_y = -5.794*inch;
         protected static final double cone_fwd_right_z = 0.332*inch;
@@ -928,14 +820,9 @@
             return VecOp.sub(bwd_right, fwd_right);
         }
     }
-
-
-    
-    /**
-     * Abstract {@link SurveyVolume}  defining the coordinate system of the u-channel plates
-
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
+    
+    /**
+     * Abstract {@link SurveyVolume}  defining the coordinate system of the u-channel plates     
      */
     public abstract static class UChannelL46Plate extends UChannelPlate {
         public final static double pocket_depth_L4 = 0.1;
@@ -1043,16 +930,12 @@
         }
        
     }
-
-    
-
+  
     /**
      * {@link SurveyVolume} volume defining the coordinate system of module L1-3
      * Reference:  @UChannelL13Bottom coordinate system
      * Origin:  hole position on mounting surface (on electron side)
      * Orientation: u - is normal to the surface pointing vertically down, v - points along module away from hybrid side (i.e. positron direction).
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     public abstract static class ModuleL13 extends BaseModule {
@@ -1119,8 +1002,7 @@
         protected double getHoleModuleCenterOffset() {
             return UChannelL13Bottom.cone_to_edge_of_plate_y - UChannelL13BottomPlate.L1_module_pin_to_edge_of_plate;
         }
-    }
-    
+    }    
     
     public static class ModuleL1Bot extends ModuleL13Bot {
 
@@ -1136,8 +1018,7 @@
             return new BasicHep3Vector(x, y, z);
         }
         
-    }
-    
+    }    
    
     public static class ModuleL1Top extends ModuleL13Top {
 
@@ -1155,9 +1036,7 @@
         }
         
     }
-    
-    
-    
+        
     public static class ModuleL2Bot extends ModuleL13Bot {
 
         public ModuleL2Bot(String name, SurveyVolume mother,
@@ -1190,10 +1069,7 @@
         }
         
     }
-    
-    
-    
-    
+        
     public static class ModuleL3Bot extends ModuleL13Bot {
 
         public ModuleL3Bot(String name, SurveyVolume mother,
@@ -1226,11 +1102,7 @@
         }
         
     }
-    
-    
-    
-   
-    
+                
     /**
      * Abstract {@link SurveyVolume} volume defining the coordinate system of module L4-6
      * 
@@ -1628,8 +1500,6 @@
      * Reference:  @ModuleL13Bot coordinate system
      * Origin:  sensor center
      * Orientation: w - is normal to the surface pointing from p-side to n-side, v - points along strips away from signal bond pads
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     public static class HalfModuleAxial extends HPSTestRunTracker2014GeometryDefinition.TestRunHalfModule {
@@ -1668,8 +1538,6 @@
      * Reference:  @ModuleL13Bot coordinate system
      * Origin:  sensor center
      * Orientation: same as axial - the module is rotated later.
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
      *
      */
     public static class HalfModuleStereo extends HPSTestRunTracker2014GeometryDefinition.TestRunHalfModule {
@@ -1873,23 +1741,21 @@
 
     }
 
-
-
-
-
-    /**
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
+    /**
+     *    
      */
     public static class LongModuleBundle extends BaseModuleBundle {
+        
         public HalfModuleBundle halfModuleAxialHole = null;
         public HalfModuleBundle halfModuleStereoHole = null;
         public HalfModuleBundle halfModuleAxialSlot = null;
         public HalfModuleBundle halfModuleStereoSlot = null;
         protected SurveyVolume coldBlock = null;
+        
         public LongModuleBundle(BaseModule m) {
             super(m);
         }
+        
         public void print() {
             if(module!=null) System.out.printf("%s: %s\n", this.getClass().getSimpleName(),module.toString());
             if(halfModuleAxialHole!=null) halfModuleAxialHole.print();
@@ -1897,13 +1763,11 @@
             if(coldBlock!=null)System.out.printf("%s: %s\n", this.getClass().getSimpleName(),coldBlock.getName());
             if(halfModuleStereoHole!=null) halfModuleStereoHole.print();
             if(halfModuleStereoSlot!=null) halfModuleStereoSlot.print();
-            }
-        }
-
-
-    /**
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
+        }
+    }
+
+    /**
+     *     
      */
     public static class LongHalfModuleBundle extends HalfModuleBundle {
         public LongHalfModuleBundle() {
@@ -1913,9 +1777,7 @@
             super(hm);
         }
     }
-    
-    
-    
+        
     /**
      * Create the half-module.
      * @param side - stereo or axial
@@ -1955,9 +1817,6 @@
         //TestRunModuleBundle bundle  = (TestRunModuleBundle)getModuleBundle(mother);
         //TestRunHalfModuleBundle halfModuleBundle;
         LongModuleBundle bundle  = (LongModuleBundle)getModuleBundle(mother);
-        
-       
-        
         
         // Build the half-module bundle and half-module
         //TODO clean this up to a separate method
@@ -1983,9 +1842,6 @@
             }
         } 
         halfModuleBundle.halfModule = halfModule;
-        
-        
-    
     
         // create the half module components 
         makeHalfModuleComponentSensor(halfModule);
@@ -1994,13 +1850,8 @@
 
         //makeHalfModuleComponentCF(halfModule);
     
-        //makeHalfModuleComponentHybrid(halfModule);
-    
-    
-    
-    
-    }
-
+        //makeHalfModuleComponentHybrid(halfModule);    
+    }
 
     protected void makeLongHalfModuleComponentKapton(BaseModule mother) {
         
@@ -2022,10 +1873,6 @@
     
     }
 
-    
-    
-    
-    
     protected HPSTestRunTracker2014GeometryDefinition.TestRunHalfModule createTestRunHalfModuleAxial(String volName,
             BaseModule mother, AlignmentCorrection alignmentCorrection,
             int layer, String half) {
@@ -2047,7 +1894,6 @@
      * @param alignmentCorrection
      * @param layer
      * @param half
-     * @return
      */
     protected LongHalfModule createLongAxialSlotHalfModule(String name, SurveyVolume mother,
             AlignmentCorrection alignmentCorrection, int layer,
@@ -2062,16 +1908,13 @@
      * @param alignmentCorrection
      * @param layer
      * @param half
-     * @return
      */
     protected LongHalfModule createLongStereoSlotHalfModule(String name, SurveyVolume mother,
             AlignmentCorrection alignmentCorrection, int layer,
             String half) {
         return new LongStereoSlotHalfModule(name, mother, alignmentCorrection, layer, half);
     }
-    
-    
-    
+
     /* (non-Javadoc)
      * @see org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition#getHalfModuleBundle(org.lcsim.geometry.compact.converter.HPSTestRunTracker2014GeometryDefinition.BaseModule, java.lang.String)
      */
@@ -2121,9 +1964,6 @@
         }
         return hm;
     }
-
-
-    
     
     /* (non-Javadoc)
      * @see org.lcsim.geometry.compact.converter.HPSTrackerBuilder#getMillepedeLayer(java.lang.String)
@@ -2149,8 +1989,6 @@
         return  getMillepedeLayer(isTopLayer, layer, isAxial, isHole);
 
     }
-    
-    
 
     /**
      * Definition relating the sensors and layer number used in millepede for this detector.
@@ -2158,7 +1996,6 @@
      * @param layer
      * @param isAxial
      * @param isHole
-     * @return
      */
     public int getMillepedeLayer(boolean isTopLayer, int layer, boolean isAxial, boolean isHole) {
         int l = -1;
@@ -2208,16 +2045,7 @@
         if(l<0) throw new RuntimeException("Error getting the millepede layer.");
         
         if(isDebug()) System.out.printf("%s: %s %d %s %s -> MP layer %d\n",getClass().getSimpleName(),isTopLayer?"top":"bottom", layer, isAxial?"axial":"stereo", isHole?"hole":"slot", l);
-
         
         return l;
     }
-
-
-   
-
 }
-
-
-
-

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.java	Wed Apr 27 11:11:32 2016
@@ -28,122 +28,122 @@
  */
 public class HPSTracker2014JavaBuilder extends HPSTestRunTracker2014JavaBuilder {
 
-	
-	
-	/**
-	 * Default constructor
-	 * @param node 
-	 */
-	public HPSTracker2014JavaBuilder(boolean debugFlag, Element node) {
-		super(debugFlag, node);
-	}
-	
-	
-	
-	
-	/**
-	 * Build the JAVA geometry objects from the geometry definition.
-	 * @param trackingVolume - the reference volume.
-	 */
-	public void build(ILogicalVolume trackingVolume) {
-
-		// build geometry
+    
+    
+    /**
+     * Default constructor
+     * @param node 
+     */
+    public HPSTracker2014JavaBuilder(boolean debugFlag, Element node) {
+        super(debugFlag, node);
+    }
+    
+    
+    
+    
+    /**
+     * Build the JAVA geometry objects from the geometry definition.
+     * @param trackingVolume - the reference volume.
+     */
+    public void build(ILogicalVolume trackingVolume) {
+
+        // build geometry
         setBuilder(createGeometryDefinition(this._debug, node));
-		
-		if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
-
-		if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
-		
-		_builder.build();
-
-		if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
-
-		if(isDebug()) System.out.printf("%s: build the JAVA geometry objects\n", getClass().getSimpleName());
-		
-		// initialize the list to store a reference to each object
-		javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
-
-		// Go through the list of volumes to build that is created in the generic builder class
-		JavaSurveyVolume tracking = new JavaSurveyVolume(_builder.getSurveyVolume(TrackingVolume.class), trackingVolume);
-		add(tracking);
-		JavaSurveyVolume chamber = new JavaGhostSurveyVolume(_builder.getSurveyVolume(PSVacuumChamber.class), tracking);
-		add(chamber);
-		setBaseTrackerGeometry(new JavaSurveyVolume(_builder.getSurveyVolume(SvtBox.class), chamber,1));
-		add(getBaseTrackerGeometry());
-		JavaSurveyVolume svtBoxBasePlate = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SvtBoxBasePlate.class), getBaseTrackerGeometry());
-		add(svtBoxBasePlate);
-
-		
-		// build modules	
-		
-		if(isDebug()) System.out.printf("%s: build JAVA modules\n", getClass().getSimpleName());
-
-		// Loop over all modules created
-		for(BaseModuleBundle mod : _builder.modules) {
-			BaseModuleBundle m = mod;
-		    if(isDebug()) { 
-				System.out.printf("%s: build module %s (layer %d half %s)\n", getClass().getSimpleName(),m.module.getName(),m.getLayer(),m.getHalf());
-				m.print();
-			}
-
-			// Find the mother among the objects using its name, should probably have a better way...
-			String name_mother = m.getMother().getName();
-			JavaSurveyVolume mother = null;
-			for(JavaSurveyVolume g : javaSurveyVolumes) {
-				if(g.getName().equals(name_mother)) {
-					mother = g;
-					break;
-				}
-			}
-			// Check that it had a mother
-			if(mother==null) throw new RuntimeException("Cound't find mother to module " + m.module.getName());
-
-			if(isDebug()) System.out.printf("%s: found mother %s to module %s\n", getClass().getSimpleName(),mother.getName(),m.module.getName());
-			
-			// put the module in the list of objects that will be added to LCDD
-			addModule(m, mother);
-			
-			if(isDebug()) System.out.printf("%s: DONE build module %s\n", getClass().getSimpleName(), m.module.getName());
-
-			
-		}
-		
-		if(isDebug()) System.out.printf("%s: DONE build JAVA modules\n", getClass().getSimpleName());
-
-		
-		//System.out.printf("%s: Built %d JAVA geometry objects\n", getClass().getSimpleName(),javaSurveyVolumes.size());
-		
-		if(isDebug()) {
-		    System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
-		    System.out.printf("%s: List of all the JAVA geometry objects built\n", this.getClass().getSimpleName());
-		    for(JavaSurveyVolume bg : javaSurveyVolumes) {
-		        System.out.printf("-------\n%s\n", bg.toString());
-		    }
-		}
-
-
-		// Set visualization features
-		//setVis();
-
-
-	}
-
-	/**
-	 * Rules for adding the JAVA module geometry.
-	 * @param bundle - module to be added
-	 * @param mother - mother JAVA geometry object
-	 */
-	private void addModule(BaseModuleBundle bundle, JavaSurveyVolume mother) {
-	    if(bundle instanceof TestRunModuleBundle) {
-	           addTestRunModule((TestRunModuleBundle) bundle, mother);
-	       } else if(bundle instanceof LongModuleBundle) {
-	           addLongModule((LongModuleBundle) bundle, mother);
-	       } else {
-	           throw new RuntimeException("The bundle is of unknown class type!");
-	       }
-	}
-	
-	/**
+        
+        if(_builder==null) throw new RuntimeException("need to set builder class before calling build!");
+
+        if(isDebug()) System.out.printf("%s: build the base geometry objects\n", getClass().getSimpleName());
+        
+        _builder.build();
+
+        if(isDebug()) System.out.printf("%s: DONE build the base geometry objects\n", getClass().getSimpleName());
+
+        if(isDebug()) System.out.printf("%s: build the JAVA geometry objects\n", getClass().getSimpleName());
+        
+        // initialize the list to store a reference to each object
+        javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
+
+        // Go through the list of volumes to build that is created in the generic builder class
+        JavaSurveyVolume tracking = new JavaSurveyVolume(_builder.getSurveyVolume(TrackingVolume.class), trackingVolume);
+        add(tracking);
+        JavaSurveyVolume chamber = new JavaGhostSurveyVolume(_builder.getSurveyVolume(PSVacuumChamber.class), tracking);
+        add(chamber);
+        setBaseTrackerGeometry(new JavaSurveyVolume(_builder.getSurveyVolume(SvtBox.class), chamber,1));
+        add(getBaseTrackerGeometry());
+        JavaSurveyVolume svtBoxBasePlate = new JavaGhostSurveyVolume(_builder.getSurveyVolume(SvtBoxBasePlate.class), getBaseTrackerGeometry());
+        add(svtBoxBasePlate);
+
+        
+        // build modules    
+        
+        if(isDebug()) System.out.printf("%s: build JAVA modules\n", getClass().getSimpleName());
+
+        // Loop over all modules created
+        for(BaseModuleBundle mod : _builder.modules) {
+            BaseModuleBundle m = mod;
+            if(isDebug()) { 
+                System.out.printf("%s: build module %s (layer %d half %s)\n", getClass().getSimpleName(),m.module.getName(),m.getLayer(),m.getHalf());
+                m.print();
+            }
+
+            // Find the mother among the objects using its name, should probably have a better way...
+            String name_mother = m.getMother().getName();
+            JavaSurveyVolume mother = null;
+            for(JavaSurveyVolume g : javaSurveyVolumes) {
+                if(g.getName().equals(name_mother)) {
+                    mother = g;
+                    break;
+                }
+            }
+            // Check that it had a mother
+            if(mother==null) throw new RuntimeException("Cound't find mother to module " + m.module.getName());
+
+            if(isDebug()) System.out.printf("%s: found mother %s to module %s\n", getClass().getSimpleName(),mother.getName(),m.module.getName());
+            
+            // put the module in the list of objects that will be added to LCDD
+            addModule(m, mother);
+            
+            if(isDebug()) System.out.printf("%s: DONE build module %s\n", getClass().getSimpleName(), m.module.getName());
+
+            
+        }
+        
+        if(isDebug()) System.out.printf("%s: DONE build JAVA modules\n", getClass().getSimpleName());
+
+        
+        //System.out.printf("%s: Built %d JAVA geometry objects\n", getClass().getSimpleName(),javaSurveyVolumes.size());
+        
+        if(isDebug()) {
+            System.out.printf("%s: DONE building the JAVA geometry objects\n", getClass().getSimpleName());
+            System.out.printf("%s: List of all the JAVA geometry objects built\n", this.getClass().getSimpleName());
+            for(JavaSurveyVolume bg : javaSurveyVolumes) {
+                System.out.printf("-------\n%s\n", bg.toString());
+            }
+        }
+
+
+        // Set visualization features
+        //setVis();
+
+
+    }
+
+    /**
+     * Rules for adding the JAVA module geometry.
+     * @param bundle - module to be added
+     * @param mother - mother JAVA geometry object
+     */
+    private void addModule(BaseModuleBundle bundle, JavaSurveyVolume mother) {
+        if(bundle instanceof TestRunModuleBundle) {
+               addTestRunModule((TestRunModuleBundle) bundle, mother);
+           } else if(bundle instanceof LongModuleBundle) {
+               addLongModule((LongModuleBundle) bundle, mother);
+           } else {
+               throw new RuntimeException("The bundle is of unknown class type!");
+           }
+    }
+    
+    /**
      * Rules for adding the LCDD module geometry.
      * @param bundle - module to be added
      * @param mother - mother LCDD geometry object
@@ -191,12 +191,12 @@
         
         
     }
-	
+    
     @Override
     public HPSTrackerGeometryDefinition createGeometryDefinition(boolean debug, Element node) {
         return new HPSTracker2014GeometryDefinition(debug, node);
     }
-	
-	
+    
+    
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
 /**
  * 
  * Updated geometry information for the HPS tracker 2014
-
+ * 
  * @author Per Hansson Adrian <[log in to unmask]>
  *
  */
@@ -93,8 +93,7 @@
 
     
     /**
-     * PI rotation around generic z-axis
-     * @return
+     * PI rotation around generic z-axis 
      */
     private static Rotation getSlotRotation() {
         return new Rotation(new Vector3D(0,0,1),Math.PI);

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerBuilder.java	Wed Apr 27 11:11:32 2016
@@ -632,7 +632,7 @@
     /**
      * Get hole or slot key name from string
      * 
-     * @param name.
+     * @param name "hole" or "slot"
      * @return hole or not boolean
      */
     public static boolean isHoleFromName(String name) {
@@ -649,10 +649,7 @@
     /**
      * Extract old definition of Test Run sensor number.
      * 
-     * @param isTopLayer - top or bottom layer
-     * @param l - layer
-     * @param isAxial - axial or stereo sensor
-     * @return
+     * @return the geometric layer according to Test Run definition
      */
     public int getOldGeomDefLayerFromVolumeName(String name) {
 
@@ -672,8 +669,7 @@
     /**
      * Get the layer number consistent with the old geometry definition.
      * 
-     * @param module name that contains layer and half information.
-     * @return the layer.
+     * @return the older layer definition
      */
     public int getOldLayerDefinition(boolean isTopLayer, int l, boolean isAxial) {
         int layer = -1;

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition.java	Wed Apr 27 11:11:32 2016
@@ -41,7 +41,7 @@
     protected static final boolean use30mradRotation = true;
     protected static final boolean useFakeHalfModuleAxialPos = false;
 
-    // Global position references	
+    // Global position references   
     protected static final double target_pos_wrt_base_plate_x = 162.3; //from Marco's 3D model
     protected static final double target_pos_wrt_base_plate_y = 80.55; //from Tim's sketchup //68.75; //from Marco's 3D model
     protected static final double target_pos_wrt_base_plate_z = 926.59; //from Marco's 3D model

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.java	Wed Apr 27 11:11:32 2016
@@ -15,158 +15,158 @@
 
 public abstract class HPSTrackerJavaBuilder implements IHPSTrackerJavaBuilder {
 
-	protected boolean _debug = false;
-	private JavaSurveyVolume baseSurveyVolume;
-	protected List<JavaSurveyVolume> javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
-	protected DetectorIdentifierHelper detectorIdentifierHelper;
-	protected IIdentifierDictionary identifierDictionary;
-	protected Subdetector subdet;
-	protected List<IDetectorElement> layerDetectorElements = new ArrayList<IDetectorElement>();
-	protected List<IDetectorElement> moduleDetectorElements = new ArrayList<IDetectorElement>();
-	protected IDetectorElement baseDetectorElement = null;
-	public HPSTrackerBuilder _builder = null;
+    protected boolean _debug = false;
+    private JavaSurveyVolume baseSurveyVolume;
+    protected List<JavaSurveyVolume> javaSurveyVolumes = new ArrayList<JavaSurveyVolume>();
+    protected DetectorIdentifierHelper detectorIdentifierHelper;
+    protected IIdentifierDictionary identifierDictionary;
+    protected Subdetector subdet;
+    protected List<IDetectorElement> layerDetectorElements = new ArrayList<IDetectorElement>();
+    protected List<IDetectorElement> moduleDetectorElements = new ArrayList<IDetectorElement>();
+    protected IDetectorElement baseDetectorElement = null;
+    public HPSTrackerBuilder _builder = null;
     protected Element node = null;
-	
-	public HPSTrackerJavaBuilder(boolean debugFlag, Element node) {
-		this._debug=debugFlag;
-		this.node  = node;
-	}	
-	
-	public abstract void build(ILogicalVolume trackingVolume);
-	public abstract HPSTrackerGeometryDefinition createGeometryDefinition(boolean debug, Element node);
+    
+    public HPSTrackerJavaBuilder(boolean debugFlag, Element node) {
+        this._debug=debugFlag;
+        this.node  = node;
+    }   
+    
+    public abstract void build(ILogicalVolume trackingVolume);
+    public abstract HPSTrackerGeometryDefinition createGeometryDefinition(boolean debug, Element node);
 
-	
-	/**
-	 * Add to list of objects.
-	 * @param geom - object to add.
-	 */
-	public void add(JavaSurveyVolume geom) {
-		javaSurveyVolumes.add(geom);
-	}
-	
-	public void setBuilder(HPSTrackerBuilder b) {
-		_builder = b;
-	}
-	
-	public void build() {
-		_builder.build();
-	}
-	
-	public void setDebug(boolean debug) {
-		_debug = debug;
-	}
-	
-	public boolean isDebug() {
-		return _debug;
-	}
+    
+    /**
+     * Add to list of objects.
+     * @param geom - object to add.
+     */
+    public void add(JavaSurveyVolume geom) {
+        javaSurveyVolumes.add(geom);
+    }
+    
+    public void setBuilder(HPSTrackerBuilder b) {
+        _builder = b;
+    }
+    
+    public void build() {
+        _builder.build();
+    }
+    
+    public void setDebug(boolean debug) {
+        _debug = debug;
+    }
+    
+    public boolean isDebug() {
+        return _debug;
+    }
 
 
-	public DetectorIdentifierHelper getDetectorIdentifierHelper() {
-		return detectorIdentifierHelper;
-	}
+    public DetectorIdentifierHelper getDetectorIdentifierHelper() {
+        return detectorIdentifierHelper;
+    }
 
-	public void setDetectorIdentifierHelper(
-			DetectorIdentifierHelper detectorIdentifierHelper) {
-		this.detectorIdentifierHelper = detectorIdentifierHelper;
-	}
+    public void setDetectorIdentifierHelper(
+            DetectorIdentifierHelper detectorIdentifierHelper) {
+        this.detectorIdentifierHelper = detectorIdentifierHelper;
+    }
 
-	public IIdentifierDictionary getIdentifierDictionary() {
-		return identifierDictionary;
-	}
+    public IIdentifierDictionary getIdentifierDictionary() {
+        return identifierDictionary;
+    }
 
-	public void setIdentifierDictionary(
-			IIdentifierDictionary identifierDictionary) {
-		this.identifierDictionary = identifierDictionary;
-	}
+    public void setIdentifierDictionary(
+            IIdentifierDictionary identifierDictionary) {
+        this.identifierDictionary = identifierDictionary;
+    }
 
 
-	public void setSubdetector(Subdetector subdet) {
-		this.subdet = subdet;
-	}
+    public void setSubdetector(Subdetector subdet) {
+        this.subdet = subdet;
+    }
 
-	public Subdetector getSubdetector() {
-		return this.subdet;
-	}
+    public Subdetector getSubdetector() {
+        return this.subdet;
+    }
 
-	
+    
 
-	
+    
 
-	// This finds specific type. I would like to use the ID for this but can't, I think.
-	// TODO there must be a factory instance to do this
-	public SiTrackerModule getModuleDetectorElement(SiTrackerModule testElement) {
-		if(isDebug()) System.out.printf("%s: getModuleDetectorElement for module  %s path: \"%s\"\n", this.getClass().getSimpleName(),testElement.getName(),testElement.getGeometry().getPathString());
-		SiTrackerModule element = null;
-		for(IDetectorElement e : moduleDetectorElements) {
-			SiTrackerModule m = (SiTrackerModule) e;
-			if(isDebug()) System.out.printf("%s: compare with module  %s path: %s\"%s\" \n", this.getClass().getSimpleName(),m.getName(),m.getGeometry().getPathString());
-			if(m.getGeometry().getPathString().equals(testElement.getGeometry().getPathString())) {
-				if(element!=null) throw new RuntimeException("two DE sharing extended ID?");
-				if(isDebug()) System.out.printf("%s: found it\n", this.getClass().getSimpleName());
-				element = m;
-			}
-		}
-		return element;
-	}
+    // This finds specific type. I would like to use the ID for this but can't, I think.
+    // TODO there must be a factory instance to do this
+    public SiTrackerModule getModuleDetectorElement(SiTrackerModule testElement) {
+        if(isDebug()) System.out.printf("%s: getModuleDetectorElement for module  %s path: \"%s\"\n", this.getClass().getSimpleName(),testElement.getName(),testElement.getGeometry().getPathString());
+        SiTrackerModule element = null;
+        for(IDetectorElement e : moduleDetectorElements) {
+            SiTrackerModule m = (SiTrackerModule) e;
+            if(isDebug()) System.out.printf("%s: compare with module  %s path: %s\"%s\" \n", this.getClass().getSimpleName(),m.getName(),m.getGeometry().getPathString());
+            if(m.getGeometry().getPathString().equals(testElement.getGeometry().getPathString())) {
+                if(element!=null) throw new RuntimeException("two DE sharing extended ID?");
+                if(isDebug()) System.out.printf("%s: found it\n", this.getClass().getSimpleName());
+                element = m;
+            }
+        }
+        return element;
+    }
 
-	
-	// Find detector elements
-	// TODO This should be using some global geometry code like DetectorElementStore?
-	public IDetectorElement getLayerDetectorElement(IExpandedIdentifier expId) {
-		IDetectorElement element = null;
-		if(isDebug()) System.out.printf("%s: search among %d layer DEs\n", this.getClass().getSimpleName(), layerDetectorElements.size());
-		for(IDetectorElement e : layerDetectorElements) {
-			if(isDebug()) System.out.printf("%s: test %s\n", this.getClass().getSimpleName(),e.getName());
-			ExpandedIdentifier eId = (ExpandedIdentifier) e.getExpandedIdentifier();
-			if(eId.equals(expId)) { // TODO order matters as expId is an interface without that function!?
-				//check that only one was found
-				if(element!=null) throw new RuntimeException("two DE sharing extended ID?");
-				if(isDebug()) System.out.printf("%s: found it\n", this.getClass().getSimpleName());
-				element = e;
-			}
+    
+    // Find detector elements
+    // TODO This should be using some global geometry code like DetectorElementStore?
+    public IDetectorElement getLayerDetectorElement(IExpandedIdentifier expId) {
+        IDetectorElement element = null;
+        if(isDebug()) System.out.printf("%s: search among %d layer DEs\n", this.getClass().getSimpleName(), layerDetectorElements.size());
+        for(IDetectorElement e : layerDetectorElements) {
+            if(isDebug()) System.out.printf("%s: test %s\n", this.getClass().getSimpleName(),e.getName());
+            ExpandedIdentifier eId = (ExpandedIdentifier) e.getExpandedIdentifier();
+            if(eId.equals(expId)) { // TODO order matters as expId is an interface without that function!?
+                //check that only one was found
+                if(element!=null) throw new RuntimeException("two DE sharing extended ID?");
+                if(isDebug()) System.out.printf("%s: found it\n", this.getClass().getSimpleName());
+                element = e;
+            }
 
-		}
-		return element;
-	}
+        }
+        return element;
+    }
 
 
-	public void addLayerDetectorElement(IDetectorElement e) {
-		IExpandedIdentifier expId = e.getExpandedIdentifier();
-		if(getLayerDetectorElement(expId) != null) 
-			throw new RuntimeException("Trying to add an existing layer detector element.");
-		layerDetectorElements.add(e);
-	}
+    public void addLayerDetectorElement(IDetectorElement e) {
+        IExpandedIdentifier expId = e.getExpandedIdentifier();
+        if(getLayerDetectorElement(expId) != null) 
+            throw new RuntimeException("Trying to add an existing layer detector element.");
+        layerDetectorElements.add(e);
+    }
 
-	public void addBaseDetectorElement(IDetectorElement e) {
-	    baseDetectorElement = e;
-	}
+    public void addBaseDetectorElement(IDetectorElement e) {
+        baseDetectorElement = e;
+    }
 
-	public IDetectorElement getBaseDetectorElement() {
-	    return baseDetectorElement;
-	}
+    public IDetectorElement getBaseDetectorElement() {
+        return baseDetectorElement;
+    }
 
-	public void addModuleDetectorElement(IDetectorElement e) {
-		if(!(e instanceof SiTrackerModule)) 
-			throw new RuntimeException("Trying to add an existing module of wrong type.");
-		if(getModuleDetectorElement((SiTrackerModule) e) != null) 
-			throw new RuntimeException("Trying to add an already existing module detector element.");
-		layerDetectorElements.add(e);
-	}
-	
+    public void addModuleDetectorElement(IDetectorElement e) {
+        if(!(e instanceof SiTrackerModule)) 
+            throw new RuntimeException("Trying to add an existing module of wrong type.");
+        if(getModuleDetectorElement((SiTrackerModule) e) != null) 
+            throw new RuntimeException("Trying to add an already existing module detector element.");
+        layerDetectorElements.add(e);
+    }
+    
 
-	/**
-	 * @return the baseTrackerGeometry
-	 */
-	public JavaSurveyVolume getBaseTrackerGeometry() {
-		return baseSurveyVolume;
-	}
+    /**
+     * @return the baseTrackerGeometry
+     */
+    public JavaSurveyVolume getBaseTrackerGeometry() {
+        return baseSurveyVolume;
+    }
 
-	/**
-	 * @param baseTrackerGeometry the baseTrackerGeometry to set
-	 */
-	public void setBaseTrackerGeometry(JavaSurveyVolume baseTrackerGeometry) {
-		this.baseSurveyVolume = baseTrackerGeometry;
-	}
+    /**
+     * @param baseTrackerGeometry the baseTrackerGeometry to set
+     */
+    public void setBaseTrackerGeometry(JavaSurveyVolume baseTrackerGeometry) {
+        this.baseSurveyVolume = baseTrackerGeometry;
+    }
 
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.java	Wed Apr 27 11:11:32 2016
@@ -10,24 +10,24 @@
 
 public abstract class HPSTrackerLCDDBuilder  implements IHPSTrackerLCDDBuilder {
 
-	public boolean _debug = false;
-	protected LCDD lcdd = null;
-	protected LCDDSurveyVolume baseSurveyVolume;
-	protected List<LCDDSurveyVolume> lcddSurveyVolumes = new ArrayList<LCDDSurveyVolume>();
-	private SensitiveDetector sensitiveDetector;
-	public HPSTrackerBuilder _builder = null;
+    public boolean _debug = false;
+    protected LCDD lcdd = null;
+    protected LCDDSurveyVolume baseSurveyVolume;
+    protected List<LCDDSurveyVolume> lcddSurveyVolumes = new ArrayList<LCDDSurveyVolume>();
+    private SensitiveDetector sensitiveDetector;
+    public HPSTrackerBuilder _builder = null;
     protected Element node;
 
-	
-	
-	public HPSTrackerLCDDBuilder(boolean debugFlag, Element node, LCDD lcdd2, SensitiveDetector sens) {
-		setDebug(debugFlag);
-		setLCDD(lcdd2);
-		setSensitiveDetector(sens);
-		setNode(node);
-	}
-	
-	/**
+    
+    
+    public HPSTrackerLCDDBuilder(boolean debugFlag, Element node, LCDD lcdd2, SensitiveDetector sens) {
+        setDebug(debugFlag);
+        setLCDD(lcdd2);
+        setSensitiveDetector(sens);
+        setNode(node);
+    }
+    
+    /**
      * Build the LCDD geometry objects.
      * @param worldVolume - the reference volume.
      */
@@ -37,93 +37,93 @@
     public abstract void setBuilder();
     
     public abstract HPSTrackerGeometryDefinition createGeometryDefinition(boolean debug, Element node);
-	
+    
 
-	public void setNode(Element node) {
+    public void setNode(Element node) {
         this.node = node;
-	}
-	
+    }
+    
     public void setSensitiveDetector(SensitiveDetector sens) {
-		this.sensitiveDetector = sens;
-	}
+        this.sensitiveDetector = sens;
+    }
 
-	public SensitiveDetector getSensitiveDetector() {
-		return this.sensitiveDetector;
-	}
+    public SensitiveDetector getSensitiveDetector() {
+        return this.sensitiveDetector;
+    }
 
-	public void setBuilder(HPSTrackerBuilder b) {
-		_builder = b;
-	}
-	
-	public HPSTrackerBuilder getBuilder() {
-	    return _builder;
-	}
-	
-	public void build() {
-		_builder.build();
-	}
-	
-	public void setDebug(boolean debug) {
-		_debug = debug;
-	}
-	
-	public boolean isDebug() {
-		return _debug;
-	}
-	
-	/**
-	 * Add to list of objects.
-	 * @param geom - object to add.
-	 */
-	public void add(LCDDSurveyVolume geom) {
-		lcddSurveyVolumes.add(geom);
-	}
+    public void setBuilder(HPSTrackerBuilder b) {
+        _builder = b;
+    }
+    
+    public HPSTrackerBuilder getBuilder() {
+        return _builder;
+    }
+    
+    public void build() {
+        _builder.build();
+    }
+    
+    public void setDebug(boolean debug) {
+        _debug = debug;
+    }
+    
+    public boolean isDebug() {
+        return _debug;
+    }
+    
+    /**
+     * Add to list of objects.
+     * @param geom - object to add.
+     */
+    public void add(LCDDSurveyVolume geom) {
+        lcddSurveyVolumes.add(geom);
+    }
 
-	
-	
+    
+    
 
-	public void setLCDD(LCDD lcdd) {
-		this.lcdd = lcdd;
-	}
+    public void setLCDD(LCDD lcdd) {
+        this.lcdd = lcdd;
+    }
 
-	public LCDD getLCDD() {
-		return lcdd;
-	}
+    public LCDD getLCDD() {
+        return lcdd;
+    }
 
-	public LCDDSurveyVolume getBaseLCDD() {
-		return baseSurveyVolume;
-	}
+    public LCDDSurveyVolume getBaseLCDD() {
+        return baseSurveyVolume;
+    }
 
-	public void setVisualization() {
-	
-		if(isDebug()) System.out.printf("%s: Set LCDD visualization for %d LCDD geometry objects \n", getClass().getSimpleName(), lcddSurveyVolumes.size());
-		for(SurveyVolumeImpl g : lcddSurveyVolumes) {
-		    String name = g.getName();
-			if(isDebug()) System.out.printf("%s: Set LCDD vis for %s \n", getClass().getSimpleName(), name);			
-			if(name.contains("base_plate")) g.setVisName("BasePlateVis");
+    public void setVisualization() {
+    
+        if(isDebug()) System.out.printf("%s: Set LCDD visualization for %d LCDD geometry objects \n", getClass().getSimpleName(), lcddSurveyVolumes.size());
+        for(SurveyVolumeImpl g : lcddSurveyVolumes) {
+            String name = g.getName();
+            if(isDebug()) System.out.printf("%s: Set LCDD vis for %s \n", getClass().getSimpleName(), name);            
+            if(name.contains("base_plate")) g.setVisName("BasePlateVis");
             else if(name.equals("base")) g.setVisName("SvtBoxVis");
-			else if(name.contains("chamber")) g.setVisName("ChamberVis");
-			else if(name.contains("support_bottom") || name.contains("support_top")) g.setVisName("SupportVolumeVis");
-			else if(name.contains("support_plate")) g.setVisName("SupportPlateVis");
-			else if(name.startsWith("module_")) {
-			    if(name.endsWith("halfmodule_axial") || name.endsWith("halfmodule_stereo")) g.setVisName("HalfModuleVis");
-			    else if(name.endsWith("cold")) g.setVisName("ColdBlockVis");
-			    else if(name.endsWith("lamination")) g.setVisName("KaptonVis");
-			    else if(name.endsWith("sensor")) g.setVisName("SensorVis");
-			    else if(name.endsWith("sensor_active")) g.setVisName("SensorVis");
-			    else if(name.endsWith("cf")) g.setVisName("CarbonFiberVis");
-			    else if(name.endsWith("hybrid")) g.setVisName("HybridVis");
-			    else {
-			        //this must be a module then?
-			        g.setVisName("ModuleVis");
-			    }
-			}
-			else {
-				if(isDebug()) System.out.printf("%s: No LCDD vis for %s \n", getClass().getSimpleName(), name);
-			}
-		}
-		if(isDebug()) System.out.printf("%s: DONE Set LCDD vis \n", getClass().getSimpleName());
-	}
-	
+            else if(name.contains("chamber")) g.setVisName("ChamberVis");
+            else if(name.contains("support_bottom") || name.contains("support_top")) g.setVisName("SupportVolumeVis");
+            else if(name.contains("support_plate")) g.setVisName("SupportPlateVis");
+            else if(name.startsWith("module_")) {
+                if(name.endsWith("halfmodule_axial") || name.endsWith("halfmodule_stereo")) g.setVisName("HalfModuleVis");
+                else if(name.endsWith("cold")) g.setVisName("ColdBlockVis");
+                else if(name.endsWith("lamination")) g.setVisName("KaptonVis");
+                else if(name.endsWith("sensor")) g.setVisName("SensorVis");
+                else if(name.endsWith("sensor_active")) g.setVisName("SensorVis");
+                else if(name.endsWith("cf")) g.setVisName("CarbonFiberVis");
+                else if(name.endsWith("hybrid")) g.setVisName("HybridVis");
+                else {
+                    //this must be a module then?
+                    g.setVisName("ModuleVis");
+                }
+            }
+            else {
+                if(isDebug()) System.out.printf("%s: No LCDD vis for %s \n", getClass().getSimpleName(), name);
+            }
+        }
+        if(isDebug()) System.out.printf("%s: DONE Set LCDD vis \n", getClass().getSimpleName());
+    }
+    
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.java	Wed Apr 27 11:11:32 2016
@@ -7,25 +7,25 @@
 
 public interface IHPSTrackerJavaBuilder {
 
-	/**
-	 * Build the JAVA geometry objects from the geometry definition.
-	 * @param trackingVolume - the reference volume.
-	 */
-	public void build(ILogicalVolume trackingVolume);
-	
-	public DetectorIdentifierHelper getDetectorIdentifierHelper();
+    /**
+     * Build the JAVA geometry objects from the geometry definition.
+     * @param trackingVolume - the reference volume.
+     */
+    public void build(ILogicalVolume trackingVolume);
+    
+    public DetectorIdentifierHelper getDetectorIdentifierHelper();
 
-	public void setDetectorIdentifierHelper(
-			DetectorIdentifierHelper detectorIdentifierHelper);
+    public void setDetectorIdentifierHelper(
+            DetectorIdentifierHelper detectorIdentifierHelper);
 
-	public IIdentifierDictionary getIdentifierDictionary();
+    public IIdentifierDictionary getIdentifierDictionary();
 
-	public void setIdentifierDictionary(
-			IIdentifierDictionary identifierDictionary);
+    public void setIdentifierDictionary(
+            IIdentifierDictionary identifierDictionary);
 
 
-	public void setSubdetector(Subdetector subdet);
+    public void setSubdetector(Subdetector subdet);
 
-	public Subdetector getSubdetector();
-	
+    public Subdetector getSubdetector();
+    
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.java	Wed Apr 27 11:11:32 2016
@@ -5,11 +5,11 @@
 
 public interface IHPSTrackerLCDDBuilder {
 
-	public  void setSensitiveDetector(SensitiveDetector sens);
+    public  void setSensitiveDetector(SensitiveDetector sens);
 
-	public  SensitiveDetector getSensitiveDetector();
-	
-	public void build(Volume worldVolume);
+    public  SensitiveDetector getSensitiveDetector();
+    
+    public void build(Volume worldVolume);
 
-	public void setVisualization();
+    public void setVisualization();
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.java	Wed Apr 27 11:11:32 2016
@@ -7,22 +7,22 @@
  * @author Per Hansson Adrian <[log in to unmask]>
  */
 public class JavaGhostSurveyVolume extends JavaSurveyVolume {
-	
-	/**
-	 * Initialize with base and mother. This is typically for a reference geometry object 
-	 * that is used for referencing coordinate systems but that doesn't have a volume itself.
-	 * @param surveyVolume - object used to get geometry definitions
-	 * @param mother - mother object
-	 */
-	public JavaGhostSurveyVolume(SurveyVolume surveyVolume, JavaSurveyVolume mother) {
-		super(surveyVolume);
-		if(isDebug()) System.out.printf("%s: constructing JAVA ghost object %s with mother %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),mother==null?"null":mother.getName());
-		setMother(mother);
-		mother.addDaughter(this);
-		setPositionAndRotation(surveyVolume);
-		if(isDebug()) System.out.printf("%s: DONE constructing JAVA object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-	}
-	
+    
+    /**
+     * Initialize with base and mother. This is typically for a reference geometry object 
+     * that is used for referencing coordinate systems but that doesn't have a volume itself.
+     * @param surveyVolume - object used to get geometry definitions
+     * @param mother - mother object
+     */
+    public JavaGhostSurveyVolume(SurveyVolume surveyVolume, JavaSurveyVolume mother) {
+        super(surveyVolume);
+        if(isDebug()) System.out.printf("%s: constructing JAVA ghost object %s with mother %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),mother==null?"null":mother.getName());
+        setMother(mother);
+        mother.addDaughter(this);
+        setPositionAndRotation(surveyVolume);
+        if(isDebug()) System.out.printf("%s: DONE constructing JAVA object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+    }
+    
 
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaSurveyVolume.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaSurveyVolume.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaSurveyVolume.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,6 @@
 import org.lcsim.detector.RotationGeant;
 import org.lcsim.detector.Transform3D;
 import org.lcsim.detector.Translation3D;
-import org.lcsim.detector.material.IMaterial;
 import org.lcsim.detector.material.MaterialStore;
 import org.lcsim.detector.solids.Box;
 import org.lcsim.geometry.util.TransformationUtils;
@@ -26,120 +25,120 @@
  * @author Per Hansson Adrian <[log in to unmask]>
  */
 public class JavaSurveyVolume extends SurveyVolumeImpl {
-	private Box box= null;
-	private ILogicalVolume volume = null;
-	private ITranslation3D pos = null;
-	private IRotation3D rot = null;
-	private IPhysicalVolume physVolume = null;
-	private JavaSurveyVolume mother = null;
-	public List<JavaSurveyVolume> daughters = new ArrayList<JavaSurveyVolume>();
-	private int componentId = -1;
-	
-	/**
-	 *  Default constructor
-	 */
-	public JavaSurveyVolume(SurveyVolume surveyVolume) {
-	    super(surveyVolume);
-	}
-
-	/**
-	 * Construct a JAVA geometry object from its geometry definition and an already built logical volume. 
-	 * This is typically used by the tracking volume.
-	 * @param surveyVolume - input geometry definition
-	 * @param vol - logical volume
-	 */
-	public JavaSurveyVolume(SurveyVolume surveyVolume, ILogicalVolume vol) {
-	    super(surveyVolume);
-		if(isDebug()) System.out.printf("%s: JavaBaseGeometry %s (given logical volume %s)\n", this.getClass().getSimpleName(),surveyVolume.getName(),vol.getName());
-		// this must be tracking volume. May change in the future and is probably weird to make this requirement here. 
-		if(!surveyVolume.getName().contains("tracking")) throw new RuntimeException("this constructor is only used with the tracking volume!?");
-		setVolume(vol);
-		// since it's tracking volume, set the pos and rotation trivially
-		Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(surveyVolume.getCoord().v(), surveyVolume.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
-		setPos(new Translation3D(0,0,0));
-		setRot(new RotationGeant(lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
-		if(isDebug()) System.out.printf("%s: DONE JavaBaseGeometry %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-	}
-	
-	/**
-	 * Construct a JAVA geometry object from its geometry definition. 
-	 * @param surveyVolume - input geometry definition
-	 * @param mother - reference to mother JAVA definition
-	 * @param volumeId - component id number 
-	 */
-	public JavaSurveyVolume(SurveyVolume surveyVolume, JavaSurveyVolume mother, int volumeId) {
-	    super(surveyVolume);
+    private Box box= null;
+    private ILogicalVolume volume = null;
+    private ITranslation3D pos = null;
+    private IRotation3D rot = null;
+    private IPhysicalVolume physVolume = null;
+    private JavaSurveyVolume mother = null;
+    public List<JavaSurveyVolume> daughters = new ArrayList<JavaSurveyVolume>();
+    private int componentId = -1;
+    
+    /**
+     *  Default constructor
+     */
+    public JavaSurveyVolume(SurveyVolume surveyVolume) {
+        super(surveyVolume);
+    }
+
+    /**
+     * Construct a JAVA geometry object from its geometry definition and an already built logical volume. 
+     * This is typically used by the tracking volume.
+     * @param surveyVolume - input geometry definition
+     * @param vol - logical volume
+     */
+    public JavaSurveyVolume(SurveyVolume surveyVolume, ILogicalVolume vol) {
+        super(surveyVolume);
+        if(isDebug()) System.out.printf("%s: JavaBaseGeometry %s (given logical volume %s)\n", this.getClass().getSimpleName(),surveyVolume.getName(),vol.getName());
+        // this must be tracking volume. May change in the future and is probably weird to make this requirement here. 
+        if(!surveyVolume.getName().contains("tracking")) throw new RuntimeException("this constructor is only used with the tracking volume!?");
+        setVolume(vol);
+        // since it's tracking volume, set the pos and rotation trivially
+        Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(surveyVolume.getCoord().v(), surveyVolume.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
+        setPos(new Translation3D(0,0,0));
+        setRot(new RotationGeant(lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
+        if(isDebug()) System.out.printf("%s: DONE JavaBaseGeometry %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+    }
+    
+    /**
+     * Construct a JAVA geometry object from its geometry definition. 
+     * @param surveyVolume - input geometry definition
+     * @param mother - reference to mother JAVA definition
+     * @param volumeId - component id number 
+     */
+    public JavaSurveyVolume(SurveyVolume surveyVolume, JavaSurveyVolume mother, int volumeId) {
+        super(surveyVolume);
         if(isDebug()) System.out.printf("%s: JavaBaseGeometry %s (volumeID %d, mother %s)\n", this.getClass().getSimpleName(),surveyVolume.getName(),volumeId,mother==null?"null":mother.getName());
-		setComponentId(volumeId);
-		setMother(mother);
-		mother.addDaughter(this);
-		buildBox();
-		buildVolume();
-		setPositionAndRotation(surveyVolume);
-		if(isDebug()) System.out.printf("%s: DONE JavaBaseGeometry %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-	}
-
-	protected boolean hasCoordinateSystemInfo() {
-		return pos!=null && rot!=null;
-	}
-	
-	
-	public void buildPhysVolume() {
-		if(isDebug()) System.out.printf("%s: build phys volume for %s with mother %s and physical mother %s\n", this.getClass().getSimpleName(),getName(),getMother().getName(),getPhysMother().getName());
-		JavaSurveyVolume physMother =  getPhysMother();
-		setPhysVolume(new PhysicalVolume(new Transform3D(getPos(), getRot()), getName(), volume, physMother.getVolume(),getComponentId()));
-	}
-	
-	public void buildBox() {
-		Hep3Vector b = VecOp.mult(0.5,getBoxDim());
-		if(isDebug()) System.out.printf("%s: build box for %s with dimensions %s \n", this.getClass().getSimpleName(),getName(), b);
-		setBox(new Box(getName() + "Box", b.x(), b.y(), b.z())); 
-	}
-	public void buildVolume() {
-		if(isDebug()) System.out.printf("%s: build volume for %s with material %s\n", this.getClass().getSimpleName(),getName(), MaterialStore.getInstance().get(getMaterial()));
-			setVolume(new LogicalVolume(getName() + "_volume", box, MaterialStore.getInstance().get(getMaterial())));
-		
-	}
-	public void setPositionAndRotation(SurveyVolume base) {
-		if(isDebug()) System.out.printf("%s: set position and rotation for volume %s\n", this.getClass().getSimpleName(),getName());
-		
-		// no mother, this must be the world/tracking volume!?
-		if(base.getMother()==null) throw new RuntimeException("trying to set coordinates w/o mother defined for "+base.getName());
-		
-		// Vector from origin to center of box locally 
-		Hep3Vector box_center_base_local = base.getCenter();
-		
-		// find the physical mother i.e. not a ghost volume and compound transformations to it
-		JavaSurveyVolume physMother =  getPhysMother();
-		if(isDebug()) System.out.printf("%s: physical mother to transform to is %s; find the transform to it\n", this.getClass().getSimpleName(),physMother.getName());
-		Transform3D trf = HPSTrackerBuilder.getTransform(base.getCoord().getTransformation(),base.getMother(),physMother.getName()); 
-		if(isDebug()) System.out.printf("%s: found transform to physical mother \n%s\n\n", this.getClass().getSimpleName(),trf.toString());
-		
-		// find the position of the center in the physical mother coord
-		Hep3Vector box_center_base = trf.transformed(box_center_base_local);
-		
-		// find the position of the center of the box in the mother coordinate system, make sure to use the physical mother coordinates
-		if(isDebug()) System.out.printf("%s: find center of box in physical mother coord %s \n", this.getClass().getSimpleName(),physMother.getName());
-		// hack since my getTransform function needs a mother TODO Fix this!
-		SurveyVolume gm = base;
-		if(isDebug()) System.out.printf("%s: look for physical mother %s starting from mother %s \n", this.getClass().getSimpleName(),physMother.getName(),gm.getMother()!=null?gm.getMother().getName():"-- no mother --");
-		while((gm=gm.getMother()).getName()!=physMother.getName()) {
-			if(isDebug()) System.out.printf("%s: gm is %s \n", this.getClass().getSimpleName(),gm.getName());
-			//gm = gm.getMother();
-		}
-		if(isDebug()) System.out.printf("%s: found physical mother %s with center at %s \n", this.getClass().getSimpleName(),gm.getName(), gm.getCenter());
-		
-		Hep3Vector mother_center = gm.getCenter();
-
-		// now calculate the position of this box center in the mother LCDD coordinates
-		Hep3Vector box_center = VecOp.sub(box_center_base, mother_center);
-
-		//Find LCDD Euler rotation angles from coordinate system unit vectors
-		//Note that this has to be rotation wrt to physical mother and not just mother as normally is the case
-		//Use apache lib to get angles, but in principle I should already have it from the trf above
-		//Hep3Vector lcdd_rot_angles = HPSTestRunTracker2014.getEulerAngles(base.getCoord().v(), base.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
-		if(isDebug()) System.out.printf("%s: find LCDD Cardan rotation angles - need to find mother to physical mother transform \n", this.getClass().getSimpleName(),physMother.getName());
-		Hep3Vector base_u = base.getCoord().u();
+        setComponentId(volumeId);
+        setMother(mother);
+        mother.addDaughter(this);
+        buildBox();
+        buildVolume();
+        setPositionAndRotation(surveyVolume);
+        if(isDebug()) System.out.printf("%s: DONE JavaBaseGeometry %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+    }
+
+    protected boolean hasCoordinateSystemInfo() {
+        return pos!=null && rot!=null;
+    }
+    
+    
+    public void buildPhysVolume() {
+        if(isDebug()) System.out.printf("%s: build phys volume for %s with mother %s and physical mother %s\n", this.getClass().getSimpleName(),getName(),getMother().getName(),getPhysMother().getName());
+        JavaSurveyVolume physMother =  getPhysMother();
+        setPhysVolume(new PhysicalVolume(new Transform3D(getPos(), getRot()), getName(), volume, physMother.getVolume(),getComponentId()));
+    }
+    
+    public void buildBox() {
+        Hep3Vector b = VecOp.mult(0.5,getBoxDim());
+        if(isDebug()) System.out.printf("%s: build box for %s with dimensions %s \n", this.getClass().getSimpleName(),getName(), b);
+        setBox(new Box(getName() + "Box", b.x(), b.y(), b.z())); 
+    }
+    public void buildVolume() {
+        if(isDebug()) System.out.printf("%s: build volume for %s with material %s\n", this.getClass().getSimpleName(),getName(), MaterialStore.getInstance().get(getMaterial()));
+            setVolume(new LogicalVolume(getName() + "_volume", box, MaterialStore.getInstance().get(getMaterial())));
+        
+    }
+    public void setPositionAndRotation(SurveyVolume base) {
+        if(isDebug()) System.out.printf("%s: set position and rotation for volume %s\n", this.getClass().getSimpleName(),getName());
+        
+        // no mother, this must be the world/tracking volume!?
+        if(base.getMother()==null) throw new RuntimeException("trying to set coordinates w/o mother defined for "+base.getName());
+        
+        // Vector from origin to center of box locally 
+        Hep3Vector box_center_base_local = base.getCenter();
+        
+        // find the physical mother i.e. not a ghost volume and compound transformations to it
+        JavaSurveyVolume physMother =  getPhysMother();
+        if(isDebug()) System.out.printf("%s: physical mother to transform to is %s; find the transform to it\n", this.getClass().getSimpleName(),physMother.getName());
+        Transform3D trf = HPSTrackerBuilder.getTransform(base.getCoord().getTransformation(),base.getMother(),physMother.getName()); 
+        if(isDebug()) System.out.printf("%s: found transform to physical mother \n%s\n\n", this.getClass().getSimpleName(),trf.toString());
+        
+        // find the position of the center in the physical mother coord
+        Hep3Vector box_center_base = trf.transformed(box_center_base_local);
+        
+        // find the position of the center of the box in the mother coordinate system, make sure to use the physical mother coordinates
+        if(isDebug()) System.out.printf("%s: find center of box in physical mother coord %s \n", this.getClass().getSimpleName(),physMother.getName());
+        // hack since my getTransform function needs a mother TODO Fix this!
+        SurveyVolume gm = base;
+        if(isDebug()) System.out.printf("%s: look for physical mother %s starting from mother %s \n", this.getClass().getSimpleName(),physMother.getName(),gm.getMother()!=null?gm.getMother().getName():"-- no mother --");
+        while((gm=gm.getMother()).getName()!=physMother.getName()) {
+            if(isDebug()) System.out.printf("%s: gm is %s \n", this.getClass().getSimpleName(),gm.getName());
+            //gm = gm.getMother();
+        }
+        if(isDebug()) System.out.printf("%s: found physical mother %s with center at %s \n", this.getClass().getSimpleName(),gm.getName(), gm.getCenter());
+        
+        Hep3Vector mother_center = gm.getCenter();
+
+        // now calculate the position of this box center in the mother LCDD coordinates
+        Hep3Vector box_center = VecOp.sub(box_center_base, mother_center);
+
+        //Find LCDD Euler rotation angles from coordinate system unit vectors
+        //Note that this has to be rotation wrt to physical mother and not just mother as normally is the case
+        //Use apache lib to get angles, but in principle I should already have it from the trf above
+        //Hep3Vector lcdd_rot_angles = HPSTestRunTracker2014.getEulerAngles(base.getCoord().v(), base.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
+        if(isDebug()) System.out.printf("%s: find LCDD Cardan rotation angles - need to find mother to physical mother transform \n", this.getClass().getSimpleName(),physMother.getName());
+        Hep3Vector base_u = base.getCoord().u();
         Hep3Vector base_v = base.getCoord().v();
         Hep3Vector base_w = base.getCoord().w();
         if(isDebug()) System.out.printf("%s: unit vectors in mother coord: %s, %s, %s\n", this.getClass().getSimpleName(),base_u.toString(),base_v.toString(),base_w.toString());
@@ -169,22 +168,22 @@
             //System.out.printf("%s: unit vectors u %s v %s w %s\n", this.getClass().getSimpleName(),base.getCoord().u().toString(),base.getCoord().v().toString(),base.getCoord().w().toString());
         }
         
-		Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(base_u, base_v, base_w, unit_u, unit_v, unit_w);
-
-
-		// Create the LCDD position
-		setPos(new Translation3D(box_center.x(), box_center.y(), box_center.z()));
-		setRot(new RotationGeant(lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
-		
-		if(isDebug()) {
-			
-		    System.out.printf("%s: SurveyVolume information for %s:\n", this.getClass().getSimpleName(), base.getName());
+        Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(base_u, base_v, base_w, unit_u, unit_v, unit_w);
+
+
+        // Create the LCDD position
+        setPos(new Translation3D(box_center.x(), box_center.y(), box_center.z()));
+        setRot(new RotationGeant(lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
+        
+        if(isDebug()) {
+            
+            System.out.printf("%s: SurveyVolume information for %s:\n", this.getClass().getSimpleName(), base.getName());
             System.out.printf("%s: box_center_base_local       %s\n", this.getClass().getSimpleName(), box_center_base_local.toString());
-			System.out.printf("%s: box_center_base             %s\n", this.getClass().getSimpleName(), box_center_base.toString());
-			System.out.printf("%s: mother center               %s\n", this.getClass().getSimpleName(), base.getMother()==null?" <no mother> ":mother_center.toString());
-			System.out.printf("%s: box_center                  %s\n", this.getClass().getSimpleName(), box_center.toString());
-			System.out.printf("%s: pos                         %s\n", this.getClass().getSimpleName(), getPos().toString());
-			Hep3Vector box_center_tracking_xcheck = HPSTrackerBuilder.transformToTracking(box_center_base_local, base);
+            System.out.printf("%s: box_center_base             %s\n", this.getClass().getSimpleName(), box_center_base.toString());
+            System.out.printf("%s: mother center               %s\n", this.getClass().getSimpleName(), base.getMother()==null?" <no mother> ":mother_center.toString());
+            System.out.printf("%s: box_center                  %s\n", this.getClass().getSimpleName(), box_center.toString());
+            System.out.printf("%s: pos                         %s\n", this.getClass().getSimpleName(), getPos().toString());
+            Hep3Vector box_center_tracking_xcheck = HPSTrackerBuilder.transformToTracking(box_center_base_local, base);
             System.out.printf("%s: box_center_tracking_xcheck  %s (for %s)\n", this.getClass().getSimpleName(), box_center_tracking_xcheck==null ? " <null> " : box_center_tracking_xcheck.toString(),base.getName());
             Hep3Vector box_center_envelope_xcheck2 = HPSTrackerBuilder.transformToParent(box_center_base_local, base, "base");
             System.out.printf("%s: box_center_base_xcheck2     %s (for %s)\n", this.getClass().getSimpleName(), box_center_envelope_xcheck2==null ? " <null> " : box_center_envelope_xcheck2.toString(),base.getName());
@@ -203,90 +202,90 @@
                 System.out.printf("%s: origin_base_in          %s\n", this.getClass().getSimpleName(), origin_base_in==null ? " <null> " : origin_base_in.toString());
             }
             System.out.printf("%s: euler                       %s\n", this.getClass().getSimpleName(), lcdd_rot_angles.toString());
-			System.out.printf("%s: rot                         %s\n", this.getClass().getSimpleName(), getRot().toString());
-			
-		}
-		
-	}
-
-	/**
-	 * Find the first non-ghost volume among parents.  
-	 * @return mother object
-	 */
-	public JavaSurveyVolume getPhysMother() {
-		//if(isDebug()) System.out.printf("%s: finding physical mother to %s\n", this.getClass().getSimpleName(), getName());
-		if(mother==null) throw new RuntimeException("Trying to get phys mother but there is no mother!");
-		if(mother instanceof JavaGhostSurveyVolume) {
-			return mother.getPhysMother();
-		} else {
-			//if(isDebug()) System.out.printf("%s: found a non-ghost volume: %s\n", this.getClass().getSimpleName(), mother.getName());
-			return mother;
-		}
-	}
-	
-	
-	public ILogicalVolume getVolume() {
-		return volume;
-	}
-	protected void setVolume(ILogicalVolume volume) {
-		this.volume = volume;
-	}
-	protected Box getBox() {
-		return box;
-	}
-	protected void setBox(Box b) {
-		box = b;
-	}	
-	protected ITranslation3D getPos() {
-		return pos;
-	}
-	protected void setPos(ITranslation3D iTranslation3D) {
-		this.pos = iTranslation3D;
-	}
-	protected IRotation3D getRot() {
-		return rot;
-	}
-	protected void setRot(IRotation3D iRotation3D) {
-		this.rot = iRotation3D;
-	}
-	public JavaSurveyVolume getMother() {
-		return mother;
-	}
-	protected void setMother(JavaSurveyVolume mother) {
-		this.mother = mother;
-	}
-	public IPhysicalVolume getPhysVolume() {
-		return physVolume;
-	}
-	protected void setPhysVolume(PhysicalVolume physVolume) {
-		this.physVolume = physVolume;
-	}
-
-	public List<JavaSurveyVolume> getDaughters() {
-		return daughters;
-	}
-
-	protected void addDaughter(JavaSurveyVolume o) {
-		getDaughters().add(o);
-	}
-
-	public int getComponentId() {
-		return componentId;
-	}
-
-	public void setComponentId(int componentId) {
-		this.componentId = componentId;
-	}
-	
-	public String toString() {
-		String s = "JavaBaseGeometry " + getName() + "\n";
-		if(getPos()!=null && getRot()!=null) {
-			s += "Position: "  + getPos().toString() + "\n";
-			s += "Rotation: " + getRot().toString() + "\n";
-		} else {
-			s+= " - no position/rotation info -\n";
-		}
-		return s;
-	}
+            System.out.printf("%s: rot                         %s\n", this.getClass().getSimpleName(), getRot().toString());
+            
+        }
+        
+    }
+
+    /**
+     * Find the first non-ghost volume among parents.  
+     * @return mother object
+     */
+    public JavaSurveyVolume getPhysMother() {
+        //if(isDebug()) System.out.printf("%s: finding physical mother to %s\n", this.getClass().getSimpleName(), getName());
+        if(mother==null) throw new RuntimeException("Trying to get phys mother but there is no mother!");
+        if(mother instanceof JavaGhostSurveyVolume) {
+            return mother.getPhysMother();
+        } else {
+            //if(isDebug()) System.out.printf("%s: found a non-ghost volume: %s\n", this.getClass().getSimpleName(), mother.getName());
+            return mother;
+        }
+    }
+    
+    
+    public ILogicalVolume getVolume() {
+        return volume;
+    }
+    protected void setVolume(ILogicalVolume volume) {
+        this.volume = volume;
+    }
+    protected Box getBox() {
+        return box;
+    }
+    protected void setBox(Box b) {
+        box = b;
+    }   
+    protected ITranslation3D getPos() {
+        return pos;
+    }
+    protected void setPos(ITranslation3D iTranslation3D) {
+        this.pos = iTranslation3D;
+    }
+    protected IRotation3D getRot() {
+        return rot;
+    }
+    protected void setRot(IRotation3D iRotation3D) {
+        this.rot = iRotation3D;
+    }
+    public JavaSurveyVolume getMother() {
+        return mother;
+    }
+    protected void setMother(JavaSurveyVolume mother) {
+        this.mother = mother;
+    }
+    public IPhysicalVolume getPhysVolume() {
+        return physVolume;
+    }
+    protected void setPhysVolume(PhysicalVolume physVolume) {
+        this.physVolume = physVolume;
+    }
+
+    public List<JavaSurveyVolume> getDaughters() {
+        return daughters;
+    }
+
+    protected void addDaughter(JavaSurveyVolume o) {
+        getDaughters().add(o);
+    }
+
+    public int getComponentId() {
+        return componentId;
+    }
+
+    public void setComponentId(int componentId) {
+        this.componentId = componentId;
+    }
+    
+    public String toString() {
+        String s = "JavaBaseGeometry " + getName() + "\n";
+        if(getPos()!=null && getRot()!=null) {
+            s += "Position: "  + getPos().toString() + "\n";
+            s += "Rotation: " + getRot().toString() + "\n";
+        } else {
+            s+= " - no position/rotation info -\n";
+        }
+        return s;
+    }
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDGhostSurveyVolume.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDGhostSurveyVolume.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDGhostSurveyVolume.java	Wed Apr 27 11:11:32 2016
@@ -10,20 +10,20 @@
  */
 public class LCDDGhostSurveyVolume extends LCDDSurveyVolume {
 
-	
-	
-	/**
-	 * Initialize with base and mother. This is typically for a reference geometry object 
-	 * that is used for referencing coordinate systems but that doesn't have a volume itself.
-	 * @param base - object used to get geometry definitions
-	 * @param mother - mother LCDD object
-	 */
-	public LCDDGhostSurveyVolume(SurveyVolume base, LCDDSurveyVolume mother) {
-		super(base);
-		if(isDebug()) System.out.printf("%s: constructing LCDD ghost object %s with mother %s\n", this.getClass().getSimpleName(),base.getName(),mother==null?"null":mother.getName());
-		setMother(mother);
-		mother.addDaughter(this);
-		if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),base.getName());
-	}
-	
+    
+    
+    /**
+     * Initialize with base and mother. This is typically for a reference geometry object 
+     * that is used for referencing coordinate systems but that doesn't have a volume itself.
+     * @param base - object used to get geometry definitions
+     * @param mother - mother LCDD object
+     */
+    public LCDDGhostSurveyVolume(SurveyVolume base, LCDDSurveyVolume mother) {
+        super(base);
+        if(isDebug()) System.out.printf("%s: constructing LCDD ghost object %s with mother %s\n", this.getClass().getSimpleName(),base.getName(),mother==null?"null":mother.getName());
+        setMother(mother);
+        mother.addDaughter(this);
+        if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),base.getName());
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDSurveyVolume.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDSurveyVolume.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDSurveyVolume.java	Wed Apr 27 11:11:32 2016
@@ -25,233 +25,233 @@
  * @author Per Hansson Adrian <[log in to unmask]>
  */
 public class LCDDSurveyVolume extends SurveyVolumeImpl  {
-	Box box= null;
-	Volume volume = null;
-	private Position pos = null;
-	private Rotation rot = null;
-	private PhysVol physVolume = null;
-	LCDD lcdd = null;
-	private LCDDSurveyVolume mother = null;
-	protected Map<String,Integer> physVolId = null;
-	public List<LCDDSurveyVolume> daughters = new ArrayList<LCDDSurveyVolume>();
-	/**
-	 *  Default constructor
-	 *  @param surveyVolume - core geometry definitions
-	 */
-	public LCDDSurveyVolume(SurveyVolume surveyVolume) {
-	   super(surveyVolume);
-	}
-	
-	/**
-	 * Initialize this object with a known volume and no mother. Typically the world volume would use this.
-	 * @param surveyVolume - core geometry definitions
-	 * @param vol - given volume
-	 */
-	public LCDDSurveyVolume(SurveyVolume surveyVolume, Volume volume) {
-		super(surveyVolume);
-		if(isDebug()) System.out.printf("%s: constructing LCDD object %s with volume name %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),volume.getName());
-		setVolume(volume);
-		if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-		Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(surveyVolume.getCoord().v(), surveyVolume.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
-		setPos(new Position(getName() + "_position", 0, 0, 0));
-		setRot(new Rotation(getName() + "_rotation",lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
-		if(isDebug()) System.out.printf("%s: DONE  %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-	}
-	
-	/**
-	 * Interface to the LCDD converter geometry for the geometry definition. 
-	 * @param surveyVolume - core geometry definition
-	 * @param lcdd - lcdd file 
-	 * @param mother - reference to mother LCDD definition
-	 */
-	public LCDDSurveyVolume(SurveyVolume surveyVolume, LCDD lcdd, LCDDSurveyVolume mother) {
-	    super(surveyVolume);
-	    if(isDebug()) System.out.printf("%s: constructing LCDD object %s with mother %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),mother==null?"null":mother.getName());
-		this.lcdd = lcdd;
-		setMother(mother);
-		mother.addDaughter(this);
-		buildBox();
-		buildVolume();
-		setPositionAndRotation(surveyVolume);
-		//buildPhysVolume(mother);
-		if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
-	}
-
-	
-	public void buildPhysVolume() {
-
-	    if(isDebug()) System.out.printf("%s: build phys volume for %s with mother %s and physical mother %s\n", this.getClass().getSimpleName(),getName(),getMother().getName(),getPhysMother().getName());
-	    LCDDSurveyVolume physMother =  getPhysMother();
-	    setPhysVolume(new PhysVol(volume, physMother.getVolume(), getPos(), getRot()));
-	    //if(isDebug()) System.out.printf("%s: build phys volume for %s\n", this.getClass().getSimpleName(),getName());
-		//setPhysVolume(new PhysVol(volume, getMother().getVolume(), getPos(), getRot()));
-	}
-	public void buildBox() {
-		if(isDebug()) System.out.printf("%s: build box for %s\n", getClass().getSimpleName(),getName());
-		setBox(new Box(getName() + "Box", getBoxDim().x(), getBoxDim().y(), getBoxDim().z())); 
-	}
-	public void buildVolume() {
-		if(isDebug()) System.out.printf("%s: build volume for %s with material %s\n", this.getClass().getSimpleName(),getName(),getMaterial());
-		try {
-			Material mat = lcdd.getMaterial(getMaterial());
-			setVolume(new Volume(getName() + "_volume", box, mat));
-		} catch (JDOMException e) {
-			e.printStackTrace();
-		}
-	}
-	
-	
-	public void setPositionAndRotation(SurveyVolume base) {
-		if(isDebug()) System.out.printf("%s: set position and rotation for volume %s\n", this.getClass().getSimpleName(),getName());
-		
-		// NOTE:
-		// This sets position and reference w.r.t. mother coordinate system. 
-		// If I'm not building that volume this will be wrong. 
-		// TODO Similar to in the JAVA converter this should be something like the physical mother.
-		
-		if(base.getMother()==null) throw new RuntimeException("trying to set coordinates w/o mother defined for "+base.getName());
-		
-		// Vector from origin to center of box locally 
-		Hep3Vector box_center_base_local = base.getCenter();
-		
-		//translate to the mother coordinate system
-		LCDDSurveyVolume physMother = getPhysMother();
-		if(isDebug()) System.out.printf("%s: physical mother to transform to is %s; find the transform to it\n", this.getClass().getSimpleName(),physMother.getName());
-		Transform3D trf = HPSTrackerBuilder.getTransform(base.getCoord().getTransformation(),base.getMother(),physMother.getName()); 
-		if(isDebug()) System.out.printf("%s: found transform to physical mother \n%s\n\n", this.getClass().getSimpleName(),trf.toString());
-		
-		// find the position of the center in the physical mother coord
-		Hep3Vector box_center_base = trf.transformed(box_center_base_local);
-		
-		// find the position of the center of the box in the mother coordinate system, make sure to use the physical mother coordinates
-		if(isDebug()) System.out.printf("%s: find center of box in physical mother coord %s \n", this.getClass().getSimpleName(),physMother.getName());
-		// hack since my getTransform function needs a mother TODO Fix this!
-		SurveyVolume gm = base;
-		if(isDebug()) System.out.printf("%s: look for physical mother %s starting from mother %s \n", this.getClass().getSimpleName(),physMother.getName(),gm.getMother()!=null?gm.getMother().getName():"-- no mother --");
-		while((gm=gm.getMother()).getName()!=physMother.getName()) {
-			if(isDebug()) System.out.printf("%s: gm is %s \n", this.getClass().getSimpleName(),gm.getName());
-			//gm = gm.getMother();
-		}
-		if(isDebug()) System.out.printf("%s: found physical mother %s with center at %s \n", this.getClass().getSimpleName(),gm.getName(), gm.getCenter());
-
-		Hep3Vector mother_center = gm.getCenter();
-		
-		// find the position of the center in the mother coord
-		Hep3Vector box_center = VecOp.sub(box_center_base, mother_center);
-		
-		//Find LCDD Euler rotation angles from coordinate system unit vectors
-		//Note that this has to be rotation wrt to physical mother and not just mother as normally is the case
-		if(isDebug()) System.out.printf("%s: find LCDD Cardan rotation angles - need to find mother to physical mother transform \n", this.getClass().getSimpleName(),physMother.getName());
-		Hep3Vector base_u = base.getCoord().u();
-		Hep3Vector base_v = base.getCoord().v();
-		Hep3Vector base_w = base.getCoord().w();
+    Box box= null;
+    Volume volume = null;
+    private Position pos = null;
+    private Rotation rot = null;
+    private PhysVol physVolume = null;
+    LCDD lcdd = null;
+    private LCDDSurveyVolume mother = null;
+    protected Map<String,Integer> physVolId = null;
+    public List<LCDDSurveyVolume> daughters = new ArrayList<LCDDSurveyVolume>();
+    /**
+     *  Default constructor
+     *  @param surveyVolume - core geometry definitions
+     */
+    public LCDDSurveyVolume(SurveyVolume surveyVolume) {
+       super(surveyVolume);
+    }
+    
+    /**
+     * Initialize this object with a known volume and no mother. Typically the world volume would use this.
+     * @param surveyVolume - core geometry definitions
+     * @param volume - given volume
+     */
+    public LCDDSurveyVolume(SurveyVolume surveyVolume, Volume volume) {
+        super(surveyVolume);
+        if(isDebug()) System.out.printf("%s: constructing LCDD object %s with volume name %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),volume.getName());
+        setVolume(volume);
+        if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+        Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(surveyVolume.getCoord().v(), surveyVolume.getCoord().w(), new BasicHep3Vector(0,1,0),new BasicHep3Vector(0,0,1));
+        setPos(new Position(getName() + "_position", 0, 0, 0));
+        setRot(new Rotation(getName() + "_rotation",lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
+        if(isDebug()) System.out.printf("%s: DONE  %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+    }
+    
+    /**
+     * Interface to the LCDD converter geometry for the geometry definition. 
+     * @param surveyVolume - core geometry definition
+     * @param lcdd - lcdd file 
+     * @param mother - reference to mother LCDD definition
+     */
+    public LCDDSurveyVolume(SurveyVolume surveyVolume, LCDD lcdd, LCDDSurveyVolume mother) {
+        super(surveyVolume);
+        if(isDebug()) System.out.printf("%s: constructing LCDD object %s with mother %s\n", this.getClass().getSimpleName(),surveyVolume.getName(),mother==null?"null":mother.getName());
+        this.lcdd = lcdd;
+        setMother(mother);
+        mother.addDaughter(this);
+        buildBox();
+        buildVolume();
+        setPositionAndRotation(surveyVolume);
+        //buildPhysVolume(mother);
+        if(isDebug()) System.out.printf("%s: DONE constructing LCDD object %s\n", this.getClass().getSimpleName(),surveyVolume.getName());
+    }
+
+    
+    public void buildPhysVolume() {
+
+        if(isDebug()) System.out.printf("%s: build phys volume for %s with mother %s and physical mother %s\n", this.getClass().getSimpleName(),getName(),getMother().getName(),getPhysMother().getName());
+        LCDDSurveyVolume physMother =  getPhysMother();
+        setPhysVolume(new PhysVol(volume, physMother.getVolume(), getPos(), getRot()));
+        //if(isDebug()) System.out.printf("%s: build phys volume for %s\n", this.getClass().getSimpleName(),getName());
+        //setPhysVolume(new PhysVol(volume, getMother().getVolume(), getPos(), getRot()));
+    }
+    public void buildBox() {
+        if(isDebug()) System.out.printf("%s: build box for %s\n", getClass().getSimpleName(),getName());
+        setBox(new Box(getName() + "Box", getBoxDim().x(), getBoxDim().y(), getBoxDim().z())); 
+    }
+    public void buildVolume() {
+        if(isDebug()) System.out.printf("%s: build volume for %s with material %s\n", this.getClass().getSimpleName(),getName(),getMaterial());
+        try {
+            Material mat = lcdd.getMaterial(getMaterial());
+            setVolume(new Volume(getName() + "_volume", box, mat));
+        } catch (JDOMException e) {
+            e.printStackTrace();
+        }
+    }
+    
+    
+    public void setPositionAndRotation(SurveyVolume base) {
+        if(isDebug()) System.out.printf("%s: set position and rotation for volume %s\n", this.getClass().getSimpleName(),getName());
+        
+        // NOTE:
+        // This sets position and reference w.r.t. mother coordinate system. 
+        // If I'm not building that volume this will be wrong. 
+        // TODO Similar to in the JAVA converter this should be something like the physical mother.
+        
+        if(base.getMother()==null) throw new RuntimeException("trying to set coordinates w/o mother defined for "+base.getName());
+        
+        // Vector from origin to center of box locally 
+        Hep3Vector box_center_base_local = base.getCenter();
+        
+        //translate to the mother coordinate system
+        LCDDSurveyVolume physMother = getPhysMother();
+        if(isDebug()) System.out.printf("%s: physical mother to transform to is %s; find the transform to it\n", this.getClass().getSimpleName(),physMother.getName());
+        Transform3D trf = HPSTrackerBuilder.getTransform(base.getCoord().getTransformation(),base.getMother(),physMother.getName()); 
+        if(isDebug()) System.out.printf("%s: found transform to physical mother \n%s\n\n", this.getClass().getSimpleName(),trf.toString());
+        
+        // find the position of the center in the physical mother coord
+        Hep3Vector box_center_base = trf.transformed(box_center_base_local);
+        
+        // find the position of the center of the box in the mother coordinate system, make sure to use the physical mother coordinates
+        if(isDebug()) System.out.printf("%s: find center of box in physical mother coord %s \n", this.getClass().getSimpleName(),physMother.getName());
+        // hack since my getTransform function needs a mother TODO Fix this!
+        SurveyVolume gm = base;
+        if(isDebug()) System.out.printf("%s: look for physical mother %s starting from mother %s \n", this.getClass().getSimpleName(),physMother.getName(),gm.getMother()!=null?gm.getMother().getName():"-- no mother --");
+        while((gm=gm.getMother()).getName()!=physMother.getName()) {
+            if(isDebug()) System.out.printf("%s: gm is %s \n", this.getClass().getSimpleName(),gm.getName());
+            //gm = gm.getMother();
+        }
+        if(isDebug()) System.out.printf("%s: found physical mother %s with center at %s \n", this.getClass().getSimpleName(),gm.getName(), gm.getCenter());
+
+        Hep3Vector mother_center = gm.getCenter();
+        
+        // find the position of the center in the mother coord
+        Hep3Vector box_center = VecOp.sub(box_center_base, mother_center);
+        
+        //Find LCDD Euler rotation angles from coordinate system unit vectors
+        //Note that this has to be rotation wrt to physical mother and not just mother as normally is the case
+        if(isDebug()) System.out.printf("%s: find LCDD Cardan rotation angles - need to find mother to physical mother transform \n", this.getClass().getSimpleName(),physMother.getName());
+        Hep3Vector base_u = base.getCoord().u();
+        Hep3Vector base_v = base.getCoord().v();
+        Hep3Vector base_w = base.getCoord().w();
         if(isDebug()) System.out.printf("%s: unit vectors in mother coord: %s, %s, %s\n", this.getClass().getSimpleName(),base_u.toString(),base_v.toString(),base_w.toString());
-		Hep3Vector unit_u = new BasicHep3Vector(1,0,0);
-		Hep3Vector unit_v = new BasicHep3Vector(0,1,0);
-		Hep3Vector unit_w = new BasicHep3Vector(0,0,1);
-		if(!base.getMother().getName().equals(physMother.getName())) {
-		    if(isDebug()) System.out.printf("%s: Need to get unit vectors in physical mother %s coord system\n", this.getClass().getSimpleName(),physMother.getName());
+        Hep3Vector unit_u = new BasicHep3Vector(1,0,0);
+        Hep3Vector unit_v = new BasicHep3Vector(0,1,0);
+        Hep3Vector unit_w = new BasicHep3Vector(0,0,1);
+        if(!base.getMother().getName().equals(physMother.getName())) {
+            if(isDebug()) System.out.printf("%s: Need to get unit vectors in physical mother %s coord system\n", this.getClass().getSimpleName(),physMother.getName());
             Transform3D trf_mother = HPSTrackerBuilder.getTransform(base.getMother().getCoord().getTransformation(),base.getMother().getMother(),physMother.getName()); 
             if(isDebug()) System.out.printf("%s: found transform from mother to physical mother \n%s\n", this.getClass().getSimpleName(),trf_mother.toString());
-			//unit_u = VecOp.unit(trf_mother.rotated(unit_u));
-			//unit_v = VecOp.unit(trf_mother.rotated(unit_v));
-			//unit_w = VecOp.unit(trf_mother.rotated(unit_w));
-			base_u = VecOp.unit(trf_mother.rotated(base_u));
+            //unit_u = VecOp.unit(trf_mother.rotated(unit_u));
+            //unit_v = VecOp.unit(trf_mother.rotated(unit_v));
+            //unit_w = VecOp.unit(trf_mother.rotated(unit_w));
+            base_u = VecOp.unit(trf_mother.rotated(base_u));
             base_v = VecOp.unit(trf_mother.rotated(base_v));
             base_w = VecOp.unit(trf_mother.rotated(base_w));
             
-		} else {
-			if(isDebug()) System.out.printf("%s: mother and physical mother is the same so unit vectors didn't change\n",getClass().getSimpleName());
-		}
-		
-		if(isDebug()) {
-		    if(isDebug()) System.out.printf("%s: final unit vectors to get Cardan angles from : \n%s, %s, %s -> %s, %s, %s \n", 
-		                                    this.getClass().getSimpleName(),
-		                                    base_u.toString(),base_v.toString(),base_w.toString(),	            
-		                                    unit_u.toString(),unit_v.toString(),unit_w.toString());
-			//System.out.printf("%s: unit vectors u %s v %s w %s\n", this.getClass().getSimpleName(),base.getCoord().u().toString(),base.getCoord().v().toString(),base.getCoord().w().toString());
-		}
+        } else {
+            if(isDebug()) System.out.printf("%s: mother and physical mother is the same so unit vectors didn't change\n",getClass().getSimpleName());
+        }
+        
+        if(isDebug()) {
+            if(isDebug()) System.out.printf("%s: final unit vectors to get Cardan angles from : \n%s, %s, %s -> %s, %s, %s \n", 
+                                            this.getClass().getSimpleName(),
+                                            base_u.toString(),base_v.toString(),base_w.toString(),              
+                                            unit_u.toString(),unit_v.toString(),unit_w.toString());
+            //System.out.printf("%s: unit vectors u %s v %s w %s\n", this.getClass().getSimpleName(),base.getCoord().u().toString(),base.getCoord().v().toString(),base.getCoord().w().toString());
+        }
         Hep3Vector lcdd_rot_angles = TransformationUtils.getCardanAngles(base_u, base_v, base_w, unit_u, unit_v, unit_w);
         
-		
-		// Create the LCDD position and rotation
-		setPos(new Position(getName() + "_position",box_center.x(), box_center.y(), box_center.z()));
-		setRot(new Rotation(getName() + "_rotation",lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
-		
-		if(isDebug()) {
-		    System.out.printf("%s: SurveyVolume information for %s:\n", this.getClass().getSimpleName(), base.getName());
+        
+        // Create the LCDD position and rotation
+        setPos(new Position(getName() + "_position",box_center.x(), box_center.y(), box_center.z()));
+        setRot(new Rotation(getName() + "_rotation",lcdd_rot_angles.x(), lcdd_rot_angles.y(), lcdd_rot_angles.z()));
+        
+        if(isDebug()) {
+            System.out.printf("%s: SurveyVolume information for %s:\n", this.getClass().getSimpleName(), base.getName());
             System.out.printf("%s: box_center_base_local  %s\n", this.getClass().getSimpleName(), box_center_base_local.toString());
-			System.out.printf("%s: box_center_base        %s\n", this.getClass().getSimpleName(), box_center_base.toString());
-			System.out.printf("%s: mother center          %s\n", this.getClass().getSimpleName(), mother_center.toString());
-			System.out.printf("%s: box_center             %s\n", this.getClass().getSimpleName(), box_center.toString());
-			System.out.printf("%s: pos                    %s\n", this.getClass().getSimpleName(), getPos().toString());
-			System.out.printf("%s: euler                  %s\n", this.getClass().getSimpleName(), lcdd_rot_angles.toString());
+            System.out.printf("%s: box_center_base        %s\n", this.getClass().getSimpleName(), box_center_base.toString());
+            System.out.printf("%s: mother center          %s\n", this.getClass().getSimpleName(), mother_center.toString());
+            System.out.printf("%s: box_center             %s\n", this.getClass().getSimpleName(), box_center.toString());
+            System.out.printf("%s: pos                    %s\n", this.getClass().getSimpleName(), getPos().toString());
+            System.out.printf("%s: euler                  %s\n", this.getClass().getSimpleName(), lcdd_rot_angles.toString());
             System.out.printf("%s: rot                    %s\n", this.getClass().getSimpleName(), getRot().toString());
-			
-			//calculate the position in tracking volume separately as a xcheck
-			Hep3Vector box_center_tracking_xcheck = HPSTrackerBuilder.transformToTracking(box_center_base_local, base);
-			System.out.printf("%s: box_center_tracking_xcheck  %s (for %s)\n", this.getClass().getSimpleName(), box_center_tracking_xcheck.toString(), base.getName());
-		}
-		
-	}
-	/**
-	 * Find the first non-ghost volume among parents.  
-	 * @return mother object
-	 */
-	public LCDDSurveyVolume getPhysMother() {
-		//if(isDebug()) System.out.printf("%s: finding physical mother to %s\n", this.getClass().getSimpleName(), getName());
-		if(mother==null) throw new RuntimeException("Trying to get phys mother but there is no mother!");
-		if(mother instanceof LCDDGhostSurveyVolume) {
-			return mother.getPhysMother();
-		} else {
-			//if(isDebug()) System.out.printf("%s: found a non-ghost volume: %s\n", this.getClass().getSimpleName(), mother.getName());
-			return mother;
-		}
-	}
-	
-	public Volume getVolume() {
-		return volume;
-	}
-	public void setVolume(Volume volume) {
-		this.volume = volume;
-	}
-	public Box getBox() {
-		return box;
-	}
-	public void setBox(Box b) {
-		box = b;
-	}	
-	public Position getPos() {
-		return pos;
-	}
-	public void setPos(Position pos) {
-		this.pos = pos;
-	}
-	public Rotation getRot() {
-		return rot;
-	}
-	public void setRot(Rotation rot) {
-		this.rot = rot;
-	}
-	public LCDDSurveyVolume getMother() {
-		return mother;
-	}
-	public void setMother(LCDDSurveyVolume mother) {
-		this.mother = mother;
-	}
-	public PhysVol getPhysVolume() {
-		return physVolume;
-	}
-	public void setPhysVolume(PhysVol physVolume) {
-		this.physVolume = physVolume;
-	}
-	public List<LCDDSurveyVolume> getDaughters() {
-		return daughters;
-	}
-	public void addDaughter(LCDDSurveyVolume o) {
-		getDaughters().add(o);
-	}
-	 public String toString() {
+            
+            //calculate the position in tracking volume separately as a xcheck
+            Hep3Vector box_center_tracking_xcheck = HPSTrackerBuilder.transformToTracking(box_center_base_local, base);
+            System.out.printf("%s: box_center_tracking_xcheck  %s (for %s)\n", this.getClass().getSimpleName(), box_center_tracking_xcheck.toString(), base.getName());
+        }
+        
+    }
+    /**
+     * Find the first non-ghost volume among parents.  
+     * @return mother object
+     */
+    public LCDDSurveyVolume getPhysMother() {
+        //if(isDebug()) System.out.printf("%s: finding physical mother to %s\n", this.getClass().getSimpleName(), getName());
+        if(mother==null) throw new RuntimeException("Trying to get phys mother but there is no mother!");
+        if(mother instanceof LCDDGhostSurveyVolume) {
+            return mother.getPhysMother();
+        } else {
+            //if(isDebug()) System.out.printf("%s: found a non-ghost volume: %s\n", this.getClass().getSimpleName(), mother.getName());
+            return mother;
+        }
+    }
+    
+    public Volume getVolume() {
+        return volume;
+    }
+    public void setVolume(Volume volume) {
+        this.volume = volume;
+    }
+    public Box getBox() {
+        return box;
+    }
+    public void setBox(Box b) {
+        box = b;
+    }   
+    public Position getPos() {
+        return pos;
+    }
+    public void setPos(Position pos) {
+        this.pos = pos;
+    }
+    public Rotation getRot() {
+        return rot;
+    }
+    public void setRot(Rotation rot) {
+        this.rot = rot;
+    }
+    public LCDDSurveyVolume getMother() {
+        return mother;
+    }
+    public void setMother(LCDDSurveyVolume mother) {
+        this.mother = mother;
+    }
+    public PhysVol getPhysVolume() {
+        return physVolume;
+    }
+    public void setPhysVolume(PhysVol physVolume) {
+        this.physVolume = physVolume;
+    }
+    public List<LCDDSurveyVolume> getDaughters() {
+        return daughters;
+    }
+    public void addDaughter(LCDDSurveyVolume o) {
+        getDaughters().add(o);
+    }
+     public String toString() {
         String s = getClass().getSimpleName() +": " + getName() + "\n";
         if(getPos()!=null && getRot()!=null)    {
             double x = Double.valueOf(getPos().getAttributeValue("x"));

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/MilleParameter.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/MilleParameter.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/MilleParameter.java	Wed Apr 27 11:11:32 2016
@@ -9,113 +9,113 @@
 
 public class MilleParameter {
     private static double corrScaleFactor = -1.;
-	private int id;
-	private double value; 
-	private double presigma;
-	private static final Map<Integer,String> dMap;
-	private static final Map<Integer,String> tMap;
-	private static final Map<Integer,String> hMap;
-	static {
-		dMap = new HashMap<Integer,String>();
-		dMap.put(1, "x");dMap.put(2, "y"); dMap.put(3, "z");
-		tMap = new HashMap<Integer,String>();
-		tMap.put(1, "");tMap.put(2, "r");
-		hMap = new HashMap<Integer,String>();
-		hMap.put(1, "t");hMap.put(2, "b");
-		}
-	public static final int half_offset = 10000;
-	public static final int type_offset = 1000; 
-	public static final int dimension_offset = 100;
-	public static enum Type {
-	    TRANSLATION(1), ROTATION(2);
-	    private int value;
-	    private Type(int value) {this.value = value;}
-	    public int getType() {return this.value;}
-	};
-	
-	public MilleParameter(String line) {
-		String[] vals = StringUtils.split(line);// line.split("\\s+");
-		if(vals.length <3) {
-			System.out.println("this line is ill-formatted (" + vals.length + ")");
-			System.out.println(line);
-			System.exit(1);
-		}
-		try {
-		//for(String v : vals) System.out.println("\"" + v + "\"");
-		setId(Integer.parseInt(vals[0]));
-		setValue( corrScaleFactor * Double.parseDouble(vals[1]) );
-		setPresigma(Double.parseDouble(vals[2]));
-		
-		} catch (NumberFormatException e) {
-			System.out.println(vals[0] + " " + vals[1] + " " + vals[2]);
-			throw new RuntimeException("problem parsing string ", e);
-		}
-	}
-	
-	public MilleParameter(int id, double value, double presigma) {
-	    setId(id);
-	    setValue(value);
-	    setPresigma(presigma);
-	}
-	
-	public String getXMLName() {
-		String d = dMap.get(getDim());
-		String t = tMap.get(getType());
-		String h = hMap.get(getHalf());
-		int s = getSensor();
-		return String.format("%s%s%d%s_align", t,d,s,h);
-		
-	}
+    private int id;
+    private double value; 
+    private double presigma;
+    private static final Map<Integer,String> dMap;
+    private static final Map<Integer,String> tMap;
+    private static final Map<Integer,String> hMap;
+    static {
+        dMap = new HashMap<Integer,String>();
+        dMap.put(1, "x");dMap.put(2, "y"); dMap.put(3, "z");
+        tMap = new HashMap<Integer,String>();
+        tMap.put(1, "");tMap.put(2, "r");
+        hMap = new HashMap<Integer,String>();
+        hMap.put(1, "t");hMap.put(2, "b");
+        }
+    public static final int half_offset = 10000;
+    public static final int type_offset = 1000; 
+    public static final int dimension_offset = 100;
+    public static enum Type {
+        TRANSLATION(1), ROTATION(2);
+        private int value;
+        private Type(int value) {this.value = value;}
+        public int getType() {return this.value;}
+    };
+    
+    public MilleParameter(String line) {
+        String[] vals = StringUtils.split(line);// line.split("\\s+");
+        if(vals.length <3) {
+            System.out.println("this line is ill-formatted (" + vals.length + ")");
+            System.out.println(line);
+            System.exit(1);
+        }
+        try {
+        //for(String v : vals) System.out.println("\"" + v + "\"");
+        setId(Integer.parseInt(vals[0]));
+        setValue( corrScaleFactor * Double.parseDouble(vals[1]) );
+        setPresigma(Double.parseDouble(vals[2]));
+        
+        } catch (NumberFormatException e) {
+            System.out.println(vals[0] + " " + vals[1] + " " + vals[2]);
+            throw new RuntimeException("problem parsing string ", e);
+        }
+    }
+    
+    public MilleParameter(int id, double value, double presigma) {
+        setId(id);
+        setValue(value);
+        setPresigma(presigma);
+    }
+    
+    public String getXMLName() {
+        String d = dMap.get(getDim());
+        String t = tMap.get(getType());
+        String h = hMap.get(getHalf());
+        int s = getSensor();
+        return String.format("%s%s%d%s_align", t,d,s,h);
+        
+    }
 
-	public int getDim() {
-		int h = (int) (getHalf() * half_offset);
-		int t = (int) (getType() * type_offset);
-		return (int) Math.floor((id- h -t)/(double)dimension_offset);
-	}
-	
-	public int getSensor() {
-		int h = (int) (getHalf() * half_offset);
-		int t = (int) (getType() * type_offset);
-		int d = (int) (getDim() * dimension_offset);
-		return (id - h - t -d);
-	}
+    public int getDim() {
+        int h = (int) (getHalf() * half_offset);
+        int t = (int) (getType() * type_offset);
+        return (int) Math.floor((id- h -t)/(double)dimension_offset);
+    }
+    
+    public int getSensor() {
+        int h = (int) (getHalf() * half_offset);
+        int t = (int) (getType() * type_offset);
+        int d = (int) (getDim() * dimension_offset);
+        return (id - h - t -d);
+    }
 
-	public int getType() {
-		int h = (int) (getHalf() * half_offset);
-		return (int) Math.floor((id -h)/(double)type_offset);
-	}
+    public int getType() {
+        int h = (int) (getHalf() * half_offset);
+        return (int) Math.floor((id -h)/(double)type_offset);
+    }
 
-	public int getHalf() {
-		return (int)Math.floor(id/(double)half_offset);
-	}
+    public int getHalf() {
+        return (int)Math.floor(id/(double)half_offset);
+    }
 
-	public int getId() {
-		return id;
-	}
+    public int getId() {
+        return id;
+    }
 
-	public void setId(int id) {
-		this.id = id;
-	}
+    public void setId(int id) {
+        this.id = id;
+    }
 
-	public double getValue() {
-		return value;
-	}
+    public double getValue() {
+        return value;
+    }
 
-	public void setValue(double value) {
-		this.value = value;
-	}
+    public void setValue(double value) {
+        this.value = value;
+    }
 
-	public double getPresigma() {
-		return presigma;
-	}
+    public double getPresigma() {
+        return presigma;
+    }
 
-	public void setPresigma(double presigma) {
-		this.presigma = presigma;
-	}
-	
-	public String toString() {
-	    return String.format("Milleparameter id=%d half=%d type=%d dim=%d sensor=%d value=%f", this.getId(), this.getHalf(), this.getType(), this.getDim(), this.getSensor(), this.getValue());
-	}
+    public void setPresigma(double presigma) {
+        this.presigma = presigma;
+    }
+    
+    public String toString() {
+        return String.format("Milleparameter id=%d half=%d type=%d dim=%d sensor=%d value=%f", this.getId(), this.getHalf(), this.getType(), this.getDim(), this.getSensor(), this.getValue());
+    }
 
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.java	Wed Apr 27 11:11:32 2016
@@ -13,26 +13,26 @@
 import org.lcsim.detector.Translation3D;
 
      /**
-	 * Class describing a simple coordinate system used to define the {@link SurveyVolume}.
-	 * 
-	 *    @author Per Hansson Adrian <[log in to unmask]>
-	 */
-	public class SurveyCoordinateSystem {
-	    private final boolean debug = false;
-		private Hep3Vector origin;
-		private Hep3Vector u;
-		private Hep3Vector v;
-		private Hep3Vector w;
+     * Class describing a simple coordinate system used to define the {@link SurveyVolume}.
+     * 
+     *    @author Per Hansson Adrian <[log in to unmask]>
+     */
+    public class SurveyCoordinateSystem {
+        private final boolean debug = false;
+        private Hep3Vector origin;
+        private Hep3Vector u;
+        private Hep3Vector v;
+        private Hep3Vector w;
 
-//		public SurveyCoordinateSystem(Hep3Vector org, Hep3Vector unit_x, Hep3Vector unit_y, Hep3Vector unit_z) {
-//			origin = org;
-//			u = unit_x;
-//			v = unit_y;
-//			w = unit_z;
-//		}
+//      public SurveyCoordinateSystem(Hep3Vector org, Hep3Vector unit_x, Hep3Vector unit_y, Hep3Vector unit_z) {
+//          origin = org;
+//          u = unit_x;
+//          v = unit_y;
+//          w = unit_z;
+//      }
 
-		
-		public SurveyCoordinateSystem(Hep3Vector ball, Hep3Vector vee, Hep3Vector flat) {
+        
+        public SurveyCoordinateSystem(Hep3Vector ball, Hep3Vector vee, Hep3Vector flat) {
             origin = ball;
             Hep3Vector ball_to_vee = VecOp.sub(vee, ball);
             u = VecOp.unit(ball_to_vee);
@@ -41,61 +41,61 @@
             v = VecOp.cross(w, u);
             check();
         }
-		
-		private void check() {
-		    checkUnitLength();
-		    checkAngles();
-		}
+        
+        private void check() {
+            checkUnitLength();
+            checkAngles();
+        }
 
-		private void checkUnitLength() {
-		    if(u.magnitude()-1>0.00001 || v.magnitude()-1>0.00001 || v.magnitude()-1>0.00001) {
-		        throw new RuntimeException("Error: the unit vectors of the  coordinate system is ill-defined " + toString());
-		    }
-		}
+        private void checkUnitLength() {
+            if(u.magnitude()-1>0.00001 || v.magnitude()-1>0.00001 || v.magnitude()-1>0.00001) {
+                throw new RuntimeException("Error: the unit vectors of the  coordinate system is ill-defined " + toString());
+            }
+        }
 
-		private void checkAngles() {
-		    if( (VecOp.dot(u, v)-1)>0.00001 ||  (VecOp.dot(u, w)-1)>0.00001 ||  (VecOp.dot(v, w)-1)>0.00001 ) {
-		        throw new RuntimeException("Error: the angles in coordinate system is ill-defined " + toString());
-		    }
-		}
-		
-		
-		/**
-		 * Transform this coordinate system to another one.
-		 * @param t
-		 */
-		public void transform(Transform3D t) {
-		    Transform3D t_this = getTransformation();
-		    Hep3Vector v = t_this.getTranslation().getTranslationVector();
-		    Hep3Vector vrot = t.rotated(v);
-		    Hep3Vector vrottrans = t.translated(vrot);
-		    origin = vrottrans;
+        private void checkAngles() {
+            if( (VecOp.dot(u, v)-1)>0.00001 ||  (VecOp.dot(u, w)-1)>0.00001 ||  (VecOp.dot(v, w)-1)>0.00001 ) {
+                throw new RuntimeException("Error: the angles in coordinate system is ill-defined " + toString());
+            }
+        }
+        
+        
+        /**
+         * Transform this coordinate system to another one.
+         * @param t
+         */
+        public void transform(Transform3D t) {
+            Transform3D t_this = getTransformation();
+            Hep3Vector v = t_this.getTranslation().getTranslationVector();
+            Hep3Vector vrot = t.rotated(v);
+            Hep3Vector vrottrans = t.translated(vrot);
+            origin = vrottrans;
             rotate(t.getRotation());
             //System.out.printf("monkey transform\n"); 
             //System.out.printf("v %s\n",v.toString());
             //System.out.printf("vrot %s\n",vrot.toString());
             //System.out.printf("vrottrans %s\n",vrottrans.toString());
-		    check();
-		}
-		
-		public void rotate(IRotation3D r) {
-			r.rotate(u);
-			r.rotate(v);
-			r.rotate(w);
-		}
+            check();
+        }
+        
+        public void rotate(IRotation3D r) {
+            r.rotate(u);
+            r.rotate(v);
+            r.rotate(w);
+        }
 
-		public void translate(Hep3Vector translation) {
-			// update origin with local translation in u,v,w
-		    //origin = VecOp.add(origin, translation);
-		    translate(new Translation3D(translation));
-		}
+        public void translate(Hep3Vector translation) {
+            // update origin with local translation in u,v,w
+            //origin = VecOp.add(origin, translation);
+            translate(new Translation3D(translation));
+        }
 
-		public void translate(Translation3D t) {
-		    origin = t.translated(getTransformation().getTranslation().getTranslationVector());
-		}
+        public void translate(Translation3D t) {
+            origin = t.translated(getTransformation().getTranslation().getTranslationVector());
+        }
 
-		
-		public void rotateApache(Rotation r) {
+        
+        public void rotateApache(Rotation r) {
             if(debug) System.out.printf("%s: apply apache rotation to this coord system\n%s\n", getClass().getSimpleName(),toString());
             this.u = new BasicHep3Vector(r.applyTo(new Vector3D(u.v())).toArray());
             this.v = new BasicHep3Vector(r.applyTo(new Vector3D(v.v())).toArray());
@@ -104,52 +104,52 @@
         }
         
         public Hep3Vector origin() {
-			return origin;
-		}
-		public Hep3Vector u() {
-			return u;
-		}
-		public Hep3Vector v() {
-			return v;
-		}
-		public Hep3Vector w() {
-			return w;
-		}
-		public void u(Hep3Vector vec) {
+            return origin;
+        }
+        public Hep3Vector u() {
+            return u;
+        }
+        public Hep3Vector v() {
+            return v;
+        }
+        public Hep3Vector w() {
+            return w;
+        }
+        public void u(Hep3Vector vec) {
             u = vec;
-		}
+        }
         public void v(Hep3Vector vec) {
             v = vec;
         }
         public void w(Hep3Vector vec) {
             w = vec;
         }
-		
+        
         public String toString() {
-			String str = "origin " + origin.toString() + "\nu " + u.toString() + "\nv " + v.toString() + "\nw " + w.toString();
-			return str;
+            String str = "origin " + origin.toString() + "\nu " + u.toString() + "\nv " + v.toString() + "\nw " + w.toString();
+            return str;
         }
-	
-		
-		/**
-		 * Find @ITransform3D to the coordinate system defined by the input. 
-		 * @return resulting 3D transform 
-		 */
-		public Transform3D getTransformation() {
-			// Find the transform between the two frames - use transform classes here (not really needed)
-			Translation3D translation = new Translation3D(origin.x(), origin.y(), origin.z());
-			//RotationGeant trackingToEnvelopeRotation = new RotationGeant(0, 0, 0);
-			Rotation3D rotation = new Rotation3D(
-					new BasicHep3Matrix(
-							u.x(),v.x(),w.x(),
-							u.y(),v.y(),w.y(),
-							u.z(),v.z(),w.z()
-							));
-			Transform3D envelopeToSupportTransform = new Transform3D(translation, rotation);
-			return envelopeToSupportTransform;
-		}
-		
-		
-		
-		
-	}
+    
+        
+        /**
+         * Find @ITransform3D to the coordinate system defined by the input. 
+         * @return resulting 3D transform 
+         */
+        public Transform3D getTransformation() {
+            // Find the transform between the two frames - use transform classes here (not really needed)
+            Translation3D translation = new Translation3D(origin.x(), origin.y(), origin.z());
+            //RotationGeant trackingToEnvelopeRotation = new RotationGeant(0, 0, 0);
+            Rotation3D rotation = new Rotation3D(
+                    new BasicHep3Matrix(
+                            u.x(),v.x(),w.x(),
+                            u.y(),v.y(),w.y(),
+                            u.z(),v.z(),w.z()
+                            ));
+            Transform3D envelopeToSupportTransform = new Transform3D(translation, rotation);
+            return envelopeToSupportTransform;
+        }
+        
+        
+        
+        
+    }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolume.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolume.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolume.java	Wed Apr 27 11:11:32 2016
@@ -20,66 +20,66 @@
  * 
  */
 public abstract class SurveyVolume {
-	protected boolean debug = false;
-	private String name;
-	private String material = "Vacuum";
-	private SurveyVolume mother = null;
-	protected List<SurveyVolume> referenceGeom = null;
-	private SurveyCoordinateSystem coord;
-	protected  Hep3Vector ballPos;
-	protected  Hep3Vector veePos;
-	protected  Hep3Vector flatPos;
-	private Hep3Vector center;
-	private Hep3Vector boxDim;
-	private AlignmentCorrection alignmentCorrections;
-	
-	public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection) {
-		setName(name);
-		setMother(m);
-		setAlignmentCorrection(alignmentCorrection);
-	}
-	
-	public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection, SurveyVolume ref) {
-		setName(name);
-		setMother(m);
-		setAlignmentCorrection(alignmentCorrection);
-		addReferenceGeom(ref);
-	}
-	
-	public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection, List<SurveyVolume> ref) {
-		setName(name);
-		setMother(m);
-		setAlignmentCorrection(alignmentCorrection);
-		addReferenceGeom(ref);
-	}
-	
-	protected abstract void setPos();
-	protected abstract void setCenter();
-	protected abstract void setBoxDim();
-
-	/**
-	 * 
-	 * Initialize the volume. 
-	 * This needs to be called at the top level implementation of the {@link SurveyVolume} to properly setup
-	 * the coordinate systems. It takes care of applying user supplied custom transformations and alignment corrections
-	 * in the order given in the function below. That order must be preserved to get a uniform behavior. 
-	 * 
-	 */
-	protected void init() {
-	    if(debug) System.out.printf("%s: init SurveyVolume %s\n",this.getClass().getSimpleName(),getName());
+    protected boolean debug = false;
+    private String name;
+    private String material = "Vacuum";
+    private SurveyVolume mother = null;
+    protected List<SurveyVolume> referenceGeom = null;
+    private SurveyCoordinateSystem coord;
+    protected  Hep3Vector ballPos;
+    protected  Hep3Vector veePos;
+    protected  Hep3Vector flatPos;
+    private Hep3Vector center;
+    private Hep3Vector boxDim;
+    private AlignmentCorrection alignmentCorrections;
+    
+    public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection) {
+        setName(name);
+        setMother(m);
+        setAlignmentCorrection(alignmentCorrection);
+    }
+    
+    public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection, SurveyVolume ref) {
+        setName(name);
+        setMother(m);
+        setAlignmentCorrection(alignmentCorrection);
+        addReferenceGeom(ref);
+    }
+    
+    public SurveyVolume(String name, SurveyVolume m, AlignmentCorrection alignmentCorrection, List<SurveyVolume> ref) {
+        setName(name);
+        setMother(m);
+        setAlignmentCorrection(alignmentCorrection);
+        addReferenceGeom(ref);
+    }
+    
+    protected abstract void setPos();
+    protected abstract void setCenter();
+    protected abstract void setBoxDim();
+
+    /**
+     * 
+     * Initialize the volume. 
+     * This needs to be called at the top level implementation of the {@link SurveyVolume} to properly setup
+     * the coordinate systems. It takes care of applying user supplied custom transformations and alignment corrections
+     * in the order given in the function below. That order must be preserved to get a uniform behavior. 
+     * 
+     */
+    protected void init() {
+        if(debug) System.out.printf("%s: init SurveyVolume %s\n",this.getClass().getSimpleName(),getName());
         setPos();
-		setCoord();
-		applyReferenceTransformation();
-		setCenter();
-		setBoxDim();
-		applyGenericCoordinateSystemCorrections();
-		applyLocalAlignmentCorrections();
-		if(debug) {
-		    //printCoordInfo();
-		    System.out.printf("%s: init of SurveyVolume %s DONE\n",this.getClass().getSimpleName(),getName());            
-		}
-	}
-	
+        setCoord();
+        applyReferenceTransformation();
+        setCenter();
+        setBoxDim();
+        applyGenericCoordinateSystemCorrections();
+        applyLocalAlignmentCorrections();
+        if(debug) {
+            //printCoordInfo();
+            System.out.printf("%s: init of SurveyVolume %s DONE\n",this.getClass().getSimpleName(),getName());            
+        }
+    }
+    
 
     private void applySurvey(Element node) {
 
@@ -378,254 +378,254 @@
      * Apply a generic correction to the coordinate system of this volume. 
      */
     protected void applyGenericCoordinateSystemCorrections() {
-	    //do nothing here unless overridden
-	   
-	}
-    
-	/**
-	 * Applies a user supplied reference transformation to the module. 
-	 * This is convenient as it allows for intermediary "virtual" mother volumes to be used 
-	 * in referencing a volume to it's physcial mother volume.
-	 */
-	protected void applyReferenceTransformation() {
-
-	        	    
-	    if(referenceGeom!=null) {
-	        
-	        if(debug) System.out.printf("%s: apply reference transformation for %s\n",this.getClass().getSimpleName(),getName());
-	        
-
-	        if(debug) System.out.printf("%s: coord system before %d ref transformations:\n%s\n",this.getClass().getSimpleName(),referenceGeom.size(),getCoord().toString());
-	        
-	        for(SurveyVolume ref : referenceGeom) {
-
-	            if(debug) {
-	                System.out.printf("%s: coord system before ref %s transform:\n%s\n",this.getClass().getSimpleName(),ref.getName(),getCoord().toString());
-	                System.out.printf("%s: Ref %s coord\n%s\n",this.getClass().getSimpleName(), ref.getName(),ref.getCoord().toString());
-	            }
-	            
-	            getCoord().transform(ref.getCoord().getTransformation());
-
-	            if(debug) System.out.printf("%s: coord system after ref %s transform:\n%s\n",this.getClass().getSimpleName(),ref.getName(),getCoord().toString());
-	            
-	        }
-
-	        if(debug) System.out.printf("%s: coord system after ref transformations:\n%s\n",this.getClass().getSimpleName(),getCoord().toString());
-	        
-	    } else {
-	        
-	        if(debug) System.out.printf("%s: no reference transformation exists for %s\n",this.getClass().getSimpleName(),getName());
-	        
-	    }
-
-	}
-	
-	/**
-	 * Apply @link AlignmentCorrection to the volume if they are supplied. 
-	 * 
-	 */
-	private void applyLocalAlignmentCorrections() {
-	    
-	    // Apply alignment corrections to local coordinate system that is already built
-	    boolean debug_local = false;
-	    if(this.coord==null) 
-	        throw new RuntimeException("no coordinate system was set before trying to apply alignment corrections.");
-
-	    if(alignmentCorrections!=null) {
-
-	        
-	        if(alignmentCorrections.getNode()!=null) {
-	            
-	            if(debug_local || debug) System.out.printf("%s: Apply survey results to %s\n",this.getClass().getSimpleName(),this.getName());
-	            
-	            applySurvey(alignmentCorrections.getNode());
-
-	            if(debug_local || debug) System.out.printf("%s: DONE Apply survey results to %s\n",this.getClass().getSimpleName(),this.getName());
-                
-	        }
-	        
-	        
-	        
-	        
-	        
-	        if(debug_local || debug) System.out.printf("%s: Apply alignment corrections to %s\n",this.getClass().getSimpleName(),this.getName());
-
-	        // translate
-	        if(alignmentCorrections.getTranslation()!=null) {			    
-
-	            if(debug_local || debug) System.out.printf("%s: Apply local translation %s\n", this.getClass().getSimpleName(),alignmentCorrections.getTranslation().toString());			    
-	            
-	            // rotate into mother coordinate system
-	            Hep3Vector translation_mother = getCoord().getTransformation().rotated(alignmentCorrections.getTranslation());
-	            
-	            if(debug_local || debug) System.out.printf("%s: after rotation apply translation %s to coordinate system\n", this.getClass().getSimpleName(),translation_mother.toString());
-	            
-	            //apply translation
-	            getCoord().translate(translation_mother);
-
-	        } else {
-	            if(debug_local || debug) System.out.printf("%s: No translation to coordinate system\n", this.getClass().getSimpleName());
-	        }
-
-	        // rotate
-	        if(alignmentCorrections.getRotation()!=null) {  
-	            
+        //do nothing here unless overridden
+       
+    }
+    
+    /**
+     * Applies a user supplied reference transformation to the module. 
+     * This is convenient as it allows for intermediary "virtual" mother volumes to be used 
+     * in referencing a volume to it's physcial mother volume.
+     */
+    protected void applyReferenceTransformation() {
+
+                    
+        if(referenceGeom!=null) {
+            
+            if(debug) System.out.printf("%s: apply reference transformation for %s\n",this.getClass().getSimpleName(),getName());
+            
+
+            if(debug) System.out.printf("%s: coord system before %d ref transformations:\n%s\n",this.getClass().getSimpleName(),referenceGeom.size(),getCoord().toString());
+            
+            for(SurveyVolume ref : referenceGeom) {
+
+                if(debug) {
+                    System.out.printf("%s: coord system before ref %s transform:\n%s\n",this.getClass().getSimpleName(),ref.getName(),getCoord().toString());
+                    System.out.printf("%s: Ref %s coord\n%s\n",this.getClass().getSimpleName(), ref.getName(),ref.getCoord().toString());
+                }
+                
+                getCoord().transform(ref.getCoord().getTransformation());
+
+                if(debug) System.out.printf("%s: coord system after ref %s transform:\n%s\n",this.getClass().getSimpleName(),ref.getName(),getCoord().toString());
+                
+            }
+
+            if(debug) System.out.printf("%s: coord system after ref transformations:\n%s\n",this.getClass().getSimpleName(),getCoord().toString());
+            
+        } else {
+            
+            if(debug) System.out.printf("%s: no reference transformation exists for %s\n",this.getClass().getSimpleName(),getName());
+            
+        }
+
+    }
+    
+    /**
+     * Apply @link AlignmentCorrection to the volume if they are supplied. 
+     * 
+     */
+    private void applyLocalAlignmentCorrections() {
+        
+        // Apply alignment corrections to local coordinate system that is already built
+        boolean debug_local = false;
+        if(this.coord==null) 
+            throw new RuntimeException("no coordinate system was set before trying to apply alignment corrections.");
+
+        if(alignmentCorrections!=null) {
+
+            
+            if(alignmentCorrections.getNode()!=null) {
+                
+                if(debug_local || debug) System.out.printf("%s: Apply survey results to %s\n",this.getClass().getSimpleName(),this.getName());
+                
+                applySurvey(alignmentCorrections.getNode());
+
+                if(debug_local || debug) System.out.printf("%s: DONE Apply survey results to %s\n",this.getClass().getSimpleName(),this.getName());
+                
+            }
+            
+            
+            
+            
+            
+            if(debug_local || debug) System.out.printf("%s: Apply alignment corrections to %s\n",this.getClass().getSimpleName(),this.getName());
+
+            // translate
+            if(alignmentCorrections.getTranslation()!=null) {               
+
+                if(debug_local || debug) System.out.printf("%s: Apply local translation %s\n", this.getClass().getSimpleName(),alignmentCorrections.getTranslation().toString());               
+                
+                // rotate into mother coordinate system
+                Hep3Vector translation_mother = getCoord().getTransformation().rotated(alignmentCorrections.getTranslation());
+                
+                if(debug_local || debug) System.out.printf("%s: after rotation apply translation %s to coordinate system\n", this.getClass().getSimpleName(),translation_mother.toString());
+                
+                //apply translation
+                getCoord().translate(translation_mother);
+
+            } else {
+                if(debug_local || debug) System.out.printf("%s: No translation to coordinate system\n", this.getClass().getSimpleName());
+            }
+
+            // rotate
+            if(alignmentCorrections.getRotation()!=null) {  
+                
                 if(debug_local || debug) {
                     System.out.printf("%s: Apply rotation matrix:\n", this.getClass().getSimpleName());   
                     TransformationUtils.printMatrix(alignmentCorrections.getRotation().getMatrix());
                     System.out.printf("%s: coord system before:\n%s\n", this.getClass().getSimpleName(),getCoord().toString());   
                 }
 
-	            
-	            // correct rotation of the local unit vectors
-	            Vector3D u_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(1,0,0));
-	            Vector3D v_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(0,1,0));
-	            Vector3D w_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(0,0,1));
-
-	            // rotate the local unit vectors to the mother coordinates
-	            
-	            Hep3Vector u_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(u_rot_local.toArray()));
-	            Hep3Vector v_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(v_rot_local.toArray()));
-	            Hep3Vector w_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(w_rot_local.toArray()));
+                
+                // correct rotation of the local unit vectors
+                Vector3D u_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(1,0,0));
+                Vector3D v_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(0,1,0));
+                Vector3D w_rot_local = alignmentCorrections.getRotation().applyTo(new Vector3D(0,0,1));
+
+                // rotate the local unit vectors to the mother coordinates
+                
+                Hep3Vector u_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(u_rot_local.toArray()));
+                Hep3Vector v_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(v_rot_local.toArray()));
+                Hep3Vector w_rot = getCoord().getTransformation().getRotation().rotated(new BasicHep3Vector(w_rot_local.toArray()));
                
-	            getCoord().u(u_rot);
-	            getCoord().v(v_rot);
-	            getCoord().w(w_rot);
+                getCoord().u(u_rot);
+                getCoord().v(v_rot);
+                getCoord().w(w_rot);
 
                 if(debug_local || debug) {
                     System.out.printf("%s: coord system after:\n%s\n", this.getClass().getSimpleName(),getCoord().toString());   
                 }
 
-	            
-	            
-
-	        } else {
-	            if(debug_local || debug) System.out.printf("%s: No rotation to coordinate system\n", this.getClass().getSimpleName());
-	        }
-
-	        if(debug_local || debug) System.out.printf("%s: coordinate system after alignment corrections:\n%s\n",this.getClass().getSimpleName(),getCoord().toString());
-
-	    } else {
+                
+                
+
+            } else {
+                if(debug_local || debug) System.out.printf("%s: No rotation to coordinate system\n", this.getClass().getSimpleName());
+            }
+
+            if(debug_local || debug) System.out.printf("%s: coordinate system after alignment corrections:\n%s\n",this.getClass().getSimpleName(),getCoord().toString());
+
+        } else {
             if(debug_local || debug) System.out.printf("%s: no alignment corrections exist for %s\n",this.getClass().getSimpleName(),this.getName());
-	    }
-
-	}
-	
-	private void setAlignmentCorrection(AlignmentCorrection alignmentCorrection) {
+        }
+
+    }
+    
+    private void setAlignmentCorrection(AlignmentCorrection alignmentCorrection) {
         this.alignmentCorrections = alignmentCorrection;
     }
     public  void setBallPos(double x, double y, double z) {
-		ballPos = new BasicHep3Vector(x,y,z);
-	}
-	public  void setVeePos(double x, double y, double z) {
-		veePos = new BasicHep3Vector(x,y,z);
-	}
-	public  void setFlatPos(double x, double y, double z) {
-		flatPos = new BasicHep3Vector(x,y,z);
-	}
-	public  Hep3Vector getBallPos() {
-		return ballPos;
-	}
-	public  Hep3Vector getVeePos() {
-		return veePos;
-	}
-	public  Hep3Vector getFlatPos() {
-		return flatPos;
-	}
-	public void setCoord() {
-		if(ballPos==null || veePos==null || flatPos==null) {
-			throw new RuntimeException("Need to set ball, vee and flat before building coord system!");
-		}
-		
-		coord = new SurveyCoordinateSystem(ballPos, veePos, flatPos);					
-		
-		if(this.debug) {
-		    System.out.printf("%s: setCoord \n%s\n", this.getClass().getSimpleName(), coord.toString());
-		}
-	}
-	public SurveyCoordinateSystem getCoord() {
-		if(coord == null) {
-			throw new RuntimeException("Need to setCoord!");
-		}
-		return coord;
-	}
-	public String getName() {
-		return name;
-	}
-	public void setName(String name) {
-		this.name = name;
-	}
-	public Hep3Vector getCenter() {
-		return center;
-	}
-	public void setCenter(Hep3Vector center) {
-		this.center = center;
-	}
-	public void setCenter(double x, double y, double z) {
-		this.center = new BasicHep3Vector(x,y,z);
-	}
-	public Hep3Vector getBoxDim() {
-		return boxDim;
-	}
-	public void setBoxDim(double x, double y, double z) {
-		this.boxDim = new BasicHep3Vector(x,y,z);
-	}
-	public SurveyVolume getMother() {
-		return mother;
-	}
-	public void setMother(SurveyVolume mother) {
-		this.mother = mother;
-	}
-	public void addReferenceGeom(SurveyVolume refGeom) {
-	    if(refGeom!=null) { // check that it's not a dummy call
-	        if(referenceGeom == null) {
-	            referenceGeom = new ArrayList<SurveyVolume>();
-	        }
-	        referenceGeom.add(refGeom);
-	    }
-	}
-	public void addReferenceGeom(List<SurveyVolume> refGeomList) {
-		if(referenceGeom == null) {
-			referenceGeom = new ArrayList<SurveyVolume>();
-		}
-		referenceGeom.addAll(refGeomList);
-	}
-	public void printSurveyPos() {
-	    if(debug) {
-	        System.out.printf("%s: Survey pos for %s:\n",getClass().getSimpleName(),getName());
-	        System.out.printf("%s: ballPos   %s\n",getClass().getSimpleName(), ballPos.toString());
-	        System.out.printf("%s: veePos    %s\n",getClass().getSimpleName(), veePos.toString());
-	        System.out.printf("%s: flatPos   %s\n",getClass().getSimpleName(), flatPos.toString());
-	    }
-	}
-	public String getMaterial() {
-		return material;
-	}
-	public void setMaterial(String material) {
-		this.material = material;
-	}
-	public String toString() {
-		String s = "==\n" + getName() + " with mother " + (getMother()==null?"<no mother>":getMother().getName()) + ":\n";
-		if( getCenter()!=null) s += "Center of box: " + getCenter().toString() + "\n";
+        ballPos = new BasicHep3Vector(x,y,z);
+    }
+    public  void setVeePos(double x, double y, double z) {
+        veePos = new BasicHep3Vector(x,y,z);
+    }
+    public  void setFlatPos(double x, double y, double z) {
+        flatPos = new BasicHep3Vector(x,y,z);
+    }
+    public  Hep3Vector getBallPos() {
+        return ballPos;
+    }
+    public  Hep3Vector getVeePos() {
+        return veePos;
+    }
+    public  Hep3Vector getFlatPos() {
+        return flatPos;
+    }
+    public void setCoord() {
+        if(ballPos==null || veePos==null || flatPos==null) {
+            throw new RuntimeException("Need to set ball, vee and flat before building coord system!");
+        }
+        
+        coord = new SurveyCoordinateSystem(ballPos, veePos, flatPos);                   
+        
+        if(this.debug) {
+            System.out.printf("%s: setCoord \n%s\n", this.getClass().getSimpleName(), coord.toString());
+        }
+    }
+    public SurveyCoordinateSystem getCoord() {
+        if(coord == null) {
+            throw new RuntimeException("Need to setCoord!");
+        }
+        return coord;
+    }
+    public String getName() {
+        return name;
+    }
+    public void setName(String name) {
+        this.name = name;
+    }
+    public Hep3Vector getCenter() {
+        return center;
+    }
+    public void setCenter(Hep3Vector center) {
+        this.center = center;
+    }
+    public void setCenter(double x, double y, double z) {
+        this.center = new BasicHep3Vector(x,y,z);
+    }
+    public Hep3Vector getBoxDim() {
+        return boxDim;
+    }
+    public void setBoxDim(double x, double y, double z) {
+        this.boxDim = new BasicHep3Vector(x,y,z);
+    }
+    public SurveyVolume getMother() {
+        return mother;
+    }
+    public void setMother(SurveyVolume mother) {
+        this.mother = mother;
+    }
+    public void addReferenceGeom(SurveyVolume refGeom) {
+        if(refGeom!=null) { // check that it's not a dummy call
+            if(referenceGeom == null) {
+                referenceGeom = new ArrayList<SurveyVolume>();
+            }
+            referenceGeom.add(refGeom);
+        }
+    }
+    public void addReferenceGeom(List<SurveyVolume> refGeomList) {
+        if(referenceGeom == null) {
+            referenceGeom = new ArrayList<SurveyVolume>();
+        }
+        referenceGeom.addAll(refGeomList);
+    }
+    public void printSurveyPos() {
+        if(debug) {
+            System.out.printf("%s: Survey pos for %s:\n",getClass().getSimpleName(),getName());
+            System.out.printf("%s: ballPos   %s\n",getClass().getSimpleName(), ballPos.toString());
+            System.out.printf("%s: veePos    %s\n",getClass().getSimpleName(), veePos.toString());
+            System.out.printf("%s: flatPos   %s\n",getClass().getSimpleName(), flatPos.toString());
+        }
+    }
+    public String getMaterial() {
+        return material;
+    }
+    public void setMaterial(String material) {
+        this.material = material;
+    }
+    public String toString() {
+        String s = "==\n" + getName() + " with mother " + (getMother()==null?"<no mother>":getMother().getName()) + ":\n";
+        if( getCenter()!=null) s += "Center of box: " + getCenter().toString() + "\n";
         if( getBoxDim()!=null) s += "Box dimensions: " + getBoxDim().toString() + "\n";
-		if(this.coord==null)   s += " No coord system \n";
-		else {
-		    s += getName() + " origin " + getCoord().origin() + " u " + getCoord().u()+ " v " + getCoord().v()+ " w " + getCoord().w();
-		}
+        if(this.coord==null)   s += " No coord system \n";
+        else {
+            s += getName() + " origin " + getCoord().origin() + " u " + getCoord().u()+ " v " + getCoord().v()+ " w " + getCoord().w();
+        }
         s += "AlignmentCorrections: \n";
-		if(this.alignmentCorrections!=null) {
-		    s += "Milleparameters: ";
-		    if(this.alignmentCorrections.getMilleParameters()!=null) {
-		        for(MilleParameter mp : this.alignmentCorrections.getMilleParameters()) s += mp.getId() + " ";
-		    } else {
-		        s += "no MP params associated.";
-		    }
-		    s +=  "(" + this.getName() + ")" + " \n";
-		} else {
-		    s+= " no alignment corrections associated.\n";
-		}
-		SurveyVolume m = getMother();
-		while(m!=null) {    
+        if(this.alignmentCorrections!=null) {
+            s += "Milleparameters: ";
+            if(this.alignmentCorrections.getMilleParameters()!=null) {
+                for(MilleParameter mp : this.alignmentCorrections.getMilleParameters()) s += mp.getId() + " ";
+            } else {
+                s += "no MP params associated.";
+            }
+            s +=  "(" + this.getName() + ")" + " \n";
+        } else {
+            s+= " no alignment corrections associated.\n";
+        }
+        SurveyVolume m = getMother();
+        while(m!=null) {    
             Hep3Vector origin_m = HPSTrackerBuilder.transformToParent(new BasicHep3Vector(0, 0, 0), this, m.getName());
             String unitVecStr = "";
             if(getCoord()!=null) {
@@ -638,12 +638,12 @@
             //origin_m = VecOp.mult(0.0393701, origin_m);
             //s += String.format("%s origin in %s : (%.4f %.4f %.4f) (inch)\n",getName(), m.getName(), origin_m.x(),origin_m.y(),origin_m.z());            
             m = m.getMother();
-		}
-		
-		
-		return s;
-	}
-	
-
-	
+        }
+        
+        
+        return s;
+    }
+    
+
+    
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeImpl.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeImpl.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeImpl.java	Wed Apr 27 11:11:32 2016
@@ -21,7 +21,7 @@
     public abstract void setPositionAndRotation(SurveyVolume base);
 
     public String getName() {
-    	return surveyVolume.getName();
+        return surveyVolume.getName();
     }
     
     protected Hep3Vector getBoxDim() {
@@ -33,7 +33,7 @@
     }
 
     public boolean isDebug() {
-    	return debug;
+        return debug;
     }
 
     public abstract String toString();

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.java	Wed Apr 27 11:11:32 2016
@@ -7,14 +7,14 @@
  * @author Per Hansson Adrian <[log in to unmask]>
  */
 public class SurveyVolumeVisualization {
-	protected String visName = "";
-	public SurveyVolumeVisualization() {}
-	public String getVisName() {
-		return visName;
-	}
-	protected void setVisName(String visName) {
-		this.visName = visName;
-	}
-	
-	
+    protected String visName = "";
+    public SurveyVolumeVisualization() {}
+    public String getVisName() {
+        return visName;
+    }
+    protected void setVisName(String visName) {
+        this.visName = visName;
+    }
+    
+    
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java	Wed Apr 27 11:11:32 2016
@@ -14,16 +14,16 @@
  * @author <a href="mailto:[log in to unmask]">Jeremy McCormick</a>
  */
 public class SvtAlignmentConstantsReader {
-	
-	private SvtAlignmentConstantsReader() {
-	}
+    
+    private SvtAlignmentConstantsReader() {
+    }
 
-	/**
-	 * Read SVT alignment constants from the conditions database table <i>svt_alignments</i> and create a list of 
-	 * <code>MilleParameter</code> objects from it.
-	 * 
-	 * @return the Millepede parameter list
-	 */
+    /**
+     * Read SVT alignment constants from the conditions database table <i>svt_alignments</i> and create a list of 
+     * <code>MilleParameter</code> objects from it.
+     * 
+     * @return the Millepede parameter list
+     */
     static List<MilleParameter> readMilleParameters() {
 
         final DatabaseConditionsManager manager = DatabaseConditionsManager.getInstance();

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java	Wed Apr 27 11:11:32 2016
@@ -8,13 +8,13 @@
 
 public class HPSMuonCalorimeter2 extends LCDDSubdetector
 {
-	HPSMuonCalorimeter2(Element e) throws JDOMException 
-	{
-		super(e);
-	}
+    HPSMuonCalorimeter2(Element e) throws JDOMException 
+    {
+        super(e);
+    }
 
-	void addToLCDD(LCDD lcdd, SensitiveDetector sens) throws JDOMException 
-	{
+    void addToLCDD(LCDD lcdd, SensitiveDetector sens) throws JDOMException 
+    {
         String name = node.getAttributeValue("name");
         System.out.println("HPSMuonCalorimeter2.addToLCDD - " + name);
         int id = node.getAttribute("id").getIntValue();
@@ -22,7 +22,7 @@
         
         Element parameters = node.getChild("parameters");
         if (parameters == null) {
-        	throw new RuntimeException("parameters element missing");
+            throw new RuntimeException("parameters element missing");
         }
                 
         double frontFaceToTarget = parameters.getAttribute("front_face_to_target").getDoubleValue();
@@ -40,16 +40,16 @@
         System.out.println("stripSpacingZ = " + stripSpacingZ);
         
         for (Object layerObject : node.getChildren("layer")) {
-        	Element layerElement = (Element)layerObject;
-        	int layerId = layerElement.getAttribute("id").getIntValue();
-        	System.out.println("layer = " + layerId);
-        	for (Object sliceObject : layerElement.getChildren("slice")) {
-        		Element sliceElement = (Element)sliceObject;
-        		if (sliceElement.getAttribute("thickness") != null) {
-        			double thickness = sliceElement.getAttribute("thickness").getDoubleValue();
-        			System.out.println("slice thickness = " + thickness);
-        		}
-        	}
+            Element layerElement = (Element)layerObject;
+            int layerId = layerElement.getAttribute("id").getIntValue();
+            System.out.println("layer = " + layerId);
+            for (Object sliceObject : layerElement.getChildren("slice")) {
+                Element sliceElement = (Element)sliceObject;
+                if (sliceElement.getAttribute("thickness") != null) {
+                    double thickness = sliceElement.getAttribute("thickness").getDoubleValue();
+                    System.out.println("slice thickness = " + thickness);
+                }
+            }
         }
-	}
+    }
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java	Wed Apr 27 11:11:32 2016
@@ -9,7 +9,6 @@
 import org.lcsim.geometry.compact.converter.HPSTestRunTracker2014GeometryDefinition;
 import org.lcsim.geometry.compact.converter.HPSTestRunTracker2014LCDDBuilder;
 import org.lcsim.geometry.compact.converter.HPSTrackerBuilder;
-import org.lcsim.geometry.compact.converter.HPSTrackerGeometryDefinition;
 import org.lcsim.geometry.compact.converter.HPSTrackerLCDDBuilder;
 import org.lcsim.geometry.compact.converter.lcdd.util.Box;
 import org.lcsim.geometry.compact.converter.lcdd.util.LCDD;
@@ -30,58 +29,58 @@
  */
 public class HPSTestRunTracker2014 extends HPSTracker2014Base
 {
-	public HPSTestRunTracker2014(Element node) throws JDOMException
-	{
-		super(node);
-	}
-
-	/* (non-Javadoc)
-	 * @see org.lcsim.geometry.compact.converter.lcdd.HPSTracker2014Base#initializeBuilder(org.lcsim.geometry.compact.converter.lcdd.util.LCDD, org.lcsim.geometry.compact.converter.lcdd.util.SensitiveDetector)
-	 */
-	protected HPSTrackerLCDDBuilder initializeBuilder(LCDD lcdd, SensitiveDetector sens) {
-	    HPSTrackerLCDDBuilder b = new HPSTestRunTracker2014LCDDBuilder(_debug,node,lcdd,sens);
-	    return b;
-	}
-	
-	
-
-	/* (non-Javadoc)
+    public HPSTestRunTracker2014(Element node) throws JDOMException
+    {
+        super(node);
+    }
+
+    /* (non-Javadoc)
+     * @see org.lcsim.geometry.compact.converter.lcdd.HPSTracker2014Base#initializeBuilder(org.lcsim.geometry.compact.converter.lcdd.util.LCDD, org.lcsim.geometry.compact.converter.lcdd.util.SensitiveDetector)
+     */
+    protected HPSTrackerLCDDBuilder initializeBuilder(LCDD lcdd, SensitiveDetector sens) {
+        HPSTrackerLCDDBuilder b = new HPSTestRunTracker2014LCDDBuilder(_debug,node,lcdd,sens);
+        return b;
+    }
+    
+    
+
+    /* (non-Javadoc)
      * @see org.lcsim.detector.converter.compact.HPSTracker2014ConverterBase#getModuleNumber(org.lcsim.geometry.compact.converter.JavaSurveyVolume)
      */
     protected int getModuleNumber(String surveyVolume) {
         return HPSTrackerBuilder.getHalfFromName(surveyVolume).equals("top") ? 0 : 1;
     }
-	
-	
-	
-	
-	
-	
-	
-	
-	
-
-	
-	
-	
-	private void makeExample(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-	
-	
-	if(_debug) {
-		System.out.println("--- makeExample ----");
-		
-	}
-
-	
-	
-	String volName = "example";
-	Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-	lcdd.add(box);
-	Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	
-	
-	
-	 org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisX = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(1., 0., 0.);
+    
+    
+    
+    
+    
+    
+    
+    
+    
+
+    
+    
+    
+    private void makeExample(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+    
+    
+    if(_debug) {
+        System.out.println("--- makeExample ----");
+        
+    }
+
+    
+    
+    String volName = "example";
+    Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+    lcdd.add(box);
+    Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+    
+    
+    
+     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisX = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(1., 0., 0.);
      org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisY = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 1., 0.);
      org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisZ = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 0., 1.);
 
@@ -131,11 +130,11 @@
      Rotation rot = new Rotation(volName + "_rotation",0,0,0);
      lcdd.add(pos);
      lcdd.add(rot);
-	
-	
+    
+    
      PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
      if(_debug) {
-    	 System.out.println("Created physical vomume " + basePV.getName());
+         System.out.println("Created physical vomume " + basePV.getName());
      }
      
      
@@ -151,153 +150,153 @@
      lcdd.add(subRot);
      PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
      if(_debug) {
-    	 System.out.println("Created physical vomume " + subBasePV.getName());
+         System.out.println("Created physical vomume " + subBasePV.getName());
      }
-	
+    
      lcdd.add(volumeSub);
      volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
 
-	
+    
      lcdd.add(volume);
-	
-	
-	
-	
-	}
-	
-	
-	private void makeExample2(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample2 ----");
-			
-		}
-		
-		String volName = "example2";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	    
-
-		
-		 org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisX = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(1., 0., 0.);
-	     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisY = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 1., 0.);
-	     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisZ = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 0., 1.);
-
-	     double alpha1 = PI / 4.;
-	     double alpha2 = PI / 4.;
-	     double alpha3 = -PI / 4.;
-
-	     org.apache.commons.math3.geometry.euclidean.threed.Rotation r123 = 
-	    		 new org.apache.commons.math3.geometry.euclidean.threed.Rotation(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ, 
-	    				 alpha1, 
-	    				 alpha2, 
-	    				 alpha3);
-	     
-	     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisXPrime = r123.applyTo(axisX);
-	     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisYPrime = r123.applyTo(axisY);
-	     org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisZPrime = r123.applyTo(axisZ);
-
-	     //if(_debug) System.out.println("axisYPrime: " + axisYPrime);
-	     //if(_debug) System.out.println("axisZPrime: " + axisZPrime);
-
-	     
-	     
-	     //double [] rotations = r123.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-	     
-	     
-	     //double [] rotations = r12.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-	     double [] rotations = r123.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-	     
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5,0,0);
-	     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-	     
-	     lcdd.add(volume);
-
-		
-		
-		
-		}
-		
-		
-		
-	private void makeExample3(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample3 ----");
-			
-		}
-		
-		String volName = "example3";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-		
-		/*
-		
-		TestRunModuleL13: survey positions before ref support_plate_top transform
-		Survey pos for module_L1t:
-		ballPos   [      25.000,      676.10,     -4.3500]
-		veePos    [      95.000,      676.10,     -4.3500]
-		flatPos   [      60.000,      670.10,     -4.3500]
-		TestRunModuleL13: Ref support_plate_top coord
-		Coordinate system: 
-		origin [      40.314,      142.71,      138.40]
-		u [     0.99955,    0.030000,      0.0000]
-		v [   -0.030000,     0.99955,      0.0000]
-		w [      0.0000,     -0.0000,      1.0000]
-		TestRunModuleL13: survey positions after ref support_plate_top transform
-		Survey pos for module_L1t:
-		ballPos   [      45.020,      819.25,      134.05]
-		veePos    [      114.99,      821.35,      134.05]
-		flatPos   [      80.184,      814.31,      134.05]
-		TestRunModuleL13: coordinate system:
-		Coordinate system: 
-		origin [      45.020,      819.25,      134.05]
-		u [     0.99955,    0.030000,      0.0000]
-		v [    0.030000,    -0.99955,      0.0000]
-		w [      0.0000,      0.0000,     -1.0000]
-		TestRunModuleL13: translation:
-		[      45.020,      819.25,      134.05]
-		TestRunModuleL13: rotation:
-		[
-		0.999549894704642 0.030000133265350216 0.0
-		0.030000133265350216 -0.999549894704642 0.0
-		0.0 0.0 -1.0
-
-		]
-		
-		
-		
-		LCDDBaseGeom: set position and rotation for volume module_L1t
+    
+    
+    
+    
+    }
+    
+    
+    private void makeExample2(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample2 ----");
+            
+        }
+        
+        String volName = "example2";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+
+        
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisX = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(1., 0., 0.);
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisY = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 1., 0.);
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisZ = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0., 0., 1.);
+
+         double alpha1 = PI / 4.;
+         double alpha2 = PI / 4.;
+         double alpha3 = -PI / 4.;
+
+         org.apache.commons.math3.geometry.euclidean.threed.Rotation r123 = 
+                 new org.apache.commons.math3.geometry.euclidean.threed.Rotation(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ, 
+                         alpha1, 
+                         alpha2, 
+                         alpha3);
+         
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisXPrime = r123.applyTo(axisX);
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisYPrime = r123.applyTo(axisY);
+         org.apache.commons.math3.geometry.euclidean.threed.Vector3D axisZPrime = r123.applyTo(axisZ);
+
+         //if(_debug) System.out.println("axisYPrime: " + axisYPrime);
+         //if(_debug) System.out.println("axisZPrime: " + axisZPrime);
+
+         
+         
+         //double [] rotations = r123.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+         
+         
+         //double [] rotations = r12.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+         double [] rotations = r123.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+         
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5,0,0);
+         Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+         
+         lcdd.add(volume);
+
+        
+        
+        
+        }
+        
+        
+        
+    private void makeExample3(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample3 ----");
+            
+        }
+        
+        String volName = "example3";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+        /*
+        
+        TestRunModuleL13: survey positions before ref support_plate_top transform
+        Survey pos for module_L1t:
+        ballPos   [      25.000,      676.10,     -4.3500]
+        veePos    [      95.000,      676.10,     -4.3500]
+        flatPos   [      60.000,      670.10,     -4.3500]
+        TestRunModuleL13: Ref support_plate_top coord
+        Coordinate system: 
+        origin [      40.314,      142.71,      138.40]
+        u [     0.99955,    0.030000,      0.0000]
+        v [   -0.030000,     0.99955,      0.0000]
+        w [      0.0000,     -0.0000,      1.0000]
+        TestRunModuleL13: survey positions after ref support_plate_top transform
+        Survey pos for module_L1t:
+        ballPos   [      45.020,      819.25,      134.05]
+        veePos    [      114.99,      821.35,      134.05]
+        flatPos   [      80.184,      814.31,      134.05]
+        TestRunModuleL13: coordinate system:
+        Coordinate system: 
+        origin [      45.020,      819.25,      134.05]
+        u [     0.99955,    0.030000,      0.0000]
+        v [    0.030000,    -0.99955,      0.0000]
+        w [      0.0000,      0.0000,     -1.0000]
+        TestRunModuleL13: translation:
+        [      45.020,      819.25,      134.05]
+        TestRunModuleL13: rotation:
+        [
+        0.999549894704642 0.030000133265350216 0.0
+        0.030000133265350216 -0.999549894704642 0.0
+        0.0 0.0 -1.0
+
+        ]
+        
+        
+        
+        LCDDBaseGeom: set position and rotation for volume module_L1t
 getEulerAngles: u [    0.030000,    -0.99955,      0.0000] v[      0.0000,      0.0000,     -1.0000] -> [      0.0000,      1.0000,      0.0000] [      0.0000,      0.0000,      1.0000]
 Input: u {0.03; -1; 0} v {0; 0; -1} u' {0; 1; 0} v' {0; 0; 1}
 rot matrix:
@@ -314,388 +313,388 @@
 LCDDBaseGeom: rot                    [Element: <rotation/>]
 LCDDBaseGeom: DONE constructing LCDD object module_L1t
 
-		
-
-		*/
-
-		Hep3Vector u = new BasicHep3Vector(1,0,0);
-		Hep3Vector v = new BasicHep3Vector(0,1,0);
-		Hep3Vector w = new BasicHep3Vector(0,0,1);
-		
-		Hep3Vector u_L1 = new BasicHep3Vector(0.99955,    0.030000,      0.0000);
-		Hep3Vector v_L1 = new BasicHep3Vector(0.030000,    -0.99955,      0.0000);
-		Hep3Vector w_L1 = new BasicHep3Vector(0.0000,      0.0000,     -1.0000);
-		
-		
-		
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u_L1.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v_L1.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w_L1.v());
-
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-		
-		Hep3Vector euler_angles = TransformationUtils.getCardanAngles(v_L1, w_L1, v, w);
-		
-		//Get the generic rotation
-		org.apache.commons.math3.geometry.euclidean.threed.Rotation r = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(v_3D_L1,w_3D_L1,v_3D, w_3D);
-		//Get the angles
-		double rotations[] = r.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-		
-		if(_debug) {
-			System.out.println("getEulerAngles gives euler_angles: " + euler_angles.toString());
-			System.out.println("manual          gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-		}
-			  
-		if((rotations[0]-euler_angles.x())>0.00001 || (rotations[1]-euler_angles.y())>0.00001 || (rotations[2]-euler_angles.z())>0.00001) {
-			//System.("closing the loop in apache rotation didn't work!");
-			//throw new RuntimeException("closing the loop in apache rotation didn't work!");
-		}
-		
-		   
-		
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*4,0,0);
-	     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("HybridVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
-		
-	
-		private void makeExample4(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample4 ----");
-			
-		}
-		
-		String volName = "example4";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	
-		 
-
-		Hep3Vector u = new BasicHep3Vector(1,0,0);
-		Hep3Vector v = new BasicHep3Vector(0,1,0);
-		Hep3Vector w = new BasicHep3Vector(0,0,1);
-	
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-		
-		
-		
-		//set up a rotation about the X axis
-	    org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -1.0*Math.PI);
-	     
-	    // find y' and z'
-	    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
-	    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
-	    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
-	    
-	    
-	    double [] rotations = r1.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-	    
-	    
-	    if(_debug) {
-	    	System.out.println("u_3D:       " + u_3D.toString());
-			System.out.println("v_3D:       " + v_3D.toString());
-			System.out.println("w_3D:       " + w_3D.toString());
-			r1.toString();
-			System.out.println("u_3D_p: " + u_3D_p.toString());
-			System.out.println("v_3D_p: " + v_3D_p.toString());
-			System.out.println("w_3D_p: " + w_3D_p.toString());
-			
-			System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-	    }
-	    
-	 	 
-		
-		//apply to unit vector
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*2,0,0);
-	     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
-		
-	
-		private void makeExample5(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-			
-			
-			if(_debug) {
-				System.out.println("--- makeExample5 ----");
-				
-			}
-			
-			String volName = "example5";
-			Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-			lcdd.add(box);
-			Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-		
-			 
-
-			Hep3Vector u = new BasicHep3Vector(1,0,0);
-			Hep3Vector v = new BasicHep3Vector(0,1,0);
-			Hep3Vector w = new BasicHep3Vector(0,0,1);
-		
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-			
-			
-			
-			//set up a rotation about the X axis
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -1.0*Math.PI);
-		     
-		    // find y' and z'
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
-		    
-		    // set up a rotation about the Z axis
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D_p, -0.03);
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r13 = r3.applyTo(r1);
-		    
-		    
-		    // find y' and z'
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D);
-		    //org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D_p);
-		    //org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D_p);
-		    //org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D_p);
-		    
-		    double [] rotations = r13.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-		    
-		    
-		    if(_debug) {
-		    	System.out.println("u_3D:       " + u_3D.toString());
-				System.out.println("v_3D:       " + v_3D.toString());
-				System.out.println("w_3D:       " + w_3D.toString());
-				r1.toString();
-				System.out.println("u_3D_p: " + u_3D_p.toString());
-				System.out.println("v_3D_p: " + v_3D_p.toString());
-				System.out.println("w_3D_p: " + w_3D_p.toString());
-				r13.toString();
-				System.out.println("u_3D_pp: " + u_3D_pp.toString());
-				System.out.println("v_3D_pp: " + v_3D_pp.toString());
-				System.out.println("w_3D_pp: " + w_3D_pp.toString());
-				System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-		    }
-		    
-		 	 
-			
-			//apply to unit vector
-			
-		     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*3,0,0);
-		     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-		     lcdd.add(pos);
-		     lcdd.add(rot);
-			
-			
-		     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + basePV.getName());
-		     }
-			
-		     
-		     volName = volName + "_sub";
-		     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-		     lcdd.add(boxSub);
-		     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-		     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-		     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-		     lcdd.add(subPos);
-		     lcdd.add(subRot);
-		     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + subBasePV.getName());
-		     }
-			
-		     lcdd.add(volumeSub);
-		     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-		     lcdd.add(volume);
-			
-			
-			
-			
-			}
-			
-		
-		
-
-		private void makeExample5b(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-			
-			
-			if(_debug) {
-				System.out.println("--- makeExample5b ----");
-				
-			}
-			
-			String volName = "example5b";
-			Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-			lcdd.add(box);
-			Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-		
-			 
-
-			Hep3Vector u = new BasicHep3Vector(1,0,0);
-			Hep3Vector v = new BasicHep3Vector(0,1,0);
-			Hep3Vector w = new BasicHep3Vector(0,0,1);
-		
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-			
-			
-			 // set up a rotation about the Z axis
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D, -0.03);
-		     
-		    // find y' and z'
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r3.applyTo(u_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r3.applyTo(v_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r3.applyTo(w_3D);
-		    
-		   
-		    
-		    double [] rotations = r3.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-		    
-		    
-		    if(_debug) {
-		    	System.out.println("u_3D:       " + u_3D.toString());
-				System.out.println("v_3D:       " + v_3D.toString());
-				System.out.println("w_3D:       " + w_3D.toString());
-				r3.toString();
-				System.out.println("u_3D_p: " + u_3D_p.toString());
-				System.out.println("v_3D_p: " + v_3D_p.toString());
-				System.out.println("w_3D_p: " + w_3D_p.toString());
-				System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-		    }
-		    
-		 	 
-			
-			//apply to unit vector
-			
-		     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*3,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1.5,0);
-		     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-		     lcdd.add(pos);
-		     lcdd.add(rot);
-			
-			
-		     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + basePV.getName());
-		     }
-			
-		     
-		     volName = volName + "_sub";
-		     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-		     lcdd.add(boxSub);
-		     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-		     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-		     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-		     lcdd.add(subPos);
-		     lcdd.add(subRot);
-		     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + subBasePV.getName());
-		     }
-			
-		     lcdd.add(volumeSub);
-		     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-		     lcdd.add(volume);
-			
-			
-			
-			
-			}
-			
-		private void makeExample3b(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-			
-			
-			if(_debug) {
-				System.out.println("--- makeExample3b ----");
-				
-			}
-			
-			String volName = "example3b";
-			Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-			lcdd.add(box);
-			Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-			
-			/*
-			
-			TestRunModuleL13: survey positions
+        
+
+        */
+
+        Hep3Vector u = new BasicHep3Vector(1,0,0);
+        Hep3Vector v = new BasicHep3Vector(0,1,0);
+        Hep3Vector w = new BasicHep3Vector(0,0,1);
+        
+        Hep3Vector u_L1 = new BasicHep3Vector(0.99955,    0.030000,      0.0000);
+        Hep3Vector v_L1 = new BasicHep3Vector(0.030000,    -0.99955,      0.0000);
+        Hep3Vector w_L1 = new BasicHep3Vector(0.0000,      0.0000,     -1.0000);
+        
+        
+        
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u_L1.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v_L1.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w_L1.v());
+
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+        
+        Hep3Vector euler_angles = TransformationUtils.getCardanAngles(v_L1, w_L1, v, w);
+        
+        //Get the generic rotation
+        org.apache.commons.math3.geometry.euclidean.threed.Rotation r = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(v_3D_L1,w_3D_L1,v_3D, w_3D);
+        //Get the angles
+        double rotations[] = r.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+        
+        if(_debug) {
+            System.out.println("getEulerAngles gives euler_angles: " + euler_angles.toString());
+            System.out.println("manual          gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+        }
+              
+        if((rotations[0]-euler_angles.x())>0.00001 || (rotations[1]-euler_angles.y())>0.00001 || (rotations[2]-euler_angles.z())>0.00001) {
+            //System.("closing the loop in apache rotation didn't work!");
+            //throw new RuntimeException("closing the loop in apache rotation didn't work!");
+        }
+        
+           
+        
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*4,0,0);
+         Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("HybridVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
+        
+    
+        private void makeExample4(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample4 ----");
+            
+        }
+        
+        String volName = "example4";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+    
+         
+
+        Hep3Vector u = new BasicHep3Vector(1,0,0);
+        Hep3Vector v = new BasicHep3Vector(0,1,0);
+        Hep3Vector w = new BasicHep3Vector(0,0,1);
+    
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+        
+        
+        
+        //set up a rotation about the X axis
+        org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -1.0*Math.PI);
+         
+        // find y' and z'
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
+        
+        
+        double [] rotations = r1.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+        
+        
+        if(_debug) {
+            System.out.println("u_3D:       " + u_3D.toString());
+            System.out.println("v_3D:       " + v_3D.toString());
+            System.out.println("w_3D:       " + w_3D.toString());
+            r1.toString();
+            System.out.println("u_3D_p: " + u_3D_p.toString());
+            System.out.println("v_3D_p: " + v_3D_p.toString());
+            System.out.println("w_3D_p: " + w_3D_p.toString());
+            
+            System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+        }
+        
+         
+        
+        //apply to unit vector
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*2,0,0);
+         Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
+        
+    
+        private void makeExample5(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+            
+            
+            if(_debug) {
+                System.out.println("--- makeExample5 ----");
+                
+            }
+            
+            String volName = "example5";
+            Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+            lcdd.add(box);
+            Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+             
+
+            Hep3Vector u = new BasicHep3Vector(1,0,0);
+            Hep3Vector v = new BasicHep3Vector(0,1,0);
+            Hep3Vector w = new BasicHep3Vector(0,0,1);
+        
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+            
+            
+            
+            //set up a rotation about the X axis
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -1.0*Math.PI);
+             
+            // find y' and z'
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
+            
+            // set up a rotation about the Z axis
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D_p, -0.03);
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r13 = r3.applyTo(r1);
+            
+            
+            // find y' and z'
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D);
+            //org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D_p);
+            //org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D_p);
+            //org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D_p);
+            
+            double [] rotations = r13.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+            
+            
+            if(_debug) {
+                System.out.println("u_3D:       " + u_3D.toString());
+                System.out.println("v_3D:       " + v_3D.toString());
+                System.out.println("w_3D:       " + w_3D.toString());
+                r1.toString();
+                System.out.println("u_3D_p: " + u_3D_p.toString());
+                System.out.println("v_3D_p: " + v_3D_p.toString());
+                System.out.println("w_3D_p: " + w_3D_p.toString());
+                r13.toString();
+                System.out.println("u_3D_pp: " + u_3D_pp.toString());
+                System.out.println("v_3D_pp: " + v_3D_pp.toString());
+                System.out.println("w_3D_pp: " + w_3D_pp.toString());
+                System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+            }
+            
+             
+            
+            //apply to unit vector
+            
+             Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*3,0,0);
+             Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+             lcdd.add(pos);
+             lcdd.add(rot);
+            
+            
+             PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + basePV.getName());
+             }
+            
+             
+             volName = volName + "_sub";
+             Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+             lcdd.add(boxSub);
+             Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+             Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+             Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+             lcdd.add(subPos);
+             lcdd.add(subRot);
+             PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + subBasePV.getName());
+             }
+            
+             lcdd.add(volumeSub);
+             volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+             lcdd.add(volume);
+            
+            
+            
+            
+            }
+            
+        
+        
+
+        private void makeExample5b(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+            
+            
+            if(_debug) {
+                System.out.println("--- makeExample5b ----");
+                
+            }
+            
+            String volName = "example5b";
+            Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+            lcdd.add(box);
+            Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+             
+
+            Hep3Vector u = new BasicHep3Vector(1,0,0);
+            Hep3Vector v = new BasicHep3Vector(0,1,0);
+            Hep3Vector w = new BasicHep3Vector(0,0,1);
+        
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+            
+            
+             // set up a rotation about the Z axis
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D, -0.03);
+             
+            // find y' and z'
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r3.applyTo(u_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r3.applyTo(v_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r3.applyTo(w_3D);
+            
+           
+            
+            double [] rotations = r3.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+            
+            
+            if(_debug) {
+                System.out.println("u_3D:       " + u_3D.toString());
+                System.out.println("v_3D:       " + v_3D.toString());
+                System.out.println("w_3D:       " + w_3D.toString());
+                r3.toString();
+                System.out.println("u_3D_p: " + u_3D_p.toString());
+                System.out.println("v_3D_p: " + v_3D_p.toString());
+                System.out.println("w_3D_p: " + w_3D_p.toString());
+                System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+            }
+            
+             
+            
+            //apply to unit vector
+            
+             Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*3,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1.5,0);
+             Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+             lcdd.add(pos);
+             lcdd.add(rot);
+            
+            
+             PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + basePV.getName());
+             }
+            
+             
+             volName = volName + "_sub";
+             Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+             lcdd.add(boxSub);
+             Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+             Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+             Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+             lcdd.add(subPos);
+             lcdd.add(subRot);
+             PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + subBasePV.getName());
+             }
+            
+             lcdd.add(volumeSub);
+             volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+             lcdd.add(volume);
+            
+            
+            
+            
+            }
+            
+        private void makeExample3b(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+            
+            
+            if(_debug) {
+                System.out.println("--- makeExample3b ----");
+                
+            }
+            
+            String volName = "example3b";
+            Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+            lcdd.add(box);
+            Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+            
+            /*
+            
+            TestRunModuleL13: survey positions
 Survey pos for module_L1b:
 ballPos   [      25.000,      661.10,      4.3500]
 veePos    [      95.000,      661.10,      4.3500]
@@ -732,11 +731,11 @@
 
 ]
 
-			
-			
-			
-			
-			LCDDBaseGeom: set position and rotation for volume module_L1b
+            
+            
+            
+            
+            LCDDBaseGeom: set position and rotation for volume module_L1b
 getEulerAngles: u [   -0.030000,     0.99955,      0.0000] v[      0.0000,      0.0000,      1.0000] -> [      0.0000,      1.0000,      0.0000] [      0.0000,      0.0000,      1.0000]
 Input: u {-0.03; 1; 0} v {0; 0; 1} u' {0; 1; 0} v' {0; 0; 1}
 rot matrix:
@@ -753,484 +752,484 @@
 LCDDBaseGeom: rot                    [Element: <rotation/>]
 LCDDBaseGeom: DONE constructing LCDD object module_L1b
 
-		
-
-			
-
-			*/
-
-			Hep3Vector u = new BasicHep3Vector(1,0,0);
-			Hep3Vector v = new BasicHep3Vector(0,1,0);
-			Hep3Vector w = new BasicHep3Vector(0,0,1);
-			
-			Hep3Vector u_L1 = new BasicHep3Vector(0.99955,    0.030000,      0.0000);
-			Hep3Vector v_L1 = new BasicHep3Vector(-0.030000,     0.99955,      0.0000);
-			Hep3Vector w_L1 = new BasicHep3Vector(0.0000,      0.0000,     1.0000);
-			
-			
-			
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u_L1.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v_L1.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w_L1.v());
-
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-			
-			Hep3Vector euler_angles = TransformationUtils.getCardanAngles(v_L1, w_L1, v, w);
-			
-			//Get the generic rotation
-			org.apache.commons.math3.geometry.euclidean.threed.Rotation r = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(v_3D_L1,w_3D_L1,v_3D, w_3D);
-			//Get the angles
-			double rotations[] = r.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-			
-			if(_debug) {
-				System.out.println("getEulerAngles gives euler_angles: " + euler_angles.toString());
-				System.out.println("manual          gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-			}
-				  
-			if((rotations[0]-euler_angles.x())>0.00001 || (rotations[1]-euler_angles.y())>0.00001 || (rotations[2]-euler_angles.z())>0.00001) {
-				//throw new RuntimeException("closing the loop in apache rotation didn't work!");
-			}
-			
-			   
-			
-			
-		     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*4,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1.5,0);
-		     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-		     lcdd.add(pos);
-		     lcdd.add(rot);
-			
-			
-		     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + basePV.getName());
-		     }
-			
-		     
-		     
-		     volName = volName + "_sub";
-		     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-		     lcdd.add(boxSub);
-		     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-		     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-		     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-		     lcdd.add(subPos);
-		     lcdd.add(subRot);
-		     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + subBasePV.getName());
-		     }
-			
-		     lcdd.add(volumeSub);
-		     volumeSub.setVisAttributes(lcdd.getVisAttributes("HybridVis"));
-
-		     lcdd.add(volume);
-			
-			
-			
-			
-			}
-			
-
-		private void makeExample6(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample6 ----");
-			
-		}
-		
-		String volName = "example6";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	    
-	    double [] rotations = {-0.5*Math.PI,0,0};
-	    
-	    
-	    if(_debug) {
-	
-			
-			System.out.println("manual set lcdd angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-	    }
-	    
-	 	 
-		
-		//apply to unit vector
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,0,0);
-	     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
-		
-		
-		
-		private void makeExample66(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-			
-			
-			if(_debug) {
-				System.out.println("--- makeExample66 ----");
-				
-			}
-			
-			String volName = "example66";
-			Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-			lcdd.add(box);
-			Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-		
-			 
-
-			Hep3Vector u = new BasicHep3Vector(1,0,0);
-			Hep3Vector v = new BasicHep3Vector(0,1,0);
-			Hep3Vector w = new BasicHep3Vector(0,0,1);
-		
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-			
-			
-			
-			//set up a rotation about the X axis
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -0.5*Math.PI);
-		     
-		    // find y' and z'
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
-		    
-		    
-		    double [] rotations = r1.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-		    
-		    
-		    if(_debug) {
-		    	System.out.println("u_3D:       " + u_3D.toString());
-				System.out.println("v_3D:       " + v_3D.toString());
-				System.out.println("w_3D:       " + w_3D.toString());
-				r1.toString();
-				System.out.println("u_3D_p: " + u_3D_p.toString());
-				System.out.println("v_3D_p: " + v_3D_p.toString());
-				System.out.println("w_3D_p: " + w_3D_p.toString());
-				
-				System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-		    }
-		    
-		 	 
-			
-			//apply to unit vector
-			
-		     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-4,0,0);
-		     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-		     lcdd.add(pos);
-		     lcdd.add(rot);
-			
-			
-		     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + basePV.getName());
-		     }
-			
-		     
-		     
-		     
-		     volName = volName + "_sub";
-		     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-		     lcdd.add(boxSub);
-		     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-		     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-		     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-		     lcdd.add(subPos);
-		     lcdd.add(subRot);
-		     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + subBasePV.getName());
-		     }
-			
-		     lcdd.add(volumeSub);
-		     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-		     lcdd.add(volume);
-			
-			
-			
-			
-			}
-		
-		
-		
-		
-		
-
-		private void makeExample7(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample7 ----");
-			
-		}
-		
-		String volName = "example7";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	    
-	    double [] rotations = {-0.5*Math.PI,0,-0.25*Math.PI};
-	    
-	    
-	    if(_debug) {
-	
-			
-			System.out.println("manual set lcdd angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-
-	    }
-	    
-	 	 
-		
-		//apply to unit vector
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1,0);
-	     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
-		
-		
-		
-	private void makeExample77(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-			
-			
-			if(_debug) {
-				System.out.println("--- makeExample77 ----");
-				
-			}
-			
-			String volName = "example77";
-			Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-			lcdd.add(box);
-			Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-		
-			 
-
-			Hep3Vector u = new BasicHep3Vector(1,0,0);
-			Hep3Vector v = new BasicHep3Vector(0,1,0);
-			Hep3Vector w = new BasicHep3Vector(0,0,1);
-		
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-			org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-			
-			
-			
-			//set up a rotation about the X axis
-		    org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -0.5*Math.PI);
-		     
-		    // find y' and z'
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
-		    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
-		    
-		    
-		  //set up a rotation about the Z xis
-		   org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D_p, -0.25*Math.PI);
-		   
-		   org.apache.commons.math3.geometry.euclidean.threed.Rotation r13 = r3.applyTo(r1);
-		   
-		   // find y'' and z''
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D);
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D);
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D);
-		    
-		   // find y'' and z'' (cross-check)
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp_2 = r3.applyTo(u_3D_p);
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp_2 = r3.applyTo(v_3D_p);
-		   org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp_2 = r3.applyTo(w_3D_p);
-		    
-		    
-		    double [] rotations = r13.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
-		    
-		    
-		    if(_debug) {
-		    	System.out.println("u_3D:       " + u_3D.toString());
-				System.out.println("v_3D:       " + v_3D.toString());
-				System.out.println("w_3D:       " + w_3D.toString());
-				r1.toString();
-				System.out.println("u_3D_p: " + u_3D_p.toString());
-				System.out.println("v_3D_p: " + v_3D_p.toString());
-				System.out.println("w_3D_p: " + w_3D_p.toString());
-				r13.toString();
-				System.out.println("u_3D_pp: " + u_3D_pp.toString());
-				System.out.println("v_3D_pp: " + v_3D_pp.toString());
-				System.out.println("w_3D_pp: " + w_3D_pp.toString());
-				
-				System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
-				
-				System.out.println("u_3D_pp_2: " + u_3D_pp_2.toString());
-				System.out.println("v_3D_pp_2: " + v_3D_pp_2.toString());
-				System.out.println("w_3D_pp_2: " + w_3D_pp_2.toString());
-		    }
-		    
-		 	 
-			
-			//apply to unit vector
-			
-		     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-4,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1,0);
-		     Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
-		     lcdd.add(pos);
-		     lcdd.add(rot);
-			
-			
-		     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + basePV.getName());
-		     }
-			
-		     
-		     
-		     
-		     volName = volName + "_sub";
-		     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-		     lcdd.add(boxSub);
-		     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-		     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-		     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-		     lcdd.add(subPos);
-		     lcdd.add(subRot);
-		     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-		     if(_debug) {
-		    	 System.out.println("Created physical vomume " + subBasePV.getName());
-		     }
-			
-		     lcdd.add(volumeSub);
-		     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-		     lcdd.add(volume);
-			
-			
-			
-			
-			}
-		
-		
-		
-
-	private void makeExample8(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-	
-	
-	if(_debug) {
-		System.out.println("--- makeExample8 ----");
-		
-	}
-	
-	String volName = "example8";
-	Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-	lcdd.add(box);
-	Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-    
-	
-	Hep3Vector u = new BasicHep3Vector(1,0,0);
-	Hep3Vector v = new BasicHep3Vector(0,1,0);
-	Hep3Vector w = new BasicHep3Vector(0,0,1);
-
-	org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-	org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-	org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-	
-	Hep3Vector u_L1 = new BasicHep3Vector(1/Math.sqrt(2),0,1/Math.sqrt(2));
-	Hep3Vector v_L1 = new BasicHep3Vector(-1/Math.sqrt(2),0,1/Math.sqrt(2));
-	Hep3Vector w_L1 = new BasicHep3Vector(0,-1,0);
-	
-	Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
-	
-	
+        
+
+            
+
+            */
+
+            Hep3Vector u = new BasicHep3Vector(1,0,0);
+            Hep3Vector v = new BasicHep3Vector(0,1,0);
+            Hep3Vector w = new BasicHep3Vector(0,0,1);
+            
+            Hep3Vector u_L1 = new BasicHep3Vector(0.99955,    0.030000,      0.0000);
+            Hep3Vector v_L1 = new BasicHep3Vector(-0.030000,     0.99955,      0.0000);
+            Hep3Vector w_L1 = new BasicHep3Vector(0.0000,      0.0000,     1.0000);
+            
+            
+            
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u_L1.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v_L1.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_L1 = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w_L1.v());
+
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+            
+            Hep3Vector euler_angles = TransformationUtils.getCardanAngles(v_L1, w_L1, v, w);
+            
+            //Get the generic rotation
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(v_3D_L1,w_3D_L1,v_3D, w_3D);
+            //Get the angles
+            double rotations[] = r.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+            
+            if(_debug) {
+                System.out.println("getEulerAngles gives euler_angles: " + euler_angles.toString());
+                System.out.println("manual          gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+            }
+                  
+            if((rotations[0]-euler_angles.x())>0.00001 || (rotations[1]-euler_angles.y())>0.00001 || (rotations[2]-euler_angles.z())>0.00001) {
+                //throw new RuntimeException("closing the loop in apache rotation didn't work!");
+            }
+            
+               
+            
+            
+             Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*4,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1.5,0);
+             Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+             lcdd.add(pos);
+             lcdd.add(rot);
+            
+            
+             PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + basePV.getName());
+             }
+            
+             
+             
+             volName = volName + "_sub";
+             Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+             lcdd.add(boxSub);
+             Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+             Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+             Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+             lcdd.add(subPos);
+             lcdd.add(subRot);
+             PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + subBasePV.getName());
+             }
+            
+             lcdd.add(volumeSub);
+             volumeSub.setVisAttributes(lcdd.getVisAttributes("HybridVis"));
+
+             lcdd.add(volume);
+            
+            
+            
+            
+            }
+            
+
+        private void makeExample6(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample6 ----");
+            
+        }
+        
+        String volName = "example6";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+        double [] rotations = {-0.5*Math.PI,0,0};
+        
+        
+        if(_debug) {
+    
+            
+            System.out.println("manual set lcdd angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+        }
+        
+         
+        
+        //apply to unit vector
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,0,0);
+         Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
+        
+        
+        
+        private void makeExample66(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+            
+            
+            if(_debug) {
+                System.out.println("--- makeExample66 ----");
+                
+            }
+            
+            String volName = "example66";
+            Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+            lcdd.add(box);
+            Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+             
+
+            Hep3Vector u = new BasicHep3Vector(1,0,0);
+            Hep3Vector v = new BasicHep3Vector(0,1,0);
+            Hep3Vector w = new BasicHep3Vector(0,0,1);
+        
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+            
+            
+            
+            //set up a rotation about the X axis
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -0.5*Math.PI);
+             
+            // find y' and z'
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
+            
+            
+            double [] rotations = r1.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+            
+            
+            if(_debug) {
+                System.out.println("u_3D:       " + u_3D.toString());
+                System.out.println("v_3D:       " + v_3D.toString());
+                System.out.println("w_3D:       " + w_3D.toString());
+                r1.toString();
+                System.out.println("u_3D_p: " + u_3D_p.toString());
+                System.out.println("v_3D_p: " + v_3D_p.toString());
+                System.out.println("w_3D_p: " + w_3D_p.toString());
+                
+                System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+            }
+            
+             
+            
+            //apply to unit vector
+            
+             Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-4,0,0);
+             Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+             lcdd.add(pos);
+             lcdd.add(rot);
+            
+            
+             PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + basePV.getName());
+             }
+            
+             
+             
+             
+             volName = volName + "_sub";
+             Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+             lcdd.add(boxSub);
+             Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+             Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+             Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+             lcdd.add(subPos);
+             lcdd.add(subRot);
+             PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + subBasePV.getName());
+             }
+            
+             lcdd.add(volumeSub);
+             volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+             lcdd.add(volume);
+            
+            
+            
+            
+            }
+        
+        
+        
+        
+        
+
+        private void makeExample7(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample7 ----");
+            
+        }
+        
+        String volName = "example7";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+        double [] rotations = {-0.5*Math.PI,0,-0.25*Math.PI};
+        
+        
+        if(_debug) {
+    
+            
+            System.out.println("manual set lcdd angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+
+        }
+        
+         
+        
+        //apply to unit vector
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1,0);
+         Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
+        
+        
+        
+    private void makeExample77(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+            
+            
+            if(_debug) {
+                System.out.println("--- makeExample77 ----");
+                
+            }
+            
+            String volName = "example77";
+            Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+            lcdd.add(box);
+            Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+             
+
+            Hep3Vector u = new BasicHep3Vector(1,0,0);
+            Hep3Vector v = new BasicHep3Vector(0,1,0);
+            Hep3Vector w = new BasicHep3Vector(0,0,1);
+        
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+            
+            
+            
+            //set up a rotation about the X axis
+            org.apache.commons.math3.geometry.euclidean.threed.Rotation r1 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(u_3D, -0.5*Math.PI);
+             
+            // find y' and z'
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_p = r1.applyTo(u_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_p = r1.applyTo(v_3D);
+            org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_p = r1.applyTo(w_3D);
+            
+            
+          //set up a rotation about the Z xis
+           org.apache.commons.math3.geometry.euclidean.threed.Rotation r3 = new org.apache.commons.math3.geometry.euclidean.threed.Rotation(w_3D_p, -0.25*Math.PI);
+           
+           org.apache.commons.math3.geometry.euclidean.threed.Rotation r13 = r3.applyTo(r1);
+           
+           // find y'' and z''
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp = r13.applyTo(u_3D);
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp = r13.applyTo(v_3D);
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp = r13.applyTo(w_3D);
+            
+           // find y'' and z'' (cross-check)
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D_pp_2 = r3.applyTo(u_3D_p);
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D_pp_2 = r3.applyTo(v_3D_p);
+           org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D_pp_2 = r3.applyTo(w_3D_p);
+            
+            
+            double [] rotations = r13.getAngles(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ);
+            
+            
+            if(_debug) {
+                System.out.println("u_3D:       " + u_3D.toString());
+                System.out.println("v_3D:       " + v_3D.toString());
+                System.out.println("w_3D:       " + w_3D.toString());
+                r1.toString();
+                System.out.println("u_3D_p: " + u_3D_p.toString());
+                System.out.println("v_3D_p: " + v_3D_p.toString());
+                System.out.println("w_3D_p: " + w_3D_p.toString());
+                r13.toString();
+                System.out.println("u_3D_pp: " + u_3D_pp.toString());
+                System.out.println("v_3D_pp: " + v_3D_pp.toString());
+                System.out.println("w_3D_pp: " + w_3D_pp.toString());
+                
+                System.out.println("gives euler_angles: (" + rotations[0] + "," + rotations[1] + "," + rotations[2] + ")");
+                
+                System.out.println("u_3D_pp_2: " + u_3D_pp_2.toString());
+                System.out.println("v_3D_pp_2: " + v_3D_pp_2.toString());
+                System.out.println("w_3D_pp_2: " + w_3D_pp_2.toString());
+            }
+            
+             
+            
+            //apply to unit vector
+            
+             Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-4,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-1,0);
+             Rotation rot = new Rotation(volName + "_rotation",rotations[0],rotations[1],rotations[2]);
+             lcdd.add(pos);
+             lcdd.add(rot);
+            
+            
+             PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + basePV.getName());
+             }
+            
+             
+             
+             
+             volName = volName + "_sub";
+             Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+             lcdd.add(boxSub);
+             Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+             Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+             Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+             lcdd.add(subPos);
+             lcdd.add(subRot);
+             PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+             if(_debug) {
+                 System.out.println("Created physical vomume " + subBasePV.getName());
+             }
+            
+             lcdd.add(volumeSub);
+             volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+             lcdd.add(volume);
+            
+            
+            
+            
+            }
+        
+        
+        
+
+    private void makeExample8(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
     
     
     if(_debug) {
-
-		
-		System.out.println("euler angles " + euler_angles.toString());
-
+        System.out.println("--- makeExample8 ----");
+        
     }
     
- 	 
-	
-	//apply to unit vector
-	
+    String volName = "example8";
+    Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+    lcdd.add(box);
+    Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+    
+    
+    Hep3Vector u = new BasicHep3Vector(1,0,0);
+    Hep3Vector v = new BasicHep3Vector(0,1,0);
+    Hep3Vector w = new BasicHep3Vector(0,0,1);
+
+    org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+    org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+    org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+    
+    Hep3Vector u_L1 = new BasicHep3Vector(1/Math.sqrt(2),0,1/Math.sqrt(2));
+    Hep3Vector v_L1 = new BasicHep3Vector(-1/Math.sqrt(2),0,1/Math.sqrt(2));
+    Hep3Vector w_L1 = new BasicHep3Vector(0,-1,0);
+    
+    Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
+    
+    
+    
+    
+    if(_debug) {
+
+        
+        System.out.println("euler angles " + euler_angles.toString());
+
+    }
+    
+     
+    
+    //apply to unit vector
+    
      Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-1,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-3,0);
      Rotation rot = new Rotation(volName + "_rotation",euler_angles.x(),euler_angles.y(),euler_angles.z());
      lcdd.add(pos);
      lcdd.add(rot);
-	
-	
+    
+    
      PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
      if(_debug) {
-    	 System.out.println("Created physical vomume " + basePV.getName());
+         System.out.println("Created physical vomume " + basePV.getName());
      }
-	
+    
      
      
      
@@ -1244,197 +1243,197 @@
      lcdd.add(subRot);
      PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
      if(_debug) {
-    	 System.out.println("Created physical vomume " + subBasePV.getName());
+         System.out.println("Created physical vomume " + subBasePV.getName());
      }
-	
+    
      lcdd.add(volumeSub);
      volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
 
      lcdd.add(volume);
-	
-	
-	
-	
-	}
-	
-		
-		
-	private void makeExample9(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample9 ----");
-			
-		}
-		
-		String volName = "example9";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	    
-		
-		Hep3Vector u = new BasicHep3Vector(1,0,0);
-		Hep3Vector v = new BasicHep3Vector(0,1,0);
-		Hep3Vector w = new BasicHep3Vector(0,0,1);
-
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-		
-		Hep3Vector u_L1 = new BasicHep3Vector(1,0,0);
-		Hep3Vector v_L1 = new BasicHep3Vector(0,0,1);
-		Hep3Vector w_L1 = new BasicHep3Vector(0,-1,0);
-		
-		Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
-		
-		
-	    
-	    
-	    if(_debug) {
-
-			
-			System.out.println("euler angles " + euler_angles.toString());
-
-	    }
-	    
-	 	 
-		
-		//apply to unit vector
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-1,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-2,0);
-	     Rotation rot = new Rotation(volName + "_rotation",euler_angles.x(),euler_angles.y(),euler_angles.z());
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
-		
-			
-	
-	
-	
-	private void makeExample10(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
-		
-		
-		if(_debug) {
-			System.out.println("--- makeExample10 ----");
-			
-		}
-		
-		String volName = "example10";
-		Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
-		lcdd.add(box);
-		Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
-	    
-		
-		Hep3Vector u = new BasicHep3Vector(1,0,0);
-		Hep3Vector v = new BasicHep3Vector(0,1,0);
-		Hep3Vector w = new BasicHep3Vector(0,0,1);
-
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
-		org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
-		
-		Hep3Vector u_L1 = new BasicHep3Vector(1/Math.sqrt(2),1/Math.sqrt(2),0);
-		Hep3Vector v_L1 = new BasicHep3Vector(0,0,1);
-		Hep3Vector w_L1 = new BasicHep3Vector(1/Math.sqrt(2),-1/Math.sqrt(2),0);
-		
-		Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
-		
-		
-	    
-	    
-	    if(_debug) {
-
-			
-			System.out.println("euler angles " + euler_angles.toString());
-
-	    }
-	    
-	 	 
-		
-		//apply to unit vector
-		
-	     Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-2,0);
-	     Rotation rot = new Rotation(volName + "_rotation",euler_angles.x(),euler_angles.y(),euler_angles.z());
-	     lcdd.add(pos);
-	     lcdd.add(rot);
-		
-		
-	     PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + basePV.getName());
-	     }
-		
-	     
-	     
-	     
-	     volName = volName + "_sub";
-	     Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
-	     lcdd.add(boxSub);
-	     Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
-	     Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
-	     Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
-	     lcdd.add(subPos);
-	     lcdd.add(subRot);
-	     PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
-	     if(_debug) {
-	    	 System.out.println("Created physical vomume " + subBasePV.getName());
-	     }
-		
-	     lcdd.add(volumeSub);
-	     volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
-
-	     lcdd.add(volume);
-		
-		
-		
-		
-		}
+    
+    
+    
+    
+    }
+    
+        
+        
+    private void makeExample9(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample9 ----");
+            
+        }
+        
+        String volName = "example9";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+        
+        Hep3Vector u = new BasicHep3Vector(1,0,0);
+        Hep3Vector v = new BasicHep3Vector(0,1,0);
+        Hep3Vector w = new BasicHep3Vector(0,0,1);
+
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+        
+        Hep3Vector u_L1 = new BasicHep3Vector(1,0,0);
+        Hep3Vector v_L1 = new BasicHep3Vector(0,0,1);
+        Hep3Vector w_L1 = new BasicHep3Vector(0,-1,0);
+        
+        Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
+        
+        
+        
+        
+        if(_debug) {
+
+            
+            System.out.println("euler angles " + euler_angles.toString());
+
+        }
+        
+         
+        
+        //apply to unit vector
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-1,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-2,0);
+         Rotation rot = new Rotation(volName + "_rotation",euler_angles.x(),euler_angles.y(),euler_angles.z());
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
+        
+            
+    
+    
+    
+    private void makeExample10(LCDD lcdd, SensitiveDetector sens) throws JDOMException {
+        
+        
+        if(_debug) {
+            System.out.println("--- makeExample10 ----");
+            
+        }
+        
+        String volName = "example10";
+        Box box = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/4.0);
+        lcdd.add(box);
+        Volume volume = new Volume(volName + "_volume", box, lcdd.getMaterial("Vacuum"));
+        
+        
+        Hep3Vector u = new BasicHep3Vector(1,0,0);
+        Hep3Vector v = new BasicHep3Vector(0,1,0);
+        Hep3Vector w = new BasicHep3Vector(0,0,1);
+
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D u_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(u.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D v_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(v.v());
+        org.apache.commons.math3.geometry.euclidean.threed.Vector3D w_3D = new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(w.v());
+        
+        Hep3Vector u_L1 = new BasicHep3Vector(1/Math.sqrt(2),1/Math.sqrt(2),0);
+        Hep3Vector v_L1 = new BasicHep3Vector(0,0,1);
+        Hep3Vector w_L1 = new BasicHep3Vector(1/Math.sqrt(2),-1/Math.sqrt(2),0);
+        
+        Hep3Vector euler_angles = TransformationUtils.getCardanAngles(u_L1, v_L1, u, v);
+        
+        
+        
+        
+        if(_debug) {
+
+            
+            System.out.println("euler angles " + euler_angles.toString());
+
+        }
+        
+         
+        
+        //apply to unit vector
+        
+         Position pos = new Position(volName + "_position",HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width*1.5*-2,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length*-2,0);
+         Rotation rot = new Rotation(volName + "_rotation",euler_angles.x(),euler_angles.y(),euler_angles.z());
+         lcdd.add(pos);
+         lcdd.add(rot);
+        
+        
+         PhysVol basePV = new PhysVol(volume, lcdd.pickMotherVolume(this), pos, rot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + basePV.getName());
+         }
+        
+         
+         
+         
+         volName = volName + "_sub";
+         Box boxSub = new Box(volName + "Box", HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_width, HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0 , HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/8.0);
+         lcdd.add(boxSub);
+         Volume volumeSub = new Volume(volName + "_volume", boxSub, lcdd.getMaterial("Vacuum"));
+         Position subPos = new Position(volName + "_position",0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/4.0*2-HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_length/8.0,HPSTestRunTracker2014GeometryDefinition.TrackerEnvelope.base_height/16.0);
+         Rotation subRot = new Rotation(volName + "_rotation",0,0,0);
+         lcdd.add(subPos);
+         lcdd.add(subRot);
+         PhysVol subBasePV = new PhysVol(volumeSub, volume, subPos, subRot);
+         if(_debug) {
+             System.out.println("Created physical vomume " + subBasePV.getName());
+         }
+        
+         lcdd.add(volumeSub);
+         volumeSub.setVisAttributes(lcdd.getVisAttributes("SensorVis"));
+
+         lcdd.add(volume);
+        
+        
+        
+        
+        }
 
    
-			
-	
-	
-			
-	
-
-	
-	
-
-	
-	
-	
-	
+            
+    
+    
+            
+    
+
+    
+    
+
+    
+    
+    
+    
 
 }
 

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker.java	Wed Apr 27 11:11:32 2016
@@ -69,7 +69,7 @@
         // layer
         for (Iterator i = node.getChildren("layer").iterator(); i.hasNext();)
         {
-        	// Modules are numbered from 0 starting in each layer.
+            // Modules are numbered from 0 starting in each layer.
             int moduleNumber = 0;
 
             Element layerElement = (Element) i.next();

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.java	Wed Apr 27 11:11:32 2016
@@ -53,79 +53,79 @@
     }
 
     // Place modules within the tracking volume.
-	private void createModulePlacements(LCDD lcdd, int sysId, String subdetName) throws DataConversionException {
-		//Volume trackingVolume = lcdd.getTrackingVolume();
-		Volume momVolume = lcdd.pickMotherVolume(this);
-		// Loop over layers.
+    private void createModulePlacements(LCDD lcdd, int sysId, String subdetName) throws DataConversionException {
+        //Volume trackingVolume = lcdd.getTrackingVolume();
+        Volume momVolume = lcdd.pickMotherVolume(this);
+        // Loop over layers.
         for (Iterator i = node.getChildren("layer").iterator(); i.hasNext();) {        
-        	Element layerElement = (Element)i.next();
-        	int layerNumber = layerElement.getAttribute("id").getIntValue();
-        	// Loop over modules within layer.
-        	for (Iterator j = layerElement.getChildren("module_placement").iterator(); j.hasNext();) {
-        	    
-        		Element modulePlacementElement = (Element)j.next();
-        		String moduleName = modulePlacementElement.getAttributeValue("name");
-        		int moduleNumber = modulePlacementElement.getAttribute("id").getIntValue();
-        		
-        		// Get the position and rotation parameters.  All must be explicitly specified.
-        		double x, y, z;
-        		double rx, ry, rz;
-        		x = modulePlacementElement.getAttribute("x").getDoubleValue();
-        		y = modulePlacementElement.getAttribute("y").getDoubleValue();
-        		z = modulePlacementElement.getAttribute("z").getDoubleValue();
-        		rx = modulePlacementElement.getAttribute("rx").getDoubleValue();
-        		ry = modulePlacementElement.getAttribute("ry").getDoubleValue();
-        		rz = modulePlacementElement.getAttribute("rz").getDoubleValue();
-        		
-        		// Place the module with position and rotation from above.
-        		String modulePlacementName = subdetName + "_" + moduleName + "_layer" + layerNumber + "_module" + moduleNumber;
-        		Position p = new Position(modulePlacementName + "_position", x, y, z);
-        		Rotation r = new Rotation(modulePlacementName + "_rotation", rx, ry, rz);
-        		lcdd.add(p);
-        		lcdd.add(r);        		        		
-        		//PhysVol modulePhysVol = new PhysVol(modules.get(moduleName), trackingVolume, p, r);
-        		PhysVol modulePhysVol = new PhysVol(modules.get(moduleName), momVolume, p, r);
-        		
-        		// Add identifier values to the placement volume.
-        		modulePhysVol.addPhysVolID("system", sysId);
-        		modulePhysVol.addPhysVolID("barrel", 0);
-        		modulePhysVol.addPhysVolID("layer", layerNumber);
-        		modulePhysVol.addPhysVolID("module", moduleNumber);        		
-        	}
-        }
-	}
+            Element layerElement = (Element)i.next();
+            int layerNumber = layerElement.getAttribute("id").getIntValue();
+            // Loop over modules within layer.
+            for (Iterator j = layerElement.getChildren("module_placement").iterator(); j.hasNext();) {
+                
+                Element modulePlacementElement = (Element)j.next();
+                String moduleName = modulePlacementElement.getAttributeValue("name");
+                int moduleNumber = modulePlacementElement.getAttribute("id").getIntValue();
+                
+                // Get the position and rotation parameters.  All must be explicitly specified.
+                double x, y, z;
+                double rx, ry, rz;
+                x = modulePlacementElement.getAttribute("x").getDoubleValue();
+                y = modulePlacementElement.getAttribute("y").getDoubleValue();
+                z = modulePlacementElement.getAttribute("z").getDoubleValue();
+                rx = modulePlacementElement.getAttribute("rx").getDoubleValue();
+                ry = modulePlacementElement.getAttribute("ry").getDoubleValue();
+                rz = modulePlacementElement.getAttribute("rz").getDoubleValue();
+                
+                // Place the module with position and rotation from above.
+                String modulePlacementName = subdetName + "_" + moduleName + "_layer" + layerNumber + "_module" + moduleNumber;
+                Position p = new Position(modulePlacementName + "_position", x, y, z);
+                Rotation r = new Rotation(modulePlacementName + "_rotation", rx, ry, rz);
+                lcdd.add(p);
+                lcdd.add(r);                                
+                //PhysVol modulePhysVol = new PhysVol(modules.get(moduleName), trackingVolume, p, r);
+                PhysVol modulePhysVol = new PhysVol(modules.get(moduleName), momVolume, p, r);
+                
+                // Add identifier values to the placement volume.
+                modulePhysVol.addPhysVolID("system", sysId);
+                modulePhysVol.addPhysVolID("barrel", 0);
+                modulePhysVol.addPhysVolID("layer", layerNumber);
+                modulePhysVol.addPhysVolID("module", moduleNumber);             
+            }
+        }
+    }
 
     // Create the module logical volumes.
-	private void createModules(LCDD lcdd, SensitiveDetector sd) {
+    private void createModules(LCDD lcdd, SensitiveDetector sd) {
         for (Iterator i = node.getChildren("module").iterator(); i.hasNext();) {
             Element module = (Element) i.next();
             String moduleName = module.getAttributeValue("name");
             moduleParameters.put(moduleName, new ModuleParameters(module));
             modules.put(moduleName, makeModule(moduleParameters.get(moduleName), sd, lcdd));
         }
-	}
-
-	private Volume makeModule(ModuleParameters params, SensitiveDetector sd, LCDD lcdd) {
-		double thickness = params.getThickness();
-		double x, y;
-		// x = params.getDimension(0);
-		// y = params.getDimension(1);
-		y = params.getDimension(0); // Y is in X plane in world coordinates.
-		x = params.getDimension(1); // X is in Y plane in world coordinates.
-		// System.out.println("making module with x = " + x + " and y = " + y);
-		Box box = new Box(params.getName() + "Box", x, y, thickness);
-		lcdd.add(box);
-
-		Volume moduleVolume = new Volume(params.getName() + "Volume", box, vacuum);
-		makeModuleComponents(moduleVolume, params, sd, lcdd);
-		lcdd.add(moduleVolume);
-
-		if (params.getVis() != null) {
-			moduleVolume.setVisAttributes(lcdd.getVisAttributes(params.getVis()));
-		}
-
-		return moduleVolume;
-	}
+    }
+
+    private Volume makeModule(ModuleParameters params, SensitiveDetector sd, LCDD lcdd) {
+        double thickness = params.getThickness();
+        double x, y;
+        // x = params.getDimension(0);
+        // y = params.getDimension(1);
+        y = params.getDimension(0); // Y is in X plane in world coordinates.
+        x = params.getDimension(1); // X is in Y plane in world coordinates.
+        // System.out.println("making module with x = " + x + " and y = " + y);
+        Box box = new Box(params.getName() + "Box", x, y, thickness);
+        lcdd.add(box);
+
+        Volume moduleVolume = new Volume(params.getName() + "Volume", box, vacuum);
+        makeModuleComponents(moduleVolume, params, sd, lcdd);
+        lcdd.add(moduleVolume);
+
+        if (params.getVis() != null) {
+            moduleVolume.setVisAttributes(lcdd.getVisAttributes(params.getVis()));
+        }
+
+        return moduleVolume;
+    }
 
     private void makeModuleComponents(Volume moduleVolume, ModuleParameters moduleParameters, SensitiveDetector sd, LCDD lcdd) {
         Box envelope = (Box) lcdd.getSolid(moduleVolume.getSolidRef());

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.java	Wed Apr 27 11:11:32 2016
@@ -61,7 +61,7 @@
                 return moduleNumber;
     }
 
-    	
+        
 
 }
 

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java	Wed Apr 27 11:11:32 2016
@@ -15,39 +15,33 @@
 /**
  * Reconstruction version of HPS ECal with crystal array.
  * 
- * @author Jeremy McCormick <[log in to unmask]>
- * @author Timothy Nelson <[log in to unmask]>
- * @version $Id: HPSEcal.java,v 1.6 2011/07/28 20:20:18 jeremy Exp $
+ * @author Jeremy McCormick, SLAC
+ * @author Timothy Nelson, SLAC
  */
-public class HPSEcal extends AbstractSubdetector
-{
+public class HPSEcal extends AbstractSubdetector {
+
     private int nx;
     private int ny;
     private double beamgap;
     private double dface;
     private boolean oddX;
 
-    public static class NeighborMap extends HashMap<Long,Set<Long>>
-    {
+    public static class NeighborMap extends HashMap<Long, Set<Long>> {
+
         IIdentifierHelper helper;
-        public NeighborMap(IIdentifierHelper helper)
-        {
+
+        public NeighborMap(IIdentifierHelper helper) {
             this.helper = helper;
         }
-        
-        public String toString()
-        {
+
+        public String toString() {
             System.out.println("NeighborMap has " + this.size() + " entries.");
             StringBuffer buff = new StringBuffer();
-            for (long id : this.keySet())
-            {
-                buff.append(helper.unpack(new Identifier(id)))
-                    .append("\n");
-                Set<Long> nei = this.get(id); 
-                for (long nid : nei)
-                {
-                    buff.append("  " + helper.unpack(new Identifier(nid)))
-                        .append("\n");
+            for (long id : this.keySet()) {
+                buff.append(helper.unpack(new Identifier(id))).append("\n");
+                Set<Long> nei = this.get(id);
+                for (long nid : nei) {
+                    buff.append("  " + helper.unpack(new Identifier(nid))).append("\n");
                 }
             }
             return buff.toString();
@@ -56,308 +50,270 @@
 
     private NeighborMap neighborMap = null;
 
-    HPSEcal(Element node) throws JDOMException
-    {
+    HPSEcal(Element node) throws JDOMException {
         super(node);
-        
+
         Element layout = node.getChild("layout");
-        
+
         nx = layout.getAttribute("nx").getIntValue();
         ny = layout.getAttribute("ny").getIntValue();
         beamgap = layout.getAttribute("beamgap").getDoubleValue();
         dface = layout.getAttribute("dface").getDoubleValue();
-        
-        if (nx % 2 != 0)
+
+        if (nx % 2 != 0) {
             oddX = true;
-     }
-    
-    public double distanceToFace()
-    {
+        }
+    }
+
+    public double distanceToFace() {
         return dface;
     }
-    
-    public double beamGap()
-    {
+
+    public double beamGap() {
         return beamgap;
     }
-    
+
     /**
      * The number of crystals in X in one section.
-     * @return
+     * 
+     * @return the number of crystals in X in one section
      */
-    public double nx()
-    {
+    public double nx() {
         return nx;
     }
-    
+
     /**
      * The number of crystals in y in one section.
-     * @return
+     * 
+     * @return the number of crystals in Y in one section
      */
-    public double ny()
-    {
+    public double ny() {
         return ny;
-    }   
-    
+    }
+
     // Class for storing neighbor incides in XY and side.
-    static class XYSide implements Comparator<XYSide>
-    {
+    static class XYSide implements Comparator<XYSide> {
+
         int x;
         int y;
         int side;
-        
-        public XYSide(int x, int y, int side)
-        {
+
+        public XYSide(int x, int y, int side) {
             this.x = x;
             this.y = y;
             this.side = side;
         }
-        
-        public int x()
-        {
+
+        public int x() {
             return x;
         }
-        
-        public int y()
-        {
+
+        public int y() {
             return y;
         }
-        
-        public int side()
-        {
+
+        public int side() {
             return side;
         }
-        
-        public boolean equals(Object o)
-        {
-            XYSide xy = (XYSide)o;
-            return xy.x() == x && xy.y() == y && xy.side() == side; 
-        }
-
-        public int compare(XYSide o1, XYSide o2)
-        {
-            if (o1.equals(o2))
-            {
+
+        public boolean equals(Object o) {
+            XYSide xy = (XYSide) o;
+            return xy.x() == x && xy.y() == y && xy.side() == side;
+        }
+
+        public int compare(XYSide o1, XYSide o2) {
+            if (o1.equals(o2)) {
                 return 0;
-            }
-            else
-            {
+            } else {
                 return -1;
             }
         }
     }
-    
+
     /**
-     * Get the neighbors for a given cell ID.  Each crystal not on an edge 
-     * has 8 neighbors.  Edge crystals have fewer.
+     * Get the neighbors for a given cell ID. Each crystal not on an edge has 8 neighbors. Edge crystals have fewer.
+     * 
      * @param id The cell ID.
      * @return A <code>Set</code> containing the cell's neighbors.
      */
-    Set<Long> getNeighbors(Long id)
-    {        
+    Set<Long> getNeighbors(Long id) {
         // Get the IDDecoder.
-        IDDecoder dec = getIDDecoder();        
-        
+        IDDecoder dec = getIDDecoder();
+
         // Set the ID.
         dec.setID(id);
-        
+
         // Get ID field values.
         int x = dec.getValue("ix");
         int y = dec.getValue("iy");
         int side = dec.getValue("side");
-       
+
         // Get field indices.
         int ix = dec.getFieldIndex("ix");
         int iy = dec.getFieldIndex("iy");
         int iside = dec.getFieldIndex("side");
-        
+
         // Get X, Y, & side neighbor data for this crystal.
         Set<XYSide> neighbors = getNeighbors(x, y, side);
 
         // Get buffer with values from current ID.
         int[] buffer = new int[dec.getFieldCount()];
-        dec.getValues(buffer);       
-        
+        dec.getValues(buffer);
+
         // Create an encoder to make neighbor IDs.
         IDEncoder enc = new IDEncoder(dec.getIDDescription());
-     
+
         // Set to hold neighbor IDs.
         Set<Long> ids = new HashSet<Long>();
-        
+
         // Loop over neighbor objects to make IDs.
-        for (XYSide xyside : neighbors)
-        {
+        for (XYSide xyside : neighbors) {
             buffer[ix] = xyside.x;
             buffer[iy] = xyside.y;
             buffer[iside] = xyside.side;
             long nId = enc.setValues(buffer);
             ids.add(nId);
         }
-        
+
         return ids;
     }
-    
-    Set<XYSide> getNeighbors(int ix, int iy, int side)
-    {
+
+    Set<XYSide> getNeighbors(int ix, int iy, int side) {
         Set<Integer> xneighbors = getXNeighbors(ix);
         Set<Integer> yneighbors = getYNeighbors(iy);
-        
+
         Set<XYSide> neighbors = new HashSet<XYSide>();
-        
-        for (Integer jx : xneighbors)
-        {
-            for (Integer jy : yneighbors)
-            {                
+
+        for (Integer jx : xneighbors) {
+            for (Integer jy : yneighbors) {
                 // Filter out self.
-                if (jx == ix && jy == iy)
-                {
+                if (jx == ix && jy == iy) {
                     continue;
                 }
-                
-                neighbors.add(new XYSide(jx,jy,side));
+
+                neighbors.add(new XYSide(jx, jy, side));
             }
         }
-        
+
         return neighbors;
     }
-    
-    Set<Integer> getXNeighbors(int ix)
-    {
+
+    Set<Integer> getXNeighbors(int ix) {
         Set<Integer> neighbors = new HashSet<Integer>();
-        
+
         // Add self.
         neighbors.add(ix);
-        
+
         // Left neighbor.
-        if (isValidX(ix - 1))
-        {
+        if (isValidX(ix - 1)) {
             neighbors.add(ix - 1);
-        }
-        else if (isValidX(ix - 2))
-        {
+        } else if (isValidX(ix - 2)) {
             neighbors.add(ix - 2);
         }
-        
+
         // Right neighbor.
-        if (isValidX(ix + 1))
-        {
+        if (isValidX(ix + 1)) {
             neighbors.add(ix + 1);
-        }
-        else if (isValidX(ix + 2))
-        {
+        } else if (isValidX(ix + 2)) {
             neighbors.add(ix + 2);
-        }                
-        
+        }
+
         return neighbors;
     }
-    
-    Set<Integer> getYNeighbors(int iy)
-    {
+
+    Set<Integer> getYNeighbors(int iy) {
         Set<Integer> neighbors = new HashSet<Integer>();
-        
+
         // Add self.
         neighbors.add(iy);
-        
+
         // Lower neighbor.
-        if (isValidY(iy - 1))
-        {
+        if (isValidY(iy - 1)) {
             neighbors.add(iy - 1);
         }
         // Upper neighbor.
-        if (isValidY(iy + 1))
-        {
+        if (isValidY(iy + 1)) {
             neighbors.add(iy + 1);
         }
-        
+
         return neighbors;
     }
-    
-    boolean isValidY(int iy)
-    {
+
+    boolean isValidY(int iy) {
         // Zero is not valid because ID scheme goes from 1.
         return iy > 0 && iy <= ny;
     }
-    
-    boolean isValidX(int ix)
-    {
+
+    boolean isValidX(int ix) {
         // Even case.
-        if (!oddX)
-        {
-            return ix >= -nx/2 && ix <= nx/2 && ix != 0;
+        if (!oddX) {
+            return ix >= -nx / 2 && ix <= nx / 2 && ix != 0;
         }
         // Odd case.
-        else
-        {
-            return ix >= (-nx-1)/2 && ix <= (nx+1)/2;
-        }
-    }
-        
+        else {
+            return ix >= (-nx - 1) / 2 && ix <= (nx + 1) / 2;
+        }
+    }
+
     /**
      * Create a map of crystal IDs to the <code>Set</code> of neighbor crystal IDs.
+     * 
      * @return A map of neighbors for each crystal ID.
      */
-    public NeighborMap getNeighborMap()
-    {
-        if (neighborMap != null)
-        {
+    public NeighborMap getNeighborMap() {
+        if (neighborMap != null) {
             return neighborMap;
         }
-       
-        // Setup the private instance of the map. 
+
+        // Setup the private instance of the map.
         neighborMap = new NeighborMap(this.getDetectorElement().getIdentifierHelper());
-        
+
         IDDecoder dec = getIDDecoder();
         IDEncoder enc = new IDEncoder(dec.getIDDescription());
-        
+
         int nfields = dec.getFieldCount();
         int[] vals = new int[nfields];
 
         vals[dec.getFieldIndex("system")] = getSystemID();
-        
+
         int idxx = dec.getFieldIndex("ix");
         int idxy = dec.getFieldIndex("iy");
-        
-        int hnx = nx;        
-        
-        // Calculate number of X for loop.  (from LCDD conv)
-        if (oddX)
-        {
+
+        int hnx = nx;
+
+        // Calculate number of X for loop. (from LCDD conv)
+        if (oddX) {
             hnx -= 1;
             hnx /= 2;
-        }
-        else
-        {
+        } else {
             hnx /= 2;
         }
-                
-        for (int side=-1; side <=1; side++)
-        {            
-            if (side == 0) continue;            
+
+        for (int side = -1; side <= 1; side++) {
+            if (side == 0)
+                continue;
             vals[dec.getFieldIndex("side")] = side;
             // Loop over y.
-            for (int iy=1; iy<=ny; iy++)
-            {       
+            for (int iy = 1; iy <= ny; iy++) {
                 // Loop over x.
-                for (int ix=0; ix<=hnx; ix++)
-                {                                                                                       
+                for (int ix = 0; ix <= hnx; ix++) {
                     // Loop for positive and negative x.
-                    for (int j=-1; j<=1; j++)
-                    {
+                    for (int j = -1; j <= 1; j++) {
                         if (j == 0)
                             continue;
-                                                
-                        vals[idxx] = ix*j;
+
+                        vals[idxx] = ix * j;
                         vals[idxy] = iy;
-                                                        
+
                         Long id = enc.setValues(vals);
                         Set<Long> neighbors = getNeighbors(id);
-                                        
+
                         neighborMap.put(id, neighbors);
                     }
                 }
             }
         }
-        
+
         return neighborMap;
-    }    
+    }
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java	Wed Apr 27 11:11:32 2016
@@ -150,7 +150,7 @@
     /**
      * The number of crystals in X in one section.
      * 
-     * @return
+     * @return the number of crystals in X in one section
      */
     public double nx() {
         return nx;
@@ -159,7 +159,7 @@
     /**
      * The number of crystals in y in one section.
      * 
-     * @return
+     * @return the number of crystals in Y in one section
      */
     public double ny() {
         return ny;

Modified: java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.java	Wed Apr 27 11:11:32 2016
@@ -9,21 +9,21 @@
 
 public class HPSTestRunTracker2014 extends AbstractTracker {
 
-	public HPSTestRunTracker2014(Element node) throws JDOMException 
-	{
-		super(node);
-	}
+    public HPSTestRunTracker2014(Element node) throws JDOMException 
+    {
+        super(node);
+    }
 
-	public void appendHepRep(HepRepFactory factory, HepRep heprep) 
-	{
+    public void appendHepRep(HepRepFactory factory, HepRep heprep) 
+    {
         DetectorElementToHepRepConverter.convert(getDetectorElement(), factory, heprep, -1, false, getVisAttributes().getColor());
-	}
-	
-	public boolean isEndcap() {
-		return false;
-	}
-	
-	public boolean isBarrel() {
-		return true;
-	}
+    }
+    
+    public boolean isEndcap() {
+        return false;
+    }
+    
+    public boolean isBarrel() {
+        return true;
+    }
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java	Wed Apr 27 11:11:32 2016
@@ -63,7 +63,8 @@
 
         final DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
         conditionsManager.addConditionsListener(new SvtDetectorSetup());
-        conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
+        //conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
+        conditionsManager.setDetector("HPS-EngRun2015-Nominal-v3", 5772);
 
         // Get the detector.
         final Detector detector = conditionsManager.getCachedConditions(Detector.class, "compact.xml").getCachedData();

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java	Wed Apr 27 11:11:32 2016
@@ -36,8 +36,8 @@
     private static final int TOTAL_NUMBER_OF_STEREO_LAYERS = 10; 
     private static final String SUBDETECTOR_NAME = "Tracker";
     
-	public static final int NUMBER_OF_READOUT_STRIPS = 639;
-	public static final int NUMBER_OF_SENSE_STRIPS = 1277;
+    public static final int NUMBER_OF_READOUT_STRIPS = 639;
+    public static final int NUMBER_OF_SENSE_STRIPS = 1277;
     
     //-----------------//
     //-----------------//
@@ -74,12 +74,12 @@
         for(HpsSiSensor sensor : sensors) {
             assertTrue("[ " + this.getClass().getSimpleName() + " ]: Sensor is of wrong type: " + sensor.getClass().getSimpleName(),
                         sensor instanceof HpsSiSensor);
-			assertTrue("[ " + this.getClass().getSimpleName() + " ]: Wrong number of readout electrodes found.",
-					sensor.getReadoutElectrodes(ChargeCarrier.HOLE).getNCells() == NUMBER_OF_READOUT_STRIPS);
-			
-			assertTrue("[ " + this.getClass().getSimpleName() + " ]: Wrong number of sense electrodes found.",
-					sensor.getSenseElectrodes(ChargeCarrier.HOLE).getNCells() == NUMBER_OF_SENSE_STRIPS);
-			LOGGER.info(sensor.toString());
+            assertTrue("[ " + this.getClass().getSimpleName() + " ]: Wrong number of readout electrodes found.",
+                    sensor.getReadoutElectrodes(ChargeCarrier.HOLE).getNCells() == NUMBER_OF_READOUT_STRIPS);
+            
+            assertTrue("[ " + this.getClass().getSimpleName() + " ]: Wrong number of sense electrodes found.",
+                    sensor.getSenseElectrodes(ChargeCarrier.HOLE).getNCells() == NUMBER_OF_SENSE_STRIPS);
+            LOGGER.info(sensor.toString());
         }
         LOGGER.info("Sensors were all initialized correctly.");
         

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java	Wed Apr 27 11:11:32 2016
@@ -18,7 +18,7 @@
 {    
    public HPSTestRunTracker2014LCDDTest(String name)
    {
-   	super(name);
+    super(name);
    }
    
    public static TestSuite suite()

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.java	Wed Apr 27 11:11:32 2016
@@ -18,7 +18,7 @@
 {    
    public HPSTracker2014LCDDTest(String name)
    {
-   	super(name);
+    super(name);
    }
    
    public static TestSuite suite()

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java	Wed Apr 27 11:11:32 2016
@@ -18,7 +18,7 @@
 {    
    public HPSTracker2014v1LCDDTest(String name)
    {
-   	super(name);
+    super(name);
    }
    
    public static TestSuite suite()

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.java	Wed Apr 27 11:11:32 2016
@@ -18,7 +18,7 @@
 {    
    public HPSTracker2014v1SurveyLCDDTest(String name)
    {
-   	super(name);
+    super(name);
    }
    
    public static TestSuite suite()

Modified: java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java	Wed Apr 27 11:11:32 2016
@@ -19,36 +19,36 @@
  */
 public class HPSTestRunTracker2014Test extends TestCase {
 
-	
-	Detector det;
-	public HPSTestRunTracker2014Test(String name) {
-		super(name);
-	}
-	
-	protected void setUp() throws Exception {
-		GeometryReader geometryReader = new GeometryReader();
-		geometryReader.setBuildDetailed(true);
-		String pathToCompactFile = "/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.xml";
+    
+    Detector det;
+    public HPSTestRunTracker2014Test(String name) {
+        super(name);
+    }
+    
+    protected void setUp() throws Exception {
+        GeometryReader geometryReader = new GeometryReader();
+        geometryReader.setBuildDetailed(true);
+        String pathToCompactFile = "/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.xml";
 
-		InputStream in = HPSTestRunTracker2014Test.class.getResourceAsStream(pathToCompactFile);
-		det = geometryReader.read(in);
-		
-		System.out.printf("%s: detector name converted: %s\n",this.getClass().getSimpleName(), det.getName());
-		
-		
-	}
-	
-	public void test() {
-		
-		
-//	    IDetectorElementStore store =  DetectorElementStore.getInstance();
-//	    System.out.printf("%s: Printing %d DE:\n",this.getClass().getSimpleName(), store.size());
-//	    System.out.printf("%s: %50s %40s %50s %50s\n",this.getClass().getSimpleName(), "name", "pos", "path","mother");
-//	    for(IDetectorElement e : store) {
-//	        System.out.printf("%s: %50s %40s %50s %50s \n",this.getClass().getSimpleName(), e.getName(),e.hasGeometryInfo()?e.getGeometry().getPosition().toString():" - ",e.hasGeometryInfo()?((PhysicalVolumePath)e.getGeometry().getPath()).toString():" - ",e.getParent()==null?" - ":e.getParent().getName());
-//	    }
-		
-		IDetectorElementStore store =  DetectorElementStore.getInstance();
+        InputStream in = HPSTestRunTracker2014Test.class.getResourceAsStream(pathToCompactFile);
+        det = geometryReader.read(in);
+        
+        System.out.printf("%s: detector name converted: %s\n",this.getClass().getSimpleName(), det.getName());
+        
+        
+    }
+    
+    public void test() {
+        
+        
+//      IDetectorElementStore store =  DetectorElementStore.getInstance();
+//      System.out.printf("%s: Printing %d DE:\n",this.getClass().getSimpleName(), store.size());
+//      System.out.printf("%s: %50s %40s %50s %50s\n",this.getClass().getSimpleName(), "name", "pos", "path","mother");
+//      for(IDetectorElement e : store) {
+//          System.out.printf("%s: %50s %40s %50s %50s \n",this.getClass().getSimpleName(), e.getName(),e.hasGeometryInfo()?e.getGeometry().getPosition().toString():" - ",e.hasGeometryInfo()?((PhysicalVolumePath)e.getGeometry().getPath()).toString():" - ",e.getParent()==null?" - ":e.getParent().getName());
+//      }
+        
+        IDetectorElementStore store =  DetectorElementStore.getInstance();
         System.out.printf("%s: Printing %d DE:\n",this.getClass().getSimpleName(), store.size());
         System.out.printf("%s: %50s %40s %50s %50s %s\n",this.getClass().getSimpleName(), "name", "pos", "path","mother", "expId");
         for(IDetectorElement e : store) {
@@ -58,8 +58,8 @@
                 expId = e.getExpandedIdentifier();
             System.out.printf("%s: %50s %40s %50s %50s %s\n",this.getClass().getSimpleName(), e.getName(),e.hasGeometryInfo()?e.getGeometry().getPosition().toString():" - ",e.hasGeometryInfo()?((PhysicalVolumePath)e.getGeometry().getPath()).toString():" - ",e.getParent()==null?" - ":e.getParent().getName(),expId==null?" no expId ":expId.toString());
         }
-		
-	}
+        
+    }
    
 
 }

Modified: java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTest.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTest.xml	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTest.xml	Wed Apr 27 11:11:32 2016
@@ -50,7 +50,7 @@
 <!--
         <constant name="tracking_region_radius" value="200.0*cm"/>
         <constant name="tracking_region_min" value="5.0*cm"/>
-        <constant name="tracking_region_zmax" value="100.0*cm"/>	
+        <constant name="tracking_region_zmax" value="100.0*cm"/>    
 
         <constant name="xCent1" value="10*cm" />
         <constant name="xCent2" value="20*cm" />

Modified: java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.xml	(original)
+++ java/branches/HPSJAVA-409/detector-model/src/test/resources/org/lcsim/geometry/subdetector/HPSTestRunTracker2014.xml	Wed Apr 27 11:11:32 2016
@@ -7,9 +7,9 @@
   </info>
   
   <define>
-	<!-- units -->
-	<constant name="mm" value="0.1*cm"/>
-	<constant name="inch" value="25.4*mm"/>
+    <!-- units -->
+    <constant name="mm" value="0.1*cm"/>
+    <constant name="inch" value="25.4*mm"/>
 
     <!-- world -->
     <constant name="world_side" value="500.0*cm" />
@@ -17,8 +17,8 @@
     <constant name="world_y" value="world_side" />
     <constant name="world_z" value="world_side" />
   
- 	 <!-- tracking region -->
- 	<constant name="tracking_region_radius" value="200.0*cm"/>
+     <!-- tracking region -->
+    <constant name="tracking_region_radius" value="200.0*cm"/>
     <constant name="tracking_region_min" value="5.0*cm"/>
     <constant name="tracking_region_zmax" value="131.8*cm"/>
  
@@ -34,7 +34,7 @@
   </materials>
   
   <display>
-	
+    
     <vis name="SensorVis" alpha="1.0" r="1.0" g="0.0" b="0.0" drawingStyle="wireframe" lineStyle="unbroken" showDaughters="true" visible="true"/>
     <vis name="ActiveSensorVis" alpha="1.0" r="1.0" g="0.0" b="0.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="true" visible="true"/>
     <vis name="CarbonFiberVis" alpha="1.0" r="0.88" g="0.88" b="0.88" drawingStyle="solid" lineStyle="unbroken" showDaughters="true" visible="true"/>
@@ -48,7 +48,7 @@
     <vis name="BasePlateVis" alpha="1.0" r="0.35" g="0.35" b="0.35" drawingStyle="solid" lineStyle="dashed" showDaughters="true" visible="true"/>
     <vis name="LayerVis" alpha="0.0" r="0.0" g="0.0" b="1.0" drawingStyle="wireframe" showDaughters="true" visible="false"/>
     <vis name="ComponentVis" alpha="0.0" r="0.0" g="0.2" b="0.4" drawingStyle="solid" showDaughters="false" visible="false"/>
-	<vis name="BeamPlaneVis" alpha="1.0" r="1.0" g="1.0" b="1.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="false" visible="true"/>
+    <vis name="BeamPlaneVis" alpha="1.0" r="1.0" g="1.0" b="1.0" drawingStyle="solid" lineStyle="unbroken" showDaughters="false" visible="true"/>
     
   </display>
   

Modified: java/branches/HPSJAVA-409/detector-model/target/antrun/build-main.xml
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/antrun/build-main.xml	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/antrun/build-main.xml	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <project name="maven-antrun-" default="main"  >
 <target name="main">
-  <mkdir dir="/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/target/test-output"/>
+  <mkdir dir="/media/work/svn/hps-java/HPSJAVA-409/detector-model/target/test-output"/>
 </target>
 </project>

Modified: java/branches/HPSJAVA-409/detector-model/target/hps-detector-model-3.4.2-SNAPSHOT-bin.jar
 =============================================================================
Binary files - no diff available.

Modified: java/branches/HPSJAVA-409/detector-model/target/hps-detector-model-3.4.2-SNAPSHOT.jar
 =============================================================================
Binary files - no diff available.

Modified: java/branches/HPSJAVA-409/detector-model/target/maven-archiver/pom.properties
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/maven-archiver/pom.properties	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/maven-archiver/pom.properties	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,5 @@
 #Generated by Maven
-#Fri Dec 04 17:58:10 CET 2015
+#Fri Apr 08 16:49:44 PDT 2016
 version=3.4.2-SNAPSHOT
 groupId=org.hps
 artifactId=hps-detector-model

Modified: java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst	Wed Apr 27 11:11:32 2016
@@ -1 +1,188 @@
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13Top.class
+org/lcsim/geometry/compact/converter/HPSTracker2014LCDDBuilder.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL46Top.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelPlate.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$HalfModuleStereo.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46TopSurveyBalls.class
+org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.class
+org/lcsim/detector/converter/compact/HPSTracker2Converter$ModuleParameters.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal3$CrystalRange.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46BottomPlate.class
+org/lcsim/geometry/compact/converter/SurveyVolumeImpl.class
+org/lcsim/detector/converter/compact/HPSTrackerConverter.class
+org/lcsim/detector/converter/compact/HPSTrackerConverter$ModuleParameters.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$Hybrid.class
+org/hps/detector/ecal/EcalCrystalChannelMap.class
+org/hps/detector/svt/SvtDetectorSetup.class
+org/lcsim/geometry/subdetector/HPSTracker2014.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL5Bot.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13BottomPlate.class
+org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.class
+org/lcsim/geometry/compact/converter/AlignmentCorrection.class
+org/lcsim/geometry/subdetector/HPSEcal3$NeighborMap.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014Base.class
+org/lcsim/geometry/compact/converter/MilleParameter.class
+org/lcsim/geometry/compact/converter/LCDDSurveyVolume.class
+org/hps/detector/ecal/HPSEcalDetectorElement$NeighborDirection.class
+org/lcsim/detector/converter/compact/HPSMuonCalorimeterConverter.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunColdBlockL45.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$SupportTop.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$HalfModuleComponent.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongHalfModuleBundle.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL4Bot.class
+org/hps/detector/ecal/geo2015/crystal/Geant4Position.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongAxialSlotHalfModule.class
+org/lcsim/geometry/subdetector/HPSTestRunTracker2014.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunHalfModuleStereo.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunModule.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL13.class
+org/lcsim/geometry/compact/converter/ReadSurveyOutput.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$SupportPlateBottom.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal4.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$Sensor.class
+org/lcsim/geometry/subdetector/HPSEcal4.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal.class
+org/hps/detector/ecal/CrystalRange.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongAxialHoleHalfModule.class
+org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL6Top.class
+org/lcsim/geometry/subdetector/HPSEcal$XYSide.class
+org/lcsim/geometry/subdetector/HPSEcal$NeighborMap.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.class
+org/hps/detector/ecal/geo2015/geoutils/CenterMass.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal3.class
+org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SupportRingL13KinMount.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$SupportPlateTop.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$HalfModuleLamination.class
+org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunColdBlockL13.class
+org/lcsim/geometry/compact/converter/SurveyVolume.class
+org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL3Top.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$SupportBottom.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2$ModuleComponentParameters.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunModuleL13.class
+org/lcsim/detector/converter/compact/subdetector/HpsTracker2.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL13Top.class
+org/lcsim/geometry/compact/converter/CompactSurveyVolume.class
+org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.class
+org/lcsim/geometry/subdetector/HPSEcal3$XY.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal2.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongStereoHalfModule.class
+org/hps/detector/ecal/geo2015/ecal/EcalSurveyData.class
+org/lcsim/geometry/subdetector/HPSTracker.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13BottomSurveyBalls.class
+org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition.class
+org/lcsim/geometry/compact/converter/HPSTracker2014v1LCDDBuilder.class
+org/hps/detector/ecal/HPSEcalAPI.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13Plate.class
+org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.class
+org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition$TestRunModuleBundle.class
+org/lcsim/geometry/compact/converter/SurveyResult.class
+org/hps/detector/ecal/geo2015/ecal/EcalNominal.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongAxialSlotHalfModuleBase.class
+org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL1Bot.class
+org/hps/detector/ecal/geo2015/base/StatFunUtils.class
+org/hps/detector/ecal/geo2015/ecal/ECalRotationCalculator.class
+org/hps/detector/ecal/geo2015/ecal/Transformations.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TrackerEnvelope.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongStereoHoleHalfModule.class
+org/lcsim/geometry/subdetector/HPSEcal3$CrystalRange.class
+org/lcsim/geometry/subdetector/HPSTracker2014v1.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$PSVacuumChamber.class
+org/lcsim/detector/tracker/silicon/HpsSiSensor.class
+org/lcsim/detector/converter/compact/HPSTestRunTracker2014Converter.class
+org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL6Bot.class
+org/lcsim/geometry/compact/converter/LCDDGhostSurveyVolume.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker$ModuleComponentParameters.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13TopSurveyBalls.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunHalfModuleBundle.class
+org/hps/detector/ecal/geo2015/crystal/CrystalTaitBryanAngleCalculator.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13TopPlate.class
+org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46Bottom.class
+org/lcsim/detector/converter/compact/HPSTracker2014Converter.class
+org/hps/detector/ecal/EcalCrystal.class
+org/lcsim/geometry/subdetector/HPSTracker2.class
+org/lcsim/geometry/compact/converter/MilleParameter$Type.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunHalfModuleAxial.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$SupportPlate.class
 org/hps/detector/ecal/HPSEcalDetectorElement$1.class
+org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.class
+org/lcsim/detector/converter/compact/HPSEcal2Converter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL13Bottom.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL2Top.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SvtBoxBasePlate.class
+org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition$TrackingVolume.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunColdBlock.class
+org/lcsim/geometry/compact/converter/JavaSurveyVolume.class
+org/lcsim/geometry/compact/converter/HPSTrackerBuilder$BaseModuleBundle.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL13Bot.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL46.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SupportRingL13TopKinMount.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL3Bot.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.class
+org/lcsim/detector/converter/compact/HPSTrackerConverter$ModuleComponentParameters.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.class
+org/hps/detector/ecal/geo2015/geoutils/Plane.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL5Top.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongStereoSlotHalfModuleBase.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$BasePlate.class
+org/lcsim/geometry/compact/converter/HPSTrackerBuilder$HalfModuleBundle.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$ActiveSensor.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46BottomSurveyBalls.class
+org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition$LongStereoSlotHalfModule.class
+org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.class
+org/lcsim/geometry/subdetector/HPSEcal3.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.class
+org/hps/detector/ecal/geo2015/base/DataLoader.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongHalfModule.class
+org/lcsim/detector/converter/compact/HPSEcalConverter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SupportRingL13BottomKinMount.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$BaseModule.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.class
+org/lcsim/geometry/subdetector/HPSEcal.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$HalfModuleAxial.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongModuleBundle.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46Plate.class
+org/lcsim/detector/converter/compact/HPSTracker2014v1Converter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46TopPlate.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL2Bot.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunModuleL45.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SvtBox.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$CSupport.class
+org/hps/detector/ecal/HPSEcalDetectorElement.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$UChannelL46Top.class
+org/lcsim/detector/converter/compact/HPSEcal4Converter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition$LongAxialSlotHalfModule.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$HalfLongModuleLamination.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2$ModuleParameters.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$SupportRing.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$TestRunHalfModule.class
+org/hps/detector/ecal/geo2015/geoutils/Vector.class
+org/hps/detector/ecal/geo2015/geoutils/Line.class
+org/hps/detector/ecal/geo2015/crystal/Crystal.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL46Bot.class
+org/lcsim/detector/converter/compact/HPSTracker2Converter.class
+org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$LongStereoSlotHalfModule.class
+org/lcsim/detector/converter/compact/HPSEcal3Converter.class
+org/lcsim/geometry/compact/converter/HPSTrackerBuilder.class
+org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition$CarbonFiber.class
+org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL4Top.class
+org/lcsim/geometry/compact/converter/HPSTracker2014v1JavaBuilder.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker$ModuleParameters.class
+org/lcsim/geometry/subdetector/HPSEcal2.class
+org/lcsim/detector/converter/compact/HPSTracker2Converter$ModuleComponentParameters.class
+org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition$ModuleL1Top.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1.class
+org/lcsim/geometry/subdetector/HPSMuonCalorimeter.class

Modified: java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst	Wed Apr 27 11:11:32 2016
@@ -1,92 +1,92 @@
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/EcalNominal.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/package-info.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/Plane.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/package-info.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2014.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/svt/SvtDetectorSetup.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDSurveyVolume.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/CompactSurveyVolume.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/Crystal.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal3.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2Converter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014Base.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/Geant4Position.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/MilleParameter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/HPSEcalDetectorElement.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal2.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/CrystalEulerAngleCalculator.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/package-info.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcalConverter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSMuonCalorimeter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/FunCheatJava.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/EcalCrystal.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/Transformations.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcal3Converter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/DataLoader.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/CenterMass.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal4.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcal4Converter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/CrystalRange.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/package-info.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/AlignmentCorrection.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/EcalCrystalChannelMap.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/package-info.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/package-info.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014Converter.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/EcalSurveyData.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerBuilder.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/Vector.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/HPSEcalAPI.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java
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-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTestRunTracker2014Converter.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal2.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeImpl.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2014v1.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaSurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerJavaBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/tracker/silicon/HpsTestRunSiSensor.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal4.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014GeometryDefinition.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014Converter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014v1Converter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcalConverter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcal3Converter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/EcalCrystal.java
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+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014LCDDBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal4.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2Converter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1JavaBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerGeometryDefinition.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/Geant4Position.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1GeometryDefinition.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/HpsTracker2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014JavaBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyCoordinateSystem.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014LCDDBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/ReadSurveyOutput.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTestRunTracker2014JavaBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/DataLoader.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014v1LCDDBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaGhostSurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/Transformations.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/CenterMass.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTracker2014ConverterBase.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSEcal4Converter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2014.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSMuonCalorimeter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/Crystal.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/HPSEcalDetectorElement.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SvtAlignmentConstantsReader.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/CrystalTaitBryanAngleCalculator.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/EcalCrystalChannelMap.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerJavaBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker2014v1.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/CrystalRange.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/Line.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/Vector.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSMuonCalorimeterConverter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTrackerLCDDBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/StatFunUtils.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/MilleParameter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/crystal/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyResult.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSMuonCalorimeter2.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/EcalNominal.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/AlignmentCorrection.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/subdetector/SvtStereoLayer.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDGhostSurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/HPSEcalAPI.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/detector/converter/compact/HPSTrackerConverter.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/HPSTracker2014GeometryDefinition.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/geoutils/Plane.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/EcalSurveyData.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/CompactSurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeImpl.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/svt/SvtDetectorSetup.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/ecal/ECalRotationCalculator.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/JavaSurveyVolume.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014Base.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSEcal3.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/hps/detector/ecal/geo2015/base/package-info.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/subdetector/HPSTracker.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/SurveyVolumeVisualization.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/IHPSTrackerLCDDBuilder.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/main/java/org/lcsim/geometry/compact/converter/LCDDSurveyVolume.java

Modified: java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/createdFiles.lst
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/createdFiles.lst	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/createdFiles.lst	Wed Apr 27 11:11:32 2016
@@ -1 +1,16 @@
+org/hps/detector/svt/SvtDetectorSetupTest.class
 org/lcsim/detector/converter/compact/HPSEcal4ConverterTest.class
+org/lcsim/detector/converter/compact/HPSMuonCalorimeterTest.class
+org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.class
+org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.class
+org/hps/detector/svt/TestRunSvtDetectorSetupTest.class
+org/hps/detector/svt/SvtDaqMappingTest.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.class
+org/lcsim/geometry/subdetector/HPSTracker2014Test.class
+org/lcsim/detector/converter/compact/HpsTestRunSiSensorConverterTest.class
+org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.class
+org/hps/detector/ecal/HPSEcalAPITest.class
+org/hps/detector/SvtAlignmentTest.class
+org/lcsim/geometry/compact/converter/lcdd/HPSEcal4LCDDTest.class

Modified: java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/inputFiles.lst
 =============================================================================
--- java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/inputFiles.lst	(original)
+++ java/branches/HPSJAVA-409/detector-model/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/inputFiles.lst	Wed Apr 27 11:11:32 2016
@@ -1,16 +1,16 @@
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/ecal/HPSEcalAPITest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/SvtAlignmentTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSEcal4ConverterTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDaqMappingTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal4LCDDTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HpsTestRunSiSensorConverterTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/TestRunSvtDetectorSetupTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTracker2014Test.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSMuonCalorimeterTest.java
-/projet/nucleon2/annie/HPS/withHPS_Java/SENA/hps_trunk_dev/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1LCDDTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/SvtAlignmentTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDaqMappingTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HpsTestRunSiSensorConverterTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014v1SurveyLCDDTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTracker2014LCDDTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSEcal4ConverterTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/SvtDetectorSetupTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/svt/TestRunSvtDetectorSetupTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014LCDDTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/compact/converter/lcdd/HPSEcal4LCDDTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTestRunTracker2014Test.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/geometry/subdetector/HPSTracker2014Test.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/hps/detector/ecal/HPSEcalAPITest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSMuonCalorimeterTest.java
+/media/work/svn/hps-java/HPSJAVA-409/detector-model/src/test/java/org/lcsim/detector/converter/compact/HPSTracker2ConverterTest.java

Modified: java/branches/HPSJAVA-409/distribution/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/distribution/pom.xml	(original)
+++ java/branches/HPSJAVA-409/distribution/pom.xml	Wed Apr 27 11:11:32 2016
@@ -13,7 +13,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>    
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/distribution/</url>
@@ -80,7 +80,7 @@
                         <binFileExtensions>
                                 <unix>.sh</unix>
                             </binFileExtensions>
-                            <extraJvmArguments>-Djava.util.logging.config.class=org.hps.logging.config.DefaultLoggingConfig</extraJvmArguments>
+                            <extraJvmArguments>-Xmx2g -Djava.util.logging.config.class=org.hps.logging.config.DefaultLoggingConfig</extraJvmArguments>
                             <programs>
                                 <program>
                                     <mainClass>org.hps.evio.EvioToLcio</mainClass>
@@ -88,35 +88,31 @@
                                 </program>
                                 <program>
                                     <mainClass>org.hps.job.JobManager</mainClass>
-                                    <id>job</id>
+                                    <id>job-manager</id>
                                 </program>
                                 <program>
                                     <mainClass>org.hps.conditions.cli.CommandLineTool</mainClass>
-                                    <id>conddb</id>
-                                </program>
-                                <program>
-                                    <mainClass>org.hps.crawler.DatacatCrawler</mainClass>
-                                    <id>crawler</id>
+                                    <id>conditions-cli</id>
                                 </program>
                                 <program>
                                     <mainClass>org.hps.run.database.RunDatabaseCommandLine</mainClass>
-                                    <id>rundb</id>
+                                    <id>run-database-cli</id>
                                 </program>
                                 <program>
                                     <mainClass>org.hps.monitoring.application.Main</mainClass>
-                                    <id>monapp</id>
+                                    <id>monitoring-app</id>
                                 </program>
                                 <program>
                                     <mainClass>org.lcsim.geometry.compact.converter.Main</mainClass>
-                                    <id>detcnv</id>
+                                    <id>detector-converter</id>
                                 </program>
                                 <program>
                                     <mainClass>org.hps.record.evio.EvioFileProducer</mainClass>
-                                    <id>evio_file_producer</id>
+                                    <id>evio-file-producer</id>
                                 </program>
                                 <program>
                                     <mainClass>org.jlab.coda.et.apps.StartEt</mainClass>
-                                    <id>et_server</id>
+                                    <id>et-server</id>
                                     <commandLineArguments>
                                         <commandLineArgument>-f</commandLineArgument>
                                         <commandLineArgument>ETBuffer</commandLineArgument>
@@ -124,6 +120,18 @@
                                         <commandLineArgument>20000</commandLineArgument>
                                         <commandLineArgument>-v</commandLineArgument>
                                     </commandLineArguments>
+                                </program>
+                                <program>
+                                    <mainClass>org.hps.crawler.MetadataWriter</mainClass>
+                                    <id>dc-create-metadata</id>
+                                </program>
+                                <program>
+                                    <mainClass>org.hps.crawler.DatacatAddFile</mainClass>
+                                    <id>dc-add-file</id>
+                                </program>
+                                <program>
+                                    <mainClass>org.hps.crawler.DatacatCrawler</mainClass>
+                                    <id>dc-crawler</id>
                                 </program>
                             </programs>
                         </configuration>

Modified: java/branches/HPSJAVA-409/distribution/src/main/java/org/hps/HPSJavaProperties.java
 =============================================================================
--- java/branches/HPSJAVA-409/distribution/src/main/java/org/hps/HPSJavaProperties.java	(original)
+++ java/branches/HPSJAVA-409/distribution/src/main/java/org/hps/HPSJavaProperties.java	Wed Apr 27 11:11:32 2016
@@ -82,6 +82,11 @@
         return this.properties.getProperty("timestamp");
     }
 
+    /**
+     * Convert this object to a string.
+     *
+     * @return this object converted to a string
+     */
     @Override
     public String toString() {
         final StringBuffer sb = new StringBuffer();

Modified: java/branches/HPSJAVA-409/ecal-event-display/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/pom.xml	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/ecal-event-display/</url>

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Association.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Association.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Association.java	Wed Apr 27 11:11:32 2016
@@ -10,52 +10,52 @@
  * @author Kyle McCarty
  */
 public final class Association {
-	private final Point parent;
-	private final Point child;
-	private final Color highlight;
-	
-	/**
-	 * <b>Association</b><br/><br/>
-	 * <code>public <b>Association</b>(Point parentCrystal, Point childCrystal, Color highlightColor)</code><br/><br/>
-	 * Creates an association between a child crystal and a parent
-	 * crystal.
-	 * @param parentCrystal - The crystal with which the child crystal
-	 * is connected.
-	 * @param childCrystal - The connected crystal.
-	 * @param highlightColor - The color in which the child crystal
-	 * should be highlighted.
-	 */
-	public Association(Point parentCrystal, Point childCrystal, Color highlightColor) {
-		parent = parentCrystal;
-		child = childCrystal;
-		highlight = highlightColor;
-	}
-	
-	/**
-	 * <b>getChildCrystal</b><br/><br/>
-	 * <code>public Point <b>getChildCrystal</b>()</code><br/><br/>
-	 * Indicates the indices for the child crystal.
-	 * @return Returns the child crystal's indices in a <code>Point
-	 * </code> object.
-	 */
-	public Point getChildCrystal() { return child; }
-	
-	/**
-	 * <b>getHighlight</b><br/><br/>
-	 * <code>public Color <b>getHighlight</b>()</code><br/><br/>
-	 * Gets the color with which the child crystal should be highlighted
-	 * whenever the parent crystal is selected.
-	 * @return Returns the highlight color as a <code>Color</code> object.
-	 */
-	public Color getHighlight() { return highlight; }
-	
-	/**
-	 * <b>getParentCrystal</b><br/><br/>
-	 * <code>public Point <b>getParentCrystal</b>()</code><br/><br/>
-	 * Indicates the indices for the parent crystal with which the
-	 * child crystal is connected.
-	 * @return Returns the parent crystal's indices in a <code>Point
-	 * </code> object.
-	 */
-	public Point getParentCrystal() { return parent; }
+    private final Point parent;
+    private final Point child;
+    private final Color highlight;
+    
+    /**
+     * <b>Association</b><br/><br/>
+     * <code>public <b>Association</b>(Point parentCrystal, Point childCrystal, Color highlightColor)</code><br/><br/>
+     * Creates an association between a child crystal and a parent
+     * crystal.
+     * @param parentCrystal - The crystal with which the child crystal
+     * is connected.
+     * @param childCrystal - The connected crystal.
+     * @param highlightColor - The color in which the child crystal
+     * should be highlighted.
+     */
+    public Association(Point parentCrystal, Point childCrystal, Color highlightColor) {
+        parent = parentCrystal;
+        child = childCrystal;
+        highlight = highlightColor;
+    }
+    
+    /**
+     * <b>getChildCrystal</b><br/><br/>
+     * <code>public Point <b>getChildCrystal</b>()</code><br/><br/>
+     * Indicates the indices for the child crystal.
+     * @return Returns the child crystal's indices in a <code>Point
+     * </code> object.
+     */
+    public Point getChildCrystal() { return child; }
+    
+    /**
+     * <b>getHighlight</b><br/><br/>
+     * <code>public Color <b>getHighlight</b>()</code><br/><br/>
+     * Gets the color with which the child crystal should be highlighted
+     * whenever the parent crystal is selected.
+     * @return Returns the highlight color as a <code>Color</code> object.
+     */
+    public Color getHighlight() { return highlight; }
+    
+    /**
+     * <b>getParentCrystal</b><br/><br/>
+     * <code>public Point <b>getParentCrystal</b>()</code><br/><br/>
+     * Indicates the indices for the parent crystal with which the
+     * child crystal is connected.
+     * @return Returns the parent crystal's indices in a <code>Point
+     * </code> object.
+     */
+    public Point getParentCrystal() { return parent; }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Cluster.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Cluster.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Cluster.java	Wed Apr 27 11:11:32 2016
@@ -11,161 +11,161 @@
  * @author Kyle McCarty
  */
 public final class Cluster {
-	private final Point center;
-	private final double energy;
-	private final double time;
-	private ArrayList<Point> hitList = new ArrayList<Point>();
-	private ArrayList<Point> shareList = new ArrayList<Point>();
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a
-	 * cluster center.
-	 * @param ix - The cluster center's x-index.
-	 * @param iy - The cluster center's y-index.
-	 */
-	public Cluster(int ix, int iy) { this(new Point(ix, iy), Double.NaN, Double.NaN); }
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a seed
-	 * hit.
-	 * @param clusterCenter - The <code>Point</code> object indicating in
-	 * which crystal the seed hit occurred.
-	 */
-	public Cluster(Point clusterCenter) { this(clusterCenter, Double.NaN, Double.NaN); }
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a
-	 * cluster center.
-	 * @param ix - The cluster center's x-index.
-	 * @param iy - The cluster center's y-index.
-	 * @param energy - The cluster's energy.
-	 */
-	public Cluster(int ix, int iy, double energy) { this(new Point(ix, iy), energy, Double.NaN); }
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a
-	 * cluster center.
-	 * @param ix - The cluster center's x-index.
-	 * @param iy - The cluster center's y-index.
-	 * @param energy - The cluster's energy.
-	 * @param time - The cluster's time-stamp.
-	 */
-	public Cluster(int ix, int iy, double energy, double time) { this(new Point(ix, iy), energy, time); }
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a seed
-	 * hit.
-	 * @param clusterCenter - The <code>Point</code> object indicating in
-	 * which crystal the seed hit occurred.
-	 * @param energy - The cluster's energy.
-	 */
-	public Cluster(Point clusterCenter, double energy) {
-		this(clusterCenter, energy, Double.NaN);
-	}
-	
-	/**
-	 * Creates a new cluster. All clusters are required to have a seed
-	 * hit.
-	 * @param clusterCenter - The <code>Point</code> object indicating in
-	 * which crystal the seed hit occurred.
-	 * @param energy - The cluster's energy.
-	 * @param time - The cluster's time-stamp.
-	 */
-	public Cluster(Point clusterCenter, double energy, double time) {
-		center = clusterCenter;
-		this.energy = energy;
-		this.time = time;
-	}
-	
-	/**
-	 * Adds an <code>Point</code> to the list of this cluster's
-	 * component hits.
-	 * @param ix - The component hit's x-coordinate.
-	 * @param iy - The component hit's y-coordinate.
-	 */
-	public void addComponentHit(int ix, int iy) { hitList.add(new Point(ix, iy)); }
-	
-	/**
-	 * Adds an <code>Point</code> to the list of this cluster's
-	 * component hits.
-	 * @param eHit - The <code>Point</code> object indicating in which
-	 * crystal the hit occurred.
-	 */
-	public void addComponentHit(Point eHit) { hitList.add(eHit); }
-	
-	/**
-	 * Adds an <code>Point</code> to the list of this cluster's shared
-	 * hits.
-	 * @param ix - The shared hit's x-coordinate.
-	 * @param iy - The shared hit's y-coordinate.
-	 */
-	public void addSharedHit(int ix, int iy) { shareList.add(new Point(ix, iy)); }
-	
-	/**
-	 * Adds an <code>Point</code> to the list of this cluster's shared
-	 * hits.
-	 * @param eHit - The <code>Point</code> object indicating in which
-	 * crystal the hit occurred.
-	 */
-	public void addSharedHit(Point eHit) { shareList.add(eHit); }
-	
-	/**
-	 * Gets the hit representing the cluster center.
-	 * @return Returns the cluster center hit as an <code>Point</code>.
-	 */
-	public Point getClusterCenter() { return center; }
-	
-	/**
-	 * Gets the cluster's energy, if it was defined when the cluster
-	 * was constructed.
-	 * @return Returns the energy of the cluster if it was defined,
-	 * and <code>NaN</code> otherwise.
-	 */
-	public double getClusterEnergy() { return energy; }
-	
-	/**
-	 * Gets the time stamp for the cluster in nanoseconds.
-	 * @return Returns the cluster's time stamp.
-	 */
-	public double getClusterTime() { return time; }
-	
-	/**
-	 * Indicates how many component hits compose this cluster. Note
-	 * that this does not include the seed hit or shared hits.
-	 * @return Returns the number of component hits in the cluster
-	 * as an <code>int</code>.
-	 */
-	public int getComponentHitCount() { return hitList.size(); }
-	
-	/**
-	 * Gets the list of hits that make up the cluster, exempting the
-	 * seed hit and shared hits.
-	 * @return Returns the cluster hits as a <code>List</code> object
-	 * composed of <code>Point</code> objects.
-	 */
-	public List<Point> getComponentHits() { return hitList; }
-	
-	/**
-	 * Indicates how many total hits compose this cluster. This includes
-	 * component hits, shared hits, and the seed hit.
-	 * @return Returns the number of component hits in the cluster
-	 * as an <code>int</code>.
-	 */
-	public int getHitCount() { return hitList.size() + shareList.size() + 1; }
-	
-	/**
-	 * Indicates how many shared hits compose this cluster. Note that
-	 * this does not include the seed hit or component hits.
-	 * @return Returns the number of shared hits in the cluster as an
-	 * <code>int</code>.
-	 */
-	public int getSharedHitCount() { return shareList.size(); }
-	
-	/**
-	 * Gets the list of hits that make up the cluster, exempting the
-	 * seed hit and component hits.
-	 * @return Returns the shared hits as a <code>List</code> object
-	 * composed of <code>Point</code> objects.
-	 */
-	public List<Point> getSharedHits() { return shareList; }
+    private final Point center;
+    private final double energy;
+    private final double time;
+    private ArrayList<Point> hitList = new ArrayList<Point>();
+    private ArrayList<Point> shareList = new ArrayList<Point>();
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a
+     * cluster center.
+     * @param ix - The cluster center's x-index.
+     * @param iy - The cluster center's y-index.
+     */
+    public Cluster(int ix, int iy) { this(new Point(ix, iy), Double.NaN, Double.NaN); }
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a seed
+     * hit.
+     * @param clusterCenter - The <code>Point</code> object indicating in
+     * which crystal the seed hit occurred.
+     */
+    public Cluster(Point clusterCenter) { this(clusterCenter, Double.NaN, Double.NaN); }
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a
+     * cluster center.
+     * @param ix - The cluster center's x-index.
+     * @param iy - The cluster center's y-index.
+     * @param energy - The cluster's energy.
+     */
+    public Cluster(int ix, int iy, double energy) { this(new Point(ix, iy), energy, Double.NaN); }
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a
+     * cluster center.
+     * @param ix - The cluster center's x-index.
+     * @param iy - The cluster center's y-index.
+     * @param energy - The cluster's energy.
+     * @param time - The cluster's time-stamp.
+     */
+    public Cluster(int ix, int iy, double energy, double time) { this(new Point(ix, iy), energy, time); }
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a seed
+     * hit.
+     * @param clusterCenter - The <code>Point</code> object indicating in
+     * which crystal the seed hit occurred.
+     * @param energy - The cluster's energy.
+     */
+    public Cluster(Point clusterCenter, double energy) {
+        this(clusterCenter, energy, Double.NaN);
+    }
+    
+    /**
+     * Creates a new cluster. All clusters are required to have a seed
+     * hit.
+     * @param clusterCenter - The <code>Point</code> object indicating in
+     * which crystal the seed hit occurred.
+     * @param energy - The cluster's energy.
+     * @param time - The cluster's time-stamp.
+     */
+    public Cluster(Point clusterCenter, double energy, double time) {
+        center = clusterCenter;
+        this.energy = energy;
+        this.time = time;
+    }
+    
+    /**
+     * Adds an <code>Point</code> to the list of this cluster's
+     * component hits.
+     * @param ix - The component hit's x-coordinate.
+     * @param iy - The component hit's y-coordinate.
+     */
+    public void addComponentHit(int ix, int iy) { hitList.add(new Point(ix, iy)); }
+    
+    /**
+     * Adds an <code>Point</code> to the list of this cluster's
+     * component hits.
+     * @param eHit - The <code>Point</code> object indicating in which
+     * crystal the hit occurred.
+     */
+    public void addComponentHit(Point eHit) { hitList.add(eHit); }
+    
+    /**
+     * Adds an <code>Point</code> to the list of this cluster's shared
+     * hits.
+     * @param ix - The shared hit's x-coordinate.
+     * @param iy - The shared hit's y-coordinate.
+     */
+    public void addSharedHit(int ix, int iy) { shareList.add(new Point(ix, iy)); }
+    
+    /**
+     * Adds an <code>Point</code> to the list of this cluster's shared
+     * hits.
+     * @param eHit - The <code>Point</code> object indicating in which
+     * crystal the hit occurred.
+     */
+    public void addSharedHit(Point eHit) { shareList.add(eHit); }
+    
+    /**
+     * Gets the hit representing the cluster center.
+     * @return Returns the cluster center hit as an <code>Point</code>.
+     */
+    public Point getClusterCenter() { return center; }
+    
+    /**
+     * Gets the cluster's energy, if it was defined when the cluster
+     * was constructed.
+     * @return Returns the energy of the cluster if it was defined,
+     * and <code>NaN</code> otherwise.
+     */
+    public double getClusterEnergy() { return energy; }
+    
+    /**
+     * Gets the time stamp for the cluster in nanoseconds.
+     * @return Returns the cluster's time stamp.
+     */
+    public double getClusterTime() { return time; }
+    
+    /**
+     * Indicates how many component hits compose this cluster. Note
+     * that this does not include the seed hit or shared hits.
+     * @return Returns the number of component hits in the cluster
+     * as an <code>int</code>.
+     */
+    public int getComponentHitCount() { return hitList.size(); }
+    
+    /**
+     * Gets the list of hits that make up the cluster, exempting the
+     * seed hit and shared hits.
+     * @return Returns the cluster hits as a <code>List</code> object
+     * composed of <code>Point</code> objects.
+     */
+    public List<Point> getComponentHits() { return hitList; }
+    
+    /**
+     * Indicates how many total hits compose this cluster. This includes
+     * component hits, shared hits, and the seed hit.
+     * @return Returns the number of component hits in the cluster
+     * as an <code>int</code>.
+     */
+    public int getHitCount() { return hitList.size() + shareList.size() + 1; }
+    
+    /**
+     * Indicates how many shared hits compose this cluster. Note that
+     * this does not include the seed hit or component hits.
+     * @return Returns the number of shared hits in the cluster as an
+     * <code>int</code>.
+     */
+    public int getSharedHitCount() { return shareList.size(); }
+    
+    /**
+     * Gets the list of hits that make up the cluster, exempting the
+     * seed hit and component hits.
+     * @return Returns the shared hits as a <code>List</code> object
+     * composed of <code>Point</code> objects.
+     */
+    public List<Point> getSharedHits() { return shareList; }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/EcalHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/EcalHit.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/EcalHit.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
      * @param energy - The raw energy of the hit.
      **/
     public EcalHit(int ix, int iy, double energy) {
-    	this(new Point(ix, iy), energy);
+        this(new Point(ix, iy), energy);
     }
     
     /**
@@ -32,7 +32,7 @@
      * @param energy - The raw energy of the hit.
      **/
     public EcalHit(Point ixy, double energy) {
-    	loc = ixy;
+        loc = ixy;
         this.energy = energy;
     }
     
@@ -44,7 +44,7 @@
      * @param time - The time-stamp for the hit.
      **/
     public EcalHit(int ix, int iy, double energy, double time) {
-    	this(new Point(ix, iy), energy, time);
+        this(new Point(ix, iy), energy, time);
     }
     
     /**
@@ -54,7 +54,7 @@
      * @param time - The time-stamp for the hit.
      **/
     public EcalHit(Point ixy, double energy, double time) {
-    	loc = ixy;
+        loc = ixy;
         this.energy = energy;
         this.time = time;
     }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Event.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Event.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/event/Event.java	Wed Apr 27 11:11:32 2016
@@ -10,119 +10,119 @@
  * @author Kyle McCarty
  */
 public final class Event {
-	private List<EcalHit> hitList;
-	private List<Point> clusterList;
-	private List<Association> connectList;
-	
-	/**
-	 * <b>Event</b><br/><br/>
-	 * <code>public <b>Event</b>()</code><br/><br/>
-	 * Creates a new <code>Event</code>.
-	 */
-	public Event() { this(10, 10, 10); }
-	
-	/**
-	 * <b>Event</b><br/><br/>
-	 * <code>public <b>Event</b>(int hits, int clusters)</code><br/><br/>
-	 * Creates a new <code>Event</code> and reserves spaces for the
-	 * given number of hits and cluster centers.
-	 * @param hits - The number of hits for which to reserve space.
-	 * @param clusters - The number of cluster centers for which to
-	 * reserve space.
-	 */
-	public Event(int hits, int clusters) { this(hits, clusters, 10); }
-	
-	/**
-	 * <b>Event</b><br/><br/>
-	 * <code>public <b>Event</b>(int hits, int clusters, int associations)</code><br/><br/>
-	 * Creates a new <code>Event</code> and reserves spaces for the
-	 * given number of hits, cluster centers, and crystal associations.
-	 * @param hits - The number of hits for which to reserve space.
-	 * @param clusters - The number of cluster centers for which to
-	 * reserve space.
-	 * @param associations - The number of crystal associations for
-	 * which to reserve space.
-	 */
-	public Event(int hits, int clusters, int associations) {
-		hitList = new ArrayList<EcalHit>(hits);
-		clusterList = new ArrayList<Point>(clusters);
-		connectList = new ArrayList<Association>(associations);
-	}
-	
-	/**
-	 * <b>Event</b><br/><br/>
-	 * <code>public <b>Event</b>(List<EcalHit> hits, List<Point> clusters, List<Association> associations)</code><br/><br/>
-	 * Creates a new <code>Event</code> and sets its contents to those
-	 * of the given lists. The crystal association list will be empty.
-	 * @param hits - The list of calorimeter hits.
-	 * @param clusters - The list of cluster centers.
-	 */
-	public Event(List<EcalHit> hits, List<Point> clusters) {
-		this(hits, clusters, new ArrayList<Association>());
-	}
-	
-	/**
-	 * <b>Event</b><br/><br/>
-	 * <code>public <b>Event</b>(List<EcalHit> hits, List<Point> clusters, List<Association> associations)</code><br/><br/>
-	 * Creates a new <code>Event</code> and sets its contents to those
-	 * of the given lists.
-	 * @param hits - The list of calorimeter hits.
-	 * @param clusters - The list of cluster centers.
-	 * @param associations - The list of crystal associations.
-	 */
-	public Event(List<EcalHit> hits, List<Point> clusters, List<Association> associations) {
-		hitList = hits;
-		clusterList = clusters;
-		connectList = associations;
-	}
-	
-	/**
-	 * <b>addAssociation</b><br/><br/>
-	 * <code>public void <b>addAssociation</b>(Association connectedCrystal)</code><br/><br/>
-	 * Adds a crystal association to the event.
-	 * @param connectedCrystal - The crystal association to add.
-	 */
-	public void addAssociation(Association connectedCrystal) {
-		connectList.add(connectedCrystal);
-	}
-	
-	/**
-	 * <b>addCluster</b><br/><br/>
-	 * <code>public void <b>addCluster</b>(Point cluster)</code><br/><br/>
-	 * Adds a cluster center to the event.
-	 * @param cluster - The cluster center to add.
-	 */
-	public void addCluster(Point cluster) { clusterList.add(cluster); }
-	
-	/**
-	 * <b>addHit</b><br/><br/>
-	 * <code>public void <b>addHit</b>(EcalHit hit)</code><br/><br/>
-	 * Adds a calorimeter hit to the event.
-	 * @param hit - The calorimeter hit to add.
-	 */
-	public void addHit(EcalHit hit) { hitList.add(hit); }
-	
-	/**
-	 * <b>getAssociations</b><br/><br/>
-	 * <code>public List<Association> <b>getAssociations</b>()</code><br/><br/>
-	 * Gets the list of associated crystals for this event.
-	 * @return Returns the associations in a <code>List</code>.
-	 */
-	public List<Association> getAssociations() { return connectList; }
-	
-	/**
-	 * <b>getClusterCenters</b><br/><br/>
-	 * <code>List<Cluster><b>getClusterCenters</b>()</code><br/><br/>
-	 * Gets the list of cluster centers for this event.
-	 * @return Returns the cluster centers in a <code>List</code>.
-	 */
-	public List<Point> getClusterCenters() { return clusterList; }
-	
-	/**
-	 * <b>getHits</b><br/><br/>
-	 * <code>public List<EcalHit> <b>getHits</b>()</code><br/><br/>
-	 * Gets the list of calorimeter hits for this event.
-	 * @return Returns the hits in a <code>List</code>.
-	 */
-	public List<EcalHit> getHits() { return hitList; }
+    private List<EcalHit> hitList;
+    private List<Point> clusterList;
+    private List<Association> connectList;
+    
+    /**
+     * <b>Event</b><br/><br/>
+     * <code>public <b>Event</b>()</code><br/><br/>
+     * Creates a new <code>Event</code>.
+     */
+    public Event() { this(10, 10, 10); }
+    
+    /**
+     * <b>Event</b><br/><br/>
+     * <code>public <b>Event</b>(int hits, int clusters)</code><br/><br/>
+     * Creates a new <code>Event</code> and reserves spaces for the
+     * given number of hits and cluster centers.
+     * @param hits - The number of hits for which to reserve space.
+     * @param clusters - The number of cluster centers for which to
+     * reserve space.
+     */
+    public Event(int hits, int clusters) { this(hits, clusters, 10); }
+    
+    /**
+     * <b>Event</b><br/><br/>
+     * <code>public <b>Event</b>(int hits, int clusters, int associations)</code><br/><br/>
+     * Creates a new <code>Event</code> and reserves spaces for the
+     * given number of hits, cluster centers, and crystal associations.
+     * @param hits - The number of hits for which to reserve space.
+     * @param clusters - The number of cluster centers for which to
+     * reserve space.
+     * @param associations - The number of crystal associations for
+     * which to reserve space.
+     */
+    public Event(int hits, int clusters, int associations) {
+        hitList = new ArrayList<EcalHit>(hits);
+        clusterList = new ArrayList<Point>(clusters);
+        connectList = new ArrayList<Association>(associations);
+    }
+    
+    /**
+     * <b>Event</b><br/><br/>
+     * <code>public <b>Event</b>(List<EcalHit> hits, List<Point> clusters, List<Association> associations)</code><br/><br/>
+     * Creates a new <code>Event</code> and sets its contents to those
+     * of the given lists. The crystal association list will be empty.
+     * @param hits - The list of calorimeter hits.
+     * @param clusters - The list of cluster centers.
+     */
+    public Event(List<EcalHit> hits, List<Point> clusters) {
+        this(hits, clusters, new ArrayList<Association>());
+    }
+    
+    /**
+     * <b>Event</b><br/><br/>
+     * <code>public <b>Event</b>(List<EcalHit> hits, List<Point> clusters, List<Association> associations)</code><br/><br/>
+     * Creates a new <code>Event</code> and sets its contents to those
+     * of the given lists.
+     * @param hits - The list of calorimeter hits.
+     * @param clusters - The list of cluster centers.
+     * @param associations - The list of crystal associations.
+     */
+    public Event(List<EcalHit> hits, List<Point> clusters, List<Association> associations) {
+        hitList = hits;
+        clusterList = clusters;
+        connectList = associations;
+    }
+    
+    /**
+     * <b>addAssociation</b><br/><br/>
+     * <code>public void <b>addAssociation</b>(Association connectedCrystal)</code><br/><br/>
+     * Adds a crystal association to the event.
+     * @param connectedCrystal - The crystal association to add.
+     */
+    public void addAssociation(Association connectedCrystal) {
+        connectList.add(connectedCrystal);
+    }
+    
+    /**
+     * <b>addCluster</b><br/><br/>
+     * <code>public void <b>addCluster</b>(Point cluster)</code><br/><br/>
+     * Adds a cluster center to the event.
+     * @param cluster - The cluster center to add.
+     */
+    public void addCluster(Point cluster) { clusterList.add(cluster); }
+    
+    /**
+     * <b>addHit</b><br/><br/>
+     * <code>public void <b>addHit</b>(EcalHit hit)</code><br/><br/>
+     * Adds a calorimeter hit to the event.
+     * @param hit - The calorimeter hit to add.
+     */
+    public void addHit(EcalHit hit) { hitList.add(hit); }
+    
+    /**
+     * <b>getAssociations</b><br/><br/>
+     * <code>public List<Association> <b>getAssociations</b>()</code><br/><br/>
+     * Gets the list of associated crystals for this event.
+     * @return Returns the associations in a <code>List</code>.
+     */
+    public List<Association> getAssociations() { return connectList; }
+    
+    /**
+     * <b>getClusterCenters</b><br/><br/>
+     * <code>List<Cluster><b>getClusterCenters</b>()</code><br/><br/>
+     * Gets the list of cluster centers for this event.
+     * @return Returns the cluster centers in a <code>List</code>.
+     */
+    public List<Point> getClusterCenters() { return clusterList; }
+    
+    /**
+     * <b>getHits</b><br/><br/>
+     * <code>public List<EcalHit> <b>getHits</b>()</code><br/><br/>
+     * Gets the list of calorimeter hits for this event.
+     * @return Returns the hits in a <code>List</code>.
+     */
+    public List<EcalHit> getHits() { return hitList; }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/EventManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/EventManager.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/EventManager.java	Wed Apr 27 11:11:32 2016
@@ -21,16 +21,16 @@
      * may be read.
      * @throws IOException Occurs if there is an error closing the file stream.
      **/
-	public void close() throws IOException;
-	
-	/**
-	 * <b>getEventNumber</b><br/><br/>
+    public void close() throws IOException;
+    
+    /**
+     * <b>getEventNumber</b><br/><br/>
      * <code>public int <b>getEventNumber</b>()</code><br/><br/>
      * Gets the ordinal number for the currently displayed event.
-	 * @return Returns the current event's ordinal number.
-	 */
-	public int getEventNumber();
-	
+     * @return Returns the current event's ordinal number.
+     */
+    public int getEventNumber();
+    
     /**
      * <b>getClusters</b><br/><br/>
      * <code>public ArrayList<Cluster> <b>getClusters</b>()</code><br/><br/>
@@ -38,17 +38,17 @@
      * @return Returns the current clusters as an <code>ArrayList
      * </code> object.
      **/
-	public List<Cluster> getClusters();
-	
-	/**
+    public List<Cluster> getClusters();
+    
+    /**
      * <b>getHits</b><br/><br/>
      * <code>public ArrayList<EcalHit> <b>getHits</b>()</code><br/><br/>
      * Allows access to the current event's list of hits.
      * @return Returns the current hits as an <code>ArrayList</code> object.
      **/
-	public List<EcalHit> getHits();
-	
-	/**
+    public List<EcalHit> getHits();
+    
+    /**
      * <b>nextEvent</b><br/><br/>
      * <code>public boolean <b>nextEvent</b>()</code><br/><br/>
      * Populates the event manager with hits and clusters from the next event.
@@ -56,8 +56,8 @@
      * </code> if it was not.
      * @throws IOException Occurs if there was a file read error.
      **/
-	public boolean nextEvent() throws IOException;
-	
+    public boolean nextEvent() throws IOException;
+    
     /**
      * <b>previousEvent</b><br/><br/>
      * <code>public boolean <b>previousEvent</b>()</code><br/><br/>
@@ -66,5 +66,5 @@
      * </code> if it was not.
      * @throws IOException Occurs if there was a file read error.
      **/
-	public boolean previousEvent() throws IOException;
+    public boolean previousEvent() throws IOException;
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/TextManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/TextManager.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/io/TextManager.java	Wed Apr 27 11:11:32 2016
@@ -53,7 +53,7 @@
     
     /**
      * Initializes an event manager that will read from the indicated file.
-     * @param filename - The path to the file containing hit information.
+     * @param file - The path to the file containing hit information.
      */
     public TextManager(File file) throws IOException {
         reader = new AdvancedReader(file);

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/EventDisplayOutputDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/EventDisplayOutputDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/EventDisplayOutputDriver.java	Wed Apr 27 11:11:32 2016
@@ -97,30 +97,30 @@
                 
                 // Only write clusters if the option is selected.
                 if(outputClusters) {
-	                // Process the clusters.
-	                for (org.lcsim.event.Cluster cluster : clusters) {
-	                    // Get the seed hit for the cluster.
-	                    CalorimeterHit seedHit = (CalorimeterHit)cluster.getCalorimeterHits().get(0);
-	                    int ix = seedHit.getIdentifierFieldValue("ix");
-	                    int iy = seedHit.getIdentifierFieldValue("iy");
-	                    double time = seedHit.getTime();
-	                    
-	                    // Get the cluster's total energy.
-	                    double energy = cluster.getEnergy();
-	                    
-	                    // Write the seed hit to start a cluster.
-	                    writer.append(String.format("Cluster\t%d\t%d\t%f\t%f%n", ix, iy, energy, time));
-	                    
-	                    // Write the component hits to the cluster.
-	                    for (CalorimeterHit hit : cluster.getCalorimeterHits()) {
-	                        // Get each component hit's x/y coordinates.
-	                        ix = hit.getIdentifierFieldValue("ix");
-	                        iy = hit.getIdentifierFieldValue("iy");
-	                        
-	                        // Write them as component hits.
-	                        writer.append(String.format("CompHit\t%d\t%d%n", ix, iy));
-	                    }
-	                }
+                    // Process the clusters.
+                    for (org.lcsim.event.Cluster cluster : clusters) {
+                        // Get the seed hit for the cluster.
+                        CalorimeterHit seedHit = (CalorimeterHit)cluster.getCalorimeterHits().get(0);
+                        int ix = seedHit.getIdentifierFieldValue("ix");
+                        int iy = seedHit.getIdentifierFieldValue("iy");
+                        double time = seedHit.getTime();
+                        
+                        // Get the cluster's total energy.
+                        double energy = cluster.getEnergy();
+                        
+                        // Write the seed hit to start a cluster.
+                        writer.append(String.format("Cluster\t%d\t%d\t%f\t%f%n", ix, iy, energy, time));
+                        
+                        // Write the component hits to the cluster.
+                        for (CalorimeterHit hit : cluster.getCalorimeterHits()) {
+                            // Get each component hit's x/y coordinates.
+                            ix = hit.getIdentifierFieldValue("ix");
+                            iy = hit.getIdentifierFieldValue("iy");
+                            
+                            // Write them as component hits.
+                            writer.append(String.format("CompHit\t%d\t%d%n", ix, iy));
+                        }
+                    }
                 }
                 
                 // Append the end of event indicator.
@@ -169,7 +169,7 @@
      * indicates that they will be output.
      */
     public void setIgnoreEmptyEvents(boolean ignoreEmptyEvents) {
-    	this.ignoreEmptyEvents = ignoreEmptyEvents;
+        this.ignoreEmptyEvents = ignoreEmptyEvents;
     }
     
     /**
@@ -179,7 +179,7 @@
      * indicates that they will be output.
      */
     public void setIgnoreNoClusterEvents(boolean ignoreNoClusterEvents) {
-    	this.ignoreNoClusterEvents = ignoreNoClusterEvents;
+        this.ignoreNoClusterEvents = ignoreNoClusterEvents;
     }
     
     /**
@@ -196,6 +196,6 @@
      * will be written and <code>false</code> that they will not.
      */
     public void setOutputClusters(boolean outputClusters) {
-    	this.outputClusters = outputClusters;
+        this.outputClusters = outputClusters;
     }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/LCIOBridgeDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/LCIOBridgeDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/lcsim/LCIOBridgeDriver.java	Wed Apr 27 11:11:32 2016
@@ -39,9 +39,9 @@
      * @param event - The LCIO event.
      */
     public void process(EventHeader event) {
-    	// If we are still updating the display, skip this event.
-    	if(updating) { return; }
-    	
+        // If we are still updating the display, skip this event.
+        if(updating) { return; }
+        
         // Make sure that this event has calorimeter hits.
         if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
             // Get the list of calorimeter hits from the event.
@@ -55,44 +55,44 @@
             
             // If this is the correct place to update, do so.
             if(eventsProcessed >= displayInterval) {
-            	// Lock the update method for the duration of the update.
-            	updating = true;
-            	
-            	// Clear the event display.
-            	eventDisplay.resetDisplay();
-            	
-            	// Add all of the hits.
-            	for(CalorimeterHit hit : hits) {
-            		// Get the hit's location and energy.
-            		int ix = hit.getIdentifierFieldValue("ix");
-            		int iy = hit.getIdentifierFieldValue("iy");
-            		double energy = hit.getRawEnergy();
-            		
-            		// Add the hit energy to the event display.
-            		eventDisplay.addHit(new EcalHit(ix, iy, energy));
-            	}
-            	
-            	// Add all the clusters.
-            	for(org.lcsim.event.Cluster cluster : clusters) {
-            		// Get the seed hit.
-            		CalorimeterHit seed = cluster.getCalorimeterHits().get(0);
-            		int ix = seed.getIdentifierFieldValue("ix");
-            		int iy = seed.getIdentifierFieldValue("iy");
-            		double energy = seed.getRawEnergy(); // FIXME: Should this be getCorrectedEnergy() instead? --JM
-            		
-            		// Add the cluster center to the event display.
-            		Cluster cc = new Cluster(ix, iy, energy);
-            		eventDisplay.addCluster(cc);
-            	}
-            	
-            	// Update the display.
-            	eventDisplay.updateDisplay();
-            	
-            	// Reset the number of events we've seen since the last update.
-            	eventsProcessed = 0;
-            	
-            	// Unlock the update method so that more events can be processed.
-            	updating = false;
+                // Lock the update method for the duration of the update.
+                updating = true;
+                
+                // Clear the event display.
+                eventDisplay.resetDisplay();
+                
+                // Add all of the hits.
+                for(CalorimeterHit hit : hits) {
+                    // Get the hit's location and energy.
+                    int ix = hit.getIdentifierFieldValue("ix");
+                    int iy = hit.getIdentifierFieldValue("iy");
+                    double energy = hit.getRawEnergy();
+                    
+                    // Add the hit energy to the event display.
+                    eventDisplay.addHit(new EcalHit(ix, iy, energy));
+                }
+                
+                // Add all the clusters.
+                for(org.lcsim.event.Cluster cluster : clusters) {
+                    // Get the seed hit.
+                    CalorimeterHit seed = cluster.getCalorimeterHits().get(0);
+                    int ix = seed.getIdentifierFieldValue("ix");
+                    int iy = seed.getIdentifierFieldValue("iy");
+                    double energy = seed.getRawEnergy(); // FIXME: Should this be getCorrectedEnergy() instead? --JM
+                    
+                    // Add the cluster center to the event display.
+                    Cluster cc = new Cluster(ix, iy, energy);
+                    eventDisplay.addCluster(cc);
+                }
+                
+                // Update the display.
+                eventDisplay.updateDisplay();
+                
+                // Reset the number of events we've seen since the last update.
+                eventsProcessed = 0;
+                
+                // Unlock the update method so that more events can be processed.
+                updating = false;
             }
         }
     }
@@ -119,14 +119,14 @@
      * a new event is displayed.
      */
     public void setDisplayInterval(String displayInterval) {
-    	// Convert the argument to an integer.
-    	int disp = Integer.parseInt(displayInterval);
-    	
-    	// If it is negative, make it zero.
-    	if(disp < 0) { disp = 0; }
-    	
-    	// Set the display interval.
-    	this.displayInterval = disp;
+        // Convert the argument to an integer.
+        int disp = Integer.parseInt(displayInterval);
+        
+        // If it is negative, make it zero.
+        if(disp < 0) { disp = 0; }
+        
+        // Set the display interval.
+        this.displayInterval = disp;
     }
     
     /**

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/ActiveViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/ActiveViewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/ActiveViewer.java	Wed Apr 27 11:11:32 2016
@@ -34,8 +34,6 @@
      * events from the indicated data source with additional status
      * fields defined by the <code>fieldNames</code> argument.
      * @param em - The data source event manager.
-     * @param fieldNames - An array of additional status fields
-     * that should be displayed.
      */
     public ActiveViewer(EventManager em) {
         // Pass any additional field values to the super class.

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/CalorimeterPanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/CalorimeterPanel.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/CalorimeterPanel.java	Wed Apr 27 11:11:32 2016
@@ -503,8 +503,8 @@
     /**
      * Determines if the crystal at the given coordinates is a active
      * or not.
-     * @param xCoor - The x-index of the crystal.
-     * @param yCoor - The y-index of the crystal.
+     * @param ix - The x-index of the crystal.
+     * @param iy - The y-index of the crystal.
      * @return Returns <code>true</code> if the crystal is active
      * and <code>false</code> if it is not.
      * @throws IndexOutOfBoundsException Occurs when either of the given
@@ -740,28 +740,28 @@
     
     /**
      * Sets whether to mirror the x-axis on the calorimeter display.
-     * @param state - <code>true</code> indicates that the axis should
+     * @param mirrorX - <code>true</code> indicates that the axis should
      * be mirrored and <code>false</code> that it should not.
      */
     public void setMirrorX(boolean mirrorX) {
-            // Process the change.
-            setMirror(mirrorX, mirrorY);
-            
-            // Throw an event.
-            throwSettingsEvent(SettingsEvent.PROPERTY_X_ORIENTATION);
+        // Process the change.
+        setMirror(mirrorX, mirrorY);
+        
+        // Throw an event.
+        throwSettingsEvent(SettingsEvent.PROPERTY_X_ORIENTATION);
     }
     
     /**
      * Sets whether to mirror the y-axis on the calorimeter display.
-     * @param state - <code>true</code> indicates that the axis should
+     * @param mirrorY - <code>true</code> indicates that the axis should
      * be mirrored and <code>false</code> that it should not.
      */
     public void setMirrorY(boolean mirrorY) {
-            // Process the change.
-            setMirror(mirrorX, mirrorY);
-            
-            // Throw an event.
-            throwSettingsEvent(SettingsEvent.PROPERTY_Y_ORIENTATION);
+        // Process the change.
+        setMirror(mirrorX, mirrorY);
+            
+        // Throw an event.
+        throwSettingsEvent(SettingsEvent.PROPERTY_Y_ORIENTATION);
     }
     
     /**

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/DataFileViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/DataFileViewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/DataFileViewer.java	Wed Apr 27 11:11:32 2016
@@ -97,9 +97,9 @@
         filterPanel.addActionListener(new ActionListener() {
             @Override
             public void actionPerformed(ActionEvent e) {
-            	// Suppress panel redrawing until the highlights are set.
-            	ecalPanel.setSuppressRedraw(true);
-            	
+                // Suppress panel redrawing until the highlights are set.
+                ecalPanel.setSuppressRedraw(true);
+                
                 // Clear the panel highlighting.
                 ecalPanel.clearHighlight();
                 

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/FileViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/FileViewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/FileViewer.java	Wed Apr 27 11:11:32 2016
@@ -178,9 +178,9 @@
             // be displayed.
             Double hitTime = crystalTimeMap.get(crystal);
             if(hitTime != null) {
-            	setStatusField(fieldNames[HIT_TIME], Double.toString(hitTime));
+                setStatusField(fieldNames[HIT_TIME], Double.toString(hitTime));
             } else {
-            	setStatusField(fieldNames[HIT_TIME], ResizableFieldPanel.NULL_VALUE);
+                setStatusField(fieldNames[HIT_TIME], ResizableFieldPanel.NULL_VALUE);
             }
         }
         // Otherwise, clear the field values.
@@ -257,7 +257,7 @@
         // Load hit time map.
         crystalTimeMap.clear();
         for(EcalHit hit : em.getHits()) {
-        	crystalTimeMap.put(new Point(toPanelX(hit.getX()), toPanelY(hit.getY())), hit.getTime());
+            crystalTimeMap.put(new Point(toPanelX(hit.getX()), toPanelY(hit.getY())), hit.getTime());
         }
         
         // Display it.

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PDataEventViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PDataEventViewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PDataEventViewer.java	Wed Apr 27 11:11:32 2016
@@ -57,7 +57,6 @@
      * Initializes a new <code>DataFileViewer</code> that reads from
      * the given event manager for event data and the given hardware
      * data file for crystal hardware data readout.
-     * @param dataSource - The manager for event data.
      * @param crystalDataFilePath - The data file for crystal hardware
      * information.
      * @throws IOException Occurs if there is an error reading from
@@ -98,9 +97,9 @@
         filterPanel.addActionListener(new ActionListener() {
             @Override
             public void actionPerformed(ActionEvent e) {
-            	// Suppress panel redrawing until the highlights are set.
-            	ecalPanel.setSuppressRedraw(true);
-            	
+                // Suppress panel redrawing until the highlights are set.
+                ecalPanel.setSuppressRedraw(true);
+                
                 // Clear the panel highlighting.
                 ecalPanel.clearHighlight();
                 

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PassiveViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PassiveViewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/PassiveViewer.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
     
     /**
      * Adds a new hit to the display.
-     * @param hit - The hit to be added.
+     * @param lcioHit - The hit to be added.
      */
     public abstract void addHit(CalorimeterHit lcioHit);
     

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/Viewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/Viewer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/ui/Viewer.java	Wed Apr 27 11:11:32 2016
@@ -122,8 +122,6 @@
     
     /**
      * Initializes the viewer window and calorimeter panel.
-     * @param statusFields - Additional fields to display in the status
-     * panel. This can not be <code>null</code>.
      * @throws NullPointerException Occurs if any of the additional field
      * arguments are <code>null</code>.
      **/
@@ -638,7 +636,7 @@
         
         JFileChooser chooser = new JFileChooser();
         if(chooser.showSaveDialog(this) == JFileChooser.CANCEL_OPTION) {
-        	return;
+            return;
         }
         
         // Parse the file name and make sure that it ends in .PNG.
@@ -646,9 +644,9 @@
         int index = filepath.lastIndexOf('.');
         if(index == -1) { filepath = filepath + ".png"; }
         else {
-        	if(filepath.substring(index + 1).compareTo("png") != 0) {
-        		filepath = filepath.substring(0, index) + ".png";
-        	}
+            if(filepath.substring(index + 1).compareTo("png") != 0) {
+                filepath = filepath.substring(0, index) + ".png";
+            }
         }
         
         // Get the lowest available file name.

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/BooleanMap.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/BooleanMap.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/BooleanMap.java	Wed Apr 27 11:11:32 2016
@@ -10,208 +10,208 @@
  * @author Kyle McCarty
  */
 public final class BooleanMap implements ColorMap<Double> {
-	// The color to display for values which pass the boolean check.
-	private Color activeColor = new Color(255, 50, 50);
-	// The color to display for values that fail the boolean check.
-	private Color inactiveColor = Color.WHITE;
-	// The critical value against which the boolean check is performed.
-	private double value = 0.0;
-	// The type of this boolean scale.
-	private final BooleanType boolType;
-	
-	/**
-	 * <b>BooleanMap</b><br/><br/>
-	 * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue)</code><br/><br/>
-	 * Defines a <code>ColorScale</code> which maps values to colors
-	 * based on a boolean comparison.
-	 * @param type - The type of boolean comparison to perform.
-	 * @param comparisonValue - The value against which the comparison
-	 * should be made.
-	 */
-	public BooleanMap(BooleanType type, double comparisonValue) {
-		// Make sure the comparison type is not null.
-		if(type == null) { throw new IllegalArgumentException("Boolean comparison type can not be null."); }
-		
-		// Define the critical value and the boolean type.
-		value = comparisonValue;
-		boolType = type;
-	}
-	
-	/**
-	 * <b>BooleanMap</b><br/><br/>
-	 * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue,
-	 * 			Color activeColor)</code><br/><br/>
-	 * Defines a <code>ColorScale</code> which maps values to colors
-	 * based on a boolean comparison.
-	 * @param type - The type of boolean comparison to perform.
-	 * @param comparisonValue - The value against which the comparison
-	 * should be made.
-	 * @param activeColor - The color in which values that pass the
-	 * comparison should be displayed.
-	 */
-	public BooleanMap(BooleanType type, double comparisonValue, Color activeColor) {
-		// Set the critical value and the boolean type.
-		this(type, comparisonValue);
-		
-		// Set the active color.
-		this.activeColor = activeColor;
-	}
-	
-	/**
-	 * <b>BooleanMap</b><br/><br/>
-	 * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue,
-	 * 			Color activeColor, Color inactiveColor)</code><br/><br/>
-	 * Defines a <code>ColorScale</code> which maps values to colors
-	 * based on a boolean comparison.
-	 * @param type - The type of boolean comparison to perform.
-	 * @param comparisonValue - The value against which the comparison
-	 * should be made.
-	 * @param activeColor - The color in which values that pass the
-	 * comparison should be displayed.
-	 * @param inactiveColor - The color in which values that fail the
-	 * comparison should be displayed.
-	 */
-	public BooleanMap(BooleanType type, double comparisonValue, Color activeColor, Color inactiveColor) {
-		// Set the critical value and the boolean type.
-		this(type, comparisonValue);
-		
-		// Set the active and inactive colors.
-		this.activeColor = activeColor;
-		this.inactiveColor = inactiveColor;
-	}
-	
-	public Color getColor(Double value) {
-		// If the argument is null, treat it is zero.
-		if(value == null) { value = 0.0; }
-		
-		// If it passes the boolean comparison, return the active color.
-		if(passes(value)) { return activeColor; }
-		
-		// Otherwise, return the inactive color.
-		else { return inactiveColor; }
-	}
-	
-	/**
-	 * <b>getActiveColor</b><br/><br/>
-	 * <code>public Color <b>getActiveColor</b>()</code><br/><br/>
-	 * Gets the color used by the scale for values which pass the
-	 * boolean comparison.
-	 * @return Returns the color as a <code>Color</code> object.
-	 */
-	public Color getActiveColor() { return activeColor; }
-	
-	/**
-	 * <b>getBooleanType</b><br/><br/>
-	 * <code>public BooleanType <b>getBooleanType</b>()</code><br/><br/>
-	 * Indicates what type of boolean comparison is performed by this
-	 * scale.
-	 * @return Returns the type of comparison as a <code>BooleanType
-	 * </code> enumerable.
-	 */
-	public BooleanType getBooleanType() { return boolType; }
-	
-	/**
-	 * <b>getComparisonValue</b><br/><br/>
-	 * <code>public double <b>getComparisonValue</b>()</code><br/><br/>
-	 * Gets the value against which the boolean comparisons are
-	 * performed.
-	 * @return Returns the value which is compared against.
-	 */
-	public double getComparisonValue() { return value; }
-	
-	/**
-	 * <b>getInactiveColor</b><br/><br/>
-	 * <code>public Color <b>getInactiveColor</b>()</code><br/><br/>
-	 * Gets the color used by the scale for values which fail the
-	 * boolean comparison.
-	 * @return Returns the color as a <code>Color</code> object.
-	 */
-	public Color getInactiveColor() { return inactiveColor; }
-	
-	/**
-	 * <b>setComparisonValue</b><br/><br/>
-	 * <code>public void <b>setComparisonValue</b>(double value)</code><br/><br/>
-	 * Sets the value against which the boolean comparison is performed.
-	 * @param value - The value to compare against.
-	 */
-	public void setComparisonValue(double value) { this.value = value; }
-	
-	/**
-	 * <b>passes</b><br/><br/>
-	 * <code>private boolean <b>passes</b>(double d)</code><br/><br/>
-	 * Determines whether a given external value passes the boolean
-	 * check or not.
-	 * @param d - The external value to compare.
-	 * @return Returns <code>true</code> if the value passes the boolean
-	 * check and <code>false</code> if it does not.
-	 */
-	private boolean passes(double d) {
-		// Perform the appropriate comparison. Note that the default
-		// case is included to satisfy the compiler -- it should not
-		// ever actually be used.
-		switch(boolType) {
-			case EQUAL_TO:
-				return d == value;
-			case NOT_EQUAL_TO:
-				return d != value;
-			case GREATER_THAN:
-				return d > value;
-			case LESS_THAN:
-				return d < value;
-			case GREATER_THAN_OR_EQUAL_TO:
-				return d >= value;
-			case LESS_THAN_OR_EQUAL_TO:
-				return d<= value;
-			default:
-				return false;
-		}
-	}
-	
-	/**
-	 * Enumerable <code>BooleanType</code> defines the type of boolean
-	 * comparison that is to be performed by the scale.
-	 */
-	public enum BooleanType {
-		/**
-		 * <b>EQUAL_TO</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] == [Comparison Value]</code>
-		 */
-		EQUAL_TO,
-		
-		/**
-		 * <b>NOT_EQUAL_TO</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] != [Comparison Value]</code>
-		 */
-		NOT_EQUAL_TO,
-		
-		/**
-		 * <b>GREATER_THAN</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] > [Comparison Value]</code>
-		 */
-		GREATER_THAN,
-		
-		/**
-		 * <b>LESS_THAN</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] < [Comparison Value]</code>
-		 */
-		LESS_THAN,
-		
-		/**
-		 * <b>GREATER_THAN_OR_EQUAL_TO</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] >= [Comparison Value]</code>
-		 */
-		GREATER_THAN_OR_EQUAL_TO,
-		
-		/**
-		 * <b>LESS_THAN_OR_EQUAL_TO</b><br/><br/>
-		 * Performs the boolean check:<br/><br/>
-		 * <code>[External Value] <= [Comparison Value]</code>
-		 */
-		LESS_THAN_OR_EQUAL_TO
-	};
+    // The color to display for values which pass the boolean check.
+    private Color activeColor = new Color(255, 50, 50);
+    // The color to display for values that fail the boolean check.
+    private Color inactiveColor = Color.WHITE;
+    // The critical value against which the boolean check is performed.
+    private double value = 0.0;
+    // The type of this boolean scale.
+    private final BooleanType boolType;
+    
+    /**
+     * <b>BooleanMap</b><br/><br/>
+     * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue)</code><br/><br/>
+     * Defines a <code>ColorScale</code> which maps values to colors
+     * based on a boolean comparison.
+     * @param type - The type of boolean comparison to perform.
+     * @param comparisonValue - The value against which the comparison
+     * should be made.
+     */
+    public BooleanMap(BooleanType type, double comparisonValue) {
+        // Make sure the comparison type is not null.
+        if(type == null) { throw new IllegalArgumentException("Boolean comparison type can not be null."); }
+        
+        // Define the critical value and the boolean type.
+        value = comparisonValue;
+        boolType = type;
+    }
+    
+    /**
+     * <b>BooleanMap</b><br/><br/>
+     * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue,
+     *          Color activeColor)</code><br/><br/>
+     * Defines a <code>ColorScale</code> which maps values to colors
+     * based on a boolean comparison.
+     * @param type - The type of boolean comparison to perform.
+     * @param comparisonValue - The value against which the comparison
+     * should be made.
+     * @param activeColor - The color in which values that pass the
+     * comparison should be displayed.
+     */
+    public BooleanMap(BooleanType type, double comparisonValue, Color activeColor) {
+        // Set the critical value and the boolean type.
+        this(type, comparisonValue);
+        
+        // Set the active color.
+        this.activeColor = activeColor;
+    }
+    
+    /**
+     * <b>BooleanMap</b><br/><br/>
+     * <code>public <b>BooleanMap</b>(BooleanType type, double comparisonValue,
+     *          Color activeColor, Color inactiveColor)</code><br/><br/>
+     * Defines a <code>ColorScale</code> which maps values to colors
+     * based on a boolean comparison.
+     * @param type - The type of boolean comparison to perform.
+     * @param comparisonValue - The value against which the comparison
+     * should be made.
+     * @param activeColor - The color in which values that pass the
+     * comparison should be displayed.
+     * @param inactiveColor - The color in which values that fail the
+     * comparison should be displayed.
+     */
+    public BooleanMap(BooleanType type, double comparisonValue, Color activeColor, Color inactiveColor) {
+        // Set the critical value and the boolean type.
+        this(type, comparisonValue);
+        
+        // Set the active and inactive colors.
+        this.activeColor = activeColor;
+        this.inactiveColor = inactiveColor;
+    }
+    
+    public Color getColor(Double value) {
+        // If the argument is null, treat it is zero.
+        if(value == null) { value = 0.0; }
+        
+        // If it passes the boolean comparison, return the active color.
+        if(passes(value)) { return activeColor; }
+        
+        // Otherwise, return the inactive color.
+        else { return inactiveColor; }
+    }
+    
+    /**
+     * <b>getActiveColor</b><br/><br/>
+     * <code>public Color <b>getActiveColor</b>()</code><br/><br/>
+     * Gets the color used by the scale for values which pass the
+     * boolean comparison.
+     * @return Returns the color as a <code>Color</code> object.
+     */
+    public Color getActiveColor() { return activeColor; }
+    
+    /**
+     * <b>getBooleanType</b><br/><br/>
+     * <code>public BooleanType <b>getBooleanType</b>()</code><br/><br/>
+     * Indicates what type of boolean comparison is performed by this
+     * scale.
+     * @return Returns the type of comparison as a <code>BooleanType
+     * </code> enumerable.
+     */
+    public BooleanType getBooleanType() { return boolType; }
+    
+    /**
+     * <b>getComparisonValue</b><br/><br/>
+     * <code>public double <b>getComparisonValue</b>()</code><br/><br/>
+     * Gets the value against which the boolean comparisons are
+     * performed.
+     * @return Returns the value which is compared against.
+     */
+    public double getComparisonValue() { return value; }
+    
+    /**
+     * <b>getInactiveColor</b><br/><br/>
+     * <code>public Color <b>getInactiveColor</b>()</code><br/><br/>
+     * Gets the color used by the scale for values which fail the
+     * boolean comparison.
+     * @return Returns the color as a <code>Color</code> object.
+     */
+    public Color getInactiveColor() { return inactiveColor; }
+    
+    /**
+     * <b>setComparisonValue</b><br/><br/>
+     * <code>public void <b>setComparisonValue</b>(double value)</code><br/><br/>
+     * Sets the value against which the boolean comparison is performed.
+     * @param value - The value to compare against.
+     */
+    public void setComparisonValue(double value) { this.value = value; }
+    
+    /**
+     * <b>passes</b><br/><br/>
+     * <code>private boolean <b>passes</b>(double d)</code><br/><br/>
+     * Determines whether a given external value passes the boolean
+     * check or not.
+     * @param d - The external value to compare.
+     * @return Returns <code>true</code> if the value passes the boolean
+     * check and <code>false</code> if it does not.
+     */
+    private boolean passes(double d) {
+        // Perform the appropriate comparison. Note that the default
+        // case is included to satisfy the compiler -- it should not
+        // ever actually be used.
+        switch(boolType) {
+            case EQUAL_TO:
+                return d == value;
+            case NOT_EQUAL_TO:
+                return d != value;
+            case GREATER_THAN:
+                return d > value;
+            case LESS_THAN:
+                return d < value;
+            case GREATER_THAN_OR_EQUAL_TO:
+                return d >= value;
+            case LESS_THAN_OR_EQUAL_TO:
+                return d<= value;
+            default:
+                return false;
+        }
+    }
+    
+    /**
+     * Enumerable <code>BooleanType</code> defines the type of boolean
+     * comparison that is to be performed by the scale.
+     */
+    public enum BooleanType {
+        /**
+         * <b>EQUAL_TO</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] == [Comparison Value]</code>
+         */
+        EQUAL_TO,
+        
+        /**
+         * <b>NOT_EQUAL_TO</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] != [Comparison Value]</code>
+         */
+        NOT_EQUAL_TO,
+        
+        /**
+         * <b>GREATER_THAN</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] > [Comparison Value]</code>
+         */
+        GREATER_THAN,
+        
+        /**
+         * <b>LESS_THAN</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] < [Comparison Value]</code>
+         */
+        LESS_THAN,
+        
+        /**
+         * <b>GREATER_THAN_OR_EQUAL_TO</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] >= [Comparison Value]</code>
+         */
+        GREATER_THAN_OR_EQUAL_TO,
+        
+        /**
+         * <b>LESS_THAN_OR_EQUAL_TO</b><br/><br/>
+         * Performs the boolean check:<br/><br/>
+         * <code>[External Value] <= [Comparison Value]</code>
+         */
+        LESS_THAN_OR_EQUAL_TO
+    };
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/ColorScale.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/ColorScale.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/ColorScale.java	Wed Apr 27 11:11:32 2016
@@ -47,8 +47,8 @@
      * value, if scaling is logarithmic.
      */
     public double getScaledMaximum() {
-    	if(linear) { return max; }
-    	else { return lMax; }
+        if(linear) { return max; }
+        else { return lMax; }
     }
     
     /**
@@ -61,8 +61,8 @@
      * value, if scaling is logarithmic.
      */
     public double getScaledMinimum() {
-    	if(linear) { return min; }
-    	else { return lMin; }
+        if(linear) { return min; }
+        else { return lMin; }
     }
     
     /**

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalEvent.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalEvent.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalEvent.java	Wed Apr 27 11:11:32 2016
@@ -14,41 +14,41 @@
  * @author Kyle McCarty
  */
 public class CrystalEvent extends AWTEvent {
-	private static final long serialVersionUID = 77198267255387212L;
-	// Stores the location of the triggering crystal.
-	private final Point crystal;
-	// The AWTEvent id for this event.
-	private static final int AWT_ID = AWTEvent.RESERVED_ID_MAX + 10;
-	
-	/**
-	 * <b>CrystalEvent</b><br/><br/>
-	 * <code>public <b>CrystalEvent</b>(Viewer parent, Point triggerCrystal)</code><br/><br/>
-	 * Creates a crystal event for the indicated crystal and triggering
-	 * component.
-	 * @param source - The triggering component.
-	 * @param triggerCrystal - The crystal associated with the event.
-	 * @throws IllegalArgumentException Occurs if the associated crystal
-	 * is <code>null</code>.
-	 */
-	public CrystalEvent(Viewer source, Point triggerCrystal) throws IllegalArgumentException {
-		// Run the superclass constructor.
-		super(source, AWT_ID);
-		
-		// Make sure that the trigger crystal is not null.
-		if(triggerCrystal == null) {
-			throw new IllegalArgumentException("Crystal events can not occur with respect to non-exstant crystals.");
-		}
-		
-		// Define the event parameters.
-		crystal = triggerCrystal;
-	}
-	
-	/**
-	 * <b>getCrystalID</b><br/><br/>
-	 * <code>public Point <b>getCrystalID</b>()</code><br/><br/>
-	 * Indicates the panel indices at which the crystal is located.
-	 * @return Returns the crystal's panel indices as a <code>Point
-	 * </code> object.
-	 */
-	public Point getCrystalID() { return crystal; }
+    private static final long serialVersionUID = 77198267255387212L;
+    // Stores the location of the triggering crystal.
+    private final Point crystal;
+    // The AWTEvent id for this event.
+    private static final int AWT_ID = AWTEvent.RESERVED_ID_MAX + 10;
+    
+    /**
+     * <b>CrystalEvent</b><br/><br/>
+     * <code>public <b>CrystalEvent</b>(Viewer parent, Point triggerCrystal)</code><br/><br/>
+     * Creates a crystal event for the indicated crystal and triggering
+     * component.
+     * @param source - The triggering component.
+     * @param triggerCrystal - The crystal associated with the event.
+     * @throws IllegalArgumentException Occurs if the associated crystal
+     * is <code>null</code>.
+     */
+    public CrystalEvent(Viewer source, Point triggerCrystal) throws IllegalArgumentException {
+        // Run the superclass constructor.
+        super(source, AWT_ID);
+        
+        // Make sure that the trigger crystal is not null.
+        if(triggerCrystal == null) {
+            throw new IllegalArgumentException("Crystal events can not occur with respect to non-exstant crystals.");
+        }
+        
+        // Define the event parameters.
+        crystal = triggerCrystal;
+    }
+    
+    /**
+     * <b>getCrystalID</b><br/><br/>
+     * <code>public Point <b>getCrystalID</b>()</code><br/><br/>
+     * Indicates the panel indices at which the crystal is located.
+     * @return Returns the crystal's panel indices as a <code>Point
+     * </code> object.
+     */
+    public Point getCrystalID() { return crystal; }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalListener.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalListener.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/CrystalListener.java	Wed Apr 27 11:11:32 2016
@@ -11,27 +11,27 @@
  * @author Kyle McCarty
  */
 public interface CrystalListener extends EventListener {
-	/**
-	 * <b>crystalActivated</b><br/><br/>
-	 * <code>public void <b>crystalActivated</b>(CrystalEvent e)</code><br/><br/>
-	 * Invoked when a crystal becomes highlighted.
-	 * @param e - An object describing the event.
-	 */
-	public void crystalActivated(CrystalEvent e);
-	
-	/**
-	 * <b>crystalDeactivated</b><br/><br/>
-	 * <code>public void <b>crystalDeactivated</b>(CrystalEvent e)</code><br/><br/>
-	 * Invoked when a crystal ceases to be highlighted.
-	 * @param e - An object describing the event.
-	 */
-	public void crystalDeactivated(CrystalEvent e);
-	
-	/**
-	 * <b>crystalClicked</b><br/><br/>
-	 * <code>public void <b>crystalClicked</b>(CrystalEvent e)</code><br/><br/>
-	 * Invoked when a crystal is clicked
-	 * @param e - An object describing the event.
-	 */
-	public void crystalClicked(CrystalEvent e);
+    /**
+     * <b>crystalActivated</b><br/><br/>
+     * <code>public void <b>crystalActivated</b>(CrystalEvent e)</code><br/><br/>
+     * Invoked when a crystal becomes highlighted.
+     * @param e - An object describing the event.
+     */
+    public void crystalActivated(CrystalEvent e);
+    
+    /**
+     * <b>crystalDeactivated</b><br/><br/>
+     * <code>public void <b>crystalDeactivated</b>(CrystalEvent e)</code><br/><br/>
+     * Invoked when a crystal ceases to be highlighted.
+     * @param e - An object describing the event.
+     */
+    public void crystalDeactivated(CrystalEvent e);
+    
+    /**
+     * <b>crystalClicked</b><br/><br/>
+     * <code>public void <b>crystalClicked</b>(CrystalEvent e)</code><br/><br/>
+     * Invoked when a crystal is clicked
+     * @param e - An object describing the event.
+     */
+    public void crystalClicked(CrystalEvent e);
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/DatabaseCheck.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/DatabaseCheck.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/DatabaseCheck.java	Wed Apr 27 11:11:32 2016
@@ -17,122 +17,122 @@
 import org.lcsim.conditions.ConditionsManager.ConditionsNotFoundException;
 
 public class DatabaseCheck {
-	private static final Set<Integer> idFailSet = new HashSet<Integer>();
-	private static final Set<Point> pointFailSet = new HashSet<Point>();
-	
-	public static void main(String[] args) throws ConditionsNotFoundException, IOException {
-		// Check that an appropriate file has been given.
-		String filepath = null;
-		if(args.length == 1) {
-			filepath = args[0];
-		}
-		
-		// If no file path was defined, throw an error.
-		if(filepath == null) {
-			throw new FileNotFoundException("No CSV mapping file defined.");
-		}
-		
-		// Initialize the local database.
-		EcalWiringManager manager = new EcalWiringManager(filepath);
-		
-		// Initialize the database.
-		int runNumber = 2000;
-		String detectorName = "HPS-Proposal2014-v7-2pt2";
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.setDetector(detectorName, runNumber);
-		
-		// Get ECAL conditions.
-		EcalConditions ecalConditions = DatabaseConditionsManager.getInstance().getEcalConditions(); 
-		
-		// Get the list of EcalChannel objects.
-		EcalChannelCollection channels = ecalConditions.getChannelCollection();
-		EcalLedCollection leds = conditionsManager.getCachedConditions(EcalLedCollection.class, "ecal_leds").getCachedData();
-		
-		// Map the LED objects to their channels.
-		Map<Integer, EcalLed> ledMap = new HashMap<Integer, EcalLed>();
+    private static final Set<Integer> idFailSet = new HashSet<Integer>();
+    private static final Set<Point> pointFailSet = new HashSet<Point>();
+    
+    public static void main(String[] args) throws ConditionsNotFoundException, IOException {
+        // Check that an appropriate file has been given.
+        String filepath = null;
+        if(args.length == 1) {
+            filepath = args[0];
+        }
+        
+        // If no file path was defined, throw an error.
+        if(filepath == null) {
+            throw new FileNotFoundException("No CSV mapping file defined.");
+        }
+        
+        // Initialize the local database.
+        EcalWiringManager manager = new EcalWiringManager(filepath);
+        
+        // Initialize the database.
+        int runNumber = 2000;
+        String detectorName = "HPS-Proposal2014-v7-2pt2";
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.setDetector(detectorName, runNumber);
+        
+        // Get ECAL conditions.
+        EcalConditions ecalConditions = DatabaseConditionsManager.getInstance().getEcalConditions(); 
+        
+        // Get the list of EcalChannel objects.
+        EcalChannelCollection channels = ecalConditions.getChannelCollection();
+        EcalLedCollection leds = conditionsManager.getCachedConditions(EcalLedCollection.class, "ecal_leds").getCachedData();
+        
+        // Map the LED objects to their channels.
+        Map<Integer, EcalLed> ledMap = new HashMap<Integer, EcalLed>();
         for (EcalLed led : leds) {
-        	ledMap.put(led.getEcalChannelId(), led);
+            ledMap.put(led.getEcalChannelId(), led);
         }
-		
-		// Perform the comparison test.
-		for(EcalChannel channel : channels) {
-			// Get the crystal point information.
-			Point crystal = new Point(channel.getX(), channel.getY());
-			
-			// Get the data from manager.
-			CrystalDataSet data = manager.getCrystalData(crystal);
-			
-			// Get the appropriate LED collection.
-			EcalLed led = ledMap.get(channel.getChannelId());
-			
-			// Perform the comparison.
-			System.out.printf("Checking Mappings for Crystal (%3d, %3d):%n", crystal.x, crystal.y);
-			System.out.printf("\tChannel ID      :: %d%n", channel.getChannelId());
-			
-			System.out.printf("\tChannel     [ %3d ] vs [ %3d ] ... ", channel.getChannel(), data.getFADCChannel());
-			if(channel.getChannel() == data.getFADCChannel()) {
-				System.out.printf("[ Success ]%n");
-			} else {
-				System.out.printf("[ Failure ]%n");
-				idFailSet.add(channel.getChannelId());
-				pointFailSet.add(crystal);
-			}
-			
-			int crate = data.getMotherboard().isTop() ? 1 : 2;
-			System.out.printf("\tCrate       [ %3d ] vs [ %3d ] ... ", channel.getCrate(), crate);
-			if(channel.getCrate() == crate) {
-				System.out.printf("[ Success ]%n");
-			} else {
-				System.out.printf("[ Failure ]%n");
-				idFailSet.add(channel.getChannelId());
-				pointFailSet.add(crystal);
-			}
-			
-			System.out.printf("\tSlot        [ %3d ] vs [ %3d ] ... ", channel.getSlot(), data.getFADCSlot());
-			if(channel.getSlot() == data.getFADCSlot()) {
-				System.out.printf("[ Success ]%n");
-			} else {
-				System.out.printf("[ Failure ]%n");
-				idFailSet.add(channel.getChannelId());
-				pointFailSet.add(crystal);
-			}
-			
-			System.out.printf("\tLED Channel [ %3d ] vs [ %3d ] ... ", led.getLedNumber(), data.getLEDChannel());
-			if(led.getLedNumber() == data.getLEDChannel()) {
-				System.out.printf("[ Success ]%n");
-			} else {
-				System.out.printf("[ Failure ]%n");
-				idFailSet.add(channel.getChannelId());
-				pointFailSet.add(crystal);
-			}
-			
-			System.out.printf("\tLED Crate   [ %3d ] vs [ %3d ] ... ", led.getCrateNumber(), crate);
-			if(led.getCrateNumber() == crate) {
-				System.out.printf("[ Success ]%n");
-			} else {
-				System.out.printf("[ Failure ]%n");
-				idFailSet.add(channel.getChannelId());
-				pointFailSet.add(crystal);
-			}
-			
-			System.out.println();
-			System.out.println();
-		}
-		
-		// Print out the failing crystals.
-		System.out.println("Crystals that Failed:");
-		for(Point fail : pointFailSet) {
-			System.out.printf("\tCrystal (%3d, %3d)%n", fail.x, fail.y);
-		}
-		if(pointFailSet.isEmpty()) {
-			System.out.println("\tNone!");
-		}
-		
-		// Indicate the database connection settings.
-		System.out.println("\n");
-		System.out.printf("Detector           :: %s%n", detectorName);
-		System.out.printf("Run Number         :: %d%n", runNumber);
-		System.out.printf("Channel Collection :: %d%n", channels.getCollectionId());
-		System.out.printf("LED Collection     :: %d%n", leds.getCollectionId());
-	}
+        
+        // Perform the comparison test.
+        for(EcalChannel channel : channels) {
+            // Get the crystal point information.
+            Point crystal = new Point(channel.getX(), channel.getY());
+            
+            // Get the data from manager.
+            CrystalDataSet data = manager.getCrystalData(crystal);
+            
+            // Get the appropriate LED collection.
+            EcalLed led = ledMap.get(channel.getChannelId());
+            
+            // Perform the comparison.
+            System.out.printf("Checking Mappings for Crystal (%3d, %3d):%n", crystal.x, crystal.y);
+            System.out.printf("\tChannel ID      :: %d%n", channel.getChannelId());
+            
+            System.out.printf("\tChannel     [ %3d ] vs [ %3d ] ... ", channel.getChannel(), data.getFADCChannel());
+            if(channel.getChannel() == data.getFADCChannel()) {
+                System.out.printf("[ Success ]%n");
+            } else {
+                System.out.printf("[ Failure ]%n");
+                idFailSet.add(channel.getChannelId());
+                pointFailSet.add(crystal);
+            }
+            
+            int crate = data.getMotherboard().isTop() ? 1 : 2;
+            System.out.printf("\tCrate       [ %3d ] vs [ %3d ] ... ", channel.getCrate(), crate);
+            if(channel.getCrate() == crate) {
+                System.out.printf("[ Success ]%n");
+            } else {
+                System.out.printf("[ Failure ]%n");
+                idFailSet.add(channel.getChannelId());
+                pointFailSet.add(crystal);
+            }
+            
+            System.out.printf("\tSlot        [ %3d ] vs [ %3d ] ... ", channel.getSlot(), data.getFADCSlot());
+            if(channel.getSlot() == data.getFADCSlot()) {
+                System.out.printf("[ Success ]%n");
+            } else {
+                System.out.printf("[ Failure ]%n");
+                idFailSet.add(channel.getChannelId());
+                pointFailSet.add(crystal);
+            }
+            
+            System.out.printf("\tLED Channel [ %3d ] vs [ %3d ] ... ", led.getLedNumber(), data.getLEDChannel());
+            if(led.getLedNumber() == data.getLEDChannel()) {
+                System.out.printf("[ Success ]%n");
+            } else {
+                System.out.printf("[ Failure ]%n");
+                idFailSet.add(channel.getChannelId());
+                pointFailSet.add(crystal);
+            }
+            
+            System.out.printf("\tLED Crate   [ %3d ] vs [ %3d ] ... ", led.getCrateNumber(), crate);
+            if(led.getCrateNumber() == crate) {
+                System.out.printf("[ Success ]%n");
+            } else {
+                System.out.printf("[ Failure ]%n");
+                idFailSet.add(channel.getChannelId());
+                pointFailSet.add(crystal);
+            }
+            
+            System.out.println();
+            System.out.println();
+        }
+        
+        // Print out the failing crystals.
+        System.out.println("Crystals that Failed:");
+        for(Point fail : pointFailSet) {
+            System.out.printf("\tCrystal (%3d, %3d)%n", fail.x, fail.y);
+        }
+        if(pointFailSet.isEmpty()) {
+            System.out.println("\tNone!");
+        }
+        
+        // Indicate the database connection settings.
+        System.out.println("\n");
+        System.out.printf("Detector           :: %s%n", detectorName);
+        System.out.printf("Run Number         :: %d%n", runNumber);
+        System.out.printf("Channel Collection :: %d%n", channels.getCollectionId());
+        System.out.printf("LED Collection     :: %d%n", leds.getCollectionId());
+    }
 }

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/GradientScale.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/GradientScale.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/GradientScale.java	Wed Apr 27 11:11:32 2016
@@ -21,9 +21,9 @@
     private int[] drgb = { 255, 255, 255 };
     
     public Color getColor(Double value) {
-    	// If the argument is null, treat it as zero.
-    	if(value == null) { value = 0.0; }
-    	
+        // If the argument is null, treat it as zero.
+        if(value == null) { value = 0.0; }
+        
         // If the value is less than the minimum, return the cold color.
         if (value < min) { return coldColor; }
         

Modified: java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/MultiGradientScale.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/MultiGradientScale.java	(original)
+++ java/branches/HPSJAVA-409/ecal-event-display/src/main/java/org/hps/monitoring/ecal/eventdisplay/util/MultiGradientScale.java	Wed Apr 27 11:11:32 2016
@@ -29,9 +29,9 @@
     }
     
     public Color getColor(Double value) {
-    	// If the value is null, treat it as zero.
-    	if(value == null) { value = 0.0; }
-    	
+        // If the value is null, treat it as zero.
+        if(value == null) { value = 0.0; }
+        
         // Get the number of colors and scales.
         int colors = colorList.size();
         int scales = scaleList.size();
@@ -48,7 +48,7 @@
         else { sValue = Math.log10(scale * value); }
         
         if(value < 1 && (Double.isNaN(sValue) || Double.isInfinite(sValue))) {
-        	return scaleList.get(0).getColor(0.0);
+            return scaleList.get(0).getColor(0.0);
         }
         
         // Otherwise, determine which scale should get the value.

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/pom.xml	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/ecal-readout-sim/</url>

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ClockSingleton.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ClockSingleton.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ClockSingleton.java	Wed Apr 27 11:11:32 2016
@@ -13,35 +13,35 @@
  */
 public class ClockSingleton {
 
-	public static final ClockSingleton _instance = new ClockSingleton();
-	private int clock;
-	//time between events (bunch spacing)
-	private double dt = 2.0;
+    public static final ClockSingleton _instance = new ClockSingleton();
+    private int clock;
+    //time between events (bunch spacing)
+    private double dt = 2.0;
 
-	private ClockSingleton() {
-	}
+    private ClockSingleton() {
+    }
 
-	public static void init() {
-		_instance.clock = 0;
-	}
+    public static void init() {
+        _instance.clock = 0;
+    }
 
-	public static int getClock() {
-		return _instance.clock;
-	}
+    public static int getClock() {
+        return _instance.clock;
+    }
 
-	public static double getTime() {
-		return _instance.dt * _instance.clock;
-	}
+    public static double getTime() {
+        return _instance.dt * _instance.clock;
+    }
 
-	public static double getDt() {
-		return _instance.dt;
-	}
+    public static double getDt() {
+        return _instance.dt;
+    }
 
-	public static void setDt(double dt) {
-		_instance.dt = dt;
-	}
+    public static void setDt(double dt) {
+        _instance.dt = dt;
+    }
 
-	public static void step() {
-		_instance.clock++;
-	}
+    public static void step() {
+        _instance.clock++;
+    }
 }

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCEcalReadoutDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCEcalReadoutDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCEcalReadoutDriver.java	Wed Apr 27 11:11:32 2016
@@ -310,7 +310,7 @@
     /**
      * Return the map of preamp signal buffers. For debug only.
      *
-     * @return
+     * @return the map of preamp signal buffers
      */
     public Map<Long, RingBuffer> getSignalMap() {
         return analogPipelines;
@@ -319,7 +319,7 @@
     /**
      * Return the map of FADC pipelines. For debug only.
      *
-     * @return
+     * @return the map of FADC pipelines
      */
     public Map<Long, FADCPipeline> getPipelineMap() {
         return digitalPipelines;
@@ -383,7 +383,7 @@
                     }
                 } else {
                     if (pedestalSubtractedValue < triggerThreshold || triggerPathHitTimes.get(cellID) + delay0 == readoutCounter) {
-//					System.out.printf("sum = %f\n",sum);
+//                  System.out.printf("sum = %f\n",sum);
                         triggerPathDelayQueue.add(new BaseRawCalorimeterHit(cellID,
                                 (int) Math.round((sum + pedestalSubtractedValue) / scaleFactor),
                                 64 * triggerPathHitTimes.get(cellID)));
@@ -460,15 +460,15 @@
         short[] adcValues = new short[readoutWindow];
         for (int i = 0; i < readoutWindow; i++) {
             adcValues[i] = (short) pipeline.getValue(readoutLatency - i - 1);
-//			if (adcValues[i] != 0) {
-//				System.out.println("getWindow: " + adcValues[i] + " at i = " + i);
-//			}
+//          if (adcValues[i] != 0) {
+//              System.out.println("getWindow: " + adcValues[i] + " at i = " + i);
+//          }
         }
         return adcValues;
     }
 
     protected List<RawTrackerHit> readWindow() {
-//		System.out.println("Reading FADC data");
+//      System.out.println("Reading FADC data");
         List<RawTrackerHit> hits = new ArrayList<RawTrackerHit>();
         for (Long cellID : digitalPipelines.keySet()) {
             short[] adcValues = getWindow(cellID);
@@ -488,7 +488,7 @@
     }
 
     protected List<RawTrackerHit> readPulses() {
-//		System.out.println("Reading FADC data");
+//      System.out.println("Reading FADC data");
         List<RawTrackerHit> hits = new ArrayList<RawTrackerHit>();
         for (Long cellID : digitalPipelines.keySet()) {
             short[] window = getWindow(cellID);
@@ -522,7 +522,7 @@
     }
 
     protected List<RawCalorimeterHit> readIntegrals() {
-//		System.out.println("Reading FADC data");
+//      System.out.println("Reading FADC data");
         List<RawCalorimeterHit> hits = new ArrayList<RawCalorimeterHit>();
         for (Long cellID : digitalPipelines.keySet()) {
             short[] window = getWindow(cellID);

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCPrimaryTriggerDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCPrimaryTriggerDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCPrimaryTriggerDriver.java	Wed Apr 27 11:11:32 2016
@@ -34,7 +34,7 @@
     private int pairCoincidence = 2;                              // Maximum allowed time difference between clusters. (4 ns clock-cycles)
     private int backgroundLevel = -1;                             // Automatically sets the cuts to achieve a predetermined background rate.
     private TriggerModule triggerModule = new TriggerModule(1.0, 0.050,
-    		6.600, 0.010, 6.600, 0.000, 13.200, 6.600, 0.0, 360, 0.0055);
+            6.600, 0.010, 6.600, 0.000, 13.200, 6.600, 0.0, 360, 0.0055);
     
     // ==================================================================
     // ==== Driver Internal Variables ===================================
@@ -77,55 +77,55 @@
      */
     @Override
     public void startOfData() {
-    	// Define plot type names.
-    	String[] plotType = new String[PLOT_COUNT];
-    	plotType[NO_CUTS] = "";
-    	plotType[ALL_CUTS] = " (Passed All Cuts)";
-    	plotType[OVER_1HIT] = " (More than 1 Hit)";
-    	plotType[OVER_2HIT] = " (More than 2 Hits)";
-    	plotType[SINGLES_CUTS] = " (Passed Single Cuts)";
-    	
-    	// Define plot type directories.
-    	String[] plotDir = new String[PLOT_COUNT];
-    	plotDir[NO_CUTS] = "NoCuts/";
-    	plotDir[ALL_CUTS] = "PassedAll/";
-    	plotDir[OVER_1HIT] = "2PlusHits/";
-    	plotDir[OVER_2HIT] = "3PlusHits/";
-    	plotDir[SINGLES_CUTS] = "PassedSingles/";
-    	
-    	// Instantiate the singles plot arrays.
-    	clusterSeedEnergy = new IHistogram1D[PLOT_COUNT];
-    	clusterHitCount = new IHistogram1D[PLOT_COUNT];
-    	clusterTotalEnergy = new IHistogram1D[PLOT_COUNT];
-    	clusterDistribution = new IHistogram2D[PLOT_COUNT];
-    	
-    	// Instantiate the pair plot arrays. Note that the pair cuts
-    	// only ever see clusters that pass the singles cuts, so the
-    	// "passed singles cuts" plots are meaningless. Thusly, the
-    	// pair plots have one fewer plot than the singles.
-    	pairEnergySum = new IHistogram1D[PLOT_COUNT - 1];
-    	pairEnergyDifference = new IHistogram1D[PLOT_COUNT - 1];
-    	pairCoplanarity = new IHistogram1D[PLOT_COUNT - 1];
-    	pairEnergySlope = new IHistogram1D[PLOT_COUNT - 1];
-    	pairEnergySum2DDistribution = new IHistogram2D[PLOT_COUNT - 1];
-    	
-    	// Instantiate the plots.
-    	for(int i = 0; i < PLOT_COUNT; i++) {
-    		System.out.println(plotDir[i] + "Cluster Seed Energy" + plotType[i]);
-    		clusterSeedEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Seed Energy" + plotType[i], 176, 0.0, 2.2);
-    		clusterHitCount[i] = aida.histogram1D(plotDir[i] + "Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
-    		clusterTotalEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Total Energy" + plotType[i], 176, 0.0, 2.2);
-    		clusterDistribution[i] = aida.histogram2D(plotDir[i] + "Cluster Seed" + plotType[i], 46, -23, 23, 11, -5.5, 5.5);
-    		
-    		if(i != PLOT_COUNT - 1) {
-    			pairEnergySum[i] = aida.histogram1D(plotDir[i] + "Pair Energy Sum" + plotType[i], 176, 0.0, 4.4);
-    			pairEnergyDifference[i] = aida.histogram1D(plotDir[i] + "Pair Energy Difference" + plotType[i], 176, 0.0, 2.2);
-    			pairCoplanarity[i] = aida.histogram1D(plotDir[i] + "Pair Coplanarity" + plotType[i], 180, 0.0, 180.0);
-    			pairEnergySlope[i] = aida.histogram1D(plotDir[i] + "Pair Energy Slope" + plotType[i], 200, 0.0, 4.0);
-    			pairEnergySum2DDistribution[i] = aida.histogram2D(plotDir[i] + "Pair Energy Sum 2D" + plotType[i], 176, 0.0, 4.4, 176, 0.0, 4.4);
-    		}
-    	}
-    	
+        // Define plot type names.
+        String[] plotType = new String[PLOT_COUNT];
+        plotType[NO_CUTS] = "";
+        plotType[ALL_CUTS] = " (Passed All Cuts)";
+        plotType[OVER_1HIT] = " (More than 1 Hit)";
+        plotType[OVER_2HIT] = " (More than 2 Hits)";
+        plotType[SINGLES_CUTS] = " (Passed Single Cuts)";
+        
+        // Define plot type directories.
+        String[] plotDir = new String[PLOT_COUNT];
+        plotDir[NO_CUTS] = "NoCuts/";
+        plotDir[ALL_CUTS] = "PassedAll/";
+        plotDir[OVER_1HIT] = "2PlusHits/";
+        plotDir[OVER_2HIT] = "3PlusHits/";
+        plotDir[SINGLES_CUTS] = "PassedSingles/";
+        
+        // Instantiate the singles plot arrays.
+        clusterSeedEnergy = new IHistogram1D[PLOT_COUNT];
+        clusterHitCount = new IHistogram1D[PLOT_COUNT];
+        clusterTotalEnergy = new IHistogram1D[PLOT_COUNT];
+        clusterDistribution = new IHistogram2D[PLOT_COUNT];
+        
+        // Instantiate the pair plot arrays. Note that the pair cuts
+        // only ever see clusters that pass the singles cuts, so the
+        // "passed singles cuts" plots are meaningless. Thusly, the
+        // pair plots have one fewer plot than the singles.
+        pairEnergySum = new IHistogram1D[PLOT_COUNT - 1];
+        pairEnergyDifference = new IHistogram1D[PLOT_COUNT - 1];
+        pairCoplanarity = new IHistogram1D[PLOT_COUNT - 1];
+        pairEnergySlope = new IHistogram1D[PLOT_COUNT - 1];
+        pairEnergySum2DDistribution = new IHistogram2D[PLOT_COUNT - 1];
+        
+        // Instantiate the plots.
+        for(int i = 0; i < PLOT_COUNT; i++) {
+            System.out.println(plotDir[i] + "Cluster Seed Energy" + plotType[i]);
+            clusterSeedEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Seed Energy" + plotType[i], 176, 0.0, 2.2);
+            clusterHitCount[i] = aida.histogram1D(plotDir[i] + "Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
+            clusterTotalEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Total Energy" + plotType[i], 176, 0.0, 2.2);
+            clusterDistribution[i] = aida.histogram2D(plotDir[i] + "Cluster Seed" + plotType[i], 46, -23, 23, 11, -5.5, 5.5);
+            
+            if(i != PLOT_COUNT - 1) {
+                pairEnergySum[i] = aida.histogram1D(plotDir[i] + "Pair Energy Sum" + plotType[i], 176, 0.0, 4.4);
+                pairEnergyDifference[i] = aida.histogram1D(plotDir[i] + "Pair Energy Difference" + plotType[i], 176, 0.0, 2.2);
+                pairCoplanarity[i] = aida.histogram1D(plotDir[i] + "Pair Coplanarity" + plotType[i], 180, 0.0, 180.0);
+                pairEnergySlope[i] = aida.histogram1D(plotDir[i] + "Pair Energy Slope" + plotType[i], 200, 0.0, 4.0);
+                pairEnergySum2DDistribution[i] = aida.histogram2D(plotDir[i] + "Pair Energy Sum 2D" + plotType[i], 176, 0.0, 4.4, 176, 0.0, 4.4);
+            }
+        }
+        
         // Make sure that a valid cluster collection name has been
         // defined. If it has not, throw an exception.
         if (clusterCollectionName == null) {
@@ -239,15 +239,15 @@
                 
                 // Fill the hit count plots for N > 1.
                 if(hitCount > 1) {
-                	// Populate the plots.
+                    // Populate the plots.
                     clusterSeedEnergy[OVER_1HIT].fill(seedEnergy);
                     clusterTotalEnergy[OVER_1HIT].fill(clusterEnergy);
                     clusterHitCount[OVER_1HIT].fill(hitCount);
                     clusterDistribution[OVER_1HIT].fill(ix, iy);
-                	
+                    
                     // Fill the hit count plots for N > 2.
                     if(hitCount > 2) {
-                    	// Populate the plots.
+                        // Populate the plots.
                         clusterSeedEnergy[OVER_2HIT].fill(seedEnergy);
                         clusterTotalEnergy[OVER_2HIT].fill(clusterEnergy);
                         clusterHitCount[OVER_2HIT].fill(hitCount);
@@ -260,14 +260,14 @@
                 // VERBOSE :: Print the seed energy comparison check.
                 if(verbose) {
                     System.out.printf("\tSeed Energy Cut    :: %.3f < %.3f < %.3f --> %b%n",
-                    		triggerModule.getCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW), seedEnergy,
-                    		triggerModule.getCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH),
-                    		triggerModule.clusterSeedEnergyCut(cluster));
+                            triggerModule.getCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW), seedEnergy,
+                            triggerModule.getCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH),
+                            triggerModule.clusterSeedEnergyCut(cluster));
                 }
                 
                 // If the cluster fails the cut, skip to the next cluster.
                 if(!triggerModule.clusterSeedEnergyCut(cluster)) {
-                	continue clusterLoop;
+                    continue clusterLoop;
                 }
                 
                 // Otherwise, note that it passed the cut.
@@ -278,13 +278,13 @@
                 // VERBOSE :: Print the hit count comparison check.
                 if(verbose) {
                     System.out.printf("\tHit Count Cut      :: %d >= %.0f --> %b%n",
-                    		hitCount, triggerModule.getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW),
-                    		triggerModule.clusterHitCountCut(cluster));
+                            hitCount, triggerModule.getCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW),
+                            triggerModule.clusterHitCountCut(cluster));
                 }
                 
                 // If the cluster fails the cut, skip to the next cluster.
                 if(!triggerModule.clusterHitCountCut(cluster)) {
-                	continue clusterLoop;
+                    continue clusterLoop;
                 }
                 
                 // Otherwise, note that it passed the cut.
@@ -295,14 +295,14 @@
                 // VERBOSE :: Print the cluster energy comparison check.
                 if(verbose) {
                     System.out.printf("\tCluster Energy Cut :: %.3f < %.3f < %.3f --> %b%n",
-                    		triggerModule.getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), clusterEnergy,
-                    		triggerModule.getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH),
-                    		triggerModule.clusterTotalEnergyCut(cluster));
+                            triggerModule.getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW), clusterEnergy,
+                            triggerModule.getCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH),
+                            triggerModule.clusterTotalEnergyCut(cluster));
                 }
                 
                 // If the cluster fails the cut, skip to the next cluster.
                 if(!triggerModule.clusterTotalEnergyCut(cluster)) {
-                	continue clusterLoop;
+                    continue clusterLoop;
                 }
                 
                 // Otherwise, note that it passed the cut.
@@ -368,7 +368,7 @@
      * Sets the maximum deviation from coplanarity that a cluster pair
      * may possess and still pass the coplanarity pair cut. Value uses
      * units of degrees.
-     * @param maxCoplanarityAngle - The parameter value.
+     * @param coplanarityHigh - The parameter value.
      */
     public void setCoplanarityHigh(double coplanarityHigh) {
         triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, coplanarityHigh);
@@ -407,7 +407,7 @@
      * Sets the lowest allowed energy a cluster pair may have and
      * still pass the cluster pair energy sum cluster cut. Value uses
      * units of GeV.
-     * @param energySumHigh - The parameter value.
+     * @param energySumLow - The parameter value.
      */
     public void setEnergySumLow(double energySumLow) {
         triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, energySumLow * EcalUtils.GeV);
@@ -544,63 +544,63 @@
         
         // Some cut values are almost always the same thing. Set those
         // here and only overwrite if necessary.
-    	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.125);
-    	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    1.300);
-    	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.200);
-    	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.700);
-    	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.500);
-    	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        2.000);
-    	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 1.200);
-    	triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
-    	triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       2);
+        triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.125);
+        triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    1.300);
+        triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.200);
+        triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.700);
+        triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.500);
+        triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        2.000);
+        triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 1.200);
+        triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
+        triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       2);
         
         // Set the variable values.
         if(backgroundLevel == 1) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         1.000);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.2);
-        	triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       20);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         1.000);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.2);
+            triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       20);
         } else if(backgroundLevel == 2) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.0);
-        	triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       20);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.0);
+            triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       20);
         } else if(backgroundLevel == 3) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.0);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.0);
         } else if(backgroundLevel == 4) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.8);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.8);
         } else if(backgroundLevel == 5) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.8);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.8);
         } else if(backgroundLevel == 6) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.6);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.6);
         } else if(backgroundLevel == 7) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.6);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.6);
         } else if(backgroundLevel == 8) {
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.500);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.500);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
         } else if(backgroundLevel == 9) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
         } else if(backgroundLevel == 10) {
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.4);
         } else if(backgroundLevel == 0) {
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.100);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    6.600);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.100);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.500);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.000);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        1.900);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 2.200);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.1);
-        	triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       35);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.100);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    6.600);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.100);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   1.500);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.000);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        1.900);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 2.200);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       1.1);
+            triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       35);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
         } else if(backgroundLevel == -1) {
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.050);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    6.600);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.010);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   6.600);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.000);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        13.200);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 6.600);
-        	triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.0);
-        	triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       360);
-        	triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW,     0.050);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_HIGH,    6.600);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.010);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   6.600);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.000);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        13.200);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 6.600);
+            triggerModule.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.0);
+            triggerModule.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       360);
+            triggerModule.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
         }
     }
     
@@ -636,16 +636,16 @@
             
             // Fill the hit count plots for N > 1.
             if(clusterPair[0].getCalorimeterHits().size() > 1 && clusterPair[1].getCalorimeterHits().size() > 1) {
-            	// Populate the plots.
+                // Populate the plots.
                 pairEnergySum[OVER_1HIT].fill(energySum);
                 pairEnergyDifference[OVER_1HIT].fill(energyDifference);
                 pairEnergySlope[OVER_1HIT].fill(energySlope);
                 pairCoplanarity[OVER_1HIT].fill(coplanarity);
                 pairEnergySum2DDistribution[OVER_1HIT].fill(clusterPair[0].getEnergy(), clusterPair[1].getEnergy());
-            	
+                
                 // Fill the hit count plots for N > 2.
                 if(clusterPair[0].getCalorimeterHits().size() > 2 && clusterPair[1].getCalorimeterHits().size() > 2) {
-                	// Populate the plots.
+                    // Populate the plots.
                     pairEnergySum[OVER_2HIT].fill(energySum);
                     pairEnergyDifference[OVER_2HIT].fill(energyDifference);
                     pairEnergySlope[OVER_2HIT].fill(energySlope);
@@ -658,7 +658,7 @@
             // =============================================================
             // If the cluster fails the cut, skip to the next pair.
             if(!triggerModule.pairEnergySumCut(clusterPair)) {
-            	continue pairLoop;
+                continue pairLoop;
             }
             
             // Otherwise, note that it passed the cut.
@@ -668,7 +668,7 @@
             // =============================================================
             // If the cluster fails the cut, skip to the next pair.
             if(!triggerModule.pairEnergyDifferenceCut(clusterPair)) {
-            	continue pairLoop;
+                continue pairLoop;
             }
             
             // Otherwise, note that it passed the cut.
@@ -678,7 +678,7 @@
             // =============================================================
             // If the cluster fails the cut, skip to the next pair.
             if(!triggerModule.pairEnergySlopeCut(clusterPair)) {
-            	continue pairLoop;
+                continue pairLoop;
             }
             
             // Otherwise, note that it passed the cut.
@@ -688,7 +688,7 @@
             // =============================================================
             // If the cluster fails the cut, skip to the next pair.
             if(!triggerModule.pairCoplanarityCut(clusterPair)) {
-            	continue pairLoop;
+                continue pairLoop;
             }
             
             // Otherwise, note that it passed the cut.
@@ -774,6 +774,6 @@
      * @param cuts - The cut string.
      */
     public void setCuts(String cuts) {
-    	triggerModule.setCutValues(false, cuts);
+        triggerModule.setCutValues(false, cuts);
     }
 }

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerDriver.java	Wed Apr 27 11:11:32 2016
@@ -532,7 +532,6 @@
     /**
      * Get a list of all unique cluster pairs in the event
      *
-     * @param ecalClusters : List of ECal clusters
      * @return list of cluster pairs
      */
     protected List<Cluster[]> getClusterPairsTopBot() {
@@ -584,7 +583,7 @@
      * Checks if the ECal clusters making up a cluster pair both have at least
      * the minimum number of hits.
      *
-     * @param clusterPair: pair of clusters
+     * @param clusterPair the pair of clusters
      * @return true if pair passes cut, false if fail
      */
     protected boolean clusterHitCount(Cluster[] clusterPair) {

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerVariableDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerVariableDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCTriggerVariableDriver.java	Wed Apr 27 11:11:32 2016
@@ -63,14 +63,14 @@
 
             //System.out.printf("%d ecal clusters in event\n", clusters.size());
             //System.out.printf("%s: %d clusters\n",this.getClass().getSimpleName(),clusters.size());
-        	//for(Cluster cl : clusters) {
-        	//	System.out.printf("%s: cl E %f x %f y %f \n",this.getClass().getSimpleName(),cl.getEnergy(),cl.getPosition()[0],cl.getPosition()[1]);
-        	//}
-        	List<Cluster> unique_clusters = this.getUniqueClusters(clusters);
-        	//System.out.printf("%s: %d unique clusters\n",this.getClass().getSimpleName(),unique_clusters.size());
-        	//for(Cluster cl : unique_clusters) {
-        	//	System.out.printf("%s: cl E %f x %f y %f \n",this.getClass().getSimpleName(),cl.getEnergy(),cl.getPosition()[0],cl.getPosition()[1]);
-        	//}
+            //for(Cluster cl : clusters) {
+            //  System.out.printf("%s: cl E %f x %f y %f \n",this.getClass().getSimpleName(),cl.getEnergy(),cl.getPosition()[0],cl.getPosition()[1]);
+            //}
+            List<Cluster> unique_clusters = this.getUniqueClusters(clusters);
+            //System.out.printf("%s: %d unique clusters\n",this.getClass().getSimpleName(),unique_clusters.size());
+            //for(Cluster cl : unique_clusters) {
+            //  System.out.printf("%s: cl E %f x %f y %f \n",this.getClass().getSimpleName(),cl.getEnergy(),cl.getPosition()[0],cl.getPosition()[1]);
+            //}
 
             updateClusterQueues(unique_clusters);
             List<Cluster[]> clusterPairs = getClusterPairsTopBot();
@@ -122,47 +122,47 @@
     
     
     private List<Cluster> getUniqueClusters(List<Cluster> clusters) {
-    	List<Cluster> unique = new ArrayList<Cluster>();
-    	for(Cluster loop_cl : clusters) {
-			ClusterCmp loop_clCmp = new ClusterCmp(loop_cl);
-    		boolean found = false;
-			for(Cluster cl : unique) {
-    			if( loop_clCmp.compareTo(cl) == 0 ) {
-    				found = true;
-    			}
-    		}
-			if( !found ) {
-				unique.add(loop_cl);
-			}
-    	}
-    	return unique;
+        List<Cluster> unique = new ArrayList<Cluster>();
+        for(Cluster loop_cl : clusters) {
+            ClusterCmp loop_clCmp = new ClusterCmp(loop_cl);
+            boolean found = false;
+            for(Cluster cl : unique) {
+                if( loop_clCmp.compareTo(cl) == 0 ) {
+                    found = true;
+                }
+            }
+            if( !found ) {
+                unique.add(loop_cl);
+            }
+        }
+        return unique;
     }
 
 
     private static class ClusterCmp implements Comparable<Cluster> {
-    	private Cluster _cluster;
-		public ClusterCmp(Cluster cl) {
-			set_cluster(cl);
-		}
-		@Override
-		public int compareTo(Cluster cl) {
-				if(cl.getEnergy()==get_cluster().getEnergy() && cl.getPosition()[0]==get_cluster().getPosition()[0] && cl.getPosition()[1]==get_cluster().getPosition()[1] ) {
-					return 0;
-				} else {
-					if( cl.getEnergy() > get_cluster().getEnergy()) {
-						return 1;
-					} else {
-						return -1;
-					}
-				}
-		}
-		public Cluster get_cluster() {
-			return _cluster;
-		}
-		public void set_cluster(Cluster _cluster) {
-			this._cluster = _cluster;
-		}
-    	
+        private Cluster _cluster;
+        public ClusterCmp(Cluster cl) {
+            set_cluster(cl);
+        }
+        @Override
+        public int compareTo(Cluster cl) {
+                if(cl.getEnergy()==get_cluster().getEnergy() && cl.getPosition()[0]==get_cluster().getPosition()[0] && cl.getPosition()[1]==get_cluster().getPosition()[1] ) {
+                    return 0;
+                } else {
+                    if( cl.getEnergy() > get_cluster().getEnergy()) {
+                        return 1;
+                    } else {
+                        return -1;
+                    }
+                }
+        }
+        public Cluster get_cluster() {
+            return _cluster;
+        }
+        public void set_cluster(Cluster _cluster) {
+            this._cluster = _cluster;
+        }
+        
     }
     
 }

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/MollerTriggerDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/MollerTriggerDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/MollerTriggerDriver.java	Wed Apr 27 11:11:32 2016
@@ -56,8 +56,8 @@
     
     @Override
     public void process(EventHeader event) {
-    	// Run the superclass process event.
-    	super.process(event);
+        // Run the superclass process event.
+        super.process(event);
     }
     
     @Override
@@ -87,29 +87,29 @@
         aMomentumAngle = aida.histogram2D("Trigger Plots :: Particle Momentum Distribution (t = 0, Passed All Cuts)", 500, -0.01, 0.06, 500, -0.04, 0.04);
         
         // Add the allowed seed crystal positions to the seed set.
-		if(useVersionOne) {
-	        // Add the allowed seed crystal positions to the seed set.
-	        // y = +/- 1, x = -11 -> -15
-	        for(int ix = -15; ix <= -11; ix++) {
-	            allowedSeedSet.add(new Point(ix, 1));
-	            allowedSeedSet.add(new Point(ix, -1));
-	        } // y = +/- 2, x = -9 -> -15
-	        for(int ix = -15; ix <= -9; ix++) {
-	            allowedSeedSet.add(new Point(ix, 2));
-	            allowedSeedSet.add(new Point(ix, -2));
-	        }
-		}
-		else {
-	        // y = +/- 1, x = -11 -> -13
-	        for(int ix = -13; ix <= -11; ix++) {
-	            allowedSeedSet.add(new Point(ix, 1));
-	            allowedSeedSet.add(new Point(ix, -1));
-	        } // y = +/- 2, x = -10 -> -14
-	        for(int ix = -14; ix <= -10; ix++) {
-	            allowedSeedSet.add(new Point(ix, 2));
-	            allowedSeedSet.add(new Point(ix, -2));
-	        }
-		}
+        if(useVersionOne) {
+            // Add the allowed seed crystal positions to the seed set.
+            // y = +/- 1, x = -11 -> -15
+            for(int ix = -15; ix <= -11; ix++) {
+                allowedSeedSet.add(new Point(ix, 1));
+                allowedSeedSet.add(new Point(ix, -1));
+            } // y = +/- 2, x = -9 -> -15
+            for(int ix = -15; ix <= -9; ix++) {
+                allowedSeedSet.add(new Point(ix, 2));
+                allowedSeedSet.add(new Point(ix, -2));
+            }
+        }
+        else {
+            // y = +/- 1, x = -11 -> -13
+            for(int ix = -13; ix <= -11; ix++) {
+                allowedSeedSet.add(new Point(ix, 1));
+                allowedSeedSet.add(new Point(ix, -1));
+            } // y = +/- 2, x = -10 -> -14
+            for(int ix = -14; ix <= -10; ix++) {
+                allowedSeedSet.add(new Point(ix, 2));
+                allowedSeedSet.add(new Point(ix, -2));
+            }
+        }
     }
     
     @Override
@@ -201,31 +201,31 @@
             // Require that the cluster pass each of the cuts in
             // order to qualify for a trigger.
             if(totalEnergyCut && seedEnergyCut && hitCountCut && positionCut) {
-            	// Increment the number of events that have passed
-            	// the cuts.
-            	passedEvents++;
-            	
-            	// If the number of passed events exceeds the prescaling
-            	// threshold, throw a trigger.
-            	if(passedEvents >= prescale) {
-            		// Reset the number of passed events.
-            		passedEvents = 0;
-            		
-	                // Add the clusters to the cut histograms.
-	                aClusterHitCount.fill(cluster.getCalorimeterHits().size());
-	                aClusterTotalEnergy.fill(cluster.getEnergy());
-	                aClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
-	                aClusterDistribution.fill(ix > 0 ? ix - 1 : ix, iy, 1);
-	                
-	                // Increment the trigger count.
-	                triggers++;
-	                
-	                // VERBOSE :: Indicate that a trigger occurred.
-	                if(verbose) { System.out.printf("\tTriggered!%n%n"); }
-	                
-	                // Return a trigger.
-	                return true;
-            	}
+                // Increment the number of events that have passed
+                // the cuts.
+                passedEvents++;
+                
+                // If the number of passed events exceeds the prescaling
+                // threshold, throw a trigger.
+                if(passedEvents >= prescale) {
+                    // Reset the number of passed events.
+                    passedEvents = 0;
+                    
+                    // Add the clusters to the cut histograms.
+                    aClusterHitCount.fill(cluster.getCalorimeterHits().size());
+                    aClusterTotalEnergy.fill(cluster.getEnergy());
+                    aClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
+                    aClusterDistribution.fill(ix > 0 ? ix - 1 : ix, iy, 1);
+                    
+                    // Increment the trigger count.
+                    triggers++;
+                    
+                    // VERBOSE :: Indicate that a trigger occurred.
+                    if(verbose) { System.out.printf("\tTriggered!%n%n"); }
+                    
+                    // Return a trigger.
+                    return true;
+                }
             }
         }
         
@@ -371,7 +371,7 @@
      * will be thrown.
      */
     public void setPrescale(int prescale) {
-    	this.prescale = prescale;
+        this.prescale = prescale;
     }
     
     /**
@@ -383,7 +383,7 @@
     public void setVerbose(boolean verbose) {
         this.verbose = verbose;
     }
-	
+    
     /**
      * Toggles whether the more inclusive acceptance region version 1
      * is used, or the slightly smaller and more exclusive acceptance
@@ -392,9 +392,9 @@
      * 1 of the acceptance region should be used and <code>false</code>
      * that version 2 should be used.
      */
-	public void setUseVersionOne(boolean useVersionOne) {
-		this.useVersionOne = useVersionOne;
-	}
+    public void setUseVersionOne(boolean useVersionOne) {
+        this.useVersionOne = useVersionOne;
+    }
     
     // ==================================================================
     // ==== AIDA Plots ==================================================

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/OccupancyAnalysisDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/OccupancyAnalysisDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/OccupancyAnalysisDriver.java	Wed Apr 27 11:11:32 2016
@@ -12,19 +12,19 @@
 import org.lcsim.util.aida.AIDA;
 
 public class OccupancyAnalysisDriver extends Driver {
-	// Internal variables.
-	private double scalingFactor = 0.05;
-	private double seedThreshold = 0.050;
-	private double beamRatio = 1.92 / 2.2;
-	private double clusterThreshold = 0.200;
+    // Internal variables.
+    private double scalingFactor = 0.05;
+    private double seedThreshold = 0.050;
+    private double beamRatio = 1.92 / 2.2;
+    private double clusterThreshold = 0.200;
     private AIDA aida = AIDA.defaultInstance();
-	private boolean ignoreBeamGapRows = false;
-	
+    private boolean ignoreBeamGapRows = false;
+    
     // LCIO Collection Names
     private String clusterCollectionName = "EcalClusters";
     private String hitCollectionName = "EcalCorrectedHits";
     
-	// Trigger plots.
+    // Trigger plots.
     IHistogram2D occupancyDistribution;
     IHistogram2D[] clusterDistribution = new IHistogram2D[2];
     IHistogram1D[] clusterHitDistribution = new IHistogram1D[2];
@@ -32,129 +32,129 @@
     IHistogram1D[] clusterEnergyDistribution = new IHistogram1D[2];
     
     public void setIgnoreBeamGapRows(boolean ignoreBeamGapRows) {
-    	this.ignoreBeamGapRows = ignoreBeamGapRows;
+        this.ignoreBeamGapRows = ignoreBeamGapRows;
     }
     
     public void setBeamRatio(double beamRatio) {
-    	this.beamRatio = beamRatio;
+        this.beamRatio = beamRatio;
     }
     
     public void setScalingFactor(double scalingFactor) {
-    	this.scalingFactor = scalingFactor;
+        this.scalingFactor = scalingFactor;
     }
     
     public void setSeedThreshold(double seedThreshold) {
-    	this.seedThreshold = seedThreshold;
+        this.seedThreshold = seedThreshold;
     }
     
     public void setClusterThreshold(double clusterThreshold) {
-    	this.clusterThreshold = clusterThreshold;
+        this.clusterThreshold = clusterThreshold;
     }
     
     public void setClusterCollectionName(String clusterCollectionName) {
-    	this.clusterCollectionName = clusterCollectionName;
+        this.clusterCollectionName = clusterCollectionName;
     }
     
     public void setHitCollectionName(String hitCollectionName) {
-    	this.hitCollectionName = hitCollectionName;
+        this.hitCollectionName = hitCollectionName;
     }
     
     @Override
     public void process(EventHeader event) {
-    	// If clusters are present, process them.
-    	if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-    		// Get the list of clusters.
-    		List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-    		
-    		// Use the clusters to populate the cluster plots.
-    		for(Cluster cluster : clusterList) {
-    			// Get the ix and iy values for the cluster.
-    			int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-    			int iy = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-    			
-    			// If we want to ignore the beam gap rows, make sure
-    			// that iy exceeds two.
-    			if(!ignoreBeamGapRows || (Math.abs(iy) > 2)) {
-	        		// If the cluster passes the seed threshold, place it in
-	        		// the level 1 plots.
-	    			if(cluster.getCalorimeterHits().get(0).getCorrectedEnergy() >= seedThreshold) {
-	    				clusterDistribution[0].fill(ix, iy, scalingFactor);
-	    				clusterHitDistribution[0].fill(cluster.getCalorimeterHits().size(), scalingFactor);
-	    				clusterEnergyDistribution[0].fill(cluster.getEnergy() * beamRatio, scalingFactor);
-	    			}
-	    			
-	    			// If the cluster energy passes the cluster threshold,
-	    			// populate the level 2 plots.
-	    			if(cluster.getEnergy() >= clusterThreshold) {
-	    				clusterDistribution[1].fill(ix, iy, scalingFactor);
-	    				clusterHitDistribution[1].fill(cluster.getCalorimeterHits().size(), scalingFactor);
-	    				clusterEnergyDistribution[1].fill(cluster.getEnergy() * beamRatio, scalingFactor);
-	    			}
-    			}
-    		}
-    	}
-    	
-    	// If the event has hits, process them.
-    	if(event.hasCollection(CalorimeterHit.class, hitCollectionName)) {
-    		// Get the list of hits.
-    		List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, hitCollectionName);
-    		
-    		// Track the energy in the top and bottom of the calorimeter.
-    		double[] energy = { 0.0, 0.0 };
-    		
-    		// Iterate over the hits.
-    		for(CalorimeterHit hit : hitList) {
-    			// Get the ix and iy values.
-    			int ix = hit.getIdentifierFieldValue("ix");
-    			int iy = hit.getIdentifierFieldValue("iy");
-    			
-    			// If we want to ignore beam gap rows, ensure that iy
-    			// is greater than 2.
-    			if(!ignoreBeamGapRows || Math.abs(iy) > 2) {
-	    			// Add the energy to the appropriate energy tracking
-	    			// variable for the calorimeter halves.
-	    			if(iy > 0) { energy[0] += hit.getCorrectedEnergy() * beamRatio; }
-	    			else { energy[1] += hit.getCorrectedEnergy() * beamRatio; }
-	    			
-	    			// Populate the occupancy distribution.
-	    			occupancyDistribution.fill(ix, iy, scalingFactor);
-    			}
-    		}
-			
-			// Populate the total calorimeter energy plot.
-			totalEnergyDistribution[0].fill(energy[0], scalingFactor);
-			totalEnergyDistribution[1].fill(energy[1], scalingFactor);
-    	}
+        // If clusters are present, process them.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the list of clusters.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Use the clusters to populate the cluster plots.
+            for(Cluster cluster : clusterList) {
+                // Get the ix and iy values for the cluster.
+                int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                int iy = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+                
+                // If we want to ignore the beam gap rows, make sure
+                // that iy exceeds two.
+                if(!ignoreBeamGapRows || (Math.abs(iy) > 2)) {
+                    // If the cluster passes the seed threshold, place it in
+                    // the level 1 plots.
+                    if(cluster.getCalorimeterHits().get(0).getCorrectedEnergy() >= seedThreshold) {
+                        clusterDistribution[0].fill(ix, iy, scalingFactor);
+                        clusterHitDistribution[0].fill(cluster.getCalorimeterHits().size(), scalingFactor);
+                        clusterEnergyDistribution[0].fill(cluster.getEnergy() * beamRatio, scalingFactor);
+                    }
+                    
+                    // If the cluster energy passes the cluster threshold,
+                    // populate the level 2 plots.
+                    if(cluster.getEnergy() >= clusterThreshold) {
+                        clusterDistribution[1].fill(ix, iy, scalingFactor);
+                        clusterHitDistribution[1].fill(cluster.getCalorimeterHits().size(), scalingFactor);
+                        clusterEnergyDistribution[1].fill(cluster.getEnergy() * beamRatio, scalingFactor);
+                    }
+                }
+            }
+        }
+        
+        // If the event has hits, process them.
+        if(event.hasCollection(CalorimeterHit.class, hitCollectionName)) {
+            // Get the list of hits.
+            List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, hitCollectionName);
+            
+            // Track the energy in the top and bottom of the calorimeter.
+            double[] energy = { 0.0, 0.0 };
+            
+            // Iterate over the hits.
+            for(CalorimeterHit hit : hitList) {
+                // Get the ix and iy values.
+                int ix = hit.getIdentifierFieldValue("ix");
+                int iy = hit.getIdentifierFieldValue("iy");
+                
+                // If we want to ignore beam gap rows, ensure that iy
+                // is greater than 2.
+                if(!ignoreBeamGapRows || Math.abs(iy) > 2) {
+                    // Add the energy to the appropriate energy tracking
+                    // variable for the calorimeter halves.
+                    if(iy > 0) { energy[0] += hit.getCorrectedEnergy() * beamRatio; }
+                    else { energy[1] += hit.getCorrectedEnergy() * beamRatio; }
+                    
+                    // Populate the occupancy distribution.
+                    occupancyDistribution.fill(ix, iy, scalingFactor);
+                }
+            }
+            
+            // Populate the total calorimeter energy plot.
+            totalEnergyDistribution[0].fill(energy[0], scalingFactor);
+            totalEnergyDistribution[1].fill(energy[1], scalingFactor);
+        }
     }
     
     @Override
     public void startOfData() {
-    	// Define the cluster distribution plots.
-    	String[] clusterDistName = { String.format("Comp Plots :: Cluster Seed Distribution [Seed Threshold %.3f GeV]", seedThreshold),
-    			String.format("Comp Plots :: Cluster Seed Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
+        // Define the cluster distribution plots.
+        String[] clusterDistName = { String.format("Comp Plots :: Cluster Seed Distribution [Seed Threshold %.3f GeV]", seedThreshold),
+                String.format("Comp Plots :: Cluster Seed Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
         clusterDistribution[0] = aida.histogram2D(clusterDistName[0], 46, -23, 23, 11, -5.5, 5.5);
         clusterDistribution[1] = aida.histogram2D(clusterDistName[1], 46, -23, 23, 11, -5.5, 5.5);
         
-    	// Define the occupancy distribution plots.
-    	String occupancyDistName = String.format("Comp Plots :: Crystal Occupancy");
-    	occupancyDistribution = aida.histogram2D(occupancyDistName, 46, -23, 23, 11, -5.5, 5.5);
-    	
+        // Define the occupancy distribution plots.
+        String occupancyDistName = String.format("Comp Plots :: Crystal Occupancy");
+        occupancyDistribution = aida.histogram2D(occupancyDistName, 46, -23, 23, 11, -5.5, 5.5);
+        
         // Define the cluster hit count distribution.
-    	String[] clusterHitDistName = { String.format("Comp Plots :: Cluster Hit Count Distribution [Seed Threshold %.3f GeV]", seedThreshold),
-    			String.format("Comp Plots :: Cluster Hit Count Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
-    	clusterHitDistribution[0] = aida.histogram1D(clusterHitDistName[0], 9, 1, 10);
-    	clusterHitDistribution[1] = aida.histogram1D(clusterHitDistName[1], 9, 1, 10);
-    	
+        String[] clusterHitDistName = { String.format("Comp Plots :: Cluster Hit Count Distribution [Seed Threshold %.3f GeV]", seedThreshold),
+                String.format("Comp Plots :: Cluster Hit Count Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
+        clusterHitDistribution[0] = aida.histogram1D(clusterHitDistName[0], 9, 1, 10);
+        clusterHitDistribution[1] = aida.histogram1D(clusterHitDistName[1], 9, 1, 10);
+        
         // Define the cluster total energy distribution.
-    	String[] clusterEnergyDistName = { String.format("Comp Plots :: Cluster Total Energy Distribution [Seed Threshold %.3f GeV]", seedThreshold),
-    			String.format("Comp Plots :: Cluster Total Energy Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
-    	clusterEnergyDistribution[0] = aida.histogram1D(clusterEnergyDistName[0], 176, 0.0, 2.2);
-    	clusterEnergyDistribution[1] = aida.histogram1D(clusterEnergyDistName[1], 176, 0.0, 2.2);
-    	
+        String[] clusterEnergyDistName = { String.format("Comp Plots :: Cluster Total Energy Distribution [Seed Threshold %.3f GeV]", seedThreshold),
+                String.format("Comp Plots :: Cluster Total Energy Distribution [Cluster Threshold %.3f GeV]", clusterThreshold) };
+        clusterEnergyDistribution[0] = aida.histogram1D(clusterEnergyDistName[0], 176, 0.0, 2.2);
+        clusterEnergyDistribution[1] = aida.histogram1D(clusterEnergyDistName[1], 176, 0.0, 2.2);
+        
         // Define the calorimeter total energy distribution.
-    	String[] totalEnergyDistName = { String.format("Comp Plots :: Calorimeter Event Energy Distribution [Top]"),
-    			String.format("Comp Plots :: Calorimeter Event Energy Distribution [Bottom]") };
-    	totalEnergyDistribution[0] = aida.histogram1D(totalEnergyDistName[0], 500, 0.0, 10.0);
-    	totalEnergyDistribution[1] = aida.histogram1D(totalEnergyDistName[1], 500, 0.0, 10.0);
+        String[] totalEnergyDistName = { String.format("Comp Plots :: Calorimeter Event Energy Distribution [Top]"),
+                String.format("Comp Plots :: Calorimeter Event Energy Distribution [Bottom]") };
+        totalEnergyDistribution[0] = aida.histogram1D(totalEnergyDistName[0], 500, 0.0, 10.0);
+        totalEnergyDistribution[1] = aida.histogram1D(totalEnergyDistName[1], 500, 0.0, 10.0);
     }
 }

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ReadoutTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ReadoutTrigger.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ReadoutTrigger.java	Wed Apr 27 11:11:32 2016
@@ -22,16 +22,16 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ReadoutTrigger extends Driver {
-	// Define settable parameters.
-	private double energySlopeParamF = 0.0055;
-	private String clusterCollectionName = "EcalClusters";
-	
-	// Define internal variables.
-	private TriggerModule trigger = new TriggerModule();
-	
-	// Define output plots.
-	private static final int NO_CUTS  = 0;
-	private static final int ALL_CUTS = 1;
+    // Define settable parameters.
+    private double energySlopeParamF = 0.0055;
+    private String clusterCollectionName = "EcalClusters";
+    
+    // Define internal variables.
+    private TriggerModule trigger = new TriggerModule();
+    
+    // Define output plots.
+    private static final int NO_CUTS  = 0;
+    private static final int ALL_CUTS = 1;
     private AIDA aida = AIDA.defaultInstance();
     private IHistogram1D[] clusterSeedEnergy;
     private IHistogram1D[] clusterHitCount;
@@ -46,267 +46,267 @@
     private IHistogram2D[] clusterDistribution;
     private IHistogram2D[] pairEnergySum2D;
     private IHistogram2D[] pairEnergySlope2D;
-	
+    
     /**
      * Instantiates cluster plots.
      */
     @Override
     public void startOfData() {
-    	// Define plot type names.
-    	String[] plotType = new String[2];
-    	plotType[NO_CUTS] = "";
-    	plotType[ALL_CUTS] = " (Passed All Cuts)";
-    	
-    	// Define plot type directories.
-    	String[] plotDir = new String[2];
-    	plotDir[NO_CUTS] = "NoCuts/";
-    	plotDir[ALL_CUTS] = "PassedAll/";
-    	
-    	// Instantiate the plots.
-    	for(int i = 0; i < 2; i++) {
-    		System.out.println(plotDir[i] + "Cluster Seed Energy" + plotType[i]);
-    		clusterSeedEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Seed Energy" + plotType[i], 88, 0.0, 1.1);
-    		clusterSeedEnergy[i].annotation().addItem("xAxisLabel", "Seed Energy (GeV)");
-    		clusterSeedEnergy[i].annotation().addItem("yAxisLabel", "Count");
-    		
-    		clusterHitCount[i] = aida.histogram1D(plotDir[i] + "Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
-    		clusterHitCount[i].annotation().addItem("xAxisLabel", "Hit Count");
-    		clusterHitCount[i].annotation().addItem("yAxisLabel", "Count");
-    		
-    		clusterTotalEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Total Energy" + plotType[i], 88, 0.0, 1.1);
-    		clusterTotalEnergy[i].annotation().addItem("xAxisLabel", "Cluster Energy (GeV)");
-    		clusterTotalEnergy[i].annotation().addItem("yAxisLabel", "Count");
-    		
-    		clusterTime[i] = aida.histogram1D(plotDir[i] + "Cluster Time" + plotType[i], 100, 0.0, 400);
-    		clusterTime[i].annotation().addItem("xAxisLabel", "Cluster Time (ns)");
-    		clusterTime[i].annotation().addItem("yAxisLabel", "Count");
-		
-			pairEnergySum[i] = aida.histogram1D(plotDir[i] + "Pair Energy Sum" + plotType[i], 88, 0.0, 2.2);
-			pairEnergySum[i].annotation().addItem("xAxisLabel", "Energy Sum (GeV)");
-			pairEnergySum[i].annotation().addItem("yAxisLabel", "Count");
-    		
-			pairEnergyDifference[i] = aida.histogram1D(plotDir[i] + "Pair Energy Difference" + plotType[i], 88, 0.0, 1.1);
-			pairEnergyDifference[i].annotation().addItem("xAxisLabel", "Energy Difference (GeV)");
-			pairEnergyDifference[i].annotation().addItem("yAxisLabel", "Count");
-    		
-			pairCoplanarity[i] = aida.histogram1D(plotDir[i] + "Pair Coplanarity" + plotType[i], 180, 0.0, 180.0);
-			pairCoplanarity[i].annotation().addItem("xAxisLabel", "Coplanarity Angle (Degrees)");
-			pairCoplanarity[i].annotation().addItem("yAxisLabel", "Count");
-    		
-			pairEnergySlope[i] = aida.histogram1D(plotDir[i] + "Pair Energy Slope" + plotType[i], 200, 0.0, 4.0);
-			pairEnergySlope[i].annotation().addItem("xAxisLabel", "Energy Slope (GeV)");
-			pairEnergySlope[i].annotation().addItem("yAxisLabel", "Count");
-    		
-			pairTime[i] = aida.histogram1D(plotDir[i] + "Pair Time" + plotType[i], 100, 0.0, 400);
-			pairTime[i].annotation().addItem("xAxisLabel", "Cluster Time (ns)");
-			pairTime[i].annotation().addItem("yAxisLabel", "Count");
-    		
-			pairCoincidence[i] = aida.histogram1D(plotDir[i] + "Pair Coincidence" + plotType[i], 8, 0.0, 32);
-			pairCoincidence[i].annotation().addItem("xAxisLabel", "Coincidence Time (ns)");
-			pairCoincidence[i].annotation().addItem("yAxisLabel", "Count");
-    		
-    		clusterDistribution[i] = aida.histogram2D(plotDir[i] + "Cluster Seed Distribution" + plotType[i], 46, -23, 23, 11, -5.5, 5.5);
-    		clusterDistribution[i].annotation().addItem("xAxisLabel", "x-Index");
-    		clusterDistribution[i].annotation().addItem("yAxisLabel", "y-Index");
-    		
-    		pairEnergySum2D[i] = aida.histogram2D(plotDir[i] + "Pair Energy Sum 2D" + plotType[i], 88, 0.0, 2.2, 88, 0.0, 2.2);
-    		pairEnergySum2D[i].annotation().addItem("xAxisLabel", "E1");
-    		pairEnergySum2D[i].annotation().addItem("yAxisLabel", "E2");
-    		
-    		pairEnergySlope2D[i] = aida.histogram2D(plotDir[i] + "Pair Energy Slope 2D" + plotType[i], 88, 0.0, 1.1, 200, 0.0, 400);
-    		pairEnergySlope2D[i].annotation().addItem("xAxisLabel", "E1");
-    		pairEnergySlope2D[i].annotation().addItem("yAxisLabel", "E2");
-    	}
+        // Define plot type names.
+        String[] plotType = new String[2];
+        plotType[NO_CUTS] = "";
+        plotType[ALL_CUTS] = " (Passed All Cuts)";
+        
+        // Define plot type directories.
+        String[] plotDir = new String[2];
+        plotDir[NO_CUTS] = "NoCuts/";
+        plotDir[ALL_CUTS] = "PassedAll/";
+        
+        // Instantiate the plots.
+        for(int i = 0; i < 2; i++) {
+            System.out.println(plotDir[i] + "Cluster Seed Energy" + plotType[i]);
+            clusterSeedEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Seed Energy" + plotType[i], 88, 0.0, 1.1);
+            clusterSeedEnergy[i].annotation().addItem("xAxisLabel", "Seed Energy (GeV)");
+            clusterSeedEnergy[i].annotation().addItem("yAxisLabel", "Count");
+            
+            clusterHitCount[i] = aida.histogram1D(plotDir[i] + "Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
+            clusterHitCount[i].annotation().addItem("xAxisLabel", "Hit Count");
+            clusterHitCount[i].annotation().addItem("yAxisLabel", "Count");
+            
+            clusterTotalEnergy[i] = aida.histogram1D(plotDir[i] + "Cluster Total Energy" + plotType[i], 88, 0.0, 1.1);
+            clusterTotalEnergy[i].annotation().addItem("xAxisLabel", "Cluster Energy (GeV)");
+            clusterTotalEnergy[i].annotation().addItem("yAxisLabel", "Count");
+            
+            clusterTime[i] = aida.histogram1D(plotDir[i] + "Cluster Time" + plotType[i], 100, 0.0, 400);
+            clusterTime[i].annotation().addItem("xAxisLabel", "Cluster Time (ns)");
+            clusterTime[i].annotation().addItem("yAxisLabel", "Count");
+        
+            pairEnergySum[i] = aida.histogram1D(plotDir[i] + "Pair Energy Sum" + plotType[i], 88, 0.0, 2.2);
+            pairEnergySum[i].annotation().addItem("xAxisLabel", "Energy Sum (GeV)");
+            pairEnergySum[i].annotation().addItem("yAxisLabel", "Count");
+            
+            pairEnergyDifference[i] = aida.histogram1D(plotDir[i] + "Pair Energy Difference" + plotType[i], 88, 0.0, 1.1);
+            pairEnergyDifference[i].annotation().addItem("xAxisLabel", "Energy Difference (GeV)");
+            pairEnergyDifference[i].annotation().addItem("yAxisLabel", "Count");
+            
+            pairCoplanarity[i] = aida.histogram1D(plotDir[i] + "Pair Coplanarity" + plotType[i], 180, 0.0, 180.0);
+            pairCoplanarity[i].annotation().addItem("xAxisLabel", "Coplanarity Angle (Degrees)");
+            pairCoplanarity[i].annotation().addItem("yAxisLabel", "Count");
+            
+            pairEnergySlope[i] = aida.histogram1D(plotDir[i] + "Pair Energy Slope" + plotType[i], 200, 0.0, 4.0);
+            pairEnergySlope[i].annotation().addItem("xAxisLabel", "Energy Slope (GeV)");
+            pairEnergySlope[i].annotation().addItem("yAxisLabel", "Count");
+            
+            pairTime[i] = aida.histogram1D(plotDir[i] + "Pair Time" + plotType[i], 100, 0.0, 400);
+            pairTime[i].annotation().addItem("xAxisLabel", "Cluster Time (ns)");
+            pairTime[i].annotation().addItem("yAxisLabel", "Count");
+            
+            pairCoincidence[i] = aida.histogram1D(plotDir[i] + "Pair Coincidence" + plotType[i], 8, 0.0, 32);
+            pairCoincidence[i].annotation().addItem("xAxisLabel", "Coincidence Time (ns)");
+            pairCoincidence[i].annotation().addItem("yAxisLabel", "Count");
+            
+            clusterDistribution[i] = aida.histogram2D(plotDir[i] + "Cluster Seed Distribution" + plotType[i], 46, -23, 23, 11, -5.5, 5.5);
+            clusterDistribution[i].annotation().addItem("xAxisLabel", "x-Index");
+            clusterDistribution[i].annotation().addItem("yAxisLabel", "y-Index");
+            
+            pairEnergySum2D[i] = aida.histogram2D(plotDir[i] + "Pair Energy Sum 2D" + plotType[i], 88, 0.0, 2.2, 88, 0.0, 2.2);
+            pairEnergySum2D[i].annotation().addItem("xAxisLabel", "E1");
+            pairEnergySum2D[i].annotation().addItem("yAxisLabel", "E2");
+            
+            pairEnergySlope2D[i] = aida.histogram2D(plotDir[i] + "Pair Energy Slope 2D" + plotType[i], 88, 0.0, 1.1, 200, 0.0, 400);
+            pairEnergySlope2D[i].annotation().addItem("xAxisLabel", "E1");
+            pairEnergySlope2D[i].annotation().addItem("yAxisLabel", "E2");
+        }
     }
     
     /**
      * Produces both uncut and cut distributions from clusters.
      */
-	@Override
-	public void process(EventHeader event) {
-		// Check for a collection of clusters.
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Get the list of clusters.
-			List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
-			
-			// Track which clusters have already been plotted.
-			Set<Cluster> plottedClustersUncut = new HashSet<Cluster>(clusters.size());
-			Set<Cluster> plottedClustersCut = new HashSet<Cluster>(clusters.size());
-			
-			// Populate a list of cluster pairs.
-			List<Cluster[]> pairs = getClusterPairs(clusters);
-			
-			// Process all cluster pairs.
-			pairLoop:
-			for(Cluster[] pair : pairs) {
-				// Get the x and y indices for each cluster in the pair.
-				int[] ix = { pair[0].getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
-						pair[1].getCalorimeterHits().get(0).getIdentifierFieldValue("ix") };
-				int[] iy = { pair[0].getCalorimeterHits().get(0).getIdentifierFieldValue("iy"),
-						pair[1].getCalorimeterHits().get(0).getIdentifierFieldValue("iy") };
-				
-				// Iterate over the clusters in the pair and plot the
-				// cluster singles distributions.
-				for(int clusterIndex = 0; clusterIndex < 2; clusterIndex++) {
-					// Only plot cluster singles distributions for
-					// clusters if they have not already been plotted.
-					// Note that this is needed because the same cluster
-					// can appear across multiple pairs.
-					if(!plottedClustersUncut.contains(pair[clusterIndex])) {
-						clusterSeedEnergy[NO_CUTS].fill(TriggerModule.getValueClusterSeedEnergy(pair[clusterIndex]));
-						clusterTotalEnergy[NO_CUTS].fill(TriggerModule.getValueClusterTotalEnergy(pair[clusterIndex]));
-						clusterHitCount[NO_CUTS].fill(TriggerModule.getValueClusterHitCount(pair[clusterIndex]));
-						clusterDistribution[NO_CUTS].fill(ix[clusterIndex], iy[clusterIndex]);
-						clusterTime[NO_CUTS].fill(pair[clusterIndex].getCalorimeterHits().get(0).getTime());
-						plottedClustersUncut.add(pair[clusterIndex]);
-					}
-				}
-				
-				// Plot the cluster pair distributions.
-				pairEnergySum[NO_CUTS].fill(TriggerModule.getValueEnergySum(pair));
-				pairEnergyDifference[NO_CUTS].fill(TriggerModule.getValueEnergyDifference(pair));
-				pairEnergySlope[NO_CUTS].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
-				pairCoplanarity[NO_CUTS].fill(TriggerModule.getValueCoplanarity(pair));
-				pairTime[NO_CUTS].fill(pair[1].getCalorimeterHits().get(0).getTime());
-				pairCoincidence[NO_CUTS].fill(TriggerModule.getValueTimeCoincidence(pair));
-				pairEnergySum2D[NO_CUTS].fill(pair[0].getEnergy(), pair[1].getEnergy());
-				if(pair[0].getEnergy() < pair[1].getEnergy()) {
-					pairEnergySlope2D[NO_CUTS].fill(pair[0].getEnergy(), TriggerModule.getClusterDistance(pair[0]));
-				} else {
-					pairEnergySlope2D[NO_CUTS].fill(pair[1].getEnergy(), TriggerModule.getClusterDistance(pair[1]));
-				}
-				
-				// Perform the cluster singles cuts.
-				if(!(trigger.clusterHitCountCut(pair[0]) && trigger.clusterHitCountCut(pair[1]))) {
-					continue pairLoop;
-				} if(!(trigger.clusterTotalEnergyCut(pair[0]) && trigger.clusterTotalEnergyCut(pair[1]))) {
-					continue pairLoop;
-				} if(!(trigger.clusterSeedEnergyCut(pair[0]) && trigger.clusterSeedEnergyCut(pair[1]))) {
-					continue pairLoop;
-				}
-				
-				// Perform the cluster pair cuts.
-				if(!trigger.pairCoplanarityCut(pair)) {
-					continue pairLoop;
-				} if(!trigger.pairEnergyDifferenceCut(pair)) {
-					continue pairLoop;
-				} if(!trigger.pairEnergySlopeCut(pair)) {
-					continue pairLoop;
-				} if(!trigger.pairEnergySumCut(pair)) {
-					continue pairLoop;
-				}
-				
-				// Iterate over the clusters in the pair and plot the
-				// cluster singles distributions.
-				for(int clusterIndex = 0; clusterIndex < 2; clusterIndex++) {
-					// Only plot cluster singles distributions for
-					// clusters if they have not already been plotted.
-					// Note that this is needed because the same cluster
-					// can appear across multiple pairs.
-					if(!plottedClustersCut.contains(pair[clusterIndex])) {
-						clusterSeedEnergy[ALL_CUTS].fill(TriggerModule.getValueClusterSeedEnergy(pair[clusterIndex]));
-						clusterTotalEnergy[ALL_CUTS].fill(TriggerModule.getValueClusterTotalEnergy(pair[clusterIndex]));
-						clusterHitCount[ALL_CUTS].fill(TriggerModule.getValueClusterHitCount(pair[clusterIndex]));
-						clusterDistribution[ALL_CUTS].fill(ix[clusterIndex], iy[clusterIndex]);
-						clusterTime[ALL_CUTS].fill(pair[clusterIndex].getCalorimeterHits().get(0).getTime());
-						plottedClustersCut.add(pair[clusterIndex]);
-					}
-				}
-				
-				// Plot the cluster pair distributions.
-				pairEnergySum[ALL_CUTS].fill(TriggerModule.getValueEnergySum(pair));
-				pairEnergyDifference[ALL_CUTS].fill(TriggerModule.getValueEnergyDifference(pair));
-				pairEnergySlope[ALL_CUTS].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
-				pairCoplanarity[ALL_CUTS].fill(TriggerModule.getValueCoplanarity(pair));
-				pairTime[ALL_CUTS].fill(pair[1].getCalorimeterHits().get(0).getTime());
-				pairCoincidence[ALL_CUTS].fill(TriggerModule.getValueTimeCoincidence(pair));
-				pairEnergySum2D[ALL_CUTS].fill(pair[0].getEnergy(), pair[1].getEnergy());
-				if(pair[0].getEnergy() < pair[1].getEnergy()) {
-					pairEnergySlope2D[ALL_CUTS].fill(pair[0].getEnergy(), TriggerModule.getClusterDistance(pair[0]));
-				} else {
-					pairEnergySlope2D[ALL_CUTS].fill(pair[1].getEnergy(), TriggerModule.getClusterDistance(pair[1]));
-				}
-				
-			}
-		}
-	}
-	
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
-	
-	public void setEnergySlopeParamF(double energySlopeParamF) {
-		this.energySlopeParamF = energySlopeParamF;
-		trigger.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, energySlopeParamF);
-	}
-	
-	public void setSeedEnergyLow(double value) {
-		trigger.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW, value);
-	}
-	
-	public void setClusterEnergyLow(double value) {
-		trigger.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, value);
-	}
-	
-	public void setClusterEnergyHigh(double value) {
-		trigger.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, value);
-	}
-	
-	public void setHitCountLow(double value) {
-		trigger.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, value);
-	}
-	
-	public void setEnergySumLow(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, value);
-	}
-	
-	public void setEnergySumHigh(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, value);
-	}
-	
-	public void setEnergyDifferenceHigh(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, value);
-	}
-	
-	public void setEnergySlopeLow(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, value);
-	}
-	
-	public void setCoplanarityHigh(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, value);
-	}
-	
-	public void setTimeCoincidence(double value) {
-		trigger.setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, value);
-	}
-	
-	/**
-	 * Creates all top/bottom pairs from the event data.
-	 * @param clusters - A list of clusters from which to form pairs.
-	 * @return Returns a <code>List</code> collection that contains
-	 * <code>Cluster</code> arrays of size two.
-	 */
-	private List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
-		// Separate the clusters into top nad bottom clusters.
-		List<Cluster> topList = new ArrayList<Cluster>();
-		List<Cluster> botList = new ArrayList<Cluster>();
-		for(Cluster cluster : clusters) {
-			if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
-				topList.add(cluster);
-			} else {
-				botList.add(cluster);
-			}
-		}
-		
-		// Create all possible top/bottom cluster pairs.
-		List<Cluster[]> pairList = new ArrayList<Cluster[]>();
-		for(Cluster topCluster : topList) {
-			for(Cluster botCluster : botList) {
-				pairList.add(new Cluster[] { topCluster, botCluster });
-			}
-		}
-		
-		// Return the pairs.
-		return pairList;
-	}
+    @Override
+    public void process(EventHeader event) {
+        // Check for a collection of clusters.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the list of clusters.
+            List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
+            
+            // Track which clusters have already been plotted.
+            Set<Cluster> plottedClustersUncut = new HashSet<Cluster>(clusters.size());
+            Set<Cluster> plottedClustersCut = new HashSet<Cluster>(clusters.size());
+            
+            // Populate a list of cluster pairs.
+            List<Cluster[]> pairs = getClusterPairs(clusters);
+            
+            // Process all cluster pairs.
+            pairLoop:
+            for(Cluster[] pair : pairs) {
+                // Get the x and y indices for each cluster in the pair.
+                int[] ix = { pair[0].getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
+                        pair[1].getCalorimeterHits().get(0).getIdentifierFieldValue("ix") };
+                int[] iy = { pair[0].getCalorimeterHits().get(0).getIdentifierFieldValue("iy"),
+                        pair[1].getCalorimeterHits().get(0).getIdentifierFieldValue("iy") };
+                
+                // Iterate over the clusters in the pair and plot the
+                // cluster singles distributions.
+                for(int clusterIndex = 0; clusterIndex < 2; clusterIndex++) {
+                    // Only plot cluster singles distributions for
+                    // clusters if they have not already been plotted.
+                    // Note that this is needed because the same cluster
+                    // can appear across multiple pairs.
+                    if(!plottedClustersUncut.contains(pair[clusterIndex])) {
+                        clusterSeedEnergy[NO_CUTS].fill(TriggerModule.getValueClusterSeedEnergy(pair[clusterIndex]));
+                        clusterTotalEnergy[NO_CUTS].fill(TriggerModule.getValueClusterTotalEnergy(pair[clusterIndex]));
+                        clusterHitCount[NO_CUTS].fill(TriggerModule.getValueClusterHitCount(pair[clusterIndex]));
+                        clusterDistribution[NO_CUTS].fill(ix[clusterIndex], iy[clusterIndex]);
+                        clusterTime[NO_CUTS].fill(pair[clusterIndex].getCalorimeterHits().get(0).getTime());
+                        plottedClustersUncut.add(pair[clusterIndex]);
+                    }
+                }
+                
+                // Plot the cluster pair distributions.
+                pairEnergySum[NO_CUTS].fill(TriggerModule.getValueEnergySum(pair));
+                pairEnergyDifference[NO_CUTS].fill(TriggerModule.getValueEnergyDifference(pair));
+                pairEnergySlope[NO_CUTS].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
+                pairCoplanarity[NO_CUTS].fill(TriggerModule.getValueCoplanarity(pair));
+                pairTime[NO_CUTS].fill(pair[1].getCalorimeterHits().get(0).getTime());
+                pairCoincidence[NO_CUTS].fill(TriggerModule.getValueTimeCoincidence(pair));
+                pairEnergySum2D[NO_CUTS].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                if(pair[0].getEnergy() < pair[1].getEnergy()) {
+                    pairEnergySlope2D[NO_CUTS].fill(pair[0].getEnergy(), TriggerModule.getClusterDistance(pair[0]));
+                } else {
+                    pairEnergySlope2D[NO_CUTS].fill(pair[1].getEnergy(), TriggerModule.getClusterDistance(pair[1]));
+                }
+                
+                // Perform the cluster singles cuts.
+                if(!(trigger.clusterHitCountCut(pair[0]) && trigger.clusterHitCountCut(pair[1]))) {
+                    continue pairLoop;
+                } if(!(trigger.clusterTotalEnergyCut(pair[0]) && trigger.clusterTotalEnergyCut(pair[1]))) {
+                    continue pairLoop;
+                } if(!(trigger.clusterSeedEnergyCut(pair[0]) && trigger.clusterSeedEnergyCut(pair[1]))) {
+                    continue pairLoop;
+                }
+                
+                // Perform the cluster pair cuts.
+                if(!trigger.pairCoplanarityCut(pair)) {
+                    continue pairLoop;
+                } if(!trigger.pairEnergyDifferenceCut(pair)) {
+                    continue pairLoop;
+                } if(!trigger.pairEnergySlopeCut(pair)) {
+                    continue pairLoop;
+                } if(!trigger.pairEnergySumCut(pair)) {
+                    continue pairLoop;
+                }
+                
+                // Iterate over the clusters in the pair and plot the
+                // cluster singles distributions.
+                for(int clusterIndex = 0; clusterIndex < 2; clusterIndex++) {
+                    // Only plot cluster singles distributions for
+                    // clusters if they have not already been plotted.
+                    // Note that this is needed because the same cluster
+                    // can appear across multiple pairs.
+                    if(!plottedClustersCut.contains(pair[clusterIndex])) {
+                        clusterSeedEnergy[ALL_CUTS].fill(TriggerModule.getValueClusterSeedEnergy(pair[clusterIndex]));
+                        clusterTotalEnergy[ALL_CUTS].fill(TriggerModule.getValueClusterTotalEnergy(pair[clusterIndex]));
+                        clusterHitCount[ALL_CUTS].fill(TriggerModule.getValueClusterHitCount(pair[clusterIndex]));
+                        clusterDistribution[ALL_CUTS].fill(ix[clusterIndex], iy[clusterIndex]);
+                        clusterTime[ALL_CUTS].fill(pair[clusterIndex].getCalorimeterHits().get(0).getTime());
+                        plottedClustersCut.add(pair[clusterIndex]);
+                    }
+                }
+                
+                // Plot the cluster pair distributions.
+                pairEnergySum[ALL_CUTS].fill(TriggerModule.getValueEnergySum(pair));
+                pairEnergyDifference[ALL_CUTS].fill(TriggerModule.getValueEnergyDifference(pair));
+                pairEnergySlope[ALL_CUTS].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
+                pairCoplanarity[ALL_CUTS].fill(TriggerModule.getValueCoplanarity(pair));
+                pairTime[ALL_CUTS].fill(pair[1].getCalorimeterHits().get(0).getTime());
+                pairCoincidence[ALL_CUTS].fill(TriggerModule.getValueTimeCoincidence(pair));
+                pairEnergySum2D[ALL_CUTS].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                if(pair[0].getEnergy() < pair[1].getEnergy()) {
+                    pairEnergySlope2D[ALL_CUTS].fill(pair[0].getEnergy(), TriggerModule.getClusterDistance(pair[0]));
+                } else {
+                    pairEnergySlope2D[ALL_CUTS].fill(pair[1].getEnergy(), TriggerModule.getClusterDistance(pair[1]));
+                }
+                
+            }
+        }
+    }
+    
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
+    
+    public void setEnergySlopeParamF(double energySlopeParamF) {
+        this.energySlopeParamF = energySlopeParamF;
+        trigger.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F, energySlopeParamF);
+    }
+    
+    public void setSeedEnergyLow(double value) {
+        trigger.setCutValue(TriggerModule.CLUSTER_SEED_ENERGY_LOW, value);
+    }
+    
+    public void setClusterEnergyLow(double value) {
+        trigger.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW, value);
+    }
+    
+    public void setClusterEnergyHigh(double value) {
+        trigger.setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH, value);
+    }
+    
+    public void setHitCountLow(double value) {
+        trigger.setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW, value);
+    }
+    
+    public void setEnergySumLow(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW, value);
+    }
+    
+    public void setEnergySumHigh(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH, value);
+    }
+    
+    public void setEnergyDifferenceHigh(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, value);
+    }
+    
+    public void setEnergySlopeLow(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW, value);
+    }
+    
+    public void setCoplanarityHigh(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH, value);
+    }
+    
+    public void setTimeCoincidence(double value) {
+        trigger.setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE, value);
+    }
+    
+    /**
+     * Creates all top/bottom pairs from the event data.
+     * @param clusters - A list of clusters from which to form pairs.
+     * @return Returns a <code>List</code> collection that contains
+     * <code>Cluster</code> arrays of size two.
+     */
+    private List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
+        // Separate the clusters into top nad bottom clusters.
+        List<Cluster> topList = new ArrayList<Cluster>();
+        List<Cluster> botList = new ArrayList<Cluster>();
+        for(Cluster cluster : clusters) {
+            if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
+                topList.add(cluster);
+            } else {
+                botList.add(cluster);
+            }
+        }
+        
+        // Create all possible top/bottom cluster pairs.
+        List<Cluster[]> pairList = new ArrayList<Cluster[]>();
+        for(Cluster topCluster : topList) {
+            for(Cluster botCluster : botList) {
+                pairList.add(new Cluster[] { topCluster, botCluster });
+            }
+        }
+        
+        // Return the pairs.
+        return pairList;
+    }
 }

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/RingBuffer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/RingBuffer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/RingBuffer.java	Wed Apr 27 11:11:32 2016
@@ -8,46 +8,46 @@
  */
 public class RingBuffer {
 
-	protected double[] array;
-	protected int ptr;
+    protected double[] array;
+    protected int ptr;
 
-	public RingBuffer(int size) {
-		array = new double[size]; //initialized to 0
-		ptr = 0;
-	}
+    public RingBuffer(int size) {
+        array = new double[size]; //initialized to 0
+        ptr = 0;
+    }
 
-	/**
-	 * 
-	 * @return value stored at current cell
-	 */
-	public double currentValue() {
-		return array[ptr];
-	}
+    /**
+     * 
+     * @return value stored at current cell
+     */
+    public double currentValue() {
+        return array[ptr];
+    }
 
-	//return content of specified cell (pos=0 for current cell)
-	public double getValue(int pos) {
-		return array[((ptr + pos) % array.length + array.length) % array.length];
-	}
+    //return content of specified cell (pos=0 for current cell)
+    public double getValue(int pos) {
+        return array[((ptr + pos) % array.length + array.length) % array.length];
+    }
 
-	/**
-	 * Clear value at current cell and step to the next one
-	 */
-	public void step() {
-		array[ptr] = 0;
-		ptr++;
-		if (ptr == array.length) {
-			ptr = 0;
-		}
-	}
+    /**
+     * Clear value at current cell and step to the next one
+     */
+    public void step() {
+        array[ptr] = 0;
+        ptr++;
+        if (ptr == array.length) {
+            ptr = 0;
+        }
+    }
 
-	/**
-	 * Add given value to specified cell
-	 * @param pos Target position relative to current cell (pos=0 for current cell)
-	 * @param val 
-	 */
-	public void addToCell(int pos, double val) {
-		array[(ptr + pos) % array.length] += val;
-	}
+    /**
+     * Add given value to specified cell
+     * @param pos Target position relative to current cell (pos=0 for current cell)
+     * @param val 
+     */
+    public void addToCell(int pos, double val) {
+        array[(ptr + pos) % array.length] += val;
+    }
 
     public int getLength() {
         return array.length;

Modified: java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/TimeEvolutionEcalReadoutDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/TimeEvolutionEcalReadoutDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-readout-sim/src/main/java/org/hps/readout/ecal/TimeEvolutionEcalReadoutDriver.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
     double t0 = 18.0;
     
     public TimeEvolutionEcalReadoutDriver() {
-		hitClass = CalorimeterHit.class;
+        hitClass = CalorimeterHit.class;
     }
 
     public void setT0(double t0) {
@@ -39,8 +39,8 @@
     protected void readHits(List<CalorimeterHit> hits) {
         for (Long cellID : eDepMap.keySet()) {
             RingBuffer eDepBuffer = eDepMap.get(cellID);
-            if (eDepBuffer.currentValue() > threshold) {            	            	            	
-            	hits.add(CalorimeterHitUtilities.create(eDepBuffer.currentValue(), readoutTime(), cellID, hitType));
+            if (eDepBuffer.currentValue() > threshold) {                                                
+                hits.add(CalorimeterHitUtilities.create(eDepBuffer.currentValue(), readoutTime(), cellID, hitType));
             }
             eDepBuffer.step();
         }

Modified: java/branches/HPSJAVA-409/ecal-recon/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/pom.xml	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/ecal-recon/</url>

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalCalibrationsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalCalibrationsDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalCalibrationsDriver.java	Wed Apr 27 11:11:32 2016
@@ -35,7 +35,7 @@
 import org.lcsim.util.aida.AIDA;
 
 /**
- * This Driver will generate a {@link org.hps.conditions.EcalCalibration} collection
+ * This Driver will generate a {@link org.hps.conditions.ecal.EcalCalibration} collection
  * from the ADC value distributions of raw ECAL data.  It may optionally insert this
  * information into the conditions database using the file's run number.
  * 
@@ -46,20 +46,20 @@
  */
 public class EcalCalibrationsDriver extends Driver {
     
-    EcalConditions ecalConditions = null;
-    DatabaseConditionsManager conditionsManager = null;
-    AIDA aida = AIDA.defaultInstance();
-    IFunctionFactory functionFactory = aida.analysisFactory().createFunctionFactory(null);
-    IFitFactory fitFactory = aida.analysisFactory().createFitFactory();
-    boolean loadCalibrations = false;
-    boolean performFit = true;
-    Integer runStart = null;
-    Integer runEnd = null;
-    File outputFile = null;
-    Set<Integer> runs = new HashSet<Integer>();
-    static DecimalFormat decimalFormat = new DecimalFormat("#.####");
-    String inputHitsCollectionName = "EcalReadoutHits";
-    static String ECAL_CALIBRATIONS = "ecal_calibrations";
+    private EcalConditions ecalConditions = null;
+    private DatabaseConditionsManager conditionsManager = null;
+    private AIDA aida = AIDA.defaultInstance();
+    private IFunctionFactory functionFactory = aida.analysisFactory().createFunctionFactory(null);
+    private IFitFactory fitFactory = aida.analysisFactory().createFitFactory();
+    private boolean loadCalibrations = false;
+    private boolean performFit = true;
+    private Integer runStart = null;
+    private Integer runEnd = null;
+    private File outputFile = null;
+    private Set<Integer> runs = new HashSet<Integer>();
+    private static DecimalFormat DECIMAL_FORMAT = new DecimalFormat("#.####");
+    private String inputHitsCollectionName = "EcalReadoutHits";
+    private static String ECAL_CALIBRATIONS = "ecal_calibrations";
     
     /**
      * Set the RawTrackerHit collection of hits to be used for the calibration.
@@ -91,7 +91,7 @@
     /**
      * Set the end run number for the conditions record.  
      * It must be >= the runEnd.
-     * @param runStart The run start number.
+     * @param runEnd The run end number.
      */
     public void setRunEnd(int runEnd) {
         if (runEnd < 0) {
@@ -216,15 +216,15 @@
             }
             
             // Truncate to 4 decimal places.
-            mean = Double.valueOf(decimalFormat.format(mean));
-            sigma = Double.valueOf(decimalFormat.format(sigma));
+            mean = Double.valueOf(DECIMAL_FORMAT.format(mean));
+            sigma = Double.valueOf(DECIMAL_FORMAT.format(sigma));
             
             // Create a new calibration object and add it to the collection, using mean for pedestal
             // and sigma for noise.
             try {
-            	calibrations.add(new EcalCalibration(channelId, mean, sigma));
+                calibrations.add(new EcalCalibration(channelId, mean, sigma));
             } catch (ConditionsObjectException e) {
-            	throw new RuntimeException("Error adding new calibration object.", e);
+                throw new RuntimeException("Error adding new calibration object.", e);
             }
         } 
         

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalConverterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalConverterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalConverterDriver.java	Wed Apr 27 11:11:32 2016
@@ -6,7 +6,6 @@
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawCalorimeterHit;
-import org.lcsim.event.base.BaseCalorimeterHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.lcio.LCIOConstants;
 import org.lcsim.util.Driver;
@@ -17,8 +16,8 @@
  * @version $Id: EcalConverterDriver.java,v 1.1 2013/02/25 22:39:24 meeg Exp $
  */
 public class EcalConverterDriver extends Driver {
-	
-	Detector detector = null;
+    
+    Detector detector = null;
 
     String rawCollectionName;
     String ecalReadoutName = "EcalHits";
@@ -59,7 +58,7 @@
     
     @Override
     public void detectorChanged(Detector detector) {
-    	this.detector = detector;
+        this.detector = detector;
     }
 
     @Override
@@ -87,8 +86,8 @@
     }
 
     private CalorimeterHit HitDtoA(RawCalorimeterHit hit) {
-    	double energy = DtoA(hit.getAmplitude(), hit.getCellID());
-    	return CalorimeterHitUtilities.create(energy, period * hit.getTimeStamp() + dt, hit.getCellID());
+        double energy = DtoA(hit.getAmplitude(), hit.getCellID());
+        return CalorimeterHitUtilities.create(energy, period * hit.getTimeStamp() + dt, hit.getCellID());
     }
 
 //    private RawCalorimeterHit HitAtoD(CalorimeterHit hit) {

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalEdepToTriggerConverterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalEdepToTriggerConverterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalEdepToTriggerConverterDriver.java	Wed Apr 27 11:11:32 2016
@@ -29,11 +29,11 @@
  * @author Holly Szumila <[log in to unmask]>
  */
 public class EcalEdepToTriggerConverterDriver extends Driver {
-	
+    
     private EcalConditions ecalConditions = null;
     
     private static final boolean isBadChannelLoaded = true;
-	
+    
     private final String ecalReadoutName = "EcalHits";
     private String inputCollection = "EcalHits";
     private String readoutCollection = "EcalCalHits";
@@ -94,7 +94,7 @@
 
     @Override
     public void detectorChanged(Detector detector) {
-    	
+        
         // ECAL combined conditions object.
         ecalConditions = DatabaseConditionsManager.getInstance().getEcalConditions();
                 
@@ -104,7 +104,7 @@
     public boolean isBadCrystal(CalorimeterHit hit) {
         // Get the channel data.
         EcalChannelConstants channelData = findChannel(hit.getCellID());
-    	
+        
         return isBadChannelLoaded ? channelData.isBadChannel() : false;
     }
 
@@ -165,8 +165,8 @@
 //        System.out.format("trigger: %f %f\n", amplitude, triggerIntegral);
 
         int truncatedIntegral = (int) Math.floor(triggerIntegral / truncateScale);
-        if (truncatedIntegral > 0) {        	
-        	return CalorimeterHitUtilities.create(truncatedIntegral, hit.getTime(), hit.getCellID());
+        if (truncatedIntegral > 0) {            
+            return CalorimeterHitUtilities.create(truncatedIntegral, hit.getTime(), hit.getCellID());
         }
         return null;
     }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverter.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverter.java	Wed Apr 27 11:11:32 2016
@@ -27,28 +27,28 @@
     private int nPeak = 3;
     
     public EcalOnlineRawConverter() {
-    	// Track changes in the DAQ configuration.
-    	ConfigurationManager.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				// Get the FADC configuration.
-				config = ConfigurationManager.getInstance().getFADCConfig();
-				// Get the number of peaks.
-				if(config.getMode() == 1) nPeak = Integer.MAX_VALUE;
-				else                      nPeak = config.getMaxPulses();
-				// Print the FADC configuration.
-				System.out.println();
-				System.out.println();
-				System.out.printf("NSA            :: %d ns%n", config.getNSA());
-				System.out.printf("NSB            :: %d ns%n", config.getNSB());
-				System.out.printf("Window Samples :: %d clock-cycles%n", config.getWindowWidth());
-				System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
-				System.out.println("======================================================================");
-				System.out.println("=== FADC Pulse-Processing Settings ===================================");
-				System.out.println("======================================================================");
-				config.printConfig();
-			}
-    	});
+        // Track changes in the DAQ configuration.
+        ConfigurationManager.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // Get the FADC configuration.
+                config = ConfigurationManager.getInstance().getFADCConfig();
+                // Get the number of peaks.
+                if(config.getMode() == 1) nPeak = Integer.MAX_VALUE;
+                else                      nPeak = config.getMaxPulses();
+                // Print the FADC configuration.
+                System.out.println();
+                System.out.println();
+                System.out.printf("NSA            :: %d ns%n", config.getNSA());
+                System.out.printf("NSB            :: %d ns%n", config.getNSB());
+                System.out.printf("Window Samples :: %d clock-cycles%n", config.getWindowWidth());
+                System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
+                System.out.println("======================================================================");
+                System.out.println("=== FADC Pulse-Processing Settings ===================================");
+                System.out.println("======================================================================");
+                config.printConfig(System.out);
+            }
+        });
     }
 
     /**
@@ -137,10 +137,10 @@
                 // search for next threshold crossing begins at end of this pulse:
                 if (ConfigurationManager.getInstance().getFADCConfig().getMode() == 1) {
                     // special case, emulating SSP:
-                	ii += 8;
+                    ii += 8;
                 } else {
                     // "normal" case, emulating FADC250:
-                	ii += config.getNSA()/nsPerSample - 1;
+                    ii += config.getNSA()/nsPerSample - 1;
                 }
 
                 // firmware limit on # of peaks:

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalOnlineRawConverterDriver.java	Wed Apr 27 11:11:32 2016
@@ -85,12 +85,12 @@
 
     @Override
     public void process(EventHeader event) {
-    	// Do not process the event if the DAQ configuration should be
-    	// used for value, but is not initialized.
-    	if(!ConfigurationManager.isInitialized()) {
-    		return;
-    	}
-    	
+        // Do not process the event if the DAQ configuration should be
+        // used for value, but is not initialized.
+        if(!ConfigurationManager.isInitialized()) {
+            return;
+        }
+        
         double timeOffset = 0.0;
         int flags = 0;
         flags += 1 << LCIOConstants.RCHBIT_TIME; //store hit time
@@ -102,12 +102,12 @@
          * This is for FADC Mode-1 data:    
          */
         if (event.hasCollection(RawTrackerHit.class, rawCollectionName)) {
-        	List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawCollectionName);
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawCollectionName);
 
-        	for (RawTrackerHit hit : hits) {
-        		newHits.addAll(converter.HitDtoA(event,hit));
-        	}
-        	event.put(ecalCollectionName, newHits, CalorimeterHit.class, flags, ecalReadoutName);
+            for (RawTrackerHit hit : hits) {
+                newHits.addAll(converter.HitDtoA(event,hit));
+            }
+            event.put(ecalCollectionName, newHits, CalorimeterHit.class, flags, ecalReadoutName);
         }
 
         /*
@@ -115,26 +115,26 @@
          */
         if (event.hasCollection(RawCalorimeterHit.class, rawCollectionName)) { 
 
-        	/*
-        	 * This is for FADC Mode-7 data:
-        	 */
-        	if (event.hasCollection(LCRelation.class, extraDataRelationsName)) { // extra information available from mode 7 readout
-        		List<LCRelation> extraDataRelations = event.get(LCRelation.class, extraDataRelationsName);
-        		for (LCRelation rel : extraDataRelations) {
-        			RawCalorimeterHit hit = (RawCalorimeterHit) rel.getFrom();
-        			GenericObject extraData = (GenericObject) rel.getTo();
-        			newHits.add(converter.HitDtoA(event,hit, extraData, timeOffset));
-        		}
-        	} else {
-        		/*
-        		 * This is for FADC Mode-3 data:
-        		 */
-        		List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, rawCollectionName);
-        		for (RawCalorimeterHit hit : hits) {
-        			newHits.add(converter.HitDtoA(event, hit, timeOffset));
-        		}
-        	}
-        	event.put(ecalCollectionName, newHits, CalorimeterHit.class, flags, ecalReadoutName);
+            /*
+             * This is for FADC Mode-7 data:
+             */
+            if (event.hasCollection(LCRelation.class, extraDataRelationsName)) { // extra information available from mode 7 readout
+                List<LCRelation> extraDataRelations = event.get(LCRelation.class, extraDataRelationsName);
+                for (LCRelation rel : extraDataRelations) {
+                    RawCalorimeterHit hit = (RawCalorimeterHit) rel.getFrom();
+                    GenericObject extraData = (GenericObject) rel.getTo();
+                    newHits.add(converter.HitDtoA(event,hit, extraData, timeOffset));
+                }
+            } else {
+                /*
+                 * This is for FADC Mode-3 data:
+                 */
+                List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, rawCollectionName);
+                for (RawCalorimeterHit hit : hits) {
+                    newHits.add(converter.HitDtoA(event, hit, timeOffset));
+                }
+            }
+            event.put(ecalCollectionName, newHits, CalorimeterHit.class, flags, ecalReadoutName);
         }
     }
 

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalPedestalCalculator.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalPedestalCalculator.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalPedestalCalculator.java	Wed Apr 27 11:11:32 2016
@@ -114,11 +114,11 @@
             }
         }
         if (uploadToDB) {
-        	try {
-        		uploadToDB();
-        	} catch (DatabaseObjectException | ConditionsObjectException | SQLException e) {
-        		throw new RuntimeException("Error uploading to database.", e);
-        	}
+            try {
+                uploadToDB();
+            } catch (DatabaseObjectException | ConditionsObjectException | SQLException e) {
+                throw new RuntimeException("Error uploading to database.", e);
+            }
         } else {
             System.out.println("!!!!!!!!!!!!!!!!!!!!!!! Not Writing Database !!!!!!!!!!!!!!!!!!!!!!!!!!");
         }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverter.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverter.java	Wed Apr 27 11:11:32 2016
@@ -41,9 +41,9 @@
  */
 public class EcalRawConverter {
 
-	/**
-	 * If true, time walk correction is performed. 
-	 */
+    /**
+     * If true, time walk correction is performed. 
+     */
     private boolean useTimeWalkCorrection = true;
     
     /**
@@ -149,42 +149,42 @@
      * for trigger emulation.
      */
     public EcalRawConverter() {
-    	// Track changes in the DAQ configuration.
-    	ConfigurationManager.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				// If the DAQ configuration should be used, load the
-				// relevant settings into the driver.
-				if(useDAQConfig) {
-					// Get the FADC configuration.
-					config = ConfigurationManager.getInstance().getFADCConfig();
-					
-					// Load the settings.
-					NSB = config.getNSB();
-					NSA = config.getNSA();
-					windowSamples = config.getWindowWidth() / 4;
-					
-					// Get the number of peaks.
-					if(config.getMode() == 1) {
-						nPeak = Integer.MAX_VALUE;
-					} else {
-						nPeak = config.getMaxPulses();
-					}
-					
-					// Print the FADC configuration.
-					System.out.println();
-					System.out.println();
-					System.out.printf("NSA            :: %d ns%n", NSA);
-					System.out.printf("NSB            :: %d ns%n", NSB);
-					System.out.printf("Window Samples :: %d clock-cycles%n", windowSamples);
-					System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
-					System.out.println("======================================================================");
-					System.out.println("=== FADC Pulse-Processing Settings ===================================");
-					System.out.println("======================================================================");
-					config.printConfig();
-				}
-			}
-    	});
+        // Track changes in the DAQ configuration.
+        ConfigurationManager.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // If the DAQ configuration should be used, load the
+                // relevant settings into the driver.
+                if(useDAQConfig) {
+                    // Get the FADC configuration.
+                    config = ConfigurationManager.getInstance().getFADCConfig();
+                    
+                    // Load the settings.
+                    NSB = config.getNSB();
+                    NSA = config.getNSA();
+                    windowSamples = config.getWindowWidth() / 4;
+                    
+                    // Get the number of peaks.
+                    if(config.getMode() == 1) {
+                        nPeak = Integer.MAX_VALUE;
+                    } else {
+                        nPeak = config.getMaxPulses();
+                    }
+                    
+                    // Print the FADC configuration.
+                    System.out.println();
+                    System.out.println();
+                    System.out.printf("NSA            :: %d ns%n", NSA);
+                    System.out.printf("NSB            :: %d ns%n", NSB);
+                    System.out.printf("Window Samples :: %d clock-cycles%n", windowSamples);
+                    System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
+                    System.out.println("======================================================================");
+                    System.out.println("=== FADC Pulse-Processing Settings ===================================");
+                    System.out.println("======================================================================");
+                    config.printConfig(System.out);
+                }
+            }
+        });
     }
     
  
@@ -313,7 +313,7 @@
      * for trigger emulation.
      */
     public void setUseDAQConfig(boolean state) {
-    	useDAQConfig = state;
+        useDAQConfig = state;
     }
     
 
@@ -325,10 +325,10 @@
         EcalChannelConstants channelData = findChannel(hit.getCellID());
         double pedestal;
         if(useDAQConfig) {
-    		//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
-    		pedestal = config.getPedestal(hit.getCellID());
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
+            pedestal = config.getPedestal(hit.getCellID());
         } else {
-        	pedestal = channelData.getCalibration().getPedestal();
+            pedestal = channelData.getCalibration().getPedestal();
         }
         
         int sum = 0;
@@ -356,10 +356,10 @@
      * Choose whether to use static pedestal from database or running pedestal from mode-7.
      */
     public double getSingleSamplePedestal(EventHeader event,long cellID) {
-    	if(useDAQConfig) {
-    		//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(cellID);
-    		return config.getPedestal(cellID);
-    	}
+        if(useDAQConfig) {
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(cellID);
+            return config.getPedestal(cellID);
+        }
         if (useRunningPedestal && event!=null) {
             if (event.hasItem("EcalRunningPedestals")) {
                 Map<EcalChannel, Double> runningPedMap = (Map<EcalChannel, Double>) event.get("EcalRunningPedestals");
@@ -536,12 +536,12 @@
         // threshold is pedestal plus threshold configuration parameter:
         final int absoluteThreshold;
         if(useDAQConfig) {
-        	//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
-        	//int leadingEdgeThreshold = ConfigurationManager.getInstance().getFADCConfig().getThreshold(channel.getChannelId());
-        	int leadingEdgeThreshold = config.getThreshold(cellID);
-        	absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
+            //int leadingEdgeThreshold = ConfigurationManager.getInstance().getFADCConfig().getThreshold(channel.getChannelId());
+            int leadingEdgeThreshold = config.getThreshold(cellID);
+            absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
         } else {
-        	absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
+            absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
         }
         
         ArrayList <Integer> thresholdCrossings = new ArrayList<Integer>();
@@ -562,10 +562,10 @@
                 // search for next threshold crossing begins at end of this pulse:
                 if(useDAQConfig && ConfigurationManager.getInstance().getFADCConfig().getMode() == 1) {
                     // special case, emulating SSP:
-                	ii += 8;
+                    ii += 8;
                 } else {
                     // "normal" case, emulating FADC250:
-                	ii += NSA/nsPerSample - 1;
+                    ii += NSA/nsPerSample - 1;
                 }
 
                 // firmware limit on # of peaks:
@@ -674,8 +674,8 @@
         EcalChannelConstants channelData = findChannel(cellID);
         
         if(useDAQConfig) {
-        	//float gain = ConfigurationManager.getInstance().getFADCConfig().getGain(ecalConditions.getChannelCollection().findGeometric(cellID));
-        	return config.getGain(cellID) * adcSum * EcalUtils.MeV;
+            //float gain = ConfigurationManager.getInstance().getFADCConfig().getGain(ecalConditions.getChannelCollection().findGeometric(cellID));
+            return config.getGain(cellID) * adcSum * EcalUtils.MeV;
         }  else if(use2014Gain) {
             if (constantGain) {
                 return adcSum * EcalUtils.gainFactor * EcalUtils.ecalReadoutPeriod;

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRawConverterDriver.java	Wed Apr 27 11:11:32 2016
@@ -18,14 +18,18 @@
 import org.lcsim.util.Driver;
 
 /**
- * This class is used to convert between collections of {@link org.lcsim.event.RawCalorimeterHit}
- * and {@link org.lcsim.event.RawTrackerHit}, objects with ADC/sample information, and
- * collections of {@link org.lcsim.event.CalorimeterHit}, objects with energy/time information.
- * 
- * org.hps.recon.ecal.EcalRawConverter is called to do most of the lower level work.
- *
- *
-*/
+ * This <code>Driver</code> converts raw ECal data collections to {@link org.lcsim.event.CalorimeterHit} collections 
+ * with energy and time information.  The {@link EcalRawConverter} does most of the low-level work.
+ * <p>
+ * The following input collections are used:
+ * <ul>
+ * <li>EcalReadoutHits<li>
+ * <li>EcalReadoutExtraDataRelations</li>
+ * <li>EcalRunningPedestals</li>
+ * </ul>
+ * <p>
+ * The results are by default written to the <b>EcalCalHits</b> output collection.
+ */
 public class EcalRawConverterDriver extends Driver {
 
     // To import database conditions
@@ -376,8 +380,8 @@
      * conditions database.
      */
     public void setUseDAQConfig(boolean state) {
-    	useDAQConfig = state;
-    	converter.setUseDAQConfig(state);
+        useDAQConfig = state;
+        converter.setUseDAQConfig(state);
     }
 
     @Override
@@ -400,18 +404,17 @@
 
     /**
      * @return false if the channel is a good one, true if it is a bad one
-     * @param CalorimeterHit
+     * @param hit the <code>CalorimeterHit</code> pointing to the channel
      */
     public boolean isBadCrystal(CalorimeterHit hit) {
         // Get the channel data.
         EcalChannelConstants channelData = findChannel(hit.getCellID());
-
         return channelData.isBadChannel();
     }
 
     /**
      * @return false if the ADC is a good one, true if it is a bad one
-     * @param CalorimeterHit
+     * @param hit the <code>CalorimeterHit</code> pointing to the FADC
      */
     public boolean isBadFADC(CalorimeterHit hit) {
         return (getCrate(hit.getCellID()) == 1 && getSlot(hit.getCellID()) == 3);
@@ -433,12 +436,12 @@
 
     @Override
     public void process(EventHeader event) {
-    	// Do not process the event if the DAQ configuration should be
-    	// used for value, but is not initialized.
-    	if(useDAQConfig && !ConfigurationManager.isInitialized()) {
-    		return;
-    	}
-    	
+        // Do not process the event if the DAQ configuration should be
+        // used for value, but is not initialized.
+        if(useDAQConfig && !ConfigurationManager.isInitialized()) {
+            return;
+        }
+        
         final int SYSTEM_TRIGGER = 0;
 //        final int SYSTEM_TRACKER = 1;
         final int SYSTEM_ECAL = 2;

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRunningPedestalDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRunningPedestalDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalRunningPedestalDriver.java	Wed Apr 27 11:11:32 2016
@@ -18,18 +18,21 @@
 import org.lcsim.util.Driver;
 
 /**
- * Calculate a running pedestal average for every channel from Mode7 FADCs. Uses
- * pedestals from the database if not available from the data.
- * 
- * May 2015:  Updated to also work on Mode1 data.
- * 
- * TODO: Use Logger.
+ * This <code>Driver</code> takes Mode-1 or Mode-7 ECal data and computes a running pedestal 
+ * average for every channel.  Pedestals from the database will be used if this is not available.
+ * <p>
+ * The following input collections are used:
+ * <ul>
+ * <li>EcalReadoutHits</li>
+ * <li>EcalReadoutExtraDataRelations</li>
+ * </ul>
+ * <p>
+ * Results are by default written to the <b>EcalRunningPedestals</b> output collection.
  * 
  * TODO: Timestamps from EVIO for some runs appear to not be monotonically increasing.
  *       This interferes with minLookbackTime, so it defaults to disabled and its setter
- *       is left private for now.
+ *       is left private for now. (Should be a JIRA item??? --JM)
  * 
- * @version $Id: ECalRunningPedestalDriver.java,v 1.0 2015/02/10 00:00:00
  * @author <[log in to unmask]>
  */
 public class EcalRunningPedestalDriver extends Driver {

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalTimeWalk.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalTimeWalk.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/EcalTimeWalk.java	Wed Apr 27 11:11:32 2016
@@ -39,11 +39,11 @@
      * Time walk parameters for pulse fitting
      */
     private static final double[] par = {
-    	0.9509,
-    	-33.21,
-    	0.2614,
-    	-0.9128,
-    	0.6251
+        0.9509,
+        -33.21,
+        0.2614,
+        -0.9128,
+        0.6251
    };
     
     /**
@@ -53,9 +53,9 @@
      * @return corrected time (ns)
      */
     public static final double correctTimeWalkPulseFitting(double time, double energy) {
-    	final double polyA = par[0] + par[1]*energy;
-    	final double polyB = par[2] + par[3] * energy + par[4] * Math.pow(energy, 2);
-    	return time - (Math.exp(polyA) + polyB);
+        final double polyA = par[0] + par[1]*energy;
+        final double polyB = par[2] + par[3] * energy + par[4] * Math.pow(energy, 2);
+        return time - (Math.exp(polyA) + polyB);
     }
     
     

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/FADCGenericHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/FADCGenericHit.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/FADCGenericHit.java	Wed Apr 27 11:11:32 2016
@@ -24,6 +24,14 @@
         this.slot = slot;
         this.channel = channel;
         this.data = data;
+    }
+    
+    public FADCGenericHit(GenericObject object) {
+        this.readoutMode = getReadoutMode(object);
+        this.crate = getCrate(object);
+        this.slot = getSlot(object);
+        this.channel = getChannel(object);
+        this.data = getData(object);
     }
 
     @Override
@@ -114,5 +122,5 @@
             data[i] = object.getIntVal(i+4);
         }
         return data;
-    }
+    }    
 }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/IterateGainFactorDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/IterateGainFactorDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/IterateGainFactorDriver.java	Wed Apr 27 11:11:32 2016
@@ -26,15 +26,15 @@
  */
 
 public class IterateGainFactorDriver extends Driver {
-	
-	private EcalConditions ecalConditions  = null;
-		
-	/**
+    
+    private EcalConditions ecalConditions  = null;
+        
+    /**
      * Set the input collection name (source).
      *
      * @param inputCollectionName the input collection name
      */
-	private String inputCollectionName = "EcalCalHits";
+    private String inputCollectionName = "EcalCalHits";
     public void setInputCollectionName(final String inputCollectionName) {
         this.inputCollectionName = inputCollectionName;
     }
@@ -116,14 +116,14 @@
      * @return the output hit collection with gain corrected energies
      */
     public List<CalorimeterHit> iterateHits(final List<CalorimeterHit> hits) {
-    	ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
+        ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
         for (final CalorimeterHit hit : hits) {
-        	double time = hit.getTime();        	
-        	long cellID = hit.getCellID();
-        	double energy = hit.getCorrectedEnergy()*gainFileGains.get(findChannelId(cellID));
-        	CalorimeterHit newHit = CalorimeterHitUtilities.create(energy, time, cellID);
-        	newHits.add(newHit);	
-        	
+            double time = hit.getTime();            
+            long cellID = hit.getCellID();
+            double energy = hit.getCorrectedEnergy()*gainFileGains.get(findChannelId(cellID));
+            CalorimeterHit newHit = CalorimeterHitUtilities.create(energy, time, cellID);
+            newHits.add(newHit);    
+            
         }
         return newHits;
     }
@@ -134,26 +134,26 @@
      */
     @Override
     public void process(final EventHeader event) {
-    	readGainFile();
-    	
-    	        // Check if output collection already exists in event which is an error.
+        readGainFile();
+        
+                // Check if output collection already exists in event which is an error.
         if (event.hasItem(outputCollectionName)) {
             throw new RuntimeException("collection " + outputCollectionName + " already exists in event");
         }
 
         // Get the input collection.
         if (event.hasCollection(CalorimeterHit.class,inputCollectionName)){
-        	final List<CalorimeterHit> inputHitCollection = event.get(CalorimeterHit.class, inputCollectionName);
+            final List<CalorimeterHit> inputHitCollection = event.get(CalorimeterHit.class, inputCollectionName);
 
-        	// Iterate the gain correction coefficient on each hit.
-        	final List<CalorimeterHit> outputHitCollection = this.iterateHits(inputHitCollection);
-        	
+            // Iterate the gain correction coefficient on each hit.
+            final List<CalorimeterHit> outputHitCollection = this.iterateHits(inputHitCollection);
+            
             int flags = 0;
             flags += 1 << LCIOConstants.RCHBIT_TIME; //store hit time
             flags += 1 << LCIOConstants.RCHBIT_LONG; //store hit position; this flag has no effect for RawCalorimeterHits
-        	
-        	// Put the collection into the event.
-        	event.put(outputCollectionName, outputHitCollection, CalorimeterHit.class, flags, ecalReadoutName);
+            
+            // Put the collection into the event.
+            event.put(outputCollectionName, outputHitCollection, CalorimeterHit.class, flags, ecalReadoutName);
         }
     }
    

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/AbstractClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/AbstractClusterer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/AbstractClusterer.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
 /**
  * This is an abstract class that {@link Clusterer} classes should implement
  * to perform a clustering algorithm on a <code>CalorimeterHit</code> collection.
- * The sub-class should implement {@link #createClusters(List)} which is 
+ * The sub-class should implement {@link #createClusters(EventHeader, List)} which is 
  * the method that should perform the clustering algorithm.
  * 
  * @see Clusterer
@@ -69,8 +69,8 @@
     
     /**
      * This is the primary method for sub-classes to implement their clustering algorithm.
-     * @param hits
-     * @return
+     * @param hits the list of hits
+     * @return the list of created clusters
      */
     public abstract List<Cluster> createClusters(EventHeader event, List<CalorimeterHit> hits);
     

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterDriver.java	Wed Apr 27 11:11:32 2016
@@ -73,7 +73,7 @@
     
     /**
      * Set the name of the input CalorimeterHit collection to use for clustering.
-     * @param inputHitcollectionName The name of the input hit collection.
+     * @param inputHitCollectionName The name of the input hit collection.
      */
     public void setInputHitCollectionName(String inputHitCollectionName) {
         this.inputHitCollectionName = inputHitCollectionName;
@@ -128,7 +128,7 @@
      * This will use a factory method which first tries to use some hard-coded names from 
      * the cluster package.  As a last resort, it will interpret the name as a canonical 
      * class name and try to instantiate it using the Class API.
-     * @param The name or canonical class name of the Clusterer.
+     * @param name The name or canonical class name of the Clusterer.
      */
     public void setClustererName(String name) {
         clusterer = ClustererFactory.create(name);

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterEnergyCorrection.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterEnergyCorrection.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterEnergyCorrection.java	Wed Apr 27 11:11:32 2016
@@ -1,89 +1,208 @@
 package org.hps.recon.ecal.cluster;
 
+import hep.physics.vec.Hep3Vector;
+
+import org.hps.detector.ecal.EcalCrystal;
+import org.hps.detector.ecal.HPSEcalDetectorElement;
+import org.jdom.DataConversionException;
+// import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.Cluster;
 import org.lcsim.event.base.BaseCluster;
+import org.lcsim.geometry.subdetector.HPSEcal3;
 
 /**
- * This is the cluster energy correction requiring the particle id 
- * uncorrected cluster energy. This is not accurate for edge crystals
- * and should be used after cluster-track matching and after position
- * corrections.
+ * This is the cluster energy correction requiring the particle id uncorrected
+ * cluster energy. This is now updated to include edge corrections and sampling
+ * fractions derived from data.
  * 
  * @author Holly Vance <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public final class ClusterEnergyCorrection {
+
+    // Variables for electron energy corrections.
+    static final double par0_em = -0.017;
+    static final double par1_em[] = { 35, -0.06738, -0.0005613, 16.42, 0.3431,
+            -2.021, 74.85, -0.3626 };
+    static final double par2_em[] = { 35, 0.933, 0.003234, 18.06, 0.24, 8.586,
+            75.08, -0.39 };
+
+    // Variables for positron energy corrections.
+    static final double par0_ep = -0.0131;
+    static final double par1_ep[] = { 35, -0.076, -0.0008183, 17.88, 0.2886,
+            -1.192, 73.12, -0.3747 };
+    static final double par2_ep[] = { 35, 0.94, 0.003713, 18.19, 0.24, 8.342,
+            72.44, -0.39 };
+
+    // Variables for photon energy corrections.
+    static final double par0_p = -0.0113;
+    static final double par1_p[] = { 35, -0.0585, -0.0008572, 16.76, 0.2784,
+            -0.07232, 72.88, -0.1685 };
+    static final double par2_p[] = { 35, 0.9307, 0.004, 18.05, 0.23, 3.027,
+            74.93, -0.34 };
+
+    /**
+     * Calculate the corrected energy for the cluster.
+     * 
+     * @param cluster
+     *            The input cluster.
+     * @return The corrected energy.
+     */
+    public static double calculateCorrectedEnergy(HPSEcal3 ecal, Cluster cluster) {
+        double rawE = cluster.getEnergy();
+        return computeCorrectedEnergy(ecal, cluster.getParticleId(), rawE,
+                cluster.getPosition()[0], cluster.getPosition()[1]);
+    }
+
+    /**
+     * Calculate the corrected energy for the cluster using track position at
+     * ecal.
+     * 
+     * @param cluster
+     *            The input cluster.
+     * @return The corrected energy.
+     */
+    public static double calculateCorrectedEnergy(HPSEcal3 ecal,
+            Cluster cluster, double ypos) {
+        double rawE = cluster.getEnergy();
+        return computeCorrectedEnergy(ecal, cluster.getParticleId(), rawE,
+                cluster.getPosition()[0], ypos);
+    }
+
+    /**
+     * Calculate the corrected energy and set on the cluster.
+     * 
+     * @param cluster
+     *            The input cluster.
+     */
+    public static void setCorrectedEnergy(HPSEcal3 ecal, BaseCluster cluster) {
+        double correctedEnergy = calculateCorrectedEnergy(ecal, cluster);
+        cluster.setEnergy(correctedEnergy);
+    }
+
+    /**
+     * Calculate the corrected energy and set on the cluster.
+     * 
+     * @param cluster
+     *            The input cluster.
+     */
+
+    public static void setCorrectedEnergy(HPSEcal3 ecal, BaseCluster cluster,
+            double ypos) {
+        double correctedEnergy = calculateCorrectedEnergy(ecal, cluster, ypos);
+        cluster.setEnergy(correctedEnergy);
+    }
+
+    /**
+     * Calculates energy correction based on cluster raw energy and particle
+     * type as per <a href=
+     * "https://misportal.jlab.org/mis/physics/hps_notes/index.cfm?note_year=2014"
+     * >HPS Note 2014-001</a>
+     * 
+     * @param pdg
+     *            Particle id as per PDG
+     * @param rawEnergy
+     *            Raw Energy of the cluster (sum of hits with shared hit
+     *            distribution)
+     * @return Corrected Energy
+     */
+
+    private static double computeCorrectedEnergy(HPSEcal3 ecal, int pdg,
+            double rawEnergy, double xpos, double ypos) {
+        // distance to beam gap edge
+        double r;
+        // Get these values from the Ecal geometry:
+        HPSEcalDetectorElement detElement = (HPSEcalDetectorElement) ecal
+                .getDetectorElement();
+        // double BEAMGAPTOP =
+        // 22.3;//ecal.getNode().getChild("layout").getAttribute("beamgapTop").getDoubleValue();//mm
+        double BEAMGAPTOP = 20.0;
+        try {
+            BEAMGAPTOP = ecal.getNode().getChild("layout")
+                    .getAttribute("beamgapTop").getDoubleValue();
+        } catch (DataConversionException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }// mm
+        double BEAMGAPBOT = -20.0;
+        try {
+            BEAMGAPBOT = -ecal.getNode().getChild("layout")
+                    .getAttribute("beamgapBottom").getDoubleValue();
+        } catch (DataConversionException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }// mm
+        double BEAMGAPTOPC = BEAMGAPTOP + 13.0;// mm
+        double BEAMGAPBOTC = BEAMGAPBOT - 13.0;// mm
+        // x-coordinates of crystals on either side of row 1 cut out
+        EcalCrystal crystalM = detElement.getCrystal(-11, 1);
+        Hep3Vector posM = crystalM.getPositionFront();
+        EcalCrystal crystalP = detElement.getCrystal(-1, 1);
+        Hep3Vector posP = crystalP.getPositionFront();
+
+        if ((xpos < posM.x()) || (xpos > posP.x())) {
+            if (ypos > 0) {
+                r = Math.abs(ypos - BEAMGAPTOP);
+            } else {
+                r = Math.abs(ypos - BEAMGAPBOT);
+            }
+        }
+        // crystals above row 1 cut out
+        else {
+            if (ypos > 0) {
+                if (ypos > (par1_em[0] + BEAMGAPTOP)) {
+                    r = Math.abs(ypos - BEAMGAPTOP);
+                } else {
+                    r = Math.abs(ypos - BEAMGAPTOPC);
+                }
+            } else {
+                if (ypos > (-par1_em[0] + BEAMGAPBOT)) {
+                    r = Math.abs(ypos - BEAMGAPBOTC);
+                } else {
+                    r = Math.abs(ypos - BEAMGAPBOT);
+                }
+            }
+        }
         
-    // Variables for electron energy corrections.
-    //Updated with recent monte carlo --7AUG15 HS. 
-    //Old values from 2014-2015 commented out to right.
-    static final double ELECTRON_ENERGY_A = 0.01004;//-0.0027;
-    static final double ELECTRON_ENERGY_B = -0.122;//-0.06;
-    static final double ELECTRON_ENERGY_C = 0.9646;//0.95;
-    
-    // Variables for positron energy corrections.
-    static final double POSITRON_ENERGY_A = 0.00711;//-0.0096;
-    static final double POSITRON_ENERGY_B = -0.1154;//-0.042;
-    static final double POSITRON_ENERGY_C = 0.9614;//0.94;
-    
-    // Variables for photon energy corrections.
-    static final double PHOTON_ENERGY_A = 0.007595;//0.0015;
-    static final double PHOTON_ENERGY_B = -0.09766;//-0.047;
-    static final double PHOTON_ENERGY_C = 0.9512;//0.94;
-          
-    /**
-     * Calculate the corrected energy for the cluster.
-     * @param cluster The input cluster.
-     * @return The corrected energy.
-     */
-    public static double calculateCorrectedEnergy(Cluster cluster) {
-        double rawE = cluster.getEnergy();
-        return computeCorrectedEnergy(cluster.getParticleId(), rawE);
-    }
-    
-    /**
-     * Calculate the corrected energy and set on the cluster.
-     * @param cluster The input cluster.
-     */
-    public static void setCorrectedEnergy(BaseCluster cluster) {
-        double correctedEnergy = calculateCorrectedEnergy(cluster);
-        cluster.setEnergy(correctedEnergy);
-    }
-                            
-    /**
-     * Calculates energy correction based on cluster raw energy and particle type as per 
-     * <a href="https://misportal.jlab.org/mis/physics/hps_notes/index.cfm?note_year=2014">HPS Note 2014-001</a>
-     * @param pdg Particle id as per PDG
-     * @param rawEnergy Raw Energy of the cluster (sum of hits with shared hit distribution)
-     * @return Corrected Energy
-     */    
-    private static double computeCorrectedEnergy(int pdg, double rawEnergy) {
-        switch(pdg) {
-            case 11: 
-                // electron             
-                return computeCorrectedEnergy(rawEnergy, ELECTRON_ENERGY_A, ELECTRON_ENERGY_B, ELECTRON_ENERGY_C);
-            case -11: 
-                // positron
-                return computeCorrectedEnergy(rawEnergy, POSITRON_ENERGY_A, POSITRON_ENERGY_B, POSITRON_ENERGY_C);
-            case 22: 
-                // photon
-                return computeCorrectedEnergy(rawEnergy, PHOTON_ENERGY_A, PHOTON_ENERGY_B, PHOTON_ENERGY_C);
-            default: 
-                // unknown 
-                return rawEnergy;
+        //Eliminates corrections at outermost edges to negative cluster energies
+        //66 for positrons, 69 is safe for electrons and photons
+        if (r > 66) {r = 66;}
+                
+        switch (pdg) {
+        case 11:
+            // electron
+            return computeCorrectedEnergy(r, rawEnergy, par0_em, par1_em,
+                    par2_em);
+        case -11:
+            // positron
+            return computeCorrectedEnergy(r, rawEnergy, par0_ep, par1_ep,
+                    par2_ep);
+        case 22:
+            // photon
+            return computeCorrectedEnergy(r, rawEnergy, par0_p, par1_p, par2_p);
+        default:
+            // unknown
+            return rawEnergy;
         }
     }
-    
-    /**
-     * Calculates the energy correction to a cluster given the variables from the fit as per
-     * <a href="https://misportal.jlab.org/mis/physics/hps_notes/index.cfm?note_year=2014">HPS Note 2014-001</a>
-     * Note that this is correct as there is a typo in the formula print in the note. 
-     * @param rawEnergy Raw energy of the cluster
+
+    /**
+     * Calculates the energy correction to a cluster given the variables from
+     * the fit as per <a href=
+     * "https://misportal.jlab.org/mis/physics/hps_notes/index.cfm?note_year=2014"
+     * >HPS Note 2014-001</a> Note that this is correct as there is a typo in
+     * the formula print in the note.
+     * 
+     * @param rawEnergy
+     *            Raw energy of the cluster
      * @param A,B,C from fitting in note
      * @return Corrected Energy
-     */   
-    private static double computeCorrectedEnergy(double rawEnergy, double varA, double varB, double varC){
-        double corrEnergy = rawEnergy / (varA / rawEnergy + varB / (Math.sqrt(rawEnergy)) + varC);
+     */
+    private static double computeCorrectedEnergy(double y, double rawEnergy,
+            double varA, double varB[], double varC[]) {
+        int ii = y < varB[0] ? 2 : 5;
+        double corrEnergy = rawEnergy/ (varA / rawEnergy+ (varB[1] - varB[ii]* Math.exp(-(y - varB[ii + 1]) * varB[ii + 2]))/ (Math.sqrt(rawEnergy)) + 
+                (varC[1] - varC[ii]* Math.exp(-(y - varC[ii + 1]) * varC[ii + 2])));
         return corrEnergy;
-    }                   
+    }
 }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterPositionCorrection.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterPositionCorrection.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterPositionCorrection.java	Wed Apr 27 11:11:32 2016
@@ -12,30 +12,29 @@
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public final class ClusterPositionCorrection {
-           
+    //Parameterizations tested in MC using v3-fieldmap
+    //Nov 2015
+      
     // Variables for electron position corrections.
-    static final double ELECTRON_POS_A1 = -0.0005813;//0.0066;
-    static final double ELECTRON_POS_A2 = 0.005738;//-0.03;
-    static final double ELECTRON_POS_A3 = -0.0309;
-    static final double ELECTRON_POS_B1 = 0.02963;//0.028;
-    static final double ELECTRON_POS_B2 = -4.289;//-0.451;
-    static final double ELECTRON_POS_B3 = 4.596;//0.465;
+    static final double ELECTRON_POS_A1 = 0.004483;
+    static final double ELECTRON_POS_A2 = -0.02884;
+    static final double ELECTRON_POS_B1 = 0.6197;
+    static final double ELECTRON_POS_B2 = -2.279;
+    static final double ELECTRON_POS_B3 = 3.66;
     
     // Variables for positron position corrections.
-    static final double POSITRON_POS_A1 = -0.0006243;//0.0072;
-    static final double POSITRON_POS_A2 = 0.006799;//-0.031;
-    static final double POSITRON_POS_A3 = -0.03141;
-    static final double POSITRON_POS_B1 = 0.0869;//0.007;
-    static final double POSITRON_POS_B2 = 2.965;//0.342;
-    static final double POSITRON_POS_B3 = 1.653;//0.108;
+    static final double POSITRON_POS_A1 = 0.006887;
+    static final double POSITRON_POS_A2 = -0.03207;
+    static final double POSITRON_POS_B1 = -0.8048;
+    static final double POSITRON_POS_B2 = 0.9366;
+    static final double POSITRON_POS_B3 = 2.628;
     
     // Variables for photon position corrections.
-    static final double PHOTON_POS_A1 = -0.0006329;//0.005;
-    static final double PHOTON_POS_A2 = 0.00595;//-0.032;
-    static final double PHOTON_POS_A3 = -0.03563;
-    static final double PHOTON_POS_B1 = 0.06444;//0.011;
-    static final double PHOTON_POS_B2 = -0.5836;//-0.037;
-    static final double PHOTON_POS_B3 = 3.508;//0.294;
+    static final double PHOTON_POS_A1 = 0.005385;
+    static final double PHOTON_POS_A2 = -0.03562;
+    static final double PHOTON_POS_B1 = -0.1948;
+    static final double PHOTON_POS_B2 = -0.7991;
+    static final double PHOTON_POS_B3 = 3.797;
     
   
     public static double[] calculateCorrectedPosition(Cluster cluster) {
@@ -59,20 +58,20 @@
      * @param pdg Particle id as per PDG
      * @param xCl Calculated x centroid position of the cluster, uncorrected, at face
      * @param rawEnergy Raw energy of the cluster (sum of hits with shared hit distribution)
-     * @return Corrected x position
+     * @return the corrected x position
      */
     private static double computeCorrectedPosition(int pdg, double xPos, double rawEnergy) {
         //double xCl = xPos / 10.0;//convert to cm
         double xCorr;
         switch(pdg) {
             case 11: //Particle is electron        
-                xCorr = positionCorrection(xPos, rawEnergy, ELECTRON_POS_A1, ELECTRON_POS_A2, ELECTRON_POS_A3, ELECTRON_POS_B1, ELECTRON_POS_B2, ELECTRON_POS_B3);
+                xCorr = positionCorrection(xPos, rawEnergy, ELECTRON_POS_A1, ELECTRON_POS_A2, ELECTRON_POS_B1, ELECTRON_POS_B2, ELECTRON_POS_B3);
                 return xCorr;
             case -11:// Particle is positron       
-                xCorr = positionCorrection(xPos, rawEnergy, POSITRON_POS_A1, POSITRON_POS_A2, POSITRON_POS_A3, POSITRON_POS_B1, POSITRON_POS_B2, POSITRON_POS_B3);
+                xCorr = positionCorrection(xPos, rawEnergy, POSITRON_POS_A1, POSITRON_POS_A2, POSITRON_POS_B1, POSITRON_POS_B2, POSITRON_POS_B3);
                 return xCorr;
             case 22: // Particle is photon      
-                xCorr = positionCorrection(xPos, rawEnergy, PHOTON_POS_A1, PHOTON_POS_A2, PHOTON_POS_A3, PHOTON_POS_B1, PHOTON_POS_B2, PHOTON_POS_B3);
+                xCorr = positionCorrection(xPos, rawEnergy, PHOTON_POS_A1, PHOTON_POS_A2, PHOTON_POS_B1, PHOTON_POS_B2, PHOTON_POS_B3);
                 return xCorr;
             default: //Unknown 
                 xCorr = xPos;
@@ -92,10 +91,10 @@
     * @param varB1
     * @param varB2
     * @param varB3
-    * @return
+    * @return the cluster position correction
     */    
-    private static double positionCorrection(double xCl, double rawEnergy, double varA1, double varA2, double varA3, double varB1, double varB2, double varB3) {
+    private static double positionCorrection(double xCl, double rawEnergy, double varA1, double varA2, double varB1, double varB2, double varB3) {
         //return ((xCl - (varB1 * rawEnergy + varB2 / Math.sqrt(rawEnergy) + varB3))/(varA1 / Math.sqrt(rawEnergy) + varA2 + 1));
-    	return ((xCl - (varB1 * rawEnergy + varB2 / Math.sqrt(rawEnergy) + varB3))/(varA1 * rawEnergy + varA2 / Math.sqrt(rawEnergy) + varA3 + 1));
+        return ((xCl - (varB1 * rawEnergy + varB2 / Math.sqrt(rawEnergy) + varB3))/(varA1 / Math.sqrt(rawEnergy) + varA2 + 1));
     }
-}
+}

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterUtilities.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClusterUtilities.java	Wed Apr 27 11:11:32 2016
@@ -199,7 +199,7 @@
     
     /**
      * Find the unique set of MCParticles that are referenced by the hits of the Cluster.
-     * @param clusters The input Cluster.
+     * @param cluster The input Cluster.
      * @return The set of unique MCParticles.
      */
     public static Set<MCParticle> findMCParticles(Cluster cluster) {  
@@ -334,7 +334,7 @@
      * Apply HPS-specific energy and position corrections to a list of clusters in place.
      * @param clusters The list of clusters.
      */
-    public static void applyCorrections(List<Cluster> clusters) {
+    public static void applyCorrections(HPSEcal3 ecal, List<Cluster> clusters) {
                 
         // Loop over the clusters.
         for (Cluster cluster : clusters) {
@@ -347,16 +347,16 @@
                 ClusterPositionCorrection.setCorrectedPosition(baseCluster);
             
                 // Apply PID based energy correction.
-                ClusterEnergyCorrection.setCorrectedEnergy(baseCluster);
-            }
-        }
-    }
-    
-    /**
-     * Apply HPS-specific energy and position corrections to a cluster.
-     * @param cluster The input cluster.
-     */
-    public static void applyCorrections(Cluster cluster) {
+                ClusterEnergyCorrection.setCorrectedEnergy(ecal, baseCluster);
+            }
+        }
+    }
+      
+    /**
+     * Apply HPS-specific energy and position corrections to a cluster without track information.
+     * @param cluster The input cluster.
+     */
+    public static void applyCorrections(HPSEcal3 ecal, Cluster cluster) {
                             
         if (cluster instanceof BaseCluster) {
             
@@ -366,7 +366,25 @@
             ClusterPositionCorrection.setCorrectedPosition(baseCluster);
             
             // Apply PID based energy correction.
-            ClusterEnergyCorrection.setCorrectedEnergy(baseCluster);
+            ClusterEnergyCorrection.setCorrectedEnergy(ecal, baseCluster);
+        }        
+    }   
+    
+    /**
+     * Apply HPS-specific energy and position corrections to a cluster with track information.
+     * @param cluster The input cluster.
+     */
+    public static void applyCorrections(HPSEcal3 ecal, Cluster cluster, double ypos) {
+        
+        if (cluster instanceof BaseCluster) {
+            
+            BaseCluster baseCluster = (BaseCluster)cluster;            
+                        
+            // Apply PID based position correction, which should happen before final energy correction.
+            ClusterPositionCorrection.setCorrectedPosition(baseCluster);
+            
+            // Apply PID based energy correction.
+            ClusterEnergyCorrection.setCorrectedEnergy(ecal, baseCluster, ypos);
         }        
     }    
         
@@ -410,7 +428,7 @@
     
     /**
      * Get the set of hits from a list of clusters.
-     * @param The input cluster list.
+     * @param clusters The input cluster list.
      * @return The list of hits from all the clusters.
      */
     public static Set<CalorimeterHit> getHits(List<Cluster> clusters) {

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClustererFactory.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClustererFactory.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ClustererFactory.java	Wed Apr 27 11:11:32 2016
@@ -38,7 +38,7 @@
      * @param name The name of the clustering algorithm.
      * @param cuts The set of cuts (can be null).
      * @return The clustering algorithm.
-     * @throw IllegalArgumentException if there is no Clusterer found with name.
+     * @throws IllegalArgumentException if there is no Clusterer found with name.
      */
     public static Clusterer create(String name, double[] cuts) {
         Clusterer clusterer;

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/CopyClusterCollectionDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/CopyClusterCollectionDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/CopyClusterCollectionDriver.java	Wed Apr 27 11:11:32 2016
@@ -111,8 +111,8 @@
 
     /**
      * Set to <code>true</code> to store hits in the output clusters.
-     *
-     * @return <code>true</code> to store hits in the output clusters
+     * 
+     * @param storeHits <code>true</code> to store hits; <code>false</code> to not store hits
      */
     public void setStoreHits(final boolean storeHits) {
         this.storeHits = storeHits;

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterDriver.java	Wed Apr 27 11:11:32 2016
@@ -22,8 +22,8 @@
  * @see GTPClusterer
  */
 public class GTPClusterDriver extends ClusterDriver {
-	/** An instance of the clustering algorithm object for producing
-	 * cluster objects. */
+    /** An instance of the clustering algorithm object for producing
+     * cluster objects. */
     private final GTPClusterer gtp;
     
     /**
@@ -112,11 +112,11 @@
      */
     @Override
     public void setWriteClusterCollection(boolean state) {
-    	// Set the flag as appropriate with the superclass.
-    	super.setWriteClusterCollection(state);
-    	
-    	// Also tell the clusterer whether it should persist its hit
-    	// collection or not.
-    	gtp.setWriteHitCollection(state);
+        // Set the flag as appropriate with the superclass.
+        super.setWriteClusterCollection(state);
+        
+        // Also tell the clusterer whether it should persist its hit
+        // collection or not.
+        gtp.setWriteHitCollection(state);
     }
 }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPClusterer.java	Wed Apr 27 11:11:32 2016
@@ -124,7 +124,7 @@
      * forms a collection of <code>Cluster</code> objects according to
      * the GTP clustering algorithm.
      * @param event - The object containing event data.
-     * @param hitList - A list of <code>CalorimeterHit</code> objects
+     * @param hits - A list of <code>CalorimeterHit</code> objects
      * from which clusters should be formed.
      */
     public List<Cluster> createClusters(EventHeader event, List<CalorimeterHit> hits) {
@@ -146,24 +146,24 @@
         // stored in LCIO format properly, it needs to separately store
         // its clusters' hits in a collection.
         if(writeHitCollection) {
-        	// Create a set to store the hits so that each one may be
-        	// stored only once.
-	        Set<CalorimeterHit> hitSet = new HashSet<CalorimeterHit>();
-	        
-	        // Loop over all clusters and add their hits to the set.
-	        for(Cluster cluster : clusterList) {
-	        	for(CalorimeterHit hit : cluster.getCalorimeterHits()) {
-	        		hitSet.add(hit);
-	        	}
-	        }
-	        
-	        // Convert the set into a List object so that it can be stored
-	        // in LCIO.
-	        List<CalorimeterHit> clusterHits = new ArrayList<CalorimeterHit>(hitSet.size());
-	        clusterHits.addAll(hitSet);
-	        
-	        // Place the list of hits into the event stream.
-	        event.put("GTPHits", hits, CalorimeterHit.class, 0);
+            // Create a set to store the hits so that each one may be
+            // stored only once.
+            Set<CalorimeterHit> hitSet = new HashSet<CalorimeterHit>();
+            
+            // Loop over all clusters and add their hits to the set.
+            for(Cluster cluster : clusterList) {
+                for(CalorimeterHit hit : cluster.getCalorimeterHits()) {
+                    hitSet.add(hit);
+                }
+            }
+            
+            // Convert the set into a List object so that it can be stored
+            // in LCIO.
+            List<CalorimeterHit> clusterHits = new ArrayList<CalorimeterHit>(hitSet.size());
+            clusterHits.addAll(hitSet);
+            
+            // Place the list of hits into the event stream.
+            event.put("GTPHits", hits, CalorimeterHit.class, 0);
         }
         
         // Return the clusters.
@@ -260,7 +260,7 @@
      * should not.
      */
     void setVerbose(boolean verbose) {
-    	this.verbose = verbose;
+        this.verbose = verbose;
     }
     
     /**
@@ -271,7 +271,7 @@
      * persisted and <code>false</code> that they will not.
      */
     void setWriteHitCollection(boolean state) {
-    	writeHitCollection = state;
+        writeHitCollection = state;
     }
     
 /**
@@ -291,7 +291,7 @@
     
     // VERBOSE :: Print the cluster window.
     if(verbose) {
-    	// Print the event header.
+        // Print the event header.
         System.out.printf("%n%nEvent:%n");
         
         // Calculate some constants.
@@ -304,9 +304,9 @@
             CalorimeterHit hit = null;
             
             for(Entry<Long, CalorimeterHit> entry : bufferMap.entrySet()) {
-            	hit = entry.getValue();
-            	System.out.printf("\t(%3d, %3d) --> %.4f (%.4f)%n", hit.getIdentifierFieldValue("ix"),
-            			hit.getIdentifierFieldValue("iy"), hit.getCorrectedEnergy(), hit.getRawEnergy());
+                hit = entry.getValue();
+                System.out.printf("\t(%3d, %3d) --> %.4f (%.4f)%n", hit.getIdentifierFieldValue("ix"),
+                        hit.getIdentifierFieldValue("iy"), hit.getCorrectedEnergy(), hit.getRawEnergy());
             }
             
             bufferNum++;
@@ -327,8 +327,8 @@
         // VERBOSE :: Print the current cluster.
         if(verbose) {
             System.out.printf("Cluster Check:%n");
-        	System.out.printf("\t(%3d, %3d) --> %.4f%n", currentHit.getIdentifierFieldValue("ix"),
-        			currentHit.getIdentifierFieldValue("iy"), currentHit.getCorrectedEnergy());
+            System.out.printf("\t(%3d, %3d) --> %.4f%n", currentHit.getIdentifierFieldValue("ix"),
+                    currentHit.getIdentifierFieldValue("iy"), currentHit.getCorrectedEnergy());
         }
         
         // Store the energy of the current hit.
@@ -337,11 +337,11 @@
         // If the hit energy is lower than the minimum threshold,
         // then we immediately reject this hit as a possible cluster.
         if (currentEnergy < seedEnergyThreshold) {
-        	// VERBOSE :: Note the reason the potential seed was
-        	//            rejected.
-        	if(verbose) { System.out.printf("\tREJECT :: Does not exceed seed threshold %.4f.%n", seedEnergyThreshold); }
-        	
-        	// Skip to the next potential seed.
+            // VERBOSE :: Note the reason the potential seed was
+            //            rejected.
+            if(verbose) { System.out.printf("\tREJECT :: Does not exceed seed threshold %.4f.%n", seedEnergyThreshold); }
+            
+            // Skip to the next potential seed.
             continue seedLoop;
         }
         
@@ -368,16 +368,16 @@
                 // is larger than then original hit. If it is, we may
                 // stop the comparison because this is not a cluster.
                 if (bufferHitEnergy > currentEnergy) {
-                	// VERBOSE :: Output the reason the potential
-                	//            seed was rejected along with the
-                	//            hit that caused it.
-                	if(verbose) {
-                    	System.out.printf("\tREJECT :: Buffer hit surpasses hit energy.");
-                    	System.out.printf("\tBUFFER HIT :: (%3d, %3d) --> %.4f%n", bufferHit.getIdentifierFieldValue("ix"),
-                    			bufferHit.getIdentifierFieldValue("iy"), bufferHit.getCorrectedEnergy(), bufferHit.getRawEnergy());
-                	}
-                	
-                	// Skip to the next potential seed.
+                    // VERBOSE :: Output the reason the potential
+                    //            seed was rejected along with the
+                    //            hit that caused it.
+                    if(verbose) {
+                        System.out.printf("\tREJECT :: Buffer hit surpasses hit energy.");
+                        System.out.printf("\tBUFFER HIT :: (%3d, %3d) --> %.4f%n", bufferHit.getIdentifierFieldValue("ix"),
+                                bufferHit.getIdentifierFieldValue("iy"), bufferHit.getCorrectedEnergy(), bufferHit.getRawEnergy());
+                    }
+                    
+                    // Skip to the next potential seed.
                     continue seedLoop;
                 }
                 
@@ -403,16 +403,16 @@
                     // If it is, we may stop the comparison because this
                     // is not a cluster.
                     if (neighborHitEnergy > currentEnergy) {
-                    	// VERBOSE :: Output the reason the potential
-                    	//            seed was rejected along with the
-                    	//            hit that caused it.
-                    	if(verbose) {
-                        	System.out.printf("\tREJECT :: Buffer hit surpasses hit energy.%n");
-                        	System.out.printf("\tBUFFER HIT :: (%3d, %3d) --> %.4f%n", neighborHit.getIdentifierFieldValue("ix"),
-                        			neighborHit.getIdentifierFieldValue("iy"), neighborHit.getCorrectedEnergy(), neighborHit.getRawEnergy());
-                    	}
-                    	
-                    	// Skip to the next potential seed.
+                        // VERBOSE :: Output the reason the potential
+                        //            seed was rejected along with the
+                        //            hit that caused it.
+                        if(verbose) {
+                            System.out.printf("\tREJECT :: Buffer hit surpasses hit energy.%n");
+                            System.out.printf("\tBUFFER HIT :: (%3d, %3d) --> %.4f%n", neighborHit.getIdentifierFieldValue("ix"),
+                                    neighborHit.getIdentifierFieldValue("iy"), neighborHit.getCorrectedEnergy(), neighborHit.getRawEnergy());
+                        }
+                        
+                        // Skip to the next potential seed.
                         continue seedLoop;
                     }
                     
@@ -436,10 +436,10 @@
         if(verbose) {
             System.out.printf("Cluster added.%n");
             System.out.printf("\t(%3d, %3d) --> %.4f GeV --> %d hits%n", cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
-            		cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"), cluster.getEnergy(), cluster.getCalorimeterHits().size());
+                    cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"), cluster.getEnergy(), cluster.getCalorimeterHits().size());
             for(CalorimeterHit hit : cluster.getCalorimeterHits()) {
-            	System.out.printf("\t\tCLUSTER HIT :: (%3d, %3d) --> %.4f%n", hit.getIdentifierFieldValue("ix"),
-            			hit.getIdentifierFieldValue("iy"), hit.getCorrectedEnergy(), hit.getRawEnergy());
+                System.out.printf("\t\tCLUSTER HIT :: (%3d, %3d) --> %.4f%n", hit.getIdentifierFieldValue("ix"),
+                        hit.getIdentifierFieldValue("iy"), hit.getCorrectedEnergy(), hit.getRawEnergy());
             }
         }
     }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterDriver.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterDriver.java	Wed Apr 27 11:11:32 2016
@@ -39,8 +39,8 @@
  * @see org.hps.record.daqconfig.DAQConfigDriver
  */
 public class GTPOnlineClusterDriver extends ClusterDriver {
-	/** An instance of the clustering algorithm object for producing
-	 * cluster objects. */
+    /** An instance of the clustering algorithm object for producing
+     * cluster objects. */
     private final GTPOnlineClusterer gtp;
     /** Indicates whether the <code>ConfigurationManager</code> object
      * should be used for clustering settings or not. */
@@ -53,29 +53,29 @@
      * @see GTPOnlineClusterer
      */
     public GTPOnlineClusterDriver() {
-    	// Instantiate the clusterer.
+        // Instantiate the clusterer.
         clusterer = ClustererFactory.create("GTPOnlineClusterer");
         gtp = (GTPOnlineClusterer) clusterer;
         
         // Track the DAQ configuration status.
         ConfigurationManager.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				// If DAQ configuration settings should be used, then
-				// update the clusterer.
-				if(useDAQConfig) {
-					// Get the GTP settings.
-					GTPConfig config = ConfigurationManager.getInstance().getGTPConfig();
-					
-					// Send the DAQ configuration settings to the clusterer.
-					gtp.setSeedLowThreshold(config.getSeedEnergyCutConfig().getLowerBound());
-					gtp.setWindowAfter(config.getTimeWindowAfter());
-					gtp.setWindowBefore(config.getTimeWindowBefore());
-					
-					// Print the updated settings.
-					logSettings();
-				}
-			}
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // If DAQ configuration settings should be used, then
+                // update the clusterer.
+                if(useDAQConfig) {
+                    // Get the GTP settings.
+                    GTPConfig config = ConfigurationManager.getInstance().getGTPConfig();
+                    
+                    // Send the DAQ configuration settings to the clusterer.
+                    gtp.setSeedLowThreshold(config.getSeedEnergyCutConfig().getLowerBound());
+                    gtp.setWindowAfter(config.getTimeWindowAfter());
+                    gtp.setWindowBefore(config.getTimeWindowBefore());
+                    
+                    // Print the updated settings.
+                    logSettings();
+                }
+            }
         });
     }
     
@@ -90,11 +90,11 @@
      */
     @Override
     public void process(EventHeader event) {
-    	// Only process an event if either the DAQ configuration is not
-    	// in use or if it has been initialized.
-    	if((useDAQConfig && ConfigurationManager.isInitialized()) || !useDAQConfig) {
-    		super.process(event);
-    	}
+        // Only process an event if either the DAQ configuration is not
+        // in use or if it has been initialized.
+        if((useDAQConfig && ConfigurationManager.isInitialized()) || !useDAQConfig) {
+            super.process(event);
+        }
     }
     
     /**
@@ -103,8 +103,8 @@
      */
     @Override
     public void startOfData() {
-    	// VERBOSE :: Output the driver settings.
-    	if(gtp.isVerbose()) { logSettings(); }
+        // VERBOSE :: Output the driver settings.
+        if(gtp.isVerbose()) { logSettings(); }
     }
     
     /**
@@ -168,23 +168,23 @@
      * @see org.hps.record.daqconfig.DAQConfigDriver
      */
     public void setUseDAQConfig(boolean state) {
-    	useDAQConfig = state;
+        useDAQConfig = state;
     }
     
     /**
      * Outputs the current GTP settings to the terminal.
      */
     private void logSettings() {
-		// Print the cluster driver header.
-		System.out.println();
-		System.out.println();
-		System.out.println("======================================================================");
-		System.out.println("=== GTP Readout Clusterer Settings ===================================");
-		System.out.println("======================================================================");
-		
-		// Output the driver settings.
-		System.out.printf("Seed Energy Threshold :: %.3f GeV%n", gtp.getSeedLowThreshold());
-		System.out.printf("Time Window (Before)  :: %.0f ns%n", gtp.getWindowBefore());
-		System.out.printf("Time Window (After)   :: %.0f ns%n", gtp.getWindowAfter());
+        // Print the cluster driver header.
+        System.out.println();
+        System.out.println();
+        System.out.println("======================================================================");
+        System.out.println("=== GTP Readout Clusterer Settings ===================================");
+        System.out.println("======================================================================");
+        
+        // Output the driver settings.
+        System.out.printf("Seed Energy Threshold :: %.3f GeV%n", gtp.getSeedLowThreshold());
+        System.out.printf("Time Window (Before)  :: %.0f ns%n", gtp.getWindowBefore());
+        System.out.printf("Time Window (After)   :: %.0f ns%n", gtp.getWindowAfter());
     }
 }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/GTPOnlineClusterer.java	Wed Apr 27 11:11:32 2016
@@ -69,10 +69,10 @@
  * @see GTPClusterer
  */
 public class GTPOnlineClusterer extends AbstractClusterer {
-	/**
-	 * The length of the temporal window for inclusing clusters that
-	 * occur before the seed hit.
-	 */
+    /**
+     * The length of the temporal window for inclusing clusters that
+     * occur before the seed hit.
+     */
     private double timeBefore = 4;
     
     /**
@@ -102,7 +102,7 @@
     
     // Diagnostic plots.
     private AIDA aida = AIDA.defaultInstance();
-    private IHistogram1D hitEnergy = aida.histogram1D("GTP(O) Cluster Plot/Hit Energy Distribution", 256, -1.0, 2.2);
+    private IHistogram1D hitEnergy = aida.histogram1D("GTP(O) Cluster Plots/Hit Energy Distribution", 256, -1.0, 2.2);
     private IHistogram1D clusterSeedEnergy = aida.histogram1D("GTP(O) Cluster Plots/Cluster Seed Energy Distribution", 176, 0.0, 2.2);
     private IHistogram1D clusterHitCount = aida.histogram1D("GTP(O) Cluster Plots/Cluster Hit Count Distribution", 9, 1, 10);
     private IHistogram1D clusterTotalEnergy = aida.histogram1D("GTP(O) Cluster Plots/Cluster Total Energy Distribution", 176, 0.0, 2.2);
@@ -128,29 +128,29 @@
      */
     @Override
     public List<Cluster> createClusters(EventHeader event, List<CalorimeterHit> hitList) {
-    	// VERBOSE :: Print the driver header.
-    	if(verbose) {
-    		System.out.println();
-    		System.out.println();
-    		System.out.println("======================================================================");
-    		System.out.println("=== GTP Readout Clusterer ============================================");
-    		System.out.println("======================================================================");
-    		
-    		// Sort the hits by x-index and then by y-index.
-        	Collections.sort(hitList, new Comparator<CalorimeterHit>() {
-				@Override
-				public int compare(CalorimeterHit firstHit, CalorimeterHit secondHit) {
-					int[] ix = { firstHit.getIdentifierFieldValue("ix"), secondHit.getIdentifierFieldValue("ix") };
-					if(ix[0] != ix[1]) { return Integer.compare(ix[0], ix[1]); }
-					else {
-						int iy[] = { firstHit.getIdentifierFieldValue("iy"), secondHit.getIdentifierFieldValue("iy") };
-						return Integer.compare(iy[0], iy[1]);
-					}
-				}
-        	});
-        	
-        	// Print the hit collection.
-        	System.out.println("Event Hit Collection:");
+        // VERBOSE :: Print the driver header.
+        if(verbose) {
+            System.out.println();
+            System.out.println();
+            System.out.println("======================================================================");
+            System.out.println("=== GTP Readout Clusterer ============================================");
+            System.out.println("======================================================================");
+            
+            // Sort the hits by x-index and then by y-index.
+            Collections.sort(hitList, new Comparator<CalorimeterHit>() {
+                @Override
+                public int compare(CalorimeterHit firstHit, CalorimeterHit secondHit) {
+                    int[] ix = { firstHit.getIdentifierFieldValue("ix"), secondHit.getIdentifierFieldValue("ix") };
+                    if(ix[0] != ix[1]) { return Integer.compare(ix[0], ix[1]); }
+                    else {
+                        int iy[] = { firstHit.getIdentifierFieldValue("iy"), secondHit.getIdentifierFieldValue("iy") };
+                        return Integer.compare(iy[0], iy[1]);
+                    }
+                }
+            });
+            
+            // Print the hit collection.
+            System.out.println("Event Hit Collection:");
             for(CalorimeterHit hit : hitList) {
                 int ix = hit.getIdentifierFieldValue("ix");
                 int iy = hit.getIdentifierFieldValue("iy");
@@ -161,7 +161,7 @@
             }
             System.out.println();
         }
-    	
+        
         // Track the valid clusters.
         List<Cluster> clusterList = new ArrayList<Cluster>();
         
@@ -183,10 +183,10 @@
         // Iterate over each hit and see if it qualifies as a seed hit.
         seedLoop:
             for(CalorimeterHit seed : hitList) {
-            	// Put the hit energy into the hit energy distribution.
-            	hitEnergy.fill(seed.getCorrectedEnergy());
-            	hitDistribution.fill(seed.getIdentifierFieldValue("ix"), seed.getIdentifierFieldValue("iy"));
-            	
+                // Put the hit energy into the hit energy distribution.
+                hitEnergy.fill(seed.getCorrectedEnergy());
+                hitDistribution.fill(seed.getIdentifierFieldValue("ix"), seed.getIdentifierFieldValue("iy"));
+                
                 // Check whether the potential seed passes the seed
                 // energy cut.
                 if(seed.getCorrectedEnergy() < seedThreshold) {
@@ -204,16 +204,16 @@
                 // energies.
                 hitLoop:
                 for(CalorimeterHit hit : hitList) {
-                	// Negative energy hits are never valid. Skip them.
-                	if(hit.getCorrectedEnergy() < 0) {
-                		continue hitLoop;
-                	}
-                	
-                	// Do not compare the potential seed hit to itself.
-                	if(hit == seed) {
-                		continue hitLoop;
-                	}
-                	
+                    // Negative energy hits are never valid. Skip them.
+                    if(hit.getCorrectedEnergy() < 0) {
+                        continue hitLoop;
+                    }
+                    
+                    // Do not compare the potential seed hit to itself.
+                    if(hit == seed) {
+                        continue hitLoop;
+                    }
+                    
                     // Check if the hit is within the spatiotemporal
                     // clustering window.
                     if(withinTimeVerificationWindow(seed, hit) && withinSpatialWindow(seed, hit)) {
@@ -246,25 +246,25 @@
                 clusterTotalEnergy.fill(protoCluster.getEnergy());
                 clusterHitCount.fill(protoCluster.getCalorimeterHits().size());
                 clusterDistribution.fill(protoCluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix"),
-                		protoCluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"));
+                        protoCluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy"));
                 
                 // Determine how much energy in the cluster is negative
                 // and how is positive.
                 double nenergy = 0.0;
                 double penergy = 0.0;
                 for(CalorimeterHit hit : protoCluster.getCalorimeterHits()) {
-                	if(hit.getCorrectedEnergy() > 0) { penergy += hit.getCorrectedEnergy(); }
-                	else { nenergy += hit.getCorrectedEnergy(); }
+                    if(hit.getCorrectedEnergy() > 0) { penergy += hit.getCorrectedEnergy(); }
+                    else { nenergy += hit.getCorrectedEnergy(); }
                 }
                 energyDistribution.fill(Math.abs(nenergy) / (penergy + Math.abs(nenergy)));
             }
         
         // VERBOSE :: Print out all the clusters in the event.
         if(verbose) {
-        	// Print the clusters.
-        	System.out.println("Event Cluster Collection:");
+            // Print the clusters.
+            System.out.println("Event Cluster Collection:");
             for(Cluster cluster : clusterList) {
-            	// Output basic cluster positional and energy data.
+                // Output basic cluster positional and energy data.
                 CalorimeterHit seedHit = cluster.getCalorimeterHits().get(0);
                 int ix = seedHit.getIdentifierFieldValue("ix");
                 int iy = seedHit.getIdentifierFieldValue("iy");
@@ -281,7 +281,7 @@
                     System.out.printf("\t\tCompHit --> %.3f GeV at (%3d, %3d) and at t = %.2f%n", henergy, hix, hiy, htime);
                 }
             }
-        	System.out.println();
+            System.out.println();
         }
         
         // VERBOSE :: Print a new line.
@@ -366,11 +366,11 @@
      * the seed hit in clock cycles.
      */
     void setWindowBefore(int cyclesBefore) {
-    	// The cluster window can not be negative.
-    	if(cyclesBefore < 0) { cyclesBefore = 0; }
-    	
-    	// Convert the window to nanoseconds and set the two time
-    	// windows appropriately.
+        // The cluster window can not be negative.
+        if(cyclesBefore < 0) { cyclesBefore = 0; }
+        
+        // Convert the window to nanoseconds and set the two time
+        // windows appropriately.
         timeBefore = cyclesBefore * 4;
         timeWindow = Math.max(timeBefore, timeAfter);
     }
@@ -384,11 +384,11 @@
      * the seed hit in clock cycles.
      */
     void setWindowAfter(int cyclesAfter) {
-    	// The cluster window can not be negative.
-    	if(cyclesAfter < 0) { cyclesAfter = 0; }
-    	
-    	// Convert the window to nanoseconds and set the two time
-    	// windows appropriately.
+        // The cluster window can not be negative.
+        if(cyclesAfter < 0) { cyclesAfter = 0; }
+        
+        // Convert the window to nanoseconds and set the two time
+        // windows appropriately.
         timeAfter = cyclesAfter * 4;
         timeWindow = Math.max(timeBefore, timeAfter);
     }
@@ -494,9 +494,9 @@
             // considered to be adjacent to ix = -1 rather than the
             // expected ix = 0. (ix = 0 does not exist.)
             else {
-            	// ix = -1 is adjacent to ix = 1 and vice versa.
+                // ix = -1 is adjacent to ix = 1 and vice versa.
                 if((six == -1 && hix == 1) || (six == 1 && hix == -1)) {
-                	return true;
+                    return true;
                 }
                 
                 // Any other combination that reaches this point is not
@@ -561,4 +561,4 @@
         // treated as within time.
         else { return false; }
     }
-}
+}

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ReconClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ReconClusterer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/ReconClusterer.java	Wed Apr 27 11:11:32 2016
@@ -289,7 +289,7 @@
                 // If the neighboring crystal exists and is not already
                 // in a cluster, add it to the list of neighboring hits.
                 if (secondaryNeighborHit != null && !hitToSeed.containsKey(secondaryNeighborHit)
-                		&& hitList.contains(secondaryNeighborHit)) {
+                        && hitList.contains(secondaryNeighborHit)) {
                     secondaryNeighborHits.add(secondaryNeighborHit);
                 }
             }
@@ -325,7 +325,7 @@
                 // If it exists, add it to the neighboring hit list.
 
                 if (clusteredNeighborHit != null && hitToSeed.get(clusteredNeighborHit) != null
-                		&& hitList.contains(clusteredNeighborHit)) {
+                        && hitList.contains(clusteredNeighborHit)) {
                     clusteredNeighborHits.add(clusteredNeighborHit);
                 }
             }
@@ -383,32 +383,32 @@
             
             // Consider time cut-is this hit in same time window as seed?
             if (useTimeCut){
-            	if(Math.abs(ihit.getTime() - iseed.getTime()) < timeWindow)
-            	{	
-            		icluster.addHit(ihit);
-            	}
+                if(Math.abs(ihit.getTime() - iseed.getTime()) < timeWindow)
+                {   
+                    icluster.addHit(ihit);
+                }
             } // end of using time cut
             else {icluster.addHit(ihit);}           
         }
 
         // Add common hits
         for (Map.Entry<CalorimeterHit, List<CalorimeterHit>> commHit : commonHits.entrySet()) {
-        	// Check that the common hit is in both time windows to their clusters
-        	CalorimeterHit seedA = commHit.getValue().get(0);
+            // Check that the common hit is in both time windows to their clusters
+            CalorimeterHit seedA = commHit.getValue().get(0);
             CalorimeterHit seedB = commHit.getValue().get(1);
-        	
+            
             boolean inTimeWithA = false;
             boolean inTimeWithB = false;
-        	// In time window with seedA?
+            // In time window with seedA?
             if (Math.abs(commHit.getKey().getTime() - seedA.getTime()) < timeWindow){
-            	inTimeWithA = true;
+                inTimeWithA = true;
             }
             
             // In time window with seedB?
             if (Math.abs(commHit.getKey().getTime() - seedB.getTime()) < timeWindow){
-            	inTimeWithB = true;
-            }
-                    	
+                inTimeWithB = true;
+            }
+                        
             double eclusterA = seedToCluster.get(seedA).getEnergy();
             double eclusterB = seedToCluster.get(seedB).getEnergy();
             double fractionA = eclusterA / (eclusterA + eclusterB);
@@ -420,25 +420,25 @@
             BaseCluster clusterB = seedToCluster.get(seedB);
 
             if (useTimeCut){
-            	// Do this if the hit is in both cluster's windows
-            	if (inTimeWithA && inTimeWithB){
-            		clusterA.addHit(commHit.getKey(), hitcontributionA);
-            		clusterB.addHit(commHit.getKey(), hitcontributionB);
-            	}
+                // Do this if the hit is in both cluster's windows
+                if (inTimeWithA && inTimeWithB){
+                    clusterA.addHit(commHit.getKey(), hitcontributionA);
+                    clusterB.addHit(commHit.getKey(), hitcontributionB);
+                }
             
-            	//If the hit is only in 1 cluster's window, add the full contribution
-            	else if(inTimeWithA ^ inTimeWithB){
-            		if(inTimeWithA){
-            			clusterA.addHit(commHit.getKey());
-            		}
-            		else{
-            			clusterB.addHit(commHit.getKey());
-            		}
-            	}
+                //If the hit is only in 1 cluster's window, add the full contribution
+                else if(inTimeWithA ^ inTimeWithB){
+                    if(inTimeWithA){
+                        clusterA.addHit(commHit.getKey());
+                    }
+                    else{
+                        clusterB.addHit(commHit.getKey());
+                    }
+                }
             } // end of using time cut
             else{
-            	clusterA.addHit(commHit.getKey(), hitcontributionA);
-        		clusterB.addHit(commHit.getKey(), hitcontributionB);           	
+                clusterA.addHit(commHit.getKey(), hitcontributionA);
+                clusterB.addHit(commHit.getKey(), hitcontributionB);            
             }
             
         }

Modified: java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/SimpleCosmicClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/SimpleCosmicClusterer.java	(original)
+++ java/branches/HPSJAVA-409/ecal-recon/src/main/java/org/hps/recon/ecal/cluster/SimpleCosmicClusterer.java	Wed Apr 27 11:11:32 2016
@@ -125,9 +125,8 @@
     }    
 
     /**
-     * This method takes a list of potential cluster hits and applies selection cuts,
-     * returning a new list that has the hit lists which did not pass the cuts removed.
-     * @param clusteredHitLists The input hit lists. 
+     * Apply selection cuts to cluster list and return filtered list.
+     * @param clusterList The input hit lists. 
      * @return The hit lists that passed the cuts.
      */
     protected List<Cluster> applyCuts(List<Cluster> clusterList) {

Modified: java/branches/HPSJAVA-409/evio/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/evio/pom.xml	(original)
+++ java/branches/HPSJAVA-409/evio/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/evio/</url>

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AbstractSvtEvioReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AbstractSvtEvioReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AbstractSvtEvioReader.java	Wed Apr 27 11:11:32 2016
@@ -12,12 +12,7 @@
 import org.hps.record.svt.SvtEvioExceptions.SvtEvioReaderException;
 import org.hps.util.Pair;
 import org.jlab.coda.jevio.BaseStructure;
-import org.jlab.coda.jevio.DataType;
 import org.jlab.coda.jevio.EvioEvent;
-import org.jlab.coda.jevio.IEvioFilter;
-import org.jlab.coda.jevio.IEvioStructure;
-import org.jlab.coda.jevio.StructureFinder;
-import org.jlab.coda.jevio.StructureType;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawTrackerHit;
@@ -31,7 +26,6 @@
  * 
  * @author Omar Moreno <[log in to unmask]>
  * @author Per Hansson Adrian <[log in to unmask]>
- * @date November 20, 2014
  *
  */
 public abstract class AbstractSvtEvioReader extends EvioReader {
@@ -39,7 +33,7 @@
     public static final String SVT_HEADER_COLLECTION_NAME = "SvtHeaders";
     
     // Initialize the logger
-    public static Logger LOGGER = Logger.getLogger(AbstractSvtEvioReader.class.getPackage().getName());
+    public static final Logger LOGGER = Logger.getLogger(AbstractSvtEvioReader.class.getPackage().getName());
     
     // A Map from DAQ pair (FPGA/Hybrid or FEB ID/FEB Hybrid ID) to the
     // corresponding sensor
@@ -47,16 +41,11 @@
                   HpsSiSensor /* Sensor */> daqPairToSensor 
                       = new HashMap<Pair<Integer, Integer>, HpsSiSensor>();
     
-    // A collection of banks that should be processed after all hits have been made
-    protected List<BaseStructure> eventBanks = new ArrayList<BaseStructure>();
-
     // Flag indicating whether the DAQ map has been setup
     protected boolean isDaqMapSetup = false;
 
     // Collections and names
     private static final String SVT_HIT_COLLECTION_NAME = "SVTRawTrackerHits";
-    List<RawTrackerHit> rawHits = new ArrayList<RawTrackerHit>();
-    List<SvtHeaderDataInfo> headers = new ArrayList<SvtHeaderDataInfo>();
 
     // Constants
     private static final String SUBDETECTOR_NAME = "Tracker";
@@ -76,6 +65,19 @@
      */
     abstract protected int getMaxRocBankTag(); 
     
+    /**
+     *  Get the minimum SVT ROC bank tag in the event.
+     *
+     *  @return Minimum SVT ROC bank tag
+     */
+    abstract protected int getMinDataBankTag(); 
+    
+    /**
+     *  Get the maximum SVT ROC bank tag in the event.
+     *
+     *  @return Maximum SVT ROC bank tag
+     */
+    abstract protected int getMaxDataBankTag(); 
 
     /**
      *  Get the SVT ROC bank number of the bank encapsulating the SVT samples.
@@ -116,14 +118,6 @@
      */
     abstract protected HpsSiSensor getSensor(int[] data);
 
-    /**
-     *  Check whether a data bank is valid i.e. contains SVT samples only.
-     * 
-     *  @param dataBank - An EVIO bank containing integer data
-     *  @return true if the bank is valid, false otherwise
-     */
-    abstract protected boolean isValidDataBank(BaseStructure dataBank);
-    
     /**
      * Check whether the samples are valid
      * 
@@ -154,125 +148,88 @@
      *  @return true if the raw hits were created successfully, false otherwise 
      * @throws SvtEvioReaderException 
      */
+    @Override
     public boolean makeHits(EvioEvent event, EventHeader lcsimEvent) throws SvtEvioReaderException {
 
         LOGGER.finest("Physics Event: " + event.toString());
         
-        // Retrieve the ROC banks encapsulated by the physics bank.  The ROC
+        // Retrieve the data banks encapsulated by the physics bank.  The ROC
         // bank range is set in the subclass.
-        List<BaseStructure> rocBanks = new ArrayList<BaseStructure>();
-        for (int rocBankTag = this.getMinRocBankTag(); 
-                rocBankTag <= this.getMaxRocBankTag(); rocBankTag++) { 
-            
-            LOGGER.finest("Retrieving ROC bank: " + rocBankTag);
-            List<BaseStructure> matchingRocBanks = this.getMatchingBanks(event, rocBankTag);
-            if (matchingRocBanks == null) { 
-                LOGGER.finest("ROC bank " + rocBankTag + " was not found!");
-                continue;
-            }
-            rocBanks.addAll(matchingRocBanks);
-        }
-        LOGGER.finest("Total ROC banks found: " + rocBanks.size());
-        
-        // Return false if ROC banks weren't found
-        if (rocBanks.isEmpty()) return false;  
+        List<BaseStructure> dataBanks = SvtEvioUtils.getDataBanks(event, this.getMinRocBankTag(), this.getMaxRocBankTag(), this.getMinDataBankTag(), this.getMaxDataBankTag());
+        
+        // Return false if data banks weren't found
+        if (dataBanks.isEmpty()) return false;  
     
         // Setup the DAQ map if it's not setup
         if (!this.isDaqMapSetup)
             this.setupDaqMap(lcsimEvent.getDetector().getSubdetector(
                     SUBDETECTOR_NAME));
 
-        // Clear the list of raw tracker hits
-        rawHits.clear();
-        
-        // Clear the list of headers
-        headers.clear();
-
-        // Loop over the SVT ROC banks and process all samples
-        for (BaseStructure rocBank : rocBanks) { 
-            
-            LOGGER.finest("ROC bank: " + rocBank.toString());
-            
-            LOGGER.finest("Processing ROC bank " + rocBank.getHeader().getTag());
-            
-            // If the ROC bank doesn't contain any data, raise an exception
-            if (rocBank.getChildCount() == 0) { 
-                throw new SvtEvioReaderException("[ " + this.getClass().getSimpleName() 
-                                + " ]: SVT bank doesn't contain any data banks.");
+        List<RawTrackerHit> rawHits = new ArrayList<RawTrackerHit>();
+        List<SvtHeaderDataInfo> headers = new ArrayList<SvtHeaderDataInfo>();
+
+        LOGGER.finest("Total data banks found: " + dataBanks.size());
+
+            // Loop over all of the data banks contained by the ROC banks and 
+        // processed them
+        for (BaseStructure dataBank : dataBanks) {
+
+            LOGGER.finest("Processing data bank: " + dataBank.toString());
+
+            // Get the int data encapsulated by the data bank
+            int[] data = dataBank.getIntData();
+            LOGGER.finest("Total number of integers contained by the data bank: " + data.length);
+
+            // Check that a complete set of samples exist
+            int sampleCount = data.length - this.getDataHeaderLength()
+                    - this.getDataTailLength();
+            LOGGER.finest("Total number of  samples: " + sampleCount);
+            if (sampleCount % 4 != 0) {
+                throw new SvtEvioReaderException("[ "
+                        + this.getClass().getSimpleName()
+                        + " ]: Size of samples array is not divisible by 4");
             }
-            
-            // Get the data banks containing the SVT samples.  
-            List<BaseStructure> dataBanks = rocBank.getChildren(); 
-            LOGGER.finest("Total data banks found: " + dataBanks.size());
-            
-            // Loop over all of the data banks contained by the ROC banks and 
-            // processed them
-            for (BaseStructure dataBank : dataBanks) { 
-        
-                LOGGER.finest("Processing data bank: " + dataBank.toString());
-                
-                // Check that the bank is valid
-                if (!this.isValidDataBank(dataBank)) continue;
-                
-                // Get the int data encapsulated by the data bank
-                int[] data = dataBank.getIntData();
-                LOGGER.finest("Total number of integers contained by the data bank: " + data.length);
-        
-                // Check that a complete set of samples exist
-                int sampleCount = data.length - this.getDataHeaderLength()
-                        - this.getDataTailLength();
-                LOGGER.finest("Total number of  samples: " + sampleCount);
-                if (sampleCount % 4 != 0) {
-                    throw new SvtEvioReaderException("[ "
-                            + this.getClass().getSimpleName()
-                            + " ]: Size of samples array is not divisible by 4");
-                }
-                
-                // extract header and tail information
-                SvtHeaderDataInfo headerData = this.extractSvtHeader(dataBank.getHeader().getNumber(), data);
-                
-                // Check that the multisample count is consistent
-                this.checkSvtSampleCount(sampleCount, headerData);
-                
-                // Add header to list
-                headers.add(headerData);
-                
-                
-                // Store the multisample headers
-                // Note that the length is not known but can't be longer than the multisample count
-                // in other words the data can be only header multisamples for example.
-                int multisampleHeaderData[] = new int[sampleCount];
-                int multisampleHeaderIndex = 0;
-
-                LOGGER.finest("sampleCount " + sampleCount);
-                
-                // Loop through all of the samples and make hits
-                for (int samplesN = 0; samplesN < sampleCount; samplesN += 4) {
-                    
-                    int[] samples = new int[4];
-                    System.arraycopy(data, this.getDataHeaderLength() + samplesN, samples, 0, samples.length);
-                    
-                    LOGGER.finest("samplesN " + samplesN + " multisampleHeaderCount " + multisampleHeaderIndex);
-                    if(SvtEvioUtils.isMultisampleHeader(samples))
-                        LOGGER.finest("this is a header multisample for apv " + SvtEvioUtils.getApvFromMultiSample(samples) + " ch " + SvtEvioUtils.getChannelNumber(samples));
-                    else 
-                        LOGGER.finest("this is a data multisample for apv " + SvtEvioUtils.getApvFromMultiSample(samples) + " ch " + SvtEvioUtils.getChannelNumber(samples));
-                    
-                    
+
+            // extract header and tail information
+            SvtHeaderDataInfo headerData = this.extractSvtHeader(dataBank.getHeader().getNumber(), data);
+
+            // Check that the multisample count is consistent
+            this.checkSvtSampleCount(sampleCount, headerData);
+
+            // Add header to list
+            headers.add(headerData);
+
+            // Store the multisample headers
+            // Note that the length is not known but can't be longer than the multisample count
+            // in other words the data can be only header multisamples for example.
+            int multisampleHeaderData[] = new int[sampleCount];
+            int multisampleHeaderIndex = 0;
+
+            LOGGER.finest("sampleCount " + sampleCount);
+
+            List<int[]> multisampleList = SvtEvioUtils.getMultisamples(data, sampleCount, this.getDataHeaderLength());
+            // Loop through all of the samples and make hits
+            for (int[] samples:multisampleList) {
+                if (SvtEvioUtils.isMultisampleHeader(samples)) {
+                    LOGGER.finest("this is a header multisample for apv " + SvtEvioUtils.getApvFromMultiSample(samples) + " ch " + SvtEvioUtils.getChannelNumber(samples));
                     // Extract data words from multisample header and update index
                     multisampleHeaderIndex += this.extractMultisampleHeaderData(samples, multisampleHeaderIndex, multisampleHeaderData);
-                    
-                    // If a set of samples is associated with an APV header or tail, skip it
-                    if (!this.isValidSampleSet(samples)) continue;
-                    rawHits.add(this.makeHit(samples));
+                } else {
+                    LOGGER.finest("this is a data multisample for apv " + SvtEvioUtils.getApvFromMultiSample(samples) + " ch " + SvtEvioUtils.getChannelNumber(samples));
                 }
-                
-                LOGGER.finest("got " +  multisampleHeaderIndex + " multisampleHeaderIndex for " + sampleCount + " sampleCount");
-                
-                // add multisample header tails to header data object
-                this.setMultiSampleHeaders(headerData, multisampleHeaderIndex, multisampleHeaderData);
-
+
+                // If a set of samples is associated with an APV header or tail, skip it
+                if (!this.isValidSampleSet(samples)) {
+                    continue;
+                }
+                rawHits.add(this.makeHit(samples));
             }
+
+            LOGGER.finest("got " + multisampleHeaderIndex + " multisampleHeaderIndex for " + sampleCount + " sampleCount");
+
+            // add multisample header tails to header data object
+            this.setMultiSampleHeaders(headerData, multisampleHeaderIndex, multisampleHeaderData);
+
         }
         
         LOGGER.finest("Total number of RawTrackerHits created: " + rawHits.size());
@@ -282,13 +239,9 @@
         // Add the collection of raw hits to the LCSim event
         lcsimEvent.put(SVT_HIT_COLLECTION_NAME, rawHits, RawTrackerHit.class, flag, READOUT_NAME);
 
-        
         // Process SVT headers
         this.processSvtHeaders(headers, lcsimEvent);
         
-       
-        
-
         return true;
     }
 
@@ -322,7 +275,7 @@
      * @param samples
      * @param index
      * @param multisampleHeaderData
-     * @return
+     * @return the length of the extracted samples or 0 if not a multisample header
      */
     protected int extractMultisampleHeaderData(int[] samples, int index, int[] multisampleHeaderData) {
         LOGGER.finest("extractMultisampleHeaderData: index " + index);
@@ -344,7 +297,7 @@
      */
     protected void checkSvtSampleCount(int sampleCount, SvtHeaderDataInfo headerData) throws SvtEvioHeaderException {
         if( sampleCount != SvtEvioUtils.getSvtTailMultisampleCount(headerData.getTail())*4)
-            throw new SvtEvioHeaderException("multisample count is not consistent with bank size.");
+            throw new SvtEvioHeaderException("ROC " + headerData.getNum() + " multisample count " + sampleCount + " is not consistent with bank size " + SvtEvioUtils.getSvtTailMultisampleCount(headerData.getTail()));
     }
     
     /**
@@ -394,26 +347,4 @@
         // Create and return a RawTrackerHit
         return new BaseRawTrackerHit(hitTime, cellID, SvtEvioUtils.getSamples(data), null, sensor);
     }
-    
-    /**
-     *  Retrieve all the banks in an event that match the given tag in their
-     *  header and are not data banks. 
-     *
-     *  @param structure : The event/bank being queried
-     *  @param tag : The tag to match
-     *  @return A collection of all bank structures that pass the filter 
-     *          provided by the event
-     */
-    protected List<BaseStructure> getMatchingBanks(BaseStructure structure, final int tag) { 
-        IEvioFilter filter = new IEvioFilter() { 
-            public boolean accept(StructureType type, IEvioStructure struc) { 
-                return (type == StructureType.BANK) 
-                        && (tag == struc.getHeader().getTag())
-                        && (struc.getHeader().getDataType() == DataType.ALSOBANK);
-            }
-        };
-        return StructureFinder.getMatchingStructures(structure, filter);
-    }
-
-   
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AugmentedSvtEvioReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AugmentedSvtEvioReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/AugmentedSvtEvioReader.java	Wed Apr 27 11:11:32 2016
@@ -32,7 +32,10 @@
     
     @Override
     protected void processSvtHeaders(List<SvtHeaderDataInfo> headers, EventHeader lcsimEvent) throws SvtEvioHeaderException {
-    
+
+
+        LOGGER.finest("Process " + headers.size() + " SVT headers for run " + lcsimEvent.getRunNumber() + " and event " + lcsimEvent.getEventNumber());
+        
         // Check that the SVT header data is valid
         // Catch the exceptions locally, add stuff to the event, then throw it again
         // and handle it outside
@@ -43,6 +46,8 @@
 
         if( !exceptions.isEmpty() ) {
 
+            LOGGER.finest("Found " + exceptions.size() + " " + SvtEvioHeaderException.class.getSimpleName() + " exceptions");
+            
             // print some debug info 
             
             List<String> exceptionNames = SvtEventHeaderChecker.getSvtEvioHeaderExceptionNames(exceptions);
@@ -68,8 +73,14 @@
                 throw new SvtEvioHeaderException(exceptions.get(0));
             
         } else { 
+            
+            LOGGER.finest("No " + SvtEvioHeaderException.class.getSimpleName() + " exceptions found for this event");
+            
             // add skimming flag - the header is OK since I would never get here otherwise
             SvtEventFlagger.voidAddHeaderCheckResultToMetaData(true, lcsimEvent);
+            
+            
+            
         }
 
         // Add SVT header data to the event

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/BasicEvioFileReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/BasicEvioFileReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/BasicEvioFileReader.java	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.record.evio.EvioEventUtilities;
 import org.hps.record.triggerbank.AbstractIntData.IntBankDefinition;
 import org.hps.record.triggerbank.HeadBankData;
@@ -33,7 +33,7 @@
         if (args.length == 0) {
             printUsage(options);
         }
-        final CommandLineParser parser = new DefaultParser();
+        final CommandLineParser parser = new PosixParser();
         CommandLine cl = null;
         try {
             cl = parser.parse(options, args);

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/DummyEventBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/DummyEventBuilder.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/DummyEventBuilder.java	Wed Apr 27 11:11:32 2016
@@ -41,7 +41,7 @@
     public void readEvioEvent(EvioEvent evioEvent) {
     }
 
-	@Override
-	public void conditionsChanged(ConditionsEvent conditionsEvent) {
-	}	
+    @Override
+    public void conditionsChanged(ConditionsEvent conditionsEvent) {
+    }   
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EcalHitWriter.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EcalHitWriter.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EcalHitWriter.java	Wed Apr 27 11:11:32 2016
@@ -212,10 +212,10 @@
         Map<Integer, List<Long>> slotMap = new HashMap<Integer, List<Long>>();
         for (Long id : hitMap.keySet()) {
             dec.setID(id);
-//			System.out.println(dec.getIDDescription());
-//			System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
+//          System.out.println(dec.getIDDescription());
+//          System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
 //            Long daqID = EcalConditions.physicalToDaqID(id);
-//			System.out.printf("physicalID %d, daqID %d\n", id, daqID);
+//          System.out.printf("physicalID %d, daqID %d\n", id, daqID);
             int slot = getSlot(id);
             if (slotMap.get(slot) == null) {
                 slotMap.put(slot, new ArrayList<Long>());
@@ -231,7 +231,7 @@
         for (int slot : slotMap.keySet()) {
             data.addUchar((byte) slot); // slot #
             data.addUint(0); // trigger #
-            data.addUlong(0); // timestamp    		
+            data.addUlong(0); // timestamp          
             List<Long> hitIDs = slotMap.get(slot);
             int nhits = hitIDs.size();
             data.addN(nhits); // number of channels
@@ -285,10 +285,10 @@
         Map<Integer, List<Long>> slotMap = new HashMap<Integer, List<Long>>();
         for (Long id : hitMap.keySet()) {
             dec.setID(id);
-//			System.out.println(dec.getIDDescription());
-//			System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
+//          System.out.println(dec.getIDDescription());
+//          System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
 //            Long daqID = EcalConditions.physicalToDaqID(id);
-//			System.out.printf("physicalID %d, daqID %d\n", id, daqID);
+//          System.out.printf("physicalID %d, daqID %d\n", id, daqID);
             int slot = getSlot(id);
             if (slotMap.get(slot) == null) {
                 slotMap.put(slot, new ArrayList<Long>());
@@ -304,7 +304,7 @@
         for (int slot : slotMap.keySet()) {
             data.addUchar((byte) slot); // slot #
             data.addUint(0); // trigger #
-            data.addUlong(0); // timestamp    		
+            data.addUlong(0); // timestamp          
             List<Long> hitIDs = slotMap.get(slot);
             int nhits = hitIDs.size();
             data.addN(nhits); // number of channels
@@ -358,10 +358,10 @@
         Map<Integer, List<Long>> slotMap = new HashMap<Integer, List<Long>>();
         for (Long id : hitMap.keySet()) {
             dec.setID(id);
-//			System.out.println(dec.getIDDescription());
-//			System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
+//          System.out.println(dec.getIDDescription());
+//          System.out.printf("ix = %d, iy = %d\n", dec.getValue("ix"), dec.getValue("iy"));
 //            Long daqID = EcalConditions.physicalToDaqID(id);
-//			System.out.printf("physicalID %d, daqID %d\n", id, daqID);
+//          System.out.printf("physicalID %d, daqID %d\n", id, daqID);
             int slot = getSlot(id);
             if (slotMap.get(slot) == null) {
                 slotMap.put(slot, new ArrayList<Long>());
@@ -380,7 +380,7 @@
 //            EvioBank slotBank = new EvioBank(EventConstants.ECAL_WINDOW_BANK_TAG, DataType.COMPOSITE, slot);
             data.addUchar((byte) slot); // slot #
             data.addUint(0); // trigger #
-            data.addUlong(0); // timestamp    		
+            data.addUlong(0); // timestamp          
             List<Long> hitIDs = slotMap.get(slot);
             int nhits = hitIDs.size();
             data.addN(nhits); // number of channels

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioReader.java	Wed Apr 27 11:11:32 2016
@@ -5,45 +5,45 @@
 import org.lcsim.event.EventHeader;
 
 /**
- *	Abstract class containing shared methods used by EVIO readers.
+ *  Abstract class containing shared methods used by EVIO readers.
  *
- *	@author Sho Uemura <[log in to unmask]>
+ *  @author Sho Uemura <[log in to unmask]>
  */
 public abstract class EvioReader {
 
-	// Debug flag
-	protected boolean debug = false;
-	
-	// Name of the hit collection that will be created
-	protected String hitCollectionName = null;
+    // Debug flag
+    protected boolean debug = false;
+    
+    // Name of the hit collection that will be created
+    protected String hitCollectionName = null;
 
-	/**
-	 *	Make a LCIO hit collection (e.g. {@link RawTrackerHit}, 
-	 * 	{@link CalorimeterHit} from raw EVIO data.
-	 * 
-	 * 	@param event : The EVIO event to read the raw data from
-	 * 	@param lcsimEvent : The LCSim event to write the collections to
-	 * 	@return True if the appropriate EVIO bank is found, false otherwise	
-	 * @throws Exception 
-	 * 
-	 */
-	abstract boolean makeHits(EvioEvent event, EventHeader lcsimEvent) throws Exception;
+    /**
+     *  Make a LCIO hit collection (e.g. {@link org.lcsim.event.RawTrackerHit}, 
+     *  {@link org.lcsim.event.CalorimeterHit} from raw EVIO data.
+     * 
+     *  @param event : The EVIO event to read the raw data from
+     *  @param lcsimEvent : The LCSim event to write the collections to
+     *  @return True if the appropriate EVIO bank is found, false otherwise 
+     * @throws Exception 
+     * 
+     */
+    abstract boolean makeHits(EvioEvent event, EventHeader lcsimEvent) throws Exception;
 
-	/**
-	 *	Set the hit collection name.
-	 * 
-	 * 	@param hitCollectionName : Name of the hit collection
-	 */
-	public void setHitCollectionName(String hitCollectionName) {
-		this.hitCollectionName = hitCollectionName;
-	}
+    /**
+     *  Set the hit collection name.
+     * 
+     *  @param hitCollectionName : Name of the hit collection
+     */
+    public void setHitCollectionName(String hitCollectionName) {
+        this.hitCollectionName = hitCollectionName;
+    }
 
-	/**
-	 *	Enable/disable debug output.
-	 * 
-	 * 	@param debug : Set to true to enable, false to disable.
-	 */
-	public void setDebug(boolean debug) {
-		this.debug = debug;
-	}
+    /**
+     *  Enable/disable debug output.
+     * 
+     *  @param debug : Set to true to enable, false to disable.
+     */
+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioToLcio.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioToLcio.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/EvioToLcio.java	Wed Apr 27 11:11:32 2016
@@ -71,7 +71,7 @@
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Sho Uemura <[log in to unmask]>
  */
-public class EvioToLcio {
+public final class EvioToLcio {
 
     /**
      * The default steering resource, which basically does nothing except print event numbers.
@@ -113,6 +113,7 @@
      */
     private static Options OPTIONS = new Options();
     static {
+        OPTIONS.addOption(new Option("h", false, "print help and exit"));
         OPTIONS.addOption(new Option("d", true, "detector name (required)"));
         OPTIONS.getOption("d").setRequired(true);
         OPTIONS.addOption(new Option("f", true, "text file containing a list of EVIO files"));
@@ -251,10 +252,11 @@
     }
 
     public void parse(String[] args) {
-        // Parse the command line options.
+        
         if (args.length == 0) {
             this.printUsage();
         }
+        
         final CommandLineParser parser = new PosixParser();
         CommandLine cl = null;
         try {
@@ -262,8 +264,13 @@
         } catch (final ParseException e) {
             throw new RuntimeException("Problem parsing command line options.", e);
         }
+        
+        if (cl.hasOption("h")) {
+            this.printUsage();
+        }
 
         // Set the log level.
+        // TODO: Remove this argument; use java logging prop instead.
         if (cl.hasOption("L")) {
             final Level level = Level.parse(cl.getOptionValue("L").toUpperCase());
 
@@ -366,6 +373,10 @@
 
         // Process the LCSim job variable definitions, if any.
         jobManager = new JobManager();
+        
+        // Initialize run manager and add as listener on conditions system.
+        RunManager runManager = RunManager.getRunManager();
+        DatabaseConditionsManager.getInstance().addConditionsListener(runManager);
         
         // Enable dry run because events will be processed individually.
         jobManager.setDryRun(true);
@@ -452,8 +463,6 @@
      * This method will execute the EVIO to LCIO conversion and optionally process the events with LCSim Drivers from a
      * steering file. Then the resultant LCIO events will be written to disk if this option is enabled in the command
      * line arguments.
-     *
-     * @param args The command line arguments.
      */
     public void run() {
 

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/LCSimEngRunEventBuilder.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/LCSimEngRunEventBuilder.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/LCSimEngRunEventBuilder.java	Wed Apr 27 11:11:32 2016
@@ -67,6 +67,11 @@
      * Modulus of TI timestamp offset (units of nanoseconds).
      */
     private final long timestampCycle = 24 * 6 * 35;
+    
+    /**
+     * The current TI time offset in nanoseconds from the run manager.
+     */
+    private Long currentTiTimeOffset = null;
 
     /**
      * Class constructor.
@@ -83,31 +88,59 @@
         intBanks.add(new IntBankDefinition(TIData.class, new int[]{sspCrateBankTag, 0xe10a}));
         intBanks.add(new IntBankDefinition(HeadBankData.class, new int[]{sspCrateBankTag, 0xe10f}));
         intBanks.add(new IntBankDefinition(TDCData.class, new int[]{0x3a, 0xe107}));
-        // ecalReader = new ECalEvioReader(0x25, 0x27);
         triggerConfigReader = new TriggerConfigEvioReader();
         svtEventFlagger = new SvtEventFlagger();
     }
 
     @Override
     public void conditionsChanged(final ConditionsEvent conditionsEvent) {
+        
         super.conditionsChanged(conditionsEvent);
         svtEventFlagger.initialize();
-    }
-
-    /**
-     * Get the time from the TI data.
+        
+        // Set TI time offset from run database.
+        setTiTimeOffsetForRun(conditionsEvent.getConditionsManager().getRun());
+    }
+    
+    /**
+     * Get TI time offset from the run database, if available.
+     * @param run the run number
+     */
+    private void setTiTimeOffsetForRun(int run) {
+        currentTiTimeOffset = null;
+        RunManager runManager = RunManager.getRunManager();
+        if (runManager.getRun() != null) {
+            if (runManager.runExists()) {
+                currentTiTimeOffset = runManager.getRunSummary().getTiTimeOffset();
+                LOGGER.info("TI time offset set to " + currentTiTimeOffset + " for run "
+                        + run + " from database");
+            } else {
+                LOGGER.warning("Run " + run 
+                        + " does not exist in the run database.");
+            }
+        } else {
+            LOGGER.info("Run manager is not initialized; TI time offset not available.");
+        }
+        /* Make sure connection is closed immediately. --JM */
+        try {
+            LOGGER.info("Closing run manager db connection ...");
+            RunManager.getRunManager().closeConnection();
+            LOGGER.info("Run manager db connection was closed.");
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Get the time from the TI data with time offset applied from run database.
      *
      * @param triggerList the TI data list
      */
     @Override
     protected long getTime(final List<AbstractIntData> triggerList) {
         long tiTimeOffset = 0;
-        try {
-            if (RunManager.getRunManager().runExists() && RunManager.getRunManager().getTriggerConfig().getTiTimeOffset() != null) {
-                tiTimeOffset = (RunManager.getRunManager().getTriggerConfig().getTiTimeOffset() / timestampCycle) * timestampCycle;
-            }
-        } catch (IllegalStateException e) {
-            // May happen if RunManager is not initialized; just ignore.
+        if (currentTiTimeOffset != null) {
+            tiTimeOffset = (currentTiTimeOffset / timestampCycle) * timestampCycle;
         }
         for (final AbstractIntData data : triggerList) {
             if (data instanceof TIData) {
@@ -137,7 +170,11 @@
         LOGGER.finest("created new LCSim event " + lcsimEvent.getEventNumber());
 
         // Put DAQ Configuration info into lcsimEvent.
-        triggerConfigReader.getDAQConfig(evioEvent, lcsimEvent);
+        try {
+            triggerConfigReader.getDAQConfig(evioEvent, lcsimEvent);
+        } catch (final Exception e) {
+            LOGGER.log(Level.SEVERE,"DAQ CONFIG BROKEN.",e);
+        }
 
         // Make RawCalorimeterHit collection, combining top and bottom section
         // of ECal into one list.

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitFunction.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitFunction.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitFunction.java	Wed Apr 27 11:11:32 2016
@@ -7,29 +7,29 @@
  * Straight line fit
  */
 public class RfFitFunction extends AbstractIFunction {
-	protected double intercept=0;
-	protected double slope=0;
-	public RfFitFunction() {
-		this("");
-	}
-	public RfFitFunction(String title) {
-		super();
-		this.variableNames=new String[]{"time"};
-		this.parameterNames=new String[]{"intercept","slope"};
+    protected double intercept=0;
+    protected double slope=0;
+    public RfFitFunction() {
+        this("");
+    }
+    public RfFitFunction(String title) {
+        super();
+        this.variableNames=new String[]{"time"};
+        this.parameterNames=new String[]{"intercept","slope"};
 
-		init(title);
-	}
-	public double value(double [] v) {
-		return  intercept + (v[0])*slope;
-	}
-	public void setParameters(double[] pars) throws IllegalArgumentException {
-		super.setParameters(pars);
-		intercept=pars[0];
-		slope=pars[1];
-	}
-	public void setParameter(String key,double value) throws IllegalArgumentException{
-		super.setParameter(key,value);
-		if      (key.equals("intercept")) intercept=value;
-		else if (key.equals("slope"))    slope=value;
-	}
+        init(title);
+    }
+    public double value(double [] v) {
+        return  intercept + (v[0])*slope;
+    }
+    public void setParameters(double[] pars) throws IllegalArgumentException {
+        super.setParameters(pars);
+        intercept=pars[0];
+        slope=pars[1];
+    }
+    public void setParameter(String key,double value) throws IllegalArgumentException{
+        super.setParameter(key,value);
+        if      (key.equals("intercept")) intercept=value;
+        else if (key.equals("slope"))    slope=value;
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitterDriver.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfFitterDriver.java	Wed Apr 27 11:11:32 2016
@@ -1,9 +1,4 @@
 package org.hps.evio;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IDataPointSet;
@@ -11,7 +6,9 @@
 import hep.aida.IFitResult;
 import hep.aida.IFitter;
 import hep.aida.IFunction;
-import hep.aida.IFunctionFactory;
+
+import java.util.ArrayList;
+import java.util.List;
 
 import org.hps.recon.ecal.FADCGenericHit;
 import org.lcsim.event.EventHeader;
@@ -19,146 +16,156 @@
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 
-/*
+/**
  * Extract RF time from waveform and put into lcsim event.
  */
 public class RfFitterDriver extends Driver {
 
-	static final double NOISE=2.0; // units = FADC
-	static final int CRATE=46;
-	static final int SLOT=13;
-	static final int CHANNELS[]={0,1};
-	static final double NSPERSAMPLE=4;
-		
+    private static final double NOISE = 2.0; // units = FADC
+    private static final int CRATE = 46;
+    private static final int SLOT = 13;
+    private static final int CHANNELS[] = {0, 1};
+    private static final double NSPERSAMPLE = 4;
 
-	// boilerplate:
-    AIDA aida = AIDA.defaultInstance();
-    IAnalysisFactory analysisFactory = aida.analysisFactory();
-    IFunctionFactory functionFactory = analysisFactory.createFunctionFactory(null);
-    IFitFactory fitFactory = analysisFactory.createFitFactory();
-    IFitter fitter=fitFactory.createFitter();
-    IDataPointSet fitData=aida.analysisFactory().createDataPointSetFactory(null).create("RF ADC DataPointSet", 2);
-    
+    // boilerplate:
+    private AIDA aida = AIDA.defaultInstance();
+    private IAnalysisFactory analysisFactory = aida.analysisFactory();
+    //private IFunctionFactory functionFactory = analysisFactory.createFunctionFactory(null);
+    private IFitFactory fitFactory = analysisFactory.createFitFactory();
+    private IFitter fitter = fitFactory.createFitter();
+    private IDataPointSet fitData = aida.analysisFactory().createDataPointSetFactory(null).create("RF ADC DataPointSet", 2);
+
     // the function used to fit the RF pulse:
-    IFunction fitFunction=new RfFitFunction();
+    private IFunction fitFunction = new RfFitFunction();
 
-    /*
-     * Check the event for an RF pulse, and, if found, fit it to get
-     * RF time and then dump it in the lcsim event.
+    /**
+     * Check the event for an RF pulse, and, if found, fit it to get RF time.
      */
-	public void process(EventHeader event) {
-		if (!event.hasCollection(GenericObject.class,"FADCGenericHits")) return;
-		
-		boolean foundRf=false;
-    	double times[]={-9999,-9999};
-    	
-    	for (GenericObject gob : event.get(GenericObject.class,"FADCGenericHits")) {
-			FADCGenericHit hit=(FADCGenericHit)gob;
-    		
-			// ignore hits not from proper RF signals based on crate/slot/channel:
-			if (hit.getCrate()!=CRATE || hit.getSlot()!=SLOT) continue;
-    		for (int ii=0; ii<CHANNELS.length; ii++) {
-				if (hit.getChannel()==CHANNELS[ii]) {
-					
-					// we found a RF readout, fit it:
-					foundRf=true;
-					times[ii] = fitPulse(hit);
-									  				    
-					break;
-				}
-			}
-		}
-		
-    	// if we found an RF readout, dump the fit result in the event:  
-    	if (foundRf) {
-    		List <RfHit> rfHits=new ArrayList<RfHit>();
-    		rfHits.add(new RfHit(times));
-	    	event.put("RFHits", rfHits, RfHit.class, 1);
-		}
-	}
+    public void process(EventHeader event) {
 
-	/*
-	 * Perform the fit to the RF pulse:
-	 */
-	public double fitPulse(FADCGenericHit hit) {
-		fitData.clear();
-		final int adcSamples[]=hit.getData();
-		//stores the number of peaks
-		int iz=0;
-		int peakBin[]={-999,-999};
-		final int threshold = 300;	
-		double fitThresh[]={-999,-999};
-		double pedVal[]={-999,-999};
-		
-		// Look for bins containing the peaks (2-3 peaks)
-		for (int ii=4; ii<adcSamples.length; ii++) {
-			// After 2 peaks, stop looking for more
-			if (iz==2){break;}
-			if ((adcSamples[ii+1]>0) && (adcSamples[ii-1]>0) && (adcSamples[ii]>threshold) && ii>8){
-				if ((adcSamples[ii]>adcSamples[ii+1]) && (adcSamples[ii]>=adcSamples[ii-1]) ){
-					
-					peakBin[iz]=ii;
-					iz++;
-				}
-			}
-		}
-		
-		
-		int jj=0;
-		// Choose peak closest to center of window (second peak, ik=1)
-		final int ik=1;
-		pedVal[ik] = (adcSamples[peakBin[ik]-6]+adcSamples[peakBin[ik]-7]+adcSamples[peakBin[ik]-8]+adcSamples[peakBin[ik]-9])/4.0;
-		fitThresh[ik]= (adcSamples[peakBin[ik]]+pedVal[ik])/3.0;
-	
-		// Initial values: we find/fit 3 points:
-		double itime[] = {-999,-999,-999};
-		double ifadc[] = {-999,-999,-999};
-		
-		// Find the points of the peak bin to peak bin-5 
-		for (int ll=0; ll<5; ll++){	
-			if ((adcSamples[peakBin[ik]-5+ll]) > fitThresh[ik]){
-				// One point is below fit threshold and two points are above	
-				if(jj==0 && (adcSamples[peakBin[ik]-6+ll] > pedVal[ik])){
-					final int zz=fitData.size();	
-					fitData.addPoint();
-					itime[zz] = peakBin[ik]-6+ll;
-					ifadc[zz] = adcSamples[peakBin[ik]-6+ll];
-					fitData.point(zz).coordinate(0).setValue(peakBin[ik]-6+ll);
-					fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-6+ll]);
-					fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
-					fitData.point(zz).coordinate(1).setErrorPlus(NOISE);		
-					jj++;	
-				}
-				final int zz=fitData.size();	
-				fitData.addPoint();
-				itime[zz] = peakBin[ik]-5+ll;
-				ifadc[zz] = adcSamples[peakBin[ik]-5+ll];
-				fitData.point(zz).coordinate(0).setValue(peakBin[ik]-5+ll);
-				fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-5+ll]);
-				fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
-				fitData.point(zz).coordinate(1).setErrorPlus(NOISE);
-					
-				jj++;
-				if (jj==3) {break;}					
-			}
-		}
-		
-		double islope = ((double)(ifadc[2]-ifadc[0]))/(itime[2]-itime[0]);
-		double icept = ifadc[1] - islope*itime[1];
-		// Initialize fit parameters:
-		fitFunction.setParameter("intercept",icept);
-		fitFunction.setParameter("slope",islope);
+        List<RfHit> rfHits = new ArrayList<RfHit>();
 
-		// this used to be turned on somewhere else on every event, dunno if it still is:
-		//Logger.getLogger("org.freehep.math.minuit").setLevel(Level.OFF);
-	
-		IFitResult fitResults = fitter.fit(fitData,fitFunction);
-		
-		// Read the time value at this location on the fit:
-		double halfVal = (adcSamples[peakBin[1]]+pedVal[1])/2.0;	
-	
-		return NSPERSAMPLE*(halfVal-fitResults.fittedParameter("intercept"))/fitResults.fittedParameter("slope");
-			
-	}
-		
+        boolean foundRf = false;
+        double times[] = {-9999, -9999};
+
+        if (event.hasCollection(GenericObject.class, "FADCGenericHits")) {
+
+            for (GenericObject gob : event.get(GenericObject.class, "FADCGenericHits")) {
+
+                FADCGenericHit hit = null;
+
+                /* Added conversion from GenericObject in case loading back from an LCIO file. --JM */
+                if (gob instanceof FADCGenericHit) {
+                    hit = (FADCGenericHit) gob;
+                } else {
+                    hit = new FADCGenericHit(gob);
+                }
+
+                // ignore hits not from proper RF signals based on crate/slot/channel:
+                if (hit.getCrate() != CRATE || hit.getSlot() != SLOT)
+                    continue;
+
+                for (int ii = 0; ii < CHANNELS.length; ii++) {
+                    if (hit.getChannel() == CHANNELS[ii]) {
+
+                        // we found a RF readout, fit it:
+                        foundRf = true;
+                        times[ii] = fitPulse(hit);
+
+                        break;
+                    }
+                }
+            }
+        }
+        if (foundRf) {
+            rfHits.add(new RfHit(times));
+        }
+        event.put("RFHits", rfHits, RfHit.class, 1);
+    }
+
+    /**
+     * Perform the fit to the RF pulse:
+     */
+    private double fitPulse(FADCGenericHit hit) {
+        fitData.clear();
+        final int adcSamples[] = hit.getData();
+        // stores the number of peaks
+        int iz = 0;
+        int peakBin[] = {-999, -999};
+        final int threshold = 300;
+        double fitThresh[] = {-999, -999};
+        double pedVal[] = {-999, -999};
+
+        // Look for bins containing the peaks (2-3 peaks)
+        for (int ii = 4; ii < adcSamples.length; ii++) {
+            // After 2 peaks, stop looking for more
+            if (iz == 2) {
+                break;
+            }
+            if ((adcSamples[ii + 1] > 0) && (adcSamples[ii - 1] > 0) && (adcSamples[ii] > threshold) && ii > 8) {
+                if ((adcSamples[ii] > adcSamples[ii + 1]) && (adcSamples[ii] >= adcSamples[ii - 1])) {
+
+                    peakBin[iz] = ii;
+                    iz++;
+                }
+            }
+        }
+
+        int jj = 0;
+        // Choose peak closest to center of window (second peak, ik=1)
+        final int ik = 1;
+        pedVal[ik] = (adcSamples[peakBin[ik] - 6] + adcSamples[peakBin[ik] - 7] + adcSamples[peakBin[ik] - 8] + adcSamples[peakBin[ik] - 9]) / 4.0;
+        fitThresh[ik] = (adcSamples[peakBin[ik]] + pedVal[ik]) / 3.0;
+
+        // Initial values: we find/fit 3 points:
+        double itime[] = {-999, -999, -999};
+        double ifadc[] = {-999, -999, -999};
+
+        // Find the points of the peak bin to peak bin-5
+        for (int ll = 0; ll < 5; ll++) {
+            if ((adcSamples[peakBin[ik] - 5 + ll]) > fitThresh[ik]) {
+                // One point is below fit threshold and two points are above
+                if (jj == 0 && (adcSamples[peakBin[ik] - 6 + ll] > pedVal[ik])) {
+                    final int zz = fitData.size();
+                    fitData.addPoint();
+                    itime[zz] = peakBin[ik] - 6 + ll;
+                    ifadc[zz] = adcSamples[peakBin[ik] - 6 + ll];
+                    fitData.point(zz).coordinate(0).setValue(peakBin[ik] - 6 + ll);
+                    fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik] - 6 + ll]);
+                    fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
+                    fitData.point(zz).coordinate(1).setErrorPlus(NOISE);
+                    jj++;
+                }
+                final int zz = fitData.size();
+                fitData.addPoint();
+                itime[zz] = peakBin[ik] - 5 + ll;
+                ifadc[zz] = adcSamples[peakBin[ik] - 5 + ll];
+                fitData.point(zz).coordinate(0).setValue(peakBin[ik] - 5 + ll);
+                fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik] - 5 + ll]);
+                fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
+                fitData.point(zz).coordinate(1).setErrorPlus(NOISE);
+
+                jj++;
+                if (jj == 3) {
+                    break;
+                }
+            }
+        }
+
+        double islope = ((double) (ifadc[2] - ifadc[0])) / (itime[2] - itime[0]);
+        double icept = ifadc[1] - islope * itime[1];
+        // Initialize fit parameters:
+        fitFunction.setParameter("intercept", icept);
+        fitFunction.setParameter("slope", islope);
+
+        // this used to be turned on somewhere else on every event, dunno if it still is:
+        // Logger.getLogger("org.freehep.math.minuit").setLevel(Level.OFF);
+
+        IFitResult fitResults = fitter.fit(fitData, fitFunction);
+
+        // Read the time value at this location on the fit:
+        double halfVal = (adcSamples[peakBin[1]] + pedVal[1]) / 2.0;
+
+        return NSPERSAMPLE * (halfVal - fitResults.fittedParameter("intercept")) / fitResults.fittedParameter("slope");
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfHit.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/RfHit.java	Wed Apr 27 11:11:32 2016
@@ -6,13 +6,13 @@
  * class to store RF times after extracting from waveform.
  */
 public class RfHit implements GenericObject {
-	private double[] times;
-	public RfHit(double[] times) { this.times=times; }
-	public int getNInt()    { return 0; }
-	public int getNFloat()  { return 0; }
-	public int getNDouble() { return times.length; }
-	public double getDoubleVal(int ii) { return times[ii]; }
-	public float  getFloatVal (int ii) { return 0; }
-	public int    getIntVal   (int ii) { return 0; }
-	public boolean isFixedSize() { return false; }
+    private double[] times;
+    public RfHit(double[] times) { this.times=times; }
+    public int getNInt()    { return 0; }
+    public int getNFloat()  { return 0; }
+    public int getNDouble() { return times.length; }
+    public double getDoubleVal(int ii) { return times[ii]; }
+    public float  getFloatVal (int ii) { return 0; }
+    public int    getIntVal   (int ii) { return 0; }
+    public boolean isFixedSize() { return false; }
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/SvtEvioReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/SvtEvioReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/SvtEvioReader.java	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,6 @@
 import org.hps.record.svt.SvtEvioExceptions.SvtEvioHeaderException;
 import org.hps.record.svt.SvtEvioExceptions.SvtEvioReaderException;
 import org.hps.util.Pair;
-import org.jlab.coda.jevio.BaseStructure;
 import org.jlab.coda.jevio.EvioEvent;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
@@ -18,8 +17,6 @@
  *  SVT EVIO reader used to convert SVT bank integer data to LCIO objects.
  * 
  *  @author Omar Moreno <[log in to unmask]>
- *  @data February 03, 2015
- *
  */
 public class SvtEvioReader extends AbstractSvtEvioReader {
 
@@ -30,6 +27,7 @@
     private static final int DATA_TAIL_LENGTH = 1; 
     public static final int MIN_ROC_BANK_TAG = 51;
     public static final int MAX_ROC_BANK_TAG = 66;
+    public static final int DATA_BANK_TAG = 3;
     private static final int ROC_BANK_NUMBER = 0; 
     
     /**
@@ -52,6 +50,16 @@
         return MAX_ROC_BANK_TAG; 
     }
     
+    @Override
+    protected int getMinDataBankTag() {
+        return DATA_BANK_TAG;
+    }
+
+    @Override
+    protected int getMaxDataBankTag() {
+        return DATA_BANK_TAG;
+    }
+
     /**
      *  Get the SVT ROC bank number of the bank encapsulating the SVT samples.
      * 
@@ -127,36 +135,13 @@
     }
     
     /**
-     *  Check whether a data bank is valid i.e. contains SVT samples only.  For
-     *  the engineering run, a valid data bank has a tag of 3.
-     * 
-     *  @param dataBank - An EVIO bank containing integer data
-     *  @return true if the bank is valid, false otherwise
-     * 
-     */
-    @Override
-    protected boolean isValidDataBank(BaseStructure dataBank) { 
-        
-        // The SVT configuration is stored in a bank with tag equal to 57614.
-        // All other event banks are invalid
-        if (dataBank.getHeader().getTag() == 57614) { 
-            
-            // Store the event bank for processing later.
-            eventBanks.add(dataBank);
-            
-            return false;
-        } else if (dataBank.getHeader().getTag() != 3) return false; 
-        
-        return true; 
-    }
-    
-    /**
      * Check whether the samples are valid. Specifically, check if the samples
      * are APV header or tails.
      * 
      * @param data : sample block of data
      * @return true if the samples are valid, false otherwise
      */
+    @Override
     protected boolean isValidSampleSet(int[] data) {
         return !(SvtEvioUtils.isMultisampleHeader(data) || SvtEvioUtils.isMultisampleTail(data));        
     }
@@ -191,9 +176,6 @@
            }
         }*/
         
-        // Clear out the event banks after they have been processed
-        eventBanks.clear();
-        
         return success;
     }
     

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunReconToEvio.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunReconToEvio.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunReconToEvio.java	Wed Apr 27 11:11:32 2016
@@ -21,96 +21,96 @@
  */
 public class TestRunReconToEvio extends Driver {
 
-	EventWriter writer;
-	String rawCalorimeterHitCollectionName = "EcalDigitizedHits";
-	String evioOutputFile = "TestRunData.evio";
-	EventBuilder builder = null;
-	private int eventsWritten = 0;
-	EcalHitWriter ecalWriter = null;
-	SVTHitWriter svtWriter = null;
-	
-	Detector detector = null;
+    EventWriter writer;
+    String rawCalorimeterHitCollectionName = "EcalDigitizedHits";
+    String evioOutputFile = "TestRunData.evio";
+    EventBuilder builder = null;
+    private int eventsWritten = 0;
+    EcalHitWriter ecalWriter = null;
+    SVTHitWriter svtWriter = null;
+    
+    Detector detector = null;
 
-	public TestRunReconToEvio() {
-	}
-	
+    public TestRunReconToEvio() {
+    }
+    
     @Override
-    public void detectorChanged(Detector detector) {    	
-    	// set the detector
+    public void detectorChanged(Detector detector) {        
+        // set the detector
         this.detector = detector;
     }
 
-	public void setEvioOutputFile(String evioOutputFile) {
-		this.evioOutputFile = evioOutputFile;
-	}
+    public void setEvioOutputFile(String evioOutputFile) {
+        this.evioOutputFile = evioOutputFile;
+    }
 
-	public void setRawCalorimeterHitCollectionName(String rawCalorimeterHitCollectionName) {
-		this.rawCalorimeterHitCollectionName = rawCalorimeterHitCollectionName;
-		if (ecalWriter != null) {
-			ecalWriter.setHitCollectionName(rawCalorimeterHitCollectionName);
-		}
-	}
+    public void setRawCalorimeterHitCollectionName(String rawCalorimeterHitCollectionName) {
+        this.rawCalorimeterHitCollectionName = rawCalorimeterHitCollectionName;
+        if (ecalWriter != null) {
+            ecalWriter.setHitCollectionName(rawCalorimeterHitCollectionName);
+        }
+    }
 
-	protected void startOfData() {
-		try {
-			writer = new EventWriter(evioOutputFile);
-		} catch (EvioException e) {
-			throw new RuntimeException(e);
-		}
+    protected void startOfData() {
+        try {
+            writer = new EventWriter(evioOutputFile);
+        } catch (EvioException e) {
+            throw new RuntimeException(e);
+        }
 
-		ecalWriter = new EcalHitWriter();
-		ecalWriter.setDetector(detector);
-		ecalWriter.setHitCollectionName(rawCalorimeterHitCollectionName);
+        ecalWriter = new EcalHitWriter();
+        ecalWriter.setDetector(detector);
+        ecalWriter.setHitCollectionName(rawCalorimeterHitCollectionName);
 
-		svtWriter = new SVTHitWriter();
-	}
+        svtWriter = new SVTHitWriter();
+    }
 
-	protected void endOfData() {
-		System.out.println(this.getClass().getSimpleName() + " - wrote " + eventsWritten + " EVIO events in job.");
-		writer.close();		
-	}
+    protected void endOfData() {
+        System.out.println(this.getClass().getSimpleName() + " - wrote " + eventsWritten + " EVIO events in job.");
+        writer.close();     
+    }
 
-	protected void process(EventHeader event) {
+    protected void process(EventHeader event) {
 
-		if (!svtWriter.hasData(event)) {
-			return;
-		}
+        if (!svtWriter.hasData(event)) {
+            return;
+        }
 
-		// Make a new EVIO event.
-		builder = new EventBuilder(0, DataType.BANK, event.getEventNumber());
+        // Make a new EVIO event.
+        builder = new EventBuilder(0, DataType.BANK, event.getEventNumber());
 
-		// Write SVTData.
-		svtWriter.writeData(event, builder);
+        // Write SVTData.
+        svtWriter.writeData(event, builder);
 
-		// Write RawCalorimeterHit collection.
-		ecalWriter.writeData(event, builder);
-//		writeRawCalorimeterHits(event);
+        // Write RawCalorimeterHit collection.
+        ecalWriter.writeData(event, builder);
+//      writeRawCalorimeterHits(event);
 
-		// Write this EVIO event.
-		writeEvioEvent();
-	}
+        // Write this EVIO event.
+        writeEvioEvent();
+    }
 
-	private void writeEvioEvent() {
-		EvioBank eventIDBank = new EvioBank(EvioEventConstants.EVENTID_BANK_TAG, DataType.UINT32, 0);
-		int[] eventID = new int[3];
-		eventID[0] = eventsWritten;
-		eventID[1] = 0; //trigger type
-		eventID[2] = 0; //status
+    private void writeEvioEvent() {
+        EvioBank eventIDBank = new EvioBank(EvioEventConstants.EVENTID_BANK_TAG, DataType.UINT32, 0);
+        int[] eventID = new int[3];
+        eventID[0] = eventsWritten;
+        eventID[1] = 0; //trigger type
+        eventID[2] = 0; //status
 
-		try {
-			eventIDBank.appendIntData(eventID);
-			builder.addChild(builder.getEvent(), eventIDBank);
-		} catch (EvioException e) {
-			throw new RuntimeException(e);
-		}
-		builder.setAllHeaderLengths();
-		try {
-			writer.writeEvent(builder.getEvent());
-			++eventsWritten;
-		} catch (EvioException e) {
-			throw new RuntimeException(e);
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		}
-	}
+        try {
+            eventIDBank.appendIntData(eventID);
+            builder.addChild(builder.getEvent(), eventIDBank);
+        } catch (EvioException e) {
+            throw new RuntimeException(e);
+        }
+        builder.setAllHeaderLengths();
+        try {
+            writer.writeEvent(builder.getEvent());
+            ++eventsWritten;
+        } catch (EvioException e) {
+            throw new RuntimeException(e);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunSvtEvioReader.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunSvtEvioReader.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/main/java/org/hps/evio/TestRunSvtEvioReader.java	Wed Apr 27 11:11:32 2016
@@ -6,7 +6,6 @@
 import org.hps.record.svt.SvtEvioUtils;
 import org.hps.record.svt.SvtHeaderDataInfo;
 import org.hps.util.Pair;
-import org.jlab.coda.jevio.BaseStructure;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.detector.tracker.silicon.HpsTestRunSiSensor;
 import org.lcsim.event.EventHeader;
@@ -18,8 +17,6 @@
  *  objects.
  * 
  *  @author Omar Moreno <[log in to unmask]>
- *  @date November 20, 2014
- *
  */
 public class TestRunSvtEvioReader extends AbstractSvtEvioReader {
 
@@ -30,6 +27,7 @@
     private static final int DATA_HEADER_LENGTH = 7;
     private static final int DATA_TAIL_LENGTH = 1; 
     private static final int MAX_FPGA_ID = 6;
+    public static final int MIN_DATA_BANK_TAG = 0;
     private static final int ROC_BANK_TAG = 3;
     private static final int ROC_BANK_NUMBER = -1; 
     
@@ -56,6 +54,16 @@
     @Override 
     protected int getMaxRocBankTag() { 
         return ROC_BANK_TAG; 
+    }
+    
+    @Override
+    protected int getMinDataBankTag() {
+        return MIN_DATA_BANK_TAG;
+    }
+
+    @Override
+    protected int getMaxDataBankTag() {
+        return MAX_FPGA_ID;
     }
     
     /**
@@ -131,26 +139,12 @@
     }
 
     /**
-     *  Check whether a data bank is valid i.e. contains SVT samples only.  For
-     *  the test run, a valid data bank has a tag in the range 0-6.
-     * 
-     *  @param dataBank - An EVIO bank containing integer data
-     *  @return true if the bank is valid, false otherwise
-     * 
-     */
-    @Override
-    protected boolean isValidDataBank(BaseStructure dataBank) { 
-        if (dataBank.getHeader().getTag() < 0 
-                || dataBank.getHeader().getTag() >= MAX_FPGA_ID) return false; 
-        return true; 
-    }
-    
-    /**
      * Check whether the samples are valid.
      * 
      * @param data : sample block of data
      * @return true if the samples are valid, false otherwise
      */
+    @Override
     protected boolean isValidSampleSet(int[] data) { 
         return true;        
     }

Modified: java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimEngRunEventBuilderTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimEngRunEventBuilderTest.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimEngRunEventBuilderTest.java	Wed Apr 27 11:11:32 2016
@@ -24,60 +24,60 @@
  */
 public class LCSimEngRunEventBuilderTest extends TestCase {
 
-	public void testLCSimEngRunEventBuilder() throws Exception {
-	    
-		// Setup database conditions.
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.setXmlConfig("/org/hps/conditions/config/conditions_dev.xml");
-		conditionsManager.setDetector("HPS-Proposal2014-v8-6pt6", 2000);
+    public void testLCSimEngRunEventBuilder() throws Exception {
+        
+        // Setup database conditions.
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.setXmlConfig("/org/hps/conditions/config/conditions_dev.xml");
+        conditionsManager.setDetector("HPS-Proposal2014-v8-6pt6", 2000);
 
-		// Configure LCIO writer.
-		new TestOutputFile(getClass().getSimpleName()).mkdirs();
-		File lcioFile = new TestOutputFile(getClass().getSimpleName() + File.separator + getClass().getSimpleName() + "_output.slcio");
-		LCIOWriter writer;
-		try {
-			writer = new LCIOWriter(lcioFile);
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		}
+        // Configure LCIO writer.
+        new TestOutputFile(getClass().getSimpleName()).mkdirs();
+        File lcioFile = new TestOutputFile(getClass().getSimpleName() + File.separator + getClass().getSimpleName() + "_output.slcio");
+        LCIOWriter writer;
+        try {
+            writer = new LCIOWriter(lcioFile);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
 
-		// Create event builder.
-		LCSimEventBuilder builder = new LCSimEngRunEventBuilder();
-		conditionsManager.addConditionsListener(builder);
-		//builder.setDetectorName("HPS-Proposal2014-v8-6pt6");
-		conditionsManager.setDetector("HPS-Proposal2014-v8-6pt6", 2744);
+        // Create event builder.
+        LCSimEventBuilder builder = new LCSimEngRunEventBuilder();
+        conditionsManager.addConditionsListener(builder);
+        //builder.setDetectorName("HPS-Proposal2014-v8-6pt6");
+        conditionsManager.setDetector("HPS-Proposal2014-v8-6pt6", 2744);
 
-		// Get remote test file.
-		FileCache cache = new FileCache();
-		File evioFile = cache.getCachedFile(new URL("http://www.lcsim.org/test/hps-java/LCSimEngRunEventBuilderTest/hps_002744.evio.0"));
+        // Get remote test file.
+        FileCache cache = new FileCache();
+        File evioFile = cache.getCachedFile(new URL("http://www.lcsim.org/test/hps-java/LCSimEngRunEventBuilderTest/hps_002744.evio.0"));
 
-		// Open the EVIO reader.
-		System.out.println("Opening file " + evioFile);
-		EvioReader reader = null;
-		try {
-			reader = new EvioReader(evioFile);
-		} catch (Exception e) {
-			throw new RuntimeException(e);
-		}
+        // Open the EVIO reader.
+        System.out.println("Opening file " + evioFile);
+        EvioReader reader = null;
+        try {
+            reader = new EvioReader(evioFile);
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
 
-		// Run the event builder on the EVIO.
-		EvioEvent evioEvent = null;
-		while ((evioEvent = reader.nextEvent()) != null) {
-			reader.parseEvent(evioEvent);
-			builder.readEvioEvent(evioEvent);
-			if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
-				try {
-					EventHeader lcsimEvent = builder.makeLCSimEvent(evioEvent);
-					System.out.println("created LCSim event #" + lcsimEvent.getEventNumber());
-					writer.write(lcsimEvent);
-				} catch (Exception e) {
-					e.printStackTrace();
-				}
-			}
-		}
+        // Run the event builder on the EVIO.
+        EvioEvent evioEvent = null;
+        while ((evioEvent = reader.nextEvent()) != null) {
+            reader.parseEvent(evioEvent);
+            builder.readEvioEvent(evioEvent);
+            if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
+                try {
+                    EventHeader lcsimEvent = builder.makeLCSimEvent(evioEvent);
+                    System.out.println("created LCSim event #" + lcsimEvent.getEventNumber());
+                    writer.write(lcsimEvent);
+                } catch (Exception e) {
+                    e.printStackTrace();
+                }
+            }
+        }
 
-		// Close the LCIO writer.
-		writer.flush();
-		writer.close();
-	}
+        // Close the LCIO writer.
+        writer.flush();
+        writer.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimTestRunEventBuilderTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimTestRunEventBuilderTest.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/LCSimTestRunEventBuilderTest.java	Wed Apr 27 11:11:32 2016
@@ -15,60 +15,60 @@
 import org.hps.record.evio.EvioEventUtilities;
 
 /**
- * 	Integration test to check the conversion of test run EVIO to LCIO 
+ *  Integration test to check the conversion of test run EVIO to LCIO 
  * 
- * 	@author Omar Moreno <[log in to unmask]>
- *	@date November 20, 2014
+ *  @author Omar Moreno <[log in to unmask]>
+ *  @date November 20, 2014
  */
 public class LCSimTestRunEventBuilderTest extends TestCase {
 
-	//-----------------//
-	//--- Constants ---//
-	//-----------------//
-	private static final String DB_CONFIGURATION
-		= "/org/hps/conditions/config/conditions_database_testrun_2012.xml";
-	
-	public void testLCSimTestRunEventBuilder() throws Exception { 
-	
-		// Configure the conditions system to retrieve test run conditions fo run 1351.
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.setXmlConfig(DB_CONFIGURATION);
-		
-		// Create the test run event builder
-		LCSimTestRunEventBuilder builder = new LCSimTestRunEventBuilder();
-		conditionsManager.addConditionsListener(builder);
+    //-----------------//
+    //--- Constants ---//
+    //-----------------//
+    private static final String DB_CONFIGURATION
+        = "/org/hps/conditions/config/conditions_database_testrun_2012.xml";
+    
+    public void testLCSimTestRunEventBuilder() throws Exception { 
+    
+        // Configure the conditions system to retrieve test run conditions fo run 1351.
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.setXmlConfig(DB_CONFIGURATION);
+        
+        // Create the test run event builder
+        LCSimTestRunEventBuilder builder = new LCSimTestRunEventBuilder();
+        conditionsManager.addConditionsListener(builder);
 
-		conditionsManager.setDetector("HPS-TestRun-v5", 1351);
+        conditionsManager.setDetector("HPS-TestRun-v5", 1351);
 
-		// Retrieve the remote test file.  The file currently being contains a
-		// subset of events from run 1351
-		FileCache cache = new FileCache();
-		File evioFile = cache.getCachedFile(new URL("http://www.lcsim.org/test/hps-java/hps1351_test.evio"));
-	
-		// Instantiate the EVIO reader and open the test file.  If the file
-		// can't be found, throw a runtime exception
-		EvioReader reader = null;
-		try {
-			reader = new EvioReader(evioFile);
-		} catch (Exception e) {
-			throw new RuntimeException(
-					"[ " + this.getClass().getSimpleName() + " ]: EVIO file couldn't be opened.");
-		}
-		
-		// Loop through all EVIO events in the file and process them using the
-		// event builder.  If the event is a physics event, process the event
-		// using the subdetector readers.
-		EvioEvent evioEvent = null;
-		while ((evioEvent = reader.nextEvent()) != null) {
-			reader.parseEvent(evioEvent);
-			builder.readEvioEvent(evioEvent);
-			if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
-				EventHeader lcsimEvent = builder.makeLCSimEvent(evioEvent);
-				System.out.println("[ " + this.getClass().getSimpleName() + " ]: Created event number " + lcsimEvent.getEventNumber());
-			}
-		}
-		
-		// Close the EVIO reader
-		reader.close();
-	}
+        // Retrieve the remote test file.  The file currently being contains a
+        // subset of events from run 1351
+        FileCache cache = new FileCache();
+        File evioFile = cache.getCachedFile(new URL("http://www.lcsim.org/test/hps-java/hps1351_test.evio"));
+    
+        // Instantiate the EVIO reader and open the test file.  If the file
+        // can't be found, throw a runtime exception
+        EvioReader reader = null;
+        try {
+            reader = new EvioReader(evioFile);
+        } catch (Exception e) {
+            throw new RuntimeException(
+                    "[ " + this.getClass().getSimpleName() + " ]: EVIO file couldn't be opened.");
+        }
+        
+        // Loop through all EVIO events in the file and process them using the
+        // event builder.  If the event is a physics event, process the event
+        // using the subdetector readers.
+        EvioEvent evioEvent = null;
+        while ((evioEvent = reader.nextEvent()) != null) {
+            reader.parseEvent(evioEvent);
+            builder.readEvioEvent(evioEvent);
+            if (EvioEventUtilities.isPhysicsEvent(evioEvent)) {
+                EventHeader lcsimEvent = builder.makeLCSimEvent(evioEvent);
+                System.out.println("[ " + this.getClass().getSimpleName() + " ]: Created event number " + lcsimEvent.getEventNumber());
+            }
+        }
+        
+        // Close the EVIO reader
+        reader.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/SvtEvioReaderTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/SvtEvioReaderTest.java	(original)
+++ java/branches/HPSJAVA-409/evio/src/test/java/org/hps/evio/SvtEvioReaderTest.java	Wed Apr 27 11:11:32 2016
@@ -25,47 +25,47 @@
     // Initialize the logger
     protected static Logger LOGGER = Logger.getLogger(SvtEvioReaderTest.class.getPackage().getName());
     
-	public void testSvtEvioReaderTest() throws Exception { 
+    public void testSvtEvioReaderTest() throws Exception { 
 
-		// Get the EVIO file that will be used to test the reader
-		FileCache fileCache = new FileCache(); 
-		File evioFile = fileCache.getCachedFile(
-				new URL("http://www.lcsim.org/test/hps-java/svt_evio_reader_test.evio")); 
+        // Get the EVIO file that will be used to test the reader
+        FileCache fileCache = new FileCache(); 
+        File evioFile = fileCache.getCachedFile(
+                new URL("http://www.lcsim.org/test/hps-java/svt_evio_reader_test.evio")); 
 
-		LOGGER.info("Opening file " + evioFile); 
+        LOGGER.info("Opening file " + evioFile); 
 
-		// Instantiate the EVIO reader and open the file
-		EvioReader evioReader = new EvioReader(evioFile); 
-	
-		// Instantiate the SVT EVIO reader
-		SvtEvioReader svtReader = new SvtEvioReader(); 
+        // Instantiate the EVIO reader and open the file
+        EvioReader evioReader = new EvioReader(evioFile); 
+    
+        // Instantiate the SVT EVIO reader
+        SvtEvioReader svtReader = new SvtEvioReader(); 
 
-		// Setup the database conditions 
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.setDetector("HPS-Proposal2014-v9-2pt2", 2000); 
+        // Setup the database conditions 
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.setDetector("HPS-Proposal2014-v9-2pt2", 2000); 
 
-		// Instantiate the event builder
-		LCSimEventBuilder eventBuilder = new LCSimEngRunEventBuilder(); 
+        // Instantiate the event builder
+        LCSimEventBuilder eventBuilder = new LCSimEngRunEventBuilder(); 
 
-		// Check that the file contains the expected number of events
-		int eventCount = evioReader.getEventCount(); 
-		LOGGER.info("File " + evioFile + " contains " + eventCount + " events."); 
+        // Check that the file contains the expected number of events
+        int eventCount = evioReader.getEventCount(); 
+        LOGGER.info("File " + evioFile + " contains " + eventCount + " events."); 
 
 
-		// Loop through the EVIO events and process them.
-		EvioEvent evioEvent = null; 
-		while ((evioEvent = evioReader.nextEvent()) != null) { 
-			evioReader.parseEvent(evioEvent); 	
+        // Loop through the EVIO events and process them.
+        EvioEvent evioEvent = null; 
+        while ((evioEvent = evioReader.nextEvent()) != null) { 
+            evioReader.parseEvent(evioEvent);   
 
-			// Only process physics events
-			if (!EvioEventUtilities.isPhysicsEvent(evioEvent)) continue;
-			LOGGER.info("Found physics event."); 	
-	
-			EventHeader lcsimEvent = eventBuilder.makeLCSimEvent(evioEvent); 
-			LOGGER.info("Created LCSim event # " + lcsimEvent.getEventNumber()); 	
+            // Only process physics events
+            if (!EvioEventUtilities.isPhysicsEvent(evioEvent)) continue;
+            LOGGER.info("Found physics event.");    
+    
+            EventHeader lcsimEvent = eventBuilder.makeLCSimEvent(evioEvent); 
+            LOGGER.info("Created LCSim event # " + lcsimEvent.getEventNumber());    
 
-			// Process the event using the SVT evio reader
-			svtReader.processEvent(evioEvent, lcsimEvent);  
-		}
-	}
+            // Process the event using the SVT evio reader
+            svtReader.processEvent(evioEvent, lcsimEvent);  
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/integration-tests/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/pom.xml	(original)
+++ java/branches/HPSJAVA-409/integration-tests/pom.xml	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
         <dependency>
             <groupId>org.hps</groupId>
             <artifactId>hps-test-data</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
+            <version>1.0-SNAPSHOT</version>
             <scope>test</scope>
             <classifier>archive</classifier>
             <type>jar</type>
@@ -31,7 +31,7 @@
         <dependency>
             <groupId>org.hps</groupId>
             <artifactId>hps-test-data</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
+            <version>1.0-SNAPSHOT</version>
             <scope>test</scope>
             <type>jar</type>
         </dependency>
@@ -51,7 +51,8 @@
                 <version>2.19</version>
                 <configuration>
                     <argLine>-server -Xmx2g -XX:MaxPermSize=512m -Djava.util.logging.config.class=org.hps.logging.config.TestLoggingConfig</argLine>
-                    <forkMode>always</forkMode>
+                    <forkCount>1</forkCount>
+                    <reuseForks>false</reuseForks>
                     <includes>
                         <include>org/hps/test/it/*Test.java</include>
                     </includes>
@@ -86,28 +87,5 @@
                 </plugins>
             </build>
         </profile> 
-        <!-- This profile activates automatically when not running tests on a SLAC Unix system with NFS access. -->
-        <profile>
-            <id>no-slac-nfs</id>
-            <activation>
-                <activeByDefault>false</activeByDefault>
-                <file>
-                    <missing>/nfs/slac/g/hps/</missing>
-                </file>
-            </activation>
-            <build>
-                <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-surefire-plugin</artifactId>
-                        <configuration>
-                            <excludes>                           
-                                <exclude>org/hps/test/it/EvioToLcioTest.java</exclude> 
-                            </excludes>
-                        </configuration>
-                    </plugin>
-                </plugins>
-            </build>        
-        </profile>  
     </profiles>    
 </project>

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/DataQualityMonitorTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/DataQualityMonitorTest.java	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/DataQualityMonitorTest.java	Wed Apr 27 11:11:32 2016
@@ -17,16 +17,14 @@
 
     private static final String CLASS_NAME = DataQualityMonitorTest.class.getSimpleName();
     private static final File OUTPUT_DIR = new File("./target/test-output/" + CLASS_NAME);
-    private static final File OUTPUT_FILE = new File(OUTPUT_DIR.getAbsolutePath() + File.separator + CLASS_NAME);
-    private static final File AIDA_FILE = new File(OUTPUT_FILE.getAbsolutePath() + ".aida");
+    private static final File OUTPUT_FILE = new File(OUTPUT_DIR.getAbsolutePath() + File.separator + CLASS_NAME + ".aida");
     private static final String STEERING_RESOURCE = "/org/hps/steering/test/DataQualityTest.lcsim";
 
     public void setUp() {
         
-        System.out.println("Setting up DQM Test");
         // Delete files if they already exist.     
-        if (AIDA_FILE.exists())
-            AIDA_FILE.delete();
+        if (OUTPUT_FILE.exists())
+            OUTPUT_FILE.delete();
 
         // Create output dir.
         OUTPUT_DIR.mkdirs();
@@ -36,11 +34,12 @@
 
     public void testQualityMonitor() {
         File dataFile = new TestDataUtility().getTestData("DataQualityMonitorTest.slcio");
-        System.out.println("running data quality job with steering resource " + STEERING_RESOURCE);
+        System.out.println("running data quality job with steering resource " + STEERING_RESOURCE + " ...");
         JobManager jobManager = new JobManager();
         jobManager.addVariableDefinition("outputFile", OUTPUT_FILE.getPath());
         jobManager.addInputFile(dataFile);
         jobManager.setup(STEERING_RESOURCE);
         jobManager.run();
+        System.out.println("Done!");
     }
 }

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/EvioToLcioTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/EvioToLcioTest.java	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/EvioToLcioTest.java	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,6 @@
 package org.hps.test.it;
 
+import java.io.File;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.logging.Level;
@@ -7,8 +8,8 @@
 
 import junit.framework.TestCase;
 
+import org.hps.data.test.TestDataUtility;
 import org.hps.evio.EvioToLcio;
-import org.hps.record.epics.EpicsData;
 import org.hps.record.scalers.ScalerData;
 import org.hps.test.util.TestOutputFile;
 import org.lcsim.event.EventHeader;
@@ -20,16 +21,6 @@
 /**
  * Basic test of converting EVIO to LCIO using the {@link org.hps.evio.EvioToLcio} command line utility on Engineering
  * Run 2015 data.
- * <p>
- * This test checks the LCIO output for the:</br>
- * <ul>
- * <li>correct number of EPICS data collections</li>
- * <li>correct number of scaler data collections</li>
- * <li>all expected event collections</li>
- * <li>scaler parameters in event header</li>
- * </ul>
- * <p>
- * The test input is the first file of run 5772 in which scaler data appears around every 100k events.
  *
  * @author Jeremy McCormick, SLAC
  */
@@ -45,12 +36,7 @@
          * Map to keep track of number of events with empty collections.
          */
         Map<String, Integer> emptyCollections = new HashMap<String, Integer>();
-
-        /**
-         * Number of EPICS data collections found.
-         */
-        int epicsDataCount = 0;
-
+       
         /**
          * Number of events processed.
          */
@@ -60,6 +46,12 @@
          * Number of scaler data collections found.
          */
         int scalerDataCount = 0;
+        
+        CheckDriver() {
+            for (String collectionName : COLLECTION_NAMES) {
+                emptyCollections.put(collectionName, new Integer(0));
+            }
+        }
 
         /**
          * Check a collection by making sure it is present in the event and incrementing a counter if it is empty.
@@ -72,13 +64,9 @@
             if (!event.hasCollection(type, name)) {
                 throw new RuntimeException("Missing " + name + " collection.");
             }
+            Integer nEmpty = emptyCollections.get(name);
             if (event.get(type, name).isEmpty()) {
-                Integer nEmpty = emptyCollections.get(name);
-                if (nEmpty == null) {
-                    nEmpty = 0;
-                }
                 ++nEmpty;
-                // System.out.println(name + " is empty in event " + event.getEventNumber());
                 emptyCollections.put(name, nEmpty);
             }
         }
@@ -88,17 +76,7 @@
                 this.checkCollection(event, COLLECTION_TYPES[i], COLLECTION_NAMES[i]);
             }
         }
-
-        private void checkEpicsData(final EventHeader event) {
-            final EpicsData epicsData = EpicsData.read(event);
-            if (epicsData != null) {
-                if (epicsData.getEpicsHeader() == null) {
-                    throw new RuntimeException("The EpicsData header is null.");
-                }
-                ++epicsDataCount;
-            }
-        }
-
+ 
         private void checkScalarData(final EventHeader event) {
             final ScalerData scalerData = ScalerData.read(event);
             if (scalerData != null) {
@@ -113,10 +91,7 @@
          */
         @Override
         public void process(final EventHeader event) {
-
-            // Find and check EPICS data.
-            this.checkEpicsData(event);
-
+          
             // Find scaler data.
             this.checkScalarData(event);
 
@@ -128,41 +103,34 @@
     }
 
     /**
-     * The number of empty collections that are allowed.
-     */
-    private static int[] ALLOWED_EMPTY = new int[] {45, 0, 0, 0};
-
-    /**
      * Names of collections to check.
      */
-    private static String[] COLLECTION_NAMES = new String[] {"EcalReadoutHits", "FADCGenericHits", "SVTRawTrackerHits",
-            "TriggerBank"};
+    private static String[] COLLECTION_NAMES = new String[] {
+        "EcalReadoutHits", 
+        "FADCGenericHits", 
+        "SVTRawTrackerHits",
+        "TriggerBank"
+    };
 
     /**
      * Classes of collections.
      */
-    private static Class<?>[] COLLECTION_TYPES = new Class<?>[] {RawTrackerHit.class, GenericObject.class,
-            RawTrackerHit.class, GenericObject.class};
-
-    /**
-     * The number of EPICS collections that should be found.
-     */
-    private static int EPICS_DATA_COUNT = 7;
-
-    /**
-     * The default input file (large file at SLAC so the pom.xml file excludes this test on non-SLAC hosts).
-     */
-    private static final String INPUT_FILE = "/nfs/slac/g/hps3/data/engrun2015/evio/hps_005772.evio.0";
+    private static Class<?>[] COLLECTION_TYPES = new Class<?>[] {
+        RawTrackerHit.class, 
+        GenericObject.class,
+        RawTrackerHit.class, 
+        GenericObject.class
+    };
 
     /**
      * The number of events that should be processed.
      */
-    private static int PROCESSED_COUNT = 251823;
+    private static int PROCESSED_COUNT = 1000;
 
     /**
      * The number of scaler data collections that should be found.
      */
-    private static int SCALER_DATA_COUNT = 3;
+    private static int SCALER_DATA_COUNT = 1;
    
     /**
      * Run the test.
@@ -171,13 +139,15 @@
      */
     public void testEvioToLcio() throws Exception {
 
+        final File inputFile = new TestDataUtility().getTestData("run5772_integrationTest.evio");
+        
         // LCIO output file.
         final TestOutputFile outputFile = new TestOutputFile(EvioToLcioTest.class, "hps_005772.slcio");
 
         // Run the command line utility.
         final String[] args = new String[] {"-l", outputFile.getPath(), "-d", "HPS-EngRun2015-Nominal-v1", "-r", "-x", 
-                "/org/hps/steering/EventMarker.lcsim", INPUT_FILE};
-        System.out.println("Running EvioToLcio on " + INPUT_FILE);
+                "/org/hps/steering/EventMarker.lcsim", inputFile.getAbsolutePath()};
+        System.out.println("Running EvioToLcio on " + inputFile.getPath());
         Logger.getLogger("org.hps.evio").setLevel(Level.WARNING);
         System.out.println("org.hps.evio logging level is " + Logger.getLogger("org.hps.evio").getLevel());
         EvioToLcio cnv = new EvioToLcio();
@@ -188,9 +158,6 @@
         System.out.println("Done running EvioToLcio!");
         System.out.println("conversion to LCIO took " + elapsed + " ms");
         
-        // Check that the conversion did not take too long.
-        //assertTrue("Conversion from EVIO to LCIO took too long.", elapsed < 2000000);
-
         // Read in the LCIO file and run the CheckDriver on it.
         System.out.println("Checking LCIO output ...");
         final LCSimLoop loop = new LCSimLoop();
@@ -209,22 +176,15 @@
         System.out.println("CheckDriver processed " + checkDriver.processedCount + " events.");
         assertEquals("Wrong number of events processed by the check Driver.", PROCESSED_COUNT, checkDriver.processedCount);
 
-        // Check that the correct number of EPICS data collections were written out.
-        System.out.println("Found " + checkDriver.epicsDataCount + " events with EPICS data.");
-        assertTrue("EPICS data count is wrong.", checkDriver.epicsDataCount == EPICS_DATA_COUNT);
-
         // Check that the correct number of scaler data collections were written out.
         System.out.println("Found " + checkDriver.scalerDataCount + " events with scaler data.");
         assertTrue("Scaler data count is wrong.", checkDriver.scalerDataCount == SCALER_DATA_COUNT);
-
-        // Check that there were not too many empty collections.  
+        
+        // Check that there were no empty output collections.
         for (int i = 0; i < COLLECTION_NAMES.length; i++) {
             final String collection = COLLECTION_NAMES[i];
             final Integer nEmpty = checkDriver.emptyCollections.get(collection);
-            if (nEmpty != null) {
-                System.out.println(collection + " had " + nEmpty + " empty collections.");
-                assertTrue(collection + " had too many empty collections.", nEmpty <= ALLOWED_EMPTY[i]);
-            }
+            assertTrue("Collection " + collection + " was empty.", nEmpty == 0);
         }
     }
 }

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/ReconSteeringTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/ReconSteeringTest.java	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/ReconSteeringTest.java	Wed Apr 27 11:11:32 2016
@@ -1,100 +1,42 @@
 package org.hps.test.it;
 
 import java.io.File;
-import java.io.IOException;
-import java.net.URL;
 
 import junit.framework.TestCase;
 
 import org.hps.data.test.TestDataUtility;
 import org.hps.job.JobManager;
-import org.lcsim.util.cache.FileCache;
 import org.lcsim.util.test.TestUtil.TestOutputFile;
 
 /**
- * Test that production MC recon steering files are not broken by running an LCSim job on them
- * using an LCIO file.
+ * Run a test job on Eng Run 2015 data.
  * 
  * @author Jeremy McCormick, SLAC
  */
 public class ReconSteeringTest extends TestCase {
     
-    /**
-     * List of steering files to run.
-     */
-    final static String[] STEERING_FILES = {
-        "EngineeringRun2014EcalRecon_Pass1.lcsim",
-        "EngineeringRun2014EcalRecon.lcsim",
-        "EngineeringRun2015EcalRecon.lcsim",
-        "EngineeringRun2015FullRecon.lcsim",
-        "EngineeringRun2015FullRecon_Pass2.lcsim",
-        "EngineeringRun2015HitRecon.lcsim",
-        "HPSTrackingDefaultsRecon.lcsim"
-    };
-            
-    /**
-     * Test recon steering files.
-     * @throws Exception if any error occurs running the recon job
-     */
-    public void testSteeringFiles() {
+    final static String STEERING_RESOURCE = "/org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim";
+              
+    public void testReconSteering() throws Exception {
         
-        File inputFile = new TestDataUtility().getTestData("tritrigv1-egsv3-triv2-g4v1_s2d6_HPS-EngRun2015-Nominal-v3_3.4.0_pairs1_1.slcio");
-        
-        for (String steeringFile : STEERING_FILES) {
-            
-            // Run the reconstruction steering file.
-            File outputFile = null;
-            try {
-                outputFile = new TestOutputFile(new File(steeringFile).getName().replace(".lcsim", ""));
-                runSteering("/org/hps/steering/recon/" + steeringFile, inputFile, outputFile);
-            } catch (Throwable e) {
-                System.err.println("Job with steering " + steeringFile + " failed!");
-                throw new RuntimeException("Recon job failed.", e);
-            }
-            
-            Runtime runtime = Runtime.getRuntime();
-            
-            int mb = 1024 * 1024;
-            
-            System.out.println("total memory: " + runtime.totalMemory() / mb);
-            System.out.println("free memory: " + runtime.freeMemory() / mb);
-            System.out.println("max memory: " + runtime.maxMemory() / mb);
-            System.out.println("used memory: " + (runtime.totalMemory() - runtime.freeMemory()) / mb);
-            
-            System.gc();
-            
-            // Create DQM output for QA.
-            try {
-                runDQM(outputFile);
-            } catch (Throwable e) {
-                throw new RuntimeException("The DQM job failed.", e);
-            }
-        }
-    }
-       
-    private void runSteering(String steeringFile, File inputFile, File outputFile) {
-        System.out.println("Testing steering file " + steeringFile + " ...");
+        File inputFile = new TestDataUtility().getTestData("run_5772_data_only.slcio");
+                           
+        File outputFile = null;
+        outputFile = new TestOutputFile(new File(STEERING_RESOURCE).getName().replace(".lcsim", ""));
+        System.out.println("Testing steering " + STEERING_RESOURCE + " ...");
         JobManager job = new JobManager();
         job.addVariableDefinition("outputFile", outputFile.getPath());
-        job.addVariableDefinition("detector", "HPS-EngRun2015-Nominal-v3");
-        job.addVariableDefinition("run", "5772");
-        job.addVariableDefinition("isMC", "true");
         job.addInputFile(inputFile);
-        job.setup(steeringFile);
+        job.setup(STEERING_RESOURCE);
+        job.setNumberOfEvents(1000);
         job.run();
-        System.out.println("Job with steering " + steeringFile + " successfully processed " + job.getLCSimLoop().getTotalCountableConsumed() + " events.");
-    }
-    
-    private void runDQM(File outputFile) {
-        System.out.println("Running DQM on " + outputFile.getPath() + " ...");
-        JobManager job = new JobManager();
-        File inputFile = new File(outputFile.getPath() + ".slcio");
-        job.addInputFile(inputFile);
-        job.addVariableDefinition("outputFile", outputFile.getPath().replace(".slcio", ""));
-        job.setup("/org/hps/steering/production/DataQualityRecon.lcsim");
-        job.run();
-        System.out.println("DQM processed " + job.getLCSimLoop().getTotalCountableConsumed() + " events from " + outputFile + ".");
+        System.out.println("Done processing " + job.getLCSimLoop().getTotalCountableConsumed() + " events.");
+                            
+        Runtime runtime = Runtime.getRuntime();
+        int mb = 1024 * 1024; 
+        System.out.printf("total memory: %d mb\n", runtime.totalMemory() / mb); 
+        System.out.printf("free memory: %d mb\n", runtime.freeMemory() / mb);
+        System.out.printf("max memory: %d mb\n", runtime.maxMemory() / mb);
+        System.out.printf("used memory: %d mb\n", (runtime.totalMemory() - runtime.freeMemory()) / mb);
     }
 }
-
-

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/SimpleSvtReadoutTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/SimpleSvtReadoutTest.java	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/java/org/hps/test/it/SimpleSvtReadoutTest.java	Wed Apr 27 11:11:32 2016
@@ -26,14 +26,14 @@
     // Collection Names
     static final String rawTrackerHitCollectionName = "SVTRawTrackerHits";
     
-	public void testSimpleSvtReadout() throws Exception { 
-				
-		File inputFile = new TestDataUtility().getTestData("ReadoutToLcioTest.slcio");
-			        
+    public void testSimpleSvtReadout() throws Exception { 
+                
+        File inputFile = new TestDataUtility().getTestData("ReadoutToLcioTest.slcio");
+                    
         outputDir.mkdirs();
         if(!outputDir.exists()){ 
-        	this.printDebug("Failed to create directory " + outputDir.getPath());
-        	throw new RuntimeException("Failed to create output directory.");
+            this.printDebug("Failed to create directory " + outputDir.getPath());
+            throw new RuntimeException("Failed to create output directory.");
         }
         
         FinalCheckDriver checker = new FinalCheckDriver();
@@ -54,25 +54,25 @@
         this.printDebug("");
         this.printDebug("===============================");
         
-	}
-	
-	class FinalCheckDriver extends Driver { 
-	
-		private int totalRawTrackerHits = 0; 
-		
-		public void process(EventHeader event){
-			if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) return;
-			List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
-		
-			totalRawTrackerHits += rawHits.size();
-		}
-		
-		public int getTotalNumberOfRawTrackerHits(){
-			return totalRawTrackerHits;
-		}
-	}
-	
-	private void printDebug(String message){
-		System.out.println("[ SimpleSvtReadoutTest ]: " + message);
-	}
+    }
+    
+    class FinalCheckDriver extends Driver { 
+    
+        private int totalRawTrackerHits = 0; 
+        
+        public void process(EventHeader event){
+            if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) return;
+            List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
+        
+            totalRawTrackerHits += rawHits.size();
+        }
+        
+        public int getTotalNumberOfRawTrackerHits(){
+            return totalRawTrackerHits;
+        }
+    }
+    
+    private void printDebug(String message){
+        System.out.println("[ SimpleSvtReadoutTest ]: " + message);
+    }
 }

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/ecalreadoutsim/EcalReadoutSimTest.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/ecalreadoutsim/EcalReadoutSimTest.lcsim	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/ecalreadoutsim/EcalReadoutSimTest.lcsim	Wed Apr 27 11:11:32 2016
@@ -32,7 +32,7 @@
         <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
             <outputFile>${outputFile}.slcio</outputFile>
         </driver>
-			
+            
         <driver name="EcalReadout" type="org.hps.readout.ecal.FADCEcalReadoutDriver">
             <coincidenceWindow>1</coincidenceWindow>
             <ecalName>Ecal</ecalName>
@@ -50,7 +50,7 @@
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>true</use2014Gain>
 <!--            <debug>true</debug>-->
-        </driver>	
+        </driver>   
 
         <driver name="EcalClusterer" type="org.hps.recon.ecal.GTPEcalClusterer">
             <ecalName>Ecal</ecalName>
@@ -63,7 +63,7 @@
             <deadTime>10</deadTime>
             <pairCoincidence>2</pairCoincidence>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout">
             <addNoise>false</addNoise>
         </driver>
@@ -74,4 +74,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/DataQualityTest.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/DataQualityTest.lcsim	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/DataQualityTest.lcsim	Wed Apr 27 11:11:32 2016
@@ -18,13 +18,12 @@
         <driver name="CleanupDriver"/>
     </execute>    
     <drivers>    
-        <!--    <driver name="DQMDatabaseDriver" type="org.hps.analysis.dataquality.DQMDatabaseDriver"/> -->
         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
-            <eventInterval>1</eventInterval>
+            <eventInterval>100</eventInterval>
         </driver>        
         <driver name="RawTrackerHitSensorSetup" type="org.lcsim.recon.tracking.digitization.sisim.config.RawTrackerHitSensorSetup"/>
         <driver name="AidaSaveDriver" type="org.lcsim.job.AidaSaveDriver">
-            <outputFileName>${outputFile}.root</outputFileName>
+            <outputFileName>${outputFile}</outputFileName>
         </driver>
         <driver name="SVTMonitoring" type="org.hps.analysis.dataquality.SvtMonitoring">
             <overwriteDB>false</overwriteDB>
@@ -48,6 +47,5 @@
             <overwriteDB>false</overwriteDB>
         </driver>
         <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver"/>
-
     </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/Dummy.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/Dummy.lcsim	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/Dummy.lcsim	Wed Apr 27 11:11:32 2016
@@ -10,4 +10,4 @@
         <driver name="DummyDriver" type="org.hps.test.util.DummyDriver"/>
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/EcalReadoutSimTest.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/EcalReadoutSimTest.lcsim	(original)
+++ java/branches/HPSJAVA-409/integration-tests/src/test/resources/org/hps/steering/test/EcalReadoutSimTest.lcsim	Wed Apr 27 11:11:32 2016
@@ -28,7 +28,7 @@
         <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
             <outputFile>${outputFile}.slcio</outputFile>
         </driver>
-			
+            
         <driver name="EcalReadout" type="org.hps.readout.ecal.FADCEcalReadoutDriver">
             <coincidenceWindow>1</coincidenceWindow>
             <ecalName>Ecal</ecalName>
@@ -46,7 +46,7 @@
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>true</use2014Gain>
 <!--            <debug>true</debug>-->
-        </driver>	
+        </driver>   
 
         <driver name="EcalClusterer" type="org.hps.recon.ecal.GTPEcalClusterer">
             <ecalName>Ecal</ecalName>
@@ -59,7 +59,7 @@
             <deadTime>10</deadTime>
             <pairCoincidence>2</pairCoincidence>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout">
             <addNoise>false</addNoise>
         </driver>
@@ -70,4 +70,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/job/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/job/pom.xml	(original)
+++ java/branches/HPSJAVA-409/job/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/job/</url>
@@ -19,5 +19,9 @@
             <groupId>org.hps</groupId>
             <artifactId>hps-detector-model</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.hps</groupId>
+            <artifactId>hps-run-database</artifactId>
+        </dependency>        
     </dependencies>
 </project>

Modified: java/branches/HPSJAVA-409/job/src/main/java/org/hps/job/JobManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/job/src/main/java/org/hps/job/JobManager.java	(original)
+++ java/branches/HPSJAVA-409/job/src/main/java/org/hps/job/JobManager.java	Wed Apr 27 11:11:32 2016
@@ -1,20 +1,25 @@
 package org.hps.job;
 
-import java.io.InputStream;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.lcsim.util.Driver;
 
 import org.hps.conditions.ConditionsDriver;
-import org.hps.conditions.database.DatabaseConditionsManager;
-import org.hps.detector.svt.SvtDetectorSetup;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
 import org.lcsim.job.JobControlManager;
-import org.lcsim.util.Driver;
 
 /**
- * Extension of standard LCSim job manager which does some HPS-specific management of the conditions system.
+ * Extension of standard LCSim job manager.
+ * <p>
+ * Provides setup of database conditions system and adds option to provide conditions system tags.
  *
  * @author Jeremy McCormick, SLAC
  */
-public class JobManager extends JobControlManager {
-
+public final class JobManager extends JobControlManager {
+    
     /**
      * Run the job manager from the command line.
      *
@@ -31,58 +36,58 @@
      * Class constructor.
      */
     public JobManager() {
+        conditionsSetup = new DatabaseConditionsManagerSetup();
+    }
+    
+    /**
+     * Get the conditions setup.
+     * @return the conditions setup
+     */
+    public DatabaseConditionsManagerSetup getDatabaseConditionsManagerSetup() {
+        return (DatabaseConditionsManagerSetup) this.conditionsSetup;
+    }
+    
+    /**
+     * Override creation of command line options.
+     * @return the overridden command line options
+     */
+    @Override
+    protected Options createCommandLineOptions() {
+        Options options = super.createCommandLineOptions();
+        options.addOption("t", "tag", true, "conditions system tag (can be used multiple times)");
+        return options;
+    }
+    
+    /**
+     * Override command line parsing.
+     * @return the overridden, parsed command line
+     */
+    @Override
+    public CommandLine parse(final String args[]) {
+        CommandLine commandLine = super.parse(args);
+        if (commandLine.hasOption("t")) {
+            Set<String> tags = new HashSet<String>();
+            for (String tag : commandLine.getOptionValues("t")) {
+                tags.add(tag);
+            }
+            getDatabaseConditionsManagerSetup().setTags(tags);
+        }
+        return commandLine;
     }
 
     /**
-     * Override setup so the conditions system can be reset.
-     * 
-     * @param is the input stream containing config information
-     */
-    public void setup(InputStream is) {
-        
-        // Add class that will setup SVT detector with conditions data (this is awkward but has to be done someplace).
-        DatabaseConditionsManager.getInstance().addConditionsListener(new SvtDetectorSetup());
-        
-        super.setup(is);
-                
-        // Setup the conditions system if there is a ConditionsDriver present.
-        this.setupConditionsDriver();
-    }
-    
-    /**
-     * Override the parent classes method that runs the job in order to perform conditions system initialization.
-     *
-     * @return <code>true</code> if job was successful
-     */
-    @Override
-    public final boolean run() {
-        
-        // Run the job.
-        final boolean result = super.run();
-
-        // Close the conditions database connection if it is open.
-        DatabaseConditionsManager.getInstance().closeConnection();
-
-        return result;
-    }
-
-    /**
-     * This method will find the {@link org.hps.conditions.ConditionsDriver} in the list of Drivers registered with the
-     * manager and then execute its initialization method, which may override the default behavior of the conditions
-     * system.
-     */
-    private void setupConditionsDriver() {
-        ConditionsDriver conditionsDriver = null;
-        for (final Driver driver : this.getDriverAdapter().getDriver().drivers()) {
+     * Initialize <code>ConditionsDriver</code> if necessary.
+     **/
+    protected void setupDrivers() {
+        super.setupDrivers();
+        for (Driver driver : this.getDriverExecList()) {
             if (driver instanceof ConditionsDriver) {
-                conditionsDriver = (ConditionsDriver) driver;
+                ConditionsDriver conditions = (ConditionsDriver) driver;
+                getConditionsSetup().setRun(conditions.getRunNumber());
+                getConditionsSetup().setDetectorName(conditions.getDetectorName());
                 break;
             }
         }
-        if (conditionsDriver != null) {
-            LOGGER.config("initializing conditions Driver");            
-            conditionsDriver.initialize();
-            LOGGER.warning("Conditions driver will be removed soon!");
-        }
     }
+
 }

Modified: java/branches/HPSJAVA-409/logging/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/logging/pom.xml	(original)
+++ java/branches/HPSJAVA-409/logging/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/logging/</url>

Modified: java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/logging.properties
 =============================================================================
--- java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/logging.properties	(original)
+++ java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/logging.properties	Wed Apr 27 11:11:32 2016
@@ -16,6 +16,9 @@
 # configure the console handler
 java.util.logging.ConsoleHandler.level = ALL
 java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
+
+# turn minuit logging off
+org.freehep.math.minuit = OFF
 
 # lcsim job
 org.lcsim.job.level = CONFIG
@@ -49,7 +52,6 @@
 # ecal-recon
 org.hps.recon.ecal.level = CONFIG
 org.hps.recon.ecal.cluster.level = WARNING
-org.hps.recon.ecal.cluster.ClusterDriver.level = WARNING
 
 # recon
 org.hps.recon.filtering.level = WARNING
@@ -75,7 +77,7 @@
 # detector-model
 org.lcsim.detector.converter.compact.level = INFO
 org.lcsim.geometry.compact.converter.level = INFO
-org.hps.detector.svt.level = ALL
+org.hps.detector.svt.level = INFO
 
 # test data
 org.hps.data.test = INFO

Modified: java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/test_logging.properties
 =============================================================================
--- java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/test_logging.properties	(original)
+++ java/branches/HPSJAVA-409/logging/src/main/resources/org/hps/logging/config/test_logging.properties	Wed Apr 27 11:11:32 2016
@@ -16,15 +16,18 @@
 # configure the console handler
 java.util.logging.ConsoleHandler.level = ALL
 java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-f
+
+# turn minuit off
+org.freehep.math.minuit = OFF
+
 # lcsim job
-org.lcsim.job.level = WARNING
+org.lcsim.job.level = CONFIG
 org.lcsim.job.EventMarkerDriver.level = OFF
 org.lcsim.job.EventPrintLoopAdapter = ALL
 
 # conditions
 org.hps.conditions.api.level = WARNING
-org.hps.conditions.database.level = CONFIG
+org.hps.conditions.database.level = WARNING
 org.hps.conditions.cli.level = WARNING
 org.hps.conditions.ecal.level = WARNING
 org.hps.conditions.svt.level = WARNING
@@ -44,12 +47,11 @@
 org.hps.crawler.level = WARNING
 
 # datacat
-org.hps.datacat.client.level = ALL
+org.hps.datacat.client.level = OFF
 
 # ecal-recon
 org.hps.recon.ecal.level = WARNING
 org.hps.recon.ecal.cluster.level = WARNING
-org.hps.recon.ecal.cluster.ClusterDriver.level = WARNING
 
 # recon
 org.hps.recon.filtering.level = WARNING
@@ -79,3 +81,6 @@
 
 # test data
 org.hps.data.test = INFO
+
+# HPS job manager
+org.hps.job.JobManager = WARNING

Modified: java/branches/HPSJAVA-409/monitoring-app/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/pom.xml	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/monitoring-app/</url>

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/EventProcessing.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/EventProcessing.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/EventProcessing.java	Wed Apr 27 11:11:32 2016
@@ -6,11 +6,14 @@
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.logging.Logger;
 
 import org.freehep.record.loop.RecordLoop.Command;
 import org.hps.conditions.database.DatabaseConditionsManager;
+import org.hps.job.DatabaseConditionsManagerSetup;
 import org.hps.job.JobManager;
 import org.hps.monitoring.application.model.ConfigurationModel;
 import org.hps.monitoring.application.model.ConnectionStatus;
@@ -34,7 +37,6 @@
 import org.jlab.coda.et.exception.EtClosedException;
 import org.jlab.coda.et.exception.EtException;
 import org.lcsim.conditions.ConditionsListener;
-import org.lcsim.conditions.ConditionsReader;
 import org.lcsim.util.Driver;
 
 /**
@@ -194,11 +196,6 @@
     private SessionState sessionState;
    
     /**
-     * The current conditions manager.
-     */ 
-    private DatabaseConditionsManager conditionsManager;
-
-    /**
      * Class constructor, which will initialize with reference to the current monitoring application and lists of extra
      * processors to add to the loop, as well as supplemental conditions listeners that activate when the conditions
      * change.
@@ -306,7 +303,7 @@
      *
      * @param configurationModel the current global {@link org.hps.monitoring.application.ConfigurationModel} object
      */
-    private void createEventBuilder(final ConfigurationModel configurationModel) {
+    private LCSimEventBuilder createEventBuilder(final ConfigurationModel configurationModel) {
 
         // Get the class for the event builder.
         final String eventBuilderClassName = configurationModel.getEventBuilderClassName();
@@ -318,9 +315,8 @@
         } catch (final Exception e) {
             throw new RuntimeException("Failed to create LCSimEventBuilder.", e);
         }
-
-        // Add the builder as a listener so it is notified when conditions change.
-        this.conditionsManager.addConditionsListener(this.sessionState.eventBuilder);
+        
+        return this.sessionState.eventBuilder; 
     }
 
     /**
@@ -464,35 +460,70 @@
             steering = configurationModel.getSteeringFile();
         } else {
             steering = configurationModel.getSteeringResource();
-        }
-
-        this.logger.config("set steering " + steering + " with type "
+            if (!steering.startsWith("/")) {
+                steering = "/" + steering;
+            }
+        }
+
+        this.logger.config("set steering " + steering + " with type " 
                 + (steeringType == SteeringType.RESOURCE ? "RESOURCE" : "FILE"));
 
         try {
             // Create the job manager. A new conditions manager is instantiated from this call but not configured.
             this.sessionState.jobManager = new JobManager();
-
-            // Set ref to current conditions manager.
-            this.conditionsManager = DatabaseConditionsManager.getInstance();
             
-            // Add conditions listeners after new database conditions manager is initialized from the job manager.
+            // Setup class for conditions system.
+            DatabaseConditionsManagerSetup conditions = new DatabaseConditionsManagerSetup();
+            
+            // Disable run manager.
+            conditions.setEnableRunManager(false);
+            
+            // Setup the event builder to translate from EVIO to LCIO.
+            LCSimEventBuilder eventBuilder = this.createEventBuilder(configurationModel);            
+            conditions.addConditionsListener(eventBuilder);
+                        
+            // Add extra conditions listeners.
             for (final ConditionsListener conditionsListener : this.sessionState.conditionsListeners) {
-                this.logger.config("adding conditions listener " + conditionsListener.getClass().getName());
-                this.conditionsManager.addConditionsListener(conditionsListener);
-            }
-
+                this.logger.config("Adding conditions listener " + conditionsListener.getClass().getName());
+                conditions.addConditionsListener(conditionsListener);
+            }
+
+            // Add detector alias.
             if (configurationModel.hasValidProperty(ConfigurationModel.DETECTOR_ALIAS_PROPERTY)) {
-                // Set a detector alias.
-                ConditionsReader.addAlias(configurationModel.getDetectorName(),
+                conditions.addAlias(configurationModel.getDetectorName(),
                         "file://" + configurationModel.getDetectorAlias());
-                this.logger.config("using detector alias " + configurationModel.getDetectorAlias());
-            }
-
-            // Setup the event builder to translate from EVIO to LCIO.
-            // This must happen before Driver setup so the builder's listeners are activated first!
-            this.createEventBuilder(configurationModel);
-
+                this.logger.config("Added detector alias " + configurationModel.getDetectorAlias() 
+                        + " for " + configurationModel.getDetectorName());
+            }
+
+            // Add conditions tag.
+            if (configurationModel.hasValidProperty(ConfigurationModel.CONDITIONS_TAG_PROPERTY)
+                    && !configurationModel.getConditionsTag().equals("")) {
+                Set<String> tags = new HashSet<String>();
+                tags.add(configurationModel.getConditionsTag());
+                this.logger.config("Added conditions tag " + configurationModel.getConditionsTag());
+                conditions.setTags(tags);
+            }
+            
+            // Set user specified job number.
+            if (configurationModel.hasValidProperty(ConfigurationModel.USER_RUN_NUMBER_PROPERTY)) {
+                final int userRun = configurationModel.getUserRunNumber();
+                this.logger.config("User run number set to " + userRun);
+                conditions.setRun(userRun);
+            }
+            
+            // Set detector name.
+            conditions.setDetectorName(configurationModel.getDetectorName());
+            
+            // Freeze the conditions system to ignore run numbers from event data.
+            if (configurationModel.hasPropertyKey(ConfigurationModel.FREEZE_CONDITIONS_PROPERTY)) {
+                this.logger.config("user configured to freeze conditions system");
+                conditions.setFreeze(configurationModel.getFreezeConditions());
+            }
+                        
+            // Register the configured conditions settings with the job manager.
+            this.sessionState.jobManager.setConditionsSetup(conditions);
+                        
             // Configure the job manager for the XML steering.
             this.sessionState.jobManager.setDryRun(true);
             if (steeringType == SteeringType.RESOURCE) {
@@ -500,32 +531,10 @@
             } else if (steeringType.equals(SteeringType.FILE)) {
                 this.setupSteeringFile(steering);
             }
-
-            // Set conditions tag if applicable.
-            if (configurationModel.hasValidProperty(ConfigurationModel.CONDITIONS_TAG_PROPERTY)
-                    && !configurationModel.getConditionsTag().equals("")) {
-                this.logger.config("conditions tag is set to " + configurationModel.getConditionsTag());
-            } else {
-                this.logger.config("conditions NOT using a tag");
-            }
-
-            // Is there a user specified run number from the JobPanel?
-            if (configurationModel.hasValidProperty(ConfigurationModel.USER_RUN_NUMBER_PROPERTY)) {
-                final int userRunNumber = configurationModel.getUserRunNumber();
-                final String detectorName = configurationModel.getDetectorName();
-                this.logger.config("setting user run number " + userRunNumber + " with detector " + detectorName);
-                conditionsManager.setDetector(detectorName, userRunNumber);
-                if (configurationModel.hasPropertyKey(ConfigurationModel.FREEZE_CONDITIONS_PROPERTY)) {
-                    // Freeze the conditions system to ignore run numbers from the events.
-                    this.logger.config("user configured to freeze conditions system");
-                    this.conditionsManager.freeze();
-                } else {
-                    // Allow run numbers to be picked up from the events.
-                    this.logger.config("user run number provided but conditions system is NOT frozen");
-                    this.conditionsManager.unfreeze();
-                }
-            }
-
+            
+            // Post-init conditions system which may freeze if run and name were provided.
+            this.sessionState.jobManager.getConditionsSetup().postInitialize();
+            
             this.logger.info("lcsim setup was successful");
 
         } catch (final Throwable t) {
@@ -592,15 +601,19 @@
             this.logger.config("added extra Driver " + driver.getName());
         }
 
-        // Enable conditions system activation from EVIO event data in case the PRESTART is missed.
-        loopConfig.add(new EvioDetectorConditionsProcessor(configurationModel.getDetectorName()));
-        this.logger.config("added EvioDetectorConditionsProcessor to job with detector "
-                + configurationModel.getDetectorName());
+        // Enable conditions activation from EVIO; not needed if conditions are frozen for the job.
+        if (!DatabaseConditionsManager.getInstance().isFrozen()) {
+            loopConfig.add(new EvioDetectorConditionsProcessor(configurationModel.getDetectorName()));
+            this.logger.config("added EvioDetectorConditionsProcessor to job with detector "
+                    + configurationModel.getDetectorName());
+        } else {
+            this.logger.config("Conditions activation from EVIO is disabled.");
+        }
 
         // Create the CompositeLoop with the configuration.
         this.sessionState.loop = new CompositeLoop(loopConfig);
 
-        this.logger.config("record loop is setup");
+        this.logger.config("Record loop is setup.");
     }
 
     /**

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/Main.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/Main.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/Main.java	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.monitoring.application.model.Configuration;
 
 /**
@@ -29,7 +29,7 @@
         final Options options = new Options();
         options.addOption(new Option("h", false, "Print help."));
         options.addOption(new Option("c", true, "Load a properties file with configuration parameters."));
-        final CommandLineParser parser = new DefaultParser();
+        final CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         final CommandLine cl;

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplication.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplication.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplication.java	Wed Apr 27 11:11:32 2016
@@ -78,7 +78,6 @@
          */
         @Override
         public void close() throws SecurityException {
-            // Does nothing.
         }
 
         /**
@@ -86,7 +85,6 @@
          */
         @Override
         public void flush() {
-            // Does nothing.
         }
 
         /**
@@ -121,8 +119,6 @@
         @Override
         public void publish(final LogRecord record) {
             super.publish(record);
-
-            // FIXME: Is this efficient? Should this always happen here?
             flush();
         }
 
@@ -295,18 +291,18 @@
             loadConfiguration(new Configuration(DEFAULT_CONFIGURATION), false);
 
             if (userConfiguration != null) {
-                // Load user configuration.
+                // Load user configuration to supplement default settings.
                 loadConfiguration(userConfiguration, true);
             }
 
-            // Enable the GUI now that initialization is complete.
+            // Enable the GUI after initialization.
             this.frame.setEnabled(true);
 
-            LOGGER.info("application initialized successfully");
+            LOGGER.info("Monitoring app initialized successfully.");
 
         } catch (final Exception e) {
-            // Don't use the ErrorHandler here because we don't know that it initialized successfully.
-            System.err.println("MonitoringApplication failed to initialize without errors!");
+            // Initialization failed so print info and die.
+            System.err.println("ERROR: MonitoringApplication failed to initialize!");
             DialogUtil.showErrorDialog(null, "Error Starting Monitoring Application",
                     "Monitoring application failed to initialize.");
             e.printStackTrace();
@@ -321,9 +317,6 @@
      */
     @Override
     public void actionPerformed(final ActionEvent e) {
-
-        // logger.finest("actionPerformed - " + e.getActionCommand());
-
         final String command = e.getActionCommand();
         if (Commands.CONNECT.equals(command)) {
             startSession();
@@ -374,7 +367,7 @@
     }
 
     /**
-     * Redirect <code>System.out</code> and <code>System.err</code> to a file chosen by a file chooser.
+     * Redirect <code>System.out</code> and <code>System.err</code> to a chosen file.
      */
     private void chooseLogFile() {
         final JFileChooser fc = new JFileChooser();
@@ -420,7 +413,7 @@
     }
 
     /**
-     * Exit from the application from exit menu item or hitting close window button.
+     * Exit from the application.
      */
     private void exit() {
         if (this.connectionModel.isConnected()) {
@@ -954,7 +947,6 @@
 
             // Add listener to push conditions changes to conditions panel.
             final List<ConditionsListener> conditionsListeners = new ArrayList<ConditionsListener>();
-            conditionsListeners.add(this.frame.getConditionsPanel().new ConditionsPanelListener());
 
             // Instantiate the event processing wrapper.
             this.processing = new EventProcessing(this, processors, drivers, conditionsListeners);
@@ -973,7 +965,7 @@
             // Start the event processing thread.
             this.processing.start();
 
-            LOGGER.info("new session successfully initialized");
+            LOGGER.info("Event processing session started.");
 
         } catch (final Exception e) {
 
@@ -989,7 +981,7 @@
                             "There was an error while starting the session." + '\n' + "See the log for details.",
                             "Session Error");
 
-            LOGGER.severe("failed to start new session");
+            LOGGER.severe("Failed to start event processing.");
         }
     }
 

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplicationFrame.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplicationFrame.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/MonitoringApplicationFrame.java	Wed Apr 27 11:11:32 2016
@@ -37,7 +37,7 @@
     /**
      * The conditions panel.
      */
-    private final ConditionsPanel conditionsPanel;
+    //private final ConditionsPanel conditionsPanel;
 
     /**
      * The dashboard panel.
@@ -150,8 +150,8 @@
         tableTabbedPane.addTab("Trigger Diagnostics", this.triggerPanel);
 
         // Add the conditions panel.
-        this.conditionsPanel = new ConditionsPanel();
-        tableTabbedPane.addTab("Detector Conditions", this.conditionsPanel);
+        //this.conditionsPanel = new ConditionsPanel();
+        //tableTabbedPane.addTab("Detector Conditions", this.conditionsPanel);
 
         // Vertical split pane in left panel.
         this.leftSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, this.dashboardPanel, tableTabbedPane);
@@ -209,9 +209,9 @@
      *
      * @return the conditions panel
      */
-    ConditionsPanel getConditionsPanel() {
-        return this.conditionsPanel;
-    }
+    //ConditionsPanel getConditionsPanel() {
+    //    return this.conditionsPanel;
+    //}
 
     /**
      * Get the panel for the dashboard.

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/SystemStatusPanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/SystemStatusPanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/SystemStatusPanel.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.hps.monitoring.application;
 
 import java.awt.BorderLayout;
@@ -81,7 +78,7 @@
         
         this.statuses.clear();
     }
-
+    
     private class SystemStatusBeeper extends TimerTask {
 
         @Override
@@ -93,7 +90,7 @@
                 }
             }
             if (isAlarming) {
-                System.out.println("beep\007");
+                Toolkit.getDefaultToolkit().beep();
             }
         }
     }

Modified: java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/util/TableExporter.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/util/TableExporter.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-app/src/main/java/org/hps/monitoring/application/util/TableExporter.java	Wed Apr 27 11:11:32 2016
@@ -33,7 +33,7 @@
 
         // Column headers.
         for (int columnIndex = 0; columnIndex < columnCount; columnIndex++) {
-            buffer.append("\"" + model.getColumnName(columnIndex) + "\"" + fieldDelimiter);
+            buffer.append("\"" + model.getColumnName(columnIndex) + "\"" + fieldDelimiter + ",");
         }
         buffer.setLength(buffer.length() - 1);
         buffer.append('\n');
@@ -47,6 +47,7 @@
                 } else {
                     buffer.append("\"" + value + "\"" + fieldDelimiter);
                 }
+                buffer.append(",");
             }
             buffer.setLength(buffer.length() - 1);
             buffer.append('\n');

Modified: java/branches/HPSJAVA-409/monitoring-drivers/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/pom.xml	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/monitoring-drivers/</url>

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/scalers/DeadtimePlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/scalers/DeadtimePlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/scalers/DeadtimePlots.java	Wed Apr 27 11:11:32 2016
@@ -9,9 +9,7 @@
 import org.hps.record.scalers.ScalerUtilities;
 import org.hps.record.scalers.ScalerUtilities.LiveTimeIndex;
 import org.jfree.chart.JFreeChart;
-import org.jfree.chart.axis.Axis;
 import org.jfree.chart.axis.DateAxis;
-import org.jfree.chart.axis.ValueAxis;
 import org.jfree.data.time.Second;
 import org.jfree.data.time.TimeSeriesCollection;
 import org.lcsim.event.EventHeader;

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/PedestalPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/PedestalPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/PedestalPlots.java	Wed Apr 27 11:11:32 2016
@@ -23,6 +23,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import org.hps.recon.tracking.SvtPlotUtils;
 //===> import org.hps.conditions.deprecated.HPSSVTCalibrationConstants;
 //===> import org.hps.conditions.deprecated.SvtUtils;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTCellIDPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTCellIDPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTCellIDPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -17,52 +17,52 @@
  */
 public class SVTCellIDPrintDriver extends Driver {
 
-	String rawTrackerHitCollectionName = "SVTData";
-	String outputFileName;
-	PrintWriter outputStream = null;
+    String rawTrackerHitCollectionName = "SVTData";
+    String outputFileName;
+    PrintWriter outputStream = null;
 
-	public SVTCellIDPrintDriver() {
-	}
+    public SVTCellIDPrintDriver() {
+    }
 
-	public void setRawTrackerHitCollectionName(String rawTrackerHitCollectionName) {
-		this.rawTrackerHitCollectionName = rawTrackerHitCollectionName;
-	}
+    public void setRawTrackerHitCollectionName(String rawTrackerHitCollectionName) {
+        this.rawTrackerHitCollectionName = rawTrackerHitCollectionName;
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	public void startOfData() {
-		if (rawTrackerHitCollectionName == null) {
-			throw new RuntimeException("The parameter ecalCollectionName was not set!");
-		}
+    public void startOfData() {
+        if (rawTrackerHitCollectionName == null) {
+            throw new RuntimeException("The parameter ecalCollectionName was not set!");
+        }
 
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(SVTData.class, rawTrackerHitCollectionName)) {
-			List<SVTData> hits = event.get(SVTData.class, rawTrackerHitCollectionName);
-			//outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
-			for (SVTData hit : hits) {
-				outputStream.printf("FPGA=%d\thybrid=%d\tchannel=%d\n", hit.getFPGAAddress(), hit.getHybridNumber(), hit.getChannelNumber());
-			}
-		}
-		if (event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {
-			List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
-			//outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
-			for (RawTrackerHit hit : hits) {
-				outputStream.printf("name=%s\tside=%d\tstrip=%d\n", hit.getDetectorElement().getName(), hit.getIdentifierFieldValue("side"), hit.getIdentifierFieldValue("strip"));
-			}
-		}
-	}
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(SVTData.class, rawTrackerHitCollectionName)) {
+            List<SVTData> hits = event.get(SVTData.class, rawTrackerHitCollectionName);
+            //outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
+            for (SVTData hit : hits) {
+                outputStream.printf("FPGA=%d\thybrid=%d\tchannel=%d\n", hit.getFPGAAddress(), hit.getHybridNumber(), hit.getChannelNumber());
+            }
+        }
+        if (event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
+            //outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
+            for (RawTrackerHit hit : hits) {
+                outputStream.printf("name=%s\tside=%d\tstrip=%d\n", hit.getDetectorElement().getName(), hit.getIdentifierFieldValue("side"), hit.getIdentifierFieldValue("strip"));
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitRecoCorrelations.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitRecoCorrelations.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitRecoCorrelations.java	Wed Apr 27 11:11:32 2016
@@ -32,7 +32,7 @@
  */
 public class SVTHitRecoCorrelations extends Driver {
 
-	//private List<AIDAFrame> plotterFrame = new ArrayList<AIDAFrame>();
+    //private List<AIDAFrame> plotterFrame = new ArrayList<AIDAFrame>();
     private List<IPlotter> plotters = new ArrayList<IPlotter>();
     private AIDA aida = AIDA.defaultInstance();                  
     private String rawTrackerHitCollectionName = "SVTRawTrackerHits";
@@ -225,7 +225,7 @@
         */
         
         //for(int i=0;i<2;++i) {
-       	//plotterFrame.get(i).pack();
+        //plotterFrame.get(i).pack();
         //    plotterFrame.get(i).setVisible(true);
         //}
     }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitReconstructionPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitReconstructionPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTHitReconstructionPlots.java	Wed Apr 27 11:11:32 2016
@@ -1,13 +1,9 @@
 package org.hps.monitoring.drivers.svt;
 
-import org.hps.monitoring.drivers.trackrecon.TrackingReconPlots;
 import hep.aida.IAnalysisFactory;
-import hep.aida.IHistogram1D;
-import hep.aida.IHistogram2D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
 import hep.aida.IProfile1D;
-import hep.aida.ref.plotter.PlotterRegion;
 
 import java.io.IOException;
 import java.util.HashMap;
@@ -16,14 +12,14 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-
+import org.hps.monitoring.drivers.trackrecon.TrackingReconPlots;
 //===> import org.hps.conditions.deprecated.SvtUtils;
 import org.hps.recon.tracking.FittedRawTrackerHit;
 import org.lcsim.detector.identifier.IIdentifier;
 import org.lcsim.detector.identifier.IIdentifierHelper;
 import org.lcsim.detector.tracker.silicon.DopedSilicon;
+import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.detector.tracker.silicon.SiSensor;
-import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.detector.tracker.silicon.SiTrackerIdentifierHelper;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawTrackerHit;
@@ -38,7 +34,7 @@
  */
 public class SVTHitReconstructionPlots extends Driver {
 
-	//private AIDAFrame plotterFrame;
+    //private AIDAFrame plotterFrame;
     private AIDA aida = AIDA.defaultInstance();
     private String fittedTrackerHitCollectionName = "SVTFittedRawTrackerHits";
     private String trackerHitCollectionName = "StripClusterer_SiTrackerHitStrip1D";
@@ -138,18 +134,18 @@
        
        // TODO: Check if this block of code is equivalent to the block commented out below
        for(SiSensor sensor : sensors){
-    	   
-                int region = computePlotterRegion(sensor);
-                if(region >= plotter1.numberOfRegions()) {
-                    throw new RuntimeException("not enough regions! (" + region + "/"+ plotter1.numberOfRegions()+ ")");
-                }
-                plotter1.region(region).plot(aida.histogram1D(sensor.getName() + "_raw_hits", 10, -0.5, 9.5));
-                plotter3.region(region).plot(aida.histogram1D(sensor.getName() + "_reco_hits", 10, -0.5, 9.5));
-                plotter2.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_hits", 10, -0.5, 9.5));
-                plotter4.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_size", 9, 0.5, 9.5));
-                plotter5.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_amp", 50, 0, 4000.0));
-                ((PlotterRegion) plotter5.region(region)).getPlot().getXAxis().setLabel("Cluster amplitude [ADC counts]");
-                plotter6.region(region).plot(aida.histogram2D(sensor.getName() + "_cluster_vs_strip", 128, 0, 640, 100, -50, 50));
+            int region = computePlotterRegion(sensor);
+            if (region >= plotter1.numberOfRegions()) {
+                throw new RuntimeException("not enough regions! (" + region + "/" + plotter1.numberOfRegions() + ")");
+            }
+            plotter1.region(region).plot(aida.histogram1D(sensor.getName() + "_raw_hits", 10, -0.5, 9.5));
+            plotter3.region(region).plot(aida.histogram1D(sensor.getName() + "_reco_hits", 10, -0.5, 9.5));
+            plotter2.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_hits", 10, -0.5, 9.5));
+            plotter4.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_size", 9, 0.5, 9.5));
+            plotter5.region(region).plot(aida.histogram1D(sensor.getName() + "_cluster_amp", 50, 0, 4000.0));
+            plotter5.style().xAxisStyle().setLabel("Cluster amplitude [ADC counts]");
+            plotter6.region(region).plot(
+                    aida.histogram2D(sensor.getName() + "_cluster_vs_strip", 128, 0, 640, 100, -50, 50));
        }
         
         /* ===> 

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SampleZeroHVBiasChecker.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SampleZeroHVBiasChecker.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SampleZeroHVBiasChecker.java	Wed Apr 27 11:11:32 2016
@@ -28,6 +28,7 @@
 import org.hps.conditions.svt.SvtBiasMyaDataReader;
 import org.hps.conditions.svt.SvtBiasMyaDataReader.SvtBiasMyaRange;
 import org.hps.conditions.svt.SvtBiasMyaDataReader.SvtBiasRunRange;
+import org.hps.recon.tracking.SvtPlotUtils;
 import org.hps.record.epics.EpicsData;
 import org.hps.record.triggerbank.AbstractIntData;
 import org.hps.record.triggerbank.HeadBankData;

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SensorOccupancyPlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SensorOccupancyPlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SensorOccupancyPlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -1,9 +1,4 @@
 package org.hps.monitoring.drivers.svt;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IHistogram1D;
@@ -13,22 +8,27 @@
 import hep.aida.IPlotterRegion;
 import hep.aida.IPlotterStyle;
 import hep.aida.ITree;
-import hep.aida.ref.plotter.Plotter;
-import hep.aida.ref.plotter.PlotterRegion;
+import hep.aida.jfree.plotter.Plotter;
+import hep.aida.jfree.plotter.PlotterRegion;
 import hep.aida.ref.rootwriter.RootFileStore;
 import hep.physics.vec.Hep3Vector;
 
-import java.util.HashSet;
-import java.util.Set;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import org.hps.monitoring.subsys.StatusCode;
 import org.hps.monitoring.subsys.Subsystem;
 import org.hps.monitoring.subsys.SystemStatus;
 import org.hps.monitoring.subsys.SystemStatusImpl;
+import org.hps.recon.tracking.SvtPlotUtils;
+import org.hps.record.triggerbank.AbstractIntData;
+import org.hps.record.triggerbank.TIData;
+import org.lcsim.detector.ITransform3D;
+import org.lcsim.detector.tracker.silicon.ChargeCarrier;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
-import org.lcsim.detector.tracker.silicon.ChargeCarrier;
 import org.lcsim.detector.tracker.silicon.SiStrips;
-import org.lcsim.detector.ITransform3D;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
 import org.lcsim.event.RawTrackerHit;
@@ -36,8 +36,6 @@
 import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
 import org.lcsim.recon.tracking.digitization.sisim.TrackerHitType;
 import org.lcsim.util.Driver;
-import org.hps.record.triggerbank.AbstractIntData;
-import org.hps.record.triggerbank.TIData;
 import org.lcsim.util.aida.AIDA;
 
 /**
@@ -51,7 +49,6 @@
     //static {
     //    hep.aida.jfree.AnalysisFactory.register();
     //}
-
     // Plotting
     private static ITree tree = null;
     private IAnalysisFactory analysisFactory = AIDA.defaultInstance().analysisFactory();
@@ -75,8 +72,6 @@
     private String triggerBankCollectionName = "TriggerBank";
     private String stripClusterCollectionName = "StripClusterer_SiTrackerHitStrip1D";
 
-    String rootFile = null;
-
     private int maxSamplePosition = -1;
     private int timeWindowWeight = 1;
     private int eventCount = 0;
@@ -108,7 +103,9 @@
     private boolean enableClusterTimeCuts = true;
     private double clusterTimeCutMax = 4.0;
     private double clusterTimeCutMin = -4.0;
-    
+
+    private boolean saveRootFile = true;
+
     public SensorOccupancyPlotsDriver() {
         maxSampleStatus = new SystemStatusImpl(Subsystem.SVT, "Checks that SVT is timed in (max sample plot)", true);
         maxSampleStatus.setStatus(StatusCode.UNKNOWN, "Status is unknown.");
@@ -194,6 +191,10 @@
 
     public void setMaxPeakOccupancy(double maxPeakOccupancy) {
         this.maxPeakOccupancy = maxPeakOccupancy;
+    }
+
+    public void setSaveRootFile(boolean saveRootFile) {
+        this.saveRootFile = saveRootFile;
     }
 
     /**
@@ -404,12 +405,12 @@
                 plotters.get("Occupancy vs Position").region(SvtPlotUtils.computePlotterRegion(sensor))
                         .plot(positionPlots.get(sensor.getName()), this.createOccupancyPlotStyle("Distance from Beam [mm]", sensor, false));
                 plotters.get("Cluster occupancy vs Position").region(SvtPlotUtils.computePlotterRegion(sensor))
-                .plot(clusterPositionPlots.get(sensor.getName()), this.createOccupancyPlotStyle("Distance from Beam [mm]", sensor, false));
+                        .plot(clusterPositionPlots.get(sensor.getName()), this.createOccupancyPlotStyle("Distance from Beam [mm]", sensor, false));
             }
             occupancyMap.put(sensor.getName(), new int[640]);
 
             if (enableMaxSamplePlots) {
-                maxSamplePositionPlots.put(sensor.getName(), histogramFactory.createHistogram1D(sensor.getName() + " - Max Sample Number", 6, 0, 6));
+                maxSamplePositionPlots.put(sensor.getName(), histogramFactory.createHistogram1D(sensor.getName() + " - Max Sample Number", 6, -0.5, 5.5));
                 plotters.get("Max Sample Number").region(SvtPlotUtils.computePlotterRegion(sensor))
                         .plot(maxSamplePositionPlots.get(sensor.getName()),
                                 this.createOccupancyPlotStyle("Max Sample Number", sensor, false));
@@ -418,12 +419,11 @@
 
         for (IPlotter plotter : plotters.values()) {
             for (int regionN = 0; regionN < plotter.numberOfRegions(); regionN++) {
-                //Plotter l;
-                //PlotterRegion region = ((PlotterRegion) ((Plotter) plotter).region(regionN));
-                //if (region..getPlottedObjects().isEmpty()) {
-                //    continue;
-                //}
-                //region.getPanel().addMouseListener(new PopupPlotterListener(region));
+                PlotterRegion region = ((PlotterRegion) ((Plotter) plotter).region(regionN));
+                if (region.getPlottedObjects().isEmpty()) {
+                    continue;
+                }
+                region.getPanel().addMouseListener(new PopupPlotterListener(region));
             }
             plotter.show();
         }
@@ -520,22 +520,22 @@
                 maxSamplePositionPlots.get(((HpsSiSensor) rawHit.getDetectorElement()).getName()).fill(maxSamplePositionFound);
             }
         }
-        
+
         // Fill the strip cluster counts if available
-        if(event.hasCollection(SiTrackerHitStrip1D.class, stripClusterCollectionName)) {
+        if (event.hasCollection(SiTrackerHitStrip1D.class, stripClusterCollectionName)) {
             List<SiTrackerHitStrip1D> stripHits1D = event.get(SiTrackerHitStrip1D.class, stripClusterCollectionName);
-            for(SiTrackerHitStrip1D h : stripHits1D) {
+            for (SiTrackerHitStrip1D h : stripHits1D) {
                 SiTrackerHitStrip1D global = h.getTransformedHit(TrackerHitType.CoordinateSystem.GLOBAL);
                 Hep3Vector pos_global = global.getPositionAsVector();
-                if(enableClusterTimeCuts) {
-                    if( h.getTime() < clusterTimeCutMax && h.getTime() > clusterTimeCutMin) 
+                if (enableClusterTimeCuts) {
+                    if (h.getTime() < clusterTimeCutMax && h.getTime() > clusterTimeCutMin) {
                         clusterPositionPlotCounts.get(((HpsSiSensor) h.getRawHits().get(0).getDetectorElement()).getName()).fill(pos_global.y());
-                } else
+                    }
+                } else {
                     clusterPositionPlotCounts.get(((HpsSiSensor) h.getRawHits().get(0).getDetectorElement()).getName()).fill(pos_global.y());
-            }
-        }
-        
-        
+                }
+            }
+        }
 
         if (enableMaxSamplePlots && eventCount > maxSampleMonitorStart && eventCount % maxSampleMonitorPeriod == 0) {
             checkMaxSample();
@@ -563,17 +563,17 @@
                         positionPlots.get(sensor.getName()).fill(stripPosition, stripOccupancy);
                     }
                 }
-                if(enablePositionPlots) {
+                if (enablePositionPlots) {
                     clusterPositionPlots.get(sensor.getName()).reset();
                     IHistogram1D h = clusterPositionPlotCounts.get(sensor.getName());
-                    for(int bin=0; bin<h.axis().bins(); ++bin) {
+                    for (int bin = 0; bin < h.axis().bins(); ++bin) {
                         int y = h.binEntries(bin);
                         double stripClusterOccupancy = (double) y / (double) eventCount;
                         double x = h.axis().binCenter(bin);
-                        clusterPositionPlots.get(sensor.getName()).fill(x,stripClusterOccupancy);
+                        clusterPositionPlots.get(sensor.getName()).fill(x, stripClusterOccupancy);
                     }
                 }
-                
+
             }
         }
 
@@ -704,14 +704,16 @@
     @Override
     public void endOfData() {
 
-        rootFile = "run" + runNumber + "_occupancy.root";
-        RootFileStore store = new RootFileStore(rootFile);
-        try {
-            store.open();
-            store.add(tree);
-            store.close();
-        } catch (IOException e) {
-            e.printStackTrace();
+        if (saveRootFile) {
+            String rootFile = "run" + runNumber + "_occupancy.root";
+            RootFileStore store = new RootFileStore(rootFile);
+            try {
+                store.open();
+                store.add(tree);
+                store.close();
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
         }
 
         System.out.println("%===============================================================================%");

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtClusterPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtClusterPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtClusterPlots.java	Wed Apr 27 11:11:32 2016
@@ -1,9 +1,4 @@
 package org.hps.monitoring.drivers.svt;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.List;
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IHistogram1D;
@@ -16,18 +11,20 @@
 import hep.aida.jfree.plotter.Plotter;
 import hep.aida.jfree.plotter.PlotterRegion;
 import hep.aida.ref.rootwriter.RootFileStore;
-import java.util.HashSet;
-import java.util.Set;
-
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hps.recon.tracking.SvtPlotUtils;
+import org.lcsim.detector.tracker.silicon.DopedSilicon;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
 import org.lcsim.util.Driver;
-
-import org.hps.recon.tracking.FittedRawTrackerHit;
-import org.lcsim.detector.tracker.silicon.DopedSilicon;
 import org.lcsim.util.aida.AIDA;
 
 /**
@@ -55,11 +52,15 @@
     private static Map<String, IHistogram1D> singleHitClusterChargePlots = new HashMap<String, IHistogram1D>();
     private static Map<String, IHistogram1D> clusterTimePlots = new HashMap<String, IHistogram1D>();
     private static Map<String, IHistogram2D> hitTimeTrigTimePlots = new HashMap<String, IHistogram2D>();
-    private static IHistogram1D[] hitTimeTrigTimePlots1D = new IHistogram1D[6];
+    private static IHistogram1D[][] hitTimeTrigTimePlots1D = new IHistogram1D[6][2];
+    private static IHistogram2D[][] hitTimeTrigTimePlots2D = new IHistogram2D[6][2];
+
+    private static final int TOP = 0;
+    private static final int BOTTOM = 1;
 
     private List<HpsSiSensor> sensors;
-    private Map<RawTrackerHit, FittedRawTrackerHit> fittedRawTrackerHitMap
-            = new HashMap<RawTrackerHit, FittedRawTrackerHit>();
+//    private Map<RawTrackerHit, FittedRawTrackerHit> fittedRawTrackerHitMap
+//            = new HashMap<RawTrackerHit, FittedRawTrackerHit>();
 
     // Detector name
     private static final String SUBDETECTOR_NAME = "Tracker";
@@ -70,10 +71,16 @@
 
     private int runNumber = -1;
 
+    private boolean saveRootFile = true;
+
     private boolean dropSmallHitEvents = true;
 
     public void setDropSmallHitEvents(boolean dropSmallHitEvents) {
         this.dropSmallHitEvents = dropSmallHitEvents;
+    }
+
+    public void setSaveRootFile(boolean saveRootFile) {
+        this.saveRootFile = saveRootFile;
     }
 
     private int computePlotterRegion(HpsSiSensor sensor) {
@@ -84,20 +91,17 @@
             } else {
                 return 6 * (sensor.getLayerNumber() - 1) + 1;
             }
-        } else {
-
-            if (sensor.isTopLayer()) {
-                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-                    return 6 * (sensor.getLayerNumber() - 7) + 2;
-                } else {
-                    return 6 * (sensor.getLayerNumber() - 7) + 3;
-                }
-            } else if (sensor.isBottomLayer()) {
-                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-                    return 6 * (sensor.getLayerNumber() - 7) + 4;
-                } else {
-                    return 6 * (sensor.getLayerNumber() - 7) + 5;
-                }
+        } else if (sensor.isTopLayer()) {
+            if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                return 6 * (sensor.getLayerNumber() - 7) + 2;
+            } else {
+                return 6 * (sensor.getLayerNumber() - 7) + 3;
+            }
+        } else if (sensor.isBottomLayer()) {
+            if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                return 6 * (sensor.getLayerNumber() - 7) + 4;
+            } else {
+                return 6 * (sensor.getLayerNumber() - 7) + 5;
             }
         }
         return -1;
@@ -158,8 +162,7 @@
     private void resetPlots() {
 
         // Clear the fitted raw hit map of old values
-        fittedRawTrackerHitMap.clear();
-
+//        fittedRawTrackerHitMap.clear();
         // Since all plots are mapped to the name of a sensor, loop 
         // through the sensors, get the corresponding plots and clear them.
         for (HpsSiSensor sensor : sensors) {
@@ -171,34 +174,40 @@
         for (IHistogram2D histogram : hitTimeTrigTimePlots.values()) {
             histogram.reset();
         }
-    }
-
-    /**
-     * Method that creates a map between a fitted raw hit and it's corresponding
-     * raw fit
-     *
-     * @param fittedHits : List of fitted hits to map
-     */
-    private void mapFittedRawHits(List<FittedRawTrackerHit> fittedHits) {
-
-        // Clear the fitted raw hit map of old values
-        fittedRawTrackerHitMap.clear();
-
-        // Loop through all fitted hits and map them to their corresponding raw hits
-        for (FittedRawTrackerHit fittedHit : fittedHits) {
-            fittedRawTrackerHitMap.put(fittedHit.getRawTrackerHit(), fittedHit);
-        }
-    }
-
-    /**
-     *
-     * @param rawHit
-     * @return
-     */
-    private FittedRawTrackerHit getFittedHit(RawTrackerHit rawHit) {
-        return fittedRawTrackerHitMap.get(rawHit);
-    }
-
+
+        for (int i = 0; i < 6; i++) {
+            for (int j = 0; j < 2; j++) {
+                hitTimeTrigTimePlots1D[i][j].reset();
+                hitTimeTrigTimePlots2D[i][j].reset();
+            }
+        }
+    }
+
+//    /**
+//     * Method that creates a map between a fitted raw hit and it's corresponding
+//     * raw fit
+//     *
+//     * @param fittedHits : List of fitted hits to map
+//     */
+//    private void mapFittedRawHits(List<FittedRawTrackerHit> fittedHits) {
+//
+//        // Clear the fitted raw hit map of old values
+//        fittedRawTrackerHitMap.clear();
+//
+//        // Loop through all fitted hits and map them to their corresponding raw hits
+//        for (FittedRawTrackerHit fittedHit : fittedHits) {
+//            fittedRawTrackerHitMap.put(fittedHit.getRawTrackerHit(), fittedHit);
+//        }
+//    }
+//
+//    /**
+//     *
+//     * @param rawHit
+//     * @return
+//     */
+//    private FittedRawTrackerHit getFittedHit(RawTrackerHit rawHit) {
+//        return fittedRawTrackerHitMap.get(rawHit);
+//    }
     protected void detectorChanged(Detector detector) {
 
         // Get the HpsSiSensor objects from the geometry
@@ -236,7 +245,7 @@
                     .plot(singleHitClusterChargePlots.get(sensor.getName()), this.createStyle(null, "Cluster Amplitude [ADC Counts]", ""));
 
             clusterTimePlots.put(sensor.getName(),
-                    histogramFactory.createHistogram1D(sensor.getName() + " - Cluster Time", 100, -50, 50));
+                    histogramFactory.createHistogram1D(sensor.getName() + " - Cluster Time", 100, -75, 50));
             plotters.get("Cluster Time").region(this.computePlotterRegion(sensor))
                     .plot(clusterTimePlots.get(sensor.getName()), this.createStyle(null, "Cluster Time [ns]", ""));
         }
@@ -245,18 +254,25 @@
         plotters.get("SVT-trigger timing top-bottom").createRegions(1, 2);
 
         hitTimeTrigTimePlots.put("Top",
-                histogramFactory.createHistogram2D("Top Cluster Time vs. Trigger Phase", 100, -50, 50, 6, 0, 24));
+                histogramFactory.createHistogram2D("Top Cluster Time vs. Trigger Phase", 100, -75, 50, 6, 0, 24));
         plotters.get("SVT-trigger timing top-bottom").region(0).plot(hitTimeTrigTimePlots.get("Top"), this.createStyle(null, "Cluster Time [ns]", "Trigger Phase[ns]"));
         hitTimeTrigTimePlots.put("Bottom",
-                histogramFactory.createHistogram2D("Bottom Cluster Time vs. Trigger Phase", 100, -50, 50, 6, 0, 24));
+                histogramFactory.createHistogram2D("Bottom Cluster Time vs. Trigger Phase", 100, -75, 50, 6, 0, 24));
         plotters.get("SVT-trigger timing top-bottom").region(1).plot(hitTimeTrigTimePlots.get("Bottom"), this.createStyle(null, "Cluster Time [ns]", "Trigger Phase[ns]"));
 
         plotters.put("SVT-trigger timing by phase", plotterFactory.create("SVT-trigger timing by phase"));
-        plotters.get("SVT-trigger timing by phase").createRegions(1, 6);
+        plotters.get("SVT-trigger timing by phase").createRegions(2, 6);
+
+        plotters.put("SVT-trigger timing and amplitude by phase", plotterFactory.create("SVT-trigger timing and amplitude by phase"));
+        plotters.get("SVT-trigger timing and amplitude by phase").createRegions(2, 6);
 
         for (int i = 0; i < 6; i++) {
-            hitTimeTrigTimePlots1D[i] = histogramFactory.createHistogram1D("Cluster Time for Phase " + i, 100, -50, 50);
-            plotters.get("SVT-trigger timing by phase").region(i).plot(hitTimeTrigTimePlots1D[i], this.createStyle(null, "Cluster Time [ns]", ""));
+            for (int j = 0; j < 2; j++) {
+                hitTimeTrigTimePlots1D[i][j] = histogramFactory.createHistogram1D(String.format("Cluster Time for Phase %d, %s", i, j == TOP ? "Top" : "Bottom"), 100, -75, 50);
+                plotters.get("SVT-trigger timing by phase").region(i + 6 * j).plot(hitTimeTrigTimePlots1D[i][j], this.createStyle(null, "Cluster Time [ns]", ""));
+                hitTimeTrigTimePlots2D[i][j] = histogramFactory.createHistogram2D(String.format("Cluster Amplitude vs. Time for Phase %d, %s", i, j == TOP ? "Top" : "Bottom"), 100, -75, 50, 100, 0, 5000.0);
+                plotters.get("SVT-trigger timing and amplitude by phase").region(i + 6 * j).plot(hitTimeTrigTimePlots2D[i][j], this.createStyle(null, "Cluster Time [ns]", "Cluster Amplitude [ADC Counts]"));
+            }
         }
 
         for (IPlotter plotter : plotters.values()) {
@@ -277,17 +293,15 @@
             runNumber = event.getRunNumber();
         }
 
-        // If the event doesn't contain fitted raw hits, skip it
-        if (!event.hasCollection(FittedRawTrackerHit.class, fittedHitsCollectionName)) {
-            return;
-        }
-
-        // Get the list of fitted hits from the event
-        List<FittedRawTrackerHit> fittedHits = event.get(FittedRawTrackerHit.class, fittedHitsCollectionName);
-
-        // Map the fitted hits to their corresponding raw hits
-        this.mapFittedRawHits(fittedHits);
-
+//        // If the event doesn't contain fitted raw hits, skip it
+//        if (!event.hasCollection(FittedRawTrackerHit.class, fittedHitsCollectionName)) {
+//            return;
+//        }
+//         Get the list of fitted hits from the event
+//        List<FittedRawTrackerHit> fittedHits = event.get(FittedRawTrackerHit.class, fittedHitsCollectionName);
+//
+//        // Map the fitted hits to their corresponding raw hits
+//        this.mapFittedRawHits(fittedHits);
         // If the event doesn't contain any clusters, skip it
         if (!event.hasCollection(SiTrackerHitStrip1D.class, clusterCollectionName)) {
             return;
@@ -318,26 +332,29 @@
             }
 
             clusterTimePlots.get(sensor.getName()).fill(cluster.getTime());
-            hitTimeTrigTimePlots1D[(int) ((event.getTimeStamp() / 4) % 6)].fill(cluster.getTime());
             if (sensor.isTopLayer()) {
+                hitTimeTrigTimePlots1D[(int) ((event.getTimeStamp() / 4) % 6)][TOP].fill(cluster.getTime());
+                hitTimeTrigTimePlots2D[(int) ((event.getTimeStamp() / 4) % 6)][TOP].fill(cluster.getTime(), cluster.getdEdx() / DopedSilicon.ENERGY_EHPAIR);
                 hitTimeTrigTimePlots.get("Top").fill(cluster.getTime(), event.getTimeStamp() % 24);
             } else {
+                hitTimeTrigTimePlots1D[(int) ((event.getTimeStamp() / 4) % 6)][BOTTOM].fill(cluster.getTime());
+                hitTimeTrigTimePlots2D[(int) ((event.getTimeStamp() / 4) % 6)][BOTTOM].fill(cluster.getTime(), cluster.getdEdx() / DopedSilicon.ENERGY_EHPAIR);
                 hitTimeTrigTimePlots.get("Bottom").fill(cluster.getTime(), event.getTimeStamp() % 24);
             }
         }
     }
 
     public void endOfData() {
-
-        String rootFile = "run" + runNumber + "_cluster_analysis.root";
-        RootFileStore store = new RootFileStore(rootFile);
-        try {
-            store.open();
-            store.add(tree);
-            store.close();
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-    }
-
+        if (saveRootFile) {
+            String rootFile = "run" + runNumber + "_cluster_analysis.root";
+            RootFileStore store = new RootFileStore(rootFile);
+            try {
+                store.open();
+                store.add(tree);
+                store.close();
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtHitPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtHitPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtHitPlots.java	Wed Apr 27 11:11:32 2016
@@ -2,6 +2,7 @@
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IHistogram1D;
+import hep.aida.IHistogram2D;
 import hep.aida.IHistogramFactory;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
@@ -9,18 +10,19 @@
 import hep.aida.ITree;
 import hep.aida.jfree.plotter.Plotter;
 import hep.aida.jfree.plotter.PlotterRegion;
-
+import hep.aida.ref.rootwriter.RootFileStore;
+
+import java.io.IOException;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
-
+
+import org.hps.recon.tracking.SvtPlotUtils;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
-import org.lcsim.util.Driver;
-import org.lcsim.geometry.Detector;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawTrackerHit;
+import org.lcsim.geometry.Detector;
+import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 
 /**
@@ -28,6 +30,8 @@
  * event.
  *
  * @author Omar Moreno <[log in to unmask]>
+ * @author Per Hansson Adrian <[log in to unmask]>
+ *
  */
 public class SvtHitPlots extends Driver {
 
@@ -38,23 +42,25 @@
 
     // Plotting
     private static ITree tree = null;
-    private IAnalysisFactory analysisFactory = AIDA.defaultInstance().analysisFactory();
-    private IPlotterFactory plotterFactory = analysisFactory.createPlotterFactory("SVT Hits");
+    private final IAnalysisFactory analysisFactory = AIDA.defaultInstance().analysisFactory();
+    private final IPlotterFactory plotterFactory = analysisFactory.createPlotterFactory("SVT Hits");
     private IHistogramFactory histogramFactory = null;
     protected Map<String, IPlotter> plotters = new HashMap<String, IPlotter>();
 
     // Histogram Maps
-    private static Map<String, IHistogram1D> hitsPerSensorPlots = new HashMap<String, IHistogram1D>();
-    private static Map<String, int[]> hitsPerSensor = new HashMap<String, int[]>();
-    private static Map<String, IHistogram1D> layersHitPlots = new HashMap<String, IHistogram1D>();
-    private static Map<String, IHistogram1D> hitCountPlots = new HashMap<String, IHistogram1D>();
-    private static Map<String, IHistogram1D> firstSamplePlots = new HashMap<String, IHistogram1D>();
+    private static final Map<String, IHistogram1D> hitsPerSensorPlots = new HashMap<String, IHistogram1D>();
+    private static final Map<String, int[]> hitsPerSensor = new HashMap<String, int[]>();
+    private static final Map<String, IHistogram1D> layersHitPlots = new HashMap<String, IHistogram1D>();
+    private static final Map<String, IHistogram1D> hitCountPlots = new HashMap<String, IHistogram1D>();
+    private static final Map<String, IHistogram1D> firstSamplePlots = new HashMap<String, IHistogram1D>();
+//    private static Map<String, IHistogram1D> firstSamplePlotsNoise = new HashMap<String, IHistogram1D>();
+    private static final Map<String, IHistogram2D> firstSamplePlotsNoisePerChannel = new HashMap<String, IHistogram2D>();
 
     private List<HpsSiSensor> sensors;
 
     private static final String SUBDETECTOR_NAME = "Tracker";
-    private String rawTrackerHitCollectionName = "SVTRawTrackerHits";
-    
+    private final String rawTrackerHitCollectionName = "SVTRawTrackerHits";
+
     // Counters
     double eventCount = 0;
     double totalHitCount = 0;
@@ -62,36 +68,23 @@
     double totalBotHitCount = 0;
 
     private boolean dropSmallHitEvents = true;
+    private static final boolean debug = false;
+    private boolean doPerChannelSamplePlots = false;
+    private int maxSampleCutForNoise = -1;
+    private boolean saveRootFile = false;
+    private String outputRootFilename = "";
+    private boolean showPlots = true;
 
     public void setDropSmallHitEvents(boolean dropSmallHitEvents) {
         this.dropSmallHitEvents = dropSmallHitEvents;
     }
 
-    private int computePlotterRegion(HpsSiSensor sensor) {
-
-        if (sensor.getLayerNumber() < 7) {
-            if (sensor.isTopLayer()) {
-                return 6 * (sensor.getLayerNumber() - 1);
-            } else {
-                return 6 * (sensor.getLayerNumber() - 1) + 1;
-            }
-        } else {
-
-            if (sensor.isTopLayer()) {
-                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-                    return 6 * (sensor.getLayerNumber() - 7) + 2;
-                } else {
-                    return 6 * (sensor.getLayerNumber() - 7) + 3;
-                }
-            } else if (sensor.isBottomLayer()) {
-                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-                    return 6 * (sensor.getLayerNumber() - 7) + 4;
-                } else {
-                    return 6 * (sensor.getLayerNumber() - 7) + 5;
-                }
-            }
-        }
-        return -1;
+    public void setDoPerChannelsSampleplots(boolean val) {
+        doPerChannelSamplePlots = val;
+    }
+
+    public void setSaveRootFile(boolean save) {
+        saveRootFile = save;
     }
 
     /**
@@ -137,6 +130,10 @@
         for (HpsSiSensor sensor : sensors) {
             hitsPerSensorPlots.get(sensor.getName()).reset();
             firstSamplePlots.get(sensor.getName()).reset();
+//            firstSamplePlotsNoise.get(sensor.getName()).reset();
+            if (doPerChannelSamplePlots) {
+                firstSamplePlotsNoisePerChannel.get(sensor.getName()).reset();
+            }
         }
 
         for (IHistogram1D histogram : layersHitPlots.values()) {
@@ -149,12 +146,13 @@
 
     }
 
+    @Override
     protected void detectorChanged(Detector detector) {
 
         // Get the HpsSiSensor objects from the geometry
         sensors = detector.getSubdetector(SUBDETECTOR_NAME).getDetectorElement().findDescendants(HpsSiSensor.class);
 
-        if (sensors.size() == 0) {
+        if (sensors.isEmpty()) {
             throw new RuntimeException("No sensors were found in this detector.");
         }
 
@@ -192,43 +190,74 @@
         plotters.get("Raw hit counts/Event").createRegions(2, 2);
 
         hitCountPlots.put("Raw hit counts/Event",
-                histogramFactory.createHistogram1D("Raw hit counts", 100, 0, 100));
+                histogramFactory.createHistogram1D("Raw hit counts", 100, 0, 500));
         plotters.get("Raw hit counts/Event").region(0).plot(hitCountPlots.get("Raw hit counts/Event"), SvtPlotUtils.createStyle(plotterFactory, "Number of Raw Hits", ""));
         hitCountPlots.put("SVT top raw hit counts/Event",
-                histogramFactory.createHistogram1D("SVT top raw hit counts", 100, 0, 100));
+                histogramFactory.createHistogram1D("SVT top raw hit counts", 100, 0, 300));
         plotters.get("Raw hit counts/Event").region(2).plot(hitCountPlots.get("SVT top raw hit counts/Event"), SvtPlotUtils.createStyle(plotterFactory, "Number of Raw Hits in Top Volume", ""));
         hitCountPlots.put("SVT bottom raw hit counts/Event",
-                histogramFactory.createHistogram1D("SVT bottom raw hit counts", 100, 0, 100));
+                histogramFactory.createHistogram1D("SVT bottom raw hit counts", 100, 0, 300));
         plotters.get("Raw hit counts/Event").region(3).plot(hitCountPlots.get("SVT bottom raw hit counts/Event"), SvtPlotUtils.createStyle(plotterFactory, "Number of Raw Bits in the Bottom Volume", ""));
 
         plotters.put("First sample distributions (pedestal shifts)", plotterFactory.create("First sample distributions (pedestal shifts)"));
         plotters.get("First sample distributions (pedestal shifts)").createRegions(6, 6);
+
+//        plotters.put("First sample distributions (pedestal shifts, MAX_SAMPLE>=4)", plotterFactory.create("First sample distributions (pedestal shifts, MAX_SAMPLE>=4)"));
+//        plotters.get("First sample distributions (pedestal shifts, MAX_SAMPLE>=4)").createRegions(6, 6);
+        if (doPerChannelSamplePlots) {
+            plotters.put("First sample channel distributions (pedestal shifts)", plotterFactory.create("First sample channel distributions (pedestal shifts)"));
+            plotters.get("First sample channel distributions (pedestal shifts)").createRegions(6, 6);
+        }
+
         for (HpsSiSensor sensor : sensors) {
             firstSamplePlots.put(sensor.getName(),
                     histogramFactory.createHistogram1D(sensor.getName() + " - first sample", 100, -500.0, 2000.0));
-            plotters.get("First sample distributions (pedestal shifts)").region(this.computePlotterRegion(sensor))
+            plotters.get("First sample distributions (pedestal shifts)").region(SvtPlotUtils.computePlotterRegion(sensor))
                     .plot(firstSamplePlots.get(sensor.getName()), this.createStyle(sensor, "First sample - pedestal [ADC counts]", ""));
+//            firstSamplePlotsNoise.put(sensor.getName(),
+//                    histogramFactory.createHistogram1D(sensor.getName() + " - first sample (MAX_SAMPLE>=4)", 100, -500.0, 2000.0));
+//            plotters.get("First sample distributions (pedestal shifts, MAX_SAMPLE>=4)").region(SvtPlotUtils.computePlotterRegion(sensor))
+//                    .plot(firstSamplePlotsNoise.get(sensor.getName()), this.createStyle(sensor, "First sample - pedestal (MAX_SAMPLE>=4) [ADC counts]", ""));
+
+            if (doPerChannelSamplePlots) {
+                firstSamplePlotsNoisePerChannel.put(sensor.getName(),
+                        histogramFactory.createHistogram2D(sensor.getName() + " channels - first sample", 640, -0.5, 639.5, 20, -500.0, 500.0));
+                plotters.get("First sample channel distributions (pedestal shifts)").region(SvtPlotUtils.computePlotterRegion(sensor))
+                        .plot(firstSamplePlotsNoisePerChannel.get(sensor.getName()), this.createStyle(sensor, "First sample channels - pedestal [ADC counts]", ""));
+            }
+
         }
 
         for (IPlotter plotter : plotters.values()) {
             for (int regionN = 0; regionN < plotter.numberOfRegions(); regionN++) {
                 PlotterRegion region = ((PlotterRegion) ((Plotter) plotter).region(regionN));
-                if (region.getPlottedObjects().size() == 0) {
+                if (region.getPlottedObjects().isEmpty()) {
                     continue;
                 }
                 region.getPanel().addMouseListener(new PopupPlotterListener(region));
             }
-            plotter.show();
-        }
-    }
-
+            if (showPlots) {
+                plotter.show();
+            }
+        }
+    }
+
+    @Override
     public void process(EventHeader event) {
 
         if (!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {
             return;
         }
 
+        if (debug && ((int) eventCount % 100 == 0)) {
+            System.out.println(this.getClass().getSimpleName() + ": processed " + String.valueOf(eventCount) + " events");
+        }
+
         eventCount++;
+
+        if (outputRootFilename.isEmpty()) {
+            outputRootFilename = "run" + String.valueOf(event.getRunNumber());
+        }
 
         // Get RawTrackerHit collection from event.
         List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
@@ -240,8 +269,31 @@
         this.clearHitMaps();
         for (RawTrackerHit rawHit : rawHits) {
             HpsSiSensor sensor = (HpsSiSensor) rawHit.getDetectorElement();
+            int channel = rawHit.getIdentifierFieldValue("strip");
+            double pedestal = sensor.getPedestal(channel, 0);
+            // Find the sample with maximum ADC count
+            int maxSample = 0;
+            double maxSampleValue = 0;
+            for (int s = 0; s < 6; ++s) {
+                if (((double) rawHit.getADCValues()[s] - pedestal) > maxSampleValue) {
+                    maxSample = s;
+                    maxSampleValue = ((double) rawHit.getADCValues()[s]) - pedestal;
+                }
+            }
+
             hitsPerSensor.get(sensor.getName())[0]++;
-            firstSamplePlots.get(sensor.getName()).fill(rawHit.getADCValues()[0] - sensor.getPedestal(rawHit.getIdentifierFieldValue("strip"), 0));
+            firstSamplePlots.get(sensor.getName()).fill(rawHit.getADCValues()[0] - pedestal);
+//            if (maxSampleCutForNoise >= 0 && maxSample >= maxSampleCutForNoise) {
+//                firstSamplePlotsNoise.get(sensor.getName()).fill(rawHit.getADCValues()[0] - pedestal);
+            if (doPerChannelSamplePlots) {
+                firstSamplePlotsNoisePerChannel.get(sensor.getName()).fill(channel, rawHit.getADCValues()[0] - pedestal);
+            }
+//            } else {
+//                firstSamplePlotsNoise.get(sensor.getName()).fill(rawHit.getADCValues()[0] - pedestal);
+//                if (doPerChannelSamplePlots) {
+//                    firstSamplePlotsNoisePerChannel.get(sensor.getName()).fill(channel, rawHit.getADCValues()[0] - pedestal);
+//                }
+//            }
         }
 
         int[] topLayersHit = new int[12];
@@ -300,6 +352,23 @@
         System.out.println("% Total Top SVT Hits/Event: " + totalTopHitCount / eventCount);
         System.out.println("% Total Bottom SVT Hits/Event: " + totalBotHitCount / eventCount);
         System.out.println("\n%================================================%");
+
+        if (saveRootFile) {
+            String rootFileName = outputRootFilename.isEmpty() ? "svthitplots.root" : outputRootFilename + "_svthitplots.root";
+            RootFileStore rootFileStore = new RootFileStore(rootFileName);
+            try {
+                rootFileStore.open();
+                rootFileStore.add(tree);
+                rootFileStore.close();
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        }
+
+    }
+
+    public void setShowPlots(boolean showPlots) {
+        this.showPlots = showPlots;
     }
 
 }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtTimingInPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtTimingInPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SvtTimingInPlots.java	Wed Apr 27 11:11:32 2016
@@ -1,35 +1,31 @@
 package org.hps.monitoring.drivers.svt;
 
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map; 
-
 import hep.aida.IAnalysisFactory;
-import hep.aida.IHistogramFactory;
 import hep.aida.IHistogram1D;
 import hep.aida.IHistogram2D;
+import hep.aida.IHistogramFactory;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
 import hep.aida.IPlotterStyle;
 import hep.aida.ITree;
 import hep.aida.ref.rootwriter.RootFileStore;
 
-import org.lcsim.util.Driver; 
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hps.recon.tracking.FittedRawTrackerHit;
+import org.hps.recon.tracking.ShapeFitParameters;
+import org.hps.record.triggerbank.SSPCluster;
+import org.hps.record.triggerbank.SSPData;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.event.EventHeader;
-import org.lcsim.event.GenericObject;
 import org.lcsim.event.LCRelation;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.geometry.Detector;
-import org.hps.recon.tracking.FittedRawTrackerHit;
-import org.hps.recon.tracking.ShapeFitParameters;
-import org.hps.record.triggerbank.AbstractIntData;
-import org.hps.record.triggerbank.SSPCluster;
-import org.hps.record.triggerbank.SSPData;
-import org.hps.record.triggerbank.SSPSinglesTrigger;
-import org.hps.record.triggerbank.TIData;
+import org.lcsim.util.Driver;
 
 /**
  *  Monitoring driver that will be used when 'timing in' the SVT.
@@ -244,51 +240,51 @@
         isEcalTopCluster = false;
         List<SSPCluster> clusters = null;
         SSPData sspData = null;
-		/*if(event.hasCollection(GenericObject.class, triggerBankCollectionName)) {
-		
-		    // Get the list of trigger banks from the event
-			List<GenericObject> triggerBanks = event.get(GenericObject.class, triggerBankCollectionName);
-
-			System.out.println("Total trigger banks: " + triggerBanks.size());
-			
-			// Loop through the collection of banks and get the SSP and TI banks.
-			for (GenericObject triggerBank : triggerBanks) { 
-			    
-			    // If the bank contains TI data, process it
-			    if (AbstractIntData.getTag(triggerBank) == TIData.BANK_TAG) { 
-			        
-			        TIData tiData = new TIData(triggerBank);
-			      
-			        // Check if the trigger is singles
-			        if (tiData.isSingle0Trigger() || tiData.isSingle1Trigger()) { 
-			            isSingleClusterTrigger = true;
-			        } 
-			        
-			    } else if (AbstractIntData.getTag(triggerBank) == SSPData.BANK_TAG) { 
-			       
-			        sspData = new SSPData(triggerBank);
-			        
-			        clusters = sspData.getClusters();
-			        
-			        for (SSPCluster cluster : clusters) { 
-			            if (cluster.getYIndex() > 0) { 
-			                isEcalTopCluster = true;
-			            }
-			        }
-			    }
-			}
-
-			if (isSingleClusterTrigger) {
-			    System.out.println("Total number of singles triggers: " + sspData.getSinglesTriggers().size());
-			    for (SSPSinglesTrigger trigger : sspData.getSinglesTriggers()) { 
-			        System.out.println("Trigger: " + trigger.toString());
-			    }
-			    System.out.println("Total number of SSP clusters: " + clusters.size());
-			    for (SSPCluster cluster : clusters) { 
-			        System.out.println("X: " + cluster.getXIndex() + " Y: " + cluster.getYIndex() + " time: " + cluster.getTime());
-			    }
-			}
-		}*/	
+        /*if(event.hasCollection(GenericObject.class, triggerBankCollectionName)) {
+        
+            // Get the list of trigger banks from the event
+            List<GenericObject> triggerBanks = event.get(GenericObject.class, triggerBankCollectionName);
+
+            System.out.println("Total trigger banks: " + triggerBanks.size());
+            
+            // Loop through the collection of banks and get the SSP and TI banks.
+            for (GenericObject triggerBank : triggerBanks) { 
+                
+                // If the bank contains TI data, process it
+                if (AbstractIntData.getTag(triggerBank) == TIData.BANK_TAG) { 
+                    
+                    TIData tiData = new TIData(triggerBank);
+                  
+                    // Check if the trigger is singles
+                    if (tiData.isSingle0Trigger() || tiData.isSingle1Trigger()) { 
+                        isSingleClusterTrigger = true;
+                    } 
+                    
+                } else if (AbstractIntData.getTag(triggerBank) == SSPData.BANK_TAG) { 
+                   
+                    sspData = new SSPData(triggerBank);
+                    
+                    clusters = sspData.getClusters();
+                    
+                    for (SSPCluster cluster : clusters) { 
+                        if (cluster.getYIndex() > 0) { 
+                            isEcalTopCluster = true;
+                        }
+                    }
+                }
+            }
+
+            if (isSingleClusterTrigger) {
+                System.out.println("Total number of singles triggers: " + sspData.getSinglesTriggers().size());
+                for (SSPSinglesTrigger trigger : sspData.getSinglesTriggers()) { 
+                    System.out.println("Trigger: " + trigger.toString());
+                }
+                System.out.println("Total number of SSP clusters: " + clusters.size());
+                for (SSPCluster cluster : clusters) { 
+                    System.out.println("X: " + cluster.getXIndex() + " Y: " + cluster.getYIndex() + " time: " + cluster.getTime());
+                }
+            }
+        }*/ 
         
         // Obtain all relations between an SVT raw hit and its corresponding
         // fit parameters.  The fit parameters are obtained from the fit to

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/PlotAndFitUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/PlotAndFitUtilities.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/PlotAndFitUtilities.java	Wed Apr 27 11:11:32 2016
@@ -50,7 +50,7 @@
     static void plot(IPlotter plotter, IBaseHistogram histogram, IPlotterStyle style, int region) {
         if (style == null)
             style = getPlotterStyle(histogram);
-        System.out.println("Putting plot in region " + region);
+        //System.out.println("Putting plot in region " + region);
         plotter.region(region).plot(histogram, style);
 
     }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/SVTOpeningAlignment.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/SVTOpeningAlignment.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/SVTOpeningAlignment.java	Wed Apr 27 11:11:32 2016
@@ -1,8 +1,8 @@
 package org.hps.monitoring.drivers.trackrecon;
 
+import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.fitAndPutParameters;
 import hep.aida.IAnalysisFactory;
 import hep.aida.IFitFactory;
-import hep.aida.IFitResult;
 import hep.aida.IFitter;
 import hep.aida.IFunction;
 import hep.aida.IFunctionFactory;
@@ -10,12 +10,13 @@
 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
 import hep.aida.IPlotterStyle;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.fitAndPutParameters;
+
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackState;
@@ -24,7 +25,6 @@
 import org.lcsim.geometry.Detector;
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
-import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.performGaussianFit;
 
 /**
  *

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackResiduals.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackResiduals.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackResiduals.java	Wed Apr 27 11:11:32 2016
@@ -1,20 +1,20 @@
 package org.hps.monitoring.drivers.trackrecon;
 
+import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.fitAndPutParameters;
+import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
 import hep.aida.IAnalysisFactory;
 import hep.aida.IFitFactory;
-import hep.aida.IFitResult;
-import hep.aida.IFitter;
 import hep.aida.IFunction;
 import hep.aida.IFunctionFactory;
 import hep.aida.IHistogram1D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
+
 import java.io.IOException;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.fitAndPutParameters;
-import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
+
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
 import org.lcsim.geometry.Detector;

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackTimePlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackTimePlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackTimePlots.java	Wed Apr 27 11:11:32 2016
@@ -7,17 +7,14 @@
 import hep.aida.IPlotterStyle;
 import hep.aida.ref.plotter.style.registry.IStyleStore;
 import hep.aida.ref.plotter.style.registry.StyleRegistry;
-
 import java.util.List;
 
 import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
 
-import org.hps.record.triggerbank.AbstractIntData;
-import org.hps.record.triggerbank.TestRunTriggerData;
 import org.lcsim.detector.tracker.silicon.DopedSilicon;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
-import org.lcsim.event.GenericObject;
+import org.lcsim.event.RawTrackerHit;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackerHit;
 import org.lcsim.fit.helicaltrack.HelicalTrackCross;
@@ -116,7 +113,7 @@
 
         for (int i = 0; i < nlayers; i++) {
             int region = computePlotterRegion(i);
-            trackHit2D[i] = aida.histogram2D("Layer " + i + " trackHit vs dt", 75, -50, 100.0, 50, -20, 20.0);
+            trackHit2D[i] = aida.histogram2D("Layer " + i + " trigger phase vs dt", 80, -20, 20.0, 6, 0, 24.0);
             plot(plotter5, trackHit2D[i], style2d, region);
             trackHitDtChan[i] = aida.histogram2D("Layer " + i + " dt vs position", 200, -20, 20, 50, -20, 20.0);
             plot(plotter6, trackHitDtChan[i], style2d, region);
@@ -124,23 +121,23 @@
         plotter.show();
         plotter3.show();
         plotter4.show();
-//         plotter5.show();"Track Time vs. dt"
-//        plotter6.show(); "Track dt vs. Channel"
+        plotter5.show();//"Track Time vs. dt"
+        plotter6.show();// "Track dt vs. Channel"
 
         for (int module = 0; module < 2; module++) {
-            trackT0[module] = aida.histogram1D((module == 0 ? "Top" : "Bottom") + " Track Time", 75, -50, 100.0);
+            trackT0[module] = aida.histogram1D((module == 0 ? "Top" : "Bottom") + " Track Time", 80, -20, 20.0);
             plot(plotter2, trackT0[module], null, module);
-            trackTrigTime[module] = aida.histogram2D((module == 0 ? "Top" : "Bottom") + " Track Time vs. Trig Time", 75, -50, 100.0, 6, -2, 22);
+            trackTrigTime[module] = aida.histogram2D((module == 0 ? "Top" : "Bottom") + " Track Time vs. Trig Time", 80, -20, 20.0, 6, 0, 24);
             plot(plotter2, trackTrigTime[module], style2d, module + 2);
 
             trackTimeRange[module] = aida.histogram1D((module == 0 ? "Top" : "Bottom") + " Track Hit Time Range", 75, 0, 30.0);
             plot(plotter7, trackTimeRange[module], null, module);
-            trackTimeMinMax[module] = aida.histogram2D((module == 0 ? "Top" : "Bottom") + " First and Last Track Hit Times", 75, -50, 100.0, 75, -50, 100.0);
+            trackTimeMinMax[module] = aida.histogram2D((module == 0 ? "Top" : "Bottom") + " First and Last Track Hit Times", 80, -20, 20.0, 80, -20, 20.0);
             plot(plotter7, trackTimeMinMax[module], style2d, module + 2);
         }
 
         plotter2.show();
-//        plotter7.show(); //"Track Hit Time Range"
+        plotter7.show(); //"Track Hit Time Range"
     }
 
     public void setHitCollection(String hitCollection) {
@@ -166,7 +163,7 @@
 
         List<Track> tracks = event.get(Track.class, trackCollectionName);
         for (Track track : tracks) {
-            int trackModule = -1;
+            int trackModule;
             if (track.getTrackerHits().get(0).getPosition()[2] > 0) {
                 trackModule = 0;
             } else {
@@ -179,7 +176,8 @@
             for (TrackerHit hitCross : track.getTrackerHits()) {
                 for (HelicalTrackStrip hit : ((HelicalTrackCross) hitCross).getStrips()) {
                     int layer = hit.layer();
-                    trackHitT0[trackModule][layer - 1].fill(hit.dEdx() / DopedSilicon.ENERGY_EHPAIR);
+                    int module = ((RawTrackerHit) hit.rawhits().get(0)).getIdentifierFieldValue("module");
+                    trackHitT0[module][layer - 1].fill(hit.dEdx() / DopedSilicon.ENERGY_EHPAIR);
                     trackTime += hit.time();
                     hitCount++;
                     if (hit.time() > maxTime) {
@@ -202,8 +200,9 @@
             for (TrackerHit hitCross : track.getTrackerHits()) {
                 for (HelicalTrackStrip hit : ((HelicalTrackCross) hitCross).getStrips()) {
                     int layer = hit.layer();
-                    trackHitDt[trackModule][layer - 1].fill(hit.time() - trackTime);
-                    trackHit2D[layer - 1].fill(trackTime, hit.time() - trackTime);
+                    int module = ((RawTrackerHit) hit.rawhits().get(0)).getIdentifierFieldValue("module");
+                    trackHitDt[module][layer - 1].fill(hit.time() - trackTime);
+                    trackHit2D[layer - 1].fill(hit.time() - trackTime, event.getTimeStamp() % 24);
                     trackHitDtChan[layer - 1].fill(hit.umeas(), hit.time() - trackTime);
                 }
             }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackingReconPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackingReconPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/TrackingReconPlots.java	Wed Apr 27 11:11:32 2016
@@ -12,14 +12,17 @@
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
-import org.hps.recon.tracking.HPSTrack;
+
+import org.hps.recon.tracking.HpsHelicalTrackFit;
+import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.Cluster;
-
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.LCIOParameters.ParameterName;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.event.Track;
+import org.lcsim.event.TrackState;
 import org.lcsim.event.TrackerHit;
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
 import org.lcsim.geometry.Detector;
@@ -267,10 +270,12 @@
             SeedTrack stEle = (SeedTrack) trk;
             SeedCandidate seedEle = stEle.getSeedCandidate();
             HelicalTrackFit ht = seedEle.getHelix();
-            HPSTrack hpstrk = new HPSTrack(ht);
+            HpsHelicalTrackFit hpstrk = new HpsHelicalTrackFit(ht);
             double svt_l12 = 900.00;//mm ~approximately...this doesn't matter much
             double ecal_face = 1393.00;//mm ~approximately ... this matters!  Should use typical shower depth...or, once have cluster match, use that value of Z
-            Hep3Vector posAtEcal = hpstrk.getPositionAtZMap(svt_l12, ecal_face, 5.0, event.getDetector().getFieldMap())[0];
+            TrackState stateAtEcal = TrackUtils.getTrackStateAtECal(trk);
+            Hep3Vector posAtEcal = new BasicHep3Vector(stateAtEcal.getReferencePoint());
+            //Hep3Vector posAtEcal = hpstrk.getPositionAtZMap(svt_l12, ecal_face, 5.0, event.getDetector().getFieldMap())[0];
             List<Cluster> clusters = event.get(Cluster.class, ecalCollectionName);
             if (clusters != null) {
                 if (debug)
@@ -282,10 +287,11 @@
                     Hep3Vector clusterPos = new BasicHep3Vector(clust.getPosition());
                     double zCluster = clusterPos.z();
                     //improve the extrapolation...use the reconstructed cluster z-position
-                    posAtEcal = hpstrk.getPositionAtZMap(svt_l12, zCluster, 5.0, event.getDetector().getFieldMap())[0];
+//                    stateAtEcal = TrackUtils.extrapolateTrackUsingFieldMap(trk, svt_l12, zCluster, 5.0, event.getDetector().getFieldMap());
+//                    posAtEcal = new BasicHep3Vector(stateAtEcal.getReferencePoint());
                     double eOverP = clust.getEnergy() / pmag;
-                    double dx = posAtEcal.x() - clusterPos.x();
-                    double dy = posAtEcal.y() - clusterPos.y();
+                    double dx = posAtEcal.y() - clusterPos.x();
+                    double dy = posAtEcal.z() - clusterPos.y();
                     heOverP.fill(eOverP);
                     hdelXECal.fill(dx);
                     hdelYECal.fill(dy);

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/V0ReconPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/V0ReconPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/trackrecon/V0ReconPlots.java	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,6 @@
 package org.hps.monitoring.drivers.trackrecon;
 
+import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
 import hep.aida.IAnalysisFactory;
 import hep.aida.IFitFactory;
 import hep.aida.IFunctionFactory;
@@ -7,12 +8,12 @@
 import hep.aida.IHistogram2D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
-import hep.aida.IPlotterStyle;
+
 import java.io.IOException;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import static org.hps.monitoring.drivers.trackrecon.PlotAndFitUtilities.plot;
+
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.ReconstructedParticle;
 import org.lcsim.event.Track;
@@ -58,7 +59,7 @@
 
     @Override
     protected void detectorChanged(Detector detector) {
-        System.out.println("V0Monitoring::detectorChanged  Setting up the plotter");
+        //System.out.println("V0Monitoring::detectorChanged  Setting up the plotter");
 
         IAnalysisFactory fac = aida.analysisFactory();
         IPlotterFactory pfac = fac.createPlotterFactory("V0 Recon");

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/BasicMonitoringPlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/BasicMonitoringPlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/BasicMonitoringPlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -18,83 +18,83 @@
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class BasicMonitoringPlotsDriver extends Driver {
-	
-	private String calHitsCollectionName = "EcalCalHits"; 
-	private String rawHitsCollectionName = "EcalReadoutHits";
-	private String clustersCollectionName = "EcalClusters";
-	
-	private IHistogram1D calHitEnergyH1D;
-	private IHistogram1D clusterEnergyH1D;
-	private IHistogram1D rawHitAmplitudeH1D;
-	private IHistogram2D calHitEnergyMapH2D;
-	
-	public BasicMonitoringPlotsDriver() {		
-	}
-	
-	public void startOfData() {		
-		
-		IAnalysisFactory.create().createHistogramFactory(null);
-		IPlotterFactory plotFactory = IAnalysisFactory.create().createPlotterFactory("ECAL Monitoring");
-		IHistogramFactory histogramFactory = IAnalysisFactory.create().createHistogramFactory(null);
-		
-		calHitEnergyH1D = histogramFactory.createHistogram1D(calHitsCollectionName + ": Energy", calHitsCollectionName + ": Energy", 200, 0.0, 2.0);
-		calHitEnergyH1D.annotation().addItem("xAxisLabel", "GeV");
-		calHitEnergyH1D.annotation().addItem("yAxisLabel", "Count");
-		IPlotter plotter = plotFactory.create("CalorimeterHits");
-		plotter.createRegion();
-		plotter.style().gridStyle().setVisible(false);
-		plotter.style().dataStyle().errorBarStyle().setVisible(false);
-		plotter.region(0).plot(calHitEnergyH1D);
-		plotter.show();
-		
-		rawHitAmplitudeH1D = histogramFactory.createHistogram1D(rawHitsCollectionName + ": Amplitude", rawHitsCollectionName + ": Amplitude", 150, 0.0, 15000.0);
-		rawHitAmplitudeH1D.annotation().addItem("xAxisLabel", "ADC Value");
-		rawHitAmplitudeH1D.annotation().addItem("yAxisLabel", "Count");
-		plotter = plotFactory.create("RawCalorimeterHits");
-		plotter.createRegion();
-		plotter.style().gridStyle().setVisible(false);
-		plotter.style().dataStyle().errorBarStyle().setVisible(false);
-		plotter.region(0).plot(rawHitAmplitudeH1D);
-		plotter.show();
-		
-		clusterEnergyH1D = histogramFactory.createHistogram1D(clustersCollectionName + ": Energy", clustersCollectionName + ": Energy", 100, 0.0, 3.0);
-		clusterEnergyH1D.annotation().addItem("xAxisLabel", "GeV");
-		clusterEnergyH1D.annotation().addItem("yAxisLabel", "Count");
-		plotter = plotFactory.create("Clusters");
-		plotter.createRegion();
-		plotter.style().gridStyle().setVisible(false);
-		plotter.style().dataStyle().errorBarStyle().setVisible(false);
-		plotter.region(0).plot(clusterEnergyH1D);
-		plotter.show();
-		
-		calHitEnergyMapH2D = histogramFactory.createHistogram2D(calHitsCollectionName + ": Energy Map", calHitsCollectionName + ": Energy Map", 47, -23.5, 23.5, 11, -5.5, 5.5);
-		plotter = plotFactory.create("CalorimeterHit Energy Map");
-		plotter.createRegion();
-		plotter.style().setParameter("hist2DStyle", "colorMap");
-		plotter.style().gridStyle().setVisible(false);
-		plotter.region(0).plot(calHitEnergyMapH2D);
-		plotter.show();
-	}
-	
-	public void process(EventHeader event) {
-		
+    
+    private String calHitsCollectionName = "EcalCalHits"; 
+    private String rawHitsCollectionName = "EcalReadoutHits";
+    private String clustersCollectionName = "EcalClusters";
+    
+    private IHistogram1D calHitEnergyH1D;
+    private IHistogram1D clusterEnergyH1D;
+    private IHistogram1D rawHitAmplitudeH1D;
+    private IHistogram2D calHitEnergyMapH2D;
+    
+    public BasicMonitoringPlotsDriver() {       
+    }
+    
+    public void startOfData() {     
+        
+        IAnalysisFactory.create().createHistogramFactory(null);
+        IPlotterFactory plotFactory = IAnalysisFactory.create().createPlotterFactory("ECAL Monitoring");
+        IHistogramFactory histogramFactory = IAnalysisFactory.create().createHistogramFactory(null);
+        
+        calHitEnergyH1D = histogramFactory.createHistogram1D(calHitsCollectionName + ": Energy", calHitsCollectionName + ": Energy", 200, 0.0, 2.0);
+        calHitEnergyH1D.annotation().addItem("xAxisLabel", "GeV");
+        calHitEnergyH1D.annotation().addItem("yAxisLabel", "Count");
+        IPlotter plotter = plotFactory.create("CalorimeterHits");
+        plotter.createRegion();
+        plotter.style().gridStyle().setVisible(false);
+        plotter.style().dataStyle().errorBarStyle().setVisible(false);
+        plotter.region(0).plot(calHitEnergyH1D);
+        plotter.show();
+        
+        rawHitAmplitudeH1D = histogramFactory.createHistogram1D(rawHitsCollectionName + ": Amplitude", rawHitsCollectionName + ": Amplitude", 150, 0.0, 15000.0);
+        rawHitAmplitudeH1D.annotation().addItem("xAxisLabel", "ADC Value");
+        rawHitAmplitudeH1D.annotation().addItem("yAxisLabel", "Count");
+        plotter = plotFactory.create("RawCalorimeterHits");
+        plotter.createRegion();
+        plotter.style().gridStyle().setVisible(false);
+        plotter.style().dataStyle().errorBarStyle().setVisible(false);
+        plotter.region(0).plot(rawHitAmplitudeH1D);
+        plotter.show();
+        
+        clusterEnergyH1D = histogramFactory.createHistogram1D(clustersCollectionName + ": Energy", clustersCollectionName + ": Energy", 100, 0.0, 3.0);
+        clusterEnergyH1D.annotation().addItem("xAxisLabel", "GeV");
+        clusterEnergyH1D.annotation().addItem("yAxisLabel", "Count");
+        plotter = plotFactory.create("Clusters");
+        plotter.createRegion();
+        plotter.style().gridStyle().setVisible(false);
+        plotter.style().dataStyle().errorBarStyle().setVisible(false);
+        plotter.region(0).plot(clusterEnergyH1D);
+        plotter.show();
+        
+        calHitEnergyMapH2D = histogramFactory.createHistogram2D(calHitsCollectionName + ": Energy Map", calHitsCollectionName + ": Energy Map", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        plotter = plotFactory.create("CalorimeterHit Energy Map");
+        plotter.createRegion();
+        plotter.style().setParameter("hist2DStyle", "colorMap");
+        plotter.style().gridStyle().setVisible(false);
+        plotter.region(0).plot(calHitEnergyMapH2D);
+        plotter.show();
+    }
+    
+    public void process(EventHeader event) {
+        
         if (event.hasCollection(CalorimeterHit.class, calHitsCollectionName)) {
             for (CalorimeterHit hit : event.get(CalorimeterHit.class, calHitsCollectionName)) {
                 calHitEnergyH1D.fill(hit.getCorrectedEnergy());
                 calHitEnergyMapH2D.fill(hit.getIdentifierFieldValue("ix"), hit.getIdentifierFieldValue("iy"), hit.getCorrectedEnergy());
             }
         }
-		
+        
         if (event.hasCollection(Cluster.class, clustersCollectionName)) {
             for (Cluster cluster : event.get(Cluster.class, clustersCollectionName)) {
                 clusterEnergyH1D.fill(cluster.getEnergy());
             }
         }
-		
-		if (event.hasCollection(RawCalorimeterHit.class, rawHitsCollectionName)) {
-			for (RawCalorimeterHit hit : event.get(RawCalorimeterHit.class, rawHitsCollectionName)) {
-				rawHitAmplitudeH1D.fill(hit.getAmplitude());
-			}
-		}
-	}
+        
+        if (event.hasCollection(RawCalorimeterHit.class, rawHitsCollectionName)) {
+            for (RawCalorimeterHit hit : event.get(RawCalorimeterHit.class, rawHitsCollectionName)) {
+                rawHitAmplitudeH1D.fill(hit.getAmplitude());
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalClusterPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalClusterPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalClusterPlots.java	Wed Apr 27 11:11:32 2016
@@ -49,15 +49,15 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class EcalClusterPlots extends Driver {
-	// Internal variables.
+    // Internal variables.
     private boolean hide = false;
     private boolean logScale = false;
-	private AIDA aida = AIDA.defaultInstance();
+    private AIDA aida = AIDA.defaultInstance();
     private double maxE = 5000 * EcalUtils.MeV;
-	private IPlotter[] plotter = new IPlotter[4];
-	private String clusterCollectionName = "EcalClusters";
-	
-	// Monitoring plot variables.
+    private IPlotter[] plotter = new IPlotter[4];
+    private String clusterCollectionName = "EcalClusters";
+    
+    // Monitoring plot variables.
     private IHistogram1D clusterCountPlot;
     private IHistogram1D clusterSizePlot;
     private IHistogram1D clusterEnergyPlot;
@@ -79,7 +79,7 @@
     private static final int TAB_CLUSTER_TIME = 2;
     private static final int TAB_CLUSTER_PAIR = 3;
     private static final String[] TAB_NAMES = { "Cluster Count Plots", "Cluster Energy Plots",
-    	"Cluster Time Plots", "Cluster Pair Plots" };
+        "Cluster Time Plots", "Cluster Pair Plots" };
     
     /**
      * Resets all of the plots for the new detector.
@@ -110,10 +110,10 @@
         
         // Apply formatting that is constant across all tabs.
         for(int tabIndex = 0; tabIndex < plotter.length; tabIndex++) {
-        	plotter[tabIndex] = plotterFactory.create(TAB_NAMES[tabIndex]);
-        	plotter[tabIndex].setTitle(TAB_NAMES[tabIndex]);
-        	plotter[tabIndex].style().dataStyle().errorBarStyle().setVisible(false);
-        	plotter[tabIndex].style().dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString());
+            plotter[tabIndex] = plotterFactory.create(TAB_NAMES[tabIndex]);
+            plotter[tabIndex].setTitle(TAB_NAMES[tabIndex]);
+            plotter[tabIndex].style().dataStyle().errorBarStyle().setVisible(false);
+            plotter[tabIndex].style().dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString());
             if(logScale) { plotter[tabIndex].style().yAxisStyle().setParameter("scale", "log"); }
         }
         
@@ -145,9 +145,9 @@
         
         // If they should not be hidden, display the tabs.
         if(!hide) {
-        	for(IPlotter tab : plotter) {
-        		tab.show();
-        	}
+            for(IPlotter tab : plotter) {
+                tab.show();
+            }
         }
     }
     
@@ -157,121 +157,121 @@
      */
     @Override
     public void process(EventHeader event) {
-    	// Check whether the event has clusters or not.
-    	if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-    		// Get the list of clusters.
-    		List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-    		
-    		// Create lists to store the clusters from the top of the
-    		// calorimeter and the bottom.
-    		List<Cluster> topList = new ArrayList<Cluster>();
-    		List<Cluster> bottomList = new ArrayList<Cluster>();
-    		
-    		// Track the highest energy cluster in the event.
-    		double maxEnergy = 0.0;
-    		
-    		// Process each of the clusters.
-    		for(Cluster cluster : clusterList) {
-    			// If this cluster has a higher energy then was seen
-    			// previously, it is now the highest energy cluster.
-				if (cluster.getEnergy() > maxEnergy) {
-					maxEnergy = cluster.getEnergy();
-				}
-				
-				
-				// Get the list of calorimeter hits and its size.
-				List<CalorimeterHit> hitList = cluster.getCalorimeterHits();
-				int hitCount = hitList.size();
-				
-				// Track cluster statistics.
-				double xEnergyWeight = 0.0;
-				double yEnergyWeight = 0.0;
-				double[] hitTimes = new double[hitCount];
-				double totalHitEnergy = 0.0;
-				
-				// Iterate over the hits and extract statistics from them.
-				for(int hitIndex = 0; hitIndex < hitCount; hitIndex++) {
-					hitTimes[hitIndex] = hitList.get(hitIndex).getTime();
-					totalHitEnergy += hitList.get(hitIndex).getRawEnergy();
-					xEnergyWeight += (hitList.get(hitIndex).getRawEnergy() * hitList.get(hitIndex).getIdentifierFieldValue("ix"));
-					yEnergyWeight += (hitList.get(hitIndex).getRawEnergy() * hitList.get(hitIndex).getIdentifierFieldValue("iy"));
-				}
-				
-				// If the cluster energy exceeds zero, plot the cluster
-				// statistics.
-				if(cluster.getEnergy() > 0) {
-					clusterSizePlot.fill(hitCount);
-					clusterTimes.fill(StatUtils.mean(hitTimes, 0, hitCount));
-					clusterTimeSigma.fill(Math.sqrt(StatUtils.variance(hitTimes, 0, hitCount)));
-					edgePlot.fill(xEnergyWeight / totalHitEnergy, yEnergyWeight / totalHitEnergy);
-				}
-				
-				// Fill the single cluster plots.
-				clusterEnergyPlot.fill(cluster.getEnergy());
-				
-    			// Cluster pairs are formed from all top/bottom cluster
-    			// combinations. To create these pairs, separate the
-    			// clusters into two lists based on their y-indices.
-    			if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix") > 0) {
-    				topList.add(cluster);
-    			} else {
-    				bottomList.add(cluster);
-    			}
-    		}
-    		
-    		// Populate the event plots.
-    		clusterCountPlot.fill(clusterList.size());
-    		if(maxEnergy > 0) { clusterMaxEnergyPlot.fill(maxEnergy); }
-    		
-    		// Create a list to store cluster pairs.
-    		List<Cluster[]> pairList = new ArrayList<Cluster[]>(topList.size() * bottomList.size());
-    		
-    		// Form pairs from all possible combinations of clusters
-    		// from the top and bottom lists.
-    		for(Cluster topCluster : topList) {
-    			for(Cluster bottomCluster : bottomList) {
-    				// Make a cluster pair array.
-    				Cluster[] pair = new Cluster[2];
-    				
-    				// The lower energy cluster goes in the second slot.
-    				if(topCluster.getEnergy() > bottomCluster.getEnergy()) {
-    					pair[0] = topCluster;
-    					pair[1] = bottomCluster;
-    				} else {
-    					pair[0] = bottomCluster;
-    					pair[1] = topCluster;
-    				}
-    				
-    				// Add the pair to the pair list.
-    				pairList.add(pair);
-    			}
-    		}
-    		
-    		// Iterate over each pair and calculate the pair cut values.
-    		for(Cluster[] pair : pairList) {
-    			// Get the energy slope value.
-    			double energySumValue = TriggerModule.getValueEnergySum(pair);
-    			double energyDifferenceValue = TriggerModule.getValueEnergyDifference(pair);
-    			double energySlopeValue = TriggerModule.getValueEnergySlope(pair, 0.005500);
-    			double coplanarityValue = TriggerModule.getValueCoplanarity(pair);
-    			double xMean = ((pair[0].getEnergy() * pair[0].getPosition()[0]) +
-    					(pair[1].getEnergy() * pair[1].getPosition()[0])) / energySumValue;
-    			double yMean = ((pair[0].getEnergy() * pair[0].getPosition()[1]) +
-    					(pair[1].getEnergy() * pair[1].getPosition()[1])) / energySumValue;
-    			
-    			// Populate the cluster pair plots.
-    			pairEnergySum.fill(energySumValue, 1);;
-    			pairEnergyDifference.fill(energyDifferenceValue, 1);
-    			pairEnergySlope.fill(energySlopeValue, 1);
-    			pairCoplanarity.fill(coplanarityValue, 1);
-    			pairEnergyPositionMeanX.fill(xMean);
-    			pairEnergyPositionMeanY.fill(yMean);
-    		}
-    	}
-    	
-    	// If the event does not contain clusters, update the "Event
-    	// Clusters" plot accordingly.
-    	else { clusterCountPlot.fill(0); }
+        // Check whether the event has clusters or not.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the list of clusters.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Create lists to store the clusters from the top of the
+            // calorimeter and the bottom.
+            List<Cluster> topList = new ArrayList<Cluster>();
+            List<Cluster> bottomList = new ArrayList<Cluster>();
+            
+            // Track the highest energy cluster in the event.
+            double maxEnergy = 0.0;
+            
+            // Process each of the clusters.
+            for(Cluster cluster : clusterList) {
+                // If this cluster has a higher energy then was seen
+                // previously, it is now the highest energy cluster.
+                if (cluster.getEnergy() > maxEnergy) {
+                    maxEnergy = cluster.getEnergy();
+                }
+                
+                
+                // Get the list of calorimeter hits and its size.
+                List<CalorimeterHit> hitList = cluster.getCalorimeterHits();
+                int hitCount = hitList.size();
+                
+                // Track cluster statistics.
+                double xEnergyWeight = 0.0;
+                double yEnergyWeight = 0.0;
+                double[] hitTimes = new double[hitCount];
+                double totalHitEnergy = 0.0;
+                
+                // Iterate over the hits and extract statistics from them.
+                for(int hitIndex = 0; hitIndex < hitCount; hitIndex++) {
+                    hitTimes[hitIndex] = hitList.get(hitIndex).getTime();
+                    totalHitEnergy += hitList.get(hitIndex).getRawEnergy();
+                    xEnergyWeight += (hitList.get(hitIndex).getRawEnergy() * hitList.get(hitIndex).getIdentifierFieldValue("ix"));
+                    yEnergyWeight += (hitList.get(hitIndex).getRawEnergy() * hitList.get(hitIndex).getIdentifierFieldValue("iy"));
+                }
+                
+                // If the cluster energy exceeds zero, plot the cluster
+                // statistics.
+                if(cluster.getEnergy() > 0) {
+                    clusterSizePlot.fill(hitCount);
+                    clusterTimes.fill(StatUtils.mean(hitTimes, 0, hitCount));
+                    clusterTimeSigma.fill(Math.sqrt(StatUtils.variance(hitTimes, 0, hitCount)));
+                    edgePlot.fill(xEnergyWeight / totalHitEnergy, yEnergyWeight / totalHitEnergy);
+                }
+                
+                // Fill the single cluster plots.
+                clusterEnergyPlot.fill(cluster.getEnergy());
+                
+                // Cluster pairs are formed from all top/bottom cluster
+                // combinations. To create these pairs, separate the
+                // clusters into two lists based on their y-indices.
+                if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix") > 0) {
+                    topList.add(cluster);
+                } else {
+                    bottomList.add(cluster);
+                }
+            }
+            
+            // Populate the event plots.
+            clusterCountPlot.fill(clusterList.size());
+            if(maxEnergy > 0) { clusterMaxEnergyPlot.fill(maxEnergy); }
+            
+            // Create a list to store cluster pairs.
+            List<Cluster[]> pairList = new ArrayList<Cluster[]>(topList.size() * bottomList.size());
+            
+            // Form pairs from all possible combinations of clusters
+            // from the top and bottom lists.
+            for(Cluster topCluster : topList) {
+                for(Cluster bottomCluster : bottomList) {
+                    // Make a cluster pair array.
+                    Cluster[] pair = new Cluster[2];
+                    
+                    // The lower energy cluster goes in the second slot.
+                    if(topCluster.getEnergy() > bottomCluster.getEnergy()) {
+                        pair[0] = topCluster;
+                        pair[1] = bottomCluster;
+                    } else {
+                        pair[0] = bottomCluster;
+                        pair[1] = topCluster;
+                    }
+                    
+                    // Add the pair to the pair list.
+                    pairList.add(pair);
+                }
+            }
+            
+            // Iterate over each pair and calculate the pair cut values.
+            for(Cluster[] pair : pairList) {
+                // Get the energy slope value.
+                double energySumValue = TriggerModule.getValueEnergySum(pair);
+                double energyDifferenceValue = TriggerModule.getValueEnergyDifference(pair);
+                double energySlopeValue = TriggerModule.getValueEnergySlope(pair, 0.005500);
+                double coplanarityValue = TriggerModule.getValueCoplanarity(pair);
+                double xMean = ((pair[0].getEnergy() * pair[0].getPosition()[0]) +
+                        (pair[1].getEnergy() * pair[1].getPosition()[0])) / energySumValue;
+                double yMean = ((pair[0].getEnergy() * pair[0].getPosition()[1]) +
+                        (pair[1].getEnergy() * pair[1].getPosition()[1])) / energySumValue;
+                
+                // Populate the cluster pair plots.
+                pairEnergySum.fill(energySumValue, 1);;
+                pairEnergyDifference.fill(energyDifferenceValue, 1);
+                pairEnergySlope.fill(energySlopeValue, 1);
+                pairCoplanarity.fill(coplanarityValue, 1);
+                pairEnergyPositionMeanX.fill(xMean);
+                pairEnergyPositionMeanY.fill(yMean);
+            }
+        }
+        
+        // If the event does not contain clusters, update the "Event
+        // Clusters" plot accordingly.
+        else { clusterCountPlot.fill(0); }
     }
     
     /**

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalDaqPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalDaqPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalDaqPlots.java	Wed Apr 27 11:11:32 2016
@@ -11,23 +11,19 @@
 
 import org.hps.conditions.database.DatabaseConditionsManager;
 import org.hps.conditions.ecal.EcalChannel;
-import org.hps.conditions.ecal.EcalConditions;
-import org.hps.detector.ecal.EcalCrystal;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.EventHeader;
 import org.lcsim.geometry.Detector;
-import org.lcsim.geometry.compact.Subdetector;
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 
-/*Conditions system imports*/
-
 /**
- * The driver <code>EcalDaqPlots</code> implements the histogram shown to the user in the fourth tab of the Monitoring Application, when using the Ecal monitoring lcsim file. It contains only a
- * sub-tab, showing the number of hits recorded by the different FADC channels. It is a very preliminary driver to monitor the DAQ status. These plots are updated continuosly.
+ * The driver <code>EcalDaqPlots</code> implements the histogram shown to the user in the fourth tab of the 
+ * Monitoring Application, when using the Ecal monitoring lcsim file. It contains only a sub-tab, showing
+ * the number of hits recorded by the different FADC channels. It is a very preliminary driver to monitor
+ * the DAQ status. These plots are updated continuously.
+ * 
  * @author Andrea Celentano
- * @TODO: integrate with the new conditions system.
- * 
  */
 public class EcalDaqPlots extends Driver {
 

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplay.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplay.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplay.java	Wed Apr 27 11:11:32 2016
@@ -13,7 +13,6 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import java.lang.IllegalArgumentException;
 
 import javax.swing.SwingUtilities;
 

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplayWithRawWaveform.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplayWithRawWaveform.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplayWithRawWaveform.java	Wed Apr 27 11:11:32 2016
@@ -13,14 +13,12 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import java.lang.IllegalArgumentException;
 
 import org.hps.monitoring.ecal.eventdisplay.ui.PDataEventViewer;
 import org.hps.monitoring.ecal.eventdisplay.ui.PEventViewer;
 import org.hps.monitoring.ecal.eventdisplay.ui.Viewer;
 import org.hps.monitoring.ecal.eventdisplay.util.CrystalEvent;
 import org.hps.monitoring.ecal.eventdisplay.util.CrystalListener;
-import org.hps.monitoring.ecal.plots.EcalMonitoringUtilities;
 import org.hps.recon.ecal.EcalUtils;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.RawTrackerHit;
@@ -54,7 +52,7 @@
     // Plotter objects and variables.
     private IPlotter plotter;
     private IPlotterFactory plotterFactory;
-    private AIDA aida = AIDA.defaultInstance();	
+    private AIDA aida = AIDA.defaultInstance(); 
 
     // LCIO Collection names.
     private String inputCollection = "EcalCalHits";
@@ -69,16 +67,16 @@
     private ArrayList<IHistogram2D> channelTimeVsEnergyPlot;
 
     // Internal variables.
-    private PEventViewer viewer;								 // Single event display.
-    private int pedSamples = 10;								 // 
-    private IPlotterStyle pstyle;								 // The plotter style for all plots.
-    private long lastEventTime = 0;								 // Tracks the time at which the last event occurred.
-    private int eventRefreshRate = 1;							 // The number of seconds before an update occurs.
-    private boolean resetOnUpdate = true;						 // Clears the event display on each update.
-    private double minEch = 10 * EcalUtils.MeV;					 // The energy scale minimum.
-    private double maxEch = 3500 * EcalUtils.MeV;				 // The energy scale maximum.
-    private int[] windowRaw = new int[NUM_CHANNELS];			 // The number of samples in a waveform for each channel.
-    private boolean[] isFirstRaw = new boolean[NUM_CHANNELS];	 // Whether a waveform plot was initiated for each channel.
+    private PEventViewer viewer;                                 // Single event display.
+    private int pedSamples = 10;                                 // 
+    private IPlotterStyle pstyle;                                // The plotter style for all plots.
+    private long lastEventTime = 0;                              // Tracks the time at which the last event occurred.
+    private int eventRefreshRate = 1;                            // The number of seconds before an update occurs.
+    private boolean resetOnUpdate = true;                        // Clears the event display on each update.
+    private double minEch = 10 * EcalUtils.MeV;                  // The energy scale minimum.
+    private double maxEch = 3500 * EcalUtils.MeV;                // The energy scale maximum.
+    private int[] windowRaw = new int[NUM_CHANNELS];             // The number of samples in a waveform for each channel.
+    private boolean[] isFirstRaw = new boolean[NUM_CHANNELS];    // Whether a waveform plot was initiated for each channel.
 
     // Plot style and title variables.
     private static final String NO_TITLE = "";

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalHitPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalHitPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalHitPlots.java	Wed Apr 27 11:11:32 2016
@@ -190,17 +190,17 @@
                 GenericObject triggerData = triggerList.get(0);
                
                 if (triggerData instanceof SSPData){
-                	// TODO: TOP, BOTTOM, OR, and AND triggers are test
-                	// run specific parameters and are not supported
-                	// by SSPData.
-                	orTrigTime  = 0; //((SSPData)triggerData).getOrTrig();
-                	topTrigTime = 0; //((SSPData)triggerData).getTopTrig();
-                	botTrigTime = 0; //((SSPData)triggerData).getBotTrig(); 
-
-                	
-                	orTrigTimePlot.fill(orTrigTime);
+                    // TODO: TOP, BOTTOM, OR, and AND triggers are test
+                    // run specific parameters and are not supported
+                    // by SSPData.
+                    orTrigTime  = 0; //((SSPData)triggerData).getOrTrig();
+                    topTrigTime = 0; //((SSPData)triggerData).getTopTrig();
+                    botTrigTime = 0; //((SSPData)triggerData).getBotTrig(); 
+
+                    
+                    orTrigTimePlot.fill(orTrigTime);
                     topTrigTimePlot.fill(topTrigTime);
-                	botTrigTimePlot.fill(botTrigTime);
+                    botTrigTimePlot.fill(botTrigTime);
 
                 }       
                 

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalLedSequenceMonitor.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalLedSequenceMonitor.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalLedSequenceMonitor.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,5 @@
 package org.hps.monitoring.ecal.plots;
+
 
 import hep.aida.IEvaluator;
 import hep.aida.IFitResult;
@@ -21,7 +22,6 @@
 import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -53,6 +53,8 @@
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 
+
+
 /* This is the driver used to determine the response of each calorimeter channel after a LED run
  * @author Andrea Celentano  <[log in to unmask]>
  */
@@ -64,16 +66,16 @@
     private static final int runNumberMax = 9999;
     private static final int nDrivers = 8;
     private static final int nSteps = 100; //should be 56 but here is to avoid seg fault
-    
-   
+
+
 
     String inputCollectionRaw = "EcalReadoutHits";
-    String inputCollection = "EcalCalHits";	
+    String inputCollection = "EcalCalHits";
     AIDA aida;
 
     DatabaseConditionsManager conditionsManager;
 
-    private EcalChannelCollection ChannelCollection;	
+    private EcalChannelCollection ChannelCollection;    
     private EcalLedCollection LedCollection;
     private EcalConditions ecalConditions;
 
@@ -88,7 +90,7 @@
     String outFileName;
 
 
-    private int runNumber = 0;	
+    private int runNumber = 0;    
     private int eventN    = 0;
     private int id,row,column,chid,ledId,driverId;
     private  int[][] expectedSequence = new int[][]{ /*A.C. it is a terrible thing to have this hard-coded here!*/
@@ -98,9 +100,9 @@
             {112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,-1}, //missing 135 is ok
             {168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223},
             //second 4 are the flasher2 sequence, BOTTOM controller 
-            {2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,-1,-1},	
+            {2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,-1,-1},    
             {56,57,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,-1}, //missing 69 is OK
-            {112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167},	
+            {112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167},    
             {168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223},
     };
     private int[][] actualSequence=new int[nDrivers][nSteps];
@@ -126,7 +128,8 @@
 
     private IFunction  fFunction,fFunction1;
     private IProfile1D   cProfile;
-    private IHistogram2D			hMeanCharge2D;
+    private IHistogram2D            hMeanCharge2D;
+    private IHistogram2D            hMeanCharge2DReferenceRatio;
     private ArrayList<IHistogram1D> hCharge;
     private ArrayList<IHistogram2D> hChargeVsEvn;
     private IPlotterFactory factory;
@@ -149,6 +152,11 @@
     private double fEvnMaxDraw=80000.;
     private double fChargeMinDraw=0.;
     private double fChargeMaxDraw=100.;
+
+    /*The reference run numbers*/
+    private int fRedReferenceID;
+    private int fBlueReferenceID;
+
 
     /*Components for user interaction*/
     private JDialog dialog;
@@ -161,6 +169,14 @@
     private LedColor m_ret=LedColor.UNKNOWN; //use UNKNONW as CANCEL button
     static Object modalMonitor = new Object();
 
+    public void setRedReferenceID(int redReference){
+        this.fRedReferenceID=redReference;
+    }
+
+    public void setBlueReferenceID(int blueReference){
+        this.fBlueReferenceID=blueReference;
+    }
+
     public void setUseRawEnergy(boolean useRawEnergy) {
         this.useRawEnergy=useRawEnergy;
     }
@@ -218,29 +234,29 @@
         conditionsManager = DatabaseConditionsManager.getInstance();
 
         LedTopMap = new HashMap< Integer , Integer >(); //key: ecal channel ID. Value:  led id
-        LedBotMap = new HashMap< Integer , Integer >();	
+        LedBotMap = new HashMap< Integer , Integer >();    
 
         LedTopMapInverted = new HashMap< Integer , Integer >(); //key: led id. Value: ecal channel id
         LedBotMapInverted = new HashMap< Integer , Integer >(); 
 
 
-        ChannelCollection = conditionsManager.getCachedConditions(EcalChannelCollection.class, "ecal_channels").getCachedData();	
+        ChannelCollection = conditionsManager.getCachedConditions(EcalChannelCollection.class, "ecal_channels").getCachedData();    
         LedCollection = conditionsManager.getCachedConditions(EcalLedCollection.class, "ecal_leds").getCachedData();
-        ecalConditions = conditionsManager.getEcalConditions();		
+        ecalConditions = conditionsManager.getEcalConditions();        
 
         for (EcalChannel channel : ChannelCollection){
             chid = channel.getChannelId();
-            for (EcalLed Led : LedCollection) {    	
-                if (Led.getEcalChannelId()==chid){
-                    if (channel.getY()>0){
-                        LedTopMap.put( chid , Led.getLedNumber() );
-                        LedTopMapInverted.put(  Led.getLedNumber(), chid  );
-                    }
-                    else if (channel.getY()<0){
-                        LedBotMap.put( chid , Led.getLedNumber() );
-                        LedBotMapInverted.put( Led.getLedNumber(), chid );                    
-                    }
-                }
+            for (EcalLed Led : LedCollection) {        
+    if (Led.getEcalChannelId()==chid){
+        if (channel.getY()>0){
+            LedTopMap.put( chid , Led.getLedNumber() );
+            LedTopMapInverted.put(  Led.getLedNumber(), chid  );
+        }
+        else if (channel.getY()<0){
+            LedBotMap.put( chid , Led.getLedNumber() );
+            LedBotMapInverted.put( Led.getLedNumber(), chid );        
+        }
+    }
             }
         }
 
@@ -250,14 +266,16 @@
         aida = AIDA.defaultInstance();
         aida.tree().cd("/");
         hMeanCharge2D = aida.histogram2D("Average LED response", 47, -23.5, 23.5, 11, -5.5, 5.5);
-
+        hMeanCharge2DReferenceRatio = aida.histogram2D("Ratio this run VS reference run", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        
         factory= aida.analysisFactory().createPlotterFactory("Ecal Led Sequence");
         pPlotter= factory.create("Drivers");
         pPlotter.createRegions(4,2);
         if (isMonitoringApp){
             pPlotter2=factory.create("Sequence Map");
-            pPlotter2.createRegions(1,1);
+            pPlotter2.createRegions(1,2);
             pPlotter2.region(0).plot(hMeanCharge2D);
+            pPlotter2.region(1).plot(hMeanCharge2DReferenceRatio);
         }   
         iTuple = new ArrayList<ITuple>(NUM_CHANNELS);   
         hCharge = new ArrayList<IHistogram1D>(NUM_CHANNELS);
@@ -269,7 +287,7 @@
 
         for (int ii=0;ii<NUM_CHANNELS;ii++){
             int row = EcalMonitoringUtilities.getRowFromHistoID(ii);
-            int column = EcalMonitoringUtilities.getColumnFromHistoID(ii);	    
+            int column = EcalMonitoringUtilities.getColumnFromHistoID(ii);        
             iTuple.add(aida.analysisFactory().createTupleFactory(aida.tree()).create("nTuple"+ii,"nTuple"+ii,"int fEvn=0 , double fCharge=0.,double fTime=0.",""));
         }
 
@@ -281,7 +299,7 @@
         pPlotter.show();
         if (isMonitoringApp) pPlotter2.show();
 
-    }		
+    }        
 
     @Override
     public void process(EventHeader event) {
@@ -292,81 +310,83 @@
             List<CalorimeterHit> hits = event.get(CalorimeterHit.class, inputCollection);
             for (CalorimeterHit hit : hits) {
 
-                column = hit.getIdentifierFieldValue("ix");
-                row = hit.getIdentifierFieldValue("iy");
-                id = EcalMonitoringUtilities.getHistoIDFromRowColumn(row, column);
-                cellID=hit.getCellID();        
-                chid = ChannelCollection.findGeometric(cellID).getChannelId();
-
-                energy = hit.getCorrectedEnergy();
-                
-                if (useRawEnergy){
-                    fillEnergy = getRawADCSum(energy,cellID);
-                }
-                else {
-                    fillEnergy = energy;
-                }
-                fillTime = hit.getTime();
-
-
-                //find the LED
-                if (row>0){
-                    ledId=LedTopMap.get(chid);
-                }
-                else if (row<0){
-                    ledId=LedBotMap.get(chid);
-                }
-                driverId=getDriver(ledId);
-                if (row<0) driverId+=4;
-
-
-
-                /*Skip the events under thr*/
-                if (energy<energyCut) continue;
-                
-                /*First, check if this led is the one in the NEXT step. Therefore, increment by 1 the step*/
-                if (iStep[driverId]==0){
+    column = hit.getIdentifierFieldValue("ix");
+    row = hit.getIdentifierFieldValue("iy");
+    id = EcalMonitoringUtilities.getHistoIDFromRowColumn(row, column);
+    cellID=hit.getCellID();        
+    chid = ChannelCollection.findGeometric(cellID).getChannelId();
+
+    energy = hit.getCorrectedEnergy();
+
+    if (useRawEnergy){
+        fillEnergy = getRawADCSum(energy,cellID);
+    }
+    else {
+        fillEnergy = energy;
+    }
+    fillTime = hit.getTime();
+
+
+    //find the LED
+    if (row>0){
+        ledId=LedTopMap.get(chid);
+    }
+    else if (row<0){
+        ledId=LedBotMap.get(chid);
+    }
+    driverId=getDriver(ledId);
+    if (row<0) driverId+=4;
+
+
+
+    /*Skip the events under thr*/
+    if (energy<energyCut) continue;
+
+    /*First, check if this led is the one in the NEXT step. Therefore, increment by 1 the step*/
+    /*
+     * if (iStep[driverId]==0){
+
                     actualSequence[driverId][iStep[driverId]]=ledId;
-                    iStep[driverId]=1;                  
+                    iStep[driverId]=1;      
                 }
                 else if ((iStep[driverId]==1)&&(ledId!=actualSequence[driverId][0])){              
-                    System.out.println("LedAnalysis:: increment step ("+iStep[driverId]+") for driver "+driverId+" . Led ID: "+ledId+" Column: "+column+" Row: "+row);                 
+                    System.out.println("LedAnalysis:: increment step ("+iStep[driverId]+") for driver "+driverId+" . Led ID: "+ledId+" Column: "+column+" Row: "+row);     
                     if (iStep[driverId]>0) drawProfiles(actualSequence[driverId][iStep[driverId]-1],driverId); 
                     actualSequence[driverId][iStep[driverId]]=ledId;
                     iStep[driverId]++;
                 }
                 else if ((iStep[driverId]>1)&&(ledId!=actualSequence[driverId][iStep[driverId]-1])&&(ledId!=actualSequence[driverId][iStep[driverId]-2])){
-                    System.out.println("LedAnalysis:: increment step ("+iStep[driverId]+") for driver "+driverId+" . Led ID: "+ledId+" Column: "+column+" Row: "+row);                 
+                    System.out.println("LedAnalysis:: increment step ("+iStep[driverId]+") for driver "+driverId+" . Led ID: "+ledId+" Column: "+column+" Row: "+row);     
                     if (iStep[driverId]>0) drawProfiles(actualSequence[driverId][iStep[driverId]-1],driverId); 
                     actualSequence[driverId][iStep[driverId]]=ledId;
                     iStep[driverId]++;
                 }
 
 
-
-
-
-
-                if (iStep[driverId]==-1) continue; /*Not yet data*/
-
-                /*Put this code here, since we want to always fill the ntuple*/
-                iTuple.get(id).fill(0,nEvents[id]);
-                iTuple.get(id).fill(1,fillEnergy);
-                iTuple.get(id).fill(2,fillTime);
-                iTuple.get(id).addRow();
-                nEvents[id]++;
-
-
-
-                /*Add a debug print */
-                if (eventN % 10000==0){
-                    System.out.println("Debug. Event "+eventN+" LED ID: "+ledId+" DRIVER ID: "+driverId+" ECAL ID: "+id+" ROW: "+row+" COLUMN: "+column+ "HISTO ID: "+id);
-                }
+                //    if (iStep[driverId]==-1) continue; 
+
+     */
+
+    if (iStep[driverId]==-1) continue; /*Not yet data*/
+
+    /*Put this code here, since we want to always fill the ntuple*/
+    iTuple.get(id).fill(0,nEvents[id]);
+    iTuple.get(id).fill(1,fillEnergy);
+    iTuple.get(id).fill(2,fillTime);
+    iTuple.get(id).addRow();
+    nEvents[id]++;
+
+
+
+    /*Add a debug print */
+    if (eventN % 10000==0){
+        System.out.println("Debug. Event "+eventN+" LED ID: "+ledId+" DRIVER ID: "+driverId+" ECAL ID: "+id+" ROW: "+row+" COLUMN: "+column+ "HISTO ID: "+id);
+    }
             }
             if (eventN % 10000==0){
-                System.out.println("\n");
-            }
-        }		
+    System.out.println("\n");
+            }
+        }        
     }
 
     /*
@@ -392,7 +412,7 @@
 
         double e,eMin,eMax;
         double t;
-        int n,nBins,nFits,nSkip;
+        int n,nBins,nSkip;
 
         int row, column;
 
@@ -400,7 +420,7 @@
         IFunctionFactory fFactory=aida.analysisFactory().createFunctionFactory(aida.tree());
 
         IFitResult fResult;
-        IFitter	   fFitter;
+        IFitter       fFitter;
 
         for (int id = 0; id < 11 * 47; id++) {
 
@@ -409,7 +429,7 @@
             row = EcalMonitoringUtilities.getRowFromHistoID(id);
             column = EcalMonitoringUtilities.getColumnFromHistoID(id);
             System.out.println("");
-            System.out.println("Doing channel: X= "+column+" Y= "+row);
+            System.out.println("Doing channel: X= "+column+" Y= "+row+ "id= "+id);
             System.out.println("Number of entries in analysis ntuple: "+iTuple.get(id).rows());
             System.out.println("Number of recognized events: "+nEvents[id]);
             /*Create the profile. Create it for all the channels, to keep sync.*/
@@ -419,9 +439,9 @@
             /*Clear previous*/
 
             if (id>0){
-                aida.tree().rm("strip");
-                aida.tree().rm("fun0");
-                aida.tree().rm("fun1");
+    aida.tree().rm("strip");
+    aida.tree().rm("fun0");
+    aida.tree().rm("fun1");
             }
             /*Create the profile.*/
             cProfile=aida.profile1D("strip",nBins,-0.5,nEvents[id]*(1-skipInitial)+0.5);
@@ -431,98 +451,79 @@
             fFunction1=fFactory.createFunctionByName("fun1","G");
 
             if (EcalMonitoringUtilities.isInHole(row,column)==true){
-                System.out.println("Channel X= "+column+" Y= "+row+" is in hole. Skip");
-                hCharge.add(aida.histogram1D("charge_"+id,200,0.,1.)); //create here the histogram to keep sync
-                System.out.println("In hole, skip");
-                continue;
+    System.out.println("Channel X= "+column+" Y= "+row+" is in hole. Skip");
+    hCharge.add(aida.histogram1D("charge_"+id,200,0.,1.)); //create here the histogram to keep sync
+    System.out.println("In hole, skip");
+    continue;
             }
             else if (nEvents[id]<nEventsMin) {
-                hCharge.add(aida.histogram1D("charge_"+id,200,0.,1.)); //create here the histogram to keep sync
-                System.err.println("LedAnalysis:: the channel X= "+column+" Y= "+row+" has not enough events "+nEvents[id]+" "+nEventsMin);
-
-                continue;
-            }			  
+    hCharge.add(aida.histogram1D("charge_"+id,200,0.,1.)); //create here the histogram to keep sync
+    System.err.println("LedAnalysis:: the channel X= "+column+" Y= "+row+" has not enough events "+nEvents[id]+" "+nEventsMin);
+
+    continue;
+            }              
 
             //Fill the profile*/
             nSkip=(int)(nEvents[id]*skipInitial);
             if (nSkip>iTuple.get(id).rows()){
-                System.out.println("Can't skip initial events?");
-                nSkip=0;
+    System.out.println("Can't skip initial events?");
+    nSkip=0;
             }
             iTuple.get(id).start();
             iTuple.get(id).skip(nSkip); //This is the work-around for those channels with charge starting from 0 and rapidly growing//
             n=0;
             iTuple.get(id).next(); 
             while ( iTuple.get(id).next() ){
-                e=iTuple.get(id).getDouble(1);
-                if (e<eMin) eMin=e;           			  
-                if (e>eMax) eMax=e;
-                cProfile.fill(1.*n,e);
-                n++;
-            }			
+    e=iTuple.get(id).getDouble(1);
+    if (e<eMin) eMin=e;                         
+    if (e>eMax) eMax=e;
+    cProfile.fill(1.*n,e);
+    n++;
+            }            
             fFitter=aida.analysisFactory().createFitFactory().createFitter("chi2","","v");
 
             if (doFullAnalysis){ 
-                //Init function parameters
-                double[] initialPars={eMax-eMin,nEvents[id]/10.,eMin};
-                if (initialPars[0]<0) initialPars[0]=0;
-                fFunction.setParameters(initialPars);
-
-                //Do the fit      
-                System.out.println("LedAnalysis:: do profile fit "+id+" "+fFitter.engineName()+" "+fFitter.fitMethodName());
-                System.out.println("LedAnalysis:: initial parameters "+initialPars[0]+" "+initialPars[1]+" "+initialPars[2]);
-                fResult=fFitter.fit(cProfile,fFunction);
-                fPars     = fResult.fittedParameters();
-                fParErrs  = fResult.errors();
-                fParNames = fResult.fittedParameterNames();			
-                System.out.println("LedAnalysis:: Status= "+fResult.fitStatus()+" "+fResult.isValid()+" Chi2 = "+fResult.quality()+" NDF: "+fResult.ndf());
-                for(int i=0; i< fResult.fittedFunction().numberOfParameters(); i++ ){
-                    System.out.println(fParNames[i]+" : "+fPars[i]+" +- "+fParErrs[i]);
-                }  
-                fFunction.setParameters(fPars);
-
-
-                //Do again the fit: it is a terrible work-around
-                nFits=0;
-                if (Double.isNaN(fParErrs[1])){
-                    fPars=fPrevPars;
-                }
-                while (Double.isNaN(fParErrs[1])){
-                    System.out.println("LedAnalysis:: redo fit");
-                    fFunction.setParameters(fPars);
-                    fResult=fFitter.fit(cProfile,fFunction);
-                    fPars     = fResult.fittedParameters();
-                    fParErrs  = fResult.errors();
-                    System.out.println("LedAnalysis:: Status= "+fResult.fitStatus()+" "+fResult.isValid()+" Chi2 = "+fResult.quality()+" NDF: "+fResult.ndf());
-                    for(int i=0; i< fResult.fittedFunction().numberOfParameters(); i++ ){
-                        System.out.println(fParNames[i]+" : "+fPars[i]+" +- "+fParErrs[i]);
-                    }  
-                    fFunction.setParameters(fPars);
-                    nFits++;
-                    if (nFits>=10){
-                        System.out.println("LedAnalysis:: Error, too many fits without convergence");
-                        break;
-                    }
-                }
-                fPrevPars=Arrays.copyOf(fPars,fPars.length);
-                System.out.println("LedAnalysis:: fit "+id+" done");  
-
-                //Now we have the tau parameter. Take ONLY the events that are with N>5*tau/
-                //As a cross-check, also verify that tau > Nevents/10, otherwise skip the first Nevents/2
-                //and emit warning
-                nSkip=(int)( fPars[1]*5);
-                if (nSkip < (nEvents[id]*skipMin)){
-                    System.out.println("LedAnalysis:: Skip number too low: "+nSkip+" Increment it to "+nEvents[id]/2);
-                    nSkip=(int)(nEvents[id]*skipMin);
-                }
-                if (nSkip > nEvents[id]){
-                    System.out.println("LedAnalysis:: Skip number too high, reduce it");
-                    nSkip=(int)(nEvents[id]*skipMin);
-                }
-
+    //Init function parameters
+    double[] initialPars={eMax-eMin,nEvents[id]/10.,eMin};
+    if (initialPars[0]<0) initialPars[0]=0;
+    fFunction.setParameters(initialPars);
+
+    //Do the fit      
+    System.out.println("LedAnalysis:: do profile fit "+id+" "+fFitter.engineName()+" "+fFitter.fitMethodName());
+    System.out.println("LedAnalysis:: initial parameters "+initialPars[0]+" "+initialPars[1]+" "+initialPars[2]);
+    fResult=fFitter.fit(cProfile,fFunction);
+    fPars     = fResult.fittedParameters();
+    fParErrs  = fResult.errors();
+    fParNames = fResult.fittedParameterNames();            
+    System.out.println("LedAnalysis:: Status= "+fResult.fitStatus()+" "+fResult.isValid()+" Chi2 = "+fResult.quality()+" NDF: "+fResult.ndf());
+    for(int i=0; i< fResult.fittedFunction().numberOfParameters(); i++ ){
+        System.out.println(fParNames[i]+" : "+fPars[i]+" +- "+fParErrs[i]);
+    }  
+    fFunction.setParameters(fPars);
+
+
+    //if fit failed, revert to simpler case
+    if ((fResult.isValid()==false)||Double.isNaN(fParErrs[0])||Double.isNaN(fParErrs[1])||Double.isNaN(fParErrs[2])){
+        System.out.println("LedAnalysis:: fit failed. Reverting to simpler case");
+        nSkip=(int)(nEvents[id]*(skipMin+skipInitial));
+    }
+    else{   
+        //Now we have the tau parameter. Take ONLY the events that are with N>5*tau/
+        //As a cross-check, also verify that tau > Nevents/10, otherwise skip the first Nevents/2
+        //and emit warning
+        nSkip=(int)( fPars[1]*5);
+        if (nSkip < (nEvents[id]*skipMin)){
+            System.out.println("LedAnalysis:: Skip number too low: "+nSkip+" Increment it to "+nEvents[id]/2);
+            nSkip=(int)(nEvents[id]*(skipMin+skipInitial));
+        }
+        if (nSkip > nEvents[id]){
+            System.out.println("LedAnalysis:: Skip number too high, reduce it");
+            nSkip=(int)(nEvents[id]*(skipMin+skipInitial));
+        }
+    }
             }
             else{
-                nSkip=(int)(nEvents[id]*(skipMin+skipInitial));
+    nSkip=(int)(nEvents[id]*(skipMin+skipInitial));
             }
 
             System.out.println("LedAnalysis:: gaus fit :: Going to skip "+nSkip+" out of "+nEvents[id]);
@@ -534,11 +535,11 @@
             iTuple.get(id).skip(nSkip); 
             n=0;
             while (iTuple.get(id).next()){
-                e=iTuple.get(id).getDouble(1);
-                t=iTuple.get(id).getDouble(2);
-                hCharge.get(id).fill(e);
-                n++;
-            }			
+    e=iTuple.get(id).getDouble(1);
+    t=iTuple.get(id).getDouble(2);
+    hCharge.get(id).fill(e);
+    n++;
+            }            
 
             /*Finally do the fit with the gaussian*/
             double[] initialPars1={hCharge.get(id).maxBinHeight(),hCharge.get(id).mean(),hCharge.get(id).rms()};
@@ -550,10 +551,10 @@
             fResult=fFitter.fit(hCharge.get(id),fFunction1);
             fPars     = fResult.fittedParameters();
             fParErrs  = fResult.errors();
-            fParNames = fResult.fittedParameterNames();			
+            fParNames = fResult.fittedParameterNames();            
             System.out.println("Status= "+fResult.fitStatus()+" "+fResult.isValid()+" Chi2 = "+fResult.quality()+" NDF: "+fResult.ndf());
             for(int i=0; i< fResult.fittedFunction().numberOfParameters(); i++ ){
-                System.out.println(fParNames[i]+" : "+fPars[i]+" +- "+fParErrs[i]);
+    System.out.println(fParNames[i]+" : "+fPars[i]+" +- "+fParErrs[i]);
             }  
             fFunction1.setParameters(fPars);
             mMean[id]=fPars[1];
@@ -572,6 +573,15 @@
             style.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString()); 
             pPlotter2.region(0).plot(hMeanCharge2D);
             pPlotter2.region(0).refresh();
+            
+            
+            style = pPlotter2.region(1).style();
+            style.setParameter("hist2DStyle", "colorMap");
+            style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+            style.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString()); 
+            pPlotter2.region(1).plot(hMeanCharge2DReferenceRatio);
+            pPlotter2.region(1).refresh();
+            
         }
         else{
             IPlotterStyle pstyle =  aida.analysisFactory().createPlotterFactory().createPlotterStyle();
@@ -581,58 +591,72 @@
             pstyle.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString());
             pstyle.setParameter("hist2DStyle", "colorMap");
             if (pPlotter2!=null){
-                pPlotter2.createRegion().plot(hMeanCharge2D,pstyle);
-                pPlotter2.show();
+    pPlotter2.createRegion().plot(hMeanCharge2D,pstyle);
+    pPlotter2.show();
             }
         }
 
         if (isMonitoringApp){
             askUploadToDBDialog();
             synchronized (modalMonitor) {
-                try{
-                    modalMonitor.wait(60000); //wait 1 minute for user interaction.
-                }
-                catch(InterruptedException excp){
-                    System.out.println("Got exception: "+excp);
-                }
+    try{
+        modalMonitor.wait(60000); //wait 1 minute for user interaction.
+    }
+    catch(InterruptedException excp){
+        System.out.println("Got exception: "+excp);
+    }
             }
             if ((m_ret!=LedColor.UNKNOWN)){
-                if (m_ret==LedColor.BLUE)    System.out.println("OK, upload to DB BLUE");
-                else System.out.println("OK, upload to DB RED");
-                try {
-                    uploadToDB(m_ret);
-                } catch (SQLException | DatabaseObjectException | ConditionsObjectException error) {
-                    throw new RuntimeException("Error uploading to the database ", error);
-                }
-
-                System.out.println("Save an Elog too");
-                uploadToElog();
+    if (m_ret==LedColor.BLUE)    System.out.println("OK, upload to DB BLUE");
+    else System.out.println("OK, upload to DB RED");
+    try {
+        uploadToDB(m_ret);
+    } catch (SQLException | DatabaseObjectException | ConditionsObjectException error) {
+        throw new RuntimeException("Error uploading to the database ", error);
+    }
+
+    System.out.println("Get reference data, produce reference ratio map");
+    compareWithReference(m_ret);
+
+    style = pPlotter2.region(1).style();
+    style.setParameter("hist2DStyle", "colorMap");
+    style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+    style.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString()); 
+    pPlotter2.region(1).plot(hMeanCharge2DReferenceRatio);
+    pPlotter2.region(1).refresh();
+    
+    System.out.println("Save an Elog too");
+    uploadToElog();
             }
             else{
-                System.out.println("Cancel pressed. Nothing to do");
-            }
-        }
+    System.out.println("Cancel pressed. Nothing to do");
+            }
+        }
+
+       
 
         /*Write a file with the LED values*/
         try {
             if (useRawEnergy){
-                outFileName=runNumber+".raw.txt";
+    outFileName=runNumber+".raw.txt";
             }
             else{
-                outFileName=runNumber+".energy.txt";
+    outFileName=runNumber+".energy.txt";
             }
             PrintWriter writer = new PrintWriter(outFileName, "UTF-8");
 
-
-            for (int id = 0; id < 11 * 47; id++) {
-
-                row = EcalMonitoringUtilities.getRowFromHistoID(id);
-                column = EcalMonitoringUtilities.getColumnFromHistoID(id);
-                if (EcalMonitoringUtilities.isInHole(row, column)) continue;
-                if ((row == 0) || (column == 0)) continue;
-
-                writer.print(column+" "+row+" "+" "+ mMean[id]+" "+mRMS[id]+"\r\n");
-
+            for (int cid = 1; cid <= 442; cid++) {/*This is a loop over the channel ID, as in the conditions system*/
+    EcalChannel cc = findChannel(cid);
+    column = cc.getX(); //This is the column
+    row = cc.getY(); //This is the row
+    id=EcalMonitoringUtilities.getHistoIDFromRowColumn(row,column);
+    row = EcalMonitoringUtilities.getRowFromHistoID(id);
+    column = EcalMonitoringUtilities.getColumnFromHistoID(id);
+    if (EcalMonitoringUtilities.isInHole(row, column)) continue;
+    if ((row == 0) || (column == 0)) continue;
+
+    writer.print(cid+" "+column+" "+row+" "+" "+ mMean[id]+" "+mRMS[id]+"\r\n");
+    
             }
             writer.close();
 
@@ -648,30 +672,31 @@
             System.out.println(ioe.getMessage());
 
         }
-
-
+        
+        
+        
+        
         System.out.println("EcalLedSequenceMonitor endOfData clear histograms"); 
-        for(int ii = 0; ii < NUM_CHANNELS; ii++) {   	
+        for(int ii = 0; ii < NUM_CHANNELS; ii++) {       
             row=EcalMonitoringUtilities.getRowFromHistoID(ii);
-            column = EcalMonitoringUtilities.getColumnFromHistoID(ii);      	  
-            hName="charge_"+ii;	 
+            column = EcalMonitoringUtilities.getColumnFromHistoID(ii);            
+            hName="charge_"+ii;     
             try{
-                aida.tree().rm(hName);
+    aida.tree().rm(hName);
             }
             catch(IllegalArgumentException ee){
-                System.out.println("Got exception "+ee);
+    System.out.println("Got exception "+ee);
             }
 
             if (!saveTuple||(isMonitoringApp)){
-                hName="nTuple"+ii;
-                try{
-                    aida.tree().rm(hName);
-                }
-                catch(IllegalArgumentException ee){
-                    System.out.println("Got exception "+ee);
-                }
-            }
-
+    hName="nTuple"+ii;
+    try{
+        aida.tree().rm(hName);
+    }
+    catch(IllegalArgumentException ee){
+        System.out.println("Got exception "+ee);
+    }
+            }
         }
         System.out.println("EcalLedSequenceMonitor endOfData clear histograms done");   
         System.out.println("endOfData end");
@@ -682,10 +707,10 @@
     /**
      * This function returns the driver number (from 0 to 3) given the LED id.
      * @param led
-     * @return
+     * @return the driver number from the LED id
      */
     public int getDriver(int led){
-        int ret=-1;	
+        int ret=-1;    
         if ((led>=2)&&(led<56)) ret=0;
         else if ((led>=56)&&(led<112)) ret=1;
         else if ((led>=112)&&(led<168)) ret=2;
@@ -698,7 +723,7 @@
      * If the gain changes (because we do a re-calibration), I do not want to include this in the LED analysis
      * @param energy
      * @param cellID
-     * @return
+     * @return the pedestal-subtracted raw energy
      */
     public double getRawADCSum(double energy,long cellID){
         EcalChannelConstants channelData = ecalConditions.getChannelConstants(ecalConditions.getChannelCollection().findGeometric(cellID));
@@ -713,8 +738,8 @@
         int x,y,id;
         double mean,rms;
         System.out.println(String.format("Uploading new led data to the database, runMin=%d, runMax=%d, tag=%s ....",
-                runNumber,runNumberMax,dbTag));
-        
+    runNumber,runNumberMax,dbTag));
+
         conditionsManager = DatabaseConditionsManager.getInstance();
         EcalLedCalibrationCollection led_calibrations =  new EcalLedCalibrationCollection();
         led_calibrations.setConnection(conditionsManager.getConnection());
@@ -743,8 +768,8 @@
         System.err.println("CollectionID:  "+collectionId);
         led_calibrations.insert();
         ConditionsRecord conditionsRecord = new ConditionsRecord(
-                led_calibrations.getCollectionId(), runNumber, runNumberMax, dbTableName, dbTableName, 
-                "Generated by LedAnalysis from Run #"+runNumber, dbTag);
+    led_calibrations.getCollectionId(), runNumber, runNumberMax, dbTableName, dbTableName, 
+    "Generated by LedAnalysis from Run #"+runNumber, dbTag);
         conditionsRecord.setConnection(conditionsManager.getConnection());
         tableMetaData = conditionsManager.findTableMetaData("conditions");
         conditionsRecord.setTableMetaData(tableMetaData);
@@ -789,6 +814,79 @@
         }
     }
 
+    private void compareWithReference(LedColor color){
+        int ID=0;
+        int x,y,chid;
+        double mean,rms,fillData=1;
+        if (color==LedColor.UNKNOWN){
+            System.out.println("LedMonitoringSequence::compare with reference, doing nothing");
+            return;
+        }
+        else if (color==LedColor.RED) ID=fRedReferenceID;
+        else if (color==LedColor.BLUE) ID=fBlueReferenceID;
+
+        conditionsManager = DatabaseConditionsManager.getInstance();
+
+
+        EcalLedCalibrationCollection referenceDataCollection =  new EcalLedCalibrationCollection();
+        referenceDataCollection.setConnection(conditionsManager.getConnection());
+
+        TableMetaData tableMetaData = conditionsManager.findTableMetaData(dbTableName);
+        referenceDataCollection.setTableMetaData(tableMetaData);
+        System.out.println("Try to get reference data from DB. Collection ID is "+ID);
+        try {
+            referenceDataCollection.select(ID);
+        } catch (SQLException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        } catch (DatabaseObjectException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
+      
+        /*Now data from the reference should be there*/
+        for (EcalLedCalibration referenceData : referenceDataCollection){
+
+            chid=referenceData.getFieldValue("ecal_channel_id");
+            mean=referenceData.getFieldValue("led_response");
+            rms=referenceData.getFieldValue("rms");
+
+            EcalChannel cc = findChannel(chid);
+            column = cc.getX(); //This is the column
+            row = cc.getY(); //This is the row
+            chid=EcalMonitoringUtilities.getHistoIDFromRowColumn(row,column);
+            row = EcalMonitoringUtilities.getRowFromHistoID(id);
+            column = EcalMonitoringUtilities.getColumnFromHistoID(id);
+            
+
+            if (mean!=0) fillData=mMean[id]/mean;
+            else fillData=1;
+            System.out.println("row= "+row+" column= "+column+" data= "+mMean[id]+" ref= "+mean+" ratio= "+fillData);
+            hMeanCharge2DReferenceRatio.fill(column,row,fillData);
+         
+          
+
+        }
+
+
+        
+        style = pPlotter2.region(0).style();
+        style.setParameter("hist2DStyle", "colorMap");
+        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString()); 
+        pPlotter2.region(0).plot(hMeanCharge2D);
+        pPlotter2.region(0).refresh();
+        
+        
+        style = pPlotter2.region(1).style();
+        style.setParameter("hist2DStyle", "colorMap");
+        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style.dataStyle().fillStyle().setParameter("showZeroHeightBins", Boolean.FALSE.toString()); 
+        pPlotter2.region(1).plot(hMeanCharge2DReferenceRatio);
+        pPlotter2.region(1).refresh();
+        
+
+    }
 
     private void drawProfiles(int ledID,int driverID){
 
@@ -836,9 +934,9 @@
         okButtonBlue = new JButton("Yes, blue");
         cancelButton = new JButton("Cancel");
         labelString = "<html> Update conditions to DB <br> for run: <br> "+runNumber+" - "+runNumberMax+" <br> ???? <br> "
-                + "Use the monitoring app to look at the map<br>"
-                + "(Tab LED sequence)<br>"
-                +"Reply in 60 seconds<br>"+"</html>";   
+    + "Use the monitoring app to look at the map<br>"
+    + "(Tab LED sequence)<br>"
+    +"Reply in 60 seconds<br>"+"</html>";   
         label = new JLabel( labelString);
 
         frame  = new JFrame("Upload to DB?");
@@ -859,49 +957,49 @@
         panel.add(cancelButton);
         panel.add(okButtonBlue);
         panel.add(okButtonRed);
-     
+
 
         frame.setVisible(true);
         okButtonBlue.addActionListener(new ActionListener(){
             public void actionPerformed(ActionEvent event)
             {
-                m_ret=LedColor.BLUE;
-                frame.dispose();    
-                synchronized(modalMonitor)
-                {
-                    System.out.println("Blue pressed");
-                    modalMonitor.notify();
-                }
-            }
-        }
-                );
+    m_ret=LedColor.BLUE;
+    frame.dispose();    
+    synchronized(modalMonitor)
+    {
+        System.out.println("Blue pressed");
+        modalMonitor.notify();
+    }
+            }
+        }
+    );
         okButtonRed.addActionListener(new ActionListener(){
             public void actionPerformed(ActionEvent event)
             {
-                m_ret=LedColor.RED;
-                frame.dispose();    
-                synchronized(modalMonitor)
-                {
-                    System.out.println("Red pressed");
-                    modalMonitor.notify();
-                }
-            }
-        }
-                );
+    m_ret=LedColor.RED;
+    frame.dispose();    
+    synchronized(modalMonitor)
+    {
+        System.out.println("Red pressed");
+        modalMonitor.notify();
+    }
+            }
+        }
+    );
 
         cancelButton.addActionListener(new ActionListener(){
             public void actionPerformed(ActionEvent event)
             {
-                m_ret=LedColor.UNKNOWN;
-                frame.dispose();   
-                synchronized(modalMonitor)
-                {
-                    System.out.println("Cancel pressed");
-                    modalMonitor.notify();
-                }
-            }
-        }
-                );
+    m_ret=LedColor.UNKNOWN;
+    frame.dispose();   
+    synchronized(modalMonitor)
+    {
+        System.out.println("Cancel pressed");
+        modalMonitor.notify();
+    }
+            }
+        }
+    );
 
         System.out.println("askUploadDB done");
     }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalMonitoringPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalMonitoringPlots.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalMonitoringPlots.java	Wed Apr 27 11:11:32 2016
@@ -59,7 +59,7 @@
 
     /**
      * Set the refresh rate for histograms in this driver
-     * @param eventRefreshRate: the refresh rate, defined as number of events to accumulate before
+     * @param eventRefreshRate the refresh rate, defined as number of events to accumulate before
      *        refreshing the plot
      */
     public void setEventRefreshRate(int eventRefreshRate) {

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalPedestalViewer.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalPedestalViewer.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalPedestalViewer.java	Wed Apr 27 11:11:32 2016
@@ -33,80 +33,80 @@
     // this has to match the one in EcalPedstalCalculator:
     private String histoNameFormat = "Ecal/Pedestals/Mode7/ped%03d";
     
-	private AIDA aida = AIDA.defaultInstance();	
-	private IPlotter plotter;
-	private IPlotterFactory plotterFactory;
-	private IPlotterStyle pstyle;
-	private PEventViewer viewer;
+    private AIDA aida = AIDA.defaultInstance(); 
+    private IPlotter plotter;
+    private IPlotterFactory plotterFactory;
+    private IPlotterStyle pstyle;
+    private PEventViewer viewer;
 
-	static final String[] colors={"red","black","blue","green","yellow","pink","cyan","magenta","brown"};
-	static final int nRows=3;
-	static final int nColumns=3;
-	private int theRegion=0;
-	
-	@Override
-	public void detectorChanged(Detector detector) {
-		plotterFactory = aida.analysisFactory().createPlotterFactory("ECal Peds");
-		plotter = plotterFactory.create("ECal Peds");
-		plotter.createRegions(nColumns,nRows);
-		// Plot dummmy histos, else null plotter regions later:
-		for (int ii=0; ii<nColumns*nRows; ii++) {
-  	    	plotter.region(ii).plot(aida.histogram1D("ASDF"+ii,100,11e9,11e11));
-		}
-		plotter.show();
-		
-		pstyle=plotterFactory.createPlotterStyle();
-		pstyle.xAxisStyle().labelStyle().setBold(true);
-		pstyle.yAxisStyle().labelStyle().setBold(true);
-		pstyle.xAxisStyle().tickLabelStyle().setBold(true);
-		pstyle.yAxisStyle().tickLabelStyle().setBold(true);
-		pstyle.xAxisStyle().lineStyle().setColor("black");
-		pstyle.yAxisStyle().lineStyle().setColor("black");
-		pstyle.xAxisStyle().lineStyle().setThickness(2);
-		pstyle.yAxisStyle().lineStyle().setThickness(2);
-		pstyle.dataStyle().errorBarStyle().setThickness(0);
-		pstyle.legendBoxStyle().setVisible(false);
-	}
-	
-	@Override
-	public void startOfData() {
-		File config = new File("ecal-mapping-config.csv");
-		if(config.exists() && config.canRead()) {
-			try { viewer = new PDataEventViewer(config.getAbsolutePath()); }
-			catch (IOException e) { viewer = new PEventViewer(); }
-		} else { viewer = new PEventViewer(); }
-		viewer.addCrystalListener(this);
-		viewer.setVisible(true);
-	}
-	
-	@Override
-	public void actionPerformed(ActionEvent ae) { }
-	
-	@Override
-	public void crystalActivated(CrystalEvent e) { }
-	
-	@Override
-	public void crystalDeactivated(CrystalEvent e) { }
+    static final String[] colors={"red","black","blue","green","yellow","pink","cyan","magenta","brown"};
+    static final int nRows=3;
+    static final int nColumns=3;
+    private int theRegion=0;
+    
+    @Override
+    public void detectorChanged(Detector detector) {
+        plotterFactory = aida.analysisFactory().createPlotterFactory("ECal Peds");
+        plotter = plotterFactory.create("ECal Peds");
+        plotter.createRegions(nColumns,nRows);
+        // Plot dummmy histos, else null plotter regions later:
+        for (int ii=0; ii<nColumns*nRows; ii++) {
+            plotter.region(ii).plot(aida.histogram1D("ASDF"+ii,100,11e9,11e11));
+        }
+        plotter.show();
+        
+        pstyle=plotterFactory.createPlotterStyle();
+        pstyle.xAxisStyle().labelStyle().setBold(true);
+        pstyle.yAxisStyle().labelStyle().setBold(true);
+        pstyle.xAxisStyle().tickLabelStyle().setBold(true);
+        pstyle.yAxisStyle().tickLabelStyle().setBold(true);
+        pstyle.xAxisStyle().lineStyle().setColor("black");
+        pstyle.yAxisStyle().lineStyle().setColor("black");
+        pstyle.xAxisStyle().lineStyle().setThickness(2);
+        pstyle.yAxisStyle().lineStyle().setThickness(2);
+        pstyle.dataStyle().errorBarStyle().setThickness(0);
+        pstyle.legendBoxStyle().setVisible(false);
+    }
+    
+    @Override
+    public void startOfData() {
+        File config = new File("ecal-mapping-config.csv");
+        if(config.exists() && config.canRead()) {
+            try { viewer = new PDataEventViewer(config.getAbsolutePath()); }
+            catch (IOException e) { viewer = new PEventViewer(); }
+        } else { viewer = new PEventViewer(); }
+        viewer.addCrystalListener(this);
+        viewer.setVisible(true);
+    }
+    
+    @Override
+    public void actionPerformed(ActionEvent ae) { }
+    
+    @Override
+    public void crystalActivated(CrystalEvent e) { }
+    
+    @Override
+    public void crystalDeactivated(CrystalEvent e) { }
 
-	@Override
-	public void crystalClicked(CrystalEvent e) {
-		aida.tree().cd("/");
-		Point ecalPoint = Viewer.toEcalPoint(e.getCrystalID());
-		if (ecalPoint.x == 0 || ecalPoint.y == 0) return;
-		if (EcalMonitoringUtilities.isInHole(ecalPoint.y,ecalPoint.x)) return;
-		final int cid=EcalMonitoringUtilities.getChannelIdFromRowColumn(ecalPoint.y,ecalPoint.x);
-	    IHistogram1D hist=aida.histogram1D(String.format(histoNameFormat,cid));
-	    if (hist==null) {
-	        System.err.println("Running the Driver?");
-	    } else {
-     	    hist.setTitle(String.format("(%d,%d)",ecalPoint.x,ecalPoint.y));
+    @Override
+    public void crystalClicked(CrystalEvent e) {
+        aida.tree().cd("/");
+        Point ecalPoint = Viewer.toEcalPoint(e.getCrystalID());
+        if (ecalPoint.x == 0 || ecalPoint.y == 0) return;
+        if (EcalMonitoringUtilities.isInHole(ecalPoint.y,ecalPoint.x)) return;
+        final int cid=EcalMonitoringUtilities.getChannelIdFromRowColumn(ecalPoint.y,ecalPoint.x);
+        IHistogram1D hist=aida.histogram1D(String.format(histoNameFormat,cid));
+        if (hist==null) {
+            System.err.println("Running the Driver?");
+        } else {
+            hist.setTitle(String.format("(%d,%d)",ecalPoint.x,ecalPoint.y));
             pstyle.dataStyle().lineStyle().setParameter("color", colors[theRegion%colors.length]);
-	        plotter.region(theRegion).clear();
-	        plotter.region(theRegion).plot(hist,pstyle);
-	        plotter.region(theRegion).refresh();
-	        theRegion=(theRegion+1)%(nColumns*nRows);
-	    }
-	}
-	
-	
+            plotter.region(theRegion).clear();
+            plotter.region(theRegion).plot(hist,pstyle);
+            plotter.region(theRegion).refresh();
+            theRegion=(theRegion+1)%(nColumns*nRows);
+        }
+    }
+    
+    
 }

Modified: java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalWindowPlotsXY.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalWindowPlotsXY.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalWindowPlotsXY.java	Wed Apr 27 11:11:32 2016
@@ -93,7 +93,7 @@
     }
 
     private void setupPlots() {
-    	System.out.println("ECAL WINDOW PLOTS START");
+        System.out.println("ECAL WINDOW PLOTS START");
         //if (plotterFrame != null) {
         //    plotterFrame.dispose();
         //}
@@ -108,8 +108,8 @@
         IPlotterStyle pstyle = plotter.style();
         pstyle.dataStyle().errorBarStyle().setVisible(false);
         plotter.createRegions(1,1);     
-    	windowPlot1 = aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : dummy", 1, -0.5, 1 - 0.5);
-    	plotter.region(0).plot(windowPlot1);
+        windowPlot1 = aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : dummy", 1, -0.5, 1 - 0.5);
+        plotter.region(0).plot(windowPlot1);
         plotter.show();
     }
 
@@ -126,15 +126,15 @@
                 dec.setID(hit.getCellID());
                 int x = dec.getValue("ix");
                 int y = dec.getValue("iy");
-//				System.out.println("got hit: x= " + x + ", y= " + y);
+//              System.out.println("got hit: x= " + x + ", y= " + y);
                 if (isFirst) {
-                	System.out.println("FIRST!!!");
+                    System.out.println("FIRST!!!");
                     isFirst=false;
-                	window=hit.getADCValues().length;
-                	windowPlot = aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Window Mode Data", window, -0.5, window - 0.5);
-                	plotter.region(0).clear();
-                	plotter.region(0).plot(windowPlot);
-                	plotter.region(0).refresh();
+                    window=hit.getADCValues().length;
+                    windowPlot = aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Window Mode Data", window, -0.5, window - 0.5);
+                    plotter.region(0).clear();
+                    plotter.region(0).plot(windowPlot);
+                    plotter.region(0).refresh();
                 
                 }
                 if (testX && x != plotX) {

Modified: java/branches/HPSJAVA-409/monitoring-util/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/pom.xml	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/monitoring-util/</url>

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/plotting/ExportPdf.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/plotting/ExportPdf.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/plotting/ExportPdf.java	Wed Apr 27 11:11:32 2016
@@ -8,6 +8,9 @@
 import java.awt.image.BufferedImage;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.logging.Logger;
 
@@ -42,12 +45,10 @@
     /**
      * Save a set of tabs containing plots to a file.
      *
-     * @param plotTabs the top level tab component (plots are actually in a set
-     * of tabs without these tabs)
+     * @param plotters the list of plotters to save (from plots in the regions)
      * @param fileName the file name
      * @param runData the list of run data to save on the cover page
-     * @throws IOException if there is a problem with the IO (e.g. writing to
-     * PDF file)
+     * @throws IOException if there is a problem with the IO (e.g. writing to PDF file)
      */
     public static void write(List<IPlotter> plotters, String fileName, List<String> runData)
             throws IOException {
@@ -70,9 +71,23 @@
         } catch (DocumentException e) {
             throw new IOException(e);
         }
+        
+        // Sort plotters so output appears the same every time.
+        ArrayList<IPlotter> sortedPlotters = new ArrayList<IPlotter>(plotters);
+        Collections.sort(sortedPlotters, new Comparator<IPlotter>() {
+           public int compare(IPlotter object1, IPlotter object2) {
+               if (object1.title() == null) {
+                   return -1;
+               }
+               if (object2.title() == null) {
+                   return 1;
+               }
+               return object1.title().compareTo(object2.title());
+           }
+        });
 
         // Write the graphics from each plotter on a new page.
-        for (IPlotter plotter : plotters) {
+        for (IPlotter plotter : sortedPlotters) {
             plotter.refresh();
             document.newPage();
             writePage(document, writer, plotter);

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/subsys/et/package-info.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/subsys/et/package-info.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/subsys/et/package-info.java	Wed Apr 27 11:11:32 2016
@@ -1,7 +1,5 @@
 /**
  * ET subsystem monitoring
- * <p>
- * {@link EtSystemMonitor} implements basic status checks of the ET system.
  * 
  * @author Jeremy McCormick, SLAC
  */

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -26,224 +26,224 @@
  * @see DiagnosticUpdatable
  */
 public abstract class AbstractTablePanel extends JPanel implements DiagnosticUpdatable {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	public static final int ORIENTATION_HORIZONTAL = 0;
-	public static final int ORIENTATION_VERTICAL   = 1;
-	
-	// Components.
-	private JLabel localHeader;
-	private JLabel globalHeader;
-	protected final JTable localTable;
-	protected final JTable globalTable;
-	
-	// Component parameters.
-	private boolean horizontal = true;
-	private Dimension userPrefSize = null;
-	private Dimension defaultPrefSize = new Dimension(0, 0);
-	
-	/**
-	 * Instantiates an <code>AbstractTablePanel</code>.
-	 * @param args Arguments to be used when generating the panel tables.
-	 */
-	public AbstractTablePanel(Object... args) {
-		// Initialize the tables.
-		JTable[] tables = initializeTables(args);
-		localTable = tables[0];
-		globalTable = tables[1];
-		add(globalTable);
-		add(localTable);
-		
-		// Set the panels to their null starting values.
-		updatePanel(null, null);
-		
-		// Define the panel layout.
-		setLayout(null);
-		
-		// Create header labels for the tables.
-		localHeader = new JLabel("Instantaneous Statistics");
-		localHeader.setHorizontalAlignment(JLabel.CENTER);
-		add(localHeader);
-		
-		globalHeader = new JLabel("Run Statistics");
-		globalHeader.setHorizontalAlignment(JLabel.CENTER);
-		add(globalHeader);
-		
-		// Track when the component changes size and reposition the
-		// components accordingly.
-		addComponentListener(new ComponentAdapter() {
-			@Override
-			public void componentResized(ComponentEvent e) { positionComponents(); }
-		});
-		
-		// Define the component preferred size.
-		defaultPrefSize.width = localTable.getPreferredSize().width +
-				ComponentUtils.hinternal + globalTable.getPreferredSize().width;
-		defaultPrefSize.height = localTable.getPreferredSize().height +
-				ComponentUtils.vinternal + globalTable.getPreferredSize().height;
-	}
-	
-	@Override
-	public Dimension getPreferredSize() {
-		// If there is a user-specified preferred size, return that.
-		if(userPrefSize == null) { return defaultPrefSize; }
-		
-		// Otherwise, return the default calculated preferred size.
-		else { return userPrefSize; }
-	}
-	
-	@Override
-	public void setBackground(Color bg) {
-		// Set the base component background.
-		super.setBackground(bg);
-		
-		// If the components have been initialized, pass the background
-		// color change to them as appropriate. Note that the tables
-		// will always retain the same background color.
-		if(localTable != null) {
-			// Set the header backgrounds.
-			localHeader.setBackground(bg);
-			globalHeader.setBackground(bg);
-		}
-	}
-	
-	@Override
-	public void setFont(Font font) {
-		// Set the base component font.
-		super.setFont(font);
-		
-		// If the components have been initialized, pass the font change
-		// to them as appropriate.
-		if(localTable != null) {
-			// Set the table fonts.
-			localTable.setFont(font);
-			globalTable.setFont(font);
-			
-			// Set the header fonts.
-			Font headerFont = font.deriveFont(Font.BOLD, (float) Math.ceil(font.getSize2D() * 1.3));
-			localHeader.setFont(headerFont);
-			globalHeader.setFont(headerFont);
-		}
-	}
-	
-	@Override
-	public void setForeground(Color fg) {
-		// Set the base component foreground.
-		super.setForeground(fg);
-		
-		// If the components have been initialized, pass the foreground
-		// color change to them as appropriate. Note that the tables
-		// will always retain the same foreground color.
-		if(localTable != null) {
-			// Set the header foregrounds.
-			localHeader.setForeground(fg);
-			globalHeader.setForeground(fg);
-		}
-	}
-	
-	/**
-	 * Sets the orientation of components on the panel.
-	 * @param orientation - The orientation identifier. Identifiers can
-	 * be obtained as static variables from the within the root object
-	 * <code>AbstractTable</code>.
-	 */
-	public void setOrientation(int orientation) {
-		if(orientation == ORIENTATION_HORIZONTAL) {
-			if(!horizontal) {
-				horizontal = true;
-				positionComponents();
-			}
-		} else if(orientation == ORIENTATION_VERTICAL) {
-			if(horizontal) {
-				horizontal = false;
-				positionComponents();
-			}
-		} else {
-			throw new IllegalArgumentException("Invalid orienation identifier.");
-		}
-	}
-	
-	@Override
-	public void setPreferredSize(Dimension preferredSize) {
-		userPrefSize = preferredSize;
-	}
-	
-	/**
-	 * Generates the two tables that are used by the component. This
-	 * must return an array of size two.
-	 * @param args - Any arguments that should be passed to the method
-	 * for generating tables.
-	 * @return Returns an array of size two, where the first index must
-	 * contain the local table and the second index the global table.
-	 */
-	protected abstract JTable[] initializeTables(Object... args);
-	
-	/**
-	 * Repositions the components to the correct places on the parent
-	 * <code>JPanel</code>. This should be run whenever the panel
-	 * changes size.
-	 */
-	private void positionComponents() {
-		// Do not update if the components have not been initialized.
-		if(localHeader == null) { return; }
-		
-		// If the components should be position horizontally...
-		if(horizontal) {
-			// The local components get the left half of the panel and the
-			// global components the right. Find half of the panel width,
-			// accounting for the internal spacing. This is an internal
-			// component, so it does not employ additional spacing between
-			// itself and the parent component's edges.
-			int compWidth = (getWidth() - 10) / 2;
-			
-			// If there is any width remaining, it goes to the spacing.
-			int horizontal = ComponentUtils.hinternal + (getWidth() - 10) % 2;
-			
-			// Place the header labels. These are given their preferred
-			// height. Note that this means a very small panel may cut off
-			// some of the components. First, get the preferred height of
-			// the label with the larger preferred height. These should be
-			// the same thing, but just in case...
-			int labelHeight = localHeader.getPreferredSize().height;
-			if(labelHeight < globalHeader.getPreferredSize().height) {
-				labelHeight = globalHeader.getPreferredSize().height;
-			}
-			
-			// Set the label sizes and positions.
-			localHeader.setBounds(0, 0, compWidth, labelHeight);
-			globalHeader.setLocation(ComponentUtils.getNextX(localHeader, horizontal), 0);
-			globalHeader.setSize(compWidth, labelHeight);
-			
-			// The tables go under their respective labels and should fill
-			// the remainder of the label height.
-			int tableY = ComponentUtils.getNextY(localHeader, ComponentUtils.vinternal);
-			localTable.setBounds(0, tableY, compWidth, localTable.getPreferredSize().height);
-			globalTable.setBounds(globalHeader.getX(), tableY, compWidth, globalTable.getPreferredSize().height);
-		}
-		
-		// Otherwise, position them vertically.
-		else {
-			// Place the header labels. These are given their preferred
-			// height. Note that this means a very small panel may cut off
-			// some of the components. First, get the preferred height of
-			// the label with the larger preferred height. These should be
-			// the same thing, but just in case...
-			int labelHeight = localHeader.getPreferredSize().height;
-			if(labelHeight < globalHeader.getPreferredSize().height) {
-				labelHeight = globalHeader.getPreferredSize().height;
-			}
-			
-			// The local components go first, taking up the entire upper
-			// width of the panel.
-			localHeader.setBounds(0, 0, getWidth(), labelHeight);
-			localTable.setBounds(0, ComponentUtils.getNextY(localHeader, ComponentUtils.vinternal),
-					getWidth(), localTable.getPreferredSize().height);
-			
-			// The global components go immediately below.
-			globalHeader.setBounds(0, ComponentUtils.getNextY(localTable, ComponentUtils.vinternal),
-					getWidth(), labelHeight);
-			globalTable.setBounds(0, ComponentUtils.getNextY(globalHeader, ComponentUtils.vinternal),
-					getWidth(), globalTable.getPreferredSize().height);
-		}
-	}
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    public static final int ORIENTATION_HORIZONTAL = 0;
+    public static final int ORIENTATION_VERTICAL   = 1;
+    
+    // Components.
+    private JLabel localHeader;
+    private JLabel globalHeader;
+    protected final JTable localTable;
+    protected final JTable globalTable;
+    
+    // Component parameters.
+    private boolean horizontal = true;
+    private Dimension userPrefSize = null;
+    private Dimension defaultPrefSize = new Dimension(0, 0);
+    
+    /**
+     * Instantiates an <code>AbstractTablePanel</code>.
+     * @param args Arguments to be used when generating the panel tables.
+     */
+    public AbstractTablePanel(Object... args) {
+        // Initialize the tables.
+        JTable[] tables = initializeTables(args);
+        localTable = tables[0];
+        globalTable = tables[1];
+        add(globalTable);
+        add(localTable);
+        
+        // Set the panels to their null starting values.
+        updatePanel(null, null);
+        
+        // Define the panel layout.
+        setLayout(null);
+        
+        // Create header labels for the tables.
+        localHeader = new JLabel("Instantaneous Statistics");
+        localHeader.setHorizontalAlignment(JLabel.CENTER);
+        add(localHeader);
+        
+        globalHeader = new JLabel("Run Statistics");
+        globalHeader.setHorizontalAlignment(JLabel.CENTER);
+        add(globalHeader);
+        
+        // Track when the component changes size and reposition the
+        // components accordingly.
+        addComponentListener(new ComponentAdapter() {
+            @Override
+            public void componentResized(ComponentEvent e) { positionComponents(); }
+        });
+        
+        // Define the component preferred size.
+        defaultPrefSize.width = localTable.getPreferredSize().width +
+                ComponentUtils.hinternal + globalTable.getPreferredSize().width;
+        defaultPrefSize.height = localTable.getPreferredSize().height +
+                ComponentUtils.vinternal + globalTable.getPreferredSize().height;
+    }
+    
+    @Override
+    public Dimension getPreferredSize() {
+        // If there is a user-specified preferred size, return that.
+        if(userPrefSize == null) { return defaultPrefSize; }
+        
+        // Otherwise, return the default calculated preferred size.
+        else { return userPrefSize; }
+    }
+    
+    @Override
+    public void setBackground(Color bg) {
+        // Set the base component background.
+        super.setBackground(bg);
+        
+        // If the components have been initialized, pass the background
+        // color change to them as appropriate. Note that the tables
+        // will always retain the same background color.
+        if(localTable != null) {
+            // Set the header backgrounds.
+            localHeader.setBackground(bg);
+            globalHeader.setBackground(bg);
+        }
+    }
+    
+    @Override
+    public void setFont(Font font) {
+        // Set the base component font.
+        super.setFont(font);
+        
+        // If the components have been initialized, pass the font change
+        // to them as appropriate.
+        if(localTable != null) {
+            // Set the table fonts.
+            localTable.setFont(font);
+            globalTable.setFont(font);
+            
+            // Set the header fonts.
+            Font headerFont = font.deriveFont(Font.BOLD, (float) Math.ceil(font.getSize2D() * 1.3));
+            localHeader.setFont(headerFont);
+            globalHeader.setFont(headerFont);
+        }
+    }
+    
+    @Override
+    public void setForeground(Color fg) {
+        // Set the base component foreground.
+        super.setForeground(fg);
+        
+        // If the components have been initialized, pass the foreground
+        // color change to them as appropriate. Note that the tables
+        // will always retain the same foreground color.
+        if(localTable != null) {
+            // Set the header foregrounds.
+            localHeader.setForeground(fg);
+            globalHeader.setForeground(fg);
+        }
+    }
+    
+    /**
+     * Sets the orientation of components on the panel.
+     * @param orientation - The orientation identifier. Identifiers can
+     * be obtained as static variables from the within the root object
+     * <code>AbstractTable</code>.
+     */
+    public void setOrientation(int orientation) {
+        if(orientation == ORIENTATION_HORIZONTAL) {
+            if(!horizontal) {
+                horizontal = true;
+                positionComponents();
+            }
+        } else if(orientation == ORIENTATION_VERTICAL) {
+            if(horizontal) {
+                horizontal = false;
+                positionComponents();
+            }
+        } else {
+            throw new IllegalArgumentException("Invalid orienation identifier.");
+        }
+    }
+    
+    @Override
+    public void setPreferredSize(Dimension preferredSize) {
+        userPrefSize = preferredSize;
+    }
+    
+    /**
+     * Generates the two tables that are used by the component. This
+     * must return an array of size two.
+     * @param args - Any arguments that should be passed to the method
+     * for generating tables.
+     * @return Returns an array of size two, where the first index must
+     * contain the local table and the second index the global table.
+     */
+    protected abstract JTable[] initializeTables(Object... args);
+    
+    /**
+     * Repositions the components to the correct places on the parent
+     * <code>JPanel</code>. This should be run whenever the panel
+     * changes size.
+     */
+    private void positionComponents() {
+        // Do not update if the components have not been initialized.
+        if(localHeader == null) { return; }
+        
+        // If the components should be position horizontally...
+        if(horizontal) {
+            // The local components get the left half of the panel and the
+            // global components the right. Find half of the panel width,
+            // accounting for the internal spacing. This is an internal
+            // component, so it does not employ additional spacing between
+            // itself and the parent component's edges.
+            int compWidth = (getWidth() - 10) / 2;
+            
+            // If there is any width remaining, it goes to the spacing.
+            int horizontal = ComponentUtils.hinternal + (getWidth() - 10) % 2;
+            
+            // Place the header labels. These are given their preferred
+            // height. Note that this means a very small panel may cut off
+            // some of the components. First, get the preferred height of
+            // the label with the larger preferred height. These should be
+            // the same thing, but just in case...
+            int labelHeight = localHeader.getPreferredSize().height;
+            if(labelHeight < globalHeader.getPreferredSize().height) {
+                labelHeight = globalHeader.getPreferredSize().height;
+            }
+            
+            // Set the label sizes and positions.
+            localHeader.setBounds(0, 0, compWidth, labelHeight);
+            globalHeader.setLocation(ComponentUtils.getNextX(localHeader, horizontal), 0);
+            globalHeader.setSize(compWidth, labelHeight);
+            
+            // The tables go under their respective labels and should fill
+            // the remainder of the label height.
+            int tableY = ComponentUtils.getNextY(localHeader, ComponentUtils.vinternal);
+            localTable.setBounds(0, tableY, compWidth, localTable.getPreferredSize().height);
+            globalTable.setBounds(globalHeader.getX(), tableY, compWidth, globalTable.getPreferredSize().height);
+        }
+        
+        // Otherwise, position them vertically.
+        else {
+            // Place the header labels. These are given their preferred
+            // height. Note that this means a very small panel may cut off
+            // some of the components. First, get the preferred height of
+            // the label with the larger preferred height. These should be
+            // the same thing, but just in case...
+            int labelHeight = localHeader.getPreferredSize().height;
+            if(labelHeight < globalHeader.getPreferredSize().height) {
+                labelHeight = globalHeader.getPreferredSize().height;
+            }
+            
+            // The local components go first, taking up the entire upper
+            // width of the panel.
+            localHeader.setBounds(0, 0, getWidth(), labelHeight);
+            localTable.setBounds(0, ComponentUtils.getNextY(localHeader, ComponentUtils.vinternal),
+                    getWidth(), localTable.getPreferredSize().height);
+            
+            // The global components go immediately below.
+            globalHeader.setBounds(0, ComponentUtils.getNextY(localTable, ComponentUtils.vinternal),
+                    getWidth(), labelHeight);
+            globalTable.setBounds(0, ComponentUtils.getNextY(globalHeader, ComponentUtils.vinternal),
+                    getWidth(), globalTable.getPreferredSize().height);
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTriggerTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTriggerTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTriggerTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -14,189 +14,189 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public abstract class AbstractTriggerTablePanel extends AbstractTwoColumnTablePanel {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	
-	// Internal variables.
-	private final int numCuts;
-	private final boolean singles;
-	
-	// Store reference index variables for local and run values.
-	private static final int GLOBAL = 0;
-	private static final int LOCAL  = 1;
-	
-	// Reference variables to the default table rows.
-	protected static final int ROW_RECON_COUNT        = 0;
-	protected static final int ROW_SSP_SIM_COUNT      = 1;
-	protected static final int ROW_SSP_BANK_COUNT     = 2;
-	protected static final int ROW_SSP_EFFICIENCY     = 3;
-	protected static final int ROW_TRIGGER_EFFICIENCY = 4;
-	protected static final int ROW_EMPTY_SPACE        = 5;
-	protected static final int ROW_CUT_FAILS_TITLE    = 6;
-	protected static final int ROW_FIRST_TRIGGER_CUT  = 7;
-	
-	/**
-	 * Instantiates an <code>AbstractTriggerTablePanel</code> with the
-	 * indicated cut names.
-	 * @param cutNames
-	 */
-	public AbstractTriggerTablePanel(String[] cutNames, boolean isSingles) {
-		// Instantiate the superclass.
-		super(makeTitle(cutNames));
-		
-		// Store the number of cuts.
-		numCuts = cutNames.length;
-		updatePanel(null, null);
-		
-		// Store whether this is a singles or pair trigger panel.
-		singles = isSingles;
-	}
-	
-	@Override
-	public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
-		// If the snapshot is null, all values should be "N/A."
-		if(runSnapshot == null || localSnapshot == null) {
-			// Output cluster count data.
-			String scalerNullValue = "---";
-			setLocalRowValue(ROW_RECON_COUNT,     scalerNullValue);
-			setLocalRowValue(ROW_SSP_SIM_COUNT,   scalerNullValue);
-			setLocalRowValue(ROW_SSP_BANK_COUNT,  scalerNullValue);
-			setGlobalRowValue(ROW_RECON_COUNT,    scalerNullValue);
-			setGlobalRowValue(ROW_SSP_SIM_COUNT,  scalerNullValue);
-			setGlobalRowValue(ROW_SSP_BANK_COUNT, scalerNullValue);
-			
-			// Output the tracked statistical data.
-			String percentNullValue = "--- / --- (---%)";
-			setLocalRowValue(ROW_SSP_EFFICIENCY,      percentNullValue);
-			setLocalRowValue(ROW_TRIGGER_EFFICIENCY,  percentNullValue);
-			setGlobalRowValue(ROW_SSP_EFFICIENCY,     percentNullValue);
-			setGlobalRowValue(ROW_TRIGGER_EFFICIENCY, percentNullValue);
-			
-			int ROW_SECOND_TRIGGER_CUT = ROW_FIRST_TRIGGER_CUT + numCuts + 2;
-			for(int cutRow = 0; cutRow < numCuts; cutRow++) {
-				setLocalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT,   percentNullValue);
-				setLocalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT,  percentNullValue);
-				setGlobalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT,  percentNullValue);
-				setGlobalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, percentNullValue);
-			}
-		} else {
-			// Get the local and run trigger statistics from the snapshot.
-			DiagnosticSnapshot[] stat = new DiagnosticSnapshot[2];
-			stat[GLOBAL] = runSnapshot;
-			stat[LOCAL] = localSnapshot;
-			
-			// Get the appropriate trigger statistical modules.
-			TriggerStatModule[][] triggerStats = new TriggerStatModule[2][2];
-			if(singles) {
-				triggerStats[LOCAL][0] = stat[LOCAL].getSingles0Stats();
-				triggerStats[LOCAL][1] = stat[LOCAL].getSingles1Stats();
-				triggerStats[GLOBAL][0] = stat[GLOBAL].getSingles0Stats();
-				triggerStats[GLOBAL][1] = stat[GLOBAL].getSingles1Stats();
-			} else {
-				triggerStats[LOCAL][0] = stat[LOCAL].getPair0Stats();
-				triggerStats[LOCAL][1] = stat[LOCAL].getPair1Stats();
-				triggerStats[GLOBAL][0] = stat[GLOBAL].getPair0Stats();
-				triggerStats[GLOBAL][1] = stat[GLOBAL].getPair1Stats();
-			}
-			
-			// Get the total number of triggers of each type.
-			int[] sspSimTriggers = new int[2];
-			int[] sspBankTriggers = new int[2];
-			int[] reconSimTriggers = new int[2];
-			int[] sspMatchedTriggers = new int[2];
-			int[] reconMatchedTriggers = new int[2];
-			
-			for(int i = 0; i < 2; i++) {
-				sspSimTriggers[i] = triggerStats[i][0].getSSPSimulatedTriggers() + triggerStats[i][1].getSSPSimulatedTriggers();
-				sspBankTriggers[i] = triggerStats[i][0].getReportedTriggers() + triggerStats[i][1].getReportedTriggers();
-				reconSimTriggers[i] = triggerStats[i][0].getReconSimulatedTriggers() + triggerStats[i][1].getReconSimulatedTriggers();
-				sspMatchedTriggers[i] = triggerStats[i][0].getMatchedSSPSimulatedTriggers() + triggerStats[i][1].getMatchedSSPSimulatedTriggers();
-				reconMatchedTriggers[i] = triggerStats[i][0].getMatchedReconSimulatedTriggers() + triggerStats[i][1].getMatchedReconSimulatedTriggers();
-			}
-			
-			// Determine the most spaces needed to display the values.
-			// Get the largest number of digits in any of the values.
-			int mostDigits = ComponentUtils.max(reconSimTriggers[LOCAL], sspBankTriggers[LOCAL],
-					sspSimTriggers[LOCAL], reconSimTriggers[GLOBAL], sspBankTriggers[GLOBAL],
-					sspSimTriggers[GLOBAL]);
-			int spaces = ComponentUtils.getDigits(mostDigits);
-			
-			// Update the single-value counters.
-			String countFormat = "%" + spaces + "d";
-			setLocalRowValue(ROW_RECON_COUNT,     String.format(countFormat, reconSimTriggers[LOCAL]));
-			setLocalRowValue(ROW_SSP_SIM_COUNT,   String.format(countFormat, sspSimTriggers[LOCAL]));
-			setLocalRowValue(ROW_SSP_BANK_COUNT,  String.format(countFormat, sspBankTriggers[LOCAL]));
-			setGlobalRowValue(ROW_RECON_COUNT,    String.format(countFormat, reconSimTriggers[GLOBAL]));
-			setGlobalRowValue(ROW_SSP_SIM_COUNT,  String.format(countFormat, sspSimTriggers[GLOBAL]));
-			setGlobalRowValue(ROW_SSP_BANK_COUNT, String.format(countFormat, sspBankTriggers[GLOBAL]));
-			
-			// Update the percentage counters.
-			String percentFormat = "%" + spaces + "d / %" + spaces + "d (%7.3f)";
-			
-			setLocalRowValue(ROW_SSP_EFFICIENCY, String.format(percentFormat, sspMatchedTriggers[LOCAL],
-					sspSimTriggers[LOCAL], (100.0 * sspMatchedTriggers[LOCAL] / sspSimTriggers[LOCAL])));
-			setLocalRowValue(ROW_TRIGGER_EFFICIENCY, String.format(percentFormat, reconMatchedTriggers[LOCAL],
-					reconSimTriggers[LOCAL], (100.0 * reconMatchedTriggers[LOCAL] / reconSimTriggers[LOCAL])));
-			setGlobalRowValue(ROW_SSP_EFFICIENCY, String.format(percentFormat, sspMatchedTriggers[GLOBAL],
-					sspSimTriggers[GLOBAL], (100.0 * sspMatchedTriggers[GLOBAL] / sspSimTriggers[GLOBAL])));
-			setGlobalRowValue(ROW_TRIGGER_EFFICIENCY, String.format(percentFormat, reconMatchedTriggers[GLOBAL],
-					reconSimTriggers[GLOBAL], (100.0 * reconMatchedTriggers[GLOBAL] / reconSimTriggers[GLOBAL])));
-			
-			int ROW_SECOND_TRIGGER_CUT = ROW_FIRST_TRIGGER_CUT + numCuts + 2;
-			for(int cutRow = 0; cutRow < numCuts; cutRow++) {
-				setLocalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT, String.format(percentFormat,
-						triggerStats[LOCAL][0].getSSPCutFailures(cutRow), triggerStats[LOCAL][0].getSSPSimulatedTriggers(),
-						(100.0 * triggerStats[LOCAL][0].getSSPCutFailures(cutRow) / triggerStats[LOCAL][0].getSSPSimulatedTriggers())));
-				setLocalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, String.format(percentFormat,
-						triggerStats[LOCAL][1].getSSPCutFailures(cutRow), triggerStats[LOCAL][1].getSSPSimulatedTriggers(),
-						(100.0 * triggerStats[LOCAL][1].getSSPCutFailures(cutRow) / triggerStats[LOCAL][1].getSSPSimulatedTriggers())));
-				setGlobalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT, String.format(percentFormat,
-						triggerStats[GLOBAL][0].getSSPCutFailures(cutRow), triggerStats[GLOBAL][0].getSSPSimulatedTriggers(),
-						(100.0 * triggerStats[GLOBAL][0].getSSPCutFailures(cutRow) / triggerStats[GLOBAL][0].getSSPSimulatedTriggers())));
-				setGlobalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, String.format(percentFormat,
-						triggerStats[GLOBAL][1].getSSPCutFailures(cutRow), triggerStats[GLOBAL][1].getSSPSimulatedTriggers(),
-						(100.0 * triggerStats[GLOBAL][1].getSSPCutFailures(cutRow) / triggerStats[GLOBAL][1].getSSPSimulatedTriggers())));
-			}
-		}
-	}
-	
-	/**
-	 * Creates the table appropriate table rows from the argument cut
-	 * names.
-	 * @param cutNames - An array containing the names of the cuts to
-	 * display.
-	 * @return Returns an array with the default table rows merged in
-	 * with the provided cut names.
-	 */
-	private static final String[] makeTitle(String[] cutNames) {
-		// Make a new array to hold all the text.
-		String[] mergedArray = new String[cutNames.length + cutNames.length + 9];
-		
-		// Define the default trigger headers.
-		mergedArray[0] = "Recon Triggers:";
-		mergedArray[1] = "SSP Sim Triggers:";
-		mergedArray[2] = "SSP Bank Triggers:";
-		mergedArray[3] = "SSP Efficiency:";
-		mergedArray[4] = "Trigger Efficiency:";
-		mergedArray[5] = "";
-		mergedArray[6] = "First Trigger Cut Failures";
-		
-		// Insert the cut names for the first trigger.
-		for(int cutIndex = 0; cutIndex < cutNames.length; cutIndex++) {
-			mergedArray[7 + cutIndex] = cutNames[cutIndex];
-		}
-		
-		// Insert the header for the second trigger cut names.
-		int startIndex = 7 + cutNames.length;
-		mergedArray[startIndex]     = "";
-		mergedArray[startIndex + 1] = "Second Trigger Cut Failures";
-		
-		// Insert the next set of cut names.
-		for(int cutIndex = 0; cutIndex < cutNames.length; cutIndex++) {
-			mergedArray[startIndex + 2 + cutIndex] = cutNames[cutIndex];
-		}
-		
-		// Return the resultant array.
-		return mergedArray;
-	}
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    
+    // Internal variables.
+    private final int numCuts;
+    private final boolean singles;
+    
+    // Store reference index variables for local and run values.
+    private static final int GLOBAL = 0;
+    private static final int LOCAL  = 1;
+    
+    // Reference variables to the default table rows.
+    protected static final int ROW_RECON_COUNT        = 0;
+    protected static final int ROW_SSP_SIM_COUNT      = 1;
+    protected static final int ROW_SSP_BANK_COUNT     = 2;
+    protected static final int ROW_SSP_EFFICIENCY     = 3;
+    protected static final int ROW_TRIGGER_EFFICIENCY = 4;
+    protected static final int ROW_EMPTY_SPACE        = 5;
+    protected static final int ROW_CUT_FAILS_TITLE    = 6;
+    protected static final int ROW_FIRST_TRIGGER_CUT  = 7;
+    
+    /**
+     * Instantiates an <code>AbstractTriggerTablePanel</code> with the
+     * indicated cut names.
+     * @param cutNames
+     */
+    public AbstractTriggerTablePanel(String[] cutNames, boolean isSingles) {
+        // Instantiate the superclass.
+        super(makeTitle(cutNames));
+        
+        // Store the number of cuts.
+        numCuts = cutNames.length;
+        updatePanel(null, null);
+        
+        // Store whether this is a singles or pair trigger panel.
+        singles = isSingles;
+    }
+    
+    @Override
+    public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
+        // If the snapshot is null, all values should be "N/A."
+        if(runSnapshot == null || localSnapshot == null) {
+            // Output cluster count data.
+            String scalerNullValue = "---";
+            setLocalRowValue(ROW_RECON_COUNT,     scalerNullValue);
+            setLocalRowValue(ROW_SSP_SIM_COUNT,   scalerNullValue);
+            setLocalRowValue(ROW_SSP_BANK_COUNT,  scalerNullValue);
+            setGlobalRowValue(ROW_RECON_COUNT,    scalerNullValue);
+            setGlobalRowValue(ROW_SSP_SIM_COUNT,  scalerNullValue);
+            setGlobalRowValue(ROW_SSP_BANK_COUNT, scalerNullValue);
+            
+            // Output the tracked statistical data.
+            String percentNullValue = "--- / --- (---%)";
+            setLocalRowValue(ROW_SSP_EFFICIENCY,      percentNullValue);
+            setLocalRowValue(ROW_TRIGGER_EFFICIENCY,  percentNullValue);
+            setGlobalRowValue(ROW_SSP_EFFICIENCY,     percentNullValue);
+            setGlobalRowValue(ROW_TRIGGER_EFFICIENCY, percentNullValue);
+            
+            int ROW_SECOND_TRIGGER_CUT = ROW_FIRST_TRIGGER_CUT + numCuts + 2;
+            for(int cutRow = 0; cutRow < numCuts; cutRow++) {
+                setLocalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT,   percentNullValue);
+                setLocalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT,  percentNullValue);
+                setGlobalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT,  percentNullValue);
+                setGlobalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, percentNullValue);
+            }
+        } else {
+            // Get the local and run trigger statistics from the snapshot.
+            DiagnosticSnapshot[] stat = new DiagnosticSnapshot[2];
+            stat[GLOBAL] = runSnapshot;
+            stat[LOCAL] = localSnapshot;
+            
+            // Get the appropriate trigger statistical modules.
+            TriggerStatModule[][] triggerStats = new TriggerStatModule[2][2];
+            if(singles) {
+                triggerStats[LOCAL][0] = stat[LOCAL].getSingles0Stats();
+                triggerStats[LOCAL][1] = stat[LOCAL].getSingles1Stats();
+                triggerStats[GLOBAL][0] = stat[GLOBAL].getSingles0Stats();
+                triggerStats[GLOBAL][1] = stat[GLOBAL].getSingles1Stats();
+            } else {
+                triggerStats[LOCAL][0] = stat[LOCAL].getPair0Stats();
+                triggerStats[LOCAL][1] = stat[LOCAL].getPair1Stats();
+                triggerStats[GLOBAL][0] = stat[GLOBAL].getPair0Stats();
+                triggerStats[GLOBAL][1] = stat[GLOBAL].getPair1Stats();
+            }
+            
+            // Get the total number of triggers of each type.
+            int[] sspSimTriggers = new int[2];
+            int[] sspBankTriggers = new int[2];
+            int[] reconSimTriggers = new int[2];
+            int[] sspMatchedTriggers = new int[2];
+            int[] reconMatchedTriggers = new int[2];
+            
+            for(int i = 0; i < 2; i++) {
+                sspSimTriggers[i] = triggerStats[i][0].getSSPSimulatedTriggers() + triggerStats[i][1].getSSPSimulatedTriggers();
+                sspBankTriggers[i] = triggerStats[i][0].getReportedTriggers() + triggerStats[i][1].getReportedTriggers();
+                reconSimTriggers[i] = triggerStats[i][0].getReconSimulatedTriggers() + triggerStats[i][1].getReconSimulatedTriggers();
+                sspMatchedTriggers[i] = triggerStats[i][0].getMatchedSSPSimulatedTriggers() + triggerStats[i][1].getMatchedSSPSimulatedTriggers();
+                reconMatchedTriggers[i] = triggerStats[i][0].getMatchedReconSimulatedTriggers() + triggerStats[i][1].getMatchedReconSimulatedTriggers();
+            }
+            
+            // Determine the most spaces needed to display the values.
+            // Get the largest number of digits in any of the values.
+            int mostDigits = ComponentUtils.max(reconSimTriggers[LOCAL], sspBankTriggers[LOCAL],
+                    sspSimTriggers[LOCAL], reconSimTriggers[GLOBAL], sspBankTriggers[GLOBAL],
+                    sspSimTriggers[GLOBAL]);
+            int spaces = ComponentUtils.getDigits(mostDigits);
+            
+            // Update the single-value counters.
+            String countFormat = "%" + spaces + "d";
+            setLocalRowValue(ROW_RECON_COUNT,     String.format(countFormat, reconSimTriggers[LOCAL]));
+            setLocalRowValue(ROW_SSP_SIM_COUNT,   String.format(countFormat, sspSimTriggers[LOCAL]));
+            setLocalRowValue(ROW_SSP_BANK_COUNT,  String.format(countFormat, sspBankTriggers[LOCAL]));
+            setGlobalRowValue(ROW_RECON_COUNT,    String.format(countFormat, reconSimTriggers[GLOBAL]));
+            setGlobalRowValue(ROW_SSP_SIM_COUNT,  String.format(countFormat, sspSimTriggers[GLOBAL]));
+            setGlobalRowValue(ROW_SSP_BANK_COUNT, String.format(countFormat, sspBankTriggers[GLOBAL]));
+            
+            // Update the percentage counters.
+            String percentFormat = "%" + spaces + "d / %" + spaces + "d (%7.3f)";
+            
+            setLocalRowValue(ROW_SSP_EFFICIENCY, String.format(percentFormat, sspMatchedTriggers[LOCAL],
+                    sspSimTriggers[LOCAL], (100.0 * sspMatchedTriggers[LOCAL] / sspSimTriggers[LOCAL])));
+            setLocalRowValue(ROW_TRIGGER_EFFICIENCY, String.format(percentFormat, reconMatchedTriggers[LOCAL],
+                    reconSimTriggers[LOCAL], (100.0 * reconMatchedTriggers[LOCAL] / reconSimTriggers[LOCAL])));
+            setGlobalRowValue(ROW_SSP_EFFICIENCY, String.format(percentFormat, sspMatchedTriggers[GLOBAL],
+                    sspSimTriggers[GLOBAL], (100.0 * sspMatchedTriggers[GLOBAL] / sspSimTriggers[GLOBAL])));
+            setGlobalRowValue(ROW_TRIGGER_EFFICIENCY, String.format(percentFormat, reconMatchedTriggers[GLOBAL],
+                    reconSimTriggers[GLOBAL], (100.0 * reconMatchedTriggers[GLOBAL] / reconSimTriggers[GLOBAL])));
+            
+            int ROW_SECOND_TRIGGER_CUT = ROW_FIRST_TRIGGER_CUT + numCuts + 2;
+            for(int cutRow = 0; cutRow < numCuts; cutRow++) {
+                setLocalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT, String.format(percentFormat,
+                        triggerStats[LOCAL][0].getSSPCutFailures(cutRow), triggerStats[LOCAL][0].getSSPSimulatedTriggers(),
+                        (100.0 * triggerStats[LOCAL][0].getSSPCutFailures(cutRow) / triggerStats[LOCAL][0].getSSPSimulatedTriggers())));
+                setLocalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, String.format(percentFormat,
+                        triggerStats[LOCAL][1].getSSPCutFailures(cutRow), triggerStats[LOCAL][1].getSSPSimulatedTriggers(),
+                        (100.0 * triggerStats[LOCAL][1].getSSPCutFailures(cutRow) / triggerStats[LOCAL][1].getSSPSimulatedTriggers())));
+                setGlobalRowValue(cutRow + ROW_FIRST_TRIGGER_CUT, String.format(percentFormat,
+                        triggerStats[GLOBAL][0].getSSPCutFailures(cutRow), triggerStats[GLOBAL][0].getSSPSimulatedTriggers(),
+                        (100.0 * triggerStats[GLOBAL][0].getSSPCutFailures(cutRow) / triggerStats[GLOBAL][0].getSSPSimulatedTriggers())));
+                setGlobalRowValue(cutRow + ROW_SECOND_TRIGGER_CUT, String.format(percentFormat,
+                        triggerStats[GLOBAL][1].getSSPCutFailures(cutRow), triggerStats[GLOBAL][1].getSSPSimulatedTriggers(),
+                        (100.0 * triggerStats[GLOBAL][1].getSSPCutFailures(cutRow) / triggerStats[GLOBAL][1].getSSPSimulatedTriggers())));
+            }
+        }
+    }
+    
+    /**
+     * Creates the table appropriate table rows from the argument cut
+     * names.
+     * @param cutNames - An array containing the names of the cuts to
+     * display.
+     * @return Returns an array with the default table rows merged in
+     * with the provided cut names.
+     */
+    private static final String[] makeTitle(String[] cutNames) {
+        // Make a new array to hold all the text.
+        String[] mergedArray = new String[cutNames.length + cutNames.length + 9];
+        
+        // Define the default trigger headers.
+        mergedArray[0] = "Recon Triggers:";
+        mergedArray[1] = "SSP Sim Triggers:";
+        mergedArray[2] = "SSP Bank Triggers:";
+        mergedArray[3] = "SSP Efficiency:";
+        mergedArray[4] = "Trigger Efficiency:";
+        mergedArray[5] = "";
+        mergedArray[6] = "First Trigger Cut Failures";
+        
+        // Insert the cut names for the first trigger.
+        for(int cutIndex = 0; cutIndex < cutNames.length; cutIndex++) {
+            mergedArray[7 + cutIndex] = cutNames[cutIndex];
+        }
+        
+        // Insert the header for the second trigger cut names.
+        int startIndex = 7 + cutNames.length;
+        mergedArray[startIndex]     = "";
+        mergedArray[startIndex + 1] = "Second Trigger Cut Failures";
+        
+        // Insert the next set of cut names.
+        for(int cutIndex = 0; cutIndex < cutNames.length; cutIndex++) {
+            mergedArray[startIndex + 2 + cutIndex] = cutNames[cutIndex];
+        }
+        
+        // Return the resultant array.
+        return mergedArray;
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTwoColumnTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTwoColumnTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/AbstractTwoColumnTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -16,94 +16,94 @@
  * @see AbstractTablePanel
  */
 public abstract class AbstractTwoColumnTablePanel extends AbstractTablePanel {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	
-	// Table models.
-	private TableTextModel localModel;
-	private TableTextModel globalModel;
-	
-	// Table model mappings.
-	private static final int COL_TITLE = 0;
-	private static final int COL_VALUE = 1;
-	
-	/**
-	 * Instantiates an <code>AbstractTwoColumnTablePanel</code> object
-	 * with the indicated row names.
-	 * @param rowNames - The names of the rows.
-	 */
-	public AbstractTwoColumnTablePanel(String[] rowNames) {
-		super((Object[]) rowNames);
-	}
-	
-	@Override
-	protected JTable[] initializeTables(Object... args) {
-		// The arguments should be a string array.
-		if(!(args instanceof String[])) {
-			throw new IllegalArgumentException("Row names must be strings!");
-		}
-		String[] rowNames = (String[]) args;
-		
-		// Initialize the table models. They should have two columns
-		// (one for values and one for headers) and a number of rows
-		// equal to the number of row names.
-		localModel = new TableTextModel(rowNames.length, 2);
-		globalModel = new TableTextModel(rowNames.length, 2);
-		
-		// Initialize the titles.
-		for(int i = 0; i < rowNames.length; i++) {
-			localModel.setValueAt(rowNames[i], i, COL_TITLE);
-			globalModel.setValueAt(rowNames[i], i, COL_TITLE);
-		}
-		updatePanel(null, null);
-		
-		// Make a cell renderer.
-		DefaultTableCellRenderer centerRenderer = new DefaultTableCellRenderer();
-		centerRenderer.setHorizontalAlignment(JLabel.CENTER);
-		
-		// Create JTable objects to display the data.
-		JTable localTable = new JTable(localModel);
-		localTable.setRowSelectionAllowed(false);
-		localTable.setColumnSelectionAllowed(false);
-		localTable.setCellSelectionEnabled(false);
-		localTable.setShowVerticalLines(false);
-		localTable.getColumnModel().getColumn(0).setMinWidth(200);
-		localTable.getColumnModel().getColumn(0).setMaxWidth(200);
-		localTable.getColumnModel().getColumn(1).setCellRenderer(centerRenderer);
-		localTable.setFont(new Font("monospaced", localTable.getFont().getStyle(), localTable.getFont().getSize()));
-		
-		JTable globalTable = new JTable(globalModel);
-		globalTable.setRowSelectionAllowed(false);
-		globalTable.setColumnSelectionAllowed(false);
-		globalTable.setCellSelectionEnabled(false);
-		globalTable.setShowVerticalLines(false);
-		globalTable.getColumnModel().getColumn(0).setMinWidth(200);
-		globalTable.getColumnModel().getColumn(0).setMaxWidth(200);
-		globalTable.getColumnModel().getColumn(1).setCellRenderer(centerRenderer);
-		globalTable.setFont(new Font("monospaced", globalTable.getFont().getStyle(), globalTable.getFont().getSize()));
-		
-		// Return the two tables.
-		return new JTable[] { localTable, globalTable };
-	}
-	
-	/**
-	 * Sets the value of the indicated row for the global statistical
-	 * table.
-	 * @param rowIndex - The row.
-	 * @param value - The new value.
-	 */
-	protected void setGlobalRowValue(int rowIndex, String value) {
-		globalModel.setValueAt(value, rowIndex, COL_VALUE);
-	}
-	
-	/**
-	 * Sets the value of the indicated row for the local statistical
-	 * table.
-	 * @param rowIndex - The row.
-	 * @param value - The new value.
-	 */
-	protected void setLocalRowValue(int rowIndex, String value) {
-		localModel.setValueAt(value, rowIndex, COL_VALUE);
-	}
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    
+    // Table models.
+    private TableTextModel localModel;
+    private TableTextModel globalModel;
+    
+    // Table model mappings.
+    private static final int COL_TITLE = 0;
+    private static final int COL_VALUE = 1;
+    
+    /**
+     * Instantiates an <code>AbstractTwoColumnTablePanel</code> object
+     * with the indicated row names.
+     * @param rowNames - The names of the rows.
+     */
+    public AbstractTwoColumnTablePanel(String[] rowNames) {
+        super((Object[]) rowNames);
+    }
+    
+    @Override
+    protected JTable[] initializeTables(Object... args) {
+        // The arguments should be a string array.
+        if(!(args instanceof String[])) {
+            throw new IllegalArgumentException("Row names must be strings!");
+        }
+        String[] rowNames = (String[]) args;
+        
+        // Initialize the table models. They should have two columns
+        // (one for values and one for headers) and a number of rows
+        // equal to the number of row names.
+        localModel = new TableTextModel(rowNames.length, 2);
+        globalModel = new TableTextModel(rowNames.length, 2);
+        
+        // Initialize the titles.
+        for(int i = 0; i < rowNames.length; i++) {
+            localModel.setValueAt(rowNames[i], i, COL_TITLE);
+            globalModel.setValueAt(rowNames[i], i, COL_TITLE);
+        }
+        updatePanel(null, null);
+        
+        // Make a cell renderer.
+        DefaultTableCellRenderer centerRenderer = new DefaultTableCellRenderer();
+        centerRenderer.setHorizontalAlignment(JLabel.CENTER);
+        
+        // Create JTable objects to display the data.
+        JTable localTable = new JTable(localModel);
+        localTable.setRowSelectionAllowed(false);
+        localTable.setColumnSelectionAllowed(false);
+        localTable.setCellSelectionEnabled(false);
+        localTable.setShowVerticalLines(false);
+        localTable.getColumnModel().getColumn(0).setMinWidth(200);
+        localTable.getColumnModel().getColumn(0).setMaxWidth(200);
+        localTable.getColumnModel().getColumn(1).setCellRenderer(centerRenderer);
+        localTable.setFont(new Font("monospaced", localTable.getFont().getStyle(), localTable.getFont().getSize()));
+        
+        JTable globalTable = new JTable(globalModel);
+        globalTable.setRowSelectionAllowed(false);
+        globalTable.setColumnSelectionAllowed(false);
+        globalTable.setCellSelectionEnabled(false);
+        globalTable.setShowVerticalLines(false);
+        globalTable.getColumnModel().getColumn(0).setMinWidth(200);
+        globalTable.getColumnModel().getColumn(0).setMaxWidth(200);
+        globalTable.getColumnModel().getColumn(1).setCellRenderer(centerRenderer);
+        globalTable.setFont(new Font("monospaced", globalTable.getFont().getStyle(), globalTable.getFont().getSize()));
+        
+        // Return the two tables.
+        return new JTable[] { localTable, globalTable };
+    }
+    
+    /**
+     * Sets the value of the indicated row for the global statistical
+     * table.
+     * @param rowIndex - The row.
+     * @param value - The new value.
+     */
+    protected void setGlobalRowValue(int rowIndex, String value) {
+        globalModel.setValueAt(value, rowIndex, COL_VALUE);
+    }
+    
+    /**
+     * Sets the value of the indicated row for the local statistical
+     * table.
+     * @param rowIndex - The row.
+     * @param value - The new value.
+     */
+    protected void setLocalRowValue(int rowIndex, String value) {
+        localModel.setValueAt(value, rowIndex, COL_VALUE);
+    }
 
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ClusterTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ClusterTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ClusterTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -14,99 +14,99 @@
  * @see AbstractTablePanel
  */
 public class ClusterTablePanel extends AbstractTwoColumnTablePanel {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	private static final String[] TABLE_TITLES = { "Recon Clusters", "SSP Clusters", "Matched Clusters",
-			"Failed (Position)", "Failed (Energy)", "Failed (Hit Count)" };
-	
-	// Table model mappings.
-	private static final int ROW_RECON_COUNT      = 0;
-	private static final int ROW_SSP_COUNT        = 1;
-	private static final int ROW_MATCHED          = 2;
-	private static final int ROW_FAILED_POSITION  = 3;
-	private static final int ROW_FAILED_ENERGY    = 4;
-	private static final int ROW_FAILED_HIT_COUNT = 5;
-	
-	/**
-	 * Instantiate a new <code>ClusterTablePanel</code>.
-	 */
-	public ClusterTablePanel() { super(TABLE_TITLES); }
-	
-	@Override
-	public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
-		// If the snapshot is null, all values should be "N/A."
-		if(localSnapshot == null || runSnapshot == null) {
-			// Output cluster count data.
-			String scalerNullValue = "---";
-			setLocalRowValue(ROW_RECON_COUNT,  scalerNullValue);
-			setLocalRowValue(ROW_SSP_COUNT,    scalerNullValue);
-			setGlobalRowValue(ROW_RECON_COUNT, scalerNullValue);
-			setGlobalRowValue(ROW_SSP_COUNT,   scalerNullValue);
-			
-			// Output the tracked statistical data.
-			String percentNullValue = "--- / --- (---%)";
-			setLocalRowValue(ROW_MATCHED,           percentNullValue);
-			setLocalRowValue(ROW_FAILED_POSITION,   percentNullValue);
-			setLocalRowValue(ROW_FAILED_ENERGY,     percentNullValue);
-			setLocalRowValue(ROW_FAILED_HIT_COUNT,  percentNullValue);
-			setGlobalRowValue(ROW_MATCHED,          percentNullValue);
-			setGlobalRowValue(ROW_FAILED_POSITION,  percentNullValue);
-			setGlobalRowValue(ROW_FAILED_ENERGY,    percentNullValue);
-			setGlobalRowValue(ROW_FAILED_HIT_COUNT, percentNullValue);
-		}
-		
-		// Otherwise, populate the table with the diagnostic data.
-		else {
-			// Get the cluster statistical banks.
-			ClusterStatModule lstat = localSnapshot.getClusterStats();
-			ClusterStatModule rstat = runSnapshot.getClusterStats();
-			
-			// Get the largest number of digits in any of the values.
-			int mostDigits = ComponentUtils.max(lstat.getReconClusterCount(), lstat.getSSPClusterCount(), lstat.getMatches(),
-					lstat.getPositionFailures(), lstat.getEnergyFailures(), lstat.getHitCountFailures(),
-					rstat.getReconClusterCount(), rstat.getSSPClusterCount(), rstat.getMatches(),
-					rstat.getPositionFailures(), rstat.getEnergyFailures(), rstat.getHitCountFailures());
-			int spaces = ComponentUtils.getDigits(mostDigits);
-			
-			// Put the number of reconstructed and SSP clusters into
-			// the tables.
-			int[] clusterValue = {
-					lstat.getReconClusterCount(),
-					lstat.getSSPClusterCount(),
-					rstat.getReconClusterCount(),
-					rstat.getSSPClusterCount()
-			};
-			String countFormat = "%" + spaces + "d";
-			setLocalRowValue(ROW_RECON_COUNT,  String.format(countFormat, clusterValue[0]));
-			setLocalRowValue(ROW_SSP_COUNT,    String.format(countFormat, clusterValue[1]));
-			setGlobalRowValue(ROW_RECON_COUNT, String.format(countFormat, clusterValue[2]));
-			setGlobalRowValue(ROW_SSP_COUNT,   String.format(countFormat, clusterValue[3]));
-			
-			// Output the tracked statistical data.
-			int total;
-			String percentFormat = "%" + spaces + "d / %" + spaces + "d (%7.3f)";
-			int[] statValue = {
-					lstat.getMatches(),
-					lstat.getPositionFailures(),
-					lstat.getEnergyFailures(),
-					lstat.getHitCountFailures(),
-					rstat.getMatches(),
-					rstat.getPositionFailures(),
-					rstat.getEnergyFailures(),
-					rstat.getHitCountFailures()
-			};
-			
-			total = lstat.getReconClusterCount();
-			setLocalRowValue(ROW_MATCHED,          String.format(percentFormat, statValue[0], total, 100.0 * statValue[0] / total));
-			setLocalRowValue(ROW_FAILED_POSITION,  String.format(percentFormat, statValue[1], total, 100.0 * statValue[1] / total));
-			setLocalRowValue(ROW_FAILED_ENERGY,    String.format(percentFormat, statValue[2], total, 100.0 * statValue[2] / total));
-			setLocalRowValue(ROW_FAILED_HIT_COUNT, String.format(percentFormat, statValue[3], total, 100.0 * statValue[3] / total));
-			
-			total = rstat.getReconClusterCount();
-			setGlobalRowValue(ROW_MATCHED,          String.format(percentFormat, statValue[4], total, 100.0 * statValue[4] / total));
-			setGlobalRowValue(ROW_FAILED_POSITION,  String.format(percentFormat, statValue[5], total, 100.0 * statValue[5] / total));
-			setGlobalRowValue(ROW_FAILED_ENERGY,    String.format(percentFormat, statValue[6], total, 100.0 * statValue[6] / total));
-			setGlobalRowValue(ROW_FAILED_HIT_COUNT, String.format(percentFormat, statValue[7], total, 100.0 * statValue[7] / total));
-		}
-	}
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    private static final String[] TABLE_TITLES = { "Recon Clusters", "SSP Clusters", "Matched Clusters",
+            "Failed (Position)", "Failed (Energy)", "Failed (Hit Count)" };
+    
+    // Table model mappings.
+    private static final int ROW_RECON_COUNT      = 0;
+    private static final int ROW_SSP_COUNT        = 1;
+    private static final int ROW_MATCHED          = 2;
+    private static final int ROW_FAILED_POSITION  = 3;
+    private static final int ROW_FAILED_ENERGY    = 4;
+    private static final int ROW_FAILED_HIT_COUNT = 5;
+    
+    /**
+     * Instantiate a new <code>ClusterTablePanel</code>.
+     */
+    public ClusterTablePanel() { super(TABLE_TITLES); }
+    
+    @Override
+    public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
+        // If the snapshot is null, all values should be "N/A."
+        if(localSnapshot == null || runSnapshot == null) {
+            // Output cluster count data.
+            String scalerNullValue = "---";
+            setLocalRowValue(ROW_RECON_COUNT,  scalerNullValue);
+            setLocalRowValue(ROW_SSP_COUNT,    scalerNullValue);
+            setGlobalRowValue(ROW_RECON_COUNT, scalerNullValue);
+            setGlobalRowValue(ROW_SSP_COUNT,   scalerNullValue);
+            
+            // Output the tracked statistical data.
+            String percentNullValue = "--- / --- (---%)";
+            setLocalRowValue(ROW_MATCHED,           percentNullValue);
+            setLocalRowValue(ROW_FAILED_POSITION,   percentNullValue);
+            setLocalRowValue(ROW_FAILED_ENERGY,     percentNullValue);
+            setLocalRowValue(ROW_FAILED_HIT_COUNT,  percentNullValue);
+            setGlobalRowValue(ROW_MATCHED,          percentNullValue);
+            setGlobalRowValue(ROW_FAILED_POSITION,  percentNullValue);
+            setGlobalRowValue(ROW_FAILED_ENERGY,    percentNullValue);
+            setGlobalRowValue(ROW_FAILED_HIT_COUNT, percentNullValue);
+        }
+        
+        // Otherwise, populate the table with the diagnostic data.
+        else {
+            // Get the cluster statistical banks.
+            ClusterStatModule lstat = localSnapshot.getClusterStats();
+            ClusterStatModule rstat = runSnapshot.getClusterStats();
+            
+            // Get the largest number of digits in any of the values.
+            int mostDigits = ComponentUtils.max(lstat.getReconClusterCount(), lstat.getSSPClusterCount(), lstat.getMatches(),
+                    lstat.getPositionFailures(), lstat.getEnergyFailures(), lstat.getHitCountFailures(),
+                    rstat.getReconClusterCount(), rstat.getSSPClusterCount(), rstat.getMatches(),
+                    rstat.getPositionFailures(), rstat.getEnergyFailures(), rstat.getHitCountFailures());
+            int spaces = ComponentUtils.getDigits(mostDigits);
+            
+            // Put the number of reconstructed and SSP clusters into
+            // the tables.
+            int[] clusterValue = {
+                    lstat.getReconClusterCount(),
+                    lstat.getSSPClusterCount(),
+                    rstat.getReconClusterCount(),
+                    rstat.getSSPClusterCount()
+            };
+            String countFormat = "%" + spaces + "d";
+            setLocalRowValue(ROW_RECON_COUNT,  String.format(countFormat, clusterValue[0]));
+            setLocalRowValue(ROW_SSP_COUNT,    String.format(countFormat, clusterValue[1]));
+            setGlobalRowValue(ROW_RECON_COUNT, String.format(countFormat, clusterValue[2]));
+            setGlobalRowValue(ROW_SSP_COUNT,   String.format(countFormat, clusterValue[3]));
+            
+            // Output the tracked statistical data.
+            int total;
+            String percentFormat = "%" + spaces + "d / %" + spaces + "d (%7.3f)";
+            int[] statValue = {
+                    lstat.getMatches(),
+                    lstat.getPositionFailures(),
+                    lstat.getEnergyFailures(),
+                    lstat.getHitCountFailures(),
+                    rstat.getMatches(),
+                    rstat.getPositionFailures(),
+                    rstat.getEnergyFailures(),
+                    rstat.getHitCountFailures()
+            };
+            
+            total = lstat.getReconClusterCount();
+            setLocalRowValue(ROW_MATCHED,          String.format(percentFormat, statValue[0], total, 100.0 * statValue[0] / total));
+            setLocalRowValue(ROW_FAILED_POSITION,  String.format(percentFormat, statValue[1], total, 100.0 * statValue[1] / total));
+            setLocalRowValue(ROW_FAILED_ENERGY,    String.format(percentFormat, statValue[2], total, 100.0 * statValue[2] / total));
+            setLocalRowValue(ROW_FAILED_HIT_COUNT, String.format(percentFormat, statValue[3], total, 100.0 * statValue[3] / total));
+            
+            total = rstat.getReconClusterCount();
+            setGlobalRowValue(ROW_MATCHED,          String.format(percentFormat, statValue[4], total, 100.0 * statValue[4] / total));
+            setGlobalRowValue(ROW_FAILED_POSITION,  String.format(percentFormat, statValue[5], total, 100.0 * statValue[5] / total));
+            setGlobalRowValue(ROW_FAILED_ENERGY,    String.format(percentFormat, statValue[6], total, 100.0 * statValue[6] / total));
+            setGlobalRowValue(ROW_FAILED_HIT_COUNT, String.format(percentFormat, statValue[7], total, 100.0 * statValue[7] / total));
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ComponentUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ComponentUtils.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ComponentUtils.java	Wed Apr 27 11:11:32 2016
@@ -11,116 +11,116 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class ComponentUtils {
-	/** The default spacing used between a horizontal edge of one
-	 * component and the horizontal edge of another. */
-	static final int hinternal = 10;
-	/** The default spacing used between a vertical edge of one
-	 * component and the vertical edge of another. */
-	static final int vinternal = 10;
-	/** The default spacing used between a horizontal edge of one
-	 * component and the edge of its parent component. */
-	static final int hexternal = 0;
-	/** The default spacing used between a vertical edge of one
-	 * component and the edge of its parent component. */
-	static final int vexternal = 0;
-	
-	/**
-	 * Gets a <code>String</code> composed of a number of instances of
-	 * character <code>c</code> equal to <code>number</code>.
-	 * @param c - The character to repeat.
-	 * @param number - The number of repetitions.
-	 * @return Returns the repeated character as a <code>String</code>.
-	 */
-	public static final String getChars(char c, int number) {
-		// Create a buffer to store the characters in.
-		StringBuffer s = new StringBuffer();
-		
-		// Add the indicated number of instances.
-		for(int i = 0; i < number; i++) {
-			s.append(c);
-		}
-		
-		// Return the string.
-		return s.toString();
-	}
-	
-	/**
-	 * Gets the number of digits in the base-10 String representation
-	 * of an integer primitive. Negative signs are not included in the
-	 * digit count.
-	 * @param value - The value of which to obtain the length.
-	 * @return Returns the number of digits in the String representation
-	 * of the argument value.
-	 */
-	public static final int getDigits(int value) {
-		return TriggerDiagnosticUtil.getDigits(value);
-	}
-	
-	/**
-	 * Gets the maximum value from a list of values.
-	 * @param values - The values to compare.
-	 * @return Returns the largest of the argument values.
-	 * @throws IllegalArgumentException Occurs if no values are given.
-	 */
-	public static final int max(int... values) throws IllegalArgumentException {
-		// Throw an error if no arguments are provided.
-		if(values == null || values.length == 0) {
-			throw new IllegalArgumentException("Can not determine maximum value from a list of 0 values.");
-		}
-		
-		// If there is only one value, return it.
-		if(values.length == 1) { return values[0]; }
-		
-		// Otherwise, get the largest value.
-		int largest = Integer.MIN_VALUE;
-		for(int value : values) {
-			if(value > largest) { largest = value; }
-		}
-		
-		// Return the result.
-		return largest;
-	}
-	
-	/**
-	 * Gets the x-coordinate immediately to the right of the given
-	 * component.
-	 * @param c - The component of which to find the edge.
-	 * @return Returns the x-coordinate as an <code>int</code> value.
-	 */
-	static final int getNextX(Component c) {
-		return getNextX(c, 0);
-	}
-	
-	/**
-	 * Gets the x-coordinate a given distance to the right edge of the
-	 * argument component.
-	 * @param c - The component of which to find the edge.
-	 * @param spacing - The additional spacing past the edge of the
-	 * component to add.
-	 * @return Returns the x-coordinate as an <code>int</code> value.
-	 */
-	static final int getNextX(Component c, int spacing) {
-		return c.getX() + c.getWidth() + spacing;
-	}
-	
-	/**
-	 * Gets the y-coordinate immediately below the given component.
-	 * @param c - The component of which to find the edge.
-	 * @return Returns the y-coordinate as an <code>int</code> value.
-	 */
-	static final int getNextY(Component c) {
-		return getNextY(c, 0);
-	}
-	
-	/**
-	 * Gets the y-coordinate a given distance below the bottom edge
-	 * of the argument component.
-	 * @param c - The component of which to find the edge.
-	 * @param spacing - The additional spacing past the edge of the
-	 * component to add.
-	 * @return Returns the y-coordinate as an <code>int</code> value.
-	 */
-	static final int getNextY(Component c, int spacing) {
-		return c.getY() + c.getHeight() + spacing;
-	}
+    /** The default spacing used between a horizontal edge of one
+     * component and the horizontal edge of another. */
+    static final int hinternal = 10;
+    /** The default spacing used between a vertical edge of one
+     * component and the vertical edge of another. */
+    static final int vinternal = 10;
+    /** The default spacing used between a horizontal edge of one
+     * component and the edge of its parent component. */
+    static final int hexternal = 0;
+    /** The default spacing used between a vertical edge of one
+     * component and the edge of its parent component. */
+    static final int vexternal = 0;
+    
+    /**
+     * Gets a <code>String</code> composed of a number of instances of
+     * character <code>c</code> equal to <code>number</code>.
+     * @param c - The character to repeat.
+     * @param number - The number of repetitions.
+     * @return Returns the repeated character as a <code>String</code>.
+     */
+    public static final String getChars(char c, int number) {
+        // Create a buffer to store the characters in.
+        StringBuffer s = new StringBuffer();
+        
+        // Add the indicated number of instances.
+        for(int i = 0; i < number; i++) {
+            s.append(c);
+        }
+        
+        // Return the string.
+        return s.toString();
+    }
+    
+    /**
+     * Gets the number of digits in the base-10 String representation
+     * of an integer primitive. Negative signs are not included in the
+     * digit count.
+     * @param value - The value of which to obtain the length.
+     * @return Returns the number of digits in the String representation
+     * of the argument value.
+     */
+    public static final int getDigits(int value) {
+        return TriggerDiagnosticUtil.getDigits(value);
+    }
+    
+    /**
+     * Gets the maximum value from a list of values.
+     * @param values - The values to compare.
+     * @return Returns the largest of the argument values.
+     * @throws IllegalArgumentException Occurs if no values are given.
+     */
+    public static final int max(int... values) throws IllegalArgumentException {
+        // Throw an error if no arguments are provided.
+        if(values == null || values.length == 0) {
+            throw new IllegalArgumentException("Can not determine maximum value from a list of 0 values.");
+        }
+        
+        // If there is only one value, return it.
+        if(values.length == 1) { return values[0]; }
+        
+        // Otherwise, get the largest value.
+        int largest = Integer.MIN_VALUE;
+        for(int value : values) {
+            if(value > largest) { largest = value; }
+        }
+        
+        // Return the result.
+        return largest;
+    }
+    
+    /**
+     * Gets the x-coordinate immediately to the right of the given
+     * component.
+     * @param c - The component of which to find the edge.
+     * @return Returns the x-coordinate as an <code>int</code> value.
+     */
+    static final int getNextX(Component c) {
+        return getNextX(c, 0);
+    }
+    
+    /**
+     * Gets the x-coordinate a given distance to the right edge of the
+     * argument component.
+     * @param c - The component of which to find the edge.
+     * @param spacing - The additional spacing past the edge of the
+     * component to add.
+     * @return Returns the x-coordinate as an <code>int</code> value.
+     */
+    static final int getNextX(Component c, int spacing) {
+        return c.getX() + c.getWidth() + spacing;
+    }
+    
+    /**
+     * Gets the y-coordinate immediately below the given component.
+     * @param c - The component of which to find the edge.
+     * @return Returns the y-coordinate as an <code>int</code> value.
+     */
+    static final int getNextY(Component c) {
+        return getNextY(c, 0);
+    }
+    
+    /**
+     * Gets the y-coordinate a given distance below the bottom edge
+     * of the argument component.
+     * @param c - The component of which to find the edge.
+     * @param spacing - The additional spacing past the edge of the
+     * component to add.
+     * @return Returns the y-coordinate as an <code>int</code> value.
+     */
+    static final int getNextY(Component c, int spacing) {
+        return c.getY() + c.getHeight() + spacing;
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/DiagnosticUpdatable.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/DiagnosticUpdatable.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/DiagnosticUpdatable.java	Wed Apr 27 11:11:32 2016
@@ -9,14 +9,15 @@
  * alter their displayed or constituent values.
  * 
  * @author Kyle McCarty <[log in to unmask]>
- * @see DiagSnapshot
+ * @see org.hps.analysis.trigger.data.DiagnosticSnapshot
  */
 public interface DiagnosticUpdatable {
-	/**
-	 * Updates the object with information from the trigger diagnostic
-	 * snapshot in the argument.
-	 * @param snapshot - The snapshot containing information with which
-	 * to update the object.
-	 */
-	public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot);
+    /**
+     * Updates the object with information from the trigger diagnostic
+     * snapshot in the argument.
+     * @param runSnapshot the accumulated snapshot
+     * @param localSnapshot The snapshot containing information with which
+     * to update the object. 
+     */
+    public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot);
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/EfficiencyTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/EfficiencyTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/EfficiencyTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -11,200 +11,200 @@
 import org.hps.analysis.trigger.util.ComponentUtils;
 
 public class EfficiencyTablePanel extends AbstractTablePanel implements DiagnosticUpdatable {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	
-	// Table models.
-	private TableTextModel localModel;
-	private TableTextModel globalModel;
-	
-	// Column/row reference variables.
-	private static final int ROWS = 7;
-	private static final int COLUMNS = 6;
-	/* private static final int COL_HEADER    = 0;
-	private static final int COL_SINGLES_0 = 1;
-	private static final int COL_SINGLES_1 = 2;
-	private static final int COL_PAIR_0    = 3;
-	private static final int COL_PAIR_1    = 4; */
-	private static final int COL_COUNT     = 5;
-	/* private static final int ROW_HEADER    = 0;
-	private static final int ROW_PULSER    = 1;
-	private static final int ROW_COSMIC    = 2;
-	private static final int ROW_SINGLES_0 = 3;
-	private static final int ROW_SINGLES_1 = 4;
-	private static final int ROW_PAIR_0    = 5;
-	private static final int ROW_PAIR_1    = 6; */
-	
-	// Global/local reference variables.
-	private static final int GLOBAL = 0;
-	private static final int LOCAL  = 1;
-	
-	// Trigger type reference variables.
-	private static final int TYPE_SINGLES_0 = TriggerStatModule.SINGLES_0;
-	private static final int TYPE_SINGLES_1 = TriggerStatModule.SINGLES_1;
-	private static final int TYPE_PAIR_0    = TriggerStatModule.PAIR_0;
-	private static final int TYPE_PAIR_1    = TriggerStatModule.PAIR_1;
-	
-	// Column/row header names.
-	private static final String[] COL_NAMES = {
-		"", "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Count"
-	};
-	private static final String[] ROW_NAMES = {
-		"", "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Pulser", "Cosmic"
-		//"", "Random", "Cosmic", "Singles 0", "Singles 1", "Pair 0", "Pair 1"
-	};
-	
-	/**
-	 * Instantiates a new <code>EfficiencyTablePanel</code>.
-	 */
-	public EfficiencyTablePanel() {
-		// Instantiate the superclass.
-		super();
-		
-		// Set the orientation to vertical.
-		setOrientation(ORIENTATION_VERTICAL);
-	}
-	
-	@Override
-	public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
-		// If there is no snapshot, the tables should all display an
-		// empty value.
-		if(runSnapshot == null || localSnapshot == null) {
-			for(int row = 1; row < ROWS; row++) {
-				for(int col = 1; col < COLUMNS; col++) {
-					localModel.setValueAt("---", row, col);
-					globalModel.setValueAt("---", row, col);
-				}
-			}
-		}
-		
-		// Otherwise, update the table cells from the snapshot data.
-		else {
-			// Get the efficiency modules.
-			DiagnosticSnapshot[] stat = new DiagnosticSnapshot[2];
-			stat[GLOBAL] = runSnapshot;
-			stat[LOCAL] = localSnapshot;
-			
-			// Get the trigger count for each trigger type for both the
-			// local and global snapshots.
-			int[][][] matched = new int[2][4][6];
-			int[][][] triggers = new int[2][4][6];
-			for(int i = 0; i < 2; i++) {
-				for(int triggerType = 0; triggerType < 6; triggerType++) {
-					// Get the total triggers seen for each type.
-					triggers[i][TYPE_SINGLES_0][triggerType] = stat[i].getSingles0Stats().getSSPSimulatedTriggers(triggerType);
-					triggers[i][TYPE_SINGLES_1][triggerType] = stat[i].getSingles1Stats().getSSPSimulatedTriggers(triggerType);
-					triggers[i][TYPE_PAIR_0][triggerType] = stat[i].getPair0Stats().getSSPSimulatedTriggers(triggerType);
-					triggers[i][TYPE_PAIR_1][triggerType] = stat[i].getPair1Stats().getSSPSimulatedTriggers(triggerType);
-					
-					// Get the total triggers matched for each type.
-					matched[i][TYPE_SINGLES_0][triggerType] = stat[i].getSingles0Stats().getMatchedSSPSimulatedTriggers(triggerType);
-					matched[i][TYPE_SINGLES_1][triggerType] = stat[i].getSingles1Stats().getMatchedSSPSimulatedTriggers(triggerType);
-					matched[i][TYPE_PAIR_0][triggerType] = stat[i].getPair0Stats().getMatchedSSPSimulatedTriggers(triggerType);
-					matched[i][TYPE_PAIR_1][triggerType] = stat[i].getPair1Stats().getMatchedSSPSimulatedTriggers(triggerType);
-				}
-			}
-			
-			// Determine the spacing needed to display the largest numerical
-			// cell value.
-			int numWidth = -1;
-			for(int tiTriggerType = 0; tiTriggerType < 6; tiTriggerType++) {
-				for(int seenTriggerType = 0; seenTriggerType < 4; seenTriggerType++) {
-					int rSize = ComponentUtils.getDigits(triggers[GLOBAL][seenTriggerType][tiTriggerType]);
-					int lSize = ComponentUtils.getDigits(triggers[LOCAL][seenTriggerType][tiTriggerType]);
-					numWidth = ComponentUtils.max(numWidth, rSize, lSize);
-				}
-			}
-			
-			// Generate the format string for the cells.
-			String format = "%" + numWidth + "d / %" + numWidth + "d";
-			
-			// Update the table.
-			for(int tiTriggerType = 0; tiTriggerType < 6; tiTriggerType++) {
-				// Fill the row/column combinations that hold trigger
-				// statistical information.
-				for(int seenTriggerType = 0; seenTriggerType < 4; seenTriggerType++) {
-					// Fill the local table cell.
-					String localText = String.format(format, matched[LOCAL][seenTriggerType][tiTriggerType],
-							triggers[LOCAL][seenTriggerType][tiTriggerType]);
-					if(triggers[LOCAL][seenTriggerType][tiTriggerType] == 0) {
-						localText = localText + " (  N/A  %)";
-					} else {
-						localText = String.format("%s (%7.3f%%)", localText,
-								(100.0 * matched[LOCAL][seenTriggerType][tiTriggerType] / triggers[LOCAL][seenTriggerType][tiTriggerType]));
-					}
-					localModel.setValueAt(localText, tiTriggerType + 1, seenTriggerType + 1);
-					
-					// Fill the global table cell.
-					String globalText = String.format(format, matched[GLOBAL][seenTriggerType][tiTriggerType],
-							triggers[GLOBAL][seenTriggerType][tiTriggerType]);
-					if(triggers[GLOBAL][seenTriggerType][tiTriggerType] == 0) {
-						globalText = globalText + " (  N/A  %)";
-					} else {
-						globalText = String.format("%s (%7.3f%%)", globalText,
-								(100.0 * matched[GLOBAL][seenTriggerType][tiTriggerType] / triggers[GLOBAL][seenTriggerType][tiTriggerType]));
-					}
-					globalModel.setValueAt(globalText, tiTriggerType + 1, seenTriggerType + 1);
-				}
-				
-				// Populate the count column.
-				localModel.setValueAt("" + stat[LOCAL].getTITriggers(tiTriggerType, true), tiTriggerType + 1, COL_COUNT);
-				globalModel.setValueAt("" + stat[GLOBAL].getTITriggers(tiTriggerType, true), tiTriggerType + 1, COL_COUNT);
-			}
-		}
-	}
-	
-	@Override
-	protected JTable[] initializeTables(Object... args) {
-		// Initialize the table models. There should be one row and
-		// one column for each type of trigger plus an additional one
-		// of each for headers.
-		localModel = new TableTextModel(ROWS, COLUMNS);
-		globalModel = new TableTextModel(ROWS, COLUMNS);
-		
-		// Set the column headers.
-		for(int col = 0; col < COLUMNS; col++) {
-			localModel.setValueAt(COL_NAMES[col], 0, col);
-			globalModel.setValueAt(COL_NAMES[col], 0, col);
-		}
-		
-		// Set the row headers.
-		for(int row = 0; row < ROWS; row++) {
-			localModel.setValueAt(ROW_NAMES[row], row, 0);
-			globalModel.setValueAt(ROW_NAMES[row], row, 0);
-		}
-		
-		// Make a cell renderer.
-		DefaultTableCellRenderer centerRenderer = new DefaultTableCellRenderer();
-		centerRenderer.setHorizontalAlignment(JLabel.CENTER);
-		
-		// Create JTable objects to display the data.
-		JTable localTable = new JTable(localModel);
-		localTable.setRowSelectionAllowed(false);
-		localTable.setColumnSelectionAllowed(false);
-		localTable.setCellSelectionEnabled(false);
-		localTable.setShowVerticalLines(false);
-		localTable.getColumnModel().getColumn(0).setMaxWidth(150);
-		localTable.getColumnModel().getColumn(COL_COUNT).setMaxWidth(150);
-		for(int col = 1; col < COLUMNS; col++) {
-			localTable.getColumnModel().getColumn(col).setCellRenderer(centerRenderer);
-		}
-		localTable.setFont(new Font("monospaced", localTable.getFont().getStyle(), localTable.getFont().getSize()));
-		
-		JTable globalTable = new JTable(globalModel);
-		globalTable.setRowSelectionAllowed(false);
-		globalTable.setColumnSelectionAllowed(false);
-		globalTable.setCellSelectionEnabled(false);
-		globalTable.setShowVerticalLines(false);
-		globalTable.getColumnModel().getColumn(0).setMaxWidth(150);
-		globalTable.getColumnModel().getColumn(COL_COUNT).setMaxWidth(150);
-		for(int col = 1; col < COLUMNS; col++) {
-			globalTable.getColumnModel().getColumn(col).setCellRenderer(centerRenderer);
-		}
-		globalTable.setFont(new Font("monospaced", globalTable.getFont().getStyle(), globalTable.getFont().getSize()));
-		
-		// Return the tables.
-		return new JTable[] { localTable, globalTable };
-	}
-	
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    
+    // Table models.
+    private TableTextModel localModel;
+    private TableTextModel globalModel;
+    
+    // Column/row reference variables.
+    private static final int ROWS = 7;
+    private static final int COLUMNS = 6;
+    /* private static final int COL_HEADER    = 0;
+    private static final int COL_SINGLES_0 = 1;
+    private static final int COL_SINGLES_1 = 2;
+    private static final int COL_PAIR_0    = 3;
+    private static final int COL_PAIR_1    = 4; */
+    private static final int COL_COUNT     = 5;
+    /* private static final int ROW_HEADER    = 0;
+    private static final int ROW_PULSER    = 1;
+    private static final int ROW_COSMIC    = 2;
+    private static final int ROW_SINGLES_0 = 3;
+    private static final int ROW_SINGLES_1 = 4;
+    private static final int ROW_PAIR_0    = 5;
+    private static final int ROW_PAIR_1    = 6; */
+    
+    // Global/local reference variables.
+    private static final int GLOBAL = 0;
+    private static final int LOCAL  = 1;
+    
+    // Trigger type reference variables.
+    private static final int TYPE_SINGLES_0 = TriggerStatModule.SINGLES_0;
+    private static final int TYPE_SINGLES_1 = TriggerStatModule.SINGLES_1;
+    private static final int TYPE_PAIR_0    = TriggerStatModule.PAIR_0;
+    private static final int TYPE_PAIR_1    = TriggerStatModule.PAIR_1;
+    
+    // Column/row header names.
+    private static final String[] COL_NAMES = {
+        "", "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Count"
+    };
+    private static final String[] ROW_NAMES = {
+        "", "Singles 0", "Singles 1", "Pair 0", "Pair 1", "Pulser", "Cosmic"
+        //"", "Random", "Cosmic", "Singles 0", "Singles 1", "Pair 0", "Pair 1"
+    };
+    
+    /**
+     * Instantiates a new <code>EfficiencyTablePanel</code>.
+     */
+    public EfficiencyTablePanel() {
+        // Instantiate the superclass.
+        super();
+        
+        // Set the orientation to vertical.
+        setOrientation(ORIENTATION_VERTICAL);
+    }
+    
+    @Override
+    public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
+        // If there is no snapshot, the tables should all display an
+        // empty value.
+        if(runSnapshot == null || localSnapshot == null) {
+            for(int row = 1; row < ROWS; row++) {
+                for(int col = 1; col < COLUMNS; col++) {
+                    localModel.setValueAt("---", row, col);
+                    globalModel.setValueAt("---", row, col);
+                }
+            }
+        }
+        
+        // Otherwise, update the table cells from the snapshot data.
+        else {
+            // Get the efficiency modules.
+            DiagnosticSnapshot[] stat = new DiagnosticSnapshot[2];
+            stat[GLOBAL] = runSnapshot;
+            stat[LOCAL] = localSnapshot;
+            
+            // Get the trigger count for each trigger type for both the
+            // local and global snapshots.
+            int[][][] matched = new int[2][4][6];
+            int[][][] triggers = new int[2][4][6];
+            for(int i = 0; i < 2; i++) {
+                for(int triggerType = 0; triggerType < 6; triggerType++) {
+                    // Get the total triggers seen for each type.
+                    triggers[i][TYPE_SINGLES_0][triggerType] = stat[i].getSingles0Stats().getSSPSimulatedTriggers(triggerType);
+                    triggers[i][TYPE_SINGLES_1][triggerType] = stat[i].getSingles1Stats().getSSPSimulatedTriggers(triggerType);
+                    triggers[i][TYPE_PAIR_0][triggerType] = stat[i].getPair0Stats().getSSPSimulatedTriggers(triggerType);
+                    triggers[i][TYPE_PAIR_1][triggerType] = stat[i].getPair1Stats().getSSPSimulatedTriggers(triggerType);
+                    
+                    // Get the total triggers matched for each type.
+                    matched[i][TYPE_SINGLES_0][triggerType] = stat[i].getSingles0Stats().getMatchedSSPSimulatedTriggers(triggerType);
+                    matched[i][TYPE_SINGLES_1][triggerType] = stat[i].getSingles1Stats().getMatchedSSPSimulatedTriggers(triggerType);
+                    matched[i][TYPE_PAIR_0][triggerType] = stat[i].getPair0Stats().getMatchedSSPSimulatedTriggers(triggerType);
+                    matched[i][TYPE_PAIR_1][triggerType] = stat[i].getPair1Stats().getMatchedSSPSimulatedTriggers(triggerType);
+                }
+            }
+            
+            // Determine the spacing needed to display the largest numerical
+            // cell value.
+            int numWidth = -1;
+            for(int tiTriggerType = 0; tiTriggerType < 6; tiTriggerType++) {
+                for(int seenTriggerType = 0; seenTriggerType < 4; seenTriggerType++) {
+                    int rSize = ComponentUtils.getDigits(triggers[GLOBAL][seenTriggerType][tiTriggerType]);
+                    int lSize = ComponentUtils.getDigits(triggers[LOCAL][seenTriggerType][tiTriggerType]);
+                    numWidth = ComponentUtils.max(numWidth, rSize, lSize);
+                }
+            }
+            
+            // Generate the format string for the cells.
+            String format = "%" + numWidth + "d / %" + numWidth + "d";
+            
+            // Update the table.
+            for(int tiTriggerType = 0; tiTriggerType < 6; tiTriggerType++) {
+                // Fill the row/column combinations that hold trigger
+                // statistical information.
+                for(int seenTriggerType = 0; seenTriggerType < 4; seenTriggerType++) {
+                    // Fill the local table cell.
+                    String localText = String.format(format, matched[LOCAL][seenTriggerType][tiTriggerType],
+                            triggers[LOCAL][seenTriggerType][tiTriggerType]);
+                    if(triggers[LOCAL][seenTriggerType][tiTriggerType] == 0) {
+                        localText = localText + " (  N/A  %)";
+                    } else {
+                        localText = String.format("%s (%7.3f%%)", localText,
+                                (100.0 * matched[LOCAL][seenTriggerType][tiTriggerType] / triggers[LOCAL][seenTriggerType][tiTriggerType]));
+                    }
+                    localModel.setValueAt(localText, tiTriggerType + 1, seenTriggerType + 1);
+                    
+                    // Fill the global table cell.
+                    String globalText = String.format(format, matched[GLOBAL][seenTriggerType][tiTriggerType],
+                            triggers[GLOBAL][seenTriggerType][tiTriggerType]);
+                    if(triggers[GLOBAL][seenTriggerType][tiTriggerType] == 0) {
+                        globalText = globalText + " (  N/A  %)";
+                    } else {
+                        globalText = String.format("%s (%7.3f%%)", globalText,
+                                (100.0 * matched[GLOBAL][seenTriggerType][tiTriggerType] / triggers[GLOBAL][seenTriggerType][tiTriggerType]));
+                    }
+                    globalModel.setValueAt(globalText, tiTriggerType + 1, seenTriggerType + 1);
+                }
+                
+                // Populate the count column.
+                localModel.setValueAt("" + stat[LOCAL].getTITriggers(tiTriggerType, true), tiTriggerType + 1, COL_COUNT);
+                globalModel.setValueAt("" + stat[GLOBAL].getTITriggers(tiTriggerType, true), tiTriggerType + 1, COL_COUNT);
+            }
+        }
+    }
+    
+    @Override
+    protected JTable[] initializeTables(Object... args) {
+        // Initialize the table models. There should be one row and
+        // one column for each type of trigger plus an additional one
+        // of each for headers.
+        localModel = new TableTextModel(ROWS, COLUMNS);
+        globalModel = new TableTextModel(ROWS, COLUMNS);
+        
+        // Set the column headers.
+        for(int col = 0; col < COLUMNS; col++) {
+            localModel.setValueAt(COL_NAMES[col], 0, col);
+            globalModel.setValueAt(COL_NAMES[col], 0, col);
+        }
+        
+        // Set the row headers.
+        for(int row = 0; row < ROWS; row++) {
+            localModel.setValueAt(ROW_NAMES[row], row, 0);
+            globalModel.setValueAt(ROW_NAMES[row], row, 0);
+        }
+        
+        // Make a cell renderer.
+        DefaultTableCellRenderer centerRenderer = new DefaultTableCellRenderer();
+        centerRenderer.setHorizontalAlignment(JLabel.CENTER);
+        
+        // Create JTable objects to display the data.
+        JTable localTable = new JTable(localModel);
+        localTable.setRowSelectionAllowed(false);
+        localTable.setColumnSelectionAllowed(false);
+        localTable.setCellSelectionEnabled(false);
+        localTable.setShowVerticalLines(false);
+        localTable.getColumnModel().getColumn(0).setMaxWidth(150);
+        localTable.getColumnModel().getColumn(COL_COUNT).setMaxWidth(150);
+        for(int col = 1; col < COLUMNS; col++) {
+            localTable.getColumnModel().getColumn(col).setCellRenderer(centerRenderer);
+        }
+        localTable.setFont(new Font("monospaced", localTable.getFont().getStyle(), localTable.getFont().getSize()));
+        
+        JTable globalTable = new JTable(globalModel);
+        globalTable.setRowSelectionAllowed(false);
+        globalTable.setColumnSelectionAllowed(false);
+        globalTable.setCellSelectionEnabled(false);
+        globalTable.setShowVerticalLines(false);
+        globalTable.getColumnModel().getColumn(0).setMaxWidth(150);
+        globalTable.getColumnModel().getColumn(COL_COUNT).setMaxWidth(150);
+        for(int col = 1; col < COLUMNS; col++) {
+            globalTable.getColumnModel().getColumn(col).setCellRenderer(centerRenderer);
+        }
+        globalTable.setFont(new Font("monospaced", globalTable.getFont().getStyle(), globalTable.getFont().getSize()));
+        
+        // Return the tables.
+        return new JTable[] { localTable, globalTable };
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/PairTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/PairTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/PairTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -7,14 +7,14 @@
  * @author Kyle McCarty
  */
 public class PairTablePanel extends AbstractTriggerTablePanel {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	private static final String[] CUT_NAMES = { "    Energy Sum:",
-		"    Energy Difference:", "    Energy Slope:", "    Coplanarity:" };
-	
-	/**
-	 * Instantiates a <code>PairTablePanel</code>.
-	 */
-	public PairTablePanel() { super(CUT_NAMES, false); }
-	
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    private static final String[] CUT_NAMES = { "    Energy Sum:",
+        "    Energy Difference:", "    Energy Slope:", "    Coplanarity:" };
+    
+    /**
+     * Instantiates a <code>PairTablePanel</code>.
+     */
+    public PairTablePanel() { super(CUT_NAMES, false); }
+    
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigPanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigPanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigPanel.java	Wed Apr 27 11:11:32 2016
@@ -12,291 +12,291 @@
 import org.hps.analysis.trigger.util.ComponentUtils;
 
 public class ShifterTrigPanel extends JPanel {
-	private static final Color BG_WARNING = new Color(255, 235, 20);
-	private static final Color BG_CRITICAL = new Color(230, 0, 0);
-	private static final Color FONT_WARNING = new Color(255, 157, 0);
-	private static final Color FONT_CRITICAL = new Color(117, 0, 0);
-	private static final long serialVersionUID = 1L;
-	
-	private JLabel panelTitle;
-	private JLabel[] fieldTitle;
-	private JLabel[] fieldValue;
-	
-	/**
-	 * Instantiates a new <code>ShifterTrigPanel</code> with the
-	 * indicated name.
-	 */
-	public ShifterTrigPanel(String name) {
-		// Instantiate a layout for the fields.
-		SpringLayout layout = new SpringLayout();
-		setLayout(layout);
-		
-		// Instantiate the header title.
-		panelTitle = new JLabel(name);
-		panelTitle.setVerticalAlignment(JLabel.CENTER);
-		panelTitle.setHorizontalAlignment(JLabel.CENTER);
-		add(panelTitle);
-		
-		// Instantiate the field title labels.
-		String[] titleName = { "Cluster Efficiency", "Singles 0 Logic Efficiency",
-				"Singles 0 Trigger Efficiency", "Singles 1 Logic Efficiency",
-				"Singles 1 Trigger Efficiency", "Pair 0 Logic Efficiency",
-				"Pair 0 Trigger Efficiency", "Pair 1 Logic Efficiency", "Pair 1 Trigger Efficiency" };
-		fieldTitle = new JLabel[titleName.length];
-		for(int index = 0; index < titleName.length; index++) {
-			fieldTitle[index] = new JLabel(titleName[index]);
-			fieldTitle[index].setVerticalAlignment(JLabel.CENTER);
-			fieldTitle[index].setHorizontalAlignment(JLabel.RIGHT);
-			fieldTitle[index].setOpaque(true);
-			add(fieldTitle[index]);
-		}
-		
-		// Instantiate the field value labels.
-		fieldValue = new JLabel[titleName.length];
-		for(int index = 0; index < titleName.length; index++) {
-			fieldValue[index] = new JLabel("");
-			fieldValue[index].setVerticalAlignment(JLabel.CENTER);
-			fieldValue[index].setHorizontalAlignment(JLabel.LEFT);
-			fieldValue[index].setOpaque(true);
-			add(fieldValue[index]);
-		}
-		
-		// Get the longest title.
-		int maxWidth = -1;
-		int maxIndex = -1;
-		for(int index = 0; index < titleName.length; index++) {
-			int width = fieldTitle[index].getFontMetrics(fieldTitle[index].getFont()).stringWidth(titleName[index]);
-			if(width > maxWidth) {
-				maxWidth = width;
-				maxIndex = index;
-			}
-		}
-		
-		// Define border edge and spacing variables.
-		String EAST = SpringLayout.EAST;
-		String WEST = SpringLayout.WEST;
-		String NORTH = SpringLayout.NORTH;
-		String SOUTH = SpringLayout.SOUTH;
-		int hinternal =  5;
-		int vinternal = 10;
-		int hexternal =  5;
-		int vexternal =  5;
-		
-		// Position the panel header.
-		layout.putConstraint(EAST,  panelTitle, hexternal, EAST,  this);
-		layout.putConstraint(WEST,  panelTitle, hexternal, WEST,  this);
-		layout.putConstraint(NORTH, panelTitle, vexternal, NORTH, this);
-		
-		// Position the field entries.
-		Component lastComp = panelTitle;
-		for(int index = 0; index < titleName.length; index++) {
-			// For all field titles except the largest, lock the right
-			// edge of the title to match the position of the largest
-			// title's right edge. The largest title is allowed to size
-			// itself to its preferred width.
-			if(index == maxIndex) {
-				layout.putConstraint(NORTH, fieldTitle[index], vinternal, SOUTH, lastComp);
-				layout.putConstraint(WEST,  fieldTitle[index], hexternal, WEST,  this);
-			} else {
-				layout.putConstraint(NORTH, fieldTitle[index], vinternal, SOUTH, lastComp);
-				layout.putConstraint(WEST,  fieldTitle[index], hexternal, WEST,  this);
-				layout.putConstraint(EAST,  fieldTitle[index],         0, EAST,  fieldTitle[maxIndex]);
-			}
-			
-			// Position the field value label to the right of the field
-			// title label. It should use up the remainder of the width
-			// allowed by the component.
-			layout.putConstraint(WEST,  fieldValue[index], hinternal, EAST,  fieldTitle[index]);
-			layout.putConstraint(EAST,  fieldValue[index], hexternal, EAST,  this);
-			layout.putConstraint(NORTH, fieldValue[index], vinternal, SOUTH, lastComp);
-			
-			// Update the "last component" to the current field title
-			// label.
-			lastComp = fieldTitle[index];
-		}
-		
-		// Update the fonts.
-		setFont(getFont());
-	}
-	
-	@Override
-	public void setBackground(Color bg) {
-		// Set the superclass background.
-		super.setBackground(bg);
-		
-		// Set the component backgrounds.
-		if(panelTitle != null) {
-			panelTitle.setBackground(bg);
-			for(int index = 0; index < fieldTitle.length; index++) {
-				fieldTitle[index].setBackground(bg);
-				
-				// If the field value label has a special alert color,
-				// then do not overwrite it.
-				if(!fieldValue[index].getBackground().equals(BG_WARNING)
-						&& !fieldValue[index].getBackground().equals(BG_CRITICAL)) {
-					fieldValue[index].setBackground(bg);
-				}
-			}
-		}
-	}
-	
-	@Override
-	public void setFont(Font font) {
-		// Set the superclass font.
-		super.setFont(font);
-		
-		// Set the component fonts.
-		if(panelTitle != null) {
-			panelTitle.setFont(font.deriveFont(Font.BOLD, (float) (font.getSize2D() * 1.5)));
-			for(int index = 0; index < fieldTitle.length; index++) {
-				fieldTitle[index].setFont(font.deriveFont(Font.BOLD));
-				fieldValue[index].setFont(font);
-			}
-		}
-	}
-	
-	@Override
-	public void setForeground(Color fg) {
-		// Set the superclass foreground.
-		super.setForeground(fg);
-		
-		// Set the component backgrounds.
-		if(panelTitle != null) {
-			panelTitle.setForeground(fg);
-			for(int index = 0; index < fieldTitle.length; index++) {
-				fieldTitle[index].setForeground(fg);
-				
-				// If the field value label has a special alert color,
-				// then do not overwrite it.
-				if(!fieldValue[index].getForeground().equals(FONT_WARNING)
-						&& !fieldValue[index].getForeground().equals(FONT_CRITICAL)) {
-					fieldValue[index].setBackground(fg);
-				}
-			}
-		}
-	}
-	
-	/**
-	 * Updates the panel statistical display with data from the
-	 * argument snapshot.
-	 * @param stat - The snapshot from which to derive statistical
-	 *               data.
-	 */
-	public void updatePanel(DiagnosticSnapshot stat) {
-		// If the snapshot is null, insert "null" values in the
-		// field panels,
-		if(stat == null) {
-			// Populate the fields with a "null" entry.
-			for(int index = 0; index < fieldValue.length; index++) {
-				fieldValue[index].setText("--- / --- (  N/A  %)");
-			}
-			
-			// No data exists, so no further processing is needed.
-			return;
-		}
-		
-		// Define index constants.
-		int RECON = 0;
-		int SSP = 1;
-		int TRIGGER_0 = 0;
-		int TRIGGER_1 = 1;
-		
-		// Get the tracked values from the snapshot.
-		int seenClusters = stat.getClusterStats().getReconClusterCount();
-		int[][] seenSinglesTriggers = {
-			{ stat.getSingles0Stats().getReconSimulatedTriggers(), stat.getSingles1Stats().getReconSimulatedTriggers() },
-			{ stat.getSingles0Stats().getSSPSimulatedTriggers(), stat.getSingles1Stats().getSSPSimulatedTriggers() }
-		};
-		int[][] seenPairTriggers = {
+    private static final Color BG_WARNING = new Color(255, 235, 20);
+    private static final Color BG_CRITICAL = new Color(230, 0, 0);
+    private static final Color FONT_WARNING = new Color(255, 157, 0);
+    private static final Color FONT_CRITICAL = new Color(117, 0, 0);
+    private static final long serialVersionUID = 1L;
+    
+    private JLabel panelTitle;
+    private JLabel[] fieldTitle;
+    private JLabel[] fieldValue;
+    
+    /**
+     * Instantiates a new <code>ShifterTrigPanel</code> with the
+     * indicated name.
+     */
+    public ShifterTrigPanel(String name) {
+        // Instantiate a layout for the fields.
+        SpringLayout layout = new SpringLayout();
+        setLayout(layout);
+        
+        // Instantiate the header title.
+        panelTitle = new JLabel(name);
+        panelTitle.setVerticalAlignment(JLabel.CENTER);
+        panelTitle.setHorizontalAlignment(JLabel.CENTER);
+        add(panelTitle);
+        
+        // Instantiate the field title labels.
+        String[] titleName = { "Cluster Efficiency", "Singles 0 Logic Efficiency",
+                "Singles 0 Trigger Efficiency", "Singles 1 Logic Efficiency",
+                "Singles 1 Trigger Efficiency", "Pair 0 Logic Efficiency",
+                "Pair 0 Trigger Efficiency", "Pair 1 Logic Efficiency", "Pair 1 Trigger Efficiency" };
+        fieldTitle = new JLabel[titleName.length];
+        for(int index = 0; index < titleName.length; index++) {
+            fieldTitle[index] = new JLabel(titleName[index]);
+            fieldTitle[index].setVerticalAlignment(JLabel.CENTER);
+            fieldTitle[index].setHorizontalAlignment(JLabel.RIGHT);
+            fieldTitle[index].setOpaque(true);
+            add(fieldTitle[index]);
+        }
+        
+        // Instantiate the field value labels.
+        fieldValue = new JLabel[titleName.length];
+        for(int index = 0; index < titleName.length; index++) {
+            fieldValue[index] = new JLabel("");
+            fieldValue[index].setVerticalAlignment(JLabel.CENTER);
+            fieldValue[index].setHorizontalAlignment(JLabel.LEFT);
+            fieldValue[index].setOpaque(true);
+            add(fieldValue[index]);
+        }
+        
+        // Get the longest title.
+        int maxWidth = -1;
+        int maxIndex = -1;
+        for(int index = 0; index < titleName.length; index++) {
+            int width = fieldTitle[index].getFontMetrics(fieldTitle[index].getFont()).stringWidth(titleName[index]);
+            if(width > maxWidth) {
+                maxWidth = width;
+                maxIndex = index;
+            }
+        }
+        
+        // Define border edge and spacing variables.
+        String EAST = SpringLayout.EAST;
+        String WEST = SpringLayout.WEST;
+        String NORTH = SpringLayout.NORTH;
+        String SOUTH = SpringLayout.SOUTH;
+        int hinternal =  5;
+        int vinternal = 10;
+        int hexternal =  5;
+        int vexternal =  5;
+        
+        // Position the panel header.
+        layout.putConstraint(EAST,  panelTitle, hexternal, EAST,  this);
+        layout.putConstraint(WEST,  panelTitle, hexternal, WEST,  this);
+        layout.putConstraint(NORTH, panelTitle, vexternal, NORTH, this);
+        
+        // Position the field entries.
+        Component lastComp = panelTitle;
+        for(int index = 0; index < titleName.length; index++) {
+            // For all field titles except the largest, lock the right
+            // edge of the title to match the position of the largest
+            // title's right edge. The largest title is allowed to size
+            // itself to its preferred width.
+            if(index == maxIndex) {
+                layout.putConstraint(NORTH, fieldTitle[index], vinternal, SOUTH, lastComp);
+                layout.putConstraint(WEST,  fieldTitle[index], hexternal, WEST,  this);
+            } else {
+                layout.putConstraint(NORTH, fieldTitle[index], vinternal, SOUTH, lastComp);
+                layout.putConstraint(WEST,  fieldTitle[index], hexternal, WEST,  this);
+                layout.putConstraint(EAST,  fieldTitle[index],         0, EAST,  fieldTitle[maxIndex]);
+            }
+            
+            // Position the field value label to the right of the field
+            // title label. It should use up the remainder of the width
+            // allowed by the component.
+            layout.putConstraint(WEST,  fieldValue[index], hinternal, EAST,  fieldTitle[index]);
+            layout.putConstraint(EAST,  fieldValue[index], hexternal, EAST,  this);
+            layout.putConstraint(NORTH, fieldValue[index], vinternal, SOUTH, lastComp);
+            
+            // Update the "last component" to the current field title
+            // label.
+            lastComp = fieldTitle[index];
+        }
+        
+        // Update the fonts.
+        setFont(getFont());
+    }
+    
+    @Override
+    public void setBackground(Color bg) {
+        // Set the superclass background.
+        super.setBackground(bg);
+        
+        // Set the component backgrounds.
+        if(panelTitle != null) {
+            panelTitle.setBackground(bg);
+            for(int index = 0; index < fieldTitle.length; index++) {
+                fieldTitle[index].setBackground(bg);
+                
+                // If the field value label has a special alert color,
+                // then do not overwrite it.
+                if(!fieldValue[index].getBackground().equals(BG_WARNING)
+                        && !fieldValue[index].getBackground().equals(BG_CRITICAL)) {
+                    fieldValue[index].setBackground(bg);
+                }
+            }
+        }
+    }
+    
+    @Override
+    public void setFont(Font font) {
+        // Set the superclass font.
+        super.setFont(font);
+        
+        // Set the component fonts.
+        if(panelTitle != null) {
+            panelTitle.setFont(font.deriveFont(Font.BOLD, (float) (font.getSize2D() * 1.5)));
+            for(int index = 0; index < fieldTitle.length; index++) {
+                fieldTitle[index].setFont(font.deriveFont(Font.BOLD));
+                fieldValue[index].setFont(font);
+            }
+        }
+    }
+    
+    @Override
+    public void setForeground(Color fg) {
+        // Set the superclass foreground.
+        super.setForeground(fg);
+        
+        // Set the component backgrounds.
+        if(panelTitle != null) {
+            panelTitle.setForeground(fg);
+            for(int index = 0; index < fieldTitle.length; index++) {
+                fieldTitle[index].setForeground(fg);
+                
+                // If the field value label has a special alert color,
+                // then do not overwrite it.
+                if(!fieldValue[index].getForeground().equals(FONT_WARNING)
+                        && !fieldValue[index].getForeground().equals(FONT_CRITICAL)) {
+                    fieldValue[index].setBackground(fg);
+                }
+            }
+        }
+    }
+    
+    /**
+     * Updates the panel statistical display with data from the
+     * argument snapshot.
+     * @param stat - The snapshot from which to derive statistical
+     *               data.
+     */
+    public void updatePanel(DiagnosticSnapshot stat) {
+        // If the snapshot is null, insert "null" values in the
+        // field panels,
+        if(stat == null) {
+            // Populate the fields with a "null" entry.
+            for(int index = 0; index < fieldValue.length; index++) {
+                fieldValue[index].setText("--- / --- (  N/A  %)");
+            }
+            
+            // No data exists, so no further processing is needed.
+            return;
+        }
+        
+        // Define index constants.
+        int RECON = 0;
+        int SSP = 1;
+        int TRIGGER_0 = 0;
+        int TRIGGER_1 = 1;
+        
+        // Get the tracked values from the snapshot.
+        int seenClusters = stat.getClusterStats().getReconClusterCount();
+        int[][] seenSinglesTriggers = {
+            { stat.getSingles0Stats().getReconSimulatedTriggers(), stat.getSingles1Stats().getReconSimulatedTriggers() },
+            { stat.getSingles0Stats().getSSPSimulatedTriggers(), stat.getSingles1Stats().getSSPSimulatedTriggers() }
+        };
+        int[][] seenPairTriggers = {
                         { stat.getPair0Stats().getReconSimulatedTriggers(), stat.getPair1Stats().getReconSimulatedTriggers() },
                         { stat.getPair0Stats().getSSPSimulatedTriggers(), stat.getPair1Stats().getSSPSimulatedTriggers() }
-		};
-		int matchedClusters = stat.getClusterStats().getMatches();
-		int[][] matchedSinglesTriggers = {
+        };
+        int matchedClusters = stat.getClusterStats().getMatches();
+        int[][] matchedSinglesTriggers = {
                         { stat.getSingles0Stats().getMatchedReconSimulatedTriggers(), stat.getSingles1Stats().getMatchedReconSimulatedTriggers() },
                         { stat.getSingles0Stats().getMatchedSSPSimulatedTriggers(), stat.getSingles1Stats().getMatchedSSPSimulatedTriggers() }
-		};
-		int[][] matchedPairTriggers = {
+        };
+        int[][] matchedPairTriggers = {
                         { stat.getPair0Stats().getMatchedReconSimulatedTriggers(), stat.getPair1Stats().getMatchedReconSimulatedTriggers() },
                         { stat.getPair0Stats().getMatchedSSPSimulatedTriggers(), stat.getPair1Stats().getMatchedSSPSimulatedTriggers() }
-		};
-		
-		// Get the largest digit of the tracked values. This should
-		// always be one of the "seen" values.
-		int mostDigits = ComponentUtils.max(seenClusters, seenSinglesTriggers[0][0], seenSinglesTriggers[0][1],
-				seenSinglesTriggers[1][0], seenSinglesTriggers[1][1], seenPairTriggers[0][0], seenPairTriggers[0][1],
-				seenPairTriggers[1][0], seenPairTriggers[1][1]);
-		int spaces = ComponentUtils.getDigits(mostDigits);
-		
-		// Populate the cluster field panel.
-		processEfficiency(seenClusters, matchedClusters, 0, spaces, 0.98, 0.94);
-		
-		// Populate the singles trigger field panels.
-		processEfficiency(seenSinglesTriggers[RECON][TRIGGER_0], matchedSinglesTriggers[RECON][TRIGGER_0], 1, spaces, 0.99, 0.95);
+        };
+        
+        // Get the largest digit of the tracked values. This should
+        // always be one of the "seen" values.
+        int mostDigits = ComponentUtils.max(seenClusters, seenSinglesTriggers[0][0], seenSinglesTriggers[0][1],
+                seenSinglesTriggers[1][0], seenSinglesTriggers[1][1], seenPairTriggers[0][0], seenPairTriggers[0][1],
+                seenPairTriggers[1][0], seenPairTriggers[1][1]);
+        int spaces = ComponentUtils.getDigits(mostDigits);
+        
+        // Populate the cluster field panel.
+        processEfficiency(seenClusters, matchedClusters, 0, spaces, 0.98, 0.94);
+        
+        // Populate the singles trigger field panels.
+        processEfficiency(seenSinglesTriggers[RECON][TRIGGER_0], matchedSinglesTriggers[RECON][TRIGGER_0], 1, spaces, 0.99, 0.95);
                 processEfficiency(seenSinglesTriggers[SSP][TRIGGER_0],   matchedSinglesTriggers[SSP][TRIGGER_0],   2, spaces, 0.99, 0.95);
                 processEfficiency(seenSinglesTriggers[RECON][TRIGGER_1], matchedSinglesTriggers[RECON][TRIGGER_1], 3, spaces, 0.99, 0.95);
                 processEfficiency(seenSinglesTriggers[SSP][TRIGGER_1],   matchedSinglesTriggers[SSP][TRIGGER_1],   4, spaces, 0.99, 0.95);
-		
-		// Populate the pair trigger field panels.
-		processEfficiency(seenPairTriggers[RECON][TRIGGER_0], matchedPairTriggers[RECON][TRIGGER_0], 5, spaces, 0.99, 0.95);
+        
+        // Populate the pair trigger field panels.
+        processEfficiency(seenPairTriggers[RECON][TRIGGER_0], matchedPairTriggers[RECON][TRIGGER_0], 5, spaces, 0.99, 0.95);
                 processEfficiency(seenPairTriggers[SSP][TRIGGER_0],   matchedPairTriggers[SSP][TRIGGER_0],   6, spaces, 0.99, 0.95);
                 processEfficiency(seenPairTriggers[RECON][TRIGGER_1], matchedPairTriggers[RECON][TRIGGER_1], 7, spaces, 0.99, 0.95);
                 processEfficiency(seenPairTriggers[SSP][TRIGGER_1],   matchedPairTriggers[SSP][TRIGGER_1],   8, spaces, 0.99, 0.95);
-	}
-	
-	/**
-	 * Updates the indicated field value using the indicated number
-	 * seen and matched elements. Automatically handles the special
-	 * case of zero seen elements and also updates the colors of the
-	 * field labels to the appropriate color based on the efficiency
-	 * and the thresholds for warnings.
-	 * @param seen - The number of elements seen.
-	 * @param matched - The number of elements matched.
-	 * @param fieldIndex - The index for the field that should display
-	 *                     the statistical data.
-	 * @param spaces - The number of spaces to giveto each displayed
-	 *                 value.
-	 * @param threshWarning - The threshold at which the "warning
-	 *                        color should be used.
-	 * @param threshCritical - The threshold at which the "critical"
-	 *                         color should be used.
-	 */
-	private void processEfficiency(int seen, int matched, int fieldIndex, int spaces, double threshWarning, double threshCritical) {
-		// Calculate the efficiency.
-		double efficiency = 100.0 * matched / seen;
-		
-		// Create the format string.
-		String format = "%" + spaces + "d / %";
-		
-		// If the number of values seen is zero, there is no
-		// percentage that can be calculated.
-		if(seen == 0) {
-			fieldValue[fieldIndex].setText(String.format(format + " (  N/A  %%)", seen, matched));
-		}
-		
-		// Otherwise, include the percentage.
-		else {
-			fieldValue[fieldIndex].setText(String.format(format + " (7.3f%%)", seen, matched, efficiency));
-		}
-		
-		// If the efficiency is below the critical threshold,
-		// change the field background to the critical color.
-		if(efficiency < threshCritical) {
-			fieldValue[fieldIndex].setBackground(BG_CRITICAL);
-			fieldValue[fieldIndex].setForeground(FONT_CRITICAL);
-		}
-		
-		// Otherwise, if the efficiency is below the warning
-		// level, set the field background to the warning color.
-		else if(efficiency < threshWarning) {
-			fieldValue[fieldIndex].setBackground(BG_WARNING);
-			fieldValue[fieldIndex].setForeground(FONT_WARNING);
-		}
-		
-		// Otherwise, use the default component background.
-		else {
-			fieldValue[fieldIndex].setBackground(getBackground());
-			fieldValue[fieldIndex].setForeground(getForeground());
-		}
-	}
+    }
+    
+    /**
+     * Updates the indicated field value using the indicated number
+     * seen and matched elements. Automatically handles the special
+     * case of zero seen elements and also updates the colors of the
+     * field labels to the appropriate color based on the efficiency
+     * and the thresholds for warnings.
+     * @param seen - The number of elements seen.
+     * @param matched - The number of elements matched.
+     * @param fieldIndex - The index for the field that should display
+     *                     the statistical data.
+     * @param spaces - The number of spaces to giveto each displayed
+     *                 value.
+     * @param threshWarning - The threshold at which the "warning
+     *                        color should be used.
+     * @param threshCritical - The threshold at which the "critical"
+     *                         color should be used.
+     */
+    private void processEfficiency(int seen, int matched, int fieldIndex, int spaces, double threshWarning, double threshCritical) {
+        // Calculate the efficiency.
+        double efficiency = 100.0 * matched / seen;
+        
+        // Create the format string.
+        String format = "%" + spaces + "d / %";
+        
+        // If the number of values seen is zero, there is no
+        // percentage that can be calculated.
+        if(seen == 0) {
+            fieldValue[fieldIndex].setText(String.format(format + " (  N/A  %%)", seen, matched));
+        }
+        
+        // Otherwise, include the percentage.
+        else {
+            fieldValue[fieldIndex].setText(String.format(format + " (7.3f%%)", seen, matched, efficiency));
+        }
+        
+        // If the efficiency is below the critical threshold,
+        // change the field background to the critical color.
+        if(efficiency < threshCritical) {
+            fieldValue[fieldIndex].setBackground(BG_CRITICAL);
+            fieldValue[fieldIndex].setForeground(FONT_CRITICAL);
+        }
+        
+        // Otherwise, if the efficiency is below the warning
+        // level, set the field background to the warning color.
+        else if(efficiency < threshWarning) {
+            fieldValue[fieldIndex].setBackground(BG_WARNING);
+            fieldValue[fieldIndex].setForeground(FONT_WARNING);
+        }
+        
+        // Otherwise, use the default component background.
+        else {
+            fieldValue[fieldIndex].setBackground(getBackground());
+            fieldValue[fieldIndex].setForeground(getForeground());
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigWindow.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigWindow.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/ShifterTrigWindow.java	Wed Apr 27 11:11:32 2016
@@ -12,25 +12,25 @@
  * to either yellow or red if the efficiencies drop too low.
  */
 public class ShifterTrigWindow extends JPanel implements DiagnosticUpdatable {
-	private static final long serialVersionUID = 1L;
-	private ShifterTrigPanel localPanel = new ShifterTrigPanel("Instantaneous");
-	private ShifterTrigPanel globalPanel = new ShifterTrigPanel("Run-Integrated");
-	
-	/**
-	 * Instantiates a new panel for displaying basic information
-	 * pertaining to trigger diagnostics.
-	 */
-	public ShifterTrigWindow() {
-		setLayout(new GridLayout(1, 2));
-		add(localPanel);
-		add(globalPanel);
-		updatePanel(null, null);
-	}
-	
-	@Override
-	public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
-		// Update each panel with the appropriate snapshot.
-		localPanel.updatePanel(localSnapshot);
-		globalPanel.updatePanel(runSnapshot);
-	}
+    private static final long serialVersionUID = 1L;
+    private ShifterTrigPanel localPanel = new ShifterTrigPanel("Instantaneous");
+    private ShifterTrigPanel globalPanel = new ShifterTrigPanel("Run-Integrated");
+    
+    /**
+     * Instantiates a new panel for displaying basic information
+     * pertaining to trigger diagnostics.
+     */
+    public ShifterTrigWindow() {
+        setLayout(new GridLayout(1, 2));
+        add(localPanel);
+        add(globalPanel);
+        updatePanel(null, null);
+    }
+    
+    @Override
+    public void updatePanel(DiagnosticSnapshot runSnapshot, DiagnosticSnapshot localSnapshot) {
+        // Update each panel with the appropriate snapshot.
+        localPanel.updatePanel(localSnapshot);
+        globalPanel.updatePanel(runSnapshot);
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/SinglesTablePanel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/SinglesTablePanel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/SinglesTablePanel.java	Wed Apr 27 11:11:32 2016
@@ -7,14 +7,14 @@
  * @author Kyle McCarty
  */
 public class SinglesTablePanel extends AbstractTriggerTablePanel {
-	// Static variables.
-	private static final long serialVersionUID = 0L;
-	private static final String[] CUT_NAMES = { "    Cluster Energy (Low):",
-		"    Cluster Energy (High):", "    Hit Count:"  };
-	
-	/**
-	 * Instantiates a <code>SinglesTablePanel</code>.
-	 */
-	public SinglesTablePanel() { super(CUT_NAMES, true); }
-	
+    // Static variables.
+    private static final long serialVersionUID = 0L;
+    private static final String[] CUT_NAMES = { "    Cluster Energy (Low):",
+        "    Cluster Energy (High):", "    Hit Count:"  };
+    
+    /**
+     * Instantiates a <code>SinglesTablePanel</code>.
+     */
+    public SinglesTablePanel() { super(CUT_NAMES, true); }
+    
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TableTextModel.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TableTextModel.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TableTextModel.java	Wed Apr 27 11:11:32 2016
@@ -11,96 +11,96 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class TableTextModel extends AbstractTableModel {
-	// Serial UID.
-	private static final long serialVersionUID = 0L;
-	
-	// Stored values.
-	private final int rows, columns;
-	private final String[][] values;
-	
-	/**
-	 * Instantiates a new <code>TableTextModel</code> with the indicated
-	 * number of rows and columns.
-	 * @param rows - The number of rows.
-	 * @param columns - The number of columns.
-	 */
-	public TableTextModel(int rows, int columns) {
-		// Make sure that the arguments for rows and columns are valid.
-		if(rows < 1) {
-			throw new IllegalArgumentException("TableTextModel must have at least one row.");
-		} else 	if(columns < 1) {
-			throw new IllegalArgumentException("TableTextModel must have at least one column.");
-		}
-		
-		// Define the number of rows and columns.
-		this.rows = rows;
-		this.columns = columns;
-		
-		// Instantiate the data storage array.
-		values = new String[rows][columns];
-	}
-	
-	@Override
-	public int getRowCount() { return rows; }
-	
-	@Override
-	public int getColumnCount() { return columns; }
-	
-	@Override
-	public Object getValueAt(int rowIndex, int columnIndex) {
-		// Ensure that the value is within the allowed range.
-		validateIndex(rowIndex, columnIndex);
-		
-		// Return the value.
-		return values[rowIndex][columnIndex];
-	}
-	
-	@Override
-	public void setValueAt(Object value, int rowIndex, int columnIndex) {
-		// If the object is a string, pass it to the preferred handler.
-		// This can also be performed if the value is null.
-		if(value == null || value instanceof String) {
-			setValueAt((String) value, rowIndex, columnIndex);
-		}
-		
-		// Otherwise, cast the object to a string and use that instead.
-		else { setValueAt(value.toString(), rowIndex, columnIndex); }
-	}
-	
-	/**
-	 * Sets the text for the indicated column and row of the table.
-	 * @param value - The new text.
-	 * @param rowIndex - The row.
-	 * @param columnIndex - The column.
-	 * @throws IndexOutOfBoundsException Occurs if the row and column
-	 * are not a valid member of table model.
-	 */
-	public void setValueAt(String value, int rowIndex, int columnIndex) throws IndexOutOfBoundsException {
-		// Ensure that the value is within the allowed range.
-		validateIndex(rowIndex, columnIndex);
-		
-		// Set the value.
-		values[rowIndex][columnIndex] = value;
-		
-		// Update the table.
-		this.fireTableCellUpdated(rowIndex, columnIndex);
-	}
-	
-	/**
-	 * Checks to make sure that a given row/column pointer refers to
-	 * an extant position in the data array. In the event that the row
-	 * and column values are not valid, an <code>IndexOutOfBounds</code>
-	 * exception is thrown.
-	 * @param rowIndex - The row index.
-	 * @param columnIndex - The column index.
-	 * @throws IndexOutOfBoundsException Occurs if the row and column
-	 * are not a valid member of the data array.
-	 */
-	private void validateIndex(int rowIndex, int columnIndex) throws IndexOutOfBoundsException {
-		if(rowIndex < 0 || rowIndex >= getRowCount()) {
-			throw new IndexOutOfBoundsException(String.format("Row index %d is out of bounds.", rowIndex));
-		} else if(columnIndex < 0 || columnIndex >= getColumnCount()) {
-			throw new IndexOutOfBoundsException(String.format("Column index %d is out of bounds.", columnIndex));
-		}
-	}
+    // Serial UID.
+    private static final long serialVersionUID = 0L;
+    
+    // Stored values.
+    private final int rows, columns;
+    private final String[][] values;
+    
+    /**
+     * Instantiates a new <code>TableTextModel</code> with the indicated
+     * number of rows and columns.
+     * @param rows - The number of rows.
+     * @param columns - The number of columns.
+     */
+    public TableTextModel(int rows, int columns) {
+        // Make sure that the arguments for rows and columns are valid.
+        if(rows < 1) {
+            throw new IllegalArgumentException("TableTextModel must have at least one row.");
+        } else  if(columns < 1) {
+            throw new IllegalArgumentException("TableTextModel must have at least one column.");
+        }
+        
+        // Define the number of rows and columns.
+        this.rows = rows;
+        this.columns = columns;
+        
+        // Instantiate the data storage array.
+        values = new String[rows][columns];
+    }
+    
+    @Override
+    public int getRowCount() { return rows; }
+    
+    @Override
+    public int getColumnCount() { return columns; }
+    
+    @Override
+    public Object getValueAt(int rowIndex, int columnIndex) {
+        // Ensure that the value is within the allowed range.
+        validateIndex(rowIndex, columnIndex);
+        
+        // Return the value.
+        return values[rowIndex][columnIndex];
+    }
+    
+    @Override
+    public void setValueAt(Object value, int rowIndex, int columnIndex) {
+        // If the object is a string, pass it to the preferred handler.
+        // This can also be performed if the value is null.
+        if(value == null || value instanceof String) {
+            setValueAt((String) value, rowIndex, columnIndex);
+        }
+        
+        // Otherwise, cast the object to a string and use that instead.
+        else { setValueAt(value.toString(), rowIndex, columnIndex); }
+    }
+    
+    /**
+     * Sets the text for the indicated column and row of the table.
+     * @param value - The new text.
+     * @param rowIndex - The row.
+     * @param columnIndex - The column.
+     * @throws IndexOutOfBoundsException Occurs if the row and column
+     * are not a valid member of table model.
+     */
+    public void setValueAt(String value, int rowIndex, int columnIndex) throws IndexOutOfBoundsException {
+        // Ensure that the value is within the allowed range.
+        validateIndex(rowIndex, columnIndex);
+        
+        // Set the value.
+        values[rowIndex][columnIndex] = value;
+        
+        // Update the table.
+        this.fireTableCellUpdated(rowIndex, columnIndex);
+    }
+    
+    /**
+     * Checks to make sure that a given row/column pointer refers to
+     * an extant position in the data array. In the event that the row
+     * and column values are not valid, an <code>IndexOutOfBounds</code>
+     * exception is thrown.
+     * @param rowIndex - The row index.
+     * @param columnIndex - The column index.
+     * @throws IndexOutOfBoundsException Occurs if the row and column
+     * are not a valid member of the data array.
+     */
+    private void validateIndex(int rowIndex, int columnIndex) throws IndexOutOfBoundsException {
+        if(rowIndex < 0 || rowIndex >= getRowCount()) {
+            throw new IndexOutOfBoundsException(String.format("Row index %d is out of bounds.", rowIndex));
+        } else if(columnIndex < 0 || columnIndex >= getColumnCount()) {
+            throw new IndexOutOfBoundsException(String.format("Column index %d is out of bounds.", columnIndex));
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TriggerDiagnosticGUIDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TriggerDiagnosticGUIDriver.java	(original)
+++ java/branches/HPSJAVA-409/monitoring-util/src/main/java/org/hps/monitoring/trigger/TriggerDiagnosticGUIDriver.java	Wed Apr 27 11:11:32 2016
@@ -9,45 +9,45 @@
 import org.lcsim.util.Driver;
 
 public class TriggerDiagnosticGUIDriver extends Driver {
-	private JFrame window = new JFrame();
-	private ClusterTablePanel clusterTable = new ClusterTablePanel();
-	private SinglesTablePanel singlesTable = new SinglesTablePanel();
-	private PairTablePanel pairTable = new PairTablePanel();
-	private EfficiencyTablePanel efficiencyTable = new EfficiencyTablePanel();
-	private String diagnosticCollectionName = "DiagnosticSnapshot";
-	
-	@Override
-	public void startOfData() {
-		window.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-		window.setSize(500, 400);
-		//window.add(clusterTable);
-		//window.add(singlesTable);
-		//window.add(pairTable);
-		window.add(efficiencyTable);
-		window.setVisible(true);
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Updates are only performed if a diagnostic snapshot object
-		// exists. Otherwise, do nothing.
-		if(event.hasCollection(DiagnosticSnapshot.class, diagnosticCollectionName)) {
-			// Get the snapshot collection.
-			List<DiagnosticSnapshot> snapshotList = event.get(DiagnosticSnapshot.class, diagnosticCollectionName);
-			
-			// Get the snapshot. There will only ever be one.
-			DiagnosticSnapshot runSnapshot = snapshotList.get(1);
-			DiagnosticSnapshot localSnapshot = snapshotList.get(0);
-			
-			// Feed it to the table.
-			clusterTable.updatePanel(runSnapshot, localSnapshot);
-			singlesTable.updatePanel(runSnapshot, localSnapshot);
-			pairTable.updatePanel(runSnapshot, localSnapshot);
-			efficiencyTable.updatePanel(runSnapshot, localSnapshot);
-		}
-	}
-	
-	public void setDiagnosticCollectionName(String name) {
-		diagnosticCollectionName = name;
-	}
+    private JFrame window = new JFrame();
+    private ClusterTablePanel clusterTable = new ClusterTablePanel();
+    private SinglesTablePanel singlesTable = new SinglesTablePanel();
+    private PairTablePanel pairTable = new PairTablePanel();
+    private EfficiencyTablePanel efficiencyTable = new EfficiencyTablePanel();
+    private String diagnosticCollectionName = "DiagnosticSnapshot";
+    
+    @Override
+    public void startOfData() {
+        window.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        window.setSize(500, 400);
+        //window.add(clusterTable);
+        //window.add(singlesTable);
+        //window.add(pairTable);
+        window.add(efficiencyTable);
+        window.setVisible(true);
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Updates are only performed if a diagnostic snapshot object
+        // exists. Otherwise, do nothing.
+        if(event.hasCollection(DiagnosticSnapshot.class, diagnosticCollectionName)) {
+            // Get the snapshot collection.
+            List<DiagnosticSnapshot> snapshotList = event.get(DiagnosticSnapshot.class, diagnosticCollectionName);
+            
+            // Get the snapshot. There will only ever be one.
+            DiagnosticSnapshot runSnapshot = snapshotList.get(1);
+            DiagnosticSnapshot localSnapshot = snapshotList.get(0);
+            
+            // Feed it to the table.
+            clusterTable.updatePanel(runSnapshot, localSnapshot);
+            singlesTable.updatePanel(runSnapshot, localSnapshot);
+            pairTable.updatePanel(runSnapshot, localSnapshot);
+            efficiencyTable.updatePanel(runSnapshot, localSnapshot);
+        }
+    }
+    
+    public void setDiagnosticCollectionName(String name) {
+        diagnosticCollectionName = name;
+    }
 }

Modified: java/branches/HPSJAVA-409/parent/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/parent/pom.xml	(original)
+++ java/branches/HPSJAVA-409/parent/pom.xml	Wed Apr 27 11:11:32 2016
@@ -6,13 +6,14 @@
     <groupId>org.hps</groupId>
     <artifactId>hps-parent</artifactId>
     <packaging>pom</packaging>
-    <version>3.4.2-SNAPSHOT</version>
+    <version>3.9-SNAPSHOT</version>
     <name>parent</name>
     <description>HPS Java parent POM</description>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <org.lcsim.cacheDir>${user.home}</org.lcsim.cacheDir>
-        <lcsimVersion>3.1.6-SNAPSHOT</lcsimVersion>
+        <lcsimVersion>3.6</lcsimVersion>
         <skipSite>false</skipSite>
         <skipPlugin>false</skipPlugin>
     </properties>
@@ -35,17 +36,22 @@
         </repository>
         <repository>
             <id>freehep-repo-public</id>
-            <name>FreeHEP Maven Public</name>
+            <name>FreeHEP</name>
             <url>http://srs.slac.stanford.edu/nexus/content/groups/freehep-maven2-public/</url>
         </repository>
         <repository>
+            <id>srs-repo-public</id>
+            <name>SRS</name>
+            <url>http://srs.slac.stanford.edu/nexus/content/groups/srs-maven2-public/</url>
+        </repository>
+        <repository>
             <id>lcsim-repo-public</id>
-            <name>LCSIM Public Maven Repository</name>
+            <name>LCSim</name>
             <url>http://srs.slac.stanford.edu/nexus/content/groups/lcsim-maven2-public/</url>
         </repository>
         <repository>
             <id>jlab-coda-repo-public</id>
-            <name>JLAB CODA Maven Repository</name>
+            <name>CODA</name>
             <url>https://coda.jlab.org/maven/</url>
         </repository>
     </repositories>
@@ -59,14 +65,14 @@
     <distributionManagement>
         <repository>
             <id>lcsim-repo-releases</id>
-            <name>LCSIM Releases maven repository</name>
-            <!--<url>http://srs.slac.stanford.edu/nexus/content/repositories/lcsim-maven2-releases/</url>-->
+            <name>LCSim Releases</name>
+            <!--<url>http://srs.slac.stanford.edu/nexus/content/repositories/lcsim-maven2-releases/</url> -->
             <url>http://scalnx-v01.slac.stanford.edu:8180/nexus/content/repositories/lcsim-maven2-releases/</url>
         </repository>
         <snapshotRepository>
             <id>lcsim-repo-snapshots</id>
-            <name>LCSIM Snapshots maven repository</name>
-            <!--<url>http://srs.slac.stanford.edu/nexus/content/repositories/lcsim-maven2-snapshot/</url>-->
+            <name>LCSim Snapshots</name>
+            <!--<url>http://srs.slac.stanford.edu/nexus/content/repositories/lcsim-maven2-snapshot/</url> -->
             <url>http://scalnx-v01.slac.stanford.edu:8180/nexus/content/repositories/lcsim-maven2-snapshot/</url>
         </snapshotRepository>
         <site>
@@ -137,117 +143,112 @@
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-util</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-detector-data</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-detector-model</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-conditions</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-ecal-recon</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-ecal-readout-sim</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-tracking</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-evio</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-recon</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-analysis</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-monitoring-drivers</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-monitoring-app</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-users</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-steering-files</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-distribution</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-ecal-event-display</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-record-util</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-monitoring-util</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-run-database</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-crawler</artifactId>
-                <version>${project.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.hps</groupId>
-                <artifactId>hps-datacat-client</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-job</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-logging</artifactId>
-                <version>${project.version}</version>
+                <version>3.9-SNAPSHOT</version>
             </dependency>
             <!-- Next are external dependencies used in multiple modules. -->
             <dependency>
@@ -278,7 +279,7 @@
             <dependency>
                 <groupId>jfreechart-aida-experimental</groupId>
                 <artifactId>jfreechart-aida-experimental</artifactId>
-                <version>1.8-SNAPSHOT</version>
+                <version>1.8</version>
                 <exclusions>
                     <exclusion>
                         <groupId>jdom</groupId>
@@ -289,6 +290,11 @@
                         <artifactId>commons-math</artifactId>
                     </exclusion>
                 </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>srs</groupId>
+                <artifactId>org-srs-datacat-client</artifactId>
+                <version>0.5-TEST3</version>
             </dependency>
         </dependencies>
     </dependencyManagement>
@@ -336,10 +342,8 @@
                 <artifactId>maven-surefire-report-plugin</artifactId>
                 <version>2.17</version>
             </plugin>
-            <plugin>
-                <groupId>org.kuali.maven.plugins</groupId>
-                <artifactId>graph-maven-plugin</artifactId>
-            </plugin>
+            <!-- <plugin> <groupId>org.kuali.maven.plugins</groupId> <artifactId>graph-maven-plugin</artifactId> 
+                </plugin> -->
         </plugins>
     </reporting>
     <build>
@@ -372,7 +376,8 @@
                     <artifactId>maven-antrun-plugin</artifactId>
                     <version>1.7</version>
                 </plugin>
-                <!-- This fixes the lifecycle not covered by plugin execution error in Eclipse. -->
+                <!-- This fixes the lifecycle not covered by plugin execution 
+                    error in Eclipse. -->
                 <plugin>
                     <groupId>org.eclipse.m2e</groupId>
                     <artifactId>lifecycle-mapping</artifactId>
@@ -399,11 +404,8 @@
                         </lifecycleMappingMetadata>
                     </configuration>
                 </plugin>
-                <plugin>
-                    <groupId>org.kuali.maven.plugins</groupId>
-                    <artifactId>graph-maven-plugin</artifactId>
-                    <version>1.2.3</version>
-                </plugin>
+                <!-- <plugin> <groupId>org.kuali.maven.plugins</groupId> 
+                    <artifactId>graph-maven-plugin</artifactId> <version>1.2.3</version> </plugin> -->
             </plugins>
         </pluginManagement>
         <plugins>
@@ -423,10 +425,7 @@
                     <target>1.7</target>
                     <showWarnings>true</showWarnings>
                     <showDeprecation>true</showDeprecation>
-                    <!--                    
-                    <staleMillis>1</staleMillis>
-                    <useIncrementalCompilation>false</useIncrementalCompilation>
-                    -->
+                    <!-- <staleMillis>1</staleMillis> <useIncrementalCompilation>false</useIncrementalCompilation> -->
                 </configuration>
             </plugin>
             <plugin>
@@ -436,7 +435,7 @@
                 <configuration>
                     <argLine>-Xmx1024m</argLine>
                     <forkMode>pertest</forkMode>
-                    <systemPropertyVariables>                    
+                    <systemPropertyVariables>
                         <org.lcsim.cacheDir>${org.lcsim.cacheDir}</org.lcsim.cacheDir>
                         <java.util.logging.config.class>org.hps.logging.config.TestLoggingConfig</java.util.logging.config.class>
                     </systemPropertyVariables>
@@ -476,7 +475,44 @@
             <plugin>
                 <artifactId>maven-resources-plugin</artifactId>
                 <version>2.7</version>
-            </plugin>            
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>2.17</version>
+                <configuration>
+                    <excludes>org/hps/users/**/*</excludes>
+                    <logViolationsToConsole>true</logViolationsToConsole>
+                    <consoleOutput>true</consoleOutput>
+                    <includeResources>true</includeResources>
+                    <includeTestResources>true</includeTestResources>
+                    <checkstyleRules>
+                        <module name="Checker">
+                            <module name="FileTabCharacter">
+                                <property name="fileExtensions" value="java,xml,lcsim,prop,properties" />
+                            </module>
+                            <module name="TreeWalker">
+                                <module name="UnusedImports">
+                                    <property name="processJavadoc" value="false" />
+                                </module>
+                                <module name="RedundantImport" />
+                                <!--                                
+                                <module name="EmptyBlock" />
+                                <module name="EmptyStatement" />
+                                -->
+                            </module>
+                        </module>
+                    </checkstyleRules>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>compile</phase>
+                        <goals>
+                            <goal>check</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
     <developers>
@@ -490,9 +526,6 @@
                 <role>release manager</role>
             </roles>
             <timezone>-8</timezone>
-            <properties>
-                <aim>jeremyslac</aim>
-            </properties>
         </developer>
         <developer>
             <name>Norman Graf</name>
@@ -503,9 +536,6 @@
                 <role>developer</role>
             </roles>
             <timezone>-8</timezone>
-            <properties>
-                <aim>ngraf137</aim>
-            </properties>
         </developer>
         <developer>
             <name>Maurik Holtrop</name>
@@ -556,7 +586,7 @@
             </roles>
             <timezone>-8</timezone>
         </developer>
-	<developer>
+        <developer>
             <name>Holly Szumila-Vance</name>
             <email>[log in to unmask]</email>
             <organization>Old Dominion University</organization>

Modified: java/branches/HPSJAVA-409/plugin/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/plugin/pom.xml	(original)
+++ java/branches/HPSJAVA-409/plugin/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/plugin/</url>

Modified: java/branches/HPSJAVA-409/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/pom.xml	(original)
+++ java/branches/HPSJAVA-409/pom.xml	Wed Apr 27 11:11:32 2016
@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <artifactId>hps-modules</artifactId>
     <packaging>pom</packaging>
@@ -10,7 +9,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>svn://svn.freehep.org/hps/java/trunk/</url>
@@ -108,7 +107,6 @@
         <module>analysis</module>
         <module>conditions</module>
         <module>crawler</module>
-        <module>datacat-client</module>
         <module>detector-data</module>
         <module>detector-model</module>
         <module>distribution</module>

Modified: java/branches/HPSJAVA-409/recon/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/recon/pom.xml	(original)
+++ java/branches/HPSJAVA-409/recon/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/recon/</url>

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalGainCalibFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalGainCalibFilter.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalGainCalibFilter.java	Wed Apr 27 11:11:32 2016
@@ -7,11 +7,11 @@
 
 public class EcalGainCalibFilter extends EventReconFilter {
 
-	private double feeCut = 0.6;
-	private double molCut = 0.6;
-	private double tMin = 16.0;
-	private double tMax = 80.0;
-	private double dtMax = 12.0;
+    private double feeCut = 0.6;
+    private double molCut = 0.6;
+    private double tMin = 16.0;
+    private double tMax = 80.0;
+    private double dtMax = 12.0;
     private String clusterCollectionName = "EcalClusters";
 
     public void setFeeCut(double feeCut) { this.feeCut = feeCut; }
@@ -27,32 +27,32 @@
     @Override
     public void process(EventHeader event) 
     {
-    	incrementEventProcessed();
+        incrementEventProcessed();
         if (!event.hasCollection(Cluster.class, clusterCollectionName)) skipEvent();
         List<Cluster> cc = event.get(Cluster.class, clusterCollectionName);
         if (cc.size() < 1) skipEvent();
         boolean keepEvent = false;
         for (Cluster c1 : cc) 
         {
-        	final double t1 = ClusterUtilities.getSeedHitTime(c1);
-        	if (t1<tMin || t1>tMax) continue;
-        	if (c1.getEnergy() > feeCut)
-        	{
-        		keepEvent = true;
-        		break;
-        	}
-        	for (Cluster c2 : cc)
-        	{
-        		final double t2 = ClusterUtilities.getSeedHitTime(c2);
-        		if (c1 == c2) continue;
-        		if (t2<tMin || t2>tMax) continue;
-        		if (Math.abs(t1-t2) > dtMax) continue;
-        		if (c1.getEnergy() + c2.getEnergy() > molCut)
-        		{
-        			keepEvent = true;
-        			break;
-        		}
-        	}
+            final double t1 = ClusterUtilities.getSeedHitTime(c1);
+            if (t1<tMin || t1>tMax) continue;
+            if (c1.getEnergy() > feeCut)
+            {
+                keepEvent = true;
+                break;
+            }
+            for (Cluster c2 : cc)
+            {
+                final double t2 = ClusterUtilities.getSeedHitTime(c2);
+                if (c1 == c2) continue;
+                if (t2<tMin || t2>tMax) continue;
+                if (Math.abs(t1-t2) > dtMax) continue;
+                if (c1.getEnergy() + c2.getEnergy() > molCut)
+                {
+                    keepEvent = true;
+                    break;
+                }
+            }
         }
         if (!keepEvent) skipEvent();
         incrementEventPassed();

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalPairsFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalPairsFilter.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/EcalPairsFilter.java	Wed Apr 27 11:11:32 2016
@@ -18,6 +18,7 @@
 
     private String clusterCollectionName = "EcalClusters";
     private double maxDt = 2.5;
+    private boolean strictPairs = false;
 
     public void setClusterCollectionName(String clusterCollectionName) {
         this.clusterCollectionName = clusterCollectionName;
@@ -27,12 +28,19 @@
         this.maxDt = maxDt;
     }
 
+    public void setStrictPairs(boolean strictPairs) {
+        this.strictPairs = strictPairs;
+    }
+
     @Override
     public void process(EventHeader event) {
         incrementEventProcessed();
         if (event.hasCollection(Cluster.class, clusterCollectionName)) {
             List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
             if (clusters.size() < 2) {
+                skipEvent();
+            }
+            if (strictPairs && clusters.size() > 2) {
                 skipEvent();
             }
             List<Double> clusterTimes = new ArrayList<Double>();
@@ -52,7 +60,7 @@
                 skipEvent();
             }
         } else {
-                skipEvent();
+            skipEvent();
         }
         incrementEventPassed();
     }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/FEEFilterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/FEEFilterDriver.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/FEEFilterDriver.java	Wed Apr 27 11:11:32 2016
@@ -1,16 +1,38 @@
 package org.hps.recon.filtering;
 
+import org.lcsim.event.Cluster;
+import org.hps.recon.ecal.cluster.ClusterUtilities;
+import org.hps.record.epics.EpicsData;
 import org.hps.record.triggerbank.AbstractIntData;
 import org.hps.record.triggerbank.TIData;
+import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
-
-import org.lcsim.event.Cluster;
-import org.lcsim.event.EventHeader;
 import org.lcsim.util.Driver;
-import org.hps.recon.ecal.cluster.ClusterUtilities;
-import org.hps.record.epics.EpicsData;
 public class FEEFilterDriver extends Driver
 {
+    //Set min seed energy value, default to 2015 run
+    private double seedCut = 0.4;
+    
+    //set min cluster energy value, default to 2015 run
+    private double clusterCut = 0.6;
+    
+    /**
+     * Set the cut value for seed energy in GeV
+     * @param seedCut
+     */
+    public void setSeedCut(double seedCut) {
+        this.seedCut = seedCut;
+    }
+    
+    /**
+     * Set the cut value for cluster energy in GeV
+     * @param clusterCut
+     */
+    public void setClusterCut(double clusterCut) {
+        this.clusterCut = clusterCut;
+    }
+    
+    
   public void process(EventHeader event) {
 
     // don't drop any events with EPICS data:
@@ -44,9 +66,10 @@
       //    ClusterUtilities.findSeedHit(cc).getRawEnergy() < 0.4)
       //  cc.Delete();
 
-      // keep events with a cluster over 600 MeV with seed over 400 MeV:
-      if (cc.getEnergy() > 0.6 && 
-          ClusterUtilities.findSeedHit(cc).getCorrectedEnergy() > 0.4)
+      // keep events with a cluster over 600 MeV with seed over 400 MeV (for 2015 running).
+        // keep events with cluster over 1.2 GeV and seed over 650 MeV for 2016 running.
+      if (cc.getEnergy() > clusterCut && 
+          ClusterUtilities.findSeedHit(cc).getCorrectedEnergy() > seedCut )
         return;
     }
 

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/MinimumHitsFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/MinimumHitsFilter.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/MinimumHitsFilter.java	Wed Apr 27 11:11:32 2016
@@ -61,7 +61,7 @@
 
 
     private boolean isHitOnTop(RawTrackerHit hit){
-    	HpsSiSensor sensor=(HpsSiSensor) hit.getDetectorElement();
+        HpsSiSensor sensor=(HpsSiSensor) hit.getDetectorElement();
         IIdentifier id=hit.getIdentifier();
         SiTrackerIdentifierHelper _sid_helper=(SiTrackerIdentifierHelper) sensor.getIdentifierHelper();
 

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/PulserScalerAndEpicsFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/PulserScalerAndEpicsFilter.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/PulserScalerAndEpicsFilter.java	Wed Apr 27 11:11:32 2016
@@ -7,101 +7,97 @@
 import java.io.File;
 import java.io.IOException;
 
-import org.lcsim.event.Cluster;
+import org.hps.conditions.ConditionsDriver;
+import org.hps.record.epics.EpicsData;
+import org.hps.record.triggerbank.AbstractIntData;
+import org.hps.record.triggerbank.TIData;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
 import org.lcsim.lcio.LCIOReader;
 import org.lcsim.lcio.LCIOWriter;
 import org.lcsim.util.Driver;
-import org.hps.conditions.ConditionsDriver;
-import org.hps.recon.ecal.cluster.ClusterUtilities;
 //import org.hps.recon.ecal.triggerbank.AbstractIntData;
 //import org.hps.recon.ecal.triggerbank.TIData;
 
-import org.hps.record.triggerbank.AbstractIntData;
-import org.hps.record.triggerbank.TIData;
-import org.hps.record.epics.EpicsData;
-import org.hps.record.scalers.ScalerData;
-
 public class PulserScalerAndEpicsFilter extends Driver{
 
-	public void process(EventHeader event) {
+    public void process(EventHeader event) {
 
-		// only keep pulser triggers:
-		if (!event.hasCollection(GenericObject.class,"TriggerBank"))
-			throw new Driver.NextEventException();
-		boolean isPulser=false;
-		for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
-		{
-			if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
-			TIData tid = new TIData(gob);
-			if (tid.isPulserTrigger())
-			{
-				isPulser=true;
-				break;
-			}
-		}
+        // only keep pulser triggers:
+        if (!event.hasCollection(GenericObject.class,"TriggerBank"))
+            throw new Driver.NextEventException();
+        boolean isPulser=false;
+        for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
+        {
+            if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
+            TIData tid = new TIData(gob);
+            if (tid.isPulserTrigger())
+            {
+                isPulser=true;
+                break;
+            }
+        }
 
-		// don't drop any events with EPICS data or scalers data
-		// (could also do this via event tag=31)
-		final EpicsData edata = EpicsData.read(event);
-		if (edata != null) return;
-		
-		if( event.hasCollection(GenericObject.class, "ScalerData"))
-			return;
+        // don't drop any events with EPICS data or scalers data
+        // (could also do this via event tag=31)
+        final EpicsData edata = EpicsData.read(event);
+        if (edata != null) return;
+        
+        if( event.hasCollection(GenericObject.class, "ScalerData"))
+            return;
 
-		if (!isPulser) throw new Driver.NextEventException();
+        if (!isPulser) throw new Driver.NextEventException();
 
 
-	}
-	/**
-	 * standalone way to run this:
-	 * 
-	 * @param arg [0] inputFile [1] outputFile [2] run number [3] detectorName (optional, default = "HPS-EngRun2015-Nominal-v1") 
-	 * @throws IOException
-	 */
-	public static void main(String arg[]) throws IOException{
-		ConditionsDriver hack = new ConditionsDriver();
-		
-		String detectorName = "HPS-EngRun2015-Nominal-v1";
-		if(arg.length >3)
-		hack.setDetectorName(arg[3]);
-		hack.setFreeze(true);
-		hack.setRunNumber(Integer.parseInt(arg[2]));
-		hack.initialize();
-		PulserScalerAndEpicsFilter pf = new PulserScalerAndEpicsFilter();
-		LCIOWriter writer = new LCIOWriter(arg[1]);
-		File file = new File(arg[0]);
-		LCIOReader reader = new LCIOReader(file);
-		System.out.println(file.getPath());
-		int nEventsKept = 0;
-		int nEvents = 0;
-		try{
-			while(true){
-				try{
-					
-					EventHeader eh = reader.read();
-					if(eh.getEventNumber() %1000 == 0){
-						//Driver.this.
-						System.out.println("PulserFitter:");
-						System.out.println("    " + nEventsKept + " events kept");
-						System.out.println("    " + nEvents + "events read");
-					}
-					nEvents ++;
-					pf.process(eh); //might throw NextEventException
-					
-					nEventsKept++;
-					writer.write(eh);
-				}catch(Driver.NextEventException e){
+    }
+    /**
+     * standalone way to run this:
+     * 
+     * @param arg [0] inputFile [1] outputFile [2] run number [3] detectorName (optional, default = "HPS-EngRun2015-Nominal-v1") 
+     * @throws IOException
+     */
+    public static void main(String arg[]) throws IOException{
+        ConditionsDriver hack = new ConditionsDriver();
+        
+        String detectorName = "HPS-EngRun2015-Nominal-v1";
+        if(arg.length >3)
+        hack.setDetectorName(arg[3]);
+        hack.setFreeze(true);
+        hack.setRunNumber(Integer.parseInt(arg[2]));
+        hack.initialize();
+        PulserScalerAndEpicsFilter pf = new PulserScalerAndEpicsFilter();
+        LCIOWriter writer = new LCIOWriter(arg[1]);
+        File file = new File(arg[0]);
+        LCIOReader reader = new LCIOReader(file);
+        System.out.println(file.getPath());
+        int nEventsKept = 0;
+        int nEvents = 0;
+        try{
+            while(true){
+                try{
+                    
+                    EventHeader eh = reader.read();
+                    if(eh.getEventNumber() %1000 == 0){
+                        //Driver.this.
+                        System.out.println("PulserFitter:");
+                        System.out.println("    " + nEventsKept + " events kept");
+                        System.out.println("    " + nEvents + "events read");
+                    }
+                    nEvents ++;
+                    pf.process(eh); //might throw NextEventException
+                    
+                    nEventsKept++;
+                    writer.write(eh);
+                }catch(Driver.NextEventException e){
 
-				}
-			}
-		}catch(IOException e){
-			e.printStackTrace();
-			reader.close();
-		}
+                }
+            }
+        }catch(IOException e){
+            e.printStackTrace();
+            reader.close();
+        }
 
 
-		writer.close();
-	}
+        writer.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/V0CandidateFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/V0CandidateFilter.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/filtering/V0CandidateFilter.java	Wed Apr 27 11:11:32 2016
@@ -4,15 +4,22 @@
 import java.util.List;
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.hps.recon.particle.ReconParticleDriver;
+import org.hps.recon.tracking.TrackData;
+import org.hps.recon.tracking.TrackType;
 import org.hps.record.epics.EpicsData;
+import org.hps.record.scalers.ScalerData;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.ReconstructedParticle;
 
 /**
  * Class to strip off trident candidates. Currently defined as: e+ e- events
- * with tracks. If the tight constraint is enabled, tracks must be matched to
- * clusters and the Ecal cluster times must be within _timingCut [2.5ns] of each
- * other.
+ * with tracks; track and vertex chi2 must be better than values defined by
+ * cuts, and track times must be within trackDtCut of each other. If the tight
+ * constraint is enabled, tracks must be matched to clusters, the Ecal cluster
+ * times must be within _timingCut [2.5ns] of each other, and there must be
+ * exactly one V0 passing all cuts.
+ *
+ * Only GBL vertices are considered.
  *
  * @author Norman A Graf
  *
@@ -20,8 +27,13 @@
  */
 public class V0CandidateFilter extends EventReconFilter {
 
-    private String _V0CandidateCollectionName = "TargetConstrainedV0Candidates";
+    private String _V0CandidateCollectionName = "UnconstrainedV0Candidates";
     private double _clusterTimingCut = 2.5;
+    private double v0Chi2Cut = 10.0;
+    private double trackChi2Cut = 20.0;
+    private double trackDtCut = 5.0;
+    private double trackPMax = 0.9;
+    private double v0PMax = 1.4;
 
     private boolean _tight = false;
     private boolean _keepEpicsDataEvents = false;
@@ -30,9 +42,15 @@
     protected void process(EventHeader event) {
         incrementEventProcessed();
         if (_keepEpicsDataEvents) {
-            // don't drop any events with EPICS data:
-            final EpicsData data = EpicsData.read(event);
-            if (data != null) {
+            // don't drop any events with EPICS or scaler data:
+            final EpicsData epicsData = EpicsData.read(event);
+            if (epicsData != null) {
+                incrementEventPassed();
+                return;
+            }
+
+            final ScalerData scalerData = ScalerData.read(event);
+            if (scalerData != null) {
                 incrementEventPassed();
                 return;
             }
@@ -41,45 +59,96 @@
             skipEvent();
         }
         List<ReconstructedParticle> V0Candidates = event.get(ReconstructedParticle.class, _V0CandidateCollectionName);
-        if (V0Candidates.isEmpty()) {
-            skipEvent();
-        }
+        int nV0 = 0; //number of good V0
+        for (ReconstructedParticle v0 : V0Candidates) {
+            ReconstructedParticle electron = v0.getParticles().get(ReconParticleDriver.ELECTRON);
+            ReconstructedParticle positron = v0.getParticles().get(ReconParticleDriver.POSITRON);
 
-        // tight requires ONLY ONE real vertex fit 
-        if (_tight) {
-            if (V0Candidates.size() != 2) {
-                skipEvent();
+            if (!TrackType.isGBL(v0.getType())) { //we only care about GBL vertices
+                continue;
             }
-            for (ReconstructedParticle rp : V0Candidates) {
-
-                ReconstructedParticle electron;
-                ReconstructedParticle positron;
-
-                List<ReconstructedParticle> fsParticles = rp.getParticles();
-                if (fsParticles.size() != 2) {
-                    skipEvent();
+            if (v0.getStartVertex().getChi2() > v0Chi2Cut) {
+                continue;
+            }
+            if (electron.getTracks().get(0).getChi2() > trackChi2Cut || positron.getTracks().get(0).getChi2() > trackChi2Cut) {
+                continue;
+            }
+            if (electron.getMomentum().magnitude() > trackPMax || positron.getMomentum().magnitude() > trackPMax) {
+                continue;
+            }
+            if (v0.getMomentum().magnitude() > v0PMax) {
+                continue;
+            }
+            double eleTime = TrackData.getTrackTime(TrackData.getTrackData(event, electron.getTracks().get(0)));
+            double posTime = TrackData.getTrackTime(TrackData.getTrackData(event, positron.getTracks().get(0)));
+            if (Math.abs(eleTime - posTime) > trackDtCut) {
+                continue;
+            }
+            if (_tight) { // tight requires cluster matches and cluster time cut
+                if (electron.getClusters().isEmpty() || positron.getClusters().isEmpty()) {
+                    continue;
                 }
-                // require both electrons to be associated with an ECal cluster
-                electron = fsParticles.get(ReconParticleDriver.ELECTRON);
-                if (electron.getClusters().isEmpty()) {
-                    skipEvent();
-                }
-                positron = fsParticles.get(ReconParticleDriver.POSITRON);
-                if (positron.getClusters().isEmpty()) {
-                    skipEvent();
-                }
-
                 // calorimeter cluster timing cut
                 // first CalorimeterHit in the list is the seed crystal
                 double t1 = ClusterUtilities.getSeedHitTime(electron.getClusters().get(0));
                 double t2 = ClusterUtilities.getSeedHitTime(positron.getClusters().get(0));
 
                 if (abs(t1 - t2) > _clusterTimingCut) {
-                    skipEvent();
+                    continue;
                 }
             }
+            nV0++;
+        }
+        if (nV0 == 0) {
+            skipEvent();
+        }
+        // tight requires ONLY ONE candidate vertex
+        if (_tight && nV0 != 1) {
+            skipEvent();
         }
         incrementEventPassed();
+    }
+
+    /**
+     * Maximum vertex chi2 for a V0 to be counted.
+     *
+     * @param v0Chi2Cut default of 10.0.
+     */
+    public void setV0Chi2Cut(double v0Chi2Cut) {
+        this.v0Chi2Cut = v0Chi2Cut;
+    }
+
+    /**
+     * Maximum track chi2 for a V0 to be counted. A V0 is rejected if either of
+     * the final state tracks has a chi2 exceeding the cut.
+     *
+     * @param trackChi2Cut default of 20.0.
+     */
+    public void setTrackChi2Cut(double trackChi2Cut) {
+        this.trackChi2Cut = trackChi2Cut;
+    }
+
+    /**
+     * Maximum track time different for a V0 to be counted.
+     *
+     * @param trackDtCut units of ns, default of 5.0
+     */
+    public void setTrackDtCut(double trackDtCut) {
+        this.trackDtCut = trackDtCut;
+    }
+
+    /**
+     * Maximum track momentum for a V0 to be counted. A V0 is rejected if either
+     * of the final state tracks has momentum exceeding this cut.
+     *
+     * @param trackPMax units of GeV, default of 0.9
+     */
+    public void setTrackPMax(double trackPMax) {
+        this.trackPMax = trackPMax;
+    }
+
+    public void setV0PMax(double v0PMax) {
+        this.v0PMax = v0PMax;
     }
 
     /**

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/HpsReconParticleDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/HpsReconParticleDriver.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/HpsReconParticleDriver.java	Wed Apr 27 11:11:32 2016
@@ -242,6 +242,7 @@
         BilliorVertexer vtxFitter = new BilliorVertexer(bField);
         // TODO: The beam size should come from the conditions database.
         vtxFitter.setBeamSize(beamSize);
+        vtxFitter.setDebug(debug);
 
         // Perform the vertexing based on the specified constraint.
         switch (constraint) {
@@ -319,7 +320,7 @@
 
             // Generate a candidate vertex and particle.
             BilliorVertex vtxFit = fitVertex(constraint, firstElectronBTrack, secondElectronBTrack);
-            ReconstructedParticle candidate = this.makeReconstructedParticle(topElectron, botElectron, vtxFit);
+            ReconstructedParticle candidate = makeReconstructedParticle(topElectron, botElectron, vtxFit);
 
             // Add the candidate vertex and particle to the
             // appropriate LCIO collection.
@@ -354,7 +355,7 @@
      * @return Returns a reconstructed particle with properties generated from
      * the child particles and vertex given as an argument.
      */
-    private ReconstructedParticle makeReconstructedParticle(ReconstructedParticle electron, ReconstructedParticle positron, BilliorVertex vtxFit) {
+    public static ReconstructedParticle makeReconstructedParticle(ReconstructedParticle electron, ReconstructedParticle positron, BilliorVertex vtxFit) {
 
         // Create a new reconstructed particle to represent the V0
         // candidate and populate it with the electron and positron.
@@ -396,9 +397,8 @@
         ((BaseReconstructedParticle) candidate).setCharge(particleCharge);
 
         // VERBOSE :: Output the fitted momentum data.
-        printDebug("Fitted momentum in tracking frame: " + fittedMomentum.toString());
-        printDebug("Fitted momentum in detector frame: " + fittedMomentum.toString());
-
+//        printDebug("Fitted momentum in tracking frame: " + fittedMomentum.toString());
+//        printDebug("Fitted momentum in detector frame: " + fittedMomentum.toString());
         // Add the ReconstructedParticle to the vertex.
         vtxFit.setAssociatedParticle(candidate);
 

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/ReconParticleDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/ReconParticleDriver.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/ReconParticleDriver.java	Wed Apr 27 11:11:32 2016
@@ -7,12 +7,14 @@
 import hep.physics.vec.VecOp;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.hps.recon.tracking.CoordinateTransformations;
+import org.hps.recon.tracking.TrackUtils;
 import org.hps.recon.utils.TrackClusterMatcher;
 import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;
@@ -22,7 +24,9 @@
 import org.lcsim.event.base.BaseCluster;
 import org.lcsim.event.base.BaseReconstructedParticle;
 import org.lcsim.geometry.Detector;
+import org.lcsim.geometry.subdetector.HPSEcal3;
 import org.lcsim.util.Driver;
+
 
 /**
  * Driver framework for generating reconstructed particles and matching clusters
@@ -44,6 +48,11 @@
     public static final int POSITRON = 1;
     public static final int MOLLER_TOP = 0;
     public static final int MOLLER_BOT = 1;
+    
+    // normalized cluster-track distance required for qualifying as a match:
+    private double MAXNSIGMAPOSITIONMATCH=30.0;
+
+    HPSEcal3 ecal;
 
     /**
      * Sets the name of the LCIO collection for beam spot constrained V0
@@ -173,6 +182,17 @@
         this.trackCollectionNames = trackCollectionNames;
     }
 
+    /**
+     * Set the requirement on cluster-track position matching in terms of N-sigma.
+     * 
+     * @param nsigma
+     */
+    public void setNSigmaPositionMatch(double nsigma) {
+        MAXNSIGMAPOSITIONMATCH=nsigma;
+    }
+    
+        
+    
     /**
      * Updates the magnetic field parameters to match the appropriate values for
      * the current detector settings.
@@ -188,6 +208,7 @@
             flipSign = -1;
         }
 
+        ecal = (HPSEcal3) detector.getSubdetector("Ecal");
         matcher.setBFieldMap(detector.getFieldMap());
 
     }
@@ -209,7 +230,7 @@
      * clusters. Clusters will be matched with tracks when this is possible.
      *
      * @param clusters - The list of event clusters.
-     * @param tracks - The list of event tracks.
+     * @param trackCollections - The list of event tracks.
      * @return Returns a <code>List</code> collection containing all of the
      * <code>ReconstructedParticle</code> objects generated from the argument
      * data.
@@ -222,15 +243,19 @@
         // Create a list of unmatched clusters. A cluster should be
         // removed from the list if a matching track is found.
         Set<Cluster> unmatchedClusters = new HashSet<Cluster>(clusters);
-
+        
+        // Create a mapping of matched clusters to corresponding tracks.
+        HashMap<Cluster, Track> clusterToTrack = new HashMap<Cluster,Track>();
+        
         // Loop through all of the track collections and try to match every
         // track to a cluster.  Allow a cluster to be matched to multiple 
         // tracks and use a probability (to be coded later) to determine what 
         // the best match is.
         // TODO: At some point, pull this out to it's own method
         for (List<Track> tracks : trackCollections) {
+       
             for (Track track : tracks) {
-
+                
                 // Create a reconstructed particle to represent the track.
                 ReconstructedParticle particle = new BaseReconstructedParticle();
 
@@ -244,6 +269,9 @@
 
                 // Derive the charge of the particle from the track.
                 ((BaseReconstructedParticle) particle).setCharge(track.getCharge() * flipSign);
+
+                // initialize PID quality to a junk value:
+                ((BaseReconstructedParticle)particle).setGoodnessOfPid(9999);
 
                 // Extrapolate the particle ID from the track. Positively
                 // charged particles are assumed to be positrons and those
@@ -254,33 +282,48 @@
                     ((BaseReconstructedParticle) particle).setParticleIdUsed(new SimpleParticleID(11, 0, 0, 0));
                 }
 
+                // normalized distance of the closest match:
+                double smallestNSigma=Double.MAX_VALUE;
+               
+                // try to find a matching cluster:
                 Cluster matchedCluster = null;
-
-                // Track the best matching cluster for the track.
-                // TODO: This should find the best match not just the first match.
-                clusterLoop:
                 for (Cluster cluster : clusters) {
-                    // Check if the cluster and track are a valid match.
-                    if (matcher.isMatch(cluster, track)) {
-
-                        // Store the matched cluster.
-                        matchedCluster = cluster;
-
-                        // Since a match has been found, the loop can be
-                        // terminated.
-                        break clusterLoop;
+
+                    // normalized distance between this cluster and track:
+                    final double thisNSigma=matcher.getNSigmaPosition(cluster, particle);
+
+                    // ignore if matching quality doesn't make the cut:
+                    if (thisNSigma > MAXNSIGMAPOSITIONMATCH) continue;
+
+                    // ignore if we already found a cluster that's a better match:
+                    if (thisNSigma > smallestNSigma) continue;
+
+                    // we found a new best cluster candidate for this track:
+                    smallestNSigma = thisNSigma;
+                    matchedCluster = cluster;
+
+                    // prefer using GBL tracks to correct (later) the clusters, for some consistency:
+                    if (track.getType() >= 32 || !clusterToTrack.containsKey(matchedCluster)) {
+                          clusterToTrack.put(matchedCluster,track);
                     }
                 }
 
                 // If a cluster was found that matches the track...
                 if (matchedCluster != null) {
+
+                    // add cluster to the particle:
                     particle.addCluster(matchedCluster);
 
-                    int pid = particle.getParticleIDUsed().getPDG();
+                    // use pid quality to store track-cluster matching quality:
+                    ((BaseReconstructedParticle)particle).setGoodnessOfPid(smallestNSigma);
+                    
+                    // propogate pid to the cluster:
+                    final int pid = particle.getParticleIDUsed().getPDG();
                     if (Math.abs(pid) == 11) {
                         ((BaseCluster) matchedCluster).setParticleId(pid);
                     }
 
+                    // unmatched clusters will (later) be used to create photon particles:
                     unmatchedClusters.remove(matchedCluster);
                 }
 
@@ -290,35 +333,40 @@
         }
 
         // Iterate over the remaining unmatched clusters.
-        if (!unmatchedClusters.isEmpty()) {
-            for (Cluster unmatchedCluster : unmatchedClusters) {
-
-                // Create a reconstructed particle to represent the unmatched cluster.
-                ReconstructedParticle particle = new BaseReconstructedParticle();
-
-                // The particle is assumed to be a photon, since it did not leave a track.
-                ((BaseReconstructedParticle) particle).setParticleIdUsed(new SimpleParticleID(22, 0, 0, 0));
-
-                int pid = particle.getParticleIDUsed().getPDG();
-                if (Math.abs(pid) != 11) {
-                    ((BaseCluster) unmatchedCluster).setParticleId(pid);
-                }
-
-                // Add the cluster to the particle.
-                particle.addCluster(unmatchedCluster);
-
-                // Set the reconstructed particle properties based on the cluster properties.
-                ((BaseReconstructedParticle) particle).setCharge(0);
-
-                // Add the particle to the reconstructed particle list.
-                particles.add(particle);
-            }
-        }
-
-        // Apply the corrections to the Ecal clusters
+        for (Cluster unmatchedCluster : unmatchedClusters) {
+
+            // Create a reconstructed particle to represent the unmatched cluster.
+            ReconstructedParticle particle = new BaseReconstructedParticle();
+
+            // The particle is assumed to be a photon, since it did not leave a track.
+            ((BaseReconstructedParticle) particle).setParticleIdUsed(new SimpleParticleID(22, 0, 0, 0));
+
+            int pid = particle.getParticleIDUsed().getPDG();
+            if (Math.abs(pid) != 11) {
+                ((BaseCluster) unmatchedCluster).setParticleId(pid);
+            }
+
+            // Add the cluster to the particle.
+            particle.addCluster(unmatchedCluster);
+
+            // Set the reconstructed particle properties based on the cluster properties.
+            ((BaseReconstructedParticle) particle).setCharge(0);
+
+            // Add the particle to the reconstructed particle list.
+            particles.add(particle);
+        }
+
+        // Apply the corrections to the Ecal clusters using track information, if available
         for (Cluster cluster : clusters) {
             if (cluster.getParticleId() != 0) {
-                ClusterUtilities.applyCorrections(cluster);
+                if (clusterToTrack.containsKey(cluster)){
+                    Track matchedT = clusterToTrack.get(cluster);
+                    double ypos = TrackUtils.getTrackStateAtECal(matchedT).getReferencePoint()[2];
+                    ClusterUtilities.applyCorrections(ecal, cluster, ypos);
+                }
+                else {
+                    ClusterUtilities.applyCorrections(ecal, cluster);               
+                }
             }
         }
 
@@ -525,7 +573,7 @@
     /**
      * Indicates whether debug text should be output or not.
      */
-    private boolean debug = false;
+    protected boolean debug = false;
 
     /**
      * The simple name of the class used for debug print statements.
@@ -622,7 +670,7 @@
     // Beam size variables.
     // The beamsize array is in the tracking frame
     /* TODO  mg-May 14, 2014:  the the beam size from the conditions db...also beam position!  */
-    protected double[] beamSize = {0.001, 0.2, 0.02};
+    protected double[] beamSize = {0.001, 0.130, 0.050}; //rough estimate from harp scans during engineering run production running
     protected double bField;
 
     //  flipSign is a kludge...

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/SimpleParticleID.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/SimpleParticleID.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/particle/SimpleParticleID.java	Wed Apr 27 11:11:32 2016
@@ -9,67 +9,67 @@
  *
  */
 public class SimpleParticleID implements ParticleID {
-	
-	int algorithmType = 0; 
-	int pdgID = UnknownPDG;
-	int type = 0; 
-	
-	double likelihood = 0.; 
-	// TODO: Need to define what other parameters are needed.
-	double[] parameters = new double[1]; 
+    
+    int algorithmType = 0; 
+    int pdgID = UnknownPDG;
+    int type = 0; 
+    
+    double likelihood = 0.; 
+    // TODO: Need to define what other parameters are needed.
+    double[] parameters = new double[1]; 
 
-	public SimpleParticleID(){}
-	
-	public SimpleParticleID(int pdgID, int algorithmType, int type, double likelihood){
-		this.pdgID = pdgID; 
-		this.algorithmType = algorithmType; 
-		this.type = type; 
-		this.likelihood = likelihood; 
-	}
-	
-	@Override
-	public int getAlgorithmType() {
-		return algorithmType;
-	}
+    public SimpleParticleID(){}
+    
+    public SimpleParticleID(int pdgID, int algorithmType, int type, double likelihood){
+        this.pdgID = pdgID; 
+        this.algorithmType = algorithmType; 
+        this.type = type; 
+        this.likelihood = likelihood; 
+    }
+    
+    @Override
+    public int getAlgorithmType() {
+        return algorithmType;
+    }
 
-	@Override
-	public double getLikelihood() {
-		return likelihood;
-	}
+    @Override
+    public double getLikelihood() {
+        return likelihood;
+    }
 
-	@Override
-	public int getPDG() {
-		return pdgID;
-	}
+    @Override
+    public int getPDG() {
+        return pdgID;
+    }
 
-	@Override
-	public double[] getParameters() {
-		return parameters;
-	}
+    @Override
+    public double[] getParameters() {
+        return parameters;
+    }
 
-	@Override
-	public int getType() {
-		return type;
-	}
-	
-	public void setAlgorithmType(int algorithmType){
-		this.algorithmType = algorithmType;
-	}
-	
-	public void setLikelihood(int likelihood){
-		this.likelihood = likelihood; 
-	}
-	
-	public void setPDG(int pdgID){
-		this.pdgID = pdgID; 
-	}
-	
-	public void setType(int type){
-		this.type = type; 
-	}
-	
-	public void setParameters(double[] parameters){
-		this.parameters = parameters;
-	}
+    @Override
+    public int getType() {
+        return type;
+    }
+    
+    public void setAlgorithmType(int algorithmType){
+        this.algorithmType = algorithmType;
+    }
+    
+    public void setLikelihood(int likelihood){
+        this.likelihood = likelihood; 
+    }
+    
+    public void setPDG(int pdgID){
+        this.pdgID = pdgID; 
+    }
+    
+    public void setType(int type){
+        this.type = type; 
+    }
+    
+    public void setParameters(double[] parameters){
+        this.parameters = parameters;
+    }
 
 }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/utils/TrackClusterMatcher.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/utils/TrackClusterMatcher.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/utils/TrackClusterMatcher.java	Wed Apr 27 11:11:32 2016
@@ -1,8 +1,4 @@
 package org.hps.recon.utils;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IHistogram1D;
@@ -13,12 +9,17 @@
 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
 
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.hps.recon.tracking.CoordinateTransformations;
+import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.Cluster;
+import org.lcsim.event.ReconstructedParticle;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackState;
 import org.lcsim.geometry.FieldMap;
-import org.hps.recon.tracking.CoordinateTransformations;
-import org.hps.recon.tracking.TrackUtils;
 
 /**
  * Utility used to determine if a track and cluster are matched.
@@ -65,6 +66,53 @@
     private double bottomClusterTrackMatchDeltaYHigh = 24; // mm 
 
     /**
+     * Rafo's parameterization of cluster-seed x/y position residuals as function of energy.
+     * 
+     * Derived using GBL/seed tracks, non-analytic extrapolation, uncorrected cluster positions,
+     * and EngRun2015-Nominal-v4-4-fieldmap detector.
+     * 
+     *  f = p0+e*(p1+e*(p2+e*(p3+e*(p4+e*p5))))
+     */
+    private static final double dxMeanTopPosiGBL[] = { 6.67414,-9.57296, 5.70647, 27.4523,-28.1103,-9.11424 };
+    private static final double dxSigmTopPosiGBL[] = { 52.6437,-478.805, 1896.73,-3761.48, 3676.77,-1408.31 };
+    private static final double dxMeanBotPosiGBL[] = { 4.13802, 15.8887,-74.2844,-9.78944, 308.541,-287.668 };
+    private static final double dxSigmBotPosiGBL[] = { 37.6513,-294.851, 1002.15,-1639.08, 1228.02,-308.754 };
+    
+    private static final double dxMeanTopElecGBL[] = {-1.6473,  5.58701, 25.3977,-17.1523,-121.025, 145.969 };
+    private static final double dxSigmTopElecGBL[] = { 48.7018,-423.599, 1592.66,-2959.99, 2668.97,-919.876 };
+    private static final double dxMeanBotElecGBL[] = {-6.63558, 83.7763,-460.451, 1275.63,-1702.83, 873.913 };
+    private static final double dxSigmBotElecGBL[] = { 47.0029,-411.784, 1586.52,-3083.37, 2985.58,-1145.53 };
+    
+    private static final double dyMeanTopPosiGBL[] = { 0.31245, 5.57585,-6.50267,-8.21688, 39.8607,-43.9661 };
+    private static final double dySigmTopPosiGBL[] = { 33.0213,-275.174, 1168.77,-2642.34, 3045.52,-1406.21 };
+    private static final double dyMeanBotPosiGBL[] = {-7.032,   74.9738,-383.972, 977.849,-1250.28, 637.75  };
+    private static final double dySigmBotPosiGBL[] = { 19.019, -83.9253, 133.813, 119.883,-546.951, 405.207 };
+    
+    private static final double dyMeanTopElecGBL[] = { 2.48498,-20.4101, 62.9689, 25.6386,-259.957, 207.145 };
+    private static final double dySigmTopElecGBL[] = { 8.65583, 120.676,-1166.43, 3811.72,-5383.19, 2787.42 };
+    private static final double dyMeanBotElecGBL[] = {-10.5228, 112.329,-489.761, 953.037,-829.96,  260.772 };
+    private static final double dySigmBotElecGBL[] = { 23.4856,-108.19,  158.7,   189.261,-682.034, 459.15  };
+
+    private static final double dxMeanTopPosiSeed[] ={ 11.6245,-28.5061, 13.0332, 59.9465,-21.1014,-63.6126 };
+    private static final double dxSigmTopPosiSeed[] ={ 61.5911,-540.596, 2077.22,-3973.22, 3704.45,-1332.07 };
+    private static final double dxMeanBotPosiSeed[] ={ 4.53394, 11.3773,-63.7127,-2.81629, 273.868,-264.709 };
+    private static final double dxSigmBotPosiSeed[] ={ 48.3163,-409.249, 1590.36,-3212.85, 3326.04,-1402.3  };
+    
+    private static final double dxMeanTopElecSeed[] ={ 2.14163,-20.8713, 76.3054,  34.894,-340.272,  295.24 };
+    private static final double dxSigmTopElecSeed[] ={ 48.585, -385.166, 1320.26,-2157.45, 1581.06,-366.012 };
+    private static final double dxMeanBotElecSeed[] ={-3.44302, 12.4687, 4.09878,-30.0057,-13.3151, 40.2707 };
+    private static final double dxSigmBotElecSeed[] ={ 48.4089,-385.494, 1341.37,-2271.52, 1814.02,-526.555 };
+
+    private static final double dyMeanTopPosiSeed[] ={-0.527741,10.4944, -18.242,-12.9155, 81.0116,-73.9773 };
+    private static final double dySigmTopPosiSeed[] ={ 37.3097, -357.55, 1607.03,-3709.55, 4282.36,-1957.91 };
+    private static final double dyMeanBotPosiSeed[] ={ 0.74392,-55.2003,  405.04,-1250.64, 1731.47,-887.262 };
+    private static final double dySigmBotPosiSeed[] ={ 25.5776,-199.731,  754.59,-1408.72, 1240.36,-400.912 };
+
+    private static final double dyMeanTopElecSeed[] ={ 2.85429,-24.0858, 69.0145, 34.1213,-297.752, 239.939 };
+    private static final double dySigmTopElecSeed[] ={ 19.9111,-53.2699,-261.915,  1593.2,-2774.01, 1605.54 };
+    private static final double dyMeanBotElecSeed[] ={-9.22963, 98.1346, -427.91, 840.225,-751.188, 250.792 };
+    private static final double dySigmBotElecSeed[] ={ 21.7909,-85.4757,-56.9423, 977.522,-1902.05, 1137.92 };
+    /**
      * Z position to start extrapolation from
      */
     double extStartPos = 700; // mm
@@ -172,6 +220,122 @@
         this.topClusterTrackMatchDeltaYLow = yLow;
         this.topClusterTrackMatchDeltaYHigh = yHigh;
     }
+
+    /**
+     * Get distance between track and cluster.
+     * 
+     * @param cluster
+     * @param track
+     * @return distance between cluster and track
+     */
+    public double getDistance(Cluster cluster,Track track) {
+        
+        // Get the cluster position
+        Hep3Vector cPos = new BasicHep3Vector(cluster.getPosition());
+        
+        // Extrapolate the track to the Ecal cluster position
+        Hep3Vector tPos = null;
+        if (this.useAnalyticExtrapolator) {
+            tPos = TrackUtils.extrapolateTrack(track, cPos.z());
+        } else {
+            TrackState trackStateAtEcal = TrackUtils.getTrackStateAtECal(track);
+            tPos = new BasicHep3Vector(trackStateAtEcal.getReferencePoint());
+            tPos = CoordinateTransformations.transformVectorToDetector(tPos);
+        }
+       
+        return Math.sqrt(Math.pow(cPos.x()-tPos.x(),2)+Math.pow(cPos.y()-tPos.y(),2));
+    }
+    
+    /**
+     * Calculate #sigma between cluster-track x/y position at calorimeter.
+     *
+     * Based on Rafo's parameterizations.  Requires non-analytic extrapolation
+     * and uncorrected cluster positions.
+     * 
+     * @param cluster = position-uncorrected cluster
+     * @param particle recon particle with tracks
+     *
+     * @return #sigma between cluster and track positions
+     */
+    public double getNSigmaPosition(Cluster cluster, ReconstructedParticle particle) {
+
+        if (particle.getTracks().size()<1) return Double.MAX_VALUE;
+          Track track=particle.getTracks().get(0);
+        
+        if (this.useAnalyticExtrapolator)
+            throw new RuntimeException("This is to be used with non-analytic extrapolator only.");
+
+        // Get the cluster position:
+        Hep3Vector cPos = new BasicHep3Vector(cluster.getPosition());
+
+        // whether track is in top half of detector:
+        final boolean isTopTrack = track.getTrackStates().get(0).getTanLambda() > 0;
+
+        // ignore if track and cluster in different halves:
+        if (isTopTrack != cPos.y()>0) return Double.MAX_VALUE;
+
+        // Get the extrapolated track position at the calorimeter:
+        TrackState trackStateAtEcal = TrackUtils.getTrackStateAtECal(track);
+        Hep3Vector tPos = new BasicHep3Vector(trackStateAtEcal.getReferencePoint());
+        tPos = CoordinateTransformations.transformVectorToDetector(tPos);
+
+        // whether it's a GBL track:
+        final boolean isGBL = track.getType() >= 32;
+       
+        // choose which parameterization of mean and sigma to use:
+        double dxMean[],dyMean[],dxSigm[],dySigm[];
+        if (particle.getCharge()>0) {
+            if (isTopTrack) {
+                dxMean = isGBL ? dxMeanTopPosiGBL : dxMeanTopPosiSeed;
+                dxSigm = isGBL ? dxSigmTopPosiGBL : dxSigmTopPosiSeed;
+                dyMean = isGBL ? dyMeanTopPosiGBL : dyMeanTopPosiSeed;
+                dySigm = isGBL ? dySigmTopPosiGBL : dySigmTopPosiSeed;
+            }
+            else {
+                dxMean = isGBL ? dxMeanBotPosiGBL : dxMeanBotPosiSeed;
+                dxSigm = isGBL ? dxSigmBotPosiGBL : dxSigmBotPosiSeed;
+                dyMean = isGBL ? dyMeanBotPosiGBL : dyMeanBotPosiSeed;
+                dySigm = isGBL ? dySigmBotPosiGBL : dySigmBotPosiSeed;
+            }
+        }
+        else if (particle.getCharge()<0) {
+            if (isTopTrack) {
+                dxMean = isGBL ? dxMeanTopElecGBL : dxMeanTopElecSeed;
+                dxSigm = isGBL ? dxSigmTopElecGBL : dxSigmTopElecSeed;
+                dyMean = isGBL ? dyMeanTopElecGBL : dyMeanTopElecSeed;
+                dySigm = isGBL ? dySigmTopElecGBL : dySigmTopElecSeed;
+            }
+            else {
+                dxMean = isGBL ? dxMeanBotElecGBL : dxMeanBotElecSeed;
+                dxSigm = isGBL ? dxSigmBotElecGBL : dxSigmBotElecSeed;
+                dyMean = isGBL ? dyMeanBotElecGBL : dyMeanBotElecSeed;
+                dySigm = isGBL ? dySigmBotElecGBL : dySigmBotElecSeed;
+            }
+        }
+        else return Double.MAX_VALUE;
+
+        // get particle energy:
+        Hep3Vector p3 = new BasicHep3Vector(track.getTrackStates().get(0).getMomentum());
+        p3 = CoordinateTransformations.transformVectorToDetector(p3);
+        double ee = p3.magnitude();
+        
+        // Rafo's parameterization isn't measured above 650 MeV/c but expected to be constant:
+        if (ee > 0.65) ee=0.65;
+
+        // calculate measured mean and sigma of deltaX and deltaY for this energy:
+        double aDxMean=0,aDxSigm=0,aDyMean=0,aDySigm=0;
+        for (int ii=dxMean.length-1; ii>=0; ii--) aDxMean = dxMean[ii] + ee*aDxMean;
+        for (int ii=dxSigm.length-1; ii>=0; ii--) aDxSigm = dxSigm[ii] + ee*aDxSigm;
+        for (int ii=dyMean.length-1; ii>=0; ii--) aDyMean = dyMean[ii] + ee*aDyMean;
+        for (int ii=dySigm.length-1; ii>=0; ii--) aDySigm = dySigm[ii] + ee*aDySigm;
+
+        // calculate nSigma between track and cluster:
+        final double nSigmaX = (cPos.x() - tPos.x() - aDxMean) / aDxSigm;
+        final double nSigmaY = (cPos.y() - tPos.y() - aDyMean) / aDySigm;
+        return Math.sqrt(nSigmaX*nSigmaX + nSigmaY*nSigmaY);
+        //return Math.sqrt( 1 / ( 1/nSigmaX/nSigmaX + 1/nSigmaY/nSigmaY ) );
+    }
+
 
     /**
      * Determine if a track is matched to a cluster. Currently, this is
@@ -363,4 +527,16 @@
             e.printStackTrace();
         }
     }
+
+    /**
+     * Class to store track-cluster matching qualities.
+     */
+    public class TrackClusterMatch {
+        private double nSigmaPositionMatch=Double.MAX_VALUE;
+        public TrackClusterMatch(ReconstructedParticle pp, Cluster cc) {
+            nSigmaPositionMatch = getNSigmaPosition(cc,pp);
+        }
+        public double getNSigmaPositionMatch() { return nSigmaPositionMatch; }
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BaseSimpleVertexer.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BaseSimpleVertexer.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BaseSimpleVertexer.java	Wed Apr 27 11:11:32 2016
@@ -12,25 +12,25 @@
 public abstract class BaseSimpleVertexer implements SimpleVertexer {
 
 
-	protected boolean _debug = false;
-	protected Vertex _fitted_vertex = null;
+    protected boolean _debug = false;
+    protected Vertex _fitted_vertex = null;
 
-	public BaseSimpleVertexer() {
-	}
+    public BaseSimpleVertexer() {
+    }
 
-	@Override
-	public abstract void fitVertex();
+    @Override
+    public abstract void fitVertex();
 
-	@Override
-	public Vertex getFittedVertex() {
-		return _fitted_vertex;
-	}
-	
-	public void clear() {
-		_fitted_vertex = null;
-	}
-	
-	public abstract boolean isValid();
-	
+    @Override
+    public Vertex getFittedVertex() {
+        return _fitted_vertex;
+    }
+    
+    public void clear() {
+        _fitted_vertex = null;
+    }
+    
+    public abstract boolean isValid();
+    
 
 }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertex.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertex.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertex.java	Wed Apr 27 11:11:32 2016
@@ -14,8 +14,8 @@
 
 /**
  * 
- *	@author Mathew Thomas Graham <[log in to unmask]>
- *	@version $Id:$
+ *  @author Mathew Thomas Graham <[log in to unmask]>
+ *  @version $Id:$
  *
  */
 public class BilliorVertex implements Vertex {
@@ -74,12 +74,12 @@
      * @param particle : The ReconstructedParticle Associated with this Vertex
      */
     public void setAssociatedParticle(ReconstructedParticle particle){
-    	this._particle = particle;
+        this._particle = particle;
     }
 
     @Override
     public boolean isPrimary() {
-    	return _isPrimary; 
+        return _isPrimary; 
     }
 
     @Override
@@ -94,7 +94,7 @@
 
     @Override
     public double getProbability() {
-    	return _probability;
+        return _probability;
     }
 
     @Override
@@ -108,7 +108,7 @@
     }
 
     // TODO: These should be pulled out and accessed by their own 
-    //		 getter methods.  
+    //       getter methods.  
     @Override
     public Map<String, Double> getParameters() {
         Map<String, Double> pars = new HashMap<String, Double>();
@@ -128,6 +128,6 @@
 
     @Override
     public ReconstructedParticle getAssociatedParticle() {
-    	return _particle; 
+        return _particle; 
     }
 }

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java	Wed Apr 27 11:11:32 2016
@@ -16,394 +16,97 @@
 
 /**
  * @version $Id: BilliorVertexer.java,v 1.3 2013/03/13 19:24:20 mgraham Exp $
- * @version Vertex tracks using least-squares method laid out by billior etal used in the HPS Java package.
+ * @version Vertex tracks using least-squares method laid out by billior etal
+ * used in the HPS Java package.
  */
 public class BilliorVertexer {
     // the value of the magnetic field in the vicinity of the vertex
     // default is a constant field along the z axis
 
     private boolean _debug = false;
-    private double _bField;
-    private boolean _beamspotConstraint = true;
-    private boolean _targetConstraint = false;
-    private double[] _beamSize = {0.001, 0.01, 0.01}; //10um in y and z
+    private final double _bField;
+    private boolean _beamspotConstraint;
+    private boolean _targetConstraint;
+    private String _constraintType;
+    private final double[] _beamSize = {0.001, 0.01, 0.01}; //10um in y and z
+    private final double[] _beamPosition = {0.0, 0.0, 0.0}; //origin
     private int _ntracks;
-    private List<Matrix> paramList = new ArrayList<Matrix>();
-    private List<Matrix> WList = new ArrayList<Matrix>();
-    private List<Matrix> DList = new ArrayList<Matrix>();
-    private List<Matrix> EList = new ArrayList<Matrix>();
-    private Matrix A;
-    private Matrix T;
-    private List<Matrix> BList = new ArrayList<Matrix>();
-    private List<Matrix> CinvList = new ArrayList<Matrix>();
-    private List<Matrix> CList = new ArrayList<Matrix>();
-    private List<Matrix> UList = new ArrayList<Matrix>();
-    private List<Matrix> dqList = new ArrayList<Matrix>();
-    private double[] _v0 = {0.0, 0.0, 0.0};
+    private double[] _v0 = {0.0, 0.0, 0.0}; //initial guess for unconstrained vertex fit
 //    private double[] _vertexPosition = {0., 0.0, 0.0};
-    private Matrix _vertexPosition = new BasicMatrix(3, 1);
-    private Matrix _covVtx = new BasicMatrix(3, 3);
-    private List<Matrix> _pFit = new ArrayList<Matrix>();
+    private Matrix _vertexPosition;
+    private Matrix _covVtx;
+    private List<Matrix> _pFit;
 
     ;//theta,phi_v,rho
-    private List<Matrix> covVtxMomList = new ArrayList<Matrix>();
-    private Matrix[][] covMomList = new Matrix[2][2];//max 2 tracks...just make this bigger for more
+    private List<Matrix> covVtxMomList;
+    private Matrix[][] covMomList;//max 2 tracks...just make this bigger for more
     private Matrix _constrainedFit;
     private Matrix _constrainedCov;
     private double _chiSq;
-     private String _constraintType="Unspecified";
-    // constructor
-    public BilliorVertexer() {
-    }
 
     public BilliorVertexer(double bField) {
         _bField = bField;
-        _constraintType="Unconstrained";
-        _beamspotConstraint =false;
+        _constraintType = "Unconstrained";
+        _beamspotConstraint = false;
         _targetConstraint = false;
     }
-    
-    public BilliorVertexer(double bField,boolean bsConst, boolean constToBS) {
+
+    public BilliorVertexer(double bField, boolean bsConst, boolean constToBS) {
         _bField = bField;
-        _beamspotConstraint =bsConst;
+        _beamspotConstraint = bsConst;
         _targetConstraint = constToBS;
-        if(_beamspotConstraint&&_targetConstraint)
+        if (_beamspotConstraint && _targetConstraint) {
             System.out.println("BilliorVertexer::Warning!!!  Setting both _beamspotConstraint and _targetConstraint to true!");
-        if(_beamspotConstraint)
-            _constraintType="BeamspotConstrained";
-        if(_targetConstraint)
-            _constraintType="TargetConstrained";
+        }
+        if (_beamspotConstraint) {
+            _constraintType = "BeamspotConstrained";
+        }
+        if (_targetConstraint) {
+            _constraintType = "TargetConstrained";
+        }
+    }
+
+    public void setDebug(boolean debug) {
+        _debug = debug;
     }
 
     public BilliorVertex fitVertex(List<BilliorTrack> tracks) {
         _ntracks = tracks.size();
         follow1985Paper(tracks);
-        if (_beamspotConstraint)
-            addV0fromBSConstraint();
-        else if (_targetConstraint)
-            constrainV0toBS();
-        Map<Integer,Hep3Vector> pFitMap=new HashMap<Integer,Hep3Vector>();
-        for(int i=0;i<tracks.size();i++){
-            Hep3Vector pFit=new BasicHep3Vector(this.getFittedMomentum(i));
-            pFitMap.put(i, pFit);            
-        }
-        Hep3Vector vert=new BasicHep3Vector(_vertexPosition.e(0, 0),_vertexPosition.e(1, 0),_vertexPosition.e(2, 0));
-        Hep3Vector vertDet=CoordinateTransformations.transformVectorToDetector(vert);
-        SymmetricMatrix covVtxDet=CoordinateTransformations.transformCovarianceToDetector(new SymmetricMatrix( _covVtx));
-        return new BilliorVertex(vertDet,covVtxDet,_chiSq,getInvMass(),pFitMap,_constraintType);
-    }
-
-    public BilliorVertex fitFastVertex(List<BilliorTrack> tracks) {
-        _ntracks = tracks.size();
-        fastVertex(tracks);
-     Hep3Vector vert=new BasicHep3Vector(_vertexPosition.e(0, 0),_vertexPosition.e(1, 0),_vertexPosition.e(2, 0));
-     return new BilliorVertex((Hep3Vector)_vertexPosition,_covVtx,_chiSq,getInvMass());
-    }
-
-    private void calculateCovariance() {
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix b = (BasicMatrix) BList.get(i);
-            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-            BasicMatrix bt = (BasicMatrix) MatrixOp.transposed(b);
-            covVtxMomList.add((MatrixOp.mult(-1, MatrixOp.mult(_covVtx, MatrixOp.mult(b, cinv)))));
-            for (int j = 0; j < _ntracks; j++) {
-                BasicMatrix bj = (BasicMatrix) BList.get(j);
-                BasicMatrix cjinv = (BasicMatrix) CinvList.get(j);
-                BasicMatrix tmp = (BasicMatrix) MatrixOp.mult(cinv, MatrixOp.mult(bt, MatrixOp.mult(_covVtx, MatrixOp.mult(bj, cjinv))));
-                if (i == j)
-                    tmp = (BasicMatrix) MatrixOp.add(tmp, cinv);
-                covMomList[i][j] = tmp;
-            }
-        }
-    }
-
-    private void calculateMomenta() {
-
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix params = (BasicMatrix) paramList.get(i);
-            BasicMatrix b = (BasicMatrix) BList.get(i);
-            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-            BasicMatrix u = (BasicMatrix) UList.get(i);
-            //not sure following line is correct...mg 10/21/10
-            BasicMatrix CinvU = (BasicMatrix) MatrixOp.mult(cinv, u);
-            BasicMatrix CinvBTdV = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(cinv, MatrixOp.mult(MatrixOp.transposed(b), _vertexPosition)));
-//            if(_debug)System.out.println(" B = "+b.toString());
-//            if(_debug)System.out.println(" cinv = "+cinv.toString());
-//            if(_debug)System.out.println(" u = "+u.toString());
-//            if(_debug)System.out.println(" CinvU = "+CinvU.toString());
-//            if(_debug)System.out.println(" CinvBTdV = "+CinvBTdV.toString());
-            BasicMatrix tmpP = (BasicMatrix) MatrixOp.add(CinvBTdV, CinvU);
-            tmpP.setElement(0, 0, tmpP.e(0, 0) + params.e(2, 0));
-            tmpP.setElement(1, 0, tmpP.e(1, 0) + params.e(3, 0));
-            tmpP.setElement(2, 0, tmpP.e(2, 0) + params.e(4, 0));
-            _pFit.add(tmpP);
-//            if(_debug)System.out.println("Track "+i+" orig parameters  = "+params);
-//            if(_debug)System.out.println("Track "+i+" deltaP  = "+MatrixOp.add(CinvBTdV, CinvU));
-//            if(_debug)System.out.println("Track " + i + " _pFit  = " + tmpP);
-        }
-    }
-
-    private void calculateVertexPosition() {
-        BasicMatrix tmpcov = new BasicMatrix(3, 3);
-        BasicMatrix tmp = new BasicMatrix(3, 1);
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix b = (BasicMatrix) BList.get(i);
-            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-            BasicMatrix u = (BasicMatrix) UList.get(i);
-//            if(_debug)System.out.println("Cinv matrix " + cinv.toString());
-//            if(_debug)System.out.println("B matrix " + b.toString());
-//            if(_debug)System.out.println("U matrix " + u.toString());
-            BasicMatrix bt = (BasicMatrix) MatrixOp.transposed(b);
-            //           if(_debug)System.out.println("Adding this to tmpcov : " + MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt))));
-            if (i == 0) {
-                tmpcov = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt)));
-                tmp = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, u)));
-            } else {
-                tmpcov = (BasicMatrix) MatrixOp.add(tmpcov, MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt))));
-                tmp = (BasicMatrix) MatrixOp.add(tmp, MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, u))));
-            }
-//            if(_debug)System.out.println("tmpCov matrix " + tmpcov.toString());
-//            if(_debug)System.out.println("tmp matrix " + tmp.toString());
-        }
-//
-//        if(_debug)System.out.println("A matrix " + A.toString());
-//        if(_debug)System.out.println("tmpCov matrix " + tmpcov.toString());
-//        if(_debug)System.out.println("sum of A and tmpCov = " + MatrixOp.add(A, tmpcov).toString());
-        _covVtx = MatrixOp.inverse(MatrixOp.add(A, tmpcov));
-//        if(_debug)System.out.println("_covVtx matrix " + _covVtx.toString());
-//        if(_debug)System.out.println("T matrix " + T.toString());
-        _vertexPosition = (BasicMatrix) MatrixOp.mult(_covVtx, MatrixOp.add(T, tmp));
-
-    }
-
-    private void makeOtherMatrices() {
-        BasicMatrix tmpA = new BasicMatrix(3, 3);
-        BasicMatrix tmpT = new BasicMatrix(3, 1);
-
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix tmpD = (BasicMatrix) DList.get(i);
-            BasicMatrix tmpE = (BasicMatrix) EList.get(i);
-            BasicMatrix dq = (BasicMatrix) dqList.get(i);
-            BasicMatrix tmpW = (BasicMatrix) WList.get(i);
-
-            if (i == 0) {
-                tmpA = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-                tmpT = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, dq));
-            } else {
-                tmpT = (BasicMatrix) MatrixOp.add(tmpT, MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, dq)));
-                tmpA = (BasicMatrix) MatrixOp.add(tmpA, MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD)));
-            }
-            BList.add(MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpE)));
-            BasicMatrix tmpC = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpE), MatrixOp.mult(tmpW, tmpE));
-            CList.add(tmpC);
-            CinvList.add(MatrixOp.inverse(tmpC));
-            UList.add(MatrixOp.mult(MatrixOp.transposed(tmpE), MatrixOp.mult(tmpW, dq)));
-
-        }
-        A = tmpA;
-        T = tmpT;
-    }
-
-    private void calculateChisq() {
-        _chiSq = 0;
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix params = (BasicMatrix) paramList.get(i);
-            BasicMatrix d = (BasicMatrix) DList.get(i);
-            BasicMatrix e = (BasicMatrix) EList.get(i);
-            BasicMatrix w = (BasicMatrix) WList.get(i);
-            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-            BasicMatrix Vtilde = (BasicMatrix) MatrixOp.mult(d, _vertexPosition);
-            BasicMatrix Trtilde = (BasicMatrix) MatrixOp.mult(e, pi);
-            BasicMatrix ptilde = (BasicMatrix) MatrixOp.add(Vtilde, Trtilde);
-            //          if(_debug)System.out.println("Vtilde = "+Vtilde);
-            //          if(_debug)System.out.println("Trtilde = "+Trtilde);
-            BasicMatrix resid = (BasicMatrix) MatrixOp.add(params, MatrixOp.mult(-1, ptilde));
-            BasicMatrix residT = (BasicMatrix) MatrixOp.transposed(resid);
-//            if(_debug)System.out.println("ptilde = "+ptilde);
-//              if(_debug)System.out.println("params = "+params);
-//            if(_debug)System.out.println("resid = "+resid);
-//            if(_debug)System.out.println("Covariance = "+MatrixOp.inverse(w));
-//             if(_debug)System.out.println("Weight = "+w);
-            _chiSq = _chiSq + (MatrixOp.mult(residT, MatrixOp.mult(w, resid))).e(0, 0);
-//            if(_debug)System.out.println("_chiSq = "+_chiSq);
-        }
-    }
-
-    private void fastVertex(List<BilliorTrack> tracks) {
-        boolean firstTrack = true;
-        BasicMatrix sumwi = new BasicMatrix(3, 3);
-        BasicMatrix sumwiXi = new BasicMatrix(3, 1);
-        BasicMatrix dX = new BasicMatrix(3, 1);
-
-        for (BilliorTrack bt : tracks) {
-            double[] par = bt.parameters();
-//            if(_debug)System.out.println("Track parameters = (" + par[0] + ", " + par[1] + ", " + par[2] + ", " + par[3] + ", " + par[4] + ")");
-            double cotth = 1. / tan(par[2]);
-            double phiv = par[3];
-            double cosf = cos(phiv);
-            double sinf = sin(phiv);
-
-            double xi = par[0] * sin(par[3]);
-            double yi = -par[0] * cos(par[3]);
-            double zi = par[1];
-
-            dX.setElement(0, 0, xi);
-            dX.setElement(1, 0, yi);
-            dX.setElement(2, 0, zi);
-
-            BasicMatrix tmpD = new BasicMatrix(2, 3);
-            tmpD.setElement(0, 0, sinf);
-            tmpD.setElement(0, 1, -cosf);
-            tmpD.setElement(1, 0, -cotth * cosf);
-            tmpD.setElement(1, 1, -cotth * sinf);
-            tmpD.setElement(1, 2, 1);
-            BasicMatrix trkCov = new BasicMatrix(2, 2);
-            trkCov.setElement(0, 0, bt.covariance().e(0, 0));
-            trkCov.setElement(0, 1, bt.covariance().e(0, 1));
-            trkCov.setElement(1, 0, bt.covariance().e(1, 0));
-            trkCov.setElement(1, 1, bt.covariance().e(1, 1));
-            BasicMatrix tmpW = (BasicMatrix) MatrixOp.inverse(trkCov);
-            BasicMatrix wi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-            if (firstTrack) {
-                sumwi = wi;
-                sumwiXi = (BasicMatrix) MatrixOp.mult(wi, dX);
-            } else {
-                sumwi = (BasicMatrix) MatrixOp.add(sumwi, wi);
-                sumwiXi = (BasicMatrix) MatrixOp.add(sumwiXi, MatrixOp.mult(wi, dX));
-            }
-            firstTrack = false;
-        }
-        _covVtx = MatrixOp.inverse(sumwi);
-        if (_debug)
-            System.out.println("fastVertex::_covVtx matrix " + _covVtx.toString());
-        _vertexPosition = (BasicMatrix) MatrixOp.mult(_covVtx, sumwiXi);
-        _chiSq = 0;
-        //get the chisq
-        for (BilliorTrack bt : tracks) {
-            double[] par = bt.parameters();
-//            if(_debug)System.out.println("Track parameters = (" + par[0] + ", " + par[1] + ", " + par[2] + ", " + par[3] + ", " + par[4] + ")");
-            double cotth = 1. / tan(par[2]);
-            double phiv = par[3];
-            double cosf = cos(phiv);
-            double sinf = sin(phiv);
-
-            double xi = par[0] * sin(par[3]);
-            double yi = -par[0] * cos(par[3]);
-            double zi = par[1];
-            //this is xi - fitted vertex now
-            dX.setElement(0, 0, xi - _vertexPosition.e(0, 0));
-            dX.setElement(1, 0, yi - _vertexPosition.e(1, 0));
-            dX.setElement(2, 0, zi - _vertexPosition.e(2, 0));
-
-            BasicMatrix tmpD = new BasicMatrix(2, 3);
-            tmpD.setElement(0, 0, sinf);
-            tmpD.setElement(0, 1, -cosf);
-            tmpD.setElement(1, 0, -cotth * cosf);
-            tmpD.setElement(1, 1, -cotth * sinf);
-            tmpD.setElement(1, 2, 1);
-            BasicMatrix trkCov = new BasicMatrix(2, 2);
-            trkCov.setElement(0, 0, bt.covariance().e(0, 0));
-            trkCov.setElement(0, 1, bt.covariance().e(0, 1));
-            trkCov.setElement(1, 0, bt.covariance().e(1, 0));
-            trkCov.setElement(1, 1, bt.covariance().e(1, 1));
-            BasicMatrix tmpW = (BasicMatrix) MatrixOp.inverse(trkCov);
-            BasicMatrix wi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-            _chiSq += MatrixOp.mult(MatrixOp.transposed(dX), MatrixOp.mult(wi, dX)).e(0, 0);
-        }
-    }
-
-    private void makeDerivativeMatrices(List<BilliorTrack> tracks) {
-
-        //DList.clear();
-        //EList.clear();
-        //paramList.clear();
-        //dqList.clear();
-        //WList.clear();
-        BasicMatrix dq = new BasicMatrix(5, 1);
-        BasicMatrix tmpW = new BasicMatrix(5, 5);
-        for (BilliorTrack bt : tracks) {
-            double[] par = bt.parameters();
-            BasicMatrix tmpPar = new BasicMatrix(5, 1);
-            tmpPar.setElement(0, 0, par[0]);
-            tmpPar.setElement(1, 0, par[1]);
-            tmpPar.setElement(2, 0, par[2]);
-            tmpPar.setElement(3, 0, par[3]);
-            tmpPar.setElement(4, 0, par[4]);
-            paramList.add(tmpPar);
-            double cotth = 1. / tan(par[2]);
-            double uu = _v0[0] * cos(par[3]) + _v0[1] * sin(par[3]);//Q
-            double vv = _v0[1] * cos(par[3]) - _v0[0] * sin(par[3]);//R
-            double eps = -vv - .5 * uu * uu * par[4];
-            double zp = _v0[2] - uu * (1 - vv * par[4]) * cotth;
-            // * phi at vertex with these parameters
-            double phiv = par[3] + uu * par[4];
-            double cosf = cos(phiv);
-            double sinf = sin(phiv);
-
-            BasicMatrix tmpD = new BasicMatrix(5, 3);
-            tmpD.setElement(0, 0, sinf);
-            tmpD.setElement(0, 1, -cosf);
-            tmpD.setElement(1, 0, -cotth * cosf);
-            tmpD.setElement(1, 1, -cotth * sinf);
-            tmpD.setElement(1, 2, 1);
-            tmpD.setElement(3, 0, -par[4] * cosf);
-            tmpD.setElement(3, 1, -par[4] * sinf);
-
-            BasicMatrix tmpE = new BasicMatrix(5, 3);
-            tmpE.setElement(0, 1, uu);
-            tmpE.setElement(0, 2, -uu * uu / 2);
-            tmpE.setElement(1, 0, uu * (1 + cotth * cotth));
-            tmpE.setElement(1, 1, -vv * cotth);
-            tmpE.setElement(1, 2, uu * vv * cotth);
-            tmpE.setElement(3, 1, 1);
-            tmpE.setElement(3, 2, -uu);
-            tmpE.setElement(2, 0, 1);  //partial(theta)/dtheta
-            tmpE.setElement(4, 2, 1); //partial (rho)/drho
-            DList.add(tmpD);
-            EList.add(tmpE);
-
-            double deps = par[0] - eps;
-            double dzp = par[1] - zp;
-            double dphi = par[3] - phiv;
-
-            dq.setElement(0, 0, deps);
-            dq.setElement(1, 0, dzp);
-            dq.setElement(3, 0, dphi);
-            dqList.add(dq);
-            tmpW = (BasicMatrix) MatrixOp.inverse(bt.covariance());
-            WList.add(tmpW);
-
-            if (_debug)
-                System.out.println("makeDerivativeMatrices::Params = \n" + tmpPar);
-            if (_debug)
-                System.out.println("D = \n" + tmpD);
-            if (_debug)
-                System.out.println("E = \n" + tmpE);
-            if (_debug)
-                System.out.println("dq = \n" + dq);
-            if (_debug)
-                System.out.println("W = \n" + tmpW);
-        }
-
-    }
-
-    /*  Add the constraint that V0 points back to beamspot
+        if (_beamspotConstraint) {
+            applyBSconstraint(true);
+        } else if (_targetConstraint) {
+            applyBSconstraint(false);
+        }
+        Map<Integer, Hep3Vector> pFitMap = new HashMap<Integer, Hep3Vector>();
+        for (int i = 0; i < tracks.size(); i++) {
+            Hep3Vector pFit = new BasicHep3Vector(this.getFittedMomentum(i));
+            pFitMap.put(i, pFit);
+        }
+        Hep3Vector vert = new BasicHep3Vector(_vertexPosition.e(0, 0), _vertexPosition.e(1, 0), _vertexPosition.e(2, 0));
+        Hep3Vector vertDet = CoordinateTransformations.transformVectorToDetector(vert);
+        SymmetricMatrix covVtxDet = CoordinateTransformations.transformCovarianceToDetector(new SymmetricMatrix(_covVtx));
+        return new BilliorVertex(vertDet, covVtxDet, _chiSq, getInvMass(), pFitMap, _constraintType);
+    }
+
+    /*  Add the constraint that V0 is at/points back to beamspot
      *  this method is based on progressive least squares fit
      *  using the unconstrained fit result as the (k-1) fit
      *
      *  all notation is taken from:
      * W. Hulsbergen, NIM 552 (2005) 566-575
      */
-    private void addV0fromBSConstraint() {
-        BasicMatrix Hk = new BasicMatrix(3 * (_ntracks + 1), 3);
+    private void applyBSconstraint(boolean pointback) {
+        String methodName = pointback ? "constrainV0toBS" : "constrainV0toTarget";
         BasicMatrix Ckm1 = new BasicMatrix(3 * (_ntracks + 1), 3 * (_ntracks + 1));
         BasicMatrix Xkm1 = new BasicMatrix(3 * (_ntracks + 1), 1);
         MatrixOp.setSubMatrix(Ckm1, _covVtx, 0, 0);
         MatrixOp.setSubMatrix(Xkm1, _vertexPosition, 0, 0);
         int n = 1;
         for (Matrix covVtxMom : covVtxMomList) {
-            if (_debug)
-                System.out.println("addV0fromBSConstraint::Track " + n + "  covVtxMom : " + covVtxMom.toString());
+            if (_debug) {
+                System.out.println(methodName + "::Track " + n + "  covVtxMom : " + covVtxMom.toString());
+            }
             MatrixOp.setSubMatrix(Ckm1, covVtxMom, 0, 3 * n);
             MatrixOp.setSubMatrix(Ckm1, MatrixOp.transposed(covVtxMom), 3 * n, 0);
             n++;
@@ -411,10 +114,12 @@
         for (int i = 0; i < _ntracks; i++) {
             BasicMatrix pi = (BasicMatrix) _pFit.get(i);
             MatrixOp.setSubMatrix(Xkm1, pi, 3 * (i + 1), 0);
-            if (_debug)
-                System.out.println("addV0fromBSConstraint::Track " + i + "  p : " + pi.toString());
-            for (int j = 0; j < _ntracks; j++)
+            if (_debug) {
+                System.out.println(methodName + "::Track " + i + "  p : " + pi.toString());
+            }
+            for (int j = 0; j < _ntracks; j++) {
                 MatrixOp.setSubMatrix(Ckm1, covMomList[i][j], 3 * (i + 1), 3 * (j + 1));
+            }
         }
 
         //  now calculate the derivative matrix for the beam constraint.
@@ -443,17 +148,96 @@
             pztot += pz;
         }
         //calculate the position of the A' at X=0
-        BasicMatrix rk = new BasicMatrix(3, 1);
-        if (_debug)
-            System.out.println("addV0fromBSConstraint::Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
-        rk.setElement(0, 0, 0);
-        rk.setElement(1, 0, 0 - (Vy - pytot / pxtot * Vx));
-        rk.setElement(2, 0, 0 - (Vz - pztot / pxtot * Vx));
-
+        BasicMatrix rk = makeRk(Vx, Vy, Vz, pxtot, pytot, pztot, pointback);
+        if (_debug) {
+            System.out.println(methodName + "::rk = " + rk);
+        }
+
+        BasicMatrix Hk = makeHk(Vx, pxtot, pytot, pztot, pointback);
+        if (_debug) {
+            System.out.println(methodName + "::Hk = " + Hk);
+        }
+
+        // the beam covariance
+        BasicMatrix Vk = new BasicMatrix(3, 3);
+        Vk.setElement(0, 0, _beamSize[0] * _beamSize[0]);
+        Vk.setElement(1, 1, _beamSize[1] * _beamSize[1]);
+        Vk.setElement(2, 2, _beamSize[2] * _beamSize[2]);
+
+        //now do the matrix operations to get the constrained parameters
+        BasicMatrix Hkt = (BasicMatrix) MatrixOp.transposed(Hk);
+        if (_debug) {
+            System.out.println(methodName + "::Ckm1Hk = " + MatrixOp.mult(Ckm1, Hk));
+        }
+
+        BasicMatrix Rk = (BasicMatrix) MatrixOp.mult(Hkt, MatrixOp.mult(Ckm1, Hk));
+        if (_debug) {
+            System.out.println("Pre Vk:  Rk = " + Rk.toString());
+        }
+        Rk = (BasicMatrix) MatrixOp.add(Rk, Vk);
+        if (_debug) {
+            System.out.println("Post Vk:  Rk = " + Rk.toString());
+        }
+        BasicMatrix Rkinv = (BasicMatrix) MatrixOp.inverse(Rk);
+        BasicMatrix Kk = (BasicMatrix) MatrixOp.mult(Ckm1, MatrixOp.mult(Hk, Rkinv));
+
+//        if(_debug)System.out.println("Ckm1 = " + Ckm1.toString());
+//        if(_debug)System.out.println("Hk = " + Hk.toString());
+//        if(_debug)System.out.println("Rk = " + Rk.toString());
+//        if(_debug)System.out.println("Vk = " + Vk.toString());
+//        if(_debug)System.out.println("rk = " + rk.toString());
+//        if(_debug)System.out.println("Kk = " + Kk.toString());
+        _constrainedFit = MatrixOp.mult(Kk, rk);
+        _constrainedFit = MatrixOp.add(_constrainedFit, Xkm1);//Xk
+
+        //ok, get the new covariance
+        BasicMatrix RkKkt = (BasicMatrix) MatrixOp.mult(Rk, MatrixOp.transposed(Kk));
+        BasicMatrix HkCkm1 = (BasicMatrix) MatrixOp.mult(Hkt, Ckm1);
+        RkKkt = (BasicMatrix) MatrixOp.mult(1, RkKkt);
+        HkCkm1 = (BasicMatrix) MatrixOp.mult(-2, HkCkm1);
+        BasicMatrix sumMatrix = (BasicMatrix) MatrixOp.mult(Kk, MatrixOp.add(HkCkm1, RkKkt));
+        _constrainedCov = (BasicMatrix) MatrixOp.add(Ckm1, sumMatrix);
+
+        //update the regular parameter names to the constrained result
+//        if(_debug)System.out.println("Without Constraint : " + _vertexPosition.toString());
+//        if(_debug)System.out.println("Without Constraint:  x= "+_vertexPosition.e(0,0));
+        //        if(_debug)System.out.println(_constrainedFit.toString());
+//         if(_debug)System.out.println("Without Constraint : " + _covVtx.toString());
+        _vertexPosition = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 0, 0, 3, 1);
+        _covVtx = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedCov, 0, 0, 3, 3);
+//        if(_debug)System.out.println("With Constraint : " + _vertexPosition.toString());
+//        if(_debug)System.out.println("With Constraint : " + _covVtx.toString());
+
+        if (_debug) {
+            System.out.println("Constrained vertex: " + _vertexPosition);
+        }
+
+        for (int i = 0; i < _ntracks; i++) {
+            BasicMatrix ptmp = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 3 * (i + 1), 0, 3, 1);
+            _pFit.set(i, ptmp);
+        }
+
+//        if(_debug)System.out.println("Unconstrained chi^2 = "+_chiSq);
+        //ok...add to the chi^2
+        if (_debug) {
+            System.out.println("Chisq contribution: " + MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
+        }
+        _chiSq += MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)).e(0, 0);
+//        if(_debug)System.out.println("Constrained chi^2 = "+_chiSq);
+    }
+
+    private BasicMatrix makeHk(double Vx, double pxtot, double pytot, double pztot, boolean bscon) {
+        BasicMatrix Hk = new BasicMatrix(3 * (_ntracks + 1), 3);
 //  ok, can set the derivitives wrt to V
-        Hk.setElement(0, 0, 0);
-        Hk.setElement(0, 1, pytot / pxtot);
-        Hk.setElement(0, 2, pztot / pxtot);
+        if (bscon) {
+            Hk.setElement(0, 0, 0);
+            Hk.setElement(0, 1, pytot / pxtot);
+            Hk.setElement(0, 2, pztot / pxtot);
+        } else {
+            Hk.setElement(0, 0, 1);
+            Hk.setElement(0, 1, 0);
+            Hk.setElement(0, 2, 0);
+        }
         Hk.setElement(1, 0, 0);
         Hk.setElement(1, 1, 1);
         Hk.setElement(1, 2, 0);
@@ -467,243 +251,67 @@
             double phiv = pi.e(1, 0);
             double rho = pi.e(2, 0);
             double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
-            double px = Pt * Math.cos(phiv);
-            double py = Pt * Math.sin(phiv);
-            double pz = Pt * 1 / Math.tan(theta);
+//            double px = Pt * Math.cos(phiv);
+//            double py = Pt * Math.sin(phiv);
+//            double pz = Pt * 1 / Math.tan(theta);
             //derivities wrt theta
             Hk.setElement(3 * (i + 1), 0, 0);
             Hk.setElement(3 * (i + 1), 1, 0);
-            Hk.setElement(3 * (i + 1), 2, -Pt / Math.pow(sin(theta), 2) * Vx);
+            if (bscon) {
+                Hk.setElement(3 * (i + 1), 2,
+                        -Pt / Math.pow(sin(theta), 2) * (Vx - _beamPosition[0]));
+            } else {
+                Hk.setElement(3 * (i + 1), 2, 0);
+            }
             //derivities wrt phi
             Hk.setElement(3 * (i + 1) + 1, 0, 0);
-            Hk.setElement(3 * (i + 1) + 1, 1,
-                    (Pt * Pt * cos(phiv) * sin(phiv) / (pxtot * pxtot)) * Vx);
-            Hk.setElement(3 * (i + 1) + 1, 2, (Pt * sin(phiv) / (pxtot * pxtot)) * Vx * pztot);
+            if (bscon) {
+                Hk.setElement(3 * (i + 1) + 1, 1,
+                        (Pt * Pt * cos(phiv) * sin(phiv) / (pxtot * pxtot)) * (Vx - _beamPosition[0]));
+                Hk.setElement(3 * (i + 1) + 1, 2,
+                        (Pt * sin(phiv) / (pxtot * pxtot)) * (Vx - _beamPosition[0]) * pztot);
+            } else {
+                Hk.setElement(3 * (i + 1) + 1, 1, 0);
+                Hk.setElement(3 * (i + 1) + 1, 2, 0);
+            }
             //derivities wrt rho
             Hk.setElement(3 * (i + 1) + 2, 0, 0);
 //            Hk.setElement(3 * (i + 1) + 2, 1,
 //                    (pytot / pxtot - 1) * (Pt / rho) * (1 / pxtot) * Vx);
 //            Hk.setElement(3 * (i + 1) + 2, 2,
 //                    (pztot / pxtot - 1) * (Pt / rho) * (1 / pxtot) * Vx);
-            Hk.setElement(3 * (i + 1) + 2, 1,
-                    (cos(phiv) * pytot / pxtot - sin(phiv)) * (Pt / rho) * (1 / pxtot) * Vx);
-            Hk.setElement(3 * (i + 1) + 2, 2,
-                    (cos(phiv) * pztot / pxtot - sin(phiv)) * (Pt / rho) * (1 / pxtot) * Vx);
+            if (bscon) {
+                Hk.setElement(3 * (i + 1) + 2, 1,
+                        (cos(phiv) * pytot / pxtot - sin(phiv)) * (Pt / rho) * (1 / pxtot) * (Vx - _beamPosition[0]));
+                Hk.setElement(3 * (i + 1) + 2, 2,
+                        (cos(phiv) * pztot / pxtot - sin(phiv)) * (Pt / rho) * (1 / pxtot) * (Vx - _beamPosition[0]));
+            } else {
+                Hk.setElement(3 * (i + 1) + 2, 1, 0);
+                Hk.setElement(3 * (i + 1) + 2, 2, 0);
+            }
             //                   if(_debug)System.out.println("pxtot = "+pxtot+"; rho = "+rho+"; Pt = "+Pt);
             //                   if(_debug)System.out.println("cos(phiv)*pytot / pxtot - sin(phiv) = "+(cos(phiv)*pytot / pxtot - sin(phiv)));
             //                   if(_debug)System.out.println("Pt/(rho*pxtot) = "+(Pt / rho) * (1 / pxtot));
         }
-        // the beam covariance
-        BasicMatrix Vk = new BasicMatrix(3, 3);
-        Vk.setElement(0, 0, _beamSize[0] * _beamSize[0]);
-        Vk.setElement(1, 1, _beamSize[1] * _beamSize[1]);
-        Vk.setElement(2, 2, _beamSize[2] * _beamSize[2]);
-
-        //now do the matrix operations to get the constrained parameters
-        BasicMatrix Hkt = (BasicMatrix) MatrixOp.transposed(Hk);
-        if (_debug)
-            System.out.println("addV0fromBSConstraint::Ckm1Hk = " + MatrixOp.mult(Ckm1, Hk));
-
-        BasicMatrix Rk = (BasicMatrix) MatrixOp.mult(Hkt, MatrixOp.mult(Ckm1, Hk));
-        if (_debug)
-            System.out.println("Pre Vk:  Rk = " + Rk.toString());
-        Rk = (BasicMatrix) MatrixOp.add(Rk, Vk);
-        if (_debug)
-            System.out.println("Post Vk:  Rk = " + Rk.toString());
-        BasicMatrix Rkinv = (BasicMatrix) MatrixOp.inverse(Rk);
-        BasicMatrix Kk = (BasicMatrix) MatrixOp.mult(Ckm1, MatrixOp.mult(Hk, Rkinv));
-
-//        if(_debug)System.out.println("Ckm1 = " + Ckm1.toString());
-//        if(_debug)System.out.println("Hk = " + Hk.toString());
-//        if(_debug)System.out.println("Rk = " + Rk.toString());
-//        if(_debug)System.out.println("Vk = " + Vk.toString());
-//        if(_debug)System.out.println("rk = " + rk.toString());
-//        if(_debug)System.out.println("Kk = " + Kk.toString());
-        _constrainedFit = MatrixOp.mult(Kk, rk);
-        _constrainedFit = MatrixOp.add(_constrainedFit, Xkm1);//Xk
-
-        //ok, get the new covariance
-        BasicMatrix RkKkt = (BasicMatrix) MatrixOp.mult(Rk, MatrixOp.transposed(Kk));
-        BasicMatrix HkCkm1 = (BasicMatrix) MatrixOp.mult(Hkt, Ckm1);
-        RkKkt = (BasicMatrix) MatrixOp.mult(1, RkKkt);
-        HkCkm1 = (BasicMatrix) MatrixOp.mult(-2, HkCkm1);
-        BasicMatrix sumMatrix = (BasicMatrix) MatrixOp.mult(Kk, MatrixOp.add(HkCkm1, RkKkt));
-        _constrainedCov = (BasicMatrix) MatrixOp.add(Ckm1, sumMatrix);
-
-        //update the regular parameter names to the constrained result
-//        if(_debug)System.out.println("Without Constraint : " + _vertexPosition.toString());
-//        if(_debug)System.out.println("Without Constraint:  x= "+_vertexPosition.e(0,0));
-        //        if(_debug)System.out.println(_constrainedFit.toString());
-//         if(_debug)System.out.println("Without Constraint : " + _covVtx.toString());
-        _vertexPosition = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 0, 0, 3, 1);
-        _covVtx = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedCov, 0, 0, 3, 3);
-//        if(_debug)System.out.println("With Constraint : " + _vertexPosition.toString());
-//        if(_debug)System.out.println("With Constraint : " + _covVtx.toString());
-
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix ptmp = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 3 * (i + 1), 0, 3, 1);
-            _pFit.set(i, ptmp);
-        }
-
-//        if(_debug)System.out.println("Unconstrained chi^2 = "+_chiSq);
-        //ok...add to the chi^2
-        if (_debug)
-            System.out.println(MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
-        _chiSq += MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)).e(0, 0);
-//        if(_debug)System.out.println("Constrained chi^2 = "+_chiSq);
-    }
-
-    private void constrainV0toBS() {
-        BasicMatrix Hk = new BasicMatrix(3 * (_ntracks + 1), 3);
-        BasicMatrix Ckm1 = new BasicMatrix(3 * (_ntracks + 1), 3 * (_ntracks + 1));
-        BasicMatrix Xkm1 = new BasicMatrix(3 * (_ntracks + 1), 1);
-        MatrixOp.setSubMatrix(Ckm1, _covVtx, 0, 0);
-        MatrixOp.setSubMatrix(Xkm1, _vertexPosition, 0, 0);
-
-        int n = 1;
-        for (Matrix covVtxMom : covVtxMomList) {
-            if (_debug)
-                System.out.println("constrainV0toBS::Track " + n + "  covVtxMom : " + covVtxMom.toString());
-            MatrixOp.setSubMatrix(Ckm1, covVtxMom, 0, 3 * n);
-            MatrixOp.setSubMatrix(Ckm1, MatrixOp.transposed(covVtxMom), 3 * n, 0);
-            n++;
-        }
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-            MatrixOp.setSubMatrix(Xkm1, pi, 3 * (i + 1), 0);
-            //           if(_debug)System.out.println("Track "+i+"  p : " + pi.toString());
-            for (int j = 0; j < _ntracks; j++)
-                MatrixOp.setSubMatrix(Ckm1, covMomList[i][j], 3 * (i + 1), 3 * (j + 1));
-        }
-        //  now calculate the derivative matrix for the beam constraint.
-        //  the beamspot is assumed to be at bvec=(0,0,0)
-        //  the V0 production position is Vbvec=(0,0,0)
-        //  where ptot=sum_i (pi)
-        //  need derivites wrt to the vertex position and momentum (theta,phi_v,rho)
-        double Vx = _vertexPosition.e(0, 0);
-        double Vy = _vertexPosition.e(1, 0);
-        double Vz = _vertexPosition.e(2, 0);
-        //first, get the sum of momenta...
-        double pxtot = 0;
-        double pytot = 0;
-        double pztot = 0;
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-            double theta = pi.e(0, 0);
-            double phiv = pi.e(1, 0);
-            double rho = pi.e(2, 0);
-            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
-            double px = Pt * Math.cos(phiv);
-            double py = Pt * Math.sin(phiv);
-            double pz = Pt * 1 / Math.tan(theta);
-            pxtot += px;
-            pytot += py;
-            pztot += pz;
-        }
+        return Hk;
+    }
+
+    private BasicMatrix makeRk(double Vx, double Vy, double Vz, double pxtot, double pytot, double pztot, boolean bscon) {
         //calculate the position of the A' at X=0
         BasicMatrix rk = new BasicMatrix(3, 1);
-        //       if(_debug)System.out.println("Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
-        rk.setElement(0, 0, -Vx);
-        rk.setElement(1, 0, -Vy);
-        rk.setElement(2, 0, -Vz);
-
-//  ok, can set the derivitives wrt to V
-        Hk.setElement(0, 0, 1);
-        Hk.setElement(0, 1, 0);
-        Hk.setElement(0, 2, 0);
-        Hk.setElement(1, 0, 0);
-        Hk.setElement(1, 1, 1);
-        Hk.setElement(1, 2, 0);
-        Hk.setElement(2, 0, 0);
-        Hk.setElement(2, 1, 0);
-        Hk.setElement(2, 2, 1);
-//ok, loop over tracks again to set the derivitives wrt track momenta (theta,phi,rho)
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-            double theta = pi.e(0, 0);
-            double phiv = pi.e(1, 0);
-            double rho = pi.e(2, 0);
-            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
-            double px = Pt * Math.cos(phiv);
-            double py = Pt * Math.sin(phiv);
-            double pz = Pt * 1 / Math.tan(theta);
-            //derivities wrt theta
-            Hk.setElement(3 * (i + 1), 0, 0);
-            Hk.setElement(3 * (i + 1), 1, 0);
-            Hk.setElement(3 * (i + 1), 2, 0);
-            //derivities wrt phi
-            Hk.setElement(3 * (i + 1) + 1, 0, 0);
-            Hk.setElement(3 * (i + 1) + 1, 1,
-                    0);
-            Hk.setElement(3 * (i + 1) + 1, 2, 0);
-            //derivities wrt rho
-            Hk.setElement(3 * (i + 1) + 2, 0, 0);
-//            Hk.setElement(3 * (i + 1) + 2, 1,
-//                    (pytot / pxtot - 1) * (Pt / rho) * (1 / pxtot) * Vx);
-//            Hk.setElement(3 * (i + 1) + 2, 2,
-//                    (pztot / pxtot - 1) * (Pt / rho) * (1 / pxtot) * Vx);
-            Hk.setElement(3 * (i + 1) + 2, 1,
-                    0);
-            Hk.setElement(3 * (i + 1) + 2, 2,
-                    0);
-            //                   if(_debug)System.out.println("pxtot = "+pxtot+"; rho = "+rho+"; Pt = "+Pt);
-            //                   if(_debug)System.out.println("cos(phiv)*pytot / pxtot - sin(phiv) = "+(cos(phiv)*pytot / pxtot - sin(phiv)));
-            //                   if(_debug)System.out.println("Pt/(rho*pxtot) = "+(Pt / rho) * (1 / pxtot));
-        }
-        // the beam covariance
-        BasicMatrix Vk = new BasicMatrix(3, 3);
-        Vk.setElement(0, 0, _beamSize[0] * _beamSize[0]);
-        Vk.setElement(1, 1, _beamSize[1] * _beamSize[1]);
-        Vk.setElement(2, 2, _beamSize[2] * _beamSize[2]);
-
-        //now do the matrix operations to get the constrained parameters
-        BasicMatrix Hkt = (BasicMatrix) MatrixOp.transposed(Hk);
-//         if(_debug)System.out.println("Ckm1Hk = " + MatrixOp.mult(Ckm1, Hk));
-
-        BasicMatrix Rk = (BasicMatrix) MatrixOp.mult(Hkt, MatrixOp.mult(Ckm1, Hk));
-//        if(_debug)System.out.println("Pre Vk:  Rk = " + Rk.toString());
-        Rk = (BasicMatrix) MatrixOp.add(Rk, Vk);
-        BasicMatrix Rkinv = (BasicMatrix) MatrixOp.inverse(Rk);
-        BasicMatrix Kk = (BasicMatrix) MatrixOp.mult(Ckm1, MatrixOp.mult(Hk, Rkinv));
-
-//        if(_debug)System.out.println("Ckm1 = " + Ckm1.toString());
-//        if(_debug)System.out.println("Hk = " + Hk.toString());
-//        if(_debug)System.out.println("Rk = " + Rk.toString());
-//        if(_debug)System.out.println("Vk = " + Vk.toString());
-//        if(_debug)System.out.println("rk = " + rk.toString());
-//        if(_debug)System.out.println("Kk = " + Kk.toString());
-        _constrainedFit = MatrixOp.mult(Kk, rk);
-        _constrainedFit = MatrixOp.add(_constrainedFit, Xkm1);//Xk
-
-        //ok, get the new covariance
-        BasicMatrix RkKkt = (BasicMatrix) MatrixOp.mult(Rk, MatrixOp.transposed(Kk));
-        BasicMatrix HkCkm1 = (BasicMatrix) MatrixOp.mult(Hkt, Ckm1);
-        RkKkt = (BasicMatrix) MatrixOp.mult(1, RkKkt);
-        HkCkm1 = (BasicMatrix) MatrixOp.mult(-2, HkCkm1);
-        BasicMatrix sumMatrix = (BasicMatrix) MatrixOp.mult(Kk, MatrixOp.add(HkCkm1, RkKkt));
-        _constrainedCov = (BasicMatrix) MatrixOp.add(Ckm1, sumMatrix);
-
-        //update the regular parameter names to the constrained result
-//        if(_debug)System.out.println("Without Constraint : " + _vertexPosition.toString());
-//        if(_debug)System.out.println("Without Constraint:  x= "+_vertexPosition.e(0,0));
-        //        if(_debug)System.out.println(_constrainedFit.toString());
-//         if(_debug)System.out.println("Without Constraint : " + _covVtx.toString());
-        _vertexPosition = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 0, 0, 3, 1);
-        _covVtx = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedCov, 0, 0, 3, 3);
-//        if(_debug)System.out.println("With Constraint : " + _vertexPosition.toString());
-//        if(_debug)System.out.println("With Constraint : " + _covVtx.toString());
-
-        for (int i = 0; i < _ntracks; i++) {
-            BasicMatrix ptmp = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 3 * (i + 1), 0, 3, 1);
-            _pFit.set(i, ptmp);
-        }
-
-//        if(_debug)System.out.println("Unconstrained chi^2 = "+_chiSq);
-        //ok...add to the chi^2
-        if (_debug)
-            System.out.println(MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
-        _chiSq += MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)).e(0, 0);
-//        if(_debug)System.out.println("Constrained chi^2 = "+_chiSq);
+        if (_debug) {
+            System.out.println("makeRk::Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
+        }
+        if (bscon) {
+            rk.setElement(0, 0, 0);
+            rk.setElement(1, 0, _beamPosition[1] - (Vy - pytot / pxtot * (Vx - _beamPosition[0])));
+            rk.setElement(2, 0, _beamPosition[2] - (Vz - pztot / pxtot * (Vx - _beamPosition[0])));
+        } else {
+            rk.setElement(0, 0, _beamPosition[0] - Vx);
+            rk.setElement(1, 0, _beamPosition[1] - Vy);
+            rk.setElement(2, 0, _beamPosition[2] - Vz);
+        }
+        return rk;
     }
 
     public void setV0(double[] v0) {
@@ -716,15 +324,23 @@
         _beamSize[2] = bs[2];
     }
 
+    public void setBeamPosition(double[] bp) {
+        _beamPosition[0] = bp[0];
+        _beamPosition[1] = bp[1];
+        _beamPosition[2] = bp[2];
+    }
+
     public void doBeamSpotConstraint(boolean bsconst) {
         _beamspotConstraint = bsconst;
-         _constraintType="BeamspotConstrained";
-        
+        _targetConstraint = false;
+        _constraintType = "BeamspotConstrained";
+
     }
 
     public void doTargetConstraint(boolean bsconst) {
+        _beamspotConstraint = false;
         _targetConstraint = bsconst;
-         _constraintType="TargetConstrained";
+        _constraintType = "TargetConstrained";
     }
 
     public double getChiSq() {
@@ -742,12 +358,12 @@
         mom[0] = Pt * Math.cos(phiv);
         mom[1] = Pt * Math.sin(phiv);
         mom[2] = Pt * 1 / Math.tan(theta);
-        if (_debug){
-            System.out.println("getFittedMomentum::  "+mom[0] + "; " + mom[1] + "; " + mom[2]);
-
-            System.out.println("pT= "+Pt+"; phi = "+phiv+"; B = "+ _bField);
-        }
-      return mom;
+        if (_debug) {
+            System.out.println("getFittedMomentum::  " + mom[0] + "; " + mom[1] + "; " + mom[2]);
+
+            System.out.println("pT= " + Pt + "; phi = " + phiv + "; B = " + _bField);
+        }
+        return mom;
     }
 
     private double getInvMass() {
@@ -772,15 +388,17 @@
         double psum = Math.sqrt(pxsum * pxsum + pysum * pysum + pzsum * pzsum);
         double evtmass = esum * esum - psum * psum;
 
-        if (evtmass > 0)
+        if (evtmass > 0) {
             return Math.sqrt(evtmass);
-        else
+        } else {
             return -99;
-    }
-
+        }
+    }
+
+    @Override
     public String toString() {
-        StringBuffer sb = new StringBuffer("Vertex at : \nx= " + _vertexPosition.e(0, 0) + " +/- " + Math.sqrt(_covVtx.e(0, 0)) + "\ny= " + _vertexPosition.e(1, 0) + " +/- " + Math.sqrt(_covVtx.e(1, 1)) + "\nz= " + _vertexPosition.e(2, 0) + " +/- " + Math.sqrt(_covVtx.e(2, 2)));
-        return sb.toString();
+        String sb = "Vertex at : \nx= " + _vertexPosition.e(0, 0) + " +/- " + Math.sqrt(_covVtx.e(0, 0)) + "\ny= " + _vertexPosition.e(1, 0) + " +/- " + Math.sqrt(_covVtx.e(1, 1)) + "\nz= " + _vertexPosition.e(2, 0) + " +/- " + Math.sqrt(_covVtx.e(2, 2));
+        return sb;
     }
 
     private void follow1985Paper(List<BilliorTrack> tracks) {
@@ -789,8 +407,8 @@
         v0.setElement(0, 0, _v0[0]);
         v0.setElement(1, 0, _v0[1]);
         v0.setElement(2, 0, _v0[2]);
-        List<Matrix> params = new ArrayList<Matrix>();
-        List<Matrix> q0s = new ArrayList<Matrix>();
+//        List<Matrix> params = new ArrayList<Matrix>();
+//        List<Matrix> q0s = new ArrayList<Matrix>();
         List<Matrix> Gs = new ArrayList<Matrix>();
         List<Matrix> Ds = new ArrayList<Matrix>();
         List<Matrix> Es = new ArrayList<Matrix>();
@@ -809,13 +427,11 @@
             tmpPar.setElement(2, 0, par[2]);
             tmpPar.setElement(3, 0, par[3]);
             tmpPar.setElement(4, 0, par[4]);
-            params.add(tmpPar);
+//            params.add(tmpPar);
             double theta = par[2];
-            double phiv = par[3];
+//            double phiv = par[3];
             double rho = par[4];
-            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
-
-
+//            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
 
             double cotth = 1. / tan(par[2]);
             double uu = v0.e(0, 0) * cos(par[3]) + v0.e(1, 0) * sin(par[3]);//Q
@@ -833,15 +449,15 @@
 
             BasicMatrix q0 = new BasicMatrix(3, 1);
             /*   this looks just wrong...
-            q0.setElement(0, 0, Pt * Math.cos(phiv));
-            q0.setElement(1, 0, Pt * Math.sin(phiv));
-            q0.setElement(2, 0, Pt * 1 / Math.tan(theta));
-            q0s.add(q0);
+             q0.setElement(0, 0, Pt * Math.cos(phiv));
+             q0.setElement(1, 0, Pt * Math.sin(phiv));
+             q0.setElement(2, 0, Pt * 1 / Math.tan(theta));
+             q0s.add(q0);
              */
             q0.setElement(0, 0, theta);
             q0.setElement(1, 0, phiVert);
             q0.setElement(2, 0, rho);
-            q0s.add(q0);
+//            q0s.add(q0);
 
             double cosf = cos(phiVert);
             double sinf = sin(phiVert);
@@ -875,10 +491,11 @@
             BasicMatrix tmpG = (BasicMatrix) MatrixOp.inverse(bt.covariance());
             Gs.add(tmpG);
 
-            if (firstTrack)
+            if (firstTrack) {
                 D0 = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpA), MatrixOp.mult(tmpG, tmpA));
-            else
+            } else {
                 D0 = (BasicMatrix) MatrixOp.add(D0, MatrixOp.mult(MatrixOp.transposed(tmpA), MatrixOp.mult(tmpG, tmpA)));
+            }
 
             BasicMatrix tmpDi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpA), MatrixOp.mult(tmpG, tmpB));
             BasicMatrix tmpEi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpB), MatrixOp.mult(tmpG, tmpB));
@@ -904,19 +521,21 @@
             BasicMatrix beIbTg = (BasicMatrix) MatrixOp.mult(b, MatrixOp.mult(MatrixOp.inverse(e), MatrixOp.mult(MatrixOp.transposed(b), g)));
             BasicMatrix MinusaTgbeIbTg = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(aTg, beIbTg));
 
-            if (firstTrack)
+            if (firstTrack) {
                 bigsum = (BasicMatrix) MatrixOp.mult(MatrixOp.add(aTg, MinusaTgbeIbTg), p);
-            else
+            } else {
                 bigsum = (BasicMatrix) MatrixOp.add(bigsum, MatrixOp.mult(MatrixOp.add(aTg, MinusaTgbeIbTg), p));
+            }
         }
         BasicMatrix covVtx = (BasicMatrix) MatrixOp.inverse(tmpCovVtx);
         BasicMatrix xtilde = (BasicMatrix) MatrixOp.mult(covVtx, bigsum);
-        if (_debug)
+        if (_debug) {
             System.out.println("follow1985Paper::Vertex at : \nx= " + xtilde.e(0, 0) + " +/- " + Math.sqrt(covVtx.e(0, 0)) + "\ny= " + xtilde.e(1, 0) + " +/- " + Math.sqrt(covVtx.e(1, 1)) + "\nz= " + xtilde.e(2, 0) + " +/- " + Math.sqrt(covVtx.e(2, 2)));
+        }
 
         //ok, now the momentum
-        List<Matrix> qtildes = new ArrayList<Matrix>();
-        List<Matrix> ptildes = new ArrayList<Matrix>();
+//        List<Matrix> qtildes = new ArrayList<Matrix>();
+//        List<Matrix> ptildes = new ArrayList<Matrix>();
         List<Matrix> C0j = new ArrayList<Matrix>();
         List<Matrix> pfit = new ArrayList<Matrix>();
         Matrix[][] Cij = new Matrix[2][2];//max 2 tracks...just make this bigger for more
@@ -934,32 +553,38 @@
             BasicMatrix second = (BasicMatrix) MatrixOp.mult(MatrixOp.inverse(e), MatrixOp.mult(MatrixOp.transposed(b), g));
             second = (BasicMatrix) MatrixOp.mult(second, p);
             BasicMatrix qtilde = (BasicMatrix) MatrixOp.add(first, second);
-            qtildes.add(qtilde);
+//            qtildes.add(qtilde);
             BasicMatrix ptilde = (BasicMatrix) MatrixOp.add(MatrixOp.mult(a, xtilde), MatrixOp.mult(b, qtilde));
-            ptildes.add(ptilde);
+//            ptildes.add(ptilde);
             chisq += MatrixOp.mult(MatrixOp.transposed(MatrixOp.add(p, MatrixOp.mult(-1, ptilde))), MatrixOp.mult(g, MatrixOp.add(p, MatrixOp.mult(-1, ptilde)))).e(0, 0);
-            if (_debug)
+            if (_debug) {
                 System.out.println("\n\nfollow1985Paper::Track #" + j);
-            if (_debug)
+            }
+            if (_debug) {
                 System.out.println("eps(meas)    = " + p.e(0, 0) + "        eps(fit)   =" + ptilde.e(0, 0));
-            if (_debug)
+            }
+            if (_debug) {
                 System.out.println("zp(meas)     = " + p.e(1, 0) + "        zp(fit)    =" + ptilde.e(1, 0));
-            if (_debug)
+            }
+            if (_debug) {
                 System.out.println("theta(meas)  = " + p.e(2, 0) + "        theta(fit) =" + ptilde.e(2, 0));
-            if (_debug)
+            }
+            if (_debug) {
                 System.out.println("phi(meas)    = " + p.e(3, 0) + "        phi(fit)   =" + ptilde.e(3, 0));
-            if (_debug)
+            }
+            if (_debug) {
                 System.out.println("rho(meas)    = " + p.e(4, 0) + "        rho(fit)   =" + ptilde.e(4, 0));
+            }
 
             BasicMatrix tmpC0j = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(covVtx, MatrixOp.mult(d, MatrixOp.inverse(e))));
             C0j.add(tmpC0j);
             for (int i = 0; i < _ntracks; i++) {
-                BasicMatrix ai = (BasicMatrix) As.get(i);
-                BasicMatrix bi = (BasicMatrix) Bs.get(i);
-                BasicMatrix di = (BasicMatrix) Ds.get(i);
-                BasicMatrix ei = (BasicMatrix) Es.get(i);
-                BasicMatrix gi = (BasicMatrix) Gs.get(i);
-                BasicMatrix pi = (BasicMatrix) pis.get(i);
+//                BasicMatrix ai = (BasicMatrix) As.get(i);
+//                BasicMatrix bi = (BasicMatrix) Bs.get(i);
+//                BasicMatrix di = (BasicMatrix) Ds.get(i);
+//                BasicMatrix ei = (BasicMatrix) Es.get(i);
+//                BasicMatrix gi = (BasicMatrix) Gs.get(i);
+//                BasicMatrix pi = (BasicMatrix) pis.get(i);
                 BasicMatrix tmpCij = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(MatrixOp.inverse(e), MatrixOp.mult(MatrixOp.transposed(d), tmpC0j)));
                 Cij[i][j] = tmpCij;
             }
@@ -970,8 +595,9 @@
             pfit.add(tmppfit);
         }
 
-        if (_debug)
+        if (_debug) {
             System.out.println("follow1985Paper::chi^2 = " + chisq);
+        }
 
         _chiSq = chisq;
         _covVtx = covVtx;

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoLineVertexer.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoLineVertexer.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoLineVertexer.java	Wed Apr 27 11:11:32 2016
@@ -20,21 +20,21 @@
  */
 public class TwoLineVertexer extends BaseSimpleVertexer {
     protected Hep3Vector A1,A2,B1,B2;
-	
-	public TwoLineVertexer() {
-		
-	}
-	
+    
+    public TwoLineVertexer() {
+        
+    }
+    
     public void setLines(Hep3Vector PA1, Hep3Vector PA2, Hep3Vector PB1, Hep3Vector PB2) {
-    	this.A1 = PA1;
-    	this.A2 = PA2;
-    	this.B1 = PB1;
-    	this.B2 = PB2;
+        this.A1 = PA1;
+        this.A2 = PA2;
+        this.B1 = PB1;
+        this.B2 = PB2;
     }
   
     public void clear() {
-    	super.clear();
-    	setLines(null,null,null,null);
+        super.clear();
+        setLines(null,null,null,null);
     }
     
     public boolean isValid() {
@@ -44,11 +44,11 @@
     
     @Override
     public void fitVertex() {
-    	assert isValid();
-    	Hep3Vector vtxPosition = getPOCALineToLine();
-		if (vtxPosition!=null) {
-			_fitted_vertex = new BaseVertex(true, "Two Line Vertexer", 0, 0, new SymmetricMatrix(0), vtxPosition, null); 
-    	}
+        assert isValid();
+        Hep3Vector vtxPosition = getPOCALineToLine();
+        if (vtxPosition!=null) {
+            _fitted_vertex = new BaseVertex(true, "Two Line Vertexer", 0, 0, new SymmetricMatrix(0), vtxPosition, null); 
+        }
     }
     
     /**
@@ -94,57 +94,57 @@
      */
     private Hep3Vector getPOCALineToLine() {
 
-		if(_debug) System.out.printf("%s: A1=%s A2=%s B1=%s B2=%s\n", this.getClass().getSimpleName(), A1.toString(), A2.toString(), B1.toString(), B2.toString());
+        if(_debug) System.out.printf("%s: A1=%s A2=%s B1=%s B2=%s\n", this.getClass().getSimpleName(), A1.toString(), A2.toString(), B1.toString(), B2.toString());
 
-    	double ya[][] = {VecOp.mult(-1,VecOp.sub(B1, A1)).v()};
-    	BasicMatrix y = (BasicMatrix)MatrixOp.transposed(new BasicMatrix(ya));
-    	Hep3Vector dB = VecOp.sub(B2, B1);
-    	Hep3Vector dA = VecOp.sub(A2, A1);
-    	BasicMatrix X = new BasicMatrix(3,2);
-    	for(int col=0;col<2;++col) {
-    		if(col==0) {
-    			X.setElement(0, col, dB.x());
-    			X.setElement(1, col, dB.y());
-    			X.setElement(2, col, dB.z());
-    		} else {
-    			X.setElement(0, col, -1*dA.x());
-    			X.setElement(1, col, -1*dA.y());
-    			X.setElement(2, col, -1*dA.z());
-    		}
-    	}
+        double ya[][] = {VecOp.mult(-1,VecOp.sub(B1, A1)).v()};
+        BasicMatrix y = (BasicMatrix)MatrixOp.transposed(new BasicMatrix(ya));
+        Hep3Vector dB = VecOp.sub(B2, B1);
+        Hep3Vector dA = VecOp.sub(A2, A1);
+        BasicMatrix X = new BasicMatrix(3,2);
+        for(int col=0;col<2;++col) {
+            if(col==0) {
+                X.setElement(0, col, dB.x());
+                X.setElement(1, col, dB.y());
+                X.setElement(2, col, dB.z());
+            } else {
+                X.setElement(0, col, -1*dA.x());
+                X.setElement(1, col, -1*dA.y());
+                X.setElement(2, col, -1*dA.z());
+            }
+        }
 
-    	BasicMatrix X_T = (BasicMatrix)MatrixOp.transposed(X);
-    	BasicMatrix XX_T = (BasicMatrix)MatrixOp.mult(X_T, X);
-		BasicMatrix IXX_T = null;
-		try {
-			IXX_T = (BasicMatrix)MatrixOp.inverse(XX_T);
-		} 
-		catch(MatrixOp.IndeterminateMatrixException e) {
-			System.out.printf("%s: caught indeterminate exception %s\n",this.getClass().getSimpleName(),e.getMessage());
-			return null;
-		}
-    	BasicMatrix X_Ty = (BasicMatrix)MatrixOp.mult(X_T,y);
-    	BasicMatrix b = (BasicMatrix)MatrixOp.mult(IXX_T, X_Ty);
-    	double t = b.e(0, 0);
-    	double s = b.e(1, 0);
-    	Hep3Vector Bpca = VecOp.add(B1, VecOp.mult(t, dB));
-    	Hep3Vector Apca = VecOp.add(A1, VecOp.mult(s, dA));
+        BasicMatrix X_T = (BasicMatrix)MatrixOp.transposed(X);
+        BasicMatrix XX_T = (BasicMatrix)MatrixOp.mult(X_T, X);
+        BasicMatrix IXX_T = null;
+        try {
+            IXX_T = (BasicMatrix)MatrixOp.inverse(XX_T);
+        } 
+        catch(MatrixOp.IndeterminateMatrixException e) {
+            System.out.printf("%s: caught indeterminate exception %s\n",this.getClass().getSimpleName(),e.getMessage());
+            return null;
+        }
+        BasicMatrix X_Ty = (BasicMatrix)MatrixOp.mult(X_T,y);
+        BasicMatrix b = (BasicMatrix)MatrixOp.mult(IXX_T, X_Ty);
+        double t = b.e(0, 0);
+        double s = b.e(1, 0);
+        Hep3Vector Bpca = VecOp.add(B1, VecOp.mult(t, dB));
+        Hep3Vector Apca = VecOp.add(A1, VecOp.mult(s, dA));
         Hep3Vector vertex = VecOp.add(Apca, VecOp.mult(0.5, VecOp.sub(Bpca, Apca)));
-    	if(_debug) {
-    		System.out.printf("y:\n%s\n",y.toString());
-    		System.out.printf("X:\n%s\n",X.toString());
-    		System.out.printf("b:\n%s\n",b.toString());
-        	Hep3Vector ymin = VecOp.add(VecOp.mult(t, dB) , VecOp.mult(s, dA) );
-        	Hep3Vector yminprime = VecOp.add(VecOp.sub(B1, A1), ymin);
-        	System.out.printf("ymin:\n%s\n",ymin.toString());
-        	System.out.printf("yminprime:\n%s\n",yminprime.toString());
-        	System.out.printf("Apca:\n%s\n",Apca.toString());
-        	System.out.printf("Bpca:\n%s\n",Bpca.toString());
-        	System.out.printf("vertex:\n%s\n",vertex.toString());
-    	}
-    	return vertex;
-    	
-    	
+        if(_debug) {
+            System.out.printf("y:\n%s\n",y.toString());
+            System.out.printf("X:\n%s\n",X.toString());
+            System.out.printf("b:\n%s\n",b.toString());
+            Hep3Vector ymin = VecOp.add(VecOp.mult(t, dB) , VecOp.mult(s, dA) );
+            Hep3Vector yminprime = VecOp.add(VecOp.sub(B1, A1), ymin);
+            System.out.printf("ymin:\n%s\n",ymin.toString());
+            System.out.printf("yminprime:\n%s\n",yminprime.toString());
+            System.out.printf("Apca:\n%s\n",Apca.toString());
+            System.out.printf("Bpca:\n%s\n",Bpca.toString());
+            System.out.printf("vertex:\n%s\n",vertex.toString());
+        }
+        return vertex;
+        
+        
     }
 
     

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoParticleVertexer.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoParticleVertexer.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoParticleVertexer.java	Wed Apr 27 11:11:32 2016
@@ -18,7 +18,7 @@
  */
 public class TwoParticleVertexer extends TwoLineVertexer {
     
-	public TwoParticleVertexer() {
+    public TwoParticleVertexer() {
     }
     public void setParticle(MCParticle track1,MCParticle track2) {
         
@@ -34,8 +34,8 @@
         Hep3Vector PB2 = this.propAlongLine(PB1, p2, dz);
         
         if(_debug) {
-        	System.out.printf("A1 %s p1 %s B1 %s p2 %s\n", PA1.toString(), p1.toString(), PB1.toString(), p2.toString());
-        	System.out.printf("A2 %s B2 %s\n", PA2.toString(), PB2.toString());
+            System.out.printf("A1 %s p1 %s B1 %s p2 %s\n", PA1.toString(), p1.toString(), PB1.toString(), p2.toString());
+            System.out.printf("A2 %s B2 %s\n", PA2.toString(), PB2.toString());
         }
         
         //set the member variables

Modified: java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoTrackFringeVertexer.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoTrackFringeVertexer.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/main/java/org/hps/recon/vertexing/TwoTrackFringeVertexer.java	Wed Apr 27 11:11:32 2016
@@ -4,14 +4,14 @@
 import hep.physics.vec.Hep3Vector;
 
 import org.hps.recon.tracking.BeamlineConstants;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.HelixConverter;
-import org.hps.recon.tracking.StraightLineTrack;
+import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.Track;
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
 import org.lcsim.fit.helicaltrack.HelixUtils;
+import org.lcsim.geometry.FieldMap;
 import org.lcsim.recon.tracking.seedtracker.SeedTrack;
-import org.lcsim.util.swim.Helix;
 
 /**
  * 
@@ -20,38 +20,42 @@
  * @author phansson
  *
  */
+
 public class TwoTrackFringeVertexer extends TwoTrackVertexer {
     protected HelixConverter converter = new HelixConverter(0.);
     
-    public void setTracks(Track track1, Track track2) {
-    	SeedTrack s1 = (SeedTrack) track1;
+    public void setTracks(Track track1, Track track2, FieldMap fieldMap) {
+        SeedTrack s1 = (SeedTrack) track1;
         HelicalTrackFit htf1 = s1.getSeedCandidate().getHelix();
-        HPSTrack hpstrk1 = new HPSTrack(htf1);
+        HpsHelicalTrackFit hpstrk1 = new HpsHelicalTrackFit(htf1);
         SeedTrack s2 = (SeedTrack) track2;
         HelicalTrackFit htf2 = s2.getSeedCandidate().getHelix();
-        HPSTrack hpstrk2 = new HPSTrack(htf2);
+        HpsHelicalTrackFit hpstrk2 = new HpsHelicalTrackFit(htf2);
         boolean debug = false;
+
+        Hep3Vector posAtConv1 = new BasicHep3Vector( TrackUtils.extrapolateTrackUsingFieldMap(track1, 100.0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0, fieldMap).getReferencePoint());
+        Hep3Vector posAtConv2 = new BasicHep3Vector( TrackUtils.extrapolateTrackUsingFieldMap(track2, 100.0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0, fieldMap).getReferencePoint());
+
+        //FIXME the straight line objects are not working
         
-        Hep3Vector posAtConv1 = hpstrk1.getPositionAtZMap(100.0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0)[0];
-        Hep3Vector posAtConv2 = hpstrk2.getPositionAtZMap(100.0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0)[0];
+        //StraightLineTrack slt1_conv = converter.Convert((Helix)hpstrk1.getTrajectory());
+        //StraightLineTrack slt2_conv = converter.Convert((Helix)hpstrk2.getTrajectory());
+        
+        //A1 = new BasicHep3Vector(slt1_conv.x0(),slt1_conv.y0(),slt1_conv.z0());
+        //B1 = new BasicHep3Vector(slt2_conv.x0(),slt2_conv.y0(),slt2_conv.z0());
 
-        StraightLineTrack slt1_conv = converter.Convert((Helix)hpstrk1.getTrajectory());
-        StraightLineTrack slt2_conv = converter.Convert((Helix)hpstrk2.getTrajectory());
+        //double YZAtConv1[] = slt1_conv.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN);
+        //double YZAtConv2[] = slt2_conv.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN);
         
-        A1 = new BasicHep3Vector(slt1_conv.x0(),slt1_conv.y0(),slt1_conv.z0());
-        B1 = new BasicHep3Vector(slt2_conv.x0(),slt2_conv.y0(),slt2_conv.z0());
-
-        double YZAtConv1[] = slt1_conv.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN);
-        double YZAtConv2[] = slt2_conv.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN);
+        //A2 = new BasicHep3Vector(BeamlineConstants.HARP_POSITION_TESTRUN,YZAtConv1[0],YZAtConv1[1]);
+        //B2 = new BasicHep3Vector(BeamlineConstants.HARP_POSITION_TESTRUN,YZAtConv2[0],YZAtConv2[1]);
         
-        A2 = new BasicHep3Vector(BeamlineConstants.HARP_POSITION_TESTRUN,YZAtConv1[0],YZAtConv1[1]);
-        B2 = new BasicHep3Vector(BeamlineConstants.HARP_POSITION_TESTRUN,YZAtConv2[0],YZAtConv2[1]);
         
         if(debug) {
             System.out.printf("%s: original track1 direction at x=0 %s  \n",this.getClass().getSimpleName(),HelixUtils.Direction(hpstrk1,0.).toString());
             System.out.printf("%s: original track2 direction at x=0 %s  \n",this.getClass().getSimpleName(),HelixUtils.Direction(hpstrk2,0.).toString());
-            System.out.printf("%s: track1 direction at conv %s  \n",this.getClass().getSimpleName(),hpstrk1.getTrajectory().getUnitTangentAtLength(0.).toString());
-            System.out.printf("%s: track2 direction at conv %s  \n",this.getClass().getSimpleName(),hpstrk2.getTrajectory().getUnitTangentAtLength(0.).toString());
+            //System.out.printf("%s: track1 direction at conv %s  \n",this.getClass().getSimpleName(),hpstrk1.getTrajectory().getUnitTangentAtLength(0.).toString());
+            //System.out.printf("%s: track2 direction at conv %s  \n",this.getClass().getSimpleName(),hpstrk2.getTrajectory().getUnitTangentAtLength(0.).toString());
            
             
             System.out.printf("%s: pos at converter track1 %s  \n",this.getClass().getSimpleName(),posAtConv1.toString());
@@ -67,5 +71,5 @@
     }
     
     
-	
+    
 }

Modified: java/branches/HPSJAVA-409/recon/src/test/java/org/hps/recon/particle/HpsReconParticleDriverTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/recon/src/test/java/org/hps/recon/particle/HpsReconParticleDriverTest.java	(original)
+++ java/branches/HPSJAVA-409/recon/src/test/java/org/hps/recon/particle/HpsReconParticleDriverTest.java	Wed Apr 27 11:11:32 2016
@@ -26,165 +26,165 @@
  */
 public class HpsReconParticleDriverTest extends TestCase { 
 
-	private static final double B_FIELD = 0.5; // Tesla
-  	double[] trackParameters = new double[5];
- 	List<Track> tracks = new ArrayList<Track>(); 
-	List<Cluster> clusters = new ArrayList<Cluster>();
-	List<ReconstructedParticle> particleTracks; 
-	HpsReconParticleDriver particleDriver = null; 
-	
-   	public void setUp() throws Exception {
-   		
-   		System.out.println("\n#=== Creating Ideal Tracks ===#\n");
+    private static final double B_FIELD = 0.5; // Tesla
+    double[] trackParameters = new double[5];
+    List<Track> tracks = new ArrayList<Track>(); 
+    List<Cluster> clusters = new ArrayList<Cluster>();
+    List<ReconstructedParticle> particleTracks; 
+    HpsReconParticleDriver particleDriver = null; 
+    
+    public void setUp() throws Exception {
+        
+        System.out.println("\n#=== Creating Ideal Tracks ===#\n");
    
-   		// Create a pair of ideal e+e- tracks in opposite detector volumes.
-   		// The e+ track is created on the bottom half of the detector while
-   		// the e- track is created on the top half.
-   		Track electronTrack = new BaseTrack(); 
-   		trackParameters[BaseTrack.D0] = 0.41051;
-   		trackParameters[BaseTrack.OMEGA] = -2.2584e-4; 
-   		trackParameters[BaseTrack.PHI] = 6.2626; 
-   		trackParameters[BaseTrack.TANLAMBDA] = 0.046548; 
-   		trackParameters[BaseTrack.Z0] = .23732; 
-   		((BaseTrack) electronTrack).setTrackParameters(trackParameters, B_FIELD);
-   		
-   		System.out.println("\n[ Track ] Electron:  \n" + electronTrack.toString());
-   		
-   		Track positronTrack = new BaseTrack();
-   		trackParameters[BaseTrack.D0] = 0.19691;
-   		trackParameters[BaseTrack.OMEGA] = 1.005e-4; 
-   		trackParameters[BaseTrack.PHI] = 6.2447; 
-   		trackParameters[BaseTrack.TANLAMBDA] = -0.024134; 
-   		trackParameters[BaseTrack.Z0] = -0.040231; 
-   		((BaseTrack) positronTrack).setTrackParameters(trackParameters, B_FIELD);
+        // Create a pair of ideal e+e- tracks in opposite detector volumes.
+        // The e+ track is created on the bottom half of the detector while
+        // the e- track is created on the top half.
+        Track electronTrack = new BaseTrack(); 
+        trackParameters[BaseTrack.D0] = 0.41051;
+        trackParameters[BaseTrack.OMEGA] = -2.2584e-4; 
+        trackParameters[BaseTrack.PHI] = 6.2626; 
+        trackParameters[BaseTrack.TANLAMBDA] = 0.046548; 
+        trackParameters[BaseTrack.Z0] = .23732; 
+        ((BaseTrack) electronTrack).setTrackParameters(trackParameters, B_FIELD);
+        
+        System.out.println("\n[ Track ] Electron:  \n" + electronTrack.toString());
+        
+        Track positronTrack = new BaseTrack();
+        trackParameters[BaseTrack.D0] = 0.19691;
+        trackParameters[BaseTrack.OMEGA] = 1.005e-4; 
+        trackParameters[BaseTrack.PHI] = 6.2447; 
+        trackParameters[BaseTrack.TANLAMBDA] = -0.024134; 
+        trackParameters[BaseTrack.Z0] = -0.040231; 
+        ((BaseTrack) positronTrack).setTrackParameters(trackParameters, B_FIELD);
 
-   		System.out.println("\n[ Track ] Positron: \n" + positronTrack.toString());
+        System.out.println("\n[ Track ] Positron: \n" + positronTrack.toString());
 
-   		// Add the tracks to the list of tracks that will be used for test
-   		// purposes.
-   		tracks.add(electronTrack);
-   		tracks.add(positronTrack);
-   		
-   		System.out.println("\n#=== Creating Ideal Ecal Clusters ===#\n");
-   		
-   		// Create a pair of ideal clusters to match the e+e- pairs created
-   		// above.  Since the properties of a cluster cannot be modified 
-   		// directly via setter methods, first create a CalorimeterHit and
-   		// then use that to create a cluster.
-   		//Hep3Vector topHitPosition = new BasicHep3Vector(190.27, 69.729, 1422.8);
-   		//BaseCalorimeterHit topHit 
-   		//	= new BaseCalorimeterHit(.4600, .4600, 0, 0, 0, topHitPosition, 0);
-   		
-   		//System.out.println("\n[ Calorimeter Hit ] Top: \n" + topHit.toString());
-   		
-   		Cluster topCluster = new BaseCluster();
-   		//((BaseCluster) topCluster).addHit(topHit);
-   		
-   		
-   		System.out.print("\n[ Cluster ] Top: " + topCluster.toString());
-   		System.out.println(" and position= ["  + topCluster.getPosition()[0] + ", " 
-   											   + topCluster.getPosition()[1] + ", " 
-   											   + topCluster.getPosition()[2] + " ]");
-   		
-   		//Hep3Vector bottomHitPosition = new BasicHep3Vector(-148.46, -39.27, 1430.5);
-   		//BaseCalorimeterHit bottomHit 
-   		//	= new BaseCalorimeterHit(1.1420, 1.1420, 0, 0, 0, bottomHitPosition, 0);
+        // Add the tracks to the list of tracks that will be used for test
+        // purposes.
+        tracks.add(electronTrack);
+        tracks.add(positronTrack);
+        
+        System.out.println("\n#=== Creating Ideal Ecal Clusters ===#\n");
+        
+        // Create a pair of ideal clusters to match the e+e- pairs created
+        // above.  Since the properties of a cluster cannot be modified 
+        // directly via setter methods, first create a CalorimeterHit and
+        // then use that to create a cluster.
+        //Hep3Vector topHitPosition = new BasicHep3Vector(190.27, 69.729, 1422.8);
+        //BaseCalorimeterHit topHit 
+        //  = new BaseCalorimeterHit(.4600, .4600, 0, 0, 0, topHitPosition, 0);
+        
+        //System.out.println("\n[ Calorimeter Hit ] Top: \n" + topHit.toString());
+        
+        Cluster topCluster = new BaseCluster();
+        //((BaseCluster) topCluster).addHit(topHit);
+        
+        
+        System.out.print("\n[ Cluster ] Top: " + topCluster.toString());
+        System.out.println(" and position= ["  + topCluster.getPosition()[0] + ", " 
+                                               + topCluster.getPosition()[1] + ", " 
+                                               + topCluster.getPosition()[2] + " ]");
+        
+        //Hep3Vector bottomHitPosition = new BasicHep3Vector(-148.46, -39.27, 1430.5);
+        //BaseCalorimeterHit bottomHit 
+        //  = new BaseCalorimeterHit(1.1420, 1.1420, 0, 0, 0, bottomHitPosition, 0);
 
-   		//System.out.println("\n[ Calorimeter Hit ] Bottom:\n " + bottomHit.toString());
-   		
-   		Cluster bottomCluster = new BaseCluster();
-   		//((BaseCluster) bottomCluster).addHit(bottomHit);
-   		
-   		System.out.print("\n[ Cluster ] bottom: " + bottomCluster.toString());
-   		System.out.println(" and position= [ " + topCluster.getPosition()[0] + ", " 
-   											   + topCluster.getPosition()[1] + ", " 
-   											   + topCluster.getPosition()[2] + " ]");
+        //System.out.println("\n[ Calorimeter Hit ] Bottom:\n " + bottomHit.toString());
+        
+        Cluster bottomCluster = new BaseCluster();
+        //((BaseCluster) bottomCluster).addHit(bottomHit);
+        
+        System.out.print("\n[ Cluster ] bottom: " + bottomCluster.toString());
+        System.out.println(" and position= [ " + topCluster.getPosition()[0] + ", " 
+                                               + topCluster.getPosition()[1] + ", " 
+                                               + topCluster.getPosition()[2] + " ]");
 
-   		// Add the clusters to the list of clusters that will be used for test
-   		// purposes.
-   		clusters.add(topCluster);
-   		clusters.add(bottomCluster);
-   		
-   		particleDriver = new HpsReconParticleDriver();
-   		particleDriver.setDebug(true);
-   	}
-   	
-   	public void testMakeReconstructedParticles(){
-   		
-   		System.out.println("\n#=== Running makeReconstructedParticles Test ===#");
-    	
-    	
-    	// Create two ReconstructedParticles with tracks only
-    	List<Cluster> emptyClusters = new ArrayList<Cluster>(); 
-    	List<List<Track>> trackCollections = new ArrayList<List<Track>>(0);
-    	trackCollections.add(tracks);
-    	particleTracks = particleDriver.makeReconstructedParticles(emptyClusters, trackCollections);
+        // Add the clusters to the list of clusters that will be used for test
+        // purposes.
+        clusters.add(topCluster);
+        clusters.add(bottomCluster);
+        
+        particleDriver = new HpsReconParticleDriver();
+        particleDriver.setDebug(true);
+    }
     
-    	//
-    	// The list contains two Tracks which should result in two 
-    	// ReconstructedParticles.
-    	//
-    	assertTrue("More particles than expected were created.", particleTracks.size() == 2);
-    	System.out.println("\nThe number of ReconstructedParticles created: " + particleTracks.size());
+    public void testMakeReconstructedParticles(){
+        
+        System.out.println("\n#=== Running makeReconstructedParticles Test ===#");
+        
+        
+        // Create two ReconstructedParticles with tracks only
+        List<Cluster> emptyClusters = new ArrayList<Cluster>(); 
+        List<List<Track>> trackCollections = new ArrayList<List<Track>>(0);
+        trackCollections.add(tracks);
+        particleTracks = particleDriver.makeReconstructedParticles(emptyClusters, trackCollections);
     
-    	for(int particleN = 0; particleN < particleTracks.size(); particleN++){
-    	
-    		//
-    		//	Check if the RecontructedParticle track is the same as the track 
-    		//	that created it
-    		// 
-    		assertTrue("The particle track does not match the track that created it",
-    					particleTracks.get(particleN).getTracks().get(0).equals(tracks.get(particleN)));
-    	
-    	
-    		//
-    		// Check that the charge of the ReconstructedParticles was set properly
-    		//
-    		assertTrue("The charge of the ReconstructedParticle is equal to zero.", 
-    					Math.abs(particleTracks.get(particleN).getCharge()) != 0);
-    		System.out.println("The charge of ReconstructedParticle number " + particleN + ": " + particleTracks.get(particleN).getCharge());
-    	
-    	
-    		//
-    		// Check that the particle ID was set correctly
-    		//
-    		assertTrue("The particle ID of the ReconstructedParticle is equal to zero.", 
-    				   particleTracks.get(particleN).getParticleIDUsed().getPDG() != 0);
-    		System.out.println("The particle ID of ReconstructedParticle number " + particleN + ": " + particleTracks.get(particleN).getParticleIDUsed().getPDG());
-    	}
-    	
-    	//
-    	// Check that the momentum of the ReconstructedParticles was set properly 
-    	// and rotated to the detector frame.
-    	//
-    	Hep3Vector electronMomentum = new BasicHep3Vector(tracks.get(0).getTrackStates().get(0).getMomentum());
-    	electronMomentum = CoordinateTransformations.transformVectorToDetector(electronMomentum);
-    	assertTrue("The momentum of the track and ReconstructedParticle don't match! Top track p = " 
-    				+ electronMomentum.toString() + " Recon particle p = " + particleTracks.get(0).getMomentum().toString(),
-    				particleTracks.get(0).getMomentum().equals(electronMomentum));
-    	
-    	System.out.println("The momentum of the first ReconstructedParticle: " + particleTracks.get(0).getMomentum().toString());
-    	
-    	Hep3Vector positronMomentum = new BasicHep3Vector(tracks.get(1).getTrackStates().get(0).getMomentum());
-    	positronMomentum = CoordinateTransformations.transformVectorToDetector(positronMomentum);
-    	assertTrue("The momentum of track and ReconstructedParticle don't march! Bottom track p = "
-    			    + positronMomentum.toString() + " Recon particle p = " + particleTracks.get(1).getMomentum().toString(),
-    			    particleTracks.get(1).getMomentum().equals(positronMomentum));
-    	
-    	System.out.println("The momentum of the second ReconstructedParticle: " + particleTracks.get(1).getMomentum().toString());
-    	
-   	}
-   	
-   	public void testVertexParticles(){
-   	
-    	// Create two ReconstructedParticles with tracks only
-    	//List<Cluster> emptyClusters = new ArrayList<Cluster>(); 
-    	//particleTracks = particleDriver.makeReconstructedParticles(emptyClusters, tracks);
+        //
+        // The list contains two Tracks which should result in two 
+        // ReconstructedParticles.
+        //
+        assertTrue("More particles than expected were created.", particleTracks.size() == 2);
+        System.out.println("\nThe number of ReconstructedParticles created: " + particleTracks.size());
+    
+        for(int particleN = 0; particleN < particleTracks.size(); particleN++){
+        
+            //
+            //  Check if the RecontructedParticle track is the same as the track 
+            //  that created it
+            // 
+            assertTrue("The particle track does not match the track that created it",
+                        particleTracks.get(particleN).getTracks().get(0).equals(tracks.get(particleN)));
+        
+        
+            //
+            // Check that the charge of the ReconstructedParticles was set properly
+            //
+            assertTrue("The charge of the ReconstructedParticle is equal to zero.", 
+                        Math.abs(particleTracks.get(particleN).getCharge()) != 0);
+            System.out.println("The charge of ReconstructedParticle number " + particleN + ": " + particleTracks.get(particleN).getCharge());
+        
+        
+            //
+            // Check that the particle ID was set correctly
+            //
+            assertTrue("The particle ID of the ReconstructedParticle is equal to zero.", 
+                       particleTracks.get(particleN).getParticleIDUsed().getPDG() != 0);
+            System.out.println("The particle ID of ReconstructedParticle number " + particleN + ": " + particleTracks.get(particleN).getParticleIDUsed().getPDG());
+        }
+        
+        //
+        // Check that the momentum of the ReconstructedParticles was set properly 
+        // and rotated to the detector frame.
+        //
+        Hep3Vector electronMomentum = new BasicHep3Vector(tracks.get(0).getTrackStates().get(0).getMomentum());
+        electronMomentum = CoordinateTransformations.transformVectorToDetector(electronMomentum);
+        assertTrue("The momentum of the track and ReconstructedParticle don't match! Top track p = " 
+                    + electronMomentum.toString() + " Recon particle p = " + particleTracks.get(0).getMomentum().toString(),
+                    particleTracks.get(0).getMomentum().equals(electronMomentum));
+        
+        System.out.println("The momentum of the first ReconstructedParticle: " + particleTracks.get(0).getMomentum().toString());
+        
+        Hep3Vector positronMomentum = new BasicHep3Vector(tracks.get(1).getTrackStates().get(0).getMomentum());
+        positronMomentum = CoordinateTransformations.transformVectorToDetector(positronMomentum);
+        assertTrue("The momentum of track and ReconstructedParticle don't march! Bottom track p = "
+                    + positronMomentum.toString() + " Recon particle p = " + particleTracks.get(1).getMomentum().toString(),
+                    particleTracks.get(1).getMomentum().equals(positronMomentum));
+        
+        System.out.println("The momentum of the second ReconstructedParticle: " + particleTracks.get(1).getMomentum().toString());
+        
+    }
+    
+    public void testVertexParticles(){
+    
+        // Create two ReconstructedParticles with tracks only
+        //List<Cluster> emptyClusters = new ArrayList<Cluster>(); 
+        //particleTracks = particleDriver.makeReconstructedParticles(emptyClusters, tracks);
 
-    	//List<ReconstructedParticle> electrons = particleTracks.subList(0, 1);
-   		//List<ReconstructedParticle> positrons = particleTracks.subList(1, 2);
-   	
-   		//particleDriver.vertexParticles(electrons, positrons);
-   		
-   	}
+        //List<ReconstructedParticle> electrons = particleTracks.subList(0, 1);
+        //List<ReconstructedParticle> positrons = particleTracks.subList(1, 2);
+    
+        //particleDriver.vertexParticles(electrons, positrons);
+        
+    }
 }

Modified: java/branches/HPSJAVA-409/record-util/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/pom.xml	(original)
+++ java/branches/HPSJAVA-409/record-util/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/record-util/</url>

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordProcessor.java	Wed Apr 27 11:11:32 2016
@@ -10,6 +10,8 @@
  */
 public abstract class AbstractRecordProcessor<RecordType> implements RecordProcessor<RecordType> {
 
+    private boolean active = true;
+    
     /**
      * End of job action.
      */
@@ -59,4 +61,12 @@
     @Override
     public void suspend() {
     }
+    
+    protected void setActive(boolean active) {
+        this.active = active;
+    }
+    
+    public boolean isActive() {
+        return this.active;
+    }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordQueue.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordQueue.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/AbstractRecordQueue.java	Wed Apr 27 11:11:32 2016
@@ -45,7 +45,8 @@
     /**
      * Class constructor with the timeout in seconds.
      *
-     * @param timeoutSeconds the timeout in seconds
+     * @param timeOutMillis the timeout in seconds
+     * @param maxSize the maximum size of the queue
      */
     public AbstractRecordQueue(final long timeOutMillis, final int maxSize) {
         this.timeOutMillis = timeOutMillis;
@@ -55,7 +56,7 @@
     /**
      * Add a record to the queue if there is space.
      *
-     * @param event the LCIO event to add
+     * @param record the LCIO event to add
      */
     // FIXME: Should drain queue if over capacity.
     public void addRecord(final RecordType record) {
@@ -102,7 +103,7 @@
      * @throws NoSuchRecordException if there are no records available from the queue
      */
     @Override
-    public void next() throws IOException, NoSuchRecordException {
+    public synchronized void next() throws IOException, NoSuchRecordException {
         try {
             if (this.timeOutMillis > 0L) {
                 // Poll the queue for the next record until timeout is exceeded.

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/RecordProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/RecordProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/RecordProcessor.java	Wed Apr 27 11:11:32 2016
@@ -45,4 +45,11 @@
      * Suspend processing action.
      */
     void suspend();
+    
+    /**
+     * Return <code>true</code> if processor is active.
+     * 
+     * @return <code>true</code> if processor is active
+     */
+    boolean isActive();
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/composite/RecordProcessorAdapter.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/composite/RecordProcessorAdapter.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/composite/RecordProcessorAdapter.java	Wed Apr 27 11:11:32 2016
@@ -44,7 +44,7 @@
     /**
      * Activate the <code>endJob</code> methods of the registered processors.
      *
-     * @param the <code>LoopEvent</code> which activated <code>finish</code>
+     * @param loopEvent the <code>LoopEvent</code> which activated <code>finish</code>
      */
     @Override
     public void finish(final LoopEvent loopEvent) {
@@ -80,7 +80,7 @@
     /**
      * Activate the <code>startJob</code> methods of the registered processors.
      *
-     * @param the <code>LoopEvent</code> which activated the start
+     * @param loopEvent the <code>LoopEvent</code> which activated the start
      */
     @Override
     public void start(final LoopEvent loopEvent) {
@@ -103,7 +103,7 @@
     /**
      * Activate the <code>suspend</code> methods of the registered processors.
      *
-     * @param the <code>LoopEvent</code> which activated <code>suspend</code>.
+     * @param loopEvent the <code>LoopEvent</code> which activated <code>suspend</code>.
      */
     @Override
     public void suspend(final LoopEvent loopEvent) {

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfig.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfig.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,8 @@
 package org.hps.record.daqconfig;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+
 
 /**
  * Class <code>DAQConfig</code> holds all of the supported parameters
@@ -47,13 +51,23 @@
     }
 
     @Override
-    public void printConfig() {
+    public void printConfig(PrintStream ps) {
         // Print the system-specific objects.
-        fadcConfig.printConfig();
-        System.out.println();
-        gtpConfig.printConfig();
-        System.out.println();
-        sspConfig.printConfig();
+        fadcConfig.printConfig(ps);
+        ps.println();
+        gtpConfig.printConfig(ps);
+        ps.println();
+        sspConfig.printConfig(ps);
     }
-    
-}
+
+    public String toString() {
+        ByteArrayOutputStream os = new ByteArrayOutputStream();
+        PrintStream ps = new PrintStream(os);
+        printConfig(ps);
+        try {
+            return os.toString("UTF8");
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfigDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfigDriver.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/DAQConfigDriver.java	Wed Apr 27 11:11:32 2016
@@ -39,57 +39,57 @@
  * @see ConfigurationManager
  */
 public class DAQConfigDriver extends Driver {
-	private int runNumber = -1;
-	private String filepath = null;
-	private boolean firstEvent = true;
-	private boolean readDataFiles = false;
-	private File[] dataFiles = new File[3];
-	private int[] crateNumber = { 46, 37, 39 };
-	
-	/**
-	 * Verifies the parameter <code>filepath</code> for the data file
-	 * repository and checks that appropriate data files exist for the
-	 * requested run number if the driver is set to read from data files.
-	 * Otherwise, this does nothing.
-	 */
-	@Override
-	public void startOfData() {
-		// Check whether to use stored data files or the EvIO data stream
-		// as the source of the DAQ settings. Nothing needs to be done
-		// in the latter case.
-		if(readDataFiles) {
-			// The user must define a data file prefix and repository
-			// location for this option to be used.
-			if(filepath == null) {
-				throw new NullPointerException("DAQ settings repository filepath must be defined.");
-			} if(runNumber == -1) {
-				throw new NullPointerException("Run number must be defined.");
-			}
-			
-			// Verify that the repository actually exist.
-			File repository = new File(filepath);
-			if(!repository.exists() || !repository.isDirectory()) {
-				throw new IllegalArgumentException("Repository location \"" + filepath + "\" must be an existing directory.");
-			}
-			
-			// Define the data file objects.
-			for(int i = 0; i < dataFiles.length; i++) {
-				try {
-					dataFiles[i] = new File(repository.getCanonicalPath() + "/" + runNumber + "_" + crateNumber[i] + ".txt");
-				} catch(IOException e) {
-					throw new RuntimeException("Error resolving absolute repository filepath.");
-				}
-			}
-			
-			// Verify that the data files actually exist.
-			for(File dataFile : dataFiles) {
-				if(!dataFile.exists() || !dataFile.canRead()) {
-					throw new IllegalArgumentException("Data file \"" + dataFile.getName() + "\" does not exist or can not be read.");
-				}
-			}
-		}
-	}
-	
+    private int runNumber = -1;
+    private String filepath = null;
+    private boolean firstEvent = true;
+    private boolean readDataFiles = false;
+    private File[] dataFiles = new File[3];
+    private int[] crateNumber = { 46, 37, 39 };
+    
+    /**
+     * Verifies the parameter <code>filepath</code> for the data file
+     * repository and checks that appropriate data files exist for the
+     * requested run number if the driver is set to read from data files.
+     * Otherwise, this does nothing.
+     */
+    @Override
+    public void startOfData() {
+        // Check whether to use stored data files or the EvIO data stream
+        // as the source of the DAQ settings. Nothing needs to be done
+        // in the latter case.
+        if(readDataFiles) {
+            // The user must define a data file prefix and repository
+            // location for this option to be used.
+            if(filepath == null) {
+                throw new NullPointerException("DAQ settings repository filepath must be defined.");
+            } if(runNumber == -1) {
+                throw new NullPointerException("Run number must be defined.");
+            }
+            
+            // Verify that the repository actually exist.
+            File repository = new File(filepath);
+            if(!repository.exists() || !repository.isDirectory()) {
+                throw new IllegalArgumentException("Repository location \"" + filepath + "\" must be an existing directory.");
+            }
+            
+            // Define the data file objects.
+            for(int i = 0; i < dataFiles.length; i++) {
+                try {
+                    dataFiles[i] = new File(repository.getCanonicalPath() + "/" + runNumber + "_" + crateNumber[i] + ".txt");
+                } catch(IOException e) {
+                    throw new RuntimeException("Error resolving absolute repository filepath.");
+                }
+            }
+            
+            // Verify that the data files actually exist.
+            for(File dataFile : dataFiles) {
+                if(!dataFile.exists() || !dataFile.canRead()) {
+                    throw new IllegalArgumentException("Data file \"" + dataFile.getName() + "\" does not exist or can not be read.");
+                }
+            }
+        }
+    }
+    
     /**
      * Checks an event for the DAQ configuration banks and passes them
      * to the <code>ConfigurationManager</code> if the driver is set to
@@ -99,28 +99,28 @@
      */
     @Override
     public void process(EventHeader event) {
-    	// If this is the first event and data files are to be read,
-    	// import the data files and generate the DAQ information.
-    	if(firstEvent && readDataFiles) {
-    		// Get the data files in the form of a data array.
-    		String[][] data;
-    		try { data = getDataFileArrays(dataFiles); }
-    		catch(IOException e) {
-				throw new RuntimeException("An error occurred when processing the data files.");
-			}
-    		
-    		// Instantiate an EvIO DAQ parser and feed it the data.
-    		EvioDAQParser daqConfig = new EvioDAQParser();
-    		for(int i = 0; i < dataFiles.length; i++) {
-        		daqConfig.parse(crateNumber[i], runNumber, data[i]);
-    		}
-    		
-    		// Update the configuration manager.
-    		ConfigurationManager.updateConfiguration(daqConfig);
-    	}
-    	
+        // If this is the first event and data files are to be read,
+        // import the data files and generate the DAQ information.
+        if(firstEvent && readDataFiles) {
+            // Get the data files in the form of a data array.
+            String[][] data;
+            try { data = getDataFileArrays(dataFiles); }
+            catch(IOException e) {
+                throw new RuntimeException("An error occurred when processing the data files.");
+            }
+            
+            // Instantiate an EvIO DAQ parser and feed it the data.
+            EvioDAQParser daqConfig = new EvioDAQParser();
+            for(int i = 0; i < dataFiles.length; i++) {
+                daqConfig.parse(crateNumber[i], runNumber, data[i]);
+            }
+            
+            // Update the configuration manager.
+            ConfigurationManager.updateConfiguration(daqConfig);
+        }
+        
         // Check if a trigger configuration bank exists.
-    	if(!readDataFiles && event.hasCollection(EvioDAQParser.class, "TriggerConfig")) {
+        if(!readDataFiles && event.hasCollection(EvioDAQParser.class, "TriggerConfig")) {
             // Get the trigger configuration bank. There should only be
             // one in the list.
             List<EvioDAQParser> configList = event.get(EvioDAQParser.class, "TriggerConfig");
@@ -134,7 +134,7 @@
         // Note that it is no longer the first event.
         firstEvent = false;
     }
-	
+    
     /**
      * Converts DAQ configuration data files into an array of strings
      * where each array entry represents a line in the configuration
@@ -152,44 +152,44 @@
      * or reading the objects in the objects referred to by the files
      * pointed to in the <code>dataFiles</code> array.
      */
-	private static final String[][] getDataFileArrays(File[] dataFiles) throws IOException {
-		// Create file readers to process the data files.
-		FileReader[] fr = new FileReader[dataFiles.length];
-		BufferedReader[] reader = new BufferedReader[dataFiles.length];
-		for(int i = 0; i < dataFiles.length; i++) {
-			fr[i] = new FileReader(dataFiles[i]);
-			reader[i] = new BufferedReader(fr[i]);
-		}
-		
-		// Generate String arrays where each entry in the array is
-		// a line from the data file.
-		String[][] data = new String[dataFiles.length][0];
-		for(int i = 0; i < dataFiles.length; i++) {
-			// Create a list to hold the raw strings.
-			List<String> rawData = new ArrayList<String>();
-			
-			// Add each line from the current data file to the list
-			// as a single entry.
-			String curLine = null;
-			while((curLine = reader[i].readLine()) != null) {
-				rawData.add(curLine);
-			}
-			
-			// Convert the list into a String array.
-			data[i] = rawData.toArray(new String[rawData.size()]);
-		}
-		
-		// Return the data array.
-		return data;
-	}
-    
-	/**
-	 * Sets the run number of the DAQ configuration being processed.
-	 * This is only used when reading from data files.
-	 * @param run - The run number of the data files to be used.
-	 */
+    private static final String[][] getDataFileArrays(File[] dataFiles) throws IOException {
+        // Create file readers to process the data files.
+        FileReader[] fr = new FileReader[dataFiles.length];
+        BufferedReader[] reader = new BufferedReader[dataFiles.length];
+        for(int i = 0; i < dataFiles.length; i++) {
+            fr[i] = new FileReader(dataFiles[i]);
+            reader[i] = new BufferedReader(fr[i]);
+        }
+        
+        // Generate String arrays where each entry in the array is
+        // a line from the data file.
+        String[][] data = new String[dataFiles.length][0];
+        for(int i = 0; i < dataFiles.length; i++) {
+            // Create a list to hold the raw strings.
+            List<String> rawData = new ArrayList<String>();
+            
+            // Add each line from the current data file to the list
+            // as a single entry.
+            String curLine = null;
+            while((curLine = reader[i].readLine()) != null) {
+                rawData.add(curLine);
+            }
+            
+            // Convert the list into a String array.
+            data[i] = rawData.toArray(new String[rawData.size()]);
+        }
+        
+        // Return the data array.
+        return data;
+    }
+    
+    /**
+     * Sets the run number of the DAQ configuration being processed.
+     * This is only used when reading from data files.
+     * @param run - The run number of the data files to be used.
+     */
     public void setRunNumber(int run) {
-    	runNumber = run;
+        runNumber = run;
     }
     
     /**
@@ -198,7 +198,7 @@
      * @param filepath - The file path of the data file repository.
      */
     public void setDataFileRepository(String filepath) {
-    	this.filepath = filepath;
+        this.filepath = filepath;
     }
     
     /**
@@ -211,6 +211,6 @@
      * should be read from the EvIO stream.
      */
     public void setReadDataFiles(boolean state) {
-    	readDataFiles = state;
+        readDataFiles = state;
     }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/EvioDAQParser.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/EvioDAQParser.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/EvioDAQParser.java	Wed Apr 27 11:11:32 2016
@@ -42,7 +42,7 @@
      * 
      * TODO: Restructure, clean up...
      */
-	/** The EvIO bank identification tag for DAQ configuration banks. */
+    /** The EvIO bank identification tag for DAQ configuration banks. */
     public static final int BANK_TAG = 0xE10E;
     
     // Stores the hardware codes for each trigger type.
@@ -204,7 +204,7 @@
      * Instantiates the <code>EvioDAQParser</code>.
      */
     public EvioDAQParser() {
-    	// Create a map to map crystals to their database channel object.
+        // Create a map to map crystals to their database channel object.
         ecalConditions = DatabaseConditionsManager.getInstance().getEcalConditions();
         for (int ii = 0; ii < 442; ii++) {
             channels.add(findChannel(ii + 1));
@@ -220,9 +220,9 @@
      * parameters.
      */
     public void parse(int crate, int runNumber, String[] configurationTables) {
-    	// Track the number of banks that have been parsed. If the
-    	// parameter values have not been populated after a certain
-    	// number of banks, there is missing information.
+        // Track the number of banks that have been parsed. If the
+        // parameter values have not been populated after a certain
+        // number of banks, there is missing information.
         nBanks++;
         
         // Create a map that maps an identifier for each configuration
@@ -256,10 +256,10 @@
      * contain the DAQ configuration parameters.
      */
     private void loadConfigMap(int crate, String[] configTables) {
-    	// Iterate over each configuration table.
+        // Iterate over each configuration table.
         for(String configTable : configTables) {
-        	// Split each table into rows and iterate over the rows.
-        	rowLoop:
+            // Split each table into rows and iterate over the rows.
+            rowLoop:
             for(String line : configTable.trim().split("\n")) {
                 // Split the first column from the row.
                 String[] cols = line.trim().split(" +", 2);
@@ -290,8 +290,8 @@
                 // This entry indicates which triggers are enabled and
                 // needs to be parsed differently than normal.
                 else if(key.startsWith("SSP_HPS_SET_IO_SRC")) {
-                	// The first "parameter value" is a hardware code
-                	// that identifies the trigger. Obtain it.
+                    // The first "parameter value" is a hardware code
+                    // that identifies the trigger. Obtain it.
                     int trig = Integer.valueOf(vals.get(1));
                     
                     // There are two trigger of each type, singles and
@@ -313,8 +313,8 @@
                 // This indicates a regular parameter that does not
                 // require any special parsing.
                 if(vals.size() > 1 && key.startsWith("SSP")) {
-                	// List the parameter by "[ROW NAME]_[KEY]" and
-                	// remove the key so that only the values remain.
+                    // List the parameter by "[ROW NAME]_[KEY]" and
+                    // remove the key so that only the values remain.
                     key += "_" + vals.remove(0);
                 }
                 
@@ -330,7 +330,7 @@
      * format of <code>[PARAMETER KEY] --> { [PARAMETER VALUES] }</code>.
      */
     public void parseConfigMap() {
-    	// Parse simple FADC data.
+        // Parse simple FADC data.
         fadcNSA    = Integer.valueOf(getConfigParameter("FADC250_NSA",      0));
         fadcNSB    = Integer.valueOf(getConfigParameter("FADC250_NSB",      0));
         fadcNPEAK  = Integer.valueOf(getConfigParameter("FADC250_NPEAK",    0));
@@ -345,12 +345,12 @@
         
         // Parse trigger data.
         for(int ii = 0; ii < 2; ii++) {
-        	// Check singles trigger cuts enabled status.
+            // Check singles trigger cuts enabled status.
             singlesNhitsEn[ii]         = getBoolConfigSSP(ii,  "SINGLES_NMIN",          1);
             singlesEnergyMinEn[ii]     = getBoolConfigSSP(ii,  "SINGLES_EMIN",          1);
             singlesEnergyMaxEn[ii]     = getBoolConfigSSP(ii,  "SINGLES_EMAX",          1);
             
-        	// Check pair trigger cuts enabled status.
+            // Check pair trigger cuts enabled status.
             pairsEnergySumMaxMinEn[ii] = getBoolConfigSSP(ii,  "PAIRS_SUMMAX_MIN",      2);
             pairsEnergyDiffEn[ii]      = getBoolConfigSSP(ii,  "PAIRS_DIFFMAX",         1);
             pairsCoplanarityEn[ii]     = getBoolConfigSSP(ii,  "PAIRS_COPLANARITY",     1);
@@ -383,7 +383,7 @@
      * used to determine if the run is a "bugged" run.
      */
     private void fixConfigMap2014Run(int runNumber) {
-    	// If this is a good run, noting should be done. Return.
+        // If this is a good run, noting should be done. Return.
         if(runNumber > 3470 || runNumber < 3100) { return; }
         
         // Populate missing GTP entries.
@@ -412,10 +412,10 @@
      * the FADC channel with which they are associated.
      */
     private void parseFADC(int crate, String key, List<String> vals) {
-    	// The FADC slot is not stored on the same line as the other
-    	// data and must be parsed and retained, as it is necessary
-    	// for handling the subsequent lines. If this line is the
-    	// FADC slot, store it.
+        // The FADC slot is not stored on the same line as the other
+        // data and must be parsed and retained, as it is necessary
+        // for handling the subsequent lines. If this line is the
+        // FADC slot, store it.
         if(key.equals("FADC250_SLOT")) {
             thisFadcSlot = Integer.valueOf(vals.get(0));
         }
@@ -449,8 +449,8 @@
      * to FADC channels 0 - 15.
      */
     private void setChannelParsFloat(int crate, int slot, Map<EcalChannel, Float> map, List<String> vals) {
-    	// Iterate over each channel and map the database channel object
-    	// to the corresponding list value.
+        // Iterate over each channel and map the database channel object
+        // to the corresponding list value.
         for(int ii = 0; ii < 16; ii++) {
             map.put(findChannel(crate, slot, ii), Float.valueOf(vals.get(ii)));
         }
@@ -468,8 +468,8 @@
      * objects representing the channel values.
      */
     private void setChannelParsInt(int crate, int slot, Map<EcalChannel, Integer> map, List<String> vals) {
-    	// Iterate over each channel and map the database channel object
-    	// to the corresponding list value.
+        // Iterate over each channel and map the database channel object
+        // to the corresponding list value.
         for(int ii = 0; ii < 16; ii++) {
             map.put(findChannel(crate, slot, ii), Integer.valueOf(vals.get(ii)));
         }
@@ -619,9 +619,9 @@
      * can not be found, an error message is passed to the logger.
      */
     public String getConfigParameter(String key, int ival) {
-    	// Check the parameter map for the requested parameter key.
+        // Check the parameter map for the requested parameter key.
         if(configMap.containsKey(key)) {
-        	// Get the list of values associated with this parameter key.
+            // Get the list of values associated with this parameter key.
             List<String> vals = configMap.get(key);
             
             // Check that the list of values contains a parameter for
@@ -639,7 +639,7 @@
         // If the key is not present...
         else {
             // If more than 2 banks have been read, the absence of a
-        	// key represents an error. Log that this has occurred.
+            // key represents an error. Log that this has occurred.
             if(nBanks > 2) {
                 Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "ConfigMap MISSING KEY:   " + key);
             }
@@ -659,13 +659,13 @@
      * if it exists, and <code>null</code> if it does not.
      */
     public EcalChannel findChannel(int crate, int fadcSlot, int fadcChan) {
-    	// Search through the database channels for a channel that
-    	// matches the the argument parameters.
+        // Search through the database channels for a channel that
+        // matches the the argument parameters.
         for (EcalChannel cc : channels) {
-        	// A channel matches the argument if the slot and channel
-        	// values are the same. Crate number must also match, but
-        	// note that EcalChannel follows a different convention
-        	// with respect to crate numbering.
+            // A channel matches the argument if the slot and channel
+            // values are the same. Crate number must also match, but
+            // note that EcalChannel follows a different convention
+            // with respect to crate numbering.
             if( ((cc.getCrate() - 1) * 2 == crate - 37) && (cc.getSlot() == fadcSlot) && (cc.getChannel() == fadcChan) ) {
                 return cc;
             }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/FADCConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/FADCConfig.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/FADCConfig.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,7 @@
 package org.hps.record.daqconfig;
 
 import java.awt.Point;
+import java.io.PrintStream;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -129,13 +130,13 @@
      * per ADC.
      */
     public float getGain(Point ixy) {
-    	// Get the channel index.
-    	Integer index = indexChannelMap.get(ixy);
-    	
-    	// If the channel index was defined, return the pedestal.
+        // Get the channel index.
+        Integer index = indexChannelMap.get(ixy);
+        
+        // If the channel index was defined, return the pedestal.
         if(index != null) { return getGain(index); }
         else {
-        	throw new IllegalArgumentException(String.format("Crystal (%3d, %3d) does not exist.", ixy.x, ixy.y));
+            throw new IllegalArgumentException(String.format("Crystal (%3d, %3d) does not exist.", ixy.x, ixy.y));
         }
     }
     
@@ -225,13 +226,13 @@
      * of ADC.
      */
     public float getPedestal(Point ixy) {
-    	// Get the channel index.
-    	Integer index = indexChannelMap.get(ixy);
-    	
-    	// If the channel index was defined, return the pedestal.
+        // Get the channel index.
+        Integer index = indexChannelMap.get(ixy);
+        
+        // If the channel index was defined, return the pedestal.
         if(index != null) { return getPedestal(index); }
         else {
-        	throw new IllegalArgumentException(String.format("Crystal (%3d, %3d) does not exist.", ixy.x, ixy.y));
+            throw new IllegalArgumentException(String.format("Crystal (%3d, %3d) does not exist.", ixy.x, ixy.y));
         }
     }
     
@@ -305,39 +306,39 @@
     }
     
     @Override
-    public void printConfig() {
-    	// Print the basic configuration information.
-        System.out.println("FADC Configuration:");
-        System.out.printf("\tMode          :: %d%n", mode);
-        System.out.printf("\tNSA           :: %d%n", nsa);
-        System.out.printf("\tNSB           :: %d%n", nsb);
-        System.out.printf("\tWindow Width  :: %d%n", windowWidth);
-        System.out.printf("\tWindow Offset :: %d%n", offset);
-        System.out.printf("\tMax Peaks     :: %d%n", maxPulses);
+    public void printConfig(PrintStream ps) {
+        // Print the basic configuration information.
+        ps.println("FADC Configuration:");
+        ps.printf("\tMode          :: %d%n", mode);
+        ps.printf("\tNSA           :: %d%n", nsa);
+        ps.printf("\tNSB           :: %d%n", nsb);
+        ps.printf("\tWindow Width  :: %d%n", windowWidth);
+        ps.printf("\tWindow Offset :: %d%n", offset);
+        ps.printf("\tMax Peaks     :: %d%n", maxPulses);
         
         // Output the pedestal/gain write-out header.
-        System.out.println("\tix\tiy\tPedestal (ADC)\tGain (MeV/ADC)\tThreshold (ADC)");
+        ps.println("\tix\tiy\tPedestal (ADC)\tGain (MeV/ADC)\tThreshold (ADC)");
         
         // Iterate over each crystal y-index.
         yLoop:
         for(int iy = -5; iy <= 5; iy++) {
-        	// iy = 0 does not exists; skip it!
-        	if(iy == 0) { continue yLoop; }
-        	
-        	// Iterate over each crystal x-index.
-        	xLoop:
-        	for(int ix = -23; ix <= 23; ix++) {
-        		// ix = 0 and the beam hole do not exist; skip these!
-        		if(ix == 0) { continue xLoop; }
-        		if((ix >= -10 && ix <= -2) && (iy == -1 || iy == 1)) {
-        			continue xLoop;
-        		}
-        		
-        		// Output the crystal indices, pedestal, and gain.
-        		int channelID = indexChannelMap.get(new Point(ix, iy));
-        		System.out.printf("\t%3d\t%3d\t%8.3f\t%8.3f\t%4d%n", ix, iy,
-        				getPedestal(channelID), getGain(channelID), getThreshold(channelID));
-        	}
+            // iy = 0 does not exists; skip it!
+            if(iy == 0) { continue yLoop; }
+            
+            // Iterate over each crystal x-index.
+            xLoop:
+            for(int ix = -23; ix <= 23; ix++) {
+                // ix = 0 and the beam hole do not exist; skip these!
+                if(ix == 0) { continue xLoop; }
+                if((ix >= -10 && ix <= -2) && (iy == -1 || iy == 1)) {
+                    continue xLoop;
+                }
+                
+                // Output the crystal indices, pedestal, and gain.
+                int channelID = indexChannelMap.get(new Point(ix, iy));
+                ps.printf("\t%3d\t%3d\t%8.3f\t%8.3f\t%4d%n", ix, iy,
+                        getPedestal(channelID), getGain(channelID), getThreshold(channelID));
+            }
         }
     }
     

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/GTPConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/GTPConfig.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/GTPConfig.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,6 @@
 package org.hps.record.daqconfig;
+
+import java.io.PrintStream;
 
 /**
  * Class <code>GTPConfig</code> stores GTP configuration settings
@@ -57,14 +59,14 @@
     }
     
     @Override
-    public void printConfig() {
+    public void printConfig(PrintStream ps) {
         // Print the configuration header.
-        System.out.println("GTP Configuration:");
+        ps.println("GTP Configuration:");
         
         // Print the GTP settings.
-        System.out.printf("\tTime Window Before :: %d clock-cycles%n", windowBefore);
-        System.out.printf("\tTime Window After  :: %d clock-cycles%n", windowAfter);
-        System.out.printf("\tSeed Energy Min    :: %5.3f GeV%n",       seedCut.getLowerBound());
+        ps.printf("\tTime Window Before :: %d clock-cycles%n", windowBefore);
+        ps.printf("\tTime Window After  :: %d clock-cycles%n", windowAfter);
+        ps.printf("\tSeed Energy Min    :: %5.3f GeV%n",       seedCut.getLowerBound());
     }
 
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/IDAQConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/IDAQConfig.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/IDAQConfig.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,6 @@
 package org.hps.record.daqconfig;
+
+import java.io.PrintStream;
 
 
 /**
@@ -20,5 +22,5 @@
      * Prints a textual representation of the configuration bank to the
      * terminal.
      */
-    public abstract void printConfig();
+    public abstract void printConfig(PrintStream ps);
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/SSPConfig.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/SSPConfig.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/daqconfig/SSPConfig.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,6 @@
 package org.hps.record.daqconfig;
+
+import java.io.PrintStream;
 
 
 /**
@@ -98,64 +100,64 @@
     }
     
     @Override
-    public void printConfig() {
+    public void printConfig(PrintStream ps) {
         // Print the configuration header.
-        System.out.println("SSP Configuration:");
+        ps.println("SSP Configuration:");
         
         // Print the singles triggers.
         for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-            System.out.printf("\tSingles Trigger %d%n", (triggerNum + 1));
-            System.out.println("\t\tCluster Energy Lower Bound Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getEnergyMinCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", singlesTrigger[triggerNum].getEnergyMinCutConfig().getLowerBound());
+            ps.printf("\tSingles Trigger %d%n", (triggerNum + 1));
+            ps.println("\t\tCluster Energy Lower Bound Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getEnergyMinCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", singlesTrigger[triggerNum].getEnergyMinCutConfig().getLowerBound());
             
-            System.out.println("\t\tCluster Energy Upper Bound Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getEnergyMaxCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", singlesTrigger[triggerNum].getEnergyMaxCutConfig().getUpperBound());
+            ps.println("\t\tCluster Energy Upper Bound Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getEnergyMaxCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", singlesTrigger[triggerNum].getEnergyMaxCutConfig().getUpperBound());
             
-            System.out.println("\t\tCluster Hit Count Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getHitCountCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %1.0f hits%n", singlesTrigger[triggerNum].getHitCountCutConfig().getLowerBound());
-            System.out.println();
+            ps.println("\t\tCluster Hit Count Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", singlesTrigger[triggerNum].getHitCountCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %1.0f hits%n", singlesTrigger[triggerNum].getHitCountCutConfig().getLowerBound());
+            ps.println();
         }
         
         // Print the pair triggers.
         for(int triggerNum = 0; triggerNum < 2; triggerNum++) {
-            System.out.printf("\tPair Trigger %d%n", (triggerNum + 1));
-            System.out.println("\t\tCluster Energy Lower Bound Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyMinCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyMinCutConfig().getLowerBound());
+            ps.printf("\tPair Trigger %d%n", (triggerNum + 1));
+            ps.println("\t\tCluster Energy Lower Bound Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyMinCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyMinCutConfig().getLowerBound());
             
-            System.out.println("\t\tCluster Energy Upper Bound Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyMaxCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyMaxCutConfig().getUpperBound());
+            ps.println("\t\tCluster Energy Upper Bound Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyMaxCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyMaxCutConfig().getUpperBound());
             
-            System.out.println("\t\tCluster Hit Count Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getHitCountCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %1.0f hits%n", pairTrigger[triggerNum].getHitCountCutConfig().getLowerBound());
+            ps.println("\t\tCluster Hit Count Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getHitCountCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %1.0f hits%n", pairTrigger[triggerNum].getHitCountCutConfig().getLowerBound());
             
-            System.out.println("\t\tPair Energy Sum Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergySumCutConfig().isEnabled());
-            System.out.printf("\t\t\tMin     :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySumCutConfig().getLowerBound());
-            System.out.printf("\t\t\tMax     :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySumCutConfig().getUpperBound());
+            ps.println("\t\tPair Energy Sum Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergySumCutConfig().isEnabled());
+            ps.printf("\t\t\tMin     :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySumCutConfig().getLowerBound());
+            ps.printf("\t\t\tMax     :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySumCutConfig().getUpperBound());
             
-            System.out.println("\t\tPair Energy Difference Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyDifferenceCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyDifferenceCutConfig().getUpperBound());
+            ps.println("\t\tPair Energy Difference Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergyDifferenceCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergyDifferenceCutConfig().getUpperBound());
             
-            System.out.println("\t\tPair Energy Slope Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().getLowerBound());
-            System.out.printf("\t\t\tParam F :: %6.4f GeV/mm%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().getParameterF());
+            ps.println("\t\tPair Energy Slope Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %5.3f GeV%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().getLowerBound());
+            ps.printf("\t\t\tParam F :: %6.4f GeV/mm%n", pairTrigger[triggerNum].getEnergySlopeCutConfig().getParameterF());
             
-            System.out.println("\t\tPair Coplanarity Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getCoplanarityCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %3.0f degrees%n", pairTrigger[triggerNum].getCoplanarityCutConfig().getUpperBound());
+            ps.println("\t\tPair Coplanarity Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getCoplanarityCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %3.0f degrees%n", pairTrigger[triggerNum].getCoplanarityCutConfig().getUpperBound());
             
-            System.out.println("\t\tPair Time Coincidence Cut");
-            System.out.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getTimeDifferenceCutConfig().isEnabled());
-            System.out.printf("\t\t\tValue   :: %1.0f clock-cycles%n", pairTrigger[triggerNum].getTimeDifferenceCutConfig().getUpperBound());
-            System.out.println();
+            ps.println("\t\tPair Time Coincidence Cut");
+            ps.printf("\t\t\tEnabled :: %b%n", pairTrigger[triggerNum].getTimeDifferenceCutConfig().isEnabled());
+            ps.printf("\t\t\tValue   :: %1.0f clock-cycles%n", pairTrigger[triggerNum].getTimeDifferenceCutConfig().getUpperBound());
+            ps.println();
         }
     }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsData.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsData.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsData.java	Wed Apr 27 11:11:32 2016
@@ -276,12 +276,13 @@
      * @param evioEvent the EVIO event
      * @return the EPICS data or <code>null</code> if it is not present in the event
      */
+    // FIXME: Not currently used.
     public static EpicsData getEpicsData(EvioEvent evioEvent) {
         
         EpicsData epicsData = null;
         
         // Is this an EPICS event?
-        if (EventTagConstant.EPICS.equals(evioEvent)) {
+        if (EventTagConstant.EPICS.matches(evioEvent)) {
 
             // Find the bank with the EPICS data string.
             final BaseStructure epicsBank = EvioBankTag.EPICS_STRING.findBank(evioEvent);

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsEvioProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsEvioProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsEvioProcessor.java	Wed Apr 27 11:11:32 2016
@@ -45,7 +45,7 @@
     public void process(final EvioEvent evioEvent) {
 
         // Is this an EPICS event?
-        if (EventTagConstant.EPICS.equals(evioEvent)) {
+        if (EventTagConstant.EPICS.matches(evioEvent)) {
 
             LOGGER.fine("processing EPICS event " + evioEvent.getEventNumber());
 

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsRunProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsRunProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/epics/EpicsRunProcessor.java	Wed Apr 27 11:11:32 2016
@@ -39,7 +39,7 @@
     private final EpicsEvioProcessor processor = new EpicsEvioProcessor();
 
     /**
-     * Create an EPICs log.
+     * Create a processor that will make a list of EPICS data.
      */
     public EpicsRunProcessor() {
     }
@@ -66,9 +66,9 @@
 
         // Add EPICS data to the collection.
         if (this.currentEpicsData != null) {
-            LOGGER.info("adding EPICS data for run " + this.currentEpicsData.getEpicsHeader().getRun() + " and timestamp " 
-                    + this.currentEpicsData.getEpicsHeader().getTimestamp() + " with seq " 
-                    + this.currentEpicsData.getEpicsHeader().getSequence());
+            LOGGER.fine("Adding EPICS data with run " + this.currentEpicsData.getEpicsHeader().getRun() + "; timestamp " 
+                    + this.currentEpicsData.getEpicsHeader().getTimestamp() + "; seq "
+                    + this.currentEpicsData.getEpicsHeader().getSequence() + ".");
             this.epicsDataSet.add(this.currentEpicsData);
         }
     }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventTagConstant.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventTagConstant.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EventTagConstant.java	Wed Apr 27 11:11:32 2016
@@ -63,7 +63,7 @@
         return tag == this.tag;
     }
     
-    public boolean equals(final EvioEvent evioEvent) {
+    public boolean matches(final EvioEvent evioEvent) {
         return evioEvent.getHeader().getTag() == this.tag;
     }
     

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioBankTag.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioBankTag.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioBankTag.java	Wed Apr 27 11:11:32 2016
@@ -25,8 +25,10 @@
     /** Scaler data bank. */
     SCALERS(57621),
     /** Trigger configuration bank. */
-    TRIGGER_CONFIG(0xE10E);
-
+    TRIGGER_CONFIG(0xE10E),
+    /** TI trigger bank. */
+    TI_TRIGGER(0xe10a);
+    
     /**
      * The bank's tag value.
      */
@@ -46,7 +48,7 @@
      *
      * @param startBank the starting bank
      * @return the first bank matching the tag or <code>null<code> if not found
-     */
+     */    
     public BaseStructure findBank(final BaseStructure startBank) {
         BaseStructure foundBank = null;
         if (this.equals(startBank)) {
@@ -60,8 +62,8 @@
             }
         }
         return foundBank;
-    }
-
+    }    
+    
     /**
      * Get the bank tag value.
      *

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioDetectorConditionsProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioDetectorConditionsProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioDetectorConditionsProcessor.java	Wed Apr 27 11:11:32 2016
@@ -39,21 +39,28 @@
      */
     @Override
     public void process(final EvioEvent evioEvent) throws Exception {
+        
         // Get the head head bank from event.
         final BaseStructure headBank = EvioEventUtilities.getHeadBank(evioEvent);
 
-        // Is the head bank present?
-        if (headBank != null) {
+        // Initialize from head bank.
+        if (headBank != null) {            
+            initializeConditions(headBank.getIntData()[1]);
+        }
+        
+        // Initialize from PRESTART.
+        if (EventTagConstant.PRESTART.matches(evioEvent)) {
+            int runNumber = EvioEventUtilities.getControlEventData(evioEvent)[1];
+            initializeConditions(runNumber);
+        }
+    }
 
-            // Get the run number from the head bank.
-            final int runNumber = headBank.getIntData()[1];
-
-            // Initialize the conditions system from the detector name and run number.
-            try {
-                ConditionsManager.defaultInstance().setDetector(this.detectorName, runNumber);
-            } catch (final ConditionsNotFoundException e) {
-                throw new RuntimeException("Error setting up conditions from EVIO head bank.", e);
-            }
+    private void initializeConditions(final int runNumber) {
+        // Initialize the conditions system from the detector name and run number.
+        try {
+            ConditionsManager.defaultInstance().setDetector(this.detectorName, runNumber);
+        } catch (final ConditionsNotFoundException e) {
+            throw new RuntimeException("Error setting up conditions from EVIO head bank.", e);
         }
     }
 
@@ -65,6 +72,7 @@
      * @param evioEvent the <code>EvioEvent</code> to process
      */
     @Override
+    // FIXME: not activated by EvioLoop
     public void startRun(final EvioEvent evioEvent) {
         // System.out.println("EvioDetectorConditionsProcessor.startRun");
         if (EvioEventUtilities.isPreStartEvent(evioEvent)) {

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java	Wed Apr 27 11:11:32 2016
@@ -14,7 +14,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.jlab.coda.jevio.EventWriter;
 import org.jlab.coda.jevio.EvioEvent;
 import org.jlab.coda.jevio.EvioReader;
@@ -51,7 +51,7 @@
      */
     public static void main(String[] args) {
 
-        DefaultParser parser = new DefaultParser();
+        PosixParser parser = new PosixParser();
 
         CommandLine commandLine = null;
         try {

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventUtilities.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioEventUtilities.java	Wed Apr 27 11:11:32 2016
@@ -13,9 +13,6 @@
 
 import org.hps.conditions.database.DatabaseConditionsManager;
 import org.hps.record.daqconfig.EvioDAQParser;
-import org.hps.record.epics.EpicsData;
-import org.hps.record.epics.EpicsHeader;
-import org.hps.record.scalers.ScalerData;
 import org.jlab.coda.jevio.BaseStructure;
 import org.jlab.coda.jevio.EvioEvent;
 import org.lcsim.conditions.ConditionsManager.ConditionsNotFoundException;
@@ -113,23 +110,18 @@
     /**
      * Get the run number from an EVIO event.
      *
-     * @return the run number
-     * @throws IllegalArgumentException if event does not have a head bank
-     */
-    public static int getRunNumber(final EvioEvent event) {
+     * @return the run number or <code>null</code> if not present in event
+     */
+    public static Integer getRunNumber(final EvioEvent event) {
         if (isControlEvent(event)) {
             return getControlEventData(event)[1];
         } else if (isPhysicsEvent(event)) {
             final BaseStructure headBank = EvioEventUtilities.getHeadBank(event);
             if (headBank != null) {
                 return headBank.getIntData()[1];
-            } else {
-                throw new IllegalArgumentException("Head bank is missing from physics event.");
-            }
-        } else {
-            // Not sure if this would ever happen.
-            throw new IllegalArgumentException("Wrong event type: " + event.getHeader().getTag());
-        }
+            } 
+        } 
+        return null;
     }
 
     /**

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileProducer.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileProducer.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileProducer.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.jlab.coda.et.EtAttachment;
 import org.jlab.coda.et.EtConstants;
 import org.jlab.coda.et.EtEvent;
@@ -195,7 +195,7 @@
     public void run(final String[] args) {
 
         // Command line parser.
-        final DefaultParser parser = new DefaultParser();
+        final PosixParser parser = new PosixParser();
 
         try {
 

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileSource.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileSource.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileSource.java	Wed Apr 27 11:11:32 2016
@@ -4,6 +4,8 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 import org.freehep.record.source.NoSuchRecordException;
 import org.hps.record.AbstractRecordQueue;
@@ -12,15 +14,15 @@
 import org.jlab.coda.jevio.EvioReader;
 
 /**
- * A basic implementation of an <tt>AbstractRecordSource</tt> for supplying <tt>EvioEvent</tt> objects to a loop from a
- * list of EVIO files.
- * <p>
- * Unlike the LCIO record source, it has no rewind or indexing capabilities.
+ * A basic implementation of an <code>AbstractRecordSource</code> for supplying <code>EvioEvent</code> objects to a 
+ * loop from a list of EVIO files.
  *
  * @author Jeremy McCormick, SLAC
  */
 public final class EvioFileSource extends AbstractRecordQueue<EvioEvent> {
 
+    private static final Logger LOGGER = Logger.getLogger(EvioFileSource.class.getPackage().getName());
+    
     /**
      * The current event.
      */
@@ -40,7 +42,12 @@
      * The reader to use for reading and parsing the EVIO data.
      */
     private EvioReader reader;
-
+    
+    /**
+     * Whether to continue on parse errors or not.
+     */
+    private boolean continueOnErrors = false;
+   
     /**
      * Constructor taking a single EVIO file.
      *
@@ -60,7 +67,15 @@
         this.files.addAll(files);
         this.openReader();
     }
-
+    
+    /**
+     * Set whether to continue on errors or not.
+     * @param continueOnErrors <code>true</code> to continue on errors
+     */
+    public void setContinueOnErrors(boolean continueOnErrors) {
+        this.continueOnErrors = continueOnErrors;
+    }
+    
     /**
      * Close the current reader.
      */
@@ -135,20 +150,26 @@
         for (;;) {
             try {
                 this.currentEvent = this.reader.parseNextEvent();
-            } catch (final EvioException e) {
-                throw new IOException(e);
+                if (this.reader.getNumEventsRemaining() == 0 && this.currentEvent == null) {
+                    this.closeReader();
+                    this.fileIndex++;
+                    if (!this.endOfFiles()) {
+                        this.openReader();
+                    } else {
+                        throw new NoSuchRecordException("End of data.");
+                    }
+                } else {
+                    LOGGER.finest("Read EVIO event " + this.currentEvent.getEventNumber() + " okay.");
+                    break;
+                }                   
+            } catch (EvioException | NegativeArraySizeException e) { 
+                LOGGER.log(Level.SEVERE, "Error parsing next EVIO event.", e);
+                if (!continueOnErrors) {
+                    throw new IOException("Fatal error parsing next EVIO event.", e);
+                }
+            } catch (Exception e) {
+                throw new IOException("Error parsing EVIO event.", e);
             }
-            if (this.currentEvent == null) {
-                this.closeReader();
-                this.fileIndex++;
-                if (!this.endOfFiles()) {
-                    this.openReader();
-                    continue;
-                } else {
-                    throw new NoSuchRecordException();
-                }
-            }
-            return;
         }
     }
 
@@ -159,10 +180,9 @@
      */
     private void openReader() {
         try {
-            System.out.println("Opening reader for file " + this.files.get(this.fileIndex) + " ...");
-            // FIXME: this should use the reader directly and cached paths should be managed externally
+            // FIXME: This should use the reader directly and MSS paths should be transformed externally.
+            LOGGER.info("opening EVIO file " + this.files.get(this.fileIndex).getPath() + " ...");
             this.reader = EvioFileUtilities.open(this.files.get(this.fileIndex), true);
-            System.out.println("Done opening file.");
         } catch (EvioException | IOException e) {
             throw new RuntimeException(e);
         }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileUtilities.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioFileUtilities.java	Wed Apr 27 11:11:32 2016
@@ -25,24 +25,7 @@
      * Milliseconds constant for conversion to/from second.
      */
     private static final long MILLISECONDS = 1000L;
-
-    /**
-     * Get a cached file path, assuming that the input file path is on the JLAB MSS e.g. it starts with "/mss".
-     *
-     * @param file the MSS file path
-     * @return the cached file path (prepends "/cache" to the path)
-     * @throws IllegalArgumentException if the file is not on the MSS (e.g. path does not start with "/mss")
-     */
-    public static File getCachedFile(final File file) {
-        if (!isMssFile(file)) {
-            throw new IllegalArgumentException("File " + file.getPath() + " is not on the JLab MSS.");
-        }
-        if (isCachedFile(file)) {
-            throw new IllegalArgumentException("File " + file.getPath() + " is already on the cache disk.");
-        }
-        return new File("/cache" + file.getPath());
-    }
-
+   
     /**
      * Get the run number from the file name.
      *
@@ -70,26 +53,6 @@
     }
 
     /**
-     * Return <code>true</code> if this is a file on the cache disk e.g. the path starts with "/cache".
-     *
-     * @param file the file
-     * @return <code>true</code> if the file is a cached file
-     */
-    public static boolean isCachedFile(final File file) {
-        return file.getPath().startsWith("/cache");
-    }
-
-    /**
-     * Return <code>true</code> if this file is on the JLAB MSS e.g. the path starts with "/mss".
-     *
-     * @param file the file
-     * @return <code>true</code> if the file is on the MSS
-     */
-    public static boolean isMssFile(final File file) {
-        return file.getPath().startsWith("/mss");
-    }
-
-    /**
      * Open an EVIO file using an <code>EvioReader</code> in memory mapping mode.
      *
      * @param file the EVIO file
@@ -98,7 +61,7 @@
      * @throws EvioException if there is an error reading the EVIO data
      */
     public static EvioReader open(final File file) throws IOException, EvioException {
-        return open(file, false);
+        return open(file, true);
     }
 
     /**
@@ -111,14 +74,11 @@
      * @throws EvioException if there is an error reading the EVIO data
      */
     public static EvioReader open(final File file, final boolean sequential) throws IOException, EvioException {
-        File openFile = file;
-        if (isMssFile(file)) {
-            openFile = getCachedFile(file);
-        }
+        LOGGER.info("opening " + file.getPath() + " in " + (sequential ? "sequential" : "mmap" + " mode"));
         final long start = System.currentTimeMillis();
-        final EvioReader reader = new EvioReader(openFile, false, sequential);
+        final EvioReader reader = new EvioReader(file, false, sequential);
         final long end = System.currentTimeMillis() - start;
-        LOGGER.info("opened " + openFile.getPath() + " in " + (double) end / (double) MILLISECONDS + " seconds in "
+        LOGGER.info("opened " + file.getPath() + " in " + (double) end / (double) MILLISECONDS + " seconds in "
                 + (sequential ? "sequential" : "mmap" + " mode"));
         return reader;
     }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoop.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoop.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoop.java	Wed Apr 27 11:11:32 2016
@@ -1,52 +1,24 @@
 package org.hps.record.evio;
 
-import org.freehep.record.loop.DefaultRecordLoop;
+import org.hps.record.AbstractRecordLoop;
+import org.jlab.coda.jevio.EvioEvent;
 
 /**
  * Implementation of a Freehep <code>RecordLoop</code> for EVIO data.
  *
  * @author Jeremy McCormick, SLAC
  */
-public class EvioLoop extends DefaultRecordLoop {
-
-    /**
-     * The record adapter.
-     */
-    private final EvioLoopAdapter adapter = new EvioLoopAdapter();
+public class EvioLoop extends AbstractRecordLoop<EvioEvent> {
 
     /**
      * Create a new record loop.
      */
     public EvioLoop() {
+        this.adapter = new EvioLoopAdapter();
         this.addLoopListener(adapter);
         this.addRecordListener(adapter);
     }
-
-    /**
-     * Add an EVIO event processor to the adapter which will be activated for every EVIO event that is processed.
-     *
-     * @param evioEventProcessor the EVIO processor to add
-     */
-    public void addEvioEventProcessor(final EvioEventProcessor evioEventProcessor) {
-        adapter.addEvioEventProcessor(evioEventProcessor);
-    }
-
-    /**
-     * Loop over events from the source.
-     *
-     * @param number the number of events to process or -1L for all events from the source
-     * @return the number of records that were processed
-     */
-    public long loop(final long number) {
-        if (number < 0L) {
-            this.execute(Command.GO, true);
-        } else {
-            this.execute(Command.GO_N, number, true);
-            this.execute(Command.STOP);
-        }
-        return this.getSupplied();
-    }
-
+  
     /**
      * Set the EVIO data source.
      *

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoopAdapter.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoopAdapter.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/evio/EvioLoopAdapter.java	Wed Apr 27 11:11:32 2016
@@ -1,14 +1,6 @@
 package org.hps.record.evio;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import org.freehep.record.loop.AbstractLoopListener;
-import org.freehep.record.loop.LoopEvent;
-import org.freehep.record.loop.LoopListener;
-import org.freehep.record.loop.RecordEvent;
-import org.freehep.record.loop.RecordListener;
+import org.hps.record.AbstractLoopAdapter;
 import org.jlab.coda.jevio.EvioEvent;
 
 /**
@@ -16,79 +8,5 @@
  *
  * @author Jeremy McCormick, SLAC
  */
-public final class EvioLoopAdapter extends AbstractLoopListener implements RecordListener, LoopListener {
-
-    /**
-     * Initialize the logger.
-     */
-    private static final Logger LOGGER = Logger.getLogger(EvioLoopAdapter.class.getPackage().getName());
-
-    /**
-     * List of event processors to activate.
-     */
-    private final List<EvioEventProcessor> processors = new ArrayList<EvioEventProcessor>();
-
-    /**
-     * Create a new loop adapter.
-     */
-    EvioLoopAdapter() {
-    }
-
-    /**
-     * Add an EVIO processor to the adapter.
-     *
-     * @param processor the EVIO processor to add to the adapter
-     */
-    void addEvioEventProcessor(final EvioEventProcessor processor) {
-        LOGGER.info("adding " + processor.getClass().getName() + " to EVIO processors");
-        this.processors.add(processor);
-    }
-
-    /**
-     * Implementation of the finish hook which activates the {@link EvioEventProcessor#endJob()} method of all
-     * registered processors.
-     */
-    @Override
-    protected void finish(final LoopEvent event) {
-        LOGGER.info("finish");
-        for (final EvioEventProcessor processor : processors) {
-            processor.endJob();
-        }
-    }
-
-    /**
-     * Primary event processing method that activates the {@link EvioEventProcessor#process(EvioEvent)} method of all
-     * registered processors.
-     *
-     * @param recordEvent the record event to process which should have an EVIO event
-     * @throws IllegalArgumentException if the record is the wrong type
-     */
-    @Override
-    public void recordSupplied(final RecordEvent recordEvent) {
-        final Object record = recordEvent.getRecord();
-        if (record instanceof EvioEvent) {
-            final EvioEvent evioEvent = EvioEvent.class.cast(record);
-            for (final EvioEventProcessor processor : processors) {
-                try {
-                    processor.process(evioEvent);
-                } catch (final Exception e) {
-                    throw new RuntimeException(e);
-                }
-            }
-        } else {
-            throw new IllegalArgumentException("The supplied record has the wrong type: " + record.getClass());
-        }
-    }
-
-    /**
-     * Implementation of the start hook which activates the {@link EvioEventProcessor#startJob()} method of all
-     * registered processors.
-     */
-    @Override
-    protected void start(final LoopEvent event) {
-        LOGGER.info("start");
-        for (final EvioEventProcessor processor : processors) {
-            processor.startJob();
-        }
-    }
+public final class EvioLoopAdapter extends AbstractLoopAdapter<EvioEvent> {
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/scalers/ScalerUtilities.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/scalers/ScalerUtilities.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/scalers/ScalerUtilities.java	Wed Apr 27 11:11:32 2016
@@ -74,7 +74,6 @@
         // [67]/[68] = CLOCK
         final double clock = (double) clockGated / (double) clockUngated;
 
-        // Compute the live times.
         final double[] liveTimes = new double[3];
         liveTimes[LiveTimeIndex.FCUP_TDC.ordinal()] = fcupTdc;
         liveTimes[LiveTimeIndex.FCUP_TRG.ordinal()] = fcupTrg;

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/svt/SvtEvioUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/svt/SvtEvioUtils.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/svt/SvtEvioUtils.java	Wed Apr 27 11:11:32 2016
@@ -1,11 +1,16 @@
 package org.hps.record.svt;
+
+import java.util.ArrayList;
+import java.util.List;
+import org.jlab.coda.jevio.BaseStructure;
+import org.jlab.coda.jevio.DataType;
+import org.jlab.coda.jevio.StructureType;
 
 
 /**
  *  A set of static utility methods used to decode SVT data.
  * 
  *  @author Omar Moreno <[log in to unmask]>
- *  @date November 20, 2014
  */
 public class SvtEvioUtils {
 
@@ -19,9 +24,7 @@
     private static final int APV_HEADER_BUFFER_ADDRESS_MASK  = 0xFF; //[8:1]
     private static final int APV_HEADER_DATA_FRAME_COUNT_MASK = 0xF; //[12:9]
     private static final int APV_HEADER_DATA_APV_NR_MASK = 0x3; //[15:13]
-    
-
-   
+      
     // TODO: Move these to constants class
     public static final int APV25_PER_HYBRID = 5;
     public static final int CHANNELS_PER_APV25 = 128;
@@ -90,13 +93,12 @@
      *  Extract and return the front end board (FEB) ID associated with the
      *  multisample tail
      *  
-     *  @param data : a multisample header
+     *  @param multisampleTail : a multisample header
      *  @return A FEB ID in the range 0-10
      */
     public static int getFebIDFromMultisampleTail(int multisampleTail) { 
         return (multisampleTail >>> 8) & FEB_MASK; 
     }
-
     
     /**
      *  Extract and return the front end board (FEB) hybrid ID associated with 
@@ -113,7 +115,7 @@
      *  Extract and return the front end board (FEB) hybrid ID associated with 
      *  the multisample tail 
      *
-     *  @param multisample : a  multisample tail
+     *  @param multisampleTail : a  multisample tail
      *  @return A FEB hybrid ID in the range 0-3
      */
     public static int getFebHybridIDFromMultisampleTail(int multisampleTail) { 
@@ -258,7 +260,7 @@
     /**
      *  Extract the error bit from the multisample header.
      *
-     *  @param data : multisample of data
+     *  @param multisampleHeader : multisample of data
      *  @return value of the error bit.  This is non-zero if there is an error.
      */
     public static int getErrorBitFromMultisampleHeader(int multisampleHeader) { 
@@ -441,6 +443,56 @@
         return samples;
     }
 
+    /**
+     *  Retrieve all the banks in an event that match the given tag in their
+     *  header and are not data banks. 
+     *
+     *  @param evioEvent : The event/bank being queried
+     *  @param tag : The tag to match
+     *  @return A collection of all bank structures that pass the filter 
+     *          provided by the event
+     */
+    public static List<BaseStructure> getROCBanks(BaseStructure evioEvent, int minROCTag, int maxROCTag) {
+        List<BaseStructure> matchingBanks = new ArrayList<BaseStructure>();
+        if (evioEvent.getChildCount() > 0) {
+            for (BaseStructure childBank : evioEvent.getChildrenList()) {
+                if (childBank.getStructureType() == StructureType.BANK
+                        && childBank.getHeader().getDataType() == DataType.ALSOBANK
+                        && childBank.getHeader().getTag() >= minROCTag
+                        && childBank.getHeader().getTag() <= maxROCTag) {
+                    matchingBanks.add(childBank);
+                }
+            }
+        }
+        return matchingBanks;
+    }
+
+    public static List<BaseStructure> getDataBanks(BaseStructure evioEvent, int minROCTag, int maxROCTag, int minDataTag, int maxDataTag) {
+        List<BaseStructure> rocBanks = getROCBanks(evioEvent, minROCTag, maxROCTag);
+        List<BaseStructure> matchingBanks = new ArrayList<BaseStructure>();
+        for (BaseStructure rocBank : rocBanks) {
+            if (rocBank.getChildCount() > 0) {
+                for (BaseStructure childBank : rocBank.getChildrenList()) {
+                    if (childBank.getHeader().getTag() >= minDataTag
+                            && childBank.getHeader().getTag() <= maxDataTag) {
+                        matchingBanks.add(childBank);
+                    }
+                }
+            }
+        }
+        return matchingBanks;
+    }
+    
+    public static List<int[]> getMultisamples(int[] data, int sampleCount, int headerLength) {
+        List<int[]> sampleList = new ArrayList<int[]>();
+        // Loop through all of the samples and make hits
+        for (int samplesN = 0; samplesN < sampleCount; samplesN += 4) {
+            int[] samples = new int[4];
+            System.arraycopy(data, headerLength + samplesN, samples, 0, samples.length);
+            sampleList.add(samples);
+        }
+        return sampleList;
+    }
 
     /**
      *  Private constructor to prevent the class from being instantiated.

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/AbstractIntData.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/AbstractIntData.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/AbstractIntData.java	Wed Apr 27 11:11:32 2016
@@ -74,7 +74,6 @@
      * Return the int bank of an AbstractIntData read from LCIO.
      *
      * @param object
-     * @return
      */
     public static int[] getBank(GenericObject object) {
         int N = object.getNInt() - 1;

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPData.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPData.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPData.java	Wed Apr 27 11:11:32 2016
@@ -175,7 +175,7 @@
      * of <code>SSPCosmicTrigger</code> objects.
      */
     public List<SSPCosmicTrigger> getCosmicTriggers() {
-    	return cosmicList;
+        return cosmicList;
     }
     
     /**
@@ -184,7 +184,7 @@
      * of <code>SSPPairTrigger</code> objects.
      */
     public List<SSPPairTrigger> getPairTriggers() {
-    	return pairList;
+        return pairList;
     }
     
     /**
@@ -193,7 +193,7 @@
      * of <code>SSPSinglesTrigger</code> objects.
      */
     public List<SSPSinglesTrigger> getSinglesTriggers() {
-    	return singlesList;
+        return singlesList;
     }
     
     /**

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPNumberedTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPNumberedTrigger.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPNumberedTrigger.java	Wed Apr 27 11:11:32 2016
@@ -10,16 +10,41 @@
  * @see SSPTrigger
  */
 public abstract class SSPNumberedTrigger extends SSPTrigger {
-	/**
-	 * Instantiates the <code>SSPNumberedTrigger</code>.
+    /**
+     * Instantiates the <code>SSPNumberedTrigger</code>.
      * @param type - The type of trigger.
      * @param time - The time at which the trigger occurred in ns.
      * @param data - The trigger bit data.
-	 */
-	public SSPNumberedTrigger(int type, int time, int data) {
-		super(type, time, data);
-	}
-	
+     */
+    public SSPNumberedTrigger(int type, int time, int data) {
+        super(type, time, data);
+    }
+    
+    /**
+     * Gets the number of the trigger which generated this object.
+     * @return Returns either <code>0</code> or </code>1</code>.
+     */
+    public abstract int getTriggerNumber();
+    
+    /**
+     * Indicates whether the trigger was reported by the trigger number
+     * 0 trigger.
+     * @return <code>true</code> if the trigger was reported by the
+     * trigger number 0 trigger and <code>false</code> if by either
+     * the trigger number 1 or an unknown trigger.
+     */
+    public abstract boolean isTrigger0();
+    
+    /**
+     * Indicates whether the trigger was reported by the trigger number
+     * 1 trigger.
+     * @return <code>true</code> if the trigger was reported by the
+     * trigger number 1 trigger and <code>false</code> if by either
+     * the trigger number 0 or an unknown trigger.
+     */
+    public abstract boolean isTrigger1();
+    
+    
     /**
      * Indicates whether the trigger was reported by the first of the
      * singles triggers.
@@ -27,6 +52,7 @@
      * first trigger and <code>false</code> if it was reported by the
      * second trigger.
      */
+    @Deprecated
     public abstract boolean isFirstTrigger();
     
     /**
@@ -36,5 +62,6 @@
      * second trigger and <code>false</code> if it was reported by
      * the first trigger.
      */
+    @Deprecated
     public abstract boolean isSecondTrigger();
-}
+}

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPPairTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPPairTrigger.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPPairTrigger.java	Wed Apr 27 11:11:32 2016
@@ -20,13 +20,30 @@
     }
     
     @Override
+    public int getTriggerNumber() {
+        if(isFirstTrigger()) { return 0; }
+        else if(isSecondTrigger()) { return 1; }
+        else { return -1; }
+    }
+    
+    @Override
+    public boolean isTrigger0() {
+        return (type == SSPData.TRIG_TYPE_PAIR0);
+    }
+    
+    @Override
+    public boolean isTrigger1() {
+        return (type == SSPData.TRIG_TYPE_PAIR1);
+    }
+    
+    @Override
     public boolean isFirstTrigger() {
-    	return (type == SSPData.TRIG_TYPE_PAIR0);
+        return isTrigger0();
     }
     
     @Override
     public boolean isSecondTrigger() {
-    	return (type == SSPData.TRIG_TYPE_PAIR1);
+        return isTrigger1();
     }
     
     /**
@@ -71,9 +88,9 @@
     
     @Override
     public String toString() {
-		return String.format("Trigger %d :: %3d ns :: ESum: %d, EDiff: %d, ESlope: %d, Coplanarity: %d",
-				isFirstTrigger() ? 1 : 2, getTime(), passCutEnergySum() ? 1 : 0,
-				passCutEnergyDifference() ? 1 : 0, passCutEnergySlope() ? 1 : 0,
-				passCutCoplanarity() ? 1 : 0);
+        return String.format("Trigger %d :: %3d ns :: ESum: %d, EDiff: %d, ESlope: %d, Coplanarity: %d",
+                isFirstTrigger() ? 1 : 2, getTime(), passCutEnergySum() ? 1 : 0,
+                passCutEnergyDifference() ? 1 : 0, passCutEnergySlope() ? 1 : 0,
+                passCutCoplanarity() ? 1 : 0);
     }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPSinglesTrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPSinglesTrigger.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/SSPSinglesTrigger.java	Wed Apr 27 11:11:32 2016
@@ -26,13 +26,30 @@
     }
     
     @Override
+    public int getTriggerNumber() {
+        if(isFirstTrigger()) { return 0; }
+        else if(isSecondTrigger()) { return 1; }
+        else { return -1; }
+    }
+    
+    @Override
+    public boolean isTrigger0() {
+        return (type == SSPData.TRIG_TYPE_SINGLES0_BOT) || (type == SSPData.TRIG_TYPE_SINGLES0_TOP);
+    }
+    
+    @Override
+    public boolean isTrigger1() {
+        return (type == SSPData.TRIG_TYPE_SINGLES1_BOT) || (type == SSPData.TRIG_TYPE_SINGLES1_TOP);
+    }
+    
+    @Override
     public boolean isFirstTrigger() {
-    	return (type == SSPData.TRIG_TYPE_SINGLES0_BOT) || (type == SSPData.TRIG_TYPE_SINGLES0_TOP);
+        return isTrigger0();
     }
     
     @Override
     public boolean isSecondTrigger() {
-    	return (type == SSPData.TRIG_TYPE_SINGLES1_BOT) || (type == SSPData.TRIG_TYPE_SINGLES1_TOP);
+        return isTrigger1();
     }
     
     /**
@@ -67,8 +84,8 @@
     
     @Override
     public String toString() {
-		return String.format("Trigger %d :: %3d ns :: EClusterLow: %d; EClusterHigh %d; HitCount: %d",
-				isFirstTrigger() ? 1 : 2, getTime(), passCutEnergyMin() ? 1 : 0,
-				passCutEnergyMax() ? 1 : 0, passCutHitCount() ? 1 : 0);
+        return String.format("Trigger %d :: %3d ns :: EClusterLow: %d; EClusterHigh %d; HitCount: %d",
+                isFirstTrigger() ? 1 : 2, getTime(), passCutEnergyMin() ? 1 : 0,
+                passCutEnergyMax() ? 1 : 0, passCutHitCount() ? 1 : 0);
     }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TIData.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TIData.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TIData.java	Wed Apr 27 11:11:32 2016
@@ -5,18 +5,25 @@
 /**
  * Class <code>TIData</code> is an implementation of abstract class
  * <code>AbstractIntData</code> that represents a TI trigger bit bank.
- * It contains both a time window length and a set of flags that track
- * whether a trigger of a given type was registered with the event to
- * which this bank is attached.
  *
  * @author Nathan Baltzell <[log in to unmask]>
  */
 public class TIData extends AbstractIntData {
-	/** The EvIO bank header tag for TI data banks. */
+
+    /**
+     * The EvIO bank header tag for TI data banks.
+     */
     public static final int BANK_TAG = 0xe10a; // EvioEventConstants.TI_TRIGGER_BANK_TAG;
-    /** The expected number of entries in the data bank. */
-    public static final int BANK_SIZE = 4;
-    
+    /**
+     * The expected number of entries in the data bank for the 2015 data.
+     */
+    private static final int BANK_SIZE_2015 = 4;
+    /**
+     * The expected number of entries in the data bank for the 2016 data (after
+     * unprescaled trigger bits were added).
+     */
+    private static final int BANK_SIZE_2016 = 5;
+
     // Store the parsed data bank parameters.
     private long time = 0;
     private boolean singles0 = false;
@@ -25,36 +32,59 @@
     private boolean pairs1 = false;
     private boolean calib = false;
     private boolean pulser = false;
-    
-    /**
-     * Creates a <code>TIData</code> bank from a raw EvIO data bank.
-     * It is expected that the EvIO reader will verify that the bank
-     * tag is of the appropriate type.
+    private boolean hasUnprescaledTriggerBits = false;
+    private boolean singles0Unprescaled = false;
+    private boolean singles1Unprescaled = false;
+    private boolean pairs0Unprescaled = false;
+    private boolean pairs1Unprescaled = false;
+    private boolean calibUnprescaled = false;
+    private boolean pulserUnprescaled = false;
+
+    /**
+     * Creates a <code>TIData</code> bank from a raw EvIO data bank. It is
+     * expected that the EvIO reader will verify that the bank tag is of the
+     * appropriate type.
+     *
      * @param bank - The EvIO data bank.
      */
     public TIData(int[] bank) {
         super(bank);
         decodeData();
     }
-    
+
     /**
      * Creates a <code>TIData</code> object from an existing LCIO
      * <code>GenericObject</code>.
+     *
      * @param tiData - The source data bank object.
      */
     public TIData(GenericObject tiData) {
         super(tiData, BANK_TAG);
         decodeData();
     }
-    
+
     @Override
     protected final void decodeData() {
-    	// Check that the data bank is the expected size. If not, throw
-    	// and exception.
-        if(this.bank.length != BANK_SIZE) {
-            throw new RuntimeException("Invalid Data Length:  " + bank.length);
-        }
-        
+        // Check that the data bank is the expected size. If not, throw
+        // and exception.
+        switch (this.bank.length) {
+            case BANK_SIZE_2015:
+//                System.out.println("2015-style TI bank");
+                break;
+            case BANK_SIZE_2016:
+//                System.out.format("2016-style TI bank, first word %x, last word %x\n", bank[0], bank[4]);
+                hasUnprescaledTriggerBits = true;
+                singles0Unprescaled = ((bank[0]) & 1) == 1;
+                singles1Unprescaled = ((bank[0] >> 1) & 1) == 1;
+                pairs0Unprescaled = ((bank[0] >> 2) & 1) == 1;
+                pairs1Unprescaled = ((bank[0] >> 3) & 1) == 1;
+                calibUnprescaled = ((bank[0] >> 4) & 1) == 1;
+                pulserUnprescaled = ((bank[0] >> 5) & 1) == 1;
+                break;
+            default:
+                throw new RuntimeException("Invalid Data Length:  " + bank.length);
+        }
+
         // Check each trigger bit to see if it is active. A value of 
         // 1 indicates a trigger of that type occurred, and 0 that it
         // did not.
@@ -64,83 +94,175 @@
         pairs1 = ((bank[0] >> 27) & 1) == 1;
         calib = ((bank[0] >> 28) & 1) == 1;
         pulser = ((bank[0] >> 29) & 1) == 1;
-        
-        // Get the unprocessed start and end times for the bank.
-        long w1 = bank[2] & 0xffffffffL;
-        long w2 = bank[3] & 0xffffffffL;
-        
-        // Process the times into units of clock-cycles.
+
+        // interpret time:
+        final long w1 = bank[2] & 0xffffffffL;
+        final long w2 = bank[3] & 0xffffffffL;
         final long timelo = w1;
         final long timehi = (w2 & 0xffff) << 32;
-        
-        // Store the time difference in nanoseconds.
         time = 4 * (timelo + timehi);
     }
-    
+
     @Override
     public int getTag() {
         return BANK_TAG;
     }
-    
-    /**
-     * Gets the time window for the bank.
-     * @return Returns the time window length in nanoseconds.
-     */
+
     public long getTime() {
         return time;
     }
-    
+
     /**
      * Indicates whether a singles 0 trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isSingle0Trigger() {
         return singles0;
     }
-    
+
     /**
      * Indicates whether a singles 1 trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isSingle1Trigger() {
         return singles1;
     }
-    
+
     /**
      * Indicates whether a pair 0 trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isPair0Trigger() {
         return pairs0;
     }
-    
+
     /**
      * Indicates whether a pair 1 trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isPair1Trigger() {
         return pairs1;
     }
-    
+
     /**
      * Indicates whether a cosmic trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isCalibTrigger() {
         return calib;
     }
-    
+
     /**
      * Indicates whether a random/pulser trigger was registered.
+     *
      * @return Returns <code>true</code> if the trigger occurred, and
      * <code>false</code> otherwise.
      */
     public boolean isPulserTrigger() {
         return pulser;
     }
-}
+
+    /**
+     * Indicates whether this TI data has unprescaled trigger bits.
+     *
+     * @return Returns <code>true</code> if the TI data has a fifth int
+     * containing unprescaled trigger bits, and <code>false</code> otherwise.
+     */
+    public boolean hasUnprescaledTriggerBits() {
+        return hasUnprescaledTriggerBits;
+    }
+
+    /**
+     * Indicates whether a singles 0 (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isSingle0UnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return singles0Unprescaled;
+    }
+
+    /**
+     * Indicates whether a singles 1 (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isSingle1UnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return singles1Unprescaled;
+    }
+
+    /**
+     * Indicates whether a pairs 0 (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isPair0UnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return pairs0Unprescaled;
+    }
+
+    /**
+     * Indicates whether a pairs 1 (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isPair1UnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return pairs1Unprescaled;
+    }
+
+    /**
+     * Indicates whether a cosmic (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isCalibUnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return calibUnprescaled;
+    }
+
+    /**
+     * Indicates whether a random/pulser (unprescaled) trigger was registered.
+     *
+     * @return Returns <code>true</code> if the trigger occurred, and
+     * <code>false</code> otherwise. Throws a RuntimeException if this data does
+     * not have unprescaled trigger bits.
+     */
+    public boolean isPulserUnprescaledTrigger() {
+        if (!hasUnprescaledTriggerBits) {
+            throw new RuntimeException("This TI data does not have unprescaled trigger bits.");
+        }
+        return pulserUnprescaled;
+    }
+}

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TiTimeOffsetEvioProcessor.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TiTimeOffsetEvioProcessor.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TiTimeOffsetEvioProcessor.java	Wed Apr 27 11:11:32 2016
@@ -55,13 +55,30 @@
             }
         }
     }
+    
+    public long getMinOffset() {
+        return this.minOffset;
+    }
+    
+    public long getMaxOffset() {
+        return this.maxOffset;
+    }
+    
+    public int getNumOutliers() {
+        return this.nOutliers;
+    }
+    
+    public long getTiTimeOffset() {
+        final long offsetRange = maxOffset - minOffset;
+        if (offsetRange > minRange && nOutliers < maxOutliers) {
+            return minOffset;
+        } else {
+            return 0L;
+        }
+    }
 
     public void updateTriggerConfig(final TriggerConfig triggerConfig) {
-        final long offsetRange = maxOffset - minOffset;
-        if (offsetRange > minRange && nOutliers < maxOutliers) {
-            triggerConfig.put(TriggerConfigVariable.TI_TIME_OFFSET, minOffset);
-        } else {
-            triggerConfig.put(TriggerConfigVariable.TI_TIME_OFFSET, 0L);
-        }
+        long tiTimeOffset = getTiTimeOffset();
+        triggerConfig.put(TriggerConfigVariable.TI_TIME_OFFSET, tiTimeOffset);
     }
 }

Modified: java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TriggerModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TriggerModule.java	(original)
+++ java/branches/HPSJAVA-409/record-util/src/main/java/org/hps/record/triggerbank/TriggerModule.java	Wed Apr 27 11:11:32 2016
@@ -44,8 +44,8 @@
  * @see SSPCluster
  */
 public final class TriggerModule {
-	/** The calorimeter mid-plane, defined by the photon beam position
-	* (30.52 mrad) at the calorimeter face (z = 1393 mm). */
+    /** The calorimeter mid-plane, defined by the photon beam position
+    * (30.52 mrad) at the calorimeter face (z = 1393 mm). */
     private static final double ORIGIN_X = 1393.0 * Math.tan(0.03052);
     
     /** The value of the parameter "F" in the energy slope equation
@@ -104,23 +104,23 @@
      * above zero) will be accepted.
      */
     public TriggerModule() {
-    	// Set the cluster singles cuts to accept all values by default.
-    	cuts.put(CLUSTER_HIT_COUNT_LOW, 0.0);
-    	cuts.put(CLUSTER_SEED_ENERGY_LOW, 0.0);
-    	cuts.put(CLUSTER_SEED_ENERGY_HIGH, Double.MAX_VALUE);
-    	cuts.put(CLUSTER_TOTAL_ENERGY_LOW, 0.0);
-    	cuts.put(CLUSTER_TOTAL_ENERGY_HIGH, Double.MAX_VALUE);
-    	
-    	// Set the cluster pair cuts to accept all values by default.
-    	cuts.put(PAIR_COPLANARITY_HIGH, 180.0);
-    	cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, Double.MAX_VALUE);
-    	cuts.put(PAIR_ENERGY_SLOPE_LOW, 0.0);
-    	cuts.put(PAIR_ENERGY_SUM_LOW, 0.0);
-    	cuts.put(PAIR_ENERGY_SUM_HIGH, Double.MAX_VALUE);
-    	cuts.put(PAIR_TIME_COINCIDENCE, Double.MAX_VALUE);
-    	
-    	// Set the default value of the energy slope parameter F.
-    	cuts.put(PAIR_ENERGY_SLOPE_F, 0.0055);
+        // Set the cluster singles cuts to accept all values by default.
+        cuts.put(CLUSTER_HIT_COUNT_LOW, 0.0);
+        cuts.put(CLUSTER_SEED_ENERGY_LOW, 0.0);
+        cuts.put(CLUSTER_SEED_ENERGY_HIGH, Double.MAX_VALUE);
+        cuts.put(CLUSTER_TOTAL_ENERGY_LOW, 0.0);
+        cuts.put(CLUSTER_TOTAL_ENERGY_HIGH, Double.MAX_VALUE);
+        
+        // Set the cluster pair cuts to accept all values by default.
+        cuts.put(PAIR_COPLANARITY_HIGH, 180.0);
+        cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, Double.MAX_VALUE);
+        cuts.put(PAIR_ENERGY_SLOPE_LOW, 0.0);
+        cuts.put(PAIR_ENERGY_SUM_LOW, 0.0);
+        cuts.put(PAIR_ENERGY_SUM_HIGH, Double.MAX_VALUE);
+        cuts.put(PAIR_TIME_COINCIDENCE, Double.MAX_VALUE);
+        
+        // Set the default value of the energy slope parameter F.
+        cuts.put(PAIR_ENERGY_SLOPE_F, 0.0055);
     }
     
     /**
@@ -142,25 +142,25 @@
      * </ul>
      */
     public TriggerModule(double... cutValues) {
-    	// Set the cuts to the default values.
-    	this();
-    	
-    	// Define the cuts in the order that they correspond to the
-    	// value arguments.
-    	String[] cutID = { CLUSTER_HIT_COUNT_LOW, CLUSTER_SEED_ENERGY_LOW, CLUSTER_SEED_ENERGY_HIGH,
-    			CLUSTER_TOTAL_ENERGY_LOW, CLUSTER_TOTAL_ENERGY_HIGH, PAIR_ENERGY_SUM_LOW, PAIR_ENERGY_SUM_HIGH,
-    			PAIR_ENERGY_DIFFERENCE_HIGH, PAIR_ENERGY_SLOPE_LOW, PAIR_COPLANARITY_HIGH, PAIR_ENERGY_SLOPE_F };
-    	
-    	// Iterate over the value arguments and assign them to the
-    	// appropriate cut.
-    	for(int i = 0; i < cutValues.length; i++) {
-    		// If more values were given then cuts exist, break from
-    		// the loop.
-    		if(i == 11) { break; }
-    		
-    		// Set the current cut to its corresponding value.
-    		cuts.put(cutID[i], cutValues[i]);
-    	}
+        // Set the cuts to the default values.
+        this();
+        
+        // Define the cuts in the order that they correspond to the
+        // value arguments.
+        String[] cutID = { CLUSTER_HIT_COUNT_LOW, CLUSTER_SEED_ENERGY_LOW, CLUSTER_SEED_ENERGY_HIGH,
+                CLUSTER_TOTAL_ENERGY_LOW, CLUSTER_TOTAL_ENERGY_HIGH, PAIR_ENERGY_SUM_LOW, PAIR_ENERGY_SUM_HIGH,
+                PAIR_ENERGY_DIFFERENCE_HIGH, PAIR_ENERGY_SLOPE_LOW, PAIR_COPLANARITY_HIGH, PAIR_ENERGY_SLOPE_F };
+        
+        // Iterate over the value arguments and assign them to the
+        // appropriate cut.
+        for(int i = 0; i < cutValues.length; i++) {
+            // If more values were given then cuts exist, break from
+            // the loop.
+            if(i == 11) { break; }
+            
+            // Set the current cut to its corresponding value.
+            cuts.put(cutID[i], cutValues[i]);
+        }
     }
     
     /**
@@ -172,14 +172,14 @@
      * specified in the argument is not valid.
      */
     public double getCutValue(String cut) throws IllegalArgumentException {
-    	// Try to get the indicated cut.
-    	Double value = cuts.get(cut);
-    	
-    	// If the cut is valid, return it.
-    	if(value != null) { return value.doubleValue(); }
-    	
-    	// Otherwise, produce an exception.
-    	else { throw new IllegalArgumentException(String.format("Cut \"%s\" does not exist.", cut)); }
+        // Try to get the indicated cut.
+        Double value = cuts.get(cut);
+        
+        // If the cut is valid, return it.
+        if(value != null) { return value.doubleValue(); }
+        
+        // Otherwise, produce an exception.
+        else { throw new IllegalArgumentException(String.format("Cut \"%s\" does not exist.", cut)); }
     }
     
     /**
@@ -190,22 +190,22 @@
      * @param config - The DAQ configuration settings.
      */
     public void loadDAQConfiguration(SinglesTriggerConfig config) {
-    	// Set the trigger values.
-    	setCutValue(CLUSTER_TOTAL_ENERGY_LOW,  config.getEnergyMinCutConfig().getLowerBound());
-    	setCutValue(CLUSTER_TOTAL_ENERGY_HIGH, config.getEnergyMaxCutConfig().getUpperBound());
-    	setCutValue(CLUSTER_HIT_COUNT_LOW,     config.getHitCountCutConfig().getLowerBound());
-    	
-    	// The remaining triggers should be set to their default values.
-    	// These settings effectively accept all possible clusters.
-    	cuts.put(PAIR_COPLANARITY_HIGH, 180.0);
-    	cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, Double.MAX_VALUE);
-    	cuts.put(PAIR_ENERGY_SLOPE_LOW, 0.0);
-    	cuts.put(PAIR_ENERGY_SUM_LOW, 0.0);
-    	cuts.put(PAIR_ENERGY_SUM_HIGH, Double.MAX_VALUE);
-    	cuts.put(PAIR_TIME_COINCIDENCE, Double.MAX_VALUE);
-    	
-    	// Set the default value of the energy slope parameter F.
-    	cuts.put(PAIR_ENERGY_SLOPE_F, 0.0055);
+        // Set the trigger values.
+        setCutValue(CLUSTER_TOTAL_ENERGY_LOW,  config.getEnergyMinCutConfig().getLowerBound());
+        setCutValue(CLUSTER_TOTAL_ENERGY_HIGH, config.getEnergyMaxCutConfig().getUpperBound());
+        setCutValue(CLUSTER_HIT_COUNT_LOW,     config.getHitCountCutConfig().getLowerBound());
+        
+        // The remaining triggers should be set to their default values.
+        // These settings effectively accept all possible clusters.
+        cuts.put(PAIR_COPLANARITY_HIGH, 180.0);
+        cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, Double.MAX_VALUE);
+        cuts.put(PAIR_ENERGY_SLOPE_LOW, 0.0);
+        cuts.put(PAIR_ENERGY_SUM_LOW, 0.0);
+        cuts.put(PAIR_ENERGY_SUM_HIGH, Double.MAX_VALUE);
+        cuts.put(PAIR_TIME_COINCIDENCE, Double.MAX_VALUE);
+        
+        // Set the default value of the energy slope parameter F.
+        cuts.put(PAIR_ENERGY_SLOPE_F, 0.0055);
     }
     
     /**
@@ -215,22 +215,22 @@
      * @param config - The DAQ configuration settings.
      */
     public void loadDAQConfiguration(PairTriggerConfig config) {
-    	// Set the trigger values.
-    	setCutValue(CLUSTER_TOTAL_ENERGY_LOW,  config.getEnergyMinCutConfig().getLowerBound());
-    	setCutValue(CLUSTER_TOTAL_ENERGY_HIGH, config.getEnergyMaxCutConfig().getUpperBound());
-    	setCutValue(CLUSTER_HIT_COUNT_LOW,     config.getHitCountCutConfig().getLowerBound());
-    	
-    	// The remaining triggers should be set to their default values.
-    	// These settings effectively accept all possible clusters.
-    	cuts.put(PAIR_COPLANARITY_HIGH, config.getCoplanarityCutConfig().getUpperBound());
-    	cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, config.getEnergyDifferenceCutConfig().getUpperBound());
-    	cuts.put(PAIR_ENERGY_SLOPE_LOW, config.getEnergySlopeCutConfig().getLowerBound());
-    	cuts.put(PAIR_ENERGY_SUM_LOW, config.getEnergySumCutConfig().getLowerBound());
-    	cuts.put(PAIR_ENERGY_SUM_HIGH, config.getEnergySumCutConfig().getUpperBound());
-    	cuts.put(PAIR_TIME_COINCIDENCE, config.getTimeDifferenceCutConfig().getUpperBound() * 4.0);
-    	
-    	// Set the default value of the energy slope parameter F.
-    	cuts.put(PAIR_ENERGY_SLOPE_F, config.getEnergySlopeCutConfig().getParameterF());
+        // Set the trigger values.
+        setCutValue(CLUSTER_TOTAL_ENERGY_LOW,  config.getEnergyMinCutConfig().getLowerBound());
+        setCutValue(CLUSTER_TOTAL_ENERGY_HIGH, config.getEnergyMaxCutConfig().getUpperBound());
+        setCutValue(CLUSTER_HIT_COUNT_LOW,     config.getHitCountCutConfig().getLowerBound());
+        
+        // The remaining triggers should be set to their default values.
+        // These settings effectively accept all possible clusters.
+        cuts.put(PAIR_COPLANARITY_HIGH, config.getCoplanarityCutConfig().getUpperBound());
+        cuts.put(PAIR_ENERGY_DIFFERENCE_HIGH, config.getEnergyDifferenceCutConfig().getUpperBound());
+        cuts.put(PAIR_ENERGY_SLOPE_LOW, config.getEnergySlopeCutConfig().getLowerBound());
+        cuts.put(PAIR_ENERGY_SUM_LOW, config.getEnergySumCutConfig().getLowerBound());
+        cuts.put(PAIR_ENERGY_SUM_HIGH, config.getEnergySumCutConfig().getUpperBound());
+        cuts.put(PAIR_TIME_COINCIDENCE, config.getTimeDifferenceCutConfig().getUpperBound() * 4.0);
+        
+        // Set the default value of the energy slope parameter F.
+        cuts.put(PAIR_ENERGY_SLOPE_F, config.getEnergySlopeCutConfig().getParameterF());
     }
     
     /**
@@ -244,76 +244,76 @@
      * identifier is not valid.
      */
     public void setCutValue(String cut, double value) throws IllegalArgumentException {
-    	// Make sure that the cut exists. If it does, change it to the
-    	// new cut value.
-    	if(cuts.containsKey(cut)) {
-    		cuts.put(cut, value);
-    	}
-    	
-    	// Otherwise, throw an exception.
-    	else { throw new IllegalArgumentException(String.format("Cut \"%s\" does not exist.", cut)); }
-    }
-    
-	/**
-	 * Sets the cluster singles cuts to the values parsed from an
-	 * argument string.
-	 * @param isSingles - Indicates whether the parser should expect
-	 * 10 cut values (for pairs) or 3 (for singles).
-	 * @param cutValues - A string representing the cuts values. This
-	 * must be formatted in the style of "Emin Emax Nmin ...".
-	 */
+        // Make sure that the cut exists. If it does, change it to the
+        // new cut value.
+        if(cuts.containsKey(cut)) {
+            cuts.put(cut, value);
+        }
+        
+        // Otherwise, throw an exception.
+        else { throw new IllegalArgumentException(String.format("Cut \"%s\" does not exist.", cut)); }
+    }
+    
+    /**
+     * Sets the cluster singles cuts to the values parsed from an
+     * argument string.
+     * @param isSingles - Indicates whether the parser should expect
+     * 10 cut values (for pairs) or 3 (for singles).
+     * @param cutValues - A string representing the cuts values. This
+     * must be formatted in the style of "Emin Emax Nmin ...".
+     */
     // TODO: Specify in JavaDoc what the order of these arguments is.
-	public void setCutValues(boolean isSingles, String cutValues) {
-		// Make sure that the string is not null.
-		if(cutValues == null) {
-			throw new NullPointerException(String.format("Cut arguments for trigger are null!"));
-		}
-		
-		// Tokenize the argument string.
-		StringTokenizer tokens = new StringTokenizer(cutValues);
-		
-		// Store the cut values. Entry format is:
-		// clusterEnergyMin clusterEnergyMax hitCountMin
-		// clusterEnergyMin clusterEnergyMax hitCountMin pairSumMin pairSumMax pairDiffMax pairSlopeMin pairSlopeF pairCoplanarityMax pairTimeCoincidence
-		double cuts[];
-		if(isSingles) { cuts = new double[] { 0.0, 8.191, 0 }; }
-		else { cuts = new double[] { 0.0, 8.191, 0, 0, 8.191, 8.191, 0, 0.0055, 180, Double.MAX_VALUE }; }
-		String[] cutNames = { "clusterEnergyMin", "clusterEnergyMax", "hitCountMin",
-				"pairSumMin", "pairSumMax", "pairDiffMax", "pairSlopeMin", "pairSlopeF",
-				"pairCoplanarityMax", "pairTimeCoincidence" };
-		
-		// Iterate over the number of cuts and extract that many values
-		// from the cut value string.
-		for(int cutNum = 0; cutNum < cuts.length; cutNum++) {
-			// If there are no more tokens left, the argument string
-			// is missing some values. Throw an exception!
-			if(tokens.hasMoreTokens()) {
-				// Get the next token from the string.
-				String arg = tokens.nextToken();
-				
-				// Try to parse the token as a double. All cut values
-				// should be rendered as doubles (or integers, which
-				// can be parsed as doubles). If it is not, the string
-				// is improperly formatted.
-				try { cuts[cutNum] = Double.parseDouble(arg); }
-				catch(NumberFormatException e) {
-					throw new NumberFormatException(String.format("Argument for \"%s\" improperly formatted: %s", cutNames[cutNum], arg));
-				}
-			}
-		}
-		
-		// Store the cuts in the trigger.
-		setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    cuts[0]);
-		setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   cuts[1]);
-		setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       cuts[2]);
-		setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         cuts[3]);
-		setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        cuts[4]);
-		setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, cuts[5]);
-		setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       cuts[6]);
-		setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         cuts[7]);
-		setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       cuts[8]);
-		setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       cuts[9]);
-	}
+    public void setCutValues(boolean isSingles, String cutValues) {
+        // Make sure that the string is not null.
+        if(cutValues == null) {
+            throw new NullPointerException(String.format("Cut arguments for trigger are null!"));
+        }
+        
+        // Tokenize the argument string.
+        StringTokenizer tokens = new StringTokenizer(cutValues);
+        
+        // Store the cut values. Entry format is:
+        // clusterEnergyMin clusterEnergyMax hitCountMin
+        // clusterEnergyMin clusterEnergyMax hitCountMin pairSumMin pairSumMax pairDiffMax pairSlopeMin pairSlopeF pairCoplanarityMax pairTimeCoincidence
+        double cuts[];
+        if(isSingles) { cuts = new double[] { 0.0, 8.191, 0 }; }
+        else { cuts = new double[] { 0.0, 8.191, 0, 0, 8.191, 8.191, 0, 0.0055, 180, Double.MAX_VALUE }; }
+        String[] cutNames = { "clusterEnergyMin", "clusterEnergyMax", "hitCountMin",
+                "pairSumMin", "pairSumMax", "pairDiffMax", "pairSlopeMin", "pairSlopeF",
+                "pairCoplanarityMax", "pairTimeCoincidence" };
+        
+        // Iterate over the number of cuts and extract that many values
+        // from the cut value string.
+        for(int cutNum = 0; cutNum < cuts.length; cutNum++) {
+            // If there are no more tokens left, the argument string
+            // is missing some values. Throw an exception!
+            if(tokens.hasMoreTokens()) {
+                // Get the next token from the string.
+                String arg = tokens.nextToken();
+                
+                // Try to parse the token as a double. All cut values
+                // should be rendered as doubles (or integers, which
+                // can be parsed as doubles). If it is not, the string
+                // is improperly formatted.
+                try { cuts[cutNum] = Double.parseDouble(arg); }
+                catch(NumberFormatException e) {
+                    throw new NumberFormatException(String.format("Argument for \"%s\" improperly formatted: %s", cutNames[cutNum], arg));
+                }
+            }
+        }
+        
+        // Store the cuts in the trigger.
+        setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    cuts[0]);
+        setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   cuts[1]);
+        setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       cuts[2]);
+        setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         cuts[3]);
+        setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        cuts[4]);
+        setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, cuts[5]);
+        setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       cuts[6]);
+        setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         cuts[7]);
+        setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       cuts[8]);
+        setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       cuts[9]);
+    }
     
     /**
      * Checks whether a cluster passes the cluster hit count cut. This
@@ -346,7 +346,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterSeedEnergyCut(Cluster cluster) {
-    	return clusterSeedEnergyCut(getValueClusterSeedEnergy(cluster));
+        return clusterSeedEnergyCut(getValueClusterSeedEnergy(cluster));
     }
     
     /**
@@ -357,7 +357,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterSeedEnergyCutHigh(Cluster cluster) {
-    	return clusterSeedEnergyCutHigh(getValueClusterSeedEnergy(cluster));
+        return clusterSeedEnergyCutHigh(getValueClusterSeedEnergy(cluster));
     }
     
     /**
@@ -368,7 +368,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterSeedEnergyCutLow(Cluster cluster) {
-    	return clusterSeedEnergyCutLow(getValueClusterSeedEnergy(cluster));
+        return clusterSeedEnergyCutLow(getValueClusterSeedEnergy(cluster));
     }
     
     /**
@@ -380,7 +380,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCut(Cluster cluster) {
-    	return clusterTotalEnergyCut(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCut(getValueClusterTotalEnergy(cluster));
     }
     
     /**
@@ -392,7 +392,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCutHigh(Cluster cluster) {
-    	return clusterTotalEnergyCutHigh(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCutHigh(getValueClusterTotalEnergy(cluster));
     }
     
     /**
@@ -404,7 +404,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCutLow(Cluster cluster) {
-    	return clusterTotalEnergyCutLow(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCutLow(getValueClusterTotalEnergy(cluster));
     }
     
     /**
@@ -416,7 +416,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCut(SSPCluster cluster) {
-    	return clusterTotalEnergyCut(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCut(getValueClusterTotalEnergy(cluster));
     }
     
     /**
@@ -428,7 +428,7 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCutHigh(SSPCluster cluster) {
-    	return clusterTotalEnergyCutHigh(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCutHigh(getValueClusterTotalEnergy(cluster));
     }
     
     /**
@@ -440,7 +440,39 @@
      * and <code>false</code> if the cluster does not.
      */
     public boolean clusterTotalEnergyCutLow(SSPCluster cluster) {
-    	return clusterTotalEnergyCutLow(getValueClusterTotalEnergy(cluster));
+        return clusterTotalEnergyCutLow(getValueClusterTotalEnergy(cluster));
+    }
+    
+    /**
+     * Gets the angle between the cluster and the centerpoint of the
+     * calorimeter.
+     * @param cluster - The cluster for which to calculate the angle.
+     * @return Returns the cluster angle as an <code>int</code> in units
+     * of degrees.
+     */
+    public static int getClusterAngle(Cluster cluster) {
+        // Get the cluster position.
+        double x = getClusterX(cluster);
+        double y = getClusterY(cluster);
+        
+        // Return the cluster angle.
+        return getClusterAngle(x, y);
+    }
+    
+    /**
+     * Gets the angle between the cluster and the centerpoint of the
+     * calorimeter.
+     * @param cluster - The cluster for which to calculate the angle.
+     * @return Returns the cluster angle as an <code>int</code> in units
+     * of degrees.
+     */
+    public static int getClusterAngle(SSPCluster cluster) {
+        // Get the cluster position.
+        double x = getClusterX(cluster);
+        double y = getClusterY(cluster);
+        
+        // Return the cluster angle.
+        return getClusterAngle(x, y);
     }
     
     /**
@@ -449,14 +481,28 @@
      * be calculated.
      * @return Returns displacement of the cluster.
      */
-    // TODO: What defines cluster distance?
     public static double getClusterDistance(Cluster cluster) {
-    	// Get the variables from the cluster.
-    	double x = getClusterX(cluster);
-    	double y = getClusterY(cluster);
-    	
-    	// Perform the calculation.
-    	return getClusterDistance(x, y);
+        // Get the variables from the cluster.
+        double x = getClusterX(cluster);
+        double y = getClusterY(cluster);
+        
+        // Perform the calculation.
+        return getClusterDistance(x, y);
+    }
+    
+    /**
+     * Calculates the distance between the origin and a cluster.
+     * @param cluster - The cluster pair from which the value should
+     * be calculated.
+     * @return Returns displacement of the cluster.
+     */
+    public static double getClusterDistance(SSPCluster cluster) {
+        // Get the variables from the cluster.
+        double x = getClusterX(cluster);
+        double y = getClusterY(cluster);
+        
+        // Perform the calculation.
+        return getClusterDistance(x, y);
     }
     
     /**
@@ -466,7 +512,7 @@
      * @return Returns the size as an <code>int</code>.
      */
     public static final double getClusterHitCount(Cluster cluster) {
-    	return cluster.getCalorimeterHits().size();
+        return cluster.getCalorimeterHits().size();
     }
     
     /**
@@ -476,7 +522,7 @@
      * @return Returns the size as an <code>int</code>.
      */
     public static final double getClusterHitCount(SSPCluster cluster) {
-    	return cluster.getHitCount();
+        return cluster.getHitCount();
     }
     
     /**
@@ -486,11 +532,11 @@
      * object.
      */
     public static final CalorimeterHit getClusterSeedHit(Cluster cluster) {
-    	if(getClusterHitCount(cluster) > 0) {
-    		return cluster.getCalorimeterHits().get(0);
-    	} else {
-    		throw new NullPointerException("Cluster does not define hits!");
-    	}
+        if(getClusterHitCount(cluster) > 0) {
+            return cluster.getCalorimeterHits().get(0);
+        } else {
+            throw new NullPointerException("Cluster does not define hits!");
+        }
     }
     
     /**
@@ -500,7 +546,7 @@
      * @return Returns the time as a <code>double</code>.
      */
     public static final double getClusterTime(Cluster cluster) {
-    	return getClusterSeedHit(cluster).getTime();
+        return getClusterSeedHit(cluster).getTime();
     }
     
     /**
@@ -510,7 +556,7 @@
      * @return Returns the time as a <code>double</code>.
      */
     public static final double getClusterTime(SSPCluster cluster) {
-    	return cluster.getTime();
+        return cluster.getTime();
     }
     
     /**
@@ -520,7 +566,7 @@
      * @return Returns the cluster x-position.
      */
     public static double getClusterX(Cluster cluster) {
-    	return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[0];
+        return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[0];
     }
     
     /**
@@ -530,7 +576,7 @@
      * @return Returns the cluster x-position.
      */
     public static double getClusterX(SSPCluster cluster) {
-    	return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[0];
+        return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[0];
     }
     
     /**
@@ -539,7 +585,7 @@
      * @return Returns the index as an <code>int</code>.
      */
     public static final int getClusterXIndex(Cluster cluster) {
-    	return getClusterSeedHit(cluster).getIdentifierFieldValue("ix");
+        return getClusterSeedHit(cluster).getIdentifierFieldValue("ix");
     }
     
     /**
@@ -548,7 +594,7 @@
      * @return Returns the index as an <code>int</code>.
      */
     public static final int getClusterXIndex(SSPCluster cluster) {
-    	return cluster.getXIndex();
+        return cluster.getXIndex();
     }
     
     /**
@@ -558,7 +604,7 @@
      * @return Returns the cluster y-position.
      */
     public static double getClusterY(Cluster cluster) {
-    	return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[1];
+        return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[1];
     }
     
     /**
@@ -568,7 +614,7 @@
      * @return Returns the cluster y-position.
      */
     public static double getClusterY(SSPCluster cluster) {
-    	return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[1];
+        return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[1];
     }
     
     /**
@@ -577,7 +623,7 @@
      * @return Returns the index as an <code>int</code>.
      */
     public static final int getClusterYIndex(Cluster cluster) {
-    	return getClusterSeedHit(cluster).getIdentifierFieldValue("iy");
+        return getClusterSeedHit(cluster).getIdentifierFieldValue("iy");
     }
     
     /**
@@ -586,7 +632,7 @@
      * @return Returns the index as an <code>int</code>.
      */
     public static final int getClusterYIndex(SSPCluster cluster) {
-    	return cluster.getYIndex();
+        return cluster.getYIndex();
     }
     
     /**
@@ -596,7 +642,7 @@
      * @return Returns the cluster z-position.
      */
     public static double getClusterZ(Cluster cluster) {
-    	return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[2];
+        return getCrystalPosition(getClusterXIndex(cluster), getClusterYIndex(cluster))[2];
     }
     
     /**
@@ -606,7 +652,7 @@
      * @return Returns the cluster z-position.
      */
     public static double getClusterZ(SSPCluster cluster) {
-    	return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[2];
+        return getCrystalPosition(cluster.getXIndex(), cluster.getYIndex())[2];
     }
     
     /**
@@ -618,48 +664,48 @@
      * first entry in the array is always the top cluster, with the
      * bottom cluster in the next position.
      */
-	public static <E> List<E[]> getTopBottomPairs(List<E> clusters, Class<E> clusterType) throws IllegalArgumentException {
-		// Ensure that only valid cluster types are processed.
-		if(!clusterType.equals(Cluster.class) && !clusterType.equals(SSPCluster.class)) {
-			throw new IllegalArgumentException("Class \"" + clusterType.getSimpleName() + "\" is not a supported cluster type.");
-		}
-		
-    	// Create a list to store top clusters, bottom clusters, and
-    	// cluster pairs.
-    	List<E> topClusters = new ArrayList<E>();
-    	List<E> botClusters = new ArrayList<E>();
-    	List<E[]> pairClusters = new ArrayList<E[]>();
-    	
-    	// Separate the cluster list into top/bottom clusters.
-    	for(E cluster : clusters) {
-    		// Process LCIO clusters...
-    		if(clusterType.equals(Cluster.class)) {
-				if(getClusterYIndex((Cluster) cluster) > 0) {
-					topClusters.add(cluster);
-				} else { botClusters.add(cluster); }
-    		}
-    		
-    		// Process SSP clusters...
-    		else if(clusterType.equals(SSPCluster.class)) {
-				if(getClusterYIndex((SSPCluster) cluster) > 0) {
-					topClusters.add(cluster);
-				} else { botClusters.add(cluster); }
-    		}
-    	}
-    	
-    	// Form all top/bottom cluster pairs.
-    	for(E topCluster : topClusters) {
-    		for(E botCluster : botClusters) {
-    			@SuppressWarnings("unchecked")
-				E[] pair = (E[]) Array.newInstance(clusterType, 2);
-    			pair[0] = topCluster;
-    			pair[1] = botCluster;
-    			pairClusters.add(pair);
-    		}
-    	}
-    	
-    	// Return the cluster pairs.
-    	return pairClusters;
+    public static <E> List<E[]> getTopBottomPairs(List<E> clusters, Class<E> clusterType) throws IllegalArgumentException {
+        // Ensure that only valid cluster types are processed.
+        if(!clusterType.equals(Cluster.class) && !clusterType.equals(SSPCluster.class)) {
+            throw new IllegalArgumentException("Class \"" + clusterType.getSimpleName() + "\" is not a supported cluster type.");
+        }
+        
+        // Create a list to store top clusters, bottom clusters, and
+        // cluster pairs.
+        List<E> topClusters = new ArrayList<E>();
+        List<E> botClusters = new ArrayList<E>();
+        List<E[]> pairClusters = new ArrayList<E[]>();
+        
+        // Separate the cluster list into top/bottom clusters.
+        for(E cluster : clusters) {
+            // Process LCIO clusters...
+            if(clusterType.equals(Cluster.class)) {
+                if(getClusterYIndex((Cluster) cluster) > 0) {
+                    topClusters.add(cluster);
+                } else { botClusters.add(cluster); }
+            }
+            
+            // Process SSP clusters...
+            else if(clusterType.equals(SSPCluster.class)) {
+                if(getClusterYIndex((SSPCluster) cluster) > 0) {
+                    topClusters.add(cluster);
+                } else { botClusters.add(cluster); }
+            }
+        }
+        
+        // Form all top/bottom cluster pairs.
+        for(E topCluster : topClusters) {
+            for(E botCluster : botClusters) {
+                @SuppressWarnings("unchecked")
+                E[] pair = (E[]) Array.newInstance(clusterType, 2);
+                pair[0] = topCluster;
+                pair[1] = botCluster;
+                pairClusters.add(pair);
+            }
+        }
+        
+        // Return the cluster pairs.
+        return pairClusters;
     }
     
     /**
@@ -671,29 +717,29 @@
      * first entry in the array is always the top cluster, with the
      * bottom cluster in the next position.
      */
-	public static List<Cluster[]> getTopBottomPairs(Cluster... clusters) {
-    	// Create a list to store top clusters, bottom clusters, and
-    	// cluster pairs.
-    	List<Cluster> topClusters = new ArrayList<Cluster>();
-    	List<Cluster> botClusters = new ArrayList<Cluster>();
-    	List<Cluster[]> pairClusters = new ArrayList<Cluster[]>();
-    	
-    	// Separate the cluster list into top/bottom clusters.
-    	for(Cluster cluster : clusters) {
-			if(getClusterYIndex(cluster) > 0) {
-				topClusters.add(cluster);
-			} else { botClusters.add(cluster); }
-    	}
-    	
-    	// Form all top/bottom cluster pairs.
-    	for(Cluster topCluster : topClusters) {
-    		for(Cluster botCluster : botClusters) {
-    			pairClusters.add(new Cluster[] { topCluster, botCluster });
-    		}
-    	}
-    	
-    	// Return the cluster pairs.
-    	return pairClusters;
+    public static List<Cluster[]> getTopBottomPairs(Cluster... clusters) {
+        // Create a list to store top clusters, bottom clusters, and
+        // cluster pairs.
+        List<Cluster> topClusters = new ArrayList<Cluster>();
+        List<Cluster> botClusters = new ArrayList<Cluster>();
+        List<Cluster[]> pairClusters = new ArrayList<Cluster[]>();
+        
+        // Separate the cluster list into top/bottom clusters.
+        for(Cluster cluster : clusters) {
+            if(getClusterYIndex(cluster) > 0) {
+                topClusters.add(cluster);
+            } else { botClusters.add(cluster); }
+        }
+        
+        // Form all top/bottom cluster pairs.
+        for(Cluster topCluster : topClusters) {
+            for(Cluster botCluster : botClusters) {
+                pairClusters.add(new Cluster[] { topCluster, botCluster });
+            }
+        }
+        
+        // Return the cluster pairs.
+        return pairClusters;
     }
     
     /**
@@ -705,29 +751,29 @@
      * The first entry in the array is always the top cluster, with
      * the bottom cluster in the next position.
      */
-	public static List<SSPCluster[]> getTopBottomPairs(SSPCluster... clusters) {
-    	// Create a list to store top clusters, bottom clusters, and
-    	// cluster pairs.
-    	List<SSPCluster> topClusters = new ArrayList<SSPCluster>();
-    	List<SSPCluster> botClusters = new ArrayList<SSPCluster>();
-    	List<SSPCluster[]> pairClusters = new ArrayList<SSPCluster[]>();
-    	
-    	// Separate the cluster list into top/bottom clusters.
-    	for(SSPCluster cluster : clusters) {
-			if(getClusterYIndex(cluster) > 0) {
-				topClusters.add(cluster);
-			} else { botClusters.add(cluster); }
-    	}
-    	
-    	// Form all top/bottom cluster pairs.
-    	for(SSPCluster topCluster : topClusters) {
-    		for(SSPCluster botCluster : botClusters) {
-    			pairClusters.add(new SSPCluster[] { topCluster, botCluster });
-    		}
-    	}
-    	
-    	// Return the cluster pairs.
-    	return pairClusters;
+    public static List<SSPCluster[]> getTopBottomPairs(SSPCluster... clusters) {
+        // Create a list to store top clusters, bottom clusters, and
+        // cluster pairs.
+        List<SSPCluster> topClusters = new ArrayList<SSPCluster>();
+        List<SSPCluster> botClusters = new ArrayList<SSPCluster>();
+        List<SSPCluster[]> pairClusters = new ArrayList<SSPCluster[]>();
+        
+        // Separate the cluster list into top/bottom clusters.
+        for(SSPCluster cluster : clusters) {
+            if(getClusterYIndex(cluster) > 0) {
+                topClusters.add(cluster);
+            } else { botClusters.add(cluster); }
+        }
+        
+        // Form all top/bottom cluster pairs.
+        for(SSPCluster topCluster : topClusters) {
+            for(SSPCluster botCluster : botClusters) {
+                pairClusters.add(new SSPCluster[] { topCluster, botCluster });
+            }
+        }
+        
+        // Return the cluster pairs.
+        return pairClusters;
     }
     
     /**
@@ -791,12 +837,12 @@
      * @return Returns the cut value.
      */
     public static double getValueCoplanarity(Cluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
-    	double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
-    	
-    	// Return the calculated value.
-    	return getValueCoplanarity(x, y);
+        // Get the variables used by the calculation.
+        double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
+        double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
+        
+        // Return the calculated value.
+        return getValueCoplanarity(x, y);
     }
     
     /**
@@ -807,12 +853,12 @@
      * @return Returns the cut value.
      */
     public static double getValueCoplanarity(SSPCluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
-    	double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
-    	
-    	// Return the calculated value.
-    	return getValueCoplanarity(x, y);
+        // Get the variables used by the calculation.
+        double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
+        double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
+        
+        // Return the calculated value.
+        return getValueCoplanarity(x, y);
     }
     
     /**
@@ -824,14 +870,14 @@
      */
     @Deprecated
     public static double getValueCoplanarityLegacy(Cluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double x[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("ix"),
-    			getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("ix") };
-    	double y[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("iy"),
-    			getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("iy") };
-    	
-    	// Return the calculated value.
-    	return getValueCoplanarityLegacy(x, y);
+        // Get the variables used by the calculation.
+        double x[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("ix"),
+                getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("ix") };
+        double y[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("iy"),
+                getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("iy") };
+        
+        // Return the calculated value.
+        return getValueCoplanarityLegacy(x, y);
     }
     
     /**
@@ -841,10 +887,10 @@
      * @return Returns the difference between the cluster energies.
      */
     public static double getValueEnergyDifference(Cluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	
-    	// Perform the calculation.
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        
+        // Perform the calculation.
         return getValueEnergyDifference(energy);
     }
     
@@ -855,10 +901,10 @@
      * @return Returns the difference between the cluster energies.
      */
     public static double getValueEnergyDifference(SSPCluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	
-    	// Perform the calculation.
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        
+        // Perform the calculation.
         return getValueEnergyDifference(energy);
     }
     
@@ -871,13 +917,13 @@
      * @return Returns the energy slope value.
      */
     public static double getValueEnergySlope(Cluster[] clusterPair, double energySlopeParamF) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
-    	double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
-    	
-    	// Perform the calculation.
-    	return getValueEnergySlope(energy, x, y, energySlopeParamF);
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
+        double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
+        
+        // Perform the calculation.
+        return getValueEnergySlope(energy, x, y, energySlopeParamF);
     }
     
     /**
@@ -889,13 +935,13 @@
      * @return Returns the energy slope value.
      */
     public static double getValueEnergySlope(SSPCluster[] clusterPair, double energySlopeParamF) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
-    	double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
-    	
-    	// Perform the calculation.
-    	return getValueEnergySlope(energy, x, y, energySlopeParamF);
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        double x[] = { getClusterX(clusterPair[0]), getClusterX(clusterPair[1]) };
+        double y[] = { getClusterY(clusterPair[0]), getClusterY(clusterPair[1]) };
+        
+        // Perform the calculation.
+        return getValueEnergySlope(energy, x, y, energySlopeParamF);
     }
     
     /**
@@ -910,15 +956,15 @@
      */
     @Deprecated
     public static double getValueEnergySlopeLegacy(Cluster[] clusterPair, double energySlopeParamF) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	double x[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("ix"),
-    			getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("ix") };
-    	double y[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("iy"),
-    			getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("iy") };
-    	
-    	// Perform the calculation.
-    	return getValueEnergySlopeLegacy(energy, x, y, energySlopeParamF);
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        double x[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("ix"),
+                getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("ix") };
+        double y[] = { getClusterSeedHit(clusterPair[0]).getIdentifierFieldValue("iy"),
+                getClusterSeedHit(clusterPair[1]).getIdentifierFieldValue("iy") };
+        
+        // Perform the calculation.
+        return getValueEnergySlopeLegacy(energy, x, y, energySlopeParamF);
     }
     
     /**
@@ -928,11 +974,11 @@
      * @return Returns the sum of the cluster energies.
      */
     public static double getValueEnergySum(Cluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	
-    	// Perform the calculation.
-    	return getValueEnergySum(energy);
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        
+        // Perform the calculation.
+        return getValueEnergySum(energy);
     }
     
     /**
@@ -942,11 +988,11 @@
      * @return Returns the sum of the cluster energies.
      */
     public static double getValueEnergySum(SSPCluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
-    	
-    	// Perform the calculation.
-    	return getValueEnergySum(energy);
+        // Get the variables used by the calculation.
+        double[] energy = { clusterPair[0].getEnergy(), clusterPair[1].getEnergy() };
+        
+        // Perform the calculation.
+        return getValueEnergySum(energy);
     }
     
     /**
@@ -956,12 +1002,12 @@
      * @return Returns the absolute difference in the cluster times..
      */
     public static double getValueTimeCoincidence(Cluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] time = { clusterPair[0].getCalorimeterHits().get(0).getTime(),
-    			clusterPair[1].getCalorimeterHits().get(0).getTime() };
-    	
-    	// Perform the calculation.
-    	return getValueTimeCoincidence(time);
+        // Get the variables used by the calculation.
+        double[] time = { clusterPair[0].getCalorimeterHits().get(0).getTime(),
+                clusterPair[1].getCalorimeterHits().get(0).getTime() };
+        
+        // Perform the calculation.
+        return getValueTimeCoincidence(time);
     }
     
     /**
@@ -971,34 +1017,34 @@
      * @return Returns the absolute difference in the cluster times..
      */
     public static double getValueTimeCoincidence(SSPCluster[] clusterPair) {
-    	// Get the variables used by the calculation.
-    	double[] time = { clusterPair[0].getTime(), clusterPair[1].getTime() };
-    	
-    	// Perform the calculation.
-    	return getValueTimeCoincidence(time);
-    }
-    
-    /**
-	 * Indicates whether the argument cluster is located in the fiducial
-	 * region or not.
-	 * @param cluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is located in
-	 * the fiducial region and <code>false</code> otherwise.
-	 */
-	public static final boolean inFiducialRegion(Cluster cluster) {
-		return inFiducialRegion(getClusterXIndex(cluster), getClusterYIndex(cluster));
-	}
-    
-    /**
-	 * Indicates whether the argument cluster is located in the fiducial
-	 * region or not.
-	 * @param cluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is located in
-	 * the fiducial region and <code>false</code> otherwise.
-	 */
-	public static final boolean inFiducialRegion(SSPCluster cluster) {
-		return inFiducialRegion(getClusterXIndex(cluster), getClusterYIndex(cluster));
-	}
+        // Get the variables used by the calculation.
+        double[] time = { clusterPair[0].getTime(), clusterPair[1].getTime() };
+        
+        // Perform the calculation.
+        return getValueTimeCoincidence(time);
+    }
+    
+    /**
+     * Indicates whether the argument cluster is located in the fiducial
+     * region or not.
+     * @param cluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is located in
+     * the fiducial region and <code>false</code> otherwise.
+     */
+    public static final boolean inFiducialRegion(Cluster cluster) {
+        return inFiducialRegion(getClusterXIndex(cluster), getClusterYIndex(cluster));
+    }
+    
+    /**
+     * Indicates whether the argument cluster is located in the fiducial
+     * region or not.
+     * @param cluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is located in
+     * the fiducial region and <code>false</code> otherwise.
+     */
+    public static final boolean inFiducialRegion(SSPCluster cluster) {
+        return inFiducialRegion(getClusterXIndex(cluster), getClusterYIndex(cluster));
+    }
     
     /**
      * Checks if a cluster pair is coplanar to the beam within a given
@@ -1080,7 +1126,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCut(Cluster[] clusterPair) {
-    	return pairEnergySumCut(getValueEnergySum(clusterPair));
+        return pairEnergySumCut(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1092,7 +1138,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCutHigh(Cluster[] clusterPair) {
-    	return pairEnergySumCutHigh(getValueEnergySum(clusterPair));
+        return pairEnergySumCutHigh(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1104,7 +1150,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCutLow(Cluster[] clusterPair) {
-    	return pairEnergySumCutLow(getValueEnergySum(clusterPair));
+        return pairEnergySumCutLow(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1117,7 +1163,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCut(SSPCluster[] clusterPair) {
-    	return pairEnergySumCut(getValueEnergySum(clusterPair));
+        return pairEnergySumCut(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1129,7 +1175,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCutHigh(SSPCluster[] clusterPair) {
-    	return pairEnergySumCutHigh(getValueEnergySum(clusterPair));
+        return pairEnergySumCutHigh(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1141,7 +1187,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairEnergySumCutLow(SSPCluster[] clusterPair) {
-    	return pairEnergySumCutLow(getValueEnergySum(clusterPair));
+        return pairEnergySumCutLow(getValueEnergySum(clusterPair));
     }
     
     /**
@@ -1153,7 +1199,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairTimeCoincidenceCut(Cluster[] clusterPair) {
-    	return pairTimeCoincidenceCut(getValueTimeCoincidence(clusterPair));
+        return pairTimeCoincidenceCut(getValueTimeCoincidence(clusterPair));
     }
     
     /**
@@ -1165,7 +1211,7 @@
      * the cut and <code>false</code> if it does not.
      */
     public boolean pairTimeCoincidenceCut(SSPCluster[] clusterPair) {
-    	return pairTimeCoincidenceCut(getValueTimeCoincidence(clusterPair));
+        return pairTimeCoincidenceCut(getValueTimeCoincidence(clusterPair));
     }
     
     /**
@@ -1243,6 +1289,18 @@
      */
     private boolean clusterTotalEnergyCutLow(double clusterEnergy) {
         return (clusterEnergy >= cuts.get(CLUSTER_TOTAL_ENERGY_LOW));
+    }
+    
+    /**
+     * Gets the angle between the cluster and the centerpoint of the
+     * calorimeter.
+     * @param x - The cluster seed x-position.
+     * @param y - The cluster seed y-position.
+     * @return Returns the cluster angle as an <code>int</code> in units
+     * of degrees.
+     */
+    private static int getClusterAngle(double x, double y) {
+        return (int) Math.round(Math.atan(x / y) * 180.0 / Math.PI);
     }
     
     /**
@@ -1266,22 +1324,22 @@
      * the x-index and either of the cases where <code>iy == 0</code>
      * or <code>|iy| > 5</code> for the y-index.
      */
-	private static double[] getCrystalPosition(int ix, int iy) throws IndexOutOfBoundsException {
-		// Make sure that the requested crystal is a valid crystal.
-		if(ix == 0 || ix < -23 || ix > 23) {
-			throw new IndexOutOfBoundsException(String.format("Value \"%d\" is invalid for field x-index.", ix));
-		} if(iy == 0 || iy < -5 || iy > 5) {
-			throw new IndexOutOfBoundsException(String.format("Value \"%d\" is invalid for field y-index.", iy));
-		}
-		
-		// Get the position map.
-		double posMap[];
-		if(ix < 1) { posMap = position[5 - iy][22 - ix]; }
-		else { posMap = position[5 - iy][23 - ix]; }
-		
-		// Return the corrected mapped position.
-		return new double[] { posMap[0], posMap[2], posMap[1] };
-	}
+    private static double[] getCrystalPosition(int ix, int iy) throws IndexOutOfBoundsException {
+        // Make sure that the requested crystal is a valid crystal.
+        if(ix == 0 || ix < -23 || ix > 23) {
+            throw new IndexOutOfBoundsException(String.format("Value \"%d\" is invalid for field x-index.", ix));
+        } if(iy == 0 || iy < -5 || iy > 5) {
+            throw new IndexOutOfBoundsException(String.format("Value \"%d\" is invalid for field y-index.", iy));
+        }
+        
+        // Get the position map.
+        double posMap[];
+        if(ix < 1) { posMap = position[5 - iy][22 - ix]; }
+        else { posMap = position[5 - iy][23 - ix]; }
+        
+        // Return the corrected mapped position.
+        return new double[] { posMap[0], posMap[2], posMap[1] };
+    }
     
     /**
      * Calculates the value used by the coplanarity cut.
@@ -1295,7 +1353,7 @@
         // Get the cluster angles.
         int[] clusterAngle = new int[2];
         for(int i = 0; i < 2; i++) {
-        	clusterAngle[i] = (int) Math.round(Math.atan(x[i] / y[i]) * 180.0 / Math.PI);
+            clusterAngle[i] = getClusterAngle(x[i], y[i]); //(int) Math.round(Math.atan(x[i] / y[i]) * 180.0 / Math.PI);
         }
         
         // Calculate the coplanarity cut value.
@@ -1343,9 +1401,9 @@
      * @return Returns the cut value.
      */
     private static double getValueEnergySlope(double energy[], double x[], double y[], double energySlopeParamF) {
-    	// Determine which cluster is the lower-energy cluster.
-    	int lei = energy[0] < energy[1] ? 0 : 1;
-    	
+        // Determine which cluster is the lower-energy cluster.
+        int lei = energy[0] < energy[1] ? 0 : 1;
+        
         // E + R*F
         // Get the low energy cluster energy.
         double slopeParamE = energy[lei];
@@ -1369,9 +1427,9 @@
      */
     @Deprecated
     private static double getValueEnergySlopeLegacy(double energy[], double x[], double y[], double energySlopeParamF) {
-    	// Determine which cluster is the lower-energy cluster.
-    	int lei = energy[0] < energy[1] ? 0 : 1;
-    	
+        // Determine which cluster is the lower-energy cluster.
+        int lei = energy[0] < energy[1] ? 0 : 1;
+        
         // E + R*F
         // Get the low energy cluster energy.
         double slopeParamE = energy[lei];
@@ -1401,52 +1459,52 @@
      * the two clusters.
      */
     private static double getValueTimeCoincidence(double[] time) {
-    	return Math.abs(time[0] - time[1]);
-    }
-    
-    /**
-	 * Indicates whether the argument cluster is located in the fiducial
-	 * region or not.
-	 * @param cluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is located in
-	 * the fiducial region and <code>false</code> otherwise.
-	 */
-	private static final boolean inFiducialRegion(int ix, int iy) {
-		// Get the x and y indices for the cluster.
-		int absx = Math.abs(ix);
-		int absy = Math.abs(iy);
-		
-		// Check if the cluster is on the top or the bottom of the
-		// calorimeter, as defined by |y| == 5. This is an edge cluster
-		// and is not in the fiducial region.
-		if(absy == 5) {
-			return false;
-		}
-		
-		// Check if the cluster is on the extreme left or right side
-		// of the calorimeter, as defined by |x| == 23. This is also
-		// and edge cluster is not in the fiducial region.
-		if(absx == 23) {
-			return false;
-		}
-		
-		// Check if the cluster is along the beam gap, as defined by
-		// |y| == 1. This is an internal edge cluster and is not in the
-		// fiducial region.
-		if(absy == 1) {
-			return false;
-		}
-		
-		// Lastly, check if the cluster falls along the beam hole, as
-		// defined by clusters with -11 <= x <= -1 and |y| == 2. This
-		// is not the fiducial region.
-		if(absy == 2 && ix <= -1 && ix >= -11) {
-			return false;
-		}
-		
-		// If all checks fail, the cluster is in the fiducial region.
-		return true;
-	}
+        return Math.abs(time[0] - time[1]);
+    }
+    
+    /**
+     * Indicates whether the argument cluster is located in the fiducial
+     * region or not.
+     * @param cluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is located in
+     * the fiducial region and <code>false</code> otherwise.
+     */
+    private static final boolean inFiducialRegion(int ix, int iy) {
+        // Get the x and y indices for the cluster.
+        int absx = Math.abs(ix);
+        int absy = Math.abs(iy);
+        
+        // Check if the cluster is on the top or the bottom of the
+        // calorimeter, as defined by |y| == 5. This is an edge cluster
+        // and is not in the fiducial region.
+        if(absy == 5) {
+            return false;
+        }
+        
+        // Check if the cluster is on the extreme left or right side
+        // of the calorimeter, as defined by |x| == 23. This is also
+        // and edge cluster is not in the fiducial region.
+        if(absx == 23) {
+            return false;
+        }
+        
+        // Check if the cluster is along the beam gap, as defined by
+        // |y| == 1. This is an internal edge cluster and is not in the
+        // fiducial region.
+        if(absy == 1) {
+            return false;
+        }
+        
+        // Lastly, check if the cluster falls along the beam hole, as
+        // defined by clusters with -11 <= x <= -1 and |y| == 2. This
+        // is not the fiducial region.
+        if(absy == 2 && ix <= -1 && ix >= -11) {
+            return false;
+        }
+        
+        // If all checks fail, the cluster is in the fiducial region.
+        return true;
+    }
     
     /**
      * Checks if a coplanarity angle is within threshold.
@@ -1522,7 +1580,7 @@
      * the cut and <code>false</code> if it does not.
      */
     private boolean pairTimeCoincidenceCut(double timeDifference) {
-    	return (timeDifference <= cuts.get(PAIR_TIME_COINCIDENCE));
+        return (timeDifference <= cuts.get(PAIR_TIME_COINCIDENCE));
     }
     
     /**
@@ -1535,193 +1593,193 @@
      * Note that in this table, position[][] = { x, z, y } by in the
      * coordinate system employed by the rest of the class.
      */
-	private static final double[][][] position = {
-		{	{ -340.003,   97.065,   87.845 }, { -324.283,   97.450,   87.875 }, { -308.648,   97.810,   87.900 },
-			{ -293.093,   98.150,   87.920 }, { -277.618,   98.470,   87.940 }, { -262.213,   98.765,   87.965 },
-			{ -246.878,   99.040,   87.980 }, { -231.603,   99.290,   87.995 }, { -216.393,   99.520,   88.010 },
-			{ -201.228,   99.725,   88.030 }, { -186.118,   99.905,   88.040 }, { -171.058,  100.070,   88.050 },
-			{ -156.038,  100.205,   88.055 }, { -141.058,  100.325,   88.070 }, { -126.113,  100.415,   88.075 },
-			{ -111.198,  100.485,   88.075 }, {  -96.313,  100.530,   88.080 }, {  -81.453,  100.555,   88.085 },
-			{  -66.608,  100.560,   88.085 }, {  -51.788,  100.540,   88.080 }, {  -36.983,  100.490,   88.075 },
-			{  -22.183,  100.425,   88.075 }, {   -7.393,  100.335,   88.070 }, {    7.393,  100.335,   88.070 },
-			{   22.183,  100.425,   88.075 }, {   36.983,  100.490,   88.075 }, {   51.793,  100.540,   88.080 },
-			{   66.613,  100.560,   88.085 }, {   81.453,  100.555,   88.085 }, {   96.313,  100.530,   88.080 },
-			{  111.198,  100.485,   88.075 }, {  126.113,  100.415,   88.075 }, {  141.053,  100.325,   88.070 },
-			{  156.038,  100.205,   88.055 }, {  171.053,  100.070,   88.050 }, {  186.118,   99.905,   88.040 },
-			{  201.228,   99.725,   88.030 }, {  216.388,   99.520,   88.010 }, {  231.608,   99.290,   87.995 },
-			{  246.878,   99.040,   87.980 }, {  262.218,   98.765,   87.965 }, {  277.623,   98.470,   87.940 },
-			{  293.098,   98.150,   87.920 }, {  308.653,   97.810,   87.900 }, {  324.288,   97.450,   87.875 },
-			{  340.008,   97.065,   87.845 }
-		},
-		{	{ -340.003,   97.040,   72.715 }, { -324.283,   97.420,   72.735 }, { -308.648,   97.785,   72.750 },
-			{ -293.093,   98.125,   72.765 }, { -277.618,   98.450,   72.785 }, { -262.213,   98.745,   72.800 },
-			{ -246.878,   99.015,   72.815 }, { -231.603,   99.265,   72.825 }, { -216.388,   99.495,   72.840 },
-			{ -201.228,   99.700,   72.850 }, { -186.118,   99.885,   72.860 }, { -171.058,  100.045,   72.865 },
-			{ -156.033,  100.185,   72.875 }, { -141.053,  100.300,   72.880 }, { -126.108,  100.395,   72.880 },
-			{ -111.193,  100.460,   72.890 }, {  -96.308,  100.510,   72.890 }, {  -81.448,  100.535,   72.895 },
-			{  -66.608,  100.535,   72.890 }, {  -51.788,  100.510,   72.890 }, {  -36.978,  100.470,   72.890 },
-			{  -22.183,  100.405,   72.880 }, {   -7.388,  100.310,   72.880 }, {    7.393,  100.310,   72.880 },
-			{   22.188,  100.405,   72.885 }, {   36.983,  100.470,   72.890 }, {   51.793,  100.510,   72.890 },
-			{   66.613,  100.535,   72.890 }, {   81.453,  100.535,   72.895 }, {   96.313,  100.510,   72.890 },
-			{  111.198,  100.460,   72.890 }, {  126.113,  100.395,   72.880 }, {  141.063,  100.300,   72.880 },
-			{  156.043,  100.185,   72.875 }, {  171.063,  100.045,   72.865 }, {  186.123,   99.885,   72.860 },
-			{  201.233,   99.700,   72.850 }, {  216.393,   99.495,   72.840 }, {  231.608,   99.265,   72.825 },
-			{  246.883,   99.015,   72.815 }, {  262.218,   98.745,   72.800 }, {  277.623,   98.450,   72.785 },
-			{  293.098,   98.125,   72.765 }, {  308.653,   97.785,   72.750 }, {  324.288,   97.420,   72.735 },
-			{  340.008,   97.040,   72.715 }
-		},
-		{	{ -340.003,   96.990,   57.600 }, { -324.283,   97.375,   57.610 }, { -308.648,   97.740,   57.625 },
-			{ -293.093,   98.080,   57.630 }, { -277.618,   98.395,   57.645 }, { -262.213,   98.700,   57.655 },
-			{ -246.873,   98.970,   57.660 }, { -231.603,   99.220,   57.670 }, { -216.383,   99.450,   57.680 },
-			{ -201.228,   99.660,   57.685 }, { -186.113,   99.840,   57.695 }, { -171.053,  100.005,   57.695 },
-			{ -156.033,  100.140,   57.700 }, { -141.053,  100.255,   57.710 }, { -126.108,  100.345,   57.710 },
-			{ -111.193,  100.420,   57.710 }, {  -96.308,  100.465,   57.715 }, {  -81.448,  100.490,   57.715 },
-			{  -66.608,  100.490,   57.715 }, {  -51.788,  100.470,   57.710 }, {  -36.978,  100.425,   57.710 },
-			{  -22.178,  100.355,   57.710 }, {   -7.388,  100.265,   57.705 }, {    7.398,  100.265,   57.705 },
-			{   22.188,  100.355,   57.710 }, {   36.988,  100.425,   57.710 }, {   51.793,  100.470,   57.710 },
-			{   66.613,  100.490,   57.715 }, {   81.458,  100.490,   57.715 }, {   96.318,  100.465,   57.715 },
-			{  111.198,  100.420,   57.710 }, {  126.118,  100.345,   57.710 }, {  141.063,  100.255,   57.710 },
-			{  156.043,  100.140,   57.700 }, {  171.063,  100.005,   57.695 }, {  186.123,   99.840,   57.695 },
-			{  201.233,   99.660,   57.685 }, {  216.393,   99.450,   57.680 }, {  231.608,   99.220,   57.670 },
-			{  246.883,   98.970,   57.660 }, {  262.218,   98.700,   57.655 }, {  277.623,   98.395,   57.645 },
-			{  293.098,   98.080,   57.630 }, {  308.653,   97.740,   57.625 }, {  324.288,   97.375,   57.610 },
-			{  340.008,   96.990,   57.600 }
-		},
-		{	{ -340.003,   96.925,   42.490 }, { -324.283,   97.305,   42.495 }, { -308.648,   97.675,   42.505 },
-			{ -293.093,   98.010,   42.510 }, { -277.618,   98.330,   42.510 }, { -262.213,   98.625,   42.515 },
-			{ -246.873,   98.900,   42.525 }, { -231.603,   99.155,   42.530 }, { -216.383,   99.385,   42.535 },
-			{ -201.223,   99.590,   42.530 }, { -186.113,   99.775,   42.535 }, { -171.048,   99.930,   42.540 },
-			{ -156.033,  100.070,   42.545 }, { -141.048,  100.185,   42.545 }, { -126.108,  100.280,   42.550 },
-			{ -111.193,  100.350,   42.545 }, {  -96.308,  100.400,   42.545 }, {  -81.448,  100.420,   42.550 },
-			{  -66.608,  100.425,   42.550 }, {  -51.788,  100.405,   42.550 }, {  -36.978,  100.355,   42.545 },
-			{  -22.178,  100.290,   42.545 }, {   -7.388,  100.200,   42.545 }, {    7.398,  100.200,   42.545 },
-			{   22.188,  100.290,   42.545 }, {   36.988,  100.355,   42.545 }, {   51.793,  100.405,   42.550 },
-			{   66.613,  100.425,   42.550 }, {   81.458,  100.420,   42.550 }, {   96.318,  100.400,   42.545 },
-			{  111.198,  100.350,   42.545 }, {  126.118,  100.280,   42.550 }, {  141.063,  100.185,   42.545 },
-			{  156.043,  100.070,   42.545 }, {  171.063,   99.930,   42.540 }, {  186.123,   99.775,   42.535 },
-			{  201.233,   99.590,   42.530 }, {  216.393,   99.385,   42.535 }, {  231.608,   99.155,   42.530 },
-			{  246.883,   98.900,   42.525 }, {  262.218,   98.625,   42.515 }, {  277.628,   98.330,   42.510 },
-			{  293.098,   98.010,   42.510 }, {  308.653,   97.675,   42.505 }, {  324.288,   97.305,   42.495 },
-			{  340.008,   96.925,   42.490 }
-		},
-		{	{ -340.003,   96.830,   27.385 }, { -324.278,   97.215,   27.385 }, { -308.648,   97.575,   27.385 },
-			{ -293.093,   97.915,   27.385 }, { -277.613,   98.240,   27.385 }, { -262.213,   98.535,   27.385 },
-			{ -246.878,   98.810,   27.385 }, { -231.603,   99.060,   27.385 }, { -216.383,   99.290,   27.385 },
-			{ -201.223,   99.495,   27.385 }, { -186.113,   99.680,   27.385 }, { -171.048,   99.840,   27.385 },
-			{ -156.033,   99.980,   27.385 }, { -141.048,  100.095,   27.385 }, { -126.103,  100.185,   27.385 },
-			{ -111.193,  100.255,   27.385 }, {  -96.303,  100.305,   27.385 }, {  -81.448,  100.330,   27.385 },
-			{  -66.608,  100.330,   27.385 }, {  -51.783,  100.310,   27.385 }, {  -36.973,  100.265,   27.385 },
-			{  -22.178,  100.200,   27.385 }, {   -7.388,  100.105,   27.385 }, {    7.403,  100.105,   27.385 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{  156.078,   99.980,   27.385 }, {  171.103,   99.840,   27.385 }, {  186.168,   99.680,   27.385 },
-			{  201.268,   99.495,   27.385 }, {  216.423,   99.290,   27.385 }, {  231.638,   99.060,   27.385 },
-			{  246.913,   98.810,   27.385 }, {  262.248,   98.535,   27.385 }, {  277.658,   98.240,   27.385 },
-			{  293.133,   97.920,   27.385 }, {  308.688,   97.575,   27.385 }, {  324.323,   97.215,   27.385 },
-			{  340.043,   96.830,   27.385 }
-		},
-		{	{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }
-		},
-		{	{ -339.998,   96.840,  -27.330 }, { -324.278,   97.225,  -27.340 }, { -308.643,   97.585,  -27.345 },
-			{ -293.093,   97.925,  -27.350 }, { -277.613,   98.245,  -27.360 }, { -262.213,   98.545,  -27.365 },
-			{ -246.868,   98.820,  -27.365 }, { -231.598,   99.070,  -27.370 }, { -216.383,   99.300,  -27.375 },
-			{ -201.223,   99.505,  -27.380 }, { -186.113,   99.690,  -27.385 }, { -171.048,   99.850,  -27.380 },
-			{ -156.028,   99.990,  -27.385 }, { -141.048,  100.100,  -27.390 }, { -126.103,  100.195,  -27.390 },
-			{ -111.193,  100.265,  -27.395 }, {  -96.303,  100.315,  -27.395 }, {  -81.443,  100.340,  -27.390 },
-			{  -66.603,  100.335,  -27.390 }, {  -51.783,  100.315,  -27.390 }, {  -36.973,  100.275,  -27.395 },
-			{  -22.173,  100.205,  -27.390 }, {   -7.383,  100.115,  -27.385 }, {    7.403,  100.115,  -27.385 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 }, {    0.000,    0.000,    0.000 },
-			{  156.088,   99.985,  -27.385 }, {  171.103,   99.845,  -27.380 }, {  186.168,   99.680,  -27.385 },
-			{  201.268,   99.495,  -27.380 }, {  216.428,   99.290,  -27.375 }, {  231.643,   99.060,  -27.370 },
-			{  246.913,   98.810,  -27.365 }, {  262.258,   98.535,  -27.365 }, {  277.658,   98.240,  -27.360 },
-			{  293.138,   97.925,  -27.350 }, {  308.688,   97.580,  -27.345 }, {  324.323,   97.215,  -27.340 },
-			{  340.043,   96.835,  -27.330 }
-		},
-		{	{ -339.998,   96.930,  -42.435 }, { -324.278,   97.315,  -42.445 }, { -308.648,   97.680,  -42.455 },
-			{ -293.093,   98.015,  -42.470 }, { -277.613,   98.340,  -42.480 }, { -262.208,   98.635,  -42.490 },
-			{ -246.873,   98.910,  -42.500 }, { -231.593,   99.160,  -42.510 }, { -216.383,   99.390,  -42.515 },
-			{ -201.223,   99.595,  -42.525 }, { -186.113,   99.780,  -42.525 }, { -171.048,   99.940,  -42.535 },
-			{ -156.028,  100.080,  -42.540 }, { -141.048,  100.195,  -42.540 }, { -126.103,  100.290,  -42.545 },
-			{ -111.193,  100.355,  -42.550 }, {  -96.303,  100.405,  -42.550 }, {  -81.443,  100.430,  -42.550 },
-			{  -66.608,  100.430,  -42.550 }, {  -51.783,  100.405,  -42.550 }, {  -36.973,  100.365,  -42.550 },
-			{  -22.178,  100.295,  -42.545 }, {   -7.388,  100.205,  -42.545 }, {    7.403,  100.205,  -42.545 },
-			{   22.193,  100.295,  -42.545 }, {   36.988,  100.365,  -42.550 }, {   51.798,  100.405,  -42.550 },
-			{   66.623,  100.430,  -42.550 }, {   81.458,  100.430,  -42.550 }, {   96.318,  100.405,  -42.550 },
-			{  111.208,  100.355,  -42.550 }, {  126.118,  100.290,  -42.545 }, {  141.063,  100.195,  -42.540 },
-			{  156.043,  100.080,  -42.540 }, {  171.063,   99.940,  -42.535 }, {  186.128,   99.780,  -42.525 },
-			{  201.238,   99.595,  -42.525 }, {  216.398,   99.390,  -42.515 }, {  231.613,   99.160,  -42.510 },
-			{  246.888,   98.910,  -42.500 }, {  262.223,   98.635,  -42.490 }, {  277.628,   98.340,  -42.480 },
-			{  293.108,   98.015,  -42.470 }, {  308.663,   97.680,  -42.455 }, {  324.293,   97.315,  -42.445 },
-			{  340.013,   96.930,  -42.435 }
-		},
-		{	{ -339.998,   97.000,  -57.540 }, { -324.278,   97.385,  -57.560 }, { -308.648,   97.745,  -57.575 },
-			{ -293.093,   98.090,  -57.595 }, { -277.613,   98.410,  -57.610 }, { -262.208,   98.705,  -57.625 },
-			{ -246.873,   98.975,  -57.640 }, { -231.593,   99.225,  -57.655 }, { -216.383,   99.455,  -57.665 },
-			{ -201.223,   99.665,  -57.675 }, { -186.113,   99.845,  -57.685 }, { -171.048,  100.010,  -57.690 },
-			{ -156.028,  100.145,  -57.700 }, { -141.048,  100.265,  -57.705 }, { -126.103,  100.355,  -57.710 },
-			{ -111.193,  100.425,  -57.710 }, {  -96.303,  100.475,  -57.720 }, {  -81.443,  100.495,  -57.715 },
-			{  -66.608,  100.500,  -57.720 }, {  -51.783,  100.480,  -57.715 }, {  -36.973,  100.430,  -57.710 },
-			{  -22.178,  100.365,  -57.710 }, {   -7.388,  100.275,  -57.705 }, {    7.403,  100.275,  -57.705 },
-			{   22.193,  100.365,  -57.710 }, {   36.988,  100.430,  -57.710 }, {   51.798,  100.480,  -57.715 },
-			{   66.623,  100.500,  -57.720 }, {   81.458,  100.495,  -57.715 }, {   96.318,  100.475,  -57.720 },
-			{  111.208,  100.425,  -57.710 }, {  126.118,  100.355,  -57.710 }, {  141.063,  100.265,  -57.705 },
-			{  156.043,  100.145,  -57.700 }, {  171.063,  100.010,  -57.690 }, {  186.128,   99.845,  -57.685 },
-			{  201.238,   99.665,  -57.675 }, {  216.398,   99.455,  -57.665 }, {  231.613,   99.225,  -57.655 },
-			{  246.888,   98.975,  -57.640 }, {  262.223,   98.705,  -57.625 }, {  277.628,   98.410,  -57.610 },
-			{  293.108,   98.090,  -57.595 }, {  308.663,   97.745,  -57.575 }, {  324.293,   97.385,  -57.560 },
-			{  340.013,   97.000,  -57.540 }
-		},
-		{	{ -339.998,   97.045,  -72.655 }, { -324.278,   97.435,  -72.680 }, { -308.648,   97.795,  -72.710 },
-			{ -293.093,   98.135,  -72.730 }, { -277.613,   98.455,  -72.750 }, { -262.208,   98.750,  -72.775 },
-			{ -246.873,   99.020,  -72.795 }, { -231.593,   99.280,  -72.810 }, { -216.383,   99.505,  -72.820 },
-			{ -201.223,   99.710,  -72.840 }, { -186.113,   99.895,  -72.850 }, { -171.048,  100.055,  -72.860 },
-			{ -156.028,  100.190,  -72.870 }, { -141.048,  100.305,  -72.880 }, { -126.103,  100.400,  -72.885 },
-			{ -111.193,  100.470,  -72.890 }, {  -96.303,  100.520,  -72.890 }, {  -81.443,  100.540,  -72.895 },
-			{  -66.608,  100.540,  -72.895 }, {  -51.783,  100.520,  -72.895 }, {  -36.973,  100.480,  -72.890 },
-			{  -22.178,  100.405,  -72.885 }, {   -7.388,  100.320,  -72.880 }, {    7.403,  100.320,  -72.880 },
-			{   22.193,  100.405,  -72.885 }, {   36.988,  100.480,  -72.890 }, {   51.798,  100.520,  -72.895 },
-			{   66.623,  100.540,  -72.895 }, {   81.458,  100.540,  -72.895 }, {   96.318,  100.520,  -72.890 },
-			{  111.208,  100.470,  -72.890 }, {  126.118,  100.400,  -72.885 }, {  141.063,  100.305,  -72.880 },
-			{  156.043,  100.190,  -72.870 }, {  171.063,  100.055,  -72.860 }, {  186.128,   99.895,  -72.850 },
-			{  201.238,   99.710,  -72.840 }, {  216.398,   99.505,  -72.820 }, {  231.613,   99.280,  -72.810 },
-			{  246.888,   99.020,  -72.795 }, {  262.223,   98.750,  -72.775 }, {  277.628,   98.455,  -72.750 },
-			{  293.108,   98.135,  -72.730 }, {  308.663,   97.795,  -72.710 }, {  324.293,   97.435,  -72.680 },
-			{  340.013,   97.045,  -72.655 }
-		},
-		{	{ -339.998,   97.070,  -87.790 }, { -324.278,   97.460,  -87.820 }, { -308.648,   97.820,  -87.850 },
-			{ -293.093,   98.160,  -87.885 }, { -277.613,   98.480,  -87.910 }, { -262.208,   98.775,  -87.935 },
-			{ -246.873,   99.050,  -87.960 }, { -231.593,   99.300,  -87.980 }, { -216.383,   99.530,  -88.000 },
-			{ -201.223,   99.735,  -88.015 }, { -186.113,   99.920,  -88.030 }, { -171.048,  100.080,  -88.045 },
-			{ -156.028,  100.215,  -88.055 }, { -141.048,  100.335,  -88.065 }, { -126.103,  100.420,  -88.070 },
-			{ -111.193,  100.490,  -88.075 }, {  -96.303,  100.540,  -88.085 }, {  -81.443,  100.565,  -88.085 },
-			{  -66.608,  100.560,  -88.085 }, {  -51.783,  100.540,  -88.085 }, {  -36.973,  100.500,  -88.080 },
-			{  -22.178,  100.430,  -88.075 }, {   -7.388,  100.340,  -88.065 }, {    7.403,  100.340,  -88.070 },
-			{   22.193,  100.430,  -88.075 }, {   36.988,  100.500,  -88.080 }, {   51.798,  100.540,  -88.085 },
-			{   66.623,  100.560,  -88.085 }, {   81.458,  100.565,  -88.085 }, {   96.318,  100.540,  -88.085 },
-			{  111.208,  100.490,  -88.075 }, {  126.118,  100.420,  -88.070 }, {  141.063,  100.335,  -88.065 },
-			{  156.043,  100.215,  -88.055 }, {  171.063,  100.080,  -88.045 }, {  186.128,   99.915,  -88.030 },
-			{  201.238,   99.735,  -88.015 }, {  216.398,   99.530,  -88.000 }, {  231.613,   99.300,  -87.980 },
-			{  246.888,   99.050,  -87.960 }, {  262.223,   98.775,  -87.935 }, {  277.628,   98.480,  -87.910 },
-			{  293.108,   98.160,  -87.885 }, {  308.663,   97.820,  -87.850 }, {  324.293,   97.460,  -87.820 },
-			{  340.013,   97.070,  -87.790 }
-		}
-	};
-}
+    private static final double[][][] position = {
+        {   { -340.003,   97.065,   87.845 }, { -324.283,   97.450,   87.875 }, { -308.648,   97.810,   87.900 },
+            { -293.093,   98.150,   87.920 }, { -277.618,   98.470,   87.940 }, { -262.213,   98.765,   87.965 },
+            { -246.878,   99.040,   87.980 }, { -231.603,   99.290,   87.995 }, { -216.393,   99.520,   88.010 },
+            { -201.228,   99.725,   88.030 }, { -186.118,   99.905,   88.040 }, { -171.058,  100.070,   88.050 },
+            { -156.038,  100.205,   88.055 }, { -141.058,  100.325,   88.070 }, { -126.113,  100.415,   88.075 },
+            { -111.198,  100.485,   88.075 }, {  -96.313,  100.530,   88.080 }, {  -81.453,  100.555,   88.085 },
+            {  -66.608,  100.560,   88.085 }, {  -51.788,  100.540,   88.080 }, {  -36.983,  100.490,   88.075 },
+            {  -22.183,  100.425,   88.075 }, {   -7.393,  100.335,   88.070 }, {    7.393,  100.335,   88.070 },
+            {   22.183,  100.425,   88.075 }, {   36.983,  100.490,   88.075 }, {   51.793,  100.540,   88.080 },
+            {   66.613,  100.560,   88.085 }, {   81.453,  100.555,   88.085 }, {   96.313,  100.530,   88.080 },
+            {  111.198,  100.485,   88.075 }, {  126.113,  100.415,   88.075 }, {  141.053,  100.325,   88.070 },
+            {  156.038,  100.205,   88.055 }, {  171.053,  100.070,   88.050 }, {  186.118,   99.905,   88.040 },
+            {  201.228,   99.725,   88.030 }, {  216.388,   99.520,   88.010 }, {  231.608,   99.290,   87.995 },
+            {  246.878,   99.040,   87.980 }, {  262.218,   98.765,   87.965 }, {  277.623,   98.470,   87.940 },
+            {  293.098,   98.150,   87.920 }, {  308.653,   97.810,   87.900 }, {  324.288,   97.450,   87.875 },
+            {  340.008,   97.065,   87.845 }
+        },
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+            {   22.193,  100.430,  -88.075 }, {   36.988,  100.500,  -88.080 }, {   51.798,  100.540,  -88.085 },
+            {   66.623,  100.560,  -88.085 }, {   81.458,  100.565,  -88.085 }, {   96.318,  100.540,  -88.085 },
+            {  111.208,  100.490,  -88.075 }, {  126.118,  100.420,  -88.070 }, {  141.063,  100.335,  -88.065 },
+            {  156.043,  100.215,  -88.055 }, {  171.063,  100.080,  -88.045 }, {  186.128,   99.915,  -88.030 },
+            {  201.238,   99.735,  -88.015 }, {  216.398,   99.530,  -88.000 }, {  231.613,   99.300,  -87.980 },
+            {  246.888,   99.050,  -87.960 }, {  262.223,   98.775,  -87.935 }, {  277.628,   98.480,  -87.910 },
+            {  293.108,   98.160,  -87.885 }, {  308.663,   97.820,  -87.850 }, {  324.293,   97.460,  -87.820 },
+            {  340.013,   97.070,  -87.790 }
+        }
+    };
+}

Modified: java/branches/HPSJAVA-409/run-database/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/pom.xml	(original)
+++ java/branches/HPSJAVA-409/run-database/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/run-database/</url>
@@ -20,8 +20,21 @@
             <artifactId>hps-record-util</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.hps</groupId>
-            <artifactId>hps-datacat-client</artifactId>
+            <groupId>srs</groupId>
+            <artifactId>org-srs-datacat-client</artifactId>
         </dependency>
     </dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <configuration>
+                    <excludes>
+                        <exclude>org/hps/run/database/RunBuilderTest.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
 </project>

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDao.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDao.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDao.java	Wed Apr 27 11:11:32 2016
@@ -16,7 +16,7 @@
      *
      * @param run the run number
      */
-    public void deleteEpicsData(EpicsType epicsType, final int run);
+    public void deleteEpicsData(EpicsType epicsType, int run);
 
     /**
      * Get EPICS data by run.
@@ -34,5 +34,5 @@
      *
      * @param epicsDataList the list of EPICS data
      */
-    void insertEpicsData(List<EpicsData> epicsDataList);   
+    void insertEpicsData(List<EpicsData> epicsDataList, int run);
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDaoImpl.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDaoImpl.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsDataDaoImpl.java	Wed Apr 27 11:11:32 2016
@@ -74,6 +74,9 @@
 
     /**
      * Delete all EPICS data for a run from the database.
+     * <p>
+     * Only the <code>epics_header</code> records are deleted and the child records
+     * are deleted automatically via a <code>CASCADE</code>.
      *
      * @param run the run number
      */
@@ -97,12 +100,12 @@
                 deleteEpicsData.setInt(1, headerId);
                 int rowsAffected = deleteEpicsData.executeUpdate();
                 if (rowsAffected == 0) {
-                    throw new SQLException("Deletion of EPICS data failed; no rows affect.");
+                    throw new SQLException("Deletion of EPICS data failed; no rows affected.");
                 }
                 deleteHeader.setInt(1, headerId);
                 rowsAffected = deleteHeader.executeUpdate();
                 if (rowsAffected == 0) {
-                    throw new SQLException("Deletion of EPICS header failed; no rows affect.");
+                    throw new SQLException("Deletion of EPICS header failed; no rows affected.");
                 }
             }
 
@@ -137,7 +140,7 @@
      * Get EPICS data by run.
      *
      * @param run the run number
-     * @param epicsType the type of EPICS data (1s or 10s)
+     * @param epicsType the type of EPICS data (2s or 20s)
      * @return the EPICS data
      */
     @Override
@@ -149,7 +152,7 @@
             final List<EpicsVariable> variables = epicsVariableDao.getEpicsVariables(epicsType);
             selectEpicsData = connection.prepareStatement("SELECT * FROM " + epicsType.getTableName() 
                     + " LEFT JOIN epics_headers ON " + epicsType.getTableName() + ".epics_header_id = epics_headers.id"
-                    + " WHERE epics_headers.run = ?");
+                    + " WHERE epics_headers.run = ? ORDER BY epics_headers.sequence");
             selectEpicsData.setInt(1, run);
             ResultSet resultSet = selectEpicsData.executeQuery();
             while (resultSet.next()) {
@@ -189,12 +192,14 @@
     /**
      * Insert a list of EPICS data into the database.
      * <p>
-     * The run number comes from the header information.
+     * By default, the run number from the header will be used, but it will be overridden
+     * if it does not match the <code>run</code> argument.  (There are a few data files
+     * where the run in the EPICS header is occassionally wrong.)
      *
      * @param epicsDataList the list of EPICS data
      */
     @Override
-    public void insertEpicsData(final List<EpicsData> epicsDataList) {
+    public void insertEpicsData(final List<EpicsData> epicsDataList, int run) {
         if (epicsDataList.isEmpty()) {
             throw new IllegalArgumentException("The EPICS data list is empty.");
         }
@@ -208,9 +213,11 @@
                 if (epicsHeader == null) {
                     throw new IllegalArgumentException("The EPICS data is missing a header.");
                 }
-                insertHeaderStatement.setInt(1, epicsHeader.getRun());
+                insertHeaderStatement.setInt(1, run); /* Don't use run from bank as it is sometimes wrong! */
                 insertHeaderStatement.setInt(2, epicsHeader.getSequence());
                 insertHeaderStatement.setInt(3, epicsHeader.getTimestamp());
+                LOGGER.finer("creating EPICs record with run = " + run + " ; seq = " 
+                        + epicsHeader.getSequence() + "; ts = " + epicsHeader.getTimestamp());
                 final int rowsCreated = insertHeaderStatement.executeUpdate();
                 if (rowsCreated == 0) {
                     throw new SQLException("Creation of EPICS header record failed; no rows affected.");
@@ -238,11 +245,11 @@
                     insertStatement.setDouble(parameterIndex, value);
                     ++parameterIndex;
                 }
-                final int dataRowsCreated = insertStatement.executeUpdate();                
+                final int dataRowsCreated = insertStatement.executeUpdate();
                 if (dataRowsCreated == 0) {
                     throw new SQLException("Creation of EPICS data failed; no rows affected.");
                 }
-                LOGGER.info("inserted EPICS data with run " + epicsHeader.getRun() + ", seq " + epicsHeader.getSequence() + "timestamp " 
+                LOGGER.finer("inserted EPICS data with run = " + run + "; seq = " + epicsHeader.getSequence() + "; ts = " 
                         + epicsHeader.getTimestamp());
                 insertStatement.close();
             }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsType.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsType.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsType.java	Wed Apr 27 11:11:32 2016
@@ -3,34 +3,35 @@
 import org.hps.record.epics.EpicsData;
 
 /**
- * Enum for representing different types of EPICS data in the run database, of which there are currently two (1s and
- * 10s).
+ * Enum for representing different types of EPICS data in the run database, of which there are currently two (2s and
+ * 20s).
  *
  * @author Jeremy McCormick, SLAC
  */
+// FIXME: move to record-util
 public enum EpicsType {
 
     /**
-     * 10S EPICS data.
+     * 20S EPICS data.
      */
-    EPICS_10S(10),
+    EPICS_20S(20),
     /**
-     * 1S EPICS data.
+     * 2S EPICS data.
      */
-    EPICS_1S(1);
+    EPICS_2S(2);
 
     /**
      * Get the type from an int.
      *
      * @param type the type from an int
      * @return the type from an int
-     * @throws IllegalArgumentException if <code>type</code> is invalid (not 1 or 10)
+     * @throws IllegalArgumentException if <code>type</code> is invalid (not 2 or 20)
      */
     public static EpicsType fromInt(final int type) {
-        if (type == EPICS_1S.type) {
-            return EPICS_1S;
-        } else if (type == EPICS_10S.type) {
-            return EPICS_10S;
+        if (type == EPICS_2S.type) {
+            return EPICS_2S;
+        } else if (type == EPICS_20S.type) {
+            return EPICS_20S;
         } else {
             throw new IllegalArgumentException("The type code is invalid (must be 1 or 10): " + type);
         }
@@ -44,9 +45,9 @@
     public static EpicsType getEpicsType(final EpicsData epicsData) {
         // FIXME: The type argument should be set on creation which would make this key check unnecessary.
         if (epicsData.getKeys().contains("MBSY2C_energy")) {
-            return EpicsType.EPICS_1S;
+            return EpicsType.EPICS_2S;
         } else {
-            return EpicsType.EPICS_10S;
+            return EpicsType.EPICS_20S;
         }
     }
 

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsVariable.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsVariable.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/EpicsVariable.java	Wed Apr 27 11:11:32 2016
@@ -2,7 +2,7 @@
 
 /**
  * Information about an EPICS variable including its name in the EPICS database, column name for the run database,
- * description of the variable, and type (either 1s or 10s).
+ * description of the variable, and type (either 2s or 20s).
  * <p>
  * This class is used to represent data from the <i>epics_variables</i> table in the run database.
  *
@@ -29,7 +29,7 @@
     private final String variableName;
 
     /**
-     * The type of the variable (1s or 10s).
+     * The type of the variable (2s or 20s).
      */
     private final EpicsType variableType;
 
@@ -53,9 +53,9 @@
      * Create an EPICs variable.
      *
      * @param variableName the name of the variable
-     * @param columnName the column name in the run db
+     * @param columnName the column name in the run database
      * @param description the variable's description
-     * @param variableType the type of the variable
+     * @param type the integer encoding of the type
      */
     public EpicsVariable(final String variableName, final String columnName, final String description, final int type) {
         this.variableName = variableName;

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunDatabaseCommandLine.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunDatabaseCommandLine.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunDatabaseCommandLine.java	Wed Apr 27 11:11:32 2016
@@ -1,62 +1,24 @@
 package org.hps.run.database;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.logging.Logger;
+import java.net.URISyntaxException;
 
 import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
 import org.hps.conditions.database.ConnectionParameters;
-import org.hps.datacat.client.DatacatClient;
-import org.hps.datacat.client.DatacatClientFactory;
-import org.hps.datacat.client.Dataset;
-import org.hps.datacat.client.DatasetMetadata;
-import org.hps.record.evio.EvioFileUtilities;
+import org.srs.datacat.client.Client;
+import org.srs.datacat.client.ClientBuilder;
 
 /**
- * Command line tool for updating the run database from EVIO files registered in the data catalog.
+ * Command line tool for inserting records into the run database.
  *
  * @author Jeremy McCormick, SLAC
  */
-public class RunDatabaseCommandLine {
-
-    /**
-     * Set of features supported by the tool.
-     */
-    static enum Feature {
-        /**
-         * Insert EPICS data.
-         */
-        EPICS,
-        /**
-         * Insert scaler data.
-         */
-        SCALERS,
-        /**
-         * Insert run summary.
-         */
-        SUMMARY,
-        /**
-         * Insert trigger config.
-         */
-        TRIGGER_CONFIG
-    }
-
-    /**
-     * Initialize the logger.
-     */
-    private static final Logger LOGGER = Logger.getLogger(RunDatabaseCommandLine.class.getPackage().getName());
-
+public final class RunDatabaseCommandLine {
+        
     /**
      * Command line options for the crawler.
      */
@@ -66,11 +28,18 @@
      * Statically define the command options.
      */
     static {
-        OPTIONS.addOption("f", "feature", true, "enable a feature");
-        OPTIONS.addOption("p", "connection-properties", true, "database connection properties file (required)");
         OPTIONS.addOption("h", "help", false, "print help and exit (overrides all other arguments)");
         OPTIONS.addOption("r", "run", true, "run to update");
-        OPTIONS.addOption("u", "update", false, "allow updating existing run in the database");
+        OPTIONS.addOption("p", "connection-properties", true, "database connection properties file (required)");       
+        OPTIONS.addOption("Y", "dry-run", false, "dry run which will not update the database");
+        OPTIONS.addOption("x", "replace", false, "allow deleting and replacing an existing run");
+        OPTIONS.addOption("s", "spreadsheet", true, "path to run database spreadsheet (CSV format)");
+        OPTIONS.addOption("d", "detector", true, "conditions system detector name");
+        OPTIONS.addOption("N", "no-evio-processing", false, "skip processing of all EVIO files");
+        OPTIONS.addOption("L", "load", false, "load back run information after inserting (for debugging)");
+        OPTIONS.addOption("u", "url", true, "data catalog URL");
+        OPTIONS.addOption("S", "site", true, "data catalog site (e.g. SLAC or JLAB)");
+        OPTIONS.addOption("f", "folder", true, "folder in datacat for dataset search");
     }
 
     /**
@@ -81,113 +50,76 @@
     public static void main(final String args[]) {
         new RunDatabaseCommandLine().parse(args).run();
     }
-
-    /**
-     * Allow updating of the database for existing runs.
-     */
-    private boolean allowUpdates = false;
-
-    /**
-     * The set of enabled features.
-     */
-    private final Set<Feature> features = new HashSet<Feature>();
-
-    /**
-     * The run manager for interacting with the run db.
-     */
-    private RunManager runManager;
-
-    /**
-     * Create a run processor from the current configuration.
-     *
-     * @return the run processor
-     */
-    private RunProcessor createEvioRunProcessor(final RunSummaryImpl runSummary, final List<File> files) {
-
-        final RunProcessor runProcessor = new RunProcessor(runSummary, files);
-
-        if (features.contains(Feature.EPICS)) {
-            runProcessor.addEpicsProcessor();
-        }
-        if (features.contains(Feature.SCALERS)) {
-            runProcessor.addScalerProcessor();
-        }
-        if (features.contains(Feature.TRIGGER_CONFIG)) {
-            runProcessor.addTriggerTimeProcessor();
-        }
-
-        return runProcessor;
-    }
-
-    /**
-     * Get the list of EVIO files for the run.
-     *
-     * @param run the run number
-     * @return the list of EVIO files from the run
-     */
-    private Map<File, Dataset> getEvioFiles(final int run) {
-        final DatacatClient datacatClient = new DatacatClientFactory().createClient();
-        final Set<String> metadata = new HashSet<String>();
-        final Map<File, Dataset> files = new HashMap<File, Dataset>();
-        metadata.add("runMin");
-        metadata.add("eventCount");
-        metadata.add("fileNumber");
-        metadata.add("endTimestamp");
-        metadata.add("startTimestamp");
-        metadata.add("hasEnd");
-        metadata.add("hasPrestart");
-        final List<Dataset> datasets = datacatClient.findDatasets("data/raw",
-                "fileFormat eq 'EVIO' AND dataType eq 'RAW' AND runMin eq " + run, metadata);
-        if (datasets.isEmpty()) {
-            throw new IllegalStateException("No EVIO datasets for run " + run + " were found in the data catalog.");
-        }
-        for (final Dataset dataset : datasets) {
-            files.put(new File(dataset.getLocations().get(0).getResource()), dataset);
-        }
-        return files;
-    }
-
-    /**
-     * Insert information for a run into the database.
-     *
-     * @param runManager the run manager for interacting with the run db
-     * @param runSummary the run summary with information about the run
-     */
-    private void insertRun(final RunManager runManager, final RunSummary runSummary) {
-
-        final RunDatabaseDaoFactory runFactory = new RunDatabaseDaoFactory(runManager.getConnection());
-
-        // Add the run summary record.
-        if (this.features.contains(Feature.SUMMARY)) {
-            LOGGER.info("inserting run summary");
-            runFactory.createRunSummaryDao().insertRunSummary(runSummary);
-        }
-
-        if (this.features.contains(Feature.EPICS)) {
-            LOGGER.info("inserting EPICS data");
-            runFactory.createEpicsDataDao().insertEpicsData(runSummary.getEpicsData());
-        }
-
-        if (this.features.contains(Feature.SCALERS)) {
-            LOGGER.info("inserting scaler data");
-            runFactory.createScalerDataDao().insertScalerData(runSummary.getScalerData(), runManager.getRun());
-        }
-
-        if (this.features.contains(Feature.TRIGGER_CONFIG)) {
-            LOGGER.info("inserting trigger config");
-            runFactory.createTriggerConfigDao().insertTriggerConfig(runSummary.getTriggerConfig(), runManager.getRun());
-        }
-    }
-
-    /**
-     * Parse command line options and return reference to <code>this</code>.
+    
+    /**
+     * Enable dry run which will not update the run database.
+     */
+    private boolean dryRun = false;
+    
+    /**
+     * Run number.
+     */
+    private int run;
+    
+    /**
+     * Path to spreadsheet CSV file.
+     */
+    private File spreadsheetFile = null;
+    
+    /**
+     * Name of detector for conditions system (default for Eng Run 2015 provided here).
+     */
+    private String detectorName = "HPS-EngRun2015-Nominal-v3";
+    
+    /**
+     * Allow replacement of existing records.
+     */
+    private boolean replace = false;
+    
+    /**
+     * Skip full EVIO file processing.
+     */
+    private boolean skipEvioProcessing = false;
+    
+    /**
+     * Load back run information after insert (for debugging).
+     */
+    private boolean reload = false;
+    
+    /**
+     * Database connection parameters.
+     */
+    private ConnectionParameters connectionParameters = null;
+    
+    /**
+     * Data catalog client interface.
+     */
+    private Client datacatClient = null;
+    
+    /**
+     * Data catalog site.
+     */
+    private String site = "JLAB";                             
+    
+    /**
+     * Data catalog URL.
+     */
+    private String url = "http://hpsweb.jlab.org/datacat/r";  
+    
+    /**
+     * Default folder for file search.
+     */
+    private String folder = "/HPS/data/raw";
+    
+    /**
+     * Parse command line options and return reference to <code>this</code> object.
      *
      * @param args the command line arguments
      * @return reference to this object
      */
-    RunDatabaseCommandLine parse(final String args[]) {
+    private RunDatabaseCommandLine parse(final String args[]) {
         try {
-            final CommandLine cl = new DefaultParser().parse(OPTIONS, args);
+            final CommandLine cl = new PosixParser().parse(OPTIONS, args);
 
             // Print help and exit.
             if (cl.hasOption("h") || args.length == 0) {
@@ -204,43 +136,74 @@
                     throw new IllegalArgumentException("Connection properties file " + dbPropFile.getPath()
                             + " does not exist.");
                 }
-                final ConnectionParameters connectionParameters = ConnectionParameters.fromProperties(dbPropFile);
-                LOGGER.config("using " + dbPropPath + " for db connection properties");
-
-                runManager = new RunManager(connectionParameters.createConnection());
-
+                connectionParameters = ConnectionParameters.fromProperties(dbPropFile);
             } else {
                 // Database connection properties file is required.
-                throw new RuntimeException("Connection properties are required.");
-            }
-
-            Integer run = null;
+                throw new RuntimeException("Connection properties are a required argument.");
+            }
+
+            // Run number.
             if (cl.hasOption("r")) {
                 run = Integer.parseInt(cl.getOptionValue("r"));
             } else {
                 throw new RuntimeException("The run number is required.");
             }
-            runManager.setRun(run);
-
+            
+            // Dry run.
+            if (cl.hasOption("Y")) {
+                this.dryRun = true;
+            }
+            
+            // Run spreadsheet.
+            if (cl.hasOption("s")) {
+                this.spreadsheetFile = new File(cl.getOptionValue("s"));
+                if (!this.spreadsheetFile.exists()) {
+                    throw new RuntimeException("The run spreadsheet " + this.spreadsheetFile.getPath() + " is inaccessible or does not exist.");
+                }
+            }
+            
+            // Detector name.
+            if (cl.hasOption("d")) {
+                this.detectorName = cl.getOptionValue("d");
+            }
+            
+            // Replace existing run.
+            if (cl.hasOption("x")) {
+                this.replace = true;
+            }
+            
+            // Skip full EVIO processing.
+            if (cl.hasOption("N")) {
+                this.skipEvioProcessing = true;
+            }
+            
+            // Load back run info at end of job.
+            if (cl.hasOption("L")) {
+                this.reload = true;
+            }
+            
+            // Data catalog URL.
+            if (cl.hasOption("u")) {
+                url = cl.getOptionValue("u");
+            }
+            
+            // Site in the data catalog.
+            if (cl.hasOption("S")) {
+                site = cl.getOptionValue("S");
+            }
+            
+            // Set folder for dataset search.
             if (cl.hasOption("f")) {
-                // Enable individual features.
-                for (final String arg : cl.getOptionValues("f")) {
-                    features.add(Feature.valueOf(arg));
-                }
-            } else {
-                // By default all features are enabled.
-                features.addAll(Arrays.asList(Feature.values()));
-            }
-            for (final Feature feature : features) {
-                LOGGER.config("feature " + feature.name() + " is enabled.");
-            }
-
-            // Allow updates to existing runs in the db.
-            if (cl.hasOption("u")) {
-                this.allowUpdates = true;
-                LOGGER.config("updating or replacing existing run data is enabled");
-            }
-
+                folder = cl.getOptionValue("f");
+            }
+            
+            // Initialize the data catalog client.
+            try {
+                datacatClient = new ClientBuilder().setUrl(url).build();
+            } catch (URISyntaxException e) {
+                throw new RuntimeException("Bad datacat URL.", e);
+            }
+            
         } catch (final ParseException e) {
             throw new RuntimeException(e);
         }
@@ -249,90 +212,21 @@
     }
 
     /**
-     * Run the job to update the information in the run database.
+     * Configure the builder from command line options and run the job to update the database.
      */
     private void run() {
-
-        LOGGER.info("starting");
-
-        final boolean runExists = runManager.runExists();
-
-        // Fail if run exists and updates are not allowed.
-        if (runExists && !allowUpdates) {
-            throw new IllegalStateException("The run " + runManager.getRun()
-                    + " already exists and updates are not allowed.");
-        }
-
-        // Get the run number configured from command line.
-        final int run = runManager.getRun();
-
-        // Get the list of EVIO files for the run using a data catalog query.
-        final Map<File, Dataset> fileDatasets = this.getEvioFiles(run);
-        final List<File> files = new ArrayList<File>(fileDatasets.keySet());
-        EvioFileUtilities.sortBySequence(files);
-
-        // Process the run's files to get information.
-        final RunSummaryImpl runSummary = new RunSummaryImpl(run);
-        final RunProcessor runProcessor = this.createEvioRunProcessor(runSummary, files);
-        try {
-            runProcessor.processRun();
-        } catch (final Exception e) {
-            throw new RuntimeException(e);
-        }
-
-        // Set number of files from datacat query.
-        runSummary.setTotalFiles(files.size());
-
-        // Set run start date.
-        this.setStartDate(fileDatasets, files, runSummary);
-
-        // Set run end date.
-        this.setEndDate(fileDatasets, files, runSummary);
-
-        // Delete existing run.
-        if (runExists) {
-            runManager.deleteRun();
-        }
-
-        // Insert run into database.
-        this.insertRun(runManager, runSummary);
-
-        // Close the database connection.
-        runManager.closeConnection();
-
-        LOGGER.info("done");
-    }
-
-    /**
-     * Set the run end date.
-     *
-     * @param fileDatasets the run's datasets
-     * @param files the run's EVIO files
-     * @param runSummary the run summary
-     */
-    private void setEndDate(final Map<File, Dataset> fileDatasets, final List<File> files,
-            final RunSummaryImpl runSummary) {
-        final Dataset lastDataset = fileDatasets.get(files.get(files.size() - 1));
-        final DatasetMetadata metadata = lastDataset.getMetadata();
-        // System.out.println("endTimestamp: " + metadata.getLong("endTimestamp"));
-        final Date endDate = new Date(metadata.getLong("endTimestamp"));
-        // System.out.println("endDate: " + startDate);
-        runSummary.setEndDate(endDate);
-        runSummary.setEndOkay(metadata.getLong("hasEnd") == 0 ? false : true);
-    }
-
-    /**
-     * Set the run start date.
-     *
-     * @param fileDatasets the run's datasets
-     * @param files the run's EVIO files
-     * @param runSummary the run summary
-     */
-    private void setStartDate(final Map<File, Dataset> fileDatasets, final List<File> files,
-            final RunSummaryImpl runSummary) {
-        final Dataset firstDataset = fileDatasets.get(files.get(0));
-        final DatasetMetadata metadata = firstDataset.getMetadata();
-        final Date startDate = new Date(metadata.getLong("startTimestamp"));
-        runSummary.setStartDate(startDate);
-    }
+        new RunDatabaseBuilder()
+            .createRunSummary(run)
+            .setFolder(folder)
+            .setDetectorName(detectorName)
+            .setConnectionParameters(connectionParameters)
+            .setDatacatClient(datacatClient)
+            .setSite(site)
+            .setDryRun(dryRun)
+            .setReplace(replace)
+            .skipEvioProcessing(skipEvioProcessing)
+            .setSpreadsheetFile(spreadsheetFile)
+            .setReload(reload)
+            .run();
+    }        
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunManager.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunManager.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunManager.java	Wed Apr 27 11:11:32 2016
@@ -6,37 +6,26 @@
 import java.util.logging.Logger;
 
 import org.hps.conditions.database.ConnectionParameters;
+import org.hps.record.daqconfig.DAQConfig;
 import org.hps.record.epics.EpicsData;
 import org.hps.record.scalers.ScalerData;
-import org.hps.record.triggerbank.TriggerConfig;
+import org.hps.record.svt.SvtConfigData;
+import org.hps.record.triggerbank.TriggerConfigData;
 import org.lcsim.conditions.ConditionsEvent;
 import org.lcsim.conditions.ConditionsListener;
 
 /**
- * Manages read-only access to the run database and creates a {@link RunSummary} for a specific run.
+ * Manages access to the run database.
  *
  * @author Jeremy McCormick, SLAC
  */
 public final class RunManager implements ConditionsListener {
 
     /**
-     * Simple class for caching data.
-     */
-    private class DataCache {
-
-        List<EpicsData> epicsData;
-        RunSummary fullRunSummary;
-        Boolean runExists;
-        RunSummary runSummary;
-        List<ScalerData> scalerData;
-        TriggerConfig triggerConfig;
-    }
-
-    /**
      * The default connection parameters for read-only access to the run database.
      */
     private static ConnectionParameters DEFAULT_CONNECTION_PARAMETERS = new ConnectionParameters("hpsuser",
-            "darkphoton", "hps_run_db", "hpsdb.jlab.org");
+            "darkphoton", "hps_run_db_v2", "hpsdb.jlab.org");
 
     /**
      * The singleton instance of the RunManager.
@@ -49,8 +38,7 @@
     private static final Logger LOGGER = Logger.getLogger(RunManager.class.getPackage().getName());
 
     /**
-     * Get the global instance of the {@link RunManager}.
-     *
+     * Get the global instance of the {@link RunManager}.     
      * @return the global instance of the {@link RunManager}
      */
     public static RunManager getRunManager() {
@@ -64,21 +52,11 @@
      * The active database connection.
      */
     private Connection connection;
-
-    /**
-     * The database connection parameters, initially set to the default parameters.
-     */
-    private final ConnectionParameters connectionParameters = DEFAULT_CONNECTION_PARAMETERS;
-
-    /**
-     * The data cache of run information.
-     */
-    private DataCache dataCache;
-
+   
     /**
      * Factory for creating database API objects.
      */
-    private final RunDatabaseDaoFactory factory;
+    private final DaoProvider factory;
 
     /**
      * The run number; the -1 value indicates that this has not been set externally yet.
@@ -86,34 +64,28 @@
     private Integer run = null;
 
     /**
+     * Class constructor.     
+     * @param connection the database connection
+     */
+    public RunManager(final Connection connection) {
+        try {
+            if (connection.isClosed()) {
+                throw new RuntimeException("The connection is already closed and cannot be used.");
+            }
+        } catch (SQLException e) {
+            throw new RuntimeException(e);
+        }
+        this.connection = connection;
+        factory = new DaoProvider(this.connection);
+    }
+    
+    /**
      * Class constructor using default connection parameters.
      */
     public RunManager() {
-        this.connection = DEFAULT_CONNECTION_PARAMETERS.createConnection();
-        this.openConnection();
-        factory = new RunDatabaseDaoFactory(this.connection);
-    }
-
-    /**
-     * Class constructor.
-     *
-     * @param connection the database connection
-     */
-    public RunManager(final Connection connection) {
-        this.connection = connection;
-        this.openConnection();
-        factory = new RunDatabaseDaoFactory(this.connection);
-    }
-
-    /**
-     * Check if the run number has been set.
-     */
-    private void checkRunNumber() {
-        if (this.run == null) {
-            throw new IllegalStateException("The run number was not set.");
-        }
-    }
-
+        this(DEFAULT_CONNECTION_PARAMETERS.createConnection());
+    }
+        
     /**
      * Close the database connection.
      */
@@ -129,7 +101,6 @@
 
     /**
      * Load new run information when conditions have changed.
-     *
      * @param conditionsEvent the event with new conditions information
      */
     @Override
@@ -138,21 +109,7 @@
     }
 
     /**
-     * Delete a run from the database.
-     *
-     * @param run the run number
-     */
-    public void deleteRun() {
-        // Create object for updating run info in the database.
-        final RunSummaryDao runSummaryDao = factory.createRunSummaryDao();
-
-        // Delete run from the database.
-        runSummaryDao.deleteFullRun(run);
-    }
-
-    /**
-     * Return the database connection.
-     *
+     * Return the database connection.     
      * @return the database connection
      */
     Connection getConnection() {
@@ -161,186 +118,159 @@
 
     /**
      * Get the EPICS data for the current run.
-     *
      * @param epicsType the type of EPICS data
      * @return the EPICS data for the current run
      */
     public List<EpicsData> getEpicsData(final EpicsType epicsType) {
-        this.checkRunNumber();
-        if (this.dataCache.epicsData == null) {
-            LOGGER.info("loading EPICS data for run " + this.run);
-            this.dataCache.epicsData = factory.createEpicsDataDao().getEpicsData(epicsType, this.run);
-        }
-        return this.dataCache.epicsData;
-    }
-
-    /**
-     * Get the EPICS variables.
-     *
+        return factory.getEpicsDataDao().getEpicsData(epicsType, this.run);
+    }
+
+    /**
+     * Get the list of EPICS variables definitions.     
      * @param epicsType the type of EPICS data
-     * @return the EPICS data for the current run
+     * @return the list of EPICS variable definitions
      */
     public List<EpicsVariable> getEpicsVariables(final EpicsType epicsType) {
-        return factory.createEpicsVariableDao().getEpicsVariables(epicsType);
-    }
-
-    /**
-     * Get the full run summary for the current run including scaler data, etc.
-     *
-     * @return the full run summary for the current run
-     */
-    public RunSummary getFullRunSummary() {
-        this.checkRunNumber();
-        if (this.dataCache.fullRunSummary == null) {
-            this.dataCache.fullRunSummary = factory.createRunSummaryDao().readFullRunSummary(this.run);
-        }
-        return this.dataCache.fullRunSummary;
-    }
-
-    /**
-     * Get the current run number.
-     *
-     * @return the run number
-     */
-    public int getRun() {
-        return run;
-    }
-
-    /**
-     * Get the complete list of run numbers from the database.
-     *
+        return factory.getEpicsVariableDao().getEpicsVariables(epicsType);
+    }
+
+    /**
+     * Get the full list of run numbers from the database.     
      * @return the complete list of run numbers
      */
     public List<Integer> getRuns() {
-        return new RunSummaryDaoImpl(this.connection).getRuns();
-    }
-
-    /**
-     * Get the full list of summaries for all runs in the database without complex data like EPICS records.
-     *
-     * @return the full list of run summaries
-     */
-    public List<RunSummary> getRunSummaries() {
-        return this.factory.createRunSummaryDao().getRunSummaries();
-    }
-
-    /**
-     * Get the run summary for the current run not including its sub-objects like scaler data.
-     *
+        return factory.getRunSummaryDao().getRuns();
+    }
+  
+    /**
+     * Get the run summary for the current run.     
      * @return the run summary for the current run
      */
     public RunSummary getRunSummary() {
-        this.checkRunNumber();
-        if (this.dataCache.runSummary == null) {
-            this.dataCache.runSummary = factory.createRunSummaryDao().getRunSummary(this.run);
-        }
-        return this.dataCache.runSummary;
-    }
-
-    /**
-     * Get the scaler data for the current run.
-     *
+        return factory.getRunSummaryDao().getRunSummary(this.run);
+    }
+
+    /**
+     * Get the scaler data for the current run.     
      * @return the scaler data for the current run
      */
     public List<ScalerData> getScalerData() {
-        this.checkRunNumber();
-        if (this.dataCache.scalerData == null) {
-            LOGGER.info("loading scaler data for run " + this.run);
-            this.dataCache.scalerData = factory.createScalerDataDao().getScalerData(run);
-        }
-        return this.dataCache.scalerData;
-    }
-
-    /**
-     * Get the trigger config for the current run.
-     *
-     * @return the trigger config for the current run
-     */
-    public TriggerConfig getTriggerConfig() {
-        this.checkRunNumber();
-        if (this.dataCache.triggerConfig == null) {
-            LOGGER.info("loading trigger config for run " + this.run);
-            this.dataCache.triggerConfig = factory.createTriggerConfigDao().getTriggerConfig(run);
-        }
-        return this.dataCache.triggerConfig;
-    }
-
-    /**
-     * Update the database with information found from crawling the files.
-     *
-     * @param runs the list of runs to update
-     * @throws SQLException if there is a database query error
-     */
-    public void insertRun(final RunSummary runSummary) throws SQLException {
-        LOGGER.info("updating run database for run " + runSummary.getRun());
-
-        // Create object for updating run info in the database.
-        final RunSummaryDao runSummaryDao = factory.createRunSummaryDao();
-
-        // Insert run summary into database.
-        runSummaryDao.insertFullRunSummary(runSummary);
-
-        LOGGER.info("done updating run database");
-    }
-
-    /**
-     * Open a new database connection from the connection parameters if the current one is closed or <code>null</code>.
-     * <p>
-     * This method does nothing if the connection is already open.
-     */
-    public void openConnection() {
-        try {
-            if (this.connection.isClosed()) {
-                LOGGER.info("creating new database connection");
-                this.connection = connectionParameters.createConnection();
-            } 
-        } catch (final SQLException e) {
-            throw new RuntimeException("Error opening database connection.", e);
-        }
-    }
+        return factory.getScalerDataDao().getScalerData(this.run);
+    }
+    
+    /**
+     * Get SVT configuration data.     
+     * @return the SVT configuration data
+     */
+    public List<SvtConfigData> getSvtConfigData() {
+        return factory.getSvtConfigDao().getSvtConfigs(this.run);
+    }
+    
+    /**
+     * Get the DAQ (trigger) configuration for the run.
+     * @return the DAQ configuration for the run
+     */
+    public DAQConfig getDAQConfig() {
+        TriggerConfigData config = factory.getTriggerConfigDao().getTriggerConfig(this.run);
+        return config.loadDAQConfig(this.run);
+    }   
 
     /**
      * Return <code>true</code> if the run exists in the database.
-     *
      * @return <code>true</code> if the run exists in the database
      */
-    public boolean runExists() {
-        this.checkRunNumber();
-        if (this.dataCache.runExists == null) {
-            this.dataCache.runExists = factory.createRunSummaryDao().runSummaryExists(this.run);
-        }
-        return this.dataCache.runExists;
-    }
-
-    /**
-     * Return <code>true</code> if the run exists in the database.
-     *
+    public boolean runExists() {      
+        return factory.getRunSummaryDao().runSummaryExists(this.run);
+    }
+
+    /**
+     * Set the run number and then load the applicable {@link RunSummary} from the database.
      * @param run the run number
-     * @return <code>true</code> if the run exists in the database
-     */
-    boolean runExists(final int run) {
-        if (this.dataCache.runExists == null) {
-            this.dataCache.runExists = factory.createRunSummaryDao().runSummaryExists(run);
-        }
-        return this.dataCache.runExists;
-    }
-
-    /**
-     * Set the run number and then load the applicable {@link RunSummary} from the database.
-     *
-     * @param run the run number
      */
     public void setRun(final int run) {
-
         if (this.run == null || run != this.run) {
-
-            LOGGER.info("setting new run " + run);
-
+            LOGGER.info("setting run " + run);
             // Set the run number.
             this.run = run;
-
-            // Reset the data cache.
-            this.dataCache = new DataCache();
-        }
-    }
+        }
+    }
+    
+    /**
+     * Get the currently active run number or <code>null</code>.
+     * @return the currently active run number of <code>null</code>
+     */
+    public Integer getRun() {
+        return this.run;
+    }
+    
+    /**
+     * Create or replace a run summary in the database.
+     * @param runSummary the run summary to update
+     * @param replaceExisting <code>true</code> to allow an existing run summary to be replaced
+     */
+    void updateRunSummary(RunSummary runSummary, boolean replaceExisting) {
+        final RunSummaryDao runSummaryDao = factory.getRunSummaryDao();
+        RunManager runManager = new RunManager();
+        runManager.setRun(runSummary.getRun());
+        if (runManager.runExists()) {
+            if (replaceExisting) {
+                runSummaryDao.updateRunSummary(runSummary);
+            } else {
+                throw new RuntimeException("Run already exists and replacement is not allowed.");
+            }
+        } else {
+            runSummaryDao.insertRunSummary(runSummary);
+        }                
+    }
+    
+    /**
+     * Create or replace the trigger config for the run.
+     * @param triggerConfig the trigger config
+     * @param replaceExisting <code>true</code> to allow an existing trigger to be replaced
+     */
+    void updateTriggerConfig(TriggerConfigData triggerConfig, boolean replaceExisting) {
+        final TriggerConfigDao configDao = factory.getTriggerConfigDao();
+        if (configDao.getTriggerConfig(run) != null) {
+            if (replaceExisting) {
+                configDao.deleteTriggerConfig(run);
+            } else {
+                throw new RuntimeException("Run already exists and replacement is not allowed.");
+            }
+        }
+        configDao.insertTriggerConfig(triggerConfig, run);
+    }
+    
+    /**
+     * Create or replace EPICS data for the run.
+     * @param epicsData the EPICS data
+     */
+    void updateEpicsData(List<EpicsData> epicsData) {
+        if (epicsData != null && !epicsData.isEmpty()) {
+            factory.getEpicsDataDao().insertEpicsData(epicsData, this.run);
+        }
+    }
+    
+    /**
+     * Create or replace scaler data for the run.
+     * @param scalerData the scaler data
+     */
+    void updateScalerData(List<ScalerData> scalerData) {
+        if (scalerData != null) {
+            factory.getScalerDataDao().insertScalerData(scalerData, this.run);
+        } 
+    }     
+    
+    /**
+     * Delete a run from the database.
+     * @param run the run number
+     */
+    void deleteRun() {        
+        factory.getEpicsDataDao().deleteEpicsData(EpicsType.EPICS_2S, run);
+        factory.getEpicsDataDao().deleteEpicsData(EpicsType.EPICS_20S, run);
+        factory.getScalerDataDao().deleteScalerData(run);
+        factory.getSvtConfigDao().deleteSvtConfigs(run);
+        factory.getTriggerConfigDao().deleteTriggerConfig(run);
+        factory.getRunSummaryDao().deleteRunSummary(run);
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummary.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummary.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummary.java	Wed Apr 27 11:11:32 2016
@@ -1,137 +1,129 @@
 package org.hps.run.database;
 
-import java.io.File;
 import java.util.Date;
-import java.util.List;
-
-import org.hps.datacat.client.DatasetFileFormat;
-import org.hps.record.epics.EpicsData;
-import org.hps.record.scalers.ScalerData;
-import org.hps.record.triggerbank.TriggerConfig;
 
 /**
- * This is an API for accessing run summary information which is persisted as a row in the <i>runs</i> table of the run
- * database.
+ * This is an API for accessing run summary information which is persisted as a row in the <i>run_summaries</i> table.
  * <p>
- * This information includes:
- * <ul>
- * <li>run number</li>
- * <li>start date</li>
- * <li>end date</li>
- * <li>number of events</li>
- * <li>number of EVIO files</li>
- * <li>whether the END event was found indicating that the DAQ did not crash</li>
- * <li>whether the run is considered good (all <code>true</code> for now)</li>
- * </ul>
- * <p>
- * It also references several complex objects including lists of {@link org.hps.record.epics.EpicsData} and
- * {@link org.hps.record.scalers.ScalerData} for the run, as well as a list of EVIO files.
+ * All timestamp fields use the Unix convention (seconds since the epoch).
  *
+ * @author Jeremy McCormick, SLAC
  * @see RunSummaryImpl
  * @see RunSummaryDao
  * @see RunSummaryDaoImpl
  * @see RunManager
- * 
- * @author Jeremy McCormick, SLAC
  */
 public interface RunSummary {
-  
+
     /**
-     * Get the creation date of this run record.
+     * Get the creation date of this record.
      *
-     * @return the creation date of this run record
+     * @return the creation date of this record
      */
     Date getCreated();
 
     /**
-     * Get the end date.
-     *
-     * @return the end date
+     * Get the END event timestamp or the timestamp from the last head bank if END is not present.
+     * 
+     * @return the last event timestamp
      */
-    Date getEndDate();
+    Integer getEndTimestamp();
 
     /**
-     * Return <code>true</code> if END event was found in the data.
-     *
-     * @return <code>true</code> if END event was in the data
+     * Get the GO event timestamp.
+     * 
+     * @return the GO event timestamp
      */
-    boolean getEndOkay();
+    Integer getGoTimestamp();
 
     /**
-     * Get the EPICS data from the run.
-     *
-     * @return the EPICS data from the run
+     * Get the livetime computed from the clock scaler.
+     * 
+     * @return the livetime computed from the clock scaler
      */
-    List<EpicsData> getEpicsData();
+    Double getLivetimeClock();
 
     /**
-     * Get the event rate (effectively the trigger rate) which is the total events divided by the number of seconds in
-     * the run.
-     *
-     * @return the event rate
+     * Get the livetime computed from the FCUP_TDC scaler.
+     * 
+     * @return the livetime computed from the FCUP_TDC scaler
      */
-    double getEventRate();
+    Double getLivetimeFcupTdc();
+
+    /**
+     * Get the livetime computed from the FCUP_TRG scaler.
+     * 
+     * @return the livetime computed from the FCUP_TRG scaler
+     */
+    Double getLivetimeFcupTrg();
+
+    /**
+     * Get the notes for the run (from the run spreadsheet).
+     * 
+     * @return the notes for the run
+     */
+    String getNotes();
+
+    /**
+     * Get the PRESTART event timestamp.
+     * 
+     * @return the PRESTART event timestamp
+     */
+    Integer getPrestartTimestamp();
 
     /**
      * Get the run number.
      *
      * @return the run number
      */
-    int getRun();
+    Integer getRun();
+   
+    /**
+     * Get the target setting for the run (string from run spreadsheet).
+     * 
+     * @return the target setting for the run
+     */
+    String getTarget();
 
     /**
-     * Return <code>true</code> if the run was okay (no major errors or data corruption occurred).
-     *
-     * @return <code>true</code> if the run was okay
+     * Get the TI time offset in ns.
+     * 
+     * @return the TI time offset in ns
      */
-    boolean getRunOkay();
+    Long getTiTimeOffset();
 
     /**
-     * Get the scaler data of this run.
+     * Get the total number of events in the run.
      *
-     * @return the scaler data of this run
+     * @return the total number of events in the run
      */
-    List<ScalerData> getScalerData();
+    Long getTotalEvents();
 
     /**
-     * Get the trigger config int values.
+     * Get the total number of EVIO files in this run.
      *
-     * @return the trigger config int values
+     * @return the total number of files in this run
      */
-    TriggerConfig getTriggerConfig();
+    Integer getTotalFiles();
 
     /**
-     * Get the start date.
-     *
-     * @return the start date
+     * Get the trigger config name (from the run spreadsheet).
+     * 
+     * @return the trigger config name
      */
-    Date getStartDate();
+    String getTriggerConfigName();
 
     /**
-     * Get the total events in the run.
-     *
-     * @return the total events in the run
+     * Get the trigger rate in KHz.
+     * 
+     * @return the trigger rate in KHz
      */
-    int getTotalEvents();
+    Double getTriggerRate();
 
     /**
-     * Get the total number of EVIO files for this run.
+     * Get the date when this record was last updated.
      *
-     * @return the total number of files for this run
-     */
-    int getTotalFiles();
-
-    /**
-     * Get the number of seconds in the run which is the difference between the start and end times.
-     *
-     * @return the total seconds in the run
-     */
-    long getTotalSeconds();
-
-    /**
-     * Get the date when this run record was last updated.
-     *
-     * @return the date when this run record was last updated
+     * @return the date when this record was last updated
      */
     Date getUpdated();
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDao.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDao.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDao.java	Wed Apr 27 11:11:32 2016
@@ -8,14 +8,7 @@
  * @author Jeremy McCormick, SLAC
  */
 interface RunSummaryDao {
-
-    /**
-     * Delete a run summary from the database including its referenced objects such as EPICS data.
-     *
-     * @param runSummary the run summary to delete
-     */
-    void deleteFullRun(int run);
-
+  
     /**
      * Delete a run summary by run number.
      *
@@ -24,26 +17,12 @@
     void deleteRunSummary(int run);
 
     /**
-     * Delete a run summary but not its objects.
-     *
-     * @param runSummary the run summary object
-     */
-    void deleteRunSummary(RunSummary runSummary);
-
-    /**
      * Get the list of run numbers.
      *
      * @return the list of run numbers
      */
     List<Integer> getRuns();
-
-    /**
-     * Get a list of run summaries without loading their objects such as EPICS data.
-     *
-     * @return the list of run summaries
-     */
-    List<RunSummary> getRunSummaries();
-
+  
     /**
      * Get a run summary by run number without loading object state.
      *
@@ -51,36 +30,13 @@
      * @return the run summary object
      */
     RunSummary getRunSummary(int run);
-
+  
     /**
-     * Insert a list of run summaries along with its referenced objects such as scaler and EPICS data.
-     *
-     * @param runSummaryList the list of run summaries
-     * @param deleteExisting <code>true</code> to allow deletion and replacement of existing run summaries
-     */
-    void insertFullRunSummaries(List<RunSummary> runSummaryList, boolean deleteExisting);
-
-    /**
-     * Insert a run summary including all its objects.
-     *
-     * @param runSummary the run summary object
-     */
-    void insertFullRunSummary(RunSummary runSummary);
-
-    /**
-     * Insert a run summary but not its objects.
+     * Insert a run summary.
      *
      * @param runSummary the run summary object
      */
     void insertRunSummary(RunSummary runSummary);
-
-    /**
-     * Read a run summary and its objects such as scaler data.
-     *
-     * @param run the run number
-     * @return the full run summary
-     */
-    RunSummary readFullRunSummary(int run);
 
     /**
      * Return <code>true</code> if a run summary exists in the database.
@@ -89,10 +45,10 @@
      * @return <code>true</code> if <code>run</code> exists in the database
      */
     boolean runSummaryExists(int run);
-
+    
     /**
-     * Update a run summary but not its objects.
-     *
+     * Update a run summary that already exists.
+     * 
      * @param runSummary the run summary to update
      */
     void updateRunSummary(RunSummary runSummary);

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDaoImpl.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDaoImpl.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryDaoImpl.java	Wed Apr 27 11:11:32 2016
@@ -5,13 +5,8 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.GregorianCalendar;
 import java.util.List;
-import java.util.TimeZone;
 import java.util.logging.Logger;
-
-import org.hps.record.epics.EpicsData;
 
 /**
  * Implementation of database operations for {@link RunSummary} objects in the run database.
@@ -21,37 +16,29 @@
 final class RunSummaryDaoImpl implements RunSummaryDao {
 
     /**
-     * SQL query strings.
-     */
-    private static final class RunSummaryQuery {
-
-        /**
-         * Delete by run number.
-         */
-        private static final String DELETE_RUN = "DELETE FROM runs WHERE run = ?";
-        /**
-         * Insert a record for a run.
-         */
-        private static final String INSERT = "INSERT INTO runs (run, start_date, end_date, nevents, nfiles, end_ok, created) VALUES(?, ?, ?, ?, ?, ?, NOW())";
-        /**
-         * Select all records.
-         */
-        private static final String SELECT_ALL = "SELECT * from runs";
-        /**
-         * Select record by run number.
-         */
-        private static final String SELECT_RUN = "SELECT run, start_date, end_date, nevents, nfiles, end_ok, run_ok, updated, created FROM runs WHERE run = ?";
-        /**
-         * Update information for a run.
-         */
-        private static final String UPDATE_RUN = "UPDATE runs SET start_date, end_date, nevents, nfiles, end_ok, run_ok WHERE run = ?";
-    }
-
-    /**
-     * Eastern time zone.
-     */
-    private static Calendar CALENDAR = new GregorianCalendar(TimeZone.getTimeZone("America/New_York"));
-
+     * Delete by run number.
+     */
+    private static final String DELETE = "DELETE FROM run_summaries WHERE run = ?";
+        
+    /**
+     * Insert a record for a run.
+     */
+    private static final String INSERT = "INSERT INTO run_summaries (run, nevents, nfiles, prestart_timestamp,"
+            + " go_timestamp, end_timestamp, trigger_rate, trigger_config_name, ti_time_offset," 
+            + " livetime_clock, livetime_fcup_tdc, livetime_fcup_trg, target, notes, created, updated)"
+            + " VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, NOW(), NOW())";
+    
+    private static final String UPDATE = "UPDATE run_summaries SET nevents = ?, nfiles = ?, prestart_timestamp = ?,"
+            + " go_timestamp = ?, end_timestamp = ?, trigger_rate = ?, trigger_config_name = ?, ti_time_offset = ?," 
+            + " livetime_clock = ?, livetime_fcup_tdc = ?, livetime_fcup_trg = ?, target = ?, notes = ?, updated = NOW()"
+            + " WHERE run = ?";
+    
+                     
+    /**
+     * Select record by run number.
+     */
+    private static final String SELECT = "SELECT * FROM run_summaries WHERE run = ?";
+           
     /**
      * Initialize the logger.
      */
@@ -61,60 +48,17 @@
      * The database connection.
      */
     private final Connection connection;
-
-    /**
-     * The database API for EPICS data.
-     */
-    private EpicsDataDao epicsDataDao = null;
-
-    /**
-     * The database API for scaler data.
-     */
-    private ScalerDataDao scalerDataDao = null;
-
-    /**
-     * The database API for integer trigger config.
-     */
-    private TriggerConfigDao triggerConfigIntDao = null;
-
+  
     /**
      * Create a new DAO object for run summary information.
      *
      * @param connection the database connection
      */
     RunSummaryDaoImpl(final Connection connection) {
-        // Set the connection.
         if (connection == null) {
             throw new IllegalArgumentException("The connection is null.");
         }
         this.connection = connection;
-
-        // Setup DAO API objects for managing complex object state.
-        epicsDataDao = new EpicsDataDaoImpl(this.connection);
-        scalerDataDao = new ScalerDataDaoImpl(this.connection);
-        triggerConfigIntDao = new TriggerConfigDaoImpl(this.connection);
-    }
-
-    /**
-     * Delete a run from the database including its referenced objects such as EPICS data.
-     *
-     * @param runSummary the run summary to delete
-     */
-    @Override
-    public void deleteFullRun(int run) {
-
-        // Delete EPICS log.
-        this.epicsDataDao.deleteEpicsData(EpicsType.EPICS_1S, run);
-        this.epicsDataDao.deleteEpicsData(EpicsType.EPICS_10S, run);
-
-        // Delete scaler data.
-        this.scalerDataDao.deleteScalerData(run);
-
-        // Delete trigger config.
-        this.triggerConfigIntDao.deleteTriggerConfigInt(run);
-
-        // Finally delete the run summary information.
-        this.deleteRunSummary(run);
     }
 
     /**
@@ -126,7 +70,7 @@
     public void deleteRunSummary(final int run) {
         PreparedStatement preparedStatement = null;
         try {
-            preparedStatement = connection.prepareStatement(RunSummaryQuery.DELETE_RUN);
+            preparedStatement = connection.prepareStatement(DELETE);
             preparedStatement.setInt(1, run);
             preparedStatement.executeUpdate();
         } catch (final SQLException e) {
@@ -141,32 +85,7 @@
             }
         }
     }
-
-    /**
-     * Delete a run summary but not its objects.
-     *
-     * @param runSummary the run summary object
-     */
-    @Override
-    public void deleteRunSummary(final RunSummary runSummary) {
-        PreparedStatement preparedStatement = null;
-        try {
-            preparedStatement = connection.prepareStatement(RunSummaryQuery.DELETE_RUN);
-            preparedStatement.setInt(1, runSummary.getRun());
-            preparedStatement.executeUpdate();
-        } catch (final SQLException e) {
-            throw new RuntimeException(e);
-        } finally {
-            if (preparedStatement != null) {
-                try {
-                    preparedStatement.close();
-                } catch (final SQLException e) {
-                    e.printStackTrace();
-                }
-            }
-        }
-    }
-
+   
     /**
      * Get the list of run numbers.
      *
@@ -177,7 +96,7 @@
         final List<Integer> runs = new ArrayList<Integer>();
         PreparedStatement preparedStatement = null;
         try {
-            preparedStatement = this.connection.prepareStatement("SELECT distinct(run) FROM runs ORDER BY run");
+            preparedStatement = this.connection.prepareStatement("SELECT distinct(run) FROM run_summaries ORDER BY run");
             final ResultSet resultSet = preparedStatement.executeQuery();
             while (resultSet.next()) {
                 final Integer run = resultSet.getInt(1);
@@ -196,47 +115,9 @@
         }
         return runs;
     }
-
-    /**
-     * Get a list of run summaries without loading their objects such as EPICS data.
-     *
-     * @return the list of run summaries
-     */
-    @Override
-    public List<RunSummary> getRunSummaries() {
-        PreparedStatement statement = null;
-        final List<RunSummary> runSummaries = new ArrayList<RunSummary>();
-        try {
-            statement = this.connection.prepareStatement(RunSummaryQuery.SELECT_ALL);
-            final ResultSet resultSet = statement.executeQuery();
-            while (resultSet.next()) {
-                final RunSummaryImpl runSummary = new RunSummaryImpl(resultSet.getInt("run"));
-                runSummary.setStartDate(resultSet.getTimestamp("start_date"));
-                runSummary.setEndDate(resultSet.getTimestamp("end_date"));
-                runSummary.setTotalEvents(resultSet.getInt("nevents"));
-                runSummary.setTotalFiles(resultSet.getInt("nfiles"));
-                runSummary.setEndOkay(resultSet.getBoolean("end_ok"));
-                runSummary.setRunOkay(resultSet.getBoolean("run_ok"));
-                runSummary.setUpdated(resultSet.getTimestamp("updated"));
-                runSummary.setCreated(resultSet.getTimestamp("created"));
-                runSummaries.add(runSummary);
-            }
-        } catch (final SQLException e) {
-            throw new RuntimeException(e);
-        } finally {
-            if (statement != null) {
-                try {
-                    statement.close();
-                } catch (final SQLException e) {
-                    e.printStackTrace();
-                }
-            }
-        }
-        return runSummaries;
-    }
-
-    /**
-     * Get a run summary by run number without loading object state.
+   
+    /**
+     * Get a run summary.
      *
      * @param run the run number
      * @return the run summary object
@@ -246,22 +127,28 @@
         PreparedStatement statement = null;
         RunSummaryImpl runSummary = null;
         try {
-            statement = this.connection.prepareStatement(RunSummaryQuery.SELECT_RUN);
+            statement = this.connection.prepareStatement(SELECT);
             statement.setInt(1, run);
             final ResultSet resultSet = statement.executeQuery();
             if (!resultSet.next()) {
-                throw new IllegalArgumentException("No record exists for run " + run + " in database.");
-            }
-
+                throw new IllegalArgumentException("Run " + run + " does not exist in database.");
+            }
             runSummary = new RunSummaryImpl(run);
-            runSummary.setStartDate(resultSet.getTimestamp("start_date"));
-            runSummary.setEndDate(resultSet.getTimestamp("end_date"));
-            runSummary.setTotalEvents(resultSet.getInt("nevents"));
+            runSummary.setTotalEvents(resultSet.getLong("nevents"));
             runSummary.setTotalFiles(resultSet.getInt("nfiles"));
-            runSummary.setEndOkay(resultSet.getBoolean("end_ok"));
-            runSummary.setRunOkay(resultSet.getBoolean("run_ok"));
+            runSummary.setPrestartTimestamp(resultSet.getInt("prestart_timestamp"));
+            runSummary.setGoTimestamp(resultSet.getInt("go_timestamp"));
+            runSummary.setEndTimestamp(resultSet.getInt("end_timestamp"));
+            runSummary.setTriggerRate(resultSet.getDouble("trigger_rate"));
+            runSummary.setTriggerConfigName(resultSet.getString("trigger_config_name"));
+            runSummary.setTiTimeOffset(resultSet.getLong("ti_time_offset"));
+            runSummary.setLivetimeClock(resultSet.getDouble("livetime_clock"));
+            runSummary.setLivetimeFcupTdc(resultSet.getDouble("livetime_fcup_tdc"));
+            runSummary.setLivetimeFcupTrg(resultSet.getDouble("livetime_fcup_trg"));
+            runSummary.setTarget(resultSet.getString("target"));
+            runSummary.setNotes(resultSet.getString("notes"));
+            runSummary.setCreated(resultSet.getTimestamp("created"));
             runSummary.setUpdated(resultSet.getTimestamp("updated"));
-            runSummary.setCreated(resultSet.getTimestamp("created"));
         } catch (final SQLException e) {
             throw new RuntimeException(e);
         } finally {
@@ -275,129 +162,9 @@
         }
         return runSummary;
     }
-
-    /**
-     * Insert a list of run summaries along with their complex state such as referenced scaler and EPICS data.
-     *
-     * @param runSummaryList the list of run summaries
-     * @param deleteExisting <code>true</code> to allow deletion and replacement of existing run summaries
-     */
-    @Override
-    public void insertFullRunSummaries(final List<RunSummary> runSummaryList, final boolean deleteExisting) {
-
-        if (runSummaryList == null) {
-            throw new IllegalArgumentException("The run summary list is null.");
-        }
-        if (runSummaryList.isEmpty()) {
-            throw new IllegalArgumentException("The run summary list is empty.");
-        }
-
-        LOGGER.info("inserting " + runSummaryList.size() + " run summaries into database");
-
-        // Turn off auto commit.
-        try {
-            LOGGER.info("turning off auto commit");
-            this.connection.setAutoCommit(false);
-        } catch (final SQLException e) {
-            throw new RuntimeException(e);
-        }
-
-        // Loop over all runs found while crawling.
-        for (final RunSummary runSummary : runSummaryList) {
-
-            final int run = runSummary.getRun();
-
-            LOGGER.info("inserting run summary for run " + run + " into database");
-
-            // Does the run exist in the database already?
-            if (this.runSummaryExists(run)) {
-                // Is deleting existing rows allowed?
-                if (deleteExisting) {
-                    LOGGER.info("deleting existing run summary");
-                    // Delete the existing rows.
-                    this.deleteFullRun(runSummary.getRun());
-                } else {
-                    // Rows exist but updating is disallowed which is a fatal error.
-                    throw new IllegalStateException("Run " + runSummary.getRun()
-                            + " already exists and updates are disallowed.");
-                }
-            }
-
-            // Insert full run summary information including sub-objects.
-            LOGGER.info("inserting run summary");
-            this.insertFullRunSummary(runSummary);
-            LOGGER.info("run summary for " + run + " inserted successfully");
-
-            try {
-                // Commit the transaction for the run.
-                LOGGER.info("committing transaction");
-                this.connection.commit();
-            } catch (final SQLException e1) {
-                try {
-                    LOGGER.severe("rolling back transaction");
-                    // Rollback the transaction if there was an error.
-                    this.connection.rollback();
-                } catch (final SQLException e2) {
-                    throw new RuntimeException(e2);
-                }
-            }
-
-            LOGGER.info("done inserting run summary " + run);
-        }
-
-        try {
-            LOGGER.info("turning auto commit on");
-            // Turn auto commit back on.
-            this.connection.setAutoCommit(true);
-        } catch (final SQLException e) {
-            e.printStackTrace();
-        }
-
-        LOGGER.info("done inserting run summaries");
-    }
-
-    /**
-     * Insert a run summary including all its objects.
-     *
-     * @param runSummary the run summary object to insert
-     */
-    @Override
-    public void insertFullRunSummary(final RunSummary runSummary) {
-
-        if (runSummary == null) {
-            throw new IllegalArgumentException("The run summary is null.");
-        }
-        
-        // Insert basic run log info.
-        this.insertRunSummary(runSummary);
-
-        // Insert EPICS data.
-        if (runSummary.getEpicsData() != null && !runSummary.getEpicsData().isEmpty()) {
-            LOGGER.info("inserting " + runSummary.getEpicsData().size() + " EPICS records");
-            epicsDataDao.insertEpicsData(runSummary.getEpicsData());
-        } else {
-            LOGGER.warning("no EPICS data to insert");
-        }
-
-        // Insert scaler data.
-        if (runSummary.getScalerData() != null && !runSummary.getScalerData().isEmpty()) {
-            LOGGER.info("inserting " + runSummary.getScalerData().size() + " scaler data records");
-            scalerDataDao.insertScalerData(runSummary.getScalerData(), runSummary.getRun());
-        } else {
-            LOGGER.warning("no scaler data to insert");
-        }
-
-        // Insert trigger config.
-        if (runSummary.getTriggerConfig() != null && !runSummary.getTriggerConfig().isEmpty()) {
-            LOGGER.info("inserting " + runSummary.getTriggerConfig().size() + " trigger config variables");
-            triggerConfigIntDao.insertTriggerConfig(runSummary.getTriggerConfig(), runSummary.getRun());
-        } else {
-            LOGGER.warning("no trigger config to insert");
-        }
-    }
-
-    /**
-     * Insert a run summary but not its objects.
+      
+    /**
+     * Insert a run summary.
      *
      * @param runSummary the run summary object
      */
@@ -405,13 +172,23 @@
     public void insertRunSummary(final RunSummary runSummary) {
         PreparedStatement preparedStatement = null;
         try {
-            preparedStatement = connection.prepareStatement(RunSummaryQuery.INSERT);
+            preparedStatement = connection.prepareStatement(INSERT);                       
             preparedStatement.setInt(1, runSummary.getRun());
-            preparedStatement.setTimestamp(2, new java.sql.Timestamp(runSummary.getStartDate().getTime()), CALENDAR);
-            preparedStatement.setTimestamp(3, new java.sql.Timestamp(runSummary.getEndDate().getTime()), CALENDAR);
-            preparedStatement.setInt(4, runSummary.getTotalEvents());
-            preparedStatement.setInt(5, runSummary.getTotalFiles());
-            preparedStatement.setBoolean(6, runSummary.getEndOkay());
+            preparedStatement.setLong(2, runSummary.getTotalEvents());
+            preparedStatement.setInt(3, runSummary.getTotalFiles());
+            /* Use setObject on the rest as they may be null. */
+            preparedStatement.setObject(4, runSummary.getPrestartTimestamp());
+            preparedStatement.setObject(5, runSummary.getGoTimestamp());
+            preparedStatement.setObject(6, runSummary.getEndTimestamp());
+            preparedStatement.setObject(7, runSummary.getTriggerRate());
+            preparedStatement.setObject(8, runSummary.getTriggerConfigName());
+            preparedStatement.setObject(9, runSummary.getTiTimeOffset());
+            preparedStatement.setObject(10, runSummary.getLivetimeClock());
+            preparedStatement.setObject(11, runSummary.getLivetimeFcupTdc());
+            preparedStatement.setObject(12, runSummary.getLivetimeFcupTrg());
+            preparedStatement.setObject(13, runSummary.getTarget());
+            preparedStatement.setObject(14, runSummary.getNotes());
+            LOGGER.fine(preparedStatement.toString());
             preparedStatement.executeUpdate();
         } catch (final SQLException e) {
             throw new RuntimeException(e);
@@ -425,34 +202,42 @@
             }
         }
     }
-
-    /**
-     * Read a run summary and its objects such as scaler data.
-     *
-     * @param run the run number
-     * @return the full run summary
-     */
-    @Override
-    public RunSummary readFullRunSummary(final int run) {
-
-        // Read main run summary but not referenced objects.
-        final RunSummaryImpl runSummary = (RunSummaryImpl) this.getRunSummary(run);
-
-        // Read EPICS data and set on RunSummary.
-        final List<EpicsData> epicsDataList = new ArrayList<EpicsData>();
-        epicsDataList.addAll(epicsDataDao.getEpicsData(EpicsType.EPICS_1S, run));
-        epicsDataList.addAll(epicsDataDao.getEpicsData(EpicsType.EPICS_10S, run));
-        runSummary.setEpicsData(epicsDataList);
-
-        // Read scaler data and set on RunSummary.
-        runSummary.setScalerData(scalerDataDao.getScalerData(run));
-
-        // Read trigger config.
-        runSummary.setTriggerConfig(triggerConfigIntDao.getTriggerConfig(run));
-
-        return runSummary;
-    }
-
+    
+    @Override
+    public void updateRunSummary(RunSummary runSummary) {
+        PreparedStatement preparedStatement = null;
+        try {
+            preparedStatement = connection.prepareStatement(UPDATE);                                   
+            preparedStatement.setLong(1, runSummary.getTotalEvents());
+            preparedStatement.setInt(2, runSummary.getTotalFiles());
+            preparedStatement.setObject(3, runSummary.getPrestartTimestamp());
+            preparedStatement.setObject(4, runSummary.getGoTimestamp());
+            preparedStatement.setObject(5, runSummary.getEndTimestamp());
+            preparedStatement.setObject(6, runSummary.getTriggerRate());
+            preparedStatement.setObject(7, runSummary.getTriggerConfigName());
+            preparedStatement.setObject(8, runSummary.getTiTimeOffset());
+            preparedStatement.setObject(9, runSummary.getLivetimeClock());
+            preparedStatement.setObject(10, runSummary.getLivetimeFcupTdc());
+            preparedStatement.setObject(11, runSummary.getLivetimeFcupTrg());
+            preparedStatement.setObject(12, runSummary.getTarget());
+            preparedStatement.setObject(13, runSummary.getNotes());
+            preparedStatement.setInt(14, runSummary.getRun());
+            LOGGER.fine(preparedStatement.toString());
+            preparedStatement.executeUpdate();
+        } catch (final SQLException e) {
+            throw new RuntimeException(e);
+        } finally {
+            if (preparedStatement != null) {
+                try {
+                    preparedStatement.close();
+                } catch (final SQLException e) {
+                    e.printStackTrace();
+                }
+            }
+        }
+    }
+    
+   
     /**
      * Return <code>true</code> if a run summary exists in the database for the run number.
      *
@@ -463,7 +248,7 @@
     public boolean runSummaryExists(final int run) {
         PreparedStatement preparedStatement = null;
         try {
-            preparedStatement = connection.prepareStatement("SELECT run FROM runs where run = ?");
+            preparedStatement = connection.prepareStatement("SELECT run FROM run_summaries where run = ?");
             preparedStatement.setInt(1, run);
             final ResultSet rs = preparedStatement.executeQuery();
             return rs.first();
@@ -479,35 +264,4 @@
             }
         }
     }
-
-    /**
-     * Update a run summary but not its complex state.
-     *
-     * @param runSummary the run summary to update
-     */
-    @Override
-    public void updateRunSummary(final RunSummary runSummary) {
-        PreparedStatement preparedStatement = null;
-        try {
-            preparedStatement = connection.prepareStatement(RunSummaryQuery.UPDATE_RUN);
-            preparedStatement.setTimestamp(1, new java.sql.Timestamp(runSummary.getStartDate().getTime()), CALENDAR);
-            preparedStatement.setTimestamp(2, new java.sql.Timestamp(runSummary.getEndDate().getTime()), CALENDAR);
-            preparedStatement.setInt(3, runSummary.getTotalEvents());
-            preparedStatement.setInt(4, runSummary.getTotalFiles());
-            preparedStatement.setBoolean(5, runSummary.getEndOkay());
-            preparedStatement.setBoolean(6, runSummary.getRunOkay());
-            preparedStatement.setInt(7, runSummary.getRun());
-            preparedStatement.executeUpdate();
-        } catch (final SQLException e) {
-            throw new RuntimeException(e);
-        } finally {
-            if (preparedStatement != null) {
-                try {
-                    preparedStatement.close();
-                } catch (final SQLException e) {
-                    e.printStackTrace();
-                }
-            }
-        }
-    }
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryImpl.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryImpl.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/RunSummaryImpl.java	Wed Apr 27 11:11:32 2016
@@ -1,40 +1,13 @@
 package org.hps.run.database;
 
-import java.io.File;
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
 import java.util.Date;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TimeZone;
-
-import org.hps.datacat.client.DatasetFileFormat;
-import org.hps.record.epics.EpicsData;
-import org.hps.record.scalers.ScalerData;
-import org.hps.record.triggerbank.TriggerConfig;
 
 /**
  * Implementation of {@link RunSummary} for retrieving information from the run database.
  *
  * @author Jeremy McCormick, SLAC
  */
-public final class RunSummaryImpl implements RunSummary {
-
-    /**
-     * Default date display format.
-     */
-    private static final DateFormat DATE_DISPLAY = new SimpleDateFormat();
-
-    static {
-        /**
-         * Set default time zone for display to East Coast (JLAB) where data was
-         * taken.
-         */
-        DATE_DISPLAY.setCalendar(new GregorianCalendar(TimeZone.getTimeZone("America/New_York")));
-    }
+final class RunSummaryImpl implements RunSummary {
 
     /**
      * Date this record was created.
@@ -42,60 +15,80 @@
     private Date created;
 
     /**
-     * End date of run.
-     */
-    private Date endDate;
-
-    /**
-     * This is <code>true</code> if the END event is found in the data.
-     */
-    private boolean endOkay;
-
-    /**
-     * The EPICS data from the run.
-     */
-    private List<EpicsData> epicsDataList;
+     * Timestamp of END event.
+     */
+    private Integer endTimestamp;
+
+    /**
+     * Timestamp of GO event.
+     */
+    private Integer goTimestamp;
+
+    /**
+     * Clock livetime calculation.
+     */
+    private Double livetimeClock;
+
+    /**
+     * FCup TDC livetime calculation.
+     */
+    private Double livetimeTdc;
+
+    /**
+     * FCup TRG livetime calculation.
+     */
+    private Double livetimeTrg;
+
+    /**
+     * Notes about the run (from spreadsheet).
+     */
+    private String notes;
+
+    /**
+     * Timestamp of PRESTART event.
+     */
+    private Integer prestartTimestamp;
 
     /**
      * The run number.
      */
-    private final int run;
-
-    /**
-     * Flag to indicate run was okay.
-     */
-    private boolean runOkay = true;
-
-    /**
-     * The scaler data for the run.
-     */
-    private List<ScalerData> scalerDataList;
-
-    /**
-     * The trigger data for the run.
-     */
-    private TriggerConfig triggerConfig;
-
-    /**
-     * Start date of run.
-     */
-    private Date startDate;
+    private final Integer run;
+
+    /**
+     * Target setup (string from run spreadsheet).
+     */
+    private String target;
+
+    /**
+     * TI time offset in ns.
+     */
+    private Long tiTimeOffset;
 
     /**
      * The total events found in the run across all files.
      */
-    private int totalEvents = -1;
+    private Long totalEvents;
 
     /**
      * The total number of files in the run.
      */
-    private int totalFiles = 0;
+    private Integer totalFiles;
+   
+    /**
+     * Name of the trigger config file.
+     */
+    private String triggerConfigName;
+
+    /**
+     * Trigger rate in KHz.
+     */
+    private double triggerRate;
 
     /**
      * Date when the run record was last updated.
      */
     private Date updated;
-    
+
     /**
      * Create a run summary.
      *
@@ -105,209 +98,174 @@
         this.run = run;
     }
 
-    /**
-     * Get the creation date of this run record.
-     *
-     * @return the creation date of this run record
-     */
+    @Override
     public Date getCreated() {
         return this.created;
     }
 
-    /**
-     * Get the end date.
-     *
-     * @return the end date
-     */
-    public Date getEndDate() {
-        return endDate;
-    }
-
-    /**
-     * Return <code>true</code> if END event was found in the data.
-     *
-     * @return <code>true</code> if END event was in the data
-     */
-    public boolean getEndOkay() {
-        return this.endOkay;
-    }
-
-    /**
-     * Get the EPICS data from the run.
-     *
-     * @return the EPICS data from the run
-     */
-    public List<EpicsData> getEpicsData() {
-        return this.epicsDataList;
-    }
-
-    /**
-     * Get the event rate (effectively the trigger rate) which is the total
-     * events divided by the number of seconds in the run.
-     *
-     * @return the event rate
-     */
-    public double getEventRate() {
-        if (this.getTotalEvents() <= 0) {
-            throw new RuntimeException("Total events is zero or invalid.");
-        }
-        return (double) this.getTotalEvents() / (double) this.getTotalSeconds();
-    }
-
-    /**
-     * Get the run number.
-     *
-     * @return the run number
-     */
-    public int getRun() {
+    @Override
+    public Integer getEndTimestamp() {
+        return endTimestamp;
+    }
+
+    @Override
+    public Integer getGoTimestamp() {
+        return goTimestamp;
+    }
+
+    @Override
+    public Double getLivetimeClock() {
+        return this.livetimeClock;
+    }
+
+    @Override
+    public Double getLivetimeFcupTdc() {
+        return this.livetimeTdc;
+    }
+
+    @Override
+    public Double getLivetimeFcupTrg() {
+        return this.livetimeTrg;
+    }
+
+    @Override
+    public String getNotes() {
+        return this.notes;
+    }
+
+    @Override
+    public Integer getPrestartTimestamp() {
+        return prestartTimestamp;
+    }
+
+    @Override
+    public Integer getRun() {
         return this.run;
     }
 
-    /**
-     * Return <code>true</code> if the run was okay (no major errors or data
-     * corruption occurred).
-     *
-     * @return <code>true</code> if the run was okay
-     */
-    public boolean getRunOkay() {
-        return this.runOkay;
-    }
-
-    /**
-     * Get the scaler data of this run.
-     *
-     * @return the scaler data of this run
-     */
-    public List<ScalerData> getScalerData() {
-        return this.scalerDataList;
-    }
-
-    /**
-     * Get the trigger config of this run.
-     *
-     * @return the trigger config of this run
-     */
-    public TriggerConfig getTriggerConfig() {
-        return triggerConfig;
-    }
-
-    /**
-     * Get the start date.
-     *
-     * @return the start date
-     */
-    public Date getStartDate() {
-        return startDate;
-    }
-
-    /**
-     * Get the total events in the run.
-     *
-     * @return the total events in the run
-     */
-    public int getTotalEvents() {
+    @Override
+    public String getTarget() {
+        return this.target;
+    }
+
+    @Override
+    public Long getTiTimeOffset() {
+        return this.tiTimeOffset;
+    }
+
+    @Override
+    public Long getTotalEvents() {
         return this.totalEvents;
     }
 
-    /**
-     * Get the total number of files for this run.
-     *
-     * @return the total number of files for this run
-     */
-    public int getTotalFiles() {
+    @Override
+    public Integer getTotalFiles() {
         return this.totalFiles;
     }
-
-    /**
-     * Get the number of seconds in the run which is the difference between the
-     * start and end times.
-     *
-     * @return the total seconds in the run
-     */
-    public long getTotalSeconds() {
-        return (endDate.getTime() - startDate.getTime()) / 1000;
-    }
-
-    /**
-     * Get the date when this run record was last updated.
-     *
-     * @return the date when this run record was last updated
-     */
+   
+    @Override
+    public String getTriggerConfigName() {
+        return this.triggerConfigName;
+    }
+
+    @Override
+    public Double getTriggerRate() {
+        return this.triggerRate;
+    }
+
+    @Override
     public Date getUpdated() {
         return updated;
     }
-    
-    /**
-     * Set the creation date of the run record.
-     *
-     * @param created the creation date of the run record
-     */
-    void setCreated(final Date created) {
+
+    /**
+     * Set the creation date of the run summary.
+     * 
+     * @param created the creation date
+     */
+    void setCreated(Date created) {
         this.created = created;
     }
 
     /**
-     * Set the start date.
-     *
-     * @param startDate the start date
-     */
-    void setEndDate(final Date endDate) {
-        this.endDate = endDate;
-    }
-
-    /**
-     * Set if end is okay.
-     *
-     * @param endOkay <code>true</code> if end is okay
-     */
-    void setEndOkay(final boolean endOkay) {
-        this.endOkay = endOkay;
-    }
-   
-    /**
-     * Set the EPICS data for the run.
-     *
-     * @param epics the EPICS data for the run
-     */
-    void setEpicsData(final List<EpicsData> epicsDataList) {
-        this.epicsDataList = epicsDataList;
-    }
-    
-    /**
-     * Set whether the run was "okay" meaning the data is usable for physics
-     * analysis.
-     *
-     * @param runOkay <code>true</code> if the run is okay
-     */
-    void setRunOkay(final boolean runOkay) {
-        this.runOkay = runOkay;
-    }
-
-    /**
-     * Set the scaler data of the run.
-     *
-     * @param scalerData the scaler data
-     */
-    void setScalerData(final List<ScalerData> scalerDataList) {
-        this.scalerDataList = scalerDataList;
-    }
-
-    /**
-     * Set the trigger config of the run.
-     *
-     * @param triggerConfig the trigger config
-     */
-    void setTriggerConfig(final TriggerConfig triggerConfig) {
-        this.triggerConfig = triggerConfig;
-    }
-
-    /**
-     * Set the start date.
-     *
-     * @param startDate the start date
-     */
-    void setStartDate(final Date startDate) {
-        this.startDate = startDate;
+     * Set the end timestamp.
+     * 
+     * @param endTimestamp the end timestamp
+     */
+    void setEndTimestamp(Integer endTimestamp) {
+        this.endTimestamp = endTimestamp;
+    }
+
+    /**
+     * Set the GO timestamp.
+     * 
+     * @param goTimestamp the GO timestamp
+     */
+    void setGoTimestamp(Integer goTimestamp) {
+        this.goTimestamp = goTimestamp;
+    }
+
+    /**
+     * Set the clock livetime. 
+     * 
+     * @param livetimeClock the clock livetime
+     */
+    void setLivetimeClock(Double livetimeClock) {
+        this.livetimeClock = livetimeClock;
+    }
+
+    /**
+     * Set the FCUP TDC livetime.
+     * 
+     * @param livetimeTdc the FCUP TDC livetime
+     */
+    void setLivetimeFcupTdc(Double livetimeTdc) {
+        this.livetimeTdc = livetimeTdc;
+    }
+
+    /**
+     * Set the FCUP TRG livetime.
+     * 
+     * @param livetimeTrg the FCUP TRG livetime
+     */
+    void setLivetimeFcupTrg(Double livetimeTrg) {
+        this.livetimeTrg = livetimeTrg;
+    }
+
+    /**
+     * Set the notes.
+     * 
+     * @param notes the notes
+     */
+    void setNotes(String notes) {
+        this.notes = notes;
+    }
+
+    /**
+     * Set the PRESTART timestamp.
+     * 
+     * @param prestartTimestamp the PRESTART timestamp
+     */
+    void setPrestartTimestamp(Integer prestartTimestamp) {
+        this.prestartTimestamp = prestartTimestamp;
+    }
+
+    /**
+     * Set the target description.
+     * 
+     * @param target the target description
+     */
+    void setTarget(String target) {
+        this.target = target;
+    }
+
+    /**
+     * Set the TI time offset in ns.
+     * 
+     * @param tiTimeOffset the TIM time offset in ns
+     */
+    void setTiTimeOffset(Long tiTimeOffset) {
+        this.tiTimeOffset = tiTimeOffset;
     }
 
     /**
@@ -315,7 +273,7 @@
      *
      * @param totalEvents the total number of physics events in the run
      */
-    void setTotalEvents(final int totalEvents) {
+    void setTotalEvents(final Long totalEvents) {
         this.totalEvents = totalEvents;
     }
 
@@ -324,37 +282,59 @@
      *
      * @param totalFiles the total number of EVIO files in the run
      */
-    void setTotalFiles(final int totalFiles) {
+    void setTotalFiles(final Integer totalFiles) {
         this.totalFiles = totalFiles;
     }
 
     /**
-     * Set the date when this run record was last updated.
-     *
-     * @param updated the date when the run record was last updated
-     */
-    void setUpdated(final Date updated) {
+     * Set the trigger config file.
+     * 
+     * @param triggerConfigName the trigger config file
+     */
+    void setTriggerConfigName(String triggerConfigName) {
+        this.triggerConfigName = triggerConfigName;
+    }
+
+    /**
+     * Set the trigger rate in KHz.
+     * 
+     * @param triggerRate the trigger rate in KHz
+     */
+    void setTriggerRate(Double triggerRate) {
+        this.triggerRate = triggerRate;
+    }
+
+    /**
+     * Set the updated date of the summary.
+     * 
+     * @param updated the updated date
+     */
+    void setUpdated(Date updated) {
         this.updated = updated;
     }
-    
-    /**
-     * Convert this object to a string.
-     *
+
+    /**
+     * Convert the object to a string.
+     * 
      * @return this object converted to a string
      */
     @Override
     public String toString() {
         return "RunSummary { " 
                 + "run: " + this.getRun() 
-                + ", startDate: " + (this.getStartDate() != null ? DATE_DISPLAY.format(this.getStartDate()) : null)
-                + ", endDate: " + (this.getEndDate() != null ? DATE_DISPLAY.format(this.getEndDate()) : null) 
-                + ", totalEvents: " + this.getTotalEvents()
-                + ", totalFiles: " + this.getTotalFiles() 
-                + ", endOkay: " + this.getEndOkay() 
-                + ", runOkay: "
-                + this.getRunOkay() 
-                + ", updated: " + this.getUpdated() 
+                + ", events: " + this.getTotalEvents() 
+                + ", files: " + this.getTotalFiles() 
                 + ", created: " + this.getCreated() 
+                + ", updated: " + this.getUpdated()
+                + ", prestartTimestamp: " + this.getPrestartTimestamp()
+                + ", goTimestamp: " + this.getGoTimestamp()
+                + ", endTimestamp: " + this.getEndTimestamp()
+                + ", triggerConfigFile: " + this.getTriggerConfigName()
+                + ", triggerRate: " + this.getTriggerRate()
+                + ", livetimeClock: " + this.getLivetimeClock()
+                + ", livetimeTdc: " + this.getLivetimeFcupTdc()
+                + ", livetimeTrg: " + this.getLivetimeFcupTrg()
+                + ", tiTimeOffset: " + this.getTiTimeOffset() 
                 + " }";
     }
 }

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/ScalerDataDaoImpl.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/ScalerDataDaoImpl.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/ScalerDataDaoImpl.java	Wed Apr 27 11:11:32 2016
@@ -18,15 +18,9 @@
 final class ScalerDataDaoImpl implements ScalerDataDao {
 
     /**
-     * SQL query strings.
+     * Insert a record.
      */
-    private static final class ScalerDataQuery {
-
-        /**
-         * Insert a record.
-         */
-        private static final String INSERT = createInsertSql();
-    }
+    private static final String INSERT = createInsertSql();    
 
     /**
      * Create insert SQL for scaler data.
@@ -102,7 +96,8 @@
         PreparedStatement selectScalers = null;
         final List<ScalerData> scalerDataList = new ArrayList<ScalerData>();
         try {
-            selectScalers = this.connection.prepareStatement("SELECT * FROM scalers WHERE run = ? ORDER BY event");
+            selectScalers = this.connection.prepareStatement("SELECT * FROM sc"
+                    + "alers WHERE run = ? ORDER BY event");
             selectScalers.setInt(1, run);
             final ResultSet resultSet = selectScalers.executeQuery();
             while (resultSet.next()) {
@@ -139,7 +134,7 @@
     public void insertScalerData(final List<ScalerData> scalerDataList, final int run) {
         PreparedStatement insertScalers = null;
         try {
-            insertScalers = this.connection.prepareStatement(ScalerDataQuery.INSERT);
+            insertScalers = this.connection.prepareStatement(INSERT);
             for (final ScalerData scalerData : scalerDataList) {
                 insertScalers.setInt(1, run);
                 insertScalers.setInt(2, scalerData.getEventId());

Modified: java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/package-info.java
 =============================================================================
--- java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/package-info.java	(original)
+++ java/branches/HPSJAVA-409/run-database/src/main/java/org/hps/run/database/package-info.java	Wed Apr 27 11:11:32 2016
@@ -1,4 +1,4 @@
 /**
- * API for accessing the HPS run database.
+ * API for accessing and updating the HPS run database.
  */
 package org.hps.run.database;

Modified: java/branches/HPSJAVA-409/steering-files/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/pom.xml	(original)
+++ java/branches/HPSJAVA-409/steering-files/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/steering-files/</url>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/analysis/StarterAnalysis.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/analysis/StarterAnalysis.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/analysis/StarterAnalysis.lcsim	Wed Apr 27 11:11:32 2016
@@ -20,4 +20,4 @@
         </driver>
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceMonitoringApp.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceMonitoringApp.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceMonitoringApp.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,9 +1,9 @@
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">         
     <execute>
-    	<driver name="EventMarkerDriver"/>
+        <driver name="EventMarkerDriver"/>
         <driver name="EcalRunningPedestal"/>
-  	    <driver name="EcalRawConverter" />    
+        <driver name="EcalRawConverter" />    
         <driver name="LedAnalysisDriver"/>
         <driver name="EcalEventDisplay" />         <!-- Ecal event display -->
         <driver name="AidaSaveDriver"/>
@@ -48,5 +48,5 @@
         <driver name="AidaSaveDriver" type="org.lcsim.job.AidaSaveDriver">
             <outputFileName>LedSequenceMonitorOut.aida</outputFileName>
         </driver>
-	</drivers>
+    </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceStandalone.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceStandalone.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalLedSequenceStandalone.lcsim	Wed Apr 27 11:11:32 2016
@@ -5,8 +5,7 @@
 	        <driver name="EcalRunningPedestal"/>
 	  	    <driver name="EcalRawConverter" />    
 	        <driver name="LedAnalysisDriver"/>
-	   <!-- <driver name="EcalEventDisplay" />    -->     <!-- Ecal event display -->
-	        <driver name="AidaSaveDriver"/>
+	        <driver name="AidaSaveDriver"/>	     
 	    </execute>           
 	    <drivers>    
 	        <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
@@ -18,13 +17,14 @@
 	        </driver>
 	        <driver name="EcalRawConverter" type="org.hps.recon.ecal.EcalRawConverterDriver">
 	            <ecalCollectionName>EcalCalHits</ecalCollectionName>
-	            <use2014Gain>false</use2014Gain>
 	            <useTimestamps>false</useTimestamps>
 	            <useTruthTime>false</useTruthTime>
 	            <useRunningPedestal>true</useRunningPedestal>
 	            <useTimeWalkCorrection>true</useTimeWalkCorrection>
+	            <nsa>60</nsa>  <!-- these are critical since the defaults in software are 100 - 20, as in prod. runs -->
+       		    <nsb>16</nsb>
 	        </driver>       
-	       <driver name="EcalEventDisplay" type="org.hps.monitoring.ecal.plots.EcalEventDisplay">
+	  <!--     <driver name="EcalEventDisplay" type="org.hps.monitoring.ecal.plots.EcalEventDisplay">
 	            <inputCollection>EcalCalHits</inputCollection>
 	            <inputCollectionRaw>EcalReadoutHits</inputCollectionRaw>
 	            <inputClusterCollection>EcalClusters</inputClusterCollection>
@@ -33,19 +33,21 @@
 	            <minEch>0.005</minEch>
 	            <eventRefreshRate>2</eventRefreshRate>
 	        </driver>
+	        -->
 	        <driver name="LedAnalysisDriver" type="org.hps.monitoring.ecal.plots.EcalLedSequenceMonitor">
 	           <isMonitoringApp>false</isMonitoringApp>
 	           <doFullAnalysis>false</doFullAnalysis>
-	           <skipMin>0.25</skipMin>
+	           <skipMin>0.2</skipMin>
 	           <skipInitial>0.05</skipInitial>    
 	           <useRawEnergy>true</useRawEnergy>
-	           <energyCut>1</energyCut>
+	           <energyCut>2.0</energyCut>
 	           <nEventsMin>300</nEventsMin>
 	           <evnMinDraw>0.</evnMinDraw>
-	           <evnMaxDraw>20000.</evnMaxDraw>
+	           <evnMaxDraw>80000.</evnMaxDraw>
+	           <saveTuple>false</saveTuple>
 	        </driver>
 	        <driver name="AidaSaveDriver" type="org.lcsim.job.AidaSaveDriver">
-	            <outputFileName>${outputFile}</outputFileName>
-	        </driver>
+	            <outputFileName>${outputFile}.LedAnalysis.aida</outputFileName>
+	        </driver>        
 		</drivers>
 	</lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringFinal.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringFinal.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringFinal.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,7 +1,7 @@
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <execute>
         <driver name="EcalRawConverter" />
-      	<driver name="EcalClusterer" />
+        <driver name="EcalClusterer" />
         <driver name="EcalMonitoringPlots" />      <!-- General plots -->
         <driver name="EcalHitPlots" />             <!-- Single hit distributions -->
         <driver name="EcalClusterPlots" />         <!-- Clusters distributions -->

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringOnly.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringOnly.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringOnly.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,7 +1,7 @@
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <execute>
         <driver name="EcalRawConverter" />
-      	<driver name="EcalClusterer" />
+        <driver name="EcalClusterer" />
         <driver name="EcalMonitoringPlots" />      <!-- General plots -->
         <driver name="EcalHitPlots" />             <!-- Single hit distributions -->
         <driver name="EcalClusterPlots" />         <!-- Clusters distributions -->

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/SvtOnlineMonitoring.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/SvtOnlineMonitoring.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/SvtOnlineMonitoring.lcsim	Wed Apr 27 11:11:32 2016
@@ -10,22 +10,27 @@
         <driver name="PedestalPlots" />-->
         <driver name="SensorOccupancy" />
         <driver name="RawTrackerHitFitterDriver" />
+        <!--<driver name="SVTPulseFitPlots" />--> 
         <driver name="TrackerHitDriver" />
         <driver name="ClusterPlots" /> 
         <driver name="CleanupDriver" />
     </execute>
     <drivers>
         <driver name="SensorOccupancy" type="org.hps.monitoring.drivers.svt.SensorOccupancyPlotsDriver" >
-        	<eventRefreshRate>100</eventRefreshRate>
+            <eventRefreshRate>100</eventRefreshRate>
             <enablePositionPlots>false</enablePositionPlots>
             <enableMaxSamplePlots>true</enableMaxSamplePlots>
             <maxSamplePosition>3</maxSamplePosition>
             <timeWindowWeight>3</timeWindowWeight>
             <resetPeriod>50000</resetPeriod>
+            <saveRootFile>false</saveRootFile>
        </driver>
-        <driver name="SvtHitPlots" type="org.hps.monitoring.drivers.svt.SvtHitPlots" />
-        <driver name="SamplesPlots" type="org.hps.monitoring.drivers.svt.SamplesPlots" />
-        <driver name="PedestalPlots" type="org.hps.monitoring.drivers.svt.PedestalPlots" />
+        <driver name="SvtHitPlots" type="org.hps.monitoring.drivers.svt.SvtHitPlots">
+            <doPerChannelsSampleplots>true</doPerChannelsSampleplots>
+            <!--<saveRootFile>false</saveRootFile>-->
+        </driver>
+        <!--<driver name="SamplesPlots" type="org.hps.monitoring.drivers.svt.SamplesPlots" />-->
+        <!--<driver name="PedestalPlots" type="org.hps.monitoring.drivers.svt.PedestalPlots" />-->
         <driver name="RawTrackerHitFitterDriver" type="org.hps.recon.tracking.RawTrackerHitFitterDriver">
             <fitAlgorithm>Linear</fitAlgorithm>
             <useTimestamps>false</useTimestamps>
@@ -41,7 +46,10 @@
             <neighborDeltaT>8.0</neighborDeltaT>
             <debug>false</debug>
         </driver>
-        <driver name="ClusterPlots" type="org.hps.monitoring.drivers.svt.SvtClusterPlots" />
+        <!--<driver name="SVTPulseFitPlots" type="org.hps.monitoring.drivers.svt.SVTPulseFitPlots" />-->
+        <driver name="ClusterPlots" type="org.hps.monitoring.drivers.svt.SvtClusterPlots">
+            <saveRootFile>false</saveRootFile>
+        </driver>
         <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver" />
     </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/TriggerDiagnosticsMonitoring.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/TriggerDiagnosticsMonitoring.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/monitoring/TriggerDiagnosticsMonitoring.lcsim	Wed Apr 27 11:11:32 2016
@@ -19,7 +19,7 @@
         <driver name="ConditionsDriver" type="org.hps.conditions.ConditionsDriver">
             <tag>pass0</tag>
         </driver>        
-        <driver name="DAQConfig" type="org.hps.recon.ecal.daqconfig.DAQConfigDriver"/>        
+        <driver name="DAQConfig" type="org.hps.record.daqconfig.DAQConfigDriver"/>
         <driver name="EcalRawConverter" type="org.hps.recon.ecal.EcalRawConverterDriver">
             <ecalCollectionName>EcalCalHits</ecalCollectionName>
             <use2014Gain>false</use2014Gain>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/V0CandidateFilter.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/V0CandidateFilter.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/production/V0CandidateFilter.lcsim	Wed Apr 27 11:11:32 2016
@@ -22,12 +22,6 @@
         <!-- Driver to strip events -->
         <driver name="StripEvent"
                 type="org.hps.recon.filtering.V0CandidateFilter">
-              <!-- Name of the V0 Candidate Collection of ReconstructedParticles -->
-              <v0CandidateCollectionName>TargetConstrainedV0Candidates</v0CandidateCollectionName>
-              <!-- Maximum difference in the ECal cluster times [ns]-->
-              <clusterTimingCut>2.5</clusterTimingCut>
-              <!-- A tight selection requires one and only one real V0 vertex --> 
-              <tightConstraint>false</tightConstraint>
               <!-- Setting this true keeps ALL events containing EPICS data -->
               <keepEpicsDataEvents>true</keepEpicsDataEvents>
         </driver>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/CommRun2014TightPairs.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/CommRun2014TightPairs.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/CommRun2014TightPairs.lcsim	Wed Apr 27 11:11:32 2016
@@ -44,7 +44,7 @@
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>false</use2014Gain>      
             <debug>true</debug>
-        </driver>	
+        </driver>   
         <driver name="EcalClusterer" type="org.hps.recon.ecal.cluster.GTPClusterDriver">
             <inputHitCollectionName>EcalCorrectedHits</inputHitCollectionName>
             <clusterWindow>1</clusterWindow>
@@ -62,7 +62,7 @@
             <energySlopeParamF>0.005500</energySlopeParamF>
             <energySlopeLow>0.4</energySlopeLow>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	      
+        </driver>         
         <driver name="AidaSaveDriver"
                 type="org.lcsim.job.AidaSaveDriver">
             <outputFileName>${outputFile}_triggerPlots</outputFileName>
@@ -73,4 +73,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/EngineeringRun2014PrescaledTriggers.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/EngineeringRun2014PrescaledTriggers.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/EngineeringRun2014PrescaledTriggers.lcsim	Wed Apr 27 11:11:32 2016
@@ -54,7 +54,7 @@
             <nsa>100</nsa>
             <nsb>20</nsb>
             <use2014Gain>false</use2014Gain> 
-        </driver>	
+        </driver>   
         <driver name="EcalClustererGTP" type="org.hps.recon.ecal.cluster.GTPClusterDriver">
             <inputHitCollectionName>EcalCorrectedHits</inputHitCollectionName>
             <outputClusterCollectionName>EcalClusters</outputClusterCollectionName>            
@@ -82,7 +82,7 @@
             <outputFileName>${outputFile}.triggers.singles0</outputFileName>
             <lcioFile>${outputFile}.singles0.slcio</lcioFile>    
             <!--<verbose>true</verbose>-->
-        </driver>	      
+        </driver>         
         <driver name="SinglesTrigger1" type="org.hps.readout.ecal.SinglesTriggerDriver">
             <clusterCollectionName>EcalClusters</clusterCollectionName>
             <deadTime>32</deadTime>
@@ -94,7 +94,7 @@
             <outputFileName>${outputFile}.triggers.singles1</outputFileName>
             <lcioFile>${outputFile}.singles1.slcio</lcioFile>            
             <!--<verbose>true</verbose>-->
-        </driver>	      
+        </driver>         
         <driver name="PairTrigger0" type="org.hps.readout.ecal.FADCPrimaryTriggerDriver">
             <clusterCollectionName>EcalClusters</clusterCollectionName>
             <deadTime>32</deadTime>
@@ -113,7 +113,7 @@
             <outputFileName>${outputFile}.triggers.pairs0</outputFileName>
             <lcioFile>${outputFile}.pairs0.slcio</lcioFile>            
             <!--<verbose>true</verbose>-->
-        </driver>	      
+        </driver>         
         <driver name="PairTrigger1" type="org.hps.readout.ecal.FADCPrimaryTriggerDriver">
             <clusterCollectionName>EcalClusters</clusterCollectionName>
             <deadTime>32</deadTime>
@@ -132,7 +132,7 @@
             <outputFileName>${outputFile}.triggers.pairs1</outputFileName>
             <lcioFile>${outputFile}.pairs1.slcio</lcioFile>
             <!--<verbose>true</verbose>-->
-        </driver>	      
+        </driver>         
         <driver name="AidaSaveDriver"
                 type="org.lcsim.job.AidaSaveDriver">
             <outputFileName>${outputFile}_triggerPlots</outputFileName>
@@ -143,4 +143,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutNoPileup.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutNoPileup.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutNoPileup.lcsim	Wed Apr 27 11:11:32 2016
@@ -48,7 +48,7 @@
             <deadTime>0</deadTime>
             <pairCoincidence>0</pairCoincidence>
             <lcioFile>${outputFile}.slcio</lcioFile>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout">
             <noPileup>true</noPileup>
         </driver>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutToEvio.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutToEvio.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014ReadoutToEvio.lcsim	Wed Apr 27 11:11:32 2016
@@ -44,7 +44,7 @@
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>true</use2014Gain>
             <!--            <debug>true</debug>-->
-        </driver>	
+        </driver>   
         <driver name="EcalClusterer" type="org.hps.recon.ecal.cluster.GTPClusterDriver">
             <inputHitCollectionName>EcalCorrectedHits</inputHitCollectionName>
             <clusterWindow>1</clusterWindow>
@@ -54,7 +54,7 @@
             <deadTime>10</deadTime>
             <pairCoincidence>2</pairCoincidence>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout" />
         <driver name="ClockDriver" type="org.hps.readout.ecal.ClockDriver"/>
         <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver">
@@ -62,4 +62,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014TruthReadoutToLcio.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014TruthReadoutToLcio.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/HPS2014TruthReadoutToLcio.lcsim	Wed Apr 27 11:11:32 2016
@@ -47,7 +47,7 @@
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>true</use2014Gain>
             <!--            <debug>true</debug>-->
-        </driver>	
+        </driver>   
         <driver name="EcalClusterer" type="org.hps.recon.ecal.cluster.GTPClusterDriver">
             <inputHitCollectionName>EcalCorrectedHits</inputHitCollectionName>
             <clusterWindow>1</clusterWindow>
@@ -57,7 +57,7 @@
             <deadTime>10</deadTime>
             <pairCoincidence>2</pairCoincidence>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout">
         </driver>
         <driver name="AidaSaveDriver"
@@ -70,4 +70,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/LcioToEvio.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/LcioToEvio.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/LcioToEvio.lcsim	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,7 @@
             <period>1</period>
             <deadTime>0</deadTime>
             <triggerDelay>0</triggerDelay>
-        </driver>	
+        </driver>   
         <driver name="TestRunReconToEvio" type="org.hps.evio.TestRunTriggeredReconToEvio">
             <evioOutputFile>${outputFile}.evio</evioOutputFile>
         </driver>
@@ -23,4 +23,4 @@
         </driver>
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunNoPileup.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunNoPileup.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunNoPileup.lcsim	Wed Apr 27 11:11:32 2016
@@ -39,7 +39,7 @@
             <clusterCollectionName>EcalTriggerClusters</clusterCollectionName>
             <deadTime>0</deadTime>
             <lcioFile>${outputFile}.slcio</lcioFile>
-        </driver>	
+        </driver>   
         <driver name="ClockDriver" type="org.hps.readout.ecal.ClockDriver"/>
         <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver"/>
     </drivers>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunReadoutToEvio.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunReadoutToEvio.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/readout/TestRunReadoutToEvio.lcsim	Wed Apr 27 11:11:32 2016
@@ -20,7 +20,7 @@
         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>
         </driver> 
-        <driver name="BadChannelFilter" type="org.hps.recon.tracking.SVTBadChannelFilterDriver" /> 		
+        <driver name="BadChannelFilter" type="org.hps.recon.tracking.SVTBadChannelFilterDriver" />      
         <driver name="EcalReadout" type="org.hps.readout.ecal.FADCEcalReadoutDriver">
             <coincidenceWindow>8</coincidenceWindow>
             <ecalName>Ecal</ecalName>
@@ -39,7 +39,7 @@
             <rawCollectionName>EcalRawHits</rawCollectionName>
             <ecalCollectionName>EcalCorrectedHits</ecalCollectionName>
             <scale>1</scale>
-        </driver>	
+        </driver>   
         <driver name="EcalTriggerFilter" type="org.hps.recon.ecal.EcalTriggerFilterDriver">
             <inputCollection>EcalCorrectedHits</inputCollection>
             <outputCollection>EcalFilteredHits</outputCollection>
@@ -55,7 +55,7 @@
             <clusterCollectionName>EcalClusters</clusterCollectionName>
             <deadTime>10</deadTime>
             <outputFileName>${outputFile}.triggers</outputFileName>
-        </driver>	
+        </driver>   
         <driver name="SimpleSVTReadout" type="org.hps.readout.svt.SimpleSvtReadout" />
         <driver name="ClockDriver" type="org.hps.readout.ecal.ClockDriver"/>
         <driver name="TestRunReconToEvio" type="org.hps.evio.TestRunTriggeredReconToEvio">

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2014EcalReconMC.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2014EcalReconMC.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2014EcalReconMC.lcsim	Wed Apr 27 11:11:32 2016
@@ -18,6 +18,7 @@
     <execute>
         <!--<driver name="EventMarkerDriver" />-->
         <driver name="EcalRunningPedestal"/>
+        <driver name="RfFitter"/>
         <driver name="EcalRawConverter" />
         <driver name="ReconClusterer" />
         <driver name="GTPOnlineClusterer" />
@@ -28,6 +29,8 @@
         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>100</eventInterval>
         </driver>
+        <driver name="RfFitter" type="org.hps.evio.RfFitterDriver"/>       
+        
      <driver name="ConditionsDriver" type="org.hps.conditions.ConditionsDriver">
        <detectorName>HPS-ECalCommissioning-v3-fieldmap</detectorName>
        <runNumber>3422</runNumber>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullRecon.lcsim	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,9 @@
       @author <a href="mailto:[log in to unmask]">Omar Moreno</a>
     -->
     <execute>
-        
+        <!--RF driver-->
+        <driver name="RfFitter"/>
+ 
         <!-- Ecal reconstruction drivers -->        
         <driver name="EcalRunningPedestal"/>
         <driver name="EcalRawConverter" />
@@ -51,7 +53,6 @@
            ReconstructedParticle types are properly set.
         -->
         <driver name="MergeTrackCollections"/>
-        <driver name="GBLOutputDriver" />
         <driver name="GBLRefitterDriver" />
         <driver name="TrackDataDriver" />
         <driver name="ReconParticleDriver" />   
@@ -61,7 +62,9 @@
     <drivers>    
         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>
-        </driver>        
+        </driver> 
+        
+        <driver name="RfFitter" type="org.hps.evio.RfFitterDriver"/>       
 
         <!-- Ecal reconstruction drivers -->
         <driver name="EcalRunningPedestal" type="org.hps.recon.ecal.EcalRunningPedestalDriver">
@@ -134,8 +137,7 @@
             <ecalClusterCollectionName>EcalClustersCorr</ecalClusterCollectionName>        
             <trackCollectionNames>MatchedTracks GBLTracks</trackCollectionNames>
         </driver>  
-        <driver name="GBLOutputDriver" type="org.hps.recon.tracking.gbl.GBLOutputDriver"/>      
-        <driver name="GBLRefitterDriver" type="org.hps.recon.tracking.gbl.HpsGblRefitter"/>
+        <driver name="GBLRefitterDriver" type="org.hps.recon.tracking.gbl.GBLRefitterDriver"/>
         <driver name="LCIOWriter" type="org.lcsim.util.loop.LCIODriver">
             <outputFilePath>${outputFile}.slcio</outputFilePath>
         </driver>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullReconMC.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullReconMC.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/recon/EngineeringRun2015FullReconMC.lcsim	Wed Apr 27 11:11:32 2016
@@ -11,6 +11,7 @@
     
         <driver name="ConditionsDriver"/>
         <driver name="EventMarkerDriver"/>
+        <driver name="RfFitter"/>
         <!-- Ecal reconstruction drivers -->        
         <driver name="EcalRawConverter" />
         <driver name="ReconClusterer" />
@@ -53,7 +54,6 @@
             ReconstructedParticle types are properly set.
          -->
         <driver name="MergeTrackCollections"/>
-        <driver name="GBLOutputDriver" />
         <driver name="GBLRefitterDriver" />
         <driver name="TrackDataDriver" />
         <driver name="ReconParticleDriver" />   
@@ -69,7 +69,9 @@
 
         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>
-        </driver>        
+        </driver>   
+        <driver name="RfFitter" type="org.hps.evio.RfFitterDriver"/>       
+             
         <driver name="RawTrackerHitSensorSetup" type="org.lcsim.recon.tracking.digitization.sisim.config.RawTrackerHitSensorSetup">
             <readoutCollections>SVTRawTrackerHits</readoutCollections>
         </driver>
@@ -119,8 +121,7 @@
             <rmsTimeCut>8.0</rmsTimeCut>
         </driver>       
         <driver name="MergeTrackCollections" type="org.hps.recon.tracking.MergeTrackCollections" />
-        <driver name="GBLOutputDriver" type="org.hps.recon.tracking.gbl.GBLOutputDriver"/>             
-        <driver name="GBLRefitterDriver" type="org.hps.recon.tracking.gbl.HpsGblRefitter"/>
+        <driver name="GBLRefitterDriver" type="org.hps.recon.tracking.gbl.GBLRefitterDriver"/>
         <driver name="EcalRawConverter" type="org.hps.recon.ecal.EcalRawConverterDriver">
             <ecalCollectionName>EcalCalHits</ecalCollectionName>
             <fixShapeParameter>true</fixShapeParameter>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/celentan/LedAnalysisFromEvio.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/celentan/LedAnalysisFromEvio.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/celentan/LedAnalysisFromEvio.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,9 +1,9 @@
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">         
     <execute>
-    	<driver name="EventMarkerDriver"/>
+        <driver name="EventMarkerDriver"/>
         <driver name="EcalRunningPedestal"/>
-  	    <driver name="EcalRawConverter" />    
+        <driver name="EcalRawConverter" />    
         <driver name="AidaSaveDriver"/>
     </execute>           
     <drivers>    
@@ -25,5 +25,5 @@
         <driver name="AidaSaveDriver" type="org.lcsim.job.AidaSaveDriver">
             <outputFileName>${outputFile}.aida</outputFileName>
         </driver>
-	</drivers>
+    </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/ClusterRecon.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/ClusterRecon.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/ClusterRecon.lcsim	Wed Apr 27 11:11:32 2016
@@ -5,7 +5,7 @@
   @author Holly Szumila <[log in to unmask]>
 -->
     <execute>
-    	<driver name="EventMarkerDriver"/>
+        <driver name="EventMarkerDriver"/>
         <driver name="EcalRunningPedestal"/>
         <driver name="EcalRawConverter" />
         <driver name="ReconClusterer" />
@@ -13,7 +13,7 @@
         <driver name="LCIOWriter"/>
     </execute>    
     <drivers>    
-   		<driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
+        <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>
         </driver> 
         <driver name="EcalRunningPedestal" type="org.hps.recon.ecal.EcalRunningPedestalDriver">

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EcalSimReadout.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EcalSimReadout.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EcalSimReadout.lcsim	Wed Apr 27 11:11:32 2016
@@ -21,11 +21,11 @@
             <eventInterval>1000</eventInterval>
         </driver>       
         <driver name="ConditionsDriver" type="org.hps.conditions.ConditionsDriver">
-     		<runNumber>0</runNumber>
-    		<freeze>true</freeze>
-    		<detectorName>HPS-ECalCommissioning-v3-fieldmap</detectorName>
-   		 </driver>
-<!--   		 <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
+            <runNumber>0</runNumber>
+            <freeze>true</freeze>
+            <detectorName>HPS-ECalCommissioning-v3-fieldmap</detectorName>
+         </driver>
+<!--         <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
             <outputFile>${outputFile}.slcio</outputFile>
             <rejectBackground>true</rejectBackground>
         </driver>-->
@@ -45,7 +45,7 @@
             <ecalCollectionName>EcalCorrectedHits</ecalCollectionName>
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>false</use2014Gain>      
-        </driver>	
+        </driver>   
         <driver name="ReconClusterer" type="org.hps.recon.ecal.cluster.ReconClusterDriver">
             <logLevel>WARNING</logLevel>
             <inputHitCollectionName>EcalCorrectedHits</inputHitCollectionName>
@@ -65,4 +65,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EngineeringRun2015EcalOnly.lcsim
 =============================================================================
Binary files - no diff available.

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/EngineeringRun2015_FEEIter_Filter.lcsim
 =============================================================================
Binary files - no diff available.

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/QuickEcalReadout.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/QuickEcalReadout.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/holly/QuickEcalReadout.lcsim	Wed Apr 27 11:11:32 2016
@@ -18,11 +18,11 @@
             <eventInterval>1000</eventInterval>
         </driver>       
         <driver name="ConditionsDriver" type="org.hps.conditions.ConditionsDriver">
-     		<runNumber>0</runNumber>
-    		<freeze>true</freeze>
-    		<detectorName>HPS-Proposal2014-v7-2pt2</detectorName>
-   		 </driver>
-   		 <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
+            <runNumber>0</runNumber>
+            <freeze>true</freeze>
+            <detectorName>HPS-Proposal2014-v7-2pt2</detectorName>
+         </driver>
+         <driver name="TestRunReconToLcio" type="org.hps.evio.TestRunTriggeredReconToLcio">
             <outputFile>${outputFile}.slcio</outputFile>
             <rejectBackground>true</rejectBackground>
         </driver>
@@ -44,4 +44,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/EcalScoring.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/EcalScoring.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/EcalScoring.lcsim	Wed Apr 27 11:11:32 2016
@@ -25,4 +25,4 @@
 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/HitTimes.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/HitTimes.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/HitTimes.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,14 +1,14 @@
 
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
-	<execute>
-		<driver name="EventMarkerDriver"/>
-		<driver name="HitTimePrintDriver"/>
-	</execute>
-	<drivers>
-		<driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
-			<eventInterval>1</eventInterval>
-		</driver>
-		<driver name="HitTimePrintDriver" type="org.hps.users.meeg.HitTimePrintDriver"/>
-	</drivers>
+    <execute>
+        <driver name="EventMarkerDriver"/>
+        <driver name="HitTimePrintDriver"/>
+    </execute>
+    <drivers>
+        <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
+            <eventInterval>1</eventInterval>
+        </driver>
+        <driver name="HitTimePrintDriver" type="org.hps.users.meeg.HitTimePrintDriver"/>
+    </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/PairsSkimmer.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/PairsSkimmer.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/PairsSkimmer.lcsim	Wed Apr 27 11:11:32 2016
@@ -44,4 +44,4 @@
         </driver>
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/SmallHits.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/SmallHits.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/SmallHits.lcsim	Wed Apr 27 11:11:32 2016
@@ -1,18 +1,18 @@
 
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
-	<execute>
-		<driver name="EventMarkerDriver"/>
-		<driver name="SVTSmallHitsDriver"/>
+    <execute>
+        <driver name="EventMarkerDriver"/>
+        <driver name="SVTSmallHitsDriver"/>
         <driver name="AidaSaveDriver"/>
-	</execute>
-	<drivers>
-		<driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
-			<eventInterval>1000</eventInterval>
-		</driver>
-		<driver name="SVTSmallHitsDriver" type="org.hps.users.meeg.SVTSmallHitsDriver"/>
+    </execute>
+    <drivers>
+        <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
+            <eventInterval>1000</eventInterval>
+        </driver>
+        <driver name="SVTSmallHitsDriver" type="org.hps.users.meeg.SVTSmallHitsDriver"/>
         <driver name="AidaSaveDriver" type="org.lcsim.job.AidaSaveDriver">
             <outputFileName>smallhits.root</outputFileName>
         </driver>
-	</drivers>
+    </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/ecal_fadc_bkgd.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/ecal_fadc_bkgd.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/ecal_fadc_bkgd.lcsim	Wed Apr 27 11:11:32 2016
@@ -10,11 +10,11 @@
         <driver name="EcalConverter" />
         <driver name="EcalClusterer" />
         <driver name="EcalTrigger" />
-<!--		<driver name="EcalPlots"/>-->
+<!--        <driver name="EcalPlots"/>-->
         <driver name="EcalFADCPlots" />
         <driver name="EcalTriggerPlots" />
         <driver name="MCParticlePlots" />
-<!--		<driver name="Writer"/>-->
+<!--        <driver name="Writer"/>-->
         <driver name="AidaSaveDriver" />
         <driver name="ClockDriver" />
     </execute>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/raw_triggers.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/raw_triggers.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/meeg/raw_triggers.lcsim	Wed Apr 27 11:11:32 2016
@@ -5,10 +5,10 @@
 -->
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <execute>
-<!--		<driver name="EventMarkerDriver"/>-->
+<!--        <driver name="EventMarkerDriver"/>-->
         <driver name="EcalClusterer" />
         <driver name="EcalTrigger" />
-<!--		<driver name="MCParticlePlots"/>-->
+<!--        <driver name="MCParticlePlots"/>-->
         <driver name="AidaSaveDriver" />
         <driver name="ClockDriver" />
     </execute>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/EngineeringRun2015FullRecon_Pass2_Gbl.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/EngineeringRun2015FullRecon_Pass2_Gbl.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/EngineeringRun2015FullRecon_Pass2_Gbl.lcsim	Wed Apr 27 11:11:32 2016
@@ -56,7 +56,7 @@
         <driver name="GBLOutputDriver" />
         <driver name="GBLRefitterDriver" />
         <driver name="TrackDataDriver" />
-        <!--<driver name="GblResidualEcalDriver" />-->
+        <driver name="GblResidualEcalDriver" />
         <!--<driver name="TrackExtrapolationTestDriver"/>-->
         <driver name="ReconParticleDriver" />  
         <!--<driver name="TrackingReconstructionPlots" />-->
@@ -162,13 +162,13 @@
             <outputFileName>${outputFile}.root</outputFileName>
         </driver>  
         <driver name="AlignmentFilterDriver" type="org.hps.recon.filtering.SvtAlignmentFilter"/>     
-        <driver name="GblResidualEcalDriver" type="org.hps.users.phansson.ECalExtrapolationDriver"/>   
+        <driver name="GblResidualEcalDriver" type="org.hps.users.phansson.GblResidualDriver"/>   
         <driver name="TrackExtrapolationTestDriver" type="org.hps.users.phansson.TrackExtrapolationTestDriver"/>   
         <driver name="TrackingReconstructionPlots" type="org.hps.users.phansson.TrackingReconstructionPlots">
             <showPlots>False</showPlots>
         </driver>
         <driver name="TimerDriver1" type="org.hps.util.TimerDriver"/>
-        <driver name="GeomChecker" type="org.hps.users.phansson.TrackingGeometryChecker"/>
+        <driver name="GeomChecker" type="org.hps.users.phansson.tools.TrackingGeometryChecker"/>
 
     </drivers>
 </lcsim>

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/TestRunOfflineRecon.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/TestRunOfflineRecon.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/phansson/TestRunOfflineRecon.lcsim	Wed Apr 27 11:11:32 2016
@@ -39,7 +39,7 @@
         </driver>
         <driver name="TrackerReconDriver" type="org.hps.recon.tracking.TrackerReconDriver">
             <debug>false</debug>
-		    <!--<strategyResource>/org/hps/recon/tracking/strategies/HPS-Test-All.xml</strategyResource>-->
+            <!--<strategyResource>/org/hps/recon/tracking/strategies/HPS-Test-All.xml</strategyResource>-->
             <strategyResource>/org/hps/recon/tracking/strategies/HPS-TestRun-357.xml</strategyResource>
         </driver>
         <driver name="EcalRawConverter" type="org.hps.recon.ecal.EcalRawConverterDriver">

Modified: java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/rafo/TestSteering.lcsim
 =============================================================================
--- java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/rafo/TestSteering.lcsim	(original)
+++ java/branches/HPSJAVA-409/steering-files/src/main/resources/org/hps/steering/users/rafo/TestSteering.lcsim	Wed Apr 27 11:11:32 2016
@@ -17,4 +17,4 @@
         </driver> 
     </drivers>
 </lcsim>
-	
+    

Modified: java/branches/HPSJAVA-409/tracking/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/pom.xml	(original)
+++ java/branches/HPSJAVA-409/tracking/pom.xml	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/tracking/</url>

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/readout/svt/FpgaData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/readout/svt/FpgaData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/readout/svt/FpgaData.java	Wed Apr 27 11:11:32 2016
@@ -39,8 +39,9 @@
 
     /**
      * 
-     * @param temperature : array containing hybrid temperatures
-     * @param tail : word present at the end of a FPGA data set
+     * @param fpgaID FPGA ID
+     * @param data : array containing hybrid temperatures
+     * @param tail : word present at the end of a FPGA data set     
      */
     public FpgaData(int fpgaID, int[] data, int tail) {
         this.fpgaID = fpgaID;

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/DumbShaperFit.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/DumbShaperFit.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/DumbShaperFit.java	Wed Apr 27 11:11:32 2016
@@ -34,7 +34,7 @@
     }
     
     public Collection<ShapeFitParameters> fitShape(int channel, short[] samples, HpsSiSensor sensor){
-    	
+        
         ShapeFitParameters fitresults = new ShapeFitParameters();
         double[] pedSub = {-99.0, -99.0, -99.0, -99.0, -99.0, -99.0};
         double maxADC = -99999;

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HelicalTrackHitDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HelicalTrackHitDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HelicalTrackHitDriver.java	Wed Apr 27 11:11:32 2016
@@ -41,15 +41,39 @@
 import org.lcsim.recon.tracking.digitization.sisim.TrackerHitType;
 
 /**
- * Driver used to create stereo hits from clusters.
- *
+ * This <code>Driver</code> creates 3D hits from SVT strip clusters of stereo pairs, which by default
+ * are read from the <b>StripClusterer_SiTrackerHitStrip1D</b> input collection.
+ * <p>
+ * The following collections will be added to the output event:
+ * <ul>
+ * <li>HelicalTrackHits</li>
+ * <li>RotatedHelicalTrackHits</li>
+ * <li>HelicalTrackHitRelations</li>
+ * <li>RotatedHelicalTrackHitRelations</li>
+ * <li>HelicalTrackMCRelations</li>
+ * <li>RotatedHelicalTrackMCRelations<li>
+ * </ul>
+ * <p>
+ * Class has the following default parameters values in the code (or from <code>EngineeringRun2015FullRecon.lcsim</code>):
+ * <ul>
+ * <li>{@link #setClusterTimeCut(double)} - 12.0 (ns)</li>
+ * <li>{@link #setMaxDt(double)} - 16.0 (ns)</li>
+ * <li>{@link #setClusterAmplitudeCut(double)} - 400.0</li>
+ * <li>{@link #setRejectGhostHits(boolean)} - <code>false</code></li>
+ * <li>{@link #setDebug(boolean)} - <code>false</code></li>
+ * <li>{@link #setEpsParallel(double)} - 0.013</li>
+ * <li>{@link #setEpsStereo(double)} - 0.01</li>
+ * <li>{@link #setSaveAxialHits(boolean)} - <code>false</code></li>
+ * <li>{@link #setStripHitsCollectionName(String)} - StripClusterer_SiTrackerHitStrip1D</li>
+ * <li>{@link #setHelicalTrackHitRelationsCollectionName(String)} - HelicalTrackHitRelations</li>
+ * <li>{@link #setHelicalTrackMCRelationsCollectionName(String)} -  HelicalTrackMCRelations</li>
+ * <li>{@link #setOutputHitCollectionName(String)} - HelicalTrackHits</li>
+ * </ul>
  *
  * @author Mathew Graham <[log in to unmask]>
  * @author Per Hansson <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
- *
  */
-// TODO: Add class documentation.
 // FIXME: The option to run using the Common geometry should be removed
 public class HelicalTrackHitDriver extends org.lcsim.fit.helicaltrack.HelicalTrackHitDriver {
 
@@ -64,8 +88,8 @@
     private final List<String> _colnames = new ArrayList<String>();
     private boolean _doTransformToTracking = true;
     private boolean _saveAxialHits = false;
-    private String _axialname = "AxialTrackHits";
-    private String _axialmcrelname = "AxialTrackHitsMCRelations";
+    private final String _axialname = "AxialTrackHits";
+    private final String _axialmcrelname = "AxialTrackHitsMCRelations";
     private boolean rejectGhostHits = false;
 
     public enum LayerGeometryType {
@@ -143,7 +167,7 @@
     public void setEpsStereo(double eps) {
         this._crosser.setEpsStereoAngle(eps);
     }
-    
+
     /**
      *
      * @param trans
@@ -199,8 +223,9 @@
         // Create an LCRelation from a HelicalTrackHit to an MC particle used to
         // create it
         List<LCRelation> mcrelations = new ArrayList<LCRelation>();
-        RelationalTable hittomc = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
+        RelationalTable hittomc = null;
         if (event.hasCollection(LCRelation.class, "SVTTrueHitRelations")) {
+            hittomc = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
             List<LCRelation> trueHitRelations = event.get(LCRelation.class, "SVTTrueHitRelations");
             for (LCRelation relation : trueHitRelations) {
                 if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
@@ -241,9 +266,11 @@
 
                     // Create a HelicalTrackStrip for this hit
                     HelicalTrackStrip strip = makeDigiStrip(h);
-                    for (RawTrackerHit rth : h.getRawHits()) {
-                        for (Object simHit : hittomc.allFrom(rth)) {
-                            strip.addMCParticle(((SimTrackerHit) simHit).getMCParticle());
+                    if (hittomc != null) {
+                        for (RawTrackerHit rth : h.getRawHits()) {
+                            for (Object simHit : hittomc.allFrom(rth)) {
+                                strip.addMCParticle(((SimTrackerHit) simHit).getMCParticle());
+                            }
                         }
                     }
 
@@ -259,10 +286,12 @@
                         if (((HpsSiSensor) h.getSensor()).isAxial()) {
                             HelicalTrack2DHit haxial = makeDigiAxialHit(h);
                             axialhits.add(haxial);
-                            List<RawTrackerHit> rl = haxial.getRawHits();
-                            for (RawTrackerHit rth : rl) {
-                                for (Object simHit : hittomc.allFrom(rth)) {
-                                    haxial.addMCParticle(((SimTrackerHit) simHit).getMCParticle());
+                            if (hittomc != null) {
+                                List<RawTrackerHit> rl = haxial.getRawHits();
+                                for (RawTrackerHit rth : rl) {
+                                    for (Object simHit : hittomc.allFrom(rth)) {
+                                        haxial.addMCParticle(((SimTrackerHit) simHit).getMCParticle());
+                                    }
                                 }
                             }
                             axialmcrelations.add(new MyLCRelation(haxial, haxial.getMCParticles()));
@@ -427,7 +456,7 @@
                     Collection<TrackerHit> htsList = hittostrip.allFrom(cross);
                     for (TrackerHit strip : htsList) {
                         Set<HelicalTrackHit> sharedCrosses = hittostrip.allTo(strip);
-                        System.out.println(sharedCrosses.size());
+//                        System.out.println(sharedCrosses.size());
                         if (sharedCrosses.size() > 1) {
 //                    this.getLogger().warning(String.format("removing possible ghost hit"));
                             iter.remove();
@@ -456,14 +485,18 @@
         helhits.addAll(stereoCrosses);
         event.put(_outname, helhits, HelicalTrackHit.class, 0);
         event.put(_hitrelname, hitrelations, LCRelation.class, 0);
-        event.put(_mcrelname, mcrelations, LCRelation.class, 0);
+        if (hittomc != null) {
+            event.put(_mcrelname, mcrelations, LCRelation.class, 0);
+        }
         if (_saveAxialHits) {
             event.put(_axialname, axialhits, HelicalTrackHit.class, 0);
-            event.put(_axialmcrelname, axialmcrelations, LCRelation.class, 0);
-            System.out.println(this.getClass().getSimpleName() + " : number of " + _axialmcrelname + " found = " + axialmcrelations.size());
+            if (hittomc != null) {
+                event.put(_axialmcrelname, axialmcrelations, LCRelation.class, 0);
+                System.out.println(this.getClass().getSimpleName() + " : number of " + _axialmcrelname + " found = " + axialmcrelations.size());
+            }
         }
         if (_doTransformToTracking) {
-            addRotatedHitsToEvent(event, stereoCrosses);
+            addRotatedHitsToEvent(event, stereoCrosses, hittomc != null);
             if (_saveAxialHits) {
                 addRotated2DHitsToEvent(event, axialhits);
             }
@@ -595,7 +628,7 @@
         return strip;
     }
 
-    private void addRotatedHitsToEvent(EventHeader event, List<HelicalTrackCross> stereohits) {
+    private void addRotatedHitsToEvent(EventHeader event, List<HelicalTrackCross> stereohits, boolean isMC) {
 
         List<HelicalTrackHit> rotatedhits = new ArrayList<HelicalTrackHit>();
         List<LCRelation> hthrelations = new ArrayList<LCRelation>();
@@ -634,10 +667,10 @@
             strip1.add(rotatedstriphits.get(0));
             strip2.add(rotatedstriphits.get(1));
             List<HelicalTrackCross> newhits = _crosser.MakeHits(strip1, strip2);
-            if(newhits.size()!=1) {
+            if (newhits.size() != 1) {
                 throw new RuntimeException("no rotated cross was created!?");
             }
-            HelicalTrackCross newhit  = newhits.get(0);
+            HelicalTrackCross newhit = newhits.get(0);
             //HelicalTrackCross newhit = new HelicalTrackCross(rotatedstriphits.get(0), rotatedstriphits.get(1));
             for (MCParticle mcp : cross.getMCParticles()) {
                 newhit.addMCParticle(mcp);
@@ -651,7 +684,9 @@
 
         event.put("Rotated" + _outname, rotatedhits, HelicalTrackHit.class, 0);
         event.put("Rotated" + _hitrelname, hthrelations, LCRelation.class, 0);
-        event.put("Rotated" + _mcrelname, mcrelations, LCRelation.class, 0);
+        if (isMC) {
+            event.put("Rotated" + _mcrelname, mcrelations, LCRelation.class, 0);
+        }
     }
 
     /*

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HitTimeTrackCheck.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HitTimeTrackCheck.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/HitTimeTrackCheck.java	Wed Apr 27 11:11:32 2016
@@ -28,9 +28,15 @@
         this.rmsTimeCut = rmsTimeCut;
     }
 
+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
+
     @Override
     public boolean checkSeed(SeedCandidate candidate) {
-//        System.out.format("seed with %d hits\n", candidate.getHits().size());
+        if (debug) {
+            System.out.format("%s: seed with %d hits\n", this.getClass().getSimpleName(), candidate.getHits().size());
+        }
         int nStrips = 0;
         double meanTime = 0;
         for (HelicalTrackHit hth : candidate.getHits()) {
@@ -50,15 +56,16 @@
         }
 //        if (nStrips<6) return true;
         seedsChecked++;
-//        rmsTime = Math.sqrt(rmsTime / nStrips);
-//        System.out.format("seed RMS %f on %d hits\n",rmsTime,nStrips);
+        if (debug) {
+            System.out.format("%s: seed RMS %f on %d hits\n", this.getClass().getSimpleName(), Math.sqrt(rmsTime / nStrips), nStrips);
+        }
         boolean passCheck = (rmsTime < minTrackHits * rmsTimeCut * rmsTimeCut);
 //        boolean passCheck = (rmsTime < minTrackHits * rmsTimeCut);
         if (passCheck) {
             seedsPassed++;
         }
         if (debug && seedsChecked % 10000 == 0) {
-            System.out.format("Checked %d seeds, %d passed (%d failed)\n", seedsChecked, seedsPassed, seedsChecked - seedsPassed);
+            System.out.format("%s: Checked %d seeds, %d passed (%d failed)\n", this.getClass().getSimpleName(), seedsChecked, seedsPassed, seedsChecked - seedsPassed);
         }
         return passCheck;
 
@@ -66,7 +73,9 @@
 
     @Override
     public boolean checkTrack(SeedTrack track) {
-//        System.out.format("track with %d hits\n", track.getTrackerHits().size());
+        if (debug) {
+            System.out.format("%s: track with %d hits\n", this.getClass().getSimpleName(), track.getTrackerHits().size());
+        }
         tracksChecked++;
         int nStrips = 0;
         double meanTime = 0;
@@ -87,13 +96,15 @@
         }
         rmsTime = Math.sqrt(rmsTime / nStrips);
 //        rmsTime = rmsTime / nStrips;
-//        System.out.format("track RMS %f on %d hits\n", rmsTime, nStrips);
+        if (debug) {
+            System.out.format("%s: track RMS %f on %d hits\n", this.getClass().getSimpleName(), rmsTime, nStrips);
+        }
         boolean passCheck = (rmsTime < rmsTimeCut);
         if (passCheck) {
             tracksPassed++;
         }
         if (debug && tracksChecked % 100 == 0) {
-            System.out.format("Checked %d tracks, %d passed (%d failed)\n", tracksChecked, tracksPassed, tracksChecked - tracksPassed);
+            System.out.format("%s: Checked %d tracks, %d passed (%d failed)\n", this.getClass().getSimpleName(), tracksChecked, tracksPassed, tracksChecked - tracksPassed);
         }
         return passCheck;
     }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NearestNeighborRMSClusterer.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NearestNeighborRMSClusterer.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NearestNeighborRMSClusterer.java	Wed Apr 27 11:11:32 2016
@@ -161,7 +161,7 @@
             double signal = base_hit.getAmp();
             double noiseRMS = 0; 
             for(int sampleN = 0; sampleN < HPSSVTConstants.TOTAL_NUMBER_OF_SAMPLES; sampleN++){
-            	noiseRMS += ((HpsSiSensor) rth.getDetectorElement()).getNoise(channel_number, sampleN);
+                noiseRMS += ((HpsSiSensor) rth.getDetectorElement()).getNoise(channel_number, sampleN);
             }
             noiseRMS = noiseRMS/HPSSVTConstants.TOTAL_NUMBER_OF_SAMPLES;
             
@@ -225,7 +225,7 @@
                 cluster_signal += hit.getAmp();
                 double strip_noise = 0; 
                 for(int sampleN = 0; sampleN < HPSSVTConstants.TOTAL_NUMBER_OF_SAMPLES; sampleN++){
-                	strip_noise += ((HpsSiSensor) hit.getRawTrackerHit().getDetectorElement()).getNoise(clustered_cell, sampleN);
+                    strip_noise += ((HpsSiSensor) hit.getRawTrackerHit().getDetectorElement()).getNoise(clustered_cell, sampleN);
                 }
                 strip_noise = strip_noise/HPSSVTConstants.TOTAL_NUMBER_OF_SAMPLES;
                 cluster_noise_squared += Math.pow(strip_noise, 2); 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NoiselessReadoutChip.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NoiselessReadoutChip.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/NoiselessReadoutChip.java	Wed Apr 27 11:11:32 2016
@@ -164,8 +164,8 @@
 
         // Loop over the channels contained in the SiElectrodeDataCollection
         for (Integer channel : data.keySet()) {
-        	
-        	if(dropBadChannels && ((HpsSiSensor) electrodes.getDetectorElement()).isBadChannel(channel)){
+            
+            if(dropBadChannels && ((HpsSiSensor) electrodes.getDetectorElement()).isBadChannel(channel)){
             //===> if (dropBadChannels && HPSSVTCalibrationConstants.isBadChannel((SiSensor) electrodes.getDetectorElement(), channel)) {
                 // System.out.format("%d bad\n", channel);
                 continue;

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/SVTBadChannelFilterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/SVTBadChannelFilterDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/SVTBadChannelFilterDriver.java	Wed Apr 27 11:11:32 2016
@@ -19,33 +19,33 @@
  */
 public class SVTBadChannelFilterDriver extends Driver {
 
-	// RawTrackerHit collection name 
+    // RawTrackerHit collection name 
     private String rawTrackerHitCollection = "SVTRawTrackerHits";
 
     @Override
     public void process(EventHeader event) {
-    	
+        
         if (event.hasCollection(RawTrackerHit.class, rawTrackerHitCollection)) {
             
-        	// Get the list of raw hits from the event
-        	List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawTrackerHitCollection);
-        	
+            // Get the list of raw hits from the event
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, rawTrackerHitCollection);
+            
             // Get the hits meta data from the event
-        	LCMetaData meta = event.getMetaData(hits);
+            LCMetaData meta = event.getMetaData(hits);
             
-        	// Iterate over all raw hits in the event.  If the raw hit is 
-        	// identified to come from a noisy/bad channel, remove it from
-        	// the list of raw hits.
+            // Iterate over all raw hits in the event.  If the raw hit is 
+            // identified to come from a noisy/bad channel, remove it from
+            // the list of raw hits.
             Iterator<RawTrackerHit> hitsIterator = hits.iterator();
             while (hitsIterator.hasNext()) {
                 
-            	RawTrackerHit hit = hitsIterator.next();
+                RawTrackerHit hit = hitsIterator.next();
                 //hit.setMetaData(meta);
                 int strip = hit.getIdentifierFieldValue("strip");
                 HpsSiSensor sensor = (HpsSiSensor) hit.getDetectorElement();
 
                 if(sensor.isBadChannel(strip)){
-                	hitsIterator.remove();
+                    hitsIterator.remove();
                 }
 
                 if (!sensor.getReadout().getHits(RawTrackerHit.class).isEmpty()) {

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/ShaperLinearFitAlgorithm.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/ShaperLinearFitAlgorithm.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/ShaperLinearFitAlgorithm.java	Wed Apr 27 11:11:32 2016
@@ -34,6 +34,7 @@
     private final int nPulses;
     final double[] amplitudes;
     final double[] amplitudeErrors;
+    private double pedestal;
     //===> private ChannelConstants channelConstants;
     private HpsSiSensor sensor;
     private int channel;
@@ -44,6 +45,7 @@
     private int nUsedSamples;
     private int firstFittedPulse;
     private int nFittedPulses;
+    private boolean fitPedestal = false;
     private boolean debug = false;
     private static final Logger minuitLoggger = Logger.getLogger("org.freehep.math.minuit");
 
@@ -61,6 +63,18 @@
         } else {
             minuitLoggger.setLevel(Level.OFF);
         }
+    }
+
+    public void setFitPedestal(boolean fitPedestal) {
+        this.fitPedestal = fitPedestal;
+    }
+
+    public boolean fitsPedestal() {
+        return fitPedestal;
+    }
+
+    public double getPedestal() {
+        return pedestal;
     }
 
     @Override
@@ -120,7 +134,11 @@
             ShapeFitParameters fit = new ShapeFitParameters();
             fit.setAmp(amplitudes[i]);
             fit.setAmpErr(amplitudeErrors[i]);
-            fit.setChiProb(Gamma.regularizedGammaQ(samples.length - 2 * nPulses, chisq));
+            if (fitPedestal) {
+                fit.setChiProb(Gamma.regularizedGammaQ(samples.length - 2 * nPulses - 1, chisq));
+            } else {
+                fit.setChiProb(Gamma.regularizedGammaQ(samples.length - 2 * nPulses, chisq));
+            }
 
             fit.setT0(min.userState().value(i));
 
@@ -177,15 +195,22 @@
                 nUsedSamples = split;
                 //fit only the first pulse
                 nFittedPulses = 1;
-                FunctionMinimum frontFit = doRecursiveFit(fitData);
+                FunctionMinimum frontFit;
+                frontFit = doRecursiveFit(fitData);
                 if (debug) {
-                    System.out.format("front fit:\tt0=%f,\tA=%f,\tchisq=%f\n", frontFit.userState().value(0), amplitudes[firstFittedPulse], frontFit.fval());
-                }
-
+                    if (fitPedestal) {
+                        System.out.format("front fit:\tt0=%f,\tA=%f,\tchisq=%f,\tpedestal=%f\n", frontFit.userState().value(0), amplitudes[firstFittedPulse], frontFit.fval(), pedestal);
+                    } else {
+                        System.out.format("front fit:\tt0=%f,\tA=%f,\tchisq=%f\n", frontFit.userState().value(0), amplitudes[firstFittedPulse], frontFit.fval());
+                    }
+                }
                 //subtract first pulse from fit input
                 for (int i = 0; i < samples.length; i++) {
                     //===> fitData[i] -= amplitudes[firstFittedPulse] * getAmplitude(HPSSVTConstants.SAMPLING_INTERVAL * i - frontFit.userState().value(0), channelConstants);
                     fitData[i] -= amplitudes[firstFittedPulse] * shape.getAmplitudePeakNorm(HPSSVTConstants.SAMPLING_INTERVAL * i - frontFit.userState().value(0));
+                    if (fitPedestal) {
+                        fitData[i] -= pedestal;
+                    }
                 }
 
                 if (debug) {
@@ -201,7 +226,14 @@
                 //fit the rest of the pulses
                 firstFittedPulse++;
                 nFittedPulses = nPulses - firstFittedPulse;
-                FunctionMinimum backFit = doRecursiveFit(fitData);
+                FunctionMinimum backFit;
+                if (fitPedestal) {
+                    fitPedestal = false;
+                    backFit = doRecursiveFit(fitData);
+                    fitPedestal = true;
+                } else {
+                    backFit = doRecursiveFit(fitData);
+                }
 
                 if (debug) {
                     System.out.format("back fit:\tt0=%f,\tA=%f,\tchisq=%f\n", backFit.userState().value(0), amplitudes[firstFittedPulse], backFit.fval());
@@ -221,7 +253,11 @@
                 FunctionMinimum combinedFit = minuitFit(combinedGuess);
 
                 if (debug) {
-                    System.out.format("combined fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f\n", combinedFit.userState().value(0), amplitudes[firstFittedPulse], combinedFit.userState().value(1), amplitudes[firstFittedPulse + 1], combinedFit.fval());
+                    if (fitPedestal) {
+                        System.out.format("combined fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f,\tpedestal=%f\n", combinedFit.userState().value(0), amplitudes[firstFittedPulse], combinedFit.userState().value(1), amplitudes[firstFittedPulse + 1], combinedFit.fval(), pedestal);
+                    } else {
+                        System.out.format("combined fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f\n", combinedFit.userState().value(0), amplitudes[firstFittedPulse], combinedFit.userState().value(1), amplitudes[firstFittedPulse + 1], combinedFit.fval());
+                    }
                 }
 
                 double newchisq = evaluateMinimum(combinedFit);
@@ -234,8 +270,11 @@
 
 //            double newchisq = evaluateMinimum(bestFit);
             if (debug) {
-                System.out.println("new chisq:\t" + bestChisq);
-                System.out.format("best fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f\n", bestFit.userState().value(0), amplitudes[firstFittedPulse], bestFit.userState().value(1), amplitudes[firstFittedPulse + 1], bestFit.fval());
+                if (fitPedestal) {
+                    System.out.format("best fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f,\tpedestal=%f\n", bestFit.userState().value(0), amplitudes[firstFittedPulse], bestFit.userState().value(1), amplitudes[firstFittedPulse + 1], bestFit.fval(), pedestal);
+                } else {
+                    System.out.format("best fit:\tt0=%f,\tA=%f,\tt0=%f,\tA=%f,\tchisq=%f\n", bestFit.userState().value(0), amplitudes[firstFittedPulse], bestFit.userState().value(1), amplitudes[firstFittedPulse + 1], bestFit.fval());
+                }
             }
             return bestFit;
         }
@@ -322,7 +361,8 @@
         if (times.length != nFittedPulses) {
             throw new RuntimeException("wrong number of parameters in doLinFit");
         }
-        RealMatrix sc_mat = new Array2DRowRealMatrix(nFittedPulses, nUsedSamples);
+        int nAmplitudes = fitPedestal ? nFittedPulses + 1 : nFittedPulses;
+        RealMatrix sc_mat = new Array2DRowRealMatrix(nAmplitudes, nUsedSamples);
         RealVector y_vec = new ArrayRealVector(nUsedSamples);
         RealVector var_vec = new ArrayRealVector(nUsedSamples);
 
@@ -330,6 +370,9 @@
             for (int i = 0; i < nFittedPulses; i++) {
                 //===> sc_mat.setEntry(i, j, getAmplitude(HPSSVTConstants.SAMPLING_INTERVAL * (firstUsedSample + j) - times[i], channelConstants) / sigma[firstUsedSample + j]);
                 sc_mat.setEntry(i, j, shape.getAmplitudePeakNorm(HPSSVTConstants.SAMPLING_INTERVAL * (firstUsedSample + j) - times[i]) / sigma[firstUsedSample + j]);
+            }
+            if (fitPedestal) {
+                sc_mat.setEntry(nFittedPulses, j, 1.0 / sigma[firstUsedSample + j]);
             }
             y_vec.setEntry(j, y[firstUsedSample + j] / sigma[firstUsedSample + j]);
             var_vec.setEntry(j, sigma[firstUsedSample + j] * sigma[firstUsedSample + j]);
@@ -344,7 +387,7 @@
             a_solver = a_cholesky.getSolver();
             solved_amplitudes = a_solver.solve(a_vec);
             amplitude_err = a_solver.solve(sc_mat.operate(var_vec));
-            if (solved_amplitudes.getMinValue() < 0) {
+            if (solved_amplitudes.getSubVector(0, nFittedPulses).getMinValue() < 0) {
                 goodFit = false;
             }
         } catch (NonPositiveDefiniteMatrixException e) {
@@ -352,8 +395,8 @@
         }
 
         if (!goodFit) {
-            solved_amplitudes = new ArrayRealVector(nFittedPulses, 0.0);
-            amplitude_err = new ArrayRealVector(nFittedPulses, Double.POSITIVE_INFINITY);
+            solved_amplitudes = new ArrayRealVector(nAmplitudes, 0.0);
+            amplitude_err = new ArrayRealVector(nAmplitudes, Double.POSITIVE_INFINITY);
         }
 
         double chisq = y_vec.subtract(sc_mat.preMultiply(solved_amplitudes)).getNorm();
@@ -361,6 +404,9 @@
         for (int i = 0; i < nFittedPulses; i++) {
             amplitudes[firstFittedPulse + i] = solved_amplitudes.getEntry(i);
             amplitudeErrors[firstFittedPulse + i] = Math.sqrt(amplitude_err.getEntry(i));
+        }
+        if (fitPedestal) {
+            pedestal = solved_amplitudes.getEntry(nFittedPulses);
         }
         return chisq;
     }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/StrategyType.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/StrategyType.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/StrategyType.java	Wed Apr 27 11:11:32 2016
@@ -4,7 +4,7 @@
 import java.util.Map;
 
 /**
- * Enum constants for different {@link Track}s based on what tracking
+ * Enum constants for different {@link org.lcsim.event.Track} objects based on what tracking
  * strategy was used.  The type is defined by comparing the tracking strategy
  * name to the name of all the enum constants.
  *  

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackData.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,13 @@
 package org.hps.recon.tracking;
 
+import java.util.List;
+import org.apache.commons.math3.util.Pair;
+import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
+import org.lcsim.event.LCRelation;
+import org.lcsim.event.RelationalTable;
+import org.lcsim.event.Track;
+import org.lcsim.event.base.BaseRelationalTable;
 
 /**
  * Generic object used to persist track data not available through a Track
@@ -155,4 +162,24 @@
     public boolean isFixedSize() {
         return true;
     }
+
+    private static Pair<EventHeader, RelationalTable> trackDataToTrackCache = null;
+
+    public static RelationalTable getTrackDataToTrackTable(EventHeader event) {
+        if (trackDataToTrackCache == null || trackDataToTrackCache.getFirst() != event) {
+            RelationalTable trackDataToTrack = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
+            List<LCRelation> hitrelations = event.get(LCRelation.class, TRACK_DATA_RELATION_COLLECTION);
+            for (LCRelation relation : hitrelations) {
+                if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
+                    trackDataToTrack.add(relation.getFrom(), relation.getTo());
+                }
+            }
+            trackDataToTrackCache = new Pair<EventHeader, RelationalTable>(event, trackDataToTrack);
+        }
+        return trackDataToTrackCache.getSecond();
+    }
+
+    public static GenericObject getTrackData(EventHeader event, Track track) {
+        return (GenericObject) getTrackDataToTrackTable(event).from(track);
+    }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackDataDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackDataDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackDataDriver.java	Wed Apr 27 11:11:32 2016
@@ -8,7 +8,6 @@
 
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
-import org.lcsim.event.GenericObject;
 import org.lcsim.event.LCRelation;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.event.RelationalTable;
@@ -16,7 +15,6 @@
 import org.lcsim.event.TrackState;
 import org.lcsim.event.TrackerHit;
 import org.lcsim.event.base.BaseLCRelation;
-import org.lcsim.event.base.BaseRelationalTable;
 import org.lcsim.fit.helicaltrack.HelicalTrackCross;
 import org.lcsim.fit.helicaltrack.HelicalTrackHit;
 import org.lcsim.fit.helicaltrack.HelicalTrackStrip;
@@ -25,8 +23,8 @@
 import org.lcsim.util.Driver;
 
 /**
- * Driver used to persist additional {@link Track} information via a
- * {@link GenericObject}.
+ * Driver used to persist additional {@link org.lcsim.event.Track} information via a 
+ * {@link org.lcsim.event.GenericObject} collection.
  *
  * @author Omar Moreno, UCSC
  * @author Sho Uemura, SLAC
@@ -34,7 +32,7 @@
 public final class TrackDataDriver extends Driver {
 
     /** logger **/
-    private static Logger LOGGER  = Logger.getLogger(TrackDataDriver.class.getPackage().getName());
+    private static final Logger LOGGER  = Logger.getLogger(TrackDataDriver.class.getPackage().getName());
     
     
     /** The B field map */
@@ -107,6 +105,7 @@
      * 
      * @param detector LCSim {@link Detector} geometry 
      */     
+    @Override
     protected void detectorChanged(Detector detector) { 
        
         // Get the field map from the detector object
@@ -121,6 +120,7 @@
      * 
      * @param event : LCSim event
      */
+    @Override
     protected void process(EventHeader event) {
 
         // Check if the event contains a collection of the type Track. If it
@@ -135,15 +135,11 @@
 
         // Get the collection of LCRelations relating RotatedHelicalTrackHits to
         // HelicalTrackHits
-        List<LCRelation> rotatedHthToHthRelations = event.get(LCRelation.class, ROTATED_HTH_REL_COL_NAME);
-        BaseRelationalTable hthToRotatedHth = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_ONE,
-                        RelationalTable.Weighting.UNWEIGHTED);
-        hthToRotatedHth.addRelations(rotatedHthToHthRelations);
 
         RelationalTable hitToStrips = TrackUtils.getHitToStripsTable(event);
         RelationalTable hitToRotated = TrackUtils.getHitToRotatedTable(event);
 
-        List<HelicalTrackHit> rotatedHths = event.get(HelicalTrackHit.class, ROTATED_HTH_COL_NAME);
+//        List<HelicalTrackHit> rotatedHths = event.get(HelicalTrackHit.class, ROTATED_HTH_COL_NAME);
 
         // Create a container that will be used to store all TrackData objects.
         List<TrackData> trackDataCollection = new ArrayList<TrackData>();
@@ -159,21 +155,21 @@
         // residuals
         List<LCRelation> trackToTrackResidualsRelations = new ArrayList<LCRelation>();
 
-        double xResidual = 0;
-        double yResidual = 0;
-
-        float totalT0 = 0;
-        float totalHits = 0;
-        float trackTime = 0;
+        double xResidual;
+        double yResidual;
+
+        float totalT0;
+        float totalHits;
+        float trackTime;
 
         int trackerVolume = -1;
 
-        boolean isFirstHit = true;
-
-        HpsSiSensor sensor = null;
-        Hep3Vector stereoHitPosition = null;
-        Hep3Vector trackPosition = null;
-        HelicalTrackHit helicalTrackHit = null;
+        boolean isFirstHit;
+
+        HpsSiSensor sensor;
+        Hep3Vector stereoHitPosition;
+        Hep3Vector trackPosition;
+        HelicalTrackHit helicalTrackHit;
 
         List<Double> t0Residuals = new ArrayList<Double>();
         List<Double> trackResidualsX = new ArrayList<Double>();
@@ -183,9 +179,7 @@
 
         // Loop over each of the track collections retrieved from the event
         for (List<Track> tracks : trackCollections) {
-            
-            
-
+                        
             // Loop over all the tracks in the event
             for (Track track : tracks) {
 
@@ -198,7 +192,10 @@
                 stereoLayers.clear();
                 isFirstHit = true;
 
-                //
+//                TrackState trackStateForResiduals = TrackUtils.getTrackStateAtLocation(track, TrackState.AtLastHit);
+//                if (trackStateForResiduals == null ) trackStateForResiduals= TrackUtils.getTrackStateAtLocation(track, TrackState.AtIP);
+                TrackState trackStateForResiduals = TrackUtils.getTrackStateAtLocation(track, TrackState.AtIP);
+                
                 // Change the position of a HelicalTrackHit to be the corrected
                 // one.
                 // FIXME: Now that multiple track collections are being used, 
@@ -216,7 +213,7 @@
                     // Extrapolate the track to the stereo hit position and
                     // calculate track residuals
                     stereoHitPosition = ((HelicalTrackHit) rotatedStereoHit).getCorrectedPosition();
-                    trackPosition = TrackUtils.extrapolateTrack(track, stereoHitPosition.x());
+                    trackPosition = TrackUtils.extrapolateTrack(trackStateForResiduals, stereoHitPosition.x());
                     xResidual = trackPosition.x() - stereoHitPosition.y();
                     yResidual = trackPosition.y() - stereoHitPosition.z();
                     trackResidualsX.add(xResidual);
@@ -230,7 +227,7 @@
                     
                     // Get the HelicalTrackHit corresponding to the 
                     // RotatedHelicalTrackHit associated with a track
-                    helicalTrackHit = (HelicalTrackHit) hthToRotatedHth.from(rotatedStereoHit);
+                    helicalTrackHit = (HelicalTrackHit) hitToRotated.from(rotatedStereoHit);
                     ((HelicalTrackHit) rotatedStereoHit).setPosition(stereoHitPosition.v());
                     stereoHitPosition = CoordinateTransformations.transformVectorToDetector(stereoHitPosition);
                     helicalTrackHit.setPosition(stereoHitPosition.v());
@@ -261,18 +258,7 @@
 
                 // Extrapolate the track to the face of the Ecal and get the TrackState
                 if( TrackType.isGBL(track.getType())) {
-                    TrackState stateLast = null;
-                    TrackState stateIP = null;
-                    for(int ist= 0; ist < track.getTrackStates().size(); ist++) {
-                        if( track.getTrackStates().get(ist).getLocation() == TrackState.AtLastHit ) 
-                            stateLast = track.getTrackStates().get(ist);
-                        if( track.getTrackStates().get(ist).getLocation() == TrackState.AtIP ) 
-                            stateIP = track.getTrackStates().get(ist);
-                    }
-                    if( stateLast == null)
-                        throw new RuntimeException("last hit track state for GBL track was not found");
-//                    TrackState stateEcal = TrackUtils.extrapolateTrackUsingFieldMap(stateLast, extStartPos, ecalPosition, stepSize, bFieldMap);
-//                    track.getTrackStates().add(stateEcal);
+                    TrackState stateIP = TrackUtils.getTrackStateAtLocation(track, TrackState.AtIP);
                     if( stateIP == null)
                         throw new RuntimeException("IP track state for GBL track was not found");
                     TrackState stateEcalIP = TrackUtils.extrapolateTrackUsingFieldMap(stateIP, extStartPos, ecalPosition, stepSize, bFieldMap);
@@ -317,7 +303,7 @@
         }
         
         // Add all collections to the event
-        event.put(TrackData.TRACK_DATA_COLLECTION, trackDataCollection, TrackTimeData.class, 0);
+        event.put(TrackData.TRACK_DATA_COLLECTION, trackDataCollection, TrackData.class, 0);
         event.put(TrackData.TRACK_DATA_RELATION_COLLECTION, trackDataRelations, LCRelation.class, 0);
         event.put(TRK_RESIDUALS_COL_NAME, trackResidualsCollection, TrackResidualsData.class, 0);
         event.put(TRK_RESIDUALS_REL_COL_NAME, trackToTrackResidualsRelations, LCRelation.class, 0);

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackQualityData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackQualityData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackQualityData.java	Wed Apr 27 11:11:32 2016
@@ -17,10 +17,7 @@
     private final double[] doubles;
 
     /**
-     * Default Ctor
-     *
-     * @param trackerVolume : The SVT volume to which the track used to
-     * calculate the residuals corresponds to.
+     * Default Ctor    
      */
     public TrackQualityData() {
         doubles = new double[2];

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackResidualsData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackResidualsData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackResidualsData.java	Wed Apr 27 11:11:32 2016
@@ -13,84 +13,84 @@
  */
 public class TrackResidualsData implements GenericObject {
 
-	List<Double> trackResidualsX = new ArrayList<Double>();
-	List<Float> trackResidualsY = new ArrayList<Float>();
-	List<Integer> layers = new ArrayList<Integer>();
-	
-	/**
-	 * Default Ctor
-	 * 
-	 * @param trackerVolume : The SVT volume to which the track used to calculate
-	 * 						  the residuals corresponds to.
-	 */
-	public TrackResidualsData(int trackerVolume, List<Integer> layers, List<Double> trackResidualsX, List<Float> trackResidualsY){
-		this.layers.addAll(layers);
-		this.layers.add(trackerVolume);
-		this.trackResidualsX.addAll(trackResidualsX);
-		this.trackResidualsY.addAll(trackResidualsY);
-	}
+    List<Double> trackResidualsX = new ArrayList<Double>();
+    List<Float> trackResidualsY = new ArrayList<Float>();
+    List<Integer> layers = new ArrayList<Integer>();
+    
+    /**
+     * Default Ctor
+     * 
+     * @param trackerVolume : The SVT volume to which the track used to calculate
+     *                        the residuals corresponds to.
+     */
+    public TrackResidualsData(int trackerVolume, List<Integer> layers, List<Double> trackResidualsX, List<Float> trackResidualsY){
+        this.layers.addAll(layers);
+        this.layers.add(trackerVolume);
+        this.trackResidualsX.addAll(trackResidualsX);
+        this.trackResidualsY.addAll(trackResidualsY);
+    }
 
-	/**
-	 * 
-	 * @return tracker volume : 0 if top 1 if bottom
-	 */
-	public int getTrackerVolume(){
-		return layers.get(layers.size() - 1);
-	}
-	
-	/**
-	 * 
-	 */
-	@Override
-	public double getDoubleVal(int index) {
-		return trackResidualsX.get(index);
-	}
+    /**
+     * 
+     * @return tracker volume : 0 if top 1 if bottom
+     */
+    public int getTrackerVolume(){
+        return layers.get(layers.size() - 1);
+    }
+    
+    /**
+     * 
+     */
+    @Override
+    public double getDoubleVal(int index) {
+        return trackResidualsX.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public float getFloatVal(int index) {
-		return trackResidualsY.get(index);
-	}
+    /**
+     * 
+     */
+    @Override
+    public float getFloatVal(int index) {
+        return trackResidualsY.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getIntVal(int index) {
-		return layers.get(index);
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getIntVal(int index) {
+        return layers.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNDouble() {
-		return trackResidualsX.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNDouble() {
+        return trackResidualsX.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNFloat() {
-		return trackResidualsY.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNFloat() {
+        return trackResidualsY.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNInt() {
-		return layers.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNInt() {
+        return layers.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public boolean isFixedSize() {
-		return false;
-	}
+    /**
+     * 
+     */
+    @Override
+    public boolean isFixedSize() {
+        return false;
+    }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackTimeData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackTimeData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackTimeData.java	Wed Apr 27 11:11:32 2016
@@ -12,124 +12,124 @@
  */
 public class TrackTimeData implements GenericObject {
 
-	List<Float> trackTimeData = new ArrayList<Float>(); 
-	List<Double> t0Residuals = new ArrayList<Double>(); 
-	List<Integer> layers = new ArrayList<Integer>(); 
-	
-	// Constants
-	private final static int SVT_VOLUME_INDEX = 0;
-	private final static int TRACK_TIME_INDEX = 1;
-	
-	/**
-	 * Default Ctor
-	 * 
-	 * @param trackTime : The mean t0 time of all hits of a track
-	 * @param trackerVolume : The SVT volume to which the track used to calculate
-	 * 						  the track time corresponds to.
-	 *
-	 */
-	public TrackTimeData(float trackerVolume, double trackTime, List<Integer> layers, List<Double> t0Residuals){
-		trackTimeData.add(trackerVolume);
-		trackTimeData.add((float) trackTime);
-		this.layers.addAll(layers);
-		this.t0Residuals.addAll(t0Residuals);
-	}
-	
-	/**
-	 *	 
-	 * 
-	 * @param layer : 
-	 * @param t0Residual : 
-	 * 
-	 */
-	private void addResidual(int layer, double t0Residual) {
-		layers.add(layer); 
-		t0Residuals.add(t0Residual);
-	}
+    List<Float> trackTimeData = new ArrayList<Float>(); 
+    List<Double> t0Residuals = new ArrayList<Double>(); 
+    List<Integer> layers = new ArrayList<Integer>(); 
+    
+    // Constants
+    private final static int SVT_VOLUME_INDEX = 0;
+    private final static int TRACK_TIME_INDEX = 1;
+    
+    /**
+     * Default Ctor
+     * 
+     * @param trackTime : The mean t0 time of all hits of a track
+     * @param trackerVolume : The SVT volume to which the track used to calculate
+     *                        the track time corresponds to.
+     *
+     */
+    public TrackTimeData(float trackerVolume, double trackTime, List<Integer> layers, List<Double> t0Residuals){
+        trackTimeData.add(trackerVolume);
+        trackTimeData.add((float) trackTime);
+        this.layers.addAll(layers);
+        this.t0Residuals.addAll(t0Residuals);
+    }
+    
+    /**
+     *   
+     * 
+     * @param layer : 
+     * @param t0Residual : 
+     * 
+     */
+    private void addResidual(int layer, double t0Residual) {
+        layers.add(layer); 
+        t0Residuals.add(t0Residual);
+    }
 
-	/**
-	 * 
-	 */
-	public double getTrackTime() { 
-	    return trackTimeData.get(TRACK_TIME_INDEX); 
-	}
-	
-	/**
-	 * 
-	 * 
-	 */
-	public double getT0Residual(int layer) { 
-	    return this.getDoubleVal(layer);
-	}
+    /**
+     * 
+     */
+    public double getTrackTime() { 
+        return trackTimeData.get(TRACK_TIME_INDEX); 
+    }
+    
+    /**
+     * 
+     * 
+     */
+    public double getT0Residual(int layer) { 
+        return this.getDoubleVal(layer);
+    }
 
-	/**
-	 * 
-	 */
-	public double getClusterTime(int layer) {
-	   return this.getTrackTime() - this.getT0Residual(layer); 
-	}
-	
-	/**
-	 * 
-	 * 
-	 */
-	public boolean isTopSvtVolume() { 
-	    return (trackTimeData.get(SVT_VOLUME_INDEX) == 0) ? true : false;
-	}
-	
-	/**
-	 * 
-	 */
-	@Override
-	public double getDoubleVal(int index) {
-		return t0Residuals.get(index);
-	}
+    /**
+     * 
+     */
+    public double getClusterTime(int layer) {
+       return this.getTrackTime() - this.getT0Residual(layer); 
+    }
+    
+    /**
+     * 
+     * 
+     */
+    public boolean isTopSvtVolume() { 
+        return (trackTimeData.get(SVT_VOLUME_INDEX) == 0) ? true : false;
+    }
+    
+    /**
+     * 
+     */
+    @Override
+    public double getDoubleVal(int index) {
+        return t0Residuals.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public float getFloatVal(int index) {
-		return trackTimeData.get(index);
-	}
+    /**
+     * 
+     */
+    @Override
+    public float getFloatVal(int index) {
+        return trackTimeData.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getIntVal(int index) {
-		return layers.get(index);
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getIntVal(int index) {
+        return layers.get(index);
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNDouble() {
-		return t0Residuals.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNDouble() {
+        return t0Residuals.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNFloat() {
-		return trackTimeData.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNFloat() {
+        return trackTimeData.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public int getNInt() {
-		return layers.size();
-	}
+    /**
+     * 
+     */
+    @Override
+    public int getNInt() {
+        return layers.size();
+    }
 
-	/**
-	 * 
-	 */
-	@Override
-	public boolean isFixedSize() {
-		return false;
-	}
+    /**
+     * 
+     */
+    @Override
+    public boolean isFixedSize() {
+        return false;
+    }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackUtils.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackUtils.java	Wed Apr 27 11:11:32 2016
@@ -1,18 +1,26 @@
 package org.hps.recon.tracking;
 
+import hep.physics.matrix.SymmetricMatrix;
+import hep.physics.vec.BasicHep3Vector;
+import hep.physics.vec.Hep3Matrix;
+import hep.physics.vec.Hep3Vector;
+import hep.physics.vec.VecOp;
+
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import hep.physics.matrix.SymmetricMatrix;
-import hep.physics.vec.BasicHep3Vector;
-import hep.physics.vec.Hep3Matrix;
-import hep.physics.vec.Hep3Vector;
-import hep.physics.vec.SpacePoint;
-import hep.physics.vec.VecOp;
+import org.apache.commons.math3.util.Pair;
+import org.hps.recon.tracking.EventQuality.Quality;
+import org.hps.recon.tracking.gbl.HelicalTrackStripGbl;
+
+import static org.lcsim.constants.Constants.fieldConversion;
 
 import org.lcsim.detector.ITransform3D;
 import org.lcsim.detector.solids.Box;
@@ -48,10 +56,6 @@
 import org.lcsim.util.swim.Helix;
 import org.lcsim.util.swim.Line;
 import org.lcsim.util.swim.Trajectory;
-import org.hps.recon.tracking.EventQuality.Quality;
-import org.hps.recon.tracking.gbl.HelicalTrackStripGbl;
-
-import static org.lcsim.constants.Constants.fieldConversion;
 
 /**
  * Assorted helper functions for the track and helix objects in lcsim. Re-use as
@@ -60,7 +64,6 @@
  * @author Omar Moreno <[log in to unmask]>
  */
 // TODO: Switch to tracking/LCsim coordinates for the extrapolation output!
-// FIXME: This class should probably be broken up into several different sets of utilities by type. --JM
 public class TrackUtils {
 
     /**
@@ -75,7 +78,7 @@
      *
      * @param track
      * @param x
-     * @return
+     * @return the position along the x-axis
      */
     public static Hep3Vector extrapolateHelixToXPlane(Track track, double x) {
         return extrapolateHelixToXPlane(getHTF(track), x);
@@ -85,13 +88,74 @@
         return extrapolateHelixToXPlane(getHTF(track), x);
     }
     
+    /** 
+     * Change reference point of helix (following L3 Internal Note 1666.)
+     * @param newRefPoint - The new reference point in XY
+     */
+    public static double[] getParametersAtNewRefPoint(double[] newRefPoint, HpsHelicalTrackFit helicalTrackFit) {
+        return getParametersAtNewRefPoint(newRefPoint, helicalTrackFit.getRefPoint(),helicalTrackFit.parameters());
+    }
+    
+    /** 
+     * Change reference point of helix (following L3 Internal Note 1666.)
+     * @param newRefPoint - The new reference point in XY
+     */
+    public static double[] getParametersAtNewRefPoint(double[] newRefPoint, double[] __refPoint, 
+                                                 double[] parameters) {
+
+        double phi0 = parameters[HelicalTrackFit.phi0Index];
+        double curvature =parameters[HelicalTrackFit.curvatureIndex];
+        double dca = parameters[HelicalTrackFit.dcaIndex];
+        double slope = parameters[HelicalTrackFit.slopeIndex]; 
+        double z0 = parameters[HelicalTrackFit.z0Index];
+
+        //take care of phi0 range if needed (this matters for dphi below I think)
+        // L3 defines it in the range [-pi,pi]
+        if(phi0 > Math.PI) 
+            phi0 -= Math.PI*2;
+        
+        double dx = newRefPoint[0] - __refPoint[0];
+        double dy = newRefPoint[1] - __refPoint[1];
+        double sinphi = Math.sin(phi0);
+        double cosphi = Math.cos(phi0);
+        double R = 1.0/curvature;
+
+        // calculate new phi
+        double phinew = Math.atan2( sinphi - dx/(R-dca) , cosphi + dy/(R-dca)  );
+
+        // difference in phi
+        // watch out for ambiguity
+        double dphi = phinew - phi0;
+        if (Math.abs( dphi ) > Math.PI) 
+            throw new RuntimeException("dphi is large " +  dphi + " from phi0 " + phi0 
+                                        + " and phinew " + phinew + " take care of the ambiguity!!??");
+        
+        // calculate new dca
+        double dcanew = dca + dx*sinphi - dy*cosphi + (dx*cosphi + dy*sinphi)*Math.tan( dphi/2. );
+
+        // path length from old to new point
+        double s = -1.0*dphi/curvature;
+
+        // new z0
+        double z0new = z0 + s*slope;
+
+        // new array
+        double[] params = new double[5];
+        params[HelicalTrackFit.phi0Index] = phinew;
+        params[HelicalTrackFit.curvatureIndex] = curvature;
+        params[HelicalTrackFit.dcaIndex] = dcanew;
+        params[HelicalTrackFit.slopeIndex] = slope;
+        params[HelicalTrackFit.z0Index] = z0new;
+        return params;
+    }
+    
 
     /**
      * Extrapolate helix to a position along the x-axis. Re-use HelixUtils.
      *
-     * @param track
+     * @param htf
      * @param x
-     * @return
+     * @return the position along the x-axis
      */
     public static Hep3Vector extrapolateHelixToXPlane(HelicalTrackFit htf, double x) {
         double s = HelixUtils.PathToXPlane(htf, x, 0., 0).get(0);
@@ -282,7 +346,7 @@
      *
      * @param track - to be extrapolated
      * @param z
-     * @return
+     * @return extrapolated position
      */
     public static Hep3Vector extrapolateTrack(Track track, double z) {
         return extrapolateTrack(track.getTrackStates().get(0),z);
@@ -293,7 +357,7 @@
      *
      * @param track - to be extrapolated
      * @param z
-     * @return
+     * @return extrapolated position
      */
     public static Hep3Vector extrapolateTrack(TrackState track, double z) {
 
@@ -329,10 +393,8 @@
     /**
      * Extrapolate track to given position, using dipole position from geometry.
      *
-     * @param helix - to be extrapolated
-     * @param track - position along the x-axis of the helix in lcsim
-     * coordiantes
-     * @return
+     * @param track - position along the x-axis of the helix in lcsim coordinates
+     * @return extrapolated position
      */
     public static Hep3Vector extrapolateTrack(Track track, double z, Detector detector) {
 
@@ -375,7 +437,7 @@
      *
      * @param helix - to be extrapolated
      * @param z - position along the x-axis of the helix in lcsim coordiantes
-     * @return
+     * @return the extrapolated position
      */
     public static Hep3Vector extrapolateTrack(HelicalTrackFit helix, double z) {
         SeedTrack trk = new SeedTrack();
@@ -800,11 +862,11 @@
     
     
     /**
-     * Transform MCParticle into a Helix object. Note that it produces the helix
-     * parameters at nominal x=0 and assumes that there is no field at x<0
-     *
-     * @param mcp MC particle to be transformed
-     * @param org origin to be used for the track 
+     * Transform MCParticle into a {@link HelicalTrackFit} object. Note that it produces the {@link HelicalTrackFit}
+     * parameters at nominal reference point at origin and assumes that there is no field at x<0
+     *
+     * @param mcp - MC particle to be transformed
+     * @param origin  - origin to be used for the track 
      * @return {@link HelicalTrackFit} object based on the MC particle
      */
     public static HelicalTrackFit getHTF(MCParticle mcp, Hep3Vector origin, double Bz) {
@@ -870,27 +932,7 @@
         return htf;
     }
 
-    public static StraightLineTrack findSLTAtZ(Track trk1, double zVal, boolean useFringe) {
-        SeedTrack s1 = (SeedTrack) trk1;
-        HelicalTrackFit htf1 = s1.getSeedCandidate().getHelix();
-        HPSTrack hpstrk1 = new HPSTrack(htf1);
-        Hep3Vector pos1;
-        if (useFringe) {
-            // broken because you need ot provide the Field Map to get this...
-//            pos1 = hpstrk1.getPositionAtZMap(100.0, zVal, 5.0)[0];            
-        } else
-            pos1 = TrackUtils.extrapolateTrack(trk1, zVal);
-        // System.out.printf("%s: Position1 at edge of fringe %s\n",this.getClass().getSimpleName(),pos1.toString());
-        Helix traj = (Helix) hpstrk1.getTrajectory();
-        if (traj == null) {
-            SpacePoint r0 = new SpacePoint(HelixUtils.PointOnHelix(htf1, 0));
-            traj = new Helix(r0, htf1.R(), htf1.phi0(), Math.atan(htf1.slope()));
-        }
-        HelixConverter converter = new HelixConverter(0.);
-        StraightLineTrack slt1 = converter.Convert(traj);
-        // System.out.printf("%s: straight line track: x0=%f,y0=%f,z0=%f dz/dx=%f dydx=%f targetY=%f targetZ=%f \n",this.getClass().getSimpleName(),slt1.x0(),slt1.y0(),slt1.z0(),slt1.dzdx(),slt1.dydx(),slt1.TargetYZ()[0],slt1.TargetYZ()[1]);
-        return slt1;
-    }
+    
 
     public static MCParticle getMatchedTruthParticle(Track track) {
         boolean debug = false;
@@ -984,24 +1026,36 @@
         return new HelicalTrackHit(pos, hitcov, dedx, time, type, rhits, detname, layer, beflag);
     }
 
+    private static Pair<EventHeader, RelationalTable> hitToStripsCache = null;
+
     public static RelationalTable getHitToStripsTable(EventHeader event) {
-        RelationalTable hitToStrips = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
-        List<LCRelation> hitrelations = event.get(LCRelation.class, "HelicalTrackHitRelations");
-        for (LCRelation relation : hitrelations)
-            if (relation != null && relation.getFrom() != null && relation.getTo() != null)
-                hitToStrips.add(relation.getFrom(), relation.getTo());
-
-        return hitToStrips;
-    }
+        if (hitToStripsCache == null || hitToStripsCache.getFirst() != event) {
+            RelationalTable hitToStrips = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
+            List<LCRelation> hitrelations = event.get(LCRelation.class, "HelicalTrackHitRelations");
+            for (LCRelation relation : hitrelations) {
+                if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
+                    hitToStrips.add(relation.getFrom(), relation.getTo());
+                }
+            }
+            hitToStripsCache = new Pair<EventHeader, RelationalTable>(event, hitToStrips);
+        }
+        return hitToStripsCache.getSecond();
+    }
+
+    private static Pair<EventHeader, RelationalTable> hitToRotatedCache = null;
 
     public static RelationalTable getHitToRotatedTable(EventHeader event) {
-
-        RelationalTable hitToRotated = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_ONE, RelationalTable.Weighting.UNWEIGHTED);
-        List<LCRelation> rotaterelations = event.get(LCRelation.class, "RotatedHelicalTrackHitRelations");
-        for (LCRelation relation : rotaterelations)
-            if (relation != null && relation.getFrom() != null && relation.getTo() != null)
-                hitToRotated.add(relation.getFrom(), relation.getTo());
-        return hitToRotated;
+        if (hitToRotatedCache == null || hitToRotatedCache.getFirst() != event) {
+            RelationalTable hitToRotated = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_ONE, RelationalTable.Weighting.UNWEIGHTED);
+            List<LCRelation> rotaterelations = event.get(LCRelation.class, "RotatedHelicalTrackHitRelations");
+            for (LCRelation relation : rotaterelations) {
+                if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
+                    hitToRotated.add(relation.getFrom(), relation.getTo());
+                }
+            }
+            hitToRotatedCache = new Pair<EventHeader, RelationalTable>(event, hitToRotated);
+        }
+        return hitToRotatedCache.getSecond();
     }
 
     public static double getTrackTime(Track track, RelationalTable hitToStrips, RelationalTable hitToRotated) {
@@ -1019,6 +1073,20 @@
         for (TrackerHit hit : track.getTrackerHits())
             hits.addAll(hitToStrips.allFrom(hitToRotated.from(hit)));
         return hits;
+    }
+
+    public static List<TrackerHit> sortHits(Collection<TrackerHit> hits) {
+        List<TrackerHit> hitList = new ArrayList<TrackerHit>(hits);
+        Collections.sort(hitList, new LayerComparator());
+        return hitList;
+    }
+
+    private static class LayerComparator implements Comparator<TrackerHit> {
+
+        @Override
+        public int compare(TrackerHit o1, TrackerHit o2) {
+            return Integer.compare(TrackUtils.getLayer(o1), TrackUtils.getLayer(o2));
+        }
     }
 
     public static boolean hasSharedStrips(Track track1, Track track2, RelationalTable hitToStrips, RelationalTable hitToRotated) {
@@ -1091,7 +1159,7 @@
      * @param trk
      * @param hitToStrips
      * @param hitToRotated
-     * @return
+     * @return isolations for all 12 strip layers
      */
     public static Double[] getIsolations(Track trk, RelationalTable hitToStrips, RelationalTable hitToRotated) {
         Double[] isolations = new Double[12];
@@ -1263,7 +1331,7 @@
      * @param r0
      * @param q
      * @param B
-     * @return
+     * @return the created trajectory
      */
     public static Trajectory getTrajectory(Hep3Vector p0, org.lcsim.spacegeom.SpacePoint r0, double q, double B) {
         SpaceVector p = new CartesianVector(p0.v());
@@ -1279,15 +1347,25 @@
             return new Line(r0, phi, lambda);
     }
 
-    public static TrackState getTrackStateAtECal(Track trk) {
+    /**
+     * Port of Track.getTrackState(int location) from the C++ LCIO API.
+     * @param trk A track.
+     * @param location A TrackState location constant
+     * @return The first matching TrackState; null if none is found.
+     */
+    public static TrackState getTrackStateAtLocation(Track trk, int location) {
         for (TrackState state : trk.getTrackStates()) {
-            if (state.getLocation() == TrackState.AtCalorimeter) {
+            if (state.getLocation() == location) {
                 return state;
             }
         }
         return null;
     }
 
+    public static TrackState getTrackStateAtECal(Track trk) {
+        return getTrackStateAtLocation(trk, TrackState.AtCalorimeter);
+    }
+    
     public static Hep3Vector getBField(Detector detector) {
         return detector.getFieldMap().getField(new BasicHep3Vector(0., 0., 500.0));
     }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackerReconDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackerReconDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/TrackerReconDriver.java	Wed Apr 27 11:11:32 2016
@@ -13,11 +13,9 @@
 import java.util.logging.Logger;
 
 import org.lcsim.event.EventHeader;
-import org.lcsim.event.LCRelation;
 import org.lcsim.event.RelationalTable;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackerHit;
-import org.lcsim.event.base.BaseRelationalTable;
 import org.lcsim.event.base.BaseTrack;
 import org.lcsim.fit.helicaltrack.HelicalTrackHit;
 import org.lcsim.geometry.Detector;
@@ -37,7 +35,7 @@
 public final class TrackerReconDriver extends Driver {
 
     private static final Logger LOGGER = Logger.getLogger(TrackerReconDriver.class.getPackage().getName());
-    
+
     // Debug flag.
     private boolean debug = false;
     // Tracks found across all events.
@@ -65,7 +63,7 @@
     private double rmsTimeCut = -1;
     private boolean rejectUncorrectedHits = true;
     private boolean rejectSharedHits = false;
-    
+
     public TrackerReconDriver() {
     }
 
@@ -145,10 +143,8 @@
 
         // Get B-field Y with no sign. Seed Tracker doesn't like signed B-field components.
         // FIXME Is this always right?
-//        this.bfield = Math.abs((detector.getFieldMap().getField(new BasicHep3Vector(0, 0, 0)).y()));
-        double zvalInTracker=500.0;//50cm...about the middle
-        Hep3Vector fieldInTracker=detector.getFieldMap().getField(new BasicHep3Vector(0, 0, zvalInTracker));
-        LOGGER.config("fieldInTracker at "+zvalInTracker+": Bx = "+fieldInTracker.x()+"; By = "+fieldInTracker.y()+"; Bz = "+fieldInTracker.z());      
+        Hep3Vector fieldInTracker = TrackUtils.getBField(detector);
+        LOGGER.config("fieldInTracker: Bx = " + fieldInTracker.x() + "; By = " + fieldInTracker.y() + "; Bz = " + fieldInTracker.z());
         this.bfield = Math.abs(fieldInTracker.y());
         LOGGER.config(String.format("%s: Set B-field to %.6f\n", this.getClass().getSimpleName(), this.bfield));
 
@@ -165,8 +161,9 @@
         //
         // 1) Driver to run Seed Tracker.
         //
-        if (!strategyResource.startsWith("/"))
+        if (!strategyResource.startsWith("/")) {
             strategyResource = "/org/hps/recon/tracking/strategies/" + strategyResource;
+        }
         List<SeedStrategy> sFinallist = StrategyXMLUtils.getStrategyListFromInputStream(this.getClass().getResourceAsStream(strategyResource));
         SeedTracker stFinal = new SeedTracker(sFinallist, this._useHPSMaterialManager, this.includeMS);
         stFinal.setApplySectorBinning(_applySectorBinning);
@@ -177,14 +174,18 @@
         stFinal.setInputCollectionName(stInputCollectionName);
         stFinal.setTrkCollectionName(trackCollectionName);
         stFinal.setBField(bfield);
-        if (debug)
+        if (debug) {
             stFinal.setDiagnostics(new SeedTrackerDiagnostics());
+        }
         // stFinal.setSectorParams(false); //this doesn't actually seem to do anything
         stFinal.setSectorParams(1, 10000);
         add(stFinal);
 
-        if (rmsTimeCut > 0)
-            stFinal.setTrackCheck(new HitTimeTrackCheck(rmsTimeCut));
+        if (rmsTimeCut > 0) {
+            HitTimeTrackCheck timeCheck = new HitTimeTrackCheck(rmsTimeCut);
+            timeCheck.setDebug(debug);
+            stFinal.setTrackCheck(timeCheck);
+        }
     }
 
     /**
@@ -198,10 +199,11 @@
 
         // Debug printouts.
         if (debug) {
-            if (event.hasCollection(HelicalTrackHit.class, stInputCollectionName))
+            if (event.hasCollection(HelicalTrackHit.class, stInputCollectionName)) {
                 System.out.println(this.getClass().getSimpleName() + ": The HelicalTrackHit collection " + stInputCollectionName + " has " + event.get(HelicalTrackHit.class, stInputCollectionName).size() + " hits.");
-            else
+            } else {
                 System.out.println(this.getClass().getSimpleName() + ": No HelicalTrackHit collection for this event");
+            }
             // Check for Tracks.
             List<Track> tracks = event.get(Track.class, trackCollectionName);
             System.out.println(this.getClass().getSimpleName() + ": The Track collection " + trackCollectionName + " has " + tracks.size() + " tracks.");
@@ -236,27 +238,13 @@
         }
 
         if (rejectSharedHits) {
-
-            RelationalTable hittostrip = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
-            List<LCRelation> hitrelations = event.get(LCRelation.class, "HelicalTrackHitRelations");
-            for (LCRelation relation : hitrelations) {
-                if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
-                    hittostrip.add(relation.getFrom(), relation.getTo());
-                }
-            }
-
-            RelationalTable hittorotated = new BaseRelationalTable(RelationalTable.Mode.ONE_TO_ONE, RelationalTable.Weighting.UNWEIGHTED);
-            List<LCRelation> rotaterelations = event.get(LCRelation.class, "RotatedHelicalTrackHitRelations");
-            for (LCRelation relation : rotaterelations) {
-                if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
-                    hittorotated.add(relation.getFrom(), relation.getTo());
-                }
-            }
+            RelationalTable hitToStrips = TrackUtils.getHitToStripsTable(event);
+            RelationalTable hitToRotated = TrackUtils.getHitToRotatedTable(event);
 
             Map<TrackerHit, List<Track>> stripsToTracks = new HashMap<TrackerHit, List<Track>>();
             for (Track track : tracks) {
                 for (TrackerHit hit : track.getTrackerHits()) {
-                    Collection<TrackerHit> htsList = hittostrip.allFrom(hittorotated.from(hit));
+                    Collection<TrackerHit> htsList = hitToStrips.allFrom(hitToRotated.from(hit));
                     for (TrackerHit strip : htsList) {
                         List<Track> sharedTracks = stripsToTracks.get(strip);
                         if (sharedTracks == null) {
@@ -272,7 +260,7 @@
             while (iter.hasNext()) {
                 Track track = iter.next();
                 for (TrackerHit hit : track.getTrackerHits()) {
-                    Collection<TrackerHit> htsList = hittostrip.allFrom(hittorotated.from(hit));
+                    Collection<TrackerHit> htsList = hitToStrips.allFrom(hitToRotated.from(hit));
                     for (TrackerHit strip : htsList) {
                         List<Track> sharedTracks = stripsToTracks.get(strip);
                         if (sharedTracks.size() > 1) {
@@ -304,15 +292,16 @@
      * @param tracks The list of <code>Track</code> objects.
      */
     private void setTrackType(List<Track> tracks) {
-        for (Track track : tracks)
+        for (Track track : tracks) {
             ((BaseTrack) track).setTrackType(BaseTrack.TrackType.Y_FIELD.ordinal());
+        }
     }
 
     @Override
     public void endOfData() {
         if (debug) {
             System.out.println("-------------------------------------------");
-            System.out.println(this.getName() + " found " + ntracks + " tracks in " + nevents + " events which is " + ((double) ntracks / (double) nevents) + " tracks per event.");
+            System.out.println(this.getName() + " with strategy " + strategyResource + " found " + ntracks + " tracks in " + nevents + " events which is " + ((double) ntracks / (double) nevents) + " tracks per event.");
         }
     }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/WTrack.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/WTrack.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/WTrack.java	Wed Apr 27 11:11:32 2016
@@ -12,9 +12,12 @@
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
 
 /**
- * Track parameterization representation.
- * 
- * @author phansson
+ * Track representation based on paper
+ * Paul Avery, CBX 98-39, June 9, 1998
+ *  
+ * Used primarily for the algorithm to intersect a helix with a generic plane in space.
+ *  
+ * @author phansson <[log in to unmask]>
  */
 public class WTrack {
 
@@ -25,7 +28,6 @@
     private boolean _debug = false;
     private final int max_iterations_intercept = 10;
     private final double epsilon_intercept = 1e-4;
-
       
     /**
      * Constructor. Assumes that b-field is in detector z direction. 
@@ -34,8 +36,8 @@
      * @param bfield value and sign of magnetic field
      */
     public WTrack(HelicalTrackFit track, double bfield) {
-    	_htf = track;
-    	//_bfield = flip ? -1.0 * bfield : bfield; // flip if needed
+        _htf = track;
+        //_bfield = flip ? -1.0 * bfield : bfield; // flip if needed
         _bfield = bfield; 
         _a = -1 * Constants.fieldConversion * _bfield * Math.signum(track.R());
         double p = track.p(Math.abs(_bfield));
@@ -185,7 +187,7 @@
      * Get point on helix at path length s in arbitrary oriented, constant magnetic field with unit vector h
      * @param s - path length
      * @param h - magnetic field unit vector
-     * @return
+     * @return get a 3D point along the helix
      */
     private Hep3Vector getPointOnHelix(double s, Hep3Vector h) {
         WTrack track = this;
@@ -224,8 +226,8 @@
     }
 
     /*
-    	Calculate the exact position of the new helix parameters at path length s in an arbitrarily oriented, 
-    	constant magnetic field point xp is the point h is a unit vector in the direction of the magnetic field.         
+        Calculate the exact position of the new helix parameters at path length s in an arbitrarily oriented, 
+        constant magnetic field point xp is the point h is a unit vector in the direction of the magnetic field.         
      * @param s - path length
      * @param h - magnetic field unit vector
      * @return track parameters
@@ -262,11 +264,9 @@
      * @param xp point on the plane
      * @param eta unit vector of the plane 
      * @param h unit vector of magnetic field
-     * @return
+     * @return the intersection point of the helix with the plane
      */
     public Hep3Vector getHelixAndPlaneIntercept(Hep3Vector xp, Hep3Vector eta, Hep3Vector h) {
-
-        
 
         int iteration = 1;
         double s_total = 0.;

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/axial/HelicalTrack2DHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/axial/HelicalTrack2DHit.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/axial/HelicalTrack2DHit.java	Wed Apr 27 11:11:32 2016
@@ -11,8 +11,8 @@
  * This class is explicitly for HPS where the length of the
  * sensors are (mostly) along the detector 
  * y-dimension ( == HelicalTrackFit x-dimension);
+ * Copied/Modified from org.lcsim.recon.tracking.helicaltrack.HelicalTrack2DHit.java
  * @author Matt Graham <[log in to unmask]>
- * Copied/Modified from org.lcsim.recon.tracking.helicaltrack.HelicalTrack2DHit.java
  */
 public class HelicalTrack2DHit  extends HelicalTrackHit {
     private double _axmin;//min value along the bend-direction..
@@ -27,8 +27,6 @@
      * @param dEdx deposited energy
      * @param time hit time
      * @param rawhits list of raw hits
-     * @param axmin minimum z for the strip
-     * @param axmax maximum z for the strip
      * @param detname detector name
      * @param layer layer number
      * @param beflag

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/FittedGblTrajectory.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/FittedGblTrajectory.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/FittedGblTrajectory.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,20 @@
 package org.hps.recon.tracking.gbl;
 
+import hep.physics.matrix.SymmetricMatrix;
+import hep.physics.vec.Hep3Vector;
+
+import java.util.Map;
+import java.util.logging.Logger;
+
+import org.apache.commons.math3.util.Pair;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
+import org.hps.recon.tracking.TrackUtils;
+import org.hps.recon.tracking.gbl.matrix.Matrix;
+import org.hps.recon.tracking.gbl.matrix.SymMatrix;
+import org.hps.recon.tracking.gbl.matrix.Vector;
 import org.lcsim.event.Track;
+import org.lcsim.fit.helicaltrack.HelicalTrackFit;
+import org.lcsim.fit.helicaltrack.HelixUtils;
 
 /**
  * A class that collects information about a fitted GBL trajectory. 
@@ -9,6 +23,9 @@
  * 
  */
 public class FittedGblTrajectory {
+    
+    public static Logger LOGGER = Logger.getLogger(FittedGblTrajectory.class.getName());
+
     public enum GBLPOINT {
         IP(0), LAST(1), VERTEX(2);
         private int numVal;
@@ -34,6 +51,7 @@
         }
         
     }
+    
     public static enum GBLPARIDX {
         QOVERP(0),YTPRIME(1),XTPRIME(2),XT(3),YT(4);
         private int _value;
@@ -44,18 +62,101 @@
             return _value;
         }
     };
+    
     private GblTrajectory _traj;
     private double _chi2;
     private double _lost;
     private int _ndf;
     private Track _seed = null;
-    private GBLTrackData _t = null;
+    private Map<Integer, Double> pathLengthMap = null;
+
+    /**
+     * Default constructor.
+     * 
+     * @param traj
+     * @param chi2
+     * @param ndf
+     * @param lost
+     */
     public FittedGblTrajectory(GblTrajectory traj, double chi2, int ndf, double lost) {
         _traj = traj;
         _chi2 = chi2;
         _ndf = ndf;
         _lost = lost;
     }
+    
+    /**
+     * Find the index (or label) of the GBL point on the trajectory from the {@link GBLPOINT}.
+     * @param point
+     * @return the index of the GBL point on the trajectory from the enum
+     */
+    public int getPointIndex(GBLPOINT point) {
+        int gblPointIndex;
+        if (point.compareTo(GBLPOINT.IP) == 0)
+            gblPointIndex = 1;
+        else if (point.compareTo(GBLPOINT.LAST) == 0)
+            gblPointIndex = _traj.getNumPoints();
+        else 
+            throw new RuntimeException("This GBL point " + point.toString() + "( " + point.name() + ") is not valid");
+        return gblPointIndex;
+    }
+    
+    
+    /**
+     * Find the corrections and covariance matrix for a particular {@link GBLPOINT}
+     * @param point
+     * @param locPar
+     * @param locCov
+     */
+    public void getResults(GBLPOINT point, Vector locPar, SymMatrix locCov) {
+        
+        // find the GBL point index
+        int gblPointIndex = getPointIndex(point);
+    
+        // get the results
+        getResults(gblPointIndex, locPar, locCov);
+
+    }
+    
+    
+    /**
+     * Find the corrections and covariance matrix for a particular point on the GBL trajectory
+     * @param iLabel
+     * @param locPar
+     * @param locCov
+     */
+    public void getResults(int iLabel, Vector locPar, SymMatrix locCov) {
+        
+        // Get the result from the trajectory
+        int ok = _traj.getResults(iLabel, locPar, locCov);
+        
+        // check that the fit was ok
+        if( ok != 0)
+            throw new RuntimeException("Trying to extract GBL corrections for fit that failed!?");
+    }
+    
+    
+    /**
+     * Find the path length to this point.
+     * @param point - {@link GBLPOINT} point
+     * @return path length
+     */
+    public double getPathLength(GBLPOINT point) {
+        int gblPointIndex = getPointIndex(point);
+        return getPathLength(gblPointIndex);
+    }
+    
+    /**
+     * Find the path length to this point.
+     * @param iLabel - GBL point index
+     * @return path length
+     */
+    public double getPathLength(int iLabel) {
+        if( !this.pathLengthMap.containsKey(iLabel) ) 
+            throw new RuntimeException("This iLabel " + iLabel + " doesn't exists in the path length map.");
+        return this.pathLengthMap.get(iLabel);
+    }
+    
     public void set_seed(Track seed) {
         _seed = seed;
     }
@@ -74,5 +175,149 @@
     public int get_ndf() {
         return _ndf;
     }
+
+    public void setPathLengthMap(Map<Integer, Double> pathLengthMap) {
+        this.pathLengthMap = pathLengthMap;
+    }
+    
+    public Map<Integer, Double> getPathLengthMap() {
+        if (this.pathLengthMap == null)
+            throw new RuntimeException("No path length map has been set on this trajectory!");
+        return this.pathLengthMap;
+    }
+
+    
+    
+    /**
+     * Get the corrected perigee parameters and covariance matrix for a point on the {@link GblTrajectory}.
+     * 
+     * FIXME the covariance matrix is not properly propagated along the trajectory right now!
+     * 
+     * @param htf - helix to be corrected
+     * @param point - {@link GBLPOINT} on the trajectory
+     * @param bfield - magnitude of B-field.
+     * @return the corrected perigee parameters and covariance matrix
+     */
+    public Pair<double[], SymmetricMatrix> getCorrectedPerigeeParameters(HelicalTrackFit htf, GBLPOINT point, double bfield) {
+        
+        // find the point on the trajectory from the GBLPOINT
+        int iLabel = getPointIndex(point);
+        
+        return getCorrectedPerigeeParameters(htf, iLabel, bfield);
+                
+    }
+
+    
+    /**
+     * Get the corrected perigee parameters and covariance matrix for a point on the {@link GblTrajectory}.
+     * 
+     * FIXME the covariance matrix is not properly propagated along the trajectory right now!
+     * 
+     * @param htf - helix to be corrected
+     * @param iLabel - label of the point on the {@link GblTrajectory}
+     * @param bfield - magnitude of B-field.
+     * @return the corrected perigee parameters
+     */
+    public Pair<double[], SymmetricMatrix> getCorrectedPerigeeParameters(HelicalTrackFit htf, int iLabel, double bfield) {
+
+        // Get corrections from GBL fit
+        Vector locPar = new Vector(5);
+        SymMatrix locCov = new SymMatrix(5);
+
+        // Extract the corrections to the track parameters and the covariance matrix from the GBL trajectory
+        getResults(iLabel, locPar, locCov); 
+
+        // Use the super class to keep track of reference point of the helix
+        HpsHelicalTrackFit helicalTrackFit = new HpsHelicalTrackFit(htf);
+        double[] refIP = helicalTrackFit.getRefPoint();
+
+        // Calculate new reference point for this point
+        // This is the intersection of the helix with the plane
+        // The trajectory has this information already in the form of a map between GBL point and path length
+        double pathLength = getPathLength(iLabel);
+        Hep3Vector refPointVec = HelixUtils.PointOnHelix(helicalTrackFit, pathLength);
+        double[] refPoint = new double[]{refPointVec.x(), refPointVec.y()};
+        
+        LOGGER.finest("pathLength " + pathLength + " -> refPointVec " + refPointVec.toString());
+        
+        // Propagate the helix to new reference point
+        double[] helixParametersAtPoint = TrackUtils.getParametersAtNewRefPoint(refPoint, helicalTrackFit);
+        
+        // Create a new helix with the new parameters and the new reference point
+        HpsHelicalTrackFit helicalTrackFitAtPoint = new HpsHelicalTrackFit(helixParametersAtPoint, helicalTrackFit.covariance(), 
+                                                        helicalTrackFit.chisq(), helicalTrackFit.ndf(), helicalTrackFit.PathMap(), 
+                                                        helicalTrackFit.ScatterMap(), refPoint);
+                
+        // find the corrected perigee track parameters at this point
+        double[] helixParametersAtPointCorrected = GblUtils.getCorrectedPerigeeParameters(locPar, helicalTrackFitAtPoint, bfield);
+        
+        // create a new helix
+        HpsHelicalTrackFit helicalTrackFitAtPointCorrected = new HpsHelicalTrackFit(helixParametersAtPointCorrected, helicalTrackFit.covariance(), 
+                helicalTrackFit.chisq(), helicalTrackFit.ndf(), helicalTrackFit.PathMap(), 
+                helicalTrackFit.ScatterMap(), refPoint);
+        
+        // change reference point back to the original one
+        double[] helixParametersAtIPCorrected = TrackUtils.getParametersAtNewRefPoint(refIP, helicalTrackFitAtPointCorrected);
+        
+        // create a new helix for the new parameters at the IP reference point
+        HpsHelicalTrackFit helicalTrackFitAtIPCorrected = new HpsHelicalTrackFit(helixParametersAtIPCorrected, helicalTrackFit.covariance(), 
+                helicalTrackFit.chisq(), helicalTrackFit.ndf(), helicalTrackFit.PathMap(), 
+                helicalTrackFit.ScatterMap(), refIP);
+        
+        
+        // Calculate the updated covariance
+        Matrix jacobian = GblUtils.getCLToPerigeeJacobian(helicalTrackFit, helicalTrackFitAtIPCorrected, bfield);
+        Matrix helixCovariance = jacobian.times(locCov.times(jacobian.transpose()));
+        SymmetricMatrix cov = new SymmetricMatrix(5);
+        for (int i = 0; i < 5; i++) {
+            for (int j = 0; j < 5; j++) {
+                if (i >= j) {
+                    cov.setElement(i, j, helixCovariance.get(i, j));
+                }
+            }
+        }
+        LOGGER.finest("corrected helix covariance:\n" + cov);
+        
+        double parameters_gbl[] = helicalTrackFitAtIPCorrected.parameters();
+        
+        return new Pair<double[], SymmetricMatrix>(parameters_gbl,cov);
+    }
+
+    
+    
+    /**
+     * Extract kinks across the trajectory.
+     * @return kinks in a {@link GBLKinkData} object.
+     */
+    public GBLKinkData getKinks() {
+        GblTrajectory traj = this._traj;
+        // get corrections from GBL fit
+        Vector locPar = new Vector(5);
+        SymMatrix locCov = new SymMatrix(5);
+        float[] lambdaKinks = new float[traj.getNumPoints() - 1];
+        double[] phiKinks = new double[traj.getNumPoints() - 1];
+
+        double oldPhi = 0, oldLambda = 0;
+        for (int i = 0; i < traj.getNumPoints(); i++) {
+            traj.getResults(i + 1, locPar, locCov); // vertex point
+            double newPhi = locPar.get(GBLPARIDX.XTPRIME.getValue());
+            double newLambda = locPar.get(GBLPARIDX.YTPRIME.getValue());
+            if (i > 0) {
+                lambdaKinks[i - 1] = (float) (newLambda - oldLambda);
+                phiKinks[i - 1] = newPhi - oldPhi;
+                //                System.out.println("phikink: " + (newPhi - oldPhi));
+            }
+            oldPhi = newPhi;
+            oldLambda = newLambda;
+        }
+
+        return new GBLKinkData(lambdaKinks, phiKinks);
+    }
+
+    
+    
+
+    
+
     
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLEventData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLEventData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLEventData.java	Wed Apr 27 11:11:32 2016
@@ -3,87 +3,87 @@
 import org.lcsim.event.GenericObject;
 
 public class GBLEventData implements GenericObject {
-	
-	/*
-	 * 
-	 * Interface enumerator to access the correct data
-	 * 
-	 */
-	private static class GBLINT {
-		public static final int RUNNR = 0;
-		public static final int BANK_INT_SIZE = 1;
-	}
-	private static class GBLDOUBLE {
-		public static final int BFIELD = 0;
-		public static final int BANK_DOUBLE_SIZE = 1;
-	}
-	// array holding the integer data
-	private int bank_int[] = new int[GBLINT.BANK_INT_SIZE];
-	private double bank_double[] = new double[GBLDOUBLE.BANK_DOUBLE_SIZE];
-	
+    
+    /*
+     * 
+     * Interface enumerator to access the correct data
+     * 
+     */
+    private static class GBLINT {
+        public static final int RUNNR = 0;
+        public static final int BANK_INT_SIZE = 1;
+    }
+    private static class GBLDOUBLE {
+        public static final int BFIELD = 0;
+        public static final int BANK_DOUBLE_SIZE = 1;
+    }
+    // array holding the integer data
+    private int bank_int[] = new int[GBLINT.BANK_INT_SIZE];
+    private double bank_double[] = new double[GBLDOUBLE.BANK_DOUBLE_SIZE];
+    
 
-	/**
-	 * Constructor with event number as parameter
-	 * @param eventNumber the event number
-	 * 
-	 */
-	public GBLEventData(int eventNumber,double Bz) {
-		setRunNr(eventNumber);
-		setBfield(Bz);
-	}
-	
-	public void setRunNr(int val) {
-		bank_int[GBLINT.RUNNR] = val;
-	}
-	
-	public int getRunNr() {
-		return this.getIntVal(GBLINT.RUNNR);
-	}
-	
-	public void setBfield(double val) {
-		bank_double[GBLDOUBLE.BFIELD] = val;
-	}
-	
-	public double getBfield() {
-		return this.getDoubleVal(GBLDOUBLE.BFIELD);
-	}
-	
-	
-	@Override
-	public int getNInt() {
-		return GBLINT.BANK_INT_SIZE;
-	}
+    /**
+     * Constructor with event number as parameter
+     * @param eventNumber the event number
+     * 
+     */
+    public GBLEventData(int eventNumber,double Bz) {
+        setRunNr(eventNumber);
+        setBfield(Bz);
+    }
+    
+    public void setRunNr(int val) {
+        bank_int[GBLINT.RUNNR] = val;
+    }
+    
+    public int getRunNr() {
+        return this.getIntVal(GBLINT.RUNNR);
+    }
+    
+    public void setBfield(double val) {
+        bank_double[GBLDOUBLE.BFIELD] = val;
+    }
+    
+    public double getBfield() {
+        return this.getDoubleVal(GBLDOUBLE.BFIELD);
+    }
+    
+    
+    @Override
+    public int getNInt() {
+        return GBLINT.BANK_INT_SIZE;
+    }
 
-	@Override
-	public int getNFloat() {
-		return 0;
-	}
+    @Override
+    public int getNFloat() {
+        return 0;
+    }
 
-	@Override
-	public int getNDouble() {
-		return GBLDOUBLE.BANK_DOUBLE_SIZE;
-	}
+    @Override
+    public int getNDouble() {
+        return GBLDOUBLE.BANK_DOUBLE_SIZE;
+    }
 
-	@Override
-	public int getIntVal(int index) {
-		return bank_int[index];
-	}
+    @Override
+    public int getIntVal(int index) {
+        return bank_int[index];
+    }
 
-	@Override
-	public float getFloatVal(int index) {
-		// TODO Auto-generated method stub
-		return 0;
-	}
+    @Override
+    public float getFloatVal(int index) {
+        // TODO Auto-generated method stub
+        return 0;
+    }
 
-	@Override
-	public double getDoubleVal(int index) {
-		return bank_double[index];
-	}
+    @Override
+    public double getDoubleVal(int index) {
+        return bank_double[index];
+    }
 
-	@Override
-	public boolean isFixedSize() {
-		// TODO Auto-generated method stub
-		return false;
-	}
+    @Override
+    public boolean isFixedSize() {
+        // TODO Auto-generated method stub
+        return false;
+    }
 
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLFileIO.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLFileIO.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLFileIO.java	Wed Apr 27 11:11:32 2016
@@ -11,8 +11,6 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import org.hps.recon.tracking.gbl.GBLOutput.ClParams;
-import org.hps.recon.tracking.gbl.GBLOutput.PerigeeParams;
 import org.hps.svt.alignment.RunAlignment;
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
 
@@ -47,11 +45,11 @@
         }
     }
     private void openFile(String fileName) {
-    	if(fileName.equalsIgnoreCase("")) {
-    		System.out.printf("%s: no file name specified \n", this.getClass().getSimpleName());
-    		System.exit(1);
-    	}
-    	try {
+        if(fileName.equalsIgnoreCase("")) {
+            System.out.printf("%s: no file name specified \n", this.getClass().getSimpleName());
+            System.exit(1);
+        }
+        try {
             _fWriter = new FileWriter(fileName);
             _pWriter = new PrintWriter(_fWriter);
         } catch (IOException ex) {
@@ -67,34 +65,34 @@
         addLine(String.format("Track perPar (R phi0 slope d0 z0) %.12f %.12f %.12f %.12f %.12f",htf.R(),htf.phi0(),htf.slope(),htf.dca(),htf.z0()));
     }
     
-    String getPerTrackParamStr(PerigeeParams perPar) {
+    String getPerTrackParamStr(GblUtils.PerigeeParams perPar) {
         return String.format("Track perPar (R theta phi d0 z0) %.12f %.12f %.12f %.12f %.12f",1.0/perPar.getKappa(),perPar.getTheta(),perPar.getPhi(),perPar.getD0(),perPar.getZ0());
     }
     
-    void printPerTrackParam(PerigeeParams perPar) {
+    void printPerTrackParam(GblUtils.PerigeeParams perPar) {
         addLine(this.getPerTrackParamStr(perPar));
     }
 
-    String getPerTrackParamTruthStr(PerigeeParams perPar) {
+    String getPerTrackParamTruthStr(GblUtils.PerigeeParams perPar) {
         return String.format("Truth perPar (kappa theta phi d0 z0) %.12f %.12f %.12f %.12f %.12f",perPar.getKappa(),perPar.getTheta(),perPar.getPhi(),perPar.getD0(),perPar.getZ0());
     }
 
-    void printPerTrackParamTruth(PerigeeParams perPar) {
+    void printPerTrackParamTruth(GblUtils.PerigeeParams perPar) {
         addLine(this.getPerTrackParamTruthStr(perPar));
     }
 
-    String getClTrackParamTruthStr(ClParams perPar) {
+    String getClTrackParamTruthStr(GblUtils.ClParams perPar) {
         return String.format("Truth clPar (q/p lambda phi xT yT) %.12f %.12f %.12f %.12f %.12f",perPar.getQoverP(),perPar.getLambda(),perPar.getPhi(),perPar.getXt(),perPar.getYt());
     }
 
-    void printClTrackParamTruth(ClParams perPar) {
+    void printClTrackParamTruth(GblUtils.ClParams perPar) {
         addLine(this.getClTrackParamTruthStr(perPar));
     }
 
-    String getClTrackParamStr(ClParams perPar) {
+    String getClTrackParamStr(GblUtils.ClParams perPar) {
         return String.format("Track clPar (q/p lambda phi xT yT) %.12f %.12f %.12f %.12f %.12f",perPar.getQoverP(),perPar.getLambda(),perPar.getPhi(),perPar.getXt(),perPar.getYt());
     }
-    void printClTrackParam(ClParams perPar) {
+    void printClTrackParam(GblUtils.ClParams perPar) {
         addLine(String.format("%s",this.getClTrackParamStr(perPar)));
     }
 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLKinkData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLKinkData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLKinkData.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,13 @@
 package org.hps.recon.tracking.gbl;
 
+import java.util.List;
+import org.apache.commons.math3.util.Pair;
+import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
+import org.lcsim.event.LCRelation;
+import org.lcsim.event.RelationalTable;
+import org.lcsim.event.Track;
+import org.lcsim.event.base.BaseRelationalTable;
 
 /**
  * Generic object used to persist GBL kink data.
@@ -94,4 +101,27 @@
     public boolean isFixedSize() {
         return true;
     }
+
+    private static Pair<EventHeader, RelationalTable> kinkDataToTrackCache = null;
+
+    public static RelationalTable getKinkDataToTrackTable(EventHeader event) {
+        if (kinkDataToTrackCache == null || kinkDataToTrackCache.getFirst() != event) {
+            RelationalTable kinkDataToTrack = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
+            if (event.hasCollection(LCRelation.class, DATA_RELATION_COLLECTION)) {
+                List<LCRelation> relations = event.get(LCRelation.class, DATA_RELATION_COLLECTION);
+                for (LCRelation relation : relations) {
+                    if (relation != null && relation.getFrom() != null && relation.getTo() != null) {
+                        kinkDataToTrack.add(relation.getFrom(), relation.getTo());
+                    }
+                }
+            }
+            kinkDataToTrackCache = new Pair<EventHeader, RelationalTable>(event, kinkDataToTrack);
+        }
+        return kinkDataToTrackCache.getSecond();
+    }
+
+    public static GenericObject getKinkData(EventHeader event, Track track) {
+        return (GenericObject) getKinkDataToTrackTable(event).from(track);
+    }
+
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutput.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutput.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutput.java	Wed Apr 27 11:11:32 2016
@@ -40,8 +40,6 @@
 import org.lcsim.geometry.subdetector.BarrelEndcapFlag;
 import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
 import org.lcsim.recon.tracking.digitization.sisim.TrackerHitType;
-import org.lcsim.recon.tracking.seedtracker.SeedCandidate;
-import org.lcsim.recon.tracking.seedtracker.SeedTrack;
 
 /**
  * Calculate the input needed for Millepede minimization.
@@ -153,15 +151,13 @@
 
     void printGBL(Track trk, List<SiTrackerHitStrip1D> stripHits, GBLTrackData gtd, List<GBLStripClusterData> stripClusterDataList, List<MCParticle> mcParticles, List<SimTrackerHit> simTrackerHits, boolean isMC) {
 
-        SeedTrack st = (SeedTrack) trk;
-        SeedCandidate seed = st.getSeedCandidate();
-        HelicalTrackFit htf = seed.getHelix();
+        HelicalTrackFit htf = TrackUtils.getHTF(trk);
 
         // Find scatter points along the path
         ScatterPoints scatters = _scattering.FindHPSScatterPoints(htf);
 
         // Hits on track
-        List<HelicalTrackHit> hits = seed.getHits();
+        List<TrackerHit> hits = trk.getTrackerHits();
 
         // Find the truth particle of the track
         MCParticle mcp = null;
@@ -171,7 +167,7 @@
         if (isMC) {
             
             // find the truth particle for this track
-            mcp = getMatchedTruthParticle(trk);
+            mcp = TrackUtils.getMatchedTruthParticle(trk);
 
             // check if this is an A' event
             for(MCParticle part : mcParticles) {
@@ -224,8 +220,8 @@
         // Use the truth helix as the initial track for GBL?
         //htf = htfTruth;
         // Get perigee parameters to curvilinear frame
-        PerigeeParams perPar = new PerigeeParams(htf, bFieldVector.z());
-        PerigeeParams perParTruth = new PerigeeParams(htfTruth, bFieldVector.z());
+        GblUtils.PerigeeParams perPar = new GblUtils.PerigeeParams(htf, bFieldVector.z());
+        GblUtils.PerigeeParams perParTruth = new GblUtils.PerigeeParams(htfTruth, bFieldVector.z());
 
         //GBLDATA
         gtd.setPerigeeTrackParameters(perPar);
@@ -236,8 +232,8 @@
 
         // Get curvilinear parameters
         if (textFile != null) {
-            ClParams clPar = new ClParams(htf, bFieldVector.z());
-            ClParams clParTruth = new ClParams(htfTruth, bFieldVector.z());
+            GblUtils.ClParams clPar = new GblUtils.ClParams(htf, bFieldVector.z());
+            GblUtils.ClParams clParTruth = new GblUtils.ClParams(htfTruth, bFieldVector.z());
             textFile.printClTrackParam(clPar);
             textFile.printClTrackParamTruth(clParTruth);
 
@@ -248,7 +244,7 @@
         }
 
         // find the projection from the I,J,K to U,V,T curvilinear coordinates
-        Hep3Matrix perToClPrj = getPerToClPrj(htf);
+        Hep3Matrix perToClPrj = GblUtils.getPerToClPrj(htf);
 
         //GBLDATA
         for (int row = 0; row < perToClPrj.getNRows(); ++row) {
@@ -326,7 +322,7 @@
                      continue;
             } 
             else {
-                hit = hits.get(ihit);
+                hit = (HelicalTrackHit) hits.get(ihit);
                 htc = (HelicalTrackCross) hit;
                 strips = htc.getStrips();
                 correctedHitPosition = hit.getCorrectedPosition();
@@ -782,171 +778,10 @@
         }
     }
 
-    MCParticle getMatchedTruthParticle(Track track) {
-        boolean debug = false;
-
-        Map<MCParticle, Integer> particlesOnTrack = new HashMap<MCParticle, Integer>();
-
-        if (debug) {
-            System.out.printf("getmatched mc particle from %d tracker hits on the track \n", track.getTrackerHits().size());
-        }
-
-        for (TrackerHit hit : track.getTrackerHits()) {
-            List<MCParticle> mcps = ((HelicalTrackHit) hit).getMCParticles();
-            if (mcps == null) {
-                System.out.printf("%s: warning, this hit (layer %d pos=%s) has no mc particles.\n", this.getClass().getSimpleName(), ((HelicalTrackHit) hit).Layer(), ((HelicalTrackHit) hit).getCorrectedPosition().toString());
-            } else {
-                if (debug) {
-                    System.out.printf("%s: this hit (layer %d pos=%s) has %d mc particles.\n", this.getClass().getSimpleName(), ((HelicalTrackHit) hit).Layer(), ((HelicalTrackHit) hit).getCorrectedPosition().toString(), mcps.size());
-                }
-                for (MCParticle mcp : mcps) {
-                    if (!particlesOnTrack.containsKey(mcp)) {
-                        particlesOnTrack.put(mcp, 0);
-                    }
-                    int c = particlesOnTrack.get(mcp);
-                    particlesOnTrack.put(mcp, c + 1);
-                }
-            }
-        }
-        if (debug) {
-            System.out.printf("Track p=[ %f, %f, %f] \n", track.getTrackStates().get(0).getMomentum()[0], track.getTrackStates().get(0).getMomentum()[1], track.getTrackStates().get(0).getMomentum()[1]);
-            System.out.printf("FOund %d particles\n", particlesOnTrack.size());
-            for (Map.Entry<MCParticle, Integer> entry : particlesOnTrack.entrySet()) {
-                System.out.printf("%d hits assigned to %d p=%s \n", entry.getValue(), entry.getKey().getPDGID(), entry.getKey().getMomentum().toString());
-            }
-        }
-        Map.Entry<MCParticle, Integer> maxEntry = null;
-        for (Map.Entry<MCParticle, Integer> entry : particlesOnTrack.entrySet()) {
-            if (maxEntry == null || entry.getValue().compareTo(maxEntry.getValue()) > 0) {
-                maxEntry = entry; //if ( maxEntry != null ) {
-            }        //    if(entry.getValue().compareTo(maxEntry.getValue()) < 0) continue;
-        }        //}
-        //maxEntry = entry;
-        if (debug) {
-            if (maxEntry != null) {
-                System.out.printf("Matched particle with pdgId=%d and mom %s to track with charge %d and momentum [%f %f %f]\n",
-                        maxEntry.getKey().getPDGID(), maxEntry.getKey().getMomentum().toString(),
-                        track.getCharge(), track.getTrackStates().get(0).getMomentum()[0], track.getTrackStates().get(0).getMomentum()[1], track.getTrackStates().get(0).getMomentum()[2]);
-            } else {
-                System.out.printf("No truth particle found on this track\n");
-            }
-        }
-        return maxEntry == null ? null : maxEntry.getKey();
-    }
-
-//    private BasicMatrix getJacPerToCl(HelicalTrackFit htf) {
-//        System.out.printf("%s: getJacPerToCl\n", this.getClass().getSimpleName());
-//        //use propoerly normalized B-field
-//        Hep3Vector Bnorm = VecOp.mult(Constants.fieldConversion, _B);
-//        //init jacobian to zero
-//        BasicMatrix j = new BasicMatrix(5, 5);
-//        initZero(j);
-//        double lambda = Math.atan(htf.slope());
-//        double q = Math.signum(htf.R());
-//        double theta = Math.PI / 2.0 - lambda;
-//        Hep3Vector T = HelixUtils.Direction(htf, 0.);
-//        Hep3Vector p = VecOp.mult(htf.p(Math.abs(_B.z())), T);
-//        double pT = htf.pT(Math.abs(_B.z()));
-//        Hep3Vector H = VecOp.mult(1. / (Bnorm.magnitude()), Bnorm);
-//        Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
-//        Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
-//        Hep3Vector U = VecOp.mult(-1, J);
-//        Hep3Vector V = VecOp.cross(T, U);
-//        double alpha = VecOp.cross(H, T).magnitude();
-//        Hep3Vector N = VecOp.mult(1. / alpha, VecOp.cross(H, T));
-//        Hep3Vector K = Z;
-//        double Q = -Bnorm.magnitude() * q / p.magnitude();
-//        double kappa = -1.0 * q * Bnorm.z() / pT;
-//
-//        if (this._debug != 0) {
-//            System.out.printf("%s: Bnorm=%s mag(Bnorm)=%f\n", this.getClass().getSimpleName(), Bnorm.toString(), Bnorm.magnitude());
-//            System.out.printf("%s: p=%s |p|=%f pT=%f\n", this.getClass().getSimpleName(), p.toString(), p.magnitude(), pT);
-//            System.out.printf("%s: q=%f\n", this.getClass().getSimpleName(), q);
-//            System.out.printf("%s: q/p=%f\n", this.getClass().getSimpleName(), q / p.magnitude());
-//            System.out.printf("%s: T=%s\n", this.getClass().getSimpleName(), T.toString());
-//            System.out.printf("%s: H=%s\n", this.getClass().getSimpleName(), H.toString());
-//            System.out.printf("%s: kappa=%f\n", this.getClass().getSimpleName(), kappa);
-//            System.out.printf("%s: alpha=%f Q=%f \n", this.getClass().getSimpleName(), alpha, Q);
-//            System.out.printf("%s: J=%s \n", this.getClass().getSimpleName(), J.toString());
-//            System.out.printf("%s: V=%s \n", this.getClass().getSimpleName(), V.toString());
-//            System.out.printf("%s: N=%s \n", this.getClass().getSimpleName(), N.toString());
-//            System.out.printf("%s: TdotJ=%f \n", this.getClass().getSimpleName(), VecOp.dot(T, J));
-//            System.out.printf("%s: VdotN=%f \n", this.getClass().getSimpleName(), VecOp.dot(V, N));
-//            System.out.printf("%s: TdotK=%f \n", this.getClass().getSimpleName(), VecOp.dot(T, K));
-//            System.out.printf("%s: UdotN=%f \n", this.getClass().getSimpleName(), VecOp.dot(U, N));
-//        }
-//
-//        j.setElement(0, 0, -1.0 * Math.sin(theta) / Bnorm.z());
-//
-//        j.setElement(0, 1, q / (p.magnitude() * Math.tan(theta)));
-//
-//        j.setElement(1, 1, -1);
-//
-//        j.setElement(1, 3, -alpha * Q * VecOp.dot(T, J) * VecOp.dot(V, N));
-//
-//        j.setElement(1, 4, -alpha * Q * VecOp.dot(T, K) * VecOp.dot(V, N));
-//
-//        j.setElement(2, 2, 1);
-//
-//        j.setElement(2, 3, -alpha * Q * VecOp.dot(T, J) * VecOp.dot(U, N) / Math.cos(lambda));
-//
-//        j.setElement(2, 4, -alpha * Q * VecOp.dot(T, K) * VecOp.dot(U, N) / Math.cos(lambda));
-//
-//        j.setElement(3, 3, -1);
-//
-//        j.setElement(4, 4, VecOp.dot(V, K));
-//
-//        if (_debug > 0) {
-//            System.out.printf("%s: lambda= J(1,1)=%f  * theta + J(1,3)=%f * eps + J(1,4)=%f * z0 \n",
-//                    this.getClass().getSimpleName(),
-//                    j.e(1, 1), j.e(1, 3), j.e(1, 4));
-//
-//        }
-//
-//        return j;
-//
-//    }
-    /**
-     * Transform MCParticle into a Helix object. Note that it produces the helix
-     * parameters at nominal x=0 and assumes that there is no field at x<0
-     *
-     * @param mcp MC particle to be transformed
-     * @return helix object based on the MC particle
-     */
-//    private HelicalTrackFit getHTF(MCParticle mcp) {
-//        Hep3Vector org = this._hpstrans.transformVectorToTracking(mcp.getOrigin());
-//        Hep3Vector p = this._hpstrans.transformVectorToTracking(mcp.getMomentum());
-//        // Move to x=0 if needed
-//        if(org.x() < 0.) { 
-//        	double dydx = p.y()/p.x();
-//        	double dzdx = p.z()/p.x();
-//        	double delta_x = -1. * org.x(); 
-//        	double y = delta_x * dydx;
-//        	double z = delta_x * dzdx;
-//        	double x = org.x() + delta_x;
-//        	if( Math.abs(x) > 1e-8) throw new RuntimeException("Error: origin is not zero!");
-//        	Hep3Vector old = org;
-//        	org = new BasicHep3Vector(x,y,z);
-//        	System.out.printf("org %s p %s -> org %s\n", old.toString(),p.toString(),org.toString());
-//        } else {
-//        	org = this._hpstrans.transformVectorToTracking(mcp.getOrigin());
-//        }
-//        
-//        
-//        
-//        HelixParamCalculator helixParamCalculator = new HelixParamCalculator(p, org, -1*((int)mcp.getCharge()), -1.0*this._B.z());
-//        double par[] = new double[5];
-//        par[HelicalTrackFit.dcaIndex] = helixParamCalculator.getDCA();
-//        par[HelicalTrackFit.slopeIndex] = helixParamCalculator.getSlopeSZPlane();
-//        par[HelicalTrackFit.phi0Index] = helixParamCalculator.getPhi0();
-//        par[HelicalTrackFit.curvatureIndex] = 1.0/helixParamCalculator.getRadius();
-//        par[HelicalTrackFit.z0Index] = helixParamCalculator.getZ0();
-//        SymmetricMatrix cov = new SymmetricMatrix(5);
-//        for(int i=0;i<cov.getNRows();++i) cov.setElement(i, i, 1.);
-//        HelicalTrackFit htf = new HelicalTrackFit(par, cov, new double[2], new int[2], null, null);
-//        return htf;
-//    }
-    private double truthTrackFitChi2(PerigeeParams perPar, PerigeeParams perParTruth, SymmetricMatrix covariance) {
+    
+    
+
+    private double truthTrackFitChi2(GblUtils.PerigeeParams perPar, GblUtils.PerigeeParams perParTruth, SymmetricMatrix covariance) {
         //re-shuffle the param vector to match the covariance order of parameters
         BasicMatrix p = new BasicMatrix(1, 5);
         p.setElement(0, 0, perPar.getD0());
@@ -1007,190 +842,6 @@
         return Math.sqrt(Math.pow(E1 + E2, 2) - VecOp.add(p1vec, p2vec).magnitudeSquared());
     }
 
-    private static BasicMatrix getPerParVector(double kappa, double theta, double phi, double d0, double z0) {
-        BasicMatrix perPar = new BasicMatrix(1, 5);
-        perPar.setElement(0, 0, kappa);
-        perPar.setElement(0, 1, theta);
-        perPar.setElement(0, 2, phi);
-        perPar.setElement(0, 3, d0);
-        perPar.setElement(0, 4, z0);
-        return perPar;
-    }
-
-    private static BasicMatrix getPerParVector(HelicalTrackFit htf, double B) {
-        if (htf != null) {
-            double kappa = -1.0 * Math.signum(B) / htf.R();
-            double theta = Math.PI / 2.0 - Math.atan(htf.slope());
-            return getPerParVector(kappa, theta, htf.phi0(), htf.dca(), htf.z0());
-        }
-        return new BasicMatrix(1, 5);
-    }
-
-    /**
-     * 
-     * Store perigee track parameters. 
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
-     */
-    public static class PerigeeParams {
-
-        private final BasicMatrix _params;
-
-        public PerigeeParams(HelicalTrackFit htf, double B) {
-            _params = getPerParVector(htf, B);
-        }
-
-        public PerigeeParams(double kappa, double theta, double phi, double d0, double z0) {
-            this._params = getPerParVector(kappa, theta, phi, d0, z0);
-        }
-
-        public BasicMatrix getParams() {
-            return _params;
-        }
-
-        public double getKappa() {
-            return _params.e(0, 0);
-        }
-
-        public double getTheta() {
-            return _params.e(0, 1);
-        }
-
-        public double getPhi() {
-            return _params.e(0, 2);
-        }
-
-        public double getD0() {
-            return _params.e(0, 3);
-        }
-
-        public double getZ0() {
-            return _params.e(0, 4);
-        }
-    }
-
-    /**
-     * Computes the projection matrix from the perigee XY plane variables dca
-     * and z0 into the curvilinear xT,yT,zT frame (U,V,T)
-     *
-     * @param htf input helix to find the track direction
-     * @return 3x3 projection matrix
-     */
-    static Hep3Matrix getPerToClPrj(HelicalTrackFit htf) {
-        Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
-        Hep3Vector T = HelixUtils.Direction(htf, 0.);
-        Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
-        Hep3Vector K = Z;
-        Hep3Vector U = VecOp.mult(-1, J);
-        Hep3Vector V = VecOp.cross(T, U);
-        Hep3Vector I = VecOp.cross(J, K);
-
-        BasicHep3Matrix trans = new BasicHep3Matrix();
-        trans.setElement(0, 0, VecOp.dot(I, U));
-        trans.setElement(0, 1, VecOp.dot(J, U));
-        trans.setElement(0, 2, VecOp.dot(K, U));
-        trans.setElement(1, 0, VecOp.dot(I, V));
-        trans.setElement(1, 1, VecOp.dot(J, V));
-        trans.setElement(1, 2, VecOp.dot(K, V));
-        trans.setElement(2, 0, VecOp.dot(I, T));
-        trans.setElement(2, 1, VecOp.dot(J, T));
-        trans.setElement(2, 2, VecOp.dot(K, T));
-        return trans;
-
-        /*
-         Hep3Vector B = new BasicHep3Vector(0, 0, 1); // TODO sign convention?
-         Hep3Vector H = VecOp.mult(1 / bfield, B);
-         Hep3Vector T = HelixUtils.Direction(helix, 0.);
-         Hep3Vector HcrossT = VecOp.cross(H, T);
-         double alpha = HcrossT.magnitude(); // this should be Bvec cross TrackDir/|B|
-         double Q = Math.abs(bfield) * q / p;
-         Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
-         Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
-         Hep3Vector K = Z;
-         Hep3Vector U = VecOp.mult(-1, J);
-         Hep3Vector V = VecOp.cross(T, U);
-         Hep3Vector I = VecOp.cross(J, K);
-         Hep3Vector N = VecOp.mult(1 / alpha, VecOp.cross(H, T)); //-cross(T,H)/alpha = -cross(T,Z) = -J
-         double UdotI = VecOp.dot(U, I); // 0,0
-         double NdotV = VecOp.dot(N, V); // 1,1?
-         double NdotU = VecOp.dot(N, U); // 0,1?
-         double TdotI = VecOp.dot(T, I); // 2,0
-         double VdotI = VecOp.dot(V, I); // 1,0
-         double VdotK = VecOp.dot(V, K); // 1,2
-         */
-    }
-
-    
-    /**
-     * 
-     * Store curvilinear track parameters. 
-     * 
-     * @author Per Hansson Adrian <[log in to unmask]>
-     *
-     */
-    public static class ClParams {
-
-        private BasicMatrix _params = new BasicMatrix(1, 5);
-
-        public ClParams(HelicalTrackFit htf, double B) {
-
-            if (htf == null) {
-                return;
-            }
-
-            Hep3Matrix perToClPrj = getPerToClPrj(htf);
-
-            double d0 = -1 * htf.dca(); //sign convention for curvilinear frame
-            double z0 = htf.z0();
-            Hep3Vector vecPer = new BasicHep3Vector(0., d0, z0);
-            //System.out.printf("%s: vecPer=%s\n",this.getClass().getSimpleName(),vecPer.toString());
-
-            Hep3Vector vecCl = VecOp.mult(perToClPrj, vecPer);
-            //System.out.printf("%s: vecCl=%s\n",this.getClass().getSimpleName(),vecCl.toString());
-            double xT = vecCl.x();
-            double yT = vecCl.y();
-            //double zT = vecCl.z();
-
-            double lambda = Math.atan(htf.slope());
-            double q = Math.signum(htf.R());
-            double qOverP = q / htf.p(Math.abs(B));
-            double phi = htf.phi0();
-
-            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), qOverP);
-            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), lambda);
-            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), phi);
-            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.XT.getValue(), xT);
-            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.YT.getValue(), yT);
-        }
-
-        public BasicMatrix getParams() {
-            return _params;
-        }
-
-        double getQoverP() {
-            return _params.e(0, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue());
-        }
-
-        double getLambda() {
-            return _params.e(0, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue());
-        }
-
-        double getPhi() {
-            return _params.e(0, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue());
-        }
-
-        double getXt() {
-            return _params.e(0, FittedGblTrajectory.GBLPARIDX.XT.getValue());
-        }
-
-        double getYt() {
-            return _params.e(0, FittedGblTrajectory.GBLPARIDX.YT.getValue());
-        }
-
-    }
-    
-    
     /**
      * 
      * {@link HelicalTrackStripGbl} that explicitly uses the given unit vectors when accessed. 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutputDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutputDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLOutputDriver.java	Wed Apr 27 11:11:32 2016
@@ -1,41 +1,30 @@
 package org.hps.recon.tracking.gbl;
 
-import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.hps.recon.tracking.EventQuality;
-import org.hps.recon.tracking.StrategyType;
-import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.LCRelation;
 import org.lcsim.event.MCParticle;
-import org.lcsim.event.RelationalTable;
 import org.lcsim.event.SimTrackerHit;
 import org.lcsim.event.Track;
-import org.lcsim.event.TrackerHit;
 import org.lcsim.event.base.MyLCRelation;
 import org.lcsim.geometry.Detector;
-import org.lcsim.lcio.LCIOConstants;
 import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
-import org.lcsim.recon.tracking.seedtracker.SeedTrack;
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 
 /**
- * This driver class is used to 1) write lcio collection of GBL info objects OR
- * 2) write GBL info into a unstructures text-based output
+ * This driver class is used to 
+ * 1) write LCIO collection of GBL info objects, or, 
+ * 2) write GBL info into a structured text-based output
  *
- * It uses a helper class that does the actual work. We will port GBL to java
- * and that will replace this driver.
+ * It uses a helper class that does the actual work. 
  *
  * @author Per Hansson Adrian <[log in to unmask]>
  * @version $Id: GBLOutputDriver.java,v 1.9 2013/11/07 03:54:58 phansson Exp $
@@ -58,15 +47,12 @@
     private int totalTracksProcessed = 0;
     private int iTrack = 0;
     private int iEvent = 0;
-    private boolean addBeamspot=false;
+    private boolean addBeamspot = false;
     private double beamspotScatAngle = 0.000001;
     private double beamspotWidthZ = 0.05;
     private double beamspotWidthY = 0.15;
-    private double beamspotTiltZOverY = 15.0*180.0/Math.PI;
-    private double beamspotPosition[] = {0,0,0};
-
-    
-    
+    private double beamspotTiltZOverY = 15.0 * 180.0 / Math.PI;
+    private double beamspotPosition[] = {0, 0, 0};
 
     public GBLOutputDriver() {
     }
@@ -95,7 +81,7 @@
 
     @Override
     public void process(EventHeader event) {
-        List<Track> tracklist = null;
+        List<Track> tracklist;
         if (event.hasCollection(Track.class, trackCollectionName)) {
             tracklist = event.get(Track.class, trackCollectionName);
             if (_debug > 0) {
@@ -107,7 +93,7 @@
 
         List<SiTrackerHitStrip1D> stripHits = event.get(SiTrackerHitStrip1D.class, "StripClusterer_SiTrackerHitStrip1D");
         if (_debug > 0) {
-            System.out.printf("%s: Got %d SiTrackerHitStrip1D in this event\n",this.getClass().getSimpleName(), stripHits.size());
+            System.out.printf("%s: Got %d SiTrackerHitStrip1D in this event\n", this.getClass().getSimpleName(), stripHits.size());
         }
 
         List<MCParticle> mcParticles = new ArrayList<MCParticle>();
@@ -143,13 +129,11 @@
         // Loop over each of the track collections retrieved from the event
         for (Track trk : tracklist) {
             totalTracks++;
-            
-            if (_debug > 0) System.out.printf("%s: PX %f bottom %d\n", this.getClass().getSimpleName(), trk.getPX(), TrackUtils.isBottomTrack(trk, 4)?1:0) ;
-            
-            //if( trk.getPX() < 0.9) continue;
-            
-            //if( TrackUtils.isBottomTrack(trk, 4)) continue;
-            
+
+            if (_debug > 0) {
+                System.out.printf("%s: PX %f bottom %d\n", this.getClass().getSimpleName(), trk.getPX(), TrackUtils.isBottomTrack(trk, 4) ? 1 : 0);
+            }
+
             if (TrackUtils.isGoodTrack(trk, tracklist, EventQuality.Quality.NONE)) {
                 if (_debug > 0) {
                     System.out.printf("%s: Print GBL output for this track\n", this.getClass().getSimpleName());
@@ -228,8 +212,8 @@
         this.isMC = isMC;
     }
 
-    public void setAddBeamspot(boolean add){
-        this.addBeamspot=add;
+    public void setAddBeamspot(boolean add) {
+        this.addBeamspot = add;
     }
 
     public double getBeamspotScatAngle() {
@@ -271,5 +255,8 @@
     public void setBeamspotPosition(double beamspotPosition[]) {
         this.beamspotPosition = beamspotPosition;
     }
-    
+
+    public void setTrackCollectionName(String trackCollectionName) {
+        this.trackCollectionName = trackCollectionName;
+    }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLRefitterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLRefitterDriver.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLRefitterDriver.java	Wed Apr 27 11:11:32 2016
@@ -11,9 +11,11 @@
 import org.hps.recon.tracking.MultipleScattering;
 import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.EventHeader;
+import org.lcsim.event.LCRelation;
 import org.lcsim.event.RelationalTable;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackerHit;
+import org.lcsim.event.base.BaseLCRelation;
 import org.lcsim.geometry.Detector;
 import org.lcsim.lcio.LCIOConstants;
 import org.lcsim.util.Driver;
@@ -26,6 +28,7 @@
 
     private String inputCollectionName = "MatchedTracks";
     private String outputCollectionName = "GBLTracks";
+    private String trackRelationCollectionName = "MatchedToGBLTrackRelations";
 
     private double bfield;
     private final MultipleScattering _scattering = new MultipleScattering(new MaterialSupervisor());
@@ -66,12 +69,21 @@
         RelationalTable hitToRotated = TrackUtils.getHitToRotatedTable(event);
 
         List<Track> refittedTracks = new ArrayList<Track>();
+        List<LCRelation> trackRelations = new ArrayList<LCRelation>();
+
+        List<GBLKinkData> kinkDataCollection = new ArrayList<GBLKinkData>();
+        List<LCRelation> kinkDataRelations = new ArrayList<LCRelation>();
 
         Map<Track, Track> inputToRefitted = new HashMap<Track, Track>();
         for (Track track : tracks) {
-            Pair<Track, GBLKinkData> newTrack = MakeGblTracks.refitTrack(TrackUtils.getHTF(track), TrackUtils.getStripHits(track, hitToStrips, hitToRotated), track.getTrackerHits(), 5, _scattering, bfield);
+            Pair<Track, GBLKinkData> newTrack = MakeGblTracks.refitTrack(TrackUtils.getHTF(track), TrackUtils.getStripHits(track, hitToStrips, hitToRotated), track.getTrackerHits(), 5, track.getType(), _scattering, bfield);
+//            newTrack.getFirst().
             refittedTracks.add(newTrack.getFirst());
+            trackRelations.add(new BaseLCRelation(track, newTrack.getFirst()));
             inputToRefitted.put(track, newTrack.getFirst());
+
+            kinkDataCollection.add(newTrack.getSecond());
+            kinkDataRelations.add(new BaseLCRelation(newTrack.getSecond(), newTrack.getFirst()));
         }
 
         if (mergeTracks) {
@@ -106,7 +118,7 @@
                         }
                     }
 
-                    Pair<Track, GBLKinkData> mergedTrack = MakeGblTracks.refitTrack(TrackUtils.getHTF(track), TrackUtils.getStripHits(track, hitToStrips, hitToRotated), allHth, 5, _scattering, bfield);
+                    Pair<Track, GBLKinkData> mergedTrack = MakeGblTracks.refitTrack(TrackUtils.getHTF(track), TrackUtils.getStripHits(track, hitToStrips, hitToRotated), allHth, 5, track.getType(), _scattering, bfield);
                     mergedTracks.add(mergedTrack.getFirst());
 //                    System.out.format("%f %f %f\n", fit.get_chi2(), inputToRefitted.get(track).getChi2(), inputToRefitted.get(otherTrack).getChi2());
 //                mergedTrackToTrackList.put(mergedTrack, new ArrayList<Track>());
@@ -131,5 +143,8 @@
         // Put the tracks back into the event and exit
         int flag = 1 << LCIOConstants.TRBIT_HITS;
         event.put(outputCollectionName, refittedTracks, Track.class, flag);
+        event.put(trackRelationCollectionName, trackRelations, LCRelation.class, 0);
+        event.put(GBLKinkData.DATA_COLLECTION, kinkDataCollection, GBLKinkData.class, 0);
+        event.put(GBLKinkData.DATA_RELATION_COLLECTION, kinkDataRelations, LCRelation.class, 0);
     }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLStripClusterData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLStripClusterData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLStripClusterData.java	Wed Apr 27 11:11:32 2016
@@ -13,55 +13,55 @@
  * @version $Id:
  */
 public class GBLStripClusterData implements GenericObject {
-	
-	/*
-	 * 
-	 * Interface enumerator to access the correct data
-	 * 
-	 */
-	public static class GBLINT {
-		public static final int ID = 0;
-		public static final int BANK_INT_SIZE = 1;
-	}
-	public static class GBLDOUBLE {
-		public static final int PATH3D = 0;
-		public static final int PATH = 1;
-		public static final int UX = 2;
-		public static final int UY = 3;
-		public static final int UZ = 4;
-		public static final int VX = 5;
-		public static final int VY = 6;
-		public static final int VZ = 7;
-		public static final int WX = 8;
-		public static final int WY = 9;
-		public static final int WZ = 10;	
-		public static final int TDIRX = 11;	
-		public static final int TDIRY = 12;	
-		public static final int TDIRZ = 13;	
-		public static final int TPHI = 14;	
-		public static final int UMEAS = 15;	
-		public static final int TPOSU = 16	;	
-		public static final int TPOSV = 17;	
-		public static final int TPOSW = 18;	
-		public static final int UMEASERR = 19;	
-		public static final int MSANGLE = 20;
-		public static final int TLAMBDA = 21;
-		
-		
-		public static final int BANK_DOUBLE_SIZE = 22;
-		
-	}
-	// array holding the integer data
-	private int bank_int[] = new int[GBLINT.BANK_INT_SIZE];
-	// array holding the double data
-	private double bank_double[] = new double[GBLDOUBLE.BANK_DOUBLE_SIZE];
-	
-	/**
-	 * Default constructor
-	 */
-	public GBLStripClusterData(int id) {
-		setId(id);
-	}
+    
+    /*
+     * 
+     * Interface enumerator to access the correct data
+     * 
+     */
+    public static class GBLINT {
+        public static final int ID = 0;
+        public static final int BANK_INT_SIZE = 1;
+    }
+    public static class GBLDOUBLE {
+        public static final int PATH3D = 0;
+        public static final int PATH = 1;
+        public static final int UX = 2;
+        public static final int UY = 3;
+        public static final int UZ = 4;
+        public static final int VX = 5;
+        public static final int VY = 6;
+        public static final int VZ = 7;
+        public static final int WX = 8;
+        public static final int WY = 9;
+        public static final int WZ = 10;    
+        public static final int TDIRX = 11; 
+        public static final int TDIRY = 12; 
+        public static final int TDIRZ = 13; 
+        public static final int TPHI = 14;  
+        public static final int UMEAS = 15; 
+        public static final int TPOSU = 16  ;   
+        public static final int TPOSV = 17; 
+        public static final int TPOSW = 18; 
+        public static final int UMEASERR = 19;  
+        public static final int MSANGLE = 20;
+        public static final int TLAMBDA = 21;
+        
+        
+        public static final int BANK_DOUBLE_SIZE = 22;
+        
+    }
+    // array holding the integer data
+    private int bank_int[] = new int[GBLINT.BANK_INT_SIZE];
+    // array holding the double data
+    private double bank_double[] = new double[GBLDOUBLE.BANK_DOUBLE_SIZE];
+    
+    /**
+     * Default constructor
+     */
+    public GBLStripClusterData(int id) {
+        setId(id);
+    }
         
         /*
         * Constructor from GenericObject
@@ -79,239 +79,239 @@
             }
             
         }
-	
-	/**
-	 * @param set track id to val
-	 */
-	public void setId(int val) {
-		bank_int[GBLINT.ID] = val;
-	}
-	
-	/**
-	 * @return track id for this object
-	 */
-	public int getId() {
-		return this.getIntVal(GBLINT.ID);
-	}
-	
-	/**
-	 * Set path length to this strip cluster
-	 * @param val
-	 */
-	public void setPath(double val) {
-		bank_double[GBLDOUBLE.PATH] = val;
-	}
-	
-	/**
-	 * Get path length to this strip cluster
-	 */
-	public double getPath() {
-		return getDoubleVal(GBLDOUBLE.PATH);
-	}
-
-	/**
-	 * Set path length to this strip cluster
-	 * @param val
-	 */
-	public void setPath3D(double val) {
-		bank_double[GBLDOUBLE.PATH3D] = val;
-	}
-	
-	/**
-	 * Get path length to this strip cluster
-	 */
-	public double getPath3D() {
-		return getDoubleVal(GBLDOUBLE.PATH3D);
-	}
-
-
-	/**
-	 *  Set and get u vector for this strip sensor
-	 */
-	public void setU(Hep3Vector u) {
-		bank_double[GBLDOUBLE.UX] = u.x();
-		bank_double[GBLDOUBLE.UY] = u.y();
-		bank_double[GBLDOUBLE.UZ] = u.z();		
-	}
-	public Hep3Vector getU() {
-		return new BasicHep3Vector(getUx(),getUy(),getUz());
-	}
-	public double getUx() {
-		return getDoubleVal(GBLDOUBLE.UX);
-	}
-	public double getUy() {
-		return getDoubleVal(GBLDOUBLE.UY);
-	}
-	public double getUz() {
-		return getDoubleVal(GBLDOUBLE.UZ);
-	}
-	
-	/**
-	 *  Set and get v vector for this strip sensor
-	 */
-
-	public void setV(Hep3Vector v) {
-		bank_double[GBLDOUBLE.VX] = v.x();
-		bank_double[GBLDOUBLE.VY] = v.y();
-		bank_double[GBLDOUBLE.VZ] = v.z();		
-	}
-	public Hep3Vector getV() {
-		return new BasicHep3Vector(getVx(),getVy(),getVz());
-	}
-	public double getVx() {
-		return getDoubleVal(GBLDOUBLE.VX);
-	}
-	public double getVy() {
-		return getDoubleVal(GBLDOUBLE.VY);
-	}
-	public double getVz() {
-		return getDoubleVal(GBLDOUBLE.VZ);
-	}
-
-	/**
-	 *  Set and get w vector for this strip sensor
-	 */
-
-	public void setW(Hep3Vector v) {
-		bank_double[GBLDOUBLE.WX] = v.x();
-		bank_double[GBLDOUBLE.WY] = v.y();
-		bank_double[GBLDOUBLE.WZ] = v.z();		
-	}
-	public Hep3Vector getW() {
-		return new BasicHep3Vector(getWx(),getWy(),getWz());
-	}
-	public double getWx() {
-		return getDoubleVal(GBLDOUBLE.WX);
-	}
-	public double getWy() {
-		return getDoubleVal(GBLDOUBLE.WY);
-	}
-	public double getWz() {
-		return getDoubleVal(GBLDOUBLE.WZ);
-	}
-
-	/**
-	 * Set track direction at this cluster
-	 * 
-	 * @param tDir
-	 */
-	public void setTrackDir(Hep3Vector v) {
-		bank_double[GBLDOUBLE.TDIRX] = v.x();
-		bank_double[GBLDOUBLE.TDIRY] = v.y();
-		bank_double[GBLDOUBLE.TDIRZ] = v.z();		
-	}
-	public Hep3Vector getTrackDirection() {
-		return new BasicHep3Vector(getTx(),getTy(),getTz());
-	}
-	public double getTx() {
-		return getDoubleVal(GBLDOUBLE.TDIRX);
-	}
-	public double getTy() {
-		return getDoubleVal(GBLDOUBLE.TDIRY);
-	}
-	public double getTz() {
-		return getDoubleVal(GBLDOUBLE.TDIRZ);
-	}
-
-	public void setTrackPhi(double phi) {
-		bank_double[GBLDOUBLE.TPHI] = phi;
-	}
-	
-	public double getTrackPhi() {
-		return getDoubleVal(GBLDOUBLE.TPHI);
-	}
-
-	public void setTrackLambda(double lambda) {
-		bank_double[GBLDOUBLE.TLAMBDA] = lambda;
-	}
-	
-	public double getTrackLambda() {
-		return getDoubleVal(GBLDOUBLE.TLAMBDA);
-	}
-
-	
-	public void setMeas(double umeas) {
-		bank_double[GBLDOUBLE.UMEAS] = umeas;
-	}
-	
-	public double getMeas() {
-		return getDoubleVal(GBLDOUBLE.UMEAS);
-	}
-	
-	public void setMeasErr(double x) {
-		bank_double[GBLDOUBLE.UMEASERR] = x;
-	}
-
-	public double getMeasErr() {
-		return getDoubleVal(GBLDOUBLE.UMEASERR);
-	}
-
-	
-	/**
-	 * Set track position in local frame
-	 * @param trkpos_meas
-	 */
-	public void setTrackPos(Hep3Vector trkpos_meas) {
-		bank_double[GBLDOUBLE.TPOSU] = trkpos_meas.x();
-		bank_double[GBLDOUBLE.TPOSV] = trkpos_meas.y();
-		bank_double[GBLDOUBLE.TPOSW] = trkpos_meas.z();
-	}
-
-	public Hep3Vector getTrackPos() {
-		return new BasicHep3Vector(getTrackPosU(),getTrackPosV(),getTrackPosW());
-	}
-	
-	public double getTrackPosU() {
-		return getDoubleVal(GBLDOUBLE.TPOSU);
-	}
-
-	public double getTrackPosV() {
-		return getDoubleVal(GBLDOUBLE.TPOSV);
-	}
-
-	public double getTrackPosW() {
-		return getDoubleVal(GBLDOUBLE.TPOSW);
-	}
-
-	public void setScatterAngle(double scatAngle) {
-		bank_double[GBLDOUBLE.MSANGLE] = scatAngle;
-	}
-	
-	public double getScatterAngle() {
-		return getDoubleVal(GBLDOUBLE.MSANGLE);
-	}
-	
-	/*
-	 * The functions below are all overide from 
-	 * @see org.lcsim.event.GenericObject#getNInt()
-	 */
-	
-	public int getNInt() {
-		return GBLINT.BANK_INT_SIZE;
-	}
-
-	public int getNFloat() {
-		return 0;
-	}
-
-	public int getNDouble() {
-		return GBLDOUBLE.BANK_DOUBLE_SIZE;
-	}
-
-	public int getIntVal(int index) {
-		return bank_int[index];
-	}
-
-	public float getFloatVal(int index) {
-		return 0;
-	}
-
-	public double getDoubleVal(int index) {
-		return bank_double[index];
-	}
-
-	public boolean isFixedSize() {
-		return false;
-	}
+    
+    /**
+     * @param val set track id to val
+     */
+    public void setId(int val) {
+        bank_int[GBLINT.ID] = val;
+    }
+    
+    /**
+     * @return track id for this object
+     */
+    public int getId() {
+        return this.getIntVal(GBLINT.ID);
+    }
+    
+    /**
+     * Set path length to this strip cluster
+     * @param val
+     */
+    public void setPath(double val) {
+        bank_double[GBLDOUBLE.PATH] = val;
+    }
+    
+    /**
+     * Get path length to this strip cluster
+     */
+    public double getPath() {
+        return getDoubleVal(GBLDOUBLE.PATH);
+    }
+
+    /**
+     * Set path length to this strip cluster
+     * @param val
+     */
+    public void setPath3D(double val) {
+        bank_double[GBLDOUBLE.PATH3D] = val;
+    }
+    
+    /**
+     * Get path length to this strip cluster
+     */
+    public double getPath3D() {
+        return getDoubleVal(GBLDOUBLE.PATH3D);
+    }
+
+
+    /**
+     *  Set and get u vector for this strip sensor
+     */
+    public void setU(Hep3Vector u) {
+        bank_double[GBLDOUBLE.UX] = u.x();
+        bank_double[GBLDOUBLE.UY] = u.y();
+        bank_double[GBLDOUBLE.UZ] = u.z();      
+    }
+    public Hep3Vector getU() {
+        return new BasicHep3Vector(getUx(),getUy(),getUz());
+    }
+    public double getUx() {
+        return getDoubleVal(GBLDOUBLE.UX);
+    }
+    public double getUy() {
+        return getDoubleVal(GBLDOUBLE.UY);
+    }
+    public double getUz() {
+        return getDoubleVal(GBLDOUBLE.UZ);
+    }
+    
+    /**
+     *  Set and get v vector for this strip sensor
+     */
+
+    public void setV(Hep3Vector v) {
+        bank_double[GBLDOUBLE.VX] = v.x();
+        bank_double[GBLDOUBLE.VY] = v.y();
+        bank_double[GBLDOUBLE.VZ] = v.z();      
+    }
+    public Hep3Vector getV() {
+        return new BasicHep3Vector(getVx(),getVy(),getVz());
+    }
+    public double getVx() {
+        return getDoubleVal(GBLDOUBLE.VX);
+    }
+    public double getVy() {
+        return getDoubleVal(GBLDOUBLE.VY);
+    }
+    public double getVz() {
+        return getDoubleVal(GBLDOUBLE.VZ);
+    }
+
+    /**
+     *  Set and get w vector for this strip sensor
+     */
+
+    public void setW(Hep3Vector v) {
+        bank_double[GBLDOUBLE.WX] = v.x();
+        bank_double[GBLDOUBLE.WY] = v.y();
+        bank_double[GBLDOUBLE.WZ] = v.z();      
+    }
+    public Hep3Vector getW() {
+        return new BasicHep3Vector(getWx(),getWy(),getWz());
+    }
+    public double getWx() {
+        return getDoubleVal(GBLDOUBLE.WX);
+    }
+    public double getWy() {
+        return getDoubleVal(GBLDOUBLE.WY);
+    }
+    public double getWz() {
+        return getDoubleVal(GBLDOUBLE.WZ);
+    }
+
+    /**
+     * Set track direction at this cluster
+     * 
+     * @param v the track direction
+     */
+    public void setTrackDir(Hep3Vector v) {
+        bank_double[GBLDOUBLE.TDIRX] = v.x();
+        bank_double[GBLDOUBLE.TDIRY] = v.y();
+        bank_double[GBLDOUBLE.TDIRZ] = v.z();       
+    }
+    public Hep3Vector getTrackDirection() {
+        return new BasicHep3Vector(getTx(),getTy(),getTz());
+    }
+    public double getTx() {
+        return getDoubleVal(GBLDOUBLE.TDIRX);
+    }
+    public double getTy() {
+        return getDoubleVal(GBLDOUBLE.TDIRY);
+    }
+    public double getTz() {
+        return getDoubleVal(GBLDOUBLE.TDIRZ);
+    }
+
+    public void setTrackPhi(double phi) {
+        bank_double[GBLDOUBLE.TPHI] = phi;
+    }
+    
+    public double getTrackPhi() {
+        return getDoubleVal(GBLDOUBLE.TPHI);
+    }
+
+    public void setTrackLambda(double lambda) {
+        bank_double[GBLDOUBLE.TLAMBDA] = lambda;
+    }
+    
+    public double getTrackLambda() {
+        return getDoubleVal(GBLDOUBLE.TLAMBDA);
+    }
+
+    
+    public void setMeas(double umeas) {
+        bank_double[GBLDOUBLE.UMEAS] = umeas;
+    }
+    
+    public double getMeas() {
+        return getDoubleVal(GBLDOUBLE.UMEAS);
+    }
+    
+    public void setMeasErr(double x) {
+        bank_double[GBLDOUBLE.UMEASERR] = x;
+    }
+
+    public double getMeasErr() {
+        return getDoubleVal(GBLDOUBLE.UMEASERR);
+    }
+
+    
+    /**
+     * Set track position in local frame
+     * @param trkpos_meas
+     */
+    public void setTrackPos(Hep3Vector trkpos_meas) {
+        bank_double[GBLDOUBLE.TPOSU] = trkpos_meas.x();
+        bank_double[GBLDOUBLE.TPOSV] = trkpos_meas.y();
+        bank_double[GBLDOUBLE.TPOSW] = trkpos_meas.z();
+    }
+
+    public Hep3Vector getTrackPos() {
+        return new BasicHep3Vector(getTrackPosU(),getTrackPosV(),getTrackPosW());
+    }
+    
+    public double getTrackPosU() {
+        return getDoubleVal(GBLDOUBLE.TPOSU);
+    }
+
+    public double getTrackPosV() {
+        return getDoubleVal(GBLDOUBLE.TPOSV);
+    }
+
+    public double getTrackPosW() {
+        return getDoubleVal(GBLDOUBLE.TPOSW);
+    }
+
+    public void setScatterAngle(double scatAngle) {
+        bank_double[GBLDOUBLE.MSANGLE] = scatAngle;
+    }
+    
+    public double getScatterAngle() {
+        return getDoubleVal(GBLDOUBLE.MSANGLE);
+    }
+    
+    /*
+     * The functions below are all overide from 
+     * @see org.lcsim.event.GenericObject#getNInt()
+     */
+    
+    public int getNInt() {
+        return GBLINT.BANK_INT_SIZE;
+    }
+
+    public int getNFloat() {
+        return 0;
+    }
+
+    public int getNDouble() {
+        return GBLDOUBLE.BANK_DOUBLE_SIZE;
+    }
+
+    public int getIntVal(int index) {
+        return bank_int[index];
+    }
+
+    public float getFloatVal(int index) {
+        return 0;
+    }
+
+    public double getDoubleVal(int index) {
+        return bank_double[index];
+    }
+
+    public boolean isFixedSize() {
+        return false;
+    }
 
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLTrackData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLTrackData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GBLTrackData.java	Wed Apr 27 11:11:32 2016
@@ -3,7 +3,6 @@
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Matrix;
 
-import org.hps.recon.tracking.gbl.GBLOutput.PerigeeParams;
 import org.lcsim.event.GenericObject;
 
 /**
@@ -61,7 +60,7 @@
     }
 
     /**
-     * @param set track id to val
+     * @param val track ID value
      */
     public void setTrackId(int val) {
         bank_int[GBLINT.ID] = val;
@@ -77,7 +76,7 @@
     /**
      * @param perPar is the perigee parameters that is added to object
      */
-    public void setPerigeeTrackParameters(PerigeeParams perPar) {
+    public void setPerigeeTrackParameters(GblUtils.PerigeeParams perPar) {
         this.bank_double[GBLDOUBLE.PERKAPPA] = perPar.getKappa();
         this.bank_double[GBLDOUBLE.PERTHETA] = perPar.getTheta();
         this.bank_double[GBLDOUBLE.PERPHI] = perPar.getPhi();
@@ -85,8 +84,8 @@
         this.bank_double[GBLDOUBLE.PERZ0] = perPar.getZ0();
     }
 
-    public PerigeeParams getPerigeeTrackParameters() {
-        return new PerigeeParams(this.bank_double[GBLDOUBLE.PERKAPPA],
+    public GblUtils.PerigeeParams getPerigeeTrackParameters() {
+        return new GblUtils.PerigeeParams(this.bank_double[GBLDOUBLE.PERKAPPA],
                 this.bank_double[GBLDOUBLE.PERTHETA],
                 this.bank_double[GBLDOUBLE.PERPHI],
                 this.bank_double[GBLDOUBLE.PERD0],

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblData.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblData.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblData.java	Wed Apr 27 11:11:32 2016
@@ -69,8 +69,8 @@
             nExt = extDer.getColumnDimension();
         }
         int nParMax = 5 + nLocal + nExt;
-//	theParameters.reserve(nParMax); // have to be sorted
-//	theDerivatives.reserve(nParMax);
+//  theParameters.reserve(nParMax); // have to be sorted
+//  theDerivatives.reserve(nParMax);
 
         if (derLocal != null) {
             for (int i = 0; i < derLocal.getColumnDimension(); ++i) // local derivatives
@@ -123,8 +123,8 @@
             nExtDer = extDer.getColumnDimension();
         }
         int nParMax = 7 + nExtDer;
-//	theParameters.reserve(nParMax); // have to be sorted
-//	theDerivatives.reserve(nParMax);
+//  theParameters.reserve(nParMax); // have to be sorted
+//  theDerivatives.reserve(nParMax);
 
         if (extDer != null) {
             for (int i = 0; i < extDer.getColumnDimension(); ++i) // external derivatives
@@ -151,14 +151,14 @@
 // * \param [in] derivatives Derivatives (vector)
 // */
 //void addDerivatives(const std::vector<unsigned int> &index,
-//		const std::vector<double> &derivatives) {
-//	for (unsigned int i = 0; i < derivatives.size(); ++i) // any derivatives
-//			{
-//		if (derivatives[i]) {
-//			theParameters.push_back(index[i]);
-//			theDerivatives.push_back(derivatives[i]);
-//		}
-//	}
+//      const std::vector<double> &derivatives) {
+//  for (unsigned int i = 0; i < derivatives.size(); ++i) // any derivatives
+//          {
+//      if (derivatives[i]) {
+//          theParameters.push_back(index[i]);
+//          theDerivatives.push_back(derivatives[i]);
+//      }
+//  }
 //}
 /// Calculate prediction for data from fit (by GblTrajectory::fit).
     void setPrediction(VVector aVector)
@@ -176,27 +176,27 @@
 // */
 //double setDownWeighting(unsigned int aMethod) {
 //
-//	double aWeight = 1.;
-//	double scaledResidual = fabs(theValue - thePrediction) * sqrt(thePrecision);
-//	if (aMethod == 1) // Tukey
-//			{
-//		if (scaledResidual < 4.6851) {
-//			aWeight = (1.0 - 0.045558 * scaledResidual * scaledResidual);
-//			aWeight *= aWeight;
-//		} else {
-//			aWeight = 0.;
-//		}
-//	} else if (aMethod == 2) //Huber
-//			{
-//		if (scaledResidual >= 1.345) {
-//			aWeight = 1.345 / scaledResidual;
-//		}
-//	} else if (aMethod == 3) //Cauchy
-//			{
-//		aWeight = 1.0 / (1.0 + (scaledResidual * scaledResidual / 5.6877));
-//	}
-//	theDownWeight = aWeight;
-//	return aWeight;
+//  double aWeight = 1.;
+//  double scaledResidual = fabs(theValue - thePrediction) * sqrt(thePrecision);
+//  if (aMethod == 1) // Tukey
+//          {
+//      if (scaledResidual < 4.6851) {
+//          aWeight = (1.0 - 0.045558 * scaledResidual * scaledResidual);
+//          aWeight *= aWeight;
+//      } else {
+//          aWeight = 0.;
+//      }
+//  } else if (aMethod == 2) //Huber
+//          {
+//      if (scaledResidual >= 1.345) {
+//          aWeight = 1.345 / scaledResidual;
+//      }
+//  } else if (aMethod == 3) //Cauchy
+//          {
+//      aWeight = 1.0 / (1.0 + (scaledResidual * scaledResidual / 5.6877));
+//  }
+//  theDownWeight = aWeight;
+//  return aWeight;
 //}
 //
 /// Calculate Chi2 contribution.

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblPoint.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblPoint.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblPoint.java	Wed Apr 27 11:11:32 2016
@@ -486,7 +486,7 @@
     {
         int ifail = 0;
 // to optimize: need only two last rows of inverse
-//	prevJacobian = aJac.InverseFast(ifail);
+//  prevJacobian = aJac.InverseFast(ifail);
 //  block matrix algebra
         Matrix CA = aJac.sub(2, 3, 3, 0).times(aJac.sub(3, 0, 0).inverse()); // C*A^-1
         Matrix DCAB = aJac.sub(2, 3, 3).minus(CA.times(aJac.sub(3, 2, 0, 3))); // D - C*A^-1 *B
@@ -531,14 +531,14 @@
         }
 
         matW.placeAt(matWt.inverse(), 0, 0);
-//	if (!matW.InvertFast()) {
-//		std::cout << " getDerivatives failed to invert matrix: "
-//				<< matW << "\n";
-//		std::cout
-//				<< " Possible reason for singular matrix: multiple GblPoints at same arc-length"
-//				<< "\n";
-//		throw std::overflow_error("Singular matrix inversion exception");
-//	}
+//  if (!matW.InvertFast()) {
+//      std::cout << " getDerivatives failed to invert matrix: "
+//              << matW << "\n";
+//      std::cout
+//              << " Possible reason for singular matrix: multiple GblPoints at same arc-length"
+//              << "\n";
+//      throw std::overflow_error("Singular matrix inversion exception");
+//  }
         matWJ.placeAt(matW.times(matJ), 0, 0);
         vecWd.placeAt(matW.times(vecd), 0, 0);
 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblTrajectory.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblTrajectory.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblTrajectory.java	Wed Apr 27 11:11:32 2016
@@ -214,7 +214,7 @@
     }
 
 /// Retrieve validity of trajectory
-    boolean isValid()
+    public boolean isValid()
     {
         return constructOK;
     }
@@ -268,7 +268,7 @@
             List<GblPoint> list = thePoints.get(iTraj);
             int size = list.size();
             // first point is offset
-            list.get(0).setOffset(numOffsets++);		// intermediate scatterers are offsets
+            list.get(0).setOffset(numOffsets++);        // intermediate scatterers are offsets
             for (int i = 1; i < size - 1; ++i) {
                 GblPoint p = list.get(i);
                 if (p.hasScatterer()) {
@@ -434,7 +434,7 @@
             aPoint.getDerivatives(0, prevW, prevWJ, prevWd); // W-, W- * J-, W- * d-
             aPoint.getDerivatives(1, nextW, nextWJ, nextWd); // W-, W- * J-, W- * d-
             Matrix sumWJ = prevWJ.plus(nextWJ);
-//?		matN = sumWJ.inverse(ierr); // N = (W- * J- + W+ * J+)^-1
+//?     matN = sumWJ.inverse(ierr); // N = (W- * J- + W+ * J+)^-1
             // derivatives for u_int
             Matrix prevNW = matN.times(prevW); // N * W-
             Matrix nextNW = matN.times(nextW); // N * W+
@@ -841,7 +841,7 @@
     /**
      * \param [in] level print level (0: minimum, >0: more)
      */
-    void printPoints(int level)
+    public void printPoints(int level)
     {
         System.out.println("GblPoints ");
 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblUtils.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/GblUtils.java	Wed Apr 27 11:11:32 2016
@@ -1,29 +1,240 @@
 package org.hps.recon.tracking.gbl;
 
+import java.util.logging.Logger;
+
 import hep.physics.matrix.BasicMatrix;
+import hep.physics.vec.BasicHep3Matrix;
+import hep.physics.vec.BasicHep3Vector;
+import hep.physics.vec.Hep3Matrix;
+import hep.physics.vec.Hep3Vector;
+import hep.physics.vec.VecOp;
+
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.MaterialSupervisor;
 import org.hps.recon.tracking.MultipleScattering;
+import org.hps.recon.tracking.gbl.matrix.Matrix;
+import org.hps.recon.tracking.gbl.matrix.Vector;
+import org.lcsim.constants.Constants;
 import org.lcsim.detector.IDetectorElement;
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
 import org.lcsim.fit.helicaltrack.HelixUtils;
 import org.lcsim.recon.tracking.seedtracker.ScatterAngle;
 
 /**
- * A class providing various utilities related to GBL
+ * A class with only static utilities related to GBL
  *
  * @author Per Hansson Adrian <[log in to unmask]>
  *
  */
 public class GblUtils {
-
+    
+    public static Logger LOGGER = Logger.getLogger(GblUtils.class.getName());
+    
+    
+    
+
+    /**
+     * Private constructor to avoid instantiation.
+     */
     private GblUtils() {
     }
+
+    
+    /**
+     * 
+     * Store local curvilinear track parameters. 
+     * 
+     * @author Per Hansson Adrian <[log in to unmask]>
+     *
+     */
+    public static class ClParams {
+    
+        private BasicMatrix _params = new BasicMatrix(1, 5);
+    
+        public ClParams(HelicalTrackFit htf, double B) {
+    
+            if (htf == null) {
+                return;
+            }
+    
+            Hep3Matrix perToClPrj = getPerToClPrj(htf);
+    
+            double d0 = -1 * htf.dca(); //sign convention for curvilinear frame
+            double z0 = htf.z0();
+            Hep3Vector vecPer = new BasicHep3Vector(0., d0, z0);
+            //System.out.printf("%s: vecPer=%s\n",this.getClass().getSimpleName(),vecPer.toString());
+    
+            Hep3Vector vecCl = VecOp.mult(perToClPrj, vecPer);
+            //System.out.printf("%s: vecCl=%s\n",this.getClass().getSimpleName(),vecCl.toString());
+            double xT = vecCl.x();
+            double yT = vecCl.y();
+            //double zT = vecCl.z();
+    
+            double lambda = Math.atan(htf.slope());
+            double q = Math.signum(htf.R());
+            double qOverP = q / htf.p(Math.abs(B));
+            double phi = htf.phi0();
+    
+            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), qOverP);
+            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), lambda);
+            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), phi);
+            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.XT.getValue(), xT);
+            _params.setElement(0, FittedGblTrajectory.GBLPARIDX.YT.getValue(), yT);
+        }
+    
+        public BasicMatrix getParams() {
+            return _params;
+        }
+    
+        double getQoverP() {
+            return _params.e(0, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue());
+        }
+    
+        double getLambda() {
+            return _params.e(0, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue());
+        }
+    
+        double getPhi() {
+            return _params.e(0, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue());
+        }
+    
+        double getXt() {
+            return _params.e(0, FittedGblTrajectory.GBLPARIDX.XT.getValue());
+        }
+    
+        double getYt() {
+            return _params.e(0, FittedGblTrajectory.GBLPARIDX.YT.getValue());
+        }
+    
+    }
+
+
+
+
+
+    /**
+     * 
+     * Store perigee track parameters. 
+     * 
+     * @author Per Hansson Adrian <[log in to unmask]>
+     *
+     */
+    public static class PerigeeParams {
+    
+        private final BasicMatrix _params;
+    
+        public PerigeeParams(HelicalTrackFit htf, double B) {
+            _params = GblUtils.getPerParVector(htf, B);
+        }
+    
+        public PerigeeParams(double kappa, double theta, double phi, double d0, double z0) {
+            this._params = GblUtils.getPerParVector(kappa, theta, phi, d0, z0);
+        }
+    
+        public BasicMatrix getParams() {
+            return _params;
+        }
+    
+        public double getKappa() {
+            return _params.e(0, 0);
+        }
+    
+        public double getTheta() {
+            return _params.e(0, 1);
+        }
+    
+        public double getPhi() {
+            return _params.e(0, 2);
+        }
+    
+        public double getD0() {
+            return _params.e(0, 3);
+        }
+    
+        public double getZ0() {
+            return _params.e(0, 4);
+        }
+    }
+
+
+
+
+
+    
+    /**
+     * Get corrected perigee parameters. 
+     * @param locPar - GBL local curvilinear corrections
+     * @param helicalTrackFit - helix
+     * @param bfield - B-field strength
+     * @return corrected parameters
+     */
+    public static double[] getCorrectedPerigeeParameters(Vector locPar, HelicalTrackFit helicalTrackFit, double bfield) {
+        
+        
+        // Explicitly assign corrections to local variables
+        double qOverPCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.QOVERP.getValue());
+        double xTPrimeCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue());
+        double yTPrimeCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue());
+        double xTCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.XT.getValue());
+        double yTCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.YT.getValue());
+
+        
+        // Get helix parameters
+        double qOverP = helicalTrackFit.curvature() / (Constants.fieldConversion * Math.abs(bfield) * Math.sqrt(1 + Math.pow(helicalTrackFit.slope(), 2)));
+        double d0 = -1.0 * helicalTrackFit.dca(); // correct for different sign convention of d0 in perigee frame
+        double z0 = helicalTrackFit.z0();
+        double phi0 = helicalTrackFit.phi0();
+        double lambda = Math.atan(helicalTrackFit.slope());
+        
+        // calculate new d0 and z0
+        Hep3Matrix perToClPrj = GblUtils.getPerToClPrj(helicalTrackFit);
+
+        Hep3Matrix clToPerPrj = VecOp.inverse(perToClPrj);
+        Hep3Vector corrPer = VecOp.mult(clToPerPrj, new BasicHep3Vector(xTCorr, yTCorr, 0.0));
+
+        //d0
+        double d0_corr = corrPer.y();
+        double dca_gbl = -1.0 * (d0 + d0_corr);
+
+        //z0
+        double z0_corr = corrPer.z();
+        double z0_gbl = z0 + z0_corr;
+
+        //calculate new slope
+        double lambda_gbl = lambda + yTPrimeCorr;
+        double slope_gbl = Math.tan(lambda_gbl);
+
+        // calculate new curvature
+        double qOverP_gbl = qOverP + qOverPCorr;
+        double C_gbl = Constants.fieldConversion * Math.abs(bfield) * qOverP_gbl / Math.cos(lambda_gbl);
+
+        //calculate new phi0
+        double phi0_gbl = phi0 + xTPrimeCorr - corrPer.x() * C_gbl;
+
+        LOGGER.info("qOverP=" + qOverP + " qOverPCorr=" + qOverPCorr + " qOverP_gbl=" + qOverP_gbl + " ==> pGbl=" + 1.0 / qOverP_gbl + " C_gbl=" + C_gbl);
+
+        LOGGER.info(String.format("corrected helix: d0=%f, z0=%f, omega=%f, tanlambda=%f, phi0=%f, p=%f", dca_gbl, z0_gbl, C_gbl, slope_gbl, phi0_gbl, Math.abs(1 / qOverP_gbl)));
+        
+        double parameters_gbl[] = new double[5];
+        parameters_gbl[HelicalTrackFit.dcaIndex] = dca_gbl;
+        parameters_gbl[HelicalTrackFit.phi0Index] = phi0_gbl;
+        parameters_gbl[HelicalTrackFit.curvatureIndex] = C_gbl;
+        parameters_gbl[HelicalTrackFit.z0Index] = z0_gbl;
+        parameters_gbl[HelicalTrackFit.slopeIndex] = slope_gbl;
+        
+        return parameters_gbl;
+        
+    }
+    
+    
+    
+    
 
     public static BasicMatrix gblSimpleJacobianLambdaPhi(double ds, double cosl, double bfac) {
         /*
          Simple jacobian: quadratic in arc length difference.
          using lambda phi as directions
-	    
+        
          @param ds: arc length difference
          @type ds: float
          @param cosl: cos(lambda)
@@ -105,4 +316,168 @@
             throw new UnsupportedOperationException("Should not happen. This problem is only solved with the MaterialSupervisor.");
         }
     }
+
+    /**
+     * Calculate the Jacobian from Curvilinear to Perigee frame. 
+     * @param helicalTrackFit - original helix
+     * @param helicalTrackFitAtIPCorrected - corrected helix at this point
+     * @param bfield - magnitude of B-field
+     * @return the Jacobian matrix from Curvilinear to Perigee frame
+     */
+    public static Matrix getCLToPerigeeJacobian(HelicalTrackFit helicalTrackFit, HpsHelicalTrackFit helicalTrackFitAtIPCorrected, double bfield) {
+        
+        /*
+         * This part is taken from:
+         // Strandlie, Wittek, NIMA 566, 2006
+         Matrix covariance_gbl = new Matrix(5, 5);
+         //helpers
+         double Bz = -Constants.fieldConversion * Math.abs(bfield); // TODO sign convention and should it be it scaled from Telsa?
+         double p = Math.abs(1 / qOverP_gbl);
+         double q = Math.signum(qOverP_gbl);
+         double tanLambda = Math.tan(lambda_gbl);
+         double cosLambda = Math.cos(lambda_gbl);
+         //        Hep3Vector B = new BasicHep3Vector(0, 0, Bz); // TODO sign convention?
+         Hep3Vector H = new BasicHep3Vector(0, 0, 1);
+         Hep3Vector T = HelixUtils.Direction(helix, 0.);
+         Hep3Vector HcrossT = VecOp.cross(H, T);
+         double alpha = HcrossT.magnitude(); // this should be Bvec cross TrackDir/|B|
+         double Q = Bz * q / p;
+         Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
+         Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
+         Hep3Vector K = Z;
+         Hep3Vector U = VecOp.mult(-1, J);
+         Hep3Vector V = VecOp.cross(T, U);
+         Hep3Vector I = VecOp.cross(J, K);
+         Hep3Vector N = VecOp.mult(1 / alpha, VecOp.cross(H, T));
+         double UdotI = VecOp.dot(U, I);
+         double NdotV = VecOp.dot(N, V);
+         double NdotU = VecOp.dot(N, U);
+         double TdotI = VecOp.dot(T, I);
+         double VdotI = VecOp.dot(V, I);
+         double VdotK = VecOp.dot(V, K);
+         covariance_gbl.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), VdotK / TdotI);
+         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 1);
+         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XT.getValue(), -alpha * Q * UdotI * NdotU / (cosLambda * TdotI));
+         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -alpha * Q * VdotI * NdotU / (cosLambda * TdotI));
+         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), -1 * Bz / cosLambda);
+         //        covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 0);
+         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), -1 * q * Bz * tanLambda / (p * cosLambda));
+         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), q * Bz * alpha * Q * tanLambda * UdotI * NdotV / (p * cosLambda * TdotI));
+         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), q * Bz * alpha * Q * tanLambda * VdotI * NdotV / (p * cosLambda * TdotI));
+         covariance_gbl.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -1 / TdotI);
+         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), -1);
+         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), alpha * Q * UdotI * NdotV / TdotI);
+         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), alpha * Q * VdotI * NdotV / TdotI);
+
+         covariance_gbl.print(15, 13);
+         */
+        
+        // Sho's magic below
+        
+        // Use projection matrix
+        //TODO should this not be the corrected helix?
+        Hep3Matrix perToClPrj = getPerToClPrj(helicalTrackFit);
+        Hep3Matrix clToPerPrj = VecOp.inverse(perToClPrj);
+        double C_gbl = helicalTrackFitAtIPCorrected.curvature();
+        double lambda_gbl = Math.atan(helicalTrackFitAtIPCorrected.slope());
+        double qOverP_gbl = helicalTrackFitAtIPCorrected.curvature() / (Constants.fieldConversion * Math.abs(bfield) * Math.sqrt(1 + Math.pow(helicalTrackFitAtIPCorrected.slope(), 2)));
+        
+        Matrix jacobian = new Matrix(5, 5);
+        jacobian.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), -clToPerPrj.e(1, 0));
+        jacobian.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -clToPerPrj.e(1, 1));
+        jacobian.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 1.0);
+        jacobian.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), clToPerPrj.e(0, 1) * C_gbl);
+        jacobian.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), Constants.fieldConversion * Math.abs(bfield) / Math.cos(lambda_gbl));
+        jacobian.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), Constants.fieldConversion * Math.abs(bfield) * qOverP_gbl * Math.tan(lambda_gbl) / Math.cos(lambda_gbl));
+        jacobian.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.XT.getValue(), clToPerPrj.e(2, 0));
+        jacobian.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), clToPerPrj.e(2, 1));
+        jacobian.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), Math.pow(Math.cos(lambda_gbl), -2.0));
+        
+        return jacobian;
+    }
+
+
+
+
+
+    /**
+     * Computes the projection matrix from the perigee XY plane variables dca
+     * and z0 into the curvilinear xT,yT,zT frame (U,V,T) with reference point (0,0,0) 
+     * for the perigee frame.
+     *
+     * @param htf input helix to find the track direction
+     * @return 3x3 projection matrix
+     */
+    static Hep3Matrix getPerToClPrj(HelicalTrackFit htf) {
+        Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
+        Hep3Vector T = HelixUtils.Direction(htf, 0.);
+        Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
+        Hep3Vector K = Z;
+        Hep3Vector U = VecOp.mult(-1, J);
+        Hep3Vector V = VecOp.cross(T, U);
+        Hep3Vector I = VecOp.cross(J, K);
+    
+        BasicHep3Matrix trans = new BasicHep3Matrix();
+        trans.setElement(0, 0, VecOp.dot(I, U));
+        trans.setElement(0, 1, VecOp.dot(J, U));
+        trans.setElement(0, 2, VecOp.dot(K, U));
+        trans.setElement(1, 0, VecOp.dot(I, V));
+        trans.setElement(1, 1, VecOp.dot(J, V));
+        trans.setElement(1, 2, VecOp.dot(K, V));
+        trans.setElement(2, 0, VecOp.dot(I, T));
+        trans.setElement(2, 1, VecOp.dot(J, T));
+        trans.setElement(2, 2, VecOp.dot(K, T));
+        return trans;
+    
+        /*
+         Hep3Vector B = new BasicHep3Vector(0, 0, 1); // TODO sign convention?
+         Hep3Vector H = VecOp.mult(1 / bfield, B);
+         Hep3Vector T = HelixUtils.Direction(helix, 0.);
+         Hep3Vector HcrossT = VecOp.cross(H, T);
+         double alpha = HcrossT.magnitude(); // this should be Bvec cross TrackDir/|B|
+         double Q = Math.abs(bfield) * q / p;
+         Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
+         Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
+         Hep3Vector K = Z;
+         Hep3Vector U = VecOp.mult(-1, J);
+         Hep3Vector V = VecOp.cross(T, U);
+         Hep3Vector I = VecOp.cross(J, K);
+         Hep3Vector N = VecOp.mult(1 / alpha, VecOp.cross(H, T)); //-cross(T,H)/alpha = -cross(T,Z) = -J
+         double UdotI = VecOp.dot(U, I); // 0,0
+         double NdotV = VecOp.dot(N, V); // 1,1?
+         double NdotU = VecOp.dot(N, U); // 0,1?
+         double TdotI = VecOp.dot(T, I); // 2,0
+         double VdotI = VecOp.dot(V, I); // 1,0
+         double VdotK = VecOp.dot(V, K); // 1,2
+         */
+    }
+
+
+
+
+
+    private static BasicMatrix getPerParVector(double kappa, double theta, double phi, double d0, double z0) {
+        BasicMatrix perPar = new BasicMatrix(1, 5);
+        perPar.setElement(0, 0, kappa);
+        perPar.setElement(0, 1, theta);
+        perPar.setElement(0, 2, phi);
+        perPar.setElement(0, 3, d0);
+        perPar.setElement(0, 4, z0);
+        return perPar;
+    }
+
+
+
+
+
+    private static BasicMatrix getPerParVector(HelicalTrackFit htf, double B) {
+        if (htf != null) {
+            double kappa = -1.0 * Math.signum(B) / htf.R();
+            double theta = Math.PI / 2.0 - Math.atan(htf.slope());
+            return getPerParVector(kappa, theta, htf.phi0(), htf.dca(), htf.z0());
+        }
+        return new BasicMatrix(1, 5);
+    }
+
+
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HelicalTrackStripGbl.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HelicalTrackStripGbl.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HelicalTrackStripGbl.java	Wed Apr 27 11:11:32 2016
@@ -13,10 +13,8 @@
 import org.lcsim.fit.helicaltrack.HelicalTrackStrip;
 
 /**
- * Encapsulates the {@HelicalTrackStrip} to make sure that the local unit vectors are 
+ * Encapsulates the {@link org.lcsim.fit.helicaltrack.HelicalTrackStrip} to make sure that the local unit vectors are
  * coming from the underlying geometry.
- * 
- * I think the base calss should change but whatever.
  * 
  * @author Per Hansson Adrian <[log in to unmask]>
  *

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HpsGblRefitter.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HpsGblRefitter.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/HpsGblRefitter.java	Wed Apr 27 11:11:32 2016
@@ -14,10 +14,12 @@
 import java.util.logging.Formatter;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.apache.commons.math3.util.Pair;
-
 import org.hps.recon.tracking.TrackUtils;
+
 import static org.hps.recon.tracking.gbl.MakeGblTracks.makeCorrectedTrack;
+
 import org.hps.recon.tracking.gbl.matrix.Matrix;
 import org.hps.recon.tracking.gbl.matrix.SymMatrix;
 import org.hps.recon.tracking.gbl.matrix.Vector;
@@ -52,6 +54,8 @@
     private final String track2GblTrackRelationName = "TrackToGBLTrack";
     private final String gblTrack2StripRelationName = "GBLTrackToStripData";
     private final String outputTrackCollectionName = "GBLTracks";
+    private final String trackRelationCollectionName = "MatchedToGBLTrackRelations";
+
 
     private MilleBinary mille;
     private String milleBinaryFileName = MilleBinary.DEFAULT_OUTPUT_FILE_NAME;
@@ -184,6 +188,8 @@
         LOGGER.info(trackFits.size() + " fitted GBL tracks before adding to event");
 
         List<Track> newTracks = new ArrayList<Track>();
+        
+        List<LCRelation> trackRelations = new ArrayList<LCRelation>();
 
         List<GBLKinkData> kinkDataCollection = new ArrayList<GBLKinkData>();
 
@@ -201,6 +207,10 @@
 
             //  Add the track to the list of tracks
             newTracks.add(trk.getFirst());
+
+            // Create relation from seed to GBL track
+            trackRelations.add(new BaseLCRelation(fittedTraj.get_seed(), trk.getFirst()));
+            
             kinkDataCollection.add(trk.getSecond());
             kinkDataRelations.add(new BaseLCRelation(trk.getSecond(), trk.getFirst()));
         }
@@ -210,6 +220,7 @@
         // Put the tracks back into the event and exit
         int flag = 1 << LCIOConstants.TRBIT_HITS;
         event.put(outputTrackCollectionName, newTracks, Track.class, flag);
+        event.put(trackRelationCollectionName, trackRelations, LCRelation.class, 0);
         event.put(GBLKinkData.DATA_COLLECTION, kinkDataCollection, GBLKinkData.class, 0);
         event.put(GBLKinkData.DATA_RELATION_COLLECTION, kinkDataRelations, LCRelation.class, 0);
 
@@ -222,12 +233,15 @@
     public static FittedGblTrajectory fit(List<GBLStripClusterData> hits, double bfac, boolean debug) {
         // path length along trajectory
         double s = 0.;
+        int iLabel;
+
 
         // jacobian to transport errors between points along the path
         Matrix jacPointToPoint = new Matrix(5, 5);
         jacPointToPoint.UnitMatrix();
         // Vector of the strip clusters used for the GBL fit
         List<GblPoint> listOfPoints = new ArrayList<GblPoint>();
+        Map<Integer, Double> pathLengthMap = new HashMap<Integer, Double>();
 
         // Store the projection from local to measurement frame for each strip cluster
         Map< Integer, Matrix> proL2m_list = new HashMap<Integer, Matrix>();
@@ -236,6 +250,10 @@
         //start trajectory at refence point (s=0) - this point has no measurement
         GblPoint ref_point = new GblPoint(jacPointToPoint);
         listOfPoints.add(ref_point);
+        
+        // save path length to each point
+        iLabel = listOfPoints.size();
+        pathLengthMap.put(iLabel, s);
 
         // Loop over strips
         int n_strips = hits.size();
@@ -323,11 +341,11 @@
             // measurement/residual in the measurement system
             // only 1D measurement in u-direction, set strip measurement direction to zero
             Vector meas = new Vector(2);
-//		double uRes = strip->GetUmeas() - strip->GetTrackPos().x(); // how can this be correct?
+//      double uRes = strip->GetUmeas() - strip->GetTrackPos().x(); // how can this be correct?
             double uRes = strip.getMeas() - strip.getTrackPos().x();
             meas.set(0, uRes);
             meas.set(1, 0.);
-//		//meas[0][0] += deltaU[iLayer] # misalignment
+//      //meas[0][0] += deltaU[iLayer] # misalignment
             Vector measErr = new Vector(2);
             measErr.set(0, strip.getMeasErr());
             measErr.set(1, 0.);
@@ -405,7 +423,10 @@
 
             // Add this GBL point to list that will be used in fit
             listOfPoints.add(point);
-            int iLabel = listOfPoints.size();
+            iLabel = listOfPoints.size();
+
+            // save path length to each point
+            pathLengthMap.put(iLabel, s);
 
             // Update MS covariance matrix 
             msCov.set(1, 1, msCov.get(1, 1) + scatErr.get(0) * scatErr.get(0));
@@ -493,8 +514,10 @@
 
         LOGGER.fine("locPar " + aCorrection.toString());
 
-//
-        return new FittedGblTrajectory(traj, dVals[0], iVals[0], dVals[1]);
+        FittedGblTrajectory fittedTraj = new FittedGblTrajectory(traj, dVals[0], iVals[0], dVals[1]);
+        fittedTraj.setPathLengthMap(pathLengthMap);
+        
+        return fittedTraj;
     }
 
     @Override

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/MakeGblTracks.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/MakeGblTracks.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/MakeGblTracks.java	Wed Apr 27 11:11:32 2016
@@ -5,22 +5,18 @@
 import hep.physics.vec.Hep3Matrix;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
+
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.apache.commons.math3.util.Pair;
 import org.hps.recon.tracking.CoordinateTransformations;
 import org.hps.recon.tracking.MultipleScattering;
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
-import static org.hps.recon.tracking.gbl.GBLOutput.getPerToClPrj;
-import org.hps.recon.tracking.gbl.matrix.Matrix;
-import org.hps.recon.tracking.gbl.matrix.SymMatrix;
-import org.hps.recon.tracking.gbl.matrix.Vector;
 import org.lcsim.constants.Constants;
 import org.lcsim.detector.ITransform3D;
 import org.lcsim.detector.tracker.silicon.ChargeCarrier;
@@ -48,7 +44,11 @@
 public class MakeGblTracks {
 
     private final static Logger LOGGER = Logger.getLogger(MakeGblTracks.class.getPackage().getName());
-
+    static {
+        LOGGER.setLevel(Level.WARNING);
+    }
+    
+    
     private MakeGblTracks() {
     }
 
@@ -60,7 +60,16 @@
         }
     }
 
-    public static Pair<Track, GBLKinkData> makeCorrectedTrack(FittedGblTrajectory fittedTraj, HelicalTrackFit helix, List<TrackerHit> trackHits, int trackType, double bfield) {
+    /**
+     * Create a new {@link BaseTrack} from a {@link FittedGblTrajectory}. 
+     * @param fittedGblTrajectory
+     * @param helicalTrackFit
+     * @param hitsOnTrack
+     * @param trackType
+     * @param bfield
+     * @return the new {@link BaseTrack} and the kinks along the {@link GblTrajectory} as a {@link Pair}.
+     */
+    public static Pair<Track, GBLKinkData> makeCorrectedTrack(FittedGblTrajectory fittedGblTrajectory, HelicalTrackFit helicalTrackFit, List<TrackerHit> hitsOnTrack, int trackType, double bfield) {
         //  Initialize the reference point to the origin
         double[] ref = new double[]{0., 0., 0.};
 
@@ -68,220 +77,41 @@
         BaseTrack trk = new BaseTrack();
 
         //  Add the hits to the track
-        for (TrackerHit hit : trackHits) {
+        for (TrackerHit hit : hitsOnTrack) {
             trk.addHit(hit);
         }
 
-        // Set state at vertex
-        Pair<double[], SymmetricMatrix> correctedHelixParams = getGblCorrectedHelixParameters(helix, fittedTraj.get_traj(), bfield, FittedGblTrajectory.GBLPOINT.IP);
+        // Set base track parameters
+        Pair<double[], SymmetricMatrix> correctedHelixParams = fittedGblTrajectory.getCorrectedPerigeeParameters(helicalTrackFit, FittedGblTrajectory.GBLPOINT.IP, bfield);
         trk.setTrackParameters(correctedHelixParams.getFirst(), bfield);// hack to set the track charge
         trk.getTrackStates().clear();
 
-        TrackState stateVertex = new BaseTrackState(correctedHelixParams.getFirst(), ref, correctedHelixParams.getSecond().asPackedArray(true), TrackState.AtIP, bfield);
-        trk.getTrackStates().add(stateVertex);
-
-        // Set state at last point
-        Pair<double[], SymmetricMatrix> correctedHelixParamsLast = getGblCorrectedHelixParameters(helix, fittedTraj.get_traj(), bfield, FittedGblTrajectory.GBLPOINT.LAST);
+        // Set state at IP
+        TrackState stateIP = new BaseTrackState(correctedHelixParams.getFirst(), ref, correctedHelixParams.getSecond().asPackedArray(true), TrackState.AtIP, bfield);
+        trk.getTrackStates().add(stateIP);
+
+        // Set state at last point on trajectory
+        Pair<double[], SymmetricMatrix> correctedHelixParamsLast = fittedGblTrajectory.getCorrectedPerigeeParameters(helicalTrackFit, FittedGblTrajectory.GBLPOINT.LAST, bfield);
         TrackState stateLast = new BaseTrackState(correctedHelixParamsLast.getFirst(), ref, correctedHelixParamsLast.getSecond().asPackedArray(true), TrackState.AtLastHit, bfield);
         trk.getTrackStates().add(stateLast);
 
-        GBLKinkData kinkData = getKinks(fittedTraj.get_traj());
+        // Extract kinks from trajectory
+        GBLKinkData kinkData = fittedGblTrajectory.getKinks();
 
         // Set other info needed
-        trk.setChisq(fittedTraj.get_chi2());
-        trk.setNDF(fittedTraj.get_ndf());
+        trk.setChisq(fittedGblTrajectory.get_chi2());
+        trk.setNDF(fittedGblTrajectory.get_ndf());
         trk.setFitSuccess(true);
         trk.setRefPointIsDCA(true);
         trk.setTrackType(TrackType.setGBL(trackType, true));
 
         //  Add the track to the list of tracks
 //            tracks.add(trk);
-        LOGGER.info(String.format("helix chi2 %f ndf %d gbl chi2 %f ndf %d\n", helix.chisqtot(), helix.ndf()[0] + helix.ndf()[1], trk.getChi2(), trk.getNDF()));
-        if (LOGGER.getLevel().intValue() <= Level.INFO.intValue()) {
-            for (int i = 0; i < 5; ++i) {
-                LOGGER.info(String.format("param %d: %.10f -> %.10f    helix-gbl= %f", i, helix.parameters()[i], trk.getTrackParameter(i), helix.parameters()[i] - trk.getTrackParameter(i)));
-            }
-        }
+        LOGGER.fine(String.format("helix chi2 %f ndf %d gbl chi2 %f ndf %d\n", helicalTrackFit.chisqtot(), helicalTrackFit.ndf()[0] + helicalTrackFit.ndf()[1], trk.getChi2(), trk.getNDF()));
         return new Pair<Track, GBLKinkData>(trk, kinkData);
     }
 
-    /**
-     * Compute the updated helix parameters and covariance matrix at a given
-     * point along the trajectory.
-     *
-     * @param helix - original seed track
-     * @param traj - fitted GBL trajectory
-     * @param point - the point along the track where the result is computed.
-     * @return corrected parameters.
-     */
-    public static Pair<double[], SymmetricMatrix> getGblCorrectedHelixParameters(HelicalTrackFit helix, GblTrajectory traj, double bfield, FittedGblTrajectory.GBLPOINT point) {
-
-        // get seed helix parameters
-        double qOverP = helix.curvature() / (Constants.fieldConversion * Math.abs(bfield) * Math.sqrt(1 + Math.pow(helix.slope(), 2)));
-        double d0 = -1.0 * helix.dca(); // correct for different sign convention of d0 in perigee frame
-        double z0 = helix.z0();
-        double phi0 = helix.phi0();
-        double lambda = Math.atan(helix.slope());
-
-        LOGGER.info("GblPoint: " + point.toString() + "( " + point.name() + ")");
-        LOGGER.info(String.format("original helix: d0=%f, z0=%f, omega=%f, tanlambda=%f, phi0=%f, p=%f", helix.dca(), helix.z0(), helix.curvature(), helix.slope(), helix.phi0(), helix.p(Math.abs(bfield))));
-        LOGGER.info("original helix covariance:\n" + helix.covariance());
-
-        // get corrections from GBL fit
-        Vector locPar = new Vector(5);
-        SymMatrix locCov = new SymMatrix(5);
-        int pointIndex;
-        if (point.compareTo(FittedGblTrajectory.GBLPOINT.IP) == 0) {
-            pointIndex = 1;
-        } else if (point.compareTo(FittedGblTrajectory.GBLPOINT.LAST) == 0) {
-            pointIndex = traj.getNumPoints();
-        } else {
-            throw new RuntimeException("This GBLPOINT " + point.toString() + "( " + point.name() + ") is not valid");
-        }
-
-        traj.getResults(pointIndex, locPar, locCov); // vertex point
-//        locCov.print(10, 8);
-        double qOverPCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.QOVERP.getValue());
-        double xTPrimeCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue());
-        double yTPrimeCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue());
-        double xTCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.XT.getValue());
-        double yTCorr = locPar.get(FittedGblTrajectory.GBLPARIDX.YT.getValue());
-
-        LOGGER.info((helix.slope() > 0 ? "top: " : "bot ") + "qOverPCorr " + qOverPCorr + " xtPrimeCorr " + xTPrimeCorr + " yTPrimeCorr " + yTPrimeCorr + " xTCorr " + xTCorr + " yTCorr " + yTCorr);
-
-        // calculate new d0 and z0
-//        Hep3Matrix perToClPrj = traj.get_track_data().getPrjPerToCl();
-        Hep3Matrix perToClPrj = getPerToClPrj(helix);
-
-        Hep3Matrix clToPerPrj = VecOp.inverse(perToClPrj);
-        Hep3Vector corrPer = VecOp.mult(clToPerPrj, new BasicHep3Vector(xTCorr, yTCorr, 0.0));
-
-        //d0
-        double d0_corr = corrPer.y();
-        double dca_gbl = -1.0 * (d0 + d0_corr);
-
-        //z0
-        double z0_corr = corrPer.z();
-        double z0_gbl = z0 + z0_corr;
-
-        //calculate new slope
-        double lambda_gbl = lambda + yTPrimeCorr;
-        double slope_gbl = Math.tan(lambda_gbl);
-
-        // calculate new curvature
-        double qOverP_gbl = qOverP + qOverPCorr;
-//        double pt_gbl = (1.0 / qOverP_gbl) * Math.cos(lambda_gbl);
-//        double C_gbl = Constants.fieldConversion * Math.abs(bfield) / pt_gbl;
-        double C_gbl = Constants.fieldConversion * Math.abs(bfield) * qOverP_gbl / Math.cos(lambda_gbl);
-
-        //calculate new phi0
-        double phi0_gbl = phi0 + xTPrimeCorr - corrPer.x() * C_gbl;
-
-        LOGGER.info("qOverP=" + qOverP + " qOverPCorr=" + qOverPCorr + " qOverP_gbl=" + qOverP_gbl + " ==> pGbl=" + 1.0 / qOverP_gbl + " C_gbl=" + C_gbl);
-
-        LOGGER.info(String.format("corrected helix: d0=%f, z0=%f, omega=%f, tanlambda=%f, phi0=%f, p=%f", dca_gbl, z0_gbl, C_gbl, slope_gbl, phi0_gbl, Math.abs(1 / qOverP_gbl)));
-
-        /*
-         // Strandlie, Wittek, NIMA 566, 2006
-         Matrix covariance_gbl = new Matrix(5, 5);
-         //helpers
-         double Bz = -Constants.fieldConversion * Math.abs(bfield); // TODO sign convention and should it be it scaled from Telsa?
-         double p = Math.abs(1 / qOverP_gbl);
-         double q = Math.signum(qOverP_gbl);
-         double tanLambda = Math.tan(lambda_gbl);
-         double cosLambda = Math.cos(lambda_gbl);
-         //        Hep3Vector B = new BasicHep3Vector(0, 0, Bz); // TODO sign convention?
-         Hep3Vector H = new BasicHep3Vector(0, 0, 1);
-         Hep3Vector T = HelixUtils.Direction(helix, 0.);
-         Hep3Vector HcrossT = VecOp.cross(H, T);
-         double alpha = HcrossT.magnitude(); // this should be Bvec cross TrackDir/|B|
-         double Q = Bz * q / p;
-         Hep3Vector Z = new BasicHep3Vector(0, 0, 1);
-         Hep3Vector J = VecOp.mult(1. / VecOp.cross(T, Z).magnitude(), VecOp.cross(T, Z));
-         Hep3Vector K = Z;
-         Hep3Vector U = VecOp.mult(-1, J);
-         Hep3Vector V = VecOp.cross(T, U);
-         Hep3Vector I = VecOp.cross(J, K);
-         Hep3Vector N = VecOp.mult(1 / alpha, VecOp.cross(H, T));
-         double UdotI = VecOp.dot(U, I);
-         double NdotV = VecOp.dot(N, V);
-         double NdotU = VecOp.dot(N, U);
-         double TdotI = VecOp.dot(T, I);
-         double VdotI = VecOp.dot(V, I);
-         double VdotK = VecOp.dot(V, K);
-         covariance_gbl.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), VdotK / TdotI);
-         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 1);
-         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XT.getValue(), -alpha * Q * UdotI * NdotU / (cosLambda * TdotI));
-         covariance_gbl.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -alpha * Q * VdotI * NdotU / (cosLambda * TdotI));
-         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), -1 * Bz / cosLambda);
-         //        covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 0);
-         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), -1 * q * Bz * tanLambda / (p * cosLambda));
-         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), q * Bz * alpha * Q * tanLambda * UdotI * NdotV / (p * cosLambda * TdotI));
-         covariance_gbl.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), q * Bz * alpha * Q * tanLambda * VdotI * NdotV / (p * cosLambda * TdotI));
-         covariance_gbl.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -1 / TdotI);
-         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), -1);
-         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), alpha * Q * UdotI * NdotV / TdotI);
-         covariance_gbl.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), alpha * Q * VdotI * NdotV / TdotI);
-
-         covariance_gbl.print(15, 13);
-         */
-        // Sho's magic
-        Matrix jacobian = new Matrix(5, 5);
-        jacobian.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.XT.getValue(), -clToPerPrj.e(1, 0));
-        jacobian.set(HelicalTrackFit.dcaIndex, FittedGblTrajectory.GBLPARIDX.YT.getValue(), -clToPerPrj.e(1, 1));
-        jacobian.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue(), 1.0);
-        jacobian.set(HelicalTrackFit.phi0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), clToPerPrj.e(0, 1) * C_gbl);
-        jacobian.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.QOVERP.getValue(), Constants.fieldConversion * Math.abs(bfield) / Math.cos(lambda_gbl));
-        jacobian.set(HelicalTrackFit.curvatureIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), Constants.fieldConversion * Math.abs(bfield) * qOverP_gbl * Math.tan(lambda_gbl) / Math.cos(lambda_gbl));
-        jacobian.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.XT.getValue(), clToPerPrj.e(2, 0));
-        jacobian.set(HelicalTrackFit.z0Index, FittedGblTrajectory.GBLPARIDX.YT.getValue(), clToPerPrj.e(2, 1));
-        jacobian.set(HelicalTrackFit.slopeIndex, FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue(), Math.pow(Math.cos(lambda_gbl), -2.0));
-
-//        jacobian.print(15, 13);
-        Matrix helixCovariance = jacobian.times(locCov.times(jacobian.transpose()));
-        SymmetricMatrix cov = new SymmetricMatrix(5);
-        for (int i = 0; i < 5; i++) {
-            for (int j = 0; j < 5; j++) {
-                if (i >= j) {
-                    cov.setElement(i, j, helixCovariance.get(i, j));
-                }
-            }
-        }
-        LOGGER.info("corrected helix covariance:\n" + cov);
-
-        double parameters_gbl[] = new double[5];
-        parameters_gbl[HelicalTrackFit.dcaIndex] = dca_gbl;
-        parameters_gbl[HelicalTrackFit.phi0Index] = phi0_gbl;
-        parameters_gbl[HelicalTrackFit.curvatureIndex] = C_gbl;
-        parameters_gbl[HelicalTrackFit.z0Index] = z0_gbl;
-        parameters_gbl[HelicalTrackFit.slopeIndex] = slope_gbl;
-
-        return new Pair<double[], SymmetricMatrix>(parameters_gbl, cov);
-    }
-
-    public static GBLKinkData getKinks(GblTrajectory traj) {
-
-        // get corrections from GBL fit
-        Vector locPar = new Vector(5);
-        SymMatrix locCov = new SymMatrix(5);
-        float[] lambdaKinks = new float[traj.getNumPoints() - 1];
-        double[] phiKinks = new double[traj.getNumPoints() - 1];
-
-        double oldPhi = 0, oldLambda = 0;
-        for (int i = 0; i < traj.getNumPoints(); i++) {
-            traj.getResults(i + 1, locPar, locCov); // vertex point
-            double newPhi = locPar.get(FittedGblTrajectory.GBLPARIDX.XTPRIME.getValue());
-            double newLambda = locPar.get(FittedGblTrajectory.GBLPARIDX.YTPRIME.getValue());
-            if (i > 0) {
-                lambdaKinks[i - 1] = (float) (newLambda - oldLambda);
-                phiKinks[i - 1] = newPhi - oldPhi;
-            }
-            oldPhi = newPhi;
-            oldLambda = newLambda;
-        }
-
-        return new GBLKinkData(lambdaKinks, phiKinks);
-    }
+    
 
     /**
      * Do a GBL fit to an arbitrary set of strip hits, with a starting value of
@@ -298,19 +128,28 @@
      * @param bfield B-field
      * @return The refitted track.
      */
-    public static Pair<Track, GBLKinkData> refitTrack(HelicalTrackFit helix, Collection<TrackerHit> stripHits, Collection<TrackerHit> hth, int nIterations, MultipleScattering scattering, double bfield) {
-        List<TrackerHit> allHthList = sortHits(hth);
-        List<TrackerHit> sortedStripHits = sortHits(stripHits);
-        FittedGblTrajectory fit = MakeGblTracks.doGBLFit(helix, sortedStripHits, scattering, bfield, 0);
+    public static Pair<Track, GBLKinkData> refitTrack(HelicalTrackFit helix, Collection<TrackerHit> stripHits, Collection<TrackerHit> hth, int nIterations, int trackType, MultipleScattering scattering, double bfield) {
+        List<TrackerHit> allHthList = TrackUtils.sortHits(hth);
+        List<TrackerHit> sortedStripHits = TrackUtils.sortHits(stripHits);
+        FittedGblTrajectory fit = doGBLFit(helix, sortedStripHits, scattering, bfield, 0);
         for (int i = 0; i < nIterations; i++) {
-            Pair<Track, GBLKinkData> newTrack = MakeGblTracks.makeCorrectedTrack(fit, helix, allHthList, 0, bfield);
+            Pair<Track, GBLKinkData> newTrack = makeCorrectedTrack(fit, helix, allHthList, trackType, bfield);
             helix = TrackUtils.getHTF(newTrack.getFirst());
-            fit = MakeGblTracks.doGBLFit(helix, sortedStripHits, scattering, bfield, 0);
-        }
-        Pair<Track, GBLKinkData> mergedTrack = MakeGblTracks.makeCorrectedTrack(fit, helix, allHthList, 0, bfield);
+            fit = doGBLFit(helix, sortedStripHits, scattering, bfield, 0);
+        }
+        Pair<Track, GBLKinkData> mergedTrack = makeCorrectedTrack(fit, helix, allHthList, trackType, bfield);
         return mergedTrack;
     }
 
+    /**
+     * Do a GBL fit to a list of {@link TrackerHit}. 
+     * @param htf - seed fit
+     * @param stripHits - list of {@link TrackerHit}.
+     * @param _scattering - estimation of the multiple scattering {@link MultipleScattering}.
+     * @param bfield - magnitude of B-field.
+     * @param debug - debug flag.
+     * @return the fitted GBL trajectory
+     */
     public static FittedGblTrajectory doGBLFit(HelicalTrackFit htf, List<TrackerHit> stripHits, MultipleScattering _scattering, double bfield, int debug) {
         List<GBLStripClusterData> stripData = makeStripData(htf, stripHits, _scattering, bfield, debug);
         double bfac = Constants.fieldConversion * bfield;
@@ -319,6 +158,15 @@
         return fit;
     }
 
+    /**
+     * Create a list of {@link GBLStripClusterData} objects that can be used as input to the GBL fitter.
+     * @param htf
+     * @param stripHits
+     * @param _scattering
+     * @param _B
+     * @param _debug
+     * @return the list of GBL strip cluster data
+     */
     public static List<GBLStripClusterData> makeStripData(HelicalTrackFit htf, List<TrackerHit> stripHits, MultipleScattering _scattering, double _B, int _debug) {
         List<GBLStripClusterData> stripClusterDataList = new ArrayList<GBLStripClusterData>();
 
@@ -480,18 +328,4 @@
 
         return strip;
     }
-
-    private static List<TrackerHit> sortHits(Collection<TrackerHit> hits) {
-        List<TrackerHit> hitList = new ArrayList<TrackerHit>(hits);
-        Collections.sort(hitList, new LayerComparator());
-        return hitList;
-    }
-
-    private static class LayerComparator implements Comparator<TrackerHit> {
-
-        @Override
-        public int compare(TrackerHit o1, TrackerHit o2) {
-            return Integer.compare(TrackUtils.getLayer(o1), TrackUtils.getLayer(o2));
-        }
-    }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/TruthResiduals.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/TruthResiduals.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/TruthResiduals.java	Wed Apr 27 11:11:32 2016
@@ -73,14 +73,14 @@
         Map<Integer, List<SimTrackerHit>> simHitsLayerMap = new HashMap<Integer, List<SimTrackerHit> >();
         Map<MCParticle, List<SimTrackerHit> > mcPartSimHitsMap = new HashMap<MCParticle, List<SimTrackerHit > >();
         for(SimTrackerHit sh : simTrackerHits) {
-        	 Hep3Vector shpos = CoordinateTransformations.transformVectorToTracking(sh.getPositionVec());
-        	if(Math.abs(shpos.x()) < 50.0) {
-        		 System.out.printf("%s: Weird hit at %s (%s) in layer %d for MC part %d org %s p %s\n",
+             Hep3Vector shpos = CoordinateTransformations.transformVectorToTracking(sh.getPositionVec());
+            if(Math.abs(shpos.x()) < 50.0) {
+                 System.out.printf("%s: Weird hit at %s (%s) in layer %d for MC part %d org %s p %s\n",
                          this.getClass().getSimpleName(),sh.getPositionVec().toString(),shpos.toString(),sh.getIdentifierFieldValue("layer"),
                          sh.getMCParticle().getPDGID(),sh.getMCParticle().getOrigin().toString(),sh.getMCParticle().getMomentum().toString());
-        		 System.exit(1);
-        	}
-        	
+                 System.exit(1);
+            }
+            
             int layer  = sh.getIdentifierFieldValue("layer");
             if(!simHitsLayerMap.containsKey(layer)) {
                 simHitsLayerMap.put(layer, new ArrayList<SimTrackerHit>());
@@ -96,28 +96,28 @@
 
         
         for(MCParticle mcp : mcPartSimHitsMap.keySet()) {
-        	this.h_mcp_org.fill(mcp.getOriginX(), mcp.getOriginY());
+            this.h_mcp_org.fill(mcp.getOriginX(), mcp.getOriginY());
         }
 
         // Find the particle responsible for the hit in each layer and compute the residual
         
         for(int layer=1;layer<13;++layer) {
-        	//System.out.printf("layer %d: \n",layer);
+            //System.out.printf("layer %d: \n",layer);
             
             List<SimTrackerHit> simHitsLayer = simHitsLayerMap.get(layer);
-        	
+            
             
             if(simHitsLayer != null ) {
-            	
-            	if(simHitsLayer.size()==2) continue;
-            	
+                
+                if(simHitsLayer.size()==2) continue;
+                
                 for(SimTrackerHit simHit : simHitsLayer) {
-                	
-                	 // Find the MC particle
+                    
+                     // Find the MC particle
                     MCParticle mcp = simHit.getMCParticle();
                     
                     if(mcp.getMomentum().magnitude()<0.5) continue;
-                	
+                    
                     // Position in tracking coord
                     Hep3Vector simHitPosTracking = CoordinateTransformations.transformVectorToTracking(simHit.getPositionVec());
                     
@@ -171,24 +171,24 @@
                     }
                     
                     if(layer == 1 && res.y() > 0.1 && this.firstWeirdTrack) {
-                    	double dx = 1.0;
-                    	double xpos = mcp.getOriginZ();
-                    	while(xpos< 100.) {
-                    		xpos += dx;
-                    		trkposExtraPolator = CoordinateTransformations.transformVectorToTracking(TrackUtils.extrapolateTrack(htfTruth,xpos));
-                    		double ypos = trkposExtraPolator.y();
-                    		trkpos_y_vs_x.fill(xpos,ypos);
-                    	}
-                    	
-                    	int idummy = 0;
-                    	while(idummy<2) {
-                    		trkpos_y_vs_x.fill(simHitPosTracking.x(),simHitPosTracking.y());
-                    		idummy++;
-                    		//System.out.printf("weird simhit res pos %s \n", simHitPosTracking.toString());
-                    	}
-                    	
-                    	this.firstWeirdTrack = false;
-                    	
+                        double dx = 1.0;
+                        double xpos = mcp.getOriginZ();
+                        while(xpos< 100.) {
+                            xpos += dx;
+                            trkposExtraPolator = CoordinateTransformations.transformVectorToTracking(TrackUtils.extrapolateTrack(htfTruth,xpos));
+                            double ypos = trkposExtraPolator.y();
+                            trkpos_y_vs_x.fill(xpos,ypos);
+                        }
+                        
+                        int idummy = 0;
+                        while(idummy<2) {
+                            trkpos_y_vs_x.fill(simHitPosTracking.x(),simHitPosTracking.y());
+                            idummy++;
+                            //System.out.printf("weird simhit res pos %s \n", simHitPosTracking.toString());
+                        }
+                        
+                        this.firstWeirdTrack = false;
+                        
                     }
                     
                 
@@ -200,12 +200,12 @@
 
   
     public IHistogram getResidual(int layer,String coord) {
-    	if( !this.res_truthsimhit.containsKey(layer) ) 
-    		throw new RuntimeException("Error the layer number is not valid");
-    	if( coord!="x" || coord!="y")
-    		throw new RuntimeException("Error the coord is not valid");
-    	IHistogram1D h = this.res_truthsimhit.get(layer).get(coord=="x"?0:1);
-    	return h;
+        if( !this.res_truthsimhit.containsKey(layer) ) 
+            throw new RuntimeException("Error the layer number is not valid");
+        if( coord!="x" || coord!="y")
+            throw new RuntimeException("Error the coord is not valid");
+        IHistogram1D h = this.res_truthsimhit.get(layer).get(coord=="x"?0:1);
+        return h;
     }
     
 

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Matrix.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Matrix.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Matrix.java	Wed Apr 27 11:11:32 2016
@@ -1,8 +1,6 @@
 package org.hps.recon.tracking.gbl.matrix;
 
-import java.io.BufferedReader;
 import java.io.PrintWriter;
-import java.io.StreamTokenizer;
 import java.text.DecimalFormat;
 import java.text.DecimalFormatSymbols;
 import java.text.NumberFormat;

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Vector.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Vector.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/recon/tracking/gbl/matrix/Vector.java	Wed Apr 27 11:11:32 2016
@@ -1,6 +1,5 @@
 package org.hps.recon.tracking.gbl.matrix;
 
-import java.io.PrintWriter;
 
 /**
  * Specializes the Matrix class to a vector.

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildCompact.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildCompact.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildCompact.java	Wed Apr 27 11:11:32 2016
@@ -23,7 +23,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 
 import org.jdom.Document;
 import org.jdom.Element;
@@ -49,361 +49,360 @@
  * Class building a new compact.xml detector based on MillepedeII input
  * corrections.
  * 
- * @author 	Per Ola Hansson Adrian <[log in to unmask]>
- * @date 	January 15, 2014 
+ * @author  Per Ola Hansson Adrian <[log in to unmask]> 
  */
 public class BuildCompact {
 
-	private static int runNumber = -1; //1351;
-	private static String detectorName = ""; //"HPS-TestRun-v7";
-	private static ConditionsManager conditionsManager = null;
-	
-	private static Options createCmdLineOpts() {
-		Options options = new Options();
-		options.addOption(new Option("c",true,"The path to the compact xml file."));
-		options.addOption(new Option("o",true,"The name of the new compact xml file."));
-		options.addOption(new Option("d",true,"Detector name."));
-		options.addOption(new Option("r",true,"Run number."));
-		
-		return options;
-	}
-	
-	private static void printHelpAndExit(Options options) {
-		HelpFormatter help = new HelpFormatter();
-		help.printHelp(" ", options);
-		System.exit(1);
-	}
-	
-	//private static buildDetector()
-
-	
-	
-	
-	
-	
-	private static class MilleParameterSet {
-		private IDetectorElement _det = null;
-		 List<MilleParameter> params = new ArrayList<MilleParameter>();
-		public MilleParameterSet(IDetectorElement d) {
-			setDetector(d);
-		}
-		public void setDetector(IDetectorElement d) {
-			_det = d;
-		}
-		public IDetectorElement getDetector() {
-			return _det;
-		}
-		public void add(MilleParameter par) {
-			params.add(par);
-		}
-		public Hep3Vector getLocalTranslation() {
-			Map<String,Double> m = new HashMap<String,Double>();
-			for(MilleParameter p : params) {
-				if (p.getType() == 1) {
-					if (p.getDim() == 1) m.put("u", p.getValue());
-					else if(p.getDim() == 2) m.put("v", p.getValue());
-					else m.put("w", p.getValue());
-				}
-			}
-			if(m.size() != 3) {
-				System.out.println("bad trans!!");
-				System.exit(1);
-			}
-			return new BasicHep3Vector(m.get("u"),m.get("v"),m.get("w"));
-			 
-		}
-		public Hep3Vector getLocalRotation() {
-			Map<String,Double> m = new HashMap<String,Double>();
-			for(MilleParameter p : params) {
-				if (p.getType() == 2) {
-					if (p.getDim() == 1) m.put("alpha",p.getValue());
-					else if(p.getDim() == 2) m.put("beta", p.getValue());
-					else m.put("gamma", p.getValue());
-				}
-			}
-			if(m.size() != 3) {
-				System.out.println("bad rot!!");
-				System.exit(1);
-			}
-			return new BasicHep3Vector(m.get("alpha"),m.get("beta"),m.get("gamma"));
-		}
-		public Hep3Vector getGlobalTranslation() {
-			ITransform3D localToGlobal = getLocalToGlobal();
-			return localToGlobal.getRotation().rotated(getLocalTranslation());
-		}
-		public double getGlobalTranslation(int d) {
-			return getGlobalTranslation().v()[d-1];
-		}
-		public Hep3Vector getGlobalRotation() {
-			ITransform3D localToGlobal = getLocalToGlobal();
-			return localToGlobal.getRotation().rotated(getLocalRotation());
-		}
-		public double getGlobalRotation(int d) {
-			return getGlobalRotation().v()[d-1];
-		}
-		public ITransform3D getLocalToGlobal() {
-			ITransform3D localToGlobal = ( (SiSensor) _det).getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
-			return localToGlobal;
-		}		
-		
-	}
-	
-	public static void main(String[] args) {
-
-		// Setup command line input
-		Options options = createCmdLineOpts();
-		if (args.length == 0) {
-			printHelpAndExit(options);
-		}
-
-		CommandLineParser parser = new DefaultParser();
-		CommandLine cl = null;
-		try {
-			cl = parser.parse(options, args);
-		} catch (ParseException e) {
-			throw new RuntimeException("Problem parsing command line options.",e);
-		}
-		
-		String compactFilename = null;  
-		if(cl.hasOption("c")) {
-			compactFilename = cl.getOptionValue("c");
-		} else {
-			printHelpAndExit(options);
-		}
-		
-		if(cl.hasOption("d")) {
-			detectorName = cl.getOptionValue("d");
-		} else {
-			printHelpAndExit(options);
-		}
-
-		if(cl.hasOption("r")) {
-			runNumber = Integer.parseInt(cl.getOptionValue("r"));
-		} else {
-			printHelpAndExit(options);
-		}
-
-		String compactFilenameNew = "compact_new.xml";
-		if(cl.hasOption("o")) {
-			compactFilenameNew = cl.getOptionValue("o");
-		}
-
-		
-		
-		File compactFile = new File(compactFilename);
-		
-		// read XML
-		SAXBuilder builder = new SAXBuilder();
-		Document compact_document = null;
-		try {
-			compact_document = (Document) builder.build(compactFile);
-		} catch (JDOMException | IOException e1) {
-			throw new RuntimeException("problem with JDOM ", e1);
-		}
-				
-		// read detector geometry
-		FileInputStream inCompact;
-		try {
-			inCompact = new FileInputStream(compactFile);
-		} catch (FileNotFoundException e) {
-			throw new RuntimeException("cannot open compact file",e);
-		}
-
-		GeometryReader reader = new GeometryReader();
-		Detector det;
-		try {
-			det = reader.read(inCompact);
-		} catch (IOException | JDOMException | ElementCreationException e) {
-			throw new RuntimeException("problem reading compact file",e);
-		}
-
-		
-		// set conditions in order to be able to determine which sensors are where in the geometry
-		setConditions(detectorName,runNumber);
-		
-		// Loop over all millepede input files and match parameters with detectors
-		
-		List<MilleParameterSet> list_det = new ArrayList<MilleParameterSet>();
-		
-		FileInputStream inMille = null;
-		BufferedReader brMille = null;
-		try {
-			for(String milleFilename : cl.getArgs()) {
-				inMille = new FileInputStream(milleFilename);
-				brMille = new BufferedReader(new InputStreamReader(inMille));
-				String line;
-				while((line = brMille.readLine()) != null) {
-					//System.out.printf("%s\n",line);
-					if(!line.contains("Parameter") && !line.contains("!")) {
-						
-						MilleParameter par = new MilleParameter(line);
-						//System.out.println(par.getXMLName() + " " + par.getValue());
-						
-						SiSensor detEle = getTrackerDetElement( det,  par);
-						if(detEle == null) {
-							System.out.println("Couldn't find detector for param " + par.getId());
-							System.exit(1);
-						}
-						System.out.println("Found detector  " + detEle.getName());
-						if(detEle.getClass().isInstance(SiSensor.class)) {
-							System.out.println("yeah");
-						}
-
-						// do we have it already?
-						MilleParameterSet useSet = null;
-						for(MilleParameterSet set : list_det) {
-							if(set.getDetector() == detEle) {
-								useSet = set;
-							}
-						}
-						
-						if (useSet == null) {
-							useSet = new MilleParameterSet(detEle);
-							list_det.add(useSet);
-						}
-						
-						//add the parameter
-						useSet.add(par);
-						
-						
-					}
-				}
-				brMille.close();
-			}
-		}
-		catch (IOException e) {
-			throw new RuntimeException("problem reading mille file",e);
-		}
-		
-		for(MilleParameterSet set : list_det) {
-			System.out.println("Detector " + set.getDetector().getName());
-			List<MilleParameter> pars = set.params;
-			for(MilleParameter p : pars) {
-				System.out.println(p.getXMLName() + " " + p.getValue());
-				Element node = findXMLNode(compact_document,p.getXMLName());
-				double value = 0.0;
-				if(p.getType() == 1){
-					value = set.getGlobalTranslation(p.getDim());
-				} else if(p.getType() == 2){
-					value = set.getGlobalRotation(p.getDim());
-				} else {
-					System.out.println("This type is illdefnied " + p.getType());
-					System.exit(1);
-				}
-				node.setAttribute("value", String.format("%.6f",value));
-			}
-			Hep3Vector u = getMeasuredCoordinate( (SiSensor )set.getDetector());
-			System.out.println("u  " + u.toString());
-			System.out.println("t (local)  " + set.getLocalTranslation().toString());
-			System.out.println("t (global) " + set.getGlobalTranslation().toString());
-			System.out.println("r (local)  " + set.getLocalRotation().toString());
-			System.out.println("r (global) " + set.getGlobalRotation().toString());
-			
-			
-		}
-
-		// Save new XML file
-		
-		XMLOutputter xmlOutput = new XMLOutputter();
-		// display nice 
-		//xmlOutput.setFormat(Format.getPrettyFormat());
-		try {
-			xmlOutput.output(compact_document, new FileWriter(compactFilenameNew));
-		} catch (IOException e) {
-			throw new RuntimeException("problem with xml output",e);
-		}
-			
-		
-		
-		
-		
-	}
-
-	private static Element findXMLNode(Document document, String name) {
-		Element rootNode = document.getRootElement();
-		List list = rootNode.getChildren("define");
-		for(int i = 0; i < list.size(); ++i ) {
-			Element node = (Element) list.get(i);
-			List llist = node.getChildren("constant");
-			//System.out.println("length of list " + llist.size());
-			for(int ii = 0; ii < llist.size(); ++ii ) {
-				Element nnode = (Element) llist.get(ii);
-				//System.out.println("node name " + nnode.getAttributeValue("name") + " " + nnode.getAttributeValue("value") );
-				//if(nnode.getAttributeValue("name").contains(name)) {
-				if(nnode.getAttributeValue("name").compareTo(name) ==0 ) {
-					return nnode;
-				}
-			}
-		}	
-		
-		return null;
-	}
-	
-	private static void setConditions(String detectorName, int run) {
-
-		try {
-			if(conditionsManager == null) {
-				conditionsManager = ConditionsManager.defaultInstance();				
-			}
-			conditionsManager.setDetector(detectorName, run);
-			
-		} catch (ConditionsNotFoundException e1) {
-			throw new RuntimeException("problem setting conditions",e1);
-		}
-		
-	}
-
-	private static SiSensor getTrackerDetElement(Detector det, MilleParameter par) {
-		List<SiSensor> sensors = det.getSubdetector("Tracker").getDetectorElement().findDescendants(SiSensor.class);
+    private static int runNumber = -1; //1351;
+    private static String detectorName = ""; //"HPS-TestRun-v7";
+    private static ConditionsManager conditionsManager = null;
+    
+    private static Options createCmdLineOpts() {
+        Options options = new Options();
+        options.addOption(new Option("c",true,"The path to the compact xml file."));
+        options.addOption(new Option("o",true,"The name of the new compact xml file."));
+        options.addOption(new Option("d",true,"Detector name."));
+        options.addOption(new Option("r",true,"Run number."));
+        
+        return options;
+    }
+    
+    private static void printHelpAndExit(Options options) {
+        HelpFormatter help = new HelpFormatter();
+        help.printHelp(" ", options);
+        System.exit(1);
+    }
+    
+    //private static buildDetector()
+
+    
+    
+    
+    
+    
+    private static class MilleParameterSet {
+        private IDetectorElement _det = null;
+         List<MilleParameter> params = new ArrayList<MilleParameter>();
+        public MilleParameterSet(IDetectorElement d) {
+            setDetector(d);
+        }
+        public void setDetector(IDetectorElement d) {
+            _det = d;
+        }
+        public IDetectorElement getDetector() {
+            return _det;
+        }
+        public void add(MilleParameter par) {
+            params.add(par);
+        }
+        public Hep3Vector getLocalTranslation() {
+            Map<String,Double> m = new HashMap<String,Double>();
+            for(MilleParameter p : params) {
+                if (p.getType() == 1) {
+                    if (p.getDim() == 1) m.put("u", p.getValue());
+                    else if(p.getDim() == 2) m.put("v", p.getValue());
+                    else m.put("w", p.getValue());
+                }
+            }
+            if(m.size() != 3) {
+                System.out.println("bad trans!!");
+                System.exit(1);
+            }
+            return new BasicHep3Vector(m.get("u"),m.get("v"),m.get("w"));
+             
+        }
+        public Hep3Vector getLocalRotation() {
+            Map<String,Double> m = new HashMap<String,Double>();
+            for(MilleParameter p : params) {
+                if (p.getType() == 2) {
+                    if (p.getDim() == 1) m.put("alpha",p.getValue());
+                    else if(p.getDim() == 2) m.put("beta", p.getValue());
+                    else m.put("gamma", p.getValue());
+                }
+            }
+            if(m.size() != 3) {
+                System.out.println("bad rot!!");
+                System.exit(1);
+            }
+            return new BasicHep3Vector(m.get("alpha"),m.get("beta"),m.get("gamma"));
+        }
+        public Hep3Vector getGlobalTranslation() {
+            ITransform3D localToGlobal = getLocalToGlobal();
+            return localToGlobal.getRotation().rotated(getLocalTranslation());
+        }
+        public double getGlobalTranslation(int d) {
+            return getGlobalTranslation().v()[d-1];
+        }
+        public Hep3Vector getGlobalRotation() {
+            ITransform3D localToGlobal = getLocalToGlobal();
+            return localToGlobal.getRotation().rotated(getLocalRotation());
+        }
+        public double getGlobalRotation(int d) {
+            return getGlobalRotation().v()[d-1];
+        }
+        public ITransform3D getLocalToGlobal() {
+            ITransform3D localToGlobal = ( (SiSensor) _det).getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
+            return localToGlobal;
+        }       
+        
+    }
+    
+    public static void main(String[] args) {
+
+        // Setup command line input
+        Options options = createCmdLineOpts();
+        if (args.length == 0) {
+            printHelpAndExit(options);
+        }
+
+        CommandLineParser parser = new PosixParser();
+        CommandLine cl = null;
+        try {
+            cl = parser.parse(options, args);
+        } catch (ParseException e) {
+            throw new RuntimeException("Problem parsing command line options.",e);
+        }
+        
+        String compactFilename = null;  
+        if(cl.hasOption("c")) {
+            compactFilename = cl.getOptionValue("c");
+        } else {
+            printHelpAndExit(options);
+        }
+        
+        if(cl.hasOption("d")) {
+            detectorName = cl.getOptionValue("d");
+        } else {
+            printHelpAndExit(options);
+        }
+
+        if(cl.hasOption("r")) {
+            runNumber = Integer.parseInt(cl.getOptionValue("r"));
+        } else {
+            printHelpAndExit(options);
+        }
+
+        String compactFilenameNew = "compact_new.xml";
+        if(cl.hasOption("o")) {
+            compactFilenameNew = cl.getOptionValue("o");
+        }
+
+        
+        
+        File compactFile = new File(compactFilename);
+        
+        // read XML
+        SAXBuilder builder = new SAXBuilder();
+        Document compact_document = null;
+        try {
+            compact_document = (Document) builder.build(compactFile);
+        } catch (JDOMException | IOException e1) {
+            throw new RuntimeException("problem with JDOM ", e1);
+        }
+                
+        // read detector geometry
+        FileInputStream inCompact;
+        try {
+            inCompact = new FileInputStream(compactFile);
+        } catch (FileNotFoundException e) {
+            throw new RuntimeException("cannot open compact file",e);
+        }
+
+        GeometryReader reader = new GeometryReader();
+        Detector det;
+        try {
+            det = reader.read(inCompact);
+        } catch (IOException | JDOMException | ElementCreationException e) {
+            throw new RuntimeException("problem reading compact file",e);
+        }
+
+        
+        // set conditions in order to be able to determine which sensors are where in the geometry
+        setConditions(detectorName,runNumber);
+        
+        // Loop over all millepede input files and match parameters with detectors
+        
+        List<MilleParameterSet> list_det = new ArrayList<MilleParameterSet>();
+        
+        FileInputStream inMille = null;
+        BufferedReader brMille = null;
+        try {
+            for(String milleFilename : cl.getArgs()) {
+                inMille = new FileInputStream(milleFilename);
+                brMille = new BufferedReader(new InputStreamReader(inMille));
+                String line;
+                while((line = brMille.readLine()) != null) {
+                    //System.out.printf("%s\n",line);
+                    if(!line.contains("Parameter") && !line.contains("!")) {
+                        
+                        MilleParameter par = new MilleParameter(line);
+                        //System.out.println(par.getXMLName() + " " + par.getValue());
+                        
+                        SiSensor detEle = getTrackerDetElement( det,  par);
+                        if(detEle == null) {
+                            System.out.println("Couldn't find detector for param " + par.getId());
+                            System.exit(1);
+                        }
+                        System.out.println("Found detector  " + detEle.getName());
+                        if(detEle.getClass().isInstance(SiSensor.class)) {
+                            System.out.println("yeah");
+                        }
+
+                        // do we have it already?
+                        MilleParameterSet useSet = null;
+                        for(MilleParameterSet set : list_det) {
+                            if(set.getDetector() == detEle) {
+                                useSet = set;
+                            }
+                        }
+                        
+                        if (useSet == null) {
+                            useSet = new MilleParameterSet(detEle);
+                            list_det.add(useSet);
+                        }
+                        
+                        //add the parameter
+                        useSet.add(par);
+                        
+                        
+                    }
+                }
+                brMille.close();
+            }
+        }
+        catch (IOException e) {
+            throw new RuntimeException("problem reading mille file",e);
+        }
+        
+        for(MilleParameterSet set : list_det) {
+            System.out.println("Detector " + set.getDetector().getName());
+            List<MilleParameter> pars = set.params;
+            for(MilleParameter p : pars) {
+                System.out.println(p.getXMLName() + " " + p.getValue());
+                Element node = findXMLNode(compact_document,p.getXMLName());
+                double value = 0.0;
+                if(p.getType() == 1){
+                    value = set.getGlobalTranslation(p.getDim());
+                } else if(p.getType() == 2){
+                    value = set.getGlobalRotation(p.getDim());
+                } else {
+                    System.out.println("This type is illdefnied " + p.getType());
+                    System.exit(1);
+                }
+                node.setAttribute("value", String.format("%.6f",value));
+            }
+            Hep3Vector u = getMeasuredCoordinate( (SiSensor )set.getDetector());
+            System.out.println("u  " + u.toString());
+            System.out.println("t (local)  " + set.getLocalTranslation().toString());
+            System.out.println("t (global) " + set.getGlobalTranslation().toString());
+            System.out.println("r (local)  " + set.getLocalRotation().toString());
+            System.out.println("r (global) " + set.getGlobalRotation().toString());
+            
+            
+        }
+
+        // Save new XML file
+        
+        XMLOutputter xmlOutput = new XMLOutputter();
+        // display nice 
+        //xmlOutput.setFormat(Format.getPrettyFormat());
+        try {
+            xmlOutput.output(compact_document, new FileWriter(compactFilenameNew));
+        } catch (IOException e) {
+            throw new RuntimeException("problem with xml output",e);
+        }
+            
+        
+        
+        
+        
+    }
+
+    private static Element findXMLNode(Document document, String name) {
+        Element rootNode = document.getRootElement();
+        List list = rootNode.getChildren("define");
+        for(int i = 0; i < list.size(); ++i ) {
+            Element node = (Element) list.get(i);
+            List llist = node.getChildren("constant");
+            //System.out.println("length of list " + llist.size());
+            for(int ii = 0; ii < llist.size(); ++ii ) {
+                Element nnode = (Element) llist.get(ii);
+                //System.out.println("node name " + nnode.getAttributeValue("name") + " " + nnode.getAttributeValue("value") );
+                //if(nnode.getAttributeValue("name").contains(name)) {
+                if(nnode.getAttributeValue("name").compareTo(name) ==0 ) {
+                    return nnode;
+                }
+            }
+        }   
+        
+        return null;
+    }
+    
+    private static void setConditions(String detectorName, int run) {
+
+        try {
+            if(conditionsManager == null) {
+                conditionsManager = ConditionsManager.defaultInstance();                
+            }
+            conditionsManager.setDetector(detectorName, run);
+            
+        } catch (ConditionsNotFoundException e1) {
+            throw new RuntimeException("problem setting conditions",e1);
+        }
+        
+    }
+
+    private static SiSensor getTrackerDetElement(Detector det, MilleParameter par) {
+        List<SiSensor> sensors = det.getSubdetector("Tracker").getDetectorElement().findDescendants(SiSensor.class);
         //List<SiTrackerModule> modules = det.getDetectorElement().findDescendants(SiTrackerModule.class);
         //System.out.printf("%d sensors\n",sensors.size());
         for (SiSensor module: sensors) {
             // Create DAQ Maps
-        	boolean isTop = ((HpsSiSensor) module).isTopLayer();
-        	int h = par.getHalf();
-        	if ((isTop && h == 1) || (!isTop && h == 2)) {
-        		int layer = ((HpsSiSensor) module).getLayerNumber();
-        		if (layer == par.getSensor()) {
-        			//found match
-        			return module;
-        		}
-        	}
+            boolean isTop = ((HpsSiSensor) module).isTopLayer();
+            int h = par.getHalf();
+            if ((isTop && h == 1) || (!isTop && h == 2)) {
+                int layer = ((HpsSiSensor) module).getLayerNumber();
+                if (layer == par.getSensor()) {
+                    //found match
+                    return module;
+                }
+            }
         }
         return null;
-		
-	}
-	
-
-	
-	private static class DetectorList<K> extends ArrayList<DetAlignConstants> {
-		//List<DetAlignConstants> _detectors = new ArrayList<DetAlignConstants>();
-		public DetectorList() {
-		}
-		
-		public boolean contains(IDetectorElement detEle) {
-			return this.get(detEle) == null ? false : true;
-		}
-		
-		public DetAlignConstants get(IDetectorElement detEle) {
-			for(DetAlignConstants d : this) {
-				if (d == detEle) {
-					return d;
-				}
-			}
-			return null;
-		}
-		public void print() {
-			System.out.println("==== " + this.size() + " detectors has alignment corrections ====");
-			for(DetAlignConstants det : this) {
-				det.print();
-			}
-		}
-		
-	}
-	
-	
-	
-	private static Hep3Vector getTrackingMeasuredCoordinate(SiSensor sensor)
+        
+    }
+    
+
+    
+    private static class DetectorList<K> extends ArrayList<DetAlignConstants> {
+        //List<DetAlignConstants> _detectors = new ArrayList<DetAlignConstants>();
+        public DetectorList() {
+        }
+        
+        public boolean contains(IDetectorElement detEle) {
+            return this.get(detEle) == null ? false : true;
+        }
+        
+        public DetAlignConstants get(IDetectorElement detEle) {
+            for(DetAlignConstants d : this) {
+                if (d == detEle) {
+                    return d;
+                }
+            }
+            return null;
+        }
+        public void print() {
+            System.out.println("==== " + this.size() + " detectors has alignment corrections ====");
+            for(DetAlignConstants det : this) {
+                det.print();
+            }
+        }
+        
+    }
+    
+    
+    
+    private static Hep3Vector getTrackingMeasuredCoordinate(SiSensor sensor)
     {
         // p-side unit vector
         ITransform3D electrodes_to_global = sensor.getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
@@ -411,8 +410,8 @@
         measuredCoordinate = VecOp.mult(VecOp.mult(CoordinateTransformations.getMatrix(),electrodes_to_global.getRotation().getRotationMatrix()), measuredCoordinate);
         return measuredCoordinate;
     }
-	
-	private static Hep3Vector getMeasuredCoordinate(SiSensor sensor)
+    
+    private static Hep3Vector getMeasuredCoordinate(SiSensor sensor)
     {
         // p-side unit vector
         ITransform3D electrodes_to_global = sensor.getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
@@ -420,127 +419,127 @@
         measuredCoordinate = VecOp.mult(electrodes_to_global.getRotation().getRotationMatrix(), measuredCoordinate);
         return measuredCoordinate;
     }
-	
-	
-	
-	private static class SiSensorDetAlignConstants extends DetAlignConstants {
-		public SiSensorDetAlignConstants(IDetectorElement det) {
-			super(det);
-		}
-		public void transform() {
-			ITransform3D localToGlobal = null;
-			if(_det.getClass().isInstance(SiSensor.class)) {
-				localToGlobal = ( (SiSensor) _det).getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
-			}
-			//Translation
-			Hep3Vector t_local = _constants.getTranslationVector();
-			Hep3Vector t_global = localToGlobal.getRotation().rotated(t_local);
-			_constants.addGlobalTranslation(t_global);
-			//Rotation
-			Hep3Vector r_local = _constants.getRotationVector();
-			Hep3Vector r_global = localToGlobal.getRotation().rotated(r_local);
-			_constants.addGlobalRotation(r_global);
-		}
-		
-	}
-	
-	private static abstract class DetAlignConstants {
-		protected IDetectorElement _det = null;
-		protected AlignConstants<String,Double> _constants = new AlignConstants<String,Double>();
-		public DetAlignConstants(IDetectorElement det) {
-			_det = det;
-		}
-		public abstract void transform();
-		public void add(MilleParameter par) {
-			this._constants.add(par);
-		}
-		public void print() {
-			System.out.println(_det.getName());
-			for(Entry<String, Double>  c : this._constants.entrySet()) {
-				System.out.println(c.getKey() + " " + c.getValue());
-			}
-			System.out.println("Local translation  " + _constants.getTranslationVector().toString());
-			System.out.println("Global translation " + _constants.getTranslationVectorGlobal().toString());
-			System.out.println("Local rotation     " + _constants.getRotationVector().toString());
-			System.out.println("Global rotation    " + _constants.getRotationVectorGlobal().toString());
-			
-
-		}
-			
-		
-	}
-	
-	
-	
-	private static class AlignConstants<K,V> extends HashMap<String,Double> {
-		List<MilleParameter> _pars = new ArrayList<MilleParameter>();
-		public AlignConstants() {
-			super();
-		}
-		public void add(MilleParameter p) {
-			_pars.add(p);
-			if (p.getType() == 1) {
-				if (p.getDim() == 1) this.put("u", p.getValue());
-				else if(p.getDim() == 2) this.put("v", p.getValue());
-				else this.put("w", p.getValue());
-			}
-			else {
-				if (p.getDim() == 1) this.put("alpha", p.getValue());
-				else if(p.getDim() == 2) this.put("beta", p.getValue());
-				else this.put("gamma", p.getValue());
-			}
-		}
-		public void print() {
-			for(Entry<String,Double> e : this.entrySet()) {
-				System.out.println(e.getKey() + " " + e.getValue());
-			}
-		}
-		public Hep3Vector getTranslationVector() {
-			if(!this.containsKey("u") || !this.containsKey("v") || !this.containsKey("w")) {
-				System.out.println("missing pars for translation");
-				print();
-				System.exit(1);
-			}
-			return new BasicHep3Vector(this.get("u"),this.get("v"),this.get("w"));
-		}
-		public Hep3Vector getTranslationVectorGlobal() {
-			if(!this.containsKey("x") || !this.containsKey("y") || !this.containsKey("z")) {
-				System.out.println("missing pars for global translation");
-				print();
-				System.exit(1);
-			}
-			return new BasicHep3Vector(this.get("x"),this.get("y"),this.get("z"));
-		}
-		public Hep3Vector getRotationVector() {
-			if(!this.containsKey("alpha") || !this.containsKey("beta") || !this.containsKey("gamma")) {
-				System.out.println("missing pars for rotation");
-				print();
-				System.exit(1);
-			}
-			return new BasicHep3Vector(this.get("alpha"),this.get("beta"),this.get("gamma"));
-		}
-		public Hep3Vector getRotationVectorGlobal() {
-			if(!this.containsKey("rx") || !this.containsKey("ry") || !this.containsKey("rz")) {
-				System.out.println("missing pars for global rotation");
-				print();
-				System.exit(1);
-			}
-			return new BasicHep3Vector(this.get("rx"),this.get("ry"),this.get("rz"));
-		}
-		private void addGlobalTranslation(Hep3Vector t) {
-			this.put("x", t.x()); 
-			this.put("y", t.y());
-			this.put("z", t.z());
-		}
-		private void addGlobalRotation(Hep3Vector t) {
-			this.put("rx", t.x()); 
-			this.put("ry", t.y());
-			this.put("rz", t.z());
-		}
-		
-		
-	}
-	
-	
+    
+    
+    
+    private static class SiSensorDetAlignConstants extends DetAlignConstants {
+        public SiSensorDetAlignConstants(IDetectorElement det) {
+            super(det);
+        }
+        public void transform() {
+            ITransform3D localToGlobal = null;
+            if(_det.getClass().isInstance(SiSensor.class)) {
+                localToGlobal = ( (SiSensor) _det).getReadoutElectrodes(ChargeCarrier.HOLE).getLocalToGlobal();
+            }
+            //Translation
+            Hep3Vector t_local = _constants.getTranslationVector();
+            Hep3Vector t_global = localToGlobal.getRotation().rotated(t_local);
+            _constants.addGlobalTranslation(t_global);
+            //Rotation
+            Hep3Vector r_local = _constants.getRotationVector();
+            Hep3Vector r_global = localToGlobal.getRotation().rotated(r_local);
+            _constants.addGlobalRotation(r_global);
+        }
+        
+    }
+    
+    private static abstract class DetAlignConstants {
+        protected IDetectorElement _det = null;
+        protected AlignConstants<String,Double> _constants = new AlignConstants<String,Double>();
+        public DetAlignConstants(IDetectorElement det) {
+            _det = det;
+        }
+        public abstract void transform();
+        public void add(MilleParameter par) {
+            this._constants.add(par);
+        }
+        public void print() {
+            System.out.println(_det.getName());
+            for(Entry<String, Double>  c : this._constants.entrySet()) {
+                System.out.println(c.getKey() + " " + c.getValue());
+            }
+            System.out.println("Local translation  " + _constants.getTranslationVector().toString());
+            System.out.println("Global translation " + _constants.getTranslationVectorGlobal().toString());
+            System.out.println("Local rotation     " + _constants.getRotationVector().toString());
+            System.out.println("Global rotation    " + _constants.getRotationVectorGlobal().toString());
+            
+
+        }
+            
+        
+    }
+    
+    
+    
+    private static class AlignConstants<K,V> extends HashMap<String,Double> {
+        List<MilleParameter> _pars = new ArrayList<MilleParameter>();
+        public AlignConstants() {
+            super();
+        }
+        public void add(MilleParameter p) {
+            _pars.add(p);
+            if (p.getType() == 1) {
+                if (p.getDim() == 1) this.put("u", p.getValue());
+                else if(p.getDim() == 2) this.put("v", p.getValue());
+                else this.put("w", p.getValue());
+            }
+            else {
+                if (p.getDim() == 1) this.put("alpha", p.getValue());
+                else if(p.getDim() == 2) this.put("beta", p.getValue());
+                else this.put("gamma", p.getValue());
+            }
+        }
+        public void print() {
+            for(Entry<String,Double> e : this.entrySet()) {
+                System.out.println(e.getKey() + " " + e.getValue());
+            }
+        }
+        public Hep3Vector getTranslationVector() {
+            if(!this.containsKey("u") || !this.containsKey("v") || !this.containsKey("w")) {
+                System.out.println("missing pars for translation");
+                print();
+                System.exit(1);
+            }
+            return new BasicHep3Vector(this.get("u"),this.get("v"),this.get("w"));
+        }
+        public Hep3Vector getTranslationVectorGlobal() {
+            if(!this.containsKey("x") || !this.containsKey("y") || !this.containsKey("z")) {
+                System.out.println("missing pars for global translation");
+                print();
+                System.exit(1);
+            }
+            return new BasicHep3Vector(this.get("x"),this.get("y"),this.get("z"));
+        }
+        public Hep3Vector getRotationVector() {
+            if(!this.containsKey("alpha") || !this.containsKey("beta") || !this.containsKey("gamma")) {
+                System.out.println("missing pars for rotation");
+                print();
+                System.exit(1);
+            }
+            return new BasicHep3Vector(this.get("alpha"),this.get("beta"),this.get("gamma"));
+        }
+        public Hep3Vector getRotationVectorGlobal() {
+            if(!this.containsKey("rx") || !this.containsKey("ry") || !this.containsKey("rz")) {
+                System.out.println("missing pars for global rotation");
+                print();
+                System.exit(1);
+            }
+            return new BasicHep3Vector(this.get("rx"),this.get("ry"),this.get("rz"));
+        }
+        private void addGlobalTranslation(Hep3Vector t) {
+            this.put("x", t.x()); 
+            this.put("y", t.y());
+            this.put("z", t.z());
+        }
+        private void addGlobalRotation(Hep3Vector t) {
+            this.put("rx", t.x()); 
+            this.put("ry", t.y());
+            this.put("rz", t.z());
+        }
+        
+        
+    }
+    
+    
 
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildMillepedeCompact.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildMillepedeCompact.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/BuildMillepedeCompact.java	Wed Apr 27 11:11:32 2016
@@ -6,22 +6,14 @@
  * created on 1/15/2014
  */
 
-import hep.physics.vec.BasicHep3Vector;
-import hep.physics.vec.Hep3Vector;
-import hep.physics.vec.VecOp;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -29,252 +21,271 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
-import org.hps.recon.tracking.CoordinateTransformations;
-import org.jdom.Attribute;
+import org.apache.commons.cli.PosixParser;
 import org.jdom.DataConversionException;
 import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
 import org.jdom.output.XMLOutputter;
-import org.lcsim.conditions.ConditionsManager;
-import org.lcsim.conditions.ConditionsManager.ConditionsNotFoundException;
-import org.lcsim.detector.IDetectorElement;
-import org.lcsim.detector.ITransform3D;
-import org.lcsim.detector.tracker.silicon.ChargeCarrier;
-import org.lcsim.detector.tracker.silicon.SiSensor;
-import org.lcsim.geometry.Detector;
-import org.lcsim.geometry.GeometryReader;
 import org.lcsim.geometry.compact.converter.MilleParameter;
-import org.lcsim.util.xml.ElementFactory.ElementCreationException;
 
 
 public class BuildMillepedeCompact {
 
-	private static String detectorName = "Tracker";
-	private static boolean replaceConstant = false;
+    private static String detectorName = "Tracker";
+    private static boolean replaceConstant = false;
     private static boolean calcNewValue = true;
     private static boolean ignoreBeamspot = true;
+    private static boolean flipRotationCorrection = false;
 
 
 
     private static Options createCmdLineOpts() {
-		Options options = new Options();
-		options.addOption(new Option("c",true,"The path to the compact xml file."));
-		options.addOption(new Option("o",true,"The name of the new compact xml file."));
-		options.addOption(new Option("r", false, "Replace correction instead of adding to it."));
+        Options options = new Options();
+        options.addOption(new Option("c",true,"The path to the compact xml file."));
+        options.addOption(new Option("o",true,"The name of the new compact xml file."));
+        options.addOption(new Option("r", false, "Replace correction instead of adding to it."));
         options.addOption(new Option("t", false, "Add a text string as a new value instead of adding to it."));
-		return options;
-	}
-	
-	private static void printHelpAndExit(Options options) {
-		HelpFormatter help = new HelpFormatter();
-		help.printHelp(" ", options);
-		System.exit(1);
-	}
-	
-		
-	public static void main(String[] args) {
-
-		// Setup command line input
-		Options options = createCmdLineOpts();
-		if (args.length == 0) {
-			printHelpAndExit(options);
-		}
-
-		CommandLineParser parser = new DefaultParser();
-		CommandLine cl = null;
-		try {
-			cl = parser.parse(options, args);
-		} catch (ParseException e) {
-			throw new RuntimeException("Problem parsing command line options.",e);
-		}
-		
-		String compactFilename = null;  
-		if(cl.hasOption("c")) {
-			compactFilename = cl.getOptionValue("c");
-		} else {
-			printHelpAndExit(options);
-		}
-		
-		String compactFilenameNew = "compact_new.xml";
-		if(cl.hasOption("o")) {
-			compactFilenameNew = cl.getOptionValue("o");
-		}
-		
-		
-		
-		if(cl.hasOption("r")) {
-		    replaceConstant = true;
-		}
-
-		if(cl.hasOption("t")) {
+        options.addOption(new Option("f",false, "Flip sign of rotation corrections."));
+        return options;
+    }
+    
+    private static void printHelpAndExit(Options options) {
+        HelpFormatter help = new HelpFormatter();
+        help.printHelp(" ", options);
+        System.exit(1);
+    }
+    
+        
+    public static void main(String[] args) {
+
+        // Setup command line input
+        Options options = createCmdLineOpts();
+        if (args.length == 0) {
+            printHelpAndExit(options);
+        }
+
+        CommandLineParser parser = new PosixParser();
+        CommandLine cl = null;
+        try {
+            cl = parser.parse(options, args);
+        } catch (ParseException e) {
+            throw new RuntimeException("Problem parsing command line options.",e);
+        }
+        
+        String compactFilename = null;  
+        if(cl.hasOption("c")) {
+            compactFilename = cl.getOptionValue("c");
+        } else {
+            printHelpAndExit(options);
+        }
+        
+        String compactFilenameNew = "compact_new.xml";
+        if(cl.hasOption("o")) {
+            compactFilenameNew = cl.getOptionValue("o");
+        }
+        
+        
+        
+        if(cl.hasOption("r")) {
+            replaceConstant = true;
+        }
+
+        if(cl.hasOption("t")) {
             calcNewValue = false;
         }
 
-		
-		File compactFile = new File(compactFilename);
-		
-		// read XML
-		SAXBuilder builder = new SAXBuilder();
-		Document compact_document = null;
-		try {
-			compact_document = (Document) builder.build(compactFile);
-		} catch (JDOMException | IOException e1) {
-			throw new RuntimeException("problem with JDOM ", e1);
-		}
-		
-		
-		
-		// Loop over all millepede input files and build a list of parameters
-		
-		List<MilleParameter> params = new ArrayList<MilleParameter>();
-		
-		FileInputStream inMille = null;
-		BufferedReader brMille = null;
-		try {
-			for(String milleFilename : cl.getArgs()) {
-				inMille = new FileInputStream(milleFilename);
-				brMille = new BufferedReader(new InputStreamReader(inMille));
-				String line;
-				while((line = brMille.readLine()) != null) {
-					//System.out.printf("%s\n",line);
-					if(!line.contains("Parameter") && !line.contains("!")) {
-						
-						MilleParameter par = new MilleParameter(line);
-						//System.out.println(par.getXMLName() + " " + par.getValue());
-						
-						if (ignoreBeamspot) {
-						    if(par.getSensor() == 98 || par.getSensor() == 99) {
-						        System.out.printf("Ignoring %s\n", par.toString());
-						        continue;
-						    }
-						}
-						System.out.printf("Adding %s\n", par.toString());
-						//add the parameter
-						params.add(par);
-						
-					}
-				}
-				brMille.close();
-			}
-		}
-		catch (IOException e) {
-			throw new RuntimeException("problem reading mille file",e);
-		}
-		
-		System.out.printf("Found %d millepede parameters\n ", params.size());
-		
-		
-
-		Element rootNode = compact_document.getRootElement();
-		List<Element> detectors = rootNode.getChildren("detectors");
-		for(Element detectorsNode : detectors) {
-		    List<Element> detectorNode = detectorsNode.getChildren("detector");
-		    if(detectorNode!=null) {
-		        System.out.println(detectorNode.size() + " detectors");
-		        for(Element detector : detectorNode) {
-		            if(detector.getAttribute("name")!=null) {
-		                if(detector.getAttributeValue("name").compareTo(detectorName)==0 ) {
-		                    System.out.println("Found " + detectorName);
-		                    for(MilleParameter p : params) {
-		                        Element node = findMillepedeConstantNode(detector,Integer.toString(p.getId()));
-		                        if(node!=null) {
+        if(cl.hasOption("f")) {
+            flipRotationCorrection = true;
+        }
+        
+        if (calcNewValue)
+            System.out.println("DO CALCULATE NEW VALUE");
+        else
+            System.out.println("DO NOT CALCULATE NEW VALUE");
+        
+        
+        
+        if (flipRotationCorrection)
+            System.out.println("DO FLIP ROTATIONS");
+        else
+            System.out.println("DO NOT FLIP ROTATIONS");
+        
+        
+        
+        File compactFile = new File(compactFilename);
+        
+        // read XML
+        SAXBuilder builder = new SAXBuilder();
+        Document compact_document = null;
+        try {
+            compact_document = (Document) builder.build(compactFile);
+        } catch (JDOMException | IOException e1) {
+            throw new RuntimeException("problem with JDOM ", e1);
+        }
+        
+        
+        
+        // Loop over all millepede input files and build a list of parameters
+        
+        List<MilleParameter> params = new ArrayList<MilleParameter>();
+        
+        FileInputStream inMille = null;
+        BufferedReader brMille = null;
+        try {
+            for(String milleFilename : cl.getArgs()) {
+                inMille = new FileInputStream(milleFilename);
+                brMille = new BufferedReader(new InputStreamReader(inMille));
+                String line;
+                while((line = brMille.readLine()) != null) {
+                    //System.out.printf("%s\n",line);
+                    if(!line.contains("Parameter") && !line.contains("!")) {
+                        
+                        MilleParameter par = new MilleParameter(line);
+                        //System.out.println(par.getXMLName() + " " + par.getValue());
+                        
+                        if (ignoreBeamspot) {
+                            if(par.getSensor() == 98 || par.getSensor() == 99) {
+                                System.out.printf("Ignoring %s\n", par.toString());
+                                continue;
+                            }
+                        }
+                        System.out.printf("Adding %s\n", par.toString());
+                        //add the parameter
+                        params.add(par);
+                        
+                    }
+                }
+                brMille.close();
+            }
+        }
+        catch (IOException e) {
+            throw new RuntimeException("problem reading mille file",e);
+        }
+        
+        System.out.printf("Found %d millepede parameters\n ", params.size());
+        
+        
+
+        Element rootNode = compact_document.getRootElement();
+        List<Element> detectors = rootNode.getChildren("detectors");
+        for(Element detectorsNode : detectors) {
+            List<Element> detectorNode = detectorsNode.getChildren("detector");
+            if(detectorNode!=null) {
+                System.out.println(detectorNode.size() + " detectors");
+                for(Element detector : detectorNode) {
+                    if(detector.getAttribute("name")!=null) {
+                        if(detector.getAttributeValue("name").compareTo(detectorName)==0 ) {
+                            System.out.println("Found " + detectorName);
+                            for(MilleParameter p : params) {
+                                Element node = findMillepedeConstantNode(detector,Integer.toString(p.getId()));
+                                if(node!=null) {
 
                                     double correction = p.getValue();
 
-		                            // have the option of adding a text value to the compact instead of actually computing the new value
-		                            if(calcNewValue) {
-
-		                                double oldValue = 0;
-		                                try {
-		                                    oldValue = node.getAttribute("value").getDoubleValue();
-		                                } catch (DataConversionException e) {
-		                                    e.printStackTrace();
-		                                }
-		                                double newValue;
-		                                if(replaceConstant) {
-		                                    newValue = correction;
-		                                } else {
-		                                    if (p.getType() == MilleParameter.Type.ROTATION.getType()) {
-		                                        newValue = oldValue - correction;
-		                                    } else {
-		                                        newValue = oldValue + correction;
-		                                    }
-		                                }
-		                                System.out.println("Update " + p.getId() + ": " + oldValue + " (corr. " + correction + ") ->  "  + newValue );
-		                                node.setAttribute("value", String.format("%.6f",newValue));
-		                            
-		                            } else {
-		                                
-		                                String oldValue = node.getAttribute("value").getValue();
-		                                
-		                                if(replaceConstant)
-		                                    throw new RuntimeException("Doesn't make sense to try and replace with the string option?");
-
-		                                if( correction != 0.0) {
-		                                    String newValue = oldValue + " + " + String.format("%.6f",correction);
-		                                    System.out.println("Update " + p.getId() + ": " + oldValue + " (corr. " + correction + ") ->  "  + newValue );
-		                                    node.setAttribute("value", newValue);
-		                                }		                                
-		                            }
-		                            
-		                        } else {
-		                            throw new RuntimeException("no element found for " + p.getId() + " check format of compact file");
-		                        }
-		                    }       
-		                }
-		            } else {
-		                throw new RuntimeException("this detector node element is not formatted correctly");
-		            }
-		        }
-		    } else {
-		        throw new RuntimeException("this detector node element is not formatted correctly");
-		    }
-		}
-
-
-		// Save new XML file
-		
-		XMLOutputter xmlOutput = new XMLOutputter();
-		// display nice 
-		//xmlOutput.setFormat(Format.getPrettyFormat());
-		try {
-			xmlOutput.output(compact_document, new FileWriter(compactFilenameNew));
-		} catch (IOException e) {
-			throw new RuntimeException("problem with xml output",e);
-		}
-			
-		
-		
-		
-		
-	}
-
-
-	private static Element findMillepedeConstantNode(Element detector, String name) {
-	    Element element_constants = detector.getChild("millepede_constants");
-	    if(element_constants==null) {
-	        throw new RuntimeException("no alignment constants in this xml file.");
-	    }
-	    List<Element> list = element_constants.getChildren("millepede_constant");
-	    for(Element element : list) {
-	        if(element.getAttribute("name")!=null) {
-	            if(element.getAttributeValue("name").compareTo(name) == 0) {
-	                return element;
-	            } 
-	        } else {
-	            throw new RuntimeException("this element is not formatted correctly");
-	        }
-	    }
-	    return null;
-	}
-
-	
-
-	
-	
-	
+                                    // have the option of adding a text value to the compact instead of actually computing the new value
+                                    if(calcNewValue) {
+
+                                        double oldValue = 0;
+                                        try {
+                                            oldValue = node.getAttribute("value").getDoubleValue();
+                                        } catch (DataConversionException e) {
+                                            e.printStackTrace();
+                                        }
+                                        double newValue;
+                                        if(replaceConstant) {
+                                            newValue = correction;
+                                        } else {
+                                            if (p.getType() == MilleParameter.Type.ROTATION.getType() && !flipRotationCorrection) {
+                                                newValue = oldValue - correction;
+                                                System.out.println("NOFLIP");
+                                            } else {
+                                                newValue = oldValue + correction;
+                                                System.out.println("FLIP");
+                                            }
+                                        }
+                                        System.out.println("Update " + p.getId() + ": " + oldValue + " (corr. " + correction + ") ->  "  + newValue );
+                                        node.setAttribute("value", String.format("%.6f",newValue));
+                                    
+                                    } else {
+                                        
+                                        String oldValue = node.getAttribute("value").getValue();
+                                        
+                                        if(replaceConstant)
+                                            throw new RuntimeException("Doesn't make sense to try and replace with the string option?");
+
+                                        if( correction != 0.0) {
+                                            String newValue;
+                                            
+                                            if (p.getType() == MilleParameter.Type.ROTATION.getType() && !flipRotationCorrection) {
+                                                newValue = oldValue + " - " + String.format("%.6f",correction);
+                                                System.out.println("NOFLIP");
+                                            } else {
+                                                newValue = oldValue + " + " + String.format("%.6f",correction);
+                                                System.out.println("FLIP");
+                                            }
+                                            
+                                            System.out.println("Update " + p.getId() + ": " + oldValue + " (corr. " + correction + ") ->  "  + newValue );
+                                            node.setAttribute("value", newValue);
+                                        }                                       
+                                    }
+                                    
+                                } else {
+                                    throw new RuntimeException("no element found for " + p.getId() + " check format of compact file");
+                                }
+                            }       
+                        }
+                    } else {
+                        throw new RuntimeException("this detector node element is not formatted correctly");
+                    }
+                }
+            } else {
+                throw new RuntimeException("this detector node element is not formatted correctly");
+            }
+        }
+
+
+        // Save new XML file
+        
+        XMLOutputter xmlOutput = new XMLOutputter();
+        // display nice 
+        //xmlOutput.setFormat(Format.getPrettyFormat());
+        try {
+            xmlOutput.output(compact_document, new FileWriter(compactFilenameNew));
+        } catch (IOException e) {
+            throw new RuntimeException("problem with xml output",e);
+        }
+            
+        
+        
+        
+        
+    }
+
+
+    private static Element findMillepedeConstantNode(Element detector, String name) {
+        Element element_constants = detector.getChild("millepede_constants");
+        if(element_constants==null) {
+            throw new RuntimeException("no alignment constants in this xml file.");
+        }
+        List<Element> list = element_constants.getChildren("millepede_constant");
+        for(Element element : list) {
+            if(element.getAttribute("name")!=null) {
+                if(element.getAttributeValue("name").compareTo(name) == 0) {
+                    return element;
+                } 
+            } else {
+                throw new RuntimeException("this element is not formatted correctly");
+            }
+        }
+        return null;
+    }
+
+    
+
+    
+    
+    
 
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/HPSStrips.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/HPSStrips.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/HPSStrips.java	Wed Apr 27 11:11:32 2016
@@ -255,7 +255,7 @@
      * Capacitance for a particular cell.  Units are pF.
      *
      * @param cell_id
-     * @return
+     * @return the capacitance for the cell (pF)
      */
     public double getCapacitance(int cell_id) // capacitance in pF
     {
@@ -266,7 +266,7 @@
      * Nominal capacitance used for throwing random noise in the sensor.
      * Calculated using middle strip.  Units are pF.
      *
-     * @return
+     * @return the nominal capacitance used for noise generation in the sensor (pF)
      */
     public double getCapacitance() {
         return getCapacitance(getNCells(0) / 2);

Modified: java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/MillepedeCompactDump.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/MillepedeCompactDump.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/java/org/hps/svt/alignment/MillepedeCompactDump.java	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,7 @@
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
@@ -28,115 +28,115 @@
 
 public class MillepedeCompactDump {
 
-	private static String detectorName = "Tracker";
+    private static String detectorName = "Tracker";
 
 
 
     private static Options createCmdLineOpts() {
-		Options options = new Options();
-		options.addOption(new Option("c",true,"The path to the compact xml file."));
-		options.addOption(new Option("o",true,"The name of the output text file."));
-		return options;
-	}
-	
-	private static void printHelpAndExit(Options options) {
-		HelpFormatter help = new HelpFormatter();
-		help.printHelp(" ", options);
-		System.exit(1);
-	}
-	
-		
-	public static void main(String[] args) {
+        Options options = new Options();
+        options.addOption(new Option("c",true,"The path to the compact xml file."));
+        options.addOption(new Option("o",true,"The name of the output text file."));
+        return options;
+    }
+    
+    private static void printHelpAndExit(Options options) {
+        HelpFormatter help = new HelpFormatter();
+        help.printHelp(" ", options);
+        System.exit(1);
+    }
+    
+        
+    public static void main(String[] args) {
 
-		// Setup command line input
-		Options options = createCmdLineOpts();
-		if (args.length == 0) {
-			printHelpAndExit(options);
-		}
+        // Setup command line input
+        Options options = createCmdLineOpts();
+        if (args.length == 0) {
+            printHelpAndExit(options);
+        }
 
-		CommandLineParser parser = new DefaultParser();
-		CommandLine cl = null;
-		try {
-			cl = parser.parse(options, args);
-		} catch (ParseException e) {
-			throw new RuntimeException("Problem parsing command line options.",e);
-		}
-		
-		String compactFilename = null;  
-		if(cl.hasOption("c")) {
-			compactFilename = cl.getOptionValue("c");
-		} else {
-			printHelpAndExit(options);
-		}
-		
-		String outputFilename = "millepede_dump.txt";// + compactFilename.replace(".xml", ".txt");
-		if(cl.hasOption("o")) {
-			outputFilename = cl.getOptionValue("o");
-		}
-		
+        CommandLineParser parser = new PosixParser();
+        CommandLine cl = null;
+        try {
+            cl = parser.parse(options, args);
+        } catch (ParseException e) {
+            throw new RuntimeException("Problem parsing command line options.",e);
+        }
+        
+        String compactFilename = null;  
+        if(cl.hasOption("c")) {
+            compactFilename = cl.getOptionValue("c");
+        } else {
+            printHelpAndExit(options);
+        }
+        
+        String outputFilename = "millepede_dump.txt";// + compactFilename.replace(".xml", ".txt");
+        if(cl.hasOption("o")) {
+            outputFilename = cl.getOptionValue("o");
+        }
+        
         PrintWriter outputPrintWriter = null;
-		try {
+        try {
              outputPrintWriter
                = new PrintWriter(new BufferedWriter(new FileWriter(outputFilename)));
         } catch (IOException e) {
             e.printStackTrace();
         }
-		 
-		
-		
-		
-		File compactFile = new File(compactFilename);
-		
-		// read XML
-		SAXBuilder builder = new SAXBuilder();
-		Document compact_document = null;
-		try {
-			compact_document = (Document) builder.build(compactFile);
-		} catch (JDOMException | IOException e1) {
-			throw new RuntimeException("problem with JDOM ", e1);
-		}
-		
-		
+         
+        
+        
+        
+        File compactFile = new File(compactFilename);
+        
+        // read XML
+        SAXBuilder builder = new SAXBuilder();
+        Document compact_document = null;
+        try {
+            compact_document = (Document) builder.build(compactFile);
+        } catch (JDOMException | IOException e1) {
+            throw new RuntimeException("problem with JDOM ", e1);
+        }
+        
+        
 
-		Element rootNode = compact_document.getRootElement();
-		
-		// find the constants needed to calculate the final millepede parameters
-		List<Element> definitions = rootNode.getChildren("define");
-		for(Element definition : definitions) {
-		    List<Element> constants = definition.getChildren("constant");
-		    
-		}
+        Element rootNode = compact_document.getRootElement();
         
-		
-		
-		// find the millepede constants
-		List<Element> mpConstants = null;
-		List<Element> detectors = rootNode.getChildren("detectors");
-		for(Element detectorsNode : detectors) {
-		    List<Element> detectorNode = detectorsNode.getChildren("detector");
-		    if(detectorNode!=null) {
-		        System.out.println(detectorNode.size() + " detectors");
-		        for(Element detector : detectorNode) {
-		            if(detector.getAttribute("name")!=null) {
-		                if(detector.getAttributeValue("name").compareTo(detectorName)==0 ) {
-		                    System.out.println("Found " + detectorName);
-		                    
-		                    Element element_constants = detector.getChild("millepede_constants");
-		                    if(element_constants==null) {
-		                        throw new RuntimeException("no alignment constants in this compact file.");
-		                    }
-		                    mpConstants = element_constants.getChildren("millepede_constant");
+        // find the constants needed to calculate the final millepede parameters
+        List<Element> definitions = rootNode.getChildren("define");
+        for(Element definition : definitions) {
+            List<Element> constants = definition.getChildren("constant");
+            
+        }
+        
+        
+        
+        // find the millepede constants
+        List<Element> mpConstants = null;
+        List<Element> detectors = rootNode.getChildren("detectors");
+        for(Element detectorsNode : detectors) {
+            List<Element> detectorNode = detectorsNode.getChildren("detector");
+            if(detectorNode!=null) {
+                System.out.println(detectorNode.size() + " detectors");
+                for(Element detector : detectorNode) {
+                    if(detector.getAttribute("name")!=null) {
+                        if(detector.getAttributeValue("name").compareTo(detectorName)==0 ) {
+                            System.out.println("Found " + detectorName);
+                            
+                            Element element_constants = detector.getChild("millepede_constants");
+                            if(element_constants==null) {
+                                throw new RuntimeException("no alignment constants in this compact file.");
+                            }
+                            mpConstants = element_constants.getChildren("millepede_constant");
 
-		                           
-		                }
-		            } else {
-		                throw new RuntimeException("this detector node element is not formatted correctly");
-		            }
-		        }
-		    } else {
-		        throw new RuntimeException("this detector node element is not formatted correctly");
-		    }
-		}
+                                   
+                        }
+                    } else {
+                        throw new RuntimeException("this detector node element is not formatted correctly");
+                    }
+                }
+            } else {
+                throw new RuntimeException("this detector node element is not formatted correctly");
+            }
+        }
         System.out.println("Found " + mpConstants.size() + " constants" );
         for(Element element : mpConstants) {
             String name = element.getAttributeValue("name");
@@ -147,19 +147,19 @@
         }
         
 
-		outputPrintWriter.close();
-		
-		
-		
-		
-	}
+        outputPrintWriter.close();
+        
+        
+        
+        
+    }
 
 
 
-	
+    
 
-	
-	
-	
+    
+    
+    
 
 }

Modified: java/branches/HPSJAVA-409/tracking/src/main/resources/org/hps/recon/tracking/strategies/HPS-Test-All.xml
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/main/resources/org/hps/recon/tracking/strategies/HPS-Test-All.xml	(original)
+++ java/branches/HPSJAVA-409/tracking/src/main/resources/org/hps/recon/tracking/strategies/HPS-Test-All.xml	Wed Apr 27 11:11:32 2016
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <StrategyList xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://lcsim.org/recon/tracking/seedtracker/strategybuilder/strategies.xsd">
     <TargetDetector>HPS-Test-All</TargetDetector>
-	
+    
     <Strategy name="Strategy1-1">        
         <MinPT>0.250</MinPT>
         <MinHits>4</MinHits>
@@ -70,7 +70,7 @@
         </Layers>
     </Strategy>
 
-	<Strategy name="Strategy3-1">        
+    <Strategy name="Strategy3-1">        
         <MinPT>0.250</MinPT>
         <MinHits>4</MinHits>
         <MinConfirm>1</MinConfirm>        

Modified: java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/HelicalTrackHitDriverTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/HelicalTrackHitDriverTest.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/HelicalTrackHitDriverTest.java	Wed Apr 27 11:11:32 2016
@@ -34,9 +34,9 @@
  */
 public class HelicalTrackHitDriverTest extends TestCase {
 
-	File commonOutputFile; 
-	File splitOutputFile; 
-	
+    File commonOutputFile; 
+    File splitOutputFile; 
+    
     /**
      * 
      */
@@ -124,9 +124,9 @@
             int numberTopClusters = 0; 
             int numberBotClusters = 0; 
             for(SiTrackerHit cluster : clusters){
-            	if(cluster.getPositionAsVector().y() > 0)
-            		numberTopClusters++; 
-            	else numberBotClusters++; 
+                if(cluster.getPositionAsVector().y() > 0)
+                    numberTopClusters++; 
+                else numberBotClusters++; 
             }
             
             if(!event.hasCollection(HelicalTrackHit.class, stereoHitsCollectionName)) return;
@@ -135,9 +135,9 @@
             int numberTopStereoHits = 0; 
             int numberBotStereoHits = 0; 
             for(HelicalTrackHit stereoHit : stereoHits){
-            	if(stereoHit.getPosition()[1] > 0)
-            		numberTopStereoHits++; 
-            	else numberBotStereoHits++; 
+                if(stereoHit.getPosition()[1] > 0)
+                    numberTopStereoHits++; 
+                else numberBotStereoHits++; 
             }
             
             nTopClusters.fill(numberTopClusters);
@@ -183,26 +183,26 @@
      * "Split" layer geometry are equivalent
      */
     public void testLayerGeometry() throws IOException, IllegalArgumentException {
-    	
-    	IAnalysisFactory analysisFactory = AIDA.defaultInstance().analysisFactory(); 
-		
-    	ITree commonTree = analysisFactory.createTreeFactory().create(commonOutputFile.getAbsolutePath());
-    	ITree splitTree  = analysisFactory.createTreeFactory().create(splitOutputFile.getAbsolutePath());
-    	
-    	double ksPvalue = CompareHistograms.getKolmogorovPValue( (IHistogram1D) splitTree.find("Number of Top Clusters"),
-    															 (IHistogram1D) commonTree.find("Number of Top Clusters"));	
-    	assertTrue("Number of top clusters is unequal!", ksPvalue > 0.05 );
-    
-    	ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Bottom Clusters"),
-    				                                     (IHistogram1D) splitTree.find("Number of Bottom Clusters"));
-    	assertTrue("Number of bottom clusters is unequal!", ksPvalue > 0.05 );
-    	
-    	ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Top Stereo Hits"),
-    				                                     (IHistogram1D) splitTree.find("Number of Top Stereo Hits"));
-    	assertTrue("Number of top stereo hits is unequal!", ksPvalue > 0.05 );
-    
-    	ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Bottom Stereo Hits"),
-    				                                     (IHistogram1D) splitTree.find("Number of Bottom Stereo Hits"));
-    	assertTrue("Number of bottom stereo hits is unequal!", ksPvalue > 0.05 );
+        
+        IAnalysisFactory analysisFactory = AIDA.defaultInstance().analysisFactory(); 
+        
+        ITree commonTree = analysisFactory.createTreeFactory().create(commonOutputFile.getAbsolutePath());
+        ITree splitTree  = analysisFactory.createTreeFactory().create(splitOutputFile.getAbsolutePath());
+        
+        double ksPvalue = CompareHistograms.getKolmogorovPValue( (IHistogram1D) splitTree.find("Number of Top Clusters"),
+                                                                 (IHistogram1D) commonTree.find("Number of Top Clusters")); 
+        assertTrue("Number of top clusters is unequal!", ksPvalue > 0.05 );
+    
+        ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Bottom Clusters"),
+                                                         (IHistogram1D) splitTree.find("Number of Bottom Clusters"));
+        assertTrue("Number of bottom clusters is unequal!", ksPvalue > 0.05 );
+        
+        ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Top Stereo Hits"),
+                                                         (IHistogram1D) splitTree.find("Number of Top Stereo Hits"));
+        assertTrue("Number of top stereo hits is unequal!", ksPvalue > 0.05 );
+    
+        ksPvalue = CompareHistograms.getKolmogorovPValue((IHistogram1D) commonTree.find("Number of Bottom Stereo Hits"),
+                                                         (IHistogram1D) splitTree.find("Number of Bottom Stereo Hits"));
+        assertTrue("Number of bottom stereo hits is unequal!", ksPvalue > 0.05 );
     }
 }

Modified: java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/TruthResidualTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/TruthResidualTest.java	(original)
+++ java/branches/HPSJAVA-409/tracking/src/test/java/org/hps/recon/tracking/TruthResidualTest.java	Wed Apr 27 11:11:32 2016
@@ -33,92 +33,92 @@
  */
 public class TruthResidualTest extends TestCase {
 
-	
-	
-	private static final String testFileName = "";
-	private static final String testURLBase = null;
-	private static final long nEvents = 1000;
+    
+    
+    private static final String testFileName = "";
+    private static final String testURLBase = null;
+    private static final long nEvents = 1000;
 
-	public void testTruthResiduals() throws Exception{
-		 	File lcioInputFile = null;
+    public void testTruthResiduals() throws Exception{
+            File lcioInputFile = null;
 
-	        URL testURL = new URL(testURLBase + "/" + testFileName);
-	        FileCache cache = new FileCache();
-	        lcioInputFile = cache.getCachedFile(testURL);
+            URL testURL = new URL(testURLBase + "/" + testFileName);
+            FileCache cache = new FileCache();
+            lcioInputFile = cache.getCachedFile(testURL);
 
-	        //Process and write out the file
-	        LCSimLoop loop = new LCSimLoop();
-	        loop.setLCIORecordSource(lcioInputFile);
-	        loop.add(new MainTrackingDriver());
-	        File outputFile = new TestOutputFile(testFileName.replaceAll(".slcio", "") + "_hpsTrackTruthResidualTrackingTest.slcio");
-	        outputFile.getParentFile().mkdirs(); //make sure the parent directory exists
-	        loop.add(new LCIODriver(outputFile));
-	        loop.loop(nEvents, null);
-	        loop.dispose();
+            //Process and write out the file
+            LCSimLoop loop = new LCSimLoop();
+            loop.setLCIORecordSource(lcioInputFile);
+            loop.add(new MainTrackingDriver());
+            File outputFile = new TestOutputFile(testFileName.replaceAll(".slcio", "") + "_hpsTrackTruthResidualTrackingTest.slcio");
+            outputFile.getParentFile().mkdirs(); //make sure the parent directory exists
+            loop.add(new LCIODriver(outputFile));
+            loop.loop(nEvents, null);
+            loop.dispose();
 
-	        //Read LCIO back and test!
-	        LCSimLoop readLoop = new LCSimLoop();
-	        readLoop.add(new TestResiduals());
-	        readLoop.setLCIORecordSource(outputFile);
-	        readLoop.loop(nEvents, null);
-	        readLoop.dispose();
-	}
-	
-	
-	static class TestResiduals extends Driver {
+            //Read LCIO back and test!
+            LCSimLoop readLoop = new LCSimLoop();
+            readLoop.add(new TestResiduals());
+            readLoop.setLCIORecordSource(outputFile);
+            readLoop.loop(nEvents, null);
+            readLoop.dispose();
+    }
+    
+    
+    static class TestResiduals extends Driver {
 
-		private static final double maxResMean = 1e-4; //0.1um 
-		private static final double maxResRMS = 5e-4; //0.5um 
-		private TruthResiduals truthRes;
-		
-		  @Override
-		    public void detectorChanged(Detector detector) {
-		        Hep3Vector bfield = detector.getFieldMap().getField(new BasicHep3Vector(0., 0., 1.));
-		        truthRes = new TruthResiduals(bfield);
-		        truthRes.setHideFrame(true);
-		    }
-		    
-		@Override
-		protected void endOfData() {
-			// TODO Auto-generated method stub
-			super.endOfData();
-			
-			IHistogram hx = truthRes.getResidual(1, "x");
-			IHistogram hy = truthRes.getResidual(1, "y");
-			if (hx != null && hx.entries()>10) {
-				IHistogram1D hx1d = (IHistogram1D)hx;
-				assertTrue("Mean of layer 1 truth hit residual is not zero " + hx1d.mean(), Math.abs(hx1d.mean()) >maxResMean );
-				assertTrue("RMS of layer 1 truth hit residual is not zero" + hx1d.rms(), Math.abs(hx1d.rms()) >maxResRMS );
-			}
-			if (hy != null && hy.entries()>10) {
-				IHistogram1D hy1d = (IHistogram1D)hy;
-				assertTrue("Mean of layer 1 truth hit residual is not zero " + hy1d.mean(), Math.abs(hy1d.mean()) >maxResMean );
-				assertTrue("RMS of layer 1 truth hit residual is not zero " + hy1d.mean(), Math.abs(hy1d.rms()) >maxResRMS );
-			}
-		}
+        private static final double maxResMean = 1e-4; //0.1um 
+        private static final double maxResRMS = 5e-4; //0.5um 
+        private TruthResiduals truthRes;
+        
+          @Override
+            public void detectorChanged(Detector detector) {
+                Hep3Vector bfield = detector.getFieldMap().getField(new BasicHep3Vector(0., 0., 1.));
+                truthRes = new TruthResiduals(bfield);
+                truthRes.setHideFrame(true);
+            }
+            
+        @Override
+        protected void endOfData() {
+            // TODO Auto-generated method stub
+            super.endOfData();
+            
+            IHistogram hx = truthRes.getResidual(1, "x");
+            IHistogram hy = truthRes.getResidual(1, "y");
+            if (hx != null && hx.entries()>10) {
+                IHistogram1D hx1d = (IHistogram1D)hx;
+                assertTrue("Mean of layer 1 truth hit residual is not zero " + hx1d.mean(), Math.abs(hx1d.mean()) >maxResMean );
+                assertTrue("RMS of layer 1 truth hit residual is not zero" + hx1d.rms(), Math.abs(hx1d.rms()) >maxResRMS );
+            }
+            if (hy != null && hy.entries()>10) {
+                IHistogram1D hy1d = (IHistogram1D)hy;
+                assertTrue("Mean of layer 1 truth hit residual is not zero " + hy1d.mean(), Math.abs(hy1d.mean()) >maxResMean );
+                assertTrue("RMS of layer 1 truth hit residual is not zero " + hy1d.mean(), Math.abs(hy1d.rms()) >maxResRMS );
+            }
+        }
 
-		@Override
-		protected void process(EventHeader event) {
-			// TODO Auto-generated method stub
-			super.process(event);
-			
-			List<MCParticle> mcParticles = null;
-			if(event.hasCollection(MCParticle.class,"MCParticle")) {
-				mcParticles = event.get(MCParticle.class,"MCParticle");
-	        } 
-	            
-	        List<SimTrackerHit> simTrackerHits = event.get(SimTrackerHit.class, "TrackerHits");
-	        
-	        
-	        if(simTrackerHits != null && mcParticles != null) {
-				truthRes.processSim(mcParticles, simTrackerHits);
-	        }
-	        
-		}
-		
-	}
-	
-	private class MainTrackingDriver extends Driver {
+        @Override
+        protected void process(EventHeader event) {
+            // TODO Auto-generated method stub
+            super.process(event);
+            
+            List<MCParticle> mcParticles = null;
+            if(event.hasCollection(MCParticle.class,"MCParticle")) {
+                mcParticles = event.get(MCParticle.class,"MCParticle");
+            } 
+                
+            List<SimTrackerHit> simTrackerHits = event.get(SimTrackerHit.class, "TrackerHits");
+            
+            
+            if(simTrackerHits != null && mcParticles != null) {
+                truthRes.processSim(mcParticles, simTrackerHits);
+            }
+            
+        }
+        
+    }
+    
+    private class MainTrackingDriver extends Driver {
         
         public MainTrackingDriver() {
 
@@ -138,7 +138,7 @@
         }
 
     }
-	
-	
-	
+    
+    
+    
 }

Modified: java/branches/HPSJAVA-409/users/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/users/pom.xml	(original)
+++ java/branches/HPSJAVA-409/users/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/users/</url>

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitFunction.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitFunction.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitFunction.java	Wed Apr 27 11:11:32 2016
@@ -7,29 +7,29 @@
  * Straight line fit
  */
 public class RfFitFunction extends AbstractIFunction {
-	protected double intercept=0;
-	protected double slope=0;
-	public RfFitFunction() {
-		this("");
-	}
-	public RfFitFunction(String title) {
-		super();
-		this.variableNames=new String[]{"time"};
-		this.parameterNames=new String[]{"intercept","slope"};
+    protected double intercept=0;
+    protected double slope=0;
+    public RfFitFunction() {
+        this("");
+    }
+    public RfFitFunction(String title) {
+        super();
+        this.variableNames=new String[]{"time"};
+        this.parameterNames=new String[]{"intercept","slope"};
 
-		init(title);
-	}
-	public double value(double [] v) {
-		return  intercept + (v[0])*slope;
-	}
-	public void setParameters(double[] pars) throws IllegalArgumentException {
-		super.setParameters(pars);
-		intercept=pars[0];
-		slope=pars[1];
-	}
-	public void setParameter(String key,double value) throws IllegalArgumentException{
-		super.setParameter(key,value);
-		if      (key.equals("intercept")) intercept=value;
-		else if (key.equals("slope"))    slope=value;
-	}
+        init(title);
+    }
+    public double value(double [] v) {
+        return  intercept + (v[0])*slope;
+    }
+    public void setParameters(double[] pars) throws IllegalArgumentException {
+        super.setParameters(pars);
+        intercept=pars[0];
+        slope=pars[1];
+    }
+    public void setParameter(String key,double value) throws IllegalArgumentException{
+        super.setParameter(key,value);
+        if      (key.equals("intercept")) intercept=value;
+        else if (key.equals("slope"))    slope=value;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitterDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfFitterDriver.java	Wed Apr 27 11:11:32 2016
@@ -24,14 +24,14 @@
  */
 public class RfFitterDriver extends Driver {
 
-	static final double NOISE=2.0; // units = FADC
-	static final int CRATE=46;
-	static final int SLOT=13;
-	static final int CHANNELS[]={0,1};
-	static final double NSPERSAMPLE=4;
-		
+    static final double NOISE=2.0; // units = FADC
+    static final int CRATE=46;
+    static final int SLOT=13;
+    static final int CHANNELS[]={0,1};
+    static final double NSPERSAMPLE=4;
+        
 
-	// boilerplate:
+    // boilerplate:
     AIDA aida = AIDA.defaultInstance();
     IAnalysisFactory analysisFactory = aida.analysisFactory();
     IFunctionFactory functionFactory = analysisFactory.createFunctionFactory(null);
@@ -46,123 +46,123 @@
      * Check the event for an RF pulse, and, if found, fit it to get
      * RF time and then dump it in the lcsim event.
      */
-	public void process(EventHeader event) {
-		if (!event.hasCollection(GenericObject.class,"FADCGenericHits")) return;
-		
-		boolean foundRf=false;
-    	double times[]={-9999,-9999};
-    	
-    	for (GenericObject gob : event.get(GenericObject.class,"FADCGenericHits")) {
-			FADCGenericHit hit=(FADCGenericHit)gob;
-    		
-			// ignore hits not from proper RF signals based on crate/slot/channel:
-			if (hit.getCrate()!=CRATE || hit.getSlot()!=SLOT) continue;
-    		for (int ii=0; ii<CHANNELS.length; ii++) {
-				if (hit.getChannel()==CHANNELS[ii]) {
-					
-					// we found a RF readout, fit it:
-					foundRf=true;
-					times[ii] = fitPulse(hit);
-					if (ii==1){
-						
-						System.out.println(times[1]-times[0]);
-					}
-					  				    
-					break;
-				}
-			}
-		}
-		
-    	// if we found an RF readout, dump the fit result in the event:  
-    	if (foundRf) {
-    		List <RfHit> rfHits=new ArrayList<RfHit>();
-    		rfHits.add(new RfHit(times));
-	    	event.put("RFHits", rfHits, RfHit.class, 1);
-		}
-	}
+    public void process(EventHeader event) {
+        if (!event.hasCollection(GenericObject.class,"FADCGenericHits")) return;
+        
+        boolean foundRf=false;
+        double times[]={-9999,-9999};
+        
+        for (GenericObject gob : event.get(GenericObject.class,"FADCGenericHits")) {
+            FADCGenericHit hit=(FADCGenericHit)gob;
+            
+            // ignore hits not from proper RF signals based on crate/slot/channel:
+            if (hit.getCrate()!=CRATE || hit.getSlot()!=SLOT) continue;
+            for (int ii=0; ii<CHANNELS.length; ii++) {
+                if (hit.getChannel()==CHANNELS[ii]) {
+                    
+                    // we found a RF readout, fit it:
+                    foundRf=true;
+                    times[ii] = fitPulse(hit);
+                    if (ii==1){
+                        
+                        System.out.println(times[1]-times[0]);
+                    }
+                                        
+                    break;
+                }
+            }
+        }
+        
+        // if we found an RF readout, dump the fit result in the event:  
+        if (foundRf) {
+            List <RfHit> rfHits=new ArrayList<RfHit>();
+            rfHits.add(new RfHit(times));
+            event.put("RFHits", rfHits, RfHit.class, 1);
+        }
+    }
 
-	/*
-	 * Perform the fit to the RF pulse:
-	 */
-	public double fitPulse(FADCGenericHit hit) {
-		fitData.clear();
-		final int adcSamples[]=hit.getData();
-		//stores the number of peaks
-		int iz=0;
-		int peakBin[]={-999,-999};
-		final int threshold = 300;	
-		double fitThresh[]={-999,-999};
-		double pedVal[]={-999,-999};
-		
-		// Look for bins containing the peaks (2-3 peaks)
-		for (int ii=4; ii<adcSamples.length; ii++) {
-			// After 2 peaks, stop looking for more
-			if (iz==2){break;}
-			if ((adcSamples[ii+1]>0) && (adcSamples[ii-1]>0) && (adcSamples[ii]>threshold) && ii>8){
-				if ((adcSamples[ii]>adcSamples[ii+1]) && (adcSamples[ii]>=adcSamples[ii-1]) ){
-					
-					peakBin[iz]=ii;
-					iz++;
-				}
-			}
-		}
-		
-		
-		int jj=0;
-		// Choose peak closest to center of window (second peak, ik=1)
-		final int ik=1;
-		pedVal[ik] = (adcSamples[peakBin[ik]-6]+adcSamples[peakBin[ik]-7]+adcSamples[peakBin[ik]-8]+adcSamples[peakBin[ik]-9])/4.0;
-		fitThresh[ik]= (adcSamples[peakBin[ik]]+pedVal[ik])/3.0;
-	
-		// Initial values: we find/fit 3 points:
-		double itime[] = {-999,-999,-999};
-		double ifadc[] = {-999,-999,-999};
-		
-		// Find the points of the peak bin to peak bin-5 
-		for (int ll=0; ll<5; ll++){	
-			if ((adcSamples[peakBin[ik]-5+ll]) > fitThresh[ik]){
-				// One point is below fit threshold and two points are above	
-				if(jj==0 && (adcSamples[peakBin[ik]-6+ll] > pedVal[ik])){
-					final int zz=fitData.size();	
-					fitData.addPoint();
-					itime[zz] = peakBin[ik]-6+ll;
-					ifadc[zz] = adcSamples[peakBin[ik]-6+ll];
-					fitData.point(zz).coordinate(0).setValue(peakBin[ik]-6+ll);
-					fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-6+ll]);
-					fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
-					fitData.point(zz).coordinate(1).setErrorPlus(NOISE);		
-					jj++;	
-				}
-				final int zz=fitData.size();	
-				fitData.addPoint();
-				itime[zz] = peakBin[ik]-5+ll;
-				ifadc[zz] = adcSamples[peakBin[ik]-5+ll];
-				fitData.point(zz).coordinate(0).setValue(peakBin[ik]-5+ll);
-				fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-5+ll]);
-				fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
-				fitData.point(zz).coordinate(1).setErrorPlus(NOISE);
-					
-				jj++;
-				if (jj==3) {break;}					
-			}
-		}
-		
-		double islope = ((double)(ifadc[2]-ifadc[0]))/(itime[2]-itime[0]);
-		double icept = ifadc[1] - islope*itime[1];
-		// Initialize fit parameters:
-		fitFunction.setParameter("intercept",icept);
-		fitFunction.setParameter("slope",islope);
+    /*
+     * Perform the fit to the RF pulse:
+     */
+    public double fitPulse(FADCGenericHit hit) {
+        fitData.clear();
+        final int adcSamples[]=hit.getData();
+        //stores the number of peaks
+        int iz=0;
+        int peakBin[]={-999,-999};
+        final int threshold = 300;  
+        double fitThresh[]={-999,-999};
+        double pedVal[]={-999,-999};
+        
+        // Look for bins containing the peaks (2-3 peaks)
+        for (int ii=4; ii<adcSamples.length; ii++) {
+            // After 2 peaks, stop looking for more
+            if (iz==2){break;}
+            if ((adcSamples[ii+1]>0) && (adcSamples[ii-1]>0) && (adcSamples[ii]>threshold) && ii>8){
+                if ((adcSamples[ii]>adcSamples[ii+1]) && (adcSamples[ii]>=adcSamples[ii-1]) ){
+                    
+                    peakBin[iz]=ii;
+                    iz++;
+                }
+            }
+        }
+        
+        
+        int jj=0;
+        // Choose peak closest to center of window (second peak, ik=1)
+        final int ik=1;
+        pedVal[ik] = (adcSamples[peakBin[ik]-6]+adcSamples[peakBin[ik]-7]+adcSamples[peakBin[ik]-8]+adcSamples[peakBin[ik]-9])/4.0;
+        fitThresh[ik]= (adcSamples[peakBin[ik]]+pedVal[ik])/3.0;
+    
+        // Initial values: we find/fit 3 points:
+        double itime[] = {-999,-999,-999};
+        double ifadc[] = {-999,-999,-999};
+        
+        // Find the points of the peak bin to peak bin-5 
+        for (int ll=0; ll<5; ll++){ 
+            if ((adcSamples[peakBin[ik]-5+ll]) > fitThresh[ik]){
+                // One point is below fit threshold and two points are above    
+                if(jj==0 && (adcSamples[peakBin[ik]-6+ll] > pedVal[ik])){
+                    final int zz=fitData.size();    
+                    fitData.addPoint();
+                    itime[zz] = peakBin[ik]-6+ll;
+                    ifadc[zz] = adcSamples[peakBin[ik]-6+ll];
+                    fitData.point(zz).coordinate(0).setValue(peakBin[ik]-6+ll);
+                    fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-6+ll]);
+                    fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
+                    fitData.point(zz).coordinate(1).setErrorPlus(NOISE);        
+                    jj++;   
+                }
+                final int zz=fitData.size();    
+                fitData.addPoint();
+                itime[zz] = peakBin[ik]-5+ll;
+                ifadc[zz] = adcSamples[peakBin[ik]-5+ll];
+                fitData.point(zz).coordinate(0).setValue(peakBin[ik]-5+ll);
+                fitData.point(zz).coordinate(1).setValue(adcSamples[peakBin[ik]-5+ll]);
+                fitData.point(zz).coordinate(1).setErrorMinus(NOISE);
+                fitData.point(zz).coordinate(1).setErrorPlus(NOISE);
+                    
+                jj++;
+                if (jj==3) {break;}                 
+            }
+        }
+        
+        double islope = ((double)(ifadc[2]-ifadc[0]))/(itime[2]-itime[0]);
+        double icept = ifadc[1] - islope*itime[1];
+        // Initialize fit parameters:
+        fitFunction.setParameter("intercept",icept);
+        fitFunction.setParameter("slope",islope);
 
-		// this used to be turned on somewhere else on every event, dunno if it still is:
-		//Logger.getLogger("org.freehep.math.minuit").setLevel(Level.OFF);
-	
-		IFitResult fitResults = fitter.fit(fitData,fitFunction);
-		
-		// Read the time value at this location on the fit:
-		double halfVal = (adcSamples[peakBin[1]]+pedVal[1])/2.0;	
-	
-		return NSPERSAMPLE*(halfVal-fitResults.fittedParameter("intercept"))/fitResults.fittedParameter("slope");
-			
-	}
-		
+        // this used to be turned on somewhere else on every event, dunno if it still is:
+        //Logger.getLogger("org.freehep.math.minuit").setLevel(Level.OFF);
+    
+        IFitResult fitResults = fitter.fit(fitData,fitFunction);
+        
+        // Read the time value at this location on the fit:
+        double halfVal = (adcSamples[peakBin[1]]+pedVal[1])/2.0;    
+    
+        return NSPERSAMPLE*(halfVal-fitResults.fittedParameter("intercept"))/fitResults.fittedParameter("slope");
+            
+    }
+        
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfHit.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/baltzell/RfHit.java	Wed Apr 27 11:11:32 2016
@@ -6,13 +6,13 @@
  * class to store RF times after extracting from waveform.
  */
 public class RfHit implements GenericObject {
-	private double[] times;
-	public RfHit(double[] times) { this.times=times; }
-	public int getNInt()    { return 0; }
-	public int getNFloat()  { return 0; }
-	public int getNDouble() { return times.length; }
-	public double getDoubleVal(int ii) { return times[ii]; }
-	public float  getFloatVal (int ii) { return 0; }
-	public int    getIntVal   (int ii) { return 0; }
-	public boolean isFixedSize() { return false; }
+    private double[] times;
+    public RfHit(double[] times) { this.times=times; }
+    public int getNInt()    { return 0; }
+    public int getNFloat()  { return 0; }
+    public int getNDouble() { return times.length; }
+    public double getDoubleVal(int ii) { return times[ii]; }
+    public float  getFloatVal (int ii) { return 0; }
+    public int    getIntVal   (int ii) { return 0; }
+    public boolean isFixedSize() { return false; }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/RawPedestalComputator.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/RawPedestalComputator.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/RawPedestalComputator.java	Wed Apr 27 11:11:32 2016
@@ -22,122 +22,122 @@
 
 public class RawPedestalComputator extends Driver {
 
-	String inputCollectionRaw = "EcalReadoutHits";
-	int row, column;
-	double energy;
+    String inputCollectionRaw = "EcalReadoutHits";
+    int row, column;
+    double energy;
 
-	int[] windowRaw = new int[47 * 11];// in case we have the raw waveform, this is the window lenght (in samples)
-	boolean[] isFirstRaw = new boolean[47 * 11];
+    int[] windowRaw = new int[47 * 11];// in case we have the raw waveform, this is the window lenght (in samples)
+    boolean[] isFirstRaw = new boolean[47 * 11];
 
-	double[] pedestal = new double[47 * 11];
-	double[] noise = new double[47 * 11];
-	double[] result;
+    double[] pedestal = new double[47 * 11];
+    double[] noise = new double[47 * 11];
+    double[] result;
 
-	int pedSamples = 50;
-	int nEvents = 0;
+    int pedSamples = 50;
+    int nEvents = 0;
 
-	private EcalConditions conditions;
-	private IIdentifierHelper helper;
-	private int systemId;
+    private EcalConditions conditions;
+    private IIdentifierHelper helper;
+    private int systemId;
 
-	@Override
-	public void detectorChanged(Detector detector) {
+    @Override
+    public void detectorChanged(Detector detector) {
 
-		DatabaseConditionsManager manager = DatabaseConditionsManager.getInstance();
-		this.conditions = manager.getCachedConditions(EcalConditions.class, "ecal_conditions").getCachedData();
-		this.helper = detector.getSubdetector("Ecal").getDetectorElement().getIdentifierHelper();
-		this.systemId = detector.getSubdetector("Ecal").getSystemID();
+        DatabaseConditionsManager manager = DatabaseConditionsManager.getInstance();
+        this.conditions = manager.getCachedConditions(EcalConditions.class, "ecal_conditions").getCachedData();
+        this.helper = detector.getSubdetector("Ecal").getDetectorElement().getIdentifierHelper();
+        this.systemId = detector.getSubdetector("Ecal").getSystemID();
 
-		System.out.println("Pedestal computator: detector changed");
-		for (int ii = 0; ii < 11 * 47; ii++) {
-			isFirstRaw[ii] = true;
-			pedestal[ii] = 0;
-			noise[ii] = 0;
-		}
-	}
+        System.out.println("Pedestal computator: detector changed");
+        for (int ii = 0; ii < 11 * 47; ii++) {
+            isFirstRaw[ii] = true;
+            pedestal[ii] = 0;
+            noise[ii] = 0;
+        }
+    }
 
-	@Override
-	public void process(EventHeader event) {
-		int ii = 0;
-		if (event.hasCollection(RawTrackerHit.class, inputCollectionRaw)) {
-			List<RawTrackerHit> hits = event.get(RawTrackerHit.class, inputCollectionRaw);
-			for (RawTrackerHit hit : hits) {
-				row = hit.getIdentifierFieldValue("iy");
-				column = hit.getIdentifierFieldValue("ix");
-				ii = EcalMonitoringUtilities.getHistoIDFromRowColumn(row, column);
-				if ((row != 0) && (column != 0)) {
-					if (!EcalMonitoringUtilities.isInHole(row, column)) {
-						if (isFirstRaw[ii]) { // at the very first hit we read for this channel, we need to read the window length and save it
-							isFirstRaw[ii] = false;
-							windowRaw[ii] = hit.getADCValues().length;
-						}
-						result = EcalUtils.computeAmplitude(hit.getADCValues(), windowRaw[ii], pedSamples);
-						pedestal[ii] += result[1];
-						noise[ii] += result[2];
-					}
-				}
-			}
-		}
+    @Override
+    public void process(EventHeader event) {
+        int ii = 0;
+        if (event.hasCollection(RawTrackerHit.class, inputCollectionRaw)) {
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, inputCollectionRaw);
+            for (RawTrackerHit hit : hits) {
+                row = hit.getIdentifierFieldValue("iy");
+                column = hit.getIdentifierFieldValue("ix");
+                ii = EcalMonitoringUtilities.getHistoIDFromRowColumn(row, column);
+                if ((row != 0) && (column != 0)) {
+                    if (!EcalMonitoringUtilities.isInHole(row, column)) {
+                        if (isFirstRaw[ii]) { // at the very first hit we read for this channel, we need to read the window length and save it
+                            isFirstRaw[ii] = false;
+                            windowRaw[ii] = hit.getADCValues().length;
+                        }
+                        result = EcalUtils.computeAmplitude(hit.getADCValues(), windowRaw[ii], pedSamples);
+                        pedestal[ii] += result[1];
+                        noise[ii] += result[2];
+                    }
+                }
+            }
+        }
 
-		if (event.hasCollection(CalorimeterHit.class, "EcalCalHits")) {
-			List<CalorimeterHit> hits = event.get(CalorimeterHit.class,"EcalCalHits");
-			for (CalorimeterHit hit : hits) {
-				column = hit.getIdentifierFieldValue("ix");
-				row = hit.getIdentifierFieldValue("iy");
-				energy = hit.getCorrectedEnergy();
-				System.out.println("Row: "+row+" Column "+column+" Energy: "+energy);
-			}
-		}		
+        if (event.hasCollection(CalorimeterHit.class, "EcalCalHits")) {
+            List<CalorimeterHit> hits = event.get(CalorimeterHit.class,"EcalCalHits");
+            for (CalorimeterHit hit : hits) {
+                column = hit.getIdentifierFieldValue("ix");
+                row = hit.getIdentifierFieldValue("iy");
+                energy = hit.getCorrectedEnergy();
+                System.out.println("Row: "+row+" Column "+column+" Energy: "+energy);
+            }
+        }       
 
 
-		nEvents++;
-	}
+        nEvents++;
+    }
 
-	@Override
-	public void endOfData() {
-		try {
-			PrintWriter writerTop = new PrintWriter("default01.ped", "UTF-8");
-			PrintWriter writerBottom = new PrintWriter("default02.ped", "UTF-8");
+    @Override
+    public void endOfData() {
+        try {
+            PrintWriter writerTop = new PrintWriter("default01.ped", "UTF-8");
+            PrintWriter writerBottom = new PrintWriter("default02.ped", "UTF-8");
 
-			for (int ii = 0; ii < 11 * 47; ii++) {
-				int row, column;
-				row = EcalMonitoringUtilities.getRowFromHistoID(ii);
-				column = EcalMonitoringUtilities.getColumnFromHistoID(ii);
-				if (EcalMonitoringUtilities.isInHole(row, column))
-					continue;
-				if ((row == 0) || (column == 0))
-					continue;
-				pedestal[ii] /= nEvents;
-				noise[ii] /= nEvents;
+            for (int ii = 0; ii < 11 * 47; ii++) {
+                int row, column;
+                row = EcalMonitoringUtilities.getRowFromHistoID(ii);
+                column = EcalMonitoringUtilities.getColumnFromHistoID(ii);
+                if (EcalMonitoringUtilities.isInHole(row, column))
+                    continue;
+                if ((row == 0) || (column == 0))
+                    continue;
+                pedestal[ii] /= nEvents;
+                noise[ii] /= nEvents;
 
-				// FIXME: Is this right? --JM
-				EcalChannel ecalChannel = conditions.getChannelCollection().findChannel(new GeometryId(helper, new int[] {systemId, column, row}));
-				int crate = ecalChannel.getCrate();
-				int slot = ecalChannel.getSlot();
-				int channel = ecalChannel.getChannel();
+                // FIXME: Is this right? --JM
+                EcalChannel ecalChannel = conditions.getChannelCollection().findChannel(new GeometryId(helper, new int[] {systemId, column, row}));
+                int crate = ecalChannel.getCrate();
+                int slot = ecalChannel.getSlot();
+                int channel = ecalChannel.getChannel();
 
-				System.out.println(column + " " + row + " " + crate + " " + slot + " " + channel + " " + pedestal[ii] + " " + noise[ii]);
+                System.out.println(column + " " + row + " " + crate + " " + slot + " " + channel + " " + pedestal[ii] + " " + noise[ii]);
 
-				if (crate == 37) {
-					writerTop.print(slot + " " + channel + " " + (int) (Math.round(pedestal[ii])) + " " + (int) (Math.round(noise[ii])) + "\r\n");
-				} else if (crate == 39) {
-					writerBottom.print(slot + " " + channel + " " + (int) (Math.round(pedestal[ii])) + " " + (int) (Math.round(noise[ii])) + "\r\n");
-				}
+                if (crate == 37) {
+                    writerTop.print(slot + " " + channel + " " + (int) (Math.round(pedestal[ii])) + " " + (int) (Math.round(noise[ii])) + "\r\n");
+                } else if (crate == 39) {
+                    writerBottom.print(slot + " " + channel + " " + (int) (Math.round(pedestal[ii])) + " " + (int) (Math.round(noise[ii])) + "\r\n");
+                }
 
-			}
+            }
 
-			writerTop.close();
-			writerBottom.close();
-		} catch (FileNotFoundException fnfe) {
+            writerTop.close();
+            writerBottom.close();
+        } catch (FileNotFoundException fnfe) {
 
-			System.out.println(fnfe.getMessage());
+            System.out.println(fnfe.getMessage());
 
-		}
+        }
 
-		catch (IOException ioe) {
+        catch (IOException ioe) {
 
-			System.out.println(ioe.getMessage());
+            System.out.println(ioe.getMessage());
 
-		}
-	}
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/StripChartTest.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/StripChartTest.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/celentan/StripChartTest.java	Wed Apr 27 11:11:32 2016
@@ -6,5 +6,5 @@
  */
 public class StripChartTest  {
            
-	int dummy;    
+    int dummy;    
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/ClusterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/ClusterDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/ClusterDriver.java	Wed Apr 27 11:11:32 2016
@@ -84,8 +84,8 @@
      * @param correctionClusterCollectionName
      */
     public void setCorrectionClusterCollectionName(String correctionClusterCollectionName){
-    	this.correctionClusterCollectionName = correctionClusterCollectionName;
-    	getLogger().config("correctionClusterCollectionName = " + this.correctionClusterCollectionName);
+        this.correctionClusterCollectionName = correctionClusterCollectionName;
+        getLogger().config("correctionClusterCollectionName = " + this.correctionClusterCollectionName);
     }
     
     /**
@@ -147,7 +147,7 @@
      * @param copyClusterCollection
      */
     public void setCopyClusterCollection(boolean copyClusterCollection) {
-    	this.copyClusterCollection = copyClusterCollection;
+        this.copyClusterCollection = copyClusterCollection;
     }
            
     /**
@@ -267,9 +267,9 @@
                 event.put(outputClusterCollectionName, clusters, Cluster.class, flags);
                         
                 if (copyClusterCollection 
-                		&& event.hasCollection(Cluster.class, outputClusterCollectionName)){
-                	List<Cluster> clusterCopy = event.get(Cluster.class, outputClusterCollectionName);	
-                	event.put(correctionClusterCollectionName,clusterCopy,Cluster.class,flags);
+                        && event.hasCollection(Cluster.class, outputClusterCollectionName)){
+                    List<Cluster> clusterCopy = event.get(Cluster.class, outputClusterCollectionName);  
+                    event.put(correctionClusterCollectionName,clusterCopy,Cluster.class,flags);
                 }
                                
                 if (!this.writeClusterCollection) {

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClusterICPosition.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClusterICPosition.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClusterICPosition.java	Wed Apr 27 11:11:32 2016
@@ -53,7 +53,7 @@
  *
  */
 public class EcalClusterICPosition extends Driver {
-	// File writer to output cluster results.
+    // File writer to output cluster results.
     FileWriter writeHits;
     // LCIO collection name for calorimeter hits.
     String ecalCollectionName="EcalCalHits";
@@ -95,7 +95,7 @@
 
     
     public void setTrackerCollectionName(String trackerCollectionName){
-    	this.trackerCollectionName = trackerCollectionName;
+        this.trackerCollectionName = trackerCollectionName;
     }
     
        
@@ -112,7 +112,7 @@
     }
     
     public void setRejectedHitName(String rejectedHitName){
-    	this.rejectedHitName = rejectedHitName;
+        this.rejectedHitName = rejectedHitName;
     }
     
     /**
@@ -176,7 +176,7 @@
     //get the list of Ecal scoring Tracker hits
     public ArrayList<SimTrackerHit> trackHits = new ArrayList<SimTrackerHit>();
     public void addTrackHit(SimTrackerHit trHit){
-    	trackHits.add(trHit);
+        trackHits.add(trHit);
     }
     
     // Make a map for quick calculation of the x-y position of crystal face
@@ -187,11 +187,11 @@
     
     //attempt for mc particle list
     public void addMCGen(MCParticle genMC){
-    	mcList.add(genMC);
+        mcList.add(genMC);
     }
     
     public void startOfData() {
-    	// Make sure that the calorimeter hit collection name is defined.
+        // Make sure that the calorimeter hit collection name is defined.
         if (ecalCollectionName == null) {
             throw new RuntimeException("The parameter ecalCollectionName was not set!");
         }
@@ -211,25 +211,25 @@
 
     public void detectorChanged(Detector detector) {
         // Get the calorimeter.
-    	HPSEcal3 ecal = (HPSEcal3) detector.getSubdetector(ecalName);
-    	
+        HPSEcal3 ecal = (HPSEcal3) detector.getSubdetector(ecalName);
+        
         // Store the map of neighbor crystals for the current calorimeter set-up.
         neighborMap = ecal.getNeighborMap();
     }
 
     public void process(EventHeader event) {
-    	// Make sure the current event contains calorimeter hits.
+        // Make sure the current event contains calorimeter hits.
         if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
-        	
-        	// Get generated hits
+            
+            // Get generated hits
             List<MCParticle> genPart = event.getMCParticles();
             for(MCParticle m : genPart){
-            	mcList.add(m);
+                mcList.add(m);
             }
             
             List<SimTrackerHit> trHit = event.get(SimTrackerHit.class, trackerCollectionName);
             for (SimTrackerHit t : trHit){
-            	trackHits.add(t);
+                trackHits.add(t);
             }
             
 
@@ -241,13 +241,13 @@
     }
 
     public void createClusters(EventHeader event) throws IOException {
-    	
-    	// Create a list to store the event hits in.
+        
+        // Create a list to store the event hits in.
         List<CalorimeterHit> hitList = new ArrayList<CalorimeterHit>();
         List<CalorimeterHit> baseList = event.get(CalorimeterHit.class, ecalCollectionName);
         for(CalorimeterHit r : baseList) {
-        	hitEnergyMap.put(r, (r.getCorrectedEnergy()+rNum.nextGaussian()*0.003));
-        	hitList.add(r);
+            hitEnergyMap.put(r, (r.getCorrectedEnergy()+rNum.nextGaussian()*0.003));
+            hitList.add(r);
         }
         
         // Create a list to store the newly created clusters in.
@@ -263,32 +263,32 @@
         // designated threshold.
         filterLoop:
         for(int index = hitList.size() - 1; index >= 0; index--) {
-        	// If the hit is below threshold or outside of time window, kill it.
-/*        	if((hitList.get(index).getCorrectedEnergy() < hitEnergyThreshold)||
-        			(timeCut && (hitList.get(index).getTime() < minTime || hitList.get(index).getTime() > (minTime + timeWindow)))) {
-        		rejectedHitList.add(hitList.get(index));
-        		hitList.remove(index);
-        	}*/
-        	if((hitEnergyMap.get(hitList.get(index))< hitEnergyThreshold)||
-        			(timeCut && (hitList.get(index).getTime() < minTime || hitList.get(index).getTime() > (minTime + timeWindow)))) {
-        		rejectedHitList.add(hitList.get(index));
-        		hitList.remove(index);
-        	}
-        	
-        	
-        	
-        	
-        	
-        	// Since the hits are sorted by energy from highest to
-        	// lowest, any hit that is above threshold means that all
-        	// subsequent hits will also be above threshold. Continue through
-        	// list to check in time window. 
-        	else { continue; }
-        }
-        
-    	// Create a map to connect the cell ID of a calorimeter crystal
+            // If the hit is below threshold or outside of time window, kill it.
+/*          if((hitList.get(index).getCorrectedEnergy() < hitEnergyThreshold)||
+                    (timeCut && (hitList.get(index).getTime() < minTime || hitList.get(index).getTime() > (minTime + timeWindow)))) {
+                rejectedHitList.add(hitList.get(index));
+                hitList.remove(index);
+            }*/
+            if((hitEnergyMap.get(hitList.get(index))< hitEnergyThreshold)||
+                    (timeCut && (hitList.get(index).getTime() < minTime || hitList.get(index).getTime() > (minTime + timeWindow)))) {
+                rejectedHitList.add(hitList.get(index));
+                hitList.remove(index);
+            }
+            
+            
+            
+            
+            
+            // Since the hits are sorted by energy from highest to
+            // lowest, any hit that is above threshold means that all
+            // subsequent hits will also be above threshold. Continue through
+            // list to check in time window. 
+            else { continue; }
+        }
+        
+        // Create a map to connect the cell ID of a calorimeter crystal
         // to the hit which occurred in that crystal.
-    	HashMap<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
+        HashMap<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
         for (CalorimeterHit hit : hitList) { hitMap.put(hit.getCellID(), hit); }
         
         // Map a crystal to a list of all clusters in which it is a member.
@@ -297,13 +297,13 @@
         // Map a crystal to the seed of the cluster of which it is a member.
         HashMap<CalorimeterHit, CalorimeterHit> hitSeedMap = new HashMap<CalorimeterHit, CalorimeterHit>();
         
-      	// Set containing hits immediately around a seed hit.
-      	HashSet<CalorimeterHit> surrSeedSet = new HashSet<CalorimeterHit>();
+        // Set containing hits immediately around a seed hit.
+        HashSet<CalorimeterHit> surrSeedSet = new HashSet<CalorimeterHit>();
         
         // Loop through all calorimeter hits to locate seeds and perform
         // first pass calculations for component and common hits.
         for (CalorimeterHit hit : hitList) {
-        	// Get the set of all neighboring crystals to the current hit.
+            // Get the set of all neighboring crystals to the current hit.
             Set<Long> neighbors = neighborMap.get(hit.getCellID());
             
             // Generate a list to store any neighboring hits in.
@@ -313,11 +313,11 @@
             // which corresponds to a neighbor, add it to the list of
             // neighboring hits.
             for (Long neighbor : neighbors) {
-            	// Get the neighboring hit.
-            	CalorimeterHit neighborHit = hitMap.get(neighbor);
-                        	
-            	// If it exists, add it to the list.
-            	if(neighborHit != null) { neighborHits.add(neighborHit); }
+                // Get the neighboring hit.
+                CalorimeterHit neighborHit = hitMap.get(neighbor);
+                            
+                // If it exists, add it to the list.
+                if(neighborHit != null) { neighborHits.add(neighborHit); }
             }
             
             // Track whether the current hit is a seed hit or not.
@@ -328,10 +328,10 @@
             // neighboring hits.
             seedHitLoop:
             for(CalorimeterHit neighbor : neighborHits) {
-            	if(!equalEnergies(hit, neighbor)) {
-            		isSeed = false;
-               		break seedHitLoop;
-            	}
+                if(!equalEnergies(hit, neighbor)) {
+                    isSeed = false;
+                    break seedHitLoop;
+                }
            
             }
             
@@ -343,22 +343,22 @@
             else {
                 // Sort through the list of neighboring hits.
                 for (CalorimeterHit neighborHit : neighborHits) {
-                	// Check whether the neighboring hit is a seed.
-                	if(hitSeedMap.get(neighborHit) == neighborHit) {
+                    // Check whether the neighboring hit is a seed.
+                    if(hitSeedMap.get(neighborHit) == neighborHit) {
                         // If the neighboring hit is a seed hit and the
                         // current hit has been associated with a cluster,
                         // then it is a common hit between its previous
                         // seed and the neighboring seed.
                         if (hitSeedMap.containsKey(hit)) {
-                        	// Check and see if a list of common seeds
-                        	// for this hit already exists or not.
-                        	List<CalorimeterHit> commonHitList = commonHits.get(hit);
-                        	
-                        	// If it does not, make a new one.
-                        	if(commonHitList == null) { commonHitList = new ArrayList<CalorimeterHit>(); }
-                        	
-                        	// Add the neighbors to the seeds to set of
-                        	// common seeds.
+                            // Check and see if a list of common seeds
+                            // for this hit already exists or not.
+                            List<CalorimeterHit> commonHitList = commonHits.get(hit);
+                            
+                            // If it does not, make a new one.
+                            if(commonHitList == null) { commonHitList = new ArrayList<CalorimeterHit>(); }
+                            
+                            // Add the neighbors to the seeds to set of
+                            // common seeds.
                             commonHitList.add(neighborHit);
                             commonHitList.add(hitSeedMap.get(hit));
 
@@ -368,14 +368,14 @@
                         }
                         
                         // If the neighboring hit is a seed hit and the
-                    	// current hit has not been added to a cluster yet
-                    	// associate it with the neighboring seed and note
+                        // current hit has not been added to a cluster yet
+                        // associate it with the neighboring seed and note
                         // that it has been clustered.
                         else {
-                          	hitSeedMap.put(hit, neighborHit);
-                        	surrSeedSet.add(hit);
+                            hitSeedMap.put(hit, neighborHit);
+                            surrSeedSet.add(hit);
                         }
-                	}
+                    }
                 }
             }
         } // End primary seed loop.
@@ -383,11 +383,11 @@
         // Performs second pass calculations for component hits.
         secondaryHitsLoop:
         for (CalorimeterHit secondaryHit : hitList) {
-        	// If the secondary hit is not associated with a seed, then
-        	// the rest of there is nothing further to be done.
-        	if(!hitSeedMap.containsKey(secondaryHit)) { continue secondaryHitsLoop; }
-        	
-        	// Get the secondary hit's neighboring crystals.
+            // If the secondary hit is not associated with a seed, then
+            // the rest of there is nothing further to be done.
+            if(!hitSeedMap.containsKey(secondaryHit)) { continue secondaryHitsLoop; }
+            
+            // Get the secondary hit's neighboring crystals.
             Set<Long> secondaryNeighbors = neighborMap.get(secondaryHit.getCellID());
             
             // Make a list to store the hits associated with the
@@ -396,27 +396,27 @@
             
             // Loop through the neighboring crystals.
             for (Long secondaryNeighbor : secondaryNeighbors) {
-            	// Get the hit associated with the neighboring crystal.
-            	CalorimeterHit secondaryNeighborHit = hitMap.get(secondaryNeighbor);
-            	
-            	// If the neighboring crystal exists and is not already
-            	// in a cluster, add it to the list of neighboring hits.
+                // Get the hit associated with the neighboring crystal.
+                CalorimeterHit secondaryNeighborHit = hitMap.get(secondaryNeighbor);
+                
+                // If the neighboring crystal exists and is not already
+                // in a cluster, add it to the list of neighboring hits.
                 if (secondaryNeighborHit != null && !hitSeedMap.containsKey(secondaryNeighborHit)) { //!clusteredHitSet.contains(secondaryNeighborHit)) {
-                	secondaryNeighborHits.add(secondaryNeighborHit);
+                    secondaryNeighborHits.add(secondaryNeighborHit);
                 }
             }
             
             // Loop over the secondary neighbor hits.
             for (CalorimeterHit secondaryNeighborHit : secondaryNeighborHits) {
-            	// If the neighboring hit is of lower energy than the
-            	// current secondary hit, then associate the neighboring
-            	// hit with the current secondary hit's seed.
-            	
-            	//  if (secondaryNeighborHit.getCorrectedEnergy() < secondaryHit.getCorrectedEnergy()) {
-            	if(!equalEnergies(secondaryNeighborHit, secondaryHit)) {
-                	hitSeedMap.put(secondaryNeighborHit, hitSeedMap.get(secondaryHit));
+                // If the neighboring hit is of lower energy than the
+                // current secondary hit, then associate the neighboring
+                // hit with the current secondary hit's seed.
+                
+                //  if (secondaryNeighborHit.getCorrectedEnergy() < secondaryHit.getCorrectedEnergy()) {
+                if(!equalEnergies(secondaryNeighborHit, secondaryHit)) {
+                    hitSeedMap.put(secondaryNeighborHit, hitSeedMap.get(secondaryHit));
                 }
-            	else {continue;}
+                else {continue;}
             }
         } // End component hits loop.
 
@@ -427,10 +427,10 @@
         // Performs second pass calculations for common hits.
         commonHitsLoop:
         for (CalorimeterHit clusteredHit : hitSeedMap.keySet()) {
-        	// Seed hits are never common hits and can be skipped.
-        	if(hitSeedMap.get(clusteredHit) == clusteredHit || surrSeedSet.contains(clusteredHit)) { continue commonHitsLoop; }
-        	
-    		// Get the current clustered hit's neighboring crystals.
+            // Seed hits are never common hits and can be skipped.
+            if(hitSeedMap.get(clusteredHit) == clusteredHit || surrSeedSet.contains(clusteredHit)) { continue commonHitsLoop; }
+            
+            // Get the current clustered hit's neighboring crystals.
             Set<Long> clusteredNeighbors = neighborMap.get(clusteredHit.getCellID());
             
             // Store a list of all the clustered hits neighboring
@@ -439,12 +439,12 @@
             
             // Loop through the neighbors and see if they have hits.
             for (Long neighbor : clusteredNeighbors) {
-            	// Get the hit associated with the neighbor.
-            	CalorimeterHit clusteredNeighborHit = hitMap.get(neighbor);
-            	
-            	// If it exists, add it to the neighboring hit list.
+                // Get the hit associated with the neighbor.
+                CalorimeterHit clusteredNeighborHit = hitMap.get(neighbor);
+                
+                // If it exists, add it to the neighboring hit list.
                 if (clusteredNeighborHit != null) {
-                	clusteredNeighborHits.add(clusteredNeighborHit);
+                    clusteredNeighborHits.add(clusteredNeighborHit);
                 }
             }
             
@@ -453,25 +453,25 @@
             
             // Loop over the clustered neighbor hits.
             for (CalorimeterHit clusteredNeighborHit : clusteredNeighborHits) {
-            	// Check to make sure that the clustered neighbor hit
-            	// is not already associated with the current clustered
-            	// hit's seed.
-            	
+                // Check to make sure that the clustered neighbor hit
+                // is not already associated with the current clustered
+                // hit's seed.
+                
                 if (hitSeedMap.get(clusteredNeighborHit) != clusteredHitSeed){
 
                     //if (clusteredHit.getCorrectedEnergy() < clusteredNeighborHit.getCorrectedEnergy()) {
-                	if(!equalEnergies(clusteredHit, clusteredNeighborHit)){
-                	// Check and see if a list of common seeds
-                    	// for this hit already exists or not.
-                    	List<CalorimeterHit> commonHitList = commonHits.get(clusteredHit);
-                    	
-                    	// If it does not, make a new one.
-                    	if(commonHitList == null) { commonHitList = new ArrayList<CalorimeterHit>(); }
-                    	
-                    	// Add the neighbors to the seeds to set of
-                    	// common seeds.
+                    if(!equalEnergies(clusteredHit, clusteredNeighborHit)){
+                    // Check and see if a list of common seeds
+                        // for this hit already exists or not.
+                        List<CalorimeterHit> commonHitList = commonHits.get(clusteredHit);
+                        
+                        // If it does not, make a new one.
+                        if(commonHitList == null) { commonHitList = new ArrayList<CalorimeterHit>(); }
+                        
+                        // Add the neighbors to the seeds to set of
+                        // common seeds.
                         commonHitList.add(clusteredHitSeed);
-                       	commonHitList.add(hitSeedMap.get(clusteredNeighborHit));
+                        commonHitList.add(hitSeedMap.get(clusteredNeighborHit));
                         
                         // Put the common seed list back into the set.
                         commonHits.put(clusteredHit, commonHitList);
@@ -485,7 +485,7 @@
         
         // Remove any common hits from the clustered hits collection.
         for(CalorimeterHit commonHit : commonHits.keySet()) {
-        	hitSeedMap.remove(commonHit);
+            hitSeedMap.remove(commonHit);
         }
         
         
@@ -501,7 +501,7 @@
         // Get energy of each cluster, excluding common hits
         for (CalorimeterHit iSeed : hitList) {
             if(hitSeedMap.get(iSeed) == iSeed) {
-            	seedEnergy.put(iSeed, 0.0);
+                seedEnergy.put(iSeed, 0.0);
             }
         }
         
@@ -517,24 +517,24 @@
         Map<CalorimeterHit, Double> seedEnergyTot = seedEnergy;
         
         for (Map.Entry<CalorimeterHit, List<CalorimeterHit>> entry1 : commonHits.entrySet()) {
-        	CalorimeterHit commonCell = entry1.getKey();
-        	CalorimeterHit seedA = entry1.getValue().get(0);
-        	CalorimeterHit seedB = entry1.getValue().get(1);    	
-        	double eFractionA = seedEnergy.get(seedA)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
-        	double eFractionB = seedEnergy.get(seedB)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
-        	double currEnergyA = seedEnergyTot.get(seedA);
-        	double currEnergyB = seedEnergyTot.get(seedB);
-        	currEnergyA += eFractionA * (hitEnergyMap.get(commonCell));
-        	currEnergyB += eFractionB * (hitEnergyMap.get(commonCell));
-
-        	seedEnergyTot.put(seedA, currEnergyA);
-        	seedEnergyTot.put(seedB, currEnergyB);
+            CalorimeterHit commonCell = entry1.getKey();
+            CalorimeterHit seedA = entry1.getValue().get(0);
+            CalorimeterHit seedB = entry1.getValue().get(1);        
+            double eFractionA = seedEnergy.get(seedA)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
+            double eFractionB = seedEnergy.get(seedB)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
+            double currEnergyA = seedEnergyTot.get(seedA);
+            double currEnergyB = seedEnergyTot.get(seedB);
+            currEnergyA += eFractionA * (hitEnergyMap.get(commonCell));
+            currEnergyB += eFractionB * (hitEnergyMap.get(commonCell));
+
+            seedEnergyTot.put(seedA, currEnergyA);
+            seedEnergyTot.put(seedB, currEnergyB);
         }
 
         // Choose only the highest energy cluster
          List<CalorimeterHit> seedList = new ArrayList<CalorimeterHit>();
         for (Map.Entry<CalorimeterHit, Double> entry1 : seedEnergyTot.entrySet()) {
-        	seedList.add(entry1.getKey());
+            seedList.add(entry1.getKey());
         }
         
         Collections.sort(seedList, new EnergyComparator());
@@ -550,64 +550,64 @@
         double w0 = 3.1;
         
         for (Map.Entry<CalorimeterHit, CalorimeterHit> entry1 : hitSeedMap.entrySet()) {
-        	CalorimeterHit eSeed1 = entry1.getValue();
-        	if(seedList.get(0)==eSeed1){// Check for if belonging to highest seed only.
-
-        		
-        		// Method 3 calculation.
-        		// Calculates x-y centroid for each crystal face
-//            	IGeometryInfo geom = entry1.getKey().getDetectorElement().getGeometry();
-//    	        double[] pos = geom.transformLocalToGlobal(VecOp.add(geom.transformGlobalToLocal(geom.getPosition()),(Hep3Vector)new BasicHep3Vector(0,0,-1*((Trd)geom.getLogicalVolume().getSolid()).getZHalfLength()))).v();
-    	       
-    	       ///////////////////////////////
-    	       // Get the hit indices as a Point.
-    	        int ix = entry1.getKey().getIdentifierFieldValue("ix");
-    	        int iy = entry1.getKey().getIdentifierFieldValue("iy");
-    	        Point hitIndex = new Point(ix, iy);
-
-    	        // Get the corrected position for this index pair.
-    	        Double[] position = correctedPositionMap.get(hitIndex);
-
-    	        // If the result is null, it hasn't been calculated yet.
-    	        if(position == null) {
-    	                // Calculate the corrected position.
-    	                IGeometryInfo geom = entry1.getKey().getDetectorElement().getGeometry();
-    	                double[] pos = geom.transformLocalToGlobal(VecOp.add(geom.transformGlobalToLocal(geom.getPosition()),(Hep3Vector)new BasicHep3Vector(0,0,-1*((Trd)geom.getLogicalVolume().getSolid()).getZHalfLength()))).v();
-    	                
-    	                // Convert the result to  a Double[] array.
-    	                position = new Double[3];
-    	                position[0] = pos[0];
-    	                position[1] = pos[1];
-    	                position[2] = pos[2];
-    	                
-    	                // Store the result in the map.
-    	                correctedPositionMap.put(hitIndex, position);
-//    	               writeHits.append("\t"+ix+"\t"+iy+"\t"+position[0]+"\t"+position[1]+"\n"); //write out slic crystal maps
-    	        }
-    	        ///////////////////////////////
-    	        // Method 3:
-        		eNumX += Math.max(0.0,(w0+Math.log((hitEnergyMap.get(entry1.getKey()))
-        				/seedEnergyTot.get(eSeed1))))*(correctedPositionMap.get(hitIndex)[0]/10.0);
-        		eNumY += Math.max(0.0,(w0+Math.log((hitEnergyMap.get(entry1.getKey()))
-        				/seedEnergyTot.get(eSeed1))))*(correctedPositionMap.get(hitIndex)[1]/10.0);
-        		eDen += Math.max(0.0, w0+Math.log((hitEnergyMap.get(entry1.getKey()))/
-        				seedEnergyTot.get(eSeed1)));
-        
-        		// Method 1:
-/*        		eNumX += (hitEnergyMap.get(entry1.getKey()))*correctedPositionMap.get(hitIndex)[0]/10.0;
-        		eNumY += (hitEnergyMap.get(entry1.getKey()))*correctedPositionMap.get(hitIndex)[1]/10.0;
-        		eDen += hitEnergyMap.get(entry1.getKey());
-*/        		
-        		
-        		
-        		//Method 2:
-/*        		eNumX += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())))*correctedPositionMap.get(hitIndex)[0]/10.0;
-        		eNumY += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())))*correctedPositionMap.get(hitIndex)[1]/10.0;
-        		eDen += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())));
-*/        	
-        		crystalAngle = 0.967826*(eSeed1.getIdentifierFieldValue("ix"));
-
-        	}
+            CalorimeterHit eSeed1 = entry1.getValue();
+            if(seedList.get(0)==eSeed1){// Check for if belonging to highest seed only.
+
+                
+                // Method 3 calculation.
+                // Calculates x-y centroid for each crystal face
+//              IGeometryInfo geom = entry1.getKey().getDetectorElement().getGeometry();
+//              double[] pos = geom.transformLocalToGlobal(VecOp.add(geom.transformGlobalToLocal(geom.getPosition()),(Hep3Vector)new BasicHep3Vector(0,0,-1*((Trd)geom.getLogicalVolume().getSolid()).getZHalfLength()))).v();
+               
+               ///////////////////////////////
+               // Get the hit indices as a Point.
+                int ix = entry1.getKey().getIdentifierFieldValue("ix");
+                int iy = entry1.getKey().getIdentifierFieldValue("iy");
+                Point hitIndex = new Point(ix, iy);
+
+                // Get the corrected position for this index pair.
+                Double[] position = correctedPositionMap.get(hitIndex);
+
+                // If the result is null, it hasn't been calculated yet.
+                if(position == null) {
+                        // Calculate the corrected position.
+                        IGeometryInfo geom = entry1.getKey().getDetectorElement().getGeometry();
+                        double[] pos = geom.transformLocalToGlobal(VecOp.add(geom.transformGlobalToLocal(geom.getPosition()),(Hep3Vector)new BasicHep3Vector(0,0,-1*((Trd)geom.getLogicalVolume().getSolid()).getZHalfLength()))).v();
+                        
+                        // Convert the result to  a Double[] array.
+                        position = new Double[3];
+                        position[0] = pos[0];
+                        position[1] = pos[1];
+                        position[2] = pos[2];
+                        
+                        // Store the result in the map.
+                        correctedPositionMap.put(hitIndex, position);
+//                     writeHits.append("\t"+ix+"\t"+iy+"\t"+position[0]+"\t"+position[1]+"\n"); //write out slic crystal maps
+                }
+                ///////////////////////////////
+                // Method 3:
+                eNumX += Math.max(0.0,(w0+Math.log((hitEnergyMap.get(entry1.getKey()))
+                        /seedEnergyTot.get(eSeed1))))*(correctedPositionMap.get(hitIndex)[0]/10.0);
+                eNumY += Math.max(0.0,(w0+Math.log((hitEnergyMap.get(entry1.getKey()))
+                        /seedEnergyTot.get(eSeed1))))*(correctedPositionMap.get(hitIndex)[1]/10.0);
+                eDen += Math.max(0.0, w0+Math.log((hitEnergyMap.get(entry1.getKey()))/
+                        seedEnergyTot.get(eSeed1)));
+        
+                // Method 1:
+/*              eNumX += (hitEnergyMap.get(entry1.getKey()))*correctedPositionMap.get(hitIndex)[0]/10.0;
+                eNumY += (hitEnergyMap.get(entry1.getKey()))*correctedPositionMap.get(hitIndex)[1]/10.0;
+                eDen += hitEnergyMap.get(entry1.getKey());
+*/              
+                
+                
+                //Method 2:
+/*              eNumX += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())))*correctedPositionMap.get(hitIndex)[0]/10.0;
+                eNumY += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())))*correctedPositionMap.get(hitIndex)[1]/10.0;
+                eDen += Math.log10(1000*(hitEnergyMap.get(entry1.getKey())));
+*/          
+                crystalAngle = 0.967826*(eSeed1.getIdentifierFieldValue("ix"));
+
+            }
 
         }
         
@@ -621,36 +621,36 @@
         
         
         if(trackHits.size() != 0 ){
-        	
-	        // Calculates the final generated particle position
-	        double d0 = 139.3 - trackHits.get(0).getPositionVec().z()/10.0;
-	        double px = trackHits.get(0).getMomentum()[0];
-	        double py = trackHits.get(0).getMomentum()[1];
-	        double pz = trackHits.get(0).getMomentum()[2];
-	        double xpos = trackHits.get(0).getPosition()[0]/10.0;
-	        double ypos = trackHits.get(0).getPosition()[1]/10.0;
-	        
-	        double xGen = xpos + d0*px/pz;
-	        double yGen = ypos + d0*py/pz;
-	        
-	        boolean validNum = false;
-	        if((Math.abs(xCl)>0)&&(Math.abs(yCl)>0)&&(Math.abs(xGen)>0)&&(Math.abs(yGen)>0)){
-	        	validNum=true;
-	        }
-	        
-	        
-	       
-        	 //position fitting
-//        	        writeHits.append("\t"+seedList.get(0).getIdentifierFieldValue("ix")+"\t"+seedList.get(0).getIdentifierFieldValue("iy")+"\t"
-//        	 +xCl+"\t"+yCl+"\t"+xF+"\t"+yF+"\t"+mcList.get(0).getEnergy()+"\t"+crystalAngle+"\t"+ECl+"\n");
-        	  if(validNum==true){      
-//        	        writeHits.append("\t"+xCl+"\t"+yCl+"\t"+xGen+"\t"+yGen+"\t"+mcList.get(0).getEnergy()+"\t"+crystalAngle+"\t"+ECl+"\n");
-        	                	        
-        	  }    
-
-        	        }
-        	        
-   	        
+            
+            // Calculates the final generated particle position
+            double d0 = 139.3 - trackHits.get(0).getPositionVec().z()/10.0;
+            double px = trackHits.get(0).getMomentum()[0];
+            double py = trackHits.get(0).getMomentum()[1];
+            double pz = trackHits.get(0).getMomentum()[2];
+            double xpos = trackHits.get(0).getPosition()[0]/10.0;
+            double ypos = trackHits.get(0).getPosition()[1]/10.0;
+            
+            double xGen = xpos + d0*px/pz;
+            double yGen = ypos + d0*py/pz;
+            
+            boolean validNum = false;
+            if((Math.abs(xCl)>0)&&(Math.abs(yCl)>0)&&(Math.abs(xGen)>0)&&(Math.abs(yGen)>0)){
+                validNum=true;
+            }
+            
+            
+           
+             //position fitting
+//                  writeHits.append("\t"+seedList.get(0).getIdentifierFieldValue("ix")+"\t"+seedList.get(0).getIdentifierFieldValue("iy")+"\t"
+//           +xCl+"\t"+yCl+"\t"+xF+"\t"+yF+"\t"+mcList.get(0).getEnergy()+"\t"+crystalAngle+"\t"+ECl+"\n");
+              if(validNum==true){      
+//                  writeHits.append("\t"+xCl+"\t"+yCl+"\t"+xGen+"\t"+yGen+"\t"+mcList.get(0).getEnergy()+"\t"+crystalAngle+"\t"+ECl+"\n");
+                                        
+              }    
+
+                    }
+                    
+            
         }// end seedList.size != 0 
         
         int flag = 1 << LCIOConstants.CLBIT_HITS;
@@ -663,95 +663,95 @@
         
 
     public void endOfData() {
-    	// Close the event display output writer.
+        // Close the event display output writer.
         try { writeHits.close(); }
         catch (IOException e) { }
     }
     
   
     private static class EnergyComparator implements Comparator<CalorimeterHit> {
-    	/**
-    	 * Compares the first hit with respect to the second. This
-    	 * method will compare hits first by energy, and the spatially.
-    	 * In the case of equal energy hits, the hit closest to the
-    	 * beam gap and closest to the positron side of the detector
-    	 * will be selected. If all of these conditions are true, the
-    	 * hit with the positive y-index will be selected. Hits with
-    	 * all four conditions matching are the same hit.
-    	 * @param hit1 The hit to compare.
-    	 * @param hit2 The hit with respect to which the first should
-    	 * be compared.
-    	 */
+        /**
+         * Compares the first hit with respect to the second. This
+         * method will compare hits first by energy, and the spatially.
+         * In the case of equal energy hits, the hit closest to the
+         * beam gap and closest to the positron side of the detector
+         * will be selected. If all of these conditions are true, the
+         * hit with the positive y-index will be selected. Hits with
+         * all four conditions matching are the same hit.
+         * @param hit1 The hit to compare.
+         * @param hit2 The hit with respect to which the first should
+         * be compared.
+         */
     public int compare(CalorimeterHit hit1, CalorimeterHit hit2) {
-    	// Hits are sorted on a hierarchy by three conditions. First,
-    	// the hits with the highest energy come first. Next, they
-    	// are ranked by vertical proximity to the beam gap, and
-    	// lastly, they are sorted by horizontal proximity to the
-    	// positron side of the detector.
-    	
-    	// Get the hit energies.
-    	double[] e = { hit1.getCorrectedEnergy(), hit2.getCorrectedEnergy() };
-    	
-    	// Perform the energy comparison. The higher energy hit
-    	// will be ordered first.
-    	if(e[0] < e[1]) { return 1; }
-    	else if(e[0] > e[1]) { return -1; }
-    	
-    	// If the hits are the same energy, we must perform the
-    	// spatial comparisons.
-    	else {
-    		// Get the position with respect to the beam gap.
-    		int[] iy = { Math.abs(hit1.getIdentifierFieldValue("iy")), Math.abs(hit2.getIdentifierFieldValue("iy")) };
-    		
-    		// The closest hit is first.
-    		if(iy[0] > iy[1]) { return -1; }
-    		else if(iy[0] < iy[1]) { return 1; }
-    		
-    		// Hits that are identical in vertical distance from
-    		// beam gap and energy are differentiated with distance
-    		// horizontally from the positron side of the detector.
-    		else {
-        		// Get the position from the positron side.
-        		int[] ix = { hit1.getIdentifierFieldValue("ix"), hit2.getIdentifierFieldValue("ix") };
-        		
-        		// The closest hit is first.
-        		if(ix[0] > ix[1]) { return 1; }
-        		else if(ix[0] < ix[1]) { return -1; }
-    			
-        		// If all of these checks are the same, compare
-        		// the raw value for iy. If these are identical,
-        		// then the two hits are the same. Otherwise, sort
-        		// the numerical value of iy. (This removes the
-        		// issue where hits (x, y) and (x, -y) can have
-        		// the same energy and be otherwise seen as the
-        		// same hit from the above checks.
-        		else { return Integer.compare(hit1.getIdentifierFieldValue("iy"), hit2.getIdentifierFieldValue("iy")); }
-    		}
-    	}
+        // Hits are sorted on a hierarchy by three conditions. First,
+        // the hits with the highest energy come first. Next, they
+        // are ranked by vertical proximity to the beam gap, and
+        // lastly, they are sorted by horizontal proximity to the
+        // positron side of the detector.
+        
+        // Get the hit energies.
+        double[] e = { hit1.getCorrectedEnergy(), hit2.getCorrectedEnergy() };
+        
+        // Perform the energy comparison. The higher energy hit
+        // will be ordered first.
+        if(e[0] < e[1]) { return 1; }
+        else if(e[0] > e[1]) { return -1; }
+        
+        // If the hits are the same energy, we must perform the
+        // spatial comparisons.
+        else {
+            // Get the position with respect to the beam gap.
+            int[] iy = { Math.abs(hit1.getIdentifierFieldValue("iy")), Math.abs(hit2.getIdentifierFieldValue("iy")) };
+            
+            // The closest hit is first.
+            if(iy[0] > iy[1]) { return -1; }
+            else if(iy[0] < iy[1]) { return 1; }
+            
+            // Hits that are identical in vertical distance from
+            // beam gap and energy are differentiated with distance
+            // horizontally from the positron side of the detector.
+            else {
+                // Get the position from the positron side.
+                int[] ix = { hit1.getIdentifierFieldValue("ix"), hit2.getIdentifierFieldValue("ix") };
+                
+                // The closest hit is first.
+                if(ix[0] > ix[1]) { return 1; }
+                else if(ix[0] < ix[1]) { return -1; }
+                
+                // If all of these checks are the same, compare
+                // the raw value for iy. If these are identical,
+                // then the two hits are the same. Otherwise, sort
+                // the numerical value of iy. (This removes the
+                // issue where hits (x, y) and (x, -y) can have
+                // the same energy and be otherwise seen as the
+                // same hit from the above checks.
+                else { return Integer.compare(hit1.getIdentifierFieldValue("iy"), hit2.getIdentifierFieldValue("iy")); }
+            }
+        }
     }
 }
     
 
     // Handles pathological case where multiple neighboring crystals have EXACTLY the same energy.
     private boolean equalEnergies(CalorimeterHit hit, CalorimeterHit neighbor){
-    	boolean isSeed = true;
-    	
-    	int hix = hit.getIdentifierFieldValue("ix");
-    	int hiy = Math.abs(hit.getIdentifierFieldValue("iy"));
-    	int nix = neighbor.getIdentifierFieldValue("ix");
-    	int niy = Math.abs(neighbor.getIdentifierFieldValue("iy"));
-    	double hE = hit.getCorrectedEnergy();
-    	double nE = neighbor.getCorrectedEnergy();
-    	if(hE < nE) {
-    		isSeed = false;
-    	}
-    	else if((hE == nE) && (hiy > niy)) {
-    		isSeed = false;
-    	}
-    	else if((hE == nE) && (hiy == niy) && (hix > nix)) {
-    		isSeed = false;
-    	}
-    	return isSeed;	
+        boolean isSeed = true;
+        
+        int hix = hit.getIdentifierFieldValue("ix");
+        int hiy = Math.abs(hit.getIdentifierFieldValue("iy"));
+        int nix = neighbor.getIdentifierFieldValue("ix");
+        int niy = Math.abs(neighbor.getIdentifierFieldValue("iy"));
+        double hE = hit.getCorrectedEnergy();
+        double nE = neighbor.getCorrectedEnergy();
+        if(hE < nE) {
+            isSeed = false;
+        }
+        else if((hE == nE) && (hiy > niy)) {
+            isSeed = false;
+        }
+        else if((hE == nE) && (hiy == niy) && (hix > nix)) {
+            isSeed = false;
+        }
+        return isSeed;  
     }
     
     

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClustererCosmics.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClustererCosmics.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalClustererCosmics.java	Wed Apr 27 11:11:32 2016
@@ -124,13 +124,13 @@
 
         // Loop over ECal hits to find cluster seeds.
         for (CalorimeterHit hit : map.values()) {
-        //	int ix = hit.getIdentifierFieldValue("ix");
+        //  int ix = hit.getIdentifierFieldValue("ix");
          //   int iy = hit.getIdentifierFieldValue("iy");
       //      System.out.println("ix = "+ix);
       //      System.out.println("iy = "+iy);
             
-              	
-        	// Cut on min seed E.
+                
+            // Cut on min seed E.
             if (hit.getRawEnergy() < seedEMin) {
                 continue;
             }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalRawConverter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalRawConverter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/EcalRawConverter.java	Wed Apr 27 11:11:32 2016
@@ -106,42 +106,42 @@
     private EcalConditions ecalConditions = null;
 
     public EcalRawConverter() {
-    	// Track changes in the DAQ configuration.
-    	ConfigurationManager.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				// If the DAQ configuration should be used, load the
-				// relevant settings into the driver.
-				if(useDAQConfig) {
-					// Get the FADC configuration.
-					config = ConfigurationManager.getInstance().getFADCConfig();
-					
-					// Load the settings.
-					NSB = config.getNSB();
-					NSA = config.getNSA();
-					windowSamples = config.getWindowWidth() / 4;
-					
-					// Get the number of peaks.
-					if(config.getMode() == 1) {
-						nPeak = Integer.MAX_VALUE;
-					} else {
-						nPeak = config.getMaxPulses();
-					}
-					
-					// Print the FADC configuration.
-					System.out.println();
-					System.out.println();
-					System.out.printf("NSA            :: %d ns%n", NSA);
-					System.out.printf("NSB            :: %d ns%n", NSB);
-					System.out.printf("Window Samples :: %d clock-cycles%n", windowSamples);
-					System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
-					System.out.println("======================================================================");
-					System.out.println("=== FADC Pulse-Processing Settings ===================================");
-					System.out.println("======================================================================");
-					config.printConfig();
-				}
-			}
-    	});
+        // Track changes in the DAQ configuration.
+        ConfigurationManager.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                // If the DAQ configuration should be used, load the
+                // relevant settings into the driver.
+                if(useDAQConfig) {
+                    // Get the FADC configuration.
+                    config = ConfigurationManager.getInstance().getFADCConfig();
+                    
+                    // Load the settings.
+                    NSB = config.getNSB();
+                    NSA = config.getNSA();
+                    windowSamples = config.getWindowWidth() / 4;
+                    
+                    // Get the number of peaks.
+                    if(config.getMode() == 1) {
+                        nPeak = Integer.MAX_VALUE;
+                    } else {
+                        nPeak = config.getMaxPulses();
+                    }
+                    
+                    // Print the FADC configuration.
+                    System.out.println();
+                    System.out.println();
+                    System.out.printf("NSA            :: %d ns%n", NSA);
+                    System.out.printf("NSB            :: %d ns%n", NSB);
+                    System.out.printf("Window Samples :: %d clock-cycles%n", windowSamples);
+                    System.out.printf("Max Peaks      :: %d peaks%n", nPeak);
+                    System.out.println("======================================================================");
+                    System.out.println("=== FADC Pulse-Processing Settings ===================================");
+                    System.out.println("======================================================================");
+                    config.printConfig(System.out);
+                }
+            }
+        });
     }
   
     public void setLeadingEdgeThreshold(double thresh) {
@@ -196,7 +196,7 @@
     }
     
     public void setUseDAQConfig(boolean state) {
-    	useDAQConfig = state;
+        useDAQConfig = state;
     }
 
     /*
@@ -206,10 +206,10 @@
         EcalChannelConstants channelData = findChannel(hit.getCellID());
         double pedestal;
         if(useDAQConfig) {
-    		//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
-    		pedestal = config.getPedestal(hit.getCellID());
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
+            pedestal = config.getPedestal(hit.getCellID());
         } else {
-        	pedestal = channelData.getCalibration().getPedestal();
+            pedestal = channelData.getCalibration().getPedestal();
         }
         
         int sum = 0;
@@ -237,10 +237,10 @@
      * Choose whether to use static pedestal from database or running pedestal from mode-7.
      */
     public double getSingleSamplePedestal(EventHeader event,long cellID) {
-    	if(useDAQConfig) {
-    		//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(cellID);
-    		return config.getPedestal(cellID);
-    	}
+        if(useDAQConfig) {
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(cellID);
+            return config.getPedestal(cellID);
+        }
         if (useRunningPedestal && event!=null) {
             if (event.hasItem("EcalRunningPedestals")) {
                 Map<EcalChannel, Double> runningPedMap = (Map<EcalChannel, Double>) event.get("EcalRunningPedestals");
@@ -409,12 +409,12 @@
         // threshold is pedestal plus threshold configuration parameter:
         final int absoluteThreshold;
         if(useDAQConfig) {
-        	//EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
-        	//int leadingEdgeThreshold = ConfigurationManager.getInstance().getFADCConfig().getThreshold(channel.getChannelId());
-        	int leadingEdgeThreshold = config.getThreshold(cellID);
-        	absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
+            //EcalChannel channel = ecalConditions.getChannelCollection().findGeometric(hit.getCellID());
+            //int leadingEdgeThreshold = ConfigurationManager.getInstance().getFADCConfig().getThreshold(channel.getChannelId());
+            int leadingEdgeThreshold = config.getThreshold(cellID);
+            absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
         } else {
-        	absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
+            absoluteThreshold = (int) (getSingleSamplePedestal(event, cellID) + leadingEdgeThreshold);
         }
         
         ArrayList <Integer> thresholdCrossings = new ArrayList<Integer>();
@@ -435,10 +435,10 @@
                 // search for next threshold crossing begins at end of this pulse:
                 if(useDAQConfig && ConfigurationManager.getInstance().getFADCConfig().getMode() == 1) {
                     // special case, emulating SSP:
-                	ii += 8;
+                    ii += 8;
                 } else {
                     // "normal" case, emulating FADC250:
-                	ii += NSA/nsPerSample - 1;
+                    ii += NSA/nsPerSample - 1;
                 }
 
                 // firmware limit on # of peaks:
@@ -532,8 +532,8 @@
         EcalChannelConstants channelData = findChannel(cellID);
         
         if(useDAQConfig) {
-        	//float gain = ConfigurationManager.getInstance().getFADCConfig().getGain(ecalConditions.getChannelCollection().findGeometric(cellID));
-        	return config.getGain(cellID) * adcSum * EcalUtils.MeV;
+            //float gain = ConfigurationManager.getInstance().getFADCConfig().getGain(ecalConditions.getChannelCollection().findGeometric(cellID));
+            return config.getGain(cellID) * adcSum * EcalUtils.MeV;
         }  else if(use2014Gain) {
             if (constantGain) {
                 return adcSum * EcalUtils.gainFactor * EcalUtils.ecalReadoutPeriod;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/HPSEcalClusterIC.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/HPSEcalClusterIC.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/holly/HPSEcalClusterIC.java	Wed Apr 27 11:11:32 2016
@@ -55,11 +55,11 @@
     }
     
     public void addSharedHit(CalorimeterHit sharedHit) {
-    	sharedHitList.add(sharedHit);
+        sharedHitList.add(sharedHit);
     }
     
     public List<CalorimeterHit> getSharedHits() {
-    	return sharedHitList;
+        return sharedHitList;
     }
     
 //    public double[] getPosition() {
@@ -155,12 +155,12 @@
         for(int i=0;i<hits.size();i++)
         {
             CalorimeterHit hit = hits.get(i);
-            //	CalorimeterIDDecoder decoder = hit.getDecoder();
-            //	decoder.setID(hit.getCellID());
-            //	double[] pos = new double[3];
-            //	pos[0] = decoder.getX();
-            //	pos[1] = decoder.getY();
-            //	pos[2] = decoder.getZ();
+            //  CalorimeterIDDecoder decoder = hit.getDecoder();
+            //  decoder.setID(hit.getCellID());
+            //  double[] pos = new double[3];
+            //  pos[0] = decoder.getX();
+            //  pos[1] = decoder.getY();
+            //  pos[2] = decoder.getZ();
             //double[] pos = hit.getPosition();
             //Find position at shower max
             IGeometryInfo geom = hit.getDetectorElement().getGeometry();
@@ -296,104 +296,104 @@
             EV[1] = E2;
             EV[2] = E3;
             // Now calculate principal axes
-	    // For eigenvalue EV, the axis is (nx, ny, nz) where:
-	    //    (Exx - EV)nx + (Exy)ny + (Exz)nz = 0
-	    //    (Eyx)nx + (Eyy - EV)ny + (Eyz)nz = 0
-	    //    (Ezx)nx + (Ezy)ny + (Ezz - EV)nz = 0
-	    // Setting nx = 1, we have:
-	    //    (Exx - EV) + (Exy)ny + (Exz)nz = 0
-	    //    (Eyx) + (Eyy - EV)ny + (Eyz)nz = 0
-	    //    (Ezx) + (Ezy)ny + (Ezz - EV)nz = 0
-	    // and so
-	    //    (Exy)ny = EV - Exx - (Exz)nz  =>  ny = (EV - Exx - Exz*nz)/Exy
-	    // What if Exy = 0? Then provided Eyz is non-zero we can write:
-	    //    (Ezx) + (Ezy)ny + (Ezz - EV)nz = 0
-	    //    ny = (Exz - (Ezz-EV)*nz)/Eyz
-	    // What if Exy = 0 and Eyz = 0 but (Eyy - EV) is non-zero?
-	    //    (Eyy - EV)ny + (Eyz)nz = 0
-	    //    ny = -(Eyz*nz)/(Eyy-EV)
-
-	    // In the pathological case where Exz = Eyz = Ezz = 0:
-	    //    (Exx - EV)nx + (Exy)ny = 0  =>  ny/nx = -(Exx-EV)/Exy
-	    //    (Eyx)nx + (Eyy - EV)ny = 0  =>  ny/nx = -Eyx/(Eyy-EV)
-	    //    (EV)nz = 0
-	    // so
-	    //     -ny/nx = (EV-Exx)/Exy = Eyx/(EV-Eyy)
-	    // But watch out for order! Recalculate eigenvalues for this pathological case.
-	    //     (EV-Exx)(EV-Eyy) = Eyx*Exy
-	    //     EV^2 - EV(Exx+Eyy) + Exx*Eyy - Eyx*Exy = 0
-	    // 
-	    // In another pathological case, Exz = Exy = 0:
-	    //    (Exx - EV)nx = 0
-	    //    (Eyy - EV)ny + (Eyz)nz = 0 => ny/nz = -(Eyz)/(Eyy-EV)
-	    //    (Ezy)ny + (Ezz - EV)nz = 0 => ny/nz = -(Ezz-EV)/(Ezy)
-	    // so we cannot set nx = 1. Instead, write:
-	    //    -ny/nz = (Eyz)/(Eyy-EV) = (Ezz-EV)/(Ezy)
-	    // Then
-	    //    (Eyz)(Ezy) = (Eyy-EV)(Ezz-EV)
-	    //    (Eyz)^2 = (Eyy)(Ezz) - (Eyy)(EV) - (Ezz)(EV) + (EV)^2
-	    //    EV^2 - EV(Eyy+Ezz) + Eyy*Ezz - Eyz*Eyz = 0
-
-	    // Handle pathological case
-	    if (Exz == 0.0 && Eyz == 0.0) {
-		// Recompute eigenvectors.
-		EV[0] = 0.5*(Exx+Eyy) + 0.5*Math.sqrt((Exx+Eyy)*(Exx+Eyy) + 4.0*Exy*Exy);
-		EV[1] = 0.5*(Exx+Eyy) - 0.5*Math.sqrt((Exx+Eyy)*(Exx+Eyy) + 4.0*Exy*Exy);
-		EV[2] = 0.0;
-		for( int i = 0 ; i < 2 ; i++ ) {
-		    double nx_over_ny = Exy / (Exx-EV[i]);
-		    double nx_unnormalized = nx_over_ny;
-		    double ny_unnormalized = 1.0;
-		    double norm = Math.sqrt(nx_unnormalized*nx_unnormalized + ny_unnormalized*ny_unnormalized);
-		    mm_PA[i][0] = ny_unnormalized/norm;
-		    mm_PA[i][1] = nx_unnormalized/norm;
-		    mm_PA[i][2] = 0.0;
-		}
-		// ... and now set third eigenvector to the z direction:
-		mm_PA[2][0] = 0.0;
-		mm_PA[2][1] = 0.0;
-		mm_PA[2][2] = 1.0;
-	    } else if (Exz == 0.0 && Exy == 0.0) {
-		// Another pathological case
-		EV[0] = 0.5*(Eyy+Ezz) + 0.5*Math.sqrt((Eyy+Ezz)*(Eyy+Ezz) + 4.0*Eyz*Eyz);
-		EV[1] = 0.5*(Eyy+Ezz) - 0.5*Math.sqrt((Eyy+Ezz)*(Eyy+Ezz) + 4.0*Eyz*Eyz);
-		EV[2] = 0.0;
-		for( int i = 0 ; i < 2 ; i++ ) {
-		    double ny_over_nz = Eyz / (Eyy-EV[i]);
-		    double ny_unnormalized = ny_over_nz;
-		    double nz_unnormalized = 1.0;
-		    double norm = Math.sqrt(ny_unnormalized*ny_unnormalized + nz_unnormalized*nz_unnormalized);
-		    mm_PA[i][0] = nz_unnormalized/norm;
-		    mm_PA[i][1] = ny_unnormalized/norm;
-		    mm_PA[i][2] = 0.0;
-		}
-		mm_PA[2][0] = 0.0;
-		mm_PA[2][1] = 0.0;
-		mm_PA[2][2] = 1.0;
-	    } else {
-		for( int i = 0 ; i < 3 ; i++ )
-		    {
-			double[] C = new double[3];
-			C[0] = 1.0;
-			C[2] = (Exy*Exy + (Eyy - EV[i])*(EV[i] - Exx))/
-			    ((Eyy - EV[i])*Exz - Eyz*Exy);
-			C[1] = (EV[i] - Exx - Exz*C[2])/Exy;
-			if (Exy == 0.0) {
-			    // Recompute
-			    if (Eyz != 0.0) {
-				// ny = (Exz - (Ezz-EV)*nz)/Eyz
-				C[1] = (Exz - (Ezz-EV[i])*C[2])/Eyz;
-			    } else {
-				// ny = -(Eyz*nz)/(Eyy-EV)
-				C[1] = -(Eyz*C[2])/(Eyy-EV[i]);
-			    }
-			}
-			double norm = Math.sqrt(C[0]*C[0] + C[1]*C[1] + C[2]*C[2]);
-			mm_PA[i][0] = C[0]/norm;
-			mm_PA[i][1] = C[1]/norm;
-			mm_PA[i][2] = C[2]/norm;
-		    }
-	    }
+        // For eigenvalue EV, the axis is (nx, ny, nz) where:
+        //    (Exx - EV)nx + (Exy)ny + (Exz)nz = 0
+        //    (Eyx)nx + (Eyy - EV)ny + (Eyz)nz = 0
+        //    (Ezx)nx + (Ezy)ny + (Ezz - EV)nz = 0
+        // Setting nx = 1, we have:
+        //    (Exx - EV) + (Exy)ny + (Exz)nz = 0
+        //    (Eyx) + (Eyy - EV)ny + (Eyz)nz = 0
+        //    (Ezx) + (Ezy)ny + (Ezz - EV)nz = 0
+        // and so
+        //    (Exy)ny = EV - Exx - (Exz)nz  =>  ny = (EV - Exx - Exz*nz)/Exy
+        // What if Exy = 0? Then provided Eyz is non-zero we can write:
+        //    (Ezx) + (Ezy)ny + (Ezz - EV)nz = 0
+        //    ny = (Exz - (Ezz-EV)*nz)/Eyz
+        // What if Exy = 0 and Eyz = 0 but (Eyy - EV) is non-zero?
+        //    (Eyy - EV)ny + (Eyz)nz = 0
+        //    ny = -(Eyz*nz)/(Eyy-EV)
+
+        // In the pathological case where Exz = Eyz = Ezz = 0:
+        //    (Exx - EV)nx + (Exy)ny = 0  =>  ny/nx = -(Exx-EV)/Exy
+        //    (Eyx)nx + (Eyy - EV)ny = 0  =>  ny/nx = -Eyx/(Eyy-EV)
+        //    (EV)nz = 0
+        // so
+        //     -ny/nx = (EV-Exx)/Exy = Eyx/(EV-Eyy)
+        // But watch out for order! Recalculate eigenvalues for this pathological case.
+        //     (EV-Exx)(EV-Eyy) = Eyx*Exy
+        //     EV^2 - EV(Exx+Eyy) + Exx*Eyy - Eyx*Exy = 0
+        // 
+        // In another pathological case, Exz = Exy = 0:
+        //    (Exx - EV)nx = 0
+        //    (Eyy - EV)ny + (Eyz)nz = 0 => ny/nz = -(Eyz)/(Eyy-EV)
+        //    (Ezy)ny + (Ezz - EV)nz = 0 => ny/nz = -(Ezz-EV)/(Ezy)
+        // so we cannot set nx = 1. Instead, write:
+        //    -ny/nz = (Eyz)/(Eyy-EV) = (Ezz-EV)/(Ezy)
+        // Then
+        //    (Eyz)(Ezy) = (Eyy-EV)(Ezz-EV)
+        //    (Eyz)^2 = (Eyy)(Ezz) - (Eyy)(EV) - (Ezz)(EV) + (EV)^2
+        //    EV^2 - EV(Eyy+Ezz) + Eyy*Ezz - Eyz*Eyz = 0
+
+        // Handle pathological case
+        if (Exz == 0.0 && Eyz == 0.0) {
+        // Recompute eigenvectors.
+        EV[0] = 0.5*(Exx+Eyy) + 0.5*Math.sqrt((Exx+Eyy)*(Exx+Eyy) + 4.0*Exy*Exy);
+        EV[1] = 0.5*(Exx+Eyy) - 0.5*Math.sqrt((Exx+Eyy)*(Exx+Eyy) + 4.0*Exy*Exy);
+        EV[2] = 0.0;
+        for( int i = 0 ; i < 2 ; i++ ) {
+            double nx_over_ny = Exy / (Exx-EV[i]);
+            double nx_unnormalized = nx_over_ny;
+            double ny_unnormalized = 1.0;
+            double norm = Math.sqrt(nx_unnormalized*nx_unnormalized + ny_unnormalized*ny_unnormalized);
+            mm_PA[i][0] = ny_unnormalized/norm;
+            mm_PA[i][1] = nx_unnormalized/norm;
+            mm_PA[i][2] = 0.0;
+        }
+        // ... and now set third eigenvector to the z direction:
+        mm_PA[2][0] = 0.0;
+        mm_PA[2][1] = 0.0;
+        mm_PA[2][2] = 1.0;
+        } else if (Exz == 0.0 && Exy == 0.0) {
+        // Another pathological case
+        EV[0] = 0.5*(Eyy+Ezz) + 0.5*Math.sqrt((Eyy+Ezz)*(Eyy+Ezz) + 4.0*Eyz*Eyz);
+        EV[1] = 0.5*(Eyy+Ezz) - 0.5*Math.sqrt((Eyy+Ezz)*(Eyy+Ezz) + 4.0*Eyz*Eyz);
+        EV[2] = 0.0;
+        for( int i = 0 ; i < 2 ; i++ ) {
+            double ny_over_nz = Eyz / (Eyy-EV[i]);
+            double ny_unnormalized = ny_over_nz;
+            double nz_unnormalized = 1.0;
+            double norm = Math.sqrt(ny_unnormalized*ny_unnormalized + nz_unnormalized*nz_unnormalized);
+            mm_PA[i][0] = nz_unnormalized/norm;
+            mm_PA[i][1] = ny_unnormalized/norm;
+            mm_PA[i][2] = 0.0;
+        }
+        mm_PA[2][0] = 0.0;
+        mm_PA[2][1] = 0.0;
+        mm_PA[2][2] = 1.0;
+        } else {
+        for( int i = 0 ; i < 3 ; i++ )
+            {
+            double[] C = new double[3];
+            C[0] = 1.0;
+            C[2] = (Exy*Exy + (Eyy - EV[i])*(EV[i] - Exx))/
+                ((Eyy - EV[i])*Exz - Eyz*Exy);
+            C[1] = (EV[i] - Exx - Exz*C[2])/Exy;
+            if (Exy == 0.0) {
+                // Recompute
+                if (Eyz != 0.0) {
+                // ny = (Exz - (Ezz-EV)*nz)/Eyz
+                C[1] = (Exz - (Ezz-EV[i])*C[2])/Eyz;
+                } else {
+                // ny = -(Eyz*nz)/(Eyy-EV)
+                C[1] = -(Eyz*C[2])/(Eyy-EV[i]);
+                }
+            }
+            double norm = Math.sqrt(C[0]*C[0] + C[1]*C[1] + C[2]*C[2]);
+            mm_PA[i][0] = C[0]/norm;
+            mm_PA[i][1] = C[1]/norm;
+            mm_PA[i][2] = C[2]/norm;
+            }
+        }
         }
         mm_NE[0] = NE1;
         mm_NE[1] = NE2;
@@ -417,7 +417,7 @@
             double dr = Math.sqrt(  (position[0]+mm_PA[0][0])*(position[0]+mm_PA[0][0]) +
                     (position[1]+mm_PA[0][1])*(position[1]+mm_PA[0][1]) +
                     (position[2]+mm_PA[0][2])*(position[2]+mm_PA[0][2]) ) -
-                    Math.sqrt(	(position[0])*(position[0]) +
+                    Math.sqrt(  (position[0])*(position[0]) +
                     (position[1])*(position[1]) +
                     (position[2])*(position[2]) ) ;
             double sign = 1.;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/jeremym/EvioFileScanner.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/jeremym/EvioFileScanner.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/jeremym/EvioFileScanner.java	Wed Apr 27 11:11:32 2016
@@ -28,7 +28,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.hps.conditions.database.ConnectionParameters;
 import org.hps.record.evio.EvioEventConstants;
 import org.hps.record.evio.EvioEventUtilities;
@@ -484,7 +484,7 @@
 
     final Set<Integer> acceptRuns = new HashSet<Integer>();
 
-    final DefaultParser parser = new DefaultParser();
+    final PosixParser parser = new PosixParser();
 
     boolean printSummary = false;
 

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ClusterAnalysisDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ClusterAnalysisDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ClusterAnalysisDriver.java	Wed Apr 27 11:11:32 2016
@@ -11,84 +11,84 @@
 import org.lcsim.util.aida.AIDA;
 
 public class ClusterAnalysisDriver extends Driver {
-	// Analysis plots.
+    // Analysis plots.
     AIDA aida = AIDA.defaultInstance();
-	IHistogram1D clusterTotalEnergy;
-	IHistogram1D clusterSeedEnergy;
-	IHistogram1D clusterHitCount;
-	IHistogram2D clusterDistribution;
-	
-	IHistogram1D fClusterTotalEnergy;
-	IHistogram1D fClusterSeedEnergy;
-	IHistogram1D fClusterHitCount;
-	IHistogram2D fClusterDistribution;
-	
-	IHistogram1D nClusterTotalEnergy;
-	IHistogram1D nClusterSeedEnergy;
-	IHistogram1D nClusterHitCount;
-	IHistogram2D nClusterDistribution;
-	
-	// Hit collection names.
-	private String clusterCollectionName = "EcalClusters";
-	
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
-	
-	@Override
-	public void startOfData() {
-		// Initialize the histograms.
-		clusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy", 110, 0.00, 2.2);
-		clusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy", 110, 0.00, 2.2);
-		clusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count", 8, 1, 9);
-		clusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
-		
-		// Initialize the filtered histograms.
-		fClusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy (Over 100 MeV)", 110, 0.00, 2.2);
-		fClusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy (Over 100 MeV)", 110, 0.00, 2.2);
-		fClusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count (Over 100 MeV)", 8, 1, 9);
-		fClusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution (Over 100 MeV)", 46, -23, 23, 11, -5.5, 5.5);
-		
-		// Initialize the more filtered histograms.
-		nClusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy (Over 100 MeV, > 1 Hit)", 110, 0.00, 2.2);
-		nClusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy (Over 100 MeV, > 1 Hit)", 110, 0.00, 2.2);
-		nClusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count (Over 100 MeV, > 1 Hit)", 8, 1, 9);
-		nClusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution (Over 100 MeV, > 1 Hit)", 46, -23, 23, 11, -5.5, 5.5);
-	}
-	
-	public void process(EventHeader event) {
-		// Check if there exists a cluster collection.
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Get the raw hit collection.
-			List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-			
-			// Output the information on each hit to the histograms.
-			for(Cluster cluster : clusterList) {
-				// Get the x and y indices for the hits.
-				int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-				int iy = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-				if(ix > 0) { ix = ix - 1; }
-				
-				// Write to the histograms.
-				clusterTotalEnergy.fill(cluster.getEnergy());
-				clusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
-				clusterHitCount.fill(cluster.getCalorimeterHits().size());
-				clusterDistribution.fill(ix, iy, 1.0);
-				
-				if(cluster.getCalorimeterHits().get(0).getCorrectedEnergy() > 0.100) {
-					fClusterTotalEnergy.fill(cluster.getEnergy());
-					fClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
-					fClusterHitCount.fill(cluster.getCalorimeterHits().size());
-					fClusterDistribution.fill(ix, iy, 1.0);
-					
-					if(cluster.getCalorimeterHits().size() > 1) {
-						nClusterTotalEnergy.fill(cluster.getEnergy());
-						nClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
-						nClusterHitCount.fill(cluster.getCalorimeterHits().size());
-						nClusterDistribution.fill(ix, iy, 1.0);
-					}
-				}
-			}
-		}
-	}
+    IHistogram1D clusterTotalEnergy;
+    IHistogram1D clusterSeedEnergy;
+    IHistogram1D clusterHitCount;
+    IHistogram2D clusterDistribution;
+    
+    IHistogram1D fClusterTotalEnergy;
+    IHistogram1D fClusterSeedEnergy;
+    IHistogram1D fClusterHitCount;
+    IHistogram2D fClusterDistribution;
+    
+    IHistogram1D nClusterTotalEnergy;
+    IHistogram1D nClusterSeedEnergy;
+    IHistogram1D nClusterHitCount;
+    IHistogram2D nClusterDistribution;
+    
+    // Hit collection names.
+    private String clusterCollectionName = "EcalClusters";
+    
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
+    
+    @Override
+    public void startOfData() {
+        // Initialize the histograms.
+        clusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy", 110, 0.00, 2.2);
+        clusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy", 110, 0.00, 2.2);
+        clusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count", 8, 1, 9);
+        clusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
+        
+        // Initialize the filtered histograms.
+        fClusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy (Over 100 MeV)", 110, 0.00, 2.2);
+        fClusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy (Over 100 MeV)", 110, 0.00, 2.2);
+        fClusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count (Over 100 MeV)", 8, 1, 9);
+        fClusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution (Over 100 MeV)", 46, -23, 23, 11, -5.5, 5.5);
+        
+        // Initialize the more filtered histograms.
+        nClusterTotalEnergy = aida.histogram1D("Cluster Plot :: Cluster Total Energy (Over 100 MeV, > 1 Hit)", 110, 0.00, 2.2);
+        nClusterSeedEnergy = aida.histogram1D("Cluster Plot :: Seed Hit Energy (Over 100 MeV, > 1 Hit)", 110, 0.00, 2.2);
+        nClusterHitCount = aida.histogram1D("Cluster Plot :: Cluster Hit Count (Over 100 MeV, > 1 Hit)", 8, 1, 9);
+        nClusterDistribution = aida.histogram2D("Cluster Plot :: Seed Hit Distribution (Over 100 MeV, > 1 Hit)", 46, -23, 23, 11, -5.5, 5.5);
+    }
+    
+    public void process(EventHeader event) {
+        // Check if there exists a cluster collection.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the raw hit collection.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Output the information on each hit to the histograms.
+            for(Cluster cluster : clusterList) {
+                // Get the x and y indices for the hits.
+                int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                int iy = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+                if(ix > 0) { ix = ix - 1; }
+                
+                // Write to the histograms.
+                clusterTotalEnergy.fill(cluster.getEnergy());
+                clusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
+                clusterHitCount.fill(cluster.getCalorimeterHits().size());
+                clusterDistribution.fill(ix, iy, 1.0);
+                
+                if(cluster.getCalorimeterHits().get(0).getCorrectedEnergy() > 0.100) {
+                    fClusterTotalEnergy.fill(cluster.getEnergy());
+                    fClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
+                    fClusterHitCount.fill(cluster.getCalorimeterHits().size());
+                    fClusterDistribution.fill(ix, iy, 1.0);
+                    
+                    if(cluster.getCalorimeterHits().size() > 1) {
+                        nClusterTotalEnergy.fill(cluster.getEnergy());
+                        nClusterSeedEnergy.fill(cluster.getCalorimeterHits().get(0).getCorrectedEnergy());
+                        nClusterHitCount.fill(cluster.getCalorimeterHits().size());
+                        nClusterDistribution.fill(ix, iy, 1.0);
+                    }
+                }
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/CountTriggersDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/CountTriggersDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/CountTriggersDriver.java	Wed Apr 27 11:11:32 2016
@@ -16,64 +16,64 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class CountTriggersDriver extends Driver {
-	// Store programmable parameters.
-	private String bankCollectionName = "TriggerBank";
-	
-	// Track the number of triggers seen for each trigger type.
-	private int[] triggers = new int[6];
-	private static final int PULSER   = 0;
-	private static final int SINGLES0 = 1;
-	private static final int SINGLES1 = 2;
-	private static final int PAIR0    = 3;
-	private static final int PAIR1    = 4;
-	private static final int COSMIC   = 5;
-	
-	/**
-	 * Outputs the total number of triggers seen for each trigger type.
-	 */
-	@Override
-	public void endOfData() {
-		System.out.println("Trigger Counts:");
-		System.out.printf("Singles 0 :: %d%n", triggers[SINGLES0]);
-		System.out.printf("Singles 1 :: %d%n", triggers[SINGLES1]);
-		System.out.printf("Pair 0    :: %d%n", triggers[PAIR0]);
-		System.out.printf("Pair 1    :: %d%n", triggers[PAIR1]);
-		System.out.printf("Pulser    :: %d%n", triggers[PULSER]);
-		System.out.printf("Cosmic    :: %d%n", triggers[COSMIC]);
-	}
-	
-	/**
-	 * Checks whether a trigger of each given type was seen by the TI
-	 * for each event and increments the total trigger count for that
-	 * type as appropriate.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		// Extract the TI bank from the data stream.
-		TIData tiBank = null;
-		if(event.hasCollection(GenericObject.class, bankCollectionName)) {
-			// Get the bank list.
-			List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-			
-			// Search through the banks and get the TI bank.
-			for(GenericObject obj : bankList) {
-				if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
-					tiBank = new TIData(obj);
-				}
-			}
-		}
-		
-		// If there is no TI bank, the event can not be processed.
-		if(tiBank == null) {
-			return;
-		}
-		
-		// Otherwise, increment the relevant trigger counts.
-		if(tiBank.isPulserTrigger()) { triggers[PULSER]++; }
-		if(tiBank.isSingle0Trigger()) { triggers[SINGLES0]++; }
-		if(tiBank.isSingle1Trigger()) { triggers[SINGLES1]++; }
-		if(tiBank.isPair0Trigger()) { triggers[PAIR0]++; }
-		if(tiBank.isPair1Trigger()) { triggers[PAIR1]++; }
-		if(tiBank.isCalibTrigger()) { triggers[COSMIC]++; }
-	}
+    // Store programmable parameters.
+    private String bankCollectionName = "TriggerBank";
+    
+    // Track the number of triggers seen for each trigger type.
+    private int[] triggers = new int[6];
+    private static final int PULSER   = 0;
+    private static final int SINGLES0 = 1;
+    private static final int SINGLES1 = 2;
+    private static final int PAIR0    = 3;
+    private static final int PAIR1    = 4;
+    private static final int COSMIC   = 5;
+    
+    /**
+     * Outputs the total number of triggers seen for each trigger type.
+     */
+    @Override
+    public void endOfData() {
+        System.out.println("Trigger Counts:");
+        System.out.printf("Singles 0 :: %d%n", triggers[SINGLES0]);
+        System.out.printf("Singles 1 :: %d%n", triggers[SINGLES1]);
+        System.out.printf("Pair 0    :: %d%n", triggers[PAIR0]);
+        System.out.printf("Pair 1    :: %d%n", triggers[PAIR1]);
+        System.out.printf("Pulser    :: %d%n", triggers[PULSER]);
+        System.out.printf("Cosmic    :: %d%n", triggers[COSMIC]);
+    }
+    
+    /**
+     * Checks whether a trigger of each given type was seen by the TI
+     * for each event and increments the total trigger count for that
+     * type as appropriate.
+     */
+    @Override
+    public void process(EventHeader event) {
+        // Extract the TI bank from the data stream.
+        TIData tiBank = null;
+        if(event.hasCollection(GenericObject.class, bankCollectionName)) {
+            // Get the bank list.
+            List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+            
+            // Search through the banks and get the TI bank.
+            for(GenericObject obj : bankList) {
+                if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
+                    tiBank = new TIData(obj);
+                }
+            }
+        }
+        
+        // If there is no TI bank, the event can not be processed.
+        if(tiBank == null) {
+            return;
+        }
+        
+        // Otherwise, increment the relevant trigger counts.
+        if(tiBank.isPulserTrigger()) { triggers[PULSER]++; }
+        if(tiBank.isSingle0Trigger()) { triggers[SINGLES0]++; }
+        if(tiBank.isSingle1Trigger()) { triggers[SINGLES1]++; }
+        if(tiBank.isPair0Trigger()) { triggers[PAIR0]++; }
+        if(tiBank.isPair1Trigger()) { triggers[PAIR1]++; }
+        if(tiBank.isCalibTrigger()) { triggers[COSMIC]++; }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/EvioAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/EvioAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/EvioAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -17,17 +17,17 @@
 import org.lcsim.util.aida.AIDA;
 
 public class EvioAnalysis extends Driver {
-	// Store index reference variables.
+    // Store index reference variables.
         private static final int RECON     = 0;
         private static final int SSP       = 1;
-	
-	// Create histogram arrays for cut distributions.
+    
+    // Create histogram arrays for cut distributions.
         private AIDA aida = AIDA.defaultInstance();
         private IHistogram1D[] clusterEnergyPlot = new IHistogram1D[2];
         private IHistogram1D[] clusterHitCountPlot = new IHistogram1D[2];
         private IHistogram1D[] clusterTimePlot = new IHistogram1D[2];
-	private IHistogram2D[] clusterSlopePlot = new IHistogram2D[2];
-	
+    private IHistogram2D[] clusterSlopePlot = new IHistogram2D[2];
+    
         private IHistogram1D[] pairClusterEnergyPlot = new IHistogram1D[2];
         private IHistogram1D[] pairHitCountPlot = new IHistogram1D[2];
         private IHistogram1D[] pairTimePlot = new IHistogram1D[2];
@@ -38,129 +38,129 @@
         private IHistogram1D[] pairCoplanarityPlot = new IHistogram1D[2];
         private IHistogram1D[] pairTriggerTimePlot = new IHistogram1D[2];
 
-	// Store programmable values.
-	private String clusterCollectionName = "EcalClusters";
-	private String bankCollectionName = "SSPData";
-	private double energySlopeParamF = 0.0055;
-	private double beamEnergy = 1.1;
-	
-	@Override
-	public void startOfData() {
-		// Store the plot source type name.
-		String[] plotType = new String[2];
-		plotType[RECON] = " (Recon)";
-		plotType[SSP] = " (SSP)";
-		
-		// Set the bin sizes based on the beam energy.
-		int bins = (int) beamEnergy * 100;
-		
-		for(int i = 0; i < 2; i++) {
-			// Instantiate the single cluster distribution plots.
-			clusterEnergyPlot[i] = aida.histogram1D("Raw/Cluster Energy" + plotType[i], bins, 0.0, beamEnergy);
-			clusterHitCountPlot[i] = aida.histogram1D("Raw/Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
-			clusterTimePlot[i] = aida.histogram1D("Raw/Cluster Time" + plotType[i], 100, 0, 400);
-			clusterSlopePlot[i] = aida.histogram2D("Raw/Cluster Energy Slope" + plotType[i], 300, 0.0, 3.0, 200, 0, 400);
-			
-			// Instantiate the cluster pair distribution plots.
-			pairSumPlot[i] = aida.histogram1D("Raw/Pair Energy Sum" + plotType[i], (int) 1.5 * bins, 0.0, 1.5 * beamEnergy);
-			pairSumEnergiesPlot[i] = aida.histogram2D("Raw/Pair 2D Energy Sum" + plotType[i], (int) 1.5 * bins, 0.0, 1.5 * beamEnergy, (int) 1.5 * bins, 0.0, 1.5 * beamEnergy);
-			pairDiffPlot[i] = aida.histogram1D("Raw/Pair Energy Difference" + plotType[i], bins, 0.0, beamEnergy);
-			pairSlopePlot[i] = aida.histogram1D("Raw/Pair Energy Slope" + plotType[i], 100, 0.0, 4.0);
-			pairCoplanarityPlot[i] = aida.histogram1D("Raw/Pair Coplanarity" + plotType[i], 180, 0.0, 180);
-		}
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Skip the event if there are no clusters.
-		if(!event.hasCollection(Cluster.class, clusterCollectionName) || !event.hasCollection(GenericObject.class, bankCollectionName)) {
-			return;
-		}
-		
-		// Get the list of clusters.
-		List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
-		
-		// Get the SSP data bank.
-		List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-		
-		// Get the SSP bank from the generic object bank list.
-		SSPData sspBank = null;
-		for(GenericObject obj : bankList) {
-			if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
-				sspBank = new SSPData(obj);
-			}
-		}
-		
-		// Make sure that the SSP bank was initialized.
-		if(sspBank == null) {
-			return;
-		}
-		
-		// Iterate over the reconstructed clusters and populate
-		// the singles plots.
-		for(Cluster cluster : clusters) {
-			// Get the cluster properties.
-			int hitCount = cluster.getCalorimeterHits().size();
-			double x = TriggerModule.getClusterX(cluster);
-			double z = TriggerModule.getClusterZ(cluster);
-			double slopeParamR = Math.sqrt((x * x) + (z * z));
-			
-			// Populate the plots.
-			clusterEnergyPlot[RECON].fill(cluster.getEnergy());
-			clusterHitCountPlot[RECON].fill(cluster.getCalorimeterHits().size());
-			clusterTimePlot[RECON].fill(cluster.getCalorimeterHits().get(0).getTime());
-			clusterSlopePlot[RECON].fill(cluster.getEnergy(), slopeParamR);
-		}
-		
-		// Get the list of pairs.
-		List<Cluster[]> pairs = makePairs(clusters);
-		
-		// Iterate over the pairs and populate the pair plots.
-		for(Cluster[] pair : pairs) {
-			pairSumPlot[RECON].fill(TriggerModule.getValueEnergySum(pair));
-			pairSumEnergiesPlot[RECON].fill(pair[0].getEnergy(), pair[1].getEnergy());
-			pairDiffPlot[RECON].fill(TriggerModule.getValueEnergyDifference(pair));
-			pairSlopePlot[RECON].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
-			pairCoplanarityPlot[RECON].fill(TriggerModule.getValueCoplanarity(pair));
-		}
-	}
-	
-	private List<Cluster[]> makePairs(List<Cluster> clusters) {
-		// Create seperate lists for top and bottom clusters.
-		List<Cluster> topList = new ArrayList<Cluster>();
-		List<Cluster> bottomList = new ArrayList<Cluster>();
-		List<Cluster[]> pairList = new ArrayList<Cluster[]>();
-		
-		// Sort the clusters into the appropriate list.
-		for(Cluster cluster : clusters) {
-			if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
-				topList.add(cluster);
-			} else {
-				bottomList.add(cluster);
-			}
-		}
-		
-		// Create all possible cluster pairs.
-		for(Cluster topCluster : topList) {
-			for(Cluster bottomCluster : bottomList) {
-				Cluster[] pair = { topCluster, bottomCluster };
-				pairList.add(pair);
-			}
-		}
-		
-		// Return the list of cluster pairs.
-		return pairList;
-	}
-	
-	public void setClusterCollectionName(String clusterCollectionName) {
-		this.clusterCollectionName = clusterCollectionName;
-	}
-	
-	public void setBankCollectionName(String bankCollectionName) {
-		this.bankCollectionName = bankCollectionName;
-	}
-	
-	public void setEnergySlopeParamF(double energySlopeParamF) {
-		this.energySlopeParamF = energySlopeParamF;
-	}
+    // Store programmable values.
+    private String clusterCollectionName = "EcalClusters";
+    private String bankCollectionName = "SSPData";
+    private double energySlopeParamF = 0.0055;
+    private double beamEnergy = 1.1;
+    
+    @Override
+    public void startOfData() {
+        // Store the plot source type name.
+        String[] plotType = new String[2];
+        plotType[RECON] = " (Recon)";
+        plotType[SSP] = " (SSP)";
+        
+        // Set the bin sizes based on the beam energy.
+        int bins = (int) beamEnergy * 100;
+        
+        for(int i = 0; i < 2; i++) {
+            // Instantiate the single cluster distribution plots.
+            clusterEnergyPlot[i] = aida.histogram1D("Raw/Cluster Energy" + plotType[i], bins, 0.0, beamEnergy);
+            clusterHitCountPlot[i] = aida.histogram1D("Raw/Cluster Hit Count" + plotType[i], 9, 0.5, 9.5);
+            clusterTimePlot[i] = aida.histogram1D("Raw/Cluster Time" + plotType[i], 100, 0, 400);
+            clusterSlopePlot[i] = aida.histogram2D("Raw/Cluster Energy Slope" + plotType[i], 300, 0.0, 3.0, 200, 0, 400);
+            
+            // Instantiate the cluster pair distribution plots.
+            pairSumPlot[i] = aida.histogram1D("Raw/Pair Energy Sum" + plotType[i], (int) 1.5 * bins, 0.0, 1.5 * beamEnergy);
+            pairSumEnergiesPlot[i] = aida.histogram2D("Raw/Pair 2D Energy Sum" + plotType[i], (int) 1.5 * bins, 0.0, 1.5 * beamEnergy, (int) 1.5 * bins, 0.0, 1.5 * beamEnergy);
+            pairDiffPlot[i] = aida.histogram1D("Raw/Pair Energy Difference" + plotType[i], bins, 0.0, beamEnergy);
+            pairSlopePlot[i] = aida.histogram1D("Raw/Pair Energy Slope" + plotType[i], 100, 0.0, 4.0);
+            pairCoplanarityPlot[i] = aida.histogram1D("Raw/Pair Coplanarity" + plotType[i], 180, 0.0, 180);
+        }
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Skip the event if there are no clusters.
+        if(!event.hasCollection(Cluster.class, clusterCollectionName) || !event.hasCollection(GenericObject.class, bankCollectionName)) {
+            return;
+        }
+        
+        // Get the list of clusters.
+        List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
+        
+        // Get the SSP data bank.
+        List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+        
+        // Get the SSP bank from the generic object bank list.
+        SSPData sspBank = null;
+        for(GenericObject obj : bankList) {
+            if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
+                sspBank = new SSPData(obj);
+            }
+        }
+        
+        // Make sure that the SSP bank was initialized.
+        if(sspBank == null) {
+            return;
+        }
+        
+        // Iterate over the reconstructed clusters and populate
+        // the singles plots.
+        for(Cluster cluster : clusters) {
+            // Get the cluster properties.
+            int hitCount = cluster.getCalorimeterHits().size();
+            double x = TriggerModule.getClusterX(cluster);
+            double z = TriggerModule.getClusterZ(cluster);
+            double slopeParamR = Math.sqrt((x * x) + (z * z));
+            
+            // Populate the plots.
+            clusterEnergyPlot[RECON].fill(cluster.getEnergy());
+            clusterHitCountPlot[RECON].fill(cluster.getCalorimeterHits().size());
+            clusterTimePlot[RECON].fill(cluster.getCalorimeterHits().get(0).getTime());
+            clusterSlopePlot[RECON].fill(cluster.getEnergy(), slopeParamR);
+        }
+        
+        // Get the list of pairs.
+        List<Cluster[]> pairs = makePairs(clusters);
+        
+        // Iterate over the pairs and populate the pair plots.
+        for(Cluster[] pair : pairs) {
+            pairSumPlot[RECON].fill(TriggerModule.getValueEnergySum(pair));
+            pairSumEnergiesPlot[RECON].fill(pair[0].getEnergy(), pair[1].getEnergy());
+            pairDiffPlot[RECON].fill(TriggerModule.getValueEnergyDifference(pair));
+            pairSlopePlot[RECON].fill(TriggerModule.getValueEnergySlope(pair, energySlopeParamF));
+            pairCoplanarityPlot[RECON].fill(TriggerModule.getValueCoplanarity(pair));
+        }
+    }
+    
+    private List<Cluster[]> makePairs(List<Cluster> clusters) {
+        // Create seperate lists for top and bottom clusters.
+        List<Cluster> topList = new ArrayList<Cluster>();
+        List<Cluster> bottomList = new ArrayList<Cluster>();
+        List<Cluster[]> pairList = new ArrayList<Cluster[]>();
+        
+        // Sort the clusters into the appropriate list.
+        for(Cluster cluster : clusters) {
+            if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
+                topList.add(cluster);
+            } else {
+                bottomList.add(cluster);
+            }
+        }
+        
+        // Create all possible cluster pairs.
+        for(Cluster topCluster : topList) {
+            for(Cluster bottomCluster : bottomList) {
+                Cluster[] pair = { topCluster, bottomCluster };
+                pairList.add(pair);
+            }
+        }
+        
+        // Return the list of cluster pairs.
+        return pairList;
+    }
+    
+    public void setClusterCollectionName(String clusterCollectionName) {
+        this.clusterCollectionName = clusterCollectionName;
+    }
+    
+    public void setBankCollectionName(String bankCollectionName) {
+        this.bankCollectionName = bankCollectionName;
+    }
+    
+    public void setEnergySlopeParamF(double energySlopeParamF) {
+        this.energySlopeParamF = energySlopeParamF;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/FADCAnalysisDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/FADCAnalysisDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/FADCAnalysisDriver.java	Wed Apr 27 11:11:32 2016
@@ -11,82 +11,82 @@
 import org.lcsim.util.aida.AIDA;
 
 public class FADCAnalysisDriver extends Driver {
-	// Analysis plots.
+    // Analysis plots.
     AIDA aida = AIDA.defaultInstance();
-	IHistogram1D rawHitEnergy;
-	IHistogram1D fadcHitEnergy;
-	IHistogram2D rawHitDistribution;
-	IHistogram2D fadcHitDistribution;
-	IHistogram2D fadcFilteredHitDistribution;
-	IHistogram1D eventRawHitCount;
-	IHistogram1D eventFADCHitCount;
-	
-	// Hit collection names.
-	private String rawHitsCollectionName = "EcalHits";
-	private String fadcHitsCollectionName = "EcalCorrectedHits";
-	
-	public void setFadcHitsCollectionName(String fadcHitsCollectionName) {
-		this.fadcHitsCollectionName = fadcHitsCollectionName;
-	}
-	
-	public void setRawHitsCollectionName(String rawHitsCollectionName) {
-		this.rawHitsCollectionName = rawHitsCollectionName;
-	}
-	
-	@Override
-	public void startOfData() {
-		// Initialize the histograms.
-		rawHitEnergy = aida.histogram1D("FADC Plot :: Raw Hit Energy", 110, 0.00, 2.2);
-		fadcHitEnergy = aida.histogram1D("FADC Plot :: FADC Hit Energy", 80, 0.00, 1.6);
-		rawHitDistribution = aida.histogram2D("FADC Plot :: Raw Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
-		fadcHitDistribution = aida.histogram2D("FADC Plot :: FADC Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
-		fadcFilteredHitDistribution = aida.histogram2D("FADC Plot :: FADC Hit Distribution Over 100 MeV", 46, -23, 23, 11, -5.5, 5.5);
-		eventRawHitCount = aida.histogram1D("FADC Plot :: Event Raw Hit Count", 159, 1, 160);
-		eventFADCHitCount = aida.histogram1D("FADC Plot :: Event FADC Hit Count", 15, 1, 16);
-	}
-	
-	public void process(EventHeader event) {
-		// Check if there exists a raw hits collection.
-		if(event.hasCollection(CalorimeterHit.class, rawHitsCollectionName)) {
-			// Get the raw hit collection.
-			List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, rawHitsCollectionName);
-			
-			// Output the information on each hit to the histograms.
-			for(CalorimeterHit hit : hitList) {
-				// Get the x and y indices for the hits.
-				int ix = hit.getIdentifierFieldValue("ix");
-				int iy = hit.getIdentifierFieldValue("iy");
-				if(ix > 0) { ix = ix - 1; }
-				
-				// Write to the histograms.
-				rawHitEnergy.fill(hit.getCorrectedEnergy());
-				rawHitDistribution.fill(ix, iy, 1.0);
-				
-				// If there are hits, fill the hit count histogram.
-				if(hitList.size() != 0) { eventRawHitCount.fill(hitList.size()); }
-			}
-		}
-		
-		// Check if there exists an FADC hits collection.
-		if(event.hasCollection(CalorimeterHit.class, fadcHitsCollectionName)) {
-			// Get the raw hit collection.
-			List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, fadcHitsCollectionName);
-			
-			// Output the information on each hit to the histograms.
-			for(CalorimeterHit hit : hitList) {
-				// Get the x and y indices for the hits.
-				int ix = hit.getIdentifierFieldValue("ix");
-				int iy = hit.getIdentifierFieldValue("iy");
-				if(ix > 0) { ix = ix - 1; }
-				
-				// Write to the histograms.
-				fadcHitEnergy.fill(hit.getCorrectedEnergy());
-				fadcHitDistribution.fill(ix, iy, 1.0);
-				if(hit.getCorrectedEnergy() > 0.100) { fadcFilteredHitDistribution.fill(ix, iy, 1.0); }
-				
-				// If there are hits, fill the hit count histogram.
-				if(hitList.size() != 0) { eventFADCHitCount.fill(hitList.size()); }
-			}
-		}
-	}
+    IHistogram1D rawHitEnergy;
+    IHistogram1D fadcHitEnergy;
+    IHistogram2D rawHitDistribution;
+    IHistogram2D fadcHitDistribution;
+    IHistogram2D fadcFilteredHitDistribution;
+    IHistogram1D eventRawHitCount;
+    IHistogram1D eventFADCHitCount;
+    
+    // Hit collection names.
+    private String rawHitsCollectionName = "EcalHits";
+    private String fadcHitsCollectionName = "EcalCorrectedHits";
+    
+    public void setFadcHitsCollectionName(String fadcHitsCollectionName) {
+        this.fadcHitsCollectionName = fadcHitsCollectionName;
+    }
+    
+    public void setRawHitsCollectionName(String rawHitsCollectionName) {
+        this.rawHitsCollectionName = rawHitsCollectionName;
+    }
+    
+    @Override
+    public void startOfData() {
+        // Initialize the histograms.
+        rawHitEnergy = aida.histogram1D("FADC Plot :: Raw Hit Energy", 110, 0.00, 2.2);
+        fadcHitEnergy = aida.histogram1D("FADC Plot :: FADC Hit Energy", 80, 0.00, 1.6);
+        rawHitDistribution = aida.histogram2D("FADC Plot :: Raw Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
+        fadcHitDistribution = aida.histogram2D("FADC Plot :: FADC Hit Distribution", 46, -23, 23, 11, -5.5, 5.5);
+        fadcFilteredHitDistribution = aida.histogram2D("FADC Plot :: FADC Hit Distribution Over 100 MeV", 46, -23, 23, 11, -5.5, 5.5);
+        eventRawHitCount = aida.histogram1D("FADC Plot :: Event Raw Hit Count", 159, 1, 160);
+        eventFADCHitCount = aida.histogram1D("FADC Plot :: Event FADC Hit Count", 15, 1, 16);
+    }
+    
+    public void process(EventHeader event) {
+        // Check if there exists a raw hits collection.
+        if(event.hasCollection(CalorimeterHit.class, rawHitsCollectionName)) {
+            // Get the raw hit collection.
+            List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, rawHitsCollectionName);
+            
+            // Output the information on each hit to the histograms.
+            for(CalorimeterHit hit : hitList) {
+                // Get the x and y indices for the hits.
+                int ix = hit.getIdentifierFieldValue("ix");
+                int iy = hit.getIdentifierFieldValue("iy");
+                if(ix > 0) { ix = ix - 1; }
+                
+                // Write to the histograms.
+                rawHitEnergy.fill(hit.getCorrectedEnergy());
+                rawHitDistribution.fill(ix, iy, 1.0);
+                
+                // If there are hits, fill the hit count histogram.
+                if(hitList.size() != 0) { eventRawHitCount.fill(hitList.size()); }
+            }
+        }
+        
+        // Check if there exists an FADC hits collection.
+        if(event.hasCollection(CalorimeterHit.class, fadcHitsCollectionName)) {
+            // Get the raw hit collection.
+            List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, fadcHitsCollectionName);
+            
+            // Output the information on each hit to the histograms.
+            for(CalorimeterHit hit : hitList) {
+                // Get the x and y indices for the hits.
+                int ix = hit.getIdentifierFieldValue("ix");
+                int iy = hit.getIdentifierFieldValue("iy");
+                if(ix > 0) { ix = ix - 1; }
+                
+                // Write to the histograms.
+                fadcHitEnergy.fill(hit.getCorrectedEnergy());
+                fadcHitDistribution.fill(ix, iy, 1.0);
+                if(hit.getCorrectedEnergy() > 0.100) { fadcFilteredHitDistribution.fill(ix, iy, 1.0); }
+                
+                // If there are hits, fill the hit count histogram.
+                if(hitList.size() != 0) { eventFADCHitCount.fill(hitList.size()); }
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/HPSEcalDataPlotsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/HPSEcalDataPlotsDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/HPSEcalDataPlotsDriver.java	Wed Apr 27 11:11:32 2016
@@ -27,22 +27,22 @@
  * @author Kyle McCarty <[log in to unmask]>
  */
 public class HPSEcalDataPlotsDriver extends Driver {
-	private String plotsGroupName= "Data Plots";
-	private String bankCollectionName = "TriggerBank";
-	private String clusterCollectionName = "EcalClusters";
-	
-	private static final int PULSER   = 0;
-	private static final int SINGLES0 = 1;
-	private static final int SINGLES1 = 2;
-	private static final int PAIR0    = 3;
-	private static final int PAIR1    = 4;
-	
-	private static final int ALL       = 0;
-	private static final int EDGE      = 1;
-	private static final int FIDUCIAL = 2;
-	
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D[][] clusterTotalEnergy = new IHistogram1D[5][3];
+    private String plotsGroupName= "Data Plots";
+    private String bankCollectionName = "TriggerBank";
+    private String clusterCollectionName = "EcalClusters";
+    
+    private static final int PULSER   = 0;
+    private static final int SINGLES0 = 1;
+    private static final int SINGLES1 = 2;
+    private static final int PAIR0    = 3;
+    private static final int PAIR1    = 4;
+    
+    private static final int ALL       = 0;
+    private static final int EDGE      = 1;
+    private static final int FIDUCIAL = 2;
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D[][] clusterTotalEnergy = new IHistogram1D[5][3];
     private IHistogram1D[][] clusterTime = new IHistogram1D[5][3];
     private IHistogram1D[][] clusterHitCount = new IHistogram1D[5][3];
     private IHistogram1D[][] clusterSeedEnergy = new IHistogram1D[5][3];
@@ -56,249 +56,249 @@
     private IHistogram2D[][] clusterSeedPosition = new IHistogram2D[5][3];
     private IHistogram2D[][] pairEnergySlope2D = new IHistogram2D[5][3];
     private IHistogram2D[][] pairCoplanarityEnergySum = new IHistogram2D[5][3];
-	
+    
     /**
      * Initializes the plots.
      */
-	@Override
-	public void startOfData() {
-		// Define trigger names.
-		String[] triggerNames = {
-			"Pulser", "Singles 0", "Singles 1", "Pair 0", "Pair 1"	
-		};
-		
-		// Define the positional names.
-		String[] positionNames = {
-				"All", "Edge", "Fiducial"
-		};
-		
-		// Instantiate the plots.
-		for(int i = 0; i < 5; i++) {
-			for(int j = 0; j < 3; j++) {
-				clusterTotalEnergy[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Cluster Total Energy", 150, 0.000, 1.500);
+    @Override
+    public void startOfData() {
+        // Define trigger names.
+        String[] triggerNames = {
+            "Pulser", "Singles 0", "Singles 1", "Pair 0", "Pair 1"  
+        };
+        
+        // Define the positional names.
+        String[] positionNames = {
+                "All", "Edge", "Fiducial"
+        };
+        
+        // Instantiate the plots.
+        for(int i = 0; i < 5; i++) {
+            for(int j = 0; j < 3; j++) {
+                clusterTotalEnergy[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
+                        + positionNames[j] + "/Cluster Total Energy", 150, 0.000, 1.500);
                 clusterTime[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Cluster Hit Time", 100, 0.0, 100.0);
+                        + positionNames[j] + "/Cluster Hit Time", 100, 0.0, 100.0);
                 clusterHitCount[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Cluster Hit Count", 10, -0.5, 9.5);
+                        + positionNames[j] + "/Cluster Hit Count", 10, -0.5, 9.5);
                 clusterSeedEnergy[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Cluster Seed Energy", 150, 0.000, 1.500);
+                        + positionNames[j] + "/Cluster Seed Energy", 150, 0.000, 1.500);
                 pairEnergySum[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Pair Energy Sum", 150, 0.000, 1.500);
+                        + positionNames[j] + "/Pair Energy Sum", 150, 0.000, 1.500);
                 pairEnergyDifference[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Pair Energy Difference", 150, 0.000, 1.500);
+                        + positionNames[j] + "/Pair Energy Difference", 150, 0.000, 1.500);
                 pairEnergySlope[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Pair Energy Slope", 100, 0.000, 4.000);
+                        + positionNames[j] + "/Pair Energy Slope", 100, 0.000, 4.000);
                 pairCoplanarity[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Pair Coplanarity", 180, 0.000, 180);
+                        + positionNames[j] + "/Pair Coplanarity", 180, 0.000, 180);
                 pairTimeCoincidence[i][j] = aida.histogram1D(plotsGroupName + "/" + triggerNames[i] + "/"
-						+ positionNames[j] + "/Pair Time Coincidence", 80, 0, 20);
+                        + positionNames[j] + "/Pair Time Coincidence", 80, 0, 20);
                 
                 clusterSeedPosition[i][j] = aida.histogram2D(plotsGroupName + "/" + triggerNames[i] + "/"
-                		+ positionNames[j] + "/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
+                        + positionNames[j] + "/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
                 pairEnergySum2D[i][j] = aida.histogram2D(plotsGroupName + "/" + triggerNames[i] + "/"
-                		+ positionNames[j] + "/Pair Energy Sum 2D", 150, 0.000, 1.500, 150, 0.000, 1.500);
+                        + positionNames[j] + "/Pair Energy Sum 2D", 150, 0.000, 1.500, 150, 0.000, 1.500);
                 pairCoplanarityEnergySum[i][j] = aida.histogram2D(plotsGroupName + "/" + triggerNames[i] + "/"
-                		+ positionNames[j] + "/Pair Energy Sum vs. Coplanarity", 150, 0.000, 1.500, 180, 0, 180);
+                        + positionNames[j] + "/Pair Energy Sum vs. Coplanarity", 150, 0.000, 1.500, 180, 0, 180);
                 pairEnergySlope2D[i][j] = aida.histogram2D(plotsGroupName + "/" + triggerNames[i] + "/"
-                		+ positionNames[j] + "/Pair Energy Slope 2D", 75, 0.000, 1.500, 100, 0.0, 400.0);
-			}
-		}
-	}
-	
-	/**
-	 * Processes the event clusters and populates distribution charts
-	 * from them for each trigger. Also creates separate plots for the
-	 * edge and fiducial regions.
-	 * @param event - The event containing LCIO collections to be used
-	 * for plot population.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		// Get the TI and SSP banks.
-		TIData tiBank = null;
-		SSPData sspBank = null;
-		if(event.hasCollection(GenericObject.class, bankCollectionName)) {
-			// Get the bank list.
-			List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-			
-			// Search through the banks and get the SSP and TI banks.
-			for(GenericObject obj : bankList) {
-				// If this is an SSP bank, parse it.
-				if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
-					sspBank = new SSPData(obj);
-				}
-				
-				// Otherwise, if this is a TI bank, parse it.
-				else if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
-					tiBank = new TIData(obj);
-				}
-			}
-		}
-		
-		// Get the list of clusters.
-		List<Cluster> clusters = null;
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			clusters = event.get(Cluster.class, clusterCollectionName);
-		}
-		
-		// Require that all collections be initialized.
-		if(sspBank == null || tiBank == null || clusters == null) {
-			return;
-		}
-		
-		// Track which triggers are active.
-		boolean[] activeTrigger = new boolean[5];
-		activeTrigger[PULSER] = tiBank.isPulserTrigger();
-		activeTrigger[SINGLES0] = tiBank.isSingle0Trigger();
-		activeTrigger[SINGLES1] = tiBank.isSingle1Trigger();
-		activeTrigger[PAIR0] = tiBank.isPair0Trigger();
-		activeTrigger[PAIR1] = tiBank.isPair1Trigger();
-		
-		// Plot all cluster properties for each trigger.
-		for(Cluster cluster : clusters) {
-			// Check whether the cluster is a fiducial or edge cluster.
-			int positional = inFiducialRegion(cluster) ? FIDUCIAL : EDGE;
-			
-			// Fill the appropriate plots for each trigger with an
-			// active trigger bit for single clusters.
-			for(int i = 0; i < 5; i++) {
-				if(activeTrigger[i]) {
-					// Populate the ALL plots.
-					clusterSeedEnergy[i][ALL].fill(TriggerModule.getValueClusterSeedEnergy(cluster));
-					clusterTotalEnergy[i][ALL].fill(cluster.getEnergy());
-					clusterHitCount[i][ALL].fill(TriggerModule.getClusterHitCount(cluster));
-					clusterTime[i][ALL].fill(TriggerModule.getClusterTime(cluster));
-					clusterSeedPosition[i][ALL].fill(TriggerModule.getClusterXIndex(cluster),
-							TriggerModule.getClusterYIndex(cluster));
-					
-					// Populate the positional plots.
-					clusterSeedEnergy[i][positional].fill(TriggerModule.getValueClusterSeedEnergy(cluster));
-					clusterTotalEnergy[i][positional].fill(cluster.getEnergy());
-					clusterHitCount[i][positional].fill(TriggerModule.getClusterHitCount(cluster));
-					clusterTime[i][positional].fill(TriggerModule.getClusterTime(cluster));
-					clusterSeedPosition[i][positional].fill(TriggerModule.getClusterXIndex(cluster),
-							TriggerModule.getClusterYIndex(cluster));
-				}
-			}
-		}
-		
-		// Plot all pair properties for each trigger.
-		List<Cluster[]> pairs = TriggerModule.getTopBottomPairs(clusters, Cluster.class);
-		for(Cluster[] pair : pairs) {
-			// Check whether the cluster is a fiducial or edge cluster.
-			boolean[] isFiducial = {
-					inFiducialRegion(pair[0]),
-					inFiducialRegion(pair[1])
-			};
-			int positional = (isFiducial[0] && isFiducial[1]) ? FIDUCIAL : EDGE;
-			
-			// Fill the appropriate plots for each trigger with an
-			// active trigger bit for single clusters.
-			for(int i = 0; i < 5; i++) {
-				if(activeTrigger[i]) {
-					// Calculate the values.
-					double energySum = TriggerModule.getValueEnergySum(pair);
-					double energyDiff = TriggerModule.getValueEnergyDifference(pair);
-					double energySlope = TriggerModule.getValueEnergySlope(pair, 0.00550);
-					double coplanarity = TriggerModule.getValueCoplanarity(pair);
-					double timeCoincidence = TriggerModule.getValueTimeCoincidence(pair);
-					
-					// Get the energy slope values.
-					Cluster lowCluster = pair[0].getEnergy() < pair[1].getEnergy() ? pair[0] : pair[1];
-					double clusterDistance = TriggerModule.getClusterDistance(lowCluster);
-					
-					// Populate the ALL plots.
-					pairEnergySum[i][ALL].fill(energySum);
-					pairEnergyDifference[i][ALL].fill(energyDiff);
-					pairEnergySlope[i][ALL].fill(energySlope);
-					pairCoplanarity[i][ALL].fill(coplanarity);
-					pairTimeCoincidence[i][ALL].fill(timeCoincidence);
-					pairEnergySum2D[i][ALL].fill(pair[0].getEnergy(), pair[1].getEnergy());
-					pairCoplanarityEnergySum[i][ALL].fill(energySum, coplanarity);
-					pairEnergySlope2D[i][ALL].fill(lowCluster.getEnergy(), clusterDistance);
-					
-					// Populate the positional plots.
-					pairEnergySum[i][positional].fill(energySum);
-					pairEnergyDifference[i][positional].fill(energyDiff);
-					pairEnergySlope[i][positional].fill(energySlope);
-					pairCoplanarity[i][positional].fill(coplanarity);
-					pairTimeCoincidence[i][positional].fill(timeCoincidence);
-					pairEnergySum2D[i][positional].fill(pair[0].getEnergy(), pair[1].getEnergy());
-					pairCoplanarityEnergySum[i][positional].fill(energySum, coplanarity);
-					pairEnergySlope2D[i][positional].fill(lowCluster.getEnergy(), clusterDistance);
-				}
-			}
-		}
-	}
-	
-	/**
-	 * Indicates whether the argument cluster is located in the fiducial
-	 * region or not.
-	 * @param cluster - The cluster to check.
-	 * @return Returns <code>true</code> if the cluster is located in
-	 * the fiducial region and <code>false</code> otherwise.
-	 */
-	private static final boolean inFiducialRegion(Cluster cluster) {
-		// Get the x and y indices for the cluster.
-		int ix   = TriggerModule.getClusterXIndex(cluster);
-		int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
-		int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
-		
-		// Check if the cluster is on the top or the bottom of the
-		// calorimeter, as defined by |y| == 5. This is an edge cluster
-		// and is not in the fiducial region.
-		if(absy == 5) {
-			return false;
-		}
-		
-		// Check if the cluster is on the extreme left or right side
-		// of the calorimeter, as defined by |x| == 23. This is also
-		// and edge cluster is not in the fiducial region.
-		if(absx == 23) {
-			return false;
-		}
-		
-		// Check if the cluster is along the beam gap, as defined by
-		// |y| == 1. This is an internal edge cluster and is not in the
-		// fiducial region.
-		if(absy == 1) {
-			return false;
-		}
-		
-		// Lastly, check if the cluster falls along the beam hole, as
-		// defined by clusters with -11 <= x <= -1 and |y| == 2. This
-		// is not the fiducial region.
-		if(absy == 2 && ix <= -1 && ix >= -11) {
-			return false;
-		}
-		
-		// If all checks fail, the cluster is in the fiducial region.
-		return true;
-	}
-	
-	/**
-	 * Sets the name of the LCIO collection containing the clusters
-	 * that are to be plotted.
-	 * @param collection - The LCIO collection name.
-	 */
-	public void setClusterCollectionName(String collection) {
-		clusterCollectionName = collection;
-	}
-	
-	/**
-	 * Defines the name of the LCIO collection containing the TI bank.
-	 * @param collection - The LCIO collection name.
-	 */
-	public void setBankCollectionName(String collection) {
-		bankCollectionName = collection;
-	}
-	
-	/**
-	 * Sets the name of the super-group folder containing all plots.
-	 * @param name - The name of the plots folder.
-	 */
-	public void setPlotsGroupName(String name) {
-		plotsGroupName = name;
-	}
+                        + positionNames[j] + "/Pair Energy Slope 2D", 75, 0.000, 1.500, 100, 0.0, 400.0);
+            }
+        }
+    }
+    
+    /**
+     * Processes the event clusters and populates distribution charts
+     * from them for each trigger. Also creates separate plots for the
+     * edge and fiducial regions.
+     * @param event - The event containing LCIO collections to be used
+     * for plot population.
+     */
+    @Override
+    public void process(EventHeader event) {
+        // Get the TI and SSP banks.
+        TIData tiBank = null;
+        SSPData sspBank = null;
+        if(event.hasCollection(GenericObject.class, bankCollectionName)) {
+            // Get the bank list.
+            List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+            
+            // Search through the banks and get the SSP and TI banks.
+            for(GenericObject obj : bankList) {
+                // If this is an SSP bank, parse it.
+                if(AbstractIntData.getTag(obj) == SSPData.BANK_TAG) {
+                    sspBank = new SSPData(obj);
+                }
+                
+                // Otherwise, if this is a TI bank, parse it.
+                else if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
+                    tiBank = new TIData(obj);
+                }
+            }
+        }
+        
+        // Get the list of clusters.
+        List<Cluster> clusters = null;
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            clusters = event.get(Cluster.class, clusterCollectionName);
+        }
+        
+        // Require that all collections be initialized.
+        if(sspBank == null || tiBank == null || clusters == null) {
+            return;
+        }
+        
+        // Track which triggers are active.
+        boolean[] activeTrigger = new boolean[5];
+        activeTrigger[PULSER] = tiBank.isPulserTrigger();
+        activeTrigger[SINGLES0] = tiBank.isSingle0Trigger();
+        activeTrigger[SINGLES1] = tiBank.isSingle1Trigger();
+        activeTrigger[PAIR0] = tiBank.isPair0Trigger();
+        activeTrigger[PAIR1] = tiBank.isPair1Trigger();
+        
+        // Plot all cluster properties for each trigger.
+        for(Cluster cluster : clusters) {
+            // Check whether the cluster is a fiducial or edge cluster.
+            int positional = inFiducialRegion(cluster) ? FIDUCIAL : EDGE;
+            
+            // Fill the appropriate plots for each trigger with an
+            // active trigger bit for single clusters.
+            for(int i = 0; i < 5; i++) {
+                if(activeTrigger[i]) {
+                    // Populate the ALL plots.
+                    clusterSeedEnergy[i][ALL].fill(TriggerModule.getValueClusterSeedEnergy(cluster));
+                    clusterTotalEnergy[i][ALL].fill(cluster.getEnergy());
+                    clusterHitCount[i][ALL].fill(TriggerModule.getClusterHitCount(cluster));
+                    clusterTime[i][ALL].fill(TriggerModule.getClusterTime(cluster));
+                    clusterSeedPosition[i][ALL].fill(TriggerModule.getClusterXIndex(cluster),
+                            TriggerModule.getClusterYIndex(cluster));
+                    
+                    // Populate the positional plots.
+                    clusterSeedEnergy[i][positional].fill(TriggerModule.getValueClusterSeedEnergy(cluster));
+                    clusterTotalEnergy[i][positional].fill(cluster.getEnergy());
+                    clusterHitCount[i][positional].fill(TriggerModule.getClusterHitCount(cluster));
+                    clusterTime[i][positional].fill(TriggerModule.getClusterTime(cluster));
+                    clusterSeedPosition[i][positional].fill(TriggerModule.getClusterXIndex(cluster),
+                            TriggerModule.getClusterYIndex(cluster));
+                }
+            }
+        }
+        
+        // Plot all pair properties for each trigger.
+        List<Cluster[]> pairs = TriggerModule.getTopBottomPairs(clusters, Cluster.class);
+        for(Cluster[] pair : pairs) {
+            // Check whether the cluster is a fiducial or edge cluster.
+            boolean[] isFiducial = {
+                    inFiducialRegion(pair[0]),
+                    inFiducialRegion(pair[1])
+            };
+            int positional = (isFiducial[0] && isFiducial[1]) ? FIDUCIAL : EDGE;
+            
+            // Fill the appropriate plots for each trigger with an
+            // active trigger bit for single clusters.
+            for(int i = 0; i < 5; i++) {
+                if(activeTrigger[i]) {
+                    // Calculate the values.
+                    double energySum = TriggerModule.getValueEnergySum(pair);
+                    double energyDiff = TriggerModule.getValueEnergyDifference(pair);
+                    double energySlope = TriggerModule.getValueEnergySlope(pair, 0.00550);
+                    double coplanarity = TriggerModule.getValueCoplanarity(pair);
+                    double timeCoincidence = TriggerModule.getValueTimeCoincidence(pair);
+                    
+                    // Get the energy slope values.
+                    Cluster lowCluster = pair[0].getEnergy() < pair[1].getEnergy() ? pair[0] : pair[1];
+                    double clusterDistance = TriggerModule.getClusterDistance(lowCluster);
+                    
+                    // Populate the ALL plots.
+                    pairEnergySum[i][ALL].fill(energySum);
+                    pairEnergyDifference[i][ALL].fill(energyDiff);
+                    pairEnergySlope[i][ALL].fill(energySlope);
+                    pairCoplanarity[i][ALL].fill(coplanarity);
+                    pairTimeCoincidence[i][ALL].fill(timeCoincidence);
+                    pairEnergySum2D[i][ALL].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                    pairCoplanarityEnergySum[i][ALL].fill(energySum, coplanarity);
+                    pairEnergySlope2D[i][ALL].fill(lowCluster.getEnergy(), clusterDistance);
+                    
+                    // Populate the positional plots.
+                    pairEnergySum[i][positional].fill(energySum);
+                    pairEnergyDifference[i][positional].fill(energyDiff);
+                    pairEnergySlope[i][positional].fill(energySlope);
+                    pairCoplanarity[i][positional].fill(coplanarity);
+                    pairTimeCoincidence[i][positional].fill(timeCoincidence);
+                    pairEnergySum2D[i][positional].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                    pairCoplanarityEnergySum[i][positional].fill(energySum, coplanarity);
+                    pairEnergySlope2D[i][positional].fill(lowCluster.getEnergy(), clusterDistance);
+                }
+            }
+        }
+    }
+    
+    /**
+     * Indicates whether the argument cluster is located in the fiducial
+     * region or not.
+     * @param cluster - The cluster to check.
+     * @return Returns <code>true</code> if the cluster is located in
+     * the fiducial region and <code>false</code> otherwise.
+     */
+    private static final boolean inFiducialRegion(Cluster cluster) {
+        // Get the x and y indices for the cluster.
+        int ix   = TriggerModule.getClusterXIndex(cluster);
+        int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
+        int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
+        
+        // Check if the cluster is on the top or the bottom of the
+        // calorimeter, as defined by |y| == 5. This is an edge cluster
+        // and is not in the fiducial region.
+        if(absy == 5) {
+            return false;
+        }
+        
+        // Check if the cluster is on the extreme left or right side
+        // of the calorimeter, as defined by |x| == 23. This is also
+        // and edge cluster is not in the fiducial region.
+        if(absx == 23) {
+            return false;
+        }
+        
+        // Check if the cluster is along the beam gap, as defined by
+        // |y| == 1. This is an internal edge cluster and is not in the
+        // fiducial region.
+        if(absy == 1) {
+            return false;
+        }
+        
+        // Lastly, check if the cluster falls along the beam hole, as
+        // defined by clusters with -11 <= x <= -1 and |y| == 2. This
+        // is not the fiducial region.
+        if(absy == 2 && ix <= -1 && ix >= -11) {
+            return false;
+        }
+        
+        // If all checks fail, the cluster is in the fiducial region.
+        return true;
+    }
+    
+    /**
+     * Sets the name of the LCIO collection containing the clusters
+     * that are to be plotted.
+     * @param collection - The LCIO collection name.
+     */
+    public void setClusterCollectionName(String collection) {
+        clusterCollectionName = collection;
+    }
+    
+    /**
+     * Defines the name of the LCIO collection containing the TI bank.
+     * @param collection - The LCIO collection name.
+     */
+    public void setBankCollectionName(String collection) {
+        bankCollectionName = collection;
+    }
+    
+    /**
+     * Sets the name of the super-group folder containing all plots.
+     * @param name - The name of the plots folder.
+     */
+    public void setPlotsGroupName(String name) {
+        plotsGroupName = name;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/InvariantMassPairDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/InvariantMassPairDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/InvariantMassPairDriver.java	Wed Apr 27 11:11:32 2016
@@ -15,255 +15,255 @@
 import org.lcsim.util.aida.AIDA;
 
 public class InvariantMassPairDriver extends Driver {
-	private int[] events = new int[3];
-	private TriggerModule[] trigger = new TriggerModule[2];
-	
-	private String gtpClusterCollectionName = "EcalClustersGTP";
-	private String particleCollectionName = "FinalStateParticles";
-	private String reconParticleCollectionName = "UnconstrainedV0Candidates";
-	
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D electronEnergyHist = aida.histogram1D("Trident Analysis/Electron Energy", 150, 0.000, 1.500);
-	private IHistogram1D positronEnergyHist = aida.histogram1D("Trident Analysis/Positron Energy", 150, 0.000, 1.500);
-	private IHistogram1D pairEnergyHist = aida.histogram1D("Trident Analysis/Energy Sum Distribution", 220, 0.00, 2.200);
-	private IHistogram2D pair2DEnergyHist = aida.histogram2D("Trident Analysis/2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1);
-	private IHistogram1D pair1MassHist = aida.histogram1D("Trident Analysis/Particle Invariant Mass (1 Hit)", 240, 0.000, 0.120);
-	private IHistogram1D pair1ModMassHist = aida.histogram1D("Trident Analysis/Particle Invariant Mass (2 Hit)", 240, 0.000, 0.120);
-	private IHistogram1D elasticElectronEnergyHist = aida.histogram1D("Trident Analysis/Trident Electron Energy", 150, 0.000, 1.500);
-	private IHistogram1D elasticPositronEnergyHist = aida.histogram1D("Trident Analysis/Trident Positron Energy", 150, 0.000, 1.500);
-	
-	@Override
-	public void startOfData() {
-		// Instantiate the pair 1 trigger.
-		trigger[0] = new TriggerModule();
-		trigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
-		trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.054);
-		trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   0.630);
-		trigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 0.540);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.180);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        0.860);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.600);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         0.0055);
-		trigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       12);
-		
-		// Instantiate the pair 1 trigger with a hit count cut of two.
-		trigger[1] = new TriggerModule();
-		trigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       2);
-		trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.054);
-		trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   0.630);
-		trigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 0.540);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.180);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        0.860);
-		trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.600);
-		trigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         0.0055);
-		trigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       12);
-	}
-	
-	@Override
-	public void endOfData() {
-		System.out.printf("Pair 1     :: %d / %d%n", events[0], events[2]);
-		System.out.printf("Pair 1 Mod :: %d / %d%n", events[1], events[2]);
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Skip the event if there is no reconstructed particle list.
-		if(!event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
-			return;
-		}
-		
-		// Get a list of all tracks in the event.
-		List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
-		
-		// Plot the energies of the electrons and positrons.
-		for(ReconstructedParticle track : trackList) {
-			// Positive tracks are assumed to be positrons.
-			if(track.getCharge() > 0) {
-				positronEnergyHist.fill(track.getMomentum().magnitude());
-			}
-			
-			// Negative tracks are assumed to be electrons.
-			else if(track.getCharge() < 0) {
-				electronEnergyHist.fill(track.getMomentum().magnitude());
-			}
-		}
-		
-		// Get track pairs.
-		List<ReconstructedParticle[]> trackPairList = getTrackPairs(trackList);
-		
-		// Populate the pair plots.
-		trackPairLoop:
-		for(ReconstructedParticle[] trackPair : trackPairList) {
-			// Note the polarity of the tracks.
-			boolean[] trackIsPositive = {
-					trackPair[0].getCharge() > 0,
-					trackPair[1].getCharge() > 0
-			};
-			
-			// Require that one track be positive and one be negative.
-			if(!(trackIsPositive[0] ^ trackIsPositive[1])) {
-				continue trackPairLoop;
-			}
-			
-			// Populate the track pair plots.
-			pairEnergyHist.fill(VecOp.add(trackPair[0].getMomentum(), trackPair[1].getMomentum()).magnitude());
-			if(trackIsPositive[0]) {
-				pair2DEnergyHist.fill(trackPair[0].getMomentum().magnitude(), trackPair[1].getMomentum().magnitude());
-			} else {
-				pair2DEnergyHist.fill(trackPair[1].getMomentum().magnitude(), trackPair[0].getMomentum().magnitude());
-			}
-		}
-		
-		// Check that the event has a collection of GTP clusters.
-		if(!event.hasCollection(Cluster.class, gtpClusterCollectionName)) {
-			return;
-		}
-		
-		// Increment the total event count.
-		events[2]++;
-		
-		// Get the GTP clusters.
-		List<Cluster> clusters = event.get(Cluster.class, gtpClusterCollectionName);
-		
-		// Get the list of top/bottom pairs.
-		List<Cluster[]> pairs = getClusterPairs(clusters);
-		
-		// Iterate over the pairs and determine if any cluster passes
-		// pair 1 trigger or the pair 1 modified trigger.
-		boolean passedPair1 = false;
-		boolean passedPair1Mod = false;
-		pairLoop:
-		for(Cluster[] pair : pairs) {
-			// Check the cluster energy cut.
-			if(!trigger[0].clusterTotalEnergyCut(pair[0])) { continue pairLoop; }
-			if(!trigger[0].clusterTotalEnergyCut(pair[1])) { continue pairLoop; }
-			
-			// Check the pair cuts.
-			if(!trigger[0].pairCoplanarityCut(pair)) { continue pairLoop; }
-			if(!trigger[0].pairEnergyDifferenceCut(pair)) { continue pairLoop; }
-			if(!trigger[0].pairEnergySumCut(pair)) { continue pairLoop; }
-			if(!trigger[0].pairEnergySlopeCut(pair)) { continue pairLoop; }
-			
-			// Check if the pair passes the singles 0 hit count cut.
-			if(trigger[0].clusterHitCountCut(pair[0]) && trigger[0].clusterHitCountCut(pair[1])) {
-				// Note that a pair passed the pair 1 trigger.
-				passedPair1 = true;
-				
-				// Check whether the pair passed the modified pair 1
-				// trigger hit count cut.
-				if(trigger[1].clusterHitCountCut(pair[0]) && trigger[1].clusterHitCountCut(pair[1])) {
-					passedPair1Mod = true;
-				}
-			} else { continue pairLoop; }
-		}
-		
-		// If no pair passed the pair 1 cut, nothing further need be done.
-		if(!passedPair1) { return; }
-		
-		// Otherwise, increment the "passed pair 1" count and the
-		// "passed pair 1 mod" count, if appropriate.
-		events[0]++;
-		if(passedPair1Mod) { events[1]++; }
-		
-		// Get the collection of reconstructed V0 candidates.
-		List<ReconstructedParticle> candidateList = event.get(ReconstructedParticle.class, reconParticleCollectionName);
-		
-		// Populate the invariant mass plot.
-		candidateLoop:
-		for(ReconstructedParticle particle : candidateList) {
-			// Track the electron and positron momenta.
-			double electronMomentum = 0.0;
-			double positronMomentum = 0.0;
-			
-			// Check that it has component particles that meet the
-			// trident condition.
-			boolean seenPositive = false;
-			boolean seenNegative = false;
-			for(ReconstructedParticle track : particle.getParticles()) {
-				// Exactly one track must be negative. Its energy is
-				// disallowed from exceeding 900 MeV.
-				if(track.getCharge() < 0) {
-					// Reject a second negative particle.
-					if(seenNegative) { continue candidateLoop; }
-					
-					// Otherwise, note that one has been seen.
-					seenNegative = true;
-					electronMomentum = track.getMomentum().magnitude();
-					
-					// Reject electrons with a momentum exceeding 900 MeV.
-					if(track.getMomentum().magnitude() > 0.900) {
-						continue candidateLoop;
-					}
-				}
-				
-				// Exactly one track must be positive. Its energy is
-				// not constrained.
-				else if(track.getCharge() > 0) {
-					// Reject a second positive particle.
-					if(seenPositive) { continue candidateLoop; }
-					
-					// Otherwise, note that one has been seen.
-					seenPositive = true;
-					positronMomentum = track.getMomentum().magnitude();
-				}
-				
-				// Lastly, reject any particle that produced a photon.
-				else { continue candidateLoop; }
-			}
-			
-			// Populate the plots.
-			pair1MassHist.fill(particle.getMass());
-			elasticElectronEnergyHist.fill(electronMomentum);
-			elasticPositronEnergyHist.fill(positronMomentum);
-			if(passedPair1Mod) { pair1ModMassHist.fill(particle.getMass()); }
-		}
-	}
-	
-	/**
-	 * Creates a list of top/bottom cluster pairs.
-	 * @param clusters - A <code>List</code> collection of objects of
-	 * type <code>Cluster</code>.
-	 * @return Returns a <code>List</code> collection of 2-entry arrays
-	 * of <code>Cluster</code> objects representing top/bottom cluster
-	 * pairs. The first entry is always the top cluster.
-	 */
-	private static final List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
-		// Separate the clusters into top and bottom clusters.
-		List<Cluster> topList = new ArrayList<Cluster>();
-		List<Cluster> botList = new ArrayList<Cluster>();
-		for(Cluster cluster : clusters) {
-			if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
-				topList.add(cluster);
-			}
-			else { botList.add(cluster); }
-		}
-		
-		// Create a list of all top/bottom pairs.
-		List<Cluster[]> pairs = new ArrayList<Cluster[]>();
-		for(Cluster topCluster : topList) {
-			for(Cluster botCluster : botList) {
-				pairs.add(new Cluster[] { topCluster, botCluster });
-			}
-		}
-		
-		// Return the list of cluster pairs.
-		return pairs;
-	}
-	
-	private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> trackList) {
-		// Create an empty list for the pairs.
-		List<ReconstructedParticle[]> pairs = new ArrayList<ReconstructedParticle[]>();
-		
-		// Add all possible pairs of tracks.
-		for(int i = 0; i < trackList.size(); i++) {
-			for(int j = i + 1; j < trackList.size(); j++) {
-				pairs.add(new ReconstructedParticle[] { trackList.get(i), trackList.get(j) });
-			}
-		}
-		
-		// Return the list of tracks.
-		return pairs;
-	}
+    private int[] events = new int[3];
+    private TriggerModule[] trigger = new TriggerModule[2];
+    
+    private String gtpClusterCollectionName = "EcalClustersGTP";
+    private String particleCollectionName = "FinalStateParticles";
+    private String reconParticleCollectionName = "UnconstrainedV0Candidates";
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D electronEnergyHist = aida.histogram1D("Trident Analysis/Electron Energy", 150, 0.000, 1.500);
+    private IHistogram1D positronEnergyHist = aida.histogram1D("Trident Analysis/Positron Energy", 150, 0.000, 1.500);
+    private IHistogram1D pairEnergyHist = aida.histogram1D("Trident Analysis/Energy Sum Distribution", 220, 0.00, 2.200);
+    private IHistogram2D pair2DEnergyHist = aida.histogram2D("Trident Analysis/2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1);
+    private IHistogram1D pair1MassHist = aida.histogram1D("Trident Analysis/Particle Invariant Mass (1 Hit)", 240, 0.000, 0.120);
+    private IHistogram1D pair1ModMassHist = aida.histogram1D("Trident Analysis/Particle Invariant Mass (2 Hit)", 240, 0.000, 0.120);
+    private IHistogram1D elasticElectronEnergyHist = aida.histogram1D("Trident Analysis/Trident Electron Energy", 150, 0.000, 1.500);
+    private IHistogram1D elasticPositronEnergyHist = aida.histogram1D("Trident Analysis/Trident Positron Energy", 150, 0.000, 1.500);
+    
+    @Override
+    public void startOfData() {
+        // Instantiate the pair 1 trigger.
+        trigger[0] = new TriggerModule();
+        trigger[0].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       1);
+        trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.054);
+        trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   0.630);
+        trigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 0.540);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.180);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        0.860);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.600);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         0.0055);
+        trigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       12);
+        
+        // Instantiate the pair 1 trigger with a hit count cut of two.
+        trigger[1] = new TriggerModule();
+        trigger[1].setCutValue(TriggerModule.CLUSTER_HIT_COUNT_LOW,       2);
+        trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_LOW,    0.054);
+        trigger[0].setCutValue(TriggerModule.CLUSTER_TOTAL_ENERGY_HIGH,   0.630);
+        trigger[0].setCutValue(TriggerModule.PAIR_COPLANARITY_HIGH,       30);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_DIFFERENCE_HIGH, 0.540);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_LOW,         0.180);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SUM_HIGH,        0.860);
+        trigger[0].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_LOW,       0.600);
+        trigger[1].setCutValue(TriggerModule.PAIR_ENERGY_SLOPE_F,         0.0055);
+        trigger[0].setCutValue(TriggerModule.PAIR_TIME_COINCIDENCE,       12);
+    }
+    
+    @Override
+    public void endOfData() {
+        System.out.printf("Pair 1     :: %d / %d%n", events[0], events[2]);
+        System.out.printf("Pair 1 Mod :: %d / %d%n", events[1], events[2]);
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Skip the event if there is no reconstructed particle list.
+        if(!event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
+            return;
+        }
+        
+        // Get a list of all tracks in the event.
+        List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
+        
+        // Plot the energies of the electrons and positrons.
+        for(ReconstructedParticle track : trackList) {
+            // Positive tracks are assumed to be positrons.
+            if(track.getCharge() > 0) {
+                positronEnergyHist.fill(track.getMomentum().magnitude());
+            }
+            
+            // Negative tracks are assumed to be electrons.
+            else if(track.getCharge() < 0) {
+                electronEnergyHist.fill(track.getMomentum().magnitude());
+            }
+        }
+        
+        // Get track pairs.
+        List<ReconstructedParticle[]> trackPairList = getTrackPairs(trackList);
+        
+        // Populate the pair plots.
+        trackPairLoop:
+        for(ReconstructedParticle[] trackPair : trackPairList) {
+            // Note the polarity of the tracks.
+            boolean[] trackIsPositive = {
+                    trackPair[0].getCharge() > 0,
+                    trackPair[1].getCharge() > 0
+            };
+            
+            // Require that one track be positive and one be negative.
+            if(!(trackIsPositive[0] ^ trackIsPositive[1])) {
+                continue trackPairLoop;
+            }
+            
+            // Populate the track pair plots.
+            pairEnergyHist.fill(VecOp.add(trackPair[0].getMomentum(), trackPair[1].getMomentum()).magnitude());
+            if(trackIsPositive[0]) {
+                pair2DEnergyHist.fill(trackPair[0].getMomentum().magnitude(), trackPair[1].getMomentum().magnitude());
+            } else {
+                pair2DEnergyHist.fill(trackPair[1].getMomentum().magnitude(), trackPair[0].getMomentum().magnitude());
+            }
+        }
+        
+        // Check that the event has a collection of GTP clusters.
+        if(!event.hasCollection(Cluster.class, gtpClusterCollectionName)) {
+            return;
+        }
+        
+        // Increment the total event count.
+        events[2]++;
+        
+        // Get the GTP clusters.
+        List<Cluster> clusters = event.get(Cluster.class, gtpClusterCollectionName);
+        
+        // Get the list of top/bottom pairs.
+        List<Cluster[]> pairs = getClusterPairs(clusters);
+        
+        // Iterate over the pairs and determine if any cluster passes
+        // pair 1 trigger or the pair 1 modified trigger.
+        boolean passedPair1 = false;
+        boolean passedPair1Mod = false;
+        pairLoop:
+        for(Cluster[] pair : pairs) {
+            // Check the cluster energy cut.
+            if(!trigger[0].clusterTotalEnergyCut(pair[0])) { continue pairLoop; }
+            if(!trigger[0].clusterTotalEnergyCut(pair[1])) { continue pairLoop; }
+            
+            // Check the pair cuts.
+            if(!trigger[0].pairCoplanarityCut(pair)) { continue pairLoop; }
+            if(!trigger[0].pairEnergyDifferenceCut(pair)) { continue pairLoop; }
+            if(!trigger[0].pairEnergySumCut(pair)) { continue pairLoop; }
+            if(!trigger[0].pairEnergySlopeCut(pair)) { continue pairLoop; }
+            
+            // Check if the pair passes the singles 0 hit count cut.
+            if(trigger[0].clusterHitCountCut(pair[0]) && trigger[0].clusterHitCountCut(pair[1])) {
+                // Note that a pair passed the pair 1 trigger.
+                passedPair1 = true;
+                
+                // Check whether the pair passed the modified pair 1
+                // trigger hit count cut.
+                if(trigger[1].clusterHitCountCut(pair[0]) && trigger[1].clusterHitCountCut(pair[1])) {
+                    passedPair1Mod = true;
+                }
+            } else { continue pairLoop; }
+        }
+        
+        // If no pair passed the pair 1 cut, nothing further need be done.
+        if(!passedPair1) { return; }
+        
+        // Otherwise, increment the "passed pair 1" count and the
+        // "passed pair 1 mod" count, if appropriate.
+        events[0]++;
+        if(passedPair1Mod) { events[1]++; }
+        
+        // Get the collection of reconstructed V0 candidates.
+        List<ReconstructedParticle> candidateList = event.get(ReconstructedParticle.class, reconParticleCollectionName);
+        
+        // Populate the invariant mass plot.
+        candidateLoop:
+        for(ReconstructedParticle particle : candidateList) {
+            // Track the electron and positron momenta.
+            double electronMomentum = 0.0;
+            double positronMomentum = 0.0;
+            
+            // Check that it has component particles that meet the
+            // trident condition.
+            boolean seenPositive = false;
+            boolean seenNegative = false;
+            for(ReconstructedParticle track : particle.getParticles()) {
+                // Exactly one track must be negative. Its energy is
+                // disallowed from exceeding 900 MeV.
+                if(track.getCharge() < 0) {
+                    // Reject a second negative particle.
+                    if(seenNegative) { continue candidateLoop; }
+                    
+                    // Otherwise, note that one has been seen.
+                    seenNegative = true;
+                    electronMomentum = track.getMomentum().magnitude();
+                    
+                    // Reject electrons with a momentum exceeding 900 MeV.
+                    if(track.getMomentum().magnitude() > 0.900) {
+                        continue candidateLoop;
+                    }
+                }
+                
+                // Exactly one track must be positive. Its energy is
+                // not constrained.
+                else if(track.getCharge() > 0) {
+                    // Reject a second positive particle.
+                    if(seenPositive) { continue candidateLoop; }
+                    
+                    // Otherwise, note that one has been seen.
+                    seenPositive = true;
+                    positronMomentum = track.getMomentum().magnitude();
+                }
+                
+                // Lastly, reject any particle that produced a photon.
+                else { continue candidateLoop; }
+            }
+            
+            // Populate the plots.
+            pair1MassHist.fill(particle.getMass());
+            elasticElectronEnergyHist.fill(electronMomentum);
+            elasticPositronEnergyHist.fill(positronMomentum);
+            if(passedPair1Mod) { pair1ModMassHist.fill(particle.getMass()); }
+        }
+    }
+    
+    /**
+     * Creates a list of top/bottom cluster pairs.
+     * @param clusters - A <code>List</code> collection of objects of
+     * type <code>Cluster</code>.
+     * @return Returns a <code>List</code> collection of 2-entry arrays
+     * of <code>Cluster</code> objects representing top/bottom cluster
+     * pairs. The first entry is always the top cluster.
+     */
+    private static final List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
+        // Separate the clusters into top and bottom clusters.
+        List<Cluster> topList = new ArrayList<Cluster>();
+        List<Cluster> botList = new ArrayList<Cluster>();
+        for(Cluster cluster : clusters) {
+            if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
+                topList.add(cluster);
+            }
+            else { botList.add(cluster); }
+        }
+        
+        // Create a list of all top/bottom pairs.
+        List<Cluster[]> pairs = new ArrayList<Cluster[]>();
+        for(Cluster topCluster : topList) {
+            for(Cluster botCluster : botList) {
+                pairs.add(new Cluster[] { topCluster, botCluster });
+            }
+        }
+        
+        // Return the list of cluster pairs.
+        return pairs;
+    }
+    
+    private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> trackList) {
+        // Create an empty list for the pairs.
+        List<ReconstructedParticle[]> pairs = new ArrayList<ReconstructedParticle[]>();
+        
+        // Add all possible pairs of tracks.
+        for(int i = 0; i < trackList.size(); i++) {
+            for(int j = i + 1; j < trackList.size(); j++) {
+                pairs.add(new ReconstructedParticle[] { trackList.get(i), trackList.get(j) });
+            }
+        }
+        
+        // Return the list of tracks.
+        return pairs;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTEAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTEAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTEAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -24,145 +24,145 @@
 import org.lcsim.util.aida.AIDA;
 
 public class MTEAnalysis extends Driver {
-	// Define track LCIO information.
-	private boolean skipBadSVT = true;
-	private String bankCollectionName = "TriggerBank";
-	private String particleCollectionName = "FinalStateParticles";
-	private static final AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D[] chargedTracksPlot = {
-			aida.histogram1D("MTE Analysis/Møller Event Tracks", 10, -0.5, 9.5),
-			aida.histogram1D("MTE Analysis/Trident Event Tracks", 10, -0.5, 9.5),
-			aida.histogram1D("MTE Analysis/Elastic Event Tracks", 10, -0.5, 9.5)
-	};
-	private IHistogram1D[] clusterCountPlot = {
-			aida.histogram1D("MTE Analysis/Møller Event Clusters", 10, -0.5, 9.5),
-			aida.histogram1D("MTE Analysis/Trident Event Clusters", 10, -0.5, 9.5),
-			aida.histogram1D("MTE Analysis/Elastic Event Clusters", 10, -0.5, 9.5)
-	};
-	private IHistogram1D[] energyPlot = {
-			aida.histogram1D("MTE Analysis/Møller Energy Sum Distribution", 220, 0, 2.2),
-			aida.histogram1D("MTE Analysis/Trident Energy Sum Distribution", 220, 0, 2.2),
-			aida.histogram1D("MTE Analysis/Elastic Energy Distribution", 110, 0, 1.5)
-	};
-	private IHistogram1D[] electronPlot = {
-			aida.histogram1D("MTE Analysis/Møller Electron Energy Distribution", 220, 0, 2.2),
-			aida.histogram1D("MTE Analysis/Trident Electron Energy Distribution", 220, 0, 2.2),
-	};
-	private IHistogram1D positronPlot = aida.histogram1D("MTE Analysis/Trident Positron Energy Distribution", 220, 0, 2.2);
-	private IHistogram2D[] energy2DPlot = {
-			aida.histogram2D("MTE Analysis/Møller 2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1),
-			aida.histogram2D("MTE Analysis/Trident 2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1),
-	};
-	private IHistogram1D timePlot = aida.histogram1D("MTE Analysis/Track Cluster Time Distribution", 4000, 0, 400);
-	private IHistogram1D timeCoincidencePlot = aida.histogram1D("MTE Analysis/Møller Time Coincidence Distribution", 1000, 0, 100);
-	private IHistogram1D timeCoincidenceAllCutsPlot = aida.histogram1D("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)", 1000, 0, 100);
-	private IHistogram1D negTrackCount = aida.histogram1D("MTE Analysis/All Negative Tracks", 10, -0.5, 9.5);
-	private IHistogram1D posTrackCount = aida.histogram1D("MTE Analysis/All Positive Event Tracks", 10, -0.5, 9.5);
-	private IHistogram1D chargedTrackCount = aida.histogram1D("MTE Analysis/All Event Event Tracks", 10, -0.5, 9.5);
-	
-	private IHistogram1D trInvariantMassAll            = aida.histogram1D("Trident/Invariant Mass",                     1500,   0.0,  1.5);
-	private IHistogram1D trInvariantMassFiducial       = aida.histogram1D("Trident/Invariant Mass (Fiducial Region)",   1500,   0.0,  1.5);
-	private IHistogram1D trTimeCoincidenceAll          = aida.histogram1D("Trident/Time Coincidence",                    300, -15.0, 15.0);
-	private IHistogram1D trTimeCoincidenceFiducial     = aida.histogram1D("Trident/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
-	private IHistogram1D trEnergySumAll                = aida.histogram1D("Trident/Energy Sum",                          300,   0.0,  1.5);
-	private IHistogram1D trEnergySumFiducial           = aida.histogram1D("Trident/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
-	private IHistogram2D trEnergySum2DAll              = aida.histogram2D("Trident/First Cluster Energy vs. Second Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D trEnergySum2DFiducial         = aida.histogram2D("Trident/First Cluster Energy vs. Second Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D trSumCoplanarityAll           = aida.histogram2D("Trident/Hardware Coplanarity vs. Energy Sum",                              300, 0, 1.5, 115,   0, 180);
-	private IHistogram2D trSumCoplanarityFiducial      = aida.histogram2D("Trident/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",            300, 0, 1.5, 115,   0, 180);
-	private IHistogram2D trSumCoplanarityCalcAll       = aida.histogram2D("Trident/Calculated Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D trSumCoplanarityCalcFiducial  = aida.histogram2D("Trident/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D trTimeEnergyAll               = aida.histogram2D("Trident/Cluster Time vs. Cluster Energy",                                  300, 0, 1.5, 100,   0, 100);
-	private IHistogram2D trTimeEnergyFiducial          = aida.histogram2D("Trident/Cluster Time vs. Cluster Energy (Fiducial Region)",                300, 0, 1.5, 100,   0, 100);
-	
-	private TriggerPlotsModule allPlots = new TriggerPlotsModule("All");
-	private TriggerPlotsModule møllerPlots = new TriggerPlotsModule("Møller");
-	private TriggerPlotsModule tridentPlots = new TriggerPlotsModule("Trident");
-	private TriggerPlotsModule elasticPlots = new TriggerPlotsModule("Elastic");
-	private static final int MØLLER  = 0;
-	private static final int TRIDENT = 1;
-	private static final int ELASTIC = 2;
-	private boolean verbose = false;
-	private boolean excludeNoTrackEvents = false;
-	private double timeCoincidenceCut = Double.MAX_VALUE;
-	private Map<String, Integer> møllerBitMap = new HashMap<String, Integer>();
-	private Map<String, Integer> tridentBitMap = new HashMap<String, Integer>();
-	private Map<String, Integer> elasticBitMap = new HashMap<String, Integer>();
-	private int møllerEvents = 0;
-	private int tridentEvents = 0;
-	private int elasticEvents = 0;
-	private int totalEvents = 0;
-	private int pair1Events = 0;
-	private int pair0Events = 0;
-	private int singles1Events = 0;
-	private int singles0Events = 0;
-	private int pulserEvents = 0;
-	
-	@Override
-	public void startOfData() {
-		for(int s0 = 0; s0 <= 1; s0++) {
-			for(int s1 = 0; s1 <= 1; s1++) {
-				for(int p0 = 0; p0 <= 1; p0++) {
-					for(int p1 = 0; p1 <= 1; p1++) {
-						for(int pulser = 0; pulser <=1; pulser++) {
-							// Set each "trigger bit."
-							boolean s0bit = (s0 == 1);
-							boolean s1bit = (s1 == 1);
-							boolean p0bit = (p0 == 1);
-							boolean p1bit = (p1 == 1);
-							boolean pulserBit = (p1 == 1);
-							
-							// Generate the bit string.
-							String bitString = getBitString(s0bit, s1bit, p0bit, p1bit, pulserBit);
-							
-							// Set a default value of zero for this bit combination.
-							møllerBitMap.put(bitString, 1);
-							tridentBitMap.put(bitString, 1);
-							elasticBitMap.put(bitString, 1);
-						}
-					}
-				}
-			}
-		}
-	}
-	
-	@Override
-	public void endOfData() {
-		System.out.println("Møller  Events   :: " + møllerEvents);
-		System.out.println("Trident Events   :: " + tridentEvents);
-		System.out.println("Elastic Events   :: " + elasticEvents);
-		System.out.println("Total Events     :: " + totalEvents);
-		System.out.println("Pair 1 Events    :: " + pair1Events);
-		System.out.println("Pair 0 Events    :: " + pair0Events);
-		System.out.println("Singles 1 Events :: " + singles1Events);
-		System.out.println("Singles 0 Events :: " + singles0Events);
-		System.out.println("Pulser Events    :: " + pulserEvents);
-		
-		System.out.println("Plsr\tS0\tS1\tP0\tP1\tMøller");
-		for(Entry<String, Integer> entry : møllerBitMap.entrySet()) {
-			System.out.println(entry.getKey() + "\t" + entry.getValue());
-		}
-		
-		System.out.println("Plsr\tS0\tS1\tP0\tP1\tTrident");
-		for(Entry<String, Integer> entry : tridentBitMap.entrySet()) {
-			System.out.println(entry.getKey() + "\t" + entry.getValue());
-		}
-		
-		System.out.println("Plsr\tS0\tS1\tP0\tP1\tElastic");
-		for(Entry<String, Integer> entry : elasticBitMap.entrySet()) {
-			System.out.println(entry.getKey() + "\t" + entry.getValue());
-		}
-	}
-	
-	private static final String getBitString(boolean s0, boolean s1, boolean p0, boolean p1, boolean pulser) {
-		return String.format("%d\t%d\t%d\t%d\t%d", (pulser ? 1 : 0), (s0 ? 1 : 0), (s1 ? 1 : 0), (p0 ? 1 : 0), (p1 ? 1 : 0));
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Check whether the SVT was active in this event.
-		final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
-		boolean svtGood = true;
+    // Define track LCIO information.
+    private boolean skipBadSVT = true;
+    private String bankCollectionName = "TriggerBank";
+    private String particleCollectionName = "FinalStateParticles";
+    private static final AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D[] chargedTracksPlot = {
+            aida.histogram1D("MTE Analysis/Møller Event Tracks", 10, -0.5, 9.5),
+            aida.histogram1D("MTE Analysis/Trident Event Tracks", 10, -0.5, 9.5),
+            aida.histogram1D("MTE Analysis/Elastic Event Tracks", 10, -0.5, 9.5)
+    };
+    private IHistogram1D[] clusterCountPlot = {
+            aida.histogram1D("MTE Analysis/Møller Event Clusters", 10, -0.5, 9.5),
+            aida.histogram1D("MTE Analysis/Trident Event Clusters", 10, -0.5, 9.5),
+            aida.histogram1D("MTE Analysis/Elastic Event Clusters", 10, -0.5, 9.5)
+    };
+    private IHistogram1D[] energyPlot = {
+            aida.histogram1D("MTE Analysis/Møller Energy Sum Distribution", 220, 0, 2.2),
+            aida.histogram1D("MTE Analysis/Trident Energy Sum Distribution", 220, 0, 2.2),
+            aida.histogram1D("MTE Analysis/Elastic Energy Distribution", 110, 0, 1.5)
+    };
+    private IHistogram1D[] electronPlot = {
+            aida.histogram1D("MTE Analysis/Møller Electron Energy Distribution", 220, 0, 2.2),
+            aida.histogram1D("MTE Analysis/Trident Electron Energy Distribution", 220, 0, 2.2),
+    };
+    private IHistogram1D positronPlot = aida.histogram1D("MTE Analysis/Trident Positron Energy Distribution", 220, 0, 2.2);
+    private IHistogram2D[] energy2DPlot = {
+            aida.histogram2D("MTE Analysis/Møller 2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1),
+            aida.histogram2D("MTE Analysis/Trident 2D Energy Distribution", 55, 0, 1.1, 55, 0, 1.1),
+    };
+    private IHistogram1D timePlot = aida.histogram1D("MTE Analysis/Track Cluster Time Distribution", 4000, 0, 400);
+    private IHistogram1D timeCoincidencePlot = aida.histogram1D("MTE Analysis/Møller Time Coincidence Distribution", 1000, 0, 100);
+    private IHistogram1D timeCoincidenceAllCutsPlot = aida.histogram1D("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)", 1000, 0, 100);
+    private IHistogram1D negTrackCount = aida.histogram1D("MTE Analysis/All Negative Tracks", 10, -0.5, 9.5);
+    private IHistogram1D posTrackCount = aida.histogram1D("MTE Analysis/All Positive Event Tracks", 10, -0.5, 9.5);
+    private IHistogram1D chargedTrackCount = aida.histogram1D("MTE Analysis/All Event Event Tracks", 10, -0.5, 9.5);
+    
+    private IHistogram1D trInvariantMassAll            = aida.histogram1D("Trident/Invariant Mass",                     1500,   0.0,  1.5);
+    private IHistogram1D trInvariantMassFiducial       = aida.histogram1D("Trident/Invariant Mass (Fiducial Region)",   1500,   0.0,  1.5);
+    private IHistogram1D trTimeCoincidenceAll          = aida.histogram1D("Trident/Time Coincidence",                    300, -15.0, 15.0);
+    private IHistogram1D trTimeCoincidenceFiducial     = aida.histogram1D("Trident/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
+    private IHistogram1D trEnergySumAll                = aida.histogram1D("Trident/Energy Sum",                          300,   0.0,  1.5);
+    private IHistogram1D trEnergySumFiducial           = aida.histogram1D("Trident/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
+    private IHistogram2D trEnergySum2DAll              = aida.histogram2D("Trident/First Cluster Energy vs. Second Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D trEnergySum2DFiducial         = aida.histogram2D("Trident/First Cluster Energy vs. Second Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D trSumCoplanarityAll           = aida.histogram2D("Trident/Hardware Coplanarity vs. Energy Sum",                              300, 0, 1.5, 115,   0, 180);
+    private IHistogram2D trSumCoplanarityFiducial      = aida.histogram2D("Trident/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",            300, 0, 1.5, 115,   0, 180);
+    private IHistogram2D trSumCoplanarityCalcAll       = aida.histogram2D("Trident/Calculated Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D trSumCoplanarityCalcFiducial  = aida.histogram2D("Trident/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D trTimeEnergyAll               = aida.histogram2D("Trident/Cluster Time vs. Cluster Energy",                                  300, 0, 1.5, 100,   0, 100);
+    private IHistogram2D trTimeEnergyFiducial          = aida.histogram2D("Trident/Cluster Time vs. Cluster Energy (Fiducial Region)",                300, 0, 1.5, 100,   0, 100);
+    
+    private TriggerPlotsModule allPlots = new TriggerPlotsModule("All");
+    private TriggerPlotsModule møllerPlots = new TriggerPlotsModule("Møller");
+    private TriggerPlotsModule tridentPlots = new TriggerPlotsModule("Trident");
+    private TriggerPlotsModule elasticPlots = new TriggerPlotsModule("Elastic");
+    private static final int MØLLER  = 0;
+    private static final int TRIDENT = 1;
+    private static final int ELASTIC = 2;
+    private boolean verbose = false;
+    private boolean excludeNoTrackEvents = false;
+    private double timeCoincidenceCut = Double.MAX_VALUE;
+    private Map<String, Integer> møllerBitMap = new HashMap<String, Integer>();
+    private Map<String, Integer> tridentBitMap = new HashMap<String, Integer>();
+    private Map<String, Integer> elasticBitMap = new HashMap<String, Integer>();
+    private int møllerEvents = 0;
+    private int tridentEvents = 0;
+    private int elasticEvents = 0;
+    private int totalEvents = 0;
+    private int pair1Events = 0;
+    private int pair0Events = 0;
+    private int singles1Events = 0;
+    private int singles0Events = 0;
+    private int pulserEvents = 0;
+    
+    @Override
+    public void startOfData() {
+        for(int s0 = 0; s0 <= 1; s0++) {
+            for(int s1 = 0; s1 <= 1; s1++) {
+                for(int p0 = 0; p0 <= 1; p0++) {
+                    for(int p1 = 0; p1 <= 1; p1++) {
+                        for(int pulser = 0; pulser <=1; pulser++) {
+                            // Set each "trigger bit."
+                            boolean s0bit = (s0 == 1);
+                            boolean s1bit = (s1 == 1);
+                            boolean p0bit = (p0 == 1);
+                            boolean p1bit = (p1 == 1);
+                            boolean pulserBit = (p1 == 1);
+                            
+                            // Generate the bit string.
+                            String bitString = getBitString(s0bit, s1bit, p0bit, p1bit, pulserBit);
+                            
+                            // Set a default value of zero for this bit combination.
+                            møllerBitMap.put(bitString, 1);
+                            tridentBitMap.put(bitString, 1);
+                            elasticBitMap.put(bitString, 1);
+                        }
+                    }
+                }
+            }
+        }
+    }
+    
+    @Override
+    public void endOfData() {
+        System.out.println("Møller  Events   :: " + møllerEvents);
+        System.out.println("Trident Events   :: " + tridentEvents);
+        System.out.println("Elastic Events   :: " + elasticEvents);
+        System.out.println("Total Events     :: " + totalEvents);
+        System.out.println("Pair 1 Events    :: " + pair1Events);
+        System.out.println("Pair 0 Events    :: " + pair0Events);
+        System.out.println("Singles 1 Events :: " + singles1Events);
+        System.out.println("Singles 0 Events :: " + singles0Events);
+        System.out.println("Pulser Events    :: " + pulserEvents);
+        
+        System.out.println("Plsr\tS0\tS1\tP0\tP1\tMøller");
+        for(Entry<String, Integer> entry : møllerBitMap.entrySet()) {
+            System.out.println(entry.getKey() + "\t" + entry.getValue());
+        }
+        
+        System.out.println("Plsr\tS0\tS1\tP0\tP1\tTrident");
+        for(Entry<String, Integer> entry : tridentBitMap.entrySet()) {
+            System.out.println(entry.getKey() + "\t" + entry.getValue());
+        }
+        
+        System.out.println("Plsr\tS0\tS1\tP0\tP1\tElastic");
+        for(Entry<String, Integer> entry : elasticBitMap.entrySet()) {
+            System.out.println(entry.getKey() + "\t" + entry.getValue());
+        }
+    }
+    
+    private static final String getBitString(boolean s0, boolean s1, boolean p0, boolean p1, boolean pulser) {
+        return String.format("%d\t%d\t%d\t%d\t%d", (pulser ? 1 : 0), (s0 ? 1 : 0), (s1 ? 1 : 0), (p0 ? 1 : 0), (p1 ? 1 : 0));
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Check whether the SVT was active in this event.
+        final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
+        boolean svtGood = true;
         for(int i = 0; i < flagNames.length; i++) {
             int[] flag = event.getIntegerParameters().get(flagNames[i]);
             if(flag == null || flag[0] == 0) {
@@ -172,437 +172,437 @@
         
         // If the SVT was bad, then skip the event.
         if(!svtGood && skipBadSVT) {
-        	return;
-        }
-        
-		if(event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
-			// Get the list of tracks.
-			List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
-			
-			// Plot the time stamps of all tracks.
-			for(ReconstructedParticle track : trackList) {
-				if(track.getClusters().size() != 0) {
-					Cluster cluster = track.getClusters().get(0);
-					timePlot.fill(cluster.getCalorimeterHits().get(0).getTime());
-				}
-			}
-			
-			if(verbose) {
-				System.out.println(trackList.size() + " tracks found.");
-				for(ReconstructedParticle track : trackList) {
-					System.out.printf("Track :: Q = %4.1f; E = %6.3f%n",
-							track.getCharge(), track.getEnergy());
-				}
-			}
-			
-			// Populate the all cluster plots.
-			List<Cluster> topClusters = new ArrayList<Cluster>();
-			List<Cluster> botClusters = new ArrayList<Cluster>();
-			List<Cluster> clusters = event.get(Cluster.class, "EcalClusters");
-			for(Cluster cluster : clusters) {
-				allPlots.addCluster(cluster);
-				if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) { topClusters.add(cluster); }
-				else { botClusters.add(cluster); }
-			}
-			
-			// Make cluster pairs.
-			List<Cluster[]> clusterPairs = new ArrayList<Cluster[]>();
-			for(Cluster topCluster : topClusters) {
-				for(Cluster botCluster : botClusters) {
-					clusterPairs.add(new Cluster[] { topCluster, botCluster });
-				}
-			}
-			
-			// Populate the all cluster pair plots.
-			for(Cluster[] pair : clusterPairs) {
-				allPlots.addClusterPair(pair);
-			}
-			
-			// Check each of the event-type conditions.
-			boolean isMøller = false;
-			boolean isTrident = false;
-			boolean isElastic = false;
-			
-			// Produce all possible pairs of tracks.
-			List<ReconstructedParticle[]> pairList = getTrackPairs(trackList);
-			
-			// Check the Møller condition. A Møller event is expected
-			// to have two tracks, both negative, with a net energy
-			// within a certain band of the beam energy.
-			møllerTrackLoop:
-			for(ReconstructedParticle[] pair : pairList) {
-				// If trackless events are to be excluded, then require
-				// that each "track" have a real track.
-				if(excludeNoTrackEvents && (pair[0].getTracks().isEmpty() || pair[1].getTracks().isEmpty())) {
-					continue møllerTrackLoop;
-				}
-				
-				// Both tracks are required to be negatively charged.
-				if(pair[0].getCharge() >= 0 || pair[1].getCharge() >= 0) {
-					continue møllerTrackLoop;
-				}
-				
-				// Both tracks must have clusters associated with them.
-				Cluster[] trackClusters = new Cluster[2];
-				for(int i = 0; i < 2; i++) {
-					// Disallow tracks with no associated clusters.
-					if(pair[i].getClusters().size() == 0) {
-						continue møllerTrackLoop;
-					}
-					
-					// Store the first cluster associated with the track.
-					trackClusters[i] = pair[i].getClusters().get(0);
-				}
-				
-				// Require that the track clusters be within a certain
-				// time window of one another.
-				CalorimeterHit[] seeds = new CalorimeterHit[2];
-				seeds[0] = trackClusters[0].getCalorimeterHits().get(0);
-				seeds[1] = trackClusters[1].getCalorimeterHits().get(0);
-				timeCoincidencePlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
-				if(Math.abs(trackClusters[0].getCalorimeterHits().get(0).getTime() - trackClusters[1].getCalorimeterHits().get(0).getTime()) > timeCoincidenceCut) {
-					continue møllerTrackLoop;
-				}
-				
-				// Require both tracks to occur within the range of
-				// 36.5 and 49 ns.
-				if(seeds[0].getTime() < 36.5 || seeds[0].getTime() > 49) {
-					continue møllerTrackLoop;
-				} if(seeds[1].getTime() < 36.5 || seeds[1].getTime() > 49) {
-					continue møllerTrackLoop;
-				}
-				
-				// No track may have an energy that exceeds 900 MeV.
-				if(pair[0].getMomentum().magnitude() >= 0.900 || pair[1].getMomentum().magnitude() >= 0.900) {
-					continue møllerTrackLoop;
-				}
-				
-				// Get the energy sum.
-				double sum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
-				
-				// "Møller-like" track pairs must have energies within
-				// an allowed energy range.
-				if(sum < 0.800 || sum > 1.500) {
-					continue møllerTrackLoop;
-				}
-				
-				//timeCoincidenceAllCutsPlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
-				
-				// Note that this is a Møller event.
-				isMøller = true;
-				
-				// Populate the Møller plots.
-				energyPlot[MØLLER].fill(sum);
-				møllerPlots.addClusterPair(trackClusters);
-				electronPlot[MØLLER].fill(pair[0].getMomentum().magnitude());
-				electronPlot[MØLLER].fill(pair[1].getMomentum().magnitude());
-				energy2DPlot[MØLLER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-			}
-			
-			// Check the elastic condition. Elastic events should be
-			// negatively and have an energy approximately equal to
-			// the beam energy.
-			elasticTrackLoop:
-			for(ReconstructedParticle track : trackList) {
-				// If trackless events are to be excluded, then require
-				// that the "track" has a real track.
-				if(excludeNoTrackEvents && track.getTracks().isEmpty()) {
-					continue elasticTrackLoop;
-				}
-				
-				// Check the elastic condition.
-				if(track.getCharge() < 0 && track.getMomentum().magnitude() >= 0.900) {
-					isElastic = true;
-					energyPlot[ELASTIC].fill(track.getMomentum().magnitude());
-					if(!track.getClusters().isEmpty()) {
-						elasticPlots.addCluster(track.getClusters().get(0));
-					}
-				}
-			}
-			
-			// Check the trident condition. Tridents are events that
-			// contain both one positive and one negative track.
-			tridentTrackLoop:
-			for(ReconstructedParticle[] pair : pairList) {
-				// If trackless events are to be excluded, then require
-				// that each "track" have a real track.
-				if(pair[0].getTracks().isEmpty() || pair[1].getTracks().isEmpty()) {
-					continue tridentTrackLoop;
-				}
-				
-				// Require that all tridents consist of a positive and
-				// negative pair.
-				boolean isPosNeg = (pair[0].getCharge() < 0 && pair[1].getCharge() > 0) || (pair[0].getCharge() > 0 && pair[1].getCharge() < 0);
-				if(!isPosNeg) { continue tridentTrackLoop; }
-				
-				// Both tracks must have clusters associated with them.
-				Cluster[] trackClusters = new Cluster[pair.length];
-				for(int i = 0; i < pair.length; i++) {
-					// Disallow tracks with no associated clusters.
-					if(pair[i].getClusters().size() == 0) {
-						continue tridentTrackLoop;
-					}
-					
-					// Store the first cluster associated with the track.
-					trackClusters[i] = pair[i].getClusters().get(0);
-				}
-				
-				// Make sure that the clusters are not the same.
-				if(trackClusters[0] == trackClusters[1]) {
-					continue tridentTrackLoop;
-				}
-				
-				// Require that tridents also be a top/bottom pair.
-				boolean isTopBot = (TriggerModule.getClusterYIndex(trackClusters[0]) > 0 && TriggerModule.getClusterYIndex(trackClusters[1]) < 0)
-						|| (TriggerModule.getClusterYIndex(trackClusters[0]) < 0 && TriggerModule.getClusterYIndex(trackClusters[1]) > 0);
-				if(!isTopBot) {
-					continue tridentTrackLoop;
-				}
-				
-				// Require that the track clusters be within a certain
-				// time window of one another.
-				CalorimeterHit[] seeds = new CalorimeterHit[2];
-				seeds[0] = trackClusters[0].getCalorimeterHits().get(0);
-				seeds[1] = trackClusters[1].getCalorimeterHits().get(0);
-				timeCoincidencePlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
-				if(Math.abs(trackClusters[0].getCalorimeterHits().get(0).getTime() - trackClusters[1].getCalorimeterHits().get(0).getTime()) > timeCoincidenceCut) {
-					continue tridentTrackLoop;
-				}
-				
-				// Require that the energy of the electron is below
-				// 900 MeV.
-				boolean electronNotElastic = (pair[0].getCharge() < 0 && pair[0].getMomentum().magnitude() < 0.900)
-						|| (pair[1].getCharge() < 0 && pair[1].getMomentum().magnitude() < 0.900);
-				if(!electronNotElastic) {
-					continue tridentTrackLoop;
-				}
-				
-				// If all tests are passed, this is a trident. Note
-				// this and populate the trident plots.
-				isTrident = true;
-				tridentPlots.addClusterPair(trackClusters);
-				if(pair[0].getCharge() > 0) {
-					positronPlot.fill(pair[1].getMomentum().magnitude());
-					electronPlot[TRIDENT].fill(pair[0].getMomentum().magnitude());
-				} else {
-					positronPlot.fill(pair[0].getMomentum().magnitude());
-					electronPlot[TRIDENT].fill(pair[1].getMomentum().magnitude());
-				}
-				energyPlot[TRIDENT].fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
-				energy2DPlot[TRIDENT].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-				
-				// Track which clusters have already been added to the
-				// singles plot so that there are no repeats.
-				Set<Cluster> plotSet = new HashSet<Cluster>();
-				Set<Cluster> plotFiducial = new HashSet<Cluster>();
-				
-				// Fill the all pairs plots.
-				double pairEnergy = trackClusters[0].getEnergy() + trackClusters[1].getEnergy();
-				trEnergySumAll.fill(pairEnergy);
-				trEnergySum2DAll.fill(trackClusters[1].getEnergy(), trackClusters[0].getEnergy());
-				trTimeCoincidenceAll.fill(RafoAnalysis.getTimeConicidence(trackClusters));
-				trSumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(trackClusters));
-				trSumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(trackClusters));
-				trInvariantMassAll.fill(RafoAnalysis.getInvariantMass(pair));
-				
-				// Fill the singles plots.
-				if(!plotSet.contains(trackClusters[0])) {
-					plotSet.add(trackClusters[0]);
-					trTimeEnergyAll.fill(trackClusters[0].getEnergy(), TriggerModule.getClusterTime(trackClusters[0]));
-				} if(!plotSet.contains(trackClusters[1])) {
-					plotSet.add(trackClusters[1]);
-					trTimeEnergyAll.fill(trackClusters[1].getEnergy(), TriggerModule.getClusterTime(trackClusters[1]));
-				}
-				
-				// Fill the fiducial plots if appropriate.
-				if(inFiducialRegion(trackClusters[0]) && inFiducialRegion(trackClusters[1])) {
-					trEnergySumFiducial.fill(pairEnergy);
-					trEnergySum2DFiducial.fill(trackClusters[1].getEnergy(), trackClusters[0].getEnergy());
-					trTimeCoincidenceFiducial.fill(RafoAnalysis.getTimeConicidence(trackClusters));
-					trSumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(trackClusters));
-					trSumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(trackClusters));
-					trInvariantMassFiducial.fill(RafoAnalysis.getInvariantMass(pair));
-				}
-				
-				// Fill the singles fiducial plots if appropriate.
-				if(!plotFiducial.contains(trackClusters[0]) && inFiducialRegion(trackClusters[0])) {
-					plotFiducial.add(trackClusters[0]);
-					trTimeEnergyFiducial.fill(trackClusters[0].getEnergy(), TriggerModule.getClusterTime(trackClusters[0]));
-				} if(!plotFiducial.contains(trackClusters[1]) && inFiducialRegion(trackClusters[1])) {
-					plotFiducial.add(trackClusters[1]);
-					trTimeEnergyFiducial.fill(trackClusters[1].getEnergy(), TriggerModule.getClusterTime(trackClusters[1]));
-				}
-			}
-			
-			if(verbose) {
-				System.out.printf("\tMøller  :: %b%n", isMøller);
-				System.out.printf("\tTrident :: %b%n", isTrident);
-				System.out.printf("\tElastic :: %b%n", isElastic);
-				System.out.println();
-			}
-			
-			// Get the TI bits.
-			String bitString = null;
-			TIData tiBank = null;
-			List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
-			for(GenericObject obj : bankList) {
-				if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
-					tiBank = new TIData(obj);
-					bitString = getBitString(tiBank.isPulserTrigger(), tiBank.isSingle0Trigger(),
-							tiBank.isSingle1Trigger(), tiBank.isPair0Trigger(), tiBank.isPair1Trigger());
-					
-					if(tiBank.isPair1Trigger()) {
-						pair1Events++;
-					} else if(tiBank.isPair0Trigger()) {
-						pair0Events++;
-					} else if(tiBank.isSingle1Trigger()) {
-						singles1Events++;
-					} else if(tiBank.isSingle0Trigger()) {
-						singles0Events++;
-					} else if(tiBank.isPulserTrigger()) {
-						pulserEvents++;
-					}
-				}
-			}
-			if(bitString == null) {
-				System.out.println("No TI data found!!");
-			}
-			
-			// Get the number of charged tracks in the event.
-			int tracks = 0;
-			int posTracks = 0;
-			int negTracks = 0;
-			for(ReconstructedParticle track : trackList) {
-				if(track.getCharge() != 0 && tiBank.isPulserTrigger()) {
-					if(excludeNoTrackEvents && !track.getTracks().isEmpty()) {
-						tracks++;
-						if(track.getCharge() > 0) { posTracks++; }
-						else { negTracks++; }
-					} else {
-						tracks++;
-						if(track.getCharge() > 0) { posTracks++; }
-						else { negTracks++; }
-					}
-				}
-			}
-			
-			// Populate the "all tracks" plots.
-			posTrackCount.fill(posTracks);
-			negTrackCount.fill(negTracks);
-			chargedTrackCount.fill(tracks);
-			
-			// Add the result to the appropriate plots and increment
-			// the appropriate trigger bit combination.
-			if(isMøller) {
-				møllerEvents++;
-				chargedTracksPlot[MØLLER].fill(tracks);
-				clusterCountPlot[MØLLER].fill(clusters.size());
-				
-				Integer val = møllerBitMap.get(bitString);
-				if(val == null) { møllerBitMap.put(bitString, 1); }
-				else { møllerBitMap.put(bitString, val + 1); }
-			} else if(isTrident) {
-				tridentEvents++;
-				chargedTracksPlot[TRIDENT].fill(tracks);
-				clusterCountPlot[TRIDENT].fill(clusters.size());
-				
-				Integer val = tridentBitMap.get(bitString);
-				if(val == null) { tridentBitMap.put(bitString, 1); }
-				else { tridentBitMap.put(bitString, val + 1); }
-			} else if(isElastic) {
-				elasticEvents++;
-				chargedTracksPlot[ELASTIC].fill(tracks);
-				clusterCountPlot[ELASTIC].fill(clusters.size());
-				
-				Integer val = elasticBitMap.get(bitString);
-				if(val == null) { elasticBitMap.put(bitString, 1); }
-				else { elasticBitMap.put(bitString, val + 1); }
-			}
-			totalEvents++;
-		}
-	}
-	
-	private static final double getCalculatedCoplanarity(Cluster[] pair) {
-		// Define the x- and y-coordinates of the clusters as well as
-		// calorimeter center.
-		final double ORIGIN_X = 42.52;
-		double x[] = { pair[0].getPosition()[0], pair[1].getPosition()[0] };
-		double y[] = { pair[0].getPosition()[1], pair[1].getPosition()[1] };
-		
+            return;
+        }
+        
+        if(event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
+            // Get the list of tracks.
+            List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
+            
+            // Plot the time stamps of all tracks.
+            for(ReconstructedParticle track : trackList) {
+                if(track.getClusters().size() != 0) {
+                    Cluster cluster = track.getClusters().get(0);
+                    timePlot.fill(cluster.getCalorimeterHits().get(0).getTime());
+                }
+            }
+            
+            if(verbose) {
+                System.out.println(trackList.size() + " tracks found.");
+                for(ReconstructedParticle track : trackList) {
+                    System.out.printf("Track :: Q = %4.1f; E = %6.3f%n",
+                            track.getCharge(), track.getEnergy());
+                }
+            }
+            
+            // Populate the all cluster plots.
+            List<Cluster> topClusters = new ArrayList<Cluster>();
+            List<Cluster> botClusters = new ArrayList<Cluster>();
+            List<Cluster> clusters = event.get(Cluster.class, "EcalClusters");
+            for(Cluster cluster : clusters) {
+                allPlots.addCluster(cluster);
+                if(cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) { topClusters.add(cluster); }
+                else { botClusters.add(cluster); }
+            }
+            
+            // Make cluster pairs.
+            List<Cluster[]> clusterPairs = new ArrayList<Cluster[]>();
+            for(Cluster topCluster : topClusters) {
+                for(Cluster botCluster : botClusters) {
+                    clusterPairs.add(new Cluster[] { topCluster, botCluster });
+                }
+            }
+            
+            // Populate the all cluster pair plots.
+            for(Cluster[] pair : clusterPairs) {
+                allPlots.addClusterPair(pair);
+            }
+            
+            // Check each of the event-type conditions.
+            boolean isMøller = false;
+            boolean isTrident = false;
+            boolean isElastic = false;
+            
+            // Produce all possible pairs of tracks.
+            List<ReconstructedParticle[]> pairList = getTrackPairs(trackList);
+            
+            // Check the Møller condition. A Møller event is expected
+            // to have two tracks, both negative, with a net energy
+            // within a certain band of the beam energy.
+            møllerTrackLoop:
+            for(ReconstructedParticle[] pair : pairList) {
+                // If trackless events are to be excluded, then require
+                // that each "track" have a real track.
+                if(excludeNoTrackEvents && (pair[0].getTracks().isEmpty() || pair[1].getTracks().isEmpty())) {
+                    continue møllerTrackLoop;
+                }
+                
+                // Both tracks are required to be negatively charged.
+                if(pair[0].getCharge() >= 0 || pair[1].getCharge() >= 0) {
+                    continue møllerTrackLoop;
+                }
+                
+                // Both tracks must have clusters associated with them.
+                Cluster[] trackClusters = new Cluster[2];
+                for(int i = 0; i < 2; i++) {
+                    // Disallow tracks with no associated clusters.
+                    if(pair[i].getClusters().size() == 0) {
+                        continue møllerTrackLoop;
+                    }
+                    
+                    // Store the first cluster associated with the track.
+                    trackClusters[i] = pair[i].getClusters().get(0);
+                }
+                
+                // Require that the track clusters be within a certain
+                // time window of one another.
+                CalorimeterHit[] seeds = new CalorimeterHit[2];
+                seeds[0] = trackClusters[0].getCalorimeterHits().get(0);
+                seeds[1] = trackClusters[1].getCalorimeterHits().get(0);
+                timeCoincidencePlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
+                if(Math.abs(trackClusters[0].getCalorimeterHits().get(0).getTime() - trackClusters[1].getCalorimeterHits().get(0).getTime()) > timeCoincidenceCut) {
+                    continue møllerTrackLoop;
+                }
+                
+                // Require both tracks to occur within the range of
+                // 36.5 and 49 ns.
+                if(seeds[0].getTime() < 36.5 || seeds[0].getTime() > 49) {
+                    continue møllerTrackLoop;
+                } if(seeds[1].getTime() < 36.5 || seeds[1].getTime() > 49) {
+                    continue møllerTrackLoop;
+                }
+                
+                // No track may have an energy that exceeds 900 MeV.
+                if(pair[0].getMomentum().magnitude() >= 0.900 || pair[1].getMomentum().magnitude() >= 0.900) {
+                    continue møllerTrackLoop;
+                }
+                
+                // Get the energy sum.
+                double sum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
+                
+                // "Møller-like" track pairs must have energies within
+                // an allowed energy range.
+                if(sum < 0.800 || sum > 1.500) {
+                    continue møllerTrackLoop;
+                }
+                
+                //timeCoincidenceAllCutsPlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
+                
+                // Note that this is a Møller event.
+                isMøller = true;
+                
+                // Populate the Møller plots.
+                energyPlot[MØLLER].fill(sum);
+                møllerPlots.addClusterPair(trackClusters);
+                electronPlot[MØLLER].fill(pair[0].getMomentum().magnitude());
+                electronPlot[MØLLER].fill(pair[1].getMomentum().magnitude());
+                energy2DPlot[MØLLER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+            }
+            
+            // Check the elastic condition. Elastic events should be
+            // negatively and have an energy approximately equal to
+            // the beam energy.
+            elasticTrackLoop:
+            for(ReconstructedParticle track : trackList) {
+                // If trackless events are to be excluded, then require
+                // that the "track" has a real track.
+                if(excludeNoTrackEvents && track.getTracks().isEmpty()) {
+                    continue elasticTrackLoop;
+                }
+                
+                // Check the elastic condition.
+                if(track.getCharge() < 0 && track.getMomentum().magnitude() >= 0.900) {
+                    isElastic = true;
+                    energyPlot[ELASTIC].fill(track.getMomentum().magnitude());
+                    if(!track.getClusters().isEmpty()) {
+                        elasticPlots.addCluster(track.getClusters().get(0));
+                    }
+                }
+            }
+            
+            // Check the trident condition. Tridents are events that
+            // contain both one positive and one negative track.
+            tridentTrackLoop:
+            for(ReconstructedParticle[] pair : pairList) {
+                // If trackless events are to be excluded, then require
+                // that each "track" have a real track.
+                if(pair[0].getTracks().isEmpty() || pair[1].getTracks().isEmpty()) {
+                    continue tridentTrackLoop;
+                }
+                
+                // Require that all tridents consist of a positive and
+                // negative pair.
+                boolean isPosNeg = (pair[0].getCharge() < 0 && pair[1].getCharge() > 0) || (pair[0].getCharge() > 0 && pair[1].getCharge() < 0);
+                if(!isPosNeg) { continue tridentTrackLoop; }
+                
+                // Both tracks must have clusters associated with them.
+                Cluster[] trackClusters = new Cluster[pair.length];
+                for(int i = 0; i < pair.length; i++) {
+                    // Disallow tracks with no associated clusters.
+                    if(pair[i].getClusters().size() == 0) {
+                        continue tridentTrackLoop;
+                    }
+                    
+                    // Store the first cluster associated with the track.
+                    trackClusters[i] = pair[i].getClusters().get(0);
+                }
+                
+                // Make sure that the clusters are not the same.
+                if(trackClusters[0] == trackClusters[1]) {
+                    continue tridentTrackLoop;
+                }
+                
+                // Require that tridents also be a top/bottom pair.
+                boolean isTopBot = (TriggerModule.getClusterYIndex(trackClusters[0]) > 0 && TriggerModule.getClusterYIndex(trackClusters[1]) < 0)
+                        || (TriggerModule.getClusterYIndex(trackClusters[0]) < 0 && TriggerModule.getClusterYIndex(trackClusters[1]) > 0);
+                if(!isTopBot) {
+                    continue tridentTrackLoop;
+                }
+                
+                // Require that the track clusters be within a certain
+                // time window of one another.
+                CalorimeterHit[] seeds = new CalorimeterHit[2];
+                seeds[0] = trackClusters[0].getCalorimeterHits().get(0);
+                seeds[1] = trackClusters[1].getCalorimeterHits().get(0);
+                timeCoincidencePlot.fill(Math.abs(seeds[0].getTime() - seeds[1].getTime()));
+                if(Math.abs(trackClusters[0].getCalorimeterHits().get(0).getTime() - trackClusters[1].getCalorimeterHits().get(0).getTime()) > timeCoincidenceCut) {
+                    continue tridentTrackLoop;
+                }
+                
+                // Require that the energy of the electron is below
+                // 900 MeV.
+                boolean electronNotElastic = (pair[0].getCharge() < 0 && pair[0].getMomentum().magnitude() < 0.900)
+                        || (pair[1].getCharge() < 0 && pair[1].getMomentum().magnitude() < 0.900);
+                if(!electronNotElastic) {
+                    continue tridentTrackLoop;
+                }
+                
+                // If all tests are passed, this is a trident. Note
+                // this and populate the trident plots.
+                isTrident = true;
+                tridentPlots.addClusterPair(trackClusters);
+                if(pair[0].getCharge() > 0) {
+                    positronPlot.fill(pair[1].getMomentum().magnitude());
+                    electronPlot[TRIDENT].fill(pair[0].getMomentum().magnitude());
+                } else {
+                    positronPlot.fill(pair[0].getMomentum().magnitude());
+                    electronPlot[TRIDENT].fill(pair[1].getMomentum().magnitude());
+                }
+                energyPlot[TRIDENT].fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
+                energy2DPlot[TRIDENT].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+                
+                // Track which clusters have already been added to the
+                // singles plot so that there are no repeats.
+                Set<Cluster> plotSet = new HashSet<Cluster>();
+                Set<Cluster> plotFiducial = new HashSet<Cluster>();
+                
+                // Fill the all pairs plots.
+                double pairEnergy = trackClusters[0].getEnergy() + trackClusters[1].getEnergy();
+                trEnergySumAll.fill(pairEnergy);
+                trEnergySum2DAll.fill(trackClusters[1].getEnergy(), trackClusters[0].getEnergy());
+                trTimeCoincidenceAll.fill(RafoAnalysis.getTimeConicidence(trackClusters));
+                trSumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(trackClusters));
+                trSumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(trackClusters));
+                trInvariantMassAll.fill(RafoAnalysis.getInvariantMass(pair));
+                
+                // Fill the singles plots.
+                if(!plotSet.contains(trackClusters[0])) {
+                    plotSet.add(trackClusters[0]);
+                    trTimeEnergyAll.fill(trackClusters[0].getEnergy(), TriggerModule.getClusterTime(trackClusters[0]));
+                } if(!plotSet.contains(trackClusters[1])) {
+                    plotSet.add(trackClusters[1]);
+                    trTimeEnergyAll.fill(trackClusters[1].getEnergy(), TriggerModule.getClusterTime(trackClusters[1]));
+                }
+                
+                // Fill the fiducial plots if appropriate.
+                if(inFiducialRegion(trackClusters[0]) && inFiducialRegion(trackClusters[1])) {
+                    trEnergySumFiducial.fill(pairEnergy);
+                    trEnergySum2DFiducial.fill(trackClusters[1].getEnergy(), trackClusters[0].getEnergy());
+                    trTimeCoincidenceFiducial.fill(RafoAnalysis.getTimeConicidence(trackClusters));
+                    trSumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(trackClusters));
+                    trSumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(trackClusters));
+                    trInvariantMassFiducial.fill(RafoAnalysis.getInvariantMass(pair));
+                }
+                
+                // Fill the singles fiducial plots if appropriate.
+                if(!plotFiducial.contains(trackClusters[0]) && inFiducialRegion(trackClusters[0])) {
+                    plotFiducial.add(trackClusters[0]);
+                    trTimeEnergyFiducial.fill(trackClusters[0].getEnergy(), TriggerModule.getClusterTime(trackClusters[0]));
+                } if(!plotFiducial.contains(trackClusters[1]) && inFiducialRegion(trackClusters[1])) {
+                    plotFiducial.add(trackClusters[1]);
+                    trTimeEnergyFiducial.fill(trackClusters[1].getEnergy(), TriggerModule.getClusterTime(trackClusters[1]));
+                }
+            }
+            
+            if(verbose) {
+                System.out.printf("\tMøller  :: %b%n", isMøller);
+                System.out.printf("\tTrident :: %b%n", isTrident);
+                System.out.printf("\tElastic :: %b%n", isElastic);
+                System.out.println();
+            }
+            
+            // Get the TI bits.
+            String bitString = null;
+            TIData tiBank = null;
+            List<GenericObject> bankList = event.get(GenericObject.class, bankCollectionName);
+            for(GenericObject obj : bankList) {
+                if(AbstractIntData.getTag(obj) == TIData.BANK_TAG) {
+                    tiBank = new TIData(obj);
+                    bitString = getBitString(tiBank.isPulserTrigger(), tiBank.isSingle0Trigger(),
+                            tiBank.isSingle1Trigger(), tiBank.isPair0Trigger(), tiBank.isPair1Trigger());
+                    
+                    if(tiBank.isPair1Trigger()) {
+                        pair1Events++;
+                    } else if(tiBank.isPair0Trigger()) {
+                        pair0Events++;
+                    } else if(tiBank.isSingle1Trigger()) {
+                        singles1Events++;
+                    } else if(tiBank.isSingle0Trigger()) {
+                        singles0Events++;
+                    } else if(tiBank.isPulserTrigger()) {
+                        pulserEvents++;
+                    }
+                }
+            }
+            if(bitString == null) {
+                System.out.println("No TI data found!!");
+            }
+            
+            // Get the number of charged tracks in the event.
+            int tracks = 0;
+            int posTracks = 0;
+            int negTracks = 0;
+            for(ReconstructedParticle track : trackList) {
+                if(track.getCharge() != 0 && tiBank.isPulserTrigger()) {
+                    if(excludeNoTrackEvents && !track.getTracks().isEmpty()) {
+                        tracks++;
+                        if(track.getCharge() > 0) { posTracks++; }
+                        else { negTracks++; }
+                    } else {
+                        tracks++;
+                        if(track.getCharge() > 0) { posTracks++; }
+                        else { negTracks++; }
+                    }
+                }
+            }
+            
+            // Populate the "all tracks" plots.
+            posTrackCount.fill(posTracks);
+            negTrackCount.fill(negTracks);
+            chargedTrackCount.fill(tracks);
+            
+            // Add the result to the appropriate plots and increment
+            // the appropriate trigger bit combination.
+            if(isMøller) {
+                møllerEvents++;
+                chargedTracksPlot[MØLLER].fill(tracks);
+                clusterCountPlot[MØLLER].fill(clusters.size());
+                
+                Integer val = møllerBitMap.get(bitString);
+                if(val == null) { møllerBitMap.put(bitString, 1); }
+                else { møllerBitMap.put(bitString, val + 1); }
+            } else if(isTrident) {
+                tridentEvents++;
+                chargedTracksPlot[TRIDENT].fill(tracks);
+                clusterCountPlot[TRIDENT].fill(clusters.size());
+                
+                Integer val = tridentBitMap.get(bitString);
+                if(val == null) { tridentBitMap.put(bitString, 1); }
+                else { tridentBitMap.put(bitString, val + 1); }
+            } else if(isElastic) {
+                elasticEvents++;
+                chargedTracksPlot[ELASTIC].fill(tracks);
+                clusterCountPlot[ELASTIC].fill(clusters.size());
+                
+                Integer val = elasticBitMap.get(bitString);
+                if(val == null) { elasticBitMap.put(bitString, 1); }
+                else { elasticBitMap.put(bitString, val + 1); }
+            }
+            totalEvents++;
+        }
+    }
+    
+    private static final double getCalculatedCoplanarity(Cluster[] pair) {
+        // Define the x- and y-coordinates of the clusters as well as
+        // calorimeter center.
+        final double ORIGIN_X = 42.52;
+        double x[] = { pair[0].getPosition()[0], pair[1].getPosition()[0] };
+        double y[] = { pair[0].getPosition()[1], pair[1].getPosition()[1] };
+        
         // Get the cluster angles.
         double[] clusterAngle = new double[2];
         for(int i = 0; i < 2; i++) {
-        	clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
-        	if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
+            clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
+            if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
         }
         
         // Calculate the coplanarity cut value.
         double clusterDiff = clusterAngle[0] - clusterAngle[1];
         return clusterDiff > 0 ? clusterDiff : clusterDiff + 360;
-	}
-	
-	public void setTimeCoincidenceCut(double value) {
-		timeCoincidenceCut = value;
-	}
-	
-	public void setExcludeNoTrackEvents(boolean state) {
-		excludeNoTrackEvents = state;
-	}
-	
-	public void setSkipBadSVT(boolean state) {
-		skipBadSVT = state;
-	}
-	
-	private static final boolean inFiducialRegion(Cluster cluster) {
-		// Get the x and y indices for the cluster.
-		int ix   = TriggerModule.getClusterXIndex(cluster);
-		int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
-		int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
-		
-		// Check if the cluster is on the top or the bottom of the
-		// calorimeter, as defined by |y| == 5. This is an edge cluster
-		// and is not in the fiducial region.
-		if(absy == 5) {
-			return false;
-		}
-		
-		// Check if the cluster is on the extreme left or right side
-		// of the calorimeter, as defined by |x| == 23. This is also
-		// and edge cluster is not in the fiducial region.
-		if(absx == 23) {
-			return false;
-		}
-		
-		// Check if the cluster is along the beam gap, as defined by
-		// |y| == 1. This is an internal edge cluster and is not in the
-		// fiducial region.
-		if(absy == 1) {
-			return false;
-		}
-		
-		// Lastly, check if the cluster falls along the beam hole, as
-		// defined by clusters with -11 <= x <= -1 and |y| == 2. This
-		// is not the fiducial region.
-		if(absy == 2 && ix <= -1 && ix >= -11) {
-			return false;
-		}
-		
-		// If all checks fail, the cluster is in the fiducial region.
-		return true;
-	}
-	
-	private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> trackList) {
-		// Create an empty list for the pairs.
-		List<ReconstructedParticle[]> pairs = new ArrayList<ReconstructedParticle[]>();
-		
-		// Add all possible pairs of tracks.
-		for(int i = 0; i < trackList.size(); i++) {
-			for(int j = i + 1; j < trackList.size(); j++) {
-				pairs.add(new ReconstructedParticle[] { trackList.get(i), trackList.get(j) });
-			}
-		}
-		
-		// Return the list of tracks.
-		return pairs;
-	}
+    }
+    
+    public void setTimeCoincidenceCut(double value) {
+        timeCoincidenceCut = value;
+    }
+    
+    public void setExcludeNoTrackEvents(boolean state) {
+        excludeNoTrackEvents = state;
+    }
+    
+    public void setSkipBadSVT(boolean state) {
+        skipBadSVT = state;
+    }
+    
+    private static final boolean inFiducialRegion(Cluster cluster) {
+        // Get the x and y indices for the cluster.
+        int ix   = TriggerModule.getClusterXIndex(cluster);
+        int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
+        int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
+        
+        // Check if the cluster is on the top or the bottom of the
+        // calorimeter, as defined by |y| == 5. This is an edge cluster
+        // and is not in the fiducial region.
+        if(absy == 5) {
+            return false;
+        }
+        
+        // Check if the cluster is on the extreme left or right side
+        // of the calorimeter, as defined by |x| == 23. This is also
+        // and edge cluster is not in the fiducial region.
+        if(absx == 23) {
+            return false;
+        }
+        
+        // Check if the cluster is along the beam gap, as defined by
+        // |y| == 1. This is an internal edge cluster and is not in the
+        // fiducial region.
+        if(absy == 1) {
+            return false;
+        }
+        
+        // Lastly, check if the cluster falls along the beam hole, as
+        // defined by clusters with -11 <= x <= -1 and |y| == 2. This
+        // is not the fiducial region.
+        if(absy == 2 && ix <= -1 && ix >= -11) {
+            return false;
+        }
+        
+        // If all checks fail, the cluster is in the fiducial region.
+        return true;
+    }
+    
+    private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> trackList) {
+        // Create an empty list for the pairs.
+        List<ReconstructedParticle[]> pairs = new ArrayList<ReconstructedParticle[]>();
+        
+        // Add all possible pairs of tracks.
+        for(int i = 0; i < trackList.size(); i++) {
+            for(int j = i + 1; j < trackList.size(); j++) {
+                pairs.add(new ReconstructedParticle[] { trackList.get(i), trackList.get(j) });
+            }
+        }
+        
+        // Return the list of tracks.
+        return pairs;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTETriggerPlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTETriggerPlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/MTETriggerPlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -15,164 +15,164 @@
 
 
 public class MTETriggerPlotsFormatter {
-	public static void main(String[] args) throws IllegalArgumentException, IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "5772-ana.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Define the 1D trigger plot names for Møllers and tridents.
-		String[] plotNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
-				"Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
-		String[] displayNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
-				"Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
-		String[] xAxisNames1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)",
-				"Coplanarity (Degrees)", "Energy Difference (GeV)", "Energy Slope (GeV)", "Energy Sum (GeV)" };
-		String yAxisName1D = "Count";
-		
-		// Define the 2D trigger plot names for Møllers and tridents.
-		String[] plotNames2D = { "Cluster Seed", "Pair Energy Sum 2D" };
-		String[] displayNames2D = { "Cluster Seed Distribution", "2D Energy Sum" };
-		String[] xAxisNames2D = { "x-Index", "Second Cluster Energy (GeV)" };
-		String[] yAxisNames2D = { "y-Index", "First Cluster Energy (GeV)" };
-		
-		// Define the 1D trigger plot names for elastics.
-		String[] plotNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
-		String[] displayNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
-		String[] xAxisNamesElastic1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)" };
-		String yAxisNameElastic1D = "Count";
-		
-		// Define the 2D trigger plot names for elastics.
-		String[] plotNamesElastic2D = { "Cluster Seed" };
-		String[] displayNamesElastic2D = { "Cluster Seed Distribution" };
-		String[] xAxisNamesElastic2D = { "x-Index" };
-		String[] yAxisNamesElastic2D = { "y-Index" };
-		
-		// Define the Møller, trident, and elastic prefixes.
-		String allPrefix = "All Trigger Plots/Pair Plots/";
-		String møllerPrefix = "Møller Trigger Plots/Pair Plots/";
-		String tridentPrefix = "Trident Trigger Plots/Pair Plots/";
-		String elasticPrefix = "Elastic Trigger Plots/Singles Plots/";
-		String allSinglesPrefix = "All Trigger Plots/Singles Plots/";
-		
-		// Define the plot type prefix.
-		String allTypeName = "All Pairs - ";
-		String møllerTypeName = "Møller - ";
-		String tridentTypeName = "Trident - ";
-		String elasticTypeName = "Elastic - ";
-		String allSinglesTypeName = "All Singles - ";
-		
-		// Define the plot type colors.
-		ColorStyle allColor = PlotsFormatter.ColorStyle.GREY;
-		ColorStyle møllerColor = PlotsFormatter.ColorStyle.MS_BLUE;
-		ColorStyle tridentColor = PlotsFormatter.ColorStyle.MS_ORANGE;
-		ColorStyle elasticColor = PlotsFormatter.ColorStyle.MS_GREEN;
-		
-		// Create a plot formatting module.
-		PlotFormatModule module = new PlotFormatModule();
-		
-		// Get the histograms and add them to the module. Start with the
-		// trident and Møller plots.
-		for(int i = 0; i < plotNames1D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram1D allPlot = (IHistogram1D) tree.find(allPrefix + plotNames1D[i]);
-			IHistogram1D møllerPlot = (IHistogram1D) tree.find(møllerPrefix + plotNames1D[i]);
-			IHistogram1D tridentPlot = (IHistogram1D) tree.find(tridentPrefix + plotNames1D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNames1D[i], yAxisName1D, allTypeName + displayNames1D[i]);
-			FormattedPlot1D møllerFormattedPlot = new FormattedPlot1D(møllerPlot, møllerColor, xAxisNames1D[i], yAxisName1D, møllerTypeName + displayNames1D[i]);
-			FormattedPlot1D tridentFormattedPlot = new FormattedPlot1D(tridentPlot, tridentColor, xAxisNames1D[i], yAxisName1D, tridentTypeName + displayNames1D[i]);
-			
-			// Add them to the module.
-			module.addPlot1D(allFormattedPlot);
-			module.addPlot1D(møllerFormattedPlot);
-			module.addPlot1D(tridentFormattedPlot);
-		}
-		for(int i = 0; i < plotNames2D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNames2D[i]);
-			IHistogram2D møllerPlot = (IHistogram2D) tree.find(møllerPrefix + plotNames2D[i]);
-			IHistogram2D tridentPlot = (IHistogram2D) tree.find(tridentPrefix + plotNames2D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], allTypeName + displayNames2D[i]);
-			FormattedPlot2D møllerFormattedPlot = new FormattedPlot2D(møllerPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], møllerTypeName + displayNames2D[i]);
-			FormattedPlot2D tridentFormattedPlot = new FormattedPlot2D(tridentPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], tridentTypeName + displayNames2D[i]);
-			
-			// Add them to the module.
-			module.addPlot2D(allFormattedPlot);
-			module.addPlot2D(møllerFormattedPlot);
-			module.addPlot2D(tridentFormattedPlot);
-		}
-		
-		// Get the histograms for the elastic plots and add them to the module.
-		for(int i = 0; i < plotNamesElastic1D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram1D allPlot = (IHistogram1D) tree.find(allSinglesPrefix + plotNames1D[i]);
-			IHistogram1D elasticPlot = (IHistogram1D) tree.find(elasticPrefix + plotNames1D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
-					allSinglesTypeName + displayNamesElastic1D[i]);
-			FormattedPlot1D elasticFormattedPlot = new FormattedPlot1D(elasticPlot, elasticColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
-					elasticTypeName + displayNamesElastic1D[i]);
-			
-			// Add them to the module.
-			module.addPlot1D(allFormattedPlot);
-			module.addPlot1D(elasticFormattedPlot);
-		}
-		for(int i = 0; i < plotNamesElastic2D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNamesElastic2D[i]);
-			IHistogram2D elasticPlot = (IHistogram2D) tree.find(møllerPrefix + plotNamesElastic2D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
-					allSinglesTypeName + plotNames2D[i]);
-			FormattedPlot2D elasticFormattedPlot = new FormattedPlot2D(elasticPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
-					elasticTypeName + displayNamesElastic2D[i]);
-			
-			// Add them to the module.
-			module.addPlot2D(allFormattedPlot);
-			module.addPlot2D(elasticFormattedPlot);
-		}
-		
-		// Add the MTE plots to the module.
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution"), elasticColor,
-				"Momentum (GeV)", "Count", "Elastic - Momentum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks"), elasticColor,
-				"Tracks", "Count", "Elastic - Tracks in Event"));
-		
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution"), møllerColor,
-				"Momentum Sum (GeV)", "Count", "Møller - Momentum Sum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution"), møllerColor,
-				"Momentum (GeV)", "Count", "Møller - Momentum (Electron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)"), møllerColor,
-				"Time (ns)", "Count", "Møller - Time Coincidence"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks"), møllerColor,
-				"Tracks", "Count", "Møller - Tracks in Event"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution"), false,
-				"First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Møller - 2D Momentum Sum"));
-		
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution"), tridentColor,
-				"Momentum Sum (GeV)", "Count", "Trident - Momentum Sum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution"), tridentColor,
-				"Momentum (GeV)", "Count", "Trident - Momentum (Electron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Positron Energy Distribution"), tridentColor,
-				"Momentum (GeV)", "Count", "Trident - Momentum (Positron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks"), tridentColor,
-				"Tracks", "Count", "Trident - Tracks in Event"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution"), false,
-				"First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Trident - 2D Momentum Sum"));
-		
-		// Display the plots.
-		module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\TestPrint\\");
-	}
+    public static void main(String[] args) throws IllegalArgumentException, IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "5772-ana.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Define the 1D trigger plot names for Møllers and tridents.
+        String[] plotNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
+                "Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
+        String[] displayNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
+                "Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
+        String[] xAxisNames1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)",
+                "Coplanarity (Degrees)", "Energy Difference (GeV)", "Energy Slope (GeV)", "Energy Sum (GeV)" };
+        String yAxisName1D = "Count";
+        
+        // Define the 2D trigger plot names for Møllers and tridents.
+        String[] plotNames2D = { "Cluster Seed", "Pair Energy Sum 2D" };
+        String[] displayNames2D = { "Cluster Seed Distribution", "2D Energy Sum" };
+        String[] xAxisNames2D = { "x-Index", "Second Cluster Energy (GeV)" };
+        String[] yAxisNames2D = { "y-Index", "First Cluster Energy (GeV)" };
+        
+        // Define the 1D trigger plot names for elastics.
+        String[] plotNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
+        String[] displayNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
+        String[] xAxisNamesElastic1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)" };
+        String yAxisNameElastic1D = "Count";
+        
+        // Define the 2D trigger plot names for elastics.
+        String[] plotNamesElastic2D = { "Cluster Seed" };
+        String[] displayNamesElastic2D = { "Cluster Seed Distribution" };
+        String[] xAxisNamesElastic2D = { "x-Index" };
+        String[] yAxisNamesElastic2D = { "y-Index" };
+        
+        // Define the Møller, trident, and elastic prefixes.
+        String allPrefix = "All Trigger Plots/Pair Plots/";
+        String møllerPrefix = "Møller Trigger Plots/Pair Plots/";
+        String tridentPrefix = "Trident Trigger Plots/Pair Plots/";
+        String elasticPrefix = "Elastic Trigger Plots/Singles Plots/";
+        String allSinglesPrefix = "All Trigger Plots/Singles Plots/";
+        
+        // Define the plot type prefix.
+        String allTypeName = "All Pairs - ";
+        String møllerTypeName = "Møller - ";
+        String tridentTypeName = "Trident - ";
+        String elasticTypeName = "Elastic - ";
+        String allSinglesTypeName = "All Singles - ";
+        
+        // Define the plot type colors.
+        ColorStyle allColor = PlotsFormatter.ColorStyle.GREY;
+        ColorStyle møllerColor = PlotsFormatter.ColorStyle.MS_BLUE;
+        ColorStyle tridentColor = PlotsFormatter.ColorStyle.MS_ORANGE;
+        ColorStyle elasticColor = PlotsFormatter.ColorStyle.MS_GREEN;
+        
+        // Create a plot formatting module.
+        PlotFormatModule module = new PlotFormatModule();
+        
+        // Get the histograms and add them to the module. Start with the
+        // trident and Møller plots.
+        for(int i = 0; i < plotNames1D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram1D allPlot = (IHistogram1D) tree.find(allPrefix + plotNames1D[i]);
+            IHistogram1D møllerPlot = (IHistogram1D) tree.find(møllerPrefix + plotNames1D[i]);
+            IHistogram1D tridentPlot = (IHistogram1D) tree.find(tridentPrefix + plotNames1D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNames1D[i], yAxisName1D, allTypeName + displayNames1D[i]);
+            FormattedPlot1D møllerFormattedPlot = new FormattedPlot1D(møllerPlot, møllerColor, xAxisNames1D[i], yAxisName1D, møllerTypeName + displayNames1D[i]);
+            FormattedPlot1D tridentFormattedPlot = new FormattedPlot1D(tridentPlot, tridentColor, xAxisNames1D[i], yAxisName1D, tridentTypeName + displayNames1D[i]);
+            
+            // Add them to the module.
+            module.addPlot1D(allFormattedPlot);
+            module.addPlot1D(møllerFormattedPlot);
+            module.addPlot1D(tridentFormattedPlot);
+        }
+        for(int i = 0; i < plotNames2D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNames2D[i]);
+            IHistogram2D møllerPlot = (IHistogram2D) tree.find(møllerPrefix + plotNames2D[i]);
+            IHistogram2D tridentPlot = (IHistogram2D) tree.find(tridentPrefix + plotNames2D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], allTypeName + displayNames2D[i]);
+            FormattedPlot2D møllerFormattedPlot = new FormattedPlot2D(møllerPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], møllerTypeName + displayNames2D[i]);
+            FormattedPlot2D tridentFormattedPlot = new FormattedPlot2D(tridentPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], tridentTypeName + displayNames2D[i]);
+            
+            // Add them to the module.
+            module.addPlot2D(allFormattedPlot);
+            module.addPlot2D(møllerFormattedPlot);
+            module.addPlot2D(tridentFormattedPlot);
+        }
+        
+        // Get the histograms for the elastic plots and add them to the module.
+        for(int i = 0; i < plotNamesElastic1D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram1D allPlot = (IHistogram1D) tree.find(allSinglesPrefix + plotNames1D[i]);
+            IHistogram1D elasticPlot = (IHistogram1D) tree.find(elasticPrefix + plotNames1D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
+                    allSinglesTypeName + displayNamesElastic1D[i]);
+            FormattedPlot1D elasticFormattedPlot = new FormattedPlot1D(elasticPlot, elasticColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
+                    elasticTypeName + displayNamesElastic1D[i]);
+            
+            // Add them to the module.
+            module.addPlot1D(allFormattedPlot);
+            module.addPlot1D(elasticFormattedPlot);
+        }
+        for(int i = 0; i < plotNamesElastic2D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNamesElastic2D[i]);
+            IHistogram2D elasticPlot = (IHistogram2D) tree.find(møllerPrefix + plotNamesElastic2D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
+                    allSinglesTypeName + plotNames2D[i]);
+            FormattedPlot2D elasticFormattedPlot = new FormattedPlot2D(elasticPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
+                    elasticTypeName + displayNamesElastic2D[i]);
+            
+            // Add them to the module.
+            module.addPlot2D(allFormattedPlot);
+            module.addPlot2D(elasticFormattedPlot);
+        }
+        
+        // Add the MTE plots to the module.
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution"), elasticColor,
+                "Momentum (GeV)", "Count", "Elastic - Momentum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks"), elasticColor,
+                "Tracks", "Count", "Elastic - Tracks in Event"));
+        
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution"), møllerColor,
+                "Momentum Sum (GeV)", "Count", "Møller - Momentum Sum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution"), møllerColor,
+                "Momentum (GeV)", "Count", "Møller - Momentum (Electron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)"), møllerColor,
+                "Time (ns)", "Count", "Møller - Time Coincidence"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks"), møllerColor,
+                "Tracks", "Count", "Møller - Tracks in Event"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution"), false,
+                "First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Møller - 2D Momentum Sum"));
+        
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution"), tridentColor,
+                "Momentum Sum (GeV)", "Count", "Trident - Momentum Sum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution"), tridentColor,
+                "Momentum (GeV)", "Count", "Trident - Momentum (Electron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Positron Energy Distribution"), tridentColor,
+                "Momentum (GeV)", "Count", "Trident - Momentum (Positron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks"), tridentColor,
+                "Tracks", "Count", "Trident - Tracks in Event"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution"), false,
+                "First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Trident - 2D Momentum Sum"));
+        
+        // Display the plots.
+        module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\TestPrint\\");
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ParticleMCAnalysisDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ParticleMCAnalysisDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/ParticleMCAnalysisDriver.java	Wed Apr 27 11:11:32 2016
@@ -13,136 +13,136 @@
 import org.lcsim.util.aida.AIDA;
 
 public class ParticleMCAnalysisDriver extends Driver {
-	// Store collection names.
-	private String particleCollectionName = "MCParticle";
-	
-	// Declare plots.
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D chargedTracksPlot = aida.histogram1D("MC Analysis/Event Tracks", 10, -0.5, 9.5);
-	private IHistogram1D allPlot = aida.histogram1D("MC Analysis/Electron Energy Distribution", 110, 0, 1.1);
-	private IHistogram1D electronPlot = aida.histogram1D("MC Analysis/Electron Energy Distribution", 110, 0, 1.1);
-	private IHistogram1D positronPlot = aida.histogram1D("MC Analysis/Positron Energy Distribution", 110, 0, 1.1);
-	private IHistogram1D momentumXPlot = aida.histogram1D("MC Analysis/Particle x-Momentum Distribution", 110, 0.0, 1.1);
-	private IHistogram1D momentumYPlot = aida.histogram1D("MC Analysis/Particle y-Momentum Distribution", 110, 0.0, 1.1);
-	private IHistogram1D momentumZPlot = aida.histogram1D("MC Analysis/Particle z-Momentum Distribution", 110, 0.0, 1.1);
-	private IHistogram1D epAnglePlot = aida.histogram1D("MC Analysis/Positron\\Electron Pair Angle Distribution", 90, 0, 180);
-	private IHistogram1D eeAnglePlot = aida.histogram1D("MC Analysis/Electron\\Electron Pair Angle Distribution", 90, 0, 180);
-	private IHistogram1D epMomentumSumPlot = aida.histogram1D("MC Analysis/Positron\\Electron Momentum Sum Distribution", 220, 0, 2.2);
-	private IHistogram1D eeMomentumSumPlot = aida.histogram1D("MC Analysis/Electron\\Electron Momentum Sum Distribution", 220, 0, 2.2);
-	private IHistogram2D momentumPlot = aida.histogram2D("MC Analysis/Particle Momentum Distribution", 100, 0.0, 0.40, 110, 0.0, 0.40);
-	private IHistogram2D epMomentumSum2DPlot = aida.histogram2D("MC Analysis/Positron\\Electron 2D Momentum Distribution", 55, 0, 1.1, 55, 0, 1.1);
-	private IHistogram2D eeMomentumSum2DPlot = aida.histogram2D("MC Analysis/Electron\\Electron 2D Momentum Distribution", 55, 0, 1.1, 55, 0, 1.1);
-	
-	@Override
-	public void process(EventHeader event) {
-		// Skip the event if there is no Monte Carlo collection.
-		if(!event.hasCollection(MCParticle.class, particleCollectionName)) {
-			return;
-		}
-		
-		// Get the list of Monte Carlo particles.
-		List<MCParticle> particleList = event.get(MCParticle.class, particleCollectionName);
-		
-		// Track the positive and negative particles.
-		List<MCParticle> electronList = new ArrayList<MCParticle>();
-		List<MCParticle> positronList = new ArrayList<MCParticle>();
-		
-		// Count the number of particles in the event.
-		int chargedParticles = 0;
-		
-		// Iterate through the particles.
-		for(MCParticle particle : particleList) {
-			// Look at only t = 0 particles.
-			if(particle.getProductionTime() == 0) {
-				// Plot the x/y momentum of each particle.
-				momentumPlot.fill(particle.getMomentum().x(), particle.getMomentum().y());
-				
-				// If the particle is charged, increment the charged
-				// particle count.
-				if(particle.getCharge() > 0) {
-					chargedParticles++;
-				}
-				
-				// Get the particle momentum in each direction.
-				momentumXPlot.fill(particle.getMomentum().x());
-				momentumYPlot.fill(particle.getMomentum().y());
-				momentumZPlot.fill(particle.getMomentum().z());
-				
-				// Populate the general momentum plot.
-				allPlot.fill(particle.getMomentum().magnitude());
-				momentumPlot.fill(particle.getMomentum().x(), particle.getMomentum().y());
-				
-				// Store each particle based on its PID and populate
-				// the appropriate plot.
-				if(particle.getPDGID() == 11) {
-					electronList.add(particle);
-					electronPlot.fill(particle.getMomentum().magnitude());
-				} else if(particle.getPDGID() == -11) {
-					positronList.add(particle);
-					positronPlot.fill(particle.getMomentum().magnitude());
-				}
-			}
-		}
-		
-		// Populate the charged particles plot.
-		chargedTracksPlot.fill(chargedParticles);
-		
-		// Form all electron/positron pairs.
-		List<MCParticle[]> epPairList = new ArrayList<MCParticle[]>();
-		for(MCParticle electron : electronList) {
-			for(MCParticle positron : positronList) {
-				epPairList.add(new MCParticle[] { electron, positron });
-			}
-		}
-		
-		// Populate the positron/electron pair plots.
-		for(MCParticle[] pair : epPairList) {
-			epAnglePlot.fill(getVectorAngle(pair[0].getMomentum(), pair[1].getMomentum()));
-			epMomentumSumPlot.fill(getVectorSum(pair[0].getMomentum(), pair[1].getMomentum()));
-			epMomentumSum2DPlot.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-		}
-		
-		// Form all electron/electron pairs.
-		List<MCParticle[]> eePairList = new ArrayList<MCParticle[]>();
-		for(int i = 0; i < electronList.size(); i++) {
-			for(int j = i + 1; j < electronList.size(); j++) {
-				eePairList.add(new MCParticle[] { electronList.get(i), electronList.get(j) });
-			}
-		}
-		
-		// Populate the electron/electron pair plots.
-		for(MCParticle[] pair : eePairList) {
-			eeAnglePlot.fill(getVectorAngle(pair[0].getMomentum(), pair[1].getMomentum()));
-			eeMomentumSumPlot.fill(getVectorSum(pair[0].getMomentum(), pair[1].getMomentum()));
-			eeMomentumSum2DPlot.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-		}
-	}
-	
-	private static final double getVectorSum(Hep3Vector v1, Hep3Vector v2) {
-		// Calculate the sum of the sum of the vector components, squared.
-		double sum = 0;
-		for(int i = 0; i < 3; i++) {
-			double elementSum = v1.v()[i] + v2.v()[i];
-			sum += (elementSum * elementSum);
-		}
-		
-		// Return the square root of the sum.
-		return Math.sqrt(sum);
-	}
-	
-	private static final double getVectorAngle(Hep3Vector v1, Hep3Vector v2) {
-		// The vector angle is defined as Acos[(v1 · v2) / (‖v1‖ × ‖v2‖)]
-		return Math.acos(getDotProduct(v1, v2) / (v1.magnitude() * v2.magnitude())) / Math.PI * 180.0;
-	}
-	
-	private static final double getDotProduct(Hep3Vector v1, Hep3Vector v2) {
-		// Calculate the sum of the vector element products.
-		int product = 0;
-		for(int i = 0; i < 3; i++) {
-			product += (v1.v()[i] * v2.v()[i]);
-		}
-		
-		// Return the result.
-		return product;
-	}
+    // Store collection names.
+    private String particleCollectionName = "MCParticle";
+    
+    // Declare plots.
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D chargedTracksPlot = aida.histogram1D("MC Analysis/Event Tracks", 10, -0.5, 9.5);
+    private IHistogram1D allPlot = aida.histogram1D("MC Analysis/Electron Energy Distribution", 110, 0, 1.1);
+    private IHistogram1D electronPlot = aida.histogram1D("MC Analysis/Electron Energy Distribution", 110, 0, 1.1);
+    private IHistogram1D positronPlot = aida.histogram1D("MC Analysis/Positron Energy Distribution", 110, 0, 1.1);
+    private IHistogram1D momentumXPlot = aida.histogram1D("MC Analysis/Particle x-Momentum Distribution", 110, 0.0, 1.1);
+    private IHistogram1D momentumYPlot = aida.histogram1D("MC Analysis/Particle y-Momentum Distribution", 110, 0.0, 1.1);
+    private IHistogram1D momentumZPlot = aida.histogram1D("MC Analysis/Particle z-Momentum Distribution", 110, 0.0, 1.1);
+    private IHistogram1D epAnglePlot = aida.histogram1D("MC Analysis/Positron\\Electron Pair Angle Distribution", 90, 0, 180);
+    private IHistogram1D eeAnglePlot = aida.histogram1D("MC Analysis/Electron\\Electron Pair Angle Distribution", 90, 0, 180);
+    private IHistogram1D epMomentumSumPlot = aida.histogram1D("MC Analysis/Positron\\Electron Momentum Sum Distribution", 220, 0, 2.2);
+    private IHistogram1D eeMomentumSumPlot = aida.histogram1D("MC Analysis/Electron\\Electron Momentum Sum Distribution", 220, 0, 2.2);
+    private IHistogram2D momentumPlot = aida.histogram2D("MC Analysis/Particle Momentum Distribution", 100, 0.0, 0.40, 110, 0.0, 0.40);
+    private IHistogram2D epMomentumSum2DPlot = aida.histogram2D("MC Analysis/Positron\\Electron 2D Momentum Distribution", 55, 0, 1.1, 55, 0, 1.1);
+    private IHistogram2D eeMomentumSum2DPlot = aida.histogram2D("MC Analysis/Electron\\Electron 2D Momentum Distribution", 55, 0, 1.1, 55, 0, 1.1);
+    
+    @Override
+    public void process(EventHeader event) {
+        // Skip the event if there is no Monte Carlo collection.
+        if(!event.hasCollection(MCParticle.class, particleCollectionName)) {
+            return;
+        }
+        
+        // Get the list of Monte Carlo particles.
+        List<MCParticle> particleList = event.get(MCParticle.class, particleCollectionName);
+        
+        // Track the positive and negative particles.
+        List<MCParticle> electronList = new ArrayList<MCParticle>();
+        List<MCParticle> positronList = new ArrayList<MCParticle>();
+        
+        // Count the number of particles in the event.
+        int chargedParticles = 0;
+        
+        // Iterate through the particles.
+        for(MCParticle particle : particleList) {
+            // Look at only t = 0 particles.
+            if(particle.getProductionTime() == 0) {
+                // Plot the x/y momentum of each particle.
+                momentumPlot.fill(particle.getMomentum().x(), particle.getMomentum().y());
+                
+                // If the particle is charged, increment the charged
+                // particle count.
+                if(particle.getCharge() > 0) {
+                    chargedParticles++;
+                }
+                
+                // Get the particle momentum in each direction.
+                momentumXPlot.fill(particle.getMomentum().x());
+                momentumYPlot.fill(particle.getMomentum().y());
+                momentumZPlot.fill(particle.getMomentum().z());
+                
+                // Populate the general momentum plot.
+                allPlot.fill(particle.getMomentum().magnitude());
+                momentumPlot.fill(particle.getMomentum().x(), particle.getMomentum().y());
+                
+                // Store each particle based on its PID and populate
+                // the appropriate plot.
+                if(particle.getPDGID() == 11) {
+                    electronList.add(particle);
+                    electronPlot.fill(particle.getMomentum().magnitude());
+                } else if(particle.getPDGID() == -11) {
+                    positronList.add(particle);
+                    positronPlot.fill(particle.getMomentum().magnitude());
+                }
+            }
+        }
+        
+        // Populate the charged particles plot.
+        chargedTracksPlot.fill(chargedParticles);
+        
+        // Form all electron/positron pairs.
+        List<MCParticle[]> epPairList = new ArrayList<MCParticle[]>();
+        for(MCParticle electron : electronList) {
+            for(MCParticle positron : positronList) {
+                epPairList.add(new MCParticle[] { electron, positron });
+            }
+        }
+        
+        // Populate the positron/electron pair plots.
+        for(MCParticle[] pair : epPairList) {
+            epAnglePlot.fill(getVectorAngle(pair[0].getMomentum(), pair[1].getMomentum()));
+            epMomentumSumPlot.fill(getVectorSum(pair[0].getMomentum(), pair[1].getMomentum()));
+            epMomentumSum2DPlot.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+        }
+        
+        // Form all electron/electron pairs.
+        List<MCParticle[]> eePairList = new ArrayList<MCParticle[]>();
+        for(int i = 0; i < electronList.size(); i++) {
+            for(int j = i + 1; j < electronList.size(); j++) {
+                eePairList.add(new MCParticle[] { electronList.get(i), electronList.get(j) });
+            }
+        }
+        
+        // Populate the electron/electron pair plots.
+        for(MCParticle[] pair : eePairList) {
+            eeAnglePlot.fill(getVectorAngle(pair[0].getMomentum(), pair[1].getMomentum()));
+            eeMomentumSumPlot.fill(getVectorSum(pair[0].getMomentum(), pair[1].getMomentum()));
+            eeMomentumSum2DPlot.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+        }
+    }
+    
+    private static final double getVectorSum(Hep3Vector v1, Hep3Vector v2) {
+        // Calculate the sum of the sum of the vector components, squared.
+        double sum = 0;
+        for(int i = 0; i < 3; i++) {
+            double elementSum = v1.v()[i] + v2.v()[i];
+            sum += (elementSum * elementSum);
+        }
+        
+        // Return the square root of the sum.
+        return Math.sqrt(sum);
+    }
+    
+    private static final double getVectorAngle(Hep3Vector v1, Hep3Vector v2) {
+        // The vector angle is defined as Acos[(v1 · v2) / (‖v1‖ × ‖v2‖)]
+        return Math.acos(getDotProduct(v1, v2) / (v1.magnitude() * v2.magnitude())) / Math.PI * 180.0;
+    }
+    
+    private static final double getDotProduct(Hep3Vector v1, Hep3Vector v2) {
+        // Calculate the sum of the vector element products.
+        int product = 0;
+        for(int i = 0; i < 3; i++) {
+            product += (v1.v()[i] * v2.v()[i]);
+        }
+        
+        // Return the result.
+        return product;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/PlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/PlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/PlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -8,120 +8,120 @@
 import java.awt.Font;
 
 public class PlotsFormatter {
-	// Define plot fonts.
-	public static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 30);
-	public static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  35);
-	public static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  45);
-	
-	// Defines the color style options for plot data.
-	public static enum ColorStyle {
-		 MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
-		  MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
-		MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
-		    RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
-		  FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
-		    TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
-		    BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
-		  PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
-		
-		private final Color fillColor;
-		private final Color lineColor;
-		
-		private ColorStyle(Color fillColor, Color lineColor) {
-			this.fillColor = fillColor;
-			this.lineColor = lineColor;
-		}
-		
-		public Color getFillColor() { return fillColor; }
-		
-		public Color getLineColor() { return lineColor; }
-	};
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	public static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the names of each plot on in the region.
-		String[] dataNames = region.getAllDataNames();
-		
-		// Check whether this is an overlay plot. Overlay plots contain
-		// more than one data name.
-		boolean overlay = (dataNames.length > 1 ? true : false);
-		
-		// Iterate over each plot in the region.
-		for(int i = 0; i < dataNames.length; i++) {
-			// Set the overlay style if needed.
-			if(overlay) {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with no fill. The color is set by the "color" argument.
-				fillStyle.setHistogramFill(false);
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarLineColor(color[i].getFillColor());
-				
-				// Set the legend text style.
-				region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
-			}
-			
-			// Otherwise, set the fill style for a single plot.
-			else {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with a fill color. The colors are defined by the
-				// "color" argument.
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarColor(color[i].getFillColor());
-				fillStyle.setHistogramBarLineColor(color[i].getLineColor());
-			}
-			
-			// Set the statistics box style.
-			region.getPlot().getStats().setVisible(true);
-			region.getPlot().getStats().setFont(BASIC_FONT);
-			
-			// Set the title font.
-			region.getPlot().getTitleObject().setFont(TITLE_FONT);
-			
-			// Set the axis tick-mark fonts.
-			region.getPlot().getXAxis().setFont(BASIC_FONT);
-			region.getPlot().getYAxis().setFont(BASIC_FONT);
-			region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-			region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 */
-	public static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
-		// Get the fill style object. 2D plots should never be overlay
-		// plots, so there should only ever be one data name.
-		JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		
-		// Set the fill style for a two-dimensional plot.
-		if(logarithmic) { fillStyle.setLogZ(true); }
-		fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
-		fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
-		
-		// Make the statistics box invisible.
-		region.getPlot().getStats().setVisible(false);
-		
-		// Set the general plot font (which is also the z-axis font).
-		region.getPlot().setFont(BASIC_FONT);
-		
-		// Set the title font.
-		region.getPlot().getTitleObject().setFont(TITLE_FONT);
-		
-		// Set the axis tick-mark fonts.
-		region.getPlot().getXAxis().setFont(BASIC_FONT);
-		region.getPlot().getYAxis().setFont(BASIC_FONT);
-		region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-		region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-	}
+    // Define plot fonts.
+    public static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 30);
+    public static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  35);
+    public static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  45);
+    
+    // Defines the color style options for plot data.
+    public static enum ColorStyle {
+         MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
+          MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
+        MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
+            RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
+          FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
+            TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
+            BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
+          PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
+        
+        private final Color fillColor;
+        private final Color lineColor;
+        
+        private ColorStyle(Color fillColor, Color lineColor) {
+            this.fillColor = fillColor;
+            this.lineColor = lineColor;
+        }
+        
+        public Color getFillColor() { return fillColor; }
+        
+        public Color getLineColor() { return lineColor; }
+    };
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    public static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the names of each plot on in the region.
+        String[] dataNames = region.getAllDataNames();
+        
+        // Check whether this is an overlay plot. Overlay plots contain
+        // more than one data name.
+        boolean overlay = (dataNames.length > 1 ? true : false);
+        
+        // Iterate over each plot in the region.
+        for(int i = 0; i < dataNames.length; i++) {
+            // Set the overlay style if needed.
+            if(overlay) {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with no fill. The color is set by the "color" argument.
+                fillStyle.setHistogramFill(false);
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarLineColor(color[i].getFillColor());
+                
+                // Set the legend text style.
+                region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
+            }
+            
+            // Otherwise, set the fill style for a single plot.
+            else {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with a fill color. The colors are defined by the
+                // "color" argument.
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarColor(color[i].getFillColor());
+                fillStyle.setHistogramBarLineColor(color[i].getLineColor());
+            }
+            
+            // Set the statistics box style.
+            region.getPlot().getStats().setVisible(true);
+            region.getPlot().getStats().setFont(BASIC_FONT);
+            
+            // Set the title font.
+            region.getPlot().getTitleObject().setFont(TITLE_FONT);
+            
+            // Set the axis tick-mark fonts.
+            region.getPlot().getXAxis().setFont(BASIC_FONT);
+            region.getPlot().getYAxis().setFont(BASIC_FONT);
+            region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+            region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     */
+    public static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
+        // Get the fill style object. 2D plots should never be overlay
+        // plots, so there should only ever be one data name.
+        JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        
+        // Set the fill style for a two-dimensional plot.
+        if(logarithmic) { fillStyle.setLogZ(true); }
+        fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
+        fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
+        
+        // Make the statistics box invisible.
+        region.getPlot().getStats().setVisible(false);
+        
+        // Set the general plot font (which is also the z-axis font).
+        region.getPlot().setFont(BASIC_FONT);
+        
+        // Set the title font.
+        region.getPlot().getTitleObject().setFont(TITLE_FONT);
+        
+        // Set the axis tick-mark fonts.
+        region.getPlot().getXAxis().setFont(BASIC_FONT);
+        region.getPlot().getYAxis().setFont(BASIC_FONT);
+        region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+        region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/RafoAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/RafoAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/RafoAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -16,431 +16,431 @@
 import org.lcsim.util.aida.AIDA;
 
 public class RafoAnalysis extends Driver {
-	private boolean useGoodSVT = false;
-	private String clusterCollectionName = "EcalClustersCorr";
-	private String particleCollectionName = "FinalStateParticles";
-	
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D t0TimeCoincidenceAll          = aida.histogram1D("Tier 0/Time Coincidence",                    300, -15.0, 15.0);
-	private IHistogram1D t0TimeCoincidenceFiducial     = aida.histogram1D("Tier 0/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
-	private IHistogram1D t0EnergySumAll                = aida.histogram1D("Tier 0/Energy Sum",                          300,   0.0,  1.5);
-	private IHistogram1D t0EnergySumFiducial           = aida.histogram1D("Tier 0/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
-	private IHistogram1D t0InvariantMassAll            = aida.histogram1D("Tier 0/Invariant Mass",                     2200,   0.0,  1.1);
-	private IHistogram2D t0EnergySum2DAll              = aida.histogram2D("Tier 0/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t0EnergySum2DFiducial         = aida.histogram2D("Tier 0/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t0SumCoplanarityAll           = aida.histogram2D("Tier 0/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t0SumCoplanarityFiducial      = aida.histogram2D("Tier 0/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t0SumCoplanarityCalcAll       = aida.histogram2D("Tier 0/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t0SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 0/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t0TimeEnergyAll               = aida.histogram2D("Tier 0/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100,   0, 100);
-	private IHistogram2D t0TimeEnergyFiducial          = aida.histogram2D("Tier 0/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100,   0, 100);
-	
-	private IHistogram1D t1TimeCoincidenceAll          = aida.histogram1D("Tier 1/Time Coincidence",                    300, -15.0, 15.0);
-	private IHistogram1D t1TimeCoincidenceFiducial     = aida.histogram1D("Tier 1/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
-	private IHistogram1D t1EnergySumAll                = aida.histogram1D("Tier 1/Energy Sum",                          300,   0.0,  1.5);
-	private IHistogram1D t1EnergySumFiducial           = aida.histogram1D("Tier 1/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
-	private IHistogram1D t1InvariantMassAll            = aida.histogram1D("Tier 1/Invariant Mass",                     2200,   0.0,  1.1);
-	private IHistogram2D t1EnergySum2DAll              = aida.histogram2D("Tier 1/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t1EnergySum2DFiducial         = aida.histogram2D("Tier 1/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t1SumCoplanarityAll           = aida.histogram2D("Tier 1/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t1SumCoplanarityFiducial      = aida.histogram2D("Tier 1/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t1SumCoplanarityCalcAll       = aida.histogram2D("Tier 1/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t1SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 1/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t1TimeEnergyAll               = aida.histogram2D("Tier 1/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100, 0, 100);
-	private IHistogram2D t1TimeEnergyFiducial          = aida.histogram2D("Tier 1/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100, 0, 100);
-	
-	private IHistogram1D t2TimeCoincidenceAll          = aida.histogram1D("Tier 2/Time Coincidence",                    300, -15.0, 15.0);
-	private IHistogram1D t2TimeCoincidenceFiducial     = aida.histogram1D("Tier 2/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
-	private IHistogram1D t2EnergySumAll                = aida.histogram1D("Tier 2/Energy Sum",                          300,   0.0,  1.5);
-	private IHistogram1D t2EnergySumFiducial           = aida.histogram1D("Tier 2/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
-	private IHistogram1D t2InvariantMassAll            = aida.histogram1D("Tier 2/Invariant Mass",                     2200,   0.0,  1.1);
-	private IHistogram2D t2EnergySum2DAll              = aida.histogram2D("Tier 2/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t2EnergySum2DFiducial         = aida.histogram2D("Tier 2/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
-	private IHistogram2D t2SumCoplanarityAll           = aida.histogram2D("Tier 2/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t2SumCoplanarityFiducial      = aida.histogram2D("Tier 2/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
-	private IHistogram2D t2SumCoplanarityCalcAll       = aida.histogram2D("Tier 2/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t2SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 2/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
-	private IHistogram2D t2TimeEnergyAll               = aida.histogram2D("Tier 2/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100,   0, 100);
-	private IHistogram2D t2TimeEnergyFiducial          = aida.histogram2D("Tier 2/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100,   0, 100);
-	
-	private int t0Events = 0;
-	private int t1Events = 0;
-	private int t2Events = 0;
-	
-	@Override
-	public void endOfData() {
-		System.out.printf("Tier 0 Events: %d%n", t0Events);
-		System.out.printf("Tier 1 Events: %d%n", t1Events);
-		System.out.printf("Tier 2 Events: %d%n", t2Events);
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Check whether the SVT was active in this event.
-		final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
-		boolean svtGood = true;
+    private boolean useGoodSVT = false;
+    private String clusterCollectionName = "EcalClustersCorr";
+    private String particleCollectionName = "FinalStateParticles";
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D t0TimeCoincidenceAll          = aida.histogram1D("Tier 0/Time Coincidence",                    300, -15.0, 15.0);
+    private IHistogram1D t0TimeCoincidenceFiducial     = aida.histogram1D("Tier 0/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
+    private IHistogram1D t0EnergySumAll                = aida.histogram1D("Tier 0/Energy Sum",                          300,   0.0,  1.5);
+    private IHistogram1D t0EnergySumFiducial           = aida.histogram1D("Tier 0/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
+    private IHistogram1D t0InvariantMassAll            = aida.histogram1D("Tier 0/Invariant Mass",                     2200,   0.0,  1.1);
+    private IHistogram2D t0EnergySum2DAll              = aida.histogram2D("Tier 0/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t0EnergySum2DFiducial         = aida.histogram2D("Tier 0/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t0SumCoplanarityAll           = aida.histogram2D("Tier 0/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t0SumCoplanarityFiducial      = aida.histogram2D("Tier 0/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t0SumCoplanarityCalcAll       = aida.histogram2D("Tier 0/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t0SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 0/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t0TimeEnergyAll               = aida.histogram2D("Tier 0/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100,   0, 100);
+    private IHistogram2D t0TimeEnergyFiducial          = aida.histogram2D("Tier 0/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100,   0, 100);
+    
+    private IHistogram1D t1TimeCoincidenceAll          = aida.histogram1D("Tier 1/Time Coincidence",                    300, -15.0, 15.0);
+    private IHistogram1D t1TimeCoincidenceFiducial     = aida.histogram1D("Tier 1/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
+    private IHistogram1D t1EnergySumAll                = aida.histogram1D("Tier 1/Energy Sum",                          300,   0.0,  1.5);
+    private IHistogram1D t1EnergySumFiducial           = aida.histogram1D("Tier 1/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
+    private IHistogram1D t1InvariantMassAll            = aida.histogram1D("Tier 1/Invariant Mass",                     2200,   0.0,  1.1);
+    private IHistogram2D t1EnergySum2DAll              = aida.histogram2D("Tier 1/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t1EnergySum2DFiducial         = aida.histogram2D("Tier 1/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t1SumCoplanarityAll           = aida.histogram2D("Tier 1/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t1SumCoplanarityFiducial      = aida.histogram2D("Tier 1/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t1SumCoplanarityCalcAll       = aida.histogram2D("Tier 1/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t1SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 1/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t1TimeEnergyAll               = aida.histogram2D("Tier 1/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100, 0, 100);
+    private IHistogram2D t1TimeEnergyFiducial          = aida.histogram2D("Tier 1/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100, 0, 100);
+    
+    private IHistogram1D t2TimeCoincidenceAll          = aida.histogram1D("Tier 2/Time Coincidence",                    300, -15.0, 15.0);
+    private IHistogram1D t2TimeCoincidenceFiducial     = aida.histogram1D("Tier 2/Time Coincidence (Fiducial Region)",  300, -15.0, 15.0);
+    private IHistogram1D t2EnergySumAll                = aida.histogram1D("Tier 2/Energy Sum",                          300,   0.0,  1.5);
+    private IHistogram1D t2EnergySumFiducial           = aida.histogram1D("Tier 2/Energy Sum (Fiducial Region)",        300,   0.0,  1.5);
+    private IHistogram1D t2InvariantMassAll            = aida.histogram1D("Tier 2/Invariant Mass",                     2200,   0.0,  1.1);
+    private IHistogram2D t2EnergySum2DAll              = aida.histogram2D("Tier 2/Top Cluster Energy vs. Bottom Cluster Energy",                   300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t2EnergySum2DFiducial         = aida.histogram2D("Tier 2/Top Cluster Energy vs. Bottom Cluster Energy (Fiducial Region)", 300, 0, 1.5, 300,   0, 1.5);
+    private IHistogram2D t2SumCoplanarityAll           = aida.histogram2D("Tier 2/Hardware Coplanarity vs. Energy Sum",                            300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t2SumCoplanarityFiducial      = aida.histogram2D("Tier 2/Hardware Coplanarity vs. Energy Sum (Fiducial Region)",          300, 0, 1.5, 115,   0, 230);
+    private IHistogram2D t2SumCoplanarityCalcAll       = aida.histogram2D("Tier 2/Calculated Coplanarity vs. Energy Sum",                          300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t2SumCoplanarityCalcFiducial  = aida.histogram2D("Tier 2/Calculated Coplanarity vs. Energy Sum (Fiducial Region)",        300, 0, 1.5, 115, 130, 230);
+    private IHistogram2D t2TimeEnergyAll               = aida.histogram2D("Tier 2/Cluster Time vs. Cluster Energy",                                300, 0, 1.5, 100,   0, 100);
+    private IHistogram2D t2TimeEnergyFiducial          = aida.histogram2D("Tier 2/Cluster Time vs. Cluster Energy (Fiducial Region)",              300, 0, 1.5, 100,   0, 100);
+    
+    private int t0Events = 0;
+    private int t1Events = 0;
+    private int t2Events = 0;
+    
+    @Override
+    public void endOfData() {
+        System.out.printf("Tier 0 Events: %d%n", t0Events);
+        System.out.printf("Tier 1 Events: %d%n", t1Events);
+        System.out.printf("Tier 2 Events: %d%n", t2Events);
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Check whether the SVT was active in this event.
+        final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
+        boolean svtGood = true;
         for(int i = 0; i < flagNames.length; i++) {
             int[] flag = event.getIntegerParameters().get(flagNames[i]);
             if(flag == null || flag[0] == 0) {
                 svtGood = false;
             }
         }
-		
+        
         // If the SVT is not properly running, skip the event.
         if(!svtGood && useGoodSVT) { return; }
         
-		// Get the list of particles, if it exists.
-		List<ReconstructedParticle> trackList = null;
-		if(event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
-			trackList = event.get(ReconstructedParticle.class, particleCollectionName);
-		}
-		
-		// Get the list of clusters, if it exists.
-		List<Cluster> clusterList = null;
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			clusterList = event.get(Cluster.class, clusterCollectionName);
-		}
-		
-		// Make sure that the cluster and track lists both exist.
-		if(clusterList == null || trackList == null) {
-			return;
-		}
-		
-		// Perform tier 1 analysis. This requires that there be at
-		// least one top/bottom cluster pair with a time difference
-		// of less then 4 ns.
-		double t1TimeThreshold = 1.5;
-		
-		// Get a list of cluster pairs.
-		List<Cluster[]> pairList = getClusterPairs(clusterList);
-		
-		// Iterate over the cluster pairs.
-		boolean t1Passed = false;
-		t1ClusterLoop:
-		for(Cluster[] pair : pairList) {
-			// Check that the time difference for the cluster pair
-			// meets the time cut.
-			if(TriggerModule.getValueTimeCoincidence(pair) <= t1TimeThreshold) {
-				// Note that the tier 1 analysis condition passed.
-				t1Passed = true;
-				
-				// Break from the loop.
-				break t1ClusterLoop;
-			}
-		}
-		
-		// Perform the additional checks for tier 2 analysis. This
-		// requires that there be at least one top/bottom track pair
-		// and that one track be positive and the other be negative.
-		
-		// Get a list of top and bottom track pairs.
-		List<ReconstructedParticle[]> trackPairList = getTrackPairs(trackList);
-		
-		// Check that at least one top/bottom track has one negative and
-		// one positive track.
-		boolean t2Passed = false;
-		t2TrackLoop:
-		for(ReconstructedParticle[] pair : trackPairList) {
-			if((pair[0].getCharge() > 0 && pair[1].getCharge() < 0) || (pair[0].getCharge() < 0 && pair[1].getCharge() > 0)) {
-				t2Passed = true;
-				break t2TrackLoop;
-			}
-		}
-		
-		// Populate the tier 0 analysis plot.
-		if(true) {
-			// Increment the number of tier 1 events found.
-			t0Events++;
-			
-			// Track which clusters have already been added to the
-			// singles plot so that there are no repeats.
-			Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
-			Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
-			
-			for(ReconstructedParticle[] pair : trackPairList) {
-				t0InvariantMassAll.fill(getInvariantMass(pair));
-			}
-			
-			for(Cluster[] pair : pairList) {
-				// Fill the all pairs plots.
-				double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
-				t0EnergySumAll.fill(pairEnergy);
-				t0EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
-				t0TimeCoincidenceAll.fill(getTimeConicidence(pair));
-				t0SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
-				t0SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				
-				// Fill the singles plots.
-				if(!plotSet.contains(pair[0])) {
-					plotSet.add(pair[0]);
-					t0TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotSet.contains(pair[1])) {
-					plotSet.add(pair[1]);
-					t0TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-				
-				// Fill the fiducial plots if appropriate.
-				if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
-					t0EnergySumFiducial.fill(pairEnergy);
-					t0EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
-					t0TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
-					t0SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
-					t0SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				}
-				
-				// Fill the singles fiducial plots if appropriate.
-				if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
-					plotFiducial.add(pair[0]);
-					t0TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
-					plotFiducial.add(pair[1]);
-					t0TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-			}
-		}
-		
-		// Populate the tier 1 analysis plots, if the conditions were met.
-		if(t1Passed) {
-			// Increment the number of tier 1 events found.
-			t1Events++;
-			
-			// Track which clusters have already been added to the
-			// singles plot so that there are no repeats.
-			Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
-			Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
-			
-			for(ReconstructedParticle[] pair : trackPairList) {
-				t1InvariantMassAll.fill(getInvariantMass(pair));
-			}
-			
-			for(Cluster[] pair : pairList) {
-				// Only include clusters that pass the time coincidence.
-				if(TriggerModule.getValueTimeCoincidence(pair) > t1TimeThreshold) {
-					continue;
-				}
-				
-				// Fill the all pairs plots.
-				double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
-				t1EnergySumAll.fill(pairEnergy);
-				t1EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
-				t1TimeCoincidenceAll.fill(getTimeConicidence(pair));
-				t1SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
-				t1SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				
-				// Fill the singles plots.
-				if(!plotSet.contains(pair[0])) {
-					plotSet.add(pair[0]);
-					t1TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotSet.contains(pair[1])) {
-					plotSet.add(pair[1]);
-					t1TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-				
-				// Fill the fiducial plots if appropriate.
-				if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
-					t1EnergySumFiducial.fill(pairEnergy);
-					t1EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
-					t1TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
-					t1SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
-					t1SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				}
-				
-				// Fill the singles fiducial plots if appropriate.
-				if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
-					plotFiducial.add(pair[0]);
-					t1TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
-					plotFiducial.add(pair[1]);
-					t1TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-			}
-		}
-		
-		// Populate the tier 2 analysis plots, if the conditions were met.
-		if(t1Passed && t2Passed) {
-			// Increment the number of tier 2 events found.
-			t2Events++;
-			
-			// Track which clusters have already been added to the
-			// singles plot so that there are no repeats.
-			Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
-			Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
-			
-			for(ReconstructedParticle[] pair : trackPairList) {
-				t2InvariantMassAll.fill(getInvariantMass(pair));
-			}
-			
-			for(Cluster[] pair : pairList) {
-				// Only include clusters that pass the time coincidence.
-				if(TriggerModule.getValueTimeCoincidence(pair) > t1TimeThreshold) {
-					continue;
-				}
-				
-				// Fill the all pairs plots.
-				double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
-				t2EnergySumAll.fill(pairEnergy);
-				t2EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
-				t2TimeCoincidenceAll.fill(getTimeConicidence(pair));
-				t2SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
-				t2SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				
-				// Fill the singles plots.
-				if(!plotSet.contains(pair[0])) {
-					plotSet.add(pair[0]);
-					t2TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotSet.contains(pair[1])) {
-					plotSet.add(pair[1]);
-					t2TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-				
-				// Fill the fiducial plots if appropriate.
-				if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
-					t2EnergySumFiducial.fill(pairEnergy);
-					t2EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
-					t2TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
-					t2SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
-					t2SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
-				}
-				
-				// Fill the singles fiducial plots if appropriate.
-				if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
-					plotFiducial.add(pair[0]);
-					t2TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
-				} if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
-					plotFiducial.add(pair[1]);
-					t2TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
-				}
-			}
-		}
-	}
-	
-	public static final double getInvariantMass(ReconstructedParticle[] pair) {
-		// Get energy.
-		double[] energy = new double[2];
-		final double electronMassSquared = Math.pow(0.00051099891, 2);
-		energy[0] = Math.sqrt(pair[0].getMomentum().magnitudeSquared() + electronMassSquared);
-		energy[1] = Math.sqrt(pair[1].getMomentum().magnitudeSquared() + electronMassSquared);
-		
-		// Calculate the invariant mass.
-		return Math.sqrt(Math.pow(energy[0] + energy[1], 2) - Math.pow(pair[0].getMomentum().x() + pair[1].getMomentum().x(), 2)
-				+ Math.pow(pair[0].getMomentum().y() + pair[1].getMomentum().y(), 2) + Math.pow(pair[0].getMomentum().z() + pair[1].getMomentum().z(), 2));
-	}
-	
-	public static final double getCalculatedCoplanarity(Cluster[] pair) {
-		// Define the x- and y-coordinates of the clusters as well as
-		// calorimeter center.
-		final double ORIGIN_X = 42.52;
-		double x[] = { pair[0].getPosition()[0], pair[1].getPosition()[0] };
-		double y[] = { pair[0].getPosition()[1], pair[1].getPosition()[1] };
-		
+        // Get the list of particles, if it exists.
+        List<ReconstructedParticle> trackList = null;
+        if(event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
+            trackList = event.get(ReconstructedParticle.class, particleCollectionName);
+        }
+        
+        // Get the list of clusters, if it exists.
+        List<Cluster> clusterList = null;
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            clusterList = event.get(Cluster.class, clusterCollectionName);
+        }
+        
+        // Make sure that the cluster and track lists both exist.
+        if(clusterList == null || trackList == null) {
+            return;
+        }
+        
+        // Perform tier 1 analysis. This requires that there be at
+        // least one top/bottom cluster pair with a time difference
+        // of less then 4 ns.
+        double t1TimeThreshold = 1.5;
+        
+        // Get a list of cluster pairs.
+        List<Cluster[]> pairList = getClusterPairs(clusterList);
+        
+        // Iterate over the cluster pairs.
+        boolean t1Passed = false;
+        t1ClusterLoop:
+        for(Cluster[] pair : pairList) {
+            // Check that the time difference for the cluster pair
+            // meets the time cut.
+            if(TriggerModule.getValueTimeCoincidence(pair) <= t1TimeThreshold) {
+                // Note that the tier 1 analysis condition passed.
+                t1Passed = true;
+                
+                // Break from the loop.
+                break t1ClusterLoop;
+            }
+        }
+        
+        // Perform the additional checks for tier 2 analysis. This
+        // requires that there be at least one top/bottom track pair
+        // and that one track be positive and the other be negative.
+        
+        // Get a list of top and bottom track pairs.
+        List<ReconstructedParticle[]> trackPairList = getTrackPairs(trackList);
+        
+        // Check that at least one top/bottom track has one negative and
+        // one positive track.
+        boolean t2Passed = false;
+        t2TrackLoop:
+        for(ReconstructedParticle[] pair : trackPairList) {
+            if((pair[0].getCharge() > 0 && pair[1].getCharge() < 0) || (pair[0].getCharge() < 0 && pair[1].getCharge() > 0)) {
+                t2Passed = true;
+                break t2TrackLoop;
+            }
+        }
+        
+        // Populate the tier 0 analysis plot.
+        if(true) {
+            // Increment the number of tier 1 events found.
+            t0Events++;
+            
+            // Track which clusters have already been added to the
+            // singles plot so that there are no repeats.
+            Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
+            Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
+            
+            for(ReconstructedParticle[] pair : trackPairList) {
+                t0InvariantMassAll.fill(getInvariantMass(pair));
+            }
+            
+            for(Cluster[] pair : pairList) {
+                // Fill the all pairs plots.
+                double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
+                t0EnergySumAll.fill(pairEnergy);
+                t0EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                t0TimeCoincidenceAll.fill(getTimeConicidence(pair));
+                t0SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                t0SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                
+                // Fill the singles plots.
+                if(!plotSet.contains(pair[0])) {
+                    plotSet.add(pair[0]);
+                    t0TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotSet.contains(pair[1])) {
+                    plotSet.add(pair[1]);
+                    t0TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+                
+                // Fill the fiducial plots if appropriate.
+                if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
+                    t0EnergySumFiducial.fill(pairEnergy);
+                    t0EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                    t0TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
+                    t0SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                    t0SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                }
+                
+                // Fill the singles fiducial plots if appropriate.
+                if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
+                    plotFiducial.add(pair[0]);
+                    t0TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
+                    plotFiducial.add(pair[1]);
+                    t0TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+            }
+        }
+        
+        // Populate the tier 1 analysis plots, if the conditions were met.
+        if(t1Passed) {
+            // Increment the number of tier 1 events found.
+            t1Events++;
+            
+            // Track which clusters have already been added to the
+            // singles plot so that there are no repeats.
+            Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
+            Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
+            
+            for(ReconstructedParticle[] pair : trackPairList) {
+                t1InvariantMassAll.fill(getInvariantMass(pair));
+            }
+            
+            for(Cluster[] pair : pairList) {
+                // Only include clusters that pass the time coincidence.
+                if(TriggerModule.getValueTimeCoincidence(pair) > t1TimeThreshold) {
+                    continue;
+                }
+                
+                // Fill the all pairs plots.
+                double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
+                t1EnergySumAll.fill(pairEnergy);
+                t1EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                t1TimeCoincidenceAll.fill(getTimeConicidence(pair));
+                t1SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                t1SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                
+                // Fill the singles plots.
+                if(!plotSet.contains(pair[0])) {
+                    plotSet.add(pair[0]);
+                    t1TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotSet.contains(pair[1])) {
+                    plotSet.add(pair[1]);
+                    t1TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+                
+                // Fill the fiducial plots if appropriate.
+                if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
+                    t1EnergySumFiducial.fill(pairEnergy);
+                    t1EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                    t1TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
+                    t1SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                    t1SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                }
+                
+                // Fill the singles fiducial plots if appropriate.
+                if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
+                    plotFiducial.add(pair[0]);
+                    t1TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
+                    plotFiducial.add(pair[1]);
+                    t1TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+            }
+        }
+        
+        // Populate the tier 2 analysis plots, if the conditions were met.
+        if(t1Passed && t2Passed) {
+            // Increment the number of tier 2 events found.
+            t2Events++;
+            
+            // Track which clusters have already been added to the
+            // singles plot so that there are no repeats.
+            Set<Cluster> plotSet = new HashSet<Cluster>(clusterList.size());
+            Set<Cluster> plotFiducial = new HashSet<Cluster>(clusterList.size());
+            
+            for(ReconstructedParticle[] pair : trackPairList) {
+                t2InvariantMassAll.fill(getInvariantMass(pair));
+            }
+            
+            for(Cluster[] pair : pairList) {
+                // Only include clusters that pass the time coincidence.
+                if(TriggerModule.getValueTimeCoincidence(pair) > t1TimeThreshold) {
+                    continue;
+                }
+                
+                // Fill the all pairs plots.
+                double pairEnergy = pair[0].getEnergy() + pair[1].getEnergy();
+                t2EnergySumAll.fill(pairEnergy);
+                t2EnergySum2DAll.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                t2TimeCoincidenceAll.fill(getTimeConicidence(pair));
+                t2SumCoplanarityCalcAll.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                t2SumCoplanarityAll.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                
+                // Fill the singles plots.
+                if(!plotSet.contains(pair[0])) {
+                    plotSet.add(pair[0]);
+                    t2TimeEnergyAll.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotSet.contains(pair[1])) {
+                    plotSet.add(pair[1]);
+                    t2TimeEnergyAll.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+                
+                // Fill the fiducial plots if appropriate.
+                if(inFiducialRegion(pair[0]) && inFiducialRegion(pair[1])) {
+                    t2EnergySumFiducial.fill(pairEnergy);
+                    t2EnergySum2DFiducial.fill(pair[1].getEnergy(), pair[0].getEnergy());
+                    t2TimeCoincidenceFiducial.fill(getTimeConicidence(pair));
+                    t2SumCoplanarityCalcFiducial.fill(pairEnergy, getCalculatedCoplanarity(pair));
+                    t2SumCoplanarityFiducial.fill(pairEnergy, TriggerModule.getValueCoplanarity(pair));
+                }
+                
+                // Fill the singles fiducial plots if appropriate.
+                if(!plotFiducial.contains(pair[0]) && inFiducialRegion(pair[0])) {
+                    plotFiducial.add(pair[0]);
+                    t2TimeEnergyFiducial.fill(pair[0].getEnergy(), TriggerModule.getClusterTime(pair[0]));
+                } if(!plotFiducial.contains(pair[1]) && inFiducialRegion(pair[1])) {
+                    plotFiducial.add(pair[1]);
+                    t2TimeEnergyFiducial.fill(pair[1].getEnergy(), TriggerModule.getClusterTime(pair[1]));
+                }
+            }
+        }
+    }
+    
+    public static final double getInvariantMass(ReconstructedParticle[] pair) {
+        // Get energy.
+        double[] energy = new double[2];
+        final double electronMassSquared = Math.pow(0.00051099891, 2);
+        energy[0] = Math.sqrt(pair[0].getMomentum().magnitudeSquared() + electronMassSquared);
+        energy[1] = Math.sqrt(pair[1].getMomentum().magnitudeSquared() + electronMassSquared);
+        
+        // Calculate the invariant mass.
+        return Math.sqrt(Math.pow(energy[0] + energy[1], 2) - Math.pow(pair[0].getMomentum().x() + pair[1].getMomentum().x(), 2)
+                + Math.pow(pair[0].getMomentum().y() + pair[1].getMomentum().y(), 2) + Math.pow(pair[0].getMomentum().z() + pair[1].getMomentum().z(), 2));
+    }
+    
+    public static final double getCalculatedCoplanarity(Cluster[] pair) {
+        // Define the x- and y-coordinates of the clusters as well as
+        // calorimeter center.
+        final double ORIGIN_X = 42.52;
+        double x[] = { pair[0].getPosition()[0], pair[1].getPosition()[0] };
+        double y[] = { pair[0].getPosition()[1], pair[1].getPosition()[1] };
+        
         // Get the cluster angles.
         double[] clusterAngle = new double[2];
         for(int i = 0; i < 2; i++) {
-        	clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
-        	if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
+            clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
+            if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
         }
         
         // Calculate the coplanarity cut value.
         double clusterDiff = clusterAngle[0] - clusterAngle[1];
         return clusterDiff > 0 ? clusterDiff : clusterDiff + 360;
-	}
-	
-	private static final boolean inFiducialRegion(Cluster cluster) {
-		// Get the x and y indices for the cluster.
-		int ix   = TriggerModule.getClusterXIndex(cluster);
-		int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
-		int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
-		
-		// Check if the cluster is on the top or the bottom of the
-		// calorimeter, as defined by |y| == 5. This is an edge cluster
-		// and is not in the fiducial region.
-		if(absy == 5) {
-			return false;
-		}
-		
-		// Check if the cluster is on the extreme left or right side
-		// of the calorimeter, as defined by |x| == 23. This is also
-		// and edge cluster is not in the fiducial region.
-		if(absx == 23) {
-			return false;
-		}
-		
-		// Check if the cluster is along the beam gap, as defined by
-		// |y| == 1. This is an internal edge cluster and is not in the
-		// fiducial region.
-		if(absy == 1) {
-			return false;
-		}
-		
-		// Lastly, check if the cluster falls along the beam hole, as
-		// defined by clusters with -11 <= x <= -1 and |y| == 2. This
-		// is not the fiducial region.
-		if(absy == 2 && ix <= -1 && ix >= -11) {
-			return false;
-		}
-		
-		// If all checks fail, the cluster is in the fiducial region.
-		return true;
-	}
-	
-	private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> tracks) {
-		// Separate the tracks into top and bottom tracks.
-		List<ReconstructedParticle> topList = new ArrayList<ReconstructedParticle>();
-		List<ReconstructedParticle> botList = new ArrayList<ReconstructedParticle>();
-		for(ReconstructedParticle track : tracks) {
-			// Make sure that the track actually contains tracks.
-			if(track.getTracks().size() > 0) {
-				// Use the tan(Λ) to differentiate "top" and "bottom"
-				// tracks from one another.
-				if(track.getTracks().get(0).getTrackStates().get(0).getTanLambda() > 0) {
-					topList.add(track);
-				} else {
-					botList.add(track);
-				}
-			}
-		}
-		
-		// Form all permutations of top and bottom tracks.
-		List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
-		for(ReconstructedParticle topTrack : topList) {
-			for(ReconstructedParticle botTrack : botList) {
-				pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
-			}
-		}
-		
-		// Return the resulting cluster pairs.
-		return pairList;
-	}
-	
-	private static final List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
-		// Separate the clusters into top and bottom clusters.
-		List<Cluster> topList = new ArrayList<Cluster>();
-		List<Cluster> botList = new ArrayList<Cluster>();
-		for(Cluster cluster : clusters) {
-			if(TriggerModule.getClusterYIndex(cluster) > 0) {
-				topList.add(cluster);
-			} else {
-				botList.add(cluster);
-			}
-		}
-		
-		// Form all permutations of top and bottom clusters.
-		List<Cluster[]> pairList = new ArrayList<Cluster[]>();
-		for(Cluster topCluster : topList) {
-			for(Cluster botCluster : botList) {
-				pairList.add(new Cluster[] { topCluster, botCluster });
-			}
-		}
-		
-		// Return the resulting cluster pairs.
-		return pairList;
-	}
-	
-	public static final double getTimeConicidence(Cluster[] pair) {
-		return TriggerModule.getClusterSeedHit(pair[1]).getTime() - TriggerModule.getClusterSeedHit(pair[0]).getTime();
-	}
-	
-	public void setUseGoodSVT(boolean state) {
-		useGoodSVT = state;
-	}
+    }
+    
+    private static final boolean inFiducialRegion(Cluster cluster) {
+        // Get the x and y indices for the cluster.
+        int ix   = TriggerModule.getClusterXIndex(cluster);
+        int absx = Math.abs(TriggerModule.getClusterXIndex(cluster));
+        int absy = Math.abs(TriggerModule.getClusterYIndex(cluster));
+        
+        // Check if the cluster is on the top or the bottom of the
+        // calorimeter, as defined by |y| == 5. This is an edge cluster
+        // and is not in the fiducial region.
+        if(absy == 5) {
+            return false;
+        }
+        
+        // Check if the cluster is on the extreme left or right side
+        // of the calorimeter, as defined by |x| == 23. This is also
+        // and edge cluster is not in the fiducial region.
+        if(absx == 23) {
+            return false;
+        }
+        
+        // Check if the cluster is along the beam gap, as defined by
+        // |y| == 1. This is an internal edge cluster and is not in the
+        // fiducial region.
+        if(absy == 1) {
+            return false;
+        }
+        
+        // Lastly, check if the cluster falls along the beam hole, as
+        // defined by clusters with -11 <= x <= -1 and |y| == 2. This
+        // is not the fiducial region.
+        if(absy == 2 && ix <= -1 && ix >= -11) {
+            return false;
+        }
+        
+        // If all checks fail, the cluster is in the fiducial region.
+        return true;
+    }
+    
+    private static final List<ReconstructedParticle[]> getTrackPairs(List<ReconstructedParticle> tracks) {
+        // Separate the tracks into top and bottom tracks.
+        List<ReconstructedParticle> topList = new ArrayList<ReconstructedParticle>();
+        List<ReconstructedParticle> botList = new ArrayList<ReconstructedParticle>();
+        for(ReconstructedParticle track : tracks) {
+            // Make sure that the track actually contains tracks.
+            if(track.getTracks().size() > 0) {
+                // Use the tan(Λ) to differentiate "top" and "bottom"
+                // tracks from one another.
+                if(track.getTracks().get(0).getTrackStates().get(0).getTanLambda() > 0) {
+                    topList.add(track);
+                } else {
+                    botList.add(track);
+                }
+            }
+        }
+        
+        // Form all permutations of top and bottom tracks.
+        List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
+        for(ReconstructedParticle topTrack : topList) {
+            for(ReconstructedParticle botTrack : botList) {
+                pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
+            }
+        }
+        
+        // Return the resulting cluster pairs.
+        return pairList;
+    }
+    
+    private static final List<Cluster[]> getClusterPairs(List<Cluster> clusters) {
+        // Separate the clusters into top and bottom clusters.
+        List<Cluster> topList = new ArrayList<Cluster>();
+        List<Cluster> botList = new ArrayList<Cluster>();
+        for(Cluster cluster : clusters) {
+            if(TriggerModule.getClusterYIndex(cluster) > 0) {
+                topList.add(cluster);
+            } else {
+                botList.add(cluster);
+            }
+        }
+        
+        // Form all permutations of top and bottom clusters.
+        List<Cluster[]> pairList = new ArrayList<Cluster[]>();
+        for(Cluster topCluster : topList) {
+            for(Cluster botCluster : botList) {
+                pairList.add(new Cluster[] { topCluster, botCluster });
+            }
+        }
+        
+        // Return the resulting cluster pairs.
+        return pairList;
+    }
+    
+    public static final double getTimeConicidence(Cluster[] pair) {
+        return TriggerModule.getClusterSeedHit(pair[1]).getTime() - TriggerModule.getClusterSeedHit(pair[0]).getTime();
+    }
+    
+    public void setUseGoodSVT(boolean state) {
+        useGoodSVT = state;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TridentTrackDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TridentTrackDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TridentTrackDriver.java	Wed Apr 27 11:11:32 2016
@@ -15,229 +15,229 @@
 import org.lcsim.util.aida.AIDA;
 
 public class TridentTrackDriver extends Driver {
-	private String finalStateCollectionName = "FinalStateParticles";
-	private String candidateCollectionName = "UnconstrainedV0Candidates";
-	
-	private int tracksCandidate = 0;
-	private int tracksFinalState = 0;
-	private int tracksCandidateCluster = 0;
-	private int tracksFinalStateCluster = 0;
-	
-	private static final int ANY_CLUSTER = 0;
-	private static final int HAS_CLUSTER = 1;
-	
-	private AIDA aida = AIDA.defaultInstance();
-	private IHistogram1D[] tracks = new IHistogram1D[2];
-	private IHistogram1D[] posTracks = new IHistogram1D[2];
-	private IHistogram1D[] negTracks = new IHistogram1D[2];
-	private IHistogram1D[] posMomentum = new IHistogram1D[2];
-	private IHistogram1D[] negMomentum = new IHistogram1D[2];
-	private IHistogram1D[] energySum = new IHistogram1D[2];
-	private IHistogram1D[] energyMomentumDiff = new IHistogram1D[2];
-	private IHistogram1D[] momentumSum = new IHistogram1D[2];
-	private IHistogram1D[] invariantMass = new IHistogram1D[2];
-	private IHistogram2D[] energySum2D = new IHistogram2D[2];
-	private IHistogram2D[] momentumSum2D = new IHistogram2D[2];
-	private IHistogram2D[] position = new IHistogram2D[2];
-	
-	@Override
-	public void startOfData() {
-		// Instantiate the "any cluster status" plots.
-		tracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (All)", 7, -0.5, 6.5);
-		posTracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (Positive)", 7, -0.5, 6.5);
-		negTracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (Negative)", 7, -0.5, 6.5);
-		posMomentum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum (Positive)", 110, 0, 1.1);
-		negMomentum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum (Negative)", 110, 0, 1.1);
-		energySum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Energy Sum", 55, 0, 2.2);
-		momentumSum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum Sum", 55, 0, 2.2);
-		energyMomentumDiff[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Energy-Momentum Difference", 55, 0, 2.2);
-		invariantMass[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Invariant Mass", 240, 0.000, 0.120);
-		energySum2D[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/2D Energy Sum", 55, 0, 1.1, 55, 0, 1.1);
-		momentumSum2D[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/2D Momentum Sum", 55, 0, 1.1, 55, 0, 1.1);
-		position[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/Track Cluster Position", 46, -23, 23, 11, -5.5, 5.5);
-		
-		// Instantiate the "has a cluster" plots.
-		tracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (All)", 7, -0.5, 6.5);
-		posTracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (Positive)", 7, -0.5, 6.5);
-		negTracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (Negative)", 7, -0.5, 6.5);
-		posMomentum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum (Positive)", 110, 0, 1.1);
-		negMomentum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum (Negative)", 110, 0, 1.1);
-		energySum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Energy Sum", 55, 0, 2.2);
-		momentumSum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum Sum", 55, 0, 2.2);
-		energyMomentumDiff[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Energy-Momentum Difference", 55, 0, 2.2);
-		invariantMass[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Invariant Mass", 240, 0.000, 0.120);
-		energySum2D[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/2D Energy Sum", 55, 0, 1.1, 55, 0, 1.1);
-		momentumSum2D[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/2D Momentum Sum", 55, 0, 1.1, 55, 0, 1.1);
-		position[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/Track Cluster Position", 46, -23, 23, 11, -5.5, 5.5);
-	}
-	
-	@Override
-	public void endOfData() {
-		System.out.printf("Tracks (Candidate)           :: %d%n", tracksCandidate);
-		System.out.printf("Tracks (Final State)         :: %d%n", tracksFinalState);
-		System.out.printf("Cluster Tracks (Candidate)   :: %d%n", tracksCandidateCluster);
-		System.out.printf("Cluster Tracks (Final State) :: %d%n", tracksFinalStateCluster);
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Check for final state particles.
-		if(event.hasCollection(ReconstructedParticle.class, finalStateCollectionName)) {
-			// Get the final state particles.
-			List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, finalStateCollectionName);
-			
-			// Store the positive and negative tracks.
-			List<ReconstructedParticle> allTrackList = new ArrayList<ReconstructedParticle>();
-			List<ReconstructedParticle> posTrackList = new ArrayList<ReconstructedParticle>();
-			List<ReconstructedParticle> negTrackList = new ArrayList<ReconstructedParticle>();
-			
-			// Store the same tracks, but limited to those with clusters.
-			List<ReconstructedParticle> allClusterTrackList = new ArrayList<ReconstructedParticle>();
-			List<ReconstructedParticle> posClusterTrackList = new ArrayList<ReconstructedParticle>();
-			List<ReconstructedParticle> negClusterTrackList = new ArrayList<ReconstructedParticle>();
-			
-			// Iterate over the tracks and populate the lists.
-			for(ReconstructedParticle track : trackList) {
-				// Skip instances with no raw tracks.
-				if(track.getTracks().size() == 0) { continue; }
-				
-				// Add the cluster to the all track list.
-				allTrackList.add(track);
-				
-				// Track the number of cluster tracks.
-				tracksFinalState++;
-				if(!track.getClusters().isEmpty()) {
-					tracksFinalStateCluster++;
-				}
-				
-				// Process the track position plots.
-				Hep3Vector trackPosAtEcal = TrackUtils.extrapolateTrack(track.getTracks().get(0), 1394.5);
-				position[ANY_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
-				
-				// Process the tracks based on charge.
-				if(track.getCharge() > 0) {
-					// Increment the counters and populate the momentum plots.
-					posTrackList.add(track);
-					posMomentum[ANY_CLUSTER].fill(track.getMomentum().magnitude());
-					
-					// Repeat for the "has clusters" plots if necessary.
-					if(track.getClusters().size() > 0) {
-						// Increment the counters and populate the
-						// momentum plot.
-						posClusterTrackList.add(track);
-						allClusterTrackList.add(track);
-						posMomentum[HAS_CLUSTER].fill(track.getMomentum().magnitude());
-						
-						// Populate the cluster position plot.
-						//int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-						//int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-						position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
-					}
-				} else if(track.getCharge() < 0) {
-					// Increment the counters and populate the momentum plots.
-					negTrackList.add(track);
-					negMomentum[ANY_CLUSTER].fill(track.getMomentum().magnitude());
-					
-					// Repeat for the "has clusters" plots if necessary.
-					if(track.getClusters().size() > 0) {
-						// Increment the counters and populate the
-						// momentum plot.
-						negClusterTrackList.add(track);
-						allClusterTrackList.add(track);
-						negMomentum[HAS_CLUSTER].fill(track.getMomentum().magnitude());
-						
-						// Populate the cluster position plot.
-						//int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-						//int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-						position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
-					}
-				} else {
-					if(track.getClusters().size() > 0) {
-						// Increment the counter.
-						allClusterTrackList.add(track);
-						
-						// Populate the cluster position plot.
-						//int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-						//int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
-						position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
-					}
-				}
-			}
-			
-			// Populate the tracks per event plots.
-			tracks[ANY_CLUSTER].fill(allTrackList.size());
-			tracks[HAS_CLUSTER].fill(allClusterTrackList.size());
-			posTracks[ANY_CLUSTER].fill(posTrackList.size());
-			posTracks[HAS_CLUSTER].fill(posClusterTrackList.size());
-			negTracks[ANY_CLUSTER].fill(negTrackList.size());
-			negTracks[HAS_CLUSTER].fill(negClusterTrackList.size());
-			
-			/// Store track pairs.
-			List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
-			List<ReconstructedParticle[]> pairClusterList = new ArrayList<ReconstructedParticle[]>();
-			
-			// Form track pairs for all tracks.
-			for(ReconstructedParticle posTrack : posTrackList) {
-				for(ReconstructedParticle negTrack : negTrackList) {
-					pairList.add(new ReconstructedParticle[] { posTrack, negTrack });
-				}
-			}
-			
-			// Form track pairs for cluster tracks.
-			for(ReconstructedParticle posTrack : posClusterTrackList) {
-				for(ReconstructedParticle negTrack : negClusterTrackList) {
-					pairClusterList.add(new ReconstructedParticle[] { posTrack, negTrack });
-				}
-			}
-			
-			// Populate the track pair plots.
-			for(ReconstructedParticle[] pair : pairList) {
-				Hep3Vector pSum = new BasicHep3Vector(
-						pair[0].getMomentum().x() + pair[1].getMomentum().x(),
-						pair[0].getMomentum().y() + pair[1].getMomentum().y(),
-						pair[0].getMomentum().z() + pair[1].getMomentum().z());
-				
-				energySum[ANY_CLUSTER].fill(pair[0].getEnergy() + pair[1].getEnergy());
-				momentumSum[ANY_CLUSTER].fill(pSum.magnitude());
-				energySum2D[ANY_CLUSTER].fill(pair[0].getEnergy(), pair[1].getEnergy());
-				momentumSum2D[ANY_CLUSTER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-				energyMomentumDiff[ANY_CLUSTER].fill(Math.abs((pair[0].getEnergy() + pair[1].getEnergy()) - pSum.magnitude()));
-			}
-			
-			// Populate the cluster track pair plots.
-			for(ReconstructedParticle[] pair : pairClusterList) {
-				Hep3Vector pSum = new BasicHep3Vector(
-						pair[0].getMomentum().x() + pair[1].getMomentum().x(),
-						pair[0].getMomentum().y() + pair[1].getMomentum().y(),
-						pair[0].getMomentum().z() + pair[1].getMomentum().z());
-				
-				energySum[HAS_CLUSTER].fill(pair[0].getEnergy() + pair[1].getEnergy());
-				momentumSum[HAS_CLUSTER].fill(pSum.magnitude());
-				energySum2D[HAS_CLUSTER].fill(pair[0].getEnergy(), pair[1].getEnergy());
-				momentumSum2D[HAS_CLUSTER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-				energyMomentumDiff[HAS_CLUSTER].fill(Math.abs((pair[0].getEnergy() + pair[1].getEnergy()) - pSum.magnitude()));
-			}
-		}
-		
-		// Check for V0 candidates.
-		if(event.hasCollection(ReconstructedParticle.class, candidateCollectionName)) {
-			// Get the candidate particles.
-			List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, candidateCollectionName);
-			
-			// Increment the counter.
-			tracksCandidate += trackList.size();
-			
-			// Increment the counter for cluster tracks.
-			for(ReconstructedParticle track : trackList) {
-				// Populate the invariant mass plot.
-				invariantMass[ANY_CLUSTER].fill(track.getMass());
-				
-				// Check for a cluster track.
-				if(track.getClusters().size() > 0) {
-					tracksCandidateCluster++;
-					invariantMass[HAS_CLUSTER].fill(track.getMass());
-				}
-			}
-		}
-	}
+    private String finalStateCollectionName = "FinalStateParticles";
+    private String candidateCollectionName = "UnconstrainedV0Candidates";
+    
+    private int tracksCandidate = 0;
+    private int tracksFinalState = 0;
+    private int tracksCandidateCluster = 0;
+    private int tracksFinalStateCluster = 0;
+    
+    private static final int ANY_CLUSTER = 0;
+    private static final int HAS_CLUSTER = 1;
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IHistogram1D[] tracks = new IHistogram1D[2];
+    private IHistogram1D[] posTracks = new IHistogram1D[2];
+    private IHistogram1D[] negTracks = new IHistogram1D[2];
+    private IHistogram1D[] posMomentum = new IHistogram1D[2];
+    private IHistogram1D[] negMomentum = new IHistogram1D[2];
+    private IHistogram1D[] energySum = new IHistogram1D[2];
+    private IHistogram1D[] energyMomentumDiff = new IHistogram1D[2];
+    private IHistogram1D[] momentumSum = new IHistogram1D[2];
+    private IHistogram1D[] invariantMass = new IHistogram1D[2];
+    private IHistogram2D[] energySum2D = new IHistogram2D[2];
+    private IHistogram2D[] momentumSum2D = new IHistogram2D[2];
+    private IHistogram2D[] position = new IHistogram2D[2];
+    
+    @Override
+    public void startOfData() {
+        // Instantiate the "any cluster status" plots.
+        tracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (All)", 7, -0.5, 6.5);
+        posTracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (Positive)", 7, -0.5, 6.5);
+        negTracks[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Tracks in Event (Negative)", 7, -0.5, 6.5);
+        posMomentum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum (Positive)", 110, 0, 1.1);
+        negMomentum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum (Negative)", 110, 0, 1.1);
+        energySum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Energy Sum", 55, 0, 2.2);
+        momentumSum[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Momentum Sum", 55, 0, 2.2);
+        energyMomentumDiff[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Energy-Momentum Difference", 55, 0, 2.2);
+        invariantMass[ANY_CLUSTER] = aida.histogram1D("Trident Analysis/All/Invariant Mass", 240, 0.000, 0.120);
+        energySum2D[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/2D Energy Sum", 55, 0, 1.1, 55, 0, 1.1);
+        momentumSum2D[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/2D Momentum Sum", 55, 0, 1.1, 55, 0, 1.1);
+        position[ANY_CLUSTER] = aida.histogram2D("Trident Analysis/All/Track Cluster Position", 46, -23, 23, 11, -5.5, 5.5);
+        
+        // Instantiate the "has a cluster" plots.
+        tracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (All)", 7, -0.5, 6.5);
+        posTracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (Positive)", 7, -0.5, 6.5);
+        negTracks[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Tracks in Event (Negative)", 7, -0.5, 6.5);
+        posMomentum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum (Positive)", 110, 0, 1.1);
+        negMomentum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum (Negative)", 110, 0, 1.1);
+        energySum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Energy Sum", 55, 0, 2.2);
+        momentumSum[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Momentum Sum", 55, 0, 2.2);
+        energyMomentumDiff[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Energy-Momentum Difference", 55, 0, 2.2);
+        invariantMass[HAS_CLUSTER] = aida.histogram1D("Trident Analysis/Cluster/Invariant Mass", 240, 0.000, 0.120);
+        energySum2D[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/2D Energy Sum", 55, 0, 1.1, 55, 0, 1.1);
+        momentumSum2D[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/2D Momentum Sum", 55, 0, 1.1, 55, 0, 1.1);
+        position[HAS_CLUSTER] = aida.histogram2D("Trident Analysis/Cluster/Track Cluster Position", 46, -23, 23, 11, -5.5, 5.5);
+    }
+    
+    @Override
+    public void endOfData() {
+        System.out.printf("Tracks (Candidate)           :: %d%n", tracksCandidate);
+        System.out.printf("Tracks (Final State)         :: %d%n", tracksFinalState);
+        System.out.printf("Cluster Tracks (Candidate)   :: %d%n", tracksCandidateCluster);
+        System.out.printf("Cluster Tracks (Final State) :: %d%n", tracksFinalStateCluster);
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Check for final state particles.
+        if(event.hasCollection(ReconstructedParticle.class, finalStateCollectionName)) {
+            // Get the final state particles.
+            List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, finalStateCollectionName);
+            
+            // Store the positive and negative tracks.
+            List<ReconstructedParticle> allTrackList = new ArrayList<ReconstructedParticle>();
+            List<ReconstructedParticle> posTrackList = new ArrayList<ReconstructedParticle>();
+            List<ReconstructedParticle> negTrackList = new ArrayList<ReconstructedParticle>();
+            
+            // Store the same tracks, but limited to those with clusters.
+            List<ReconstructedParticle> allClusterTrackList = new ArrayList<ReconstructedParticle>();
+            List<ReconstructedParticle> posClusterTrackList = new ArrayList<ReconstructedParticle>();
+            List<ReconstructedParticle> negClusterTrackList = new ArrayList<ReconstructedParticle>();
+            
+            // Iterate over the tracks and populate the lists.
+            for(ReconstructedParticle track : trackList) {
+                // Skip instances with no raw tracks.
+                if(track.getTracks().size() == 0) { continue; }
+                
+                // Add the cluster to the all track list.
+                allTrackList.add(track);
+                
+                // Track the number of cluster tracks.
+                tracksFinalState++;
+                if(!track.getClusters().isEmpty()) {
+                    tracksFinalStateCluster++;
+                }
+                
+                // Process the track position plots.
+                Hep3Vector trackPosAtEcal = TrackUtils.extrapolateTrack(track.getTracks().get(0), 1394.5);
+                position[ANY_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
+                
+                // Process the tracks based on charge.
+                if(track.getCharge() > 0) {
+                    // Increment the counters and populate the momentum plots.
+                    posTrackList.add(track);
+                    posMomentum[ANY_CLUSTER].fill(track.getMomentum().magnitude());
+                    
+                    // Repeat for the "has clusters" plots if necessary.
+                    if(track.getClusters().size() > 0) {
+                        // Increment the counters and populate the
+                        // momentum plot.
+                        posClusterTrackList.add(track);
+                        allClusterTrackList.add(track);
+                        posMomentum[HAS_CLUSTER].fill(track.getMomentum().magnitude());
+                        
+                        // Populate the cluster position plot.
+                        //int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                        //int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+                        position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
+                    }
+                } else if(track.getCharge() < 0) {
+                    // Increment the counters and populate the momentum plots.
+                    negTrackList.add(track);
+                    negMomentum[ANY_CLUSTER].fill(track.getMomentum().magnitude());
+                    
+                    // Repeat for the "has clusters" plots if necessary.
+                    if(track.getClusters().size() > 0) {
+                        // Increment the counters and populate the
+                        // momentum plot.
+                        negClusterTrackList.add(track);
+                        allClusterTrackList.add(track);
+                        negMomentum[HAS_CLUSTER].fill(track.getMomentum().magnitude());
+                        
+                        // Populate the cluster position plot.
+                        //int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                        //int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+                        position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
+                    }
+                } else {
+                    if(track.getClusters().size() > 0) {
+                        // Increment the counter.
+                        allClusterTrackList.add(track);
+                        
+                        // Populate the cluster position plot.
+                        //int ix = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                        //int iy = track.getClusters().get(0).getCalorimeterHits().get(0).getIdentifierFieldValue("iy");
+                        position[HAS_CLUSTER].fill(trackPosAtEcal.x(), trackPosAtEcal.y());
+                    }
+                }
+            }
+            
+            // Populate the tracks per event plots.
+            tracks[ANY_CLUSTER].fill(allTrackList.size());
+            tracks[HAS_CLUSTER].fill(allClusterTrackList.size());
+            posTracks[ANY_CLUSTER].fill(posTrackList.size());
+            posTracks[HAS_CLUSTER].fill(posClusterTrackList.size());
+            negTracks[ANY_CLUSTER].fill(negTrackList.size());
+            negTracks[HAS_CLUSTER].fill(negClusterTrackList.size());
+            
+            /// Store track pairs.
+            List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
+            List<ReconstructedParticle[]> pairClusterList = new ArrayList<ReconstructedParticle[]>();
+            
+            // Form track pairs for all tracks.
+            for(ReconstructedParticle posTrack : posTrackList) {
+                for(ReconstructedParticle negTrack : negTrackList) {
+                    pairList.add(new ReconstructedParticle[] { posTrack, negTrack });
+                }
+            }
+            
+            // Form track pairs for cluster tracks.
+            for(ReconstructedParticle posTrack : posClusterTrackList) {
+                for(ReconstructedParticle negTrack : negClusterTrackList) {
+                    pairClusterList.add(new ReconstructedParticle[] { posTrack, negTrack });
+                }
+            }
+            
+            // Populate the track pair plots.
+            for(ReconstructedParticle[] pair : pairList) {
+                Hep3Vector pSum = new BasicHep3Vector(
+                        pair[0].getMomentum().x() + pair[1].getMomentum().x(),
+                        pair[0].getMomentum().y() + pair[1].getMomentum().y(),
+                        pair[0].getMomentum().z() + pair[1].getMomentum().z());
+                
+                energySum[ANY_CLUSTER].fill(pair[0].getEnergy() + pair[1].getEnergy());
+                momentumSum[ANY_CLUSTER].fill(pSum.magnitude());
+                energySum2D[ANY_CLUSTER].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                momentumSum2D[ANY_CLUSTER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+                energyMomentumDiff[ANY_CLUSTER].fill(Math.abs((pair[0].getEnergy() + pair[1].getEnergy()) - pSum.magnitude()));
+            }
+            
+            // Populate the cluster track pair plots.
+            for(ReconstructedParticle[] pair : pairClusterList) {
+                Hep3Vector pSum = new BasicHep3Vector(
+                        pair[0].getMomentum().x() + pair[1].getMomentum().x(),
+                        pair[0].getMomentum().y() + pair[1].getMomentum().y(),
+                        pair[0].getMomentum().z() + pair[1].getMomentum().z());
+                
+                energySum[HAS_CLUSTER].fill(pair[0].getEnergy() + pair[1].getEnergy());
+                momentumSum[HAS_CLUSTER].fill(pSum.magnitude());
+                energySum2D[HAS_CLUSTER].fill(pair[0].getEnergy(), pair[1].getEnergy());
+                momentumSum2D[HAS_CLUSTER].fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+                energyMomentumDiff[HAS_CLUSTER].fill(Math.abs((pair[0].getEnergy() + pair[1].getEnergy()) - pSum.magnitude()));
+            }
+        }
+        
+        // Check for V0 candidates.
+        if(event.hasCollection(ReconstructedParticle.class, candidateCollectionName)) {
+            // Get the candidate particles.
+            List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, candidateCollectionName);
+            
+            // Increment the counter.
+            tracksCandidate += trackList.size();
+            
+            // Increment the counter for cluster tracks.
+            for(ReconstructedParticle track : trackList) {
+                // Populate the invariant mass plot.
+                invariantMass[ANY_CLUSTER].fill(track.getMass());
+                
+                // Check for a cluster track.
+                if(track.getClusters().size() > 0) {
+                    tracksCandidateCluster++;
+                    invariantMass[HAS_CLUSTER].fill(track.getMass());
+                }
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerPlotsModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerPlotsModule.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerPlotsModule.java	Wed Apr 27 11:11:32 2016
@@ -8,8 +8,8 @@
 import org.lcsim.util.aida.AIDA;
 
 public class TriggerPlotsModule {
-	// Define plots.
-	private AIDA aida = AIDA.defaultInstance();
+    // Define plots.
+    private AIDA aida = AIDA.defaultInstance();
     private IHistogram1D singleSeedEnergy;
     private IHistogram1D singleHitCount;
     private IHistogram1D singleTotalEnergy;
@@ -25,43 +25,43 @@
     private IHistogram2D pairDistribution;
     private IHistogram2D pairEnergySum2D;
     
-	public TriggerPlotsModule(String moduleName) {
-		singleSeedEnergy     = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Seed Energy",  176,   0.0,   1.1);
-		singleHitCount       = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Hit Count",      9,   0.5,   9.5);
-		singleTotalEnergy    = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Total Energy", 176,   0.0,   1.1);
-		singleDistribution   = aida.histogram2D(moduleName + " Trigger Plots/Singles Plots/Cluster Seed",          46, -23.0,  23.0,  11, -5.5, 5.5);
-		pairSeedEnergy       = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Seed Energy",     176,   0.0,   1.1);
-		pairHitCount         = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Hit Count",         9,   0.5,   9.5);
-		pairTotalEnergy      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Total Energy",    176,   0.0,   1.1);
-		pairEnergySum        = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Sum",         176,   0.0,   2.2);
-		pairEnergyDifference = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Difference",  176,   0.0,   1.1);
-		pairCoplanarity      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Coplanarity",        180,   0.0, 180.0);
-		pairEnergySlope      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Slope",       200,   0.0,   3.0);
-		pairDistribution     = aida.histogram2D(moduleName + " Trigger Plots/Pair Plots/Cluster Seed",             46, -23.0,  23.0,  11, -5.5, 5.5);
-		pairEnergySum2D      = aida.histogram2D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Sum 2D",      110,   0.0,   1.1, 110,  0.0, 1.1);
-	}
-	
-	public void addCluster(Cluster cluster) {
-		singleSeedEnergy.fill(TriggerModule.getValueClusterSeedEnergy(cluster));
-		singleHitCount.fill(TriggerModule.getValueClusterHitCount(cluster));
-		singleTotalEnergy.fill(TriggerModule.getValueClusterTotalEnergy(cluster));
-		singleDistribution.fill(TriggerModule.getClusterXIndex(cluster), TriggerModule.getClusterYIndex(cluster));
-	}
-	
-	public void addClusterPair(Cluster[] pair) {
-		// Populate the singles plots.
-		for(Cluster cluster : pair) {
-			pairSeedEnergy.fill(TriggerModule.getValueClusterSeedEnergy(cluster));
-			pairHitCount.fill(TriggerModule.getValueClusterHitCount(cluster));
-			pairTotalEnergy.fill(TriggerModule.getValueClusterTotalEnergy(cluster));
-			pairDistribution.fill(TriggerModule.getClusterXIndex(cluster), TriggerModule.getClusterYIndex(cluster));
-		}
-		
-		// Populate the pair plots.
-		pairEnergySum.fill(TriggerModule.getValueEnergySum(pair));
-		pairEnergyDifference.fill(TriggerModule.getValueEnergyDifference(pair));
-		pairCoplanarity.fill(TriggerModule.getValueCoplanarity(pair));
-		pairEnergySlope.fill(TriggerModule.getValueEnergySlope(pair, 0.0055));
-		pairEnergySum2D.fill(TriggerModule.getValueClusterTotalEnergy(pair[0]), TriggerModule.getValueClusterTotalEnergy(pair[1]));
-	}
+    public TriggerPlotsModule(String moduleName) {
+        singleSeedEnergy     = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Seed Energy",  176,   0.0,   1.1);
+        singleHitCount       = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Hit Count",      9,   0.5,   9.5);
+        singleTotalEnergy    = aida.histogram1D(moduleName + " Trigger Plots/Singles Plots/Cluster Total Energy", 176,   0.0,   1.1);
+        singleDistribution   = aida.histogram2D(moduleName + " Trigger Plots/Singles Plots/Cluster Seed",          46, -23.0,  23.0,  11, -5.5, 5.5);
+        pairSeedEnergy       = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Seed Energy",     176,   0.0,   1.1);
+        pairHitCount         = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Hit Count",         9,   0.5,   9.5);
+        pairTotalEnergy      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Cluster Total Energy",    176,   0.0,   1.1);
+        pairEnergySum        = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Sum",         176,   0.0,   2.2);
+        pairEnergyDifference = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Difference",  176,   0.0,   1.1);
+        pairCoplanarity      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Coplanarity",        180,   0.0, 180.0);
+        pairEnergySlope      = aida.histogram1D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Slope",       200,   0.0,   3.0);
+        pairDistribution     = aida.histogram2D(moduleName + " Trigger Plots/Pair Plots/Cluster Seed",             46, -23.0,  23.0,  11, -5.5, 5.5);
+        pairEnergySum2D      = aida.histogram2D(moduleName + " Trigger Plots/Pair Plots/Pair Energy Sum 2D",      110,   0.0,   1.1, 110,  0.0, 1.1);
+    }
+    
+    public void addCluster(Cluster cluster) {
+        singleSeedEnergy.fill(TriggerModule.getValueClusterSeedEnergy(cluster));
+        singleHitCount.fill(TriggerModule.getValueClusterHitCount(cluster));
+        singleTotalEnergy.fill(TriggerModule.getValueClusterTotalEnergy(cluster));
+        singleDistribution.fill(TriggerModule.getClusterXIndex(cluster), TriggerModule.getClusterYIndex(cluster));
+    }
+    
+    public void addClusterPair(Cluster[] pair) {
+        // Populate the singles plots.
+        for(Cluster cluster : pair) {
+            pairSeedEnergy.fill(TriggerModule.getValueClusterSeedEnergy(cluster));
+            pairHitCount.fill(TriggerModule.getValueClusterHitCount(cluster));
+            pairTotalEnergy.fill(TriggerModule.getValueClusterTotalEnergy(cluster));
+            pairDistribution.fill(TriggerModule.getClusterXIndex(cluster), TriggerModule.getClusterYIndex(cluster));
+        }
+        
+        // Populate the pair plots.
+        pairEnergySum.fill(TriggerModule.getValueEnergySum(pair));
+        pairEnergyDifference.fill(TriggerModule.getValueEnergyDifference(pair));
+        pairCoplanarity.fill(TriggerModule.getValueCoplanarity(pair));
+        pairEnergySlope.fill(TriggerModule.getValueEnergySlope(pair, 0.0055));
+        pairEnergySum2D.fill(TriggerModule.getValueClusterTotalEnergy(pair[0]), TriggerModule.getValueClusterTotalEnergy(pair[1]));
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerProcessAnalysisDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerProcessAnalysisDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/TriggerProcessAnalysisDriver.java	Wed Apr 27 11:11:32 2016
@@ -21,768 +21,768 @@
 import org.lcsim.util.aida.AIDA;
 
 public class TriggerProcessAnalysisDriver extends Driver {
-	private int eventsProcessed = 0;
-	private int møllersProcessed = 0;
-	private boolean checkSVT = false;
-	private int tridentsProcessed = 0;
-	private int gblMøllersProcessed = 0;
-	private int gblTridentsProcessed = 0;
-	private double timeCoincidence = 2.5;
-	private double elasticThreshold = 0.800;
-	private double møllerLowerRange = 0.900;
-	private double møllerUpperRange = 1.200;
-	private AIDA aida = AIDA.defaultInstance();
-	private boolean checkTriggerTimeWindow = false;
-	private String clusterCollectionName = "EcalClustersCorr";
-	private String particleCollectionName = "FinalStateParticles";
-	
-	// Define trident cluster-track matched condition plots.
-	private IHistogram1D trctmInvariantMass = aida.histogram1D("Tridents CTMatched/Invariant Mass", 140, 0.0, 0.070);
-	private IHistogram1D trctmInstancesInEvent = aida.histogram1D("Tridents CTMatched/Instances in Event", 9, 0.5, 9.5);
-	private IHistogram1D trctmEnergySum1D = aida.histogram1D("Tridents CTMatched/Cluster Energy Sum", 150, 0.000, 1.500);
-	private IHistogram1D trctmMomentumSum1D = aida.histogram1D("Tridents CTMatched/Track Momentum Sum", 150, 0.000, 1.500);
-	private IHistogram1D trctmElectronEnergy = aida.histogram1D("Tridents CTMatched/Electron Cluster Energy", 150, 0.000, 1.500);
-	private IHistogram1D trctmElectronMomentum = aida.histogram1D("Tridents CTMatched/Electron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram1D trctmPositronEnergy = aida.histogram1D("Tridents CTMatched/Positron Cluster Energy", 150, 0.000, 1.500);
-	private IHistogram1D trctmPositronMomentum = aida.histogram1D("Tridents CTMatched/Positron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram1D trctmTimeCoincidence = aida.histogram1D("Tridents CTMatched/Time Coincidence", 100, -4, 4);
-	private IHistogram2D trctmClusterPosition = aida.histogram2D("Tridents CTMatched/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
-	private IHistogram2D trctmEnergySum2D = aida.histogram2D("Tridents CTMatched/Cluster Energy Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D trctmTrackPosition = aida.histogram2D("Tridents CTMatched/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
-	private IHistogram2D trctmMomentumSum2D = aida.histogram2D("Tridents CTMatched/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D trctmESumCoplanarity = aida.histogram2D("Tridents CTMatched/Cluster Energy Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	private IHistogram2D trctmPSumCoplanarity = aida.histogram2D("Tridents CTMatched/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	
-	// Define the Møller cluster-track matched condition plots.
-	private IHistogram1D møctmInvariantMass = aida.histogram1D("Møller CTMatched/Invariant Mass", 140, 0.0, 0.070);
-	private IHistogram1D møctmInstancesInEvent = aida.histogram1D("Møller CTMatched/Instances in Event", 9, 0.5, 9.5);
-	private IHistogram1D møctmEnergySum1D = aida.histogram1D("Møller CTMatched/Cluster Energy Sum", 150, 0.000, 1.500);
-	private IHistogram1D møctmMomentumSum1D = aida.histogram1D("Møller CTMatched/Track Momentum Sum", 150, 0.000, 1.500);
-	private IHistogram1D møctmElectronEnergy = aida.histogram1D("Møller CTMatched/Electron Cluster Energy", 150, 0.000, 1.500);
-	private IHistogram1D møctmElectronMomentum = aida.histogram1D("Møller CTMatched/Electron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram1D møctmTimeCoincidence = aida.histogram1D("Møller CTMatched/Time Coincidence", 100, -4, 4);
-	private IHistogram2D møctmClusterPosition = aida.histogram2D("Møller CTMatched/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
-	private IHistogram2D møctmEnergySum2D = aida.histogram2D("Møller CTMatched/Cluster Energy Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D møctmTrackPosition = aida.histogram2D("Møller CTMatched/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
-	private IHistogram2D møctmMomentumSum2D = aida.histogram2D("Møller CTMatched/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D møctmESumCoplanarity = aida.histogram2D("Møller CTMatched/Cluster Energy Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	private IHistogram2D møctmPSumCoplanarity = aida.histogram2D("Møller CTMatched/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	
-	// Define the Møller track-only condition plots.
-	private IHistogram1D møgblTimeCoincidence = aida.histogram1D("Møller Track-Only/Time Coincidence", 100, -4, 4);
-	private IHistogram1D møgblInvariantMass = aida.histogram1D("Møller Track-Only/Invariant Mass", 140, 0.0, 0.070);
-	private IHistogram1D møgblInstancesInEvent = aida.histogram1D("Møller Track-Only/Instances in Event", 9, 0.5, 9.5);
-	private IHistogram1D møgblMomentumSum1D = aida.histogram1D("Møller Track-Only/Track Momentum Sum", 150, 0.000, 1.500);
-	private IHistogram1D møgblElectronMomentum = aida.histogram1D("Møller Track-Only/Electron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram2D møgblTrackPosition = aida.histogram2D("Møller Track-Only/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
-	private IHistogram2D møgblMomentumSum2D = aida.histogram2D("Møller Track-Only/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D møgblPSumCoplanarity = aida.histogram2D("Møller Track-Only/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	
-	// Define the GBL trident condition plots.
-	private IHistogram1D trgblInvariantMass = aida.histogram1D("Tridents Track-Only/Invariant Mass", 140, 0.0, 0.070);
-	private IHistogram1D trgblInstancesInEvent = aida.histogram1D("Tridents Track-Only/Instances in Event", 9, 0.5, 9.5);
-	private IHistogram1D trgblMomentumSum1D = aida.histogram1D("Tridents Track-Only/Track Momentum Sum", 150, 0.000, 1.500);
-	private IHistogram1D trgblElectronMomentum = aida.histogram1D("Tridents Track-Only/Electron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram1D trgblPositronMomentum = aida.histogram1D("Tridents Track-Only/Positron Track Momentum", 150, 0.000, 1.500);
-	private IHistogram1D trgblTimeCoincidence = aida.histogram1D("Tridents Track-Only/Time Coincidence", 100, -4, 4);
-	private IHistogram2D trgblTrackPosition = aida.histogram2D("Tridents Track-Only/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
-	private IHistogram2D trgblMomentumSum2D = aida.histogram2D("Tridents Track-Only/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
-	private IHistogram2D trgblPSumCoplanarity = aida.histogram2D("Tridents Track-Only/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
-	
-	@Override
-	public void endOfData() {
-		// Calculate the scaling factor for Hertz.
-		double scale = 19000.0 / eventsProcessed;
-		
-		System.out.println("Processed " + eventsProcessed + " events.");
-		System.out.println("Processed " + møllersProcessed + " Møller events");
-		System.out.println("\tAcceptance :: " + (100.0 * møllersProcessed / eventsProcessed) + "%");
-		System.out.println("\tRate       :: " + (møllersProcessed * scale) + " Hz");
-		
-		System.out.println("Processed " + tridentsProcessed + " trident events");
-		System.out.println("\tAcceptance :: " + (100.0 * tridentsProcessed / eventsProcessed) + "%");
-		System.out.println("\tRate       :: " + (tridentsProcessed * scale) + " Hz");
-		
-		System.out.println("Processed " + gblMøllersProcessed + " track-only Møller events");
-		System.out.println("\tAcceptance :: " + (100.0 * gblMøllersProcessed / eventsProcessed) + "%");
-		System.out.println("\tRate       :: " + (gblMøllersProcessed * scale) + " Hz");
-		
-		System.out.println("Processed " + gblTridentsProcessed + " Rafo trident events");
-		System.out.println("\tAcceptance :: " + (100.0 * gblTridentsProcessed / eventsProcessed) + "%");
-		System.out.println("\tRate       :: " + (gblTridentsProcessed * scale) + " Hz");
-	}
-	
-	@Override
-	public void process(EventHeader event) {
-		// Check whether the SVT was active in this event and, if so,
-		// skip it. This can be disabled through the steering file for
-		// Monte Carlo data, where the "SVT" is always active.
-		if(checkSVT) {
-			final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
-			boolean svtGood = true;
-	        for(int i = 0; i < flagNames.length; i++) {
-	            int[] flag = event.getIntegerParameters().get(flagNames[i]);
-	            if(flag == null || flag[0] == 0) {
-	                svtGood = false;
-	            }
-	        }
-	        if(!svtGood) { return; }
-		}
+    private int eventsProcessed = 0;
+    private int møllersProcessed = 0;
+    private boolean checkSVT = false;
+    private int tridentsProcessed = 0;
+    private int gblMøllersProcessed = 0;
+    private int gblTridentsProcessed = 0;
+    private double timeCoincidence = 2.5;
+    private double elasticThreshold = 0.800;
+    private double møllerLowerRange = 0.900;
+    private double møllerUpperRange = 1.200;
+    private AIDA aida = AIDA.defaultInstance();
+    private boolean checkTriggerTimeWindow = false;
+    private String clusterCollectionName = "EcalClustersCorr";
+    private String particleCollectionName = "FinalStateParticles";
+    
+    // Define trident cluster-track matched condition plots.
+    private IHistogram1D trctmInvariantMass = aida.histogram1D("Tridents CTMatched/Invariant Mass", 140, 0.0, 0.070);
+    private IHistogram1D trctmInstancesInEvent = aida.histogram1D("Tridents CTMatched/Instances in Event", 9, 0.5, 9.5);
+    private IHistogram1D trctmEnergySum1D = aida.histogram1D("Tridents CTMatched/Cluster Energy Sum", 150, 0.000, 1.500);
+    private IHistogram1D trctmMomentumSum1D = aida.histogram1D("Tridents CTMatched/Track Momentum Sum", 150, 0.000, 1.500);
+    private IHistogram1D trctmElectronEnergy = aida.histogram1D("Tridents CTMatched/Electron Cluster Energy", 150, 0.000, 1.500);
+    private IHistogram1D trctmElectronMomentum = aida.histogram1D("Tridents CTMatched/Electron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram1D trctmPositronEnergy = aida.histogram1D("Tridents CTMatched/Positron Cluster Energy", 150, 0.000, 1.500);
+    private IHistogram1D trctmPositronMomentum = aida.histogram1D("Tridents CTMatched/Positron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram1D trctmTimeCoincidence = aida.histogram1D("Tridents CTMatched/Time Coincidence", 100, -4, 4);
+    private IHistogram2D trctmClusterPosition = aida.histogram2D("Tridents CTMatched/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
+    private IHistogram2D trctmEnergySum2D = aida.histogram2D("Tridents CTMatched/Cluster Energy Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D trctmTrackPosition = aida.histogram2D("Tridents CTMatched/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
+    private IHistogram2D trctmMomentumSum2D = aida.histogram2D("Tridents CTMatched/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D trctmESumCoplanarity = aida.histogram2D("Tridents CTMatched/Cluster Energy Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    private IHistogram2D trctmPSumCoplanarity = aida.histogram2D("Tridents CTMatched/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    
+    // Define the Møller cluster-track matched condition plots.
+    private IHistogram1D møctmInvariantMass = aida.histogram1D("Møller CTMatched/Invariant Mass", 140, 0.0, 0.070);
+    private IHistogram1D møctmInstancesInEvent = aida.histogram1D("Møller CTMatched/Instances in Event", 9, 0.5, 9.5);
+    private IHistogram1D møctmEnergySum1D = aida.histogram1D("Møller CTMatched/Cluster Energy Sum", 150, 0.000, 1.500);
+    private IHistogram1D møctmMomentumSum1D = aida.histogram1D("Møller CTMatched/Track Momentum Sum", 150, 0.000, 1.500);
+    private IHistogram1D møctmElectronEnergy = aida.histogram1D("Møller CTMatched/Electron Cluster Energy", 150, 0.000, 1.500);
+    private IHistogram1D møctmElectronMomentum = aida.histogram1D("Møller CTMatched/Electron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram1D møctmTimeCoincidence = aida.histogram1D("Møller CTMatched/Time Coincidence", 100, -4, 4);
+    private IHistogram2D møctmClusterPosition = aida.histogram2D("Møller CTMatched/Cluster Seed Position", 46, -23, 23, 11, -5.5, 5.5);
+    private IHistogram2D møctmEnergySum2D = aida.histogram2D("Møller CTMatched/Cluster Energy Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D møctmTrackPosition = aida.histogram2D("Møller CTMatched/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
+    private IHistogram2D møctmMomentumSum2D = aida.histogram2D("Møller CTMatched/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D møctmESumCoplanarity = aida.histogram2D("Møller CTMatched/Cluster Energy Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    private IHistogram2D møctmPSumCoplanarity = aida.histogram2D("Møller CTMatched/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    
+    // Define the Møller track-only condition plots.
+    private IHistogram1D møgblTimeCoincidence = aida.histogram1D("Møller Track-Only/Time Coincidence", 100, -4, 4);
+    private IHistogram1D møgblInvariantMass = aida.histogram1D("Møller Track-Only/Invariant Mass", 140, 0.0, 0.070);
+    private IHistogram1D møgblInstancesInEvent = aida.histogram1D("Møller Track-Only/Instances in Event", 9, 0.5, 9.5);
+    private IHistogram1D møgblMomentumSum1D = aida.histogram1D("Møller Track-Only/Track Momentum Sum", 150, 0.000, 1.500);
+    private IHistogram1D møgblElectronMomentum = aida.histogram1D("Møller Track-Only/Electron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram2D møgblTrackPosition = aida.histogram2D("Møller Track-Only/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
+    private IHistogram2D møgblMomentumSum2D = aida.histogram2D("Møller Track-Only/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D møgblPSumCoplanarity = aida.histogram2D("Møller Track-Only/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    
+    // Define the GBL trident condition plots.
+    private IHistogram1D trgblInvariantMass = aida.histogram1D("Tridents Track-Only/Invariant Mass", 140, 0.0, 0.070);
+    private IHistogram1D trgblInstancesInEvent = aida.histogram1D("Tridents Track-Only/Instances in Event", 9, 0.5, 9.5);
+    private IHistogram1D trgblMomentumSum1D = aida.histogram1D("Tridents Track-Only/Track Momentum Sum", 150, 0.000, 1.500);
+    private IHistogram1D trgblElectronMomentum = aida.histogram1D("Tridents Track-Only/Electron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram1D trgblPositronMomentum = aida.histogram1D("Tridents Track-Only/Positron Track Momentum", 150, 0.000, 1.500);
+    private IHistogram1D trgblTimeCoincidence = aida.histogram1D("Tridents Track-Only/Time Coincidence", 100, -4, 4);
+    private IHistogram2D trgblTrackPosition = aida.histogram2D("Tridents Track-Only/Extrapolated Track Position", 200, -400, 400, 55, -110, 110);
+    private IHistogram2D trgblMomentumSum2D = aida.histogram2D("Tridents Track-Only/Track Momentum Sum 2D", 300, 0.000, 1.500, 300, 0.000, 1.500);
+    private IHistogram2D trgblPSumCoplanarity = aida.histogram2D("Tridents Track-Only/Track Momentum Sum vs. Coplanarity", 300, 0.000, 1.500, 360, 0, 360);
+    
+    @Override
+    public void endOfData() {
+        // Calculate the scaling factor for Hertz.
+        double scale = 19000.0 / eventsProcessed;
+        
+        System.out.println("Processed " + eventsProcessed + " events.");
+        System.out.println("Processed " + møllersProcessed + " Møller events");
+        System.out.println("\tAcceptance :: " + (100.0 * møllersProcessed / eventsProcessed) + "%");
+        System.out.println("\tRate       :: " + (møllersProcessed * scale) + " Hz");
+        
+        System.out.println("Processed " + tridentsProcessed + " trident events");
+        System.out.println("\tAcceptance :: " + (100.0 * tridentsProcessed / eventsProcessed) + "%");
+        System.out.println("\tRate       :: " + (tridentsProcessed * scale) + " Hz");
+        
+        System.out.println("Processed " + gblMøllersProcessed + " track-only Møller events");
+        System.out.println("\tAcceptance :: " + (100.0 * gblMøllersProcessed / eventsProcessed) + "%");
+        System.out.println("\tRate       :: " + (gblMøllersProcessed * scale) + " Hz");
+        
+        System.out.println("Processed " + gblTridentsProcessed + " Rafo trident events");
+        System.out.println("\tAcceptance :: " + (100.0 * gblTridentsProcessed / eventsProcessed) + "%");
+        System.out.println("\tRate       :: " + (gblTridentsProcessed * scale) + " Hz");
+    }
+    
+    @Override
+    public void process(EventHeader event) {
+        // Check whether the SVT was active in this event and, if so,
+        // skip it. This can be disabled through the steering file for
+        // Monte Carlo data, where the "SVT" is always active.
+        if(checkSVT) {
+            final String[] flagNames = { "svt_bias_good", "svt_burstmode_noise_good", "svt_position_good" };
+            boolean svtGood = true;
+            for(int i = 0; i < flagNames.length; i++) {
+                int[] flag = event.getIntegerParameters().get(flagNames[i]);
+                if(flag == null || flag[0] == 0) {
+                    svtGood = false;
+                }
+            }
+            if(!svtGood) { return; }
+        }
         
         // Track the number of events with good SVT.
         eventsProcessed++;
         
-		// Check if the event has a collection of tracks. If it exists,
+        // Check if the event has a collection of tracks. If it exists,
         // extract it. Otherwise, skip the event.
-		if(!event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
-			return;
-		}
-		List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
-		
-		// Check if the event has a collection of clusters. If it
-		// exists, extract it. Otherwise, skip the event.
-		if(!event.hasCollection(Cluster.class, clusterCollectionName)) {
-			return;
-		}
-		List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-		
-		// Get cluster-track matched top/bottom pairs.
-		List<ReconstructedParticle[]> gblMatchedPairs = getTopBottomTracksGBL(trackList);
-		List<ReconstructedParticle[]> ctMatchedPairs  = getTopBottomTracksCTMatched(trackList);
-		
-		System.out.println("CTM Pairs :: " + ctMatchedPairs.size());
-		System.out.println("GBL Pairs :: " + gblMatchedPairs.size());
-		
-		// Get the trident and Møller tracks for the matched track
-		// and cluster pair condition sets.
-		List<ReconstructedParticle[]> møllers     = getMøllerTracksCTMatched(ctMatchedPairs);
-		List<ReconstructedParticle[]> møllersGBL  = getMøllerTracksGBL(gblMatchedPairs, event);
-		List<ReconstructedParticle[]> tridents    = getTridentTracksCTMatched(ctMatchedPairs);
-		List<ReconstructedParticle[]> tridentsGBL = getTridentClustersGBL(gblMatchedPairs, TriggerModule.getTopBottomPairs(clusterList, Cluster.class), event);
-		
-		// Track how many events had tridents and Møllers.
-		if(!møllers.isEmpty()) { møllersProcessed++; }
-		if(!tridents.isEmpty()) { tridentsProcessed++; }
-		if(!møllersGBL.isEmpty()) { gblMøllersProcessed++; }
-		if(!tridentsGBL.isEmpty()) { gblTridentsProcessed++; }
-		
-		// Produce Møller cluster-track matched plots.
-		møctmInstancesInEvent.fill(møllers.size());
-		for(ReconstructedParticle[] pair : møllers) {
-			// Get the track clusters.
-			Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			
-			// Populate the cluster plots.
-			møctmElectronEnergy.fill(trackClusters[0].getEnergy());
-			møctmElectronEnergy.fill(trackClusters[1].getEnergy());
-			møctmEnergySum1D.fill(TriggerModule.getValueEnergySum(trackClusters));
-			møctmEnergySum2D.fill(trackClusters[0].getEnergy(), trackClusters[1].getEnergy());
-			møctmESumCoplanarity.fill(TriggerModule.getValueEnergySum(trackClusters), getCalculatedCoplanarity(trackClusters));
-			møctmTimeCoincidence.fill(TriggerModule.getClusterTime(trackClusters[0]) - TriggerModule.getClusterTime(trackClusters[1]));
-			møctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[0]), TriggerModule.getClusterYIndex(trackClusters[0]));
-			møctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[1]), TriggerModule.getClusterYIndex(trackClusters[1]));
-			
-			// Populate the momentum plots.
-			møctmInvariantMass.fill(getInvariantMass(pair));
-			møctmElectronMomentum.fill(pair[0].getMomentum().magnitude());
-			møctmElectronMomentum.fill(pair[1].getMomentum().magnitude());
-			møctmMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
-			møctmMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-			møctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
-			møctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
-			møctmPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
-					getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
-		}
-		
-		// Produce trident cluster-track matched plots.
-		trctmInstancesInEvent.fill(tridents.size());
-		for(ReconstructedParticle[] pair : tridents) {
-			// Get the electron and positron tracks.
-			ReconstructedParticle electronTrack = pair[pair[0].getCharge() < 0 ? 0 : 1];
-			ReconstructedParticle positronTrack = pair[pair[0].getCharge() > 0 ? 0 : 1];
-			
-			// Get the track clusters.
-			Cluster electronCluster = electronTrack.getClusters().get(0);
-			Cluster positronCluster = positronTrack.getClusters().get(0);
-			Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			
-			// Populate the cluster plots.
-			trctmElectronEnergy.fill(electronCluster.getEnergy());
-			trctmPositronEnergy.fill(positronCluster.getEnergy());
-			trctmEnergySum2D.fill(pair[0].getEnergy(), pair[1].getEnergy());
-			trctmEnergySum1D.fill(TriggerModule.getValueEnergySum(trackClusters));
-			trctmESumCoplanarity.fill(TriggerModule.getValueEnergySum(trackClusters), getCalculatedCoplanarity(trackClusters));
-			trctmTimeCoincidence.fill(TriggerModule.getClusterTime(trackClusters[0]) - TriggerModule.getClusterTime(trackClusters[1]));
-			trctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[0]), TriggerModule.getClusterYIndex(trackClusters[0]));
-			trctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[1]), TriggerModule.getClusterYIndex(trackClusters[1]));
-			
-			// Populate the momentum plots.
-			trctmInvariantMass.fill(getInvariantMass(pair));
-			trctmElectronMomentum.fill(electronTrack.getMomentum().magnitude());
-			trctmPositronMomentum.fill(positronTrack.getMomentum().magnitude());
-			trctmMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
-			trctmMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-			trctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
-			trctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
-			trctmPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
-					getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
-		}
-		
-		// Produce the Møller track-only plots.
-		møgblInstancesInEvent.fill(møllersGBL.size());
-		RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
-		RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
-		for(ReconstructedParticle pair[] : møllersGBL) {
-			// Get the tracks and track times.
-			Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
-			double times[] = {
-					TrackUtils.getTrackTime(tracks[0], hitToStrips, hitToRotated),
-					TrackUtils.getTrackTime(tracks[1], hitToStrips, hitToRotated)	
-			};
-			
-			// Fill the plots.
-			møgblTimeCoincidence.fill(times[0] - times[1]);
-			møgblInvariantMass.fill(getInvariantMass(pair));
-			møgblElectronMomentum.fill(pair[0].getMomentum().magnitude());
-			møgblElectronMomentum.fill(pair[1].getMomentum().magnitude());
-			møgblMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
-			møgblMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-			møgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
-			møgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
-			møgblPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
-					getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
-		}
-		
-		// Produce track-only trident plots.
-		trgblInstancesInEvent.fill(tridentsGBL.size());
-		for(ReconstructedParticle[] pair : tridentsGBL) {
-			// Get the tracks and track times.
-			Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
-			double times[] = {
-					TrackUtils.getTrackTime(tracks[0], hitToStrips, hitToRotated),
-					TrackUtils.getTrackTime(tracks[1], hitToStrips, hitToRotated)	
-			};
-			
-			// Get the positron and the electron.
-			ReconstructedParticle positron = pair[0].getCharge() > 0 ? pair[0] : pair[1];
-			ReconstructedParticle electron = pair[0].getCharge() < 0 ? pair[0] : pair[1];
-			
-			// Fill the plots.
-			trgblTimeCoincidence.fill(times[0] - times[1]);
-			trgblInvariantMass.fill(getInvariantMass(pair));
-			trgblElectronMomentum.fill(electron.getMomentum().magnitude());
-			trgblPositronMomentum.fill(positron.getMomentum().magnitude());
-			trgblMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
-			trgblMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
-			trgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
-			trgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
-			trgblPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
-					getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
-		}
-	}
-	
-	public void setCheckSVT(boolean state) {
-		checkSVT = state;
-	}
-	
-	public void setCheckTriggerTimeWindow(boolean state) {
-		checkTriggerTimeWindow = state;
-	}
-	
-	/**
-	 * Gets a list of all possible GBL top/bottom track pairs. These
-	 * tracks are not guaranteed to have a matched cluster.
-	 * @param trackList - A list of all possible tracks.
-	 * @return Returns a list of track pairs.
-	 */
-	private static final List<ReconstructedParticle[]> getTopBottomTracksGBL(List<ReconstructedParticle> trackList) {
-		// Separate the tracks into top and bottom tracks based on
-		// the value of tan(Λ). Use only GBL tracks to avoid track
-		// duplication.
-		List<ReconstructedParticle> topTracks = new ArrayList<ReconstructedParticle>();
-		List<ReconstructedParticle> botTracks = new ArrayList<ReconstructedParticle>();
-		trackLoop:
-		for(ReconstructedParticle track : trackList) {
-			// Require that the ReconstructedParticle contain an actual
-			// Track object.
-			if(track.getTracks().isEmpty()) {
-				continue trackLoop;
-			}
-			
-			// Ignore tracks that are not GBL tracks.
-			if(!TrackType.isGBL(track.getType())) {
-				continue trackLoop;
-			}
-			
-			// If the above tests pass, the ReconstructedParticle has
-			// a track and is also a GBL track. Separate it into either
-			// a top or a bottom track based on its tan(Λ) value.
-			if(track.getTracks().get(0).getTrackStates().get(0).getTanLambda() > 0) {
-				topTracks.add(track);
-			} else {
-				botTracks.add(track);
-			}
-		}
-		
-		// Form all top/bottom pairs with the unique tracks.
-		List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
-		for(ReconstructedParticle topTrack : topTracks) {
-			for(ReconstructedParticle botTrack : botTracks) {
-				pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
-			}
-		}
-		
-		// Return the result.
-		return pairList;
-	}
-	
-	/**
-	 * Produces pairs of tracks. The track pairs are required to be
-	 * matched to a cluster and the associated clusters must form a
-	 * top/bottom pair. If more than one track points to the same
-	 * cluster, only the first track is retained.
-	 * @param trackList - A list of all tracks.
-	 * @return Returns a list of track pairs meeting the aforementioned
-	 * conditions.
-	 */
-	private static final List<ReconstructedParticle[]> getTopBottomTracksCTMatched(List<ReconstructedParticle> trackList) {
-		// Track clusters that have already been seen to prevent clusters
-		// that have duplicate tracks from reappearing.
-		Set<Cluster> clusterSet = new HashSet<Cluster>();
-		
-		// Separate the tracks into top and bottom tracks based on
-		// the track cluster. Filter out tracks with no clusters.
-		List<ReconstructedParticle> topTracks = new ArrayList<ReconstructedParticle>();
-		List<ReconstructedParticle> botTracks = new ArrayList<ReconstructedParticle>();
-		trackLoop:
-		for(ReconstructedParticle track : trackList) {
-			// Check if the track has a cluster. If not, skip it.
-			if(track.getClusters().isEmpty()) {
-				continue trackLoop;
-			}
-			
-			// If the track doesn't have actual tracks, skip it.
-			if(track.getTracks().isEmpty()) {
-				continue trackLoop;
-			}
-			
-			// Check if the track cluster has already seen.
-			Cluster trackCluster = track.getClusters().get(0);
-			if(clusterSet.contains(trackCluster)) {
-				continue trackLoop;
-			}
-			
-			// If the track has a unique cluster, add it to the proper
-			// list based on the cluster y-index.
-			clusterSet.add(trackCluster);
-			if(TriggerModule.getClusterYIndex(trackCluster) > 0) {
-				topTracks.add(track);
-			} else {
-				botTracks.add(track);
-			}
-		}
-		
-		// Form all top/bottom pairs with the unique tracks.
-		List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
-		for(ReconstructedParticle topTrack : topTracks) {
-			for(ReconstructedParticle botTrack : botTracks) {
-				pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
-			}
-		}
-		
-		// Return the result.
-		return pairList;
-	}
-	
-	private final List<ReconstructedParticle[]> getTridentClustersGBL(List<ReconstructedParticle[]> pairList, List<Cluster[]> clusterList, EventHeader event) {
-		// Store the set of track pairs that meet the trident condition.
-		List<ReconstructedParticle[]> tridentTracks = new ArrayList<ReconstructedParticle[]>();
-		
-		// Extract track relational tables from the event object.
-		RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
-		RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
-		
-		// Tracks will not be considered for trident analysis unless there
-		// is at least one top/bottom cluster pair within the time window.
-		boolean passesClusterCondition = false;
-		tridentClusterLoop:
-		for(Cluster[] pair : clusterList) {
-			// Ignore clusters that are too far apart temporally.
-			if(TriggerModule.getValueTimeCoincidence(pair) > timeCoincidence) {
-				continue tridentClusterLoop;
-			}
-			
-			// Require that the cluster pair be top/bottom.
-			boolean hasTop = TriggerModule.getClusterYIndex(pair[0]) > 0 || TriggerModule.getClusterYIndex(pair[1]) > 0;
-			boolean hasBot = TriggerModule.getClusterYIndex(pair[0]) < 0 || TriggerModule.getClusterYIndex(pair[1]) < 0;
-			if(!hasTop || !hasBot) {
-				continue tridentClusterLoop;
-			}
-			
-			// If the cluster passes, mark that it has done so and skip
-			// the rest. Only one pair need pass.
-			passesClusterCondition = true;
-			break tridentClusterLoop;
-		}
-		
-		// If no cluster pair passed the cluster condition, no tracks
-		// are allowed to pass either.
-		if(!passesClusterCondition) {
-			return tridentTracks;
-		}
-		
-		// Next, check the track pair list. A track pair must have a
-		// positive and a negative track and must also be within the
-		// time coincidence window.
-		tridentTrackLoop:
-		for(ReconstructedParticle[] pair : pairList) {
-			// Check that there is at least one positive and one negative
-			// track in the pair.
-			boolean hasPositive = pair[0].getCharge() > 0 || pair[1].getCharge() > 0;
-			boolean hasNegative = pair[0].getCharge() < 0 || pair[1].getCharge() < 0;
-			if(!hasPositive || !hasNegative) {
-				break tridentTrackLoop;
-			}
-			
-			// Check that the track pair passes the time cut.
-			double times[] = {
-				TrackUtils.getTrackTime(pair[0].getTracks().get(0), hitToStrips, hitToRotated),
-				TrackUtils.getTrackTime(pair[1].getTracks().get(0), hitToStrips, hitToRotated)	
-			};
-			
-			if(Math.abs(times[0] - times[1]) > timeCoincidence) {
-				continue tridentTrackLoop;
-			}
-			
-			// Require that the negative track have less than the
-			// elastic threshold momentum to exclude elastic electrons.
-			if(pair[0].getCharge() < 0 && pair[0].getMomentum().magnitude() > elasticThreshold
-					|| pair[1].getCharge() < 0 && pair[1].getMomentum().magnitude() > elasticThreshold) {
-				continue tridentTrackLoop;
-			}
-			
-			// If the track passes both, it is considered a trident pair.
-			tridentTracks.add(pair);
-		}
-		
-		// Return the resultant pairs.
-		return tridentTracks;
-	}
-	
-	/**
-	 * Gets a list track pairs that meet the trident condition defined
-	 * using tracks with matched calorimeter clusters. A pair meets the
-	 * cluster/track matched trident condition is it meets the following:
-	 * <ul><li>Both tracks have matched clusters.</li>
-	 * <li>Has one positive track.</li>
-	 * <li>Has one negative track.</li>
-	 * <li>Clusters have a time coincidence of 2.5 ns or less.</li>
-	 * <li>The electron momentum is below 900 MeV.</li></ul>
-	 * @param pairList - A <code>List</code> collection of parameterized
-	 * type <code>ReconstructedParticle[]</code> containing all valid
-	 * top/bottom pairs of tracks with matched clusters. These will be
-	 * tested to see if they meet the process criteria.
-	 * @return Returns a list containing pairs of tracks that meet the
-	 * trident condition.
-	 */
-	private final List<ReconstructedParticle[]> getTridentTracksCTMatched(List<ReconstructedParticle[]> pairList) {
-		// Store the set of track pairs that meet the trident condition.
-		List<ReconstructedParticle[]> tridentTracks = new ArrayList<ReconstructedParticle[]>();
-		
-		// Loop over the filtered pair list and apply the trident
-		// condition test.
-		tridentLoop:
-		for(ReconstructedParticle[] pair : pairList) {
-			// There must be one positive and one negative track.
-			ReconstructedParticle electron = null;
-			ReconstructedParticle positron = null;
-			if(pair[0].getCharge() > 0) { positron = pair[0]; }
-			else if(pair[1].getCharge() > 0) { positron = pair[1]; }
-			if(pair[0].getCharge() < 0) { electron = pair[0]; }
-			else if(pair[1].getCharge() < 0) { electron = pair[1]; }
-			if(electron == null || positron == null) {
-				continue tridentLoop;
-			}
-			
-			// Make sure that the clusters are not the same. This should
-			// not actually ever be possible...
-			if(pair[0].getClusters().get(0) == pair[1].getClusters().get(0)) {
-				continue tridentLoop;
-			}
-			
-			// The clusters must within a limited time window.
-			/*
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			if(TriggerModule.getValueTimeCoincidence(trackClusters) > timeCoincidence) {
-				continue tridentLoop;
-			}
-			*/
-			
-			// The clusters must be coincidental within an energy
-			// dependent coincidence window.
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			if(!isCoincidental(trackClusters)) {
-				continue tridentLoop;
-			}
-			
-			// Require that the electron in the pair have an energy
-			// below the elastic threshold to exclude elastic electrons.
-			if(electron.getMomentum().magnitude() >= elasticThreshold) {
-				continue tridentLoop;
-			}
-			
-			// Require that all clusters occur within the trigger time
-			// window to exclude accidentals.
-			if(checkTriggerTimeWindow) {
-				if(!inTriggerWindow(trackClusters[0]) || !inTriggerWindow(trackClusters[1])) {
-					continue tridentLoop;
-				}
-			}
-			
-			// If all the above conditions are met, the pair is to be
-			// considered a trident pair. Add it to the list.
-			tridentTracks.add(pair);
-		}
-		
-		// Return the list of pairs that passed the condition.
-		return tridentTracks;
-	}
-	
-	private final List<ReconstructedParticle[]> getMøllerTracksGBL(List<ReconstructedParticle[]> pairList, EventHeader event) {
-		// Store the set of track pairs that meet the Møller condition.
-		List<ReconstructedParticle[]> møllerTracks = new ArrayList<ReconstructedParticle[]>();
-		
-		// Extract track relational tables from the event object.
-		RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
-		RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
-		
-		// Loop over the filtered pair list and apply the Møller
-		// condition test.
-		møllerLoop:
-		for(ReconstructedParticle[] pair : pairList) {
-			// Both tracks must be negatively charged.
-			if(pair[0].getCharge() > 0 || pair[1].getCharge() > 0) {
-				continue møllerLoop;
-			}
-			
-			// The clusters must within a limited time window.
-			double times[] = {
-				TrackUtils.getTrackTime(pair[0].getTracks().get(0), hitToStrips, hitToRotated),
-				TrackUtils.getTrackTime(pair[1].getTracks().get(0), hitToStrips, hitToRotated)	
-			};
-			
-			if(Math.abs(times[0] - times[1]) > timeCoincidence) {
-				continue møllerLoop;
-			}
-			
-			// Require that the electrons in the pair have energies
-			// below the elastic threshold to exclude said electrons.
-			if(pair[0].getMomentum().magnitude() > elasticThreshold || pair[1].getMomentum().magnitude() > elasticThreshold) {
-				continue møllerLoop;
-			}
-			
-			// Require that the energy of the pair be within a range
-			// that is sufficiently "Møller-like."
-			double momentumSum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
-			if(momentumSum < møllerLowerRange || momentumSum > møllerUpperRange) {
-				continue møllerLoop;
-			}
-			
-			// If all the above conditions are met, the pair is to be
-			// considered a trident pair. Add it to the list.
-			møllerTracks.add(pair);
-		}
-		
-		// Return the list of pairs that passed the condition.
-		return møllerTracks;
-	}
-	
-	/**
-	 * Gets a list track pairs that meet the Møller condition defined
-	 * using tracks with matched calorimeter clusters. A pair meets the
-	 * cluster/track matched Møller condition is it meets the following:
-	 * <ul><li>Both tracks have matched clusters.</li>
-	 * <li>Both tracks are negative.</li>
-	 * <li>Clusters have a time coincidence of 2.5 ns or less.</li>
-	 * <li>The electron momenta are below 900 MeV.</li>
-	 * <li>The momentum sum of the tracks is in the range <code>800 MeV
-	 * ≤ p1 + p2 ≤ 1500 MeV</li></ul>
-	 * @param pairList - A <code>List</code> collection of parameterized
-	 * type <code>ReconstructedParticle[]</code> containing all valid
-	 * top/bottom pairs of tracks with matched clusters. These will be
-	 * tested to see if they meet the process criteria.
-	 * @return Returns a list containing pairs of tracks that meet the
-	 * Møller condition.
-	 */
-	private final List<ReconstructedParticle[]> getMøllerTracksCTMatched(List<ReconstructedParticle[]> pairList) {
-		// Store the set of track pairs that meet the Møller condition.
-		List<ReconstructedParticle[]> møllerTracks = new ArrayList<ReconstructedParticle[]>();
-		
-		// Loop over the filtered pair list and apply the Møller
-		// condition test.
-		møllerLoop:
-		for(ReconstructedParticle[] pair : pairList) {
-			// Both tracks must be negatively charged.
-			if(pair[0].getCharge() > 0 || pair[1].getCharge() > 0) {
-				continue møllerLoop;
-			}
-			
-			// The clusters must within a limited time window.
-			/*
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			if(TriggerModule.getValueTimeCoincidence(trackClusters) > timeCoincidence) {
-				continue møllerLoop;
-			}
-			*/
-			
-			// The clusters must be coincidental within an energy
-			// dependent coincidence window.
-			Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
-			if(!isCoincidental(trackClusters)) {
-				continue møllerLoop;
-			}
-			
-			// Require that the electrons in the pair have energies
-			// below the elastic threshold to exclude said electrons.
-			if(pair[0].getMomentum().magnitude() > elasticThreshold || pair[1].getMomentum().magnitude() > elasticThreshold) {
-				continue møllerLoop;
-			}
-			
-			// Require that the energy of the pair be within a range
-			// that is sufficiently "Møller-like."
-			double momentumSum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
-			if(momentumSum < møllerLowerRange || momentumSum > møllerUpperRange) {
-				continue møllerLoop;
-			}
-			
-			// Require that all clusters occur within the trigger time
-			// window to exclude accidentals.
-			if(checkTriggerTimeWindow) {
-				if(!inTriggerWindow(trackClusters[0]) || !inTriggerWindow(trackClusters[1])) {
-					continue møllerLoop;
-				}
-			}
-			
-			// If all the above conditions are met, the pair is to be
-			// considered a trident pair. Add it to the list.
-			møllerTracks.add(pair);
-		}
-		
-		// Return the list of pairs that passed the condition.
-		return møllerTracks;
-	}
-	
-	/**
-	 * Calculates the approximate invariant mass for a pair of tracks
-	 * from their momentum. This assumes that the particles are either
-	 * electrons or positrons, and thusly have a sufficiently small
-	 * mass term that it can be safely excluded.
-	 * @param pair - The track pair for which to calculate the invariant
-	 * mass.
-	 * @return Returns the approximate invariant mass in units of GeV.
-	 */
-	private static final double getInvariantMass(ReconstructedParticle[] pair) {
-		// Get the momentum squared.
-		double p2 = Math.pow(pair[0].getMomentum().magnitude() + pair[1].getMomentum().magnitude(), 2);
-		
-		// Get the remaining terms.
-		double xPro = pair[0].getMomentum().x() + pair[1].getMomentum().x();
-		double yPro = pair[0].getMomentum().y() + pair[1].getMomentum().y();
-		double zPro = pair[0].getMomentum().z() + pair[1].getMomentum().z();
-		
-		// Calculate the invariant mass.
-		return Math.sqrt(p2 - Math.pow(xPro, 2) - Math.pow(yPro, 2) - Math.pow(zPro, 2));
-	}
-	
-	/**
-	 * Calculates the coplanarity angle between two points, specified
-	 * by a double array. The array must be of the format (x, y, z).
-	 * @param position - The first position array.
-	 * @param otherPosition - The second position array.
-	 * @return Returns the coplanarity angle between the points in units
-	 * of degrees.
-	 */
-	private static final double getCalculatedCoplanarity(double[] position, double[] otherPosition) {
-		// Define the x- and y-coordinates of the clusters as well as
-		// calorimeter center.
-		final double ORIGIN_X = 42.52;
-		double x[] = { position[0], otherPosition[0] };
-		double y[] = { position[1], otherPosition[1] };
-		
+        if(!event.hasCollection(ReconstructedParticle.class, particleCollectionName)) {
+            return;
+        }
+        List<ReconstructedParticle> trackList = event.get(ReconstructedParticle.class, particleCollectionName);
+        
+        // Check if the event has a collection of clusters. If it
+        // exists, extract it. Otherwise, skip the event.
+        if(!event.hasCollection(Cluster.class, clusterCollectionName)) {
+            return;
+        }
+        List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+        
+        // Get cluster-track matched top/bottom pairs.
+        List<ReconstructedParticle[]> gblMatchedPairs = getTopBottomTracksGBL(trackList);
+        List<ReconstructedParticle[]> ctMatchedPairs  = getTopBottomTracksCTMatched(trackList);
+        
+        System.out.println("CTM Pairs :: " + ctMatchedPairs.size());
+        System.out.println("GBL Pairs :: " + gblMatchedPairs.size());
+        
+        // Get the trident and Møller tracks for the matched track
+        // and cluster pair condition sets.
+        List<ReconstructedParticle[]> møllers     = getMøllerTracksCTMatched(ctMatchedPairs);
+        List<ReconstructedParticle[]> møllersGBL  = getMøllerTracksGBL(gblMatchedPairs, event);
+        List<ReconstructedParticle[]> tridents    = getTridentTracksCTMatched(ctMatchedPairs);
+        List<ReconstructedParticle[]> tridentsGBL = getTridentClustersGBL(gblMatchedPairs, TriggerModule.getTopBottomPairs(clusterList, Cluster.class), event);
+        
+        // Track how many events had tridents and Møllers.
+        if(!møllers.isEmpty()) { møllersProcessed++; }
+        if(!tridents.isEmpty()) { tridentsProcessed++; }
+        if(!møllersGBL.isEmpty()) { gblMøllersProcessed++; }
+        if(!tridentsGBL.isEmpty()) { gblTridentsProcessed++; }
+        
+        // Produce Møller cluster-track matched plots.
+        møctmInstancesInEvent.fill(møllers.size());
+        for(ReconstructedParticle[] pair : møllers) {
+            // Get the track clusters.
+            Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            
+            // Populate the cluster plots.
+            møctmElectronEnergy.fill(trackClusters[0].getEnergy());
+            møctmElectronEnergy.fill(trackClusters[1].getEnergy());
+            møctmEnergySum1D.fill(TriggerModule.getValueEnergySum(trackClusters));
+            møctmEnergySum2D.fill(trackClusters[0].getEnergy(), trackClusters[1].getEnergy());
+            møctmESumCoplanarity.fill(TriggerModule.getValueEnergySum(trackClusters), getCalculatedCoplanarity(trackClusters));
+            møctmTimeCoincidence.fill(TriggerModule.getClusterTime(trackClusters[0]) - TriggerModule.getClusterTime(trackClusters[1]));
+            møctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[0]), TriggerModule.getClusterYIndex(trackClusters[0]));
+            møctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[1]), TriggerModule.getClusterYIndex(trackClusters[1]));
+            
+            // Populate the momentum plots.
+            møctmInvariantMass.fill(getInvariantMass(pair));
+            møctmElectronMomentum.fill(pair[0].getMomentum().magnitude());
+            møctmElectronMomentum.fill(pair[1].getMomentum().magnitude());
+            møctmMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
+            møctmMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+            møctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
+            møctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
+            møctmPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
+                    getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
+        }
+        
+        // Produce trident cluster-track matched plots.
+        trctmInstancesInEvent.fill(tridents.size());
+        for(ReconstructedParticle[] pair : tridents) {
+            // Get the electron and positron tracks.
+            ReconstructedParticle electronTrack = pair[pair[0].getCharge() < 0 ? 0 : 1];
+            ReconstructedParticle positronTrack = pair[pair[0].getCharge() > 0 ? 0 : 1];
+            
+            // Get the track clusters.
+            Cluster electronCluster = electronTrack.getClusters().get(0);
+            Cluster positronCluster = positronTrack.getClusters().get(0);
+            Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            
+            // Populate the cluster plots.
+            trctmElectronEnergy.fill(electronCluster.getEnergy());
+            trctmPositronEnergy.fill(positronCluster.getEnergy());
+            trctmEnergySum2D.fill(pair[0].getEnergy(), pair[1].getEnergy());
+            trctmEnergySum1D.fill(TriggerModule.getValueEnergySum(trackClusters));
+            trctmESumCoplanarity.fill(TriggerModule.getValueEnergySum(trackClusters), getCalculatedCoplanarity(trackClusters));
+            trctmTimeCoincidence.fill(TriggerModule.getClusterTime(trackClusters[0]) - TriggerModule.getClusterTime(trackClusters[1]));
+            trctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[0]), TriggerModule.getClusterYIndex(trackClusters[0]));
+            trctmClusterPosition.fill(TriggerModule.getClusterXIndex(trackClusters[1]), TriggerModule.getClusterYIndex(trackClusters[1]));
+            
+            // Populate the momentum plots.
+            trctmInvariantMass.fill(getInvariantMass(pair));
+            trctmElectronMomentum.fill(electronTrack.getMomentum().magnitude());
+            trctmPositronMomentum.fill(positronTrack.getMomentum().magnitude());
+            trctmMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
+            trctmMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+            trctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
+            trctmTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
+            trctmPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
+                    getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
+        }
+        
+        // Produce the Møller track-only plots.
+        møgblInstancesInEvent.fill(møllersGBL.size());
+        RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
+        RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
+        for(ReconstructedParticle pair[] : møllersGBL) {
+            // Get the tracks and track times.
+            Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
+            double times[] = {
+                    TrackUtils.getTrackTime(tracks[0], hitToStrips, hitToRotated),
+                    TrackUtils.getTrackTime(tracks[1], hitToStrips, hitToRotated)   
+            };
+            
+            // Fill the plots.
+            møgblTimeCoincidence.fill(times[0] - times[1]);
+            møgblInvariantMass.fill(getInvariantMass(pair));
+            møgblElectronMomentum.fill(pair[0].getMomentum().magnitude());
+            møgblElectronMomentum.fill(pair[1].getMomentum().magnitude());
+            møgblMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
+            møgblMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+            møgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
+            møgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
+            møgblPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
+                    getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
+        }
+        
+        // Produce track-only trident plots.
+        trgblInstancesInEvent.fill(tridentsGBL.size());
+        for(ReconstructedParticle[] pair : tridentsGBL) {
+            // Get the tracks and track times.
+            Track[] tracks = { pair[0].getTracks().get(0), pair[1].getTracks().get(0) };
+            double times[] = {
+                    TrackUtils.getTrackTime(tracks[0], hitToStrips, hitToRotated),
+                    TrackUtils.getTrackTime(tracks[1], hitToStrips, hitToRotated)   
+            };
+            
+            // Get the positron and the electron.
+            ReconstructedParticle positron = pair[0].getCharge() > 0 ? pair[0] : pair[1];
+            ReconstructedParticle electron = pair[0].getCharge() < 0 ? pair[0] : pair[1];
+            
+            // Fill the plots.
+            trgblTimeCoincidence.fill(times[0] - times[1]);
+            trgblInvariantMass.fill(getInvariantMass(pair));
+            trgblElectronMomentum.fill(electron.getMomentum().magnitude());
+            trgblPositronMomentum.fill(positron.getMomentum().magnitude());
+            trgblMomentumSum1D.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude());
+            trgblMomentumSum2D.fill(pair[0].getMomentum().magnitude(), pair[1].getMomentum().magnitude());
+            trgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[0]).x(), TrackUtils.getTrackPositionAtEcal(tracks[0]).y());
+            trgblTrackPosition.fill(TrackUtils.getTrackPositionAtEcal(tracks[1]).x(), TrackUtils.getTrackPositionAtEcal(tracks[1]).y());
+            trgblPSumCoplanarity.fill(VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude(),
+                    getCalculatedCoplanarity(new Track[] { pair[0].getTracks().get(0), pair[1].getTracks().get(0) }));
+        }
+    }
+    
+    public void setCheckSVT(boolean state) {
+        checkSVT = state;
+    }
+    
+    public void setCheckTriggerTimeWindow(boolean state) {
+        checkTriggerTimeWindow = state;
+    }
+    
+    /**
+     * Gets a list of all possible GBL top/bottom track pairs. These
+     * tracks are not guaranteed to have a matched cluster.
+     * @param trackList - A list of all possible tracks.
+     * @return Returns a list of track pairs.
+     */
+    private static final List<ReconstructedParticle[]> getTopBottomTracksGBL(List<ReconstructedParticle> trackList) {
+        // Separate the tracks into top and bottom tracks based on
+        // the value of tan(Λ). Use only GBL tracks to avoid track
+        // duplication.
+        List<ReconstructedParticle> topTracks = new ArrayList<ReconstructedParticle>();
+        List<ReconstructedParticle> botTracks = new ArrayList<ReconstructedParticle>();
+        trackLoop:
+        for(ReconstructedParticle track : trackList) {
+            // Require that the ReconstructedParticle contain an actual
+            // Track object.
+            if(track.getTracks().isEmpty()) {
+                continue trackLoop;
+            }
+            
+            // Ignore tracks that are not GBL tracks.
+            if(!TrackType.isGBL(track.getType())) {
+                continue trackLoop;
+            }
+            
+            // If the above tests pass, the ReconstructedParticle has
+            // a track and is also a GBL track. Separate it into either
+            // a top or a bottom track based on its tan(Λ) value.
+            if(track.getTracks().get(0).getTrackStates().get(0).getTanLambda() > 0) {
+                topTracks.add(track);
+            } else {
+                botTracks.add(track);
+            }
+        }
+        
+        // Form all top/bottom pairs with the unique tracks.
+        List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
+        for(ReconstructedParticle topTrack : topTracks) {
+            for(ReconstructedParticle botTrack : botTracks) {
+                pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
+            }
+        }
+        
+        // Return the result.
+        return pairList;
+    }
+    
+    /**
+     * Produces pairs of tracks. The track pairs are required to be
+     * matched to a cluster and the associated clusters must form a
+     * top/bottom pair. If more than one track points to the same
+     * cluster, only the first track is retained.
+     * @param trackList - A list of all tracks.
+     * @return Returns a list of track pairs meeting the aforementioned
+     * conditions.
+     */
+    private static final List<ReconstructedParticle[]> getTopBottomTracksCTMatched(List<ReconstructedParticle> trackList) {
+        // Track clusters that have already been seen to prevent clusters
+        // that have duplicate tracks from reappearing.
+        Set<Cluster> clusterSet = new HashSet<Cluster>();
+        
+        // Separate the tracks into top and bottom tracks based on
+        // the track cluster. Filter out tracks with no clusters.
+        List<ReconstructedParticle> topTracks = new ArrayList<ReconstructedParticle>();
+        List<ReconstructedParticle> botTracks = new ArrayList<ReconstructedParticle>();
+        trackLoop:
+        for(ReconstructedParticle track : trackList) {
+            // Check if the track has a cluster. If not, skip it.
+            if(track.getClusters().isEmpty()) {
+                continue trackLoop;
+            }
+            
+            // If the track doesn't have actual tracks, skip it.
+            if(track.getTracks().isEmpty()) {
+                continue trackLoop;
+            }
+            
+            // Check if the track cluster has already seen.
+            Cluster trackCluster = track.getClusters().get(0);
+            if(clusterSet.contains(trackCluster)) {
+                continue trackLoop;
+            }
+            
+            // If the track has a unique cluster, add it to the proper
+            // list based on the cluster y-index.
+            clusterSet.add(trackCluster);
+            if(TriggerModule.getClusterYIndex(trackCluster) > 0) {
+                topTracks.add(track);
+            } else {
+                botTracks.add(track);
+            }
+        }
+        
+        // Form all top/bottom pairs with the unique tracks.
+        List<ReconstructedParticle[]> pairList = new ArrayList<ReconstructedParticle[]>();
+        for(ReconstructedParticle topTrack : topTracks) {
+            for(ReconstructedParticle botTrack : botTracks) {
+                pairList.add(new ReconstructedParticle[] { topTrack, botTrack });
+            }
+        }
+        
+        // Return the result.
+        return pairList;
+    }
+    
+    private final List<ReconstructedParticle[]> getTridentClustersGBL(List<ReconstructedParticle[]> pairList, List<Cluster[]> clusterList, EventHeader event) {
+        // Store the set of track pairs that meet the trident condition.
+        List<ReconstructedParticle[]> tridentTracks = new ArrayList<ReconstructedParticle[]>();
+        
+        // Extract track relational tables from the event object.
+        RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
+        RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
+        
+        // Tracks will not be considered for trident analysis unless there
+        // is at least one top/bottom cluster pair within the time window.
+        boolean passesClusterCondition = false;
+        tridentClusterLoop:
+        for(Cluster[] pair : clusterList) {
+            // Ignore clusters that are too far apart temporally.
+            if(TriggerModule.getValueTimeCoincidence(pair) > timeCoincidence) {
+                continue tridentClusterLoop;
+            }
+            
+            // Require that the cluster pair be top/bottom.
+            boolean hasTop = TriggerModule.getClusterYIndex(pair[0]) > 0 || TriggerModule.getClusterYIndex(pair[1]) > 0;
+            boolean hasBot = TriggerModule.getClusterYIndex(pair[0]) < 0 || TriggerModule.getClusterYIndex(pair[1]) < 0;
+            if(!hasTop || !hasBot) {
+                continue tridentClusterLoop;
+            }
+            
+            // If the cluster passes, mark that it has done so and skip
+            // the rest. Only one pair need pass.
+            passesClusterCondition = true;
+            break tridentClusterLoop;
+        }
+        
+        // If no cluster pair passed the cluster condition, no tracks
+        // are allowed to pass either.
+        if(!passesClusterCondition) {
+            return tridentTracks;
+        }
+        
+        // Next, check the track pair list. A track pair must have a
+        // positive and a negative track and must also be within the
+        // time coincidence window.
+        tridentTrackLoop:
+        for(ReconstructedParticle[] pair : pairList) {
+            // Check that there is at least one positive and one negative
+            // track in the pair.
+            boolean hasPositive = pair[0].getCharge() > 0 || pair[1].getCharge() > 0;
+            boolean hasNegative = pair[0].getCharge() < 0 || pair[1].getCharge() < 0;
+            if(!hasPositive || !hasNegative) {
+                break tridentTrackLoop;
+            }
+            
+            // Check that the track pair passes the time cut.
+            double times[] = {
+                TrackUtils.getTrackTime(pair[0].getTracks().get(0), hitToStrips, hitToRotated),
+                TrackUtils.getTrackTime(pair[1].getTracks().get(0), hitToStrips, hitToRotated)  
+            };
+            
+            if(Math.abs(times[0] - times[1]) > timeCoincidence) {
+                continue tridentTrackLoop;
+            }
+            
+            // Require that the negative track have less than the
+            // elastic threshold momentum to exclude elastic electrons.
+            if(pair[0].getCharge() < 0 && pair[0].getMomentum().magnitude() > elasticThreshold
+                    || pair[1].getCharge() < 0 && pair[1].getMomentum().magnitude() > elasticThreshold) {
+                continue tridentTrackLoop;
+            }
+            
+            // If the track passes both, it is considered a trident pair.
+            tridentTracks.add(pair);
+        }
+        
+        // Return the resultant pairs.
+        return tridentTracks;
+    }
+    
+    /**
+     * Gets a list track pairs that meet the trident condition defined
+     * using tracks with matched calorimeter clusters. A pair meets the
+     * cluster/track matched trident condition is it meets the following:
+     * <ul><li>Both tracks have matched clusters.</li>
+     * <li>Has one positive track.</li>
+     * <li>Has one negative track.</li>
+     * <li>Clusters have a time coincidence of 2.5 ns or less.</li>
+     * <li>The electron momentum is below 900 MeV.</li></ul>
+     * @param pairList - A <code>List</code> collection of parameterized
+     * type <code>ReconstructedParticle[]</code> containing all valid
+     * top/bottom pairs of tracks with matched clusters. These will be
+     * tested to see if they meet the process criteria.
+     * @return Returns a list containing pairs of tracks that meet the
+     * trident condition.
+     */
+    private final List<ReconstructedParticle[]> getTridentTracksCTMatched(List<ReconstructedParticle[]> pairList) {
+        // Store the set of track pairs that meet the trident condition.
+        List<ReconstructedParticle[]> tridentTracks = new ArrayList<ReconstructedParticle[]>();
+        
+        // Loop over the filtered pair list and apply the trident
+        // condition test.
+        tridentLoop:
+        for(ReconstructedParticle[] pair : pairList) {
+            // There must be one positive and one negative track.
+            ReconstructedParticle electron = null;
+            ReconstructedParticle positron = null;
+            if(pair[0].getCharge() > 0) { positron = pair[0]; }
+            else if(pair[1].getCharge() > 0) { positron = pair[1]; }
+            if(pair[0].getCharge() < 0) { electron = pair[0]; }
+            else if(pair[1].getCharge() < 0) { electron = pair[1]; }
+            if(electron == null || positron == null) {
+                continue tridentLoop;
+            }
+            
+            // Make sure that the clusters are not the same. This should
+            // not actually ever be possible...
+            if(pair[0].getClusters().get(0) == pair[1].getClusters().get(0)) {
+                continue tridentLoop;
+            }
+            
+            // The clusters must within a limited time window.
+            /*
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            if(TriggerModule.getValueTimeCoincidence(trackClusters) > timeCoincidence) {
+                continue tridentLoop;
+            }
+            */
+            
+            // The clusters must be coincidental within an energy
+            // dependent coincidence window.
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            if(!isCoincidental(trackClusters)) {
+                continue tridentLoop;
+            }
+            
+            // Require that the electron in the pair have an energy
+            // below the elastic threshold to exclude elastic electrons.
+            if(electron.getMomentum().magnitude() >= elasticThreshold) {
+                continue tridentLoop;
+            }
+            
+            // Require that all clusters occur within the trigger time
+            // window to exclude accidentals.
+            if(checkTriggerTimeWindow) {
+                if(!inTriggerWindow(trackClusters[0]) || !inTriggerWindow(trackClusters[1])) {
+                    continue tridentLoop;
+                }
+            }
+            
+            // If all the above conditions are met, the pair is to be
+            // considered a trident pair. Add it to the list.
+            tridentTracks.add(pair);
+        }
+        
+        // Return the list of pairs that passed the condition.
+        return tridentTracks;
+    }
+    
+    private final List<ReconstructedParticle[]> getMøllerTracksGBL(List<ReconstructedParticle[]> pairList, EventHeader event) {
+        // Store the set of track pairs that meet the Møller condition.
+        List<ReconstructedParticle[]> møllerTracks = new ArrayList<ReconstructedParticle[]>();
+        
+        // Extract track relational tables from the event object.
+        RelationalTable<?, ?> hitToStrips = TrackUtils.getHitToStripsTable(event);
+        RelationalTable<?, ?> hitToRotated = TrackUtils.getHitToRotatedTable(event);
+        
+        // Loop over the filtered pair list and apply the Møller
+        // condition test.
+        møllerLoop:
+        for(ReconstructedParticle[] pair : pairList) {
+            // Both tracks must be negatively charged.
+            if(pair[0].getCharge() > 0 || pair[1].getCharge() > 0) {
+                continue møllerLoop;
+            }
+            
+            // The clusters must within a limited time window.
+            double times[] = {
+                TrackUtils.getTrackTime(pair[0].getTracks().get(0), hitToStrips, hitToRotated),
+                TrackUtils.getTrackTime(pair[1].getTracks().get(0), hitToStrips, hitToRotated)  
+            };
+            
+            if(Math.abs(times[0] - times[1]) > timeCoincidence) {
+                continue møllerLoop;
+            }
+            
+            // Require that the electrons in the pair have energies
+            // below the elastic threshold to exclude said electrons.
+            if(pair[0].getMomentum().magnitude() > elasticThreshold || pair[1].getMomentum().magnitude() > elasticThreshold) {
+                continue møllerLoop;
+            }
+            
+            // Require that the energy of the pair be within a range
+            // that is sufficiently "Møller-like."
+            double momentumSum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
+            if(momentumSum < møllerLowerRange || momentumSum > møllerUpperRange) {
+                continue møllerLoop;
+            }
+            
+            // If all the above conditions are met, the pair is to be
+            // considered a trident pair. Add it to the list.
+            møllerTracks.add(pair);
+        }
+        
+        // Return the list of pairs that passed the condition.
+        return møllerTracks;
+    }
+    
+    /**
+     * Gets a list track pairs that meet the Møller condition defined
+     * using tracks with matched calorimeter clusters. A pair meets the
+     * cluster/track matched Møller condition is it meets the following:
+     * <ul><li>Both tracks have matched clusters.</li>
+     * <li>Both tracks are negative.</li>
+     * <li>Clusters have a time coincidence of 2.5 ns or less.</li>
+     * <li>The electron momenta are below 900 MeV.</li>
+     * <li>The momentum sum of the tracks is in the range <code>800 MeV
+     * ≤ p1 + p2 ≤ 1500 MeV</li></ul>
+     * @param pairList - A <code>List</code> collection of parameterized
+     * type <code>ReconstructedParticle[]</code> containing all valid
+     * top/bottom pairs of tracks with matched clusters. These will be
+     * tested to see if they meet the process criteria.
+     * @return Returns a list containing pairs of tracks that meet the
+     * Møller condition.
+     */
+    private final List<ReconstructedParticle[]> getMøllerTracksCTMatched(List<ReconstructedParticle[]> pairList) {
+        // Store the set of track pairs that meet the Møller condition.
+        List<ReconstructedParticle[]> møllerTracks = new ArrayList<ReconstructedParticle[]>();
+        
+        // Loop over the filtered pair list and apply the Møller
+        // condition test.
+        møllerLoop:
+        for(ReconstructedParticle[] pair : pairList) {
+            // Both tracks must be negatively charged.
+            if(pair[0].getCharge() > 0 || pair[1].getCharge() > 0) {
+                continue møllerLoop;
+            }
+            
+            // The clusters must within a limited time window.
+            /*
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            if(TriggerModule.getValueTimeCoincidence(trackClusters) > timeCoincidence) {
+                continue møllerLoop;
+            }
+            */
+            
+            // The clusters must be coincidental within an energy
+            // dependent coincidence window.
+            Cluster[] trackClusters = { pair[0].getClusters().get(0), pair[1].getClusters().get(0) };
+            if(!isCoincidental(trackClusters)) {
+                continue møllerLoop;
+            }
+            
+            // Require that the electrons in the pair have energies
+            // below the elastic threshold to exclude said electrons.
+            if(pair[0].getMomentum().magnitude() > elasticThreshold || pair[1].getMomentum().magnitude() > elasticThreshold) {
+                continue møllerLoop;
+            }
+            
+            // Require that the energy of the pair be within a range
+            // that is sufficiently "Møller-like."
+            double momentumSum = VecOp.add(pair[0].getMomentum(), pair[1].getMomentum()).magnitude();
+            if(momentumSum < møllerLowerRange || momentumSum > møllerUpperRange) {
+                continue møllerLoop;
+            }
+            
+            // Require that all clusters occur within the trigger time
+            // window to exclude accidentals.
+            if(checkTriggerTimeWindow) {
+                if(!inTriggerWindow(trackClusters[0]) || !inTriggerWindow(trackClusters[1])) {
+                    continue møllerLoop;
+                }
+            }
+            
+            // If all the above conditions are met, the pair is to be
+            // considered a trident pair. Add it to the list.
+            møllerTracks.add(pair);
+        }
+        
+        // Return the list of pairs that passed the condition.
+        return møllerTracks;
+    }
+    
+    /**
+     * Calculates the approximate invariant mass for a pair of tracks
+     * from their momentum. This assumes that the particles are either
+     * electrons or positrons, and thusly have a sufficiently small
+     * mass term that it can be safely excluded.
+     * @param pair - The track pair for which to calculate the invariant
+     * mass.
+     * @return Returns the approximate invariant mass in units of GeV.
+     */
+    private static final double getInvariantMass(ReconstructedParticle[] pair) {
+        // Get the momentum squared.
+        double p2 = Math.pow(pair[0].getMomentum().magnitude() + pair[1].getMomentum().magnitude(), 2);
+        
+        // Get the remaining terms.
+        double xPro = pair[0].getMomentum().x() + pair[1].getMomentum().x();
+        double yPro = pair[0].getMomentum().y() + pair[1].getMomentum().y();
+        double zPro = pair[0].getMomentum().z() + pair[1].getMomentum().z();
+        
+        // Calculate the invariant mass.
+        return Math.sqrt(p2 - Math.pow(xPro, 2) - Math.pow(yPro, 2) - Math.pow(zPro, 2));
+    }
+    
+    /**
+     * Calculates the coplanarity angle between two points, specified
+     * by a double array. The array must be of the format (x, y, z).
+     * @param position - The first position array.
+     * @param otherPosition - The second position array.
+     * @return Returns the coplanarity angle between the points in units
+     * of degrees.
+     */
+    private static final double getCalculatedCoplanarity(double[] position, double[] otherPosition) {
+        // Define the x- and y-coordinates of the clusters as well as
+        // calorimeter center.
+        final double ORIGIN_X = 42.52;
+        double x[] = { position[0], otherPosition[0] };
+        double y[] = { position[1], otherPosition[1] };
+        
         // Get the cluster angles.
         double[] clusterAngle = new double[2];
         for(int i = 0; i < 2; i++) {
-        	clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
-        	if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
+            clusterAngle[i] = Math.atan2(y[i], x[i] - ORIGIN_X) * 180 / Math.PI;
+            if(clusterAngle[i] <= 0) { clusterAngle[i] += 360; }
         }
         
         // Calculate the coplanarity cut value.
         double clusterDiff = clusterAngle[0] - clusterAngle[1];
         return clusterDiff > 0 ? clusterDiff : clusterDiff + 360;
-	}
-	
-	/**
-	 * Calculates the coplanarity angle of a pair of clusters.
-	 * @param pair - The pair of clusters for which to calculate the
-	 * coplanarity angle.
-	 * @return Returns the coplanarity angle between the two clusters
-	 * in degrees.
-	 */
-	private static final double getCalculatedCoplanarity(Cluster[] pair) {
-		return getCalculatedCoplanarity(pair[0].getPosition(), pair[1].getPosition());
-	}
-	
-	/**
-	 * Calculates the coplanarity angle of a pair of tracks. The track
-	 * is extrapolated to the calorimeter face and its position there
-	 * used for the arguments in the calculation.
-	 * @param pair - The pair of tracks for which to calculate the
-	 * coplanarity angle.
-	 * @return Returns the coplanarity angle between the two tracks
-	 * in degrees.
-	 */
-	private static final double getCalculatedCoplanarity(Track[] pair) {
-		return getCalculatedCoplanarity(TrackUtils.getTrackPositionAtEcal(pair[0]).v(), TrackUtils.getTrackPositionAtEcal(pair[1]).v());
-	}
-	
-	private static final boolean inTriggerWindow(Cluster cluster) {
-		// Get the cluster time.
-		double clusterTime = TriggerModule.getClusterTime(cluster);
-		
-		// Check that it is within the allowed bounds.
-		return (35 <= clusterTime && clusterTime <= 50);
-	}
-	
-	private static final boolean isCoincidental(Cluster[] pair) {
-		// Get the energy sum and the time coincidence.
-		double energySum = pair[0].getEnergy() + pair[1].getEnergy();
-		double timeCoincidence = TriggerModule.getValueTimeCoincidence(pair);
-		
-		// Get the upper and lower bounds of the allowed range.
-		double mean = getTimeDependenceMean(energySum);
-		double threeSigma = 3.0 * getTimeDependenceSigma(energySum);
-		double lowerBound = mean - threeSigma;
-		double upperBound = mean + threeSigma;
-		
-		// Perform the time coincidence check.
-		return (lowerBound <= timeCoincidence && timeCoincidence <= upperBound);
-	}
-	
-	private static final double getTimeDependenceMean(double energySum) {
-		// Define the fit parameters.
-		double[] param = { 0.289337, -2.81998, 9.03475, -12.93, 8.71476, -2.26969 };
-		
-		// Calculate the mean.
-		return param[0] + energySum * (param[1] + energySum * (param[2] + energySum * (param[3] + energySum * (param[4] + energySum * (param[5])))));
-	}
-	
-	private static final double getTimeDependenceSigma(double energySum) {
-		// Define the fit parameters.
-		double[] param = { 4.3987, -24.2371, 68.9567, -98.2586, 67.562, -17.8987 };
-		
-		// Calculate the standard deviation.
-		return param[0] + energySum * (param[1] + energySum * (param[2] + energySum * (param[3] + energySum * (param[4] + energySum * (param[5])))));
-	}
+    }
+    
+    /**
+     * Calculates the coplanarity angle of a pair of clusters.
+     * @param pair - The pair of clusters for which to calculate the
+     * coplanarity angle.
+     * @return Returns the coplanarity angle between the two clusters
+     * in degrees.
+     */
+    private static final double getCalculatedCoplanarity(Cluster[] pair) {
+        return getCalculatedCoplanarity(pair[0].getPosition(), pair[1].getPosition());
+    }
+    
+    /**
+     * Calculates the coplanarity angle of a pair of tracks. The track
+     * is extrapolated to the calorimeter face and its position there
+     * used for the arguments in the calculation.
+     * @param pair - The pair of tracks for which to calculate the
+     * coplanarity angle.
+     * @return Returns the coplanarity angle between the two tracks
+     * in degrees.
+     */
+    private static final double getCalculatedCoplanarity(Track[] pair) {
+        return getCalculatedCoplanarity(TrackUtils.getTrackPositionAtEcal(pair[0]).v(), TrackUtils.getTrackPositionAtEcal(pair[1]).v());
+    }
+    
+    private static final boolean inTriggerWindow(Cluster cluster) {
+        // Get the cluster time.
+        double clusterTime = TriggerModule.getClusterTime(cluster);
+        
+        // Check that it is within the allowed bounds.
+        return (35 <= clusterTime && clusterTime <= 50);
+    }
+    
+    private static final boolean isCoincidental(Cluster[] pair) {
+        // Get the energy sum and the time coincidence.
+        double energySum = pair[0].getEnergy() + pair[1].getEnergy();
+        double timeCoincidence = TriggerModule.getValueTimeCoincidence(pair);
+        
+        // Get the upper and lower bounds of the allowed range.
+        double mean = getTimeDependenceMean(energySum);
+        double threeSigma = 3.0 * getTimeDependenceSigma(energySum);
+        double lowerBound = mean - threeSigma;
+        double upperBound = mean + threeSigma;
+        
+        // Perform the time coincidence check.
+        return (lowerBound <= timeCoincidence && timeCoincidence <= upperBound);
+    }
+    
+    private static final double getTimeDependenceMean(double energySum) {
+        // Define the fit parameters.
+        double[] param = { 0.289337, -2.81998, 9.03475, -12.93, 8.71476, -2.26969 };
+        
+        // Calculate the mean.
+        return param[0] + energySum * (param[1] + energySum * (param[2] + energySum * (param[3] + energySum * (param[4] + energySum * (param[5])))));
+    }
+    
+    private static final double getTimeDependenceSigma(double energySum) {
+        // Define the fit parameters.
+        double[] param = { 4.3987, -24.2371, 68.9567, -98.2586, 67.562, -17.8987 };
+        
+        // Calculate the standard deviation.
+        return param[0] + energySum * (param[1] + energySum * (param[2] + energySum * (param[3] + energySum * (param[4] + energySum * (param[5])))));
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/AddPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/AddPlots.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/AddPlots.java	Wed Apr 27 11:11:32 2016
@@ -14,241 +14,241 @@
 import hep.aida.ITree;
 
 public class AddPlots {
-	
-	public static void main(String[] args) throws IllegalArgumentException, IOException {
-		// Define the root directory for the plots.
-		String rootDir = null;
-		
-		// Get the option identifier from the command arguments.
-		boolean isHelp = false;
-		boolean isFileList = false;
-		boolean isDirectory = false;
-		if(args.length > 0) {
-			if(args[0].compareTo("-h") == 0) { isHelp = true; }
-			else if(args[0].compareTo("-f") == 0) { isFileList = true; }
-			else if(args[0].compareTo("-d") == 0) { isDirectory = true; }
-		} else {
-			System.err.println("Insufficient arguments. See \"AddPlots -h\"");
-			System.exit(1);
-		}
-		
-		// Process the command line argument.
-		List<File> plotFiles = new ArrayList<File>();
-		if(isHelp) {
-			System.out.println("Usage:");
-			System.out.println("\tAddPlots -d [PLOT_DIRECTORY]");
-			System.out.println("\tAddPlots -f [PLOT_FILE] [PLOT_FILE] ...");
-			System.exit(0);
-		} else if(isDirectory) {
-			// Make sure that a directory is specified.
-			if(args.length < 2) {
-				System.err.println("Insufficient arguments. Must specify at least two files.");
-				System.exit(1);
-			}
-			
-			// Get the plot directory from the second argument.
-			File plotDirectory = new File(args[1]);
-			
-			// Verify that it exists and is a directory.
-			if(!plotDirectory.exists()) {
-				System.err.println("File path does not exist.");
-				System.exit(1);
-			} if(!plotDirectory.isDirectory()) {
-				System.err.println("Indicated path must be a directory.");
-				System.exit(1);
-			}
-			
-			// Store the root directory.
-			rootDir = plotDirectory.getAbsolutePath() + "/";
-			
-			// Extract the AIDA files from the directory.
-			for(File file : plotDirectory.listFiles()) {
-				System.out.println(file.getName());
-				int indexOfExtension = file.getName().lastIndexOf('.');
-				if(indexOfExtension == -1) { continue; }
-				if(file.getName().substring(indexOfExtension).compareToIgnoreCase(".aida") == 0) {
-					plotFiles.add(file);
-				}
-			}
-			
-			// Debug status print.
-			System.out.println("Processing plots in directory \"" + plotDirectory.getAbsolutePath() + "\"");
-		} else if(isFileList) {
-			// Make sure that at least one file was specified.
-			if(args.length < 3) {
-				System.err.println("Insufficient arguments. Must specify at least two files.");
-				System.exit(1);
-			}
-			
-			// Get the root directory.
-			rootDir = System.getProperty("user.dir") + "/";
-			
-			// Create and verify the specified files.
-			for(int i = 1; i < args.length; i++) {
-				// Create the file object and make sure that it exists.
-				File file = new File(args[i]);
-				if(!file.exists()) {
-					System.err.println("Specified file does not exist: " + args[i]);
-					System.exit(1);
-				}
-				
-				// Add it to the file list.
-				plotFiles.add(file);
-			}
-		} else {
-			System.err.println("Option \"" + args[0] + "\" is not recognized.");
-			System.exit(1);
-		}
-		
-		// Make sure that there are actually files.
-		if(plotFiles.isEmpty()) {
-			System.err.println("No AIDA files found!");
-			System.exit(1);
-		}
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFiles.get(0).getAbsolutePath());
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Get the histograms names.
-		List<String> objectNameList = getTreeFiles(tree);
-		
-		// Separate the plots into 1D and 2D plots and extract their
-		// bin sizes and other properties.
-		List<Integer> xBins1D = new ArrayList<Integer>();
-		List<Double> xBins1DMin = new ArrayList<Double>();
-		List<Double> xBins1DMax = new ArrayList<Double>();
-		List<Integer> xBins2D = new ArrayList<Integer>();
-		List<Double> xBins2DMin = new ArrayList<Double>();
-		List<Double> xBins2DMax = new ArrayList<Double>();
-		List<Integer> yBins2D = new ArrayList<Integer>();
-		List<Double> yBins2DMin = new ArrayList<Double>();
-		List<Double> yBins2DMax = new ArrayList<Double>();
-		List<String> histogramNames1D = new ArrayList<String>();
-		List<String> histogramNames2D = new ArrayList<String>();
-		for(String objectName : objectNameList) {
-			// Get the object.
-			IManagedObject object = tree.find(objectName);
-			
-			// If it is a 1D histogram, process it.
-			if(object instanceof IHistogram1D) {
-				// Add the object to the 1D histogram list.
-				histogramNames1D.add(objectName);
-				
-				// Get the bin size.
-				IHistogram1D plot = (IHistogram1D) object;
-				xBins1D.add(plot.axis().bins());
-				xBins1DMin.add(plot.axis().lowerEdge());
-				xBins1DMax.add(plot.axis().upperEdge());
-			}
-			
-			// If it is a 1D histogram, process it.
-			else if(object instanceof IHistogram2D) {
-				// Add the object to the 2D histogram list.
-				histogramNames2D.add(objectName);
-				
-				// Get the bin size.
-				IHistogram2D plot = (IHistogram2D) object;
-				xBins2D.add(plot.xAxis().bins());
-				xBins2DMin.add(plot.xAxis().lowerEdge());
-				xBins2DMax.add(plot.xAxis().upperEdge());
-				yBins2D.add(plot.yAxis().bins());
-				yBins2DMin.add(plot.yAxis().lowerEdge());
-				yBins2DMax.add(plot.yAxis().upperEdge());
-			}
-		}
-		
-		// Create plots corresponding to each of the plot objects.
-		AIDA aida = AIDA.defaultInstance();
-		List<IHistogram1D> histograms1D = new ArrayList<IHistogram1D>(histogramNames1D.size());
-		List<IHistogram2D> histograms2D = new ArrayList<IHistogram2D>(histogramNames2D.size());
-		for(int i = 0; i < histogramNames1D.size(); i++) {
-			IHistogram1D histogram = aida.histogram1D(histogramNames1D.get(i), xBins1D.get(i), xBins1DMin.get(i), xBins1DMax.get(i));
-			histograms1D.add(histogram);
-		}
-		for(int i = 0; i < histogramNames2D.size(); i++) {
-			IHistogram2D histogram = aida.histogram2D(histogramNames2D.get(i), xBins2D.get(i), xBins2DMin.get(i), xBins2DMax.get(i), yBins2D.get(i), yBins2DMin.get(i), yBins2DMax.get(i));
-			histograms2D.add(histogram);
-		}
-		
-		// Iterate over each file and add their entries to the compiled
-		// plots.
-		for(File file : plotFiles) {
-			// Open the file.
-			ITree fileTree = af.createTreeFactory().create(file.getAbsolutePath());
-			
-			// For each plot, get the equivalent plot from the file
-			// and add each bin entry to the compiled plot.
-			for(int i = 0; i < histogramNames1D.size(); i++) {
-				// Get the histogram object.
-				IHistogram1D histogram = (IHistogram1D) fileTree.find(histogramNames1D.get(i));
-				
-				// Iterate over the bins.
-				for(int x = 0; x < xBins1D.get(i); x++) {
-					// Get the entries in this bin and the bin average.
-					int entries = histogram.binEntries(x);
-					double average = histogram.binMean(x);
-					
-					// Add the entries to the compiled plot.
-					for(int j = 0; j < entries; j++) {
-						histograms1D.get(i).fill(average);
-					}
-				}
-			}
-			for(int i = 0; i < histogramNames2D.size(); i++) {
-				// Get the histogram object.
-				IHistogram2D histogram = (IHistogram2D) fileTree.find(histogramNames2D.get(i));
-				
-				// Iterate over the bins.
-				for(int x = 0; x < xBins2D.get(i); x++) {
-					for(int y = 0; y < yBins2D.get(i); y++) {
-						// Get the entries in this bin and the bin average.
-						int entries = histogram.binEntries(x, y);
-						double averageX = histogram.binMeanX(x, y);
-						double averageY = histogram.binMeanY(x, y);
-						
-						// Add the entries to the compiled plot.
-						for(int j = 0; j < entries; j++) {
-							histograms2D.get(i).fill(averageX, averageY);
-						}
-					}
-				}
-			}
-		}
-		
-		// Save the compiled plots to a new file.
-		aida.saveAs(rootDir + "compiled-plots.aida");
-		System.out.println("Plots written to path " + rootDir + "compiled-plots.aida");
-	}
-	
-	private static final List<String> getTreeFiles(ITree tree) {
-		return getTreeFiles(tree, "/");
-	}
-	
-	private static final List<String> getTreeFiles(ITree tree, String rootDir) {
-		// Make a list to contain the plot names.
-		List<String> list = new ArrayList<String>();
-		
-		// Iterate over the objects at the indicated directory of the tree.
-		String objectNames[] = tree.listObjectNames(rootDir);
-		for(String objectName : objectNames) {
-			// Convert the object name to a char array and check the
-			// last character. Directories end in '/'.
-			char[] plotChars = objectName.toCharArray();
-			
-			// If the object is a directory, process any objects inside
-			// of it as well.
-			if(plotChars[plotChars.length - 1] == '/') {
-				List<String> dirList = getTreeFiles(tree, objectName);
-				list.addAll(dirList);
-			}
-			
-			// Otherwise, just add the object to the list.
-			else { list.add(objectName); }
-		}
-		
-		// Return the compiled list.
-		return list;
-	}
+    
+    public static void main(String[] args) throws IllegalArgumentException, IOException {
+        // Define the root directory for the plots.
+        String rootDir = null;
+        
+        // Get the option identifier from the command arguments.
+        boolean isHelp = false;
+        boolean isFileList = false;
+        boolean isDirectory = false;
+        if(args.length > 0) {
+            if(args[0].compareTo("-h") == 0) { isHelp = true; }
+            else if(args[0].compareTo("-f") == 0) { isFileList = true; }
+            else if(args[0].compareTo("-d") == 0) { isDirectory = true; }
+        } else {
+            System.err.println("Insufficient arguments. See \"AddPlots -h\"");
+            System.exit(1);
+        }
+        
+        // Process the command line argument.
+        List<File> plotFiles = new ArrayList<File>();
+        if(isHelp) {
+            System.out.println("Usage:");
+            System.out.println("\tAddPlots -d [PLOT_DIRECTORY]");
+            System.out.println("\tAddPlots -f [PLOT_FILE] [PLOT_FILE] ...");
+            System.exit(0);
+        } else if(isDirectory) {
+            // Make sure that a directory is specified.
+            if(args.length < 2) {
+                System.err.println("Insufficient arguments. Must specify at least two files.");
+                System.exit(1);
+            }
+            
+            // Get the plot directory from the second argument.
+            File plotDirectory = new File(args[1]);
+            
+            // Verify that it exists and is a directory.
+            if(!plotDirectory.exists()) {
+                System.err.println("File path does not exist.");
+                System.exit(1);
+            } if(!plotDirectory.isDirectory()) {
+                System.err.println("Indicated path must be a directory.");
+                System.exit(1);
+            }
+            
+            // Store the root directory.
+            rootDir = plotDirectory.getAbsolutePath() + "/";
+            
+            // Extract the AIDA files from the directory.
+            for(File file : plotDirectory.listFiles()) {
+                System.out.println(file.getName());
+                int indexOfExtension = file.getName().lastIndexOf('.');
+                if(indexOfExtension == -1) { continue; }
+                if(file.getName().substring(indexOfExtension).compareToIgnoreCase(".aida") == 0) {
+                    plotFiles.add(file);
+                }
+            }
+            
+            // Debug status print.
+            System.out.println("Processing plots in directory \"" + plotDirectory.getAbsolutePath() + "\"");
+        } else if(isFileList) {
+            // Make sure that at least one file was specified.
+            if(args.length < 3) {
+                System.err.println("Insufficient arguments. Must specify at least two files.");
+                System.exit(1);
+            }
+            
+            // Get the root directory.
+            rootDir = System.getProperty("user.dir") + "/";
+            
+            // Create and verify the specified files.
+            for(int i = 1; i < args.length; i++) {
+                // Create the file object and make sure that it exists.
+                File file = new File(args[i]);
+                if(!file.exists()) {
+                    System.err.println("Specified file does not exist: " + args[i]);
+                    System.exit(1);
+                }
+                
+                // Add it to the file list.
+                plotFiles.add(file);
+            }
+        } else {
+            System.err.println("Option \"" + args[0] + "\" is not recognized.");
+            System.exit(1);
+        }
+        
+        // Make sure that there are actually files.
+        if(plotFiles.isEmpty()) {
+            System.err.println("No AIDA files found!");
+            System.exit(1);
+        }
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFiles.get(0).getAbsolutePath());
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Get the histograms names.
+        List<String> objectNameList = getTreeFiles(tree);
+        
+        // Separate the plots into 1D and 2D plots and extract their
+        // bin sizes and other properties.
+        List<Integer> xBins1D = new ArrayList<Integer>();
+        List<Double> xBins1DMin = new ArrayList<Double>();
+        List<Double> xBins1DMax = new ArrayList<Double>();
+        List<Integer> xBins2D = new ArrayList<Integer>();
+        List<Double> xBins2DMin = new ArrayList<Double>();
+        List<Double> xBins2DMax = new ArrayList<Double>();
+        List<Integer> yBins2D = new ArrayList<Integer>();
+        List<Double> yBins2DMin = new ArrayList<Double>();
+        List<Double> yBins2DMax = new ArrayList<Double>();
+        List<String> histogramNames1D = new ArrayList<String>();
+        List<String> histogramNames2D = new ArrayList<String>();
+        for(String objectName : objectNameList) {
+            // Get the object.
+            IManagedObject object = tree.find(objectName);
+            
+            // If it is a 1D histogram, process it.
+            if(object instanceof IHistogram1D) {
+                // Add the object to the 1D histogram list.
+                histogramNames1D.add(objectName);
+                
+                // Get the bin size.
+                IHistogram1D plot = (IHistogram1D) object;
+                xBins1D.add(plot.axis().bins());
+                xBins1DMin.add(plot.axis().lowerEdge());
+                xBins1DMax.add(plot.axis().upperEdge());
+            }
+            
+            // If it is a 1D histogram, process it.
+            else if(object instanceof IHistogram2D) {
+                // Add the object to the 2D histogram list.
+                histogramNames2D.add(objectName);
+                
+                // Get the bin size.
+                IHistogram2D plot = (IHistogram2D) object;
+                xBins2D.add(plot.xAxis().bins());
+                xBins2DMin.add(plot.xAxis().lowerEdge());
+                xBins2DMax.add(plot.xAxis().upperEdge());
+                yBins2D.add(plot.yAxis().bins());
+                yBins2DMin.add(plot.yAxis().lowerEdge());
+                yBins2DMax.add(plot.yAxis().upperEdge());
+            }
+        }
+        
+        // Create plots corresponding to each of the plot objects.
+        AIDA aida = AIDA.defaultInstance();
+        List<IHistogram1D> histograms1D = new ArrayList<IHistogram1D>(histogramNames1D.size());
+        List<IHistogram2D> histograms2D = new ArrayList<IHistogram2D>(histogramNames2D.size());
+        for(int i = 0; i < histogramNames1D.size(); i++) {
+            IHistogram1D histogram = aida.histogram1D(histogramNames1D.get(i), xBins1D.get(i), xBins1DMin.get(i), xBins1DMax.get(i));
+            histograms1D.add(histogram);
+        }
+        for(int i = 0; i < histogramNames2D.size(); i++) {
+            IHistogram2D histogram = aida.histogram2D(histogramNames2D.get(i), xBins2D.get(i), xBins2DMin.get(i), xBins2DMax.get(i), yBins2D.get(i), yBins2DMin.get(i), yBins2DMax.get(i));
+            histograms2D.add(histogram);
+        }
+        
+        // Iterate over each file and add their entries to the compiled
+        // plots.
+        for(File file : plotFiles) {
+            // Open the file.
+            ITree fileTree = af.createTreeFactory().create(file.getAbsolutePath());
+            
+            // For each plot, get the equivalent plot from the file
+            // and add each bin entry to the compiled plot.
+            for(int i = 0; i < histogramNames1D.size(); i++) {
+                // Get the histogram object.
+                IHistogram1D histogram = (IHistogram1D) fileTree.find(histogramNames1D.get(i));
+                
+                // Iterate over the bins.
+                for(int x = 0; x < xBins1D.get(i); x++) {
+                    // Get the entries in this bin and the bin average.
+                    int entries = histogram.binEntries(x);
+                    double average = histogram.binMean(x);
+                    
+                    // Add the entries to the compiled plot.
+                    for(int j = 0; j < entries; j++) {
+                        histograms1D.get(i).fill(average);
+                    }
+                }
+            }
+            for(int i = 0; i < histogramNames2D.size(); i++) {
+                // Get the histogram object.
+                IHistogram2D histogram = (IHistogram2D) fileTree.find(histogramNames2D.get(i));
+                
+                // Iterate over the bins.
+                for(int x = 0; x < xBins2D.get(i); x++) {
+                    for(int y = 0; y < yBins2D.get(i); y++) {
+                        // Get the entries in this bin and the bin average.
+                        int entries = histogram.binEntries(x, y);
+                        double averageX = histogram.binMeanX(x, y);
+                        double averageY = histogram.binMeanY(x, y);
+                        
+                        // Add the entries to the compiled plot.
+                        for(int j = 0; j < entries; j++) {
+                            histograms2D.get(i).fill(averageX, averageY);
+                        }
+                    }
+                }
+            }
+        }
+        
+        // Save the compiled plots to a new file.
+        aida.saveAs(rootDir + "compiled-plots.aida");
+        System.out.println("Plots written to path " + rootDir + "compiled-plots.aida");
+    }
+    
+    private static final List<String> getTreeFiles(ITree tree) {
+        return getTreeFiles(tree, "/");
+    }
+    
+    private static final List<String> getTreeFiles(ITree tree, String rootDir) {
+        // Make a list to contain the plot names.
+        List<String> list = new ArrayList<String>();
+        
+        // Iterate over the objects at the indicated directory of the tree.
+        String objectNames[] = tree.listObjectNames(rootDir);
+        for(String objectName : objectNames) {
+            // Convert the object name to a char array and check the
+            // last character. Directories end in '/'.
+            char[] plotChars = objectName.toCharArray();
+            
+            // If the object is a directory, process any objects inside
+            // of it as well.
+            if(plotChars[plotChars.length - 1] == '/') {
+                List<String> dirList = getTreeFiles(tree, objectName);
+                list.addAll(dirList);
+            }
+            
+            // Otherwise, just add the object to the list.
+            else { list.add(objectName); }
+        }
+        
+        // Return the compiled list.
+        return list;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot.java	Wed Apr 27 11:11:32 2016
@@ -1,25 +1,25 @@
 package org.hps.users.kmccarty.plots;
 
 public abstract class FormattedPlot {
-	private final String xAxis;
-	private final String yAxis;
-	private final String plotName;
-	
-	public FormattedPlot(String xAxis, String yAxis, String plotName) {
-		this.xAxis = xAxis;
-		this.yAxis = yAxis;
-		this.plotName = plotName;
-	}
-	
-	public String getPlotName() {
-		return plotName;
-	}
-	
-	public String getXAxisName() {
-		return xAxis;
-	}
-	
-	public String getYAxisName() {
-		return yAxis;
-	}
+    private final String xAxis;
+    private final String yAxis;
+    private final String plotName;
+    
+    public FormattedPlot(String xAxis, String yAxis, String plotName) {
+        this.xAxis = xAxis;
+        this.yAxis = yAxis;
+        this.plotName = plotName;
+    }
+    
+    public String getPlotName() {
+        return plotName;
+    }
+    
+    public String getXAxisName() {
+        return xAxis;
+    }
+    
+    public String getYAxisName() {
+        return yAxis;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot1D.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot1D.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot1D.java	Wed Apr 27 11:11:32 2016
@@ -5,37 +5,37 @@
 import hep.aida.IHistogram1D;
 
 public class FormattedPlot1D extends FormattedPlot {
-	private final ColorStyle style;
-	private final IHistogram1D plot;
-	private final double axisRange;
-	
-	public FormattedPlot1D(IHistogram1D plot, ColorStyle style, String xAxis, String yAxis, String plotName) {
-		super(xAxis, yAxis, plotName);
-		this.plot = plot;
-		this.style = style;
-		this.axisRange = -1;
-	}
-	
-	public FormattedPlot1D(IHistogram1D plot, ColorStyle style, String xAxis, String yAxis, String plotName, double axisRange) {
-		super(xAxis, yAxis, plotName);
-		this.plot = plot;
-		this.style = style;
-		this.axisRange = axisRange;
-	}
-	
-	public IHistogram1D getPlot() {
-		return plot;
-	}
-	
-	public ColorStyle getColorStyle() {
-		return style;
-	}
-	
-	public boolean definesAxisRange() {
-		return axisRange != -1;
-	}
-	
-	public double getAxisRange() {
-		return axisRange;
-	}
+    private final ColorStyle style;
+    private final IHistogram1D plot;
+    private final double axisRange;
+    
+    public FormattedPlot1D(IHistogram1D plot, ColorStyle style, String xAxis, String yAxis, String plotName) {
+        super(xAxis, yAxis, plotName);
+        this.plot = plot;
+        this.style = style;
+        this.axisRange = -1;
+    }
+    
+    public FormattedPlot1D(IHistogram1D plot, ColorStyle style, String xAxis, String yAxis, String plotName, double axisRange) {
+        super(xAxis, yAxis, plotName);
+        this.plot = plot;
+        this.style = style;
+        this.axisRange = axisRange;
+    }
+    
+    public IHistogram1D getPlot() {
+        return plot;
+    }
+    
+    public ColorStyle getColorStyle() {
+        return style;
+    }
+    
+    public boolean definesAxisRange() {
+        return axisRange != -1;
+    }
+    
+    public double getAxisRange() {
+        return axisRange;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot2D.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot2D.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/FormattedPlot2D.java	Wed Apr 27 11:11:32 2016
@@ -3,48 +3,48 @@
 import hep.aida.IHistogram2D;
 
 public class FormattedPlot2D extends FormattedPlot {
-	private final IHistogram2D plot;
-	private final boolean logarithmic;
-	private final double xAxisRange;
-	private final double yAxisRange;
-	
-	public FormattedPlot2D(IHistogram2D plot, boolean logarithmic, String xAxis, String yAxis, String plotName) {
-		super(xAxis, yAxis, plotName);
-		this.plot = plot;
-		this.xAxisRange = -1;
-		this.yAxisRange = -1;
-		this.logarithmic = logarithmic;
-	}
-	
-	public FormattedPlot2D(IHistogram2D plot, boolean logarithmic, String xAxis, String yAxis, String plotName, double xAxisRange, double yAxisRange) {
-		super(xAxis, yAxis, plotName);
-		this.plot = plot;
-		this.xAxisRange = xAxisRange;
-		this.yAxisRange = yAxisRange;
-		this.logarithmic = logarithmic;
-	}
-	
-	public IHistogram2D getPlot() {
-		return plot;
-	}
-	
-	public boolean isLogarithmic() {
-		return logarithmic;
-	}
-	
-	public boolean definesXAxisRange() {
-		return xAxisRange != -1;
-	}
-	
-	public boolean definesYAxisRange() {
-		return yAxisRange != -1;
-	}
-	
-	public double getXAxisRange() {
-		return xAxisRange;
-	}
-	
-	public double getYAxisRange() {
-		return yAxisRange;
-	}
+    private final IHistogram2D plot;
+    private final boolean logarithmic;
+    private final double xAxisRange;
+    private final double yAxisRange;
+    
+    public FormattedPlot2D(IHistogram2D plot, boolean logarithmic, String xAxis, String yAxis, String plotName) {
+        super(xAxis, yAxis, plotName);
+        this.plot = plot;
+        this.xAxisRange = -1;
+        this.yAxisRange = -1;
+        this.logarithmic = logarithmic;
+    }
+    
+    public FormattedPlot2D(IHistogram2D plot, boolean logarithmic, String xAxis, String yAxis, String plotName, double xAxisRange, double yAxisRange) {
+        super(xAxis, yAxis, plotName);
+        this.plot = plot;
+        this.xAxisRange = xAxisRange;
+        this.yAxisRange = yAxisRange;
+        this.logarithmic = logarithmic;
+    }
+    
+    public IHistogram2D getPlot() {
+        return plot;
+    }
+    
+    public boolean isLogarithmic() {
+        return logarithmic;
+    }
+    
+    public boolean definesXAxisRange() {
+        return xAxisRange != -1;
+    }
+    
+    public boolean definesYAxisRange() {
+        return yAxisRange != -1;
+    }
+    
+    public double getXAxisRange() {
+        return xAxisRange;
+    }
+    
+    public double getYAxisRange() {
+        return yAxisRange;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotFormatModule.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotFormatModule.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotFormatModule.java	Wed Apr 27 11:11:32 2016
@@ -17,189 +17,189 @@
 import java.util.List;
 
 public class PlotFormatModule {
-	private String width = "2000";
-	private String height = "1200";
-	private List<FormattedPlot1D> formattedPlots1D = new ArrayList<FormattedPlot1D>();
-	private List<FormattedPlot2D> formattedPlots2D = new ArrayList<FormattedPlot2D>();
-	
-	public void addPlot1D(FormattedPlot1D plot) {
-		formattedPlots1D.add(plot);
-	}
-	
-	public void addPlot2D(FormattedPlot2D plot) {
-		formattedPlots2D.add(plot);
-	}
-	
-	public void setDisplayHeight(int height) {
-		this.height = "" + height;
-	}
-	
-	public void setDisplayWidth(int width) {
-		this.width = "" + width;
-	}
-	
-	public void displayPlots() {
-		try { processPlots(null); }
-		catch (IOException e) { e.printStackTrace(); }
-	}
-	
-	public void savePlots(String filePath) throws IOException {
-		processPlots(filePath);
-	}
-	
-	private void processPlots(String filePath) throws IOException {
-		// Create a plotter factory.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		IPlotterFactory plotterFactory = af.createPlotterFactory();
-		
-		// Format and display the 1D plots.
-		for(FormattedPlot1D formattedPlot : formattedPlots1D) {
-			// Get the plot.
-			IHistogram1D plot = formattedPlot.getPlot();
-			
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(plot.title());
-			plotter.createRegions(1);
-			plotter.region(0).plot(plot);
-			
-			// Set the axis range.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			if(formattedPlot.definesAxisRange()) {
-				region.getPlot().getXAxis().setMax(formattedPlot.getAxisRange());
-			}
-			
-			// Format the axis labels.
-			region.getPlot().setTitle(formattedPlot.getPlotName());
-			region.getPlot().getXAxis().setLabel(formattedPlot.getXAxisName());
-			region.getPlot().getYAxis().setLabel(formattedPlot.getYAxisName());
-			
-			// Format the fonts and general plot presentation.
-			PlotsFormatter.setDefault1DStyle(region, new ColorStyle[] { formattedPlot.getColorStyle() });
-			
-			// Set the plotter dimensions.
-			plotter.setParameter("plotterWidth", width);
-			plotter.setParameter("plotterHeight", height);
-			
-			// If the file path is null, display the plots. Otherwise,
-			// save them to the destination folder.
-			if(filePath == null) { plotter.show(); }
-			else {
-				File plotFile = new File(filePath + formattedPlot.getPlotName() + ".png");
-				if(plotFile.exists()) { plotFile.delete(); }
-				plotter.writeToFile(filePath + formattedPlot.getPlotName() + ".png");
-				System.out.printf("Saved plot \"%s\" to path: %s%n", formattedPlot.getPlotName(), filePath + formattedPlot.getPlotName() + ".png");
-			}
-		}
-		
-		// Format and display the 2D plots.
-		for(FormattedPlot2D formattedPlot : formattedPlots2D) {
-			// Get the plot.
-			IHistogram2D plot = formattedPlot.getPlot();
-			
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(formattedPlot.getPlotName());
-			plotter.createRegions(1);
-			plotter.region(0).plot(plot);
-			
-			// Set the axis range.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			if(formattedPlot.definesXAxisRange()) {
-				region.getPlot().getXAxis().setMax(formattedPlot.getXAxisRange());
-			} if(formattedPlot.definesYAxisRange()) {
-				region.getPlot().getYAxis().setMax(formattedPlot.getYAxisRange());
-			}
-			
-			// Format the axis labels.
-			region.getPlot().setTitle(formattedPlot.getPlotName());
-			region.getPlot().getXAxis().setLabel(formattedPlot.getXAxisName());
-			region.getPlot().getYAxis().setLabel(formattedPlot.getYAxisName());
-			
-			// Format the fonts and general plot presentation.
-			PlotsFormatter.setDefault2DStyle(region, formattedPlot.isLogarithmic());
-			
-			// Set the plotter dimensions.
-			plotter.setParameter("plotterWidth", width);
-			plotter.setParameter("plotterHeight", height);
-			
-			// If the file path is null, display the plots. Otherwise,
-			// save them to the destination folder.
-			if(filePath == null) { plotter.show(); }
-			else {
-				File plotFile = new File(filePath + formattedPlot.getPlotName() + ".png");
-				if(plotFile.exists()) { plotFile.delete(); }
-				plotter.writeToFile(filePath + formattedPlot.getPlotName() + ".png");
-				System.out.printf("Saved plot \"%s\" to path: %s%n", formattedPlot.getPlotName(), filePath + formattedPlot.getPlotName() + ".png");
-			}
-		}
-	}
-	
-	public void exportPlots(String filePath) throws IOException {
-		// Export the 1D plots in a text format.
-		for(FormattedPlot1D plot : formattedPlots1D) {
-			exportPlot(filePath, plot);
-		}
-		
-		// Export the 2D plots in a text format.
-		for(FormattedPlot2D plot : formattedPlots2D) {
-			exportPlot(filePath, plot);
-		}
-	}
-	
-	private static final void exportPlot(String filePath, FormattedPlot plot) throws IOException {
-		// Check if this is a one or two dimensional plot.
-		boolean is1D = plot instanceof FormattedPlot1D;
-		
-		// Create a file object for the plot.
-		String plotPath = filePath + plot.getPlotName() + (is1D ? ".aida1D" : ".aida2D");
-		File datFile = new File(plotPath);
-		
-		// If the plot file already exists, delete it.
-		if(datFile.exists()) { datFile.delete(); }
-		
-		// Create a new file for the plot to occupy.
-		datFile.createNewFile();
-		
-		// Get the textual form of the plot.
-		String plotText = null;
-		if(is1D) { plotText = toTextFormat(((FormattedPlot1D) plot).getPlot()); }
-		else { plotText = toTextFormat(((FormattedPlot2D) plot).getPlot()); }
-		
-		// Write the plot text to the file.
-		BufferedWriter writer = new BufferedWriter(new FileWriter(datFile));
-		writer.write(plotText);
-		writer.close();
-		
-		// Note that the file was written.
-		System.out.printf("Plot \"%s\" was exported to path: %s%n", plot.getPlotName(), plotPath);
-	}
-	
-	private static final String toTextFormat(IHistogram1D plot) {
-		// Create a buffer to hold the converted plot.
-		StringBuffer buffer = new StringBuffer();
-		
-		// Iterate over the bins and output the plot in the format of
-		// "[BIN_MEAN] [BIN_VALUE]" with a tab delimiter.
-		for(int bin = 0; bin < plot.axis().bins(); bin++) {
-			buffer.append(String.format("%f\t%f%n", plot.binMean(bin), plot.binHeight(bin)));
-		}
-		
-		// Return the converted file.
-		return buffer.toString();
-	}
-	
-	private static final String toTextFormat(IHistogram2D plot) {
-		// Create a buffer to hold the converted plot.
-		StringBuffer buffer = new StringBuffer();
-		
-		// Iterate over the bins and output the plot in the format of
-		// "[X_BIN_MEAN] [Y_BIN_MEAN] [BIN_VALUE]" with a tab delimiter.
-		for(int xBin = 0; xBin < plot.xAxis().bins(); xBin++) {
-			for(int yBin = 0; yBin < plot.yAxis().bins(); yBin++) {
-				buffer.append(String.format("%f\t%f\t%f%n", plot.binMeanX(xBin, yBin), plot.binMeanY(xBin, yBin), plot.binHeight(xBin, yBin)));
-			}
-		}
-		
-		// Return the converted file.
-		return buffer.toString();
-	}
+    private String width = "2000";
+    private String height = "1200";
+    private List<FormattedPlot1D> formattedPlots1D = new ArrayList<FormattedPlot1D>();
+    private List<FormattedPlot2D> formattedPlots2D = new ArrayList<FormattedPlot2D>();
+    
+    public void addPlot1D(FormattedPlot1D plot) {
+        formattedPlots1D.add(plot);
+    }
+    
+    public void addPlot2D(FormattedPlot2D plot) {
+        formattedPlots2D.add(plot);
+    }
+    
+    public void setDisplayHeight(int height) {
+        this.height = "" + height;
+    }
+    
+    public void setDisplayWidth(int width) {
+        this.width = "" + width;
+    }
+    
+    public void displayPlots() {
+        try { processPlots(null); }
+        catch (IOException e) { e.printStackTrace(); }
+    }
+    
+    public void savePlots(String filePath) throws IOException {
+        processPlots(filePath);
+    }
+    
+    private void processPlots(String filePath) throws IOException {
+        // Create a plotter factory.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        IPlotterFactory plotterFactory = af.createPlotterFactory();
+        
+        // Format and display the 1D plots.
+        for(FormattedPlot1D formattedPlot : formattedPlots1D) {
+            // Get the plot.
+            IHistogram1D plot = formattedPlot.getPlot();
+            
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(plot.title());
+            plotter.createRegions(1);
+            plotter.region(0).plot(plot);
+            
+            // Set the axis range.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            if(formattedPlot.definesAxisRange()) {
+                region.getPlot().getXAxis().setMax(formattedPlot.getAxisRange());
+            }
+            
+            // Format the axis labels.
+            region.getPlot().setTitle(formattedPlot.getPlotName());
+            region.getPlot().getXAxis().setLabel(formattedPlot.getXAxisName());
+            region.getPlot().getYAxis().setLabel(formattedPlot.getYAxisName());
+            
+            // Format the fonts and general plot presentation.
+            PlotsFormatter.setDefault1DStyle(region, new ColorStyle[] { formattedPlot.getColorStyle() });
+            
+            // Set the plotter dimensions.
+            plotter.setParameter("plotterWidth", width);
+            plotter.setParameter("plotterHeight", height);
+            
+            // If the file path is null, display the plots. Otherwise,
+            // save them to the destination folder.
+            if(filePath == null) { plotter.show(); }
+            else {
+                File plotFile = new File(filePath + formattedPlot.getPlotName() + ".png");
+                if(plotFile.exists()) { plotFile.delete(); }
+                plotter.writeToFile(filePath + formattedPlot.getPlotName() + ".png");
+                System.out.printf("Saved plot \"%s\" to path: %s%n", formattedPlot.getPlotName(), filePath + formattedPlot.getPlotName() + ".png");
+            }
+        }
+        
+        // Format and display the 2D plots.
+        for(FormattedPlot2D formattedPlot : formattedPlots2D) {
+            // Get the plot.
+            IHistogram2D plot = formattedPlot.getPlot();
+            
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(formattedPlot.getPlotName());
+            plotter.createRegions(1);
+            plotter.region(0).plot(plot);
+            
+            // Set the axis range.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            if(formattedPlot.definesXAxisRange()) {
+                region.getPlot().getXAxis().setMax(formattedPlot.getXAxisRange());
+            } if(formattedPlot.definesYAxisRange()) {
+                region.getPlot().getYAxis().setMax(formattedPlot.getYAxisRange());
+            }
+            
+            // Format the axis labels.
+            region.getPlot().setTitle(formattedPlot.getPlotName());
+            region.getPlot().getXAxis().setLabel(formattedPlot.getXAxisName());
+            region.getPlot().getYAxis().setLabel(formattedPlot.getYAxisName());
+            
+            // Format the fonts and general plot presentation.
+            PlotsFormatter.setDefault2DStyle(region, formattedPlot.isLogarithmic());
+            
+            // Set the plotter dimensions.
+            plotter.setParameter("plotterWidth", width);
+            plotter.setParameter("plotterHeight", height);
+            
+            // If the file path is null, display the plots. Otherwise,
+            // save them to the destination folder.
+            if(filePath == null) { plotter.show(); }
+            else {
+                File plotFile = new File(filePath + formattedPlot.getPlotName() + ".png");
+                if(plotFile.exists()) { plotFile.delete(); }
+                plotter.writeToFile(filePath + formattedPlot.getPlotName() + ".png");
+                System.out.printf("Saved plot \"%s\" to path: %s%n", formattedPlot.getPlotName(), filePath + formattedPlot.getPlotName() + ".png");
+            }
+        }
+    }
+    
+    public void exportPlots(String filePath) throws IOException {
+        // Export the 1D plots in a text format.
+        for(FormattedPlot1D plot : formattedPlots1D) {
+            exportPlot(filePath, plot);
+        }
+        
+        // Export the 2D plots in a text format.
+        for(FormattedPlot2D plot : formattedPlots2D) {
+            exportPlot(filePath, plot);
+        }
+    }
+    
+    private static final void exportPlot(String filePath, FormattedPlot plot) throws IOException {
+        // Check if this is a one or two dimensional plot.
+        boolean is1D = plot instanceof FormattedPlot1D;
+        
+        // Create a file object for the plot.
+        String plotPath = filePath + plot.getPlotName() + (is1D ? ".aida1D" : ".aida2D");
+        File datFile = new File(plotPath);
+        
+        // If the plot file already exists, delete it.
+        if(datFile.exists()) { datFile.delete(); }
+        
+        // Create a new file for the plot to occupy.
+        datFile.createNewFile();
+        
+        // Get the textual form of the plot.
+        String plotText = null;
+        if(is1D) { plotText = toTextFormat(((FormattedPlot1D) plot).getPlot()); }
+        else { plotText = toTextFormat(((FormattedPlot2D) plot).getPlot()); }
+        
+        // Write the plot text to the file.
+        BufferedWriter writer = new BufferedWriter(new FileWriter(datFile));
+        writer.write(plotText);
+        writer.close();
+        
+        // Note that the file was written.
+        System.out.printf("Plot \"%s\" was exported to path: %s%n", plot.getPlotName(), plotPath);
+    }
+    
+    private static final String toTextFormat(IHistogram1D plot) {
+        // Create a buffer to hold the converted plot.
+        StringBuffer buffer = new StringBuffer();
+        
+        // Iterate over the bins and output the plot in the format of
+        // "[BIN_MEAN] [BIN_VALUE]" with a tab delimiter.
+        for(int bin = 0; bin < plot.axis().bins(); bin++) {
+            buffer.append(String.format("%f\t%f%n", plot.binMean(bin), plot.binHeight(bin)));
+        }
+        
+        // Return the converted file.
+        return buffer.toString();
+    }
+    
+    private static final String toTextFormat(IHistogram2D plot) {
+        // Create a buffer to hold the converted plot.
+        StringBuffer buffer = new StringBuffer();
+        
+        // Iterate over the bins and output the plot in the format of
+        // "[X_BIN_MEAN] [Y_BIN_MEAN] [BIN_VALUE]" with a tab delimiter.
+        for(int xBin = 0; xBin < plot.xAxis().bins(); xBin++) {
+            for(int yBin = 0; yBin < plot.yAxis().bins(); yBin++) {
+                buffer.append(String.format("%f\t%f\t%f%n", plot.binMeanX(xBin, yBin), plot.binMeanY(xBin, yBin), plot.binHeight(xBin, yBin)));
+            }
+        }
+        
+        // Return the converted file.
+        return buffer.toString();
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/PlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -8,120 +8,120 @@
 import java.awt.Font;
 
 public class PlotsFormatter {
-	// Define plot fonts.
-	public static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 30);
-	public static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  35);
-	public static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  45);
-	
-	// Defines the color style options for plot data.
-	public static enum ColorStyle {
-		 MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
-		  MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
-		MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
-		    RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
-		  FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
-		    TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
-		    BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
-		  PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
-		
-		private final Color fillColor;
-		private final Color lineColor;
-		
-		private ColorStyle(Color fillColor, Color lineColor) {
-			this.fillColor = fillColor;
-			this.lineColor = lineColor;
-		}
-		
-		public Color getFillColor() { return fillColor; }
-		
-		public Color getLineColor() { return lineColor; }
-	};
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	public static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the names of each plot on in the region.
-		String[] dataNames = region.getAllDataNames();
-		
-		// Check whether this is an overlay plot. Overlay plots contain
-		// more than one data name.
-		boolean overlay = (dataNames.length > 1 ? true : false);
-		
-		// Iterate over each plot in the region.
-		for(int i = 0; i < dataNames.length; i++) {
-			// Set the overlay style if needed.
-			if(overlay) {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with no fill. The color is set by the "color" argument.
-				fillStyle.setHistogramFill(false);
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarLineColor(color[i].getFillColor());
-				
-				// Set the legend text style.
-				region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
-			}
-			
-			// Otherwise, set the fill style for a single plot.
-			else {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with a fill color. The colors are defined by the
-				// "color" argument.
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarColor(color[i].getFillColor());
-				fillStyle.setHistogramBarLineColor(color[i].getLineColor());
-			}
-			
-			// Set the statistics box style.
-			region.getPlot().getStats().setVisible(true);
-			region.getPlot().getStats().setFont(BASIC_FONT);
-			
-			// Set the title font.
-			region.getPlot().getTitleObject().setFont(TITLE_FONT);
-			
-			// Set the axis tick-mark fonts.
-			region.getPlot().getXAxis().setFont(BASIC_FONT);
-			region.getPlot().getYAxis().setFont(BASIC_FONT);
-			region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-			region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 */
-	public static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
-		// Get the fill style object. 2D plots should never be overlay
-		// plots, so there should only ever be one data name.
-		JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		
-		// Set the fill style for a two-dimensional plot.
-		if(logarithmic) { fillStyle.setLogZ(true); }
-		fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
-		fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
-		
-		// Make the statistics box invisible.
-		region.getPlot().getStats().setVisible(false);
-		
-		// Set the general plot font (which is also the z-axis font).
-		region.getPlot().setFont(BASIC_FONT);
-		
-		// Set the title font.
-		region.getPlot().getTitleObject().setFont(TITLE_FONT);
-		
-		// Set the axis tick-mark fonts.
-		region.getPlot().getXAxis().setFont(BASIC_FONT);
-		region.getPlot().getYAxis().setFont(BASIC_FONT);
-		region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-		region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-	}
+    // Define plot fonts.
+    public static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 30);
+    public static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  35);
+    public static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  45);
+    
+    // Defines the color style options for plot data.
+    public static enum ColorStyle {
+         MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
+          MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
+        MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
+            RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
+          FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
+            TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
+            BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
+          PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
+        
+        private final Color fillColor;
+        private final Color lineColor;
+        
+        private ColorStyle(Color fillColor, Color lineColor) {
+            this.fillColor = fillColor;
+            this.lineColor = lineColor;
+        }
+        
+        public Color getFillColor() { return fillColor; }
+        
+        public Color getLineColor() { return lineColor; }
+    };
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    public static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the names of each plot on in the region.
+        String[] dataNames = region.getAllDataNames();
+        
+        // Check whether this is an overlay plot. Overlay plots contain
+        // more than one data name.
+        boolean overlay = (dataNames.length > 1 ? true : false);
+        
+        // Iterate over each plot in the region.
+        for(int i = 0; i < dataNames.length; i++) {
+            // Set the overlay style if needed.
+            if(overlay) {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with no fill. The color is set by the "color" argument.
+                fillStyle.setHistogramFill(false);
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarLineColor(color[i].getFillColor());
+                
+                // Set the legend text style.
+                region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
+            }
+            
+            // Otherwise, set the fill style for a single plot.
+            else {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with a fill color. The colors are defined by the
+                // "color" argument.
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarColor(color[i].getFillColor());
+                fillStyle.setHistogramBarLineColor(color[i].getLineColor());
+            }
+            
+            // Set the statistics box style.
+            region.getPlot().getStats().setVisible(true);
+            region.getPlot().getStats().setFont(BASIC_FONT);
+            
+            // Set the title font.
+            region.getPlot().getTitleObject().setFont(TITLE_FONT);
+            
+            // Set the axis tick-mark fonts.
+            region.getPlot().getXAxis().setFont(BASIC_FONT);
+            region.getPlot().getYAxis().setFont(BASIC_FONT);
+            region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+            region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     */
+    public static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
+        // Get the fill style object. 2D plots should never be overlay
+        // plots, so there should only ever be one data name.
+        JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        
+        // Set the fill style for a two-dimensional plot.
+        if(logarithmic) { fillStyle.setLogZ(true); }
+        fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
+        fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
+        
+        // Make the statistics box invisible.
+        region.getPlot().getStats().setVisible(false);
+        
+        // Set the general plot font (which is also the z-axis font).
+        region.getPlot().setFont(BASIC_FONT);
+        
+        // Set the title font.
+        region.getPlot().getTitleObject().setFont(TITLE_FONT);
+        
+        // Set the axis tick-mark fonts.
+        region.getPlot().getXAxis().setFont(BASIC_FONT);
+        region.getPlot().getYAxis().setFont(BASIC_FONT);
+        region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+        region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/InvariantMassPlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/InvariantMassPlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/InvariantMassPlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -19,317 +19,317 @@
 import hep.aida.ref.plotter.PlotterRegion;
 
 public class InvariantMassPlotsFormatter {
-	// Define plot fonts.
-	private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
-	private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
-	private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
-	
-	// Defines the color style options for plot data.
-	private enum ColorStyle {
-		 MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
-		  MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
-		MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
-		    RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
-		  FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
-		    TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
-		    BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
-		  PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
-		
-		private final Color fillColor;
-		private final Color lineColor;
-		
-		private ColorStyle(Color fillColor, Color lineColor) {
-			this.fillColor = fillColor;
-			this.lineColor = lineColor;
-		}
-		
-		public Color getFillColor() { return fillColor; }
-		
-		public Color getLineColor() { return lineColor; }
-	};
-		
-	/**
-	 * Loads all plots in a file and formats them according to the
-	 * indicated style.
-	 * @param args - Unused default executable parameter.
-	 * @throws IOException Occurs if there is an issue opening the file.
-	 */
-	public static void main(String[] args) throws IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String[] plotFile = {
-				rootDir + "temp.aida"
-		};
-		
-		// Define the run numbers for each file.
-		String[] runNumber = { "1 Hits", "2 Hits" };
-		
-		// Define the scaling factors for each plot.
-		double scaleFactor = 13.254;
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree[] tree = new ITree[plotFile.length];
-		for(int i = 0; i < plotFile.length; i++) {
-			tree[i] = af.createTreeFactory().create(plotFile[i]);
-			if(tree[i] == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		}
-		
-		// Get the histograms.
-		IHistogram1D[] invariantMassPlots = new IHistogram1D[3];
-		invariantMassPlots[0] = (IHistogram1D) tree[0].find("Trident Analysis/Particle Invariant Mass (1 Hit)");
-		invariantMassPlots[1] = (IHistogram1D) tree[0].find("Trident Analysis/Particle Invariant Mass (2 Hit)");
-		IHistogram1D electronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Electron Energy");
-		IHistogram1D positronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Positron Energy");
-		IHistogram1D energySumPlot = (IHistogram1D) tree[0].find("Trident Analysis/Energy Sum Distribution");
-		IHistogram2D energySum2DPlot = (IHistogram2D) tree[0].find("Trident Analysis/2D Energy Distribution");
-		IHistogram1D tridentElectronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Trident Electron Energy");
-		IHistogram1D tridentPositronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Trident Positron Energy");
-		
-		// Define the plot titles and arrays.
-		IHistogram[] plots = { electronEnergyPlot, positronEnergyPlot, energySumPlot, tridentElectronEnergyPlot, tridentPositronEnergyPlot };
-		String[] titles = { "Electron Energy", "Positron Energy", "Energy Sum", "Trident Electron Energy", "Trident Positron Energy" };
-		String[] xTitles = { "Energy (GeV)", "Energy (GeV)", "Energy Sum (GeV)", "Energy (GeV)", "Energy (GeV)" };
-		
-		// Re-bin the histograms to have 5-times larger bins. First,
-		// get the bin count and upper and lower bounds of the plot.
-		int bins = invariantMassPlots[0].axis().bins();
-		double low = invariantMassPlots[0].axis().binLowerEdge(0);
-		double high = invariantMassPlots[0].axis().binUpperEdge(invariantMassPlots[0].axis().bins() - 1);
-		
-		// Create new plots with the larger bin sizes.
-		AIDA aida = AIDA.defaultInstance();
-		IHistogram1D[] newPlot = new IHistogram1D[2];
-		newPlot[0] = aida.histogram1D("Particle Invariant Mass (1 Hit)", bins / 5, low, high);
-		newPlot[1] = aida.histogram1D("Particle Invariant Mass (2 Hit)", bins / 5, low, high);
-		
-		// Populate the new plots with the data from the old ones.
-		for(int j = 0; j < 2; j++) {
-			for(int i = 0; i < bins; i++) {
-				int entries = invariantMassPlots[j].binEntries(i);
-				double center = invariantMassPlots[j].axis().binCenter(i);
-				for(int k = 0; k < entries; k++) {
-					newPlot[j].fill(center);
-				}
-			}
-		}
-		
-		// Replace the old plots.
-		invariantMassPlots = newPlot;
-		
-		// Create a plotter factory.
-		IPlotterFactory plotterFactory = af.createPlotterFactory();
-		
-		// Format and display the basic histograms.
-		for(int i = 0; i < plots.length; i++) {
-			// Scale the histogram by the appropriate scaling factor.
-			plots[i].scale(1.0 / scaleFactor);
-			
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(titles[i]);
-			plotter.createRegions(1);
-			plotter.region(0).plot(plots[i]);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle(titles[i]);
-			region.getPlot().getXAxis().setLabel(xTitles[i]);
-			region.getPlot().getYAxis().setLabel("Rate (Hz)");
-			
-			// Format the fonts and general plot presentation.
-			setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Format and display the 2D histogram.
-		energySum2DPlot.scale(1.0 / scaleFactor);
-		IPlotter plotter2D = plotterFactory.create("2D Energy Sum");
-		plotter2D.createRegions(1);
-		plotter2D.region(0).plot(energySum2DPlot);
-		
-		// Format the axis labels.
-		PlotterRegion region2D = (PlotterRegion) plotter2D.region(0);
-		region2D.getPlot().setTitle("2D Energy Sum");
-		region2D.getPlot().getXAxis().setLabel("Electron Energy (GeV)");
-		region2D.getPlot().getYAxis().setLabel("Positron Energy (GeV)");
-		
-		// Format the fonts and general plot presentation.
-		setDefault2DStyle(region2D, false);
-		
-		// Show the plot.
-		plotter2D.setParameter("plotterWidth", "2000");
-		plotter2D.setParameter("plotterHeight", "1200");
-		plotter2D.show();
-		
-		// Format and display the histograms.
-		for(int i = 0; i < 2; i++) {
-			// Scale the histogram by the appropriate scaling factor.
-			invariantMassPlots[i].scale(1.0 / scaleFactor);
-			
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create("Particle Invariant Mass (" + runNumber[i] + ")");
-			plotter.createRegions(1);
-			plotter.region(0).plot(invariantMassPlots[i]);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle("Particle Invariant Mass (" + runNumber[i] + ")");
-			region.getPlot().getXAxis().setLabel("Invariant Mass (GeV)");
-			region.getPlot().getYAxis().setLabel("Rate (Hz)");
-			
-			// Format the fonts and general plot presentation.
-			setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Note which plot is the numerator and which is the denominator.
-		int numerator   = 0;
-		int denominator = 1;
-		
-		// Create a new histogram to display the ratios of the rates.
-		IHistogram1D ratioPlot = AIDA.defaultInstance().histogram1D("Invariant Mass Ratio (" + runNumber[numerator] + " / "
-				+ runNumber[denominator] + ")", invariantMassPlots[0].axis().bins(),
-				invariantMassPlots[0].axis().lowerEdge(), invariantMassPlots[0].axis().upperEdge());
-		
-		// Iterate over each bin.
-		for(int bin = 0; bin < invariantMassPlots[0].axis().bins(); bin++) {
-			// Calculate the ratio.
-			double ratio = invariantMassPlots[numerator].binHeight(bin) / invariantMassPlots[denominator].binHeight(bin);
-			
-			// If the ratio is either not a number of infinite, skip
-			// this bin.
-			if(Double.isNaN(ratio) || Double.isInfinite(ratio)) { continue; }
-			
-			// Populate the ratio plot bin.
-			ratioPlot.fill(invariantMassPlots[0].axis().binCenter(bin), ratio);
-		}
-		
-		// Create a plotter and plotting region for the plot.
-		IPlotter plotter = plotterFactory.create("Invariant Mass Ratio (5411 / 5554)");
-		plotter.createRegions(1);
-		plotter.region(0).plot(ratioPlot);
-		
-		// Format the axis labels.
-		PlotterRegion region = (PlotterRegion) plotter.region(0);
-		region.getPlot().setTitle("Invariant Mass Ratio (" + runNumber[numerator] + " / " + runNumber[denominator] + ")");
-		region.getPlot().getXAxis().setLabel("Invariant Mass (GeV)");
-		region.getPlot().getXAxis().setMin(0.010);
-		region.getPlot().getXAxis().setMax(0.060);
-		region.getPlot().getYAxis().setLabel("Ratio");
-		
-		// Format the fonts and general plot presentation.
-		setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-		
-		// Disable the error bars.
-		JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		fillStyle.setShowErrorBars(false);
-		
-		// Show the plot.
-		plotter.setParameter("plotterWidth", "2000");
-		plotter.setParameter("plotterHeight", "1200");
-		plotter.show();
-		
-		// Close the trees.
-		for(int i = 0; i < plotFile.length; i++) {
-			tree[i].close();
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the names of each plot on in the region.
-		String[] dataNames = region.getAllDataNames();
-		
-		// Check whether this is an overlay plot. Overlay plots contain
-		// more than one data name.
-		boolean overlay = (dataNames.length > 1 ? true : false);
-		
-		// Iterate over each plot in the region.
-		for(int i = 0; i < dataNames.length; i++) {
-			// Set the overlay style if needed.
-			if(overlay) {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with no fill. The color is set by the "color" argument.
-				fillStyle.setHistogramFill(false);
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarLineColor(color[i].getFillColor());
-				
-				// Set the legend text style.
-				region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
-			}
-			
-			// Otherwise, set the fill style for a single plot.
-			else {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with a fill color. The colors are defined by the
-				// "color" argument.
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarColor(color[i].getFillColor());
-				fillStyle.setHistogramBarLineColor(color[i].getLineColor());
-			}
-			
-			// Set the statistics box style.
-			region.getPlot().getStats().setVisible(true);
-			region.getPlot().getStats().setFont(BASIC_FONT);
-			
-			// Set the title font.
-			region.getPlot().getTitleObject().setFont(TITLE_FONT);
-			
-			// Set the axis tick-mark fonts.
-			region.getPlot().getXAxis().setFont(BASIC_FONT);
-			region.getPlot().getYAxis().setFont(BASIC_FONT);
-			region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-			region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 */
-	private static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
-		// Get the fill style object. 2D plots should never be overlay
-		// plots, so there should only ever be one data name.
-		JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		
-		// Set the fill style for a two-dimensional plot.
-		if(logarithmic) { fillStyle.setLogZ(true); }
-		fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
-		fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
-		
-		// Make the statistics box invisible.
-		region.getPlot().getStats().setVisible(false);
-		
-		// Set the general plot font (which is also the z-axis font).
-		region.getPlot().setFont(BASIC_FONT);
-		
-		// Set the title font.
-		region.getPlot().getTitleObject().setFont(TITLE_FONT);
-		
-		// Set the axis tick-mark fonts.
-		region.getPlot().getXAxis().setFont(BASIC_FONT);
-		region.getPlot().getYAxis().setFont(BASIC_FONT);
-		region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-		region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-	}
+    // Define plot fonts.
+    private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
+    private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
+    private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
+    
+    // Defines the color style options for plot data.
+    private enum ColorStyle {
+         MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
+          MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
+        MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
+            RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
+          FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
+            TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
+            BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
+          PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
+        
+        private final Color fillColor;
+        private final Color lineColor;
+        
+        private ColorStyle(Color fillColor, Color lineColor) {
+            this.fillColor = fillColor;
+            this.lineColor = lineColor;
+        }
+        
+        public Color getFillColor() { return fillColor; }
+        
+        public Color getLineColor() { return lineColor; }
+    };
+        
+    /**
+     * Loads all plots in a file and formats them according to the
+     * indicated style.
+     * @param args - Unused default executable parameter.
+     * @throws IOException Occurs if there is an issue opening the file.
+     */
+    public static void main(String[] args) throws IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String[] plotFile = {
+                rootDir + "temp.aida"
+        };
+        
+        // Define the run numbers for each file.
+        String[] runNumber = { "1 Hits", "2 Hits" };
+        
+        // Define the scaling factors for each plot.
+        double scaleFactor = 13.254;
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree[] tree = new ITree[plotFile.length];
+        for(int i = 0; i < plotFile.length; i++) {
+            tree[i] = af.createTreeFactory().create(plotFile[i]);
+            if(tree[i] == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        }
+        
+        // Get the histograms.
+        IHistogram1D[] invariantMassPlots = new IHistogram1D[3];
+        invariantMassPlots[0] = (IHistogram1D) tree[0].find("Trident Analysis/Particle Invariant Mass (1 Hit)");
+        invariantMassPlots[1] = (IHistogram1D) tree[0].find("Trident Analysis/Particle Invariant Mass (2 Hit)");
+        IHistogram1D electronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Electron Energy");
+        IHistogram1D positronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Positron Energy");
+        IHistogram1D energySumPlot = (IHistogram1D) tree[0].find("Trident Analysis/Energy Sum Distribution");
+        IHistogram2D energySum2DPlot = (IHistogram2D) tree[0].find("Trident Analysis/2D Energy Distribution");
+        IHistogram1D tridentElectronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Trident Electron Energy");
+        IHistogram1D tridentPositronEnergyPlot = (IHistogram1D) tree[0].find("Trident Analysis/Trident Positron Energy");
+        
+        // Define the plot titles and arrays.
+        IHistogram[] plots = { electronEnergyPlot, positronEnergyPlot, energySumPlot, tridentElectronEnergyPlot, tridentPositronEnergyPlot };
+        String[] titles = { "Electron Energy", "Positron Energy", "Energy Sum", "Trident Electron Energy", "Trident Positron Energy" };
+        String[] xTitles = { "Energy (GeV)", "Energy (GeV)", "Energy Sum (GeV)", "Energy (GeV)", "Energy (GeV)" };
+        
+        // Re-bin the histograms to have 5-times larger bins. First,
+        // get the bin count and upper and lower bounds of the plot.
+        int bins = invariantMassPlots[0].axis().bins();
+        double low = invariantMassPlots[0].axis().binLowerEdge(0);
+        double high = invariantMassPlots[0].axis().binUpperEdge(invariantMassPlots[0].axis().bins() - 1);
+        
+        // Create new plots with the larger bin sizes.
+        AIDA aida = AIDA.defaultInstance();
+        IHistogram1D[] newPlot = new IHistogram1D[2];
+        newPlot[0] = aida.histogram1D("Particle Invariant Mass (1 Hit)", bins / 5, low, high);
+        newPlot[1] = aida.histogram1D("Particle Invariant Mass (2 Hit)", bins / 5, low, high);
+        
+        // Populate the new plots with the data from the old ones.
+        for(int j = 0; j < 2; j++) {
+            for(int i = 0; i < bins; i++) {
+                int entries = invariantMassPlots[j].binEntries(i);
+                double center = invariantMassPlots[j].axis().binCenter(i);
+                for(int k = 0; k < entries; k++) {
+                    newPlot[j].fill(center);
+                }
+            }
+        }
+        
+        // Replace the old plots.
+        invariantMassPlots = newPlot;
+        
+        // Create a plotter factory.
+        IPlotterFactory plotterFactory = af.createPlotterFactory();
+        
+        // Format and display the basic histograms.
+        for(int i = 0; i < plots.length; i++) {
+            // Scale the histogram by the appropriate scaling factor.
+            plots[i].scale(1.0 / scaleFactor);
+            
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(titles[i]);
+            plotter.createRegions(1);
+            plotter.region(0).plot(plots[i]);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle(titles[i]);
+            region.getPlot().getXAxis().setLabel(xTitles[i]);
+            region.getPlot().getYAxis().setLabel("Rate (Hz)");
+            
+            // Format the fonts and general plot presentation.
+            setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Format and display the 2D histogram.
+        energySum2DPlot.scale(1.0 / scaleFactor);
+        IPlotter plotter2D = plotterFactory.create("2D Energy Sum");
+        plotter2D.createRegions(1);
+        plotter2D.region(0).plot(energySum2DPlot);
+        
+        // Format the axis labels.
+        PlotterRegion region2D = (PlotterRegion) plotter2D.region(0);
+        region2D.getPlot().setTitle("2D Energy Sum");
+        region2D.getPlot().getXAxis().setLabel("Electron Energy (GeV)");
+        region2D.getPlot().getYAxis().setLabel("Positron Energy (GeV)");
+        
+        // Format the fonts and general plot presentation.
+        setDefault2DStyle(region2D, false);
+        
+        // Show the plot.
+        plotter2D.setParameter("plotterWidth", "2000");
+        plotter2D.setParameter("plotterHeight", "1200");
+        plotter2D.show();
+        
+        // Format and display the histograms.
+        for(int i = 0; i < 2; i++) {
+            // Scale the histogram by the appropriate scaling factor.
+            invariantMassPlots[i].scale(1.0 / scaleFactor);
+            
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create("Particle Invariant Mass (" + runNumber[i] + ")");
+            plotter.createRegions(1);
+            plotter.region(0).plot(invariantMassPlots[i]);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle("Particle Invariant Mass (" + runNumber[i] + ")");
+            region.getPlot().getXAxis().setLabel("Invariant Mass (GeV)");
+            region.getPlot().getYAxis().setLabel("Rate (Hz)");
+            
+            // Format the fonts and general plot presentation.
+            setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Note which plot is the numerator and which is the denominator.
+        int numerator   = 0;
+        int denominator = 1;
+        
+        // Create a new histogram to display the ratios of the rates.
+        IHistogram1D ratioPlot = AIDA.defaultInstance().histogram1D("Invariant Mass Ratio (" + runNumber[numerator] + " / "
+                + runNumber[denominator] + ")", invariantMassPlots[0].axis().bins(),
+                invariantMassPlots[0].axis().lowerEdge(), invariantMassPlots[0].axis().upperEdge());
+        
+        // Iterate over each bin.
+        for(int bin = 0; bin < invariantMassPlots[0].axis().bins(); bin++) {
+            // Calculate the ratio.
+            double ratio = invariantMassPlots[numerator].binHeight(bin) / invariantMassPlots[denominator].binHeight(bin);
+            
+            // If the ratio is either not a number of infinite, skip
+            // this bin.
+            if(Double.isNaN(ratio) || Double.isInfinite(ratio)) { continue; }
+            
+            // Populate the ratio plot bin.
+            ratioPlot.fill(invariantMassPlots[0].axis().binCenter(bin), ratio);
+        }
+        
+        // Create a plotter and plotting region for the plot.
+        IPlotter plotter = plotterFactory.create("Invariant Mass Ratio (5411 / 5554)");
+        plotter.createRegions(1);
+        plotter.region(0).plot(ratioPlot);
+        
+        // Format the axis labels.
+        PlotterRegion region = (PlotterRegion) plotter.region(0);
+        region.getPlot().setTitle("Invariant Mass Ratio (" + runNumber[numerator] + " / " + runNumber[denominator] + ")");
+        region.getPlot().getXAxis().setLabel("Invariant Mass (GeV)");
+        region.getPlot().getXAxis().setMin(0.010);
+        region.getPlot().getXAxis().setMax(0.060);
+        region.getPlot().getYAxis().setLabel("Ratio");
+        
+        // Format the fonts and general plot presentation.
+        setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+        
+        // Disable the error bars.
+        JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        fillStyle.setShowErrorBars(false);
+        
+        // Show the plot.
+        plotter.setParameter("plotterWidth", "2000");
+        plotter.setParameter("plotterHeight", "1200");
+        plotter.show();
+        
+        // Close the trees.
+        for(int i = 0; i < plotFile.length; i++) {
+            tree[i].close();
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the names of each plot on in the region.
+        String[] dataNames = region.getAllDataNames();
+        
+        // Check whether this is an overlay plot. Overlay plots contain
+        // more than one data name.
+        boolean overlay = (dataNames.length > 1 ? true : false);
+        
+        // Iterate over each plot in the region.
+        for(int i = 0; i < dataNames.length; i++) {
+            // Set the overlay style if needed.
+            if(overlay) {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with no fill. The color is set by the "color" argument.
+                fillStyle.setHistogramFill(false);
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarLineColor(color[i].getFillColor());
+                
+                // Set the legend text style.
+                region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
+            }
+            
+            // Otherwise, set the fill style for a single plot.
+            else {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with a fill color. The colors are defined by the
+                // "color" argument.
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarColor(color[i].getFillColor());
+                fillStyle.setHistogramBarLineColor(color[i].getLineColor());
+            }
+            
+            // Set the statistics box style.
+            region.getPlot().getStats().setVisible(true);
+            region.getPlot().getStats().setFont(BASIC_FONT);
+            
+            // Set the title font.
+            region.getPlot().getTitleObject().setFont(TITLE_FONT);
+            
+            // Set the axis tick-mark fonts.
+            region.getPlot().getXAxis().setFont(BASIC_FONT);
+            region.getPlot().getYAxis().setFont(BASIC_FONT);
+            region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+            region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     */
+    private static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
+        // Get the fill style object. 2D plots should never be overlay
+        // plots, so there should only ever be one data name.
+        JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        
+        // Set the fill style for a two-dimensional plot.
+        if(logarithmic) { fillStyle.setLogZ(true); }
+        fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
+        fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
+        
+        // Make the statistics box invisible.
+        region.getPlot().getStats().setVisible(false);
+        
+        // Set the general plot font (which is also the z-axis font).
+        region.getPlot().setFont(BASIC_FONT);
+        
+        // Set the title font.
+        region.getPlot().getTitleObject().setFont(TITLE_FONT);
+        
+        // Set the axis tick-mark fonts.
+        region.getPlot().getXAxis().setFont(BASIC_FONT);
+        region.getPlot().getYAxis().setFont(BASIC_FONT);
+        region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+        region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTEPlotFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTEPlotFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTEPlotFormatter.java	Wed Apr 27 11:11:32 2016
@@ -19,308 +19,308 @@
 import hep.aida.ref.plotter.PlotterRegion;
 
 public class MTEPlotFormatter {
-	// Define plot fonts.
-	private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
-	private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
-	private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
-	
-	// Defines the color style options for plot data.
-	private enum ColorStyle {
-		 MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
-		  MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
-		MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
-		    RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
-		  FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
-		    TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
-		    BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
-		  PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
-		
-		private final Color fillColor;
-		private final Color lineColor;
-		
-		private ColorStyle(Color fillColor, Color lineColor) {
-			this.fillColor = fillColor;
-			this.lineColor = lineColor;
-		}
-		
-		public Color getFillColor() { return fillColor; }
-		
-		public Color getLineColor() { return lineColor; }
-	};
-		
-	/**
-	 * Loads all plots in a file and formats them according to the
-	 * indicated style.
-	 * @param args - Unused default executable parameter.
-	 * @throws IOException Occurs if there is an issue opening the file.
-	 */
-	public static void main(String[] args) throws IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "temp.aida";
-		
-		// Define the scaling factors for each plot.
-		double scaleFactor = 1;
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Define index references for each event type.
-		int MOLLER  = 0;
-		int TRIDENT = 1;
-		int ELASTIC = 2;
-		
-		// Get the histograms.
-		IHistogram1D[] trackCountPlots = new IHistogram1D[3];
-		trackCountPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks");
-		trackCountPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks");
-		trackCountPlots[ELASTIC] = (IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks");
-		
-		IHistogram1D[] energyPlots = new IHistogram1D[3];
-		energyPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution");
-		energyPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution");
-		energyPlots[ELASTIC] = (IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution");
-		
-		IHistogram1D[] energySumPlots = new IHistogram1D[2];
-		energySumPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution");
-		energySumPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution");
-		
-		IHistogram2D[] energy2DPlots = new IHistogram2D[2];
-		energy2DPlots[MOLLER]  = (IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution");
-		energy2DPlots[TRIDENT] = (IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution");
-		
-		// Create a plotter factory.
-		IPlotterFactory plotterFactory = af.createPlotterFactory();
-		
-		// Format the track count plots.
-		for(IHistogram1D trackCountPlot : trackCountPlots) {
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(trackCountPlot.title());
-			plotter.createRegions(1);
-			plotter.region(0).plot(trackCountPlot);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle(trackCountPlot.title());
-			region.getPlot().getXAxis().setLabel("Number of Tracks");
-			region.getPlot().getYAxis().setLabel("Count");
-			
-			// Format the fonts and general plot presentation.
-			setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Format the electron energy plots.
-		for(IHistogram1D energyPlot : energyPlots) {
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(energyPlot.title());
-			plotter.createRegions(1);
-			plotter.region(0).plot(energyPlot);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle(energyPlot.title());
-			region.getPlot().getXAxis().setLabel("Track Energy (GeV)");
-			region.getPlot().getYAxis().setLabel("Count");
-			
-			// Format the fonts and general plot presentation.
-			setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Format the energy sum plots.
-		for(IHistogram1D energySumPlot : energySumPlots) {
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(energySumPlot.title());
-			plotter.createRegions(1);
-			plotter.region(0).plot(energySumPlot);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle(energySumPlot.title());
-			region.getPlot().getXAxis().setLabel("Track Energy (GeV)");
-			region.getPlot().getYAxis().setLabel("Count");
-			
-			// Format the fonts and general plot presentation.
-			setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Format the 2D energy sum plots.
-		for(IHistogram2D energy2DPlot : energy2DPlots) {
-			// Create a plotter and plotting region for the plot.
-			IPlotter plotter = plotterFactory.create(energy2DPlot.title());
-			plotter.createRegions(1);
-			plotter.region(0).plot(energy2DPlot);
-			
-			// Format the axis labels.
-			PlotterRegion region = (PlotterRegion) plotter.region(0);
-			region.getPlot().setTitle(energy2DPlot.title());
-			region.getPlot().getXAxis().setLabel("First Track Energy (GeV)");
-			region.getPlot().getYAxis().setLabel("Second Track Energy (GeV)");
-			
-			
-			// Format the fonts and general plot presentation.
-			setDefault2DStyle(region, false);
-			
-			// Show the plot.
-			plotter.setParameter("plotterWidth", "2000");
-			plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Disable the error bars.
-		//JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		//fillStyle.setShowErrorBars(false);
-		
-		// Close the tree.
-		tree.close();
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the names of each plot on in the region.
-		String[] dataNames = region.getAllDataNames();
-		
-		// Check whether this is an overlay plot. Overlay plots contain
-		// more than one data name.
-		boolean overlay = (dataNames.length > 1 ? true : false);
-		
-		// Iterate over each plot in the region.
-		for(int i = 0; i < dataNames.length; i++) {
-			// Set the overlay style if needed.
-			if(overlay) {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with no fill. The color is set by the "color" argument.
-				fillStyle.setHistogramFill(false);
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarLineColor(color[i].getFillColor());
-				
-				// Set the legend text style.
-				region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
-			}
-			
-			// Otherwise, set the fill style for a single plot.
-			else {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with a fill color. The colors are defined by the
-				// "color" argument.
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarColor(color[i].getFillColor());
-				fillStyle.setHistogramBarLineColor(color[i].getLineColor());
-			}
-			
-			// Set the statistics box style.
-			region.getPlot().getStats().setVisible(true);
-			region.getPlot().getStats().setFont(BASIC_FONT);
-			
-			// Set the title font.
-			region.getPlot().getTitleObject().setFont(TITLE_FONT);
-			
-			// Set the axis tick-mark fonts.
-			region.getPlot().getXAxis().setFont(BASIC_FONT);
-			region.getPlot().getYAxis().setFont(BASIC_FONT);
-			region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-			region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 */
-	private static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
-		// Get the fill style object. 2D plots should never be overlay
-		// plots, so there should only ever be one data name.
-		JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		
-		// Set the fill style for a two-dimensional plot.
-		if(logarithmic) { fillStyle.setLogZ(true); }
-		fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
-		fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
-		
-		// Make the statistics box invisible.
-		region.getPlot().getStats().setVisible(false);
-		
-		// Set the general plot font (which is also the z-axis font).
-		region.getPlot().setFont(BASIC_FONT);
-		
-		// Set the title font.
-		region.getPlot().getTitleObject().setFont(TITLE_FONT);
-		
-		// Set the axis tick-mark fonts.
-		region.getPlot().getXAxis().setFont(BASIC_FONT);
-		region.getPlot().getYAxis().setFont(BASIC_FONT);
-		region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-		region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-	}
-	
-	/**
-	 * Recursive method that gets all object names from a tree that
-	 * are not directories. Method should not be called directly, but
-	 * rather called only through the <code>getHistograms(ITree)</code>
-	 * method.
-	 * @param tree - The tree from which to obtain the object names.
-	 * @param directory - The directory in which to search for objects.
-	 * @param list - The list in which to place the objects.
-	 * @return Returns the <code>List</code> collection that was given
-	 * as an argument.
-	 */
-	private static final List<String> getHistograms(ITree tree, String directory, List<String> list) {
-		// Get the list of objects in the directory.
-		String[] treeObjects = tree.listObjectNames(directory);
-		
-		// Print the objects.
-		for(String objectName : treeObjects) {
-			// Check if the object is a directory.
-			boolean isDirectory = isDirectory(objectName);
-			
-			// If the object is a directory, get the histograms from it.
-			if(isDirectory) {
-				getHistograms(tree, objectName, list);
-			}
-			
-			// If the object is a plot, add it to the list.
-			else { list.add(objectName); }
-		}
-		
-		// Return the list.
-		return list;
-	}
-	
-	/**
-	 * Checks whether a tree object is a directory.
-	 * @param object - The object to check.
-	 * @return Returns <code>true</code> if the object is a directory
-	 * and <code>false</code> otherwise.
-	 */
-	private static final boolean isDirectory(String object) {
-		return (object.toCharArray()[object.length() - 1] == '/');
-	}
+    // Define plot fonts.
+    private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
+    private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
+    private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
+    
+    // Defines the color style options for plot data.
+    private enum ColorStyle {
+         MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
+          MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
+        MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
+            RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
+          FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
+            TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
+            BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
+          PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
+        
+        private final Color fillColor;
+        private final Color lineColor;
+        
+        private ColorStyle(Color fillColor, Color lineColor) {
+            this.fillColor = fillColor;
+            this.lineColor = lineColor;
+        }
+        
+        public Color getFillColor() { return fillColor; }
+        
+        public Color getLineColor() { return lineColor; }
+    };
+        
+    /**
+     * Loads all plots in a file and formats them according to the
+     * indicated style.
+     * @param args - Unused default executable parameter.
+     * @throws IOException Occurs if there is an issue opening the file.
+     */
+    public static void main(String[] args) throws IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "temp.aida";
+        
+        // Define the scaling factors for each plot.
+        double scaleFactor = 1;
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Define index references for each event type.
+        int MOLLER  = 0;
+        int TRIDENT = 1;
+        int ELASTIC = 2;
+        
+        // Get the histograms.
+        IHistogram1D[] trackCountPlots = new IHistogram1D[3];
+        trackCountPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks");
+        trackCountPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks");
+        trackCountPlots[ELASTIC] = (IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks");
+        
+        IHistogram1D[] energyPlots = new IHistogram1D[3];
+        energyPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution");
+        energyPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution");
+        energyPlots[ELASTIC] = (IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution");
+        
+        IHistogram1D[] energySumPlots = new IHistogram1D[2];
+        energySumPlots[MOLLER]  = (IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution");
+        energySumPlots[TRIDENT] = (IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution");
+        
+        IHistogram2D[] energy2DPlots = new IHistogram2D[2];
+        energy2DPlots[MOLLER]  = (IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution");
+        energy2DPlots[TRIDENT] = (IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution");
+        
+        // Create a plotter factory.
+        IPlotterFactory plotterFactory = af.createPlotterFactory();
+        
+        // Format the track count plots.
+        for(IHistogram1D trackCountPlot : trackCountPlots) {
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(trackCountPlot.title());
+            plotter.createRegions(1);
+            plotter.region(0).plot(trackCountPlot);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle(trackCountPlot.title());
+            region.getPlot().getXAxis().setLabel("Number of Tracks");
+            region.getPlot().getYAxis().setLabel("Count");
+            
+            // Format the fonts and general plot presentation.
+            setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Format the electron energy plots.
+        for(IHistogram1D energyPlot : energyPlots) {
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(energyPlot.title());
+            plotter.createRegions(1);
+            plotter.region(0).plot(energyPlot);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle(energyPlot.title());
+            region.getPlot().getXAxis().setLabel("Track Energy (GeV)");
+            region.getPlot().getYAxis().setLabel("Count");
+            
+            // Format the fonts and general plot presentation.
+            setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Format the energy sum plots.
+        for(IHistogram1D energySumPlot : energySumPlots) {
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(energySumPlot.title());
+            plotter.createRegions(1);
+            plotter.region(0).plot(energySumPlot);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle(energySumPlot.title());
+            region.getPlot().getXAxis().setLabel("Track Energy (GeV)");
+            region.getPlot().getYAxis().setLabel("Count");
+            
+            // Format the fonts and general plot presentation.
+            setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Format the 2D energy sum plots.
+        for(IHistogram2D energy2DPlot : energy2DPlots) {
+            // Create a plotter and plotting region for the plot.
+            IPlotter plotter = plotterFactory.create(energy2DPlot.title());
+            plotter.createRegions(1);
+            plotter.region(0).plot(energy2DPlot);
+            
+            // Format the axis labels.
+            PlotterRegion region = (PlotterRegion) plotter.region(0);
+            region.getPlot().setTitle(energy2DPlot.title());
+            region.getPlot().getXAxis().setLabel("First Track Energy (GeV)");
+            region.getPlot().getYAxis().setLabel("Second Track Energy (GeV)");
+            
+            
+            // Format the fonts and general plot presentation.
+            setDefault2DStyle(region, false);
+            
+            // Show the plot.
+            plotter.setParameter("plotterWidth", "2000");
+            plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Disable the error bars.
+        //JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        //fillStyle.setShowErrorBars(false);
+        
+        // Close the tree.
+        tree.close();
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the names of each plot on in the region.
+        String[] dataNames = region.getAllDataNames();
+        
+        // Check whether this is an overlay plot. Overlay plots contain
+        // more than one data name.
+        boolean overlay = (dataNames.length > 1 ? true : false);
+        
+        // Iterate over each plot in the region.
+        for(int i = 0; i < dataNames.length; i++) {
+            // Set the overlay style if needed.
+            if(overlay) {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with no fill. The color is set by the "color" argument.
+                fillStyle.setHistogramFill(false);
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarLineColor(color[i].getFillColor());
+                
+                // Set the legend text style.
+                region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
+            }
+            
+            // Otherwise, set the fill style for a single plot.
+            else {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with a fill color. The colors are defined by the
+                // "color" argument.
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarColor(color[i].getFillColor());
+                fillStyle.setHistogramBarLineColor(color[i].getLineColor());
+            }
+            
+            // Set the statistics box style.
+            region.getPlot().getStats().setVisible(true);
+            region.getPlot().getStats().setFont(BASIC_FONT);
+            
+            // Set the title font.
+            region.getPlot().getTitleObject().setFont(TITLE_FONT);
+            
+            // Set the axis tick-mark fonts.
+            region.getPlot().getXAxis().setFont(BASIC_FONT);
+            region.getPlot().getYAxis().setFont(BASIC_FONT);
+            region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+            region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     */
+    private static final void setDefault2DStyle(PlotterRegion region, boolean logarithmic) {
+        // Get the fill style object. 2D plots should never be overlay
+        // plots, so there should only ever be one data name.
+        JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        
+        // Set the fill style for a two-dimensional plot.
+        if(logarithmic) { fillStyle.setLogZ(true); }
+        fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
+        fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
+        
+        // Make the statistics box invisible.
+        region.getPlot().getStats().setVisible(false);
+        
+        // Set the general plot font (which is also the z-axis font).
+        region.getPlot().setFont(BASIC_FONT);
+        
+        // Set the title font.
+        region.getPlot().getTitleObject().setFont(TITLE_FONT);
+        
+        // Set the axis tick-mark fonts.
+        region.getPlot().getXAxis().setFont(BASIC_FONT);
+        region.getPlot().getYAxis().setFont(BASIC_FONT);
+        region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+        region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+    }
+    
+    /**
+     * Recursive method that gets all object names from a tree that
+     * are not directories. Method should not be called directly, but
+     * rather called only through the <code>getHistograms(ITree)</code>
+     * method.
+     * @param tree - The tree from which to obtain the object names.
+     * @param directory - The directory in which to search for objects.
+     * @param list - The list in which to place the objects.
+     * @return Returns the <code>List</code> collection that was given
+     * as an argument.
+     */
+    private static final List<String> getHistograms(ITree tree, String directory, List<String> list) {
+        // Get the list of objects in the directory.
+        String[] treeObjects = tree.listObjectNames(directory);
+        
+        // Print the objects.
+        for(String objectName : treeObjects) {
+            // Check if the object is a directory.
+            boolean isDirectory = isDirectory(objectName);
+            
+            // If the object is a directory, get the histograms from it.
+            if(isDirectory) {
+                getHistograms(tree, objectName, list);
+            }
+            
+            // If the object is a plot, add it to the list.
+            else { list.add(objectName); }
+        }
+        
+        // Return the list.
+        return list;
+    }
+    
+    /**
+     * Checks whether a tree object is a directory.
+     * @param object - The object to check.
+     * @return Returns <code>true</code> if the object is a directory
+     * and <code>false</code> otherwise.
+     */
+    private static final boolean isDirectory(String object) {
+        return (object.toCharArray()[object.length() - 1] == '/');
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTETriggerPlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTETriggerPlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/MTETriggerPlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -15,164 +15,164 @@
 
 
 public class MTETriggerPlotsFormatter {
-	public static void main(String[] args) throws IllegalArgumentException, IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "5772-ana.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Define the 1D trigger plot names for Møllers and tridents.
-		String[] plotNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
-				"Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
-		String[] displayNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
-				"Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
-		String[] xAxisNames1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)",
-				"Coplanarity (Degrees)", "Energy Difference (GeV)", "Energy Slope (GeV)", "Energy Sum (GeV)" };
-		String yAxisName1D = "Count";
-		
-		// Define the 2D trigger plot names for Møllers and tridents.
-		String[] plotNames2D = { "Cluster Seed", "Pair Energy Sum 2D" };
-		String[] displayNames2D = { "Cluster Seed Distribution", "2D Energy Sum" };
-		String[] xAxisNames2D = { "x-Index", "Second Cluster Energy (GeV)" };
-		String[] yAxisNames2D = { "y-Index", "First Cluster Energy (GeV)" };
-		
-		// Define the 1D trigger plot names for elastics.
-		String[] plotNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
-		String[] displayNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
-		String[] xAxisNamesElastic1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)" };
-		String yAxisNameElastic1D = "Count";
-		
-		// Define the 2D trigger plot names for elastics.
-		String[] plotNamesElastic2D = { "Cluster Seed" };
-		String[] displayNamesElastic2D = { "Cluster Seed Distribution" };
-		String[] xAxisNamesElastic2D = { "x-Index" };
-		String[] yAxisNamesElastic2D = { "y-Index" };
-		
-		// Define the Møller, trident, and elastic prefixes.
-		String allPrefix = "All Trigger Plots/Pair Plots/";
-		String møllerPrefix = "Møller Trigger Plots/Pair Plots/";
-		String tridentPrefix = "Trident Trigger Plots/Pair Plots/";
-		String elasticPrefix = "Elastic Trigger Plots/Singles Plots/";
-		String allSinglesPrefix = "All Trigger Plots/Singles Plots/";
-		
-		// Define the plot type prefix.
-		String allTypeName = "All Pairs - ";
-		String møllerTypeName = "Møller - ";
-		String tridentTypeName = "Trident - ";
-		String elasticTypeName = "Elastic - ";
-		String allSinglesTypeName = "All Singles - ";
-		
-		// Define the plot type colors.
-		ColorStyle allColor = PlotsFormatter.ColorStyle.GREY;
-		ColorStyle møllerColor = PlotsFormatter.ColorStyle.MS_BLUE;
-		ColorStyle tridentColor = PlotsFormatter.ColorStyle.MS_ORANGE;
-		ColorStyle elasticColor = PlotsFormatter.ColorStyle.MS_GREEN;
-		
-		// Create a plot formatting module.
-		PlotFormatModule module = new PlotFormatModule();
-		
-		// Get the histograms and add them to the module. Start with the
-		// trident and Møller plots.
-		for(int i = 0; i < plotNames1D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram1D allPlot = (IHistogram1D) tree.find(allPrefix + plotNames1D[i]);
-			IHistogram1D møllerPlot = (IHistogram1D) tree.find(møllerPrefix + plotNames1D[i]);
-			IHistogram1D tridentPlot = (IHistogram1D) tree.find(tridentPrefix + plotNames1D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNames1D[i], yAxisName1D, allTypeName + displayNames1D[i]);
-			FormattedPlot1D møllerFormattedPlot = new FormattedPlot1D(møllerPlot, møllerColor, xAxisNames1D[i], yAxisName1D, møllerTypeName + displayNames1D[i]);
-			FormattedPlot1D tridentFormattedPlot = new FormattedPlot1D(tridentPlot, tridentColor, xAxisNames1D[i], yAxisName1D, tridentTypeName + displayNames1D[i]);
-			
-			// Add them to the module.
-			module.addPlot1D(allFormattedPlot);
-			module.addPlot1D(møllerFormattedPlot);
-			module.addPlot1D(tridentFormattedPlot);
-		}
-		for(int i = 0; i < plotNames2D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNames2D[i]);
-			IHistogram2D møllerPlot = (IHistogram2D) tree.find(møllerPrefix + plotNames2D[i]);
-			IHistogram2D tridentPlot = (IHistogram2D) tree.find(tridentPrefix + plotNames2D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], allTypeName + displayNames2D[i]);
-			FormattedPlot2D møllerFormattedPlot = new FormattedPlot2D(møllerPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], møllerTypeName + displayNames2D[i]);
-			FormattedPlot2D tridentFormattedPlot = new FormattedPlot2D(tridentPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], tridentTypeName + displayNames2D[i]);
-			
-			// Add them to the module.
-			module.addPlot2D(allFormattedPlot);
-			module.addPlot2D(møllerFormattedPlot);
-			module.addPlot2D(tridentFormattedPlot);
-		}
-		
-		// Get the histograms for the elastic plots and add them to the module.
-		for(int i = 0; i < plotNamesElastic1D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram1D allPlot = (IHistogram1D) tree.find(allSinglesPrefix + plotNames1D[i]);
-			IHistogram1D elasticPlot = (IHistogram1D) tree.find(elasticPrefix + plotNames1D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
-					allSinglesTypeName + displayNamesElastic1D[i]);
-			FormattedPlot1D elasticFormattedPlot = new FormattedPlot1D(elasticPlot, elasticColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
-					elasticTypeName + displayNamesElastic1D[i]);
-			
-			// Add them to the module.
-			module.addPlot1D(allFormattedPlot);
-			module.addPlot1D(elasticFormattedPlot);
-		}
-		for(int i = 0; i < plotNamesElastic2D.length; i++) {
-			// Get the Møller and trident plots.
-			IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNamesElastic2D[i]);
-			IHistogram2D elasticPlot = (IHistogram2D) tree.find(møllerPrefix + plotNamesElastic2D[i]);
-			
-			// Make a formatted plot for each.
-			FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
-					allSinglesTypeName + plotNames2D[i]);
-			FormattedPlot2D elasticFormattedPlot = new FormattedPlot2D(elasticPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
-					elasticTypeName + displayNamesElastic2D[i]);
-			
-			// Add them to the module.
-			module.addPlot2D(allFormattedPlot);
-			module.addPlot2D(elasticFormattedPlot);
-		}
-		
-		// Add the MTE plots to the module.
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution"), elasticColor,
-				"Momentum (GeV)", "Count", "Elastic - Momentum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks"), elasticColor,
-				"Tracks", "Count", "Elastic - Tracks in Event"));
-		
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution"), møllerColor,
-				"Momentum Sum (GeV)", "Count", "Møller - Momentum Sum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution"), møllerColor,
-				"Momentum (GeV)", "Count", "Møller - Momentum (Electron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)"), møllerColor,
-				"Time (ns)", "Count", "Møller - Time Coincidence"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks"), møllerColor,
-				"Tracks", "Count", "Møller - Tracks in Event"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution"), false,
-				"First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Møller - 2D Momentum Sum"));
-		
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution"), tridentColor,
-				"Momentum Sum (GeV)", "Count", "Trident - Momentum Sum"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution"), tridentColor,
-				"Momentum (GeV)", "Count", "Trident - Momentum (Electron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Positron Energy Distribution"), tridentColor,
-				"Momentum (GeV)", "Count", "Trident - Momentum (Positron)"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks"), tridentColor,
-				"Tracks", "Count", "Trident - Tracks in Event"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution"), false,
-				"First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Trident - 2D Momentum Sum"));
-		
-		// Display the plots.
-		module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\TestPrint\\");
-	}
+    public static void main(String[] args) throws IllegalArgumentException, IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "5772-ana.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Define the 1D trigger plot names for Møllers and tridents.
+        String[] plotNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
+                "Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
+        String[] displayNames1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy",
+                "Pair Coplanarity", "Pair Energy Difference", "Pair Energy Slope", "Pair Energy Sum" };
+        String[] xAxisNames1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)",
+                "Coplanarity (Degrees)", "Energy Difference (GeV)", "Energy Slope (GeV)", "Energy Sum (GeV)" };
+        String yAxisName1D = "Count";
+        
+        // Define the 2D trigger plot names for Møllers and tridents.
+        String[] plotNames2D = { "Cluster Seed", "Pair Energy Sum 2D" };
+        String[] displayNames2D = { "Cluster Seed Distribution", "2D Energy Sum" };
+        String[] xAxisNames2D = { "x-Index", "Second Cluster Energy (GeV)" };
+        String[] yAxisNames2D = { "y-Index", "First Cluster Energy (GeV)" };
+        
+        // Define the 1D trigger plot names for elastics.
+        String[] plotNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
+        String[] displayNamesElastic1D = { "Cluster Hit Count", "Cluster Seed Energy", "Cluster Total Energy" };
+        String[] xAxisNamesElastic1D = { "Hit Count", "Seed Energy (GeV)", "Total Energy (GeV)" };
+        String yAxisNameElastic1D = "Count";
+        
+        // Define the 2D trigger plot names for elastics.
+        String[] plotNamesElastic2D = { "Cluster Seed" };
+        String[] displayNamesElastic2D = { "Cluster Seed Distribution" };
+        String[] xAxisNamesElastic2D = { "x-Index" };
+        String[] yAxisNamesElastic2D = { "y-Index" };
+        
+        // Define the Møller, trident, and elastic prefixes.
+        String allPrefix = "All Trigger Plots/Pair Plots/";
+        String møllerPrefix = "Møller Trigger Plots/Pair Plots/";
+        String tridentPrefix = "Trident Trigger Plots/Pair Plots/";
+        String elasticPrefix = "Elastic Trigger Plots/Singles Plots/";
+        String allSinglesPrefix = "All Trigger Plots/Singles Plots/";
+        
+        // Define the plot type prefix.
+        String allTypeName = "All Pairs - ";
+        String møllerTypeName = "Møller - ";
+        String tridentTypeName = "Trident - ";
+        String elasticTypeName = "Elastic - ";
+        String allSinglesTypeName = "All Singles - ";
+        
+        // Define the plot type colors.
+        ColorStyle allColor = PlotsFormatter.ColorStyle.GREY;
+        ColorStyle møllerColor = PlotsFormatter.ColorStyle.MS_BLUE;
+        ColorStyle tridentColor = PlotsFormatter.ColorStyle.MS_ORANGE;
+        ColorStyle elasticColor = PlotsFormatter.ColorStyle.MS_GREEN;
+        
+        // Create a plot formatting module.
+        PlotFormatModule module = new PlotFormatModule();
+        
+        // Get the histograms and add them to the module. Start with the
+        // trident and Møller plots.
+        for(int i = 0; i < plotNames1D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram1D allPlot = (IHistogram1D) tree.find(allPrefix + plotNames1D[i]);
+            IHistogram1D møllerPlot = (IHistogram1D) tree.find(møllerPrefix + plotNames1D[i]);
+            IHistogram1D tridentPlot = (IHistogram1D) tree.find(tridentPrefix + plotNames1D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNames1D[i], yAxisName1D, allTypeName + displayNames1D[i]);
+            FormattedPlot1D møllerFormattedPlot = new FormattedPlot1D(møllerPlot, møllerColor, xAxisNames1D[i], yAxisName1D, møllerTypeName + displayNames1D[i]);
+            FormattedPlot1D tridentFormattedPlot = new FormattedPlot1D(tridentPlot, tridentColor, xAxisNames1D[i], yAxisName1D, tridentTypeName + displayNames1D[i]);
+            
+            // Add them to the module.
+            module.addPlot1D(allFormattedPlot);
+            module.addPlot1D(møllerFormattedPlot);
+            module.addPlot1D(tridentFormattedPlot);
+        }
+        for(int i = 0; i < plotNames2D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNames2D[i]);
+            IHistogram2D møllerPlot = (IHistogram2D) tree.find(møllerPrefix + plotNames2D[i]);
+            IHistogram2D tridentPlot = (IHistogram2D) tree.find(tridentPrefix + plotNames2D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], allTypeName + displayNames2D[i]);
+            FormattedPlot2D møllerFormattedPlot = new FormattedPlot2D(møllerPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], møllerTypeName + displayNames2D[i]);
+            FormattedPlot2D tridentFormattedPlot = new FormattedPlot2D(tridentPlot, i == 0 ? true : false, xAxisNames2D[i], yAxisNames2D[i], tridentTypeName + displayNames2D[i]);
+            
+            // Add them to the module.
+            module.addPlot2D(allFormattedPlot);
+            module.addPlot2D(møllerFormattedPlot);
+            module.addPlot2D(tridentFormattedPlot);
+        }
+        
+        // Get the histograms for the elastic plots and add them to the module.
+        for(int i = 0; i < plotNamesElastic1D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram1D allPlot = (IHistogram1D) tree.find(allSinglesPrefix + plotNames1D[i]);
+            IHistogram1D elasticPlot = (IHistogram1D) tree.find(elasticPrefix + plotNames1D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot1D allFormattedPlot = new FormattedPlot1D(allPlot, allColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
+                    allSinglesTypeName + displayNamesElastic1D[i]);
+            FormattedPlot1D elasticFormattedPlot = new FormattedPlot1D(elasticPlot, elasticColor, xAxisNamesElastic1D[i], yAxisNameElastic1D,
+                    elasticTypeName + displayNamesElastic1D[i]);
+            
+            // Add them to the module.
+            module.addPlot1D(allFormattedPlot);
+            module.addPlot1D(elasticFormattedPlot);
+        }
+        for(int i = 0; i < plotNamesElastic2D.length; i++) {
+            // Get the Møller and trident plots.
+            IHistogram2D allPlot = (IHistogram2D) tree.find(allPrefix + plotNamesElastic2D[i]);
+            IHistogram2D elasticPlot = (IHistogram2D) tree.find(møllerPrefix + plotNamesElastic2D[i]);
+            
+            // Make a formatted plot for each.
+            FormattedPlot2D allFormattedPlot = new FormattedPlot2D(allPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
+                    allSinglesTypeName + plotNames2D[i]);
+            FormattedPlot2D elasticFormattedPlot = new FormattedPlot2D(elasticPlot, i == 0 ? true : false, xAxisNamesElastic2D[i], yAxisNamesElastic2D[i],
+                    elasticTypeName + displayNamesElastic2D[i]);
+            
+            // Add them to the module.
+            module.addPlot2D(allFormattedPlot);
+            module.addPlot2D(elasticFormattedPlot);
+        }
+        
+        // Add the MTE plots to the module.
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Energy Distribution"), elasticColor,
+                "Momentum (GeV)", "Count", "Elastic - Momentum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Elastic Event Tracks"), elasticColor,
+                "Tracks", "Count", "Elastic - Tracks in Event"));
+        
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Energy Sum Distribution"), møllerColor,
+                "Momentum Sum (GeV)", "Count", "Møller - Momentum Sum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Electron Energy Distribution"), møllerColor,
+                "Momentum (GeV)", "Count", "Møller - Momentum (Electron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Time Coincidence Distribution (All Møller Cuts)"), møllerColor,
+                "Time (ns)", "Count", "Møller - Time Coincidence"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Møller Event Tracks"), møllerColor,
+                "Tracks", "Count", "Møller - Tracks in Event"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Møller 2D Energy Distribution"), false,
+                "First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Møller - 2D Momentum Sum"));
+        
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Energy Sum Distribution"), tridentColor,
+                "Momentum Sum (GeV)", "Count", "Trident - Momentum Sum"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Electron Energy Distribution"), tridentColor,
+                "Momentum (GeV)", "Count", "Trident - Momentum (Electron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Positron Energy Distribution"), tridentColor,
+                "Momentum (GeV)", "Count", "Trident - Momentum (Positron)"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MTE Analysis/Trident Event Tracks"), tridentColor,
+                "Tracks", "Count", "Trident - Tracks in Event"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MTE Analysis/Trident 2D Energy Distribution"), false,
+                "First Track Momentum (GeV)", "Second Track Momentum (GeV)", "Trident - 2D Momentum Sum"));
+        
+        // Display the plots.
+        module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\TestPrint\\");
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/ParticleMCAnalysisPlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/ParticleMCAnalysisPlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/ParticleMCAnalysisPlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -13,43 +13,43 @@
 import org.hps.users.kmccarty.plots.PlotsFormatter.ColorStyle;
 
 public class ParticleMCAnalysisPlotsFormatter {
-	public static void main(String[] args) throws IllegalArgumentException, IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "moller-mc-out_triggerPlots.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Create a plot formatting module.
-		PlotFormatModule module = new PlotFormatModule();
-		
-		// Define the plot color.
-		ColorStyle plotColor = ColorStyle.MS_BLUE;
-		
-		// Define the plots to be read.
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron Energy Distribution"),
-				plotColor, "Electron Energy (GeV)", "Count", "Electron Energy Distribution"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron\\Electron Momentum Sum Distribution"),
-				plotColor, "Momentum Sum (GeV)", "Count", "Momentum Sum Distribution"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron\\Electron Pair Angle Distribution"),
-				plotColor, "Momentum Sum (GeV)", "Count", "Pair Angle Distribution"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle x-Momentum Distribution"),
-				plotColor, "Momentum (GeV)", "Count", "Particle x-Momentum Distribution"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle y-Momentum Distribution"),
-				plotColor, "Momentum (GeV)", "Count", "Particle y-Momentum Distribution"));
-		module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle z-Momentum Distribution"),
-				plotColor, "Momentum (GeV)", "Count", "Particle z-Momentum Distribution"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MC Analysis/Electron\\Electron 2D Momentum Distribution"),
-				true, "Particle 1 Momentum (GeV)", "Particle 2 Momentum (GeV)", "2D Momentum Sum Distribution"));
-		module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MC Analysis/Particle Momentum Distribution"),
-				true, "px (GeV)", "py (GeV)", "Particle x/y Momentum Distribution"));
-		
-		// Display the plots.
-		module.displayPlots();
-	}
+    public static void main(String[] args) throws IllegalArgumentException, IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "moller-mc-out_triggerPlots.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Create a plot formatting module.
+        PlotFormatModule module = new PlotFormatModule();
+        
+        // Define the plot color.
+        ColorStyle plotColor = ColorStyle.MS_BLUE;
+        
+        // Define the plots to be read.
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron Energy Distribution"),
+                plotColor, "Electron Energy (GeV)", "Count", "Electron Energy Distribution"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron\\Electron Momentum Sum Distribution"),
+                plotColor, "Momentum Sum (GeV)", "Count", "Momentum Sum Distribution"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Electron\\Electron Pair Angle Distribution"),
+                plotColor, "Momentum Sum (GeV)", "Count", "Pair Angle Distribution"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle x-Momentum Distribution"),
+                plotColor, "Momentum (GeV)", "Count", "Particle x-Momentum Distribution"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle y-Momentum Distribution"),
+                plotColor, "Momentum (GeV)", "Count", "Particle y-Momentum Distribution"));
+        module.addPlot1D(new FormattedPlot1D((IHistogram1D) tree.find("MC Analysis/Particle z-Momentum Distribution"),
+                plotColor, "Momentum (GeV)", "Count", "Particle z-Momentum Distribution"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MC Analysis/Electron\\Electron 2D Momentum Distribution"),
+                true, "Particle 1 Momentum (GeV)", "Particle 2 Momentum (GeV)", "2D Momentum Sum Distribution"));
+        module.addPlot2D(new FormattedPlot2D((IHistogram2D) tree.find("MC Analysis/Particle Momentum Distribution"),
+                true, "px (GeV)", "py (GeV)", "Particle x/y Momentum Distribution"));
+        
+        // Display the plots.
+        module.displayPlots();
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/RafoTridentFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/RafoTridentFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/RafoTridentFormatter.java	Wed Apr 27 11:11:32 2016
@@ -13,101 +13,101 @@
 import hep.aida.ITree;
 
 public class RafoTridentFormatter {
-	/**
-	 * Loads all plots in a file and formats them according to the
-	 * indicated style.
-	 * @param args - Unused default executable parameter.
-	 * @throws IOException Occurs if there is an issue opening the file.
-	 */
-	public static void main(String[] args) throws IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "mte-out.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Declare the histogram names.
-		String energySumName = "Energy Sum";
-		String timeCoincidenceName = "Time Coincidence";
-		String timeEnergy2DName = "Cluster Time vs. Cluster Energy";
-		String hCoplanaritySum2DName = "Hardware Coplanarity vs. Energy Sum";
-		String coplanaritySum2DName = "Calculated Coplanarity vs. Energy Sum";
-		String energySum2DName = "Top Cluster Energy vs. Bottom Cluster Energy";
-		String fiducial = " (Fiducial Region)";
-		
-		// Get the histograms.
-		IHistogram1D[] energySum = {
-				(IHistogram1D) tree.find("Trident/" + energySumName),
-				(IHistogram1D) tree.find("Trident/" + energySumName + fiducial)
-		};
-		IHistogram1D[] timeCoincidence = {
-				(IHistogram1D) tree.find("Trident/" + timeCoincidenceName),
-				(IHistogram1D) tree.find("Trident/" + timeCoincidenceName + fiducial)
-		};
-		IHistogram2D[] coplanaritySum = {
-				(IHistogram2D) tree.find("Trident/" + coplanaritySum2DName),
-				(IHistogram2D) tree.find("Trident/" + coplanaritySum2DName + fiducial)
-		};
-		IHistogram2D[] hcoplanaritySum = {
-				(IHistogram2D) tree.find("Trident/" + hCoplanaritySum2DName),
-				(IHistogram2D) tree.find("Trident/" + hCoplanaritySum2DName + fiducial)
-		};
-		IHistogram2D[] energySum2D = {
-				(IHistogram2D) tree.find("Trident/" + energySum2DName),
-				(IHistogram2D) tree.find("Trident/" + energySum2DName + fiducial)
-		};
-		IHistogram2D[] timeEnergy = {
-				(IHistogram2D) tree.find("Trident/" + timeEnergy2DName),
-				(IHistogram2D) tree.find("Trident/" + timeEnergy2DName + fiducial)
-		};
-		
-		// Define the scaling factors for each plot.
-		double scaleFactor = 19000.0 / 9736969.0;
-		
-		// Define the plot titles and arrays for 1D plots.
-		IHistogram1D[][] plots = { energySum, timeCoincidence  };
-		String titles[] = { energySumName, timeCoincidenceName, coplanaritySum2DName, hCoplanaritySum2DName, energySum2DName, timeEnergy2DName };
-		String[] xTitles = { "Energy (GeV)", "Time Difference (ns)" };
-		String yTitle = "Rate (Hz)";
-		
-		// Define the plot titles and arrays for 2D plots.
-		IHistogram2D[][] plots2D = { coplanaritySum, hcoplanaritySum, energySum2D, timeEnergy };
-		String[] titles2D = { coplanaritySum2DName, hCoplanaritySum2DName, energySum2DName, timeEnergy2DName };
-		String[] xTitles2D = { "Coplanarity (Degrees)", "Coplanarity (Degrees)", "Top Cluster Energy (GeV)", "Time Coincidence (ns)" };
-		String[] yTitles2D = { "Energy Sum (GeV)", "Energy Sum (GeV)", "Bottom Cluster Energy (GeV)", "Energy Sum (GeV)" };
-		String zTitle2D = "Rate (Hz)";
-		
-		// Create a plot formatting module.
-		PlotFormatModule module = new PlotFormatModule();
-		
-		// Define the plot color.
-		ColorStyle plotColor = ColorStyle.MS_BLUE;
-		
-		// Define the plots to be read.
-		for(int i = 0; i < plots.length; i++) {
-			plots[i][0].scale(scaleFactor);
-			plots[i][1].scale(scaleFactor);
-			module.addPlot1D(new FormattedPlot1D(plots[i][0], plotColor, xTitles[i], yTitle, titles[i]));
-			module.addPlot1D(new FormattedPlot1D(plots[i][1], plotColor, xTitles[i],  yTitle, titles[i] + fiducial));
-		}
-		for(int i = 0; i < plots2D.length; i++) {
-			plots2D[i][0].scale(scaleFactor);
-			plots2D[i][1].scale(scaleFactor);
-			module.addPlot2D(new FormattedPlot2D(plots2D[i][0], false, xTitles2D[i], yTitles2D[i], titles2D[i]));
-			module.addPlot2D(new FormattedPlot2D(plots2D[i][1], false, xTitles2D[i], yTitles2D[i], titles2D[i] + fiducial));
-		}
-		
-		// Display the plots.
-		//module.displayPlots();
-		module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\run-5772\\RafoPlots\\");
-		module.exportPlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\run-5772\\RafoPlots\\");
-		
-		// Close the tree.
-		tree.close();
-	}
+    /**
+     * Loads all plots in a file and formats them according to the
+     * indicated style.
+     * @param args - Unused default executable parameter.
+     * @throws IOException Occurs if there is an issue opening the file.
+     */
+    public static void main(String[] args) throws IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "mte-out.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Declare the histogram names.
+        String energySumName = "Energy Sum";
+        String timeCoincidenceName = "Time Coincidence";
+        String timeEnergy2DName = "Cluster Time vs. Cluster Energy";
+        String hCoplanaritySum2DName = "Hardware Coplanarity vs. Energy Sum";
+        String coplanaritySum2DName = "Calculated Coplanarity vs. Energy Sum";
+        String energySum2DName = "Top Cluster Energy vs. Bottom Cluster Energy";
+        String fiducial = " (Fiducial Region)";
+        
+        // Get the histograms.
+        IHistogram1D[] energySum = {
+                (IHistogram1D) tree.find("Trident/" + energySumName),
+                (IHistogram1D) tree.find("Trident/" + energySumName + fiducial)
+        };
+        IHistogram1D[] timeCoincidence = {
+                (IHistogram1D) tree.find("Trident/" + timeCoincidenceName),
+                (IHistogram1D) tree.find("Trident/" + timeCoincidenceName + fiducial)
+        };
+        IHistogram2D[] coplanaritySum = {
+                (IHistogram2D) tree.find("Trident/" + coplanaritySum2DName),
+                (IHistogram2D) tree.find("Trident/" + coplanaritySum2DName + fiducial)
+        };
+        IHistogram2D[] hcoplanaritySum = {
+                (IHistogram2D) tree.find("Trident/" + hCoplanaritySum2DName),
+                (IHistogram2D) tree.find("Trident/" + hCoplanaritySum2DName + fiducial)
+        };
+        IHistogram2D[] energySum2D = {
+                (IHistogram2D) tree.find("Trident/" + energySum2DName),
+                (IHistogram2D) tree.find("Trident/" + energySum2DName + fiducial)
+        };
+        IHistogram2D[] timeEnergy = {
+                (IHistogram2D) tree.find("Trident/" + timeEnergy2DName),
+                (IHistogram2D) tree.find("Trident/" + timeEnergy2DName + fiducial)
+        };
+        
+        // Define the scaling factors for each plot.
+        double scaleFactor = 19000.0 / 9736969.0;
+        
+        // Define the plot titles and arrays for 1D plots.
+        IHistogram1D[][] plots = { energySum, timeCoincidence  };
+        String titles[] = { energySumName, timeCoincidenceName, coplanaritySum2DName, hCoplanaritySum2DName, energySum2DName, timeEnergy2DName };
+        String[] xTitles = { "Energy (GeV)", "Time Difference (ns)" };
+        String yTitle = "Rate (Hz)";
+        
+        // Define the plot titles and arrays for 2D plots.
+        IHistogram2D[][] plots2D = { coplanaritySum, hcoplanaritySum, energySum2D, timeEnergy };
+        String[] titles2D = { coplanaritySum2DName, hCoplanaritySum2DName, energySum2DName, timeEnergy2DName };
+        String[] xTitles2D = { "Coplanarity (Degrees)", "Coplanarity (Degrees)", "Top Cluster Energy (GeV)", "Time Coincidence (ns)" };
+        String[] yTitles2D = { "Energy Sum (GeV)", "Energy Sum (GeV)", "Bottom Cluster Energy (GeV)", "Energy Sum (GeV)" };
+        String zTitle2D = "Rate (Hz)";
+        
+        // Create a plot formatting module.
+        PlotFormatModule module = new PlotFormatModule();
+        
+        // Define the plot color.
+        ColorStyle plotColor = ColorStyle.MS_BLUE;
+        
+        // Define the plots to be read.
+        for(int i = 0; i < plots.length; i++) {
+            plots[i][0].scale(scaleFactor);
+            plots[i][1].scale(scaleFactor);
+            module.addPlot1D(new FormattedPlot1D(plots[i][0], plotColor, xTitles[i], yTitle, titles[i]));
+            module.addPlot1D(new FormattedPlot1D(plots[i][1], plotColor, xTitles[i],  yTitle, titles[i] + fiducial));
+        }
+        for(int i = 0; i < plots2D.length; i++) {
+            plots2D[i][0].scale(scaleFactor);
+            plots2D[i][1].scale(scaleFactor);
+            module.addPlot2D(new FormattedPlot2D(plots2D[i][0], false, xTitles2D[i], yTitles2D[i], titles2D[i]));
+            module.addPlot2D(new FormattedPlot2D(plots2D[i][1], false, xTitles2D[i], yTitles2D[i], titles2D[i] + fiducial));
+        }
+        
+        // Display the plots.
+        //module.displayPlots();
+        module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\run-5772\\RafoPlots\\");
+        module.exportPlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\run-5772\\RafoPlots\\");
+        
+        // Close the tree.
+        tree.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/SingleTriggerPlotsFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/SingleTriggerPlotsFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/SingleTriggerPlotsFormatter.java	Wed Apr 27 11:11:32 2016
@@ -13,151 +13,151 @@
 import hep.aida.ITree;
 
 public class SingleTriggerPlotsFormatter {
-	
-	public static void main(String[] args) throws IllegalArgumentException, IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "trident-readout-full.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Define plots variables.
-		int UNCUT     = 0;
-		int TRIGGERED = 1;
-		String[] plotsDir = { "NoCuts/", "PassedAll/" };
-		int PLOT_HIT_COUNT      = 0;
-		int PLOT_SEED_ENERGY    = 1;
-		int PLOT_CLUSTER_ENERGY = 2;
-		int PLOT_COPLANARITY    = 3;
-		int PLOT_ENERGY_SUM     = 4;
-		int PLOT_ENERGY_DIFF    = 5;
-		int PLOT_ENERGY_SLOPE   = 6;
-		int PLOT_SEED_DIST      = 0;
-		int PLOT_ENERGY_SUM_2D  = 1;
-		
-		// Define the internal plot names.
-		String[] plotNameInternal1D = new String[7];
-		String[] plotNameInternal2D = new String[2];
-		plotNameInternal1D[PLOT_HIT_COUNT]      = "Cluster Hit Count";
-		plotNameInternal1D[PLOT_SEED_ENERGY]    = "Cluster Seed Energy";
-		plotNameInternal1D[PLOT_CLUSTER_ENERGY] = "Cluster Total Energy";
-		plotNameInternal1D[PLOT_COPLANARITY]    = "Pair Coplanarity";
-		plotNameInternal1D[PLOT_ENERGY_SUM]     = "Pair Energy Sum";
-		plotNameInternal1D[PLOT_ENERGY_DIFF]    = "Pair Energy Difference";
-		plotNameInternal1D[PLOT_ENERGY_SLOPE]   = "Pair Energy Slope";
-		plotNameInternal2D[PLOT_SEED_DIST]      = "Cluster Seed";
-		plotNameInternal2D[PLOT_ENERGY_SUM_2D]  = "Pair Energy Sum 2D";
-		
-		// Define the plot display names.
-		String[] plotName1D = new String[7];
-		String[] plotName2D = new String[2];
-		for(int j = 0; j < plotNameInternal1D.length; j++) {
-			plotName1D[j] = plotNameInternal1D[j];
-		}
-		for(int j = 0; j < plotNameInternal2D.length; j++) {
-			plotName2D[j] = plotNameInternal2D[j];
-		}
-		plotName1D[PLOT_ENERGY_SUM]    = "1D Pair Energy Sum";
-		plotName2D[PLOT_SEED_DIST]     = "Cluster Seed Distribution";
-		plotName2D[PLOT_ENERGY_SUM_2D] = "2D Pair Energy Sum";
-		
-		String[] xTitles1D = new String[plotName1D.length];
-		String[] xTitles2D = new String[plotName2D.length];
-		xTitles1D[PLOT_HIT_COUNT]      = "Hit Count";
-		xTitles1D[PLOT_SEED_ENERGY]    = "Seed Energy (GeV)";
-		xTitles1D[PLOT_CLUSTER_ENERGY] = "Cluster Energy (GeV)";
-		xTitles1D[PLOT_COPLANARITY]    = "Coplanarity Angle (Degrees)";
-		xTitles1D[PLOT_ENERGY_SUM]     = "Energy Sum (GeV)";
-		xTitles1D[PLOT_ENERGY_DIFF]    = "Energy Difference (GeV)";
-		xTitles1D[PLOT_ENERGY_SLOPE]   = "Energy Slope (GeV)";
-		xTitles2D[PLOT_SEED_DIST]      = "x-Index";
-		xTitles2D[PLOT_ENERGY_SUM_2D]  = "First Cluster Energy (GeV)";
-		String yTitle1D = "Count";
-		String[] yTitles2D = new String[plotName2D.length];
-		yTitles2D[PLOT_SEED_DIST]      = "y-Index";
-		yTitles2D[PLOT_ENERGY_SUM_2D]  = "Second Cluster Energy (GeV)";
-		
-		// Define axis ranges.
-		double[] axisRanges1D = new double[plotName1D.length];
-		axisRanges1D[PLOT_HIT_COUNT]      = -1;
-		axisRanges1D[PLOT_SEED_ENERGY]    = 1.1;
-		axisRanges1D[PLOT_CLUSTER_ENERGY] = 1.1;
-		axisRanges1D[PLOT_COPLANARITY]    = 180;
-		axisRanges1D[PLOT_ENERGY_SUM]     = 2.2;
-		axisRanges1D[PLOT_ENERGY_DIFF]    = 1.1;
-		axisRanges1D[PLOT_ENERGY_SLOPE]   = 2.4;
-		double[] xAxisRanges2D = new double[plotName2D.length];
-		double[] yAxisRanges2D = new double[plotName2D.length];
-		xAxisRanges2D[PLOT_SEED_DIST]      = -1;
-		xAxisRanges2D[PLOT_ENERGY_SUM_2D]  = 1.1;
-		yAxisRanges2D[PLOT_SEED_DIST]      = -1;
-		yAxisRanges2D[PLOT_ENERGY_SUM_2D]  = 1.1;
-		
-		// Define the plot names.
-		String[][] plotLocations1D = new String[plotsDir.length][plotNameInternal1D.length];
-		String[][] plotLocations2D = new String[plotsDir.length][plotNameInternal2D.length];
-		for(int i = 0; i < plotsDir.length; i++) {
-			for(int j = 0; j < plotNameInternal1D.length; j++) {
-				plotLocations1D[i][j] = plotsDir[i] + plotNameInternal1D[j];
-			}
-		}
-		for(int i = 0; i < plotsDir.length; i++) {
-			for(int j = 0; j < plotNameInternal2D.length; j++) {
-				plotLocations2D[i][j] = plotsDir[i] + plotNameInternal2D[j];
-			}
-		}
-		
-		// Create a plot formatting module.
-		PlotFormatModule module = new PlotFormatModule();
-		
-		// Load the plot objects.
-		for(int i = 0; i < plotName1D.length; i++) {
-			// Get the uncut and triggered plots.
-			IHistogram1D uncutPlot = (IHistogram1D) tree.find(plotLocations1D[UNCUT][i]);
-			IHistogram1D triggeredPlot = (IHistogram1D) tree.find(plotLocations1D[TRIGGERED][i] + " (Passed All Cuts)");
-			
-			// Make a formatted plot for each.
-			FormattedPlot1D uncutFormattedPlot;
-			FormattedPlot1D triggeredFormattedPlot;
-			if(axisRanges1D[i] != -1) {
-				uncutFormattedPlot = new FormattedPlot1D(uncutPlot, PlotsFormatter.ColorStyle.GREY, xTitles1D[i], yTitle1D, plotName1D[i] + " (No Cuts)", axisRanges1D[i]);
-				triggeredFormattedPlot = new FormattedPlot1D(triggeredPlot, PlotsFormatter.ColorStyle.MS_GREEN, xTitles1D[i], yTitle1D, plotName1D[i] + " (Triggered)", axisRanges1D[i]);
-			} else {
-				uncutFormattedPlot = new FormattedPlot1D(uncutPlot, PlotsFormatter.ColorStyle.GREY, xTitles1D[i], yTitle1D, plotName1D[i] + " (No Cuts)");
-				triggeredFormattedPlot = new FormattedPlot1D(triggeredPlot, PlotsFormatter.ColorStyle.MS_GREEN, xTitles1D[i], yTitle1D, plotName1D[i] + " (Triggered)");
-			}
-			
-			// Add the plots to the module.
-			module.addPlot1D(uncutFormattedPlot);
-			module.addPlot1D(triggeredFormattedPlot);
-		}
-		for(int i = 0; i < plotName2D.length; i++) {
-			// Get the uncut and triggered plots.
-			IHistogram2D uncutPlot = (IHistogram2D) tree.find(plotLocations2D[UNCUT][i]);
-			IHistogram2D triggeredPlot = (IHistogram2D) tree.find(plotLocations2D[TRIGGERED][i] + " (Passed All Cuts)");
-			
-			// Make a formatted plot for each.
-			FormattedPlot2D uncutFormattedPlot;
-			FormattedPlot2D triggeredFormattedPlot;
-			if(xAxisRanges2D[i] != -1) {
-				uncutFormattedPlot = new FormattedPlot2D(uncutPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (No Cuts)", xAxisRanges2D[i], yAxisRanges2D[i]);
-				triggeredFormattedPlot = new FormattedPlot2D(triggeredPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (Triggered)", xAxisRanges2D[i], yAxisRanges2D[i]);
-			} else {
-				uncutFormattedPlot = new FormattedPlot2D(uncutPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (No Cuts)");
-				triggeredFormattedPlot = new FormattedPlot2D(triggeredPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (Triggered)");
-			}
-			
-			// Add the plots to the module.
-			module.addPlot2D(uncutFormattedPlot);
-			module.addPlot2D(triggeredFormattedPlot);
-		}
-		
-		// Save the plots.
-		module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\MonteCarlo\\Trident\\Trigger\\");
-	}
+    
+    public static void main(String[] args) throws IllegalArgumentException, IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "trident-readout-full.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Define plots variables.
+        int UNCUT     = 0;
+        int TRIGGERED = 1;
+        String[] plotsDir = { "NoCuts/", "PassedAll/" };
+        int PLOT_HIT_COUNT      = 0;
+        int PLOT_SEED_ENERGY    = 1;
+        int PLOT_CLUSTER_ENERGY = 2;
+        int PLOT_COPLANARITY    = 3;
+        int PLOT_ENERGY_SUM     = 4;
+        int PLOT_ENERGY_DIFF    = 5;
+        int PLOT_ENERGY_SLOPE   = 6;
+        int PLOT_SEED_DIST      = 0;
+        int PLOT_ENERGY_SUM_2D  = 1;
+        
+        // Define the internal plot names.
+        String[] plotNameInternal1D = new String[7];
+        String[] plotNameInternal2D = new String[2];
+        plotNameInternal1D[PLOT_HIT_COUNT]      = "Cluster Hit Count";
+        plotNameInternal1D[PLOT_SEED_ENERGY]    = "Cluster Seed Energy";
+        plotNameInternal1D[PLOT_CLUSTER_ENERGY] = "Cluster Total Energy";
+        plotNameInternal1D[PLOT_COPLANARITY]    = "Pair Coplanarity";
+        plotNameInternal1D[PLOT_ENERGY_SUM]     = "Pair Energy Sum";
+        plotNameInternal1D[PLOT_ENERGY_DIFF]    = "Pair Energy Difference";
+        plotNameInternal1D[PLOT_ENERGY_SLOPE]   = "Pair Energy Slope";
+        plotNameInternal2D[PLOT_SEED_DIST]      = "Cluster Seed";
+        plotNameInternal2D[PLOT_ENERGY_SUM_2D]  = "Pair Energy Sum 2D";
+        
+        // Define the plot display names.
+        String[] plotName1D = new String[7];
+        String[] plotName2D = new String[2];
+        for(int j = 0; j < plotNameInternal1D.length; j++) {
+            plotName1D[j] = plotNameInternal1D[j];
+        }
+        for(int j = 0; j < plotNameInternal2D.length; j++) {
+            plotName2D[j] = plotNameInternal2D[j];
+        }
+        plotName1D[PLOT_ENERGY_SUM]    = "1D Pair Energy Sum";
+        plotName2D[PLOT_SEED_DIST]     = "Cluster Seed Distribution";
+        plotName2D[PLOT_ENERGY_SUM_2D] = "2D Pair Energy Sum";
+        
+        String[] xTitles1D = new String[plotName1D.length];
+        String[] xTitles2D = new String[plotName2D.length];
+        xTitles1D[PLOT_HIT_COUNT]      = "Hit Count";
+        xTitles1D[PLOT_SEED_ENERGY]    = "Seed Energy (GeV)";
+        xTitles1D[PLOT_CLUSTER_ENERGY] = "Cluster Energy (GeV)";
+        xTitles1D[PLOT_COPLANARITY]    = "Coplanarity Angle (Degrees)";
+        xTitles1D[PLOT_ENERGY_SUM]     = "Energy Sum (GeV)";
+        xTitles1D[PLOT_ENERGY_DIFF]    = "Energy Difference (GeV)";
+        xTitles1D[PLOT_ENERGY_SLOPE]   = "Energy Slope (GeV)";
+        xTitles2D[PLOT_SEED_DIST]      = "x-Index";
+        xTitles2D[PLOT_ENERGY_SUM_2D]  = "First Cluster Energy (GeV)";
+        String yTitle1D = "Count";
+        String[] yTitles2D = new String[plotName2D.length];
+        yTitles2D[PLOT_SEED_DIST]      = "y-Index";
+        yTitles2D[PLOT_ENERGY_SUM_2D]  = "Second Cluster Energy (GeV)";
+        
+        // Define axis ranges.
+        double[] axisRanges1D = new double[plotName1D.length];
+        axisRanges1D[PLOT_HIT_COUNT]      = -1;
+        axisRanges1D[PLOT_SEED_ENERGY]    = 1.1;
+        axisRanges1D[PLOT_CLUSTER_ENERGY] = 1.1;
+        axisRanges1D[PLOT_COPLANARITY]    = 180;
+        axisRanges1D[PLOT_ENERGY_SUM]     = 2.2;
+        axisRanges1D[PLOT_ENERGY_DIFF]    = 1.1;
+        axisRanges1D[PLOT_ENERGY_SLOPE]   = 2.4;
+        double[] xAxisRanges2D = new double[plotName2D.length];
+        double[] yAxisRanges2D = new double[plotName2D.length];
+        xAxisRanges2D[PLOT_SEED_DIST]      = -1;
+        xAxisRanges2D[PLOT_ENERGY_SUM_2D]  = 1.1;
+        yAxisRanges2D[PLOT_SEED_DIST]      = -1;
+        yAxisRanges2D[PLOT_ENERGY_SUM_2D]  = 1.1;
+        
+        // Define the plot names.
+        String[][] plotLocations1D = new String[plotsDir.length][plotNameInternal1D.length];
+        String[][] plotLocations2D = new String[plotsDir.length][plotNameInternal2D.length];
+        for(int i = 0; i < plotsDir.length; i++) {
+            for(int j = 0; j < plotNameInternal1D.length; j++) {
+                plotLocations1D[i][j] = plotsDir[i] + plotNameInternal1D[j];
+            }
+        }
+        for(int i = 0; i < plotsDir.length; i++) {
+            for(int j = 0; j < plotNameInternal2D.length; j++) {
+                plotLocations2D[i][j] = plotsDir[i] + plotNameInternal2D[j];
+            }
+        }
+        
+        // Create a plot formatting module.
+        PlotFormatModule module = new PlotFormatModule();
+        
+        // Load the plot objects.
+        for(int i = 0; i < plotName1D.length; i++) {
+            // Get the uncut and triggered plots.
+            IHistogram1D uncutPlot = (IHistogram1D) tree.find(plotLocations1D[UNCUT][i]);
+            IHistogram1D triggeredPlot = (IHistogram1D) tree.find(plotLocations1D[TRIGGERED][i] + " (Passed All Cuts)");
+            
+            // Make a formatted plot for each.
+            FormattedPlot1D uncutFormattedPlot;
+            FormattedPlot1D triggeredFormattedPlot;
+            if(axisRanges1D[i] != -1) {
+                uncutFormattedPlot = new FormattedPlot1D(uncutPlot, PlotsFormatter.ColorStyle.GREY, xTitles1D[i], yTitle1D, plotName1D[i] + " (No Cuts)", axisRanges1D[i]);
+                triggeredFormattedPlot = new FormattedPlot1D(triggeredPlot, PlotsFormatter.ColorStyle.MS_GREEN, xTitles1D[i], yTitle1D, plotName1D[i] + " (Triggered)", axisRanges1D[i]);
+            } else {
+                uncutFormattedPlot = new FormattedPlot1D(uncutPlot, PlotsFormatter.ColorStyle.GREY, xTitles1D[i], yTitle1D, plotName1D[i] + " (No Cuts)");
+                triggeredFormattedPlot = new FormattedPlot1D(triggeredPlot, PlotsFormatter.ColorStyle.MS_GREEN, xTitles1D[i], yTitle1D, plotName1D[i] + " (Triggered)");
+            }
+            
+            // Add the plots to the module.
+            module.addPlot1D(uncutFormattedPlot);
+            module.addPlot1D(triggeredFormattedPlot);
+        }
+        for(int i = 0; i < plotName2D.length; i++) {
+            // Get the uncut and triggered plots.
+            IHistogram2D uncutPlot = (IHistogram2D) tree.find(plotLocations2D[UNCUT][i]);
+            IHistogram2D triggeredPlot = (IHistogram2D) tree.find(plotLocations2D[TRIGGERED][i] + " (Passed All Cuts)");
+            
+            // Make a formatted plot for each.
+            FormattedPlot2D uncutFormattedPlot;
+            FormattedPlot2D triggeredFormattedPlot;
+            if(xAxisRanges2D[i] != -1) {
+                uncutFormattedPlot = new FormattedPlot2D(uncutPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (No Cuts)", xAxisRanges2D[i], yAxisRanges2D[i]);
+                triggeredFormattedPlot = new FormattedPlot2D(triggeredPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (Triggered)", xAxisRanges2D[i], yAxisRanges2D[i]);
+            } else {
+                uncutFormattedPlot = new FormattedPlot2D(uncutPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (No Cuts)");
+                triggeredFormattedPlot = new FormattedPlot2D(triggeredPlot, true, xTitles2D[i], yTitles2D[i], plotName2D[i] + " (Triggered)");
+            }
+            
+            // Add the plots to the module.
+            module.addPlot2D(uncutFormattedPlot);
+            module.addPlot2D(triggeredFormattedPlot);
+        }
+        
+        // Save the plots.
+        module.savePlots("C:\\Users\\Kyle\\Desktop\\EnergyShift\\MonteCarlo\\Trident\\Trigger\\");
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TridentTrackFormatter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TridentTrackFormatter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TridentTrackFormatter.java	Wed Apr 27 11:11:32 2016
@@ -16,187 +16,187 @@
 import hep.aida.ref.plotter.PlotterRegion;
 
 public class TridentTrackFormatter {
-	/**
-	 * Loads all plots in a file and formats them according to the
-	 * indicated style.
-	 * @param args - Unused default executable parameter.
-	 * @throws IOException Occurs if there is an issue opening the file.
-	 */
-	public static void main(String[] args) throws IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\tmp\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String plotFile = rootDir + "trident-out.aida";
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree tree = af.createTreeFactory().create(plotFile);
-		if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		
-		// Declare the histogram names.
-		String trackName = "Tracks in Event (All)";
-		String posTrackName = "Tracks in Event (Positive)";
-		String negTrackName = "Tracks in Event (Negative)";
-		String posMomentumName = "Momentum (Positive)";
-		String negMomentumName = "Momentum (Negative)";
-		String energySumName = "Energy Sum";
-		String momentumSumName = "Momentum Sum";
-		String energyMomentumDiffName = "Energy-Momentum Difference";
-		String invariantMassName = "Invariant Mass";
-		String energySum2DName = "2D Energy Sum";
-		String momentumSum2DName = "2D Momentum Sum";
-		String positionName = "Track Cluster Position";
-		
-		// Get the histograms.
-		IHistogram1D[] tracks = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + trackName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + trackName)
-		};
-		IHistogram1D[] posTracks = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + posTrackName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + posTrackName)
-		};
-		IHistogram1D[] negTracks = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + negTrackName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + negTrackName)
-		};
-		IHistogram1D[] posMomentum = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + posMomentumName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + posMomentumName)
-		};
-		IHistogram1D[] negMomentum = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + negMomentumName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + negMomentumName)
-		};
-		IHistogram1D[] energySum = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + energySumName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + energySumName)
-		};
-		IHistogram1D[] momentumSum = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + momentumSumName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + momentumSumName)
-		};
-		IHistogram1D[] energyMomentumDiff = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + energyMomentumDiffName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + energyMomentumDiffName)
-		};
-		IHistogram1D[] invariantMass = {
-				(IHistogram1D) tree.find("Trident Analysis/All/" + invariantMassName),
-				(IHistogram1D) tree.find("Trident Analysis/Cluster/" + invariantMassName)
-		};
-		IHistogram2D[] energySum2D = {
-				(IHistogram2D) tree.find("Trident Analysis/All/" + energySum2DName),
-				(IHistogram2D) tree.find("Trident Analysis/Cluster/" + energySum2DName)
-		};
-		IHistogram2D[] momentumSum2D = {
-				(IHistogram2D) tree.find("Trident Analysis/All/" + momentumSum2DName),
-				(IHistogram2D) tree.find("Trident Analysis/Cluster/" + momentumSum2DName)
-		};
-		IHistogram2D[] position = {
-				(IHistogram2D) tree.find("Trident Analysis/All/" + positionName),
-				(IHistogram2D) tree.find("Trident Analysis/Cluster/" + positionName)
-		};
-		
-		// Re-bin the histograms to have 5-times larger bins. First,
-		// get the bin count and upper and lower bounds of the plot.
-		int bins = invariantMass[0].axis().bins();
-		double low = invariantMass[0].axis().binLowerEdge(0);
-		double high = invariantMass[0].axis().binUpperEdge(invariantMass[0].axis().bins() - 1);
-		
-		// Create new plots with the larger bin sizes.
-		AIDA aida = AIDA.defaultInstance();
-		IHistogram1D[] newPlot = new IHistogram1D[2];
-		newPlot[0] = aida.histogram1D(invariantMassName, bins / 5, low, high);
-		newPlot[1] = aida.histogram1D("Cluster " + invariantMassName, bins / 5, low, high);
-		
-		// Populate the new plots with the data from the old ones.
-		for(int j = 0; j < 2; j++) {
-			for(int i = 0; i < bins; i++) {
-				int entries = invariantMass[j].binEntries(i);
-				double center = invariantMass[j].axis().binCenter(i);
-				for(int k = 0; k < entries; k++) {
-					newPlot[j].fill(center);
-				}
-			}
-		}
-		
-		// Replace the old plots.
-		invariantMass = newPlot;
-		
-		// Define the scaling factors for each plot.
-		double scaleFactor = 1;
-		
-		// Define the plot titles and arrays for 1D plots.
-		IHistogram[][] plots = { tracks, posTracks, negTracks, posMomentum, negMomentum, energySum, momentumSum, energyMomentumDiff, invariantMass };
-		String[] titles = { trackName, posTrackName, negTrackName, posMomentumName, negMomentumName, energySumName, momentumSumName,
-				energyMomentumDiffName, invariantMassName };
-		String[] xTitles = { "Tracks", "Tracks", "Tracks", "Momentum (GeV)", "Momentum (GeV)", "Energy Sum (GeV)", "Momentum Sum (GeV)",
-				"|E_Cluster - P_Track| (GeV)", "Invariant Mass (GeV)" };
-		String yTitle = "Count";
-		
-		// Define the plot titles and arrays for 2D plots.
-		IHistogram2D[][] plots2D = { energySum2D, momentumSum2D, position };
-		String[] titles2D = { energySum2DName, momentumSum2DName, positionName };
-		String[] xTitles2D = { "Positive Cluster Energy", "Positive Track Momentum", "x-Index" };
-		String[] yTitles2D = { "Negative Cluster Energy", "Negative Track Momentum", "y-Index" };
-		String zTitle2D = "Count";
-		
-		// Create a plotter factory.
-		IPlotterFactory plotterFactory = af.createPlotterFactory();
-		
-		// Format and display the basic histograms.
-		for(int i = 0; i < plots.length; i++) {
-			for(int j = 0; j < 2; j++) {
-				// Scale the histogram by the appropriate scaling factor.
-				plots[i][j].scale(1.0 / scaleFactor);
-				
-				// Create a plotter and plotting region for the plot.
-				IPlotter plotter = plotterFactory.create((j == 1 ? "Cluster " : "") + titles[i]);
-				plotter.createRegions(1);
-				plotter.region(0).plot(plots[i][j]);
-				
-				// Format the axis labels.
-				PlotterRegion region = (PlotterRegion) plotter.region(0);
-				region.getPlot().setTitle((j == 1 ? "Cluster " : "") + titles[i]);
-				region.getPlot().getXAxis().setLabel(xTitles[i]);
-				region.getPlot().getYAxis().setLabel(yTitle);
-				
-				// Format the fonts and general plot presentation.
-				PlotsFormatter.setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
-				
-				// Show the plot.
-				plotter.setParameter("plotterWidth", "2000");
-				plotter.setParameter("plotterHeight", "1200");
-				plotter.show();
-			}
-		}
-		
-		// Format and display the 2D histogram.
-		for(int i = 0; i < plots2D.length; i++) {
-			for(int j = 0; j < 2; j++) {
-				plots2D[i][j].scale(1.0 / scaleFactor);
-				IPlotter plotter2D = plotterFactory.create((j == 1 ? "Cluster " : "") + titles2D[i]);
-				plotter2D.createRegions(1);
-				plotter2D.region(0).plot(plots2D[i][j]);
-				
-				// Format the axis labels.
-				PlotterRegion region2D = (PlotterRegion) plotter2D.region(0);
-				region2D.getPlot().setTitle((j == 1 ? "Cluster " : "") + titles2D[i]);
-				region2D.getPlot().getXAxis().setLabel(xTitles2D[i]);
-				region2D.getPlot().getYAxis().setLabel(yTitles2D[i]);
-				
-				// Format the fonts and general plot presentation.
-				PlotsFormatter.setDefault2DStyle(region2D, true);
-				
-				// Show the plot.
-				plotter2D.setParameter("plotterWidth", "2000");
-				plotter2D.setParameter("plotterHeight", "1200");
-				plotter2D.show();
-			}
-		}
-		
-		// Close the tree.
-		tree.close();
-	}
+    /**
+     * Loads all plots in a file and formats them according to the
+     * indicated style.
+     * @param args - Unused default executable parameter.
+     * @throws IOException Occurs if there is an issue opening the file.
+     */
+    public static void main(String[] args) throws IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\tmp\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String plotFile = rootDir + "trident-out.aida";
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree tree = af.createTreeFactory().create(plotFile);
+        if(tree == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        
+        // Declare the histogram names.
+        String trackName = "Tracks in Event (All)";
+        String posTrackName = "Tracks in Event (Positive)";
+        String negTrackName = "Tracks in Event (Negative)";
+        String posMomentumName = "Momentum (Positive)";
+        String negMomentumName = "Momentum (Negative)";
+        String energySumName = "Energy Sum";
+        String momentumSumName = "Momentum Sum";
+        String energyMomentumDiffName = "Energy-Momentum Difference";
+        String invariantMassName = "Invariant Mass";
+        String energySum2DName = "2D Energy Sum";
+        String momentumSum2DName = "2D Momentum Sum";
+        String positionName = "Track Cluster Position";
+        
+        // Get the histograms.
+        IHistogram1D[] tracks = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + trackName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + trackName)
+        };
+        IHistogram1D[] posTracks = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + posTrackName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + posTrackName)
+        };
+        IHistogram1D[] negTracks = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + negTrackName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + negTrackName)
+        };
+        IHistogram1D[] posMomentum = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + posMomentumName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + posMomentumName)
+        };
+        IHistogram1D[] negMomentum = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + negMomentumName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + negMomentumName)
+        };
+        IHistogram1D[] energySum = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + energySumName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + energySumName)
+        };
+        IHistogram1D[] momentumSum = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + momentumSumName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + momentumSumName)
+        };
+        IHistogram1D[] energyMomentumDiff = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + energyMomentumDiffName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + energyMomentumDiffName)
+        };
+        IHistogram1D[] invariantMass = {
+                (IHistogram1D) tree.find("Trident Analysis/All/" + invariantMassName),
+                (IHistogram1D) tree.find("Trident Analysis/Cluster/" + invariantMassName)
+        };
+        IHistogram2D[] energySum2D = {
+                (IHistogram2D) tree.find("Trident Analysis/All/" + energySum2DName),
+                (IHistogram2D) tree.find("Trident Analysis/Cluster/" + energySum2DName)
+        };
+        IHistogram2D[] momentumSum2D = {
+                (IHistogram2D) tree.find("Trident Analysis/All/" + momentumSum2DName),
+                (IHistogram2D) tree.find("Trident Analysis/Cluster/" + momentumSum2DName)
+        };
+        IHistogram2D[] position = {
+                (IHistogram2D) tree.find("Trident Analysis/All/" + positionName),
+                (IHistogram2D) tree.find("Trident Analysis/Cluster/" + positionName)
+        };
+        
+        // Re-bin the histograms to have 5-times larger bins. First,
+        // get the bin count and upper and lower bounds of the plot.
+        int bins = invariantMass[0].axis().bins();
+        double low = invariantMass[0].axis().binLowerEdge(0);
+        double high = invariantMass[0].axis().binUpperEdge(invariantMass[0].axis().bins() - 1);
+        
+        // Create new plots with the larger bin sizes.
+        AIDA aida = AIDA.defaultInstance();
+        IHistogram1D[] newPlot = new IHistogram1D[2];
+        newPlot[0] = aida.histogram1D(invariantMassName, bins / 5, low, high);
+        newPlot[1] = aida.histogram1D("Cluster " + invariantMassName, bins / 5, low, high);
+        
+        // Populate the new plots with the data from the old ones.
+        for(int j = 0; j < 2; j++) {
+            for(int i = 0; i < bins; i++) {
+                int entries = invariantMass[j].binEntries(i);
+                double center = invariantMass[j].axis().binCenter(i);
+                for(int k = 0; k < entries; k++) {
+                    newPlot[j].fill(center);
+                }
+            }
+        }
+        
+        // Replace the old plots.
+        invariantMass = newPlot;
+        
+        // Define the scaling factors for each plot.
+        double scaleFactor = 1;
+        
+        // Define the plot titles and arrays for 1D plots.
+        IHistogram[][] plots = { tracks, posTracks, negTracks, posMomentum, negMomentum, energySum, momentumSum, energyMomentumDiff, invariantMass };
+        String[] titles = { trackName, posTrackName, negTrackName, posMomentumName, negMomentumName, energySumName, momentumSumName,
+                energyMomentumDiffName, invariantMassName };
+        String[] xTitles = { "Tracks", "Tracks", "Tracks", "Momentum (GeV)", "Momentum (GeV)", "Energy Sum (GeV)", "Momentum Sum (GeV)",
+                "|E_Cluster - P_Track| (GeV)", "Invariant Mass (GeV)" };
+        String yTitle = "Count";
+        
+        // Define the plot titles and arrays for 2D plots.
+        IHistogram2D[][] plots2D = { energySum2D, momentumSum2D, position };
+        String[] titles2D = { energySum2DName, momentumSum2DName, positionName };
+        String[] xTitles2D = { "Positive Cluster Energy", "Positive Track Momentum", "x-Index" };
+        String[] yTitles2D = { "Negative Cluster Energy", "Negative Track Momentum", "y-Index" };
+        String zTitle2D = "Count";
+        
+        // Create a plotter factory.
+        IPlotterFactory plotterFactory = af.createPlotterFactory();
+        
+        // Format and display the basic histograms.
+        for(int i = 0; i < plots.length; i++) {
+            for(int j = 0; j < 2; j++) {
+                // Scale the histogram by the appropriate scaling factor.
+                plots[i][j].scale(1.0 / scaleFactor);
+                
+                // Create a plotter and plotting region for the plot.
+                IPlotter plotter = plotterFactory.create((j == 1 ? "Cluster " : "") + titles[i]);
+                plotter.createRegions(1);
+                plotter.region(0).plot(plots[i][j]);
+                
+                // Format the axis labels.
+                PlotterRegion region = (PlotterRegion) plotter.region(0);
+                region.getPlot().setTitle((j == 1 ? "Cluster " : "") + titles[i]);
+                region.getPlot().getXAxis().setLabel(xTitles[i]);
+                region.getPlot().getYAxis().setLabel(yTitle);
+                
+                // Format the fonts and general plot presentation.
+                PlotsFormatter.setDefault1DStyle(region, new ColorStyle[] { ColorStyle.GREY });
+                
+                // Show the plot.
+                plotter.setParameter("plotterWidth", "2000");
+                plotter.setParameter("plotterHeight", "1200");
+                plotter.show();
+            }
+        }
+        
+        // Format and display the 2D histogram.
+        for(int i = 0; i < plots2D.length; i++) {
+            for(int j = 0; j < 2; j++) {
+                plots2D[i][j].scale(1.0 / scaleFactor);
+                IPlotter plotter2D = plotterFactory.create((j == 1 ? "Cluster " : "") + titles2D[i]);
+                plotter2D.createRegions(1);
+                plotter2D.region(0).plot(plots2D[i][j]);
+                
+                // Format the axis labels.
+                PlotterRegion region2D = (PlotterRegion) plotter2D.region(0);
+                region2D.getPlot().setTitle((j == 1 ? "Cluster " : "") + titles2D[i]);
+                region2D.getPlot().getXAxis().setLabel(xTitles2D[i]);
+                region2D.getPlot().getYAxis().setLabel(yTitles2D[i]);
+                
+                // Format the fonts and general plot presentation.
+                PlotsFormatter.setDefault2DStyle(region2D, true);
+                
+                // Show the plot.
+                plotter2D.setParameter("plotterWidth", "2000");
+                plotter2D.setParameter("plotterHeight", "1200");
+                plotter2D.show();
+            }
+        }
+        
+        // Close the tree.
+        tree.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TriggerPlotsFormat.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TriggerPlotsFormat.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/kmccarty/plots/formatter/TriggerPlotsFormat.java	Wed Apr 27 11:11:32 2016
@@ -20,331 +20,331 @@
 import hep.aida.ref.plotter.PlotterRegion;
 
 public class TriggerPlotsFormat {
-	// Define plot fonts.
-	private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
-	private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
-	private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
-	
-	// Defines the color style options for plot data.
-	private enum ColorStyle {
-		 MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
-		  MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
-		MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
-		    RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
-		  FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
-		    TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
-		    BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
-		  PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
-		
-		private final Color fillColor;
-		private final Color lineColor;
-		
-		private ColorStyle(Color fillColor, Color lineColor) {
-			this.fillColor = fillColor;
-			this.lineColor = lineColor;
-		}
-		
-		public Color getFillColor() { return fillColor; }
-		
-		public Color getLineColor() { return lineColor; }
-	};
-		
-	/**
-	 * Loads all plots in a file and formats them according to the
-	 * indicated style.
-	 * @param args - Unused default executable parameter.
-	 * @throws IOException Occurs if there is an issue opening the file.
-	 */
-	public static void main(String[] args) throws IOException {
-		// Define the root directory for the plots.
-		String rootDir = "D:\\cygwin64\\home\\Kyle\\beam-plots\\base\\";
-		//String rootDir = "D:\\cygwin64\\home\\Kyle\\aprime-plots\\base\\readout-plots\\";
-		
-		// Define the new name of the file containing the trigger plots.
-		String[] plotFile = {
-				rootDir + "compiled-plots.aida"
-				//rootDir + "15-MeV\\compiled-plots.aida",
-				//rootDir + "20-MeV\\compiled-plots.aida",
-				//rootDir + "30-MeV\\compiled-plots.aida",
-				//rootDir + "40-MeV\\compiled-plots.aida",
-				//rootDir + "50-MeV\\compiled-plots.aida"
-		};
-		
-		// Define the names of each plot. This will be used for the
-		// legend in the case of multiple plots.
-		String[] treeName = {
-			"Background",
-			"15 MeV A'",
-			"20 MeV A'",
-			"30 MeV A'",
-			"40 MeV A'",
-			"50 MeV A'"
-		};
-		
-		// Define the color style for the plots.
-		ColorStyle[] dataColorStyle = {
-				ColorStyle.GREY,
-				ColorStyle.MS_GREEN,
-				ColorStyle.MS_BLUE,
-				ColorStyle.MS_ORANGE,
-				ColorStyle.MS_RED,
-				ColorStyle.TEAL,
-				ColorStyle.CRIMSON,
-				ColorStyle.FOREST
-		};
-		
-		// Get the plots file and open it.
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITree[] tree = new ITree[plotFile.length];
-		for(int i = 0; i < plotFile.length; i++) {
-			tree[i] = af.createTreeFactory().create(plotFile[i]);
-			if(tree[i] == null) { throw new IllegalArgumentException("Unable to load plot file."); }
-		}
-		
-		// Get a list of all the histograms in the file.
-		List<List<String>> treeHistograms = new ArrayList<List<String>>(plotFile.length);
-		for(int i = 0; i < plotFile.length; i++) {
-			treeHistograms.add(getHistograms(tree[i], "/NoCuts/"));//, "/PassedAll/"));
-		}
-		
-		// Create a plotter factory.
-		IPlotterFactory plotterFactory = af.createPlotterFactory();
-		
-		// Plot each histogram and format it.
-		for(String histogram : treeHistograms.get(0)) {
-			// Get the plot from the tree and verify that it is a 1D
-			// or 2D histogram. Other types are not supported.
-			IManagedObject histObject = tree[0].find(histogram);
-			if(!(histObject instanceof IHistogram1D) && !(histObject instanceof IHistogram2D)) {
-				continue;
-			}
-			
-			// Obtain the histogram object.
-			IBaseHistogram hist;
-			if(histObject instanceof IHistogram1D) { hist = (IHistogram1D) histObject; }
-			else { hist = (IHistogram2D) histObject; }
-			
-			// Define whether this is an overlay plot and whether
-			// this is a one or two dimensional plot.
-			boolean overlay = plotFile.length > 1;
-			boolean twoDimensional = hist instanceof IHistogram2D;
-			
-			// Generate the plotter and set its title. The plotter will
-			// use the title of the first tree's plot.
-			String plotTitle = hist.title();
-			IPlotter plotter = plotterFactory.create(plotTitle);
-			
-			// For single plots and one-dimensional overlay plots,
-			// there should only be a single plotter region.
-			if(!twoDimensional || !overlay) { plotter.createRegions(1); }
-			
-			// For two-dimensional overlay plots, create a region for
-			// each plot individually.
-			else { plotter.createRegions(2, (int) Math.ceil(plotFile.length / 2.0)); }
-			
-			// Find the histogram in each of the trees and plot them
-			// all on the same region.
-			for(int i = 0; i < plotFile.length; i++) {
-				// Get the histogram from the tree.
-				IManagedObject treeObject = tree[i].find(histogram);
-				IBaseHistogram treeHist;
-				if(treeObject instanceof IHistogram1D) { treeHist = (IHistogram1D) treeObject; }
-				else { treeHist = (IHistogram2D) treeObject; }
-				
-				// Display the plot.
-				if(treeHist != null) {
-					// Set the title of plot to the name associated with
-					// its tree. This ensures that the correct name will
-					// appear on the legend.
-					if(plotFile.length > 1) {
-						treeHist.setTitle(treeName[i]);
-					}
-					
-					// Plot the tree's data in the plotter region.
-					if(!twoDimensional || !overlay) { plotter.region(0).plot(treeHist); }
-					else {
-						plotter.region(i).plot(treeHist);
-						setDefault2DStyle(((PlotterRegion) plotter.region(i)), dataColorStyle);
-					}
-				}
-			}
-			
-			// Format the plot region.
-			if(!twoDimensional) { setDefault1DStyle(((PlotterRegion) plotter.region(0)), dataColorStyle); }
-			else { setDefault2DStyle(((PlotterRegion) plotter.region(0)), dataColorStyle); }
-			
-			// Show the plotter.
-			plotter.region(0).setTitle(plotTitle);
-			plotter.setParameter("plotterWidth", "750");
-			plotter.setParameter("plotterHeight", "600");
-			//plotter.setParameter("plotterWidth", "2000");
-			//plotter.setParameter("plotterHeight", "1200");
-			plotter.show();
-		}
-		
-		// Close the trees.
-		for(int i = 0; i < plotFile.length; i++) {
-			tree[i].close();
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the names of each plot on in the region.
-		String[] dataNames = region.getAllDataNames();
-		
-		// Check whether this is an overlay plot. Overlay plots contain
-		// more than one data name.
-		boolean overlay = (dataNames.length > 1 ? true : false);
-		
-		// Iterate over each plot in the region.
-		for(int i = 0; i < dataNames.length; i++) {
-			// Set the overlay style if needed.
-			if(overlay) {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with no fill. The color is set by the "color" argument.
-				fillStyle.setHistogramFill(false);
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarLineColor(color[i].getFillColor());
-				
-				// Set the legend text style.
-				region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
-			}
-			
-			// Otherwise, set the fill style for a single plot.
-			else {
-				// Get the fill style for the current data type.
-				JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
-				
-				// Set the histogram style to display thick-lined bars
-				// with a fill color. The colors are defined by the
-				// "color" argument.
-				fillStyle.setHistogramBarLineWidth(3);
-				fillStyle.setHistogramBarColor(color[i].getFillColor());
-				fillStyle.setHistogramBarLineColor(color[i].getLineColor());
-			}
-			
-			// Set the statistics box style.
-			region.getPlot().getStats().setVisible(true);
-			region.getPlot().getStats().setFont(BASIC_FONT);
-			
-			// Set the title font.
-			region.getPlot().getTitleObject().setFont(TITLE_FONT);
-			
-			// Set generic axis titles.
-			region.getPlot().getXAxis().setLabel("Data Label (Unit)");
-			region.getPlot().getYAxis().setLabel("Count");
-			
-			// Set the axis tick-mark fonts.
-			region.getPlot().getXAxis().setFont(BASIC_FONT);
-			region.getPlot().getYAxis().setFont(BASIC_FONT);
-			region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-			region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-		}
-	}
-	
-	/**
-	 * Sets the plot display formatting for 1D plots.
-	 * @param region - The plotter region to format.
-	 * @param color - The data color settings to use.
-	 */
-	private static final void setDefault2DStyle(PlotterRegion region, ColorStyle[] color) {
-		// Get the fill style object. 2D plots should never be overlay
-		// plots, so there should only ever be one data name.
-		JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
-		
-		// Set the fill style for a two-dimensional plot.
-		fillStyle.setLogZ(true);
-		fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
-		fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
-		
-		// Make the statistics box invisible.
-		region.getPlot().getStats().setVisible(false);
-		
-		// Set the general plot font (which is also the z-axis font).
-		region.getPlot().setFont(BASIC_FONT);
-		
-		// Set the title font.
-		region.getPlot().getTitleObject().setFont(TITLE_FONT);
-		
-		// Set generic axis titles.
-		region.getPlot().getXAxis().setLabel("Data Label (Unit)");
-		region.getPlot().getYAxis().setLabel("Data Label (Unit)");
-		
-		// Set the axis tick-mark fonts.
-		region.getPlot().getXAxis().setFont(BASIC_FONT);
-		region.getPlot().getYAxis().setFont(BASIC_FONT);
-		region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
-		region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
-	}
-	
-	/**
-	 * Gets a list of all objects that are not directories in a tree.
-	 * @param tree - The tree from which to extract the object names.
-	 * @return Returns the object names as <code>String</code> objects
-	 * in a <code>List</code> collection.
-	 */
-	private static final List<String> getHistograms(ITree tree) {
-		return getHistograms(tree, "/");
-	}
-	
-	/**
-	 * Gets a list of all objects that are not directories in a tree.
-	 * @param tree - The tree from which to extract the object names.
-	 * @return Returns the object names as <code>String</code> objects
-	 * in a <code>List</code> collection.
-	 */
-	private static final List<String> getHistograms(ITree tree, String rootDir) {
-		return getHistograms(tree, rootDir, new ArrayList<String>());
-	}
-	
-	/**
-	 * Recursive method that gets all object names from a tree that
-	 * are not directories. Method should not be called directly, but
-	 * rather called only through the <code>getHistograms(ITree)</code>
-	 * method.
-	 * @param tree - The tree from which to obtain the object names.
-	 * @param directory - The directory in which to search for objects.
-	 * @param list - The list in which to place the objects.
-	 * @return Returns the <code>List</code> collection that was given
-	 * as an argument.
-	 */
-	private static final List<String> getHistograms(ITree tree, String directory, List<String> list) {
-		// Get the list of objects in the directory.
-		String[] treeObjects = tree.listObjectNames(directory);
-		
-		// Print the objects.
-		for(String objectName : treeObjects) {
-			// Check if the object is a directory.
-			boolean isDirectory = isDirectory(objectName);
-			
-			// If the object is a directory, get the histograms from it.
-			if(isDirectory) {
-				getHistograms(tree, objectName, list);
-			}
-			
-			// If the object is a plot, add it to the list.
-			else { list.add(objectName); }
-		}
-		
-		// Return the list.
-		return list;
-	}
-	
-	/**
-	 * Checks whether a tree object is a directory.
-	 * @param object - The object to check.
-	 * @return Returns <code>true</code> if the object is a directory
-	 * and <code>false</code> otherwise.
-	 */
-	private static final boolean isDirectory(String object) {
-		return (object.toCharArray()[object.length() - 1] == '/');
-	}
+    // Define plot fonts.
+    private static final Font BASIC_FONT = new Font("Calibri", Font.PLAIN, 20);
+    private static final Font AXIS_FONT  = new Font("Calibri", Font.BOLD,  25);
+    private static final Font TITLE_FONT = new Font("Calibri", Font.BOLD,  35);
+    
+    // Defines the color style options for plot data.
+    private enum ColorStyle {
+         MS_BLUE(new Color( 79, 129, 189), new Color( 36,  64,  97)), MS_ORANGE(new Color(247, 150,  70), new Color(152,  72,   6)),
+          MS_RED(new Color(192,  80,  77), new Color( 99,  36,  35)),      GREY(new Color(166, 166, 166), new Color( 89,  89,  89)),
+        MS_GREEN(new Color(155, 187,  89), new Color( 79,  98,  40)),   CRIMSON(new Color(161,   0,   0), new Color(104,   0,   0)),
+            RUST(new Color(161,  80,   0), new Color(105,  80,   0)),    YELLOW(new Color(161, 161,   0), new Color(122, 109,   8)),
+          FOREST(new Color( 65, 102,   0), new Color( 37,  79,   0)),     GREEN(new Color(  7, 132,  70), new Color(  7,  82,  30)),
+            TEAL(new Color(  0, 130, 130), new Color(  0,  90, 100)),  CERULEAN(new Color(  0,  86, 130), new Color(  0,  28,  83)),
+            BLUE(new Color(  0,  33, 203), new Color(  0,   0, 137)),    INDIGO(new Color( 68,  10, 127), new Color(  0,   0,  61)),
+          PURPLE(new Color(106,   0, 106), new Color( 63,   0,  56)),   FUSCHIA(new Color(119,   0,  60), new Color( 60,   0,  60));
+        
+        private final Color fillColor;
+        private final Color lineColor;
+        
+        private ColorStyle(Color fillColor, Color lineColor) {
+            this.fillColor = fillColor;
+            this.lineColor = lineColor;
+        }
+        
+        public Color getFillColor() { return fillColor; }
+        
+        public Color getLineColor() { return lineColor; }
+    };
+        
+    /**
+     * Loads all plots in a file and formats them according to the
+     * indicated style.
+     * @param args - Unused default executable parameter.
+     * @throws IOException Occurs if there is an issue opening the file.
+     */
+    public static void main(String[] args) throws IOException {
+        // Define the root directory for the plots.
+        String rootDir = "D:\\cygwin64\\home\\Kyle\\beam-plots\\base\\";
+        //String rootDir = "D:\\cygwin64\\home\\Kyle\\aprime-plots\\base\\readout-plots\\";
+        
+        // Define the new name of the file containing the trigger plots.
+        String[] plotFile = {
+                rootDir + "compiled-plots.aida"
+                //rootDir + "15-MeV\\compiled-plots.aida",
+                //rootDir + "20-MeV\\compiled-plots.aida",
+                //rootDir + "30-MeV\\compiled-plots.aida",
+                //rootDir + "40-MeV\\compiled-plots.aida",
+                //rootDir + "50-MeV\\compiled-plots.aida"
+        };
+        
+        // Define the names of each plot. This will be used for the
+        // legend in the case of multiple plots.
+        String[] treeName = {
+            "Background",
+            "15 MeV A'",
+            "20 MeV A'",
+            "30 MeV A'",
+            "40 MeV A'",
+            "50 MeV A'"
+        };
+        
+        // Define the color style for the plots.
+        ColorStyle[] dataColorStyle = {
+                ColorStyle.GREY,
+                ColorStyle.MS_GREEN,
+                ColorStyle.MS_BLUE,
+                ColorStyle.MS_ORANGE,
+                ColorStyle.MS_RED,
+                ColorStyle.TEAL,
+                ColorStyle.CRIMSON,
+                ColorStyle.FOREST
+        };
+        
+        // Get the plots file and open it.
+        IAnalysisFactory af = IAnalysisFactory.create();
+        ITree[] tree = new ITree[plotFile.length];
+        for(int i = 0; i < plotFile.length; i++) {
+            tree[i] = af.createTreeFactory().create(plotFile[i]);
+            if(tree[i] == null) { throw new IllegalArgumentException("Unable to load plot file."); }
+        }
+        
+        // Get a list of all the histograms in the file.
+        List<List<String>> treeHistograms = new ArrayList<List<String>>(plotFile.length);
+        for(int i = 0; i < plotFile.length; i++) {
+            treeHistograms.add(getHistograms(tree[i], "/NoCuts/"));//, "/PassedAll/"));
+        }
+        
+        // Create a plotter factory.
+        IPlotterFactory plotterFactory = af.createPlotterFactory();
+        
+        // Plot each histogram and format it.
+        for(String histogram : treeHistograms.get(0)) {
+            // Get the plot from the tree and verify that it is a 1D
+            // or 2D histogram. Other types are not supported.
+            IManagedObject histObject = tree[0].find(histogram);
+            if(!(histObject instanceof IHistogram1D) && !(histObject instanceof IHistogram2D)) {
+                continue;
+            }
+            
+            // Obtain the histogram object.
+            IBaseHistogram hist;
+            if(histObject instanceof IHistogram1D) { hist = (IHistogram1D) histObject; }
+            else { hist = (IHistogram2D) histObject; }
+            
+            // Define whether this is an overlay plot and whether
+            // this is a one or two dimensional plot.
+            boolean overlay = plotFile.length > 1;
+            boolean twoDimensional = hist instanceof IHistogram2D;
+            
+            // Generate the plotter and set its title. The plotter will
+            // use the title of the first tree's plot.
+            String plotTitle = hist.title();
+            IPlotter plotter = plotterFactory.create(plotTitle);
+            
+            // For single plots and one-dimensional overlay plots,
+            // there should only be a single plotter region.
+            if(!twoDimensional || !overlay) { plotter.createRegions(1); }
+            
+            // For two-dimensional overlay plots, create a region for
+            // each plot individually.
+            else { plotter.createRegions(2, (int) Math.ceil(plotFile.length / 2.0)); }
+            
+            // Find the histogram in each of the trees and plot them
+            // all on the same region.
+            for(int i = 0; i < plotFile.length; i++) {
+                // Get the histogram from the tree.
+                IManagedObject treeObject = tree[i].find(histogram);
+                IBaseHistogram treeHist;
+                if(treeObject instanceof IHistogram1D) { treeHist = (IHistogram1D) treeObject; }
+                else { treeHist = (IHistogram2D) treeObject; }
+                
+                // Display the plot.
+                if(treeHist != null) {
+                    // Set the title of plot to the name associated with
+                    // its tree. This ensures that the correct name will
+                    // appear on the legend.
+                    if(plotFile.length > 1) {
+                        treeHist.setTitle(treeName[i]);
+                    }
+                    
+                    // Plot the tree's data in the plotter region.
+                    if(!twoDimensional || !overlay) { plotter.region(0).plot(treeHist); }
+                    else {
+                        plotter.region(i).plot(treeHist);
+                        setDefault2DStyle(((PlotterRegion) plotter.region(i)), dataColorStyle);
+                    }
+                }
+            }
+            
+            // Format the plot region.
+            if(!twoDimensional) { setDefault1DStyle(((PlotterRegion) plotter.region(0)), dataColorStyle); }
+            else { setDefault2DStyle(((PlotterRegion) plotter.region(0)), dataColorStyle); }
+            
+            // Show the plotter.
+            plotter.region(0).setTitle(plotTitle);
+            plotter.setParameter("plotterWidth", "750");
+            plotter.setParameter("plotterHeight", "600");
+            //plotter.setParameter("plotterWidth", "2000");
+            //plotter.setParameter("plotterHeight", "1200");
+            plotter.show();
+        }
+        
+        // Close the trees.
+        for(int i = 0; i < plotFile.length; i++) {
+            tree[i].close();
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    private static final void setDefault1DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the names of each plot on in the region.
+        String[] dataNames = region.getAllDataNames();
+        
+        // Check whether this is an overlay plot. Overlay plots contain
+        // more than one data name.
+        boolean overlay = (dataNames.length > 1 ? true : false);
+        
+        // Iterate over each plot in the region.
+        for(int i = 0; i < dataNames.length; i++) {
+            // Set the overlay style if needed.
+            if(overlay) {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with no fill. The color is set by the "color" argument.
+                fillStyle.setHistogramFill(false);
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarLineColor(color[i].getFillColor());
+                
+                // Set the legend text style.
+                region.getPlot().getLegend().setFont(new Font("Calibri", Font.PLAIN, 20));
+            }
+            
+            // Otherwise, set the fill style for a single plot.
+            else {
+                // Get the fill style for the current data type.
+                JASHist1DHistogramStyle fillStyle = (JASHist1DHistogramStyle) region.getDataForName(dataNames[i]).getStyle();
+                
+                // Set the histogram style to display thick-lined bars
+                // with a fill color. The colors are defined by the
+                // "color" argument.
+                fillStyle.setHistogramBarLineWidth(3);
+                fillStyle.setHistogramBarColor(color[i].getFillColor());
+                fillStyle.setHistogramBarLineColor(color[i].getLineColor());
+            }
+            
+            // Set the statistics box style.
+            region.getPlot().getStats().setVisible(true);
+            region.getPlot().getStats().setFont(BASIC_FONT);
+            
+            // Set the title font.
+            region.getPlot().getTitleObject().setFont(TITLE_FONT);
+            
+            // Set generic axis titles.
+            region.getPlot().getXAxis().setLabel("Data Label (Unit)");
+            region.getPlot().getYAxis().setLabel("Count");
+            
+            // Set the axis tick-mark fonts.
+            region.getPlot().getXAxis().setFont(BASIC_FONT);
+            region.getPlot().getYAxis().setFont(BASIC_FONT);
+            region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+            region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+        }
+    }
+    
+    /**
+     * Sets the plot display formatting for 1D plots.
+     * @param region - The plotter region to format.
+     * @param color - The data color settings to use.
+     */
+    private static final void setDefault2DStyle(PlotterRegion region, ColorStyle[] color) {
+        // Get the fill style object. 2D plots should never be overlay
+        // plots, so there should only ever be one data name.
+        JASHist2DHistogramStyle fillStyle = (JASHist2DHistogramStyle) region.getDataForName(region.getAllDataNames()[0]).getStyle();
+        
+        // Set the fill style for a two-dimensional plot.
+        fillStyle.setLogZ(true);
+        fillStyle.setHistStyle(JASHist2DHistogramStyle.STYLE_COLORMAP);
+        fillStyle.setColorMapScheme(JASHist2DHistogramStyle.COLORMAP_RAINBOW);
+        
+        // Make the statistics box invisible.
+        region.getPlot().getStats().setVisible(false);
+        
+        // Set the general plot font (which is also the z-axis font).
+        region.getPlot().setFont(BASIC_FONT);
+        
+        // Set the title font.
+        region.getPlot().getTitleObject().setFont(TITLE_FONT);
+        
+        // Set generic axis titles.
+        region.getPlot().getXAxis().setLabel("Data Label (Unit)");
+        region.getPlot().getYAxis().setLabel("Data Label (Unit)");
+        
+        // Set the axis tick-mark fonts.
+        region.getPlot().getXAxis().setFont(BASIC_FONT);
+        region.getPlot().getYAxis().setFont(BASIC_FONT);
+        region.getPlot().getXAxis().getLabelObject().setFont(AXIS_FONT);
+        region.getPlot().getYAxis().getLabelObject().setFont(AXIS_FONT);
+    }
+    
+    /**
+     * Gets a list of all objects that are not directories in a tree.
+     * @param tree - The tree from which to extract the object names.
+     * @return Returns the object names as <code>String</code> objects
+     * in a <code>List</code> collection.
+     */
+    private static final List<String> getHistograms(ITree tree) {
+        return getHistograms(tree, "/");
+    }
+    
+    /**
+     * Gets a list of all objects that are not directories in a tree.
+     * @param tree - The tree from which to extract the object names.
+     * @return Returns the object names as <code>String</code> objects
+     * in a <code>List</code> collection.
+     */
+    private static final List<String> getHistograms(ITree tree, String rootDir) {
+        return getHistograms(tree, rootDir, new ArrayList<String>());
+    }
+    
+    /**
+     * Recursive method that gets all object names from a tree that
+     * are not directories. Method should not be called directly, but
+     * rather called only through the <code>getHistograms(ITree)</code>
+     * method.
+     * @param tree - The tree from which to obtain the object names.
+     * @param directory - The directory in which to search for objects.
+     * @param list - The list in which to place the objects.
+     * @return Returns the <code>List</code> collection that was given
+     * as an argument.
+     */
+    private static final List<String> getHistograms(ITree tree, String directory, List<String> list) {
+        // Get the list of objects in the directory.
+        String[] treeObjects = tree.listObjectNames(directory);
+        
+        // Print the objects.
+        for(String objectName : treeObjects) {
+            // Check if the object is a directory.
+            boolean isDirectory = isDirectory(objectName);
+            
+            // If the object is a directory, get the histograms from it.
+            if(isDirectory) {
+                getHistograms(tree, objectName, list);
+            }
+            
+            // If the object is a plot, add it to the list.
+            else { list.add(objectName); }
+        }
+        
+        // Return the list.
+        return list;
+    }
+    
+    /**
+     * Checks whether a tree object is a directory.
+     * @param object - The object to check.
+     * @return Returns <code>true</code> if the object is a directory
+     * and <code>false</code> otherwise.
+     */
+    private static final boolean isDirectory(String object) {
+        return (object.toCharArray()[object.length() - 1] == '/');
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FADCVariableTriggerFEEDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FADCVariableTriggerFEEDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FADCVariableTriggerFEEDriver.java	Wed Apr 27 11:11:32 2016
@@ -25,64 +25,64 @@
     // ==================================================================
     // ==== Trigger Cut Default Parameters ==============================
     // ==================================================================
-    private int minHitCount = 1;								// Minimum required cluster hit count threshold. (Hits)			
-    private double seedEnergyHigh = Double.MAX_VALUE;			// Maximum allowed cluster seed energy. (GeV)
-    private double seedEnergyLow = Double.MIN_VALUE;			// Minimum required cluster seed energy. (GeV)
-    private double clusterEnergyHigh = 1.5 * EcalUtils.GeV;		// Maximum allowed cluster total energy. (GeV)
-    private double clusterEnergyLow = .1 * EcalUtils.GeV;		// Minimum required cluster total energy. (GeV)
-    private double energySumHigh = 1.9 * EcalUtils.GeV;			// Maximum allowed pair energy sum. (GeV)
-    private double energySumLow = 0.0 * EcalUtils.GeV;			// Minimum required pair energy sum. (GeV)
-    private double energyDifferenceHigh = 2.2 * EcalUtils.GeV;	// Maximum allowed pair energy difference. (GeV)
-    private double energySlopeLow = 1.1;						// Minimum required pair energy slope value.
-    private double coplanarityHigh = 35;						// Maximum allowed pair coplanarity deviation. (Degrees)
+    private int minHitCount = 1;                                // Minimum required cluster hit count threshold. (Hits)         
+    private double seedEnergyHigh = Double.MAX_VALUE;           // Maximum allowed cluster seed energy. (GeV)
+    private double seedEnergyLow = Double.MIN_VALUE;            // Minimum required cluster seed energy. (GeV)
+    private double clusterEnergyHigh = 1.5 * EcalUtils.GeV;     // Maximum allowed cluster total energy. (GeV)
+    private double clusterEnergyLow = .1 * EcalUtils.GeV;       // Minimum required cluster total energy. (GeV)
+    private double energySumHigh = 1.9 * EcalUtils.GeV;         // Maximum allowed pair energy sum. (GeV)
+    private double energySumLow = 0.0 * EcalUtils.GeV;          // Minimum required pair energy sum. (GeV)
+    private double energyDifferenceHigh = 2.2 * EcalUtils.GeV;  // Maximum allowed pair energy difference. (GeV)
+    private double energySlopeLow = 1.1;                        // Minimum required pair energy slope value.
+    private double coplanarityHigh = 35;                        // Maximum allowed pair coplanarity deviation. (Degrees)
     
     // ==================================================================
     // ==== Trigger General Default Parameters ==========================
     // ==================================================================
-    private String clusterCollectionName = "EcalClusters";		// Name for the LCIO cluster collection.
-    private int pairCoincidence = 2;							// Maximum allowed time difference between clusters. (4 ns clock-cycles)
-    private double energySlopeParamF = 0.005500;				// A parameter value used for the energy slope calculation.
-    private double originX = 1393.0 * Math.tan(0.03052);		// ECal mid-plane, defined by photon beam position (30.52 mrad) at ECal face (z=1393 mm)
-    private int backgroundLevel = -1;							// Automatically sets the cuts to achieve a predetermined background rate.
+    private String clusterCollectionName = "EcalClusters";      // Name for the LCIO cluster collection.
+    private int pairCoincidence = 2;                            // Maximum allowed time difference between clusters. (4 ns clock-cycles)
+    private double energySlopeParamF = 0.005500;                // A parameter value used for the energy slope calculation.
+    private double originX = 1393.0 * Math.tan(0.03052);        // ECal mid-plane, defined by photon beam position (30.52 mrad) at ECal face (z=1393 mm)
+    private int backgroundLevel = -1;                           // Automatically sets the cuts to achieve a predetermined background rate.
     
     // ==================================================================
     // ==== Driver Internal Variables ===================================
     // ==================================================================
-    private Queue<List<Cluster>> topClusterQueue = null;	// Store clusters on the top half of the calorimeter.
-    private Queue<List<Cluster>> botClusterQueue = null;	// Store clusters on the bottom half of the calorimeter.
-    private int allClusters = 0;								// Track the number of clusters processed.
-    private int allPairs = 0;									// Track the number of cluster pairs processed.
-    private int clusterTotalEnergyCount = 0;					// Track the clusters which pass the total energy cut.
-    private int clusterSeedEnergyCount = 0;						// Track the clusters which pass the seed energy cut.
-    private int clusterHitCountCount = 0;						// Track the clusters which pass the hit count cut.
-    private int pairEnergySumCount = 0;							// Track the pairs which pass the energy sum cut.
-    private int pairEnergyDifferenceCount = 0;					// Track the pairs which pass the energy difference cut.
-    private int pairEnergySlopeCount = 0;						// Track the pairs which pass the energy slope cut.
-    private int pairCoplanarityCount = 0;						// Track the pairs which pass the coplanarity cut.
+    private Queue<List<Cluster>> topClusterQueue = null;    // Store clusters on the top half of the calorimeter.
+    private Queue<List<Cluster>> botClusterQueue = null;    // Store clusters on the bottom half of the calorimeter.
+    private int allClusters = 0;                                // Track the number of clusters processed.
+    private int allPairs = 0;                                   // Track the number of cluster pairs processed.
+    private int clusterTotalEnergyCount = 0;                    // Track the clusters which pass the total energy cut.
+    private int clusterSeedEnergyCount = 0;                     // Track the clusters which pass the seed energy cut.
+    private int clusterHitCountCount = 0;                       // Track the clusters which pass the hit count cut.
+    private int pairEnergySumCount = 0;                         // Track the pairs which pass the energy sum cut.
+    private int pairEnergyDifferenceCount = 0;                  // Track the pairs which pass the energy difference cut.
+    private int pairEnergySlopeCount = 0;                       // Track the pairs which pass the energy slope cut.
+    private int pairCoplanarityCount = 0;                       // Track the pairs which pass the coplanarity cut.
     
     /**
      * Prints out the results of the trigger at the end of the run.
      */
     @Override
     public void endOfData() {
-    	// Print out the results of the trigger cuts.
-    	System.out.printf("Trigger Processing Results%n");
-    	System.out.printf("\tSingle-Cluster Cuts%n");
-    	System.out.printf("\t\tTotal Clusters Processed     :: %d%n", allClusters);
-    	System.out.printf("\t\tPassed Seed Energy Cut       :: %d%n", clusterSeedEnergyCount);
-    	System.out.printf("\t\tPassed Hit Count Cut         :: %d%n", clusterHitCountCount);
-    	System.out.printf("\t\tPassed Total Energy Cut      :: %d%n", clusterTotalEnergyCount);
-    	System.out.printf("%n");
-    	System.out.printf("\tCluster Pair Cuts%n");
-    	System.out.printf("\t\tTotal Pairs Processed        :: %d%n", allPairs);
-    	System.out.printf("\t\tPassed Energy Sum Cut        :: %d%n", pairEnergySumCount);
-    	System.out.printf("\t\tPassed Energy Difference Cut :: %d%n", pairEnergyDifferenceCount);
-    	System.out.printf("\t\tPassed Energy Slope Cut      :: %d%n", pairEnergySlopeCount);
-    	System.out.printf("\t\tPassed Coplanarity Cut       :: %d%n", pairCoplanarityCount);
-    	System.out.printf("%n");
-    	System.out.printf("\tTrigger Count :: %d%n", numTriggers);
-    	
-    	// Run the superclass method.
+        // Print out the results of the trigger cuts.
+        System.out.printf("Trigger Processing Results%n");
+        System.out.printf("\tSingle-Cluster Cuts%n");
+        System.out.printf("\t\tTotal Clusters Processed     :: %d%n", allClusters);
+        System.out.printf("\t\tPassed Seed Energy Cut       :: %d%n", clusterSeedEnergyCount);
+        System.out.printf("\t\tPassed Hit Count Cut         :: %d%n", clusterHitCountCount);
+        System.out.printf("\t\tPassed Total Energy Cut      :: %d%n", clusterTotalEnergyCount);
+        System.out.printf("%n");
+        System.out.printf("\tCluster Pair Cuts%n");
+        System.out.printf("\t\tTotal Pairs Processed        :: %d%n", allPairs);
+        System.out.printf("\t\tPassed Energy Sum Cut        :: %d%n", pairEnergySumCount);
+        System.out.printf("\t\tPassed Energy Difference Cut :: %d%n", pairEnergyDifferenceCount);
+        System.out.printf("\t\tPassed Energy Slope Cut      :: %d%n", pairEnergySlopeCount);
+        System.out.printf("\t\tPassed Coplanarity Cut       :: %d%n", pairCoplanarityCount);
+        System.out.printf("%n");
+        System.out.printf("\tTrigger Count :: %d%n", numTriggers);
+        
+        // Run the superclass method.
         super.endOfData();
     }
     
@@ -92,53 +92,53 @@
      */
     @Override
     public void process(EventHeader event) {
-    	// Process the list of clusters for the event, if it exists.
+        // Process the list of clusters for the event, if it exists.
         if (event.hasCollection(Cluster.class, clusterCollectionName)) {
-        	// Get the collection of clusters.
-        	List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-        	
-        	// Create a list to hold clusters which pass the single
-        	// cluster cuts.
-        	List<Cluster> goodClusterList = new ArrayList<Cluster>(clusterList.size());
-        	
-        	// Sort through the cluster list and add clusters that pass
-        	// the single cluster cuts to the good list.
-        	clusterLoop:
-        	for(Cluster cluster : clusterList) {
-        		// Increment the number of processed clusters.
-        		allClusters++;
-        		
-        		// ==== Seed Hit Energy Cut ====================================
-        		// =============================================================
-        		// If the cluster fails the cut, skip to the next cluster.
-        		if(!clusterSeedEnergyCut(cluster)) { continue clusterLoop; }
-        		
-        		// Otherwise, note that it passed the cut.
-        		clusterSeedEnergyCount++;
-        		
-        		// ==== Cluster Hit Count Cut ==================================
-        		// =============================================================
-        		// If the cluster fails the cut, skip to the next cluster.
-        		if(!clusterHitCountCut(cluster)) { continue clusterLoop; }
-        		
-        		// Otherwise, note that it passed the cut.
-        		clusterHitCountCount++;
-        		
-        		// ==== Cluster Total Energy Cut ===============================
-        		// =============================================================
-        		// If the cluster fails the cut, skip to the next cluster.
-        		if(!clusterTotalEnergyCut(cluster)) { continue clusterLoop; }
-        		
-        		// Otherwise, note that it passed the cut.
-        		clusterTotalEnergyCount++;
-        		
-        		// A cluster that passes all of the single-cluster cuts
-        		// can be used in cluster pairs.
-        		goodClusterList.add(cluster);
-        	}
-        	
-        	// Put the good clusters into the cluster queue.
-        	updateClusterQueues(goodClusterList);
+            // Get the collection of clusters.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Create a list to hold clusters which pass the single
+            // cluster cuts.
+            List<Cluster> goodClusterList = new ArrayList<Cluster>(clusterList.size());
+            
+            // Sort through the cluster list and add clusters that pass
+            // the single cluster cuts to the good list.
+            clusterLoop:
+            for(Cluster cluster : clusterList) {
+                // Increment the number of processed clusters.
+                allClusters++;
+                
+                // ==== Seed Hit Energy Cut ====================================
+                // =============================================================
+                // If the cluster fails the cut, skip to the next cluster.
+                if(!clusterSeedEnergyCut(cluster)) { continue clusterLoop; }
+                
+                // Otherwise, note that it passed the cut.
+                clusterSeedEnergyCount++;
+                
+                // ==== Cluster Hit Count Cut ==================================
+                // =============================================================
+                // If the cluster fails the cut, skip to the next cluster.
+                if(!clusterHitCountCut(cluster)) { continue clusterLoop; }
+                
+                // Otherwise, note that it passed the cut.
+                clusterHitCountCount++;
+                
+                // ==== Cluster Total Energy Cut ===============================
+                // =============================================================
+                // If the cluster fails the cut, skip to the next cluster.
+                if(!clusterTotalEnergyCut(cluster)) { continue clusterLoop; }
+                
+                // Otherwise, note that it passed the cut.
+                clusterTotalEnergyCount++;
+                
+                // A cluster that passes all of the single-cluster cuts
+                // can be used in cluster pairs.
+                goodClusterList.add(cluster);
+            }
+            
+            // Put the good clusters into the cluster queue.
+            updateClusterQueues(goodClusterList);
         }
         
         // Perform the superclass event processing.
@@ -152,7 +152,7 @@
      * be set. Actual background rates equal about (5 * backgroundLevel) kHz.
      */
     public void setBackgroundLevel(int backgroundLevel) {
-    	this.backgroundLevel = backgroundLevel;
+        this.backgroundLevel = backgroundLevel;
     }
     
     /**
@@ -215,7 +215,7 @@
      * @param energySlopeLow - The parameter value.
      */
     public void setEnergySlopeLow(double energySlopeLow) {
-    	this.energySlopeLow = energySlopeLow;
+        this.energySlopeLow = energySlopeLow;
     }
     
     /**
@@ -299,12 +299,12 @@
      */
     @Override
     public void startOfData() {
-    	// Make sure that a valid cluster collection name has been
-    	// defined. If it has not, throw an exception.
+        // Make sure that a valid cluster collection name has been
+        // defined. If it has not, throw an exception.
         if (clusterCollectionName == null) {
             throw new RuntimeException("The parameter clusterCollectionName was not set!");
         }
-    	
+        
         // Initialize the top and bottom cluster queues.
         topClusterQueue = new LinkedList<List<Cluster>>();
         botClusterQueue = new LinkedList<List<Cluster>>();
@@ -345,9 +345,9 @@
         for (Cluster botCluster : botClusterQueue.element()) {
             for (List<Cluster> topClusters : topClusterQueue) {
                 for (Cluster topCluster : topClusters) {
-                	// The first cluster in a pair should always be
-                	// the higher energy cluster. If the top cluster
-                	// is higher energy, it goes first.
+                    // The first cluster in a pair should always be
+                    // the higher energy cluster. If the top cluster
+                    // is higher energy, it goes first.
                     if (topCluster.getEnergy() > botCluster.getEnergy()) {
                         Cluster[] clusterPair = {topCluster, botCluster};
                         clusterPairs.add(clusterPair);
@@ -366,24 +366,24 @@
         return clusterPairs;
     }
     
-	/**
-	 * Determines if the event produces a trigger.
-	 * 
-	 * @return Returns <code>true</code> if the event produces a trigger
-	 * and <code>false</code> if it does not.
-	 */
-	@Override
-	protected boolean triggerDecision(EventHeader event) {
-    	// If there is a list of clusters present for this event,
-    	// check whether it passes the trigger conditions.
-    	if (event.hasCollection(Cluster.class, clusterCollectionName)) {
-        	return testTrigger();
+    /**
+     * Determines if the event produces a trigger.
+     * 
+     * @return Returns <code>true</code> if the event produces a trigger
+     * and <code>false</code> if it does not.
+     */
+    @Override
+    protected boolean triggerDecision(EventHeader event) {
+        // If there is a list of clusters present for this event,
+        // check whether it passes the trigger conditions.
+        if (event.hasCollection(Cluster.class, clusterCollectionName)) {
+            return testTrigger();
         }
         
         // Otherwise, this event can not produce a trigger and should
         // return false automatically.
         else { return false; }
-	}
+    }
     
     /**
      * Checks whether the argument cluster possesses the minimum
@@ -394,7 +394,7 @@
      * and <code>false</code> if the cluster does not.
      */
     private boolean clusterHitCountCut(Cluster cluster) {
-    	return (getValueClusterHitCount(cluster) >= minHitCount);
+        return (getValueClusterHitCount(cluster) >= minHitCount);
     }
     
     /**
@@ -406,12 +406,12 @@
      * and <code>false</code> if the cluster does not.
      */
     private boolean clusterSeedEnergyCut(Cluster cluster) {
-    	// Get the cluster seed energy.
-    	double energy = getValueClusterSeedEnergy(cluster);
-    	
-    	// Check that it is above the minimum threshold and below the
-    	// maximum threshold.
-    	return (energy < seedEnergyHigh) && (energy > seedEnergyLow);
+        // Get the cluster seed energy.
+        double energy = getValueClusterSeedEnergy(cluster);
+        
+        // Check that it is above the minimum threshold and below the
+        // maximum threshold.
+        return (energy < seedEnergyHigh) && (energy > seedEnergyLow);
     }
     
     /**
@@ -423,12 +423,12 @@
      * and <code>false</code> if the cluster does not.
      */
     private boolean clusterTotalEnergyCut(Cluster cluster) {
-    	// Get the total cluster energy.
-    	double energy = getValueClusterTotalEnergy(cluster);
-    	
-    	// Check that it is above the minimum threshold and below the
-    	// maximum threshold.
-    	return (energy < clusterEnergyHigh) && (energy > clusterEnergyLow);
+        // Get the total cluster energy.
+        double energy = getValueClusterTotalEnergy(cluster);
+        
+        // Check that it is above the minimum threshold and below the
+        // maximum threshold.
+        return (energy < clusterEnergyHigh) && (energy > clusterEnergyLow);
     }
     
     /**
@@ -450,7 +450,7 @@
      * @return Returns the cut value.
      */
     private double getValueClusterTotalEnergy(Cluster cluster) {
-    	return cluster.getEnergy();
+        return cluster.getEnergy();
     }
     
     /**
@@ -461,7 +461,7 @@
      * @return Returns the cut value.
      */
     private int getValueClusterHitCount(Cluster cluster) {
-    	return cluster.getCalorimeterHits().size();
+        return cluster.getCalorimeterHits().size();
     }
     
     /**
@@ -472,7 +472,7 @@
      * @return Returns the cut value.
      */
     private double getValueClusterSeedEnergy(Cluster cluster) {
-    	return cluster.getCalorimeterHits().get(0).getCorrectedEnergy();
+        return cluster.getCalorimeterHits().get(0).getCorrectedEnergy();
     }
     
     /**
@@ -483,16 +483,16 @@
      * @return Returns the cut value.
      */
     private double getValueCoplanarity(Cluster[] clusterPair) {
-    	// Get the cluster angles.
-    	double[] clusterAngle = new double[2];
-    	for(int i = 0; i < 2; i++) {
+        // Get the cluster angles.
+        double[] clusterAngle = new double[2];
+        for(int i = 0; i < 2; i++) {
             double position[] = clusterPair[i].getCalorimeterHits().get(0).getPosition();
             //clusterAngle[i] = Math.toDegrees(Math.atan2(position[1], position[0] - originX));
             //clusterAngle[i] = (clusterAngle[i] + 180.0) % 180.0;
             clusterAngle[i] = (Math.toDegrees(Math.atan2(position[1], position[0] - originX)) + 180.0) % 180.0;
-    	}
-    	
-    	// Calculate the coplanarity cut value.
+        }
+        
+        // Calculate the coplanarity cut value.
         return Math.abs(clusterAngle[1] - clusterAngle[0]);
     }
     
@@ -504,7 +504,7 @@
      * @return Returns the cut value.
      */
     private double getValueEnergyDifference(Cluster[] clusterPair) {
-    	return clusterPair[0].getEnergy() - clusterPair[1].getEnergy();
+        return clusterPair[0].getEnergy() - clusterPair[1].getEnergy();
     }
     
     /**
@@ -515,15 +515,15 @@
      * @return Returns the cut value.
      */
     private double getValueEnergySlope(Cluster[] clusterPair) {
-    	// E + R*F
-    	// Get the low energy cluster energy.
-    	double slopeParamE = clusterPair[1].getEnergy();
-    	
-    	// Get the low energy cluster radial distance.
-    	double slopeParamR = getClusterDistance(clusterPair[1]);
-    	
-    	// Calculate the energy slope.
-    	return slopeParamE + slopeParamR * energySlopeParamF;
+        // E + R*F
+        // Get the low energy cluster energy.
+        double slopeParamE = clusterPair[1].getEnergy();
+        
+        // Get the low energy cluster radial distance.
+        double slopeParamR = getClusterDistance(clusterPair[1]);
+        
+        // Calculate the energy slope.
+        return slopeParamE + slopeParamR * energySlopeParamF;
     }
     
     /**
@@ -534,7 +534,7 @@
      * @return Returns the cut value.
      */
     private double getValueEnergySum(Cluster[] clusterPair) {
-    	return clusterPair[0].getEnergy() + clusterPair[1].getEnergy();
+        return clusterPair[0].getEnergy() + clusterPair[1].getEnergy();
     }
     
     /**
@@ -570,7 +570,7 @@
      * @return true if pair is found, false otherwise
      */
     private boolean pairEnergySlopeCut(Cluster[] clusterPair) {
-    	return (getValueEnergySlope(clusterPair) > energySlopeLow);
+        return (getValueEnergySlope(clusterPair) > energySlopeLow);
     }
     
     /**
@@ -582,175 +582,175 @@
      * the cut and <code>false</code> if it does not.
      */
     private boolean pairEnergySumCut(Cluster[] clusterPair) {
-    	// Get the energy sum value.
-    	double energySum = getValueEnergySum(clusterPair);
-    	
-    	// Check that it is within the allowed range.
+        // Get the energy sum value.
+        double energySum = getValueEnergySum(clusterPair);
+        
+        // Check that it is within the allowed range.
         return (energySum < energySumHigh) && (energySum > energySumLow);
     }
-	
+    
     private void setBackgroundCuts(int backgroundLevel) {
-    	// Make sure that the background level is valid.
-    	if(backgroundLevel < 1 || backgroundLevel > 10) {
-    		throw new RuntimeException(String.format("Trigger cuts are undefined for background level %d.", backgroundLevel));
-    	}
-    	
-    	// Otherwise, set the trigger cuts. Certain cuts are constant
-    	// across all background levels.
-    	clusterEnergyLow = 0.000;
-    	seedEnergyLow = 0.100;
-    	
-    	// Set the variable values.
-    	if(backgroundLevel == 1) {
-    		clusterEnergyHigh = 1.700;
-    		seedEnergyHigh = 1.300;
-    		energySumLow = 0.400;
-    		energySumHigh = 2.00;
-    		energyDifferenceHigh = 1.500;
-    		energySlopeLow = 1.0;
-    		coplanarityHigh = 40;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 2) {
-    		clusterEnergyHigh = 1.600;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.300;
-    		energySumHigh = 2.00;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.8;
-    		coplanarityHigh = 40;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 3) {
-    		clusterEnergyHigh = 1.600;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.200;
-    		energySumHigh = 2.000;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.7;
-    		coplanarityHigh = 40;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 4) {
-    		clusterEnergyHigh = 1.500;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.500;
-    		energySumHigh = 1.950;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.6;
-    		coplanarityHigh = 40;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 5) {
-    		clusterEnergyHigh = 1.500;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.400;
-    		energySumHigh = 2.000;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.6;
-    		coplanarityHigh = 45;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 6) {
-    		clusterEnergyHigh = 1.500;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.200;
-    		energySumHigh = 1.950;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.6;
-    		coplanarityHigh = 55;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 7) {
-    		clusterEnergyHigh = 1.700;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.200;
-    		energySumHigh = 2.000;
-    		energyDifferenceHigh = 1.500;
-    		energySlopeLow = 0.6;
-    		coplanarityHigh = 60;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 8) {
-    		clusterEnergyHigh = 1.700;
-    		seedEnergyHigh = 1.300;
-    		energySumLow = 0.200;
-    		energySumHigh = 2.000;
-    		energyDifferenceHigh = 1.500;
-    		energySlopeLow = 0.6;
-    		coplanarityHigh = 65;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 9) {
-    		clusterEnergyHigh = 1.500;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.400;
-    		energySumHigh = 1.950;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.5;
-    		coplanarityHigh = 60;
-    		minHitCount = 2;
-    	} else if(backgroundLevel == 10) {
-    		clusterEnergyHigh = 1.500;
-    		seedEnergyHigh = 1.200;
-    		energySumLow = 0.400;
-    		energySumHigh = 2.000;
-    		energyDifferenceHigh = 1.400;
-    		energySlopeLow = 0.5;
-    		coplanarityHigh = 65;
-    		minHitCount = 2;
-    	}
-    }
-    
-	/**
-	 * Tests all of the current cluster pairs for triggers.
-	 * 
-	 * @return Returns <code>true</code> if one of the cluster pairs
-	 * passes all of the cluster cuts and <code>false</code> otherwise.
-	 */
+        // Make sure that the background level is valid.
+        if(backgroundLevel < 1 || backgroundLevel > 10) {
+            throw new RuntimeException(String.format("Trigger cuts are undefined for background level %d.", backgroundLevel));
+        }
+        
+        // Otherwise, set the trigger cuts. Certain cuts are constant
+        // across all background levels.
+        clusterEnergyLow = 0.000;
+        seedEnergyLow = 0.100;
+        
+        // Set the variable values.
+        if(backgroundLevel == 1) {
+            clusterEnergyHigh = 1.700;
+            seedEnergyHigh = 1.300;
+            energySumLow = 0.400;
+            energySumHigh = 2.00;
+            energyDifferenceHigh = 1.500;
+            energySlopeLow = 1.0;
+            coplanarityHigh = 40;
+            minHitCount = 2;
+        } else if(backgroundLevel == 2) {
+            clusterEnergyHigh = 1.600;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.300;
+            energySumHigh = 2.00;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.8;
+            coplanarityHigh = 40;
+            minHitCount = 2;
+        } else if(backgroundLevel == 3) {
+            clusterEnergyHigh = 1.600;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.200;
+            energySumHigh = 2.000;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.7;
+            coplanarityHigh = 40;
+            minHitCount = 2;
+        } else if(backgroundLevel == 4) {
+            clusterEnergyHigh = 1.500;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.500;
+            energySumHigh = 1.950;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.6;
+            coplanarityHigh = 40;
+            minHitCount = 2;
+        } else if(backgroundLevel == 5) {
+            clusterEnergyHigh = 1.500;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.400;
+            energySumHigh = 2.000;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.6;
+            coplanarityHigh = 45;
+            minHitCount = 2;
+        } else if(backgroundLevel == 6) {
+            clusterEnergyHigh = 1.500;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.200;
+            energySumHigh = 1.950;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.6;
+            coplanarityHigh = 55;
+            minHitCount = 2;
+        } else if(backgroundLevel == 7) {
+            clusterEnergyHigh = 1.700;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.200;
+            energySumHigh = 2.000;
+            energyDifferenceHigh = 1.500;
+            energySlopeLow = 0.6;
+            coplanarityHigh = 60;
+            minHitCount = 2;
+        } else if(backgroundLevel == 8) {
+            clusterEnergyHigh = 1.700;
+            seedEnergyHigh = 1.300;
+            energySumLow = 0.200;
+            energySumHigh = 2.000;
+            energyDifferenceHigh = 1.500;
+            energySlopeLow = 0.6;
+            coplanarityHigh = 65;
+            minHitCount = 2;
+        } else if(backgroundLevel == 9) {
+            clusterEnergyHigh = 1.500;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.400;
+            energySumHigh = 1.950;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.5;
+            coplanarityHigh = 60;
+            minHitCount = 2;
+        } else if(backgroundLevel == 10) {
+            clusterEnergyHigh = 1.500;
+            seedEnergyHigh = 1.200;
+            energySumLow = 0.400;
+            energySumHigh = 2.000;
+            energyDifferenceHigh = 1.400;
+            energySlopeLow = 0.5;
+            coplanarityHigh = 65;
+            minHitCount = 2;
+        }
+    }
+    
+    /**
+     * Tests all of the current cluster pairs for triggers.
+     * 
+     * @return Returns <code>true</code> if one of the cluster pairs
+     * passes all of the cluster cuts and <code>false</code> otherwise.
+     */
     private boolean testTrigger() {
-    	// Get the list of cluster pairs.
-    	List<Cluster[]> clusterPairs = getClusterPairsTopBot();
+        // Get the list of cluster pairs.
+        List<Cluster[]> clusterPairs = getClusterPairsTopBot();
         
         // Iterate over the cluster pairs and perform each of the cluster
         // pair cuts on them. A cluster pair that passes all of the
         // cuts registers as a trigger.
-    	pairLoop:
+        pairLoop:
         for (Cluster[] clusterPair : clusterPairs) {
-    		// Increment the number of processed cluster pairs.
-    		allPairs++;
-    		
-    		// ==== Pair Energy Sum Cut ====================================
-    		// =============================================================
-    		// If the cluster fails the cut, skip to the next pair.
-    		if(!pairEnergySumCut(clusterPair)) { continue pairLoop; }
-    		
-    		// Otherwise, note that it passed the cut.
-    		pairEnergySumCount++;
-        	
-    		// ==== Pair Energy Difference Cut =============================
-    		// =============================================================
-    		// If the cluster fails the cut, skip to the next pair.
-    		if(!pairEnergyDifferenceCut(clusterPair)) { continue pairLoop; }
-    		
-    		// Otherwise, note that it passed the cut.
-    		pairEnergyDifferenceCount++;
-    		
-    		// ==== Pair Energy Slope Cut ==================================
-    		// =============================================================
-    		// If the cluster fails the cut, skip to the next pair.
-    		//if(!energyDistanceCut(clusterPair)) { continue pairLoop; }
-    		if(!pairEnergySlopeCut(clusterPair)) { continue pairLoop; }
-    		
-    		// Otherwise, note that it passed the cut.
-    		pairEnergySlopeCount++;
-    		
-    		// ==== Pair Coplanarity Cut ===================================
-    		// =============================================================
-    		// If the cluster fails the cut, skip to the next pair.
-    		if(!pairCoplanarityCut(clusterPair)) { continue pairLoop; }
-    		
-    		// Otherwise, note that it passed the cut.
-    		pairCoplanarityCount++;
-    		
-    		// Clusters that pass all of the pair cuts produce a trigger.
-    		return true;
+            // Increment the number of processed cluster pairs.
+            allPairs++;
+            
+            // ==== Pair Energy Sum Cut ====================================
+            // =============================================================
+            // If the cluster fails the cut, skip to the next pair.
+            if(!pairEnergySumCut(clusterPair)) { continue pairLoop; }
+            
+            // Otherwise, note that it passed the cut.
+            pairEnergySumCount++;
+            
+            // ==== Pair Energy Difference Cut =============================
+            // =============================================================
+            // If the cluster fails the cut, skip to the next pair.
+            if(!pairEnergyDifferenceCut(clusterPair)) { continue pairLoop; }
+            
+            // Otherwise, note that it passed the cut.
+            pairEnergyDifferenceCount++;
+            
+            // ==== Pair Energy Slope Cut ==================================
+            // =============================================================
+            // If the cluster fails the cut, skip to the next pair.
+            //if(!energyDistanceCut(clusterPair)) { continue pairLoop; }
+            if(!pairEnergySlopeCut(clusterPair)) { continue pairLoop; }
+            
+            // Otherwise, note that it passed the cut.
+            pairEnergySlopeCount++;
+            
+            // ==== Pair Coplanarity Cut ===================================
+            // =============================================================
+            // If the cluster fails the cut, skip to the next pair.
+            if(!pairCoplanarityCut(clusterPair)) { continue pairLoop; }
+            
+            // Otherwise, note that it passed the cut.
+            pairCoplanarityCount++;
+            
+            // Clusters that pass all of the pair cuts produce a trigger.
+            return true;
         }
         
         // If the loop terminates without producing a trigger, there
-    	// are no cluster pairs which meet the trigger conditions.
+        // are no cluster pairs which meet the trigger conditions.
         return false;
     }
     
@@ -761,14 +761,14 @@
      * @param clusterList - The clusters to add to the queues.
      */
     private void updateClusterQueues(List<Cluster> clusterList) {
-    	// Create lists to store the top and bottom clusters.
+        // Create lists to store the top and bottom clusters.
         ArrayList<Cluster> topClusterList = new ArrayList<Cluster>();
         ArrayList<Cluster> botClusterList = new ArrayList<Cluster>();
         
         // Loop over the clusters in the cluster list.
         for (Cluster cluster : clusterList) {
-        	// If the cluster is on the top of the calorimeter, it
-        	// goes into the top cluster list.
+            // If the cluster is on the top of the calorimeter, it
+            // goes into the top cluster list.
             if (cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("iy") > 0) {
                 topClusterList.add(cluster);
             }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger.java	Wed Apr 27 11:11:32 2016
@@ -15,209 +15,209 @@
  * @author Luca Colaneri
  */
 public class FEETrigger extends TriggerDriver {
-	// Store the LCIO cluster collection name.
-	private String clusterCollectionName = "EcalClusters";
-	
-	// Store the cluster total energy trigger threshold.
-	private double energyThreshold = 1.5;
-	
-	// Track the number of over-threshold clusters in each region.
-	private int zone1Count = 0;
-	private int zone2Count = 0;
-	private int zone3Count = 0;
-	
+    // Store the LCIO cluster collection name.
+    private String clusterCollectionName = "EcalClusters";
+    
+    // Store the cluster total energy trigger threshold.
+    private double energyThreshold = 1.5;
+    
+    // Track the number of over-threshold clusters in each region.
+    private int zone1Count = 0;
+    private int zone2Count = 0;
+    private int zone3Count = 0;
+    
     // The number of cluster over threshold that must occur in a region
-	// before a trigger occurs.
-	private int zone1Prescaling = 50;
-	private int zone2Prescaling = 10;
-	
-	/**
-	 * Sets the energy threshold required for a cluster to be counted.
-	 * 
-	 * @param energyThreshold - The energy threshold in GeV.
-	 */
-	public void setEnergyThreshold(int energyThreshold) {
-		this.energyThreshold = energyThreshold;
-	}
-	
-	/**
-	 * Sets the number of events over threshold which must occur in the
-	 * first region in order for a trigger to occur.
-	 * 
-	 * @param zone1Prescaling - The number of over-threshold clusters needed
-	 * for a trigger.
-	 */
-	public void setZone1Prescaling(int zone1Prescaling) {
-		this.zone1Prescaling = zone1Prescaling;
-	}
-	
-	/**
-	 * Sets the number of events over threshold which must occur in the
-	 * second region in order for a trigger to occur.
-	 * 
-	 * @param zone2Prescaling - The number of over-threshold clusters needed
-	 * for a trigger.
-	 */
-	public void setZone2Prescaling(int zone2Prescaling) {
-		this.zone2Prescaling = zone2Prescaling;
-	}
-	
-	/**
-	 * Checks if any clusters exist over the set energy threshold and,
-	 * if they do, increments the appropriate over-threshold count
-	 * variable for the zone in which the cluster resides.
-	 * 
-	 * @param event - The event from which clusters should be extracted.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Get the list of clusters from the event.
-			List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-			
-			// Loop over the clusters and check for any that pass the threshold.
-			for(Cluster cluster : clusterList) {
-				// Check if the current cluster exceeds the energy
-				// threshold. If it does not, continue to the next
-				// cluster in the list.
-				if(cluster.getEnergy() > energyThreshold) {
-					// Get the x-index of the seed hit.
-					int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-					
-					// Determine in which region the cluster is located
-					// and increment the counter for that region. Zones
-					// are defined as:
-					// Zone 1 is -13 < ix < -4 and 14 < ix < 21  MISTAKE!!! it's all reversed!! remember!!!
-					// Zone 2 is -20 < ix < -14 and ix > 20
-					// Zone 3 is -23 <= ix < -18
+    // before a trigger occurs.
+    private int zone1Prescaling = 50;
+    private int zone2Prescaling = 10;
+    
+    /**
+     * Sets the energy threshold required for a cluster to be counted.
+     * 
+     * @param energyThreshold - The energy threshold in GeV.
+     */
+    public void setEnergyThreshold(int energyThreshold) {
+        this.energyThreshold = energyThreshold;
+    }
+    
+    /**
+     * Sets the number of events over threshold which must occur in the
+     * first region in order for a trigger to occur.
+     * 
+     * @param zone1Prescaling - The number of over-threshold clusters needed
+     * for a trigger.
+     */
+    public void setZone1Prescaling(int zone1Prescaling) {
+        this.zone1Prescaling = zone1Prescaling;
+    }
+    
+    /**
+     * Sets the number of events over threshold which must occur in the
+     * second region in order for a trigger to occur.
+     * 
+     * @param zone2Prescaling - The number of over-threshold clusters needed
+     * for a trigger.
+     */
+    public void setZone2Prescaling(int zone2Prescaling) {
+        this.zone2Prescaling = zone2Prescaling;
+    }
+    
+    /**
+     * Checks if any clusters exist over the set energy threshold and,
+     * if they do, increments the appropriate over-threshold count
+     * variable for the zone in which the cluster resides.
+     * 
+     * @param event - The event from which clusters should be extracted.
+     */
+    @Override
+    public void process(EventHeader event) {
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the list of clusters from the event.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Loop over the clusters and check for any that pass the threshold.
+            for(Cluster cluster : clusterList) {
+                // Check if the current cluster exceeds the energy
+                // threshold. If it does not, continue to the next
+                // cluster in the list.
+                if(cluster.getEnergy() > energyThreshold) {
+                    // Get the x-index of the seed hit.
+                    int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                    
+                    // Determine in which region the cluster is located
+                    // and increment the counter for that region. Zones
+                    // are defined as:
+                    // Zone 1 is -13 < ix < -4 and 14 < ix < 21  MISTAKE!!! it's all reversed!! remember!!!
+                    // Zone 2 is -20 < ix < -14 and ix > 20
+                    // Zone 3 is -23 <= ix < -18
                                         //V3
                                         /*
-					if( ix > 18 || ix < -22) { zone3Count++; }
-					if(ix < 19 && ix  > 12 )  { zone2Count++; }
-					if((ix > 4 && ix < 13) || (ix > -23 && ix < -14)) { zone1Count++; }
+                    if( ix > 18 || ix < -22) { zone3Count++; }
+                    if(ix < 19 && ix  > 12 )  { zone2Count++; }
+                    if((ix > 4 && ix < 13) || (ix > -23 && ix < -14)) { zone1Count++; }
                                         */
                                         //V2
                                         /*
-					if( ix > 18 ) { zone3Count++; }
-					if(ix < 19 && ix  > 12 || ix <-20)  { zone2Count++; }
-					if((ix > 4 && ix < 13) || (ix > -21 && ix < -14)) { zone1Count++; }
+                    if( ix > 18 ) { zone3Count++; }
+                    if(ix < 19 && ix  > 12 || ix <-20)  { zone2Count++; }
+                    if((ix > 4 && ix < 13) || (ix > -21 && ix < -14)) { zone1Count++; }
                                         */
                                         
                                         //v4/*
                                         /*
                                         if( ix > 19 || ix < -22) { zone3Count++; }
-					if(ix < 20 && ix  > 12 || ix <-20 && ix > -23)  { zone2Count++; }
-					if((ix > 4 && ix < 13) || (ix > -21 && ix < -14)) { zone1Count++; }
+                    if(ix < 20 && ix  > 12 || ix <-20 && ix > -23)  { zone2Count++; }
+                    if((ix > 4 && ix < 13) || (ix > -21 && ix < -14)) { zone1Count++; }
                                         */
                                         //V prova
                                        /* 
-					if( ix != 50 ) { zone2Count++; }
-					*/
+                    if( ix != 50 ) { zone2Count++; }
+                    */
                                         //V6
                                         /*
                                         if( ix > 19 || ix < -22) { zone3Count++; }
-					if(ix < 20 && ix  > 8 || ix <-16 && ix > -23)  { zone2Count++; }
-					if((ix > 4 && ix < 9) || (ix > -17 && ix < -14)) { zone1Count++; }
+                    if(ix < 20 && ix  > 8 || ix <-16 && ix > -23)  { zone2Count++; }
+                    if((ix > 4 && ix < 9) || (ix > -17 && ix < -14)) { zone1Count++; }
                                         */
                                         //V7
                                         /*
                                         if( ix > 19 || ix < -22) { zone3Count++; }
-					if(ix < 20 && ix  > 15 )  { zone2Count++; }
-					if((ix > 5 && ix < 16) || (ix > -23 && ix < -14)) { zone1Count++; }
+                    if(ix < 20 && ix  > 15 )  { zone2Count++; }
+                    if((ix > 5 && ix < 16) || (ix > -23 && ix < -14)) { zone1Count++; }
                                         */
                                         //V8
                                         /*
                                         if( ix > 19 || ix < -17) { zone3Count++; } //x1
-					if(ix < 20 && ix  > 9 )  { zone2Count++; }//x10
-					if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
+                    if(ix < 20 && ix  > 9 )  { zone2Count++; }//x10
+                    if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
                                         }*/
                                          //V9
                                         /*
                                         if( ix > 19 || ix < -21) { zone3Count++; } //x1
-					if(ix < 20 && ix  > 9 || ix > -22 && ix <-17)  { zone2Count++; }//x10
-					if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
+                    if(ix < 20 && ix  > 9 || ix > -22 && ix <-17)  { zone2Count++; }//x10
+                    if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
                                         */ 
                                         //10
                                         
                                         /*
                                         if( ix > 19 || ix < -22) { zone3Count++; } //x1
-					if(ix < 20 && ix  > 9 || ix > -22 && ix <-17)  { zone2Count++; }//x10
-					if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
+                    if(ix < 20 && ix  > 9 || ix > -22 && ix <-17)  { zone2Count++; }//x10
+                    if((ix > 5 && ix < 10) || (ix > -18 && ix < -14)) { zone1Count++; }    //x50
                                         */
                                         
                                         //V11
                                         
                                         if( ix > 19 || ix < -22) { zone3Count++; } //x1
-					if(ix < 20 && ix  > 11 || ix > -22 && ix <-19)  { zone2Count++; }//x10
-					if((ix > 5 && ix < 12) || (ix > -20 && ix < -14)) { zone1Count++; }    //x50
+                    if(ix < 20 && ix  > 11 || ix > -22 && ix <-19)  { zone2Count++; }//x10
+                    if((ix > 5 && ix < 12) || (ix > -20 && ix < -14)) { zone1Count++; }    //x50
                                 
                                 }
-			}
-		}
-		
-		// Run the superclass event processing.
-		super.process(event);
-	}
-	
-	/**
-	 * Checks whether or not a trigger occurred.
-	 * 
-	 * @param event - The event on which to base the trigger decision.
-	 * @return Returns <code>true</code> if a trigger occurred and <code>
-	 * false</code> if a trigger did not.
-	 */
-	@Override
-	protected boolean triggerDecision(EventHeader event) {
-		// Check if the event has clusters. An event with no clusters
-		// should never result in a trigger.
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Check if any of the zone counts are high enough to trigger.
-			return triggerTest();
-		}
-		
-		// Events without clusters can not trigger.
-		else { return false; }
-	}
-	
-	/**
-	 * Checks if any of the regional counts are sufficiently high to
-	 * register a trigger.
-	 * 
-	 * @return Returns <code>true</code> if a region has enough clusters
-	 * to trigger and <code>false</code> otherwise.
-	 */
-	private boolean triggerTest() {
-		// Track whether a trigger occurred.
-		boolean trigger = false;
-		
-		// If any clusters occur in zone 3, reset the count and note
-		// that a trigger occurred.
-		if(zone3Count > 0) {
-			zone3Count = 0;
+            }
+        }
+        
+        // Run the superclass event processing.
+        super.process(event);
+    }
+    
+    /**
+     * Checks whether or not a trigger occurred.
+     * 
+     * @param event - The event on which to base the trigger decision.
+     * @return Returns <code>true</code> if a trigger occurred and <code>
+     * false</code> if a trigger did not.
+     */
+    @Override
+    protected boolean triggerDecision(EventHeader event) {
+        // Check if the event has clusters. An event with no clusters
+        // should never result in a trigger.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Check if any of the zone counts are high enough to trigger.
+            return triggerTest();
+        }
+        
+        // Events without clusters can not trigger.
+        else { return false; }
+    }
+    
+    /**
+     * Checks if any of the regional counts are sufficiently high to
+     * register a trigger.
+     * 
+     * @return Returns <code>true</code> if a region has enough clusters
+     * to trigger and <code>false</code> otherwise.
+     */
+    private boolean triggerTest() {
+        // Track whether a trigger occurred.
+        boolean trigger = false;
+        
+        // If any clusters occur in zone 3, reset the count and note
+        // that a trigger occurred.
+        if(zone3Count > 0) {
+            zone3Count = 0;
                          if(zone2Count==zone2Prescaling){zone2Count=0;}
                          if(zone1Count==zone1Prescaling){zone1Count=0;}
-			trigger = true;
-		}
-		
-		// If zone 2 has sufficient clusters (100 by default) to
-		// trigger, reset its count and note that a trigger occurred.
-		else if(zone2Count == zone2Prescaling) {
-			zone2Count = 0;
+            trigger = true;
+        }
+        
+        // If zone 2 has sufficient clusters (100 by default) to
+        // trigger, reset its count and note that a trigger occurred.
+        else if(zone2Count == zone2Prescaling) {
+            zone2Count = 0;
                         if(zone3Count>0){zone3Count=0;}
                         if(zone1Count==zone1Prescaling){zone1Count=0;}
-			trigger = true;
-		}
-		
-		// If zone 3 has sufficient clusters (1000 by default) to
-		// trigger, reset its count and note that a trigger occurred.
-		else if(zone1Count == zone1Prescaling) {
-			zone1Count = 0;
+            trigger = true;
+        }
+        
+        // If zone 3 has sufficient clusters (1000 by default) to
+        // trigger, reset its count and note that a trigger occurred.
+        else if(zone1Count == zone1Prescaling) {
+            zone1Count = 0;
                         if(zone3Count>0){zone3Count=0;}
                         if(zone2Count==zone2Prescaling){zone2Count=0;}
-			trigger = true;
-		}
-		
-		// Return whether or not a trigger occurred.
-		return trigger;
-	}
+            trigger = true;
+        }
+        
+        // Return whether or not a trigger occurred.
+        return trigger;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger2.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger2.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/FEETrigger2.java	Wed Apr 27 11:11:32 2016
@@ -15,159 +15,159 @@
  * @author Luca Colaneri
  */
 public class FEETrigger2 extends TriggerDriver {
-	// Store the LCIO cluster collection name.
-	private String clusterCollectionName = "EcalClusters";
-	
-	// Store the cluster total energy trigger threshold.
-	private double energyThreshold = 1.5;
-	
-	// Track the number of over-threshold clusters in each region.
-	private int zone1Count = 0;
-	private int zone2Count = 0;
-	private int zone3Count = 0;
+    // Store the LCIO cluster collection name.
+    private String clusterCollectionName = "EcalClusters";
+    
+    // Store the cluster total energy trigger threshold.
+    private double energyThreshold = 1.5;
+    
+    // Track the number of over-threshold clusters in each region.
+    private int zone1Count = 0;
+    private int zone2Count = 0;
+    private int zone3Count = 0;
         private int zone4Count = 0;
-	
+    
     // The number of cluster over threshold that must occur in a region
-	// before a trigger occurs.
-	private int zone1Prescaling = 1000;
-	private int zone2Prescaling = 70;
-	private int zone4Prescaling = 200;
-	/**
-	 * Sets the energy threshold required for a cluster to be counted.
-	 * 
-	 * @param energyThreshold - The energy threshold in GeV.
-	 */
-	public void setEnergyThreshold(int energyThreshold) {
-		this.energyThreshold = energyThreshold;
-	}
-	
-	/**
-	 * Sets the number of events over threshold which must occur in the
-	 * first region in order for a trigger to occur.
-	 * 
-	 * @param zone1Prescaling - The number of over-threshold clusters needed
-	 * for a trigger.
-	 */
-	public void setZone1Prescaling(int zone1Prescaling) {
-		this.zone1Prescaling = zone1Prescaling;
-	}
-	
-	/**
-	 * Sets the number of events over threshold which must occur in the
-	 * second region in order for a trigger to occur.
-	 * 
-	 * @param zone2Prescaling - The number of over-threshold clusters needed
-	 * for a trigger.
-	 */
-	public void setZone2Prescaling(int zone2Prescaling) {
-		this.zone2Prescaling = zone2Prescaling;
-	}
-	
-	/**
-	 * Checks if any clusters exist over the set energy threshold and,
-	 * if they do, increments the appropriate over-threshold count
-	 * variable for the zone in which the cluster resides.
-	 * 
-	 * @param event - The event from which clusters should be extracted.
-	 */
-	@Override
-	public void process(EventHeader event) {
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Get the list of clusters from the event.
-			List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
-			
-			// Loop over the clusters and check for any that pass the threshold.
-			for(Cluster cluster : clusterList) {
-				// Check if the current cluster exceeds the energy
-				// threshold. If it does not, continue to the next
-				// cluster in the list.
-				if(cluster.getEnergy() > energyThreshold) {
-					// Get the x-index of the seed hit.
-					int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
-					
-					// Determine in which region the cluster is located
-					// and increment the counter for that region. Zones
-					// are defined as:
-					// Zone 1 is -13 < ix < -4 and 14 < ix < 21
-					// Zone 2 is -20 < ix < -14 and ix > 20
-					// Zone 3 is -23 <= ix < -19
-					if(-23 <= ix && ix < -19) { zone3Count++; }
-					if((-20 < ix && ix < -14))  { zone2Count++; }
-					if((-13 < ix && ix < -4) || (14 < ix && ix < 21)) { zone1Count++; }
+    // before a trigger occurs.
+    private int zone1Prescaling = 1000;
+    private int zone2Prescaling = 70;
+    private int zone4Prescaling = 200;
+    /**
+     * Sets the energy threshold required for a cluster to be counted.
+     * 
+     * @param energyThreshold - The energy threshold in GeV.
+     */
+    public void setEnergyThreshold(int energyThreshold) {
+        this.energyThreshold = energyThreshold;
+    }
+    
+    /**
+     * Sets the number of events over threshold which must occur in the
+     * first region in order for a trigger to occur.
+     * 
+     * @param zone1Prescaling - The number of over-threshold clusters needed
+     * for a trigger.
+     */
+    public void setZone1Prescaling(int zone1Prescaling) {
+        this.zone1Prescaling = zone1Prescaling;
+    }
+    
+    /**
+     * Sets the number of events over threshold which must occur in the
+     * second region in order for a trigger to occur.
+     * 
+     * @param zone2Prescaling - The number of over-threshold clusters needed
+     * for a trigger.
+     */
+    public void setZone2Prescaling(int zone2Prescaling) {
+        this.zone2Prescaling = zone2Prescaling;
+    }
+    
+    /**
+     * Checks if any clusters exist over the set energy threshold and,
+     * if they do, increments the appropriate over-threshold count
+     * variable for the zone in which the cluster resides.
+     * 
+     * @param event - The event from which clusters should be extracted.
+     */
+    @Override
+    public void process(EventHeader event) {
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Get the list of clusters from the event.
+            List<Cluster> clusterList = event.get(Cluster.class, clusterCollectionName);
+            
+            // Loop over the clusters and check for any that pass the threshold.
+            for(Cluster cluster : clusterList) {
+                // Check if the current cluster exceeds the energy
+                // threshold. If it does not, continue to the next
+                // cluster in the list.
+                if(cluster.getEnergy() > energyThreshold) {
+                    // Get the x-index of the seed hit.
+                    int ix = cluster.getCalorimeterHits().get(0).getIdentifierFieldValue("ix");
+                    
+                    // Determine in which region the cluster is located
+                    // and increment the counter for that region. Zones
+                    // are defined as:
+                    // Zone 1 is -13 < ix < -4 and 14 < ix < 21
+                    // Zone 2 is -20 < ix < -14 and ix > 20
+                    // Zone 3 is -23 <= ix < -19
+                    if(-23 <= ix && ix < -19) { zone3Count++; }
+                    if((-20 < ix && ix < -14))  { zone2Count++; }
+                    if((-13 < ix && ix < -4) || (14 < ix && ix < 21)) { zone1Count++; }
                                         if(ix>20){zone4Count++;}
-				}
-			}
-		}
-		
-		// Run the superclass event processing.
-		super.process(event);
-	}
-	
-	/**
-	 * Checks whether or not a trigger occurred.
-	 * 
-	 * @param event - The event on which to base the trigger decision.
-	 * @return Returns <code>true</code> if a trigger occurred and <code>
-	 * false</code> if a trigger did not.
-	 */
-	@Override
-	protected boolean triggerDecision(EventHeader event) {
-		// Check if the event has clusters. An event with no clusters
-		// should never result in a trigger.
-		if(event.hasCollection(Cluster.class, clusterCollectionName)) {
-			// Check if any of the zone counts are high enough to trigger.
-			return triggerTest();
-		}
-		
-		// Events without clusters can not trigger.
-		else { return false; }
-	}
-	
-	/**
-	 * Checks if any of the regional counts are sufficiently high to
-	 * register a trigger.
-	 * 
-	 * @return Returns <code>true</code> if a region has enough clusters
-	 * to trigger and <code>false</code> otherwise.
-	 */
-	private boolean triggerTest() {
-		// Track whether a trigger occurred.
-		boolean trigger = false;
-		
-		// If any clusters occur in zone 3, reset the count and note
-		// that a trigger occurred.
-		if(zone3Count > 0) {
-			zone3Count = 0;
+                }
+            }
+        }
+        
+        // Run the superclass event processing.
+        super.process(event);
+    }
+    
+    /**
+     * Checks whether or not a trigger occurred.
+     * 
+     * @param event - The event on which to base the trigger decision.
+     * @return Returns <code>true</code> if a trigger occurred and <code>
+     * false</code> if a trigger did not.
+     */
+    @Override
+    protected boolean triggerDecision(EventHeader event) {
+        // Check if the event has clusters. An event with no clusters
+        // should never result in a trigger.
+        if(event.hasCollection(Cluster.class, clusterCollectionName)) {
+            // Check if any of the zone counts are high enough to trigger.
+            return triggerTest();
+        }
+        
+        // Events without clusters can not trigger.
+        else { return false; }
+    }
+    
+    /**
+     * Checks if any of the regional counts are sufficiently high to
+     * register a trigger.
+     * 
+     * @return Returns <code>true</code> if a region has enough clusters
+     * to trigger and <code>false</code> otherwise.
+     */
+    private boolean triggerTest() {
+        // Track whether a trigger occurred.
+        boolean trigger = false;
+        
+        // If any clusters occur in zone 3, reset the count and note
+        // that a trigger occurred.
+        if(zone3Count > 0) {
+            zone3Count = 0;
                          if(zone2Count==zone2Prescaling){zone2Count=0;}
                          if(zone1Count==zone1Prescaling){zone1Count=0;}
-			trigger = true;
-		}
-		
-		// If zone 2 has sufficient clusters (100 by default) to
-		// trigger, reset its count and note that a trigger occurred.
-		else if(zone2Count == zone2Prescaling) {
-			zone2Count = 0;
+            trigger = true;
+        }
+        
+        // If zone 2 has sufficient clusters (100 by default) to
+        // trigger, reset its count and note that a trigger occurred.
+        else if(zone2Count == zone2Prescaling) {
+            zone2Count = 0;
                         if(zone3Count>0){zone3Count=0;}
                         if(zone1Count==zone1Prescaling){zone1Count=0;}
-			trigger = true;
-		}
-		
-		// If zone 3 has sufficient clusters (1000 by default) to
-		// trigger, reset its count and note that a trigger occurred.
-		else if(zone1Count == zone1Prescaling) {
-			zone1Count = 0;
+            trigger = true;
+        }
+        
+        // If zone 3 has sufficient clusters (1000 by default) to
+        // trigger, reset its count and note that a trigger occurred.
+        else if(zone1Count == zone1Prescaling) {
+            zone1Count = 0;
                         if(zone3Count>0){zone3Count=0;}
                         if(zone2Count==zone2Prescaling){zone2Count=0;}
-			trigger = true;
-		}
-		else if(zone4Count == zone4Prescaling) {
-			zone4Count = 0;
+            trigger = true;
+        }
+        else if(zone4Count == zone4Prescaling) {
+            zone4Count = 0;
                         if(zone3Count>0){zone3Count=0;}
                         if(zone2Count==zone2Prescaling){zone2Count=0;}
                         if(zone1Count==zone1Prescaling){zone1Count=0;}
-			trigger = true;
-		}
-		// Return whether or not a trigger occurred.
-		return trigger;
-	}
+            trigger = true;
+        }
+        // Return whether or not a trigger occurred.
+        return trigger;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/LCIOReadScript.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/LCIOReadScript.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/LCIOReadScript.java	Wed Apr 27 11:11:32 2016
@@ -10,91 +10,91 @@
 import org.lcsim.lcio.LCIOWriter;
 
 public class LCIOReadScript {
-	public static void main(String[] args) {
-		// Make sure there arguments are valid.
-		if(args.length != 2) {
-			System.err.println("Error: Arguments must be [Input_File] [Output_File]");
-			System.exit(1);
-		}
-		
-		// Set the input/output files.
-		File inputFile = new File(args[0]);
-		File outputFile = new File(args[1]);
-		
-		// Make sure that the input file exists.
-		if(!inputFile.canRead()) {
-			System.err.println("Error: Input file can not be found.");
-			System.exit(1);
-		}
-		
-		// Create an LCIO reader to read it in.
-		LCIOReader reader = null;
-		try { reader = new LCIOReader(inputFile); }
-		catch(IOException e) {
-			e.printStackTrace();
-			System.exit(1);
-		}
-		
-		// Create an LCIO writer to output the new file.
-		LCIOWriter writer = null;
-		try { writer = new LCIOWriter(outputFile); }
-		catch(IOException e) {
-			e.printStackTrace();
-			System.exit(1);
-		}
-		
-		// Keep looping through events until there are no more.
-		while(true) {
-			// Try to get an event.
-			EventHeader event = null;
-			try { event = reader.read(); }
-			catch(IOException e) { }
-			
-			// If the event is still null, there either was no event
-			// or an error occurred.
-			if(event == null) { break; }
-			
-			// Get the event number to print a status update.
-			int num = event.getEventNumber();
-			if(num % 10000 == 0) { System.out.println("Parsing event " + num + "."); }
-			
-			// See if the MCParticle collection exists.
-			if(event.hasCollection(MCParticle.class, "MCParticle")) {
-				// Get the MCParticle collection from the event.
-				ArrayList<MCParticle> particleList = (ArrayList<MCParticle>) event.get(MCParticle.class, "MCParticle");
-				
-				// Remove the MCParticle collection from the event.
-				event.remove("MCParticle");
-				
-				// Make a new list for good particles which pass some test.
-				ArrayList<MCParticle> goodParticles = new ArrayList<MCParticle>();
-				
-				// Sort through the list of MCParticle objects in the
-				// full list and add good ones to the good list.
-				for(MCParticle p : particleList) {
-					if(p.getEnergy() >= 2.1) { goodParticles.add(p); }
-				}
-				
-				// Write the good particles back to the event.
-				event.put("MCParticle", goodParticles);
-			}
-			
-			// Write the event back out to the new file.
-			try { writer.write(event); }
-			catch(IOException e) {
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-		
-		// Close the reader and writer.
-		try {
-			reader.close();
-			writer.close();
-		}
-		catch(IOException e) {
-			e.printStackTrace();
-			System.exit(1);
-		}
-	}
+    public static void main(String[] args) {
+        // Make sure there arguments are valid.
+        if(args.length != 2) {
+            System.err.println("Error: Arguments must be [Input_File] [Output_File]");
+            System.exit(1);
+        }
+        
+        // Set the input/output files.
+        File inputFile = new File(args[0]);
+        File outputFile = new File(args[1]);
+        
+        // Make sure that the input file exists.
+        if(!inputFile.canRead()) {
+            System.err.println("Error: Input file can not be found.");
+            System.exit(1);
+        }
+        
+        // Create an LCIO reader to read it in.
+        LCIOReader reader = null;
+        try { reader = new LCIOReader(inputFile); }
+        catch(IOException e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+        
+        // Create an LCIO writer to output the new file.
+        LCIOWriter writer = null;
+        try { writer = new LCIOWriter(outputFile); }
+        catch(IOException e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+        
+        // Keep looping through events until there are no more.
+        while(true) {
+            // Try to get an event.
+            EventHeader event = null;
+            try { event = reader.read(); }
+            catch(IOException e) { }
+            
+            // If the event is still null, there either was no event
+            // or an error occurred.
+            if(event == null) { break; }
+            
+            // Get the event number to print a status update.
+            int num = event.getEventNumber();
+            if(num % 10000 == 0) { System.out.println("Parsing event " + num + "."); }
+            
+            // See if the MCParticle collection exists.
+            if(event.hasCollection(MCParticle.class, "MCParticle")) {
+                // Get the MCParticle collection from the event.
+                ArrayList<MCParticle> particleList = (ArrayList<MCParticle>) event.get(MCParticle.class, "MCParticle");
+                
+                // Remove the MCParticle collection from the event.
+                event.remove("MCParticle");
+                
+                // Make a new list for good particles which pass some test.
+                ArrayList<MCParticle> goodParticles = new ArrayList<MCParticle>();
+                
+                // Sort through the list of MCParticle objects in the
+                // full list and add good ones to the good list.
+                for(MCParticle p : particleList) {
+                    if(p.getEnergy() >= 2.1) { goodParticles.add(p); }
+                }
+                
+                // Write the good particles back to the event.
+                event.put("MCParticle", goodParticles);
+            }
+            
+            // Write the event back out to the new file.
+            try { writer.write(event); }
+            catch(IOException e) {
+                e.printStackTrace();
+                System.exit(1);
+            }
+        }
+        
+        // Close the reader and writer.
+        try {
+            reader.close();
+            writer.close();
+        }
+        catch(IOException e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/rate.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/rate.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/rate.java	Wed Apr 27 11:11:32 2016
@@ -435,15 +435,15 @@
      nevents++;
      
      
-    	/* natha's code for trigger
-    	List <AbstractIntData> aids = event.get(AbstractIntData.class, "TriggerBank");
-    	for (AbstractIntData aid : aids) {
-    		if (aid.getTag() == TIData.BANK_TAG) {
-    			TIData tt=(TIData)aid;
-    			if (!tt.isSingle1Trigger()) return;
+        /* natha's code for trigger
+        List <AbstractIntData> aids = event.get(AbstractIntData.class, "TriggerBank");
+        for (AbstractIntData aid : aids) {
+            if (aid.getTag() == TIData.BANK_TAG) {
+                TIData tt=(TIData)aid;
+                if (!tt.isSingle1Trigger()) return;
                         break;
-    		}
-    	}
+            }
+        }
      */ //nathans code for trigger end
      
     

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/ratesim.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/ratesim.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/luca/ratesim.java	Wed Apr 27 11:11:32 2016
@@ -238,15 +238,15 @@
      nevents++;
      
      
-    	/* natha's code for trigger
-    	List <AbstractIntData> aids = event.get(AbstractIntData.class, "TriggerBank");
-    	for (AbstractIntData aid : aids) {
-    		if (aid.getTag() == TIData.BANK_TAG) {
-    			TIData tt=(TIData)aid;
-    			if (!tt.isSingle1Trigger()) return;
+        /* natha's code for trigger
+        List <AbstractIntData> aids = event.get(AbstractIntData.class, "TriggerBank");
+        for (AbstractIntData aid : aids) {
+            if (aid.getTag() == TIData.BANK_TAG) {
+                TIData tt=(TIData)aid;
+                if (!tt.isSingle1Trigger()) return;
                         break;
-    		}
-    	}
+            }
+        }
      */ //nathans code for trigger end
      
     

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/FilterMCBunches.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/FilterMCBunches.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/FilterMCBunches.java	Wed Apr 27 11:11:32 2016
@@ -17,7 +17,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.MCParticle;
 import org.lcsim.event.RawCalorimeterHit;
@@ -70,7 +70,7 @@
     public static void main(String[] args) {
         // Set up command line parsing.
         Options options = createCommandLineOptions();
-        CommandLineParser parser = new DefaultParser();
+        CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         CommandLine cl = null;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalAnalogPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalAnalogPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalAnalogPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -22,67 +22,67 @@
  */
 public class HPSEcalAnalogPrintDriver extends Driver {
 
-	Subdetector ecal;
-	IDDecoder dec;
-	String ecalName;
-	String ecalReadoutName = "EcalHits";
-	String ecalCollectionName = null;
-	String outputFileName;
-	PrintWriter outputStream = null;
-	int flags;
+    Subdetector ecal;
+    IDDecoder dec;
+    String ecalName;
+    String ecalReadoutName = "EcalHits";
+    String ecalCollectionName = null;
+    String outputFileName;
+    PrintWriter outputStream = null;
+    int flags;
 
-	public HPSEcalAnalogPrintDriver() {
-	}
+    public HPSEcalAnalogPrintDriver() {
+    }
 
-	public void setEcalCollectionName(String ecalCollectionName) {
-		this.ecalCollectionName = ecalCollectionName;
-	}
+    public void setEcalCollectionName(String ecalCollectionName) {
+        this.ecalCollectionName = ecalCollectionName;
+    }
 
-	public void setEcalName(String ecalName) {
-		this.ecalName = ecalName;
-	}
+    public void setEcalName(String ecalName) {
+        this.ecalName = ecalName;
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	@Override
-	public void startOfData() {
-		if (ecalCollectionName == null) {
-			throw new RuntimeException("The parameter ecalCollectionName was not set!");
-		}
+    @Override
+    public void startOfData() {
+        if (ecalCollectionName == null) {
+            throw new RuntimeException("The parameter ecalCollectionName was not set!");
+        }
 
-		if (ecalName == null) {
-			throw new RuntimeException("The parameter ecalName was not set!");
-		}
+        if (ecalName == null) {
+            throw new RuntimeException("The parameter ecalName was not set!");
+        }
 
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void detectorChanged(Detector detector) {
-		// Get the Subdetector.
-		ecal = (Subdetector) detector.getSubdetector(ecalName);
-		dec = ecal.getIDDecoder();
-	}
+    public void detectorChanged(Detector detector) {
+        // Get the Subdetector.
+        ecal = (Subdetector) detector.getSubdetector(ecalName);
+        dec = ecal.getIDDecoder();
+    }
 
-	@Override
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
-			//outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
-			List<CalorimeterHit> hits = event.get(CalorimeterHit.class, ecalCollectionName);
-			for (CalorimeterHit hit : hits) {
-				dec.setID(hit.getCellID());
-				outputStream.printf("%d\t%d\t%f\t%f\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTime(), hit.getRawEnergy());
-			}
-		}
-	}
+    @Override
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
+            //outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
+            List<CalorimeterHit> hits = event.get(CalorimeterHit.class, ecalCollectionName);
+            for (CalorimeterHit hit : hits) {
+                dec.setID(hit.getCellID());
+                outputStream.printf("%d\t%d\t%f\t%f\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTime(), hit.getRawEnergy());
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalDigitalPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalDigitalPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalDigitalPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -22,70 +22,70 @@
  */
 public class HPSEcalDigitalPrintDriver extends Driver {
 
-	Subdetector ecal;
-	IDDecoder dec;
-	String ecalName = "Ecal";
-	String ecalReadoutName = "EcalHits";
-	String ecalCollectionName = "EcalRawHits";
-	String outputFileName;
-	PrintWriter outputStream = null;
-	int timeScale = 1;
-	int flags;
+    Subdetector ecal;
+    IDDecoder dec;
+    String ecalName = "Ecal";
+    String ecalReadoutName = "EcalHits";
+    String ecalCollectionName = "EcalRawHits";
+    String outputFileName;
+    PrintWriter outputStream = null;
+    int timeScale = 1;
+    int flags;
 
-	public HPSEcalDigitalPrintDriver() {
-	}
+    public HPSEcalDigitalPrintDriver() {
+    }
 
-	public void setTimeScale(int timeScale) {
-		this.timeScale = timeScale;
-	}
+    public void setTimeScale(int timeScale) {
+        this.timeScale = timeScale;
+    }
 
-	public void setEcalCollectionName(String ecalCollectionName) {
-		this.ecalCollectionName = ecalCollectionName;
-	}
+    public void setEcalCollectionName(String ecalCollectionName) {
+        this.ecalCollectionName = ecalCollectionName;
+    }
 
-	public void setEcalName(String ecalName) {
-		this.ecalName = ecalName;
-	}
+    public void setEcalName(String ecalName) {
+        this.ecalName = ecalName;
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	public void startOfData() {
-		if (ecalCollectionName == null) {
-			throw new RuntimeException("The parameter ecalCollectionName was not set!");
-		}
+    public void startOfData() {
+        if (ecalCollectionName == null) {
+            throw new RuntimeException("The parameter ecalCollectionName was not set!");
+        }
 
-		if (ecalName == null) {
-			throw new RuntimeException("The parameter ecalName was not set!");
-		}
+        if (ecalName == null) {
+            throw new RuntimeException("The parameter ecalName was not set!");
+        }
 
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void detectorChanged(Detector detector) {
-		// Get the Subdetector.
-		ecal = (Subdetector) detector.getSubdetector(ecalName);
-		dec = ecal.getIDDecoder();
-	}
+    public void detectorChanged(Detector detector) {
+        // Get the Subdetector.
+        ecal = (Subdetector) detector.getSubdetector(ecalName);
+        dec = ecal.getIDDecoder();
+    }
 
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(RawCalorimeterHit.class, ecalCollectionName)) {
-			List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, ecalCollectionName);
-			//outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
-			for (RawCalorimeterHit hit : hits) {
-				dec.setID(hit.getCellID());
-				outputStream.printf("%d\t%d\t%d\t%d\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTimeStamp() * timeScale, hit.getAmplitude());
-			}
-		}
-	}
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(RawCalorimeterHit.class, ecalCollectionName)) {
+            List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, ecalCollectionName);
+            //outputStream.println("Reading RawCalorimeterHit from event " + event.getEventNumber());
+            for (RawCalorimeterHit hit : hits) {
+                dec.setID(hit.getCellID());
+                outputStream.printf("%d\t%d\t%d\t%d\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTimeStamp() * timeScale, hit.getAmplitude());
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalRawTrackerHitPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalRawTrackerHitPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSEcalRawTrackerHitPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -22,68 +22,68 @@
  */
 public class HPSEcalRawTrackerHitPrintDriver extends Driver {
 
-	Subdetector ecal;
-	IDDecoder dec;
-	String ecalName = "Ecal";
-	String ecalReadoutName = "EcalHits";
-	String ecalCollectionName = "EcalRawHits";
-	String outputFileName;
-	PrintWriter outputStream = null;
-	int flags;
+    Subdetector ecal;
+    IDDecoder dec;
+    String ecalName = "Ecal";
+    String ecalReadoutName = "EcalHits";
+    String ecalCollectionName = "EcalRawHits";
+    String outputFileName;
+    PrintWriter outputStream = null;
+    int flags;
 
-	public HPSEcalRawTrackerHitPrintDriver() {
-	}
+    public HPSEcalRawTrackerHitPrintDriver() {
+    }
 
-	public void setEcalCollectionName(String ecalCollectionName) {
-		this.ecalCollectionName = ecalCollectionName;
-	}
+    public void setEcalCollectionName(String ecalCollectionName) {
+        this.ecalCollectionName = ecalCollectionName;
+    }
 
-	public void setEcalName(String ecalName) {
-		this.ecalName = ecalName;
-	}
+    public void setEcalName(String ecalName) {
+        this.ecalName = ecalName;
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	public void startOfData() {
-		if (ecalCollectionName == null) {
-			throw new RuntimeException("The parameter ecalCollectionName was not set!");
-		}
+    public void startOfData() {
+        if (ecalCollectionName == null) {
+            throw new RuntimeException("The parameter ecalCollectionName was not set!");
+        }
 
-		if (ecalName == null) {
-			throw new RuntimeException("The parameter ecalName was not set!");
-		}
+        if (ecalName == null) {
+            throw new RuntimeException("The parameter ecalName was not set!");
+        }
 
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void detectorChanged(Detector detector) {
-		// Get the Subdetector.
-		ecal = (Subdetector) detector.getSubdetector(ecalName);
-		dec = ecal.getIDDecoder();
-	}
+    public void detectorChanged(Detector detector) {
+        // Get the Subdetector.
+        ecal = (Subdetector) detector.getSubdetector(ecalName);
+        dec = ecal.getIDDecoder();
+    }
 
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(RawTrackerHit.class, ecalCollectionName)) {
-			//outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
-			List<RawTrackerHit> hits = event.get(RawTrackerHit.class, ecalCollectionName);
-			for (RawTrackerHit hit : hits) {
-				dec.setID(hit.getCellID());
-				outputStream.printf("%d\t%d\t%d\t%d\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTime(), hit.getADCValues().length);
-				for (int i = 0; i < hit.getADCValues().length; i++) {
-					outputStream.printf("%d\n", hit.getADCValues()[i]);
-				}
-			}
-		}
-	}
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(RawTrackerHit.class, ecalCollectionName)) {
+            //outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
+            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, ecalCollectionName);
+            for (RawTrackerHit hit : hits) {
+                dec.setID(hit.getCellID());
+                outputStream.printf("%d\t%d\t%d\t%d\n", dec.getValue("ix"), dec.getValue("iy"), hit.getTime(), hit.getADCValues().length);
+                for (int i = 0; i < hit.getADCValues().length; i++) {
+                    outputStream.printf("%d\n", hit.getADCValues()[i]);
+                }
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSGenericRawTrackerHitPrintDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSGenericRawTrackerHitPrintDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/HPSGenericRawTrackerHitPrintDriver.java	Wed Apr 27 11:11:32 2016
@@ -20,42 +20,42 @@
  */
 public class HPSGenericRawTrackerHitPrintDriver extends Driver {
 
-	String outputFileName;
-	PrintWriter outputStream = null;
+    String outputFileName;
+    PrintWriter outputStream = null;
 
-	public HPSGenericRawTrackerHitPrintDriver() {
-	}
+    public HPSGenericRawTrackerHitPrintDriver() {
+    }
 
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
+    public void setOutputFileName(String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
 
-	public void startOfData() {
-		if (outputFileName != null) {
-			try {
-				outputStream = new PrintWriter(outputFileName);
-			} catch (IOException ex) {
-				throw new RuntimeException("Invalid outputFilePath!");
-			}
-		} else {
-			outputStream = new PrintWriter(System.out, true);
-		}
-	}
+    public void startOfData() {
+        if (outputFileName != null) {
+            try {
+                outputStream = new PrintWriter(outputFileName);
+            } catch (IOException ex) {
+                throw new RuntimeException("Invalid outputFilePath!");
+            }
+        } else {
+            outputStream = new PrintWriter(System.out, true);
+        }
+    }
 
-	public void process(EventHeader event) {
-		// Get the list of ECal hits.
-		if (event.hasCollection(RawTrackerHit.class)) {
-			//outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
-			List<List<RawTrackerHit>> listOfLists = event.get(RawTrackerHit.class);
-			for (List<RawTrackerHit> hits : listOfLists) {
-				outputStream.printf("List with %d RawTrackerHits:\n", hits.size());
-				for (RawTrackerHit hit : hits) {
-					outputStream.printf("%d\t%d\n", hit.getCellID(), hit.getADCValues().length);
-					for (int i = 0; i < hit.getADCValues().length; i++) {
-						outputStream.printf("%d\n", hit.getADCValues()[i]);
-					}
-				}
-			}
-		}
-	}
+    public void process(EventHeader event) {
+        // Get the list of ECal hits.
+        if (event.hasCollection(RawTrackerHit.class)) {
+            //outputStream.println("Reading RawTrackerHits from event " + event.getEventNumber());
+            List<List<RawTrackerHit>> listOfLists = event.get(RawTrackerHit.class);
+            for (List<RawTrackerHit> hits : listOfLists) {
+                outputStream.printf("List with %d RawTrackerHits:\n", hits.size());
+                for (RawTrackerHit hit : hits) {
+                    outputStream.printf("%d\t%d\n", hit.getCellID(), hit.getADCValues().length);
+                    for (int i = 0; i < hit.getADCValues().length; i++) {
+                        outputStream.printf("%d\n", hit.getADCValues()[i]);
+                    }
+                }
+            }
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/LCIOTrackAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/LCIOTrackAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/LCIOTrackAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -24,7 +24,7 @@
  * @author Sho Uemura <[log in to unmask]>
  */
 // TODO: This is an exact duplicate of the class in the analysis.example package.
-//		 One of them should be sandboxed
+//       One of them should be sandboxed
 public class LCIOTrackAnalysis {
 
     protected Track track;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/MergeMCBunches.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/MergeMCBunches.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/MergeMCBunches.java	Wed Apr 27 11:11:32 2016
@@ -13,7 +13,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.MCParticle;
 import org.lcsim.event.SimCalorimeterHit;
@@ -49,7 +49,7 @@
     public static void main(String[] args) {
         // Set up command line parsing.
         Options options = createCommandLineOptions();
-        CommandLineParser parser = new DefaultParser();
+        CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         CommandLine cl = null;
@@ -191,4 +191,4 @@
             throw new RuntimeException(e);
         }
     }
-}
+}

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/SvtChargeIntegrator.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/SvtChargeIntegrator.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/SvtChargeIntegrator.java	Wed Apr 27 11:11:32 2016
@@ -6,17 +6,19 @@
 import java.io.IOException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.TimeZone;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
@@ -26,6 +28,7 @@
 import org.hps.conditions.svt.SvtBiasConstant.SvtBiasConstantCollection;
 import org.hps.conditions.svt.SvtMotorPosition;
 import org.hps.conditions.svt.SvtMotorPosition.SvtMotorPositionCollection;
+import org.hps.conditions.svt.SvtTimingConstants;
 import org.hps.run.database.RunManager;
 
 /**
@@ -35,9 +38,9 @@
 public class SvtChargeIntegrator {
 
     private static final double angleTolerance = 1e-4;
+    private static final double burstModeNoiseEfficiency = 0.965;
 
     /**
-     * Load SVT HV bias constants into the conditions database.
      *
      * @param args the command line arguments (requires a CSV run/file log file
      * and a MYA dump file.)
@@ -48,8 +51,9 @@
         options.addOption(new Option("r", false, "use per-run CSV log file (default is per-file)"));
         options.addOption(new Option("t", false, "use TI timestamp instead of Unix time (higher precision, but requires TI time offset in run DB)"));
         options.addOption(new Option("c", false, "get TI time offset from CSV log file instead of run DB"));
-
-        final CommandLineParser parser = new DefaultParser();
+        options.addOption(new Option("e", true, "header error file"));
+
+        final CommandLineParser parser = new PosixParser();
         CommandLine cl = null;
         try {
             cl = parser.parse(options, args);
@@ -61,6 +65,26 @@
         boolean useTI = cl.hasOption("t");
         boolean useCrawlerTI = cl.hasOption("c");
 
+        Map<Integer, Long> runErrorMap = new HashMap<Integer, Long>();
+        if (cl.hasOption("e")) {
+            try {
+                BufferedReader br = new BufferedReader(new FileReader(cl.getOptionValue("e")));
+                String line;
+                System.err.println("header error file header: " + br.readLine()); //discard the first line
+                while ((line = br.readLine()) != null) {
+                    String arr[] = line.split(" +");
+                    int run = Integer.parseInt(arr[1]);
+                    long errorTime = Long.parseLong(arr[4]);
+                    runErrorMap.put(run, errorTime);
+//                    System.out.format("%d %d\n", run, errorTime);
+                }
+            } catch (FileNotFoundException ex) {
+                Logger.getLogger(SvtChargeIntegrator.class.getName()).log(Level.SEVERE, null, ex);
+            } catch (IOException ex) {
+                Logger.getLogger(SvtChargeIntegrator.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        }
+
         if (cl.getArgs().length != 2) {
             printUsage(options);
             return;
@@ -88,9 +112,9 @@
             String line;
             System.err.println("myaData header: " + br.readLine()); //discard the first line
             if (perRun) {
-                System.out.println("run_num\tnominal_position\tnEvents\ttotalQ\ttotalQ_withbias\ttotalQ_atnom\tgatedQ\tgatedQ_withbias\tgatedQ_atnom");
+                System.out.println("run_num\tnominal_position\tnEvents\ttotalQ\ttotalQ_withbias\ttotalQ_atnom\ttotalQ_noerror\tgatedQ\tgatedQ_withbias\tgatedQ_atnom\tgatedQ_noerror\tgoodQ\tgoodQ_withbias\tgoodQ_atnom\tgoodQ_noerror");
             } else {
-                System.out.println("run_num\tfile_num\tnominal_position\tnEvents\ttotalQ\ttotalQ_withbias\ttotalQ_atnom\tgatedQ\tgatedQ_withbias\tgatedQ_atnom");
+                System.out.println("run_num\tfile_num\tnominal_position\tnEvents\ttotalQ\ttotalQ_withbias\ttotalQ_atnom\ttotalQ_noerror\tgatedQ\tgatedQ_withbias\tgatedQ_atnom\tgatedQ_noerror\tgoodQ\tgoodQ_withbias\tgoodQ_atnom\tgoodQ_noerror");
             }
 
             int currentRun = 0;
@@ -98,6 +122,7 @@
             double nominalAngleBottom = -999;
             String nominalPosition = null;
             long tiTimeOffset = 0;
+            double efficiency = 0;
             SvtBiasConstantCollection svtBiasConstants = null;
             SvtMotorPositionCollection svtPositionConstants = null;
             SvtAlignmentConstant.SvtAlignmentConstantCollection alignmentConstants = null;
@@ -120,10 +145,10 @@
                 if (runNum != currentRun) {
                     if (useTI && !useCrawlerTI) {
                         RunManager.getRunManager().setRun(runNum);
-                        if (!RunManager.getRunManager().runExists() || RunManager.getRunManager().getTriggerConfig().getTiTimeOffset() == null) {
+                        if (!RunManager.getRunManager().runExists() || RunManager.getRunManager().getRunSummary().getTiTimeOffset() == null) {
                             continue;
                         }
-                        tiTimeOffset = RunManager.getRunManager().getTriggerConfig().getTiTimeOffset();
+                        tiTimeOffset = RunManager.getRunManager().getRunSummary().getTiTimeOffset();
                         if (tiTimeOffset == 0) {
                             continue;
                         }
@@ -169,7 +194,20 @@
                         alignmentConstants = null;
                         nominalPosition = "unknown";
                     }
-
+                    efficiency = burstModeNoiseEfficiency;
+                    SvtTimingConstants svtTimingConstants;
+                    try {
+                        svtTimingConstants = DatabaseConditionsManager.getInstance().getCachedConditions(SvtTimingConstants.SvtTimingConstantsCollection.class, "svt_timing_constants").getCachedData().get(0);
+                    } catch (Exception ex) {
+                        svtTimingConstants = null;
+                    }
+                    if (svtTimingConstants != null) {
+                        if (svtTimingConstants.getOffsetTime() > 27) {
+                            efficiency *= 2.0 / 3.0; // bad latency: drop 2 out of 6 trigger phases
+                        }// otherwise, we have good latency
+                    } else {
+                        efficiency = 0;
+                    }//no latency info in conditions: give up
                     currentRun = runNum;
                 }
 
@@ -194,22 +232,40 @@
                     if (firstTI == 0 || lastTI == 0) {
                         continue;
                     }
-                    startDate = new Date((long) ((firstTI + tiTimeOffset) / 1e6));
-                    endDate = new Date((long) ((lastTI + tiTimeOffset) / 1e6));
+                    startDate = new Date((firstTI + tiTimeOffset) / 1000000);
+                    endDate = new Date((lastTI + tiTimeOffset) / 1000000);
                 } else {
                     if (firstTime == 0 || lastTime == 0) {
                         continue;
                     }
                     startDate = new Date(firstTime * 1000);
                     endDate = new Date(lastTime * 1000);
+                }
+
+                Long errorTime = runErrorMap.get(runNum);
+                Date errorDate = null;
+                if (errorTime != null) {
+                    errorDate = new Date(errorTime / 1000000);
+                    boolean isGood = Math.abs(errorDate.getTime() - startDate.getTime()) < 10 * 60 * 60 * 1000; //10 hours
+                    if (!isGood && useTI) {
+                        errorDate = new Date((errorTime + tiTimeOffset) / 1000000);
+//                        boolean isPlusOffsetGood = Math.abs(errorDatePlusOffset.getTime() - startDate.getTime()) < 10 * 60 * 60 * 1000; //10 hours
+//                        System.out.format("%d, %d, %d: %s (good: %b), %s (good: %b)\n", runNum, errorTime, tiTimeOffset, errorDate, isGood, errorDatePlusOffset, isPlusOffsetGood);
+                    }
                 }
 
                 double totalCharge = 0;
                 double totalChargeWithBias = 0;
                 double totalChargeWithBiasAtNominal = 0;
+                double totalChargeWithBiasAtNominalNoError = 0;
                 double totalGatedCharge = 0;
                 double totalGatedChargeWithBias = 0;
                 double totalGatedChargeWithBiasAtNominal = 0;
+                double totalGatedChargeWithBiasAtNominalNoError = 0;
+                double totalGoodCharge = 0;
+                double totalGoodChargeWithBias = 0;
+                double totalGoodChargeWithBiasAtNominal = 0;
+                double totalGoodChargeWithBiasAtNominalNoError = 0;
                 br.mark(1000);
 
                 while ((line = br.readLine()) != null) {
@@ -268,27 +324,41 @@
                         long dtStart = Math.max(startDate.getTime(), lastDate.getTime());
                         long dtEnd = Math.min(date.getTime(), endDate.getTime());
                         double dt = (dtEnd - dtStart) / 1000.0;
+                        double errorDt = 0;
                         if (biasConstant != null) {
                             long biasStart = Math.max(dtStart, biasConstant.getStart());
                             long biasEnd = Math.min(dtEnd, biasConstant.getEnd());
-                            biasDt = (biasEnd - biasStart) / 1000.0;
+                            biasDt = Math.max(0, biasEnd - biasStart) / 1000.0;
                             if (positionConstant != null) {
                                 long positionStart = Math.max(biasStart, positionConstant.getStart());
                                 long positionEnd = Math.min(biasEnd, positionConstant.getEnd());
-                                positionDt = (positionEnd - positionStart) / 1000.0;
+                                positionDt = Math.max(0, positionEnd - positionStart) / 1000.0;
+
+                                long errorEnd = positionStart;
+                                if (errorDate == null) {
+                                    errorEnd = positionEnd;
+                                } else if (errorDate.getTime() > dtStart) {
+                                    errorEnd = Math.min(positionEnd, errorDate.getTime());
+                                }
+                                errorDt = Math.max(0, errorEnd - positionStart) / 1000.0;
                             }
                         }
-                        double dq = dt * current; // nC
-                        double dqGated = dt * current * livetime; // nC
 //                        System.out.format("start %d end %d date %d lastDate %d current %f dt %f\n", startDate.getTime(), endDate.getTime(), date.getTime(), lastDate.getTime(), current, dt);
-                        totalCharge += dq;
-                        totalGatedCharge += dqGated;
+                        totalCharge += dt * current; // nC
+                        totalGatedCharge += dt * current * livetime;
+                        totalGoodCharge += dt * current * livetime * efficiency;
                         if (biasGood) {
                             totalChargeWithBias += biasDt * current;
                             totalGatedChargeWithBias += biasDt * current * livetime;
+                            totalGoodChargeWithBias += biasDt * current * livetime * efficiency;
                             if (positionGood) {
                                 totalChargeWithBiasAtNominal += positionDt * current;
                                 totalGatedChargeWithBiasAtNominal += positionDt * current * livetime;
+                                totalGoodChargeWithBiasAtNominal += positionDt * current * livetime * efficiency;
+
+                                totalChargeWithBiasAtNominalNoError += errorDt * current;
+                                totalGatedChargeWithBiasAtNominalNoError += errorDt * current * livetime;
+                                totalGoodChargeWithBiasAtNominalNoError += errorDt * current * livetime * efficiency;
                             }
                         }
                     }
@@ -304,11 +374,11 @@
                 }
                 if (perRun) {
                     int nEvents = Integer.parseInt(record.get(9));
-                    System.out.format("%d\t%s\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", runNum, nominalPosition, nEvents, totalCharge, totalChargeWithBias, totalChargeWithBiasAtNominal, totalGatedCharge, totalGatedChargeWithBias, totalGatedChargeWithBiasAtNominal);
+                    System.out.format("%d\t%s\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", runNum, nominalPosition, nEvents, totalCharge, totalChargeWithBias, totalChargeWithBiasAtNominal, totalChargeWithBiasAtNominalNoError, totalGatedCharge, totalGatedChargeWithBias, totalGatedChargeWithBiasAtNominal, totalGatedChargeWithBiasAtNominalNoError, totalGoodCharge, totalGoodChargeWithBias, totalGoodChargeWithBiasAtNominal, totalGoodChargeWithBiasAtNominalNoError);
                 } else {
                     int fileNum = Integer.parseInt(record.get(1));
                     int nEvents = Integer.parseInt(record.get(2));
-                    System.out.format("%d\t%d\t%s\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", runNum, fileNum, nominalPosition, nEvents, totalCharge, totalChargeWithBias, totalChargeWithBiasAtNominal, totalGatedCharge, totalGatedChargeWithBias, totalGatedChargeWithBiasAtNominal);
+                    System.out.format("%d\t%d\t%s\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", runNum, fileNum, nominalPosition, nEvents, totalCharge, totalChargeWithBias, totalChargeWithBiasAtNominal, totalChargeWithBiasAtNominalNoError, totalGatedCharge, totalGatedChargeWithBias, totalGatedChargeWithBiasAtNominal, totalGatedChargeWithBiasAtNominalNoError, totalGoodCharge, totalGoodChargeWithBias, totalGoodChargeWithBiasAtNominal, totalGoodChargeWithBiasAtNominalNoError);
                 }
             }
         } catch (Exception ex) {

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/TridentMCFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/TridentMCFilter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/meeg/TridentMCFilter.java	Wed Apr 27 11:11:32 2016
@@ -16,8 +16,45 @@
  */
 public class TridentMCFilter extends EventReconFilter {
 
+    private boolean requireFrontHits = false;
+    private double minL12Kink = -1;
+    private double maxL12Kink = -1;
+    private double minL1Kink = -1;
+    private double maxL1Kink = -1;
+    private double minL2Kink = -1;
+    private double maxL2Kink = -1;
+
+    public void setMinL12Kink(double minL12Kink) {
+        this.minL12Kink = minL12Kink;
+    }
+
+    public void setMaxL12Kink(double maxL12Kink) {
+        this.maxL12Kink = maxL12Kink;
+    }
+
+    public void setMinL1Kink(double minL1Kink) {
+        this.minL1Kink = minL1Kink;
+    }
+
+    public void setMaxL1Kink(double maxL1Kink) {
+        this.maxL1Kink = maxL1Kink;
+    }
+
+    public void setMinL2Kink(double minL2Kink) {
+        this.minL2Kink = minL2Kink;
+    }
+
+    public void setMaxL2Kink(double maxL2Kink) {
+        this.maxL2Kink = maxL2Kink;
+    }
+
+    public void setRequireFrontHits(boolean requireFrontHits) {
+        this.requireFrontHits = requireFrontHits;
+    }
+
     @Override
     public void process(EventHeader event) {
+        incrementEventProcessed();
         List<MCParticle> MCParticles = event.getMCParticles();
 
         List<MCParticle> tridentParticles = null;
@@ -39,7 +76,11 @@
         int nElectronsWithTracks = 0, nPositronsWithTracks = 0;
         MCParticle electron = null, positron = null;
 
+        particleLoop:
         for (MCParticle particle : tridentParticles) {
+            if (!trackHitMap.containsKey(particle)) {
+                continue;
+            }
             Set<Integer> layers = trackHitMap.get(particle).keySet();
             int pairCount = 0;
             for (Integer layer : layers) {
@@ -47,31 +88,74 @@
                     pairCount++;
                 }
             }
-            boolean hasTrack = (pairCount >= 5);
+            if (pairCount < 5) {
+                continue;
+            }
+            if (requireFrontHits) {
+                for (int i = 1; i < 5; i++) {
+                    if (!layers.contains(i)) {
+                        continue particleLoop;
+                    }
+                }
+            }
 
-            if (hasTrack && particle.getCharge() < 0) {
+            if (particle.getCharge() < 0) {
                 nElectronsWithTracks++;
                 electron = particle;
             }
-            if (hasTrack && particle.getCharge() > 0) {
+            if (particle.getCharge() > 0) {
                 nPositronsWithTracks++;
                 positron = particle;
             }
         }
 
         if (electron == null || positron == null) {
-            System.out.println("not enough trident daughters with tracks");
+//            System.out.println("not enough trident daughters with tracks");
             skipEvent();
         }
 
         if (nElectronsWithTracks > 1 || nPositronsWithTracks > 1) {
-            System.out.println("too many trident daughters with tracks");
+//            System.out.println("too many trident daughters with tracks");
             skipEvent();
         }
 
-//        double deflection12_ele = KinkAnalysisDriver.deflection(trackHitMap.get(electron), 0, 4);
-//        double deflection12_pos = KinkAnalysisDriver.deflection(trackHitMap.get(positron), 0, 4);
+        double deflection12_ele = KinkAnalysisDriver.deflection(trackHitMap.get(electron), 0, 4);
+        double deflection12_pos = KinkAnalysisDriver.deflection(trackHitMap.get(positron), 0, 4);
+        double deflection1_ele = KinkAnalysisDriver.deflection(trackHitMap.get(electron), 0, 2);
+        double deflection1_pos = KinkAnalysisDriver.deflection(trackHitMap.get(positron), 0, 2);
+        double deflection2_ele = KinkAnalysisDriver.deflection(trackHitMap.get(electron), 2, 4);
+        double deflection2_pos = KinkAnalysisDriver.deflection(trackHitMap.get(positron), 2, 4);
+        if (minL12Kink > 0) {
+            if (Math.abs(deflection12_ele) < minL12Kink && Math.abs(deflection12_pos) < minL12Kink) {
+                skipEvent();
+            }
+        }
+        if (maxL12Kink > 0) {
+            if (Math.abs(deflection12_ele) > maxL12Kink || Math.abs(deflection12_pos) > maxL12Kink) {
+                skipEvent();
+            }
+        }
+        if (minL1Kink > 0) {
+            if (Math.abs(deflection1_ele) < minL1Kink && Math.abs(deflection1_pos) < minL1Kink) {
+                skipEvent();
+            }
+        }
+        if (maxL1Kink > 0) {
+            if (Math.abs(deflection1_ele) > maxL1Kink || Math.abs(deflection1_pos) > maxL1Kink) {
+                skipEvent();
+            }
+        }
+        if (minL2Kink > 0) {
+            if (Math.abs(deflection2_ele) < minL2Kink && Math.abs(deflection2_pos) < minL2Kink) {
+                skipEvent();
+            }
+        }
+        if (maxL2Kink > 0) {
+            if (Math.abs(deflection2_ele) > maxL2Kink || Math.abs(deflection2_pos) > maxL2Kink) {
+                skipEvent();
+            }
+        }
+
         incrementEventPassed();
-
     }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/ExamplePlotter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/ExamplePlotter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/ExamplePlotter.java	Wed Apr 27 11:11:32 2016
@@ -4,6 +4,7 @@
 import hep.aida.IHistogram1D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
+import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
 
 import java.io.IOException;
@@ -12,9 +13,10 @@
 import java.util.logging.Logger;
 
 import org.hps.recon.tracking.BeamlineConstants;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.HelixConverter;
 import org.hps.recon.tracking.StraightLineTrack;
+import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.Track;
 import org.lcsim.fit.helicaltrack.HelicalTrackFit;
@@ -76,15 +78,9 @@
             aida.histogram1D("Track Momentum (Pz)").fill(trk.getTrackStates().get(0).getMomentum()[0]);
             aida.histogram1D("Track Chi2").fill(trk.getChi2());
 
-            SeedTrack stEle = (SeedTrack) trk;
-            SeedCandidate seedEle = stEle.getSeedCandidate();
-            HelicalTrackFit ht = seedEle.getHelix();
-            HelixConverter converter = new HelixConverter(0);
-            StraightLineTrack slt = converter.Convert(ht);
-            HPSTrack hpstrack = new HPSTrack(ht);
-            Hep3Vector[] trkatconver = hpstrack.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
-            aida.histogram1D("X (mm) @ Converter").fill(trkatconver[0].x()); // y tracker frame?
-            aida.histogram1D("Y (mm) @ Converter").fill(trkatconver[0].y()); // z tracker frame?
+            Hep3Vector trkatconver = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk, 100.0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0, event.getDetector().getFieldMap()).getReferencePoint());
+            aida.histogram1D("X (mm) @ Converter").fill(trkatconver.x()); // y tracker frame?
+            aida.histogram1D("Y (mm) @ Converter").fill(trkatconver.y()); // z tracker frame?
 
         }
     }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HPSTrackerHit.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HPSTrackerHit.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HPSTrackerHit.java	Wed Apr 27 11:11:32 2016
@@ -16,23 +16,23 @@
         double t0;
         double amp;                
       public HPSTrackerHit(
-    		long id,
-    		int time,
-    		short[] adcValues, double t0, double Amp) {
-    	this.cellId = id;
-    	this.packedID = new Identifier(id);
-    	this.time = time;
-    	this.adcValues = adcValues;
+            long id,
+            int time,
+            short[] adcValues, double t0, double Amp) {
+        this.cellId = id;
+        this.packedID = new Identifier(id);
+        this.time = time;
+        this.adcValues = adcValues;
         this.t0=t0;
         this.amp=Amp;        
     }
       
       public HPSTrackerHit(
-    		RawTrackerHit rth, double t0, double Amp) {
-    	this.cellId = rth.getCellID();
-    	this.packedID = new Identifier(rth.getCellID());
-    	this.time = rth.getTime();
-    	this.adcValues = rth.getADCValues();
+            RawTrackerHit rth, double t0, double Amp) {
+        this.cellId = rth.getCellID();
+        this.packedID = new Identifier(rth.getCellID());
+        this.time = rth.getTime();
+        this.adcValues = rth.getADCValues();
         this.t0=t0;
         this.amp=Amp;        
     }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HelicalTrackHitResidualsDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HelicalTrackHitResidualsDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/HelicalTrackHitResidualsDriver.java	Wed Apr 27 11:11:32 2016
@@ -16,10 +16,11 @@
 import java.util.logging.Logger;
 
 
+
 //===> import org.hps.conditions.deprecated.SvtUtils;
 import org.hps.recon.tracking.EventQuality;
 import org.hps.recon.tracking.TrackUtils;
-import org.hps.users.phansson.TrigRateDriver;
+import org.hps.users.phansson.testrun.TrigRateDriver;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.RawTrackerHit;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/SVTRawTrackerHitThresholdDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/SVTRawTrackerHitThresholdDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/SVTRawTrackerHitThresholdDriver.java	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,7 @@
  * @author Matt Graham
  */
 // TODO: Check that this Driver works as expected after it was updated to use 
-// 		 the database conditions system.
+//       the database conditions system.
 public class SVTRawTrackerHitThresholdDriver extends Driver {
 
     private String rawTrackerHitCollectionName = "RawTrackerHitMaker_RawTrackerHits";

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TrackExtrapolationAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TrackExtrapolationAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TrackExtrapolationAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -5,13 +5,14 @@
 import hep.aida.IHistogram2D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
+import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
 
 import java.util.List;
 import java.util.Map;
 
 import org.hps.recon.tracking.BeamlineConstants;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.HelixConverter;
 import org.hps.recon.tracking.StraightLineTrack;
 import org.hps.recon.tracking.TrackUtils;
@@ -99,10 +100,9 @@
                 charge = 0;//make plot look pretty
 //            System.out.println("Charge = " + charge + "; isTop = " + isTop);
 
-            HPSTrack hpstrk=null;
-                hpstrk = new HPSTrack(ht);
-//            Hep3Vector posAtConv = hpstrk.getPositionAtZ(zAtConverter, -101, -100, 0.1);
-            Hep3Vector posAtConv = hpstrk.getPositionAtZMap(100,BeamlineConstants.HARP_POSITION_TESTRUN , 5.0)[0];
+            HpsHelicalTrackFit hpstrk=null;
+                hpstrk = new HpsHelicalTrackFit(ht);
+                Hep3Vector posAtConv = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk, 100, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0, event.getDetector().getFieldMap()).getReferencePoint());
             double useThisx=posAtConv.x();
             double useThisy=posAtConv.y();
             
@@ -123,7 +123,7 @@
                 aida.histogram1D("Negative Y (mm) @ Converter").fill(useThisy);
             }
 //            Hep3Vector posAtConvShort = hpstrk.getPositionAtZ(zAtConverter, -0.1, 0, 0.01);
-            Hep3Vector posAtConvShort = hpstrk.getPositionAtZMap(0,BeamlineConstants.HARP_POSITION_TESTRUN, 5.0)[0];
+            Hep3Vector posAtConvShort = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk, 0, BeamlineConstants.HARP_POSITION_TESTRUN, 5.0, event.getDetector().getFieldMap()).getReferencePoint());
             aida.histogram2D("Extrapolated X: short vs long fringe").fill(posAtConvShort.x(), posAtConv.x());
             aida.histogram2D("Extrapolated Y: short vs long fringe").fill(posAtConvShort.y(), posAtConv.y());
 
@@ -144,7 +144,8 @@
 //                Hep3Vector posAtEcalHPS = hpstrk.getPositionAtZMap(750,zCluster, 5.0);
                 double zCluster=clust.getPosition()[2];
  //               double zCluster=1450.0;
-                 Hep3Vector posAtEcalHPS = hpstrk.getPositionAtZMap(750,zCluster, 5.0)[0];
+                Hep3Vector posAtEcalHPS = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk, 750, zCluster, 5.0, event.getDetector().getFieldMap()).getReferencePoint());
+
                 Hep3Vector posAtEcalExtend= TrackUtils.extrapolateTrack(trk,zCluster);
                 aida.histogram2D("ECal Extrapolation X :  HPS vs Extend").fill( posAtEcalExtend.y(),posAtEcalHPS.x()-posAtEcalExtend.y());
                 aida.histogram2D("ECal Extrapolation Y :  HPS vs Extend").fill( posAtEcalExtend.z(),posAtEcalHPS.y()-posAtEcalExtend.z());

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TwoTrackAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TwoTrackAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/mgraham/TwoTrackAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -17,10 +17,12 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import org.apache.commons.lang3.NotImplementedException;
 import org.hps.recon.tracking.BeamlineConstants;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.HelixConverter;
 import org.hps.recon.tracking.StraightLineTrack;
+import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackerHit;
@@ -273,10 +275,11 @@
             HelicalTrackFit ht = seedEle.getHelix();
             HelixConverter converter = new HelixConverter(0);
             StraightLineTrack slt = converter.Convert(ht);
-            HPSTrack hpstrack = new HPSTrack(ht);
-            Hep3Vector[] trkatconver = hpstrack.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
-            aida.histogram1D("X (mm) @ Converter using Map").fill(trkatconver[0].x()); // y tracker frame?
-            aida.histogram1D("Y (mm) @ Converter using Map").fill(trkatconver[0].y()); // z tracker frame?
+            HpsHelicalTrackFit hpstrack = new HpsHelicalTrackFit(ht);
+            Hep3Vector trkatconver = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk, 100, BeamlineConstants.HARP_POSITION_TESTRUN, 1, event.getDetector().getFieldMap()).getReferencePoint());
+
+            aida.histogram1D("X (mm) @ Converter using Map").fill(trkatconver.x()); // y tracker frame?
+            aida.histogram1D("Y (mm) @ Converter using Map").fill(trkatconver.y()); // z tracker frame?
             if (slt != null) {
                 aida.histogram1D("X (mm) @ Converter using SLT").fill(slt.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN)[0]); // y tracker frame?
                 aida.histogram1D("Y (mm) @ Converter using SLT").fill(slt.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN)[1]); // z tracker frame?
@@ -320,9 +323,9 @@
 //            HPSTrack hpstrack2 = new HPSTrack(ht2);
 //            Hep3Vector[] trkatconver2 = hpstrack2.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION, 1);
 
-            HPSTrack hpstrack1 = new HPSTrack(ht1);
+            HpsHelicalTrackFit hpstrack1 = new HpsHelicalTrackFit(ht1);
             Hep3Vector[] trkatconver1 = {new BasicHep3Vector(), new BasicHep3Vector(0, 0, 0)};
-            HPSTrack hpstrack2 = new HPSTrack(ht2);
+            HpsHelicalTrackFit hpstrack2 = new HpsHelicalTrackFit(ht2);
             Hep3Vector[] trkatconver2 = {new BasicHep3Vector(), new BasicHep3Vector(0, 0, 0)};;
             if (isMC) {
                 double[] t1 = slt1.getYZAtX(BeamlineConstants.HARP_POSITION_TESTRUN);
@@ -330,8 +333,9 @@
                 trkatconver1[0] = new BasicHep3Vector(t1[0], t1[1], BeamlineConstants.HARP_POSITION_TESTRUN);
                 trkatconver2[0] = new BasicHep3Vector(t2[0], t2[1], BeamlineConstants.HARP_POSITION_TESTRUN);
             } else {
-                trkatconver1 = hpstrack1.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
-                trkatconver2 = hpstrack2.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
+                throw new NotImplementedException("Need to implement using TrackUtils to extrapolate tracks!");
+                //trkatconver1 = hpstrack1.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
+                //trkatconver2 = hpstrack2.getPositionAtZMap(100, BeamlineConstants.HARP_POSITION_TESTRUN, 1);
             }
             List<TrackerHit> hitsOnTrack1 = trk1.getTrackerHits();
             int layer1;
@@ -508,9 +512,10 @@
                             posvec[1] = slt1.getYZAtX(z)[1];
                             posvec[2] = z;
                         } else {
-                            Hep3Vector[] trk1atz = hpstrack1.getPositionAtZMap(100, z, 1);
-                            posvec[0] = trk1atz[0].x();
-                            posvec[1] = trk1atz[0].y();
+                            Hep3Vector trk1atz = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk1, 100, z, 1, event.getDetector().getFieldMap()).getReferencePoint());
+
+                            posvec[0] = trk1atz.x();
+                            posvec[1] = trk1atz.y();
                             posvec[2] = z;
                         }
                         Trk1.add(posvec);
@@ -592,9 +597,10 @@
                             posvec2[1] = slt2.getYZAtX(z)[1];
                             posvec2[2] = z;
                         } else {
-                            Hep3Vector[] trk2atz = hpstrack2.getPositionAtZMap(100, z, 1);
-                            posvec2[0] = trk2atz[0].x();
-                            posvec2[1] = trk2atz[0].y();
+                            Hep3Vector trk2atz = new BasicHep3Vector(TrackUtils.extrapolateTrackUsingFieldMap(trk2, 100, z, 1, event.getDetector().getFieldMap()).getReferencePoint());
+
+                            posvec2[0] = trk2atz.x();
+                            posvec2[1] = trk2atz.y();
                             posvec2[2] = z;
                         }
                         Trk2.add(posvec2);

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/EcalScoringPlaneDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/EcalScoringPlaneDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/EcalScoringPlaneDriver.java	Wed Apr 27 11:11:32 2016
@@ -23,136 +23,136 @@
  */
 public class EcalScoringPlaneDriver extends Driver {
 
-	boolean verbose = false;
-	
-	// Collection Names
-	String ecalScoringPlaneHitsCollectionName = "TrackerHitsECal";
-	String tracksCollectionName = "MatchedTracks";
-	String trackToScoringPlaneHitRelationsName = "TrackToEcalScoringPlaneHitRelations";
-	String trackToMCParticleRelationsName = "TrackToMCParticleRelations";
-	
-	/**
-	 * Enable/disable verbose mode
-	 * 
-	 * @param verbose : set true to enable, false otherwise
-	 */
-	public void setVerbose(boolean verbose){
-		this.verbose = verbose; 
-	}
-	
-	@Override
-	protected void process(EventHeader event){
-		
-		// If the event doesn't have a collection of Tracks, skip it
-		if(!event.hasCollection(Track.class, tracksCollectionName)) return;
-		
-		// If the event doesn't have a collection of Ecal scoring plane hits, 
-		// skip it
-		if(!event.hasCollection(SimTrackerHit.class, ecalScoringPlaneHitsCollectionName)) return;
-		
-		// Get the collection of tracks from the event
-		List<Track> tracks = event.get(Track.class, tracksCollectionName);
-		
-		// Get the collection of Ecal scoring plane hits from the event
-		List<SimTrackerHit> scoringPlaneHits = event.get(SimTrackerHit.class, ecalScoringPlaneHitsCollectionName);
-		
-		// Create a collection to hold the scoring plane hits that were found to match
-		// a track
-		List<SimTrackerHit> matchedScoringPlaneHits = new ArrayList<SimTrackerHit>(); 
-		
-		// Create a collection of LCRelations between a track and the scoring plane hit
-		List<LCRelation> trackToScoringPlaneHitRelations = new ArrayList<LCRelation>();
-	
-		// Create a collection of LCRelations between a track and its corresponding MC particle
-		List<LCRelation> trackToMCParticleRelations = new ArrayList<LCRelation>();
-	
-		MCParticle particle = null;
-		for(Track track : tracks){
-		
-			// Get the MC particle associated with this track
-			particle = this.getMCParticleAssociatedWithTrack(track);
-			// If the MC particle is null, then the hits associated with the
-			// track did not have an MC particle associated with them
-			// TODO: Find out why some hits don't have any MC particles associated with them
-			if(particle == null) continue;
-		
-			// Add an LCRelation between the track and the corresponding MC particle
-			trackToMCParticleRelations.add(new BaseLCRelation(track, particle));
-			
-			// Loop over all of the scoring plane hits and check if the associated MC particle
-			// matches the one from the track
-			for(SimTrackerHit scoringPlaneHit : scoringPlaneHits){
-	
-				// If the MC particles don't match, move on to the next particle
-				if(!(scoringPlaneHit.getMCParticle() == particle)) continue; 
-					
-				this.printVerbose("Found a match between a track and a scoring plane hit.");
-				
-				// If a match is found, add the scoring plane hit to the list of matched hits and
-				// an LCRelation between the track and the scoring plane.
-				matchedScoringPlaneHits.add(scoringPlaneHit);
-				trackToScoringPlaneHitRelations.add(new BaseLCRelation(track, scoringPlaneHit));
-				
-				// Once a match is found, there is no need to loop through the rest of the list
-				break;
-			}
-		}
-		
-		// Store all of the collections in the event
-		event.put(ecalScoringPlaneHitsCollectionName, matchedScoringPlaneHits, SimTrackerHit.class, 0);
-		event.put(trackToScoringPlaneHitRelationsName, trackToScoringPlaneHitRelations, LCRelation.class, 0);
-		event.put(trackToMCParticleRelationsName, trackToMCParticleRelations, LCRelation.class, 0);
-	}
-	
-	/**
-	 * Print a message if verbose has been enabled.
-	 *  
-	 * @param message : message to print.
-	 */
-	private void printVerbose(String message){
-		if(verbose)
-			System.out.println(this.getClass().getSimpleName() + ": " + message);
-	}
-	
-	/**
-	 * Get the MC particle associated with a track.
-	 * 
-	 * @param track : Track to get the MC particle for
-	 * @return The MC particle associated with the track
-	 */
-	private MCParticle getMCParticleAssociatedWithTrack(Track track){
-		
-		Map <MCParticle, int[]>mcParticleMultiplicity = new HashMap<MCParticle, int[]>();
-		MCParticle particle;
-		for(TrackerHit hit : track.getTrackerHits()){
-		
-				// If one of the tracker hits doesn't have any MC particles associated
-				// with it, return null for now.
-				if(((HelicalTrackHit) hit).getMCParticles().size() == 0){
-					this.printVerbose("HelicalTrackHit is not associated with any MC particles.");
-					return null;
-				}
-				
-				particle = ((HelicalTrackHit) hit).getMCParticles().get(0);
-				if(!mcParticleMultiplicity.containsKey(particle)){
-					mcParticleMultiplicity.put(particle, new int[1]);
-					mcParticleMultiplicity.get(particle)[0] = 0;
-				}
-				
-				mcParticleMultiplicity.get(particle)[0]++;
-				
-		}
-		
-		// Look for the MC particle that occurs the most of the track
-		int maxValue = 0;
-		particle = null;
-		for(Map.Entry<MCParticle, int[]> entry : mcParticleMultiplicity.entrySet()){
-			if(maxValue < entry.getValue()[0]){
-				particle = entry.getKey();
-				maxValue = entry.getValue()[0];
-			}
-		}
-		
-		return particle;
-	}
+    boolean verbose = false;
+    
+    // Collection Names
+    String ecalScoringPlaneHitsCollectionName = "TrackerHitsECal";
+    String tracksCollectionName = "MatchedTracks";
+    String trackToScoringPlaneHitRelationsName = "TrackToEcalScoringPlaneHitRelations";
+    String trackToMCParticleRelationsName = "TrackToMCParticleRelations";
+    
+    /**
+     * Enable/disable verbose mode
+     * 
+     * @param verbose : set true to enable, false otherwise
+     */
+    public void setVerbose(boolean verbose){
+        this.verbose = verbose; 
+    }
+    
+    @Override
+    protected void process(EventHeader event){
+        
+        // If the event doesn't have a collection of Tracks, skip it
+        if(!event.hasCollection(Track.class, tracksCollectionName)) return;
+        
+        // If the event doesn't have a collection of Ecal scoring plane hits, 
+        // skip it
+        if(!event.hasCollection(SimTrackerHit.class, ecalScoringPlaneHitsCollectionName)) return;
+        
+        // Get the collection of tracks from the event
+        List<Track> tracks = event.get(Track.class, tracksCollectionName);
+        
+        // Get the collection of Ecal scoring plane hits from the event
+        List<SimTrackerHit> scoringPlaneHits = event.get(SimTrackerHit.class, ecalScoringPlaneHitsCollectionName);
+        
+        // Create a collection to hold the scoring plane hits that were found to match
+        // a track
+        List<SimTrackerHit> matchedScoringPlaneHits = new ArrayList<SimTrackerHit>(); 
+        
+        // Create a collection of LCRelations between a track and the scoring plane hit
+        List<LCRelation> trackToScoringPlaneHitRelations = new ArrayList<LCRelation>();
+    
+        // Create a collection of LCRelations between a track and its corresponding MC particle
+        List<LCRelation> trackToMCParticleRelations = new ArrayList<LCRelation>();
+    
+        MCParticle particle = null;
+        for(Track track : tracks){
+        
+            // Get the MC particle associated with this track
+            particle = this.getMCParticleAssociatedWithTrack(track);
+            // If the MC particle is null, then the hits associated with the
+            // track did not have an MC particle associated with them
+            // TODO: Find out why some hits don't have any MC particles associated with them
+            if(particle == null) continue;
+        
+            // Add an LCRelation between the track and the corresponding MC particle
+            trackToMCParticleRelations.add(new BaseLCRelation(track, particle));
+            
+            // Loop over all of the scoring plane hits and check if the associated MC particle
+            // matches the one from the track
+            for(SimTrackerHit scoringPlaneHit : scoringPlaneHits){
+    
+                // If the MC particles don't match, move on to the next particle
+                if(!(scoringPlaneHit.getMCParticle() == particle)) continue; 
+                    
+                this.printVerbose("Found a match between a track and a scoring plane hit.");
+                
+                // If a match is found, add the scoring plane hit to the list of matched hits and
+                // an LCRelation between the track and the scoring plane.
+                matchedScoringPlaneHits.add(scoringPlaneHit);
+                trackToScoringPlaneHitRelations.add(new BaseLCRelation(track, scoringPlaneHit));
+                
+                // Once a match is found, there is no need to loop through the rest of the list
+                break;
+            }
+        }
+        
+        // Store all of the collections in the event
+        event.put(ecalScoringPlaneHitsCollectionName, matchedScoringPlaneHits, SimTrackerHit.class, 0);
+        event.put(trackToScoringPlaneHitRelationsName, trackToScoringPlaneHitRelations, LCRelation.class, 0);
+        event.put(trackToMCParticleRelationsName, trackToMCParticleRelations, LCRelation.class, 0);
+    }
+    
+    /**
+     * Print a message if verbose has been enabled.
+     *  
+     * @param message : message to print.
+     */
+    private void printVerbose(String message){
+        if(verbose)
+            System.out.println(this.getClass().getSimpleName() + ": " + message);
+    }
+    
+    /**
+     * Get the MC particle associated with a track.
+     * 
+     * @param track : Track to get the MC particle for
+     * @return The MC particle associated with the track
+     */
+    private MCParticle getMCParticleAssociatedWithTrack(Track track){
+        
+        Map <MCParticle, int[]>mcParticleMultiplicity = new HashMap<MCParticle, int[]>();
+        MCParticle particle;
+        for(TrackerHit hit : track.getTrackerHits()){
+        
+                // If one of the tracker hits doesn't have any MC particles associated
+                // with it, return null for now.
+                if(((HelicalTrackHit) hit).getMCParticles().size() == 0){
+                    this.printVerbose("HelicalTrackHit is not associated with any MC particles.");
+                    return null;
+                }
+                
+                particle = ((HelicalTrackHit) hit).getMCParticles().get(0);
+                if(!mcParticleMultiplicity.containsKey(particle)){
+                    mcParticleMultiplicity.put(particle, new int[1]);
+                    mcParticleMultiplicity.get(particle)[0] = 0;
+                }
+                
+                mcParticleMultiplicity.get(particle)[0]++;
+                
+        }
+        
+        // Look for the MC particle that occurs the most of the track
+        int maxValue = 0;
+        particle = null;
+        for(Map.Entry<MCParticle, int[]> entry : mcParticleMultiplicity.entrySet()){
+            if(maxValue < entry.getValue()[0]){
+                particle = entry.getKey();
+                maxValue = entry.getValue()[0];
+            }
+        }
+        
+        return particle;
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ExtrapolationAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ExtrapolationAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ExtrapolationAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -30,312 +30,312 @@
  */
 public class ExtrapolationAnalysis  extends Driver {
 
-	AIDA aida = null;
-	List<IPlotter> plotters;
-
-	Hep3Vector bField = null;
-	
-	boolean verbose = false;
-	
-	// Collection Names
-	String matchedEcalScoringPlaneHitsCollectionName = "MatchedTrackerHitsEcal";
-	String trackToScoringPlaneHitRelationsName = "TrackToEcalScoringPlaneHitRelations";
-	String trackToMCParticleRelationsName = "TrackToMCParticleRelations";
-	
-	/**
-	 * Enable/disable verbose mode
-	 * 
-	 * @param verbose : true to enable, false otherwise
-	 */
-	public void setVerbose(boolean verbose){
-		this.verbose = verbose; 
-	}
-	
-	public void detectorChanged(Detector detector){
-		
-		// Get the magnetic field from the geometry
-		bField = detector.getFieldMap().getField(new BasicHep3Vector(0,0,0));
-		
-		//-----------------------//
-		//--- Setup all plots ---//
-		//-----------------------//
-		
-		// Setup AIDA
-		aida = AIDA.defaultInstance();
-		aida.tree().cd("/");
-	
-		// Instantiate a list to hold the collection of plotters
-		plotters = new ArrayList<IPlotter>();
-		IPlotter plotter = null; 
-		
-		//--- Plots of scoring plane positions ---//
-		//----------------------------------------//
-		plotter = PlotUtils.setupPlotter("Positions of Scoring plane hits matched to tracks", 2, 2);
-		PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - x", 0, "x (mm)",
-				aida.histogram1D("Scoring plane hit position - x", 100, -400, 400));
-		PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - y", 1, "y (mm)",
-				aida.histogram1D("Scoring plane hit position - y", 100, -200, 200));
-		PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - z", 2, "z (mm)",
-				aida.histogram1D("Scoring plane hit position - z", 100, 1000, 1500));
-		PlotUtils.setup2DRegion(plotter, "Scoring plane hit position - x-y", 3, "x (mm)", "y (mm)", 
-				aida.histogram2D("Scoring plane hit position - x-y", 100, -400, 400, 100, -200, 200));
-		plotters.add(plotter);	
-
-		//--- Plots of residuals at scoring plane ---//
-		//-------------------------------------------//
-		plotter = PlotUtils.setupPlotter("Residuals at scoring plane", 3, 3);
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at scoring plane", 0, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Top electron tracks - Bend plane residual at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at scoring plane", 0, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Top positron tracks - Bend plane residual at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at scoring plane", 1, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Bottom electron tracks - Bend plane residuals at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at scoring plane", 1, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Bottom positron tracks - Bend plane residuals at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Bend plane residuals at scoring plane", 2, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Bend plane residuals at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Bend plane residuals at scoring plane", 2, "x_{ep} - x_{sp} (mm)",
-				aida.histogram1D("Bend plane residuals at scoring plane", 60, -30, 30));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at scoring plane", 3,"y_{ep} - y_{sp} (mm)", 
-				aida.histogram1D("Top electron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at scoring plane", 3,"y_{ep} - y_{sp} (mm)", 
-				aida.histogram1D("Top positron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at scoring plane", 4,"y_{ep} - y_{sp} (mm)", 
-				aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at scoring plane", 4,"y_{ep} - y_{sp} (mm)", 
-				aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
-		PlotUtils.setup1DRegion(plotter, "Non-bend plane residuals at scoring plane", 5,"y_{ep} - y_{sp} (mm)", 
-				aida.histogram1D("Non-bend plane residuals at scoring plane", 30, -15, 15));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at scoring plane", 6, "z_{ep} - z_{sp} (mm)",
-				aida.histogram1D("Top electron tracks - z residuals at scoring plane", 10, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at scoring plane", 6, "z_{ep} - z_{sp} (mm)",
-				aida.histogram1D("Top positron tracks - z residuals at scoring plane", 10, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
-				aida.histogram1D("Bottom electron tracks - z residuals at scoring plane", 10, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
-				aida.histogram1D("Bottom positron tracks - z residuals at scoring plane", 10, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
-				aida.histogram1D("z residuals at scoring plane", 10, -5, 5));
-		plotters.add(plotter);	
-		
-		//--- Plots of residuals at target ---//
-		//------------------------------------//
-		plotter = PlotUtils.setupPlotter("Residuals at target", 3, 3);
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at target", 0, "x_{ep} - x_{t} (mm)",
-				aida.histogram1D("Top electron tracks - Bend plane residual at target", 40, -4, 4));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at target", 0, "x_{ep} - x_{t} (mm)",
-				aida.histogram1D("Top positron tracks - Bend plane residual at target", 40, -4, 4));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at target", 1, "x_{ep} - x_{t} (mm)",
-				aida.histogram1D("Bottom electron tracks - Bend plane residuals at target", 40, -4, 4));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at target", 1, "x_{ep} - x_{t} (mm)",
-				aida.histogram1D("Bottom positron tracks - Bend plane residuals at target", 40, -4, 4));
-		PlotUtils.setup1DRegion(plotter, "Bend plane residuals at target", 2, "x_{ep} - x_{t} (mm)",
-				aida.histogram1D("Bend plane residuals at target", 40, -4, 4));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at target", 3, "y_{ep} - y_{t} (mm)",
-				aida.histogram1D("Top electron tracks - Non-bend plane residuals at target", 20, -2, 2));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at target", 3, "y_{ep} - y_{t} (mm)",
-				aida.histogram1D("Top positron tracks - Non-bend plane residuals at target", 20, -2, 2));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at target", 4, "y_{ep} - y_{t} (mm)",
-				aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at target", 20, -2, 2));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at target", 4, "y_{ep} - y_{t} (mm)",
-				aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at target", 20, -2, 2));
-		PlotUtils.setup1DRegion(plotter, "Non-bend plane residuals at target", 5, "y_{ep} - y_{t} (mm)",
-				aida.histogram1D("Non-bend plane residuals at target", 20, -2, 2));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at target", 6, "z_{ep} - z_{t} (mm)",
-				aida.histogram1D("Top electron tracks - z residuals at target", 50, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at target", 6, "z_{ep} - z_{t} (mm)",
-				aida.histogram1D("Top positron tracks - z residuals at target", 50, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at target", 7, "z_{ep} - z_{t} (mm)",
-				aida.histogram1D("Bottom electron tracks - z residuals at target", 50, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at target", 7, "z_{ep} - z_{t} (mm)",
-				aida.histogram1D("Bottom positron tracks - z residuals at target", 50, -5, 5));
-		PlotUtils.setup1DRegion(plotter, "z residuals at target", 8, "z_{ep} - z_{t} (mm)",
-				aida.histogram1D("z residuals at target", 50, -5, 5));
-		plotters.add(plotter);	
-		
-		//--- Plot of residuals at scoring plane vs momentum ---//
-		//------------------------------------------------------//
-		plotter = PlotUtils.setupPlotter("Residuals vs Momentum", 2, 2);
-		PlotUtils.setup2DRegion(plotter, "Bend plane residuals vs momentum at scoring plane", 0, 
-				"Momentum (GeV)", "x_{ep} - x_{sp} (mm)",
-				aida.histogram2D("Bend plane residuals vs momentum at scoring plane", 5, 0, 2.5, 60, -30, 30));
-		PlotUtils.setup2DRegion(plotter, "Non-bend plane residuals vs momentum at scoring plane", 1, 
-				"Momentum (GeV)", "y_{ep} - y_{sp} (mm)",
-				aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane", 5, 0, 2.5, 60, -30, 30));
-		PlotUtils.setup2DRegion(plotter, "Bend plane residuals vs momentum at target", 2, 
-				"Momentum (GeV)", "x_{ep} - x_{t} (mm)",
-				aida.histogram2D("Bend plane residuals vs momentum at target", 5, 0, 2.5, 60, -3, 3));
-		PlotUtils.setup2DRegion(plotter, "Non-bend plane residuals vs momentum at target", 3, 
-				"Momentum (GeV)", "y_{ep} - y_{t} (mm)",
-				aida.histogram2D("Non-bend plane residuals vs momentum at target", 5, 0, 2.5, 50, -2.5, 2.5));
-		plotters.add(plotter);
-		
-		for(IPlotter iPlotter : plotters){
-			iPlotter.show(); 
-		}
-		
-	}
-	
-	public void process(EventHeader event){
-	
-		// If the event doesn't contain an LCRelation between a track and its 
-		// corresponding ECal scoring plane hit, skip the event.
-		if(!event.hasCollection(LCRelation.class, trackToScoringPlaneHitRelationsName)) return;
-		
-		List<LCRelation> trackToScoringPlaneHitRelations = event.get(LCRelation.class, trackToScoringPlaneHitRelationsName);
-		
-		for(LCRelation trackToScoringPlaneHitRelation : trackToScoringPlaneHitRelations){
-		
-			// Get the track
-			Track track = (Track) trackToScoringPlaneHitRelation.getFrom();
-			
-			// Get the track momentum
-			double[] momentum = BaseTrackState.computeMomentum(track.getTrackStates().get(0), bField.y());
-			double p = Math.sqrt(momentum[0]*momentum[0] + momentum[1]*momentum[1] + momentum[2]*momentum[2]);
-			this.printVerbose("Track momentum: " + p);
-			
-			// Get the corresponding scoring plane hit
-			SimTrackerHit scoringPlaneHit = (SimTrackerHit) trackToScoringPlaneHitRelation.getTo();
-			Hep3Vector scoringPlaneHitPosition = scoringPlaneHit.getPositionVec();
-			this.printVerbose("Scoring plane hit position: " + scoringPlaneHitPosition.toString());
-			
-			// Fill the scoring plane position histograms
-			aida.histogram1D("Scoring plane hit position - x").fill(scoringPlaneHitPosition.x());
-			aida.histogram1D("Scoring plane hit position - y").fill(scoringPlaneHitPosition.y());
-			aida.histogram1D("Scoring plane hit position - z").fill(scoringPlaneHitPosition.z());
-			aida.histogram2D("Scoring plane hit position - x-y").fill(scoringPlaneHitPosition.x(), scoringPlaneHitPosition.y());
-		
-			// Extrapolate the track to the scoring plane position
-			Hep3Vector trackPositionAtScoringPlane = TrackUtils.extrapolateTrack(track, scoringPlaneHitPosition.z());
-			this.printVerbose("Extrapolated track position: " + trackPositionAtScoringPlane.toString());
-				
-			// Find the residual between the extrapolated track position and the scoring plane hit position
-			double deltaX = trackPositionAtScoringPlane.x() - scoringPlaneHitPosition.x();
-			double deltaY = trackPositionAtScoringPlane.y() - scoringPlaneHitPosition.y();
-			// This should be 0 but it serves as a sanity check.
-			double deltaZ = trackPositionAtScoringPlane.z() - scoringPlaneHitPosition.z();
-		
-			if(track.getTrackerHits().get(0).getPosition()[2] > 0){
-				if(track.getTrackStates().get(0).getOmega() > 0){
-					aida.histogram1D("Top positron tracks - Bend plane residual at scoring plane").fill(deltaX);
-					aida.histogram1D("Top positron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
-					aida.histogram1D("Top positron tracks - z residuals at scoring plane").fill(deltaZ);	
-				} else { 
-					aida.histogram1D("Top electron tracks - Bend plane residual at scoring plane").fill(deltaX);
-					aida.histogram1D("Top electron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
-					aida.histogram1D("Top electron tracks - z residuals at scoring plane").fill(deltaZ);	
-				}
-			} else { 
-				if(track.getTrackStates().get(0).getOmega() > 0){
-					aida.histogram1D("Bottom positron tracks - Bend plane residuals at scoring plane").fill(deltaX);
-					aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
-					aida.histogram1D("Bottom positron tracks - z residuals at scoring plane").fill(deltaZ);
-				} else { 
-					aida.histogram1D("Bottom electron tracks - Bend plane residuals at scoring plane").fill(deltaX);
-					aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
-					aida.histogram1D("Bottom electron tracks - z residuals at scoring plane").fill(deltaZ);
-				}
-			}
-
-			aida.histogram1D("Bend plane residuals at scoring plane").fill(deltaX);
-			aida.histogram1D("Non-bend plane residuals at scoring plane").fill(deltaY);
-			aida.histogram1D("z residuals at target").fill(deltaZ);
-			aida.histogram2D("Bend plane residuals vs momentum at scoring plane").fill(p, deltaX);
-			aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane").fill(p, deltaY);
-		}
-		
-		if(!event.hasCollection(LCRelation.class, trackToMCParticleRelationsName)) return;
-		
-		List<LCRelation> trackToMCParticleRelations = event.get(LCRelation.class, trackToMCParticleRelationsName);
-		
-		for(LCRelation trackToMCParticleRelation : trackToMCParticleRelations){
-			
-			// Get the track
-			Track track = (Track) trackToMCParticleRelation.getFrom();
-			
-			// Get the track momentum
-			double[] momentum = BaseTrackState.computeMomentum(track.getTrackStates().get(0), bField.y());
-			double p = Math.sqrt(momentum[0]*momentum[0] + momentum[1]*momentum[1] + momentum[2]*momentum[2]);
-			this.printVerbose("Track momentum: " + p);
-
-			// Get the corresponding MC particle
-			MCParticle particle = (MCParticle) trackToMCParticleRelation.getTo();
-			
-			// Extrapolate the track to the origin
-			Hep3Vector trackPositionAtOrigin = TrackUtils.extrapolateTrack(track, particle.getOriginZ());
-			
-			// Find the residual between the extrapolated track and the position of the scoring plane at the origin
-			double deltaX = trackPositionAtOrigin.x() - particle.getOriginX();
-			double deltaY = trackPositionAtOrigin.y() - particle.getOriginY();
-			double deltaZ = trackPositionAtOrigin.z() - particle.getOriginZ();
-			
-			if(track.getTrackerHits().get(0).getPosition()[2] > 0){
-				if(track.getTrackStates().get(0).getOmega() > 0){
-					aida.histogram1D("Top positron tracks - Bend plane residual at target").fill(deltaX);
-					aida.histogram1D("Top positron tracks - Non-bend plane residuals at target").fill(deltaY);
-					aida.histogram1D("Top positron tracks - z residuals at target").fill(deltaZ);
-				} else { 
-					aida.histogram1D("Top electron tracks - Bend plane residual at target").fill(deltaX);
-					aida.histogram1D("Top electron tracks - Non-bend plane residuals at target").fill(deltaY);
-					aida.histogram1D("Top electron tracks - z residuals at target").fill(deltaZ);
-				}
-			} else { 
-				
-				if(track.getTrackStates().get(0).getOmega() > 0){
-					aida.histogram1D("Bottom positron tracks - Bend plane residuals at target").fill(deltaX);
-					aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at target").fill(deltaY);
-					aida.histogram1D("Bottom positron tracks - z residuals at target").fill(deltaZ);
-				} else { 
-					aida.histogram1D("Bottom electron tracks - Bend plane residuals at target").fill(deltaX);
-					aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at target").fill(deltaY);
-					aida.histogram1D("Bottom electron tracks - z residuals at target").fill(deltaZ);
-				}
-			}
-			
-			aida.histogram1D("Bend plane residuals at target").fill(deltaX);
-			aida.histogram1D("Non-bend plane residuals at target").fill(deltaY);
-			aida.histogram1D("z residuals at target").fill(deltaZ);
-			aida.histogram2D("Bend plane residuals vs momentum at target").fill(p, deltaX);
-			aida.histogram2D("Non-bend plane residuals vs momentum at target").fill(p, deltaY);
-		}
-	}
-	
-	@Override
-	protected void endOfData(){
-		
-		IHistogram2D histogram = aida.histogram2D("Bend plane residuals vs momentum at scoring plane");
-		int binsX = histogram.xAxis().bins();
-		for(int binX = 0; binX < binsX; binX++){
-			PlotUtils.getYProjection(binX, histogram);
-		}
-		
-		histogram = aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane");
-		binsX = histogram.xAxis().bins();
-		for(int binX = 0; binX < binsX; binX++){
-			PlotUtils.getYProjection(binX, histogram);
-		}
-	
-		histogram = aida.histogram2D("Bend plane residuals vs momentum at target");
-		binsX = histogram.xAxis().bins();
-		for(int binX = 0; binX < binsX; binX++){
-			PlotUtils.getYProjection(binX, histogram);
-		}
-		
-		histogram = aida.histogram2D("Non-bend plane residuals vs momentum at target");
-		binsX = histogram.xAxis().bins();
-		for(int binX = 0; binX < binsX; binX++){
-			PlotUtils.getYProjection(binX, histogram);
-		}
-	}
-	
-	/**
-	 * Print a message if verbose has been enabled.
-	 *  
-	 * @param message : message to print.
-	 */
-	private void printVerbose(String message){
-		if(verbose)
-			System.out.println(this.getClass().getSimpleName() + ": " + message);
-	}
-	
+    AIDA aida = null;
+    List<IPlotter> plotters;
+
+    Hep3Vector bField = null;
+    
+    boolean verbose = false;
+    
+    // Collection Names
+    String matchedEcalScoringPlaneHitsCollectionName = "MatchedTrackerHitsEcal";
+    String trackToScoringPlaneHitRelationsName = "TrackToEcalScoringPlaneHitRelations";
+    String trackToMCParticleRelationsName = "TrackToMCParticleRelations";
+    
+    /**
+     * Enable/disable verbose mode
+     * 
+     * @param verbose : true to enable, false otherwise
+     */
+    public void setVerbose(boolean verbose){
+        this.verbose = verbose; 
+    }
+    
+    public void detectorChanged(Detector detector){
+        
+        // Get the magnetic field from the geometry
+        bField = detector.getFieldMap().getField(new BasicHep3Vector(0,0,0));
+        
+        //-----------------------//
+        //--- Setup all plots ---//
+        //-----------------------//
+        
+        // Setup AIDA
+        aida = AIDA.defaultInstance();
+        aida.tree().cd("/");
+    
+        // Instantiate a list to hold the collection of plotters
+        plotters = new ArrayList<IPlotter>();
+        IPlotter plotter = null; 
+        
+        //--- Plots of scoring plane positions ---//
+        //----------------------------------------//
+        plotter = PlotUtils.setupPlotter("Positions of Scoring plane hits matched to tracks", 2, 2);
+        PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - x", 0, "x (mm)",
+                aida.histogram1D("Scoring plane hit position - x", 100, -400, 400));
+        PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - y", 1, "y (mm)",
+                aida.histogram1D("Scoring plane hit position - y", 100, -200, 200));
+        PlotUtils.setup1DRegion(plotter, "Scoring plane hit position - z", 2, "z (mm)",
+                aida.histogram1D("Scoring plane hit position - z", 100, 1000, 1500));
+        PlotUtils.setup2DRegion(plotter, "Scoring plane hit position - x-y", 3, "x (mm)", "y (mm)", 
+                aida.histogram2D("Scoring plane hit position - x-y", 100, -400, 400, 100, -200, 200));
+        plotters.add(plotter);  
+
+        //--- Plots of residuals at scoring plane ---//
+        //-------------------------------------------//
+        plotter = PlotUtils.setupPlotter("Residuals at scoring plane", 3, 3);
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at scoring plane", 0, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Top electron tracks - Bend plane residual at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at scoring plane", 0, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Top positron tracks - Bend plane residual at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at scoring plane", 1, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Bottom electron tracks - Bend plane residuals at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at scoring plane", 1, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Bottom positron tracks - Bend plane residuals at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Bend plane residuals at scoring plane", 2, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Bend plane residuals at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Bend plane residuals at scoring plane", 2, "x_{ep} - x_{sp} (mm)",
+                aida.histogram1D("Bend plane residuals at scoring plane", 60, -30, 30));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at scoring plane", 3,"y_{ep} - y_{sp} (mm)", 
+                aida.histogram1D("Top electron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at scoring plane", 3,"y_{ep} - y_{sp} (mm)", 
+                aida.histogram1D("Top positron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at scoring plane", 4,"y_{ep} - y_{sp} (mm)", 
+                aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at scoring plane", 4,"y_{ep} - y_{sp} (mm)", 
+                aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at scoring plane", 30, -15, 15));
+        PlotUtils.setup1DRegion(plotter, "Non-bend plane residuals at scoring plane", 5,"y_{ep} - y_{sp} (mm)", 
+                aida.histogram1D("Non-bend plane residuals at scoring plane", 30, -15, 15));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at scoring plane", 6, "z_{ep} - z_{sp} (mm)",
+                aida.histogram1D("Top electron tracks - z residuals at scoring plane", 10, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at scoring plane", 6, "z_{ep} - z_{sp} (mm)",
+                aida.histogram1D("Top positron tracks - z residuals at scoring plane", 10, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
+                aida.histogram1D("Bottom electron tracks - z residuals at scoring plane", 10, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
+                aida.histogram1D("Bottom positron tracks - z residuals at scoring plane", 10, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "z residuals at scoring plane", 7, "z_{ep} - z_{sp} (mm)",
+                aida.histogram1D("z residuals at scoring plane", 10, -5, 5));
+        plotters.add(plotter);  
+        
+        //--- Plots of residuals at target ---//
+        //------------------------------------//
+        plotter = PlotUtils.setupPlotter("Residuals at target", 3, 3);
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at target", 0, "x_{ep} - x_{t} (mm)",
+                aida.histogram1D("Top electron tracks - Bend plane residual at target", 40, -4, 4));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Bend plane residuals at target", 0, "x_{ep} - x_{t} (mm)",
+                aida.histogram1D("Top positron tracks - Bend plane residual at target", 40, -4, 4));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at target", 1, "x_{ep} - x_{t} (mm)",
+                aida.histogram1D("Bottom electron tracks - Bend plane residuals at target", 40, -4, 4));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Bend plane residuals at target", 1, "x_{ep} - x_{t} (mm)",
+                aida.histogram1D("Bottom positron tracks - Bend plane residuals at target", 40, -4, 4));
+        PlotUtils.setup1DRegion(plotter, "Bend plane residuals at target", 2, "x_{ep} - x_{t} (mm)",
+                aida.histogram1D("Bend plane residuals at target", 40, -4, 4));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at target", 3, "y_{ep} - y_{t} (mm)",
+                aida.histogram1D("Top electron tracks - Non-bend plane residuals at target", 20, -2, 2));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - Non-bend plane residuals at target", 3, "y_{ep} - y_{t} (mm)",
+                aida.histogram1D("Top positron tracks - Non-bend plane residuals at target", 20, -2, 2));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at target", 4, "y_{ep} - y_{t} (mm)",
+                aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at target", 20, -2, 2));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - Non-bend plane residuals at target", 4, "y_{ep} - y_{t} (mm)",
+                aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at target", 20, -2, 2));
+        PlotUtils.setup1DRegion(plotter, "Non-bend plane residuals at target", 5, "y_{ep} - y_{t} (mm)",
+                aida.histogram1D("Non-bend plane residuals at target", 20, -2, 2));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at target", 6, "z_{ep} - z_{t} (mm)",
+                aida.histogram1D("Top electron tracks - z residuals at target", 50, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Top tracks - z residuals at target", 6, "z_{ep} - z_{t} (mm)",
+                aida.histogram1D("Top positron tracks - z residuals at target", 50, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at target", 7, "z_{ep} - z_{t} (mm)",
+                aida.histogram1D("Bottom electron tracks - z residuals at target", 50, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "Bottom tracks - z residuals at target", 7, "z_{ep} - z_{t} (mm)",
+                aida.histogram1D("Bottom positron tracks - z residuals at target", 50, -5, 5));
+        PlotUtils.setup1DRegion(plotter, "z residuals at target", 8, "z_{ep} - z_{t} (mm)",
+                aida.histogram1D("z residuals at target", 50, -5, 5));
+        plotters.add(plotter);  
+        
+        //--- Plot of residuals at scoring plane vs momentum ---//
+        //------------------------------------------------------//
+        plotter = PlotUtils.setupPlotter("Residuals vs Momentum", 2, 2);
+        PlotUtils.setup2DRegion(plotter, "Bend plane residuals vs momentum at scoring plane", 0, 
+                "Momentum (GeV)", "x_{ep} - x_{sp} (mm)",
+                aida.histogram2D("Bend plane residuals vs momentum at scoring plane", 5, 0, 2.5, 60, -30, 30));
+        PlotUtils.setup2DRegion(plotter, "Non-bend plane residuals vs momentum at scoring plane", 1, 
+                "Momentum (GeV)", "y_{ep} - y_{sp} (mm)",
+                aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane", 5, 0, 2.5, 60, -30, 30));
+        PlotUtils.setup2DRegion(plotter, "Bend plane residuals vs momentum at target", 2, 
+                "Momentum (GeV)", "x_{ep} - x_{t} (mm)",
+                aida.histogram2D("Bend plane residuals vs momentum at target", 5, 0, 2.5, 60, -3, 3));
+        PlotUtils.setup2DRegion(plotter, "Non-bend plane residuals vs momentum at target", 3, 
+                "Momentum (GeV)", "y_{ep} - y_{t} (mm)",
+                aida.histogram2D("Non-bend plane residuals vs momentum at target", 5, 0, 2.5, 50, -2.5, 2.5));
+        plotters.add(plotter);
+        
+        for(IPlotter iPlotter : plotters){
+            iPlotter.show(); 
+        }
+        
+    }
+    
+    public void process(EventHeader event){
+    
+        // If the event doesn't contain an LCRelation between a track and its 
+        // corresponding ECal scoring plane hit, skip the event.
+        if(!event.hasCollection(LCRelation.class, trackToScoringPlaneHitRelationsName)) return;
+        
+        List<LCRelation> trackToScoringPlaneHitRelations = event.get(LCRelation.class, trackToScoringPlaneHitRelationsName);
+        
+        for(LCRelation trackToScoringPlaneHitRelation : trackToScoringPlaneHitRelations){
+        
+            // Get the track
+            Track track = (Track) trackToScoringPlaneHitRelation.getFrom();
+            
+            // Get the track momentum
+            double[] momentum = BaseTrackState.computeMomentum(track.getTrackStates().get(0), bField.y());
+            double p = Math.sqrt(momentum[0]*momentum[0] + momentum[1]*momentum[1] + momentum[2]*momentum[2]);
+            this.printVerbose("Track momentum: " + p);
+            
+            // Get the corresponding scoring plane hit
+            SimTrackerHit scoringPlaneHit = (SimTrackerHit) trackToScoringPlaneHitRelation.getTo();
+            Hep3Vector scoringPlaneHitPosition = scoringPlaneHit.getPositionVec();
+            this.printVerbose("Scoring plane hit position: " + scoringPlaneHitPosition.toString());
+            
+            // Fill the scoring plane position histograms
+            aida.histogram1D("Scoring plane hit position - x").fill(scoringPlaneHitPosition.x());
+            aida.histogram1D("Scoring plane hit position - y").fill(scoringPlaneHitPosition.y());
+            aida.histogram1D("Scoring plane hit position - z").fill(scoringPlaneHitPosition.z());
+            aida.histogram2D("Scoring plane hit position - x-y").fill(scoringPlaneHitPosition.x(), scoringPlaneHitPosition.y());
+        
+            // Extrapolate the track to the scoring plane position
+            Hep3Vector trackPositionAtScoringPlane = TrackUtils.extrapolateTrack(track, scoringPlaneHitPosition.z());
+            this.printVerbose("Extrapolated track position: " + trackPositionAtScoringPlane.toString());
+                
+            // Find the residual between the extrapolated track position and the scoring plane hit position
+            double deltaX = trackPositionAtScoringPlane.x() - scoringPlaneHitPosition.x();
+            double deltaY = trackPositionAtScoringPlane.y() - scoringPlaneHitPosition.y();
+            // This should be 0 but it serves as a sanity check.
+            double deltaZ = trackPositionAtScoringPlane.z() - scoringPlaneHitPosition.z();
+        
+            if(track.getTrackerHits().get(0).getPosition()[2] > 0){
+                if(track.getTrackStates().get(0).getOmega() > 0){
+                    aida.histogram1D("Top positron tracks - Bend plane residual at scoring plane").fill(deltaX);
+                    aida.histogram1D("Top positron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
+                    aida.histogram1D("Top positron tracks - z residuals at scoring plane").fill(deltaZ);    
+                } else { 
+                    aida.histogram1D("Top electron tracks - Bend plane residual at scoring plane").fill(deltaX);
+                    aida.histogram1D("Top electron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
+                    aida.histogram1D("Top electron tracks - z residuals at scoring plane").fill(deltaZ);    
+                }
+            } else { 
+                if(track.getTrackStates().get(0).getOmega() > 0){
+                    aida.histogram1D("Bottom positron tracks - Bend plane residuals at scoring plane").fill(deltaX);
+                    aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
+                    aida.histogram1D("Bottom positron tracks - z residuals at scoring plane").fill(deltaZ);
+                } else { 
+                    aida.histogram1D("Bottom electron tracks - Bend plane residuals at scoring plane").fill(deltaX);
+                    aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at scoring plane").fill(deltaY);
+                    aida.histogram1D("Bottom electron tracks - z residuals at scoring plane").fill(deltaZ);
+                }
+            }
+
+            aida.histogram1D("Bend plane residuals at scoring plane").fill(deltaX);
+            aida.histogram1D("Non-bend plane residuals at scoring plane").fill(deltaY);
+            aida.histogram1D("z residuals at target").fill(deltaZ);
+            aida.histogram2D("Bend plane residuals vs momentum at scoring plane").fill(p, deltaX);
+            aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane").fill(p, deltaY);
+        }
+        
+        if(!event.hasCollection(LCRelation.class, trackToMCParticleRelationsName)) return;
+        
+        List<LCRelation> trackToMCParticleRelations = event.get(LCRelation.class, trackToMCParticleRelationsName);
+        
+        for(LCRelation trackToMCParticleRelation : trackToMCParticleRelations){
+            
+            // Get the track
+            Track track = (Track) trackToMCParticleRelation.getFrom();
+            
+            // Get the track momentum
+            double[] momentum = BaseTrackState.computeMomentum(track.getTrackStates().get(0), bField.y());
+            double p = Math.sqrt(momentum[0]*momentum[0] + momentum[1]*momentum[1] + momentum[2]*momentum[2]);
+            this.printVerbose("Track momentum: " + p);
+
+            // Get the corresponding MC particle
+            MCParticle particle = (MCParticle) trackToMCParticleRelation.getTo();
+            
+            // Extrapolate the track to the origin
+            Hep3Vector trackPositionAtOrigin = TrackUtils.extrapolateTrack(track, particle.getOriginZ());
+            
+            // Find the residual between the extrapolated track and the position of the scoring plane at the origin
+            double deltaX = trackPositionAtOrigin.x() - particle.getOriginX();
+            double deltaY = trackPositionAtOrigin.y() - particle.getOriginY();
+            double deltaZ = trackPositionAtOrigin.z() - particle.getOriginZ();
+            
+            if(track.getTrackerHits().get(0).getPosition()[2] > 0){
+                if(track.getTrackStates().get(0).getOmega() > 0){
+                    aida.histogram1D("Top positron tracks - Bend plane residual at target").fill(deltaX);
+                    aida.histogram1D("Top positron tracks - Non-bend plane residuals at target").fill(deltaY);
+                    aida.histogram1D("Top positron tracks - z residuals at target").fill(deltaZ);
+                } else { 
+                    aida.histogram1D("Top electron tracks - Bend plane residual at target").fill(deltaX);
+                    aida.histogram1D("Top electron tracks - Non-bend plane residuals at target").fill(deltaY);
+                    aida.histogram1D("Top electron tracks - z residuals at target").fill(deltaZ);
+                }
+            } else { 
+                
+                if(track.getTrackStates().get(0).getOmega() > 0){
+                    aida.histogram1D("Bottom positron tracks - Bend plane residuals at target").fill(deltaX);
+                    aida.histogram1D("Bottom positron tracks - Non-bend plane residuals at target").fill(deltaY);
+                    aida.histogram1D("Bottom positron tracks - z residuals at target").fill(deltaZ);
+                } else { 
+                    aida.histogram1D("Bottom electron tracks - Bend plane residuals at target").fill(deltaX);
+                    aida.histogram1D("Bottom electron tracks - Non-bend plane residuals at target").fill(deltaY);
+                    aida.histogram1D("Bottom electron tracks - z residuals at target").fill(deltaZ);
+                }
+            }
+            
+            aida.histogram1D("Bend plane residuals at target").fill(deltaX);
+            aida.histogram1D("Non-bend plane residuals at target").fill(deltaY);
+            aida.histogram1D("z residuals at target").fill(deltaZ);
+            aida.histogram2D("Bend plane residuals vs momentum at target").fill(p, deltaX);
+            aida.histogram2D("Non-bend plane residuals vs momentum at target").fill(p, deltaY);
+        }
+    }
+    
+    @Override
+    protected void endOfData(){
+        
+        IHistogram2D histogram = aida.histogram2D("Bend plane residuals vs momentum at scoring plane");
+        int binsX = histogram.xAxis().bins();
+        for(int binX = 0; binX < binsX; binX++){
+            PlotUtils.getYProjection(binX, histogram);
+        }
+        
+        histogram = aida.histogram2D("Non-bend plane residuals vs momentum at scoring plane");
+        binsX = histogram.xAxis().bins();
+        for(int binX = 0; binX < binsX; binX++){
+            PlotUtils.getYProjection(binX, histogram);
+        }
+    
+        histogram = aida.histogram2D("Bend plane residuals vs momentum at target");
+        binsX = histogram.xAxis().bins();
+        for(int binX = 0; binX < binsX; binX++){
+            PlotUtils.getYProjection(binX, histogram);
+        }
+        
+        histogram = aida.histogram2D("Non-bend plane residuals vs momentum at target");
+        binsX = histogram.xAxis().bins();
+        for(int binX = 0; binX < binsX; binX++){
+            PlotUtils.getYProjection(binX, histogram);
+        }
+    }
+    
+    /**
+     * Print a message if verbose has been enabled.
+     *  
+     * @param message : message to print.
+     */
+    private void printVerbose(String message){
+        if(verbose)
+            System.out.println(this.getClass().getSimpleName() + ": " + message);
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/LheToStdhep.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/LheToStdhep.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/LheToStdhep.java	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,7 @@
 import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.JDOMException;
@@ -32,248 +32,248 @@
  * TODO: Make this converter more generic.
  */
 public class LheToStdhep {
-	
-	private static final int N_PARTICLE_INDEX = 0;
-	private static final int PDG_ID_INDEX = 1;
-	private static final int STATUS_INDEX = 2; 
-	private static final int FIRST_MOTHER_INDEX = 3; 
-	private static final int SECOND_MOTHER_INDEX = 4; 
-	private static final int FIRST_DAUGHTER_INDEX = 5; 
-	private static final int SECOND_DAUGHTER_INDEX = 6; 
-	
-	private static double sigmaX = 0.2;
-	private static double sigmaY = 0.02;
-	private static double sigmaZ = 0.0;
-	
-	private static double offsetX = 0;
-	private static double offsetY = 0;
-	private static double offsetZ = 0.03;
-	
-	static int eventNumber = 0; 
-	
-	
-	public static void main(String[] args) throws IOException{
-
-		String lheFileName = null; 
-		String stdhepFileName = "output.stdhep";
-		
-		// Instantiate te command line parser
-		CommandLineParser parser = new DefaultParser(); 
-
-		// Create the Options
-		// TODO: Add ability to parse list of files.
-		// Allow a user to pass tag.gz files
-		Options options = new Options(); 
-		options.addOption("i", "input", true, "Input LHE file name");
-		options.addOption("o", "output", true, "Output Stdhep file name");
-		
-		try { 
-			// Parse the command line arguments
-			CommandLine line = parser.parse(options, args);
-			
-			// If the file is not specified, notify the user and exit the program
-			if(!line.hasOption("i")){
-				System.out.println("Please specify an LHE file to process");
-				System.exit(0);
-			}
-			lheFileName = line.getOptionValue("i");
-		
-			// Check if the user has specified the output file name and that the
-			// extension is stdhep.  If not, add the extension
-			if(line.hasOption("o")){
-				stdhepFileName = line.getOptionValue("o");
-			}
-		} catch(ParseException e){
-			System.out.println("Unexpected exception: " + e.getMessage());
-		}
-		
-		convertToStdhep(lheFileName, stdhepFileName);
-		
-	}
-
-	/**
-	 * 
-	 */
-	static private void convertToStdhep(String lheFileName, String stdhepFileName) throws IOException{
-		List<Element> events = readLhe(lheFileName);
-
-		StdhepWriter writer = new StdhepWriter(
-						   	stdhepFileName,
-						   	"Import Stdhep Events",
-						   	"Imported from LHE generated from MadGraph",
-						   	events.size()
-							);
-		writer.setCompatibilityMode(false);
-		
-		for(Element event : events){
-			writeEvent(event, writer);
-		}
-		writer.close();
-	}
-
-	/**
-	 * 
-	 */
-	private static List<Element> readLhe(String lheFileName){
-		
-		// Instantiate the SAX parser used to build the JDOM document
-		SAXBuilder builder = new SAXBuilder(); 
-		
-		// Open the lhe file
-		File lheFile = new File(lheFileName);
-			
-		// Parse the lhe file and build the JDOM document
-		Document document = null;
-		List<Element> eventNodes = null; 
-		try {
-			
-			document = (Document) builder.build(lheFile);
-			
-			// Get the root node
-			Element rootNode = document.getRootElement(); 
-			
-			// Get a list of all nodes of type event
-			eventNodes = rootNode.getChildren("event");
-		
-		} catch (JDOMException e) {
-			e.printStackTrace();
-			
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-		
-		return eventNodes; 
-	}
-
-	/**
-	 * 
-	 */
-	private static void writeEvent(Element event, StdhepWriter writer) throws IOException{
-		
-		int numberOfParticles = 0; 
-		int particleIndex = 0;
-		int pdgID[] = null; 
-		int particleStatus[] = null;
-		int motherParticles[] = null; 
-		int daughterParticles[] = null; 
-		double particleMomentum[] = null;
-		double particleVertex[] = null; 
-		
-		Random generator = new Random(); 
-		
-		eventNumber++; 
-		
-		System.out.println("#================================================#\n#");
-		System.out.println("# Event: " + eventNumber);
-		
-		
-		// Get the text within the event element node.  An element node contains
-		// information describing the event and it's particles.  The PDG ID of
-		// a particle along with it's kinematics is listed on it's own line.
-		// In order to parse the information for each particle, the text is 
-		// split using the newline character as a delimiter.  
-		String[] eventData = event.getTextTrim().split("\n");	
-	 
-		for(int datumIndex = 0; datumIndex < eventData.length; datumIndex++){
-			
-			// Split a line by whitespace
-			String[] eventTokens = eventData[datumIndex].split("\\s+");
-		
-			if(datumIndex == 0){
-				
-				numberOfParticles = Integer.valueOf(eventTokens[N_PARTICLE_INDEX]);
-				System.out.println("# Number of particles: " + numberOfParticles + "\n#");
-				System.out.println("#================================================#");
-		
-				// Reset all arrays used to build the Stdhep event
-				particleIndex = 0; 
-				particleStatus = new int[numberOfParticles];
-				pdgID = new int[numberOfParticles];
-				motherParticles = new int[numberOfParticles*2];
-				daughterParticles = new int[numberOfParticles*2];
-				particleMomentum = new double[numberOfParticles*5];
-				particleVertex = new double[numberOfParticles*4];
-			
-				continue;
-			}
-	
-			// Get the PDG ID of the particle
-			pdgID[particleIndex] = Integer.valueOf(eventTokens[PDG_ID_INDEX]);
-			
-			
-			System.out.println(">>> PDG ID: " + pdgID[particleIndex]);
-			
-			// Get the status of the particle (initial state = -1, final state = 1, resonance = 2)
-			particleStatus[particleIndex] = Integer.valueOf(eventTokens[STATUS_INDEX]);
-			if(particleStatus[particleIndex] == -1) particleStatus[particleIndex] = 3; 
-			System.out.println(">>>> Particle Status: " + particleStatus[particleIndex]);
-			
-			 // Get the mothers of a particle.  If the particle is a trident electron, then assign it
-			 // a mother value of 10 so it's distinguishable from the beam electron.
-			if(pdgID[particleIndex] == 611){
-				motherParticles[particleIndex*2] = 10;
-				// If the PDG ID is equal to 611/-611 (trident electron) change it back to 11/-11. 
-				// Otherwise, SLIC won't do anything with them.
-				pdgID[particleIndex] = 11;
-			} else if(pdgID[particleIndex] == -611){
-				motherParticles[particleIndex*2] = 10;
-				pdgID[particleIndex] = -11; 
-			} else {
-				motherParticles[particleIndex*2] = Integer.valueOf(eventTokens[FIRST_MOTHER_INDEX]);
-			}
-	        motherParticles[particleIndex*2 + 1] = Integer.valueOf(eventTokens[SECOND_MOTHER_INDEX]);
-	        System.out.println(">>>> Mothers: 1) " + motherParticles[particleIndex*2] + " 2) " + motherParticles[particleIndex*2 + 1]);
-	        
-	        // Get the daughter particles
-	        daughterParticles[particleIndex*2] = Integer.valueOf(eventTokens[FIRST_DAUGHTER_INDEX]);
-	        daughterParticles[particleIndex*2 + 1] = Integer.valueOf(eventTokens[SECOND_DAUGHTER_INDEX]);
-	        System.out.println(">>>> Daughter: 1) " + daughterParticles[particleIndex*2] + " 2) " + daughterParticles[particleIndex*2 + 1]);
-	        
-	        // Get the particle momentum, its mass and energy
-	        particleMomentum[particleIndex*5] = Double.valueOf(eventTokens[7]);		// px
-	        particleMomentum[particleIndex*5 + 1] = Double.valueOf(eventTokens[8]);	// py   
-	        particleMomentum[particleIndex*5 + 2] = Double.valueOf(eventTokens[9]); // pz
-	        particleMomentum[particleIndex*5 + 3] = Double.valueOf(eventTokens[10]); // Particle Energy
-	        particleMomentum[particleIndex*5 + 4] = Double.valueOf(eventTokens[11]); // Particle Mass
-	        
-	        // Rotate the particle by 30 mrad around the beam axis
-	        Hep3Vector rotatedMomentum = 
-	        		rotateToDetector(particleMomentum[particleIndex*5], 
-	        				particleMomentum[particleIndex*5+1], 
-	        				particleMomentum[particleIndex*5+1]);
-	        
-	        particleMomentum[particleIndex*5] = rotatedMomentum.x();
-	        particleMomentum[particleIndex*5 + 1] = rotatedMomentum.y();
-	        particleMomentum[particleIndex*5 + 2] = rotatedMomentum.z();
-
-	        // Set the origin of the particle
-	        Hep3Vector rotatedVertex = rotateToDetector(sigmaX*generator.nextGaussian() + offsetX, 
-	        		sigmaY*generator.nextGaussian() + offsetY, 
-	        		sigmaZ*generator.nextGaussian() + offsetZ);
-	        particleVertex[particleIndex*4] = rotatedVertex.x();
-	        particleVertex[particleIndex*4+1] = rotatedVertex.y();
-	        particleVertex[particleIndex*4+2] = rotatedVertex.z();
-	        particleVertex[particleIndex*4+3] = 0; 
-	        
-	        // Increment the particle number
-	        particleIndex++;
-	        
-			System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>");
-		}
-		
-		// Create the Stdhep event and write it 
-	    StdhepEvent stdhepEvent = new StdhepEvent(eventNumber, numberOfParticles, particleStatus, 
-	    		pdgID, motherParticles, daughterParticles, particleMomentum, particleVertex);
-	    writer.writeRecord(stdhepEvent);
-	}
-
-	/**
-	 * 
-	 */
-	private static Hep3Vector rotateToDetector(double x, double y, double z){
-		IRotation3D rotation = new RotationGeant(0.0, 0.03, 0.0);
-		Hep3Vector vector = new BasicHep3Vector(x, y, z);
-		return rotation.rotated(vector);
-	}
+    
+    private static final int N_PARTICLE_INDEX = 0;
+    private static final int PDG_ID_INDEX = 1;
+    private static final int STATUS_INDEX = 2; 
+    private static final int FIRST_MOTHER_INDEX = 3; 
+    private static final int SECOND_MOTHER_INDEX = 4; 
+    private static final int FIRST_DAUGHTER_INDEX = 5; 
+    private static final int SECOND_DAUGHTER_INDEX = 6; 
+    
+    private static double sigmaX = 0.2;
+    private static double sigmaY = 0.02;
+    private static double sigmaZ = 0.0;
+    
+    private static double offsetX = 0;
+    private static double offsetY = 0;
+    private static double offsetZ = 0.03;
+    
+    static int eventNumber = 0; 
+    
+    
+    public static void main(String[] args) throws IOException{
+
+        String lheFileName = null; 
+        String stdhepFileName = "output.stdhep";
+        
+        // Instantiate te command line parser
+        CommandLineParser parser = new PosixParser(); 
+
+        // Create the Options
+        // TODO: Add ability to parse list of files.
+        // Allow a user to pass tag.gz files
+        Options options = new Options(); 
+        options.addOption("i", "input", true, "Input LHE file name");
+        options.addOption("o", "output", true, "Output Stdhep file name");
+        
+        try { 
+            // Parse the command line arguments
+            CommandLine line = parser.parse(options, args);
+            
+            // If the file is not specified, notify the user and exit the program
+            if(!line.hasOption("i")){
+                System.out.println("Please specify an LHE file to process");
+                System.exit(0);
+            }
+            lheFileName = line.getOptionValue("i");
+        
+            // Check if the user has specified the output file name and that the
+            // extension is stdhep.  If not, add the extension
+            if(line.hasOption("o")){
+                stdhepFileName = line.getOptionValue("o");
+            }
+        } catch(ParseException e){
+            System.out.println("Unexpected exception: " + e.getMessage());
+        }
+        
+        convertToStdhep(lheFileName, stdhepFileName);
+        
+    }
+
+    /**
+     * 
+     */
+    static private void convertToStdhep(String lheFileName, String stdhepFileName) throws IOException{
+        List<Element> events = readLhe(lheFileName);
+
+        StdhepWriter writer = new StdhepWriter(
+                            stdhepFileName,
+                            "Import Stdhep Events",
+                            "Imported from LHE generated from MadGraph",
+                            events.size()
+                            );
+        writer.setCompatibilityMode(false);
+        
+        for(Element event : events){
+            writeEvent(event, writer);
+        }
+        writer.close();
+    }
+
+    /**
+     * 
+     */
+    private static List<Element> readLhe(String lheFileName){
+        
+        // Instantiate the SAX parser used to build the JDOM document
+        SAXBuilder builder = new SAXBuilder(); 
+        
+        // Open the lhe file
+        File lheFile = new File(lheFileName);
+            
+        // Parse the lhe file and build the JDOM document
+        Document document = null;
+        List<Element> eventNodes = null; 
+        try {
+            
+            document = (Document) builder.build(lheFile);
+            
+            // Get the root node
+            Element rootNode = document.getRootElement(); 
+            
+            // Get a list of all nodes of type event
+            eventNodes = rootNode.getChildren("event");
+        
+        } catch (JDOMException e) {
+            e.printStackTrace();
+            
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+        
+        return eventNodes; 
+    }
+
+    /**
+     * 
+     */
+    private static void writeEvent(Element event, StdhepWriter writer) throws IOException{
+        
+        int numberOfParticles = 0; 
+        int particleIndex = 0;
+        int pdgID[] = null; 
+        int particleStatus[] = null;
+        int motherParticles[] = null; 
+        int daughterParticles[] = null; 
+        double particleMomentum[] = null;
+        double particleVertex[] = null; 
+        
+        Random generator = new Random(); 
+        
+        eventNumber++; 
+        
+        System.out.println("#================================================#\n#");
+        System.out.println("# Event: " + eventNumber);
+        
+        
+        // Get the text within the event element node.  An element node contains
+        // information describing the event and it's particles.  The PDG ID of
+        // a particle along with it's kinematics is listed on it's own line.
+        // In order to parse the information for each particle, the text is 
+        // split using the newline character as a delimiter.  
+        String[] eventData = event.getTextTrim().split("\n");   
+     
+        for(int datumIndex = 0; datumIndex < eventData.length; datumIndex++){
+            
+            // Split a line by whitespace
+            String[] eventTokens = eventData[datumIndex].split("\\s+");
+        
+            if(datumIndex == 0){
+                
+                numberOfParticles = Integer.valueOf(eventTokens[N_PARTICLE_INDEX]);
+                System.out.println("# Number of particles: " + numberOfParticles + "\n#");
+                System.out.println("#================================================#");
+        
+                // Reset all arrays used to build the Stdhep event
+                particleIndex = 0; 
+                particleStatus = new int[numberOfParticles];
+                pdgID = new int[numberOfParticles];
+                motherParticles = new int[numberOfParticles*2];
+                daughterParticles = new int[numberOfParticles*2];
+                particleMomentum = new double[numberOfParticles*5];
+                particleVertex = new double[numberOfParticles*4];
+            
+                continue;
+            }
+    
+            // Get the PDG ID of the particle
+            pdgID[particleIndex] = Integer.valueOf(eventTokens[PDG_ID_INDEX]);
+            
+            
+            System.out.println(">>> PDG ID: " + pdgID[particleIndex]);
+            
+            // Get the status of the particle (initial state = -1, final state = 1, resonance = 2)
+            particleStatus[particleIndex] = Integer.valueOf(eventTokens[STATUS_INDEX]);
+            if(particleStatus[particleIndex] == -1) particleStatus[particleIndex] = 3; 
+            System.out.println(">>>> Particle Status: " + particleStatus[particleIndex]);
+            
+             // Get the mothers of a particle.  If the particle is a trident electron, then assign it
+             // a mother value of 10 so it's distinguishable from the beam electron.
+            if(pdgID[particleIndex] == 611){
+                motherParticles[particleIndex*2] = 10;
+                // If the PDG ID is equal to 611/-611 (trident electron) change it back to 11/-11. 
+                // Otherwise, SLIC won't do anything with them.
+                pdgID[particleIndex] = 11;
+            } else if(pdgID[particleIndex] == -611){
+                motherParticles[particleIndex*2] = 10;
+                pdgID[particleIndex] = -11; 
+            } else {
+                motherParticles[particleIndex*2] = Integer.valueOf(eventTokens[FIRST_MOTHER_INDEX]);
+            }
+            motherParticles[particleIndex*2 + 1] = Integer.valueOf(eventTokens[SECOND_MOTHER_INDEX]);
+            System.out.println(">>>> Mothers: 1) " + motherParticles[particleIndex*2] + " 2) " + motherParticles[particleIndex*2 + 1]);
+            
+            // Get the daughter particles
+            daughterParticles[particleIndex*2] = Integer.valueOf(eventTokens[FIRST_DAUGHTER_INDEX]);
+            daughterParticles[particleIndex*2 + 1] = Integer.valueOf(eventTokens[SECOND_DAUGHTER_INDEX]);
+            System.out.println(">>>> Daughter: 1) " + daughterParticles[particleIndex*2] + " 2) " + daughterParticles[particleIndex*2 + 1]);
+            
+            // Get the particle momentum, its mass and energy
+            particleMomentum[particleIndex*5] = Double.valueOf(eventTokens[7]);     // px
+            particleMomentum[particleIndex*5 + 1] = Double.valueOf(eventTokens[8]); // py   
+            particleMomentum[particleIndex*5 + 2] = Double.valueOf(eventTokens[9]); // pz
+            particleMomentum[particleIndex*5 + 3] = Double.valueOf(eventTokens[10]); // Particle Energy
+            particleMomentum[particleIndex*5 + 4] = Double.valueOf(eventTokens[11]); // Particle Mass
+            
+            // Rotate the particle by 30 mrad around the beam axis
+            Hep3Vector rotatedMomentum = 
+                    rotateToDetector(particleMomentum[particleIndex*5], 
+                            particleMomentum[particleIndex*5+1], 
+                            particleMomentum[particleIndex*5+1]);
+            
+            particleMomentum[particleIndex*5] = rotatedMomentum.x();
+            particleMomentum[particleIndex*5 + 1] = rotatedMomentum.y();
+            particleMomentum[particleIndex*5 + 2] = rotatedMomentum.z();
+
+            // Set the origin of the particle
+            Hep3Vector rotatedVertex = rotateToDetector(sigmaX*generator.nextGaussian() + offsetX, 
+                    sigmaY*generator.nextGaussian() + offsetY, 
+                    sigmaZ*generator.nextGaussian() + offsetZ);
+            particleVertex[particleIndex*4] = rotatedVertex.x();
+            particleVertex[particleIndex*4+1] = rotatedVertex.y();
+            particleVertex[particleIndex*4+2] = rotatedVertex.z();
+            particleVertex[particleIndex*4+3] = 0; 
+            
+            // Increment the particle number
+            particleIndex++;
+            
+            System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>");
+        }
+        
+        // Create the Stdhep event and write it 
+        StdhepEvent stdhepEvent = new StdhepEvent(eventNumber, numberOfParticles, particleStatus, 
+                pdgID, motherParticles, daughterParticles, particleMomentum, particleVertex);
+        writer.writeRecord(stdhepEvent);
+    }
+
+    /**
+     * 
+     */
+    private static Hep3Vector rotateToDetector(double x, double y, double z){
+        IRotation3D rotation = new RotationGeant(0.0, 0.03, 0.0);
+        Hep3Vector vector = new BasicHep3Vector(x, y, z);
+        return rotation.rotated(vector);
+    }
 
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/PlotUtils.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/PlotUtils.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/PlotUtils.java	Wed Apr 27 11:11:32 2016
@@ -20,71 +20,71 @@
  */
 public class PlotUtils {
 
-	// Default ctor
-	public PlotUtils(){}	
+    // Default ctor
+    public PlotUtils(){}    
 
-	public static IPlotter setupPlotter(String title, int regionX, int regionY){
-	    IPlotter plotter = AIDA.defaultInstance().analysisFactory().createPlotterFactory().create(title);
-	    plotter.setTitle(title);
-	    
-	    if(regionX < 0 || regionY < 0) throw new RuntimeException("Region dimensions need to be greater than 0!");
-	    else if(regionX != 0 || regionY != 0) plotter.createRegions(regionX, regionY);
-	    
-	    plotter.style().statisticsBoxStyle().setVisible(false);
-	    plotter.style().dataStyle().errorBarStyle().setVisible(false);
-	    plotter.setParameter("plotterWidth", "800");
-	    plotter.setParameter("plotterHeight", "800");
-	    
-	    return plotter;
-	    
-	}
+    public static IPlotter setupPlotter(String title, int regionX, int regionY){
+        IPlotter plotter = AIDA.defaultInstance().analysisFactory().createPlotterFactory().create(title);
+        plotter.setTitle(title);
+        
+        if(regionX < 0 || regionY < 0) throw new RuntimeException("Region dimensions need to be greater than 0!");
+        else if(regionX != 0 || regionY != 0) plotter.createRegions(regionX, regionY);
+        
+        plotter.style().statisticsBoxStyle().setVisible(false);
+        plotter.style().dataStyle().errorBarStyle().setVisible(false);
+        plotter.setParameter("plotterWidth", "800");
+        plotter.setParameter("plotterHeight", "800");
+        
+        return plotter;
+        
+    }
     
     public static void setup2DRegion(IPlotter plotter, String title, int region, String xTitle, String yTitle, IHistogram2D histo){
-    	
-    	// Check if the specified region is valid
-    	if(region > plotter.numberOfRegions()) 
-    		throw new RuntimeException("Region is invalid! " + title + " contains " + plotter.numberOfRegions() + " regions");
-    	
-		plotter.region(region).style().xAxisStyle().setLabel(xTitle);
-		plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
-		plotter.region(region).style().yAxisStyle().setLabel(yTitle);
-		plotter.region(region).style().yAxisStyle().labelStyle().setFontSize(14);
-		plotter.region(region).style().xAxisStyle().setVisible(true);
-		plotter.region(region).style().yAxisStyle().setVisible(true);
-		plotter.region(region).style().setParameter("hist2DStyle", "colorMap");
-    	plotter.region(region).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-    	
-    	if(histo != null) plotter.region(region).plot(histo);
+        
+        // Check if the specified region is valid
+        if(region > plotter.numberOfRegions()) 
+            throw new RuntimeException("Region is invalid! " + title + " contains " + plotter.numberOfRegions() + " regions");
+        
+        plotter.region(region).style().xAxisStyle().setLabel(xTitle);
+        plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
+        plotter.region(region).style().yAxisStyle().setLabel(yTitle);
+        plotter.region(region).style().yAxisStyle().labelStyle().setFontSize(14);
+        plotter.region(region).style().xAxisStyle().setVisible(true);
+        plotter.region(region).style().yAxisStyle().setVisible(true);
+        plotter.region(region).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(region).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        
+        if(histo != null) plotter.region(region).plot(histo);
     }
    
     public static void setup2DRegion(IPlotter plotter, String title, int region, String xTitle, String yTitle, ICloud2D cloud, IPlotterStyle style){
-    	
-    	// Check if the specified region is valid
-    	if(region > plotter.numberOfRegions()) 
-    		throw new RuntimeException("Region is invalid! " + title + " contains " + plotter.numberOfRegions() + " regions");
-    	
-		plotter.region(region).style().xAxisStyle().setLabel(xTitle);
-		plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
-		String[] pars = plotter.region(region).style().xAxisStyle().availableParameters();
-		plotter.region(region).style().yAxisStyle().setLabel(yTitle);
-		plotter.region(region).style().yAxisStyle().labelStyle().setFontSize(14);
-		plotter.region(region).style().xAxisStyle().setVisible(true);
-		plotter.region(region).style().yAxisStyle().setVisible(true);
-		plotter.region(region).style().setParameter("showAsScatterPlot", "true");
-    	
-    	if(cloud != null) plotter.region(region).plot(cloud, style);
+        
+        // Check if the specified region is valid
+        if(region > plotter.numberOfRegions()) 
+            throw new RuntimeException("Region is invalid! " + title + " contains " + plotter.numberOfRegions() + " regions");
+        
+        plotter.region(region).style().xAxisStyle().setLabel(xTitle);
+        plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
+        String[] pars = plotter.region(region).style().xAxisStyle().availableParameters();
+        plotter.region(region).style().yAxisStyle().setLabel(yTitle);
+        plotter.region(region).style().yAxisStyle().labelStyle().setFontSize(14);
+        plotter.region(region).style().xAxisStyle().setVisible(true);
+        plotter.region(region).style().yAxisStyle().setVisible(true);
+        plotter.region(region).style().setParameter("showAsScatterPlot", "true");
+        
+        if(cloud != null) plotter.region(region).plot(cloud, style);
     }
     
     
     public static void setup1DRegion(IPlotter plotter, String title, int region, String xTitle, IHistogram1D histo){
-    	
-		plotter.region(region).style().xAxisStyle().setLabel(xTitle);
-		plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
-		plotter.region(region).style().xAxisStyle().setVisible(true);
-		plotter.region(region).style().dataStyle().fillStyle().setVisible(false);
-		plotter.region(region).style().dataStyle().lineStyle().setThickness(3);
-		
-		if(histo != null) plotter.region(region).plot(histo);
+        
+        plotter.region(region).style().xAxisStyle().setLabel(xTitle);
+        plotter.region(region).style().xAxisStyle().labelStyle().setFontSize(14);
+        plotter.region(region).style().xAxisStyle().setVisible(true);
+        plotter.region(region).style().dataStyle().fillStyle().setVisible(false);
+        plotter.region(region).style().dataStyle().lineStyle().setThickness(3);
+        
+        if(histo != null) plotter.region(region).plot(histo);
     }
     
     /**
@@ -98,7 +98,7 @@
         int ix = (layer - 1) / 2;
         int iy = 0;
         if (!((HpsSiSensor) sensor).isTopLayer()){ 
-        	iy += 2;
+            iy += 2;
         }
         if (layer % 2 == 0) {
             iy += 1;
@@ -108,35 +108,35 @@
     }
    
     public static IHistogram1D getYProjection(int binX, IHistogram2D histogram){
-    	int binsY = histogram.yAxis().bins();
-    	double yMin = histogram.yAxis().lowerEdge();
-    	double yMax = histogram.yAxis().upperEdge(); 
-    	
-    	IHistogram1D projection 
-    		= AIDA.defaultInstance().histogram1D(histogram.title() + "_" + binX, binsY, yMin, yMax);
-    	projection.reset();
-    	
-    	double dataY = 0; 
-    	for(int binY = 0; binY < binsY; binY++){
-    		dataY = histogram.binEntries(binX, binY);
-    		projection.fill(yMin, dataY);
-    		yMin++;
-    	}
-    	
-    	return projection; 
+        int binsY = histogram.yAxis().bins();
+        double yMin = histogram.yAxis().lowerEdge();
+        double yMax = histogram.yAxis().upperEdge(); 
+        
+        IHistogram1D projection 
+            = AIDA.defaultInstance().histogram1D(histogram.title() + "_" + binX, binsY, yMin, yMax);
+        projection.reset();
+        
+        double dataY = 0; 
+        for(int binY = 0; binY < binsY; binY++){
+            dataY = histogram.binEntries(binX, binY);
+            projection.fill(yMin, dataY);
+            yMin++;
+        }
+        
+        return projection; 
     }
     
     public static double[] fitToGuassian(IHistogram1D histogram){
-    	
-    	double[] fitParameters = {0, 0};
-    	IFitter fitter = AIDA.defaultInstance().analysisFactory().createFitFactory().createFitter();
-    	IFitResult fitResult = fitter.fit(histogram, "g");
-    	int meanIndex  = fitResult.fittedFunction().indexOfParameter("mean");
-    	fitParameters[0] = fitResult.fittedParameters()[meanIndex];
+        
+        double[] fitParameters = {0, 0};
+        IFitter fitter = AIDA.defaultInstance().analysisFactory().createFitFactory().createFitter();
+        IFitResult fitResult = fitter.fit(histogram, "g");
+        int meanIndex  = fitResult.fittedFunction().indexOfParameter("mean");
+        fitParameters[0] = fitResult.fittedParameters()[meanIndex];
 
-    	int sigmaIndex  = fitResult.fittedFunction().indexOfParameter("sigma");
-    	fitParameters[1] = fitResult.fittedParameters()[sigmaIndex];
-    	
-		return fitParameters;
+        int sigmaIndex  = fitResult.fittedFunction().indexOfParameter("sigma");
+        fitParameters[1] = fitResult.fittedParameters()[sigmaIndex];
+        
+        return fitParameters;
     }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ReconstructedParticleChecker.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ReconstructedParticleChecker.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/ReconstructedParticleChecker.java	Wed Apr 27 11:11:32 2016
@@ -29,92 +29,92 @@
  *
  */
 public class ReconstructedParticleChecker extends Driver {
-	
-	private AIDA aida; 
-	private List<IPlotter> plotters = new ArrayList<IPlotter>(); 
+    
+    private AIDA aida; 
+    private List<IPlotter> plotters = new ArrayList<IPlotter>(); 
 
-	IHistogram1D xPositionResidual;
-	IHistogram1D yPositionResidual;
-	IHistogram1D zPositionResidual;
-	IHistogram1D r;
-	
-	// Collection Names
-	private String finalStateParticlesCollectionName = "FinalStateParticles";
-	
-	boolean debug = true; 
-	int plotterIndex = 0; 
-	
-	public ReconstructedParticleChecker(){} 
-	
-	protected void detectorChanged(Detector detector){
-		super.detectorChanged(detector);
-		
-		// Setup AIDA
-		aida = AIDA.defaultInstance(); 
-		aida.tree().cd("/");
-		
-		plotters.add(PlotUtils.setupPlotter("Track-Cluster Position Residual", 2, 2));
-		xPositionResidual = aida.histogram1D("x Residual", 100, -100, 100);
-		yPositionResidual = aida.histogram1D("y Residual", 100, -100, 100);
-		zPositionResidual = aida.histogram1D("z Residual", 100, -100, 100);
-		r = aida.histogram1D("r", 100, -100, 100);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "x Residual", 0, "delta x [mm]", xPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "y Residual", 1, "delta y [mm]", yPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "z Residual", 2, "delta z [mm]", zPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "r", 3, "r [mm]", r);
-		
-		
-		for(IPlotter plotter : plotters){
-			plotter.show(); 
-		}
-	}
-	
-	public void process(EventHeader event){
-		
-		// If the event doesn't contain any final state reconstructed 
-		// particles, skip the event 
-		if(!event.hasCollection(ReconstructedParticle.class, finalStateParticlesCollectionName)){
-			this.printDebug("Event does not contain ReconstructedParticles");
-			return;
-		}
-		
-		// Get the collections of reconstructed final state particles from the
-		// event
-		List<ReconstructedParticle> finalStateParticles 
-			= event.get(ReconstructedParticle.class, finalStateParticlesCollectionName); 
-				
-	
-		// Loop over all of the reconstructed particles in the event
-		for(ReconstructedParticle finalStateParticle : finalStateParticles){
-			
-			// Get the list of clusters from the event
-			List<Cluster> ecalClusters = finalStateParticle.getClusters(); 
-				this.printDebug("Number of Ecal clusters: " + ecalClusters.size()); 
-			if(ecalClusters.isEmpty()){
-				this.printDebug("Number of Ecal clusters: " + ecalClusters.size()); 
-				this.printDebug("List of Ecal cluster is empty ... skipping");
-				continue; 
-			}
-			
-			// Get the list of tracks from the event
-			List<Track> tracks = finalStateParticle.getTracks(); 
-			if(tracks.isEmpty()){
-				this.printDebug("List of tracks is empty ... skipping");
-				continue; 
-			}
-		
-			Hep3Vector ecalPosition = new BasicHep3Vector(ecalClusters.get(0).getPosition()); 
-			Hep3Vector trackPositionAtEcal = TrackUtils.extrapolateTrack(tracks.get(0),ecalPosition.z()); 
-			xPositionResidual.fill(trackPositionAtEcal.x() - ecalPosition.x());
-			yPositionResidual.fill(trackPositionAtEcal.y() - ecalPosition.y());
-			zPositionResidual.fill(trackPositionAtEcal.z() - ecalPosition.z());
-			r.fill(VecOp.sub(trackPositionAtEcal, ecalPosition).magnitude());
-		}
-		
-	}
-	
-	private void printDebug(String debugMessage){
-		if(debug)
-			System.out.println(this.getClass().getSimpleName() + ": " + debugMessage); 
-	}
+    IHistogram1D xPositionResidual;
+    IHistogram1D yPositionResidual;
+    IHistogram1D zPositionResidual;
+    IHistogram1D r;
+    
+    // Collection Names
+    private String finalStateParticlesCollectionName = "FinalStateParticles";
+    
+    boolean debug = true; 
+    int plotterIndex = 0; 
+    
+    public ReconstructedParticleChecker(){} 
+    
+    protected void detectorChanged(Detector detector){
+        super.detectorChanged(detector);
+        
+        // Setup AIDA
+        aida = AIDA.defaultInstance(); 
+        aida.tree().cd("/");
+        
+        plotters.add(PlotUtils.setupPlotter("Track-Cluster Position Residual", 2, 2));
+        xPositionResidual = aida.histogram1D("x Residual", 100, -100, 100);
+        yPositionResidual = aida.histogram1D("y Residual", 100, -100, 100);
+        zPositionResidual = aida.histogram1D("z Residual", 100, -100, 100);
+        r = aida.histogram1D("r", 100, -100, 100);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "x Residual", 0, "delta x [mm]", xPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "y Residual", 1, "delta y [mm]", yPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "z Residual", 2, "delta z [mm]", zPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "r", 3, "r [mm]", r);
+        
+        
+        for(IPlotter plotter : plotters){
+            plotter.show(); 
+        }
+    }
+    
+    public void process(EventHeader event){
+        
+        // If the event doesn't contain any final state reconstructed 
+        // particles, skip the event 
+        if(!event.hasCollection(ReconstructedParticle.class, finalStateParticlesCollectionName)){
+            this.printDebug("Event does not contain ReconstructedParticles");
+            return;
+        }
+        
+        // Get the collections of reconstructed final state particles from the
+        // event
+        List<ReconstructedParticle> finalStateParticles 
+            = event.get(ReconstructedParticle.class, finalStateParticlesCollectionName); 
+                
+    
+        // Loop over all of the reconstructed particles in the event
+        for(ReconstructedParticle finalStateParticle : finalStateParticles){
+            
+            // Get the list of clusters from the event
+            List<Cluster> ecalClusters = finalStateParticle.getClusters(); 
+                this.printDebug("Number of Ecal clusters: " + ecalClusters.size()); 
+            if(ecalClusters.isEmpty()){
+                this.printDebug("Number of Ecal clusters: " + ecalClusters.size()); 
+                this.printDebug("List of Ecal cluster is empty ... skipping");
+                continue; 
+            }
+            
+            // Get the list of tracks from the event
+            List<Track> tracks = finalStateParticle.getTracks(); 
+            if(tracks.isEmpty()){
+                this.printDebug("List of tracks is empty ... skipping");
+                continue; 
+            }
+        
+            Hep3Vector ecalPosition = new BasicHep3Vector(ecalClusters.get(0).getPosition()); 
+            Hep3Vector trackPositionAtEcal = TrackUtils.extrapolateTrack(tracks.get(0),ecalPosition.z()); 
+            xPositionResidual.fill(trackPositionAtEcal.x() - ecalPosition.x());
+            yPositionResidual.fill(trackPositionAtEcal.y() - ecalPosition.y());
+            zPositionResidual.fill(trackPositionAtEcal.z() - ecalPosition.z());
+            r.fill(VecOp.sub(trackPositionAtEcal, ecalPosition).magnitude());
+        }
+        
+    }
+    
+    private void printDebug(String debugMessage){
+        if(debug)
+            System.out.println(this.getClass().getSimpleName() + ": " + debugMessage); 
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SharedHitAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SharedHitAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SharedHitAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -98,14 +98,14 @@
     }
     
     
-	protected void detectorChanged(Detector detector){
-
-	    for (int layer = 1; layer <= 6; layer++) { 
-	        
-	        topLayerToStereoHit.put(layer, new ArrayList<TrackerHit>());
-	        bottomLayerToStereoHit.put(layer, new ArrayList<TrackerHit>());
-	    }
-	    
+    protected void detectorChanged(Detector detector){
+
+        for (int layer = 1; layer <= 6; layer++) { 
+            
+            topLayerToStereoHit.put(layer, new ArrayList<TrackerHit>());
+            bottomLayerToStereoHit.put(layer, new ArrayList<TrackerHit>());
+        }
+        
         tree = IAnalysisFactory.create().createTreeFactory().create();
         histogramFactory = IAnalysisFactory.create().createHistogramFactory(tree);
         
@@ -159,18 +159,18 @@
         plotters.get("Track Parameters").region(4).plot(trackPlots.get("tan_lambda"), this.createStyle(1, "", ""));
         plotters.get("Track Parameters").region(4).plot(trackPlots.get("tan_lambda - shared strip hit"),  this.createStyle(2, "", ""));
         plotters.get("Track Parameters").region(4).plot(trackPlots.get("tan_lambda - l1 Isolation"),  this.createStyle(3, "", ""));
-	
-		for (IPlotter plotter : plotters.values()) { 
-			plotter.show();
-		}
-	}
-	
-	@SuppressWarnings({ "unchecked", "rawtypes" })
+    
+        for (IPlotter plotter : plotters.values()) { 
+            plotter.show();
+        }
+    }
+    
+    @SuppressWarnings({ "unchecked", "rawtypes" })
     public void process(EventHeader event){
 
         // If the event doesn't have any tracks, skip it    
-		if(!event.hasCollection(Track.class, trackCollectionName)) return;
-    	
+        if(!event.hasCollection(Track.class, trackCollectionName)) return;
+        
         // Get the collection of tracks from the event
         List<Track> tracks = event.get(Track.class, trackCollectionName);
         
@@ -198,13 +198,13 @@
         this.mapStereoHits(stereoHits);
         
         // Loop over all of the tracks in the event
-    	for(Track track : tracks){
-    	
-    	    boolean sharedHitTrack = false;
+        for(Track track : tracks){
+        
+            boolean sharedHitTrack = false;
            boolean l1Isolation = true;
-    	    
-    	    // Fill the track parameter plots
-    	    
+            
+            // Fill the track parameter plots
+            
             // Loop through all of the stereo hits associated with a track
             for (TrackerHit rotatedStereoHit : track.getTrackerHits()) { 
                
@@ -277,15 +277,15 @@
                 trackPlots.get("tan_lambda - l1 Isolation").fill(TrackUtils.getTanLambda(track));
                 trackPlots.get("chi2 - l1 Isolation").fill(track.getChi2());
             }
-    	}
-	}
-	
+        }
+    }
+    
     private void mapStereoHits(List<TrackerHit> stereoHits) { 
        
-	    for (int layer = 1; layer <= 6; layer++) { 
-	        topLayerToStereoHit.get(layer).clear();
-	        bottomLayerToStereoHit.get(layer).clear();;
-	    }
+        for (int layer = 1; layer <= 6; layer++) { 
+            topLayerToStereoHit.get(layer).clear();
+            bottomLayerToStereoHit.get(layer).clear();;
+        }
         
         for (TrackerHit stereoHit : stereoHits) {
             HpsSiSensor sensor = (HpsSiSensor) ((RawTrackerHit) stereoHit.getRawHits().get(0)).getDetectorElement();

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtClusterAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtClusterAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtClusterAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -50,28 +50,28 @@
     // Plotting
     ITree tree; 
     IHistogramFactory histogramFactory; 
-	IPlotterFactory plotterFactory = IAnalysisFactory.create().createPlotterFactory();
-	protected Map<String, IPlotter> plotters = new HashMap<String, IPlotter>(); 
-	
-	// All clusters
-	private Map<String, IHistogram1D> clusterChargePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> singleHitClusterChargePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> multHitClusterChargePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> signalToNoisePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> singleHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> multHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> clusterSizePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> clusterTimePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram2D> clusterChargeVsTimePlots = new HashMap<String, IHistogram2D>();
-
-	// Clusters on track
-	private Map<String, IHistogram1D> trackClusterChargePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> trackHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> trackClusterTimePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram2D> trackClusterChargeVsMomentum = new HashMap<String, IHistogram2D>();
-	private Map<String, IHistogram2D> trackClusterChargeVsCosTheta = new HashMap<String, IHistogram2D>();
-	private Map<String, IHistogram2D> trackClusterChargeVsSinPhi = new HashMap<String, IHistogram2D>();
-	
+    IPlotterFactory plotterFactory = IAnalysisFactory.create().createPlotterFactory();
+    protected Map<String, IPlotter> plotters = new HashMap<String, IPlotter>(); 
+    
+    // All clusters
+    private Map<String, IHistogram1D> clusterChargePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> singleHitClusterChargePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> multHitClusterChargePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> signalToNoisePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> singleHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> multHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> clusterSizePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> clusterTimePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram2D> clusterChargeVsTimePlots = new HashMap<String, IHistogram2D>();
+
+    // Clusters on track
+    private Map<String, IHistogram1D> trackClusterChargePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> trackHitSignalToNoisePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> trackClusterTimePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram2D> trackClusterChargeVsMomentum = new HashMap<String, IHistogram2D>();
+    private Map<String, IHistogram2D> trackClusterChargeVsCosTheta = new HashMap<String, IHistogram2D>();
+    private Map<String, IHistogram2D> trackClusterChargeVsSinPhi = new HashMap<String, IHistogram2D>();
+    
     // Detector name
     private static final String SUBDETECTOR_NAME = "Tracker";
     
@@ -92,29 +92,29 @@
     
     private int computePlotterRegion(HpsSiSensor sensor) {
 
-		if (sensor.getLayerNumber() < 7) {
-			if (sensor.isTopLayer()) {
-				return 6*(sensor.getLayerNumber() - 1); 
-			} else { 
-				return 6*(sensor.getLayerNumber() - 1) + 1;
-			} 
-		} else { 
-		
-			if (sensor.isTopLayer()) {
-				if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-					return 6*(sensor.getLayerNumber() - 7) + 2;
-				} else { 
-					return 6*(sensor.getLayerNumber() - 7) + 3;
-				}
-			} else if (sensor.isBottomLayer()) {
-				if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-					return 6*(sensor.getLayerNumber() - 7) + 4;
-				} else {
-					return 6*(sensor.getLayerNumber() - 7) + 5;
-				}
-			}
-		}
-		return -1; 
+        if (sensor.getLayerNumber() < 7) {
+            if (sensor.isTopLayer()) {
+                return 6*(sensor.getLayerNumber() - 1); 
+            } else { 
+                return 6*(sensor.getLayerNumber() - 1) + 1;
+            } 
+        } else { 
+        
+            if (sensor.isTopLayer()) {
+                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                    return 6*(sensor.getLayerNumber() - 7) + 2;
+                } else { 
+                    return 6*(sensor.getLayerNumber() - 7) + 3;
+                }
+            } else if (sensor.isBottomLayer()) {
+                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                    return 6*(sensor.getLayerNumber() - 7) + 4;
+                } else {
+                    return 6*(sensor.getLayerNumber() - 7) + 5;
+                }
+            }
+        }
+        return -1; 
     }
     
     protected void detectorChanged(Detector detector) {
@@ -249,12 +249,12 @@
                                                           .get(sensor.getName()));
         }
         
-		for (IPlotter plotter : plotters.values()) { 
-			plotter.show();
-		}
-    }
-
-	@SuppressWarnings({ "unchecked", "rawtypes" })
+        for (IPlotter plotter : plotters.values()) { 
+            plotter.show();
+        }
+    }
+
+    @SuppressWarnings({ "unchecked", "rawtypes" })
     public void process(EventHeader event) { 
      
         if (runNumber == -1) runNumber = event.getRunNumber();
@@ -354,18 +354,18 @@
         this.mapReconstructedParticlesToTracks(tracks, fsParticles);
        
         // Loop over all of the tracks in the event
-    	for(Track track : tracks){
+        for(Track track : tracks){
 
             // Calculate the momentum of the track
             double p = this.getReconstructedParticle(track).getMomentum().magnitude();
-    	    
-    	    for (TrackerHit rotatedStereoHit : track.getTrackerHits()) { 
-    	    
-    	        // Get the HelicalTrackHit corresponding to the RotatedHelicalTrackHit
-    	        // associated with a track
+            
+            for (TrackerHit rotatedStereoHit : track.getTrackerHits()) { 
+            
+                // Get the HelicalTrackHit corresponding to the RotatedHelicalTrackHit
+                // associated with a track
                 Set<TrackerHit> trackClusters = stereoHitToClusters.allFrom(hthToRotatedHth.from(rotatedStereoHit));
-    	        
-    	        for (TrackerHit trackCluster : trackClusters) { 
+                
+                for (TrackerHit trackCluster : trackClusters) { 
                 
                     // Get the raw hits composing this cluster and use them to calculate the amplitude of the hit
                     double amplitudeSum = 0;
@@ -405,9 +405,9 @@
                     trackClusterChargeVsCosTheta.get(sensor.getName()).fill(TrackUtils.getCosTheta(track), amplitudeSum);
                     trackClusterChargeVsSinPhi.get(sensor.getName()).fill(Math.sin(TrackUtils.getPhi0(track)), amplitudeSum);
                     //trackClusterTimePlots.get(sensor.getName()).fill(trackCluster.time());
-    	        }
-    	    }
-    	}
+                }
+            }
+        }
     }
     
     public void endOfData() { 

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtDataRates.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtDataRates.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtDataRates.java	Wed Apr 27 11:11:32 2016
@@ -12,81 +12,81 @@
 
 public class SvtDataRates extends Driver {
 
-	//Map<VOLUMES, double[]> rawHitsPerLayer = new HashMap<VOLUMES, double[]>(); 
-	double[][] rawHitsPerLayer = new double[12][4];
-	
-	//public enum VOLUMES { TOP, BOTTOM };
-	
-	// Collection Names
-	String rawTrackerHitCollectionName = "SVTRawTrackerHits";
+    //Map<VOLUMES, double[]> rawHitsPerLayer = new HashMap<VOLUMES, double[]>(); 
+    double[][] rawHitsPerLayer = new double[12][4];
+    
+    //public enum VOLUMES { TOP, BOTTOM };
+    
+    // Collection Names
+    String rawTrackerHitCollectionName = "SVTRawTrackerHits";
 
-	double totalEvents = 0; 
-	int totalLayersPerVolume = 0; 
-	
-	public SvtDataRates(){}
-	
-	//static { 
-	//	hep.aida.jfree.AnalysisFactory.register();
-	//}
-	
-	protected void detectorChanged(Detector detector){
-	
-		List<HpsSiSensor> sensors = detector.getDetectorElement().findDescendants(HpsSiSensor.class);
-		for(HpsSiSensor sensor : sensors){
-			this.printDebug("Layer: " + sensor.getLayerNumber() + " Module: " + sensor.getModuleNumber());
-		}
-		totalLayersPerVolume = sensors.size()/2;
-		//for(VOLUMES volume : VOLUMES.values()){
-		//	rawHitsPerLayer.put(volume, new double[totalLayersPerVolume]);
-		//}
-	}
-	
-	protected void process(EventHeader event){
-		
-		if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)){
-			return;
-		}
-		
-		totalEvents++; 
-		
-		List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
-		for(RawTrackerHit rawHit : rawHits){
-			
-			HpsSiSensor sensor = (HpsSiSensor) rawHit.getDetectorElement(); 
-			int layer = sensor.getLayerNumber();
-			int module = sensor.getModuleNumber();
-			//if(sensor.isTopLayer()){
-			//	rawHitsPerLayer.get(VOLUMES.TOP)[layer]++;
-			//} else { 
-			//	rawHitsPerLayer.get(VOLUMES.BOTTOM)[layer]++;
-			//}
-			
-			rawHitsPerLayer[layer-1][module]++;
-		}
-	}
-	
-	protected void endOfData(){
-	
-		//for(VOLUMES volume : VOLUMES.values()){
-			//System.out.println("Volume: " + volume);
-			//System.out.println("Hits per layer per event: ");
-			//for(int layer = 0; layer < totalLayersPerVolume; layer++){
-			//	System.out.println("Layer: " + (layer+1) + ": " + rawHitsPerLayer.get(volume)[layer]/totalEvents); 
-			//}
-		//}
-		
-		for(int layer = 0; layer < 12; layer++){
-			
-			for(int module = 0; module < 4; module++){
-				System.out.println("Layer: " + layer + 
-									" Module: " + module + 
-									" Hits Per Layer: " + rawHitsPerLayer[layer][module]/totalEvents); 
-			}
-		}
-	}
+    double totalEvents = 0; 
+    int totalLayersPerVolume = 0; 
+    
+    public SvtDataRates(){}
+    
+    //static { 
+    //  hep.aida.jfree.AnalysisFactory.register();
+    //}
+    
+    protected void detectorChanged(Detector detector){
+    
+        List<HpsSiSensor> sensors = detector.getDetectorElement().findDescendants(HpsSiSensor.class);
+        for(HpsSiSensor sensor : sensors){
+            this.printDebug("Layer: " + sensor.getLayerNumber() + " Module: " + sensor.getModuleNumber());
+        }
+        totalLayersPerVolume = sensors.size()/2;
+        //for(VOLUMES volume : VOLUMES.values()){
+        //  rawHitsPerLayer.put(volume, new double[totalLayersPerVolume]);
+        //}
+    }
+    
+    protected void process(EventHeader event){
+        
+        if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)){
+            return;
+        }
+        
+        totalEvents++; 
+        
+        List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
+        for(RawTrackerHit rawHit : rawHits){
+            
+            HpsSiSensor sensor = (HpsSiSensor) rawHit.getDetectorElement(); 
+            int layer = sensor.getLayerNumber();
+            int module = sensor.getModuleNumber();
+            //if(sensor.isTopLayer()){
+            //  rawHitsPerLayer.get(VOLUMES.TOP)[layer]++;
+            //} else { 
+            //  rawHitsPerLayer.get(VOLUMES.BOTTOM)[layer]++;
+            //}
+            
+            rawHitsPerLayer[layer-1][module]++;
+        }
+    }
+    
+    protected void endOfData(){
+    
+        //for(VOLUMES volume : VOLUMES.values()){
+            //System.out.println("Volume: " + volume);
+            //System.out.println("Hits per layer per event: ");
+            //for(int layer = 0; layer < totalLayersPerVolume; layer++){
+            //  System.out.println("Layer: " + (layer+1) + ": " + rawHitsPerLayer.get(volume)[layer]/totalEvents); 
+            //}
+        //}
+        
+        for(int layer = 0; layer < 12; layer++){
+            
+            for(int module = 0; module < 4; module++){
+                System.out.println("Layer: " + layer + 
+                                    " Module: " + module + 
+                                    " Hits Per Layer: " + rawHitsPerLayer[layer][module]/totalEvents); 
+            }
+        }
+    }
 
-	private void printDebug(String debugMessage){
-		System.out.println(this.getClass().getSimpleName() + ": " + debugMessage);
-	}
-	
+    private void printDebug(String debugMessage){
+        System.out.println(this.getClass().getSimpleName() + ": " + debugMessage);
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtHitCorrelations.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtHitCorrelations.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtHitCorrelations.java	Wed Apr 27 11:11:32 2016
@@ -28,12 +28,12 @@
  */
 public class SvtHitCorrelations extends Driver {
 
-	// TODO: Add documentation
-	static { 
-	    hep.aida.jfree.AnalysisFactory.register();
-	}
+    // TODO: Add documentation
+    static { 
+        hep.aida.jfree.AnalysisFactory.register();
+    }
    
-	// Plotting
+    // Plotting
     ITree tree; 
     IHistogramFactory histogramFactory;
     IPlotterFactory plotterFactory = IAnalysisFactory.create().createPlotterFactory();
@@ -59,46 +59,46 @@
     boolean enableBottomAxialAxial = false;
     boolean enableBottomAxialStereo = false;
     
-	/**
-	 * 
-	 */
-	public void setEnableTopAxialAxial(boolean enableTopAxialAxial){
-		this.enableTopAxialAxial = enableTopAxialAxial;
-	}
-
-	/**
-	 * 
-	 */
-	public void setEnableTopAxialStereo(boolean enableTopAxialStereo){
-	    this.enableTopAxialStereo = enableTopAxialStereo; 
-	}
-	
-	/**
-	 * 
-	 */
-	public void setEnableBottomAxialAxial(boolean enableBottomAxialAxial){
-		this.enableBottomAxialAxial = enableBottomAxialAxial;
-	}
-	
-	/**
-	 * 
-	 */
-	public void setEnableBottomAxialStereo(boolean enableBottomAxialStereo){
-	    this.enableBottomAxialStereo = enableBottomAxialStereo; 
-	}
-    
-	/**
-	 * 
-	 */
-	private int computePlotterRegion(HpsSiSensor firstSensor, HpsSiSensor secondSensor) {
-	    return (this.getLayerNumber(firstSensor) - 1) + (this.getLayerNumber(secondSensor) - 1)*6;    
-	}
-	
-	protected void detectorChanged(Detector detector){
-	   
+    /**
+     * 
+     */
+    public void setEnableTopAxialAxial(boolean enableTopAxialAxial){
+        this.enableTopAxialAxial = enableTopAxialAxial;
+    }
+
+    /**
+     * 
+     */
+    public void setEnableTopAxialStereo(boolean enableTopAxialStereo){
+        this.enableTopAxialStereo = enableTopAxialStereo; 
+    }
+    
+    /**
+     * 
+     */
+    public void setEnableBottomAxialAxial(boolean enableBottomAxialAxial){
+        this.enableBottomAxialAxial = enableBottomAxialAxial;
+    }
+    
+    /**
+     * 
+     */
+    public void setEnableBottomAxialStereo(boolean enableBottomAxialStereo){
+        this.enableBottomAxialStereo = enableBottomAxialStereo; 
+    }
+    
+    /**
+     * 
+     */
+    private int computePlotterRegion(HpsSiSensor firstSensor, HpsSiSensor secondSensor) {
+        return (this.getLayerNumber(firstSensor) - 1) + (this.getLayerNumber(secondSensor) - 1)*6;    
+    }
+    
+    protected void detectorChanged(Detector detector){
+       
         tree = IAnalysisFactory.create().createTreeFactory().create();
         histogramFactory = IAnalysisFactory.create().createHistogramFactory(tree);
-	
+    
         sensors = detector.getSubdetector(SUBDETECTOR_NAME).getDetectorElement().findDescendants(HpsSiSensor.class);
 
         if (sensors.size() == 0) {
@@ -178,55 +178,55 @@
         }
 
         for (IPlotter plotter : plotters.values()) plotter.show();
-	}
-	
-	public void process(EventHeader event){
-	
+    }
+    
+    public void process(EventHeader event){
+    
         if (runNumber == -1) runNumber = event.getRunNumber();
-	    
-		if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) return;
-	
-		List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
-		
-		String plotName = "";
-		for(RawTrackerHit firstRawHit : rawHits){
-	
-			HpsSiSensor firstSensor = (HpsSiSensor) firstRawHit.getDetectorElement();
-			int firstChannel = firstRawHit.getIdentifierFieldValue("strip");
-			
-			for(RawTrackerHit secondRawHit : rawHits){
-			
-				HpsSiSensor secondSensor = (HpsSiSensor) secondRawHit.getDetectorElement();
-				int secondChannel = secondRawHit.getIdentifierFieldValue("strip");
-			
-				if(firstSensor.isTopLayer() && secondSensor.isTopLayer()){
-					if(enableTopAxialAxial && firstSensor.isAxial() && secondSensor.isAxial()){
-						
-					    plotName = "Top Axial Layer " + this.getLayerNumber(firstSensor) 
-					                + " vs Top Axial Layer " + this.getLayerNumber(secondSensor); 
-					    topAxialAxialPlots.get(plotName).fill(firstChannel, secondChannel);
-					} else if (enableTopAxialStereo && firstSensor.isAxial() && secondSensor.isStereo()) { 
-					    
-					    plotName = "Top Axial Layer " + this.getLayerNumber(firstSensor) 
-					                + " vs Top Stereo Layer " + this.getLayerNumber(secondSensor); 
-					    topAxialStereoPlots.get(plotName).fill(firstChannel, secondChannel);
-					}
-				} else if (firstSensor.isBottomLayer() && secondSensor.isBottomLayer()) { 
-					if(enableBottomAxialAxial && firstSensor.isAxial() && secondSensor.isAxial()){
-						
-					    plotName = "Bottom Axial Layer " + this.getLayerNumber(firstSensor) 
-					                + " vs Bottom Axial Layer " + this.getLayerNumber(secondSensor); 
-					    bottomAxialAxialPlots.get(plotName).fill(firstChannel, secondChannel);
-					} else if (enableBottomAxialStereo && firstSensor.isAxial() && secondSensor.isStereo()) { 
-					    
-					    plotName = "Bottom Axial Layer " + this.getLayerNumber(firstSensor) 
-					                + " vs Bottom Stereo Layer " + this.getLayerNumber(secondSensor); 
-					    bottomAxialStereoPlots.get(plotName).fill(firstChannel, secondChannel);
-					}
-				}
-			}
-		}
-	}
+        
+        if(!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) return;
+    
+        List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
+        
+        String plotName = "";
+        for(RawTrackerHit firstRawHit : rawHits){
+    
+            HpsSiSensor firstSensor = (HpsSiSensor) firstRawHit.getDetectorElement();
+            int firstChannel = firstRawHit.getIdentifierFieldValue("strip");
+            
+            for(RawTrackerHit secondRawHit : rawHits){
+            
+                HpsSiSensor secondSensor = (HpsSiSensor) secondRawHit.getDetectorElement();
+                int secondChannel = secondRawHit.getIdentifierFieldValue("strip");
+            
+                if(firstSensor.isTopLayer() && secondSensor.isTopLayer()){
+                    if(enableTopAxialAxial && firstSensor.isAxial() && secondSensor.isAxial()){
+                        
+                        plotName = "Top Axial Layer " + this.getLayerNumber(firstSensor) 
+                                    + " vs Top Axial Layer " + this.getLayerNumber(secondSensor); 
+                        topAxialAxialPlots.get(plotName).fill(firstChannel, secondChannel);
+                    } else if (enableTopAxialStereo && firstSensor.isAxial() && secondSensor.isStereo()) { 
+                        
+                        plotName = "Top Axial Layer " + this.getLayerNumber(firstSensor) 
+                                    + " vs Top Stereo Layer " + this.getLayerNumber(secondSensor); 
+                        topAxialStereoPlots.get(plotName).fill(firstChannel, secondChannel);
+                    }
+                } else if (firstSensor.isBottomLayer() && secondSensor.isBottomLayer()) { 
+                    if(enableBottomAxialAxial && firstSensor.isAxial() && secondSensor.isAxial()){
+                        
+                        plotName = "Bottom Axial Layer " + this.getLayerNumber(firstSensor) 
+                                    + " vs Bottom Axial Layer " + this.getLayerNumber(secondSensor); 
+                        bottomAxialAxialPlots.get(plotName).fill(firstChannel, secondChannel);
+                    } else if (enableBottomAxialStereo && firstSensor.isAxial() && secondSensor.isStereo()) { 
+                        
+                        plotName = "Bottom Axial Layer " + this.getLayerNumber(firstSensor) 
+                                    + " vs Bottom Stereo Layer " + this.getLayerNumber(secondSensor); 
+                        bottomAxialStereoPlots.get(plotName).fill(firstChannel, secondChannel);
+                    }
+                }
+            }
+        }
+    }
 
     public void endOfData() { 
       
@@ -240,12 +240,12 @@
             e.printStackTrace();
         }
     }
-	
-	
-	private int getLayerNumber(HpsSiSensor sensor) {
-	   return (int) Math.ceil(((double) sensor.getLayerNumber())/2); 
-	}
-	
+    
+    
+    private int getLayerNumber(HpsSiSensor sensor) {
+       return (int) Math.ceil(((double) sensor.getLayerNumber())/2); 
+    }
+    
     IPlotterStyle createStyle(String xAxisTitle, String yAxisTitle) { 
        
         // Create a default style
@@ -279,5 +279,5 @@
        
         return style;
     }
-	
+    
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtQA.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtQA.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtQA.java	Wed Apr 27 11:11:32 2016
@@ -54,7 +54,7 @@
 
     int channelNumber = 0;
     int plotterIndex = 0;
-    int apvNumber = 0;	
+    int apvNumber = 0;  
     double totalNumberEvents = 0;
     double totalNumberOfRawHitEvents = 0;
     double[] totalTopSamples = new double[6];
@@ -210,7 +210,7 @@
      * 
      */
     public void setEnableTotalNumberOfHitsPlots(boolean enableTotalNumberOfHitsPlots){
-    	this.enableTotalNumberOfHitsPlots = enableTotalNumberOfHitsPlots;
+        this.enableTotalNumberOfHitsPlots = enableTotalNumberOfHitsPlots;
     }
 
     /**
@@ -391,13 +391,13 @@
         }
         
         if(enableTotalNumberOfHitsPlots){
-        	title = "Total Number of RawTrackerHits";
-        	plotters.add(PlotUtils.setupPlotter(title, 0, 0));
-        	plotters.get(plotterIndex).style().statisticsBoxStyle().setVisible(true);
-        	histo1D = aida.histogram1D(title, 100, 0, 75);
-        	histos1D.add(histo1D);
-        	PlotUtils.setup1DRegion(plotters.get(plotterIndex), title, 0, "Number of RawTrackerHits", histo1D);
-        	plotterIndex++;
+            title = "Total Number of RawTrackerHits";
+            plotters.add(PlotUtils.setupPlotter(title, 0, 0));
+            plotters.get(plotterIndex).style().statisticsBoxStyle().setVisible(true);
+            histo1D = aida.histogram1D(title, 100, 0, 75);
+            histos1D.add(histo1D);
+            PlotUtils.setup1DRegion(plotters.get(plotterIndex), title, 0, "Number of RawTrackerHits", histo1D);
+            plotterIndex++;
         }
 
         for(IPlotter plotter : plotters) plotter.show();
@@ -488,7 +488,7 @@
                     aida.histogram1D(title).fill(sample);
                 }
                 title = "Shaper Signal Amplitude";
-                aida.histogram1D(title).fill(fit.getAmp());	    
+                aida.histogram1D(title).fill(fit.getAmp());     
                 System.out.println("Amplitude: " + fit.getAmp());
                 title="t0";
                 aida.histogram1D(title).fill(fit.getT0());
@@ -595,9 +595,9 @@
                                 topSamples[sampleN-1] += samples[sampleN-1] - sensor.getPedestal(channel, sampleN-1);
                             }
                             else{
-                            	aida.histogram2D("APV Sample Number vs Sample Amplitude - Bottom").fill(sampleN, samples[sampleN-1] - sensor.getPedestal(channel, sampleN-1));
-                            	totalBottomSamples[sampleN-1]++;
-                            	bottomSamples[sampleN-1] += samples[sampleN - 1] - sensor.getPedestal(channel, sampleN-1);
+                                aida.histogram2D("APV Sample Number vs Sample Amplitude - Bottom").fill(sampleN, samples[sampleN-1] - sensor.getPedestal(channel, sampleN-1));
+                                totalBottomSamples[sampleN-1]++;
+                                bottomSamples[sampleN-1] += samples[sampleN - 1] - sensor.getPedestal(channel, sampleN-1);
                             }
                         }
                     }
@@ -659,7 +659,7 @@
                         int channel = ((RawTrackerHit) hts.rawhits().get(0)).getIdentifierFieldValue("strip");
                         
                         if(sensorName.equals("all")){
-                        	aida.histogram2D(sensor.getName() + " - t0 Resolution vs Channel #").fill(channel, meanT0 - hts.time());
+                            aida.histogram2D(sensor.getName() + " - t0 Resolution vs Channel #").fill(channel, meanT0 - hts.time());
                         } else {
                         if(sensor.getName().equals(sensorName)){
                             aida.histogram1D(sensorName + " - Hit Time Resolution").fill(meanT0 - hts.time());
@@ -675,67 +675,67 @@
 
     @Override
         public void endOfData(){
-    		String title;
-    		
-
-    		
+            String title;
+            
+
+            
             String plotName;
-    		if(enableOccupancy){
-    			for(HpsSiSensor sensor : sensors){
-    				title = sensor.getName() + " - Occupancy";
-    				// Scale the hits per channel by the number of events
-    				aida.histogram1D(title).scale(1/totalNumberEvents);
-    				
-    				// Write the occupancies to a file
-    				if(sensor.isTopLayer()){
-    					plotName = outputFile + "_top_";
-    				} else { 
-    					plotName = outputFile + "_bottom_";
-    				}
-    				
-					if(sensor.getLayerNumber() < 10){
-						plotName += "0" + sensor.getLayerNumber() + ".dat";
-					} else {
-						plotName += sensor.getLayerNumber() + ".dat";
-					}
-    			
-	    			// Open the output files stream
-	                if(plotName != null){
-	                	try{
-	                		output = new BufferedWriter(new FileWriter(plotName)); 
-                			for(int channel = 0; channel < 640; channel++){
-                				output.write(channel + " " + aida.histogram1D(title).binHeight(channel) + "\n");
-                			}
-                			output.close();
-	                	} catch(Exception e) {
-	                		System.out.println(this.getClass().getSimpleName() + " :Error! " + e.getMessage());
-	                	}
-	                }
-    			}
-    		}
-    		
-    		if(enableT0Plots){
-    			int bins = aida.histogram1D(sensorName + " - Hit Time Resolution").axis().bins();
-    			for(int bin = 0; bin < bins; bin++){
-    				System.out.println(bin + "        " + aida.histogram1D(sensorName + " - Hit Time Resolution").binHeight(bin));
-    			}
-    		}
-    	
-            	
-            	/*
+            if(enableOccupancy){
                 for(HpsSiSensor sensor : sensors){
-                    	if(outputFile != null && sensorName.equals(sensor.getName())){
-                    		try{
-                    			for(int channel = 0; channel < 639; channel++){
-    								output.write(channel + " " + this.getOccupancy(sensor, channel) + "\n");
-    							}
-                    			output.close();
-                    		} catch(IOException e){
-                    			System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
-                    		}
-                    	}
-                	
-                	System.out.println("%===================================================================%");
+                    title = sensor.getName() + " - Occupancy";
+                    // Scale the hits per channel by the number of events
+                    aida.histogram1D(title).scale(1/totalNumberEvents);
+                    
+                    // Write the occupancies to a file
+                    if(sensor.isTopLayer()){
+                        plotName = outputFile + "_top_";
+                    } else { 
+                        plotName = outputFile + "_bottom_";
+                    }
+                    
+                    if(sensor.getLayerNumber() < 10){
+                        plotName += "0" + sensor.getLayerNumber() + ".dat";
+                    } else {
+                        plotName += sensor.getLayerNumber() + ".dat";
+                    }
+                
+                    // Open the output files stream
+                    if(plotName != null){
+                        try{
+                            output = new BufferedWriter(new FileWriter(plotName)); 
+                            for(int channel = 0; channel < 640; channel++){
+                                output.write(channel + " " + aida.histogram1D(title).binHeight(channel) + "\n");
+                            }
+                            output.close();
+                        } catch(Exception e) {
+                            System.out.println(this.getClass().getSimpleName() + " :Error! " + e.getMessage());
+                        }
+                    }
+                }
+            }
+            
+            if(enableT0Plots){
+                int bins = aida.histogram1D(sensorName + " - Hit Time Resolution").axis().bins();
+                for(int bin = 0; bin < bins; bin++){
+                    System.out.println(bin + "        " + aida.histogram1D(sensorName + " - Hit Time Resolution").binHeight(bin));
+                }
+            }
+        
+                
+                /*
+                for(HpsSiSensor sensor : sensors){
+                        if(outputFile != null && sensorName.equals(sensor.getName())){
+                            try{
+                                for(int channel = 0; channel < 639; channel++){
+                                    output.write(channel + " " + this.getOccupancy(sensor, channel) + "\n");
+                                }
+                                output.close();
+                            } catch(IOException e){
+                                System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
+                            }
+                        }
+                    
+                    System.out.println("%===================================================================%");
                     System.out.println(sensor.getName() + " Bad Channels");
                     System.out.println("%===================================================================%");
                     for(int index = 0; index < 640; index++){
@@ -769,21 +769,21 @@
             }
             
             if(enableSamples){
-            	double sigma = 0;
-            	double[] topMean = new double[6];
-            	double[] bottomMean = new double[6];
-            	
+                double sigma = 0;
+                double[] topMean = new double[6];
+                double[] bottomMean = new double[6];
+                
                 System.out.println("%===================================================================% \n");
-            	for(int index = 0; index < topSamples.length; index++){
-            		topMean[index] = topSamples[index]/totalTopSamples[index];
-            		System.out.println("Top sample " + index + " mean: " + topMean[index]);
-            	}
-            	
+                for(int index = 0; index < topSamples.length; index++){
+                    topMean[index] = topSamples[index]/totalTopSamples[index];
+                    System.out.println("Top sample " + index + " mean: " + topMean[index]);
+                }
+                
                 System.out.println("\n%===================================================================% \n");
-            	for(int index = 0; index < bottomSamples.length; index++){
-            		bottomMean[index] = bottomSamples[index]/totalBottomSamples[index];
-            		System.out.println("Bottom sample " + index + " mean: " + bottomMean[index]);
-            	}
+                for(int index = 0; index < bottomSamples.length; index++){
+                    bottomMean[index] = bottomSamples[index]/totalBottomSamples[index];
+                    System.out.println("Bottom sample " + index + " mean: " + bottomMean[index]);
+                }
                 System.out.println("\n%===================================================================% \n");
             }
         }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -46,8 +46,8 @@
     IPlotterFactory plotterFactory = IAnalysisFactory.create().createPlotterFactory();
     protected Map<String, IPlotter> plotters = new HashMap<String, IPlotter>();
     private Map<String, IHistogram1D> trackPlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> clusterChargePlots = new HashMap<String, IHistogram1D>();
-	private Map<String, IHistogram1D> clusterSizePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> clusterChargePlots = new HashMap<String, IHistogram1D>();
+    private Map<String, IHistogram1D> clusterSizePlots = new HashMap<String, IHistogram1D>();
 
     private List<HpsSiSensor> sensors;
     private Map<RawTrackerHit, LCRelation> fittedRawTrackerHitMap 
@@ -64,67 +64,67 @@
 
     private int runNumber = -1; 
     
-	int npositive = 0;
-	int nnegative = 0;
-	double ntracks = 0;
-	double ntracksTop = 0;
-	double ntracksBottom = 0;
-	double nTwoTracks = 0;
-	double nevents = 0;
-
-	double d0Cut = -9999;
-	
-	// Flags 
-	boolean electronCut = false;
-	boolean positronCut = false;
-	
+    int npositive = 0;
+    int nnegative = 0;
+    double ntracks = 0;
+    double ntracksTop = 0;
+    double ntracksBottom = 0;
+    double nTwoTracks = 0;
+    double nevents = 0;
+
+    double d0Cut = -9999;
+    
+    // Flags 
+    boolean electronCut = false;
+    boolean positronCut = false;
+    
     /**
      *  Default Constructor
      */    
-	public SvtTrackAnalysis(){
-	}
-	
-	public void setEnableElectronCut(boolean electronCut) {
-	    this.electronCut = electronCut;
-	}
-
-	public void setEnablePositronCut(boolean positronCut) {
-	    this.positronCut = positronCut;
-	}
-
-	public void setD0Cut(double d0Cut) {
-	   this.d0Cut = d0Cut; 
-	}
-	
-	private int computePlotterRegion(HpsSiSensor sensor) {
-
-		if (sensor.getLayerNumber() < 7) {
-			if (sensor.isTopLayer()) {
-				return 6*(sensor.getLayerNumber() - 1); 
-			} else { 
-				return 6*(sensor.getLayerNumber() - 1) + 1;
-			} 
-		} else { 
-		
-			if (sensor.isTopLayer()) {
-				if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-					return 6*(sensor.getLayerNumber() - 7) + 2;
-				} else { 
-					return 6*(sensor.getLayerNumber() - 7) + 3;
-				}
-			} else if (sensor.isBottomLayer()) {
-				if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
-					return 6*(sensor.getLayerNumber() - 7) + 4;
-				} else {
-					return 6*(sensor.getLayerNumber() - 7) + 5;
-				}
-			}
-		}
-		return -1; 
-    }
-	
-	protected void detectorChanged(Detector detector){
-	
+    public SvtTrackAnalysis(){
+    }
+    
+    public void setEnableElectronCut(boolean electronCut) {
+        this.electronCut = electronCut;
+    }
+
+    public void setEnablePositronCut(boolean positronCut) {
+        this.positronCut = positronCut;
+    }
+
+    public void setD0Cut(double d0Cut) {
+       this.d0Cut = d0Cut; 
+    }
+    
+    private int computePlotterRegion(HpsSiSensor sensor) {
+
+        if (sensor.getLayerNumber() < 7) {
+            if (sensor.isTopLayer()) {
+                return 6*(sensor.getLayerNumber() - 1); 
+            } else { 
+                return 6*(sensor.getLayerNumber() - 1) + 1;
+            } 
+        } else { 
+        
+            if (sensor.isTopLayer()) {
+                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                    return 6*(sensor.getLayerNumber() - 7) + 2;
+                } else { 
+                    return 6*(sensor.getLayerNumber() - 7) + 3;
+                }
+            } else if (sensor.isBottomLayer()) {
+                if (sensor.getSide() == HpsSiSensor.POSITRON_SIDE) {
+                    return 6*(sensor.getLayerNumber() - 7) + 4;
+                } else {
+                    return 6*(sensor.getLayerNumber() - 7) + 5;
+                }
+            }
+        }
+        return -1; 
+    }
+    
+    protected void detectorChanged(Detector detector){
+    
         tree = IAnalysisFactory.create().createTreeFactory().create();
         histogramFactory = IAnalysisFactory.create().createHistogramFactory(tree);
         
@@ -195,66 +195,66 @@
             
         }
 
-		//--- Track Extrapolation ---//
-		//---------------------------//	
-		/*plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal"));
-		plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal", 200, -350, 350, 200, -100, 100));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        //--- Track Extrapolation ---//
+        //---------------------------// 
+        /*plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal"));
+        plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal", 200, -350, 350, 200, -100, 100));
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style();
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Harp"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Harp", 200, -200, 200, 100, -50, 50));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
 
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal: curvature < 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal: curvature < 0",200, -350, 350, 200, -100, 100));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Harp: curvature < 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Harp: curvature < 0", 200, -200, 200, 100, -50, 50));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal: curvature > 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal: curvature > 0", 200, -350, 350, 200, -100, 100));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Harp: curvature > 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Harp: curvature > 0", 200, -200, 200, 100, -50, 50));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		
-		plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal: Two Tracks"));
-		plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal: Two Tracks", 200, -350, 350, 200, -100, 100));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        
+        plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Ecal: Two Tracks"));
+        plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Ecal: Two Tracks", 200, -350, 350, 200, -100, 100));
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style();
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Track Position at Harp: Two Tracks"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("Track Position at Harp: Two Tracks", 200, -200, 200, 100, -50, 50));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        
         
         //--- Momentum ---//
         //----------------//
@@ -262,99 +262,99 @@
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Px", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Py"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Py", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Pz"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Pz", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
-		
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Px: C > 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Px: C > 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Py: C > 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Py: C > 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Pz: C > 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Pz: C > 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
-		
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Px: C < 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Px: C < 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Py: C < 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Py: C < 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Pz: C < 0"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Pz: C < 0", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
-		
+        nPlotters++;
+        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("Px: Two Tracks"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("Px: Two Tracks", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
+        nPlotters++;
         
         plotters.add(aida.analysisFactory().createPlotterFactory().create("E over P"));
         plotters.get(nPlotters).region(0).plot(aida.histogram1D("E over P", 100, 0, 5));
         plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
         plotters.get(nPlotters).style().dataStyle().errorBarStyle().setVisible(false);
-		nPlotters++;
-		   
-		plotters.add(aida.analysisFactory().createPlotterFactory().create("E versus P"));
-	    plotters.get(nPlotters).region(0).plot(aida.histogram2D("E versus P", 100, 0, 1500, 100, 0, 4000));
-	    plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-	    plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-	    plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-	    nPlotters++;
+        nPlotters++;
+           
+        plotters.add(aida.analysisFactory().createPlotterFactory().create("E versus P"));
+        plotters.get(nPlotters).region(0).plot(aida.histogram2D("E versus P", 100, 0, 1500, 100, 0, 4000));
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
         
         //--- Cluster Matching ---//
         //------------------------//        
         plotters.add(aida.analysisFactory().createPlotterFactory().create("XY Difference between Ecal Cluster and Track Position"));
         plotters.get(nPlotters).region(0).plot(aida.histogram2D("XY Difference between Ecal Cluster and Track Position", 200, -200, 200, 100, -50, 50));
-		plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
-    	plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
-		nPlotters++;
-		*/
-		for (IPlotter plotter : plotters.values()) { 
-			plotter.show();
-		}
-	}
-	
-	@SuppressWarnings({ "unchecked", "rawtypes" })
+        plotters.get(nPlotters).region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotters.get(nPlotters).region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotters.get(nPlotters).style().statisticsBoxStyle().setVisible(false);
+        nPlotters++;
+        */
+        for (IPlotter plotter : plotters.values()) { 
+            plotter.show();
+        }
+    }
+    
+    @SuppressWarnings({ "unchecked", "rawtypes" })
     public void process(EventHeader event){
-		nevents++;
-
-		// Get the run number from the event
+        nevents++;
+
+        // Get the run number from the event
         if (runNumber == -1) runNumber = event.getRunNumber();
-		
+        
         // If the event doesn't have any tracks, skip it    
-		if(!event.hasCollection(Track.class, trackCollectionName)) return;
-    	
+        if(!event.hasCollection(Track.class, trackCollectionName)) return;
+        
         // Get the collection of tracks from the event
         List<Track> tracks = event.get(Track.class, trackCollectionName);
         
@@ -386,17 +386,17 @@
         trackPlots.get("Number of tracks").fill(tracks.size());
         
         // Loop over all of the tracks in the event
-    	for(Track track : tracks){
-    	    
-    	    if (TrackUtils.getR(track) < 0 && electronCut) continue;
-    	    
-    	    if (TrackUtils.getR(track) > 0 && positronCut) continue;
-    	    
-    	    if (d0Cut != -9999 && Math.abs(TrackUtils.getDoca(track)) < d0Cut) continue;
-    	    
-    	    trackPlots.get("Track charge").fill(TrackUtils.getR(track), 1);
-    
-    	    // Fill the track parameter plots
+        for(Track track : tracks){
+            
+            if (TrackUtils.getR(track) < 0 && electronCut) continue;
+            
+            if (TrackUtils.getR(track) > 0 && positronCut) continue;
+            
+            if (d0Cut != -9999 && Math.abs(TrackUtils.getDoca(track)) < d0Cut) continue;
+            
+            trackPlots.get("Track charge").fill(TrackUtils.getR(track), 1);
+    
+            // Fill the track parameter plots
             trackPlots.get("doca").fill(TrackUtils.getDoca(track));
             trackPlots.get("z0").fill(TrackUtils.getZ0(track));
             trackPlots.get("sin(phi0)").fill(TrackUtils.getPhi0(track));
@@ -444,8 +444,8 @@
             }
         }
     }
-	
-	public void endOfData() { 
+    
+    public void endOfData() { 
         
         String rootFile = "run" + runNumber + "_track_analysis.root";
         RootFileStore store = new RootFileStore(rootFile);
@@ -473,7 +473,7 @@
             fittedRawTrackerHitMap.put(FittedRawTrackerHit.getRawTrackerHit(fittedHit), fittedHit);
         }
     }
-	
+    
     /**
      * 
      * @param rawHit
@@ -489,101 +489,101 @@
 
             /*
             ntracks++;
-    		Hep3Vector positionEcal = TrackUtils.getTrackPositionAtEcal(track);
-    		System.out.println("Position at Ecal: " + positionEcal);
-    		Hep3Vector positionConverter = TrackUtils.extrapolateTrack(track,-700);
-    	
-    		aida.histogram2D("Track Position at Ecal").fill(positionEcal.y(), positionEcal.z());
-    		aida.histogram2D("Track Position at Harp").fill(positionConverter.y(), positionConverter.z());
-
-    		if(positionEcal.z() > 0 ) ntracksTop++;
-    		else if(positionEcal.z() < 0) ntracksBottom++;
+            Hep3Vector positionEcal = TrackUtils.getTrackPositionAtEcal(track);
+            System.out.println("Position at Ecal: " + positionEcal);
+            Hep3Vector positionConverter = TrackUtils.extrapolateTrack(track,-700);
+        
+            aida.histogram2D("Track Position at Ecal").fill(positionEcal.y(), positionEcal.z());
+            aida.histogram2D("Track Position at Harp").fill(positionConverter.y(), positionConverter.z());
+
+            if(positionEcal.z() > 0 ) ntracksTop++;
+            else if(positionEcal.z() < 0) ntracksBottom++;
             */
-    		
-    	
+            
+        
             /*    
-    		aida.histogram1D("Px").fill(track.getTrackStates().get(0).getMomentum()[0]);
-    		aida.histogram1D("Py").fill(track.getTrackStates().get(0).getMomentum()[1]);
-    		aida.histogram1D("Pz").fill(track.getTrackStates().get(0).getMomentum()[2]);
-    		aida.histogram1D("ChiSquared").fill(track.getChi2());
-    		
-    		if(Math.signum(TrackUtils.getR(track)) < 0){
-    			aida.histogram2D("Track Position at Ecal: curvature < 0").fill(positionEcal.y(), positionEcal.z());
-    			aida.histogram2D("Track Position at Harp: curvature < 0").fill(positionConverter.y(), positionConverter.z());
-        		aida.histogram1D("Px: C < 0").fill(track.getTrackStates().get(0).getMomentum()[0]);
-        		aida.histogram1D("Py: C < 0").fill(track.getTrackStates().get(0).getMomentum()[1]);
-        		aida.histogram1D("Pz: C < 0").fill(track.getTrackStates().get(0).getMomentum()[2]);
-        		nnegative++;
-    		} else if(Math.signum(TrackUtils.getR(track)) > 0){
-    			aida.histogram2D("Track Position at Ecal: curvature > 0").fill(positionEcal.y(), positionEcal.z());
-    			aida.histogram2D("Track Position at Harp: curvature > 0").fill(positionConverter.y(), positionConverter.z());
-        		aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[0]);
-        		aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[1]);
-        		aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[2]);
-        		npositive++;
-    		}
-    		
-    		if(tracks.size() > 1){
-    			aida.histogram2D("Track Position at Ecal: Two Tracks").fill(positionEcal.y(), positionEcal.z());
-    			aida.histogram2D("Track Position at Harp: Two Tracks").fill(positionConverter.y(), positionConverter.z()); 
-    			aida.histogram1D("Px: Two Tracks").fill(track.getTrackStates().get(0).getMomentum()[0]);
-    			if(tracks.size() == 2) nTwoTracks++;
-    		}
-    		
-    		trackToEcalPosition.put(positionEcal, track);
-    		ecalPos.add(positionEcal);  		
-    	}
-    	
-    	if(!event.hasCollection(Cluster.class, "EcalClusters")) return;
-    	List<Cluster> clusters = event.get(Cluster.class, "EcalClusters");
-    	
-
-    	for(Hep3Vector ecalP : ecalPos){
-        	double xdiff = 1000; 
-        	double ydiff = 1000;
-    		for(Cluster cluster : clusters){
-    			double xd = ecalP.y() - cluster.getPosition()[0];
-    			double yd = ecalP.z() - cluster.getPosition()[1];  
-    			if(yd < ydiff){
-    				xdiff = xd;
-    				ydiff = yd;
-    				trackToCluster.put(trackToEcalPosition.get(ecalP),cluster);
-    			}
-    		}
-    		clusters.remove(trackToCluster.get(trackToEcalPosition.get(ecalP)));
-    		aida.histogram2D("XY Difference between Ecal Cluster and Track Position").fill(xdiff, ydiff);
-    	}
-    	
-    	for(Map.Entry<Track, Cluster> entry : trackToCluster.entrySet()){
-    		double Energy = entry.getValue().getEnergy();
-    		Track track = entry.getKey();
-    		double pTotal = Math.sqrt(track.getTrackStates().get(0).getMomentum()[0]*track.getTrackStates().get(0).getMomentum()[0] + track.getTrackStates().get(0).getMomentum()[1]*track.getTrackStates().get(0).getMomentum()[1] + track.getTrackStates().get(0).getMomentum()[2]*track.getTrackStates().get(0).getMomentum()[2]);
-    		
-    		double ep = Energy/(pTotal*1000);
-    		
-    		System.out.println("Energy: " + Energy + "P: " + pTotal + " E over P: " + ep);
-    		
-    		aida.histogram1D("E over P").fill(ep);
-    		aida.histogram2D("E versus P").fill(Energy, pTotal*1000);
-    	}
-    	
-    	for(Cluster cluster : clusters){
-    		double[] clusterPosition = cluster.getPosition();
-    		
-    		System.out.println("Cluster Position: [" + clusterPosition[0] + ", " + clusterPosition[1] + ", " + clusterPosition[2]+ "]");
-    	}
-    	
-    	double ratio = nnegative/npositive;
-    	System.out.println("Ratio of Negative to Position Tracks: " + ratio);
-	
-    	double tracksRatio = ntracks/nevents;
-    	double tracksTopRatio = ntracksTop/nevents;
-    	double tracksBottomRatio = ntracksBottom/nevents;
-    	double twoTrackRatio = nTwoTracks/nevents;
-    	System.out.println("Number of tracks per event: " + tracksRatio);
-    	System.out.println("Number of top tracks per event: " + tracksTopRatio);
-    	System.out.println("Number of bottom tracks per event: " + tracksBottomRatio);
-    	System.out.println("Number of two track events: " + twoTrackRatio);
-	}*/
-
-
+            aida.histogram1D("Px").fill(track.getTrackStates().get(0).getMomentum()[0]);
+            aida.histogram1D("Py").fill(track.getTrackStates().get(0).getMomentum()[1]);
+            aida.histogram1D("Pz").fill(track.getTrackStates().get(0).getMomentum()[2]);
+            aida.histogram1D("ChiSquared").fill(track.getChi2());
+            
+            if(Math.signum(TrackUtils.getR(track)) < 0){
+                aida.histogram2D("Track Position at Ecal: curvature < 0").fill(positionEcal.y(), positionEcal.z());
+                aida.histogram2D("Track Position at Harp: curvature < 0").fill(positionConverter.y(), positionConverter.z());
+                aida.histogram1D("Px: C < 0").fill(track.getTrackStates().get(0).getMomentum()[0]);
+                aida.histogram1D("Py: C < 0").fill(track.getTrackStates().get(0).getMomentum()[1]);
+                aida.histogram1D("Pz: C < 0").fill(track.getTrackStates().get(0).getMomentum()[2]);
+                nnegative++;
+            } else if(Math.signum(TrackUtils.getR(track)) > 0){
+                aida.histogram2D("Track Position at Ecal: curvature > 0").fill(positionEcal.y(), positionEcal.z());
+                aida.histogram2D("Track Position at Harp: curvature > 0").fill(positionConverter.y(), positionConverter.z());
+                aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[0]);
+                aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[1]);
+                aida.histogram1D("Px: C > 0").fill(track.getTrackStates().get(0).getMomentum()[2]);
+                npositive++;
+            }
+            
+            if(tracks.size() > 1){
+                aida.histogram2D("Track Position at Ecal: Two Tracks").fill(positionEcal.y(), positionEcal.z());
+                aida.histogram2D("Track Position at Harp: Two Tracks").fill(positionConverter.y(), positionConverter.z()); 
+                aida.histogram1D("Px: Two Tracks").fill(track.getTrackStates().get(0).getMomentum()[0]);
+                if(tracks.size() == 2) nTwoTracks++;
+            }
+            
+            trackToEcalPosition.put(positionEcal, track);
+            ecalPos.add(positionEcal);          
+        }
+        
+        if(!event.hasCollection(Cluster.class, "EcalClusters")) return;
+        List<Cluster> clusters = event.get(Cluster.class, "EcalClusters");
+        
+
+        for(Hep3Vector ecalP : ecalPos){
+            double xdiff = 1000; 
+            double ydiff = 1000;
+            for(Cluster cluster : clusters){
+                double xd = ecalP.y() - cluster.getPosition()[0];
+                double yd = ecalP.z() - cluster.getPosition()[1];  
+                if(yd < ydiff){
+                    xdiff = xd;
+                    ydiff = yd;
+                    trackToCluster.put(trackToEcalPosition.get(ecalP),cluster);
+                }
+            }
+            clusters.remove(trackToCluster.get(trackToEcalPosition.get(ecalP)));
+            aida.histogram2D("XY Difference between Ecal Cluster and Track Position").fill(xdiff, ydiff);
+        }
+        
+        for(Map.Entry<Track, Cluster> entry : trackToCluster.entrySet()){
+            double Energy = entry.getValue().getEnergy();
+            Track track = entry.getKey();
+            double pTotal = Math.sqrt(track.getTrackStates().get(0).getMomentum()[0]*track.getTrackStates().get(0).getMomentum()[0] + track.getTrackStates().get(0).getMomentum()[1]*track.getTrackStates().get(0).getMomentum()[1] + track.getTrackStates().get(0).getMomentum()[2]*track.getTrackStates().get(0).getMomentum()[2]);
+            
+            double ep = Energy/(pTotal*1000);
+            
+            System.out.println("Energy: " + Energy + "P: " + pTotal + " E over P: " + ep);
+            
+            aida.histogram1D("E over P").fill(ep);
+            aida.histogram2D("E versus P").fill(Energy, pTotal*1000);
+        }
+        
+        for(Cluster cluster : clusters){
+            double[] clusterPosition = cluster.getPosition();
+            
+            System.out.println("Cluster Position: [" + clusterPosition[0] + ", " + clusterPosition[1] + ", " + clusterPosition[2]+ "]");
+        }
+        
+        double ratio = nnegative/npositive;
+        System.out.println("Ratio of Negative to Position Tracks: " + ratio);
+    
+        double tracksRatio = ntracks/nevents;
+        double tracksTopRatio = ntracksTop/nevents;
+        double tracksBottomRatio = ntracksBottom/nevents;
+        double twoTrackRatio = nTwoTracks/nevents;
+        System.out.println("Number of tracks per event: " + tracksRatio);
+        System.out.println("Number of top tracks per event: " + tracksTopRatio);
+        System.out.println("Number of bottom tracks per event: " + tracksBottomRatio);
+        System.out.println("Number of two track events: " + twoTrackRatio);
+    }*/
+
+

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackRecoEfficiency.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackRecoEfficiency.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/SvtTrackRecoEfficiency.java	Wed Apr 27 11:11:32 2016
@@ -100,7 +100,7 @@
      * Set the name of the file to output efficiency data to
      */
     public void setEfficiencyOutputFile(String efficiencyOutputFile){
-    	this.efficiencyOutputFile = efficiencyOutputFile;
+        this.efficiencyOutputFile = efficiencyOutputFile;
     }
 
     /**
@@ -124,31 +124,31 @@
      * @param message : debug message
      */
     private void printDebug(String message){
-    	if(debug){
-    		System.out.println(this.getClass().getSimpleName() + ": " + message);
-    	}
+        if(debug){
+            System.out.println(this.getClass().getSimpleName() + ": " + message);
+        }
     }
     
     /**
      * 
      */
     protected void detectorChanged(Detector detector){
-    	super.detectorChanged(detector);
-    	
-    	sensors = detector.getSubdetector("Tracker").getDetectorElement().findDescendants(HpsSiSensor.class);
-    	
+        super.detectorChanged(detector);
+        
+        sensors = detector.getSubdetector("Tracker").getDetectorElement().findDescendants(HpsSiSensor.class);
+        
         // setup AIDA
         aida = AIDA.defaultInstance();
         aida.tree().cd("/");
         
         // Open the output file stream
         if(efficiencyOutputFile != null && momentumOutputFile != null){
-        	try{
-        		efficiencyOutput = new BufferedWriter(new FileWriter(efficiencyOutputFile));
+            try{
+                efficiencyOutput = new BufferedWriter(new FileWriter(efficiencyOutputFile));
                 momentumOutput = new BufferedWriter(new FileWriter(momentumOutputFile));
-        	} catch(Exception e){
-        		System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
-        	}
+            } catch(Exception e){
+                System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
+            }
         }
         
         // Get the total number of SVT layers
@@ -164,28 +164,28 @@
         }
 
         if(trackingEfficiencyPlots){
-        	plotters.add(PlotUtils.setupPlotter("Track Momentum", 0, 0));
-        	histo1D.add(aida.histogram1D("Momentum - Reconstructed Tracks", 14, 0, 5.6));
-        	PlotUtils.setup1DRegion(plotters.get(plotterIndex), "Reconstructed Tracks", 0, "Momentum [GeV]", histo1D.get(histo1DIndex));
+            plotters.add(PlotUtils.setupPlotter("Track Momentum", 0, 0));
+            histo1D.add(aida.histogram1D("Momentum - Reconstructed Tracks", 14, 0, 5.6));
+            PlotUtils.setup1DRegion(plotters.get(plotterIndex), "Reconstructed Tracks", 0, "Momentum [GeV]", histo1D.get(histo1DIndex));
             histo1DIndex++;            
             histo1D.add(aida.histogram1D("Momentum - Findable Tracks", 14, 0, 5.6));
-        	PlotUtils.setup1DRegion(plotters.get(plotterIndex), "Findable Tracks", 0, "Momentum [GeV]", histo1D.get(histo1DIndex));
-        	plotterIndex++;
-        	histo1DIndex++;
+            PlotUtils.setup1DRegion(plotters.get(plotterIndex), "Findable Tracks", 0, "Momentum [GeV]", histo1D.get(histo1DIndex));
+            plotterIndex++;
+            histo1DIndex++;
         }
         
         for(IPlotter plotter : plotters){
-        	plotter.show();
+            plotter.show();
         }
     }
     
     private String samplesToString(short[] samples){
-    	String sampleList = "[ ";
-    	for(short sample : samples){
-    		sampleList += Short.toString(sample) + ", ";
-    	}
-    	sampleList += "]";
-    	return sampleList;
+        String sampleList = "[ ";
+        for(short sample : samples){
+            sampleList += Short.toString(sample) + ", ";
+        }
+        sampleList += "]";
+        return sampleList;
     }
 
     /**
@@ -196,7 +196,7 @@
     @Override
     protected void process(EventHeader event){
         
-    	// For now, only look at events with a single track
+        // For now, only look at events with a single track
         if(event.get(Track.class, trackCollectionName).size() > 1) return;
         eventNumber++;
 
@@ -204,46 +204,46 @@
         if(!event.hasCollection(SimTrackerHit.class, simTrackerHitCollectionName)) return;
         List<SimTrackerHit> simTrackerHits = event.get(SimTrackerHit.class, simTrackerHitCollectionName);
         this.printDebug("\nEvent " + eventNumber + " contains " + simTrackerHits.size() + " SimTrackerHits");
-    	// Loop through all SimTrackerHits and confirm that a corresponding RawTrackerHit was created
-    	for(SimTrackerHit simTrackHit : simTrackerHits){
-    		
-    		this.printDebug("SimTrackerHit Layer Number: " + simTrackHit.getLayerNumber());
-    	}
+        // Loop through all SimTrackerHits and confirm that a corresponding RawTrackerHit was created
+        for(SimTrackerHit simTrackHit : simTrackerHits){
+            
+            this.printDebug("SimTrackerHit Layer Number: " + simTrackHit.getLayerNumber());
+        }
 
         // Get the list of RawTrackerHits and add them to the sensor readout
         List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
         String volume; 
         for(RawTrackerHit rawHit : rawHits){
-        	HpsSiSensor sensor = (HpsSiSensor) rawHit.getDetectorElement();
-        	if(sensor.isTopLayer()){
-        		volume = "Top Volume ";
-        	} else { 
-        		volume = "Bottom Volume ";
-        	}
-    		this.printDebug(volume + "RawTrackerHit Channel #: " + rawHit.getIdentifierFieldValue("strip") + " Layer Number: " + rawHit.getLayerNumber()
-    				+ " Samples: " + samplesToString(rawHit.getADCValues()));
+            HpsSiSensor sensor = (HpsSiSensor) rawHit.getDetectorElement();
+            if(sensor.isTopLayer()){
+                volume = "Top Volume ";
+            } else { 
+                volume = "Bottom Volume ";
+            }
+            this.printDebug(volume + "RawTrackerHit Channel #: " + rawHit.getIdentifierFieldValue("strip") + " Layer Number: " + rawHit.getLayerNumber()
+                    + " Samples: " + samplesToString(rawHit.getADCValues()));
             ((HpsSiSensor) rawHit.getDetectorElement()).getReadout().addHit(rawHit);
         }
         
         if(event.hasCollection(SiTrackerHit.class, siTrackerHitCollectionName)){
-        	List<SiTrackerHit> hitlist = event.get(SiTrackerHit.class, siTrackerHitCollectionName);
-        	for(SiTrackerHit siTrackerHit : hitlist){
-    			this.printDebug("Cluster is comprised by the following raw hits:");
-        		for(RawTrackerHit rawHit : siTrackerHit.getRawHits()){
-            		this.printDebug("RawTrackerHit Channel #: " + rawHit.getIdentifierFieldValue("strip") + " Layer Number: " + rawHit.getLayerNumber());
-        		}
-        	}
+            List<SiTrackerHit> hitlist = event.get(SiTrackerHit.class, siTrackerHitCollectionName);
+            for(SiTrackerHit siTrackerHit : hitlist){
+                this.printDebug("Cluster is comprised by the following raw hits:");
+                for(RawTrackerHit rawHit : siTrackerHit.getRawHits()){
+                    this.printDebug("RawTrackerHit Channel #: " + rawHit.getIdentifierFieldValue("strip") + " Layer Number: " + rawHit.getLayerNumber());
+                }
+            }
         }
         
         // Get the MC Particles associated with the SimTrackerHits
         List<MCParticle> mcParticles = event.getMCParticles();
         if(debug){
-        	String particleList = "[ ";
-        	for(MCParticle mcParticle : mcParticles){
-        		particleList += mcParticle.getPDGID() + ", ";
-        	}
-        	particleList += "]";
-        	this.printDebug("MC Particles: " + particleList);
+            String particleList = "[ ";
+            for(MCParticle mcParticle : mcParticles){
+                particleList += mcParticle.getPDGID() + ", ";
+            }
+            particleList += "]";
+            this.printDebug("MC Particles: " + particleList);
         }
         
         // Get the magnetic field
@@ -264,10 +264,10 @@
                 Set<SimTrackerHit> trackerHits = findable.getSimTrackerHits(mcParticle);
                 if(this.isSameSvtVolume(trackerHits)){
                     if(debug){
-                    	this.printDebug("Track is findable");
-                    	this.printDebug("MC particle momentum: " + mcParticle.getMomentum().toString());
-                    }
-                    	
+                        this.printDebug("Track is findable");
+                        this.printDebug("MC particle momentum: " + mcParticle.getMomentum().toString());
+                    }
+                        
                     findableTracks++;
                     trackIsFindable = true;      
                 }
@@ -303,8 +303,8 @@
         
         if(!mcParticles.isEmpty() && trackingEfficiencyPlots){
             // If the list still contains MC Particles, a matching track wasn't found
-        	this.printDebug("No matching track found");
-        	
+            this.printDebug("No matching track found");
+            
             // Check that all stereoHits were correctly assigned to an MCParticle
             for(MCParticle mcParticle : mcParticles){
                 
@@ -326,7 +326,7 @@
                 
                 // Determine if the MC particle passed through the top or bottom SVT volume
                 for(SimTrackerHit simHit : simHits){
-                	HpsSiSensor sensor = (HpsSiSensor) simHit.getDetectorElement();
+                    HpsSiSensor sensor = (HpsSiSensor) simHit.getDetectorElement();
                     if(sensor.isTopLayer()){
                         this.printDebug("MC Particle passed through the top layer");
                         isTopTrack = true;
@@ -376,7 +376,7 @@
     {
         int volumeIndex = 0;
         for(SimTrackerHit simTrackerHit : simTrackerHits){
-        	HpsSiSensor sensor = (HpsSiSensor) simTrackerHit.getDetectorElement();
+            HpsSiSensor sensor = (HpsSiSensor) simTrackerHit.getDetectorElement();
             if(sensor.isTopLayer()) volumeIndex++;
             else volumeIndex--;
         }
@@ -454,24 +454,24 @@
    @Override
    public void endOfData()
    { 
-	   
+       
        if(trackingEfficiencyPlots && efficiencyOutputFile != null && momentumOutputFile != null){
-	   	   try{ 
-	   		   int bins = aida.histogram1D("Momentum - Findable Tracks").axis().bins();
-	   		   for(int index = 0; index < bins; index++){
-	   			   if(aida.histogram1D("Momentum - Reconstructed Tracks").binEntries(index) == 0) efficiencyOutput.write(index + " " + 0 + "\n");
-	   			   else	efficiencyOutput.write(index + " " + aida.histogram1D("Momentum - Reconstructed Tracks").binEntries(index) + "\n");
-	   			   
+           try{ 
+               int bins = aida.histogram1D("Momentum - Findable Tracks").axis().bins();
+               for(int index = 0; index < bins; index++){
+                   if(aida.histogram1D("Momentum - Reconstructed Tracks").binEntries(index) == 0) efficiencyOutput.write(index + " " + 0 + "\n");
+                   else efficiencyOutput.write(index + " " + aida.histogram1D("Momentum - Reconstructed Tracks").binEntries(index) + "\n");
+                   
                    if(aida.histogram1D("Momentum - Findable Tracks").binEntries(index) == 0) momentumOutput.write(index + " " + 0 + "\n");
-	   			   else momentumOutput.write(index + " " + aida.histogram1D("Momentum - Findable Tracks").binEntries(index) + "\n");
-	   		   }
-	   		   efficiencyOutput.close();
+                   else momentumOutput.write(index + " " + aida.histogram1D("Momentum - Findable Tracks").binEntries(index) + "\n");
+               }
+               efficiencyOutput.close();
                momentumOutput.close();
-	   	   } catch(IOException e){
-	   		   System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
-	   	   }
+           } catch(IOException e){
+               System.out.println(this.getClass().getSimpleName() + ": Error! " + e.getMessage());
+           }
        } 
-	   
+       
         System.out.println("%===============================================================%");
         System.out.println("%============== Track Reconstruction Efficiencies ==============%");
         System.out.println("%===============================================================%\n%");

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/TestRunTrackReconEfficiency.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/TestRunTrackReconEfficiency.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/omoreno/TestRunTrackReconEfficiency.java	Wed Apr 27 11:11:32 2016
@@ -60,18 +60,18 @@
     boolean topTrigger = false;
      
     // Collection Names
-    String stereoHitCollectionName 		= "HelicalTrackHits";
-    String trackCollectionName 			= "MatchedTracks";
-    String ecalClustersCollectionName 	= "EcalClusters";
-    String triggerDataCollectionName 	= "TriggerBank";
+    String stereoHitCollectionName      = "HelicalTrackHits";
+    String trackCollectionName          = "MatchedTracks";
+    String ecalClustersCollectionName   = "EcalClusters";
+    String triggerDataCollectionName    = "TriggerBank";
     
     // Plots
     IHistogram1D findableTrackMomentum; 
     IHistogram1D totalTrackMomentum; 
-	IHistogram1D xPositionResidual;
-	IHistogram1D yPositionResidual;
-	IHistogram1D zPositionResidual;
-	IHistogram1D r;
+    IHistogram1D xPositionResidual;
+    IHistogram1D yPositionResidual;
+    IHistogram1D zPositionResidual;
+    IHistogram1D r;
 
     /**
      * Dflt Ctor
@@ -89,7 +89,7 @@
      * 
      */
     public void setThresholdEnergy(double thresholdEnergy){
-    	this.thresholdEnergy = thresholdEnergy;
+        this.thresholdEnergy = thresholdEnergy;
     }
 
     public void setClusterEnergyDifference(double energyDifference){ 
@@ -117,15 +117,15 @@
         plotterIndex++;
 
         // Create plot for diffence in track and cluster position
-		plotters.add(PlotUtils.setupPlotter("Track-Cluster Position Residual", 2, 2));
-		xPositionResidual = aida.histogram1D("x Residual", 100, -100, 100);
-		yPositionResidual = aida.histogram1D("y Residual", 100, -100, 100);
-		zPositionResidual = aida.histogram1D("z Residual", 100, -100, 100);
-		r = aida.histogram1D("r", 100, -100, 100);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "x Residual", 0, "delta x [mm]", xPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "y Residual", 1, "delta y [mm]", yPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "z Residual", 2, "delta z [mm]", zPositionResidual);
-		PlotUtils.setup1DRegion(plotters.get(plotterIndex), "r", 3, "r [mm]", r);
+        plotters.add(PlotUtils.setupPlotter("Track-Cluster Position Residual", 2, 2));
+        xPositionResidual = aida.histogram1D("x Residual", 100, -100, 100);
+        yPositionResidual = aida.histogram1D("y Residual", 100, -100, 100);
+        zPositionResidual = aida.histogram1D("z Residual", 100, -100, 100);
+        r = aida.histogram1D("r", 100, -100, 100);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "x Residual", 0, "delta x [mm]", xPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "y Residual", 1, "delta y [mm]", yPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "z Residual", 2, "delta z [mm]", zPositionResidual);
+        PlotUtils.setup1DRegion(plotters.get(plotterIndex), "r", 3, "r [mm]", r);
         plotterIndex++; 
 
         // Show all of the plotters
@@ -154,138 +154,138 @@
         // If the event has a single Ecal cluster satisfying the threshold cut, 
         // check if there is a track that is well matched to the cluster
         if(ecalClusters.size() == 1){
-        	Cluster ecalCluster = ecalClusters.get(0);
-        	
-        	// If the cluster is above the energy threshold, then the track should
-        	// be findable
-        	if(!isClusterAboveEnergyThreshold(ecalCluster)) return;
-        	findableSingleTracks++;
-        	
-        	double[] clusterPosition = ecalCluster.getPosition();
-        	
-        	if(clusterPosition[0] > 0 && clusterPosition[1] > 0) 	   findableSingleTracksQuad1++;
-        	else if(clusterPosition[0] < 0 && clusterPosition[1] > 0) findableSingleTracksQuad2++;
-        	else if(clusterPosition[0] < 0 && clusterPosition[1] < 0) findableSingleTracksQuad3++;
-        	else if(clusterPosition[0] > 0 && clusterPosition[1] < 0) findableSingleTracksQuad4++;	
-        	
-        	if(!isClusterMatchedToTrack(ecalCluster, tracks)) return;
-        	foundSingleTracks++;
-
-        	if(clusterPosition[0] > 0 && clusterPosition[1] > 0) 	   foundSingleTracksQuad1++;
-        	else if(clusterPosition[0] < 0 && clusterPosition[1] > 0) foundSingleTracksQuad2++;
-        	else if(clusterPosition[0] < 0 && clusterPosition[1] < 0) foundSingleTracksQuad3++;
-        	else if(clusterPosition[0] > 0 && clusterPosition[1] < 0) foundSingleTracksQuad4++;	
+            Cluster ecalCluster = ecalClusters.get(0);
+            
+            // If the cluster is above the energy threshold, then the track should
+            // be findable
+            if(!isClusterAboveEnergyThreshold(ecalCluster)) return;
+            findableSingleTracks++;
+            
+            double[] clusterPosition = ecalCluster.getPosition();
+            
+            if(clusterPosition[0] > 0 && clusterPosition[1] > 0)       findableSingleTracksQuad1++;
+            else if(clusterPosition[0] < 0 && clusterPosition[1] > 0) findableSingleTracksQuad2++;
+            else if(clusterPosition[0] < 0 && clusterPosition[1] < 0) findableSingleTracksQuad3++;
+            else if(clusterPosition[0] > 0 && clusterPosition[1] < 0) findableSingleTracksQuad4++;  
+            
+            if(!isClusterMatchedToTrack(ecalCluster, tracks)) return;
+            foundSingleTracks++;
+
+            if(clusterPosition[0] > 0 && clusterPosition[1] > 0)       foundSingleTracksQuad1++;
+            else if(clusterPosition[0] < 0 && clusterPosition[1] > 0) foundSingleTracksQuad2++;
+            else if(clusterPosition[0] < 0 && clusterPosition[1] < 0) foundSingleTracksQuad3++;
+            else if(clusterPosition[0] > 0 && clusterPosition[1] < 0) foundSingleTracksQuad4++; 
         }
         
         // Only look at events which have two Ecal cluster 
         if(ecalClusters.size() != 2) return;
 
         // Check that the Ecal clusters are in opposite Ecal volumes. If 
-       	// they don't, skip the event.
-       	if(!hasClustersInOppositeVolumes(ecalClusters)){
-       		this.printDebug("Ecal clusters are not in opposite volumes");
-       		return;
-       	}
-       	nOppositeVolume++;
+        // they don't, skip the event.
+        if(!hasClustersInOppositeVolumes(ecalClusters)){
+            this.printDebug("Ecal clusters are not in opposite volumes");
+            return;
+        }
+        nOppositeVolume++;
       
-       	// Check that the Ecal clusters lie within some pre-defined window. If
-       	// they don't, skip the event. 
+        // Check that the Ecal clusters lie within some pre-defined window. If
+        // they don't, skip the event. 
         if(!isClusterWithinWindow(ecalClusters.get(0)) || !isClusterWithinWindow(ecalClusters.get(1))){
-        		this.printDebug("Ecal cluster falls outside of window.");
-        		return;        	
+                this.printDebug("Ecal cluster falls outside of window.");
+                return;         
         }
         nWithinWindow++;
        
         // Check that the Ecal clusters are above the threshold energy.  If 
         // they don't, skip the event.
         if(!isClusterAboveEnergyThreshold(ecalClusters.get(0)) || !isClusterAboveEnergyThreshold(ecalClusters.get(1))){
-        		this.printDebug("Ecal cluster energies are below threshold.");
-        		return;        	        	
-        }
-       	nAboveThreshold++;
+                this.printDebug("Ecal cluster energies are below threshold.");
+                return;                     
+        }
+        nAboveThreshold++;
  
-       	// Check that the difference between the Ecal cluster energies is 
+        // Check that the difference between the Ecal cluster energies is 
         // reasonable
-       	double energyDiff = Math.abs(ecalClusters.get(0).getEnergy() - ecalClusters.get(1).getEnergy()); 
-       	if(energyDiff > energyDifference){
-       		this.printDebug("The energy difference between the two clusters is too great.");
-       		return;
-       	}
+        double energyDiff = Math.abs(ecalClusters.get(0).getEnergy() - ecalClusters.get(1).getEnergy()); 
+        if(energyDiff > energyDifference){
+            this.printDebug("The energy difference between the two clusters is too great.");
+            return;
+        }
        
         // Check if the event contains a collection of tracks.  If it doesn't,
         // move on to the next event.
         if(!event.hasCollection(Track.class, trackCollectionName)){
-        	this.printDebug("Event doesn't contain a collection of tracks!");
-        	return;
+            this.printDebug("Event doesn't contain a collection of tracks!");
+            return;
         }
 
 
         // If there are no tracks in the collection, move on to the next event. 
         if(tracks.isEmpty()){
-        	this.printDebug("Event doesn't contain any tracks!");
-        	return;  
+            this.printDebug("Event doesn't contain any tracks!");
+            return;  
         }
        
         // Sort the tracks by SVT volume
-    	topTracks = new ArrayList<Track>();
-    	botTracks = new ArrayList<Track>();
+        topTracks = new ArrayList<Track>();
+        botTracks = new ArrayList<Track>();
         for(Track track : tracks){
-    		if(track.getTrackStates().get(0).getZ0() > 0)  topTracks.add(track);
-    		else if(track.getTrackStates().get(0).getZ0() < 0) botTracks.add(track);
-    	}
-        
-       	// Get the trigger information from the event
-       	List<GenericObject> triggerData = event.get(GenericObject.class, triggerDataCollectionName);
-       	GenericObject triggerDatum = triggerData.get(0);
-       	if(triggerDatum.getIntVal(4) > 0){
-       		this.printDebug("Ecal triggered by top cluster");
-       		topTrigger = true;
-       	} else if(triggerDatum.getIntVal(5) > 0){
-       		this.printDebug("Ecal triggered by bottom cluster");       		
-       		topTrigger = false;
-       	}
-       	
-       	// Match a track to the trigger cluster
-       	Cluster matchedCluster = null; 
-       	for(Cluster ecalCluster : ecalClusters){
-       		if(ecalCluster.getPosition()[1] > 0 && topTrigger){
-       			if(!isClusterMatchedToTrack(ecalCluster, topTracks)){
-       				this.printDebug("Trigger cluster-track match was not found.");
-       				return;
-       			}
-       			matchedCluster = ecalCluster; 
-       			findableBottomTracks++;
-       			break;
-       		} else if( ecalCluster.getPosition()[1] < 0 && !topTrigger){
-       			if(!isClusterMatchedToTrack(ecalCluster, botTracks)){
-       				this.printDebug("Trigger cluster-track match was not found.");
-       				return;
-       			}
-       			matchedCluster = ecalCluster;
-       			findableTopTracks++;
-       			break;
-       		}
-       	}
-       	if(matchedCluster != null) ecalClusters.remove(matchedCluster);
-       	nTrigClusterTrackMatch++;
-       	
+            if(track.getTrackStates().get(0).getZ0() > 0)  topTracks.add(track);
+            else if(track.getTrackStates().get(0).getZ0() < 0) botTracks.add(track);
+        }
+        
+        // Get the trigger information from the event
+        List<GenericObject> triggerData = event.get(GenericObject.class, triggerDataCollectionName);
+        GenericObject triggerDatum = triggerData.get(0);
+        if(triggerDatum.getIntVal(4) > 0){
+            this.printDebug("Ecal triggered by top cluster");
+            topTrigger = true;
+        } else if(triggerDatum.getIntVal(5) > 0){
+            this.printDebug("Ecal triggered by bottom cluster");            
+            topTrigger = false;
+        }
+        
+        // Match a track to the trigger cluster
+        Cluster matchedCluster = null; 
+        for(Cluster ecalCluster : ecalClusters){
+            if(ecalCluster.getPosition()[1] > 0 && topTrigger){
+                if(!isClusterMatchedToTrack(ecalCluster, topTracks)){
+                    this.printDebug("Trigger cluster-track match was not found.");
+                    return;
+                }
+                matchedCluster = ecalCluster; 
+                findableBottomTracks++;
+                break;
+            } else if( ecalCluster.getPosition()[1] < 0 && !topTrigger){
+                if(!isClusterMatchedToTrack(ecalCluster, botTracks)){
+                    this.printDebug("Trigger cluster-track match was not found.");
+                    return;
+                }
+                matchedCluster = ecalCluster;
+                findableTopTracks++;
+                break;
+            }
+        }
+        if(matchedCluster != null) ecalClusters.remove(matchedCluster);
+        nTrigClusterTrackMatch++;
+        
         // If the cluster passes all requirements, then there is likely a track
         // associated with it
         findableTracks++;
         
         // Now check if a track is associated with the non-trigger cluster
         if(topTrigger){
-       			if(!isClusterMatchedToTrack(ecalClusters.get(0), botTracks)){
-       				this.printDebug("Non trigger cluster-track match was not found.");
-       				return;
-       			}
-       			totalBottomTracks++;
+                if(!isClusterMatchedToTrack(ecalClusters.get(0), botTracks)){
+                    this.printDebug("Non trigger cluster-track match was not found.");
+                    return;
+                }
+                totalBottomTracks++;
         } else if(!topTrigger){
-       			if(!isClusterMatchedToTrack(ecalClusters.get(0), topTracks)){
-       				this.printDebug("Non trigger cluster-track match was not found.");
-       				return;
-       			}        	       
-       			totalTopTracks++;
+                if(!isClusterMatchedToTrack(ecalClusters.get(0), topTracks)){
+                    this.printDebug("Non trigger cluster-track match was not found.");
+                    return;
+                }                  
+                totalTopTracks++;
         } 
         ++totalTracks; 
     }    
@@ -305,67 +305,67 @@
      * 
      */
     private boolean isClusterWithinWindow(Cluster clusterPosition){
-    	return true;
+        return true;
     }
     
     /**
      * 
      */
     private boolean isClusterAboveEnergyThreshold(Cluster ecalCluster){
-    	if(ecalCluster.getEnergy() > thresholdEnergy) return true;
-    	return false;
+        if(ecalCluster.getEnergy() > thresholdEnergy) return true;
+        return false;
     }
      
     /**
      * 
      */
     private boolean hasClustersInOppositeVolumes(List<Cluster> ecalClusters){
-    	this.printPosition(ecalClusters.get(0).getPosition());
-    	this.printPosition(ecalClusters.get(1).getPosition());
-    	if((ecalClusters.get(0).getPosition()[1] > 0 && ecalClusters.get(1).getPosition()[1] < 0)
-    			|| (ecalClusters.get(0).getPosition()[1] < 0 && ecalClusters.get(1).getPosition()[1] > 0)){
-    		return true; 	
-    	}
-    	return false;
+        this.printPosition(ecalClusters.get(0).getPosition());
+        this.printPosition(ecalClusters.get(1).getPosition());
+        if((ecalClusters.get(0).getPosition()[1] > 0 && ecalClusters.get(1).getPosition()[1] < 0)
+                || (ecalClusters.get(0).getPosition()[1] < 0 && ecalClusters.get(1).getPosition()[1] > 0)){
+            return true;    
+        }
+        return false;
     }
     
     /**
      * 
      */
     private boolean isClusterMatchedToTrack(Cluster cluster, List<Track> tracks){
-    	Hep3Vector clusterPos = new BasicHep3Vector(cluster.getPosition());
-    	double rMax = Double.MAX_VALUE;
-    	Track matchedTrack = null; 
-    	for(Track track : tracks){
-    		
-    		Hep3Vector trkPosAtShowerMax = TrackUtils.extrapolateTrack(track,clusterPos.z());
-    		if(Double.isNaN(trkPosAtShowerMax.x()) || Double.isNaN(trkPosAtShowerMax.y())){
-    			this.printDebug("Invalid track position");
-    			return false; 
-    		}
-    		this.printDebug("Track position at shower max: " + trkPosAtShowerMax.toString());
+        Hep3Vector clusterPos = new BasicHep3Vector(cluster.getPosition());
+        double rMax = Double.MAX_VALUE;
+        Track matchedTrack = null; 
+        for(Track track : tracks){
+            
+            Hep3Vector trkPosAtShowerMax = TrackUtils.extrapolateTrack(track,clusterPos.z());
+            if(Double.isNaN(trkPosAtShowerMax.x()) || Double.isNaN(trkPosAtShowerMax.y())){
+                this.printDebug("Invalid track position");
+                return false; 
+            }
+            this.printDebug("Track position at shower max: " + trkPosAtShowerMax.toString());
  
-    		// Find the distance between the track position at shower
-    		// max and the cluster position
-    		double r = VecOp.sub(trkPosAtShowerMax, clusterPos).magnitude();
-    		this.printDebug("Distance between Ecal cluster and track position at shower max: " + r + " mm");
-        	
-    		// Check if the track is the closest to the cluster.  If it is, then
-    		// save the track and contineu looping over all other tracks
-    		if (r < rMax /*&& r <= maxTrackClusterDistance*/) {
-    			rMax = r;
-    			matchedTrack = track;
-    		}
-    	}
-    	if(matchedTrack != null) return true;
-    	return false;
+            // Find the distance between the track position at shower
+            // max and the cluster position
+            double r = VecOp.sub(trkPosAtShowerMax, clusterPos).magnitude();
+            this.printDebug("Distance between Ecal cluster and track position at shower max: " + r + " mm");
+            
+            // Check if the track is the closest to the cluster.  If it is, then
+            // save the track and contineu looping over all other tracks
+            if (r < rMax /*&& r <= maxTrackClusterDistance*/) {
+                rMax = r;
+                matchedTrack = track;
+            }
+        }
+        if(matchedTrack != null) return true;
+        return false;
     }
     
     /**
      * 
      */
     private void printPosition(double[] position){
-    	this.printDebug("[ " + position[0] + ", " + position[1] + ", " + position[2] + " ]");
+        this.printDebug("[ " + position[0] + ", " + position[1] + ", " + position[2] + " ]");
     }
     
     
@@ -373,28 +373,28 @@
     public void endOfData(){ 
         System.out.println("%===================================================================% \n");
         if(findableSingleTracks > 0){
-        	System.out.println("% Total single track efficiency: " + foundSingleTracks + " / " + findableSingleTracks + " = " + (foundSingleTracks/findableSingleTracks)*100 + "%");
+            System.out.println("% Total single track efficiency: " + foundSingleTracks + " / " + findableSingleTracks + " = " + (foundSingleTracks/findableSingleTracks)*100 + "%");
         }
         if(findableSingleTracksQuad1 > 0){
-        	System.out.println("% Total single track efficiency - Quad 1: " + foundSingleTracksQuad1 + " / " + findableSingleTracksQuad1 + " = " + (foundSingleTracksQuad1/findableSingleTracksQuad1)*100 + "%");
+            System.out.println("% Total single track efficiency - Quad 1: " + foundSingleTracksQuad1 + " / " + findableSingleTracksQuad1 + " = " + (foundSingleTracksQuad1/findableSingleTracksQuad1)*100 + "%");
         }
         if(findableSingleTracksQuad2 > 0){
-        	System.out.println("% Total single track efficiency - Quad 2: " + foundSingleTracksQuad2 + " / " + findableSingleTracksQuad2 + " = " + (foundSingleTracksQuad2/findableSingleTracksQuad2)*100 + "%");
+            System.out.println("% Total single track efficiency - Quad 2: " + foundSingleTracksQuad2 + " / " + findableSingleTracksQuad2 + " = " + (foundSingleTracksQuad2/findableSingleTracksQuad2)*100 + "%");
         }
         if(findableSingleTracksQuad3 > 0){
-        	System.out.println("% Total single track efficiency - Quad 3: " + foundSingleTracksQuad3 + " / " + findableSingleTracksQuad3 + " = " + (foundSingleTracksQuad3/findableSingleTracksQuad3)*100 + "%");
+            System.out.println("% Total single track efficiency - Quad 3: " + foundSingleTracksQuad3 + " / " + findableSingleTracksQuad3 + " = " + (foundSingleTracksQuad3/findableSingleTracksQuad3)*100 + "%");
         }
         if(findableSingleTracksQuad4 > 0){
-        	System.out.println("% Total single track efficiency - Quad 4: " + foundSingleTracksQuad4 + " / " + findableSingleTracksQuad4 + " = " + (foundSingleTracksQuad4/findableSingleTracksQuad4)*100 + "%");
+            System.out.println("% Total single track efficiency - Quad 4: " + foundSingleTracksQuad4 + " / " + findableSingleTracksQuad4 + " = " + (foundSingleTracksQuad4/findableSingleTracksQuad4)*100 + "%");
         }
         if(nOppositeVolume > 0){
-        	System.out.println("% Total events passing opposite volume requirement: " + nOppositeVolume + " / " + eventNumber + " = " + (nOppositeVolume/eventNumber)*100 + "%");
+            System.out.println("% Total events passing opposite volume requirement: " + nOppositeVolume + " / " + eventNumber + " = " + (nOppositeVolume/eventNumber)*100 + "%");
         }
         if(nAboveThreshold > 0){
-        	System.out.println("% Total events with both clusters above energy threshold: " + nAboveThreshold + " / " + eventNumber + " = " + (nAboveThreshold/eventNumber)*100 + "%");
+            System.out.println("% Total events with both clusters above energy threshold: " + nAboveThreshold + " / " + eventNumber + " = " + (nAboveThreshold/eventNumber)*100 + "%");
         }
         if(nTrigClusterTrackMatch > 0){
-        	System.out.println("% Total events with a trigger cluster-track match: " + nTrigClusterTrackMatch + " / " + eventNumber + " = " + (nTrigClusterTrackMatch/eventNumber)*100 + "%");
+            System.out.println("% Total events with a trigger cluster-track match: " + nTrigClusterTrackMatch + " / " + eventNumber + " = " + (nTrigClusterTrackMatch/eventNumber)*100 + "%");
         }
         if(findableTracks > 0){
             System.out.println("% Total Track Reconstruction Efficiency: " + totalTracks + " / " + findableTracks + " = " + (totalTracks / findableTracks) * 100 + "%");

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/CmpGenToFittedTracksDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/CmpGenToFittedTracksDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/CmpGenToFittedTracksDriver.java	Wed Apr 27 11:11:32 2016
@@ -12,6 +12,7 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import org.hps.users.phansson.testrun.TrigRateDriver;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.Track;
 import org.lcsim.event.TrackerHit;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DataTrackerFakeHitDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DataTrackerFakeHitDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/DataTrackerFakeHitDriver.java	Wed Apr 27 11:11:32 2016
@@ -16,10 +16,12 @@
 import java.util.List;
 import java.util.Set;
 
+
 //===> import org.hps.conditions.deprecated.SvtUtils;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.TrackUtils;
 import org.hps.recon.tracking.TrackerHitUtils;
+import org.hps.recon.tracking.WTrack;
 import org.lcsim.detector.IDetectorElement;
 import org.lcsim.detector.ITransform3D;
 import org.lcsim.detector.ITranslation3D;
@@ -194,12 +196,12 @@
 
 
         // Obtain the tracks from the event
-        if (!event.hasCollection(HPSTrack.class, trackCollectionName)) {
+        if (!event.hasCollection(HpsHelicalTrackFit.class, trackCollectionName)) {
             this.printDebug("No HPSTracks were found, skipping event");
             simHits = null;
             return;
         }
-        List<HPSTrack> tracks = event.get(HPSTrack.class, trackCollectionName);
+        List<HpsHelicalTrackFit> tracks = event.get(HpsHelicalTrackFit.class, trackCollectionName);
 
         if (debug) {
             System.out.println(this.getClass().getSimpleName() + ": found " + tracks.size() + " tracks (" + this.trackCollectionName + ")");
@@ -223,13 +225,13 @@
             System.out.println(this.getClass().getSimpleName() + ": Add hits for " + tracks.size() + " tracks (" + this.trackCollectionName + ")");
         }
 
-        for (HPSTrack helix : tracks) {
+        for (HpsHelicalTrackFit helix : tracks) {
             if (debug) {
                 System.out.println(this.getClass().getSimpleName() + ": trying to add hits for this track");
             }
 
             // Get the MC Particle associated with this track
-            MCParticle mcParticle = helix.getMCParticle();
+            MCParticle mcParticle = helix.getMcParticle();
 
             if (debug) {
                 System.out.println(this.getClass().getSimpleName() + helix.toString());
@@ -238,8 +240,8 @@
                 System.out.println(this.getClass().getSimpleName() + ": create a WTrack object");
             }
 
-            WTrack wtrack = new WTrack(helix, Math.abs(_bfield.z()), true); //remove sign from B-field (assumed to go along z-direction)
-
+            WTrack wtrack = new WTrack(helix, Math.abs(_bfield.z())); 
+            
             if (debug) {
                 System.out.println(this.getClass().getSimpleName() + ": " + wtrack.toString());
 

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/FastTrackResidualDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/FastTrackResidualDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/FastTrackResidualDriver.java	Wed Apr 27 11:11:32 2016
@@ -78,11 +78,11 @@
     }
     
     public void detectorChanged(Detector detector) {
-	// Get the Subdetector.
-	ecal = detector.getSubdetector(ecalName);
-
-	// Cache ref to decoder.
-	dec = ecal.getIDDecoder();
+    // Get the Subdetector.
+    ecal = detector.getSubdetector(ecalName);
+
+    // Cache ref to decoder.
+    dec = ecal.getIDDecoder();
         
         //Ecal geometry
         crystalX = (13.3 + 16.0) / 2;
@@ -793,7 +793,7 @@
                 style.setParameter("hist2DStyle", "colorMap");
                 style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
                 ((PlotterRegion) plotter_ecalhitmult.region(idx)).getPlot().setAllowUserInteraction(false);
-		((PlotterRegion) plotter_ecalhitmult.region(idx)).getPlot().setAllowPopupMenus(false);
+        ((PlotterRegion) plotter_ecalhitmult.region(idx)).getPlot().setAllowPopupMenus(false);
           }
                
         

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ParticleHelixProducer.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ParticleHelixProducer.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/ParticleHelixProducer.java	Wed Apr 27 11:11:32 2016
@@ -13,7 +13,7 @@
 import java.util.List;
 
 import org.hps.analysis.ecal.HPSMCParticlePlotsDriver;
-import org.hps.recon.tracking.HPSTrack;
+import org.hps.recon.tracking.HpsHelicalTrackFit;
 import org.hps.recon.tracking.TrackerHitUtils;
 import org.lcsim.constants.Constants;
 import org.lcsim.event.EventHeader;
@@ -137,7 +137,7 @@
 
         //Make new tracks based on the MC particles
         //List<HelicalTrackFit> tracks = new ArrayList<HelicalTrackFit>();
-        List<HPSTrack> tracks = new ArrayList<HPSTrack>();
+        List<HpsHelicalTrackFit> tracks = new ArrayList<HpsHelicalTrackFit>();
 
         if (event.hasCollection(MCParticle.class)) {
             List<MCParticle> mcparticles = event.get(MCParticle.class).get(0);
@@ -251,7 +251,7 @@
                     pars[3] = hpc.getZ0();
                     pars[4] = hpc.getSlopeSZPlane();
                     //HelicalTrackFit htf = this.trackUtils.makeHelicalTrackFit(pars);
-                    HPSTrack htf = this.makeHPSTrack(pars, part);
+                    HpsHelicalTrackFit htf = this.makeHPSTrack(pars, part);
                     tracks.add(htf);
                     if (debug) {
                         System.out.println(this.getClass().getSimpleName() + ": MC particle created HelicalTrackFit " + htf.toString());
@@ -281,7 +281,7 @@
         }
 
         this.printDebug("created " + tracks.size() + " MC particle helix tracks");
-        event.put(this.trackOutputCollectionName, tracks, HPSTrack.class, 0);
+        event.put(this.trackOutputCollectionName, tracks, HpsHelicalTrackFit.class, 0);
         _totalTracks += tracks.size();
     }
 
@@ -292,9 +292,12 @@
      * @param mcParticle : MC particle associated to this HelicalTrackFit
      * @return HpsHelicalTrackFit :
      */
-    public HPSTrack makeHPSTrack(double[] helixParameters, MCParticle mcParticle) {
-        return new HPSTrack(helixParameters, new SymmetricMatrix(5), new double[2], new int[2],
-                new HashMap<HelicalTrackHit, Double>(), new HashMap<HelicalTrackHit, MultipleScatter>(), mcParticle);
+    public HpsHelicalTrackFit makeHPSTrack(double[] helixParameters, MCParticle mcParticle) {
+        HpsHelicalTrackFit helicalTrackFit = new HpsHelicalTrackFit(helixParameters, new SymmetricMatrix(5), new double[2], new int[2],
+                new HashMap<HelicalTrackHit, Double>(), new HashMap<HelicalTrackHit, MultipleScatter>());
+        helicalTrackFit.setMcParticle(mcParticle);
+        return  helicalTrackFit;
+        
     }
 
     /**

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SimpleResiduals.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SimpleResiduals.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/SimpleResiduals.java	Wed Apr 27 11:11:32 2016
@@ -98,11 +98,11 @@
     }
     
     public void detectorChanged(Detector detector) {
-	// Get the Subdetector.
-	ecal = detector.getSubdetector(ecalName);
-
-	// Cache ref to decoder.
-	dec = ecal.getIDDecoder();
+    // Get the Subdetector.
+    ecal = detector.getSubdetector(ecalName);
+
+    // Cache ref to decoder.
+    dec = ecal.getIDDecoder();
     }
     
     public SimpleResiduals() {

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrackingReconstructionPlots.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrackingReconstructionPlots.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TrackingReconstructionPlots.java	Wed Apr 27 11:11:32 2016
@@ -50,7 +50,8 @@
 import org.lcsim.util.aida.AIDA;
 
 /**
- *
+ * Analysis class to check recon.
+ * 
  * @author phansson
  */
 public class TrackingReconstructionPlots extends Driver {
@@ -89,12 +90,10 @@
     IPlotter plotter55;
     IPlotter plotter6;
     IPlotter plotter66;
-    IPlotter plotter7;
     IPlotter plotter8;
     IPlotter plotter88;
     IPlotter plotter888;
     IPlotter plotter8888;
-    IPlotter plotter9;
     IPlotter top1;
     IPlotter top2;
     IPlotter top3;
@@ -114,11 +113,11 @@
     private boolean showPlots = true;
     private double _bfield;
     private static Logger LOGGER = Logger.getLogger(TrackingReconstructionPlots.class.getName());
+    private List<HpsSiSensor> sensors = new ArrayList<HpsSiSensor>();
 
     @Override
     protected void detectorChanged(Detector detector) {
         aida.tree().cd("/");
-        List<HpsSiSensor> sensors = new ArrayList<HpsSiSensor>();
         for(HpsSiSensor s : detector.getDetectorElement().findDescendants(HpsSiSensor.class)) {
             if(s.getName().startsWith("module_") && s.getName().endsWith("sensor0")) {
                 sensors.add(s);
@@ -128,833 +127,15 @@
         
         Hep3Vector bfieldvec = detector.getFieldMap().getField(new BasicHep3Vector(0., 0., 1.));
         _bfield = bfieldvec.y();
-
-        IAnalysisFactory fac = aida.analysisFactory();
-        plotter = fac.createPlotterFactory().create("HPS Tracking Plots");
-        plotter.setTitle("Momentum");
-        IPlotterStyle style = plotter.style();
-        style.dataStyle().fillStyle().setColor("yellow");
-        style.dataStyle().errorBarStyle().setVisible(false);
-        plotter.createRegions(2, 2);
-        //plotterFrame.addPlotter(plotter);
-
-        trkPx = aida.histogram1D("Track Momentum (Px)", 25, -0.25, 0.25);
-        IHistogram1D trkPy = aida.histogram1D("Track Momentum (Py)", 25, -0.5, 0.5);
-        IHistogram1D trkPz = aida.histogram1D("Track Momentum (Pz)", 25, 0, 1.5);
-        IHistogram1D trkChi2 = aida.histogram1D("Track Chi2", 25, 0, 25.0);
-
-        plotter.region(0).plot(trkPx);
-        plotter.region(1).plot(trkPy);
-        plotter.region(2).plot(trkPz);
-        plotter.region(3).plot(trkChi2);
-
-        if(showPlots) plotter.show();
-
-//   ******************************************************************
-        top1 = fac.createPlotterFactory().create("Top Tracking Plots");
-        top1.setTitle("Top Momentum");
-        IPlotterStyle stop1 = top1.style();
-        stop1.dataStyle().fillStyle().setColor("green");
-        stop1.dataStyle().errorBarStyle().setVisible(false);
-        top1.createRegions(2, 2);
-        //topFrame.addPlotter(top1);
-
-        IHistogram1D toptrkPx = aida.histogram1D("Top Track Momentum (Px)", 25, -0.25, 0.25);
-        IHistogram1D toptrkPy = aida.histogram1D("Top Track Momentum (Py)", 25, -0.5, 0.5);
-        IHistogram1D toptrkPz = aida.histogram1D("Top Track Momentum (Pz)", 25, 0, 1.5);
-        IHistogram1D toptrkChi2 = aida.histogram1D("Top Track Chi2", 25, 0, 25.0);
-
-        top1.region(0).plot(toptrkPx);
-        top1.region(1).plot(toptrkPy);
-        top1.region(2).plot(toptrkPz);
-        top1.region(3).plot(toptrkChi2);
-
-        if(showPlots) top1.show();
-
-        bot1 = fac.createPlotterFactory().create("Bottom Tracking Plots");
-        bot1.setTitle("Bottom Momentum");
-        IPlotterStyle sbot1 = bot1.style();
-        sbot1.dataStyle().fillStyle().setColor("blue");
-        sbot1.dataStyle().errorBarStyle().setVisible(false);
-        bot1.createRegions(2, 2);
-        //bottomFrame.addPlotter(bot1);
-
-        IHistogram1D bottrkPx = aida.histogram1D("Bottom Track Momentum (Px)", 25, -0.25, 0.25);
-        IHistogram1D bottrkPy = aida.histogram1D("Bottom Track Momentum (Py)", 25, -0.5, 0.5);
-        IHistogram1D bottrkPz = aida.histogram1D("Bottom Track Momentum (Pz)", 25, 0, 1.5);
-        IHistogram1D bottrkChi2 = aida.histogram1D("Bottom Track Chi2", 25, 0, 25.0);
-
-        bot1.region(0).plot(bottrkPx);
-        bot1.region(1).plot(bottrkPy);
-        bot1.region(2).plot(bottrkPz);
-        bot1.region(3).plot(bottrkChi2);
-
-        if(showPlots) bot1.show();
-
-//   ******************************************************************
-        IHistogram1D trkd0 = aida.histogram1D("d0 ", 25, -10.0, 10.0);
-        IHistogram1D trkphi = aida.histogram1D("sinphi ", 25, -0.2, 0.2);
-        IHistogram1D trkomega = aida.histogram1D("omega ", 25, -0.0025, 0.0025);
-        IHistogram1D trklam = aida.histogram1D("tan(lambda) ", 25, -0.1, 0.1);
-        IHistogram1D trkz0 = aida.histogram1D("z0 ", 25, -6.0, 6.0);
-
-        plotter22 = fac.createPlotterFactory().create("HPS Track Params");
-        plotter22.setTitle("Track parameters");
-        //plotterFrame.addPlotter(plotter22);
-        IPlotterStyle style22 = plotter22.style();
-        style22.dataStyle().fillStyle().setColor("yellow");
-        style22.dataStyle().errorBarStyle().setVisible(false);
-        plotter22.createRegions(2, 3);
-        plotter22.region(0).plot(trkd0);
-        plotter22.region(1).plot(trkphi);
-        plotter22.region(2).plot(trkomega);
-        plotter22.region(3).plot(trklam);
-        plotter22.region(4).plot(trkz0);
-        
-        if(showPlots) plotter22.show();
-
- //   ******************************************************************
-
-        
-         trkd0 = aida.histogram1D("d0 Top", 25, -10.0, 10.0);
-         trkphi = aida.histogram1D("sinphi Top", 25, -0.2, 0.2);
-         trkomega = aida.histogram1D("omega Top", 25, -0.0025, 0.0025);
-         trklam = aida.histogram1D("tan(lambda) Top", 25, -0.1, 0.1);
-         trkz0 = aida.histogram1D("z0 Top", 25, -6.0, 6.0);
-
-        plotter2221 = fac.createPlotterFactory().create("HPS Track Params");
-        plotter2221.setTitle("Track parameters");
-        //plotterFrame.addPlotter(plotter22);
-        IPlotterStyle style2221 = plotter2221.style();
-        style2221.dataStyle().fillStyle().setColor("yellow");
-        style2221.dataStyle().errorBarStyle().setVisible(false);
-        plotter2221.createRegions(2, 3);
-        plotter2221.region(0).plot(trkd0);
-        plotter2221.region(1).plot(trkphi);
-        plotter2221.region(2).plot(trkomega);
-        plotter2221.region(3).plot(trklam);
-        plotter2221.region(4).plot(trkz0);
-        
-        if(showPlots) plotter2221.show();
-        
-        
-   //   ******************************************************************
-
-        
-        trkd0 = aida.histogram1D("d0 Bottom", 25, -10.0, 10.0);
-        trkphi = aida.histogram1D("sinphi Bottom", 25, -0.2, 0.2);
-        trkomega = aida.histogram1D("omega Bottom", 25, -0.0025, 0.0025);
-        trklam = aida.histogram1D("tan(lambda) Bottom", 25, -0.1, 0.1);
-        trkz0 = aida.histogram1D("z0 Bottom", 25, -6.0, 6.0);
-
-       plotter2222 = fac.createPlotterFactory().create("HPS Track Params");
-       plotter2222.setTitle("Track parameters");
-       //plotterFrame.addPlotter(plotter22);
-       IPlotterStyle style2222 = plotter2222.style();
-       style2222.dataStyle().fillStyle().setColor("yellow");
-       style2222.dataStyle().errorBarStyle().setVisible(false);
-       plotter2222.createRegions(2, 3);
-       plotter2222.region(0).plot(trkd0);
-       plotter2222.region(1).plot(trkphi);
-       plotter2222.region(2).plot(trkomega);
-       plotter2222.region(3).plot(trklam);
-       plotter2222.region(4).plot(trkz0);
-       
-       if(showPlots) plotter2222.show();
-        
-        
-        
-   //   ******************************************************************
-
-        
-        plotter2 = fac.createPlotterFactory().create("HPS Tracking Plots");
-        plotter2.setTitle("Track extrapolation");
-        //plotterFrame.addPlotter(plotter2);
-        IPlotterStyle style2 = plotter2.style();
-        style2.dataStyle().fillStyle().setColor("yellow");
-        style2.dataStyle().errorBarStyle().setVisible(false);
-        plotter2.createRegions(2, 4);
-        IHistogram1D xAtConverter = aida.histogram1D("X (mm) @ Z=-60cm", 50, -50, 50);
-        IHistogram1D yAtConverter = aida.histogram1D("Y (mm) @ Z=-60cm", 50, -20, 20);
-        IHistogram1D xAtColl = aida.histogram1D("X (mm) @ Z=-150cm", 50, -200, 200);
-        IHistogram1D yAtColl = aida.histogram1D("Y (mm) @ Z=-150cm", 50, -200, 200);
-        IHistogram1D xAtEcal = aida.histogram1D("X (mm) @ ECAL", 50, -500, 500);
-        IHistogram1D yAtEcal = aida.histogram1D("Y (mm) @ ECAL", 50, -100, 100);
-        IHistogram1D xAtEcal2 = aida.histogram1D("X (mm) @ ECAL (Pz>1)", 50, -500, 500);
-        IHistogram1D yAtEcal2 = aida.histogram1D("Y (mm) @ ECAL (Pz>1)", 50, -100, 100);
-
-        plotter2.region(0).plot(xAtConverter);
-        plotter2.region(4).plot(yAtConverter);
-        plotter2.region(1).plot(xAtColl);
-        plotter2.region(5).plot(yAtColl);
-        plotter2.region(2).plot(xAtEcal);
-        plotter2.region(6).plot(yAtEcal);
-        plotter2.region(3).plot(xAtEcal2);
-        plotter2.region(7).plot(yAtEcal2);
-        
-        if(showPlots) plotter2.show();
-
-   //   ******************************************************************
-        
-        plotter222 = fac.createPlotterFactory().create("HPS Tracking Plots");
-        plotter222.setTitle("HPS Tracking Plots");
-        //plotterFrame.addPlotter(plotter222);
-        IPlotterStyle style222 = plotter222.style();
-        style222.dataStyle().fillStyle().setColor("yellow");
-        style222.dataStyle().errorBarStyle().setVisible(false);
-        plotter222.createRegions(2, 2);
-        
-        IHistogram1D nHits = aida.histogram1D("Hits per Track", 4, 3, 7);
-        nTracks = aida.histogram1D("Tracks per Event", 3, 0, 3);
-        IHistogram1D nHitsCluster = aida.histogram1D("Hits in Cluster (HitOnTrack)", 4, 0, 4);
-
-       
-        plotter222.region(0).plot(nHits);
-        plotter222.region(1).plot(nTracks);
-        plotter222.region(2).plot(nHitsCluster);
-        
-        if(showPlots) plotter222.show();
-   
-        
-   //   ******************************************************************
-        
-        plotter22299 = fac.createPlotterFactory().create("HPS Tracking Plots Top");
-        plotter22299.setTitle("HPS Tracking Plots Top");
-        //plotterFrame.addPlotter(plotter22299);
-        IPlotterStyle style22299 = plotter22299.style();
-        style22299.dataStyle().fillStyle().setColor("yellow");
-        style22299.dataStyle().errorBarStyle().setVisible(false);
-        plotter22299.createRegions(2, 2);
-        
-        IHistogram1D nHitsTop = aida.histogram1D("Hits per Track Top", 4, 3, 7);
-        nTracksTop = aida.histogram1D("Tracks per Event Top", 3, 0, 3);
-        IHistogram1D nHitsClusterTop = aida.histogram1D("Hits in Cluster (HitOnTrack) Top", 4, 0, 4);
-
-       
-        plotter22299.region(0).plot(nHitsTop);
-        plotter22299.region(1).plot(nTracksTop);
-        plotter22299.region(2).plot(nHitsClusterTop);
-        
-        if(showPlots) plotter22299.show();
-   
-//   ******************************************************************
-        
-        plotter22298 = fac.createPlotterFactory().create("HPS Tracking Plots Bottom");
-        plotter22298.setTitle("HPS Tracking Plots Bottom");
-        //plotterFrame.addPlotter(plotter22298);
-        IPlotterStyle style22298 = plotter22298.style();
-        style22298.dataStyle().fillStyle().setColor("yellow");
-        style22298.dataStyle().errorBarStyle().setVisible(false);
-        plotter22298.createRegions(2, 2);
-        
-        IHistogram1D nHitsBot = aida.histogram1D("Hits per Track Bot", 4, 3, 7);
-        nTracksBot = aida.histogram1D("Tracks per Event Bot", 3, 0, 3);
-        IHistogram1D nHitsClusterBot = aida.histogram1D("Hits in Cluster (HitOnTrack) Bot", 4, 0, 4);
-
-       
-        plotter22298.region(0).plot(nHitsBot);
-        plotter22298.region(1).plot(nTracksBot);
-        plotter22298.region(2).plot(nHitsClusterBot);
-        
-        if(showPlots) plotter22298.show();
-   
-        
-        //   ******************************************************************
-        
-        
-        plotter2223 = fac.createPlotterFactory().create("Cluster Amp Plots");
-        plotter2223.setTitle("Other");
-        //plotterFrame.addPlotter(plotter222);
-        IPlotterStyle style2223 = plotter2223.style();
-        style2223.dataStyle().fillStyle().setColor("yellow");
-        style2223.dataStyle().errorBarStyle().setVisible(false);
-        plotter2223.createRegions(2, 2);
-        
-       
-
-        IHistogram1D amp = aida.histogram1D("Amp (HitOnTrack)", 50, 0, 5000);
-        IHistogram1D ampcl = aida.histogram1D("Cluster Amp (HitOnTrack)", 50, 0, 5000);
-        IHistogram1D amp2 = aida.histogram1D("Amp Pz>0.8 (HitOnTrack)", 50, 0, 5000);
-        IHistogram1D ampcl2 = aida.histogram1D("Cluster Amp Pz>0.8 (HitOnTrack)", 50, 0, 5000);
-      
-        
-        plotter2223.region(0).plot(amp);
-        plotter2223.region(1).plot(amp2);
-        plotter2223.region(2).plot(ampcl);
-        plotter2223.region(3).plot(ampcl2);
-        
-        if(showPlots) plotter2223.show();
-   
-//   ******************************************************************
-        
-        
-        plotter2224 = fac.createPlotterFactory().create("t0 Plots");
-        plotter2224.setTitle("Other");
-        IPlotterStyle style2224 = plotter2224.style();
-        style2224.dataStyle().fillStyle().setColor("yellow");
-        style2224.dataStyle().errorBarStyle().setVisible(false);
-        plotter2224.createRegions(2, 2);
-                
-        IHistogram1D t0 = aida.histogram1D("t0 (HitOnTrack)", 50, -100, 100);
-        IHistogram1D t0cl = aida.histogram1D("Cluster t0 (HitOnTrack)", 50, -100, 100);
-        IHistogram1D t02 = aida.histogram1D("t0 Pz>0.8 (HitOnTrack)", 50, -100, 100);
-        IHistogram1D t0cl2 = aida.histogram1D("Cluster t0 Pz>0.8 (HitOnTrack)", 50, -100, 100);
-        
-        plotter2224.region(0).plot(t0);
-        plotter2224.region(1).plot(t0cl);
-        plotter2224.region(2).plot(t02);
-        plotter2224.region(3).plot(t0cl2);
-
-        if(showPlots) plotter2224.show();
-   
-        
-        //   ******************************************************************
-          
-        plotter3 = fac.createPlotterFactory().create("HPS Layer Residual Plots");
-        plotter3.setTitle("Layer Residuals");
-        //plotterFrame.addPlotter(plotter3);
-        IPlotterStyle style3 = plotter3.style();
-        style3.dataStyle().fillStyle().setColor("yellow");
-        style3.dataStyle().errorBarStyle().setVisible(false);
-        plotter3.createRegions(6, 2);
-
-       
-
-        IHistogram1D mod1ResX = aida.histogram1D("Layer 1 Residual X(mm)", 25, -1, 1);
-        IHistogram1D mod1ResY = aida.histogram1D("Layer 1 Residual Y(mm)", 25, -0.04, 0.04);
-
-        IHistogram1D mod2ResX = aida.histogram1D("Layer 2 Residual X(mm)", 25, -2, 2);
-        IHistogram1D mod2ResY = aida.histogram1D("Layer 2 Residual Y(mm)", 25, -1, 1);
-
-        IHistogram1D mod3ResX = aida.histogram1D("Layer 3 Residual X(mm)", 25, -2.5, 2.5);
-        IHistogram1D mod3ResY = aida.histogram1D("Layer 3 Residual Y(mm)", 25, -1.5, 1.5);
-
-        IHistogram1D mod4ResX = aida.histogram1D("Layer 4 Residual X(mm)", 25, -3.0, 3.0);
-        IHistogram1D mod4ResY = aida.histogram1D("Layer 4 Residual Y(mm)", 25, -2, 2);
-
-        IHistogram1D mod5ResX = aida.histogram1D("Layer 5 Residual X(mm)", 25, -4, 4);
-        IHistogram1D mod5ResY = aida.histogram1D("Layer 5 Residual Y(mm)", 25, -3, 3);
-
-        IHistogram1D mod6ResX = aida.histogram1D("Layer 6 Residual X(mm)", 25, -5, 5);
-        IHistogram1D mod6ResY = aida.histogram1D("Layer 6 Residual Y(mm)", 25, -3, 3);
-
-        plotter3.region(0).plot(mod1ResX);
-        plotter3.region(2).plot(mod2ResX);
-        plotter3.region(4).plot(mod3ResX);
-        plotter3.region(6).plot(mod4ResX);
-        plotter3.region(8).plot(mod5ResX);
-        plotter3.region(10).plot(mod6ResX);
-
-        plotter3.region(1).plot(mod1ResY);
-        plotter3.region(3).plot(mod2ResY);
-        plotter3.region(5).plot(mod3ResY);
-        plotter3.region(7).plot(mod4ResY);
-        plotter3.region(9).plot(mod5ResY);
-        plotter3.region(11).plot(mod6ResY);
-               
-        if(showPlots) plotter3.show();
-        
-        
-        
-        plotter3_11 = fac.createPlotterFactory().create("HPS Strip Residual Plots");
-        plotter3_11.setTitle("Strip Residuals (Top)");
-        //plotterFrame.addPlotter(plotter3_11);
-        IPlotterStyle style3_11 = plotter3_11.style();
-        style3_11.dataStyle().fillStyle().setColor("yellow");
-        style3_11.dataStyle().errorBarStyle().setVisible(false);
-        plotter3_11.createRegions(6, 6);
-        int i=0;
-        for(HpsSiSensor sensor : sensors) {
-            double min = 0.0;
-            double max = 0.0;
-            if(sensor.getName().contains("L1")) {
-                min=-0.04; max=0.04;
-            } else if(sensor.getName().contains("L2")) {
-                min=-1; max=1;
-            } else if(sensor.getName().contains("L3")) {
-                min=-1.5; max=1.5;
-            } else if(sensor.getName().contains("L4")) {
-                min=-3; max=3;
-            } else if(sensor.getName().contains("L5")) {
-                min=-4; max=4;
-            } else if(sensor.getName().contains("L6")) {
-                min=-5; max=5;
-            } else {
-                throw new RuntimeException("Invalid sensor name: " + sensor.getName());
-            }
-           IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip residual (mm)", 50, min, max);
-            plotter3_11.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter3_11.show();
-        
-
-        plotter3_1 = fac.createPlotterFactory().create("HPS Residual Plots (Single hit per layer)");
-        plotter3_1.setTitle("Residuals (Top)");
-        //plotterFrame.addPlotter(plotter3_1);
-        IPlotterStyle style3_1 = plotter3_1.style();
-        style3_1.dataStyle().fillStyle().setColor("yellow");
-        style3_1.dataStyle().errorBarStyle().setVisible(false);
-        plotter3_1.createRegions(6, 2);
-        
-        IHistogram1D mod1ResX_Top = aida.histogram1D("Layer 1 Residual X(mm) Top", 25, -1, 1);
-        IHistogram1D mod1ResY_Top = aida.histogram1D("Layer 1 Residual Y(mm) Top", 25, -0.04, 0.04);
-
-        IHistogram1D mod2ResX_Top = aida.histogram1D("Layer 2 Residual X(mm) Top", 25, -2, 2);
-        IHistogram1D mod2ResY_Top = aida.histogram1D("Layer 2 Residual Y(mm) Top", 25, -1, 1);
-
-        IHistogram1D mod3ResX_Top = aida.histogram1D("Layer 3 Residual X(mm) Top", 25, -2.5, 2.5);
-        IHistogram1D mod3ResY_Top = aida.histogram1D("Layer 3 Residual Y(mm) Top", 25, -1.5, 1.5);
-
-        IHistogram1D mod4ResX_Top = aida.histogram1D("Layer 4 Residual X(mm) Top", 25, -3.0, 3.0);
-        IHistogram1D mod4ResY_Top = aida.histogram1D("Layer 4 Residual Y(mm) Top", 25, -2, 2);
-
-        IHistogram1D mod5ResX_Top = aida.histogram1D("Layer 5 Residual X(mm) Top", 25, -4, 4);
-        IHistogram1D mod5ResY_Top = aida.histogram1D("Layer 5 Residual Y(mm) Top", 25, -3, 3);
-
-        IHistogram1D mod6ResX_Top = aida.histogram1D("Layer 6 Residual X(mm) Top", 25, -5, 5);
-        IHistogram1D mod6ResY_Top = aida.histogram1D("Layer 6 Residual Y(mm) Top", 25, -3, 3);
-
-        
-        plotter3_1.region(0).plot(mod1ResX_Top);
-        plotter3_1.region(2).plot(mod2ResX_Top);
-        plotter3_1.region(4).plot(mod3ResX_Top);
-        plotter3_1.region(6).plot(mod4ResX_Top);
-        plotter3_1.region(8).plot(mod5ResX_Top);
-        plotter3_1.region(10).plot(mod6ResX_Top);
-
-        plotter3_1.region(1).plot(mod1ResY_Top);
-        plotter3_1.region(3).plot(mod2ResY_Top);
-        plotter3_1.region(5).plot(mod3ResY_Top);
-        plotter3_1.region(7).plot(mod4ResY_Top);
-        plotter3_1.region(9).plot(mod5ResY_Top);
-        plotter3_1.region(11).plot(mod6ResY_Top);
-
-        if(showPlots) plotter3_1.show();
-        
-        plotter3_2 = fac.createPlotterFactory().create("HPS Residual Plots (Single strip cluster per layer)");
-        plotter3_2.setTitle("Residuals (Bottom)");
-        //plotterFrame.addPlotter(plotter3_2);
-        IPlotterStyle style3_2 = plotter3_2.style();
-        style3_2.dataStyle().fillStyle().setColor("yellow");
-        style3_2.dataStyle().errorBarStyle().setVisible(false);
-        plotter3_2.createRegions(6, 2);
-
-        IHistogram1D mod1ResX_Bottom = aida.histogram1D("Layer 1 Residual X(mm) Bottom", 25, -1, 1);
-        IHistogram1D mod1ResY_Bottom = aida.histogram1D("Layer 1 Residual Y(mm) Bottom", 25, -0.04, 0.04);
-
-        IHistogram1D mod2ResX_Bottom = aida.histogram1D("Layer 2 Residual X(mm) Bottom", 25, -2, 2);
-        IHistogram1D mod2ResY_Bottom = aida.histogram1D("Layer 2 Residual Y(mm) Bottom", 25, -1, 1);
-
-        IHistogram1D mod3ResX_Bottom = aida.histogram1D("Layer 3 Residual X(mm) Bottom", 25, -2.5, 2.5);
-        IHistogram1D mod3ResY_Bottom = aida.histogram1D("Layer 3 Residual Y(mm) Bottom", 25, -1.5, 1.5);
-
-        IHistogram1D mod4ResX_Bottom = aida.histogram1D("Layer 4 Residual X(mm) Bottom", 25, -3.0, 3.0);
-        IHistogram1D mod4ResY_Bottom = aida.histogram1D("Layer 4 Residual Y(mm) Bottom", 25, -2, 2);
-
-        IHistogram1D mod5ResX_Bottom = aida.histogram1D("Layer 5 Residual X(mm) Bottom", 25, -4, 4);
-        IHistogram1D mod5ResY_Bottom = aida.histogram1D("Layer 5 Residual Y(mm) Bottom", 25, -3, 3);
-
-        IHistogram1D mod6ResX_Bottom = aida.histogram1D("Layer 6 Residual X(mm) Bottom", 25, -5, 5);
-        IHistogram1D mod6ResY_Bottom = aida.histogram1D("Layer 6 Residual Y(mm) Bottom", 25, -3, 3);
-
-        plotter3_2.region(0).plot(mod1ResX_Bottom);
-        plotter3_2.region(2).plot(mod2ResX_Bottom);
-        plotter3_2.region(4).plot(mod3ResX_Bottom);
-        plotter3_2.region(6).plot(mod4ResX_Bottom);
-        plotter3_2.region(8).plot(mod5ResX_Bottom);
-        plotter3_2.region(10).plot(mod6ResX_Bottom);
-
-        plotter3_2.region(1).plot(mod1ResY_Bottom);
-        plotter3_2.region(3).plot(mod2ResY_Bottom);
-        plotter3_2.region(5).plot(mod3ResY_Bottom);
-        plotter3_2.region(7).plot(mod4ResY_Bottom);
-        plotter3_2.region(9).plot(mod5ResY_Bottom);
-        plotter3_2.region(11).plot(mod6ResY_Bottom);
-        
-        if(showPlots) plotter3_2.show();
-
-        plotter4 = fac.createPlotterFactory().create("HPS Track and ECal Plots");
-        plotter4.setTitle("Track and ECal Correlations");
-        //plotterFrame.addPlotter(plotter4);
-        IPlotterStyle style4 = plotter4.style();
-        style4.setParameter("hist2DStyle", "colorMap");
-        style4.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style4.dataStyle().fillStyle().setColor("yellow");
-        style4.dataStyle().errorBarStyle().setVisible(false);
-        plotter4.createRegions(2, 3);
-
-        IHistogram2D eVsP = aida.histogram2D("Energy Vs Momentum", 50, 0, 0.50, 50, 0, 1.5);
-        IHistogram1D eOverP = aida.histogram1D("Energy Over Momentum", 50, 0, 2);
-
-        IHistogram1D distX = aida.histogram1D("deltaX", 50, -100, 100);
-        IHistogram1D distY = aida.histogram1D("deltaY", 50, -40, 40);
-
-        IHistogram2D xEcalVsTrk = aida.histogram2D("X ECal Vs Track", 100, -400, 400, 100, -400, 400);
-        IHistogram2D yEcalVsTrk = aida.histogram2D("Y ECal Vs Track", 100, -100, 100, 100, -100, 100);
-
-        plotter4.region(0).plot(eVsP);
-        plotter4.region(3).plot(eOverP);
-        plotter4.region(1).plot(distX);
-        plotter4.region(4).plot(distY);
-        plotter4.region(2).plot(xEcalVsTrk);
-        plotter4.region(5).plot(yEcalVsTrk);
-
-        if(showPlots) plotter4.show();
-
-        //   ******************************************************************
-        top2 = fac.createPlotterFactory().create("Top ECal Plots");
-        top2.setTitle("Top ECal Correlations");
-        IPlotterStyle stop2 = top2.style();
-        stop2.dataStyle().fillStyle().setColor("green");
-        stop2.dataStyle().errorBarStyle().setVisible(false);
-        stop2.setParameter("hist2DStyle", "colorMap");
-        stop2.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        top2.createRegions(2, 3);
-        //topFrame.addPlotter(top2);
-
-        IHistogram2D topeVsP = aida.histogram2D("Top Energy Vs Momentum", 50, 0, 0.500, 50, 0, 1.5);
-        IHistogram1D topeOverP = aida.histogram1D("Top Energy Over Momentum", 50, 0, 2);
-
-        IHistogram1D topdistX = aida.histogram1D("Top deltaX", 50, -100, 100);
-        IHistogram1D topdistY = aida.histogram1D("Top deltaY", 50, -40, 40);
-
-        IHistogram2D topxEcalVsTrk = aida.histogram2D("Top X ECal Vs Track", 100, -400, 400, 100, -100, 100);
-        IHistogram2D topyEcalVsTrk = aida.histogram2D("Top Y ECal Vs Track", 100, 0, 100, 100, 0, 100);
-
-        top2.region(0).plot(topeVsP);
-        top2.region(3).plot(topeOverP);
-        top2.region(1).plot(topdistX);
-        top2.region(4).plot(topdistY);
-        top2.region(2).plot(topxEcalVsTrk);
-        top2.region(5).plot(topyEcalVsTrk);
-
-        if(showPlots) top2.show();
-        
-        bot2 = fac.createPlotterFactory().create("Bottom ECal Plots");
-        bot2.setTitle("Bottom ECal Correlations");
-        IPlotterStyle sbot2 = bot2.style();
-        sbot2.dataStyle().fillStyle().setColor("green");
-        sbot2.dataStyle().errorBarStyle().setVisible(false);
-        sbot2.setParameter("hist2DStyle", "colorMap");
-        sbot2.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        bot2.createRegions(2, 3);
-        //bottomFrame.addPlotter(bot2);
-
-        IHistogram2D BottomeVsP = aida.histogram2D("Bottom Energy Vs Momentum", 50, 0, 0.500, 50, 0, 1.5);
-        IHistogram1D BottomeOverP = aida.histogram1D("Bottom Energy Over Momentum", 50, 0, 2);
-
-        IHistogram1D BottomdistX = aida.histogram1D("Bottom deltaX", 50, -100, 100);
-        IHistogram1D BottomdistY = aida.histogram1D("Bottom deltaY", 50, -40, 40);
-
-        IHistogram2D BottomxEcalVsTrk = aida.histogram2D("Bottom X ECal Vs Track", 100, -400, 400, 100, -400, 400);
-        IHistogram2D BottomyEcalVsTrk = aida.histogram2D("Bottom Y ECal Vs Track", 100, -100, 0, 100, -100, 0);
-
-        bot2.region(0).plot(BottomeVsP);
-        bot2.region(3).plot(BottomeOverP);
-        bot2.region(1).plot(BottomdistX);
-        bot2.region(4).plot(BottomdistY);
-        bot2.region(2).plot(BottomxEcalVsTrk);
-        bot2.region(5).plot(BottomyEcalVsTrk);
-
-        if(showPlots) bot2.show();
-        
-        
-        //   ******************************************************************
-        top3 = fac.createPlotterFactory().create("Top ECal Plots");
-        top3.setTitle("Top ECal More Correlations");
-        IPlotterStyle stop3 = top3.style();
-        stop3.dataStyle().fillStyle().setColor("green");
-        stop3.dataStyle().errorBarStyle().setVisible(false);
-        stop3.setParameter("hist2DStyle", "colorMap");
-        stop3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        top3.createRegions(1, 2);
-        //topFrame.addPlotter(top3);
-
-        IHistogram2D topdistXvsX = aida.histogram2D("Top deltaX vs X", 51, -400, 400, 25, -100, 100);
-        IHistogram2D topdistYvsY = aida.histogram2D("Top deltaY vs Y", 51, 0, 100, 25, -40, 40);
-
-        top3.region(0).plot(topdistXvsX);
-        top3.region(1).plot(topdistYvsY);
-
-        if(showPlots) top3.show();
-        
-        bot3 = fac.createPlotterFactory().create("Bottom ECal Plots");
-        bot3.setTitle("Bottom ECal More Correlations");
-        IPlotterStyle sbot3 = bot3.style();
-        sbot3.dataStyle().fillStyle().setColor("green");
-        sbot3.dataStyle().errorBarStyle().setVisible(false);
-        sbot3.setParameter("hist2DStyle", "colorMap");
-        sbot3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        bot3.createRegions(1, 2);
-        //bottomFrame.addPlotter(bot3);
-
-        IHistogram2D botdistXvsX = aida.histogram2D("Bottom deltaX vs X", 51, -400, 400, 25, -100, 100);
-        IHistogram2D botdistYvsY = aida.histogram2D("Bottom deltaY vs Y", 51, -100, 0, 25, -40, 40);
-
-        bot3.region(0).plot(botdistXvsX);
-        bot3.region(1).plot(botdistYvsY);
-
-        if(showPlots) bot3.show();
-        
-        //   ******************************************************************
-        top4 = fac.createPlotterFactory().create("Track Matching Plots");
-        top4.setTitle("Track Matching Plots");
-        IPlotterStyle stop4 = top4.style();
-        stop4.dataStyle().fillStyle().setColor("green");
-        stop4.dataStyle().errorBarStyle().setVisible(false);
-        stop4.setParameter("hist2DStyle", "colorMap");
-        stop4.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        top4.createRegions(2, 3);
-        //topFrame.addPlotter(top4);
-
-        IHistogram1D trackmatchN = aida.histogram1D("Tracks matched", 3, 0, 3);
-        IHistogram1D toptrackmatchN = aida.histogram1D("Tracks matched Top", 3, 0, 3);
-        IHistogram1D bottrackmatchN = aida.histogram1D("Tracks matched Bottom", 3, 0, 3);
-        IHistogram1D trackmatchN2 = aida.histogram1D("Tracks matched (Pz>0.8)", 3, 0, 3);
-        IHistogram1D toptrackmatchN2 = aida.histogram1D("Tracks matched Top (Pz>0.8)", 3, 0, 3);
-        IHistogram1D bottrackmatchN2 = aida.histogram1D("Tracks matched Bottom (Pz>0.8)", 3, 0, 3);
-        
-        top4.region(0).plot(trackmatchN);
-        top4.region(1).plot(toptrackmatchN);
-        top4.region(2).plot(bottrackmatchN);
-        top4.region(3).plot(trackmatchN2);
-        top4.region(4).plot(toptrackmatchN2);
-        top4.region(5).plot(bottrackmatchN2);
-
-        if(showPlots) top4.show();
-        
-        //   ******************************************************************
-        top44 = fac.createPlotterFactory().create("e+e- Plots");
-        top44.setTitle("e+e- Plots");
-        IPlotterStyle stop44 = top44.style();
-        stop44.dataStyle().fillStyle().setColor("green");
-        stop44.dataStyle().errorBarStyle().setVisible(false);
-        stop44.setParameter("hist2DStyle", "colorMap");
-        stop44.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        top44.createRegions(2,4);
-        //topFrame.addPlotter(top44);
-
-        IHistogram2D trackPCorr = aida.histogram2D("p(e-) vs p(e+) max", 25, 0, 1.2, 25, 0, 1.2);
-        IHistogram1D ne = aida.histogram1D("n(e-)", 3, 0, 3);
-        IHistogram1D np = aida.histogram1D("n(e+)", 3, 0, 3);
-        IHistogram1D pem = aida.histogram1D("p(e-) max", 25, 0, 1.5);
-        IHistogram1D pe = aida.histogram1D("p(e-)", 25, 0, 1.5);
-        IHistogram1D ppm = aida.histogram1D("p(e+) max", 25, 0, 1.5);
-        IHistogram1D pp = aida.histogram1D("p(e+)", 25, 0, 1.5);
-        
-        top44.region(0).plot(trackPCorr);
-        top44.region(1).plot(ne);
-        top44.region(2).plot(np);
-        top44.region(3).plot(pe);
-        top44.region(4).plot(pp);
-        top44.region(5).plot(pem);
-        top44.region(6).plot(ppm);
-        
-        if(showPlots) top44.show();
-        
-        
-        
-//   ******************************************************************
-        plotter5 = fac.createPlotterFactory().create("HPS Hit Positions");
-        plotter5.setTitle("Hit Positions:  Top");
-        //plotterFrame.addPlotter(plotter5);
-        IPlotterStyle style5 = plotter5.style();
-        style5.setParameter("hist2DStyle", "colorMap");
-        style5.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style5.dataStyle().fillStyle().setColor("yellow");
-        style5.dataStyle().errorBarStyle().setVisible(false);
-        plotter5.createRegions(1, 2);
-
-        IHistogram2D l1Pos = aida.histogram2D("Layer 1 HTH Position:  Top", 50, -55, 55, 55, -25, 25);
-        IHistogram2D l7Pos = aida.histogram2D("Layer 7 HTH Position:  Top", 50, -55, 55, 55, -25, 25);
-
-        plotter5.region(0).plot(l1Pos);
-        plotter5.region(1).plot(l7Pos);
-        
-        if(showPlots) plotter5.show();
-        
-        plotter5_1 = fac.createPlotterFactory().create("HPS Hit Positions");
-        plotter5_1.setTitle("Hit Positions:  Bottom");
-        //plotterFrame.addPlotter(plotter5_1);
-        IPlotterStyle style5_1 = plotter5_1.style();
-        style5_1.setParameter("hist2DStyle", "colorMap");
-        style5_1.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style5_1.dataStyle().fillStyle().setColor("yellow");
-        style5_1.dataStyle().errorBarStyle().setVisible(false);
-        plotter5_1.createRegions(1, 2);
-
-        
-        IHistogram2D l1PosBot = aida.histogram2D("Layer 1 HTH Position:  Bottom", 50, -55, 55, 55, -25, 25);
-        IHistogram2D l7PosBot = aida.histogram2D("Layer 7 HTH Position:  Bottom", 50, -55, 55, 55, -25, 25);
-        plotter5_1.region(0).plot(l1PosBot);
-        plotter5_1.region(1).plot(l7PosBot);
-
-        if(showPlots) plotter5_1.show();
-
-        plotter55 = fac.createPlotterFactory().create("HPS Hit Positions");
-        plotter55.setTitle("Helical Track Hits");
-        //plotterFrame.addPlotter(plotter55);
-        IPlotterStyle style55 = plotter55.style();
-        style55.dataStyle().fillStyle().setColor("Green");
-        style55.dataStyle().errorBarStyle().setVisible(false);
-        style55.dataStyle().markerStyle().setSize(20);
-        plotter55.createRegions(1, 2);
-
-        IProfile avgLayersTopPlot = aida.profile1D("Number of Stereo Hits per layer in Top Half", 13, 0, 13);
-        IProfile avgLayersBottomPlot = aida.profile1D("Number of Stereo Hits per layer in Bottom Half", 13, 0, 13);
-
-        plotter55.region(0).plot(avgLayersTopPlot);
-        plotter55.region(1).plot(avgLayersBottomPlot);
-
-        if(showPlots) plotter55.show();
-
-        plotter6 = fac.createPlotterFactory().create("HPS ECAL Hit Positions");
-        plotter6.setTitle("ECAL Positions");
-        //plotterFrame.addPlotter(plotter6);
-        IPlotterStyle style6 = plotter6.style();
-        style6.setParameter("hist2DStyle", "colorMap");
-        style6.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style6.dataStyle().fillStyle().setColor("yellow");
-        style6.dataStyle().errorBarStyle().setVisible(false);
-        plotter6.createRegions(4, 2);
-
-        IHistogram2D topECal = aida.histogram2D("Top ECal Cluster Position", 50, -400, 400, 10, 0, 100);
-        IHistogram2D botECal = aida.histogram2D("Bottom ECal Cluster Position", 50, -400, 400, 10, -100, 0);
-        IHistogram2D topECal1 = aida.histogram2D("Top ECal Cluster Position (>0 tracks)", 50, -400, 400, 10, 0, 100);
-        IHistogram2D botECal1 = aida.histogram2D("Bottom ECal Cluster Position (>0 tracks)", 50, -400, 400, 10, -100, 0);
-        IHistogram2D topECal2 = aida.histogram2D("Top ECal Cluster Position (E>0.1,>0 tracks)", 50, -400, 400, 10, 0, 100);
-        IHistogram2D botECal2 = aida.histogram2D("Bottom ECal Cluster Position (E>0.1,>0 tracks)", 50, -400, 400, 10, -100, 0);
-        IHistogram2D topECal3 = aida.histogram2D("Top ECal Cluster Position w_E (E>0.1,>0 tracks)", 50, -400, 400, 10, 0, 100);
-        IHistogram2D botECal3 = aida.histogram2D("Bottom ECal Cluster Position w_E (E>0.1,>0 tracks)", 50, -400, 400, 10, -100, 0);
-
-        plotter6.region(0).plot(topECal);
-        plotter6.region(1).plot(botECal);
-        plotter6.region(2).plot(topECal1);
-        plotter6.region(3).plot(botECal1);
-        plotter6.region(4).plot(topECal2);
-        plotter6.region(5).plot(botECal2);
-        plotter6.region(6).plot(topECal3);
-        plotter6.region(7).plot(botECal3);
-        
-        if(showPlots) plotter6.show();
-        
-        
-        plotter66 = fac.createPlotterFactory().create("HPS ECAL Basic Plots");
-        plotter66.setTitle("ECAL Basic Plots");
-        //plotterFrame.addPlotter(plotter6);
-        IPlotterStyle style66 = plotter66.style();
-        style66.dataStyle().fillStyle().setColor("yellow");
-        style66.dataStyle().errorBarStyle().setVisible(false);
-        plotter66.createRegions(2, 2);
-
-        IHistogram1D topECalE = aida.histogram1D("Top ECal Cluster Energy", 50, 0, 2);
-        IHistogram1D botECalE = aida.histogram1D("Bottom ECal Cluster Energy", 50, 0, 2);
-        IHistogram1D topECalN = aida.histogram1D("Number of Clusters Top", 6, 0, 6);
-        IHistogram1D botECalN = aida.histogram1D("Number of Clusters Bot", 6, 0, 6);
-        
-        plotter66.region(0).plot(topECalE);
-        plotter66.region(1).plot(botECalE);
-        plotter66.region(2).plot(botECalN);
-        plotter66.region(3).plot(topECalN);
-        
-        if(showPlots) plotter66.show();
-        
-        
-        plotter7 = fac.createPlotterFactory().create("HPS ECAL Hit Positions");
-        plotter7.setTitle("Basic Misc Stuff");
-        //plotterFrame.addPlotter(plotter7);
-        IPlotterStyle style7 = plotter7.style();
-        style7.setParameter("hist2DStyle", "colorMap");
-        style7.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style7.dataStyle().fillStyle().setColor("yellow");
-        style7.dataStyle().errorBarStyle().setVisible(false);
-        plotter7.createRegions(2, 2);
-
-        IHistogram2D quadrants = aida.histogram2D("Charge vs Slope", 2, -1, 1, 2, -1, 1);
-        plotter7.region(0).plot(quadrants);
-        
-        if(showPlots) plotter7.show();
-        
-        plotter8 = fac.createPlotterFactory().create("HPS Strip Hit From Stereo Multiplicity");
-        plotter8.setTitle("Strip Hit Multiplicity");
-        //plotterFrame.addPlotter(plotter8);
-        IPlotterStyle style8 = plotter8.style();
-        style8.dataStyle().fillStyle().setColor("yellow");
-        style8.dataStyle().errorBarStyle().setVisible(false);
-        plotter8.createRegions(6, 6);
-        i=0;
-        for(SiSensor sensor : sensors) {
-            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits from stereo", 10, 0, 10);
-            plotter8.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter8.show();
-        
-        plotter88 = fac.createPlotterFactory().create("HPS Strip Hit Multiplicity");
-        plotter88.setTitle("Strip Hit Multiplicity");
-        //plotterFrame.addPlotter(plotter88);
-        plotter88.setStyle(style8);
-        plotter88.createRegions(6, 6);
-        i=0;
-        for(SiSensor sensor : sensors) {
-            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits", 10, 0, 10);
-            plotter88.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter88.show();
-        
-        
-        plotter9 = fac.createPlotterFactory().create("HPS Strip Hit On Track Multiplicity");
-        plotter9.setTitle("Strip Hit Multiplicity");
-        //plotterFrame.addPlotter(plotter9);
-        IPlotterStyle style9 = plotter9.style();
-        style9.dataStyle().fillStyle().setColor("yellow");
-        style9.dataStyle().errorBarStyle().setVisible(false);
-        plotter9.createRegions(6, 6);
-        i=0;
-        for(SiSensor sensor : sensors) {
-            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits on track", 3, 0, 3);
-            plotter9.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter9.show();
-        
-        
-        plotter888 = fac.createPlotterFactory().create("HPS Strip Hit Isolation");
-        plotter888.setTitle("Strip Hit Isolation");
-        //plotterFrame.addPlotter(plotter88);
-        plotter888.setStyle(style8);
-        plotter888.createRegions(6, 6);
-        i=0;
-        for(SiSensor sensor : sensors) {
-            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits iso", 50, 0, 5);
-            plotter888.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter888.show();
-        
-        plotter8888 = fac.createPlotterFactory().create("HPS Strip Hit On Track Isolation");
-        plotter8888.setTitle("Strip Hit On Track Isolation");
-        //plotterFrame.addPlotter(plotter88);
-        plotter8888.setStyle(style8);
-        plotter8888.createRegions(6, 6);
-        i=0;
-        for(SiSensor sensor : sensors) {
-            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits iso on track", 50, 0, 5);
-            plotter8888.region(i).plot(resX);
-            i++;
-        }
-
-        if(showPlots) plotter8888.show();
-
-
+        
+        setupPlots();
     }
+    
+    
+    
+    
+    
+    
 
     public TrackingReconstructionPlots() {
         LOGGER.setLevel(Level.WARNING);
@@ -1170,13 +351,8 @@
 
             int isTop = -1;
             if (trk.getTrackerHits().get(0).getPosition()[2] > 0) {
-                isTop = 0;//make plot look pretty
-            }
-            int charge = trk.getCharge();
-            if (charge > 0) {
-                charge = 0;//make plot look pretty
-            }//            System.out.println("Charge = " + charge + "; isTop = " + isTop);
-            aida.histogram2D("Charge vs Slope").fill(charge, isTop);
+                isTop = 0;
+            }
             if (isTop == 0) {
                 aida.histogram1D("Top Track Momentum (Px)").fill(trk.getTrackStates().get(0).getMomentum()[1]);
                 aida.histogram1D("Top Track Momentum (Py)").fill(trk.getTrackStates().get(0).getMomentum()[2]);
@@ -1304,8 +480,6 @@
                     layersBot[htc.Layer() - 1]++;
                     Hep3Vector sensorPos = ((SiSensor) ((RawTrackerHit) htc.getRawHits().get(0)).getDetectorElement()).getGeometry().getPosition();
                     if (htc.Layer() == 1) {
-//                    System.out.println(sensorPos.toString());
-//                    System.out.println("Hit X = " + x + "; Hit Y = " + y);
                         aida.histogram2D("Layer 1 HTH Position:  Bottom").fill(x - sensorPos.x(), y - sensorPos.y());
                     }
                     if (htc.Layer() == 7) {
@@ -1319,7 +493,7 @@
                         double clusterSum = 0;
                         double clusterT0 = 0;
                         int nHitsCluster = 0;
-                                
+                        
                         for (RawTrackerHit rawHit : (List<RawTrackerHit>) hts.rawhits()) {
                             if(event.hasCollection(LCRelation.class, "SVTFittedRawTrackerHits")) {
                                 List<LCRelation> fittedHits = event.get(LCRelation.class, "SVTFittedRawTrackerHits");
@@ -1361,7 +535,6 @@
             }
             
             for(Map.Entry<HpsSiSensor,Integer> sensor : stripHitsOnTrack.entrySet()) {
-                aida.histogram1D(sensor.getKey().getName() + " strip hits on track").fill(sensor.getValue());
                 aida.histogram1D(sensor.getKey().getName() + " strip hits iso on track").fill(stripHitsIsoOnTrack.get(sensor.getKey()));
             }
             
@@ -1645,6 +818,813 @@
 
 
     
+    
+private void setupPlots() {
+        
+        
+        IAnalysisFactory fac = aida.analysisFactory();
+        plotter = fac.createPlotterFactory().create("HPS Tracking Plots");
+        plotter.setTitle("Momentum");
+        IPlotterStyle style = plotter.style();
+        style.dataStyle().fillStyle().setColor("yellow");
+        style.dataStyle().errorBarStyle().setVisible(false);
+        plotter.createRegions(2, 2);
+        //plotterFrame.addPlotter(plotter);
+
+        trkPx = aida.histogram1D("Track Momentum (Px)", 25, -0.25, 0.25);
+        IHistogram1D trkPy = aida.histogram1D("Track Momentum (Py)", 25, -0.5, 0.5);
+        IHistogram1D trkPz = aida.histogram1D("Track Momentum (Pz)", 25, 0, 1.5);
+        IHistogram1D trkChi2 = aida.histogram1D("Track Chi2", 25, 0, 25.0);
+
+        plotter.region(0).plot(trkPx);
+        plotter.region(1).plot(trkPy);
+        plotter.region(2).plot(trkPz);
+        plotter.region(3).plot(trkChi2);
+
+        if(showPlots) plotter.show();
+
+//   ******************************************************************
+        top1 = fac.createPlotterFactory().create("Top Tracking Plots");
+        top1.setTitle("Top Momentum");
+        IPlotterStyle stop1 = top1.style();
+        stop1.dataStyle().fillStyle().setColor("green");
+        stop1.dataStyle().errorBarStyle().setVisible(false);
+        top1.createRegions(2, 2);
+        //topFrame.addPlotter(top1);
+
+        IHistogram1D toptrkPx = aida.histogram1D("Top Track Momentum (Px)", 25, -0.25, 0.25);
+        IHistogram1D toptrkPy = aida.histogram1D("Top Track Momentum (Py)", 25, -0.5, 0.5);
+        IHistogram1D toptrkPz = aida.histogram1D("Top Track Momentum (Pz)", 25, 0, 1.5);
+        IHistogram1D toptrkChi2 = aida.histogram1D("Top Track Chi2", 25, 0, 25.0);
+
+        top1.region(0).plot(toptrkPx);
+        top1.region(1).plot(toptrkPy);
+        top1.region(2).plot(toptrkPz);
+        top1.region(3).plot(toptrkChi2);
+
+        if(showPlots) top1.show();
+
+        bot1 = fac.createPlotterFactory().create("Bottom Tracking Plots");
+        bot1.setTitle("Bottom Momentum");
+        IPlotterStyle sbot1 = bot1.style();
+        sbot1.dataStyle().fillStyle().setColor("blue");
+        sbot1.dataStyle().errorBarStyle().setVisible(false);
+        bot1.createRegions(2, 2);
+        //bottomFrame.addPlotter(bot1);
+
+        IHistogram1D bottrkPx = aida.histogram1D("Bottom Track Momentum (Px)", 25, -0.25, 0.25);
+        IHistogram1D bottrkPy = aida.histogram1D("Bottom Track Momentum (Py)", 25, -0.5, 0.5);
+        IHistogram1D bottrkPz = aida.histogram1D("Bottom Track Momentum (Pz)", 25, 0, 1.5);
+        IHistogram1D bottrkChi2 = aida.histogram1D("Bottom Track Chi2", 25, 0, 25.0);
+
+        bot1.region(0).plot(bottrkPx);
+        bot1.region(1).plot(bottrkPy);
+        bot1.region(2).plot(bottrkPz);
+        bot1.region(3).plot(bottrkChi2);
+
+        if(showPlots) bot1.show();
+
+//   ******************************************************************
+        IHistogram1D trkd0 = aida.histogram1D("d0 ", 25, -10.0, 10.0);
+        IHistogram1D trkphi = aida.histogram1D("sinphi ", 25, -0.2, 0.2);
+        IHistogram1D trkomega = aida.histogram1D("omega ", 25, -0.0025, 0.0025);
+        IHistogram1D trklam = aida.histogram1D("tan(lambda) ", 25, -0.1, 0.1);
+        IHistogram1D trkz0 = aida.histogram1D("z0 ", 25, -6.0, 6.0);
+
+        plotter22 = fac.createPlotterFactory().create("HPS Track Params");
+        plotter22.setTitle("Track parameters");
+        //plotterFrame.addPlotter(plotter22);
+        IPlotterStyle style22 = plotter22.style();
+        style22.dataStyle().fillStyle().setColor("yellow");
+        style22.dataStyle().errorBarStyle().setVisible(false);
+        plotter22.createRegions(2, 3);
+        plotter22.region(0).plot(trkd0);
+        plotter22.region(1).plot(trkphi);
+        plotter22.region(2).plot(trkomega);
+        plotter22.region(3).plot(trklam);
+        plotter22.region(4).plot(trkz0);
+        
+        if(showPlots) plotter22.show();
+
+ //   ******************************************************************
+
+        
+         trkd0 = aida.histogram1D("d0 Top", 25, -10.0, 10.0);
+         trkphi = aida.histogram1D("sinphi Top", 25, -0.2, 0.2);
+         trkomega = aida.histogram1D("omega Top", 25, -0.0025, 0.0025);
+         trklam = aida.histogram1D("tan(lambda) Top", 25, -0.1, 0.1);
+         trkz0 = aida.histogram1D("z0 Top", 25, -6.0, 6.0);
+
+        plotter2221 = fac.createPlotterFactory().create("HPS Track Params");
+        plotter2221.setTitle("Track parameters");
+        //plotterFrame.addPlotter(plotter22);
+        IPlotterStyle style2221 = plotter2221.style();
+        style2221.dataStyle().fillStyle().setColor("yellow");
+        style2221.dataStyle().errorBarStyle().setVisible(false);
+        plotter2221.createRegions(2, 3);
+        plotter2221.region(0).plot(trkd0);
+        plotter2221.region(1).plot(trkphi);
+        plotter2221.region(2).plot(trkomega);
+        plotter2221.region(3).plot(trklam);
+        plotter2221.region(4).plot(trkz0);
+        
+        if(showPlots) plotter2221.show();
+        
+        
+   //   ******************************************************************
+
+        
+        trkd0 = aida.histogram1D("d0 Bottom", 25, -10.0, 10.0);
+        trkphi = aida.histogram1D("sinphi Bottom", 25, -0.2, 0.2);
+        trkomega = aida.histogram1D("omega Bottom", 25, -0.0025, 0.0025);
+        trklam = aida.histogram1D("tan(lambda) Bottom", 25, -0.1, 0.1);
+        trkz0 = aida.histogram1D("z0 Bottom", 25, -6.0, 6.0);
+
+       plotter2222 = fac.createPlotterFactory().create("HPS Track Params");
+       plotter2222.setTitle("Track parameters");
+       //plotterFrame.addPlotter(plotter22);
+       IPlotterStyle style2222 = plotter2222.style();
+       style2222.dataStyle().fillStyle().setColor("yellow");
+       style2222.dataStyle().errorBarStyle().setVisible(false);
+       plotter2222.createRegions(2, 3);
+       plotter2222.region(0).plot(trkd0);
+       plotter2222.region(1).plot(trkphi);
+       plotter2222.region(2).plot(trkomega);
+       plotter2222.region(3).plot(trklam);
+       plotter2222.region(4).plot(trkz0);
+       
+       if(showPlots) plotter2222.show();
+        
+        
+        
+   //   ******************************************************************
+
+        
+        plotter2 = fac.createPlotterFactory().create("HPS Tracking Plots");
+        plotter2.setTitle("Track extrapolation");
+        //plotterFrame.addPlotter(plotter2);
+        IPlotterStyle style2 = plotter2.style();
+        style2.dataStyle().fillStyle().setColor("yellow");
+        style2.dataStyle().errorBarStyle().setVisible(false);
+        plotter2.createRegions(2, 4);
+        IHistogram1D xAtConverter = aida.histogram1D("X (mm) @ Z=-60cm", 50, -50, 50);
+        IHistogram1D yAtConverter = aida.histogram1D("Y (mm) @ Z=-60cm", 50, -20, 20);
+        IHistogram1D xAtColl = aida.histogram1D("X (mm) @ Z=-150cm", 50, -200, 200);
+        IHistogram1D yAtColl = aida.histogram1D("Y (mm) @ Z=-150cm", 50, -200, 200);
+        IHistogram1D xAtEcal = aida.histogram1D("X (mm) @ ECAL", 50, -500, 500);
+        IHistogram1D yAtEcal = aida.histogram1D("Y (mm) @ ECAL", 50, -100, 100);
+        IHistogram1D xAtEcal2 = aida.histogram1D("X (mm) @ ECAL (Pz>1)", 50, -500, 500);
+        IHistogram1D yAtEcal2 = aida.histogram1D("Y (mm) @ ECAL (Pz>1)", 50, -100, 100);
+
+        plotter2.region(0).plot(xAtConverter);
+        plotter2.region(4).plot(yAtConverter);
+        plotter2.region(1).plot(xAtColl);
+        plotter2.region(5).plot(yAtColl);
+        plotter2.region(2).plot(xAtEcal);
+        plotter2.region(6).plot(yAtEcal);
+        plotter2.region(3).plot(xAtEcal2);
+        plotter2.region(7).plot(yAtEcal2);
+        
+        if(showPlots) plotter2.show();
+
+   //   ******************************************************************
+        
+        plotter222 = fac.createPlotterFactory().create("HPS Tracking Plots");
+        plotter222.setTitle("HPS Tracking Plots");
+        //plotterFrame.addPlotter(plotter222);
+        IPlotterStyle style222 = plotter222.style();
+        style222.dataStyle().fillStyle().setColor("yellow");
+        style222.dataStyle().errorBarStyle().setVisible(false);
+        plotter222.createRegions(2, 2);
+        
+        IHistogram1D nHits = aida.histogram1D("Hits per Track", 4, 3, 7);
+        nTracks = aida.histogram1D("Tracks per Event", 3, 0, 3);
+        IHistogram1D nHitsCluster = aida.histogram1D("Hits in Cluster (HitOnTrack)", 4, 0, 4);
+
+       
+        plotter222.region(0).plot(nHits);
+        plotter222.region(1).plot(nTracks);
+        plotter222.region(2).plot(nHitsCluster);
+        
+        if(showPlots) plotter222.show();
+   
+        
+   //   ******************************************************************
+        
+        plotter22299 = fac.createPlotterFactory().create("HPS Tracking Plots Top");
+        plotter22299.setTitle("HPS Tracking Plots Top");
+        //plotterFrame.addPlotter(plotter22299);
+        IPlotterStyle style22299 = plotter22299.style();
+        style22299.dataStyle().fillStyle().setColor("yellow");
+        style22299.dataStyle().errorBarStyle().setVisible(false);
+        plotter22299.createRegions(2, 2);
+        
+        IHistogram1D nHitsTop = aida.histogram1D("Hits per Track Top", 4, 3, 7);
+        nTracksTop = aida.histogram1D("Tracks per Event Top", 3, 0, 3);
+        IHistogram1D nHitsClusterTop = aida.histogram1D("Hits in Cluster (HitOnTrack) Top", 4, 0, 4);
+
+       
+        plotter22299.region(0).plot(nHitsTop);
+        plotter22299.region(1).plot(nTracksTop);
+        plotter22299.region(2).plot(nHitsClusterTop);
+        
+        if(showPlots) plotter22299.show();
+   
+//   ******************************************************************
+        
+        plotter22298 = fac.createPlotterFactory().create("HPS Tracking Plots Bottom");
+        plotter22298.setTitle("HPS Tracking Plots Bottom");
+        //plotterFrame.addPlotter(plotter22298);
+        IPlotterStyle style22298 = plotter22298.style();
+        style22298.dataStyle().fillStyle().setColor("yellow");
+        style22298.dataStyle().errorBarStyle().setVisible(false);
+        plotter22298.createRegions(2, 2);
+        
+        IHistogram1D nHitsBot = aida.histogram1D("Hits per Track Bot", 4, 3, 7);
+        nTracksBot = aida.histogram1D("Tracks per Event Bot", 3, 0, 3);
+        IHistogram1D nHitsClusterBot = aida.histogram1D("Hits in Cluster (HitOnTrack) Bot", 4, 0, 4);
+
+       
+        plotter22298.region(0).plot(nHitsBot);
+        plotter22298.region(1).plot(nTracksBot);
+        plotter22298.region(2).plot(nHitsClusterBot);
+        
+        if(showPlots) plotter22298.show();
+   
+        
+        //   ******************************************************************
+        
+        
+        plotter2223 = fac.createPlotterFactory().create("Cluster Amp Plots");
+        plotter2223.setTitle("Other");
+        //plotterFrame.addPlotter(plotter222);
+        IPlotterStyle style2223 = plotter2223.style();
+        style2223.dataStyle().fillStyle().setColor("yellow");
+        style2223.dataStyle().errorBarStyle().setVisible(false);
+        plotter2223.createRegions(2, 2);
+        
+       
+
+        IHistogram1D amp = aida.histogram1D("Amp (HitOnTrack)", 50, 0, 5000);
+        IHistogram1D ampcl = aida.histogram1D("Cluster Amp (HitOnTrack)", 50, 0, 5000);
+        IHistogram1D amp2 = aida.histogram1D("Amp Pz>0.8 (HitOnTrack)", 50, 0, 5000);
+        IHistogram1D ampcl2 = aida.histogram1D("Cluster Amp Pz>0.8 (HitOnTrack)", 50, 0, 5000);
+      
+        
+        plotter2223.region(0).plot(amp);
+        plotter2223.region(1).plot(amp2);
+        plotter2223.region(2).plot(ampcl);
+        plotter2223.region(3).plot(ampcl2);
+        
+        if(showPlots) plotter2223.show();
+   
+//   ******************************************************************
+        
+        
+        plotter2224 = fac.createPlotterFactory().create("t0 Plots");
+        plotter2224.setTitle("Other");
+        IPlotterStyle style2224 = plotter2224.style();
+        style2224.dataStyle().fillStyle().setColor("yellow");
+        style2224.dataStyle().errorBarStyle().setVisible(false);
+        plotter2224.createRegions(2, 2);
+                
+        IHistogram1D t0 = aida.histogram1D("t0 (HitOnTrack)", 50, -100, 100);
+        IHistogram1D t0cl = aida.histogram1D("Cluster t0 (HitOnTrack)", 50, -100, 100);
+        IHistogram1D t02 = aida.histogram1D("t0 Pz>0.8 (HitOnTrack)", 50, -100, 100);
+        IHistogram1D t0cl2 = aida.histogram1D("Cluster t0 Pz>0.8 (HitOnTrack)", 50, -100, 100);
+        
+        plotter2224.region(0).plot(t0);
+        plotter2224.region(1).plot(t0cl);
+        plotter2224.region(2).plot(t02);
+        plotter2224.region(3).plot(t0cl2);
+
+        if(showPlots) plotter2224.show();
+   
+        
+        //   ******************************************************************
+          
+        plotter3 = fac.createPlotterFactory().create("HPS Layer Residual Plots");
+        plotter3.setTitle("Layer Residuals");
+        //plotterFrame.addPlotter(plotter3);
+        IPlotterStyle style3 = plotter3.style();
+        style3.dataStyle().fillStyle().setColor("yellow");
+        style3.dataStyle().errorBarStyle().setVisible(false);
+        plotter3.createRegions(6, 2);
+
+       
+
+        IHistogram1D mod1ResX = aida.histogram1D("Layer 1 Residual X(mm)", 25, -1, 1);
+        IHistogram1D mod1ResY = aida.histogram1D("Layer 1 Residual Y(mm)", 25, -0.04, 0.04);
+
+        IHistogram1D mod2ResX = aida.histogram1D("Layer 2 Residual X(mm)", 25, -2, 2);
+        IHistogram1D mod2ResY = aida.histogram1D("Layer 2 Residual Y(mm)", 25, -1, 1);
+
+        IHistogram1D mod3ResX = aida.histogram1D("Layer 3 Residual X(mm)", 25, -2.5, 2.5);
+        IHistogram1D mod3ResY = aida.histogram1D("Layer 3 Residual Y(mm)", 25, -1.5, 1.5);
+
+        IHistogram1D mod4ResX = aida.histogram1D("Layer 4 Residual X(mm)", 25, -3.0, 3.0);
+        IHistogram1D mod4ResY = aida.histogram1D("Layer 4 Residual Y(mm)", 25, -2, 2);
+
+        IHistogram1D mod5ResX = aida.histogram1D("Layer 5 Residual X(mm)", 25, -4, 4);
+        IHistogram1D mod5ResY = aida.histogram1D("Layer 5 Residual Y(mm)", 25, -3, 3);
+
+        IHistogram1D mod6ResX = aida.histogram1D("Layer 6 Residual X(mm)", 25, -5, 5);
+        IHistogram1D mod6ResY = aida.histogram1D("Layer 6 Residual Y(mm)", 25, -3, 3);
+
+        plotter3.region(0).plot(mod1ResX);
+        plotter3.region(2).plot(mod2ResX);
+        plotter3.region(4).plot(mod3ResX);
+        plotter3.region(6).plot(mod4ResX);
+        plotter3.region(8).plot(mod5ResX);
+        plotter3.region(10).plot(mod6ResX);
+
+        plotter3.region(1).plot(mod1ResY);
+        plotter3.region(3).plot(mod2ResY);
+        plotter3.region(5).plot(mod3ResY);
+        plotter3.region(7).plot(mod4ResY);
+        plotter3.region(9).plot(mod5ResY);
+        plotter3.region(11).plot(mod6ResY);
+               
+        if(showPlots) plotter3.show();
+        
+        
+        
+        plotter3_11 = fac.createPlotterFactory().create("HPS Strip Residual Plots");
+        plotter3_11.setTitle("Strip Residuals (Top)");
+        //plotterFrame.addPlotter(plotter3_11);
+        IPlotterStyle style3_11 = plotter3_11.style();
+        style3_11.dataStyle().fillStyle().setColor("yellow");
+        style3_11.dataStyle().errorBarStyle().setVisible(false);
+        plotter3_11.createRegions(6, 6);
+        int i=0;
+        for(HpsSiSensor sensor : sensors) {
+            double min = 0.0;
+            double max = 0.0;
+            if(sensor.getName().contains("L1")) {
+                min=-0.04; max=0.04;
+            } else if(sensor.getName().contains("L2")) {
+                min=-1; max=1;
+            } else if(sensor.getName().contains("L3")) {
+                min=-1.5; max=1.5;
+            } else if(sensor.getName().contains("L4")) {
+                min=-3; max=3;
+            } else if(sensor.getName().contains("L5")) {
+                min=-4; max=4;
+            } else if(sensor.getName().contains("L6")) {
+                min=-5; max=5;
+            } else {
+                throw new RuntimeException("Invalid sensor name: " + sensor.getName());
+            }
+           IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip residual (mm)", 50, min, max);
+            plotter3_11.region(i).plot(resX);
+            i++;
+        }
+
+        if(showPlots) plotter3_11.show();
+        
+
+        plotter3_1 = fac.createPlotterFactory().create("HPS Residual Plots (Single hit per layer)");
+        plotter3_1.setTitle("Residuals (Top)");
+        //plotterFrame.addPlotter(plotter3_1);
+        IPlotterStyle style3_1 = plotter3_1.style();
+        style3_1.dataStyle().fillStyle().setColor("yellow");
+        style3_1.dataStyle().errorBarStyle().setVisible(false);
+        plotter3_1.createRegions(6, 2);
+        
+        IHistogram1D mod1ResX_Top = aida.histogram1D("Layer 1 Residual X(mm) Top", 25, -1, 1);
+        IHistogram1D mod1ResY_Top = aida.histogram1D("Layer 1 Residual Y(mm) Top", 25, -0.04, 0.04);
+
+        IHistogram1D mod2ResX_Top = aida.histogram1D("Layer 2 Residual X(mm) Top", 25, -2, 2);
+        IHistogram1D mod2ResY_Top = aida.histogram1D("Layer 2 Residual Y(mm) Top", 25, -1, 1);
+
+        IHistogram1D mod3ResX_Top = aida.histogram1D("Layer 3 Residual X(mm) Top", 25, -2.5, 2.5);
+        IHistogram1D mod3ResY_Top = aida.histogram1D("Layer 3 Residual Y(mm) Top", 25, -1.5, 1.5);
+
+        IHistogram1D mod4ResX_Top = aida.histogram1D("Layer 4 Residual X(mm) Top", 25, -3.0, 3.0);
+        IHistogram1D mod4ResY_Top = aida.histogram1D("Layer 4 Residual Y(mm) Top", 25, -2, 2);
+
+        IHistogram1D mod5ResX_Top = aida.histogram1D("Layer 5 Residual X(mm) Top", 25, -4, 4);
+        IHistogram1D mod5ResY_Top = aida.histogram1D("Layer 5 Residual Y(mm) Top", 25, -3, 3);
+
+        IHistogram1D mod6ResX_Top = aida.histogram1D("Layer 6 Residual X(mm) Top", 25, -5, 5);
+        IHistogram1D mod6ResY_Top = aida.histogram1D("Layer 6 Residual Y(mm) Top", 25, -3, 3);
+
+        
+        plotter3_1.region(0).plot(mod1ResX_Top);
+        plotter3_1.region(2).plot(mod2ResX_Top);
+        plotter3_1.region(4).plot(mod3ResX_Top);
+        plotter3_1.region(6).plot(mod4ResX_Top);
+        plotter3_1.region(8).plot(mod5ResX_Top);
+        plotter3_1.region(10).plot(mod6ResX_Top);
+
+        plotter3_1.region(1).plot(mod1ResY_Top);
+        plotter3_1.region(3).plot(mod2ResY_Top);
+        plotter3_1.region(5).plot(mod3ResY_Top);
+        plotter3_1.region(7).plot(mod4ResY_Top);
+        plotter3_1.region(9).plot(mod5ResY_Top);
+        plotter3_1.region(11).plot(mod6ResY_Top);
+
+        if(showPlots) plotter3_1.show();
+        
+        plotter3_2 = fac.createPlotterFactory().create("HPS Residual Plots (Single strip cluster per layer)");
+        plotter3_2.setTitle("Residuals (Bottom)");
+        //plotterFrame.addPlotter(plotter3_2);
+        IPlotterStyle style3_2 = plotter3_2.style();
+        style3_2.dataStyle().fillStyle().setColor("yellow");
+        style3_2.dataStyle().errorBarStyle().setVisible(false);
+        plotter3_2.createRegions(6, 2);
+
+        IHistogram1D mod1ResX_Bottom = aida.histogram1D("Layer 1 Residual X(mm) Bottom", 25, -1, 1);
+        IHistogram1D mod1ResY_Bottom = aida.histogram1D("Layer 1 Residual Y(mm) Bottom", 25, -0.04, 0.04);
+
+        IHistogram1D mod2ResX_Bottom = aida.histogram1D("Layer 2 Residual X(mm) Bottom", 25, -2, 2);
+        IHistogram1D mod2ResY_Bottom = aida.histogram1D("Layer 2 Residual Y(mm) Bottom", 25, -1, 1);
+
+        IHistogram1D mod3ResX_Bottom = aida.histogram1D("Layer 3 Residual X(mm) Bottom", 25, -2.5, 2.5);
+        IHistogram1D mod3ResY_Bottom = aida.histogram1D("Layer 3 Residual Y(mm) Bottom", 25, -1.5, 1.5);
+
+        IHistogram1D mod4ResX_Bottom = aida.histogram1D("Layer 4 Residual X(mm) Bottom", 25, -3.0, 3.0);
+        IHistogram1D mod4ResY_Bottom = aida.histogram1D("Layer 4 Residual Y(mm) Bottom", 25, -2, 2);
+
+        IHistogram1D mod5ResX_Bottom = aida.histogram1D("Layer 5 Residual X(mm) Bottom", 25, -4, 4);
+        IHistogram1D mod5ResY_Bottom = aida.histogram1D("Layer 5 Residual Y(mm) Bottom", 25, -3, 3);
+
+        IHistogram1D mod6ResX_Bottom = aida.histogram1D("Layer 6 Residual X(mm) Bottom", 25, -5, 5);
+        IHistogram1D mod6ResY_Bottom = aida.histogram1D("Layer 6 Residual Y(mm) Bottom", 25, -3, 3);
+
+        plotter3_2.region(0).plot(mod1ResX_Bottom);
+        plotter3_2.region(2).plot(mod2ResX_Bottom);
+        plotter3_2.region(4).plot(mod3ResX_Bottom);
+        plotter3_2.region(6).plot(mod4ResX_Bottom);
+        plotter3_2.region(8).plot(mod5ResX_Bottom);
+        plotter3_2.region(10).plot(mod6ResX_Bottom);
+
+        plotter3_2.region(1).plot(mod1ResY_Bottom);
+        plotter3_2.region(3).plot(mod2ResY_Bottom);
+        plotter3_2.region(5).plot(mod3ResY_Bottom);
+        plotter3_2.region(7).plot(mod4ResY_Bottom);
+        plotter3_2.region(9).plot(mod5ResY_Bottom);
+        plotter3_2.region(11).plot(mod6ResY_Bottom);
+        
+        if(showPlots) plotter3_2.show();
+
+        plotter4 = fac.createPlotterFactory().create("HPS Track and ECal Plots");
+        plotter4.setTitle("Track and ECal Correlations");
+        //plotterFrame.addPlotter(plotter4);
+        IPlotterStyle style4 = plotter4.style();
+        style4.setParameter("hist2DStyle", "colorMap");
+        style4.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style4.dataStyle().fillStyle().setColor("yellow");
+        style4.dataStyle().errorBarStyle().setVisible(false);
+        plotter4.createRegions(2, 3);
+
+        IHistogram2D eVsP = aida.histogram2D("Energy Vs Momentum", 50, 0, 0.50, 50, 0, 1.5);
+        IHistogram1D eOverP = aida.histogram1D("Energy Over Momentum", 50, 0, 2);
+
+        IHistogram1D distX = aida.histogram1D("deltaX", 50, -100, 100);
+        IHistogram1D distY = aida.histogram1D("deltaY", 50, -40, 40);
+
+        IHistogram2D xEcalVsTrk = aida.histogram2D("X ECal Vs Track", 100, -400, 400, 100, -400, 400);
+        IHistogram2D yEcalVsTrk = aida.histogram2D("Y ECal Vs Track", 100, -100, 100, 100, -100, 100);
+
+        plotter4.region(0).plot(eVsP);
+        plotter4.region(3).plot(eOverP);
+        plotter4.region(1).plot(distX);
+        plotter4.region(4).plot(distY);
+        plotter4.region(2).plot(xEcalVsTrk);
+        plotter4.region(5).plot(yEcalVsTrk);
+
+        if(showPlots) plotter4.show();
+
+        //   ******************************************************************
+        top2 = fac.createPlotterFactory().create("Top ECal Plots");
+        top2.setTitle("Top ECal Correlations");
+        IPlotterStyle stop2 = top2.style();
+        stop2.dataStyle().fillStyle().setColor("green");
+        stop2.dataStyle().errorBarStyle().setVisible(false);
+        stop2.setParameter("hist2DStyle", "colorMap");
+        stop2.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        top2.createRegions(2, 3);
+        //topFrame.addPlotter(top2);
+
+        IHistogram2D topeVsP = aida.histogram2D("Top Energy Vs Momentum", 50, 0, 0.500, 50, 0, 1.5);
+        IHistogram1D topeOverP = aida.histogram1D("Top Energy Over Momentum", 50, 0, 2);
+
+        IHistogram1D topdistX = aida.histogram1D("Top deltaX", 50, -100, 100);
+        IHistogram1D topdistY = aida.histogram1D("Top deltaY", 50, -40, 40);
+
+        IHistogram2D topxEcalVsTrk = aida.histogram2D("Top X ECal Vs Track", 100, -400, 400, 100, -100, 100);
+        IHistogram2D topyEcalVsTrk = aida.histogram2D("Top Y ECal Vs Track", 100, 0, 100, 100, 0, 100);
+
+        top2.region(0).plot(topeVsP);
+        top2.region(3).plot(topeOverP);
+        top2.region(1).plot(topdistX);
+        top2.region(4).plot(topdistY);
+        top2.region(2).plot(topxEcalVsTrk);
+        top2.region(5).plot(topyEcalVsTrk);
+
+        if(showPlots) top2.show();
+        
+        bot2 = fac.createPlotterFactory().create("Bottom ECal Plots");
+        bot2.setTitle("Bottom ECal Correlations");
+        IPlotterStyle sbot2 = bot2.style();
+        sbot2.dataStyle().fillStyle().setColor("green");
+        sbot2.dataStyle().errorBarStyle().setVisible(false);
+        sbot2.setParameter("hist2DStyle", "colorMap");
+        sbot2.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        bot2.createRegions(2, 3);
+        //bottomFrame.addPlotter(bot2);
+
+        IHistogram2D BottomeVsP = aida.histogram2D("Bottom Energy Vs Momentum", 50, 0, 0.500, 50, 0, 1.5);
+        IHistogram1D BottomeOverP = aida.histogram1D("Bottom Energy Over Momentum", 50, 0, 2);
+
+        IHistogram1D BottomdistX = aida.histogram1D("Bottom deltaX", 50, -100, 100);
+        IHistogram1D BottomdistY = aida.histogram1D("Bottom deltaY", 50, -40, 40);
+
+        IHistogram2D BottomxEcalVsTrk = aida.histogram2D("Bottom X ECal Vs Track", 100, -400, 400, 100, -400, 400);
+        IHistogram2D BottomyEcalVsTrk = aida.histogram2D("Bottom Y ECal Vs Track", 100, -100, 0, 100, -100, 0);
+
+        bot2.region(0).plot(BottomeVsP);
+        bot2.region(3).plot(BottomeOverP);
+        bot2.region(1).plot(BottomdistX);
+        bot2.region(4).plot(BottomdistY);
+        bot2.region(2).plot(BottomxEcalVsTrk);
+        bot2.region(5).plot(BottomyEcalVsTrk);
+
+        if(showPlots) bot2.show();
+        
+        
+        //   ******************************************************************
+        top3 = fac.createPlotterFactory().create("Top ECal Plots");
+        top3.setTitle("Top ECal More Correlations");
+        IPlotterStyle stop3 = top3.style();
+        stop3.dataStyle().fillStyle().setColor("green");
+        stop3.dataStyle().errorBarStyle().setVisible(false);
+        stop3.setParameter("hist2DStyle", "colorMap");
+        stop3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        top3.createRegions(1, 2);
+        //topFrame.addPlotter(top3);
+
+        IHistogram2D topdistXvsX = aida.histogram2D("Top deltaX vs X", 51, -400, 400, 25, -100, 100);
+        IHistogram2D topdistYvsY = aida.histogram2D("Top deltaY vs Y", 51, 0, 100, 25, -40, 40);
+
+        top3.region(0).plot(topdistXvsX);
+        top3.region(1).plot(topdistYvsY);
+
+        if(showPlots) top3.show();
+        
+        bot3 = fac.createPlotterFactory().create("Bottom ECal Plots");
+        bot3.setTitle("Bottom ECal More Correlations");
+        IPlotterStyle sbot3 = bot3.style();
+        sbot3.dataStyle().fillStyle().setColor("green");
+        sbot3.dataStyle().errorBarStyle().setVisible(false);
+        sbot3.setParameter("hist2DStyle", "colorMap");
+        sbot3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        bot3.createRegions(1, 2);
+        //bottomFrame.addPlotter(bot3);
+
+        IHistogram2D botdistXvsX = aida.histogram2D("Bottom deltaX vs X", 51, -400, 400, 25, -100, 100);
+        IHistogram2D botdistYvsY = aida.histogram2D("Bottom deltaY vs Y", 51, -100, 0, 25, -40, 40);
+
+        bot3.region(0).plot(botdistXvsX);
+        bot3.region(1).plot(botdistYvsY);
+
+        if(showPlots) bot3.show();
+        
+        //   ******************************************************************
+        top4 = fac.createPlotterFactory().create("Track Matching Plots");
+        top4.setTitle("Track Matching Plots");
+        IPlotterStyle stop4 = top4.style();
+        stop4.dataStyle().fillStyle().setColor("green");
+        stop4.dataStyle().errorBarStyle().setVisible(false);
+        stop4.setParameter("hist2DStyle", "colorMap");
+        stop4.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        top4.createRegions(2, 3);
+        //topFrame.addPlotter(top4);
+
+        IHistogram1D trackmatchN = aida.histogram1D("Tracks matched", 3, 0, 3);
+        IHistogram1D toptrackmatchN = aida.histogram1D("Tracks matched Top", 3, 0, 3);
+        IHistogram1D bottrackmatchN = aida.histogram1D("Tracks matched Bottom", 3, 0, 3);
+        IHistogram1D trackmatchN2 = aida.histogram1D("Tracks matched (Pz>0.8)", 3, 0, 3);
+        IHistogram1D toptrackmatchN2 = aida.histogram1D("Tracks matched Top (Pz>0.8)", 3, 0, 3);
+        IHistogram1D bottrackmatchN2 = aida.histogram1D("Tracks matched Bottom (Pz>0.8)", 3, 0, 3);
+        
+        top4.region(0).plot(trackmatchN);
+        top4.region(1).plot(toptrackmatchN);
+        top4.region(2).plot(bottrackmatchN);
+        top4.region(3).plot(trackmatchN2);
+        top4.region(4).plot(toptrackmatchN2);
+        top4.region(5).plot(bottrackmatchN2);
+
+        if(showPlots) top4.show();
+        
+        //   ******************************************************************
+        top44 = fac.createPlotterFactory().create("e+e- Plots");
+        top44.setTitle("e+e- Plots");
+        IPlotterStyle stop44 = top44.style();
+        stop44.dataStyle().fillStyle().setColor("green");
+        stop44.dataStyle().errorBarStyle().setVisible(false);
+        stop44.setParameter("hist2DStyle", "colorMap");
+        stop44.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        top44.createRegions(2,4);
+        //topFrame.addPlotter(top44);
+
+        IHistogram2D trackPCorr = aida.histogram2D("p(e-) vs p(e+) max", 25, 0, 1.2, 25, 0, 1.2);
+        IHistogram1D ne = aida.histogram1D("n(e-)", 3, 0, 3);
+        IHistogram1D np = aida.histogram1D("n(e+)", 3, 0, 3);
+        IHistogram1D pem = aida.histogram1D("p(e-) max", 25, 0, 1.5);
+        IHistogram1D pe = aida.histogram1D("p(e-)", 25, 0, 1.5);
+        IHistogram1D ppm = aida.histogram1D("p(e+) max", 25, 0, 1.5);
+        IHistogram1D pp = aida.histogram1D("p(e+)", 25, 0, 1.5);
+        
+        top44.region(0).plot(trackPCorr);
+        top44.region(1).plot(ne);
+        top44.region(2).plot(np);
+        top44.region(3).plot(pe);
+        top44.region(4).plot(pp);
+        top44.region(5).plot(pem);
+        top44.region(6).plot(ppm);
+        
+        if(showPlots) top44.show();
+        
+        
+        
+//   ******************************************************************
+        plotter5 = fac.createPlotterFactory().create("HPS Hit Positions");
+        plotter5.setTitle("Hit Positions:  Top");
+        //plotterFrame.addPlotter(plotter5);
+        IPlotterStyle style5 = plotter5.style();
+        style5.setParameter("hist2DStyle", "colorMap");
+        style5.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style5.dataStyle().fillStyle().setColor("yellow");
+        style5.dataStyle().errorBarStyle().setVisible(false);
+        plotter5.createRegions(1, 2);
+
+        IHistogram2D l1Pos = aida.histogram2D("Layer 1 HTH Position:  Top", 50, -55, 55, 55, -25, 25);
+        IHistogram2D l7Pos = aida.histogram2D("Layer 7 HTH Position:  Top", 50, -55, 55, 55, -25, 25);
+
+        plotter5.region(0).plot(l1Pos);
+        plotter5.region(1).plot(l7Pos);
+        
+        if(showPlots) plotter5.show();
+        
+        plotter5_1 = fac.createPlotterFactory().create("HPS Hit Positions");
+        plotter5_1.setTitle("Hit Positions:  Bottom");
+        //plotterFrame.addPlotter(plotter5_1);
+        IPlotterStyle style5_1 = plotter5_1.style();
+        style5_1.setParameter("hist2DStyle", "colorMap");
+        style5_1.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style5_1.dataStyle().fillStyle().setColor("yellow");
+        style5_1.dataStyle().errorBarStyle().setVisible(false);
+        plotter5_1.createRegions(1, 2);
+
+        
+        IHistogram2D l1PosBot = aida.histogram2D("Layer 1 HTH Position:  Bottom", 50, -55, 55, 55, -25, 25);
+        IHistogram2D l7PosBot = aida.histogram2D("Layer 7 HTH Position:  Bottom", 50, -55, 55, 55, -25, 25);
+        plotter5_1.region(0).plot(l1PosBot);
+        plotter5_1.region(1).plot(l7PosBot);
+
+        if(showPlots) plotter5_1.show();
+
+        plotter55 = fac.createPlotterFactory().create("HPS Hit Positions");
+        plotter55.setTitle("Helical Track Hits");
+        //plotterFrame.addPlotter(plotter55);
+        IPlotterStyle style55 = plotter55.style();
+        style55.dataStyle().fillStyle().setColor("Green");
+        style55.dataStyle().errorBarStyle().setVisible(false);
+        style55.dataStyle().markerStyle().setSize(20);
+        plotter55.createRegions(1, 2);
+
+        IProfile avgLayersTopPlot = aida.profile1D("Number of Stereo Hits per layer in Top Half", 13, 0, 13);
+        IProfile avgLayersBottomPlot = aida.profile1D("Number of Stereo Hits per layer in Bottom Half", 13, 0, 13);
+
+        plotter55.region(0).plot(avgLayersTopPlot);
+        plotter55.region(1).plot(avgLayersBottomPlot);
+
+        if(showPlots) plotter55.show();
+
+        plotter6 = fac.createPlotterFactory().create("HPS ECAL Hit Positions");
+        plotter6.setTitle("ECAL Positions");
+        //plotterFrame.addPlotter(plotter6);
+        IPlotterStyle style6 = plotter6.style();
+        style6.setParameter("hist2DStyle", "colorMap");
+        style6.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        style6.dataStyle().fillStyle().setColor("yellow");
+        style6.dataStyle().errorBarStyle().setVisible(false);
+        plotter6.createRegions(4, 2);
+
+        IHistogram2D topECal = aida.histogram2D("Top ECal Cluster Position", 50, -400, 400, 10, 0, 100);
+        IHistogram2D botECal = aida.histogram2D("Bottom ECal Cluster Position", 50, -400, 400, 10, -100, 0);
+        IHistogram2D topECal1 = aida.histogram2D("Top ECal Cluster Position (>0 tracks)", 50, -400, 400, 10, 0, 100);
+        IHistogram2D botECal1 = aida.histogram2D("Bottom ECal Cluster Position (>0 tracks)", 50, -400, 400, 10, -100, 0);
+        IHistogram2D topECal2 = aida.histogram2D("Top ECal Cluster Position (E>0.1,>0 tracks)", 50, -400, 400, 10, 0, 100);
+        IHistogram2D botECal2 = aida.histogram2D("Bottom ECal Cluster Position (E>0.1,>0 tracks)", 50, -400, 400, 10, -100, 0);
+        IHistogram2D topECal3 = aida.histogram2D("Top ECal Cluster Position w_E (E>0.1,>0 tracks)", 50, -400, 400, 10, 0, 100);
+        IHistogram2D botECal3 = aida.histogram2D("Bottom ECal Cluster Position w_E (E>0.1,>0 tracks)", 50, -400, 400, 10, -100, 0);
+
+        plotter6.region(0).plot(topECal);
+        plotter6.region(1).plot(botECal);
+        plotter6.region(2).plot(topECal1);
+        plotter6.region(3).plot(botECal1);
+        plotter6.region(4).plot(topECal2);
+        plotter6.region(5).plot(botECal2);
+        plotter6.region(6).plot(topECal3);
+        plotter6.region(7).plot(botECal3);
+        
+        if(showPlots) plotter6.show();
+        
+        
+        plotter66 = fac.createPlotterFactory().create("HPS ECAL Basic Plots");
+        plotter66.setTitle("ECAL Basic Plots");
+        //plotterFrame.addPlotter(plotter6);
+        IPlotterStyle style66 = plotter66.style();
+        style66.dataStyle().fillStyle().setColor("yellow");
+        style66.dataStyle().errorBarStyle().setVisible(false);
+        plotter66.createRegions(2, 2);
+
+        IHistogram1D topECalE = aida.histogram1D("Top ECal Cluster Energy", 50, 0, 2);
+        IHistogram1D botECalE = aida.histogram1D("Bottom ECal Cluster Energy", 50, 0, 2);
+        IHistogram1D topECalN = aida.histogram1D("Number of Clusters Top", 6, 0, 6);
+        IHistogram1D botECalN = aida.histogram1D("Number of Clusters Bot", 6, 0, 6);
+        
+        plotter66.region(0).plot(topECalE);
+        plotter66.region(1).plot(botECalE);
+        plotter66.region(2).plot(botECalN);
+        plotter66.region(3).plot(topECalN);
+        
+        if(showPlots) plotter66.show();
+        
+        
+        
+        
+        plotter8 = fac.createPlotterFactory().create("HPS Strip Hit From Stereo Multiplicity");
+        plotter8.setTitle("Strip Hit Multiplicity");
+        //plotterFrame.addPlotter(plotter8);
+        IPlotterStyle style8 = plotter8.style();
+        style8.dataStyle().fillStyle().setColor("yellow");
+        style8.dataStyle().errorBarStyle().setVisible(false);
+        plotter8.createRegions(6, 6);
+        i=0;
+        for(SiSensor sensor : sensors) {
+            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits from stereo", 10, 0, 10);
+            plotter8.region(i).plot(resX);
+            i++;
+        }
+
+        if(showPlots) plotter8.show();
+        
+        plotter88 = fac.createPlotterFactory().create("HPS Strip Hit Multiplicity");
+        plotter88.setTitle("Strip Hit Multiplicity");
+        //plotterFrame.addPlotter(plotter88);
+        plotter88.setStyle(style8);
+        plotter88.createRegions(6, 6);
+        i=0;
+        for(SiSensor sensor : sensors) {
+            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits", 10, 0, 10);
+            plotter88.region(i).plot(resX);
+            i++;
+        }
+
+        if(showPlots) plotter88.show();
+        
+        
+        
+        
+        
+        plotter888 = fac.createPlotterFactory().create("HPS Strip Hit Isolation");
+        plotter888.setTitle("Strip Hit Isolation");
+        //plotterFrame.addPlotter(plotter88);
+        plotter888.setStyle(style8);
+        plotter888.createRegions(6, 6);
+        i=0;
+        for(SiSensor sensor : sensors) {
+            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits iso", 50, 0, 5);
+            plotter888.region(i).plot(resX);
+            i++;
+        }
+
+        if(showPlots) plotter888.show();
+        
+        plotter8888 = fac.createPlotterFactory().create("HPS Strip Hit On Track Isolation");
+        plotter8888.setTitle("Strip Hit On Track Isolation");
+        //plotterFrame.addPlotter(plotter88);
+        plotter8888.setStyle(style8);
+        plotter8888.createRegions(6, 6);
+        i=0;
+        for(SiSensor sensor : sensors) {
+            IHistogram1D resX = aida.histogram1D(sensor.getName() + " strip hits iso on track", 50, 0, 5);
+            plotter8888.region(i).plot(resX);
+            i++;
+        }
+
+        if(showPlots) plotter8888.show();
+
+
+    }
+    
+    
+    
+    
     private Cluster findClosestCluster(Hep3Vector posonhelix, List<Cluster> clusters) {
         Cluster closest = null;
         double minDist = 9999;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TriggerTurnOnAnalysis.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TriggerTurnOnAnalysis.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TriggerTurnOnAnalysis.java	Wed Apr 27 11:11:32 2016
@@ -10,12 +10,15 @@
 import hep.aida.IHistogramFactory;
 import hep.aida.IPlotter;
 import hep.physics.vec.Hep3Vector;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.hps.analysis.ecal.HPSMCParticlePlotsDriver;
+import org.hps.users.phansson.testrun.TrigRateDriver;
 import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TruthMomentumResolutionDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TruthMomentumResolutionDriver.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/phansson/TruthMomentumResolutionDriver.java	Wed Apr 27 11:11:32 2016
@@ -18,6 +18,7 @@
 import java.util.logging.Logger;
 
 import org.hps.analysis.ecal.HPSMCParticlePlotsDriver;
+import org.hps.users.phansson.testrun.TrigRateDriver;
 import org.lcsim.constants.Constants;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.MCParticle;

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/rafo/test1.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/rafo/test1.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/rafo/test1.java	Wed Apr 27 11:11:32 2016
@@ -4,15 +4,15 @@
 import org.lcsim.util.Driver;
 
 public class test1 extends Driver {
-	private int clusterID;
+    private int clusterID;
     
-	public void process(EventHeader event) {
-    	System.out.println("The cluster ID = " + clusterID);
-	}
+    public void process(EventHeader event) {
+        System.out.println("The cluster ID = " + clusterID);
+    }
     
-	public void setClusterID(int clusterID) {
-    	this.clusterID = clusterID;
-	}
+    public void setClusterID(int clusterID) {
+        this.clusterID = clusterID;
+    }
 }
 
 

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/GetChargeFromScalersMultirun.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/GetChargeFromScalersMultirun.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/GetChargeFromScalersMultirun.java	Wed Apr 27 11:11:32 2016
@@ -18,144 +18,144 @@
  *
  */
 public class GetChargeFromScalersMultirun {
-	private static ArrayList<String> runs;
-	private static ArrayList<Date> starts;
-	private static ArrayList<Date> ends;
+    private static ArrayList<String> runs;
+    private static ArrayList<Date> starts;
+    private static ArrayList<Date> ends;
 
-	public static void main(String[] arg) throws FileNotFoundException, ParseException{
-		String inputFile = arg[0];
-		String timingInfoFile = arg[1];
-		String outputFile = arg[2];
-		
-		
-		readTimingInfoFile(timingInfoFile);
-		
-		Map map = getCharges(runs, starts, ends, inputFile);
-		mergeBiasIntervals(map);
-		
-		ArrayList<String> keys = new ArrayList(map.keySet());
-		Collections.sort(keys);
-		
-		
-		PrintWriter pw = new PrintWriter(new File(outputFile));
-		for(String s : keys){
-			pw.println(s + "\t" + map.get(s));
-			System.out.println(s + "\t" + map.get(s));
-		}
-		pw.close();
-	}
+    public static void main(String[] arg) throws FileNotFoundException, ParseException{
+        String inputFile = arg[0];
+        String timingInfoFile = arg[1];
+        String outputFile = arg[2];
+        
+        
+        readTimingInfoFile(timingInfoFile);
+        
+        Map map = getCharges(runs, starts, ends, inputFile);
+        mergeBiasIntervals(map);
+        
+        ArrayList<String> keys = new ArrayList(map.keySet());
+        Collections.sort(keys);
+        
+        
+        PrintWriter pw = new PrintWriter(new File(outputFile));
+        for(String s : keys){
+            pw.println(s + "\t" + map.get(s));
+            System.out.println(s + "\t" + map.get(s));
+        }
+        pw.close();
+    }
 
-	static void readTimingInfoFile(String s) throws FileNotFoundException, ParseException{
-		Scanner scanner = new Scanner(new File(s));
-		scanner.useDelimiter("[\n\t]");
-		runs = new ArrayList();
-		starts = new ArrayList();
-		ends = new ArrayList();
-		DateFormat df = new SimpleDateFormat("MM/dd/yyyy HH:mm:ss z");
-		
-		while(scanner.hasNext()){
-			runs.add(scanner.next());
-			String n = scanner.next();
-			if(n.matches("\\d+"))
-				starts.add(new Date(Long.parseLong(n)));
-			else 
-				starts.add(df.parse(n));
-			n = scanner.next();
-			if(n.matches("\\d+"))
-				ends.add(new Date(Long.parseLong(n)));
-			else 
-				ends.add(df.parse(n));
-			
-		}
-		scanner.close();
-	}
-	
-	
-	
-	
-	
-	/**
-	 * returns charge in microCoulombs
-	 * @param runs names of the runs   
-	 * @param starts starting times of the runs
-	 * @param ends ending times of the runs
-	 * @param file the mya file that we need to use
-	 * @return a map relating the runs to the charges (uC).  
-	 * @throws FileNotFoundException
-	 */
-	
-	static Map<String, Double> getCharges(ArrayList<String> runs, ArrayList<Date> starts, ArrayList<Date> ends, String file) throws FileNotFoundException{
-		Scanner s = new Scanner(new File(file));
-		HashMap<String, Double> map = new HashMap();
-		long prev = 0;
-		long time = 0;
-		for(int i = 0; i< runs.size(); i++){
-			long endt = ends.get(i).getTime();
-			long startt = starts.get(i).getTime();
-			
-			double charge = 0;
-			boolean started = false;
-			double prevval = 0;
-			if(time > endt){
-				s.close();
-				s = new Scanner(new File(file));
-			}
-			inner : while(s.hasNext()){
-				String var = s.next();
-				prev = time;
-				time = s.nextLong()*1000; //convert from s to ms
+    static void readTimingInfoFile(String s) throws FileNotFoundException, ParseException{
+        Scanner scanner = new Scanner(new File(s));
+        scanner.useDelimiter("[\n\t]");
+        runs = new ArrayList();
+        starts = new ArrayList();
+        ends = new ArrayList();
+        DateFormat df = new SimpleDateFormat("MM/dd/yyyy HH:mm:ss z");
+        
+        while(scanner.hasNext()){
+            runs.add(scanner.next());
+            String n = scanner.next();
+            if(n.matches("\\d+"))
+                starts.add(new Date(Long.parseLong(n)));
+            else 
+                starts.add(df.parse(n));
+            n = scanner.next();
+            if(n.matches("\\d+"))
+                ends.add(new Date(Long.parseLong(n)));
+            else 
+                ends.add(df.parse(n));
+            
+        }
+        scanner.close();
+    }
+    
+    
+    
+    
+    
+    /**
+     * returns charge in microCoulombs
+     * @param runs names of the runs   
+     * @param starts starting times of the runs
+     * @param ends ending times of the runs
+     * @param file the mya file that we need to use
+     * @return a map relating the runs to the charges (uC).  
+     * @throws FileNotFoundException
+     */
+    
+    static Map<String, Double> getCharges(ArrayList<String> runs, ArrayList<Date> starts, ArrayList<Date> ends, String file) throws FileNotFoundException{
+        Scanner s = new Scanner(new File(file));
+        HashMap<String, Double> map = new HashMap();
+        long prev = 0;
+        long time = 0;
+        for(int i = 0; i< runs.size(); i++){
+            long endt = ends.get(i).getTime();
+            long startt = starts.get(i).getTime();
+            
+            double charge = 0;
+            boolean started = false;
+            double prevval = 0;
+            if(time > endt){
+                s.close();
+                s = new Scanner(new File(file));
+            }
+            inner : while(s.hasNext()){
+                String var = s.next();
+                prev = time;
+                time = s.nextLong()*1000; //convert from s to ms
 
-				double val = s.nextDouble();
-				if(!var.equals("scaler_calc1"))
-					continue;
-				
-				if(!started && time> startt){ //first sample in the run
-					charge += (val)/2.*(time-startt);
-					started= true;
-				}
-				
-				else if(time > startt && endt > time){ //middle samples in the run
-					charge += (val/*+prevval*/)/*/2.*/*(time-prev);
-					
-				}
-				
-				if(endt < time){ //last sample that is in the run
-					charge += (/*prev*/val)/2.*(endt-prev);
-					break inner;
-				}
-				prevval = val;
-			}
-			charge/=1e6;
-			map.put(runs.get(i), charge);
-		}
-		s.close();
-		return map;
+                double val = s.nextDouble();
+                if(!var.equals("scaler_calc1"))
+                    continue;
+                
+                if(!started && time> startt){ //first sample in the run
+                    charge += (val)/2.*(time-startt);
+                    started= true;
+                }
+                
+                else if(time > startt && endt > time){ //middle samples in the run
+                    charge += (val/*+prevval*/)/*/2.*/*(time-prev);
+                    
+                }
+                
+                if(endt < time){ //last sample that is in the run
+                    charge += (/*prev*/val)/2.*(endt-prev);
+                    break inner;
+                }
+                prevval = val;
+            }
+            charge/=1e6;
+            map.put(runs.get(i), charge);
+        }
+        s.close();
+        return map;
 
-	}
-	
-	/**
-	 * If the subsections of the runs in which the bias is on are labeled according to a scheme,
-	they will be added together.  
-	for instance, 5779a, 5779b, 5779c, etc. will be added up as 5779bias.   
-	 * @param map the map of run names (and portions of runs that have bias labeled as [run number][a,b,c,d...],
-	 * corresponding to the total charge in that run (or piece of a run).  
-	 */
-	static void mergeBiasIntervals(Map<String, Double> map){
-		Map<String, Double> map2 = new HashMap();
-		for(Map.Entry<String, Double> entry : map.entrySet()){
-			String key1 = entry.getKey();
-			if(!entry.getKey().matches("\\d+a"))
-					continue;
-			double charge = entry.getValue();
-			for(Map.Entry<String, Double> entry2 : map.entrySet()){
-				if(entry2.getKey().matches(key1.substring(0, 4) + "[b-z]"))
-						charge += entry2.getValue();
-			}
-			map2.put(key1.substring(0, 4) + "bias", charge);
-			
-		}
-		for(Map.Entry<String, Double> e : map2.entrySet()){
-			map.put(e.getKey(), e.getValue());
-		}
-	}
+    }
+    
+    /**
+     * If the subsections of the runs in which the bias is on are labeled according to a scheme,
+    they will be added together.  
+    for instance, 5779a, 5779b, 5779c, etc. will be added up as 5779bias.   
+     * @param map the map of run names (and portions of runs that have bias labeled as [run number][a,b,c,d...],
+     * corresponding to the total charge in that run (or piece of a run).  
+     */
+    static void mergeBiasIntervals(Map<String, Double> map){
+        Map<String, Double> map2 = new HashMap();
+        for(Map.Entry<String, Double> entry : map.entrySet()){
+            String key1 = entry.getKey();
+            if(!entry.getKey().matches("\\d+a"))
+                    continue;
+            double charge = entry.getValue();
+            for(Map.Entry<String, Double> entry2 : map.entrySet()){
+                if(entry2.getKey().matches(key1.substring(0, 4) + "[b-z]"))
+                        charge += entry2.getValue();
+            }
+            map2.put(key1.substring(0, 4) + "bias", charge);
+            
+        }
+        for(Map.Entry<String, Double> e : map2.entrySet()){
+            map.put(e.getKey(), e.getValue());
+        }
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/HitrateHistograms.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/HitrateHistograms.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/HitrateHistograms.java	Wed Apr 27 11:11:32 2016
@@ -19,109 +19,109 @@
 import org.lcsim.util.Driver;
 
 public class HitrateHistograms extends Driver{
-	HashMap<String, IHistogram2D[]> hist2d = new HashMap<String, IHistogram2D[]>();
+    HashMap<String, IHistogram2D[]> hist2d = new HashMap<String, IHistogram2D[]>();
 
-	IAnalysisFactory af = IAnalysisFactory.create();
-	IHistogramFactory hf = af.createHistogramFactory(af.createTreeFactory().create());
-	IPlotterFactory pf = af.createPlotterFactory();
-	public HitrateHistograms(){
-		addHistograms2D("Ecal", 1, -30, 30, -8, 16);
-		addHistograms2D("muon", 8, -30, 30, -8, 16);
+    IAnalysisFactory af = IAnalysisFactory.create();
+    IHistogramFactory hf = af.createHistogramFactory(af.createTreeFactory().create());
+    IPlotterFactory pf = af.createPlotterFactory();
+    public HitrateHistograms(){
+        addHistograms2D("Ecal", 1, -30, 30, -8, 16);
+        addHistograms2D("muon", 8, -30, 30, -8, 16);
 
-		try {
-			ecalDecoder = new IDDecoder(new IDDescriptor("system:0:6,layer:6:2,ix:8:-8,iy:16:-6"));
-		} catch (IDException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
+        try {
+            ecalDecoder = new IDDecoder(new IDDescriptor("system:0:6,layer:6:2,ix:8:-8,iy:16:-6"));
+        } catch (IDException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
 
 
 
-	}
-	private void addHistograms2D(String detector, int nLayers, int ixMin, int ixMax,  int iyMin, int iyMax){
-		IPlotter plotter1 = pf.create("detector");
-		int nx = (int)Math.ceil(Math.sqrt(nLayers));
-		int ny = (int)Math.ceil(nLayers/(double)nx);
-		plotter1.createRegions(nx, ny);
+    }
+    private void addHistograms2D(String detector, int nLayers, int ixMin, int ixMax,  int iyMin, int iyMax){
+        IPlotter plotter1 = pf.create("detector");
+        int nx = (int)Math.ceil(Math.sqrt(nLayers));
+        int ny = (int)Math.ceil(nLayers/(double)nx);
+        plotter1.createRegions(nx, ny);
 
-		hist2d.put(detector,new IHistogram2D[nLayers]);
-		for(int i = 0; i< nLayers; i++){
-			hist2d.get(detector)[i] 
-			                     = hf.createHistogram2D(detector + " layer " + (i+1), ixMax-ixMin, ixMin, ixMax, iyMax-iyMin, iyMin, iyMax);
-			plotter1.region(i).plot(hist2d.get(detector)[i]);
+        hist2d.put(detector,new IHistogram2D[nLayers]);
+        for(int i = 0; i< nLayers; i++){
+            hist2d.get(detector)[i] 
+                                 = hf.createHistogram2D(detector + " layer " + (i+1), ixMax-ixMin, ixMin, ixMax, iyMax-iyMin, iyMin, iyMax);
+            plotter1.region(i).plot(hist2d.get(detector)[i]);
 
-		}
-	}
+        }
+    }
 
 
-	IDDecoder ecalDecoder;
-	private float recency;
+    IDDecoder ecalDecoder;
+    private float recency;
 
-	public void process(EventHeader header){
+    public void process(EventHeader header){
 
 
-		//System.out.println(header.keys());
+        //System.out.println(header.keys());
 
 
-		for(SIOSimCalorimeterHit hit: header.get(SIOSimCalorimeterHit.class,"EcalHits")){
-			int fieldCount = hit.getIDDecoder().getFieldCount();
-			ecalDecoder.setID(hit.getCellID());
-			int ix = ecalDecoder.getValue("ix");
-			int iy = ecalDecoder.getValue("iy");
-			int layer = ecalDecoder.getValue("layer");
-			hist2d.get("Ecal")[layer].fill(ix, iy);
-		}
-		
-		
-		/*if(recency != 0)
-		for(IHistogram2D[] hists : hist2d.values()){
-			for(IHistogram2D hist : hists){
-				hf.
-			}
-		}*/
-		//}
-	}
-	/**
-	 * "recency" is a parameter used to determine how to time-weight the 
-	 * histogram so that the more recent events are more highly weighted.
-	 * A recency of zero means that there is no time weightedness.
-	 * A recency of R means that each event is weighted by a factor of (1-R)^n,
-	 * where n is the number of events that have taken place since the event shown.
-	 * @param recency
-	 */
-	//public void setRecency(float recency){
-	//this.recency = recency;
-	//}
+        for(SIOSimCalorimeterHit hit: header.get(SIOSimCalorimeterHit.class,"EcalHits")){
+            int fieldCount = hit.getIDDecoder().getFieldCount();
+            ecalDecoder.setID(hit.getCellID());
+            int ix = ecalDecoder.getValue("ix");
+            int iy = ecalDecoder.getValue("iy");
+            int layer = ecalDecoder.getValue("layer");
+            hist2d.get("Ecal")[layer].fill(ix, iy);
+        }
+        
+        
+        /*if(recency != 0)
+        for(IHistogram2D[] hists : hist2d.values()){
+            for(IHistogram2D hist : hists){
+                hf.
+            }
+        }*/
+        //}
+    }
+    /**
+     * "recency" is a parameter used to determine how to time-weight the 
+     * histogram so that the more recent events are more highly weighted.
+     * A recency of zero means that there is no time weightedness.
+     * A recency of R means that each event is weighted by a factor of (1-R)^n,
+     * where n is the number of events that have taken place since the event shown.
+     * @param recency
+     */
+    //public void setRecency(float recency){
+    //this.recency = recency;
+    //}
 
-	public void startOfData(){
+    public void startOfData(){
 
-	}
-	public void endOfData(){
+    }
+    public void endOfData(){
 
-		for(String name : hist2d.keySet()){
-			IHistogram2D[] hists = hist2d.get(name);
-			System.out.println(name);
-			for(int i = 0; i< hists.length; i++){
-				double max = hists[i].maxBinHeight();
-				double total = hists[i].sumAllBinHeights();
-				double ratioPercent = 100.*max/(double)total;
-				System.out.printf("  layer %d: %.2f %% of hits were in the most populated bin\n",i, ratioPercent);
-			}
-		}
-	}
-	public static void main(String arg[]) throws IOException{
-		LCIOReader lcReader = new LCIOReader(new File(arg[0]));
-		HitrateHistograms driver = new HitrateHistograms();
-		driver.startOfData();
-		for(int i=0;i<1000;i++){
-			EventHeader event = lcReader.read();
+        for(String name : hist2d.keySet()){
+            IHistogram2D[] hists = hist2d.get(name);
+            System.out.println(name);
+            for(int i = 0; i< hists.length; i++){
+                double max = hists[i].maxBinHeight();
+                double total = hists[i].sumAllBinHeights();
+                double ratioPercent = 100.*max/(double)total;
+                System.out.printf("  layer %d: %.2f %% of hits were in the most populated bin\n",i, ratioPercent);
+            }
+        }
+    }
+    public static void main(String arg[]) throws IOException{
+        LCIOReader lcReader = new LCIOReader(new File(arg[0]));
+        HitrateHistograms driver = new HitrateHistograms();
+        driver.startOfData();
+        for(int i=0;i<1000;i++){
+            EventHeader event = lcReader.read();
 
-			if(event == null)
-				break;
-			driver.process(event);
+            if(event == null)
+                break;
+            driver.process(event);
 
-		}
-		driver.endOfData();
-	}
+        }
+        driver.endOfData();
+    }
 
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/PulserFilter.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/PulserFilter.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/PulserFilter.java	Wed Apr 27 11:11:32 2016
@@ -25,65 +25,65 @@
 
 public class PulserFilter extends Driver{
 
-	public void process(EventHeader event) {
+    public void process(EventHeader event) {
 
-		// only keep pulser triggers:
-		if (!event.hasCollection(GenericObject.class,"TriggerBank"))
-			throw new Driver.NextEventException();
-		boolean isPulser=false;
-		for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
-		{
-			if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
-			TIData tid = new TIData(gob);
-			if (tid.isPulserTrigger())
-			{
-				isPulser=true;
-				break;
-			}
-		}
+        // only keep pulser triggers:
+        if (!event.hasCollection(GenericObject.class,"TriggerBank"))
+            throw new Driver.NextEventException();
+        boolean isPulser=false;
+        for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
+        {
+            if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
+            TIData tid = new TIData(gob);
+            if (tid.isPulserTrigger())
+            {
+                isPulser=true;
+                break;
+            }
+        }
 
-		// don't drop any events with EPICS data or scalers data
-		// (could also do this via event tag=31)
-		final EpicsData edata = EpicsData.read(event);
-		if (edata != null) return;
-		ScalerData sdata = ScalerData.read(event);
-		if(sdata != null) return;
+        // don't drop any events with EPICS data or scalers data
+        // (could also do this via event tag=31)
+        final EpicsData edata = EpicsData.read(event);
+        if (edata != null) return;
+        ScalerData sdata = ScalerData.read(event);
+        if(sdata != null) return;
 
-		if (!isPulser) throw new Driver.NextEventException();
+        if (!isPulser) throw new Driver.NextEventException();
 
 
-	}
+    }
 
-	public static void main(String arg[]) throws IOException{
-		ConditionsDriver hack = new ConditionsDriver();
-		hack.setDetectorName("HPS-EngRun2015-Nominal-v1");
-		hack.setFreeze(true);
-		hack.setRunNumber(Integer.parseInt(arg[2]));
-		hack.initialize();
-		PulserFilter pf = new PulserFilter();
-		LCIOWriter writer = new LCIOWriter(arg[1]);
-		File file = new File(arg[0]);
-		LCIOReader reader = new LCIOReader(file);
-		System.out.println(file.getPath());
+    public static void main(String arg[]) throws IOException{
+        ConditionsDriver hack = new ConditionsDriver();
+        hack.setDetectorName("HPS-EngRun2015-Nominal-v1");
+        hack.setFreeze(true);
+        hack.setRunNumber(Integer.parseInt(arg[2]));
+        hack.initialize();
+        PulserFilter pf = new PulserFilter();
+        LCIOWriter writer = new LCIOWriter(arg[1]);
+        File file = new File(arg[0]);
+        LCIOReader reader = new LCIOReader(file);
+        System.out.println(file.getPath());
 
-		try{
-			while(true){
-				try{
-					EventHeader eh = reader.read();
-					if(eh.getEventNumber() %100 == 0)
-						System.out.println(eh.getEventNumber());
-					pf.process(eh);
-					writer.write(eh);
-				}catch(Driver.NextEventException e){
+        try{
+            while(true){
+                try{
+                    EventHeader eh = reader.read();
+                    if(eh.getEventNumber() %100 == 0)
+                        System.out.println(eh.getEventNumber());
+                    pf.process(eh);
+                    writer.write(eh);
+                }catch(Driver.NextEventException e){
 
-				}
-			}
-		}catch(IOException e){
-			e.printStackTrace();
-			reader.close();
-		}
+                }
+            }
+        }catch(IOException e){
+            e.printStackTrace();
+            reader.close();
+        }
 
 
-		writer.close();
-	}
+        writer.close();
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/StyleUtil.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/StyleUtil.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/StyleUtil.java	Wed Apr 27 11:11:32 2016
@@ -1,56 +1,195 @@
 package org.hps.users.spaul;
 
+import java.awt.Component;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
 import java.util.Arrays;
+import java.util.Random;
 
-import hep.aida.IAnalysisFactory;
-import hep.aida.IFunction;
-import hep.aida.IPlotterRegion;
+import javax.imageio.ImageIO;
+
+import hep.aida.*;
+import hep.aida.ref.plotter.PlotterUtilities;
 
 public class StyleUtil {
-	
-	public static void stylize(IPlotterRegion r, String title, String lx, String ly, double xmin, double xmax, double ymin, double ymax){
-		r.setTitle(title);
-		stylize(r, lx, ly);
-		r.setXLimits(xmin, xmax);
-		r.setYLimits(ymin, ymax);
-	}
-	public static void stylize(IPlotterRegion r, String title, String lx, String ly){
-		r.setTitle(title);
-		stylize(r, lx, ly);
-	}
-	public static void stylize(IPlotterRegion r, String lx, String ly){
-		
-		r.style().titleStyle().textStyle().setFontSize(22);
-		r.style().xAxisStyle().setLabel(lx);
-		r.style().xAxisStyle().labelStyle().setFontSize(16);
-		r.style().xAxisStyle().tickLabelStyle().setFontSize(14);
-		r.style().yAxisStyle().setLabel(ly);
-		r.style().yAxisStyle().labelStyle().setFontSize(16);
-		r.style().yAxisStyle().tickLabelStyle().setFontSize(14);
-		r.style().statisticsBoxStyle().setParameter("backgroundColor", "white");
-		r.style().statisticsBoxStyle().boxStyle().backgroundStyle().setColor("White");
-		r.style().statisticsBoxStyle().boxStyle().backgroundStyle().setParameter("color", "white");
-		r.style().statisticsBoxStyle().boxStyle().backgroundStyle().setOpacity(100);
-		System.out.println(Arrays.toString(r.style().dataStyle().availableParameters()));
-		r.style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-		r.style().dataStyle().fillStyle().setParameter("showZeroHeightBins", "false");
-		//r.style().dataStyle().setParameter("showDataInStatisticsBox", "false");
-		r.style().setParameter("hist2DStyle", "colorMap");
-		//r.style().dataBoxStyle()
-	}
-	static void addHorizontalLine(IPlotterRegion r, double y, String name){
-		IAnalysisFactory af = IAnalysisFactory.create();
-		IFunction f = af.createFunctionFactory(af.createTreeFactory().create()).createFunctionByName(name, "p0");
-		f.setParameter("p0", y);
-		r.plot(f);
-	}
-	public static void addParabola(IPlotterRegion region, double p0,
-			double p1, double p2, String string) {
-		IAnalysisFactory af = IAnalysisFactory.create();
-		IFunction f = af.createFunctionFactory(af.createTreeFactory().create()).createFunctionByName(string, "p2");
-		f.setParameter("p0", p0);
-		f.setParameter("p1", p1);
-		f.setParameter("p2", p2);
-		region.plot(f);
-	}
+    
+    public static void stylize(IPlotterRegion r, String title, String lx, String ly, double xmin, double xmax, double ymin, double ymax){
+        r.setTitle(title);
+        stylize(r, lx, ly);
+        r.setXLimits(xmin, xmax);
+        r.setYLimits(ymin, ymax);
+    }
+    public static void stylize(IPlotterRegion r, String title, String lx, String ly){
+        r.setTitle(title);
+        stylize(r, lx, ly);
+    }
+    public static void stylize(IPlotterRegion r, String lx, String ly){
+        
+        r.style().titleStyle().textStyle().setFontSize(22);
+        r.style().xAxisStyle().setLabel(lx);
+        r.style().xAxisStyle().labelStyle().setFontSize(16);
+        r.style().xAxisStyle().tickLabelStyle().setFontSize(14);
+        r.style().yAxisStyle().setLabel(ly);
+        r.style().yAxisStyle().labelStyle().setFontSize(16);
+        r.style().yAxisStyle().tickLabelStyle().setFontSize(14);
+        //  r.style().statisticsBoxStyle().set;
+        //debugPrint());
+        r.style().legendBoxStyle().textStyle().setFontSize(16);
+        r.style().statisticsBoxStyle().textStyle().setFontSize(16);
+        
+        //r.style().dataStyle().showInLegendBox(false);
+        
+        r.style().legendBoxStyle().boxStyle().foregroundStyle().setOpacity(1.0);
+        r.style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        r.style().dataStyle().fillStyle().setParameter("showZeroHeightBins", "false");
+        //debugPrint(r.style().dataStyle().availableParameters()));
+        //r.style().dataStyle().setParameter("showDataInStatisticsBox", "false");
+        r.style().setParameter("hist2DStyle", "colorMap");
+        //r.style().dataBoxStyle()
+    }
+    public static void addHorizontalLine(IPlotterRegion r, double y, String name){
+        IAnalysisFactory af = IAnalysisFactory.create();
+        IFunction f = af.createFunctionFactory(af.createTreeFactory().create()).createFunctionByName(name, "p0");
+        f.setParameter("p0", y);
+        r.plot(f);
+    }
+    public static void addParabola(IPlotterRegion region, double p0,
+            double p1, double p2, String string) {
+        IAnalysisFactory af = IAnalysisFactory.create();
+        IFunction f = af.createFunctionFactory(af.createTreeFactory().create()).createFunctionByName(string, "p2");
+        f.setParameter("p0", p0);
+        f.setParameter("p1", p1);
+        f.setParameter("p2", p2);
+        region.plot(f);
+    }
+    public static void noFillHistogramBars(IPlotterRegion region) {
+        region.style().dataStyle().setParameter("fillHistogramBars", "false");
+        region.style().dataStyle().fillStyle().setVisible(false);
+        
+
+        region.style().dataStyle().lineStyle().setParameter("colorRotateMethod", "regionOverlayIndex");
+        region.style().dataStyle().lineStyle().setParameter("colorRotate", "black, red, green, blue");
+        region.style().dataStyle().lineStyle().setParameter("thickness", "3");
+        region.style().dataStyle().outlineStyle().setParameter("colorRotateMethod", "regionOverlayIndex");
+        //debug = true;
+        debugPrint(region.style().dataStyle().outlineStyle().availableParameters());
+        region.style().dataStyle().outlineStyle().setParameter("colorRotate", "black, red, green, blue");
+        region.style().dataStyle().outlineStyle().setParameter("thickness", "3");
+        region.style().dataStyle().errorBarStyle().setVisible(false);
+        debugPrint(region.style().dataStyle().lineStyle().availableParameterOptions("colorRotateMethod"));
+    }
+    public static void setSize(IPlotter p, int width, int height){
+        p.setParameter("plotterWidth", width +"");
+        p.setParameter("plotterHeight", height +"");
+    }
+    
+    public static void setLog(IPlotterRegion r){
+
+        r.style().yAxisStyle().setParameter("scale", "log");
+        r.style().gridStyle().setUnits(100);
+        debugPrint(r.style().gridStyle().availableParameters()); 
+        
+    }
+    static boolean debug = false;
+    static void debugPrint(String[] stuff){
+        if(debug){
+            System.out.println(Arrays.toString(stuff));
+        }
+    }
+    public static void main(String arg[]){
+        IAnalysisFactory af = IAnalysisFactory.create();
+        IHistogramFactory hf = af.createHistogramFactory(af.createTreeFactory().create());
+        
+        IPlotter p = af.createPlotterFactory().create();
+        debugPrint(p.availableParameters());
+        p.createRegions(1, 2);
+        IHistogram1D h1 = hf.createHistogram1D("blah", 100, -5, 5);
+        IHistogram1D h2 = hf.createHistogram1D("bleh", 100, -5, 5);
+        Random random = new Random();
+        for(int i = 0; i< 100000; i++){
+            h1.fill(random.nextGaussian());
+            h2.fill(random.nextGaussian()*2);
+        }
+        hideLegendAndStats(p.region(1));
+        noFillHistogramBars(p.region(0));
+        stylize(p.region(0), "title", "x axis label", "y axis label");
+        stylize(p.region(1), "stuff", "x axis label", "y axis label");
+        p.region(0).plot(h1);
+        p.region(0).plot(h2);
+        
+
+        IHistogram2D h3 = hf.createHistogram2D("blah", 100, -5, 5, 100, -5,5);
+        
+        for(int i = 0; i< 100000; i++){
+            h3.fill(random.nextGaussian(), random.nextGaussian());
+        }
+        
+        p.region(1).plot(h3);
+        
+        
+        
+        p.show();
+        
+        p = af.createPlotterFactory().create();
+        debugPrint(p.availableParameters());
+        p.createRegions(1, 2);
+        
+        p.region(0).plot(h1);
+        setLog(p.region(0));
+        
+        
+        
+        p.show();
+    }
+    public static void hideLegendAndStats(IPlotterRegion r){
+        r.style().statisticsBoxStyle().setVisible(false);
+        r.style().legendBoxStyle().setVisible(false);
+    }
+    public static IPlotterStyle smoothCurveStyle(IPlotterFactory pf) {
+        IPlotterStyle style = pf.createPlotterStyle();
+        debugPrint(style.dataStyle().availableParameters());
+        
+        style.dataStyle().markerStyle().setVisible(false);
+        
+        return style;
+    }
+    public static void writeToFile(IPlotter plotter, String filename, String filetype){
+        //JFrame frame = new JFrame()
+        //if(plotter.)
+        //plotter.hide();
+        //plotter.show();
+        //PlotterUtilities.writeToFile(plotter, filename, filetype, null);
+        try {
+            
+            
+            //PlotterUtilities.writeToFile(plotter, filename, filetype, null);
+            Thread.sleep(1000);
+            Component c = PlotterUtilities.componentForPlotter(plotter);
+            int width = Integer.parseInt(plotter.parameterValue("plotterWidth"));
+            int height = Integer.parseInt(plotter.parameterValue("plotterHeight"));
+            if(width <= 0){
+                width = 300;
+                plotter.setParameter("plotterWidth", Integer.toString(width));
+            }
+            if(height <= 0){
+                height = 300;
+
+                plotter.setParameter("plotterHeight", Integer.toString(height));
+            }
+            
+            c.setSize(width, height);
+            BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+            Graphics2D graphics2D = image.createGraphics();
+            c.paint(graphics2D);
+            ImageIO.write(image,filetype, new File(filename));
+            Runtime.getRuntime().exec("open " + filename);
+            System.out.println("saved");
+            
+        } catch (Exception e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
+        
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/SumEverything.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/SumEverything.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/SumEverything.java	Wed Apr 27 11:11:32 2016
@@ -2,6 +2,10 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.lcsim.util.aida.AIDA;
 
 import hep.aida.IAnalysisFactory;
 import hep.aida.IHistogram1D;
@@ -15,75 +19,163 @@
 // full of aida output files.  Then add up all of the histograms in each sub folder,
 // and put the sums in separate files in a folder called "sums"
 public class SumEverything {
-	public static void main(String arg[]) throws IllegalArgumentException, IOException{
-		if(arg.length > 1){
-			twoArg(arg[0], arg[1]);
-		}
-		else{
-			oneArg(arg[0]);
-		}
-	}
-	static void oneArg(String indir) throws IllegalArgumentException, IOException{
-		File outdir = new File(indir + "/sums");
-		outdir.mkdir();
-		for(File subdirf : new File(indir).listFiles()){
-			String subdir = subdirf.getAbsolutePath();
-			if(subdir.matches(".*/sums/?"))
-				continue;
-			String split[] = subdir.split("/");
-			String outfile = indir + "/sums/" + split[split.length-1] + ".aida";
-			twoArg(subdir, outfile);
-		}
-		new File(indir + "/sums/total.aida").delete();
-		twoArg(outdir.getAbsolutePath(), indir + "/sums/total.aida");
-		
-	}
+    public static void main(String arg[]) throws IllegalArgumentException, IOException{
+        if(arg.length == 2){
+            twoArg(arg[0], arg[1]);
+        }
+        else if(arg.length == 1){
+            oneArg(arg[0]);
+        }
+        else 
+            polyArg(arg);
+    }
+    static void oneArg(final String indir) throws IllegalArgumentException, IOException{
+        File outdir = new File(indir + "/sums");
+        outdir.mkdir();
+        ArrayList<Thread> threads = new ArrayList<Thread>();
+        for(final File subdirf : new File(indir).listFiles()){
+            Thread t = new Thread(){
+                public void run(){
 
-	static void twoArg(String indir, String out) throws IllegalArgumentException, IOException{
-		IAnalysisFactory af = IAnalysisFactory.create();
-		ITreeFactory tf = af.createTreeFactory();
-		new File(out).delete();
-		ITree tree0 = tf.create(out, "xml", false, true);
-		IHistogramFactory hf = af.createHistogramFactory(tree0);
-		
+                    String subdir = subdirf.getAbsolutePath();
+                    if(subdir.matches(".*/sums/?"))
+                        return;
+                    String split[] = subdir.split("/");
+                    String outfile = indir + "/sums/" + split[split.length-1] + ".aida";
+                    try {
+                        twoArg(subdir, outfile);
+                    } catch (IllegalArgumentException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                    } catch (IOException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                    }
+                }
+            };
+            threads.add(t);
+            t.start();
+        }
+        for(Thread t : threads){
+            try {
+                t.join();
+            } catch (InterruptedException e) {
+                // TODO Auto-generated catch block
+                e.printStackTrace();
+            }
+        }
+        new File(indir + "/sums/total.aida").delete();
+        twoArg(outdir.getAbsolutePath(), indir + "/sums/total.aida");
 
-		int j = 0;
-		for(File s : new File(indir).listFiles()){
-			ITree tree = af.createTreeFactory().create(s.getAbsolutePath(),"xml");
+    }
 
-			
-			if(j == 0){
-				String [] names = tree.listObjectNames();
-				tree0.mount("/tmp", tree, "/");
-				for(String name : names){
-					Object o = tree.find(name);
-					if(o instanceof IHistogram1D || o instanceof IHistogram2D)
-						tree0.cp("/tmp/" + name, name);
-				}
-				tree0.unmount("/tmp");
-				tree.close();
-				
-			}
-			else{
-				//tree.
-				String [] names = tree.listObjectNames();
-				tree0.mount("/tmp", tree, "/");
-				for(String name : names){
-					Object o = tree.find(name);
-					if(o instanceof IHistogram1D)
-						((IHistogram1D)tree0.find(name)).add((IHistogram1D)o);
-					if(o instanceof IHistogram2D)
-						((IHistogram2D)tree0.find(name)).add((IHistogram2D)o);
-				}
-				tree0.unmount("/tmp");
-				tree.close();
-			}
 
-			tree.close();
-			j++;
-			System.out.println(j + " files have been read");
-		}
-		tree0.commit();
-	}
+
+    static void twoArg(String indir, String out) throws IllegalArgumentException, IOException{
+
+        run(new File(indir).listFiles(), out);
+    }
+    static void run(File[] files, String out) throws IllegalArgumentException, IOException{
+        
+        long timeStart = System.currentTimeMillis();
+        IAnalysisFactory af = IAnalysisFactory.create();
+        //AIDA.defaultInstance().
+        ITreeFactory tf = af.createTreeFactory();
+        new File(out).delete();
+        ITree outtree = tf.createTree(out, "xml", ITreeFactory.RECREATE);
+        IHistogramFactory hf = af.createHistogramFactory(outtree);
+        int j = 0;
+        String names[] = null;
+        for(File s : files){
+            System.gc();
+            if(!s.getAbsolutePath().endsWith("aida"))
+                continue;
+            try{
+                
+                ITree tree = tf.createTree(s.getAbsolutePath(), "xml", ITreeFactory.READONLY);//.create(s.getAbsolutePath(),"xml");
+
+
+                if(j == 0){
+                    names = tree.listObjectNames("/", true);
+                    System.out.println(Arrays.toString(names));
+                    //outtree.mount("/tmp", tree, "/");
+                    for(String name : names){
+                        if(name.endsWith("/")){
+                            outtree.mkdirs(name);
+                            continue;
+                        }
+                        Object o = tree.find(name);
+                        if(o instanceof IHistogram1D)
+                            hf.createCopy(name,(IHistogram1D)o);
+                        if(o instanceof IHistogram2D)
+                            hf.createCopy(name,(IHistogram2D)o);
+                        
+                    }
+                    //outtree.unmount("/tmp");
+                    //tree.close();
+
+                }
+                else{
+                    //tree.
+                    //String [] names = tree.listObjectNames("/", true);
+                    //outtree.mount("/tmp", tree, "/");
+                    //System.out.println(Arrays.toString(names));
+                    for(String name : names){
+                        if(name.endsWith("/"))
+                            continue;
+                        Object o = null;
+                        try{
+                            o = tree.find(name);
+                        } catch(IllegalArgumentException e){
+                            System.err.println("couldn't find object called " + name +  " in file " + s);
+                            throw e;
+                        }
+                        if(o instanceof IHistogram1D){
+                            if(((IHistogram1D)o).allEntries() != 0)
+                            ((IHistogram1D)outtree.find(name)).add((IHistogram1D)o);
+                        }
+                        if(o instanceof IHistogram2D)
+                            if(((IHistogram2D)o).allEntries() != 0)
+                            ((IHistogram2D)outtree.find(name)).add((IHistogram2D)o);
+                    }
+                    //outtree.unmount("/tmp");
+                    //tree.close();
+                }
+
+                tree.close();
+                j++;
+                System.out.println(j + " files have been read (" +(System.currentTimeMillis()-timeStart)/j + " ms per file)");
+
+            } catch(IllegalArgumentException e){
+                //print the filename
+                System.out.println("Exception happened at file " + s.getAbsolutePath());
+
+                e.printStackTrace();
+            }
+
+        }
+        outtree.commit();
+        System.out.println("summed file " + out +" commited.  Total time = " + (System.currentTimeMillis()-timeStart)/1000 + " seconds");
+    
+    }
+
+    static void polyArg(String[] arg) throws IllegalArgumentException, IOException{
+        ArrayList<File> files = new ArrayList<File>();
+        boolean nextIsOutput = false;
+        for(String a : arg){
+            if(a.equals("-o")){
+                nextIsOutput = true; 
+                continue;
+            }
+            if(nextIsOutput){
+                run(files.toArray(new File[0]), a);
+                nextIsOutput = false;
+                files.clear();
+                continue;
+            }
+            files.add(new File(a));
+
+        }
+    }
 }
 

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/BinGenerator.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/BinGenerator.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/BinGenerator.java	Wed Apr 27 11:11:32 2016
@@ -5,76 +5,86 @@
 import java.io.PrintWriter;
 
 public class BinGenerator {
-	public static void main(String arg[]) throws FileNotFoundException{
-		int nBins = 20;
+    public static void main(String arg[]) throws FileNotFoundException{
+        int nBins = 32;
 
-		PrintStream pw = new PrintStream("generatedbins.txt");
-		pw.println(nBins);
-		double[] thetaBins = getThetaBins(nBins);
-		for(int i = 0; i< nBins; i++){
-			double thetaMin = thetaBins[i];
-			double thetaMax = thetaBins[i+1];
-			double phiBounds[] = getPhiBounds(thetaMin, thetaMax);
-			pw.printf("%d %.4f %.4f ", phiBounds.length/2, thetaMin, thetaMax);
-			for(int j = 0; j< phiBounds.length; j++){
-				pw.printf("%.4f ", phiBounds[j]);
-			}
-			pw.println();
-		}
-		ShowCustomBinning.main(new String[]{"generatedbins.txt"});
+        PrintStream pw = new PrintStream("generatedbins.txt");
+        pw.println(nBins);
+        double[] thetaBins = getThetaBins(nBins);
+        for(int i = 0; i< nBins; i++){
+            double thetaMin = thetaBins[i];
+            double thetaMax = thetaBins[i+1];
+            double phiBounds[] = getPhiBounds(thetaMin, thetaMax);
+            pw.printf("%d %.4f %.4f ", phiBounds.length/2, thetaMin, thetaMax);
+            for(int j = 0; j< phiBounds.length; j++){
+                pw.printf("%.4f ", phiBounds[j]);
+            }
+            pw.println();
+        }
+        ShowCustomBinning.main(new String[]{"generatedbins.txt"});
 
-	}
+    }
 
-	private static double[] getThetaBins(int nBins){
-		/*double thetaMin = 0.035;
-		double dTheta = .2/nBins;
-		double[] bins = new double[nBins +1];
-		for(int i = 0; i< nBins+1; i++){
-			bins[i] = thetaMin+dTheta*i;
-		}
-		return bins; */
-		double thetaMax = .145;
-		double thetaMin = .035;
+    private static double[] getThetaBins(int nBins){
+        /*double thetaMin = 0.035;
+        double dTheta = .2/nBins;
+        double[] bins = new double[nBins +1];
+        for(int i = 0; i< nBins+1; i++){
+            bins[i] = thetaMin+dTheta*i;
+        }
+        return bins; */
+        double thetaMax = .200;
+        double thetaMin = .040;
 
-		double[] bins = new double[nBins +1];
-		double xMin = 1/(thetaMax*thetaMax);
-		double xMax = 1/(thetaMin*thetaMin);
-		for(int i = 0; i< nBins+1; i++){
-			double x = xMax - i*(xMax-xMin)/nBins;
-			bins[i] = Math.pow(x, -.5);
-		}
-		return bins;
-	}
-	private static double[] getPhiBounds(double thetaMin, double thetaMax){
-		double phiBins[] = new double[6];
-		double dphi = .01; 
-		int edgeNumber = 0;
+        double[] bins = new double[nBins +1];
+        for(int i = 0; i<nBins+1; i++){
+            bins[i] = thetaMin+i*(thetaMax-thetaMin)/nBins;
+        }
+        return bins;
+        /*double xMin = 1/(thetaMax*thetaMax);
+        double xMax = 1/(thetaMin*thetaMin);
+        for(int i = 0; i< nBins+1; i++){
+            double x = xMax - i*(xMax-xMin)/nBins;
+            bins[i] = Math.pow(x, -.5);
+        }
+        return bins;*/
+    }
+    private static double[] getPhiBounds(double thetaMin, double thetaMax){
+        double phiBins[] = new double[6];
+        double dphi = .01; 
+        int edgeNumber = 0;
 
-		boolean prevInRange = false;
-		for(double phi = 0; phi< 3.14; phi+= dphi){
-			boolean inRange = EcalUtil.fid_ECal_spherical(thetaMin, phi) && EcalUtil.fid_ECal_spherical(thetaMax, phi)
-								&& EcalUtil.fid_ECal_spherical(thetaMin, -phi) && EcalUtil.fid_ECal_spherical(thetaMax, -phi);
-			if(inRange && !prevInRange)
-				phiBins[edgeNumber++] = phi;
-			if(prevInRange && !inRange)
-				phiBins[edgeNumber++] = phi-dphi;
-			prevInRange = inRange;	
-		}
-		if(phiBins[2] == 0)
-			return new double[]{phiBins[0], phiBins[1]};
-		if(phiBins[4] == 0)
-			return new double[]{phiBins[0], phiBins[1],phiBins[2], phiBins[3]};
-		
-		//3 segments: choose the largest two
-		if(phiBins[4] != 0 && phiBins[1] - phiBins[0] > phiBins[3]-phiBins[2] && phiBins[5] - phiBins[4] > phiBins[3]-phiBins[2]){
-			return new double[]{phiBins[0], phiBins[1],phiBins[4], phiBins[5]};
-		}
-		if(phiBins[4] != 0 && phiBins[3] - phiBins[2] > phiBins[1]-phiBins[0] && phiBins[5] - phiBins[4] > phiBins[1]-phiBins[0]){
-			return new double[]{phiBins[2], phiBins[3],phiBins[4], phiBins[5]};
-		}
-		return new double[]{phiBins[0], phiBins[1],phiBins[2], phiBins[3]};
-		
-		
-	}
+        boolean prevInRange = false;
+        for(double phi = 0; phi< 3.14; phi+= dphi){
+            
+            // make the angular cuts on the tracks such that the particles that go into that cut 
+            // are expected to be within 4 mm (~= 2 times the angular resolution of 1.5 mrad) of 
+            // the ecal cuts.  
+            double d = 4;
+            
+            boolean inRange = EcalUtil.fid_ECal_spherical_more_strict(thetaMin, phi, d) && EcalUtil.fid_ECal_spherical_more_strict(thetaMax, phi, d)
+                                && EcalUtil.fid_ECal_spherical_more_strict(thetaMin, -phi, d) && EcalUtil.fid_ECal_spherical_more_strict(thetaMax, -phi, d);
+            if(inRange && !prevInRange)
+                phiBins[edgeNumber++] = phi;
+            if(prevInRange && !inRange)
+                phiBins[edgeNumber++] = phi-dphi;
+            prevInRange = inRange;  
+        }
+        if(phiBins[2] == 0)
+            return new double[]{phiBins[0], phiBins[1]};
+        if(phiBins[4] == 0)
+            return new double[]{phiBins[0], phiBins[1],phiBins[2], phiBins[3]};
+        
+        //3 segments: choose the largest two
+        if(phiBins[4] != 0 && phiBins[1] - phiBins[0] > phiBins[3]-phiBins[2] && phiBins[5] - phiBins[4] > phiBins[3]-phiBins[2]){
+            return new double[]{phiBins[0], phiBins[1],phiBins[4], phiBins[5]};
+        }
+        if(phiBins[4] != 0 && phiBins[3] - phiBins[2] > phiBins[1]-phiBins[0] && phiBins[5] - phiBins[4] > phiBins[1]-phiBins[0]){
+            return new double[]{phiBins[2], phiBins[3],phiBins[4], phiBins[5]};
+        }
+        return new double[]{phiBins[0], phiBins[1],phiBins[2], phiBins[3]};
+        
+        
+    }
 
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/CustomBinning.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/CustomBinning.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/CustomBinning.java	Wed Apr 27 11:11:32 2016
@@ -5,92 +5,76 @@
 import java.util.Scanner;
 
 public class CustomBinning {
-	public CustomBinning(File f) throws FileNotFoundException{
-		Scanner s = new Scanner(f);
+    public CustomBinning(File f) throws FileNotFoundException{
+        Scanner s = new Scanner(f);
 
-		nTheta = s.nextInt();  //number of bins in theta;
-		thetaMax = new double[nTheta];
-		thetaMin = new double[nTheta];
-		
-		phiMax = new double[nTheta][];
-		phiMin = new double[nTheta][];
-		int i = 0;
-		while(s.hasNext()){ //new row
-			int nPhi = s.nextInt();
-			thetaMin[i] = s.nextDouble();
-			thetaMax[i] = s.nextDouble();
-			
-			phiMax[i] = new double[nPhi];
-			phiMin[i] = new double[nPhi];
-			for(int j = 0; j<nPhi; j++){
-				phiMin[i][j] = s.nextDouble();
-				phiMax[i][j] = s.nextDouble();
-			}
-			i++;
-		}
-	}
-	double[][] phiMax;
-	double[][] phiMin;
-	public double thetaMax[], thetaMin[];
-	public int nTheta;
+        nTheta = s.nextInt();  //number of bins in theta;
+        thetaMax = new double[nTheta];
+        thetaMin = new double[nTheta];
+        
+        phiMax = new double[nTheta][];
+        phiMin = new double[nTheta][];
+        int i = 0;
+        while(s.hasNext()){ //new row
+            int nPhi = s.nextInt();
+            thetaMin[i] = s.nextDouble();
+            thetaMax[i] = s.nextDouble();
+            
+            phiMax[i] = new double[nPhi];
+            phiMin[i] = new double[nPhi];
+            for(int j = 0; j<nPhi; j++){
+                phiMin[i][j] = s.nextDouble();
+                phiMax[i][j] = s.nextDouble();
+            }
+            i++;
+        }
+    }
+    double[][] phiMax;
+    double[][] phiMin;
+    public double thetaMax[], thetaMin[];
+    public int nTheta;
 
-	double getSteradians(int binNumber){
-		double t1 = thetaMin[binNumber];
-		double t2 = thetaMax[binNumber];
-		double dCos = Math.cos(t1)-Math.cos(t2);
-		double dPhiTot = 0;
-		for(int i = 0; i< phiMax[binNumber].length; i++){
-			dPhiTot += phiMax[binNumber][i]-phiMin[binNumber][i];
-		}
-		return 2*dPhiTot*dCos;  //factor of two because top and bottom
-	}
-	boolean inRange(double theta, double phi){
-		phi = Math.abs(phi);
-		/*int i =(int) Math.floor((theta-theta0)/deltaTheta);
-		if(i>= nTheta || i<0)
-			return false;*/
-		if(theta > thetaMax[nTheta-1] || theta < thetaMin[0])
-			return false;
-		int i;
-		boolean found = false;
-		for(i = 0; i< nTheta; i++){
-			if(theta > thetaMin[i] && theta < thetaMax[i]){
-				found = true;
-				break;
-			}
-		}
-		if(!found)
-			return false;
-		
-		for(int j = 0; j<phiMax[i].length; j++){
-			if(phi>phiMin[i][j] && phi< phiMax[i][j])
-				return true;
-		}
-		return false;
+    double getSteradians(int binNumber){
+        double t1 = thetaMin[binNumber];
+        double t2 = thetaMax[binNumber];
+        double dCos = Math.cos(t1)-Math.cos(t2);
+        double dPhiTot = 0;
+        for(int i = 0; i< phiMax[binNumber].length; i++){
+            dPhiTot += phiMax[binNumber][i]-phiMin[binNumber][i];
+        }
+        return 2*dPhiTot*dCos;  //factor of two because top and bottom
+    }
+    boolean inRange(double theta, double phi){
+        phi = Math.abs(phi);
+        /*int i =(int) Math.floor((theta-theta0)/deltaTheta);
+        if(i>= nTheta || i<0)
+            return false;*/
+        if(theta > thetaMax[nTheta-1] || theta < thetaMin[0])
+            return false;
+        int i;
+        boolean found = false;
+        for(i = 0; i< nTheta; i++){
+            if(theta > thetaMin[i] && theta < thetaMax[i]){
+                found = true;
+                break;
+            }
+        }
+        if(!found)
+            return false;
+        
+        for(int j = 0; j<phiMax[i].length; j++){
+            if(phi>phiMin[i][j] && phi< phiMax[i][j])
+                return true;
+        }
+        return false;
 
-	}
-	public double getTotSteradians() {
-		double tot = 0;
-		for(int i = 0; i<nTheta; i++){
-			tot += getSteradians(i);
-		}
-		return tot;
-	}
-	/**
-	 * @param bin
-	 * @param a = 2E/M
-	 * @return the integral of 1/sin^4(th/2)*cos^2(th/2)/(1+a*sin^2(th/2)) times dPhi,
-	 * which appears in the integral of mott scattering.
-	 */
-	public double mottIntegralFactor(double a, int bin){
-		double dPhi = 0;
-		for(int i = 0; i< phiMax[bin].length; i++)
-			dPhi += 2*(phiMax[bin][0] - phiMin[bin][0]); //factor of 2 from top and bottom
-		
-		double csc2 = Math.pow(Math.sin(thetaMax[bin]/2), -2);
-		double Imax = (-csc2+(1+a)*Math.log(a+2*csc2));
-		       csc2 = Math.pow(Math.sin(thetaMin[bin]/2), -2);
-		double Imin = (-csc2+(1+a)*Math.log(a+2*csc2));
-		return 2*dPhi*(Imax-Imin);
-	}
+    }
+    public double getTotSteradians() {
+        double tot = 0;
+        for(int i = 0; i<nTheta; i++){
+            tot += getSteradians(i);
+        }
+        return tot;
+    }
+
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/DisplayHistograms.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/DisplayHistograms.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/DisplayHistograms.java	Wed Apr 27 11:11:32 2016
@@ -3,7 +3,8 @@
 import java.io.IOException;
 
 public class DisplayHistograms {
-	public static void main(String arg[]) throws IllegalArgumentException, IOException{
-		MakeHistograms.main(new String[]{arg[0]});
-	}
+    public static void main(String arg[]) throws IllegalArgumentException, IOException{
+        //System.out.println("dognabo");
+        MakeHistograms.main(new String[]{arg[0]});
+    }
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/EcalUtil.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/EcalUtil.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/EcalUtil.java	Wed Apr 27 11:11:32 2016
@@ -12,153 +12,232 @@
 import org.lcsim.event.Cluster;
 
 public class EcalUtil {
-	/**
-	 * Holly's algorithm.  
-	 * @param x x position of cluster
-	 * @param y y position of cluster
-	 * @param e energy of cluster
-	 * @param pid type of particle (11 = electron; -1 = positron)
-	 * @return array of doubles
-	 * <br> [0] theta = atan(py/pz)
-	 * <br> [1] phi = atan(px/pz) 
-	 */
-	static double [] toHollysCoordinates(double x, double y, double e, int pid){
-		if(pid == 11){
-			return new double[]{0.00071 * y +0.000357, 0.00071*x + 0.00003055*e + 0.04572/e +0.0006196};
-		} else if(pid == -11){
-			return new double[]{0.00071 * y +0.000357, 0.00071*x - 0.0006465*e + 0.045757/e +0.003465};
-		}
-		return null;
-	}
-	
-	static double getSteradians(double x, double y, double e,int pid, double dA){
-		double thetaPhi[] = toHollysCoordinates(x, y, e, pid);
-		return .00071*.00071*dA/Math.sqrt(thetaPhi[0]*thetaPhi[0]+ thetaPhi[1]*thetaPhi[1]+1);
-	}
-	
-	static boolean isSeedEdge(Cluster c){
-		CalorimeterHit seedhit  = (CalorimeterHit)c.getCalorimeterHits().get(0);
-		//	seedhit
-		int ix = seedhit.getIdentifierFieldValue("ix");
-		int iy = seedhit.getIdentifierFieldValue("iy");
-
-		//seedhit.get
-		return isEdge(ix, iy);
-	}
-	static boolean isEdge(int ix, int iy){
-		if(iy == 5 || iy == 1 || iy == -1 || iy == -5)
-			return true;
-		if(ix == -23 || ix == 23)
-			return true;
-		if((iy == 2 || iy == -2) && (ix >=-11 && ix <= -1))
-			return true;
-		return false;
-	}
-	public static boolean fid_ECal(Cluster c){
-		return fid_ECal(c.getPosition()[0], c.getPosition()[1]);
-	}
-	public static boolean fid_ECal(double x, double y)
-	{
-		y = Math.abs(y);
-
-		boolean in_fid = false;
-		double x_edge_low = -262.74;
-		double x_edge_high = 347.7;
-		double y_edge_low = 33.54;
-		double y_edge_high = 75.18;
-
-		double x_gap_low = -106.66;
-		double x_gap_high = 42.17;
-		double y_gap_high = 47.18;
-
-		y = Math.abs(y);
-
-		if( x > x_edge_low && x < x_edge_high && y > y_edge_low && y < y_edge_high )
-		{
-			if( !(x > x_gap_low && x < x_gap_high && y > y_edge_low && y < y_gap_high) )
-			{
-				in_fid = true;
-			}
-		}
-
-		return in_fid;
-	}
-	static double[] toSphericalFromBeam(double pxpz, double pypz){
-		double x = pxpz, y = pypz, z = 1;
-		double beamTilt = .03057;
-		double xtemp = Math.cos(beamTilt)*x - Math.sin(beamTilt)*z;
-		double ztemp = Math.cos(beamTilt)*z + Math.sin(beamTilt)*x;
-		double ytemp = y;
-		
-		double theta = Math.atan(Math.hypot(xtemp, ytemp)/ ztemp);
-		double phi = Math.atan2(ytemp, xtemp);
-		
-		
-		return new double[]{theta, phi};
-	}
-	static Map<Integer, double[]> map = new HashMap();
-	static void readMap() throws FileNotFoundException{
-		Scanner s = new Scanner(new File("ecal_positions.txt"));
-
-		
-		while(s.hasNext()){
-			int ix =s.nextInt();
-			int iy = s.nextInt();
-			double x = s.nextDouble();
-			double y =s.nextDouble();
-			map.put(ix+100*iy, new double[]{x, y});
-			
-		}
-		s.close();
-	}
-	static double getArea(int ix, int iy){
-		int ixp = ix+1;
-		if(ixp == 0)
-			ixp = 1;
-		int ixm = ix-1;
-		if(ixm == 0)
-			ixm = -1;
-		double[] plus = map.get(ixp+100*(iy+1));
-		double[] minus = map.get(ixm+100*(iy-1));
-		return (plus[0]-minus[0])*(plus[1]-minus[1])/4;
-	}
-	
-	public static double[] getThetaPhiSpherical(double x,double y){
-		double hcoord[] = toHollysCoordinates(x,y, 1.056, 11);
-		return toSphericalFromBeam(Math.tan(hcoord[1]),Math.tan(hcoord[0]));
-	}
-	/*beam tilt*/
-	static double tilt = .03057;
-	//assuming FEE electron.
-
-	public static double[] getXY(double theta, double phi){
-		
-		double ux = Math.cos(phi)*Math.sin(theta)*Math.cos(tilt)+Math.cos(theta)*Math.sin(tilt);
-		double uy = Math.sin(phi)*Math.sin(theta);
-		double uz = Math.cos(theta)*Math.cos(tilt)-Math.cos(phi)*Math.sin(theta)*Math.sin(tilt);
-		double pxpz = ux/uz;
-		double pypz = uy/uz;
-		//holly's coordinates:
-		double h1 = Math.atan(pypz);
-		double h2 = Math.atan(pxpz);
-		//0.00071 * y +0.000357,
-		//0.00071*x + 0.00003055*e + 0.04572/e +0.0006196
-		double y = (h1-0.000357)/0.00071;
-		double e = 1.056;
-		double x = (h2 - 0.00003055*e - 0.04572/e -0.0006196)/0.00071;
-		return new double[]{x,y};
-	}
-	public static boolean fid_ECal_spherical(double theta, double phi){
-		double[] xy = getXY(theta, phi);
-		double x = xy[0];
-		double y = xy[1];
-		return fid_ECal(x, y);
-	}
-	public static void main(String arg[]){
-		double x = 0, y = 0;
-		double sp[] = getThetaPhiSpherical(x,y); 
-		System.out.println(Arrays.toString(getXY(sp[0], sp[1])));
-	}
+    
+    static int[] getCrystalIndex(Cluster c){
+        if(map == null){
+            try{
+                readMap();
+            }catch(Exception e){
+                e.printStackTrace();
+            }
+        }
+        c.getPosition();
+        int bestix = 0, bestiy = 0;
+        double bestdist = 100000;
+
+        double cx = c.getPosition()[0];
+        double cy = c.getPosition()[1];
+        for(int ix = -23; ix<= 23; ix++){
+            if(!map.containsKey(200+ix))
+                continue;
+            double x = map.get(200+ix)[0];
+            if(Math.abs(x-cx)<bestdist){
+                bestdist = Math.abs(x-cx);
+                bestix = ix;
+            }
+        }
+        
+        bestdist = 100000;
+        for(int iy = -5; iy<= 5; iy++){
+            if(!map.containsKey(100*iy + bestix))
+                continue;
+            double y = map.get(100*iy + bestix)[1];
+            if(Math.abs(y-cy)<bestdist){
+                bestdist = Math.abs(y-cy);
+                bestiy = iy;
+            }
+        }
+        return new int[]{bestix, bestiy}; 
+    }
+    
+    
+    /**
+     * Holly's algorithm.  
+     * @param x x position of cluster
+     * @param y y position of cluster
+     * @param e energy of cluster
+     * @param pid type of particle (11 = electron; -1 = positron)
+     * @return array of doubles
+     * <br> [0] theta = atan(py/pz)
+     * <br> [1] phi = atan(px/pz) 
+     */
+    static double [] toHollysCoordinates(double x, double y, double e, int pid){
+        if(pid == 11){
+            return new double[]{0.00071 * y +0.000357, 0.00071*x + 0.00003055*e + 0.04572/e +0.0006196};
+        } else if(pid == -11){
+            return new double[]{0.00071 * y +0.000357, 0.00071*x - 0.0006465*e + 0.045757/e +0.003465};
+        }
+        return null;
+    }
+    
+    static double getSteradians(double x, double y, double e,int pid, double dA){
+        double thetaPhi[] = toHollysCoordinates(x, y, e, pid);
+        return .00071*.00071*dA/Math.sqrt(thetaPhi[0]*thetaPhi[0]+ thetaPhi[1]*thetaPhi[1]+1);
+    }
+    
+    static boolean isSeedEdge(Cluster c){
+        CalorimeterHit seedhit  = (CalorimeterHit)c.getCalorimeterHits().get(0);
+        //  seedhit
+        int ix = seedhit.getIdentifierFieldValue("ix");
+        int iy = seedhit.getIdentifierFieldValue("iy");
+
+        //seedhit.get
+        return isEdge(ix, iy);
+    }
+    static boolean isEdge(int ix, int iy){
+        if(iy == 5 || iy == 1 || iy == -1 || iy == -5)
+            return true;
+        if(ix == -23 || ix == 23)
+            return true;
+        if((iy == 2 || iy == -2) && (ix >=-11 && ix <= -1))
+            return true;
+        return false;
+    }
+    public static boolean fid_ECal(Cluster c){
+        return fid_ECal(c.getPosition()[0], c.getPosition()[1]);
+    }
+    public static boolean fid_ECal(double x, double y)
+    {
+        y = Math.abs(y);
+
+        boolean in_fid = false;
+        double x_edge_low = -262.74;
+        double x_edge_high = 347.7;
+        double y_edge_low = 33.54;
+        double y_edge_high = 75.18;
+
+        double x_gap_low = -106.66;
+        double x_gap_high = 42.17;
+        double y_gap_high = 47.18;
+
+        y = Math.abs(y);
+
+        if( x > x_edge_low && x < x_edge_high && y > y_edge_low && y < y_edge_high )
+        {
+            if( !(x > x_gap_low && x < x_gap_high && y > y_edge_low && y < y_gap_high) )
+            {
+                in_fid = true;
+            }
+        }
+
+        return in_fid;
+    }
+    /**
+     * 
+     * @param x
+     * @param y
+     * @param d the additional distance from the edge of the ecal in addition
+     *       to what is required by fid_Cal(double, double)
+     * @return
+     */
+    public static boolean fid_ecal_more_strict(double x, double y, double d){
+        y = Math.abs(y);
+
+        boolean in_fid = false;
+         
+        double x_edge_low = -262.74 + d;
+        double x_edge_high = 347.7 - d;
+        double y_edge_low = 33.54 + d;
+        double y_edge_high = 75.18 - d;
+
+        double x_gap_low = -106.66 - d;
+        double x_gap_high = 42.17 + d;
+        double y_gap_high = 47.18 + d;
+
+        y = Math.abs(y);
+
+        if( x > x_edge_low && x < x_edge_high && y > y_edge_low && y < y_edge_high )
+        {
+            if( !(x > x_gap_low && x < x_gap_high && y > y_edge_low && y < y_gap_high) )
+            {
+                in_fid = true;
+            }
+        }
+
+        return in_fid;
+    }
+    static double[] toSphericalFromBeam(double pxpz, double pypz){
+        double x = pxpz, y = pypz, z = 1;
+        double beamTilt = .03057;
+        double xtemp = Math.cos(beamTilt)*x - Math.sin(beamTilt)*z;
+        double ztemp = Math.cos(beamTilt)*z + Math.sin(beamTilt)*x;
+        double ytemp = y;
+        
+        double theta = Math.atan(Math.hypot(xtemp, ytemp)/ ztemp);
+        double phi = Math.atan2(ytemp, xtemp);
+        
+        
+        return new double[]{theta, phi};
+    }
+    static Map<Integer, double[]> map ;
+    static void readMap() throws FileNotFoundException{
+        Scanner s = new Scanner(new File(System.getenv("HOME") + "/ecal_positions.txt"));
+        map = new HashMap();
+        
+        while(s.hasNext()){
+            int ix =s.nextInt();
+            int iy = s.nextInt();
+            double x = s.nextDouble();
+            double y =s.nextDouble();
+            map.put(ix+100*iy, new double[]{x, y});
+            
+        }
+        s.close();
+    }
+    static double getArea(int ix, int iy){
+        int ixp = ix+1;
+        if(ixp == 0)
+            ixp = 1;
+        int ixm = ix-1;
+        if(ixm == 0)
+            ixm = -1;
+        double[] plus = map.get(ixp+100*(iy+1));
+        double[] minus = map.get(ixm+100*(iy-1));
+        return (plus[0]-minus[0])*(plus[1]-minus[1])/4;
+    }
+    
+    public static double[] getThetaPhiSpherical(double x,double y){
+        double hcoord[] = toHollysCoordinates(x,y, 1.056, 11);
+        return toSphericalFromBeam(Math.tan(hcoord[1]),Math.tan(hcoord[0]));
+    }
+    /*beam tilt*/
+    static double tilt = .03057;
+    //assuming FEE electron.
+
+    public static double[] getXY(double theta, double phi){
+        
+        double ux = Math.cos(phi)*Math.sin(theta)*Math.cos(tilt)+Math.cos(theta)*Math.sin(tilt);
+        double uy = Math.sin(phi)*Math.sin(theta);
+        double uz = Math.cos(theta)*Math.cos(tilt)-Math.cos(phi)*Math.sin(theta)*Math.sin(tilt);
+        double pxpz = ux/uz;
+        double pypz = uy/uz;
+        //holly's coordinates:
+        double h1 = Math.atan(pypz);
+        double h2 = Math.atan(pxpz);
+        //0.00071 * y +0.000357,
+        //0.00071*x + 0.00003055*e + 0.04572/e +0.0006196
+        double y = (h1-0.000357)/0.00071;
+        double e = 1.056;
+        double x = (h2 - 0.00003055*e - 0.04572/e -0.0006196)/0.00071;
+        return new double[]{x,y};
+    }
+    public static boolean fid_ECal_spherical(double theta, double phi){
+        double[] xy = getXY(theta, phi);
+        double x = xy[0];
+        double y = xy[1];
+        return fid_ECal(x, y);
+    }
+    public static boolean fid_ECal_spherical_more_strict(double theta, double phi, double d){
+        double[] xy = getXY(theta, phi);
+        double x = xy[0];
+        double y = xy[1];
+        return fid_ecal_more_strict(x, y, d);
+    }
+    public static void main(String arg[]){
+        double x = 0, y = 0;
+        double sp[] = getThetaPhiSpherical(x,y); 
+        System.out.println(Arrays.toString(getXY(sp[0], sp[1])));
+    }
 }
-	
-
+    
+

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MakeHistograms.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MakeHistograms.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/MakeHistograms.java	Wed Apr 27 11:11:32 2016
@@ -2,12 +2,15 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.Date;
 import java.util.List;
 
 import org.hps.conditions.ConditionsDriver;
+import org.hps.recon.tracking.TrackType;
 import org.hps.record.triggerbank.AbstractIntData;
 import org.hps.record.triggerbank.TIData;
 import org.lcsim.event.CalorimeterHit;
@@ -15,9 +18,12 @@
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
 import org.lcsim.event.ReconstructedParticle;
+import org.lcsim.event.Track;
+import org.lcsim.event.TrackState;
 import org.lcsim.lcio.LCIOReader;
 
 import hep.aida.IAnalysisFactory;
+import hep.aida.IDataPointSetFactory;
 import hep.aida.IHistogram1D;
 import hep.aida.IHistogram2D;
 import hep.aida.IHistogramFactory;
@@ -29,232 +35,448 @@
 import org.hps.users.spaul.StyleUtil;
 
 public class MakeHistograms {
-	static boolean display = false;
-	static CustomBinning cb;
-	public static void main(String arg[]) throws IllegalArgumentException, IOException{
-		if(arg.length == 1){
-			File file = new File(arg[0]);
-			String path = arg[0];
-			if(file.isDirectory()){
-				org.hps.users.spaul.SumEverything.main(new String[]{path, "temp.aida"});
-				path = "temp.aida";
-			}
-			IAnalysisFactory af = IAnalysisFactory.create();
-			 ITreeFactory tf = af.createTreeFactory();
-			ITree tree0 = tf.create(path, "xml");
-			extractHistograms(tree0);
-			setupPlotter(af);
-			
-		} else{
-
-			String input = arg[0];
-			String output = arg[1];
-			cb = new CustomBinning(new File(arg[2]));
-			if(arg.length == 5)
-				display = true;
-			IAnalysisFactory af = IAnalysisFactory.create();
-			ITree tree = af.createTreeFactory().create(output,"xml",false,true);
-			IHistogramFactory hf = af.createHistogramFactory(tree);
-			setupHistograms(hf);
-			if(display){
-				setupPlotter(af);
-			}
-			ConditionsDriver hack = new ConditionsDriver();
-			//hack.setXmlConfigResource("/u/group/hps/hps_soft/detector-data/detectors/HPS-EngRun2015-Nominal-v3");
-			hack.setDetectorName("HPS-EngRun2015-Nominal-v3");
-			hack.setFreeze(true);
-			hack.setRunNumber(Integer.parseInt(arg[3]));
-			hack.initialize();
-			LCIOReader reader = new LCIOReader(new File(input));
-			//reader.open(input);
-			//reader.
-			EventHeader event = reader.read();
-			int nEvents = 0;
-			try{
-				outer : while(event != null){
-					processEvent(event);
-
-					//System.out.println(Q2);
-
-					event = reader.read();
-				}
-			} catch (Exception e){
-				e.printStackTrace();
-			}
-			tree.commit();
-			tree.close();
-		}
-
-	}
-	
-	static IHistogram2D h1, h2, h2a, h2b, h2c;
-	static IHistogram2D h4,h4a;
-	static IHistogram1D h3, h3a;
-	static IHistogram1D h5, h6;
-	
-	private static void extractHistograms(ITree tree0) {
-		h2 = (IHistogram2D) tree0.find("theta vs phi");
-		h2a = (IHistogram2D) tree0.find("theta vs phi cut");
-		h2b = (IHistogram2D) tree0.find("theta vs phi cut alt");
-		h2c = (IHistogram2D) tree0.find("theta vs phi alt");
-		
-		h3 = (IHistogram1D) tree0.find("theta");
-		h4 = (IHistogram2D) tree0.find("px\\/pz vs py\\/pz");
-		h4a = (IHistogram2D) tree0.find("px\\/pz vs py\\/pz cut");
-		h5 = (IHistogram1D) tree0.find("energy");
-		
-	}
-	static void setupHistograms(IHistogramFactory hf){
-		//h1 = hf.createHistogram2D("px\\/pz vs py\\/pz", 160, -.16, .24, 160, -.2, .2);
-		
-		
-		
-		
-		h2 = hf.createHistogram2D("theta vs phi", 300, 0, .3, 314, -3.14, 3.14);
-		
-		h2a = hf.createHistogram2D("theta vs phi cut", 300, 0, .3, 314, -3.14, 3.14);
-
-		double thetaBins[] = new double[cb.nTheta+1];
-		for(int i = 0; i<cb.nTheta; i++){
-			thetaBins[i] = cb.thetaMin[i];
-		}
-		
-		thetaBins[thetaBins.length-1] = cb.thetaMax[cb.nTheta-1];
-
-		double phiBins[] = new double[315];
-		for(int i = 0; i<315; i++){
-			phiBins[i] = i/50.-3.14;  //every 10 mrad;
-		}
-		
-		//identical to h2a, except different binning
-		h2b = hf.createHistogram2D("theta vs phi cut alt", "theta vs phi cut alt", thetaBins, phiBins);
-		h2c = hf.createHistogram2D("theta vs phi alt", "theta vs phi alt", thetaBins, phiBins);
-		
-		h3 = hf.createHistogram1D("theta", "theta", thetaBins);
-
-		h4 = hf.createHistogram2D("px\\/pz vs py\\/pz", 160, -.16, .24, 160, -.2, .2);
-		h4a = hf.createHistogram2D("px\\/pz vs py\\/pz cut", 160, -.16, .24, 160, -.2, .2);
-		
-		h5 = hf.createHistogram1D("energy", 75, 0, 1.5);
-	}
-	static void setupPlotter(IAnalysisFactory af){
-		IPlotterFactory pf = af.createPlotterFactory();
-		IPlotter p = pf.create();
-		p.createRegions(2,2);
-		p.region(0).plot(h2);
-
-		StyleUtil.stylize(p.region(0), "theta", "phi");
-		p.region(1).plot(h2a);
-		StyleUtil.stylize(p.region(1), "theta", "phi");
-		p.region(2).plot(h3);
-		StyleUtil.stylize(p.region(2), "theta", "# of particles");
-		p.region(3).plot(h5);
-		StyleUtil.stylize(p.region(3), "energy", "# of particles");
-		
-		p.show();
-		//new window for the next plot
-		IPlotter p2 = pf.create();
-		p2.region(0).plot(h2b);
-		StyleUtil.stylize(p2.region(0), "theta", "phi");
-		
-		p2.show();
-		
-		//new window for the next plot
-		IPlotter p3 = pf.create();
-		p3.region(0).plot(h2c);
-		StyleUtil.stylize(p3.region(0), "theta", "phi");
-		
-		p3.show();
-		
-		//new window for the next plot
-		IPlotter p4 = pf.create();
-		p4.region(0).plot(h4);
-		StyleUtil.stylize(p4.region(0), "px/pz", "py/pz");
-		
-		p4.show();
-		
-		//new window for the next plot
-		IPlotter p5 = pf.create();
-		p5.region(0).plot(h4a);
-		StyleUtil.stylize(p5.region(0), "px/pz", "py/pz");
-		
-		p5.show();
-	}
-	private static void processEvent(EventHeader event) {
-		if(event.getEventNumber() %1000 == 0)
-			System.out.println("event number " + event.getEventNumber());
-		
-		for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
-		{
-			if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
-			TIData tid = new TIData(gob);
-			if (!tid.isSingle1Trigger())
-			{
-				return;
-			}
-		}
-		List<ReconstructedParticle> particles = event.get(ReconstructedParticle.class, "FinalStateParticles");
-
-		for(ReconstructedParticle p : particles){
-
-			boolean isGood = addParticle(p);
-
-
-		}
-	}
-
-	static double eMin = .8;
-	static double eMax = 1.2;
-	static double beamEnergy = 1.057;
-
-	static double beamTilt = .03057;
-	static double maxChi2 = 50;
-	static boolean addParticle(ReconstructedParticle part){
-		
-		if(part.getTracks().size() == 0)
-			return false;
-		if(part.getTracks().get(0).getChi2()>maxChi2){
-			return false;
-		}
-		if(part.getClusters().size() == 0)
-			return false;
-		Cluster c = part.getClusters().get(0);
-		double time = c.getCalorimeterHits().get(0).getTime();
-		if(EcalUtil.fid_ECal(c)){
-			if(c.getCalorimeterHits().size() < 3)
-				return false;
-			if(time>40 && time <48)
-				h5.fill(c.getEnergy());
-			if(c.getEnergy() > eMin && c.getEnergy() < eMax && (time >40 && time < 48)) {
-
-				Hep3Vector p = part.getMomentum();
-				
-				double px = p.x(), pz = p.z();
-				double pxtilt = px*Math.cos(beamTilt)-pz*Math.sin(beamTilt);
-				double py = p.y();
-				double pztilt = pz*Math.cos(beamTilt)+px*Math.sin(beamTilt);
-
-				double theta = Math.atan(Math.hypot(pxtilt, py)/pztilt);
-				double phi =Math.atan2(py, pxtilt);
-
-				h2.fill(theta, phi);
-				h2c.fill(theta, phi);
-				
-				h4.fill(px/pz, py/pz);
-				
-				if(cb.inRange(theta, phi)){
-					h2a.fill(theta, phi);
-					h2b.fill(theta, phi);
-					h3.fill(theta);
-					h4a.fill(px/pz, py/pz);
-				}
-
-
-				return true;
-			}
-
-		}
-		return false;
-	}
-
+    
+    
+    
+    static boolean display = false;
+    static CustomBinning cb;
+    public static void main(String arg[]) throws IllegalArgumentException, IOException{
+        if(arg.length == 1){
+            File file = new File(arg[0]);
+            String path = arg[0];
+            if(file.isDirectory()){
+                org.hps.users.spaul.SumEverything.main(new String[]{path, "temp.aida"});
+                path = "temp.aida";
+            }
+            IAnalysisFactory af = IAnalysisFactory.create();
+            ITreeFactory tf = af.createTreeFactory();
+            ITree tree0 = tf.create(path, "xml");
+            extractHistograms(tree0);
+            setupPlotter(af);
+
+        } else{
+
+            String input = arg[0];
+            String output = arg[1];
+            cb = new CustomBinning(new File(arg[2]));
+            if(arg[arg.length -1].equals("display"))
+                display = true;
+            IAnalysisFactory af = IAnalysisFactory.create();
+            ITree tree = af.createTreeFactory().create(output,"xml",false,true);
+            IHistogramFactory hf = af.createHistogramFactory(tree);
+            setupHistograms(hf);
+            if(display){
+                setupPlotter(af);
+            }
+            ConditionsDriver hack = new ConditionsDriver();
+            //hack.setXmlConfigResource("/u/group/hps/hps_soft/detector-data/detectors/HPS-EngRun2015-Nominal-v3");
+            hack.setDetectorName("HPS-EngRun2015-Nominal-v3");
+            hack.setFreeze(true);
+            hack.setRunNumber(Integer.parseInt(arg[3]));
+            
+            hack.initialize();
+            beamTiltY = Double.parseDouble(arg[4]);
+            beamTiltX = Double.parseDouble(arg[5]);
+            LCIOReader reader = new LCIOReader(new File(input));
+            //reader.open(input);
+            //reader.
+            EventHeader event = reader.read();
+            int nEvents = 0;
+            try{
+                outer : while(event != null){
+                    processEvent(event);
+
+                    //System.out.println(Q2);
+
+                    event = reader.read();
+                }
+            } catch (Exception e){
+                e.printStackTrace();
+            }
+            tree.commit();
+            tree.close();
+        }
+
+    }
+
+    static IHistogram2D h1, h2, h2a, h2b, h2c;
+    static IHistogram2D h4,h4a;
+    static IHistogram1D h3, /*h3a,*/ h3_t, h3_b;
+    static IHistogram1D h5, h5a; 
+    //static IHistogram2D h6, h6a;
+    static IHistogram1D h7, h7a;
+    static IHistogram1D h8;
+    static IHistogram1D h9_t, h9_b;
+    static IHistogram1D h10_t, h10_b;
+    private static IHistogram1D h4y;
+
+    private static void extractHistograms(ITree tree0) {
+        h1 = (IHistogram2D) tree0.find("theta vs energy");
+
+        h2 = (IHistogram2D) tree0.find("theta vs phi");
+        h2a = (IHistogram2D) tree0.find("theta vs phi cut");
+        h2b = (IHistogram2D) tree0.find("theta vs phi cut alt");
+        h2c = (IHistogram2D) tree0.find("theta vs phi alt");
+
+        h3 = (IHistogram1D) tree0.find("theta");
+        //h3a = (IHistogram1D) tree0.find("theta isolated ");
+        h3_t = (IHistogram1D) tree0.find("theta top");
+        h3_b = (IHistogram1D) tree0.find("theta bottom");
+        
+        h4 = (IHistogram2D) tree0.find("px\\/pz vs py\\/pz");
+        h4a = (IHistogram2D) tree0.find("px\\/pz vs py\\/pz cut");
+        System.out.println(h4a.xAxis().bins());
+        h5 = (IHistogram1D) tree0.find("energy top");
+        h5 = (IHistogram1D) tree0.find("energy bottom");
+
+//      h6 = (IHistogram2D) tree0.find("cluster");
+//      h6a = (IHistogram2D) tree0.find("cluster matched");
+        h7 = (IHistogram1D) tree0.find("y top");
+        h7a = (IHistogram1D) tree0.find("y bottom");
+        h8 = (IHistogram1D) tree0.find("seed energy");
+        
+
+        h9_t = (IHistogram1D) tree0.find("pz top");
+        h9_b = (IHistogram1D) tree0.find("pz bottom");
+        
+
+        h10_t = (IHistogram1D) tree0.find("clustsize top");
+        h10_b = (IHistogram1D) tree0.find("clustsize bottom");
+
+    }
+    static void setupHistograms(IHistogramFactory hf){
+        //h1 = hf.createHistogram2D("px\\/pz vs py\\/pz", 160, -.16, .24, 160, -.2, .2);
+
+
+
+
+        h2 = hf.createHistogram2D("theta vs phi", 300, 0, .3, 314, -3.14, 3.14);
+
+        h2a = hf.createHistogram2D("theta vs phi cut", 300, 0, .3, 314, -3.14, 3.14);
+
+        double thetaBins[] = new double[cb.nTheta+1];
+        for(int i = 0; i<cb.nTheta; i++){
+            thetaBins[i] = cb.thetaMin[i];
+        }
+
+        thetaBins[thetaBins.length-1] = cb.thetaMax[cb.nTheta-1];
+
+        double phiBins[] = new double[315];
+        for(int i = 0; i<315; i++){
+            phiBins[i] = i/50.-3.14;  //every 10 mrad;
+        }
+
+        double eBins[] = new double[66];
+        for(int i = 0; i<66; i++){
+            eBins[i] = i/50.;  //every 20 MeV up to 1300 MeV
+        }
+
+
+        h1 = hf.createHistogram2D("theta vs energy", "theta vs energy", thetaBins, eBins);
+
+
+        //identical to h2a, except different binning
+        h2b = hf.createHistogram2D("theta vs phi cut alt", "theta vs phi cut alt", thetaBins, phiBins);
+        h2c = hf.createHistogram2D("theta vs phi alt", "theta vs phi alt", thetaBins, phiBins);
+
+        h3 = hf.createHistogram1D("theta", "theta", thetaBins);
+//      h3a = hf.createHistogram1D("theta isolated ", "theta isolated", thetaBins);
+
+        h3_t = hf.createHistogram1D("theta top", "theta top", thetaBins);
+        h3_b = hf.createHistogram1D("theta bottom", "theta bottom", thetaBins);
+
+        
+        h4 = hf.createHistogram2D("px\\/pz vs py\\/pz", 300, -.16, .24, 300, -.2, .2);
+        h4a = hf.createHistogram2D("px\\/pz vs py\\/pz cut", 300, -.16, .24, 300, -.2, .2);
+        h4y = hf.createHistogram1D("py\\pz", 1200, -.06, .06);
+        
+        h5 = hf.createHistogram1D("energy top", 75, 0, 1.5);
+        h5a = hf.createHistogram1D("energy bottom", 75, 0, 1.5);
+        
+
+        h9_t = hf.createHistogram1D("pz top", 75, 0, 1.5);
+        h9_b = hf.createHistogram1D("pz bottom", 75, 0, 1.5);
+        
+//      h6 = hf.createHistogram2D("cluster", 47, -23.5, 23.5, 11, -5.5, 5.5);
+//      h6a = hf.createHistogram2D("cluster matched", 47, -23.5, 23.5, 11, -5.5, 5.5);
+
+        h7 = hf.createHistogram1D("y top", 500, 0, 100);
+
+        h7a = hf.createHistogram1D("y bottom", 500, 0, 100);
+
+        h8 = hf.createHistogram1D("seed energy", 120, 0, 1.2);
+        
+        h10_t = hf.createHistogram1D("clustsize top", 10,0, 10);
+        h10_b = hf.createHistogram1D("clustsize bottom", 10,0, 10);
+    }
+    static void setupPlotter(IAnalysisFactory af){
+        IPlotterFactory pf = af.createPlotterFactory();
+        IPlotter p = pf.create();
+        p.createRegions(2,2);
+        p.region(0).plot(h2);
+        StyleUtil.stylize(p.region(0), "theta", "phi");
+//      p.region(1).plot(h3a);
+        StyleUtil.stylize(p.region(1), "theta", "# of particles");
+        p.region(2).plot(h9_t);
+        p.region(2).plot(h9_b);
+        StyleUtil.noFillHistogramBars(p.region(2));
+        StyleUtil.stylize(p.region(2), "pztilt" ,"pztilt", "# of particles");
+        p.region(3).plot(h5);
+        p.region(3).plot(h5a);
+        StyleUtil.noFillHistogramBars(p.region(3));
+        StyleUtil.stylize(p.region(3), "energy", "# of particles");
+
+        p.show();
+        
+        //new window for the next plot
+        IPlotter p2 = pf.create();
+        p2.region(0).plot(h2b);
+        //IDataPointSetFactory dpsf = af.createDataPointSetFactory(af.createTreeFactory().create());
+
+        StyleUtil.stylize(p2.region(0), "theta", "phi");
+
+        p2.show();
+
+        //new window for the next plot
+        IPlotter p3 = pf.create();
+        p3.region(0).plot(h2c);
+        StyleUtil.stylize(p3.region(0), "theta", "phi");
+
+        p3.show();
+
+        //new window for the next plot
+        IPlotter p4 = pf.create();
+        p4.region(0).plot(h4);
+        StyleUtil.stylize(p4.region(0), "px/pz", "py/pz");
+
+        p4.show();
+
+        //new window for the next plot
+        IPlotter p5 = pf.create();
+        p5.region(0).plot(h4a);
+        StyleUtil.stylize(p5.region(0), "px/pz", "py/pz");
+
+        p5.show();
+
+        IPlotter p6 = pf.create("efficiency");
+        p6.createRegions(1,2);
+//      p6.region(0).plot(h6);
+        StyleUtil.stylize(p6.region(0), "ix", "iy");
+//      p6.region(1).plot(h6a);
+        StyleUtil.stylize(p6.region(1), "ix", "iy");
+        p6.show();
+
+        IPlotter p7 = pf.create("theta vs energy");
+        //p6.createRegions(1,2);
+        p7.region(0).plot(h1);
+        StyleUtil.stylize(p7.region(0), "theta", "energy");
+        //      StyleUtil.stylize(p6.region(1), "ix", "iy");
+        p7.show();
+
+        IPlotter p8 = pf.create("y");
+        //p6.createRegions(1,2);
+        p8.region(0).plot(h7);
+        p8.region(0).plot(h7a);
+        StyleUtil.stylize(p8.region(0), "y", "# of particles");
+        //      StyleUtil.stylize(p6.region(1), "ix", "iy");
+        p8.show();
+        
+        IPlotter p9 = pf.create("theta: top vs. bottom");
+        //p6.createRegions(1,2);
+        p9.region(0).plot(h3_t);
+        p9.region(0).plot(h3_b);
+        StyleUtil.stylize(p9.region(0), "theta", "theta", "# of particles");
+        StyleUtil.noFillHistogramBars(p9.region(0));
+                //StyleUtil.stylize(p6.region(1), "ix", "iy");
+        p9.show();
+        
+        IPlotter p10 = pf.create("seed energy");
+        //p6.createRegions(1,2);
+        p10.createRegions(2,1);
+        p10.region(0).plot(h8);
+        StyleUtil.stylize(p10.region(0), "seed energy", "seed energy (GeV)", "# of particles");
+        
+        p10.region(1).plot(h10_t);
+        p10.region(1).plot(h10_b);
+        StyleUtil.noFillHistogramBars(p10.region(1));
+        StyleUtil.stylize(p10.region(1), "clust size", "n ecal hits", "# of particles");
+        
+        //StyleUtil.noFillHistogramBars(p10.region(0));
+                //StyleUtil.stylize(p6.region(1), "ix", "iy");
+        p10.show();
+
+    }
+    private static void processEvent(EventHeader event) {
+        if(event.getEventNumber() %10000 == 0)
+            System.out.println("event number " + event.getEventNumber());
+
+        for (GenericObject gob : event.get(GenericObject.class,"TriggerBank"))
+        {
+            if (!(AbstractIntData.getTag(gob) == TIData.BANK_TAG)) continue;
+            TIData tid = new TIData(gob);
+            if (!tid.isSingle1Trigger())
+            {
+                return;
+            }
+        }
+        List<ReconstructedParticle> particles = event.get(ReconstructedParticle.class, "FinalStateParticles");
+        particles = RemoveDuplicateParticles.removeDuplicateParticles(particles);
+        outer : for(ReconstructedParticle p : particles){
+            
+
+            boolean isGood = addParticle(p);
+            
+
+        }
+        
+    }
+
+    
+
+    static double eMin = .8;
+    static double eMax = 1.2;
+    static double beamEnergy = 1.057;
+
+    static double beamTiltX = .03057;
+    static double beamTiltY;
+    static double maxChi2 = 50;
+    //maximum difference between the reconstructed energy and momentum
+    static double maxdE = .5;
+
+    static double seedEnergyCut = .4;
+
+
+    static boolean addParticle(ReconstructedParticle part){
+        if(part.getTracks().size() != 0){
+            if(part.getMomentum().magnitudeSquared() > .8
+                    && part.getTracks().get(0).getChi2() > maxChi2){
+                h4y.fill(part.getMomentum().y()/part.getMomentum().z());
+            }
+        }
+        if(part.getCharge() != -1)
+            return false;
+        if(part.getClusters().size() == 0)
+            return false;
+        Cluster c = part.getClusters().get(0);
+        double time = c.getCalorimeterHits().get(0).getTime();
+
+        if(!(time>40 && time <50))
+            return false;
+        double seedEnergy = 0;
+        for(CalorimeterHit hit : c.getCalorimeterHits()){
+            if(hit.getCorrectedEnergy() > seedEnergy)
+                seedEnergy = hit.getCorrectedEnergy();
+        }
+        h8.fill(seedEnergy);
+        
+        
+        if(seedEnergy < seedEnergyCut)
+            return false;
+        
+        if(c.getPosition()[1] > 0){
+            h10_t.fill(c.getSize());
+        }
+        else{ 
+            h10_b.fill(c.getSize());
+        }
+        
+        
+        if(c.getCalorimeterHits().size() < 3)
+            return false;
+        
+
+        if(c.getEnergy() > eMin && c.getEnergy() < eMax){
+            if(c.getPosition()[1] > 0)
+                h7.fill(c.getPosition()[1]);
+            else if(c.getPosition()[1] < 0)
+                h7a.fill(-c.getPosition()[1]);
+        }
+        
+        if(EcalUtil.fid_ECal(c)){
+            
+            if(c.getPosition()[1] > 0){
+                h5.fill(c.getEnergy());
+            }
+            else{ 
+                h5a.fill(c.getEnergy());
+            }
+            if(part.getTracks().size() == 0)
+                return false;
+            Track t = part.getTracks().get(0);
+            if(t.getChi2()>maxChi2){
+                return false;
+            }
+            if(!TrackType.isGBL(t.getType()))
+                return false;
+            
+            
+            
+            Hep3Vector p = part.getMomentum();
+
+
+
+            double px = p.x(), pz = p.z();
+            double pxtilt = px*Math.cos(beamTiltX)-pz*Math.sin(beamTiltX);
+            double py = p.y();
+            double pztilt = pz*Math.cos(beamTiltX)+px*Math.sin(beamTiltX);
+            
+            double pytilt = py*Math.cos(beamTiltY)-pztilt*Math.sin(beamTiltY);
+            pztilt = pz*Math.cos(beamTiltY) + pytilt*Math.sin(beamTiltY);
+
+            if(Math.abs(pztilt - c.getEnergy()) > maxdE)
+                return false;
+            if(c.getPosition()[1] > 0)
+                h9_t.fill(pztilt);
+            else
+                h9_b.fill(pztilt);
+
+            double theta = Math.atan(Math.hypot(pxtilt, pytilt)/pztilt);
+            double phi =Math.atan2(pytilt, pxtilt);
+            boolean inRange = cb.inRange(theta, phi);
+            if(inRange)
+                h1.fill(theta, c.getEnergy());
+
+
+
+            if(c.getEnergy() > eMin && c.getEnergy() < eMax) {
+
+
+
+                h2.fill(theta, phi);
+                h2c.fill(theta, phi);
+
+                h4.fill(px/pz, py/pz);
+                //h4y.fill(py/pz);
+
+                if(inRange){
+
+                    //System.out.println(c.getEnergy() + " " + t.getType());
+                    /*for(TrackState ts : t.getTrackStates()){
+                        if(ts.getLocation() == TrackState.AtIP)
+                            System.out.println(Arrays.toString( 
+                                    ts.getReferencePoint()));
+                    }*/
+                    h2a.fill(theta, phi);
+                    h2b.fill(theta, phi);
+                    
+                    h3.fill(theta);
+                    if(py > 0)
+                        h3_t.fill(theta);
+                    else 
+                        h3_b.fill(theta);
+                    //if(h3_t.sumBinHeights()+h3_b.sumBinHeights() != h3.sumBinHeights())
+                        //System.out.println("NABO ERROR");
+                    
+                    
+                    h4a.fill(px/pz, py/pz);
+                }
+
+
+                return true;
+            }
+
+        }
+        return false;
+    }
+    
 }

Modified: java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinning.java
 =============================================================================
--- java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinning.java	(original)
+++ java/branches/HPSJAVA-409/users/src/main/java/org/hps/users/spaul/feecc/ShowCustomBinning.java	Wed Apr 27 11:11:32 2016
@@ -2,10 +2,16 @@
 
 import java.awt.Canvas;
 import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
 import java.io.File;
 import java.io.FileNotFoundException;
-
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
 import javax.swing.JFrame;
 
 import hep.aida.IAnalysisFactory;
@@ -18,201 +24,277 @@
 import hep.aida.ITreeFactory;
 
 public class ShowCustomBinning extends Canvas{
-	/**
-	 * show Rafo's fiducial cuts translated into rotated theta and phi, 
-	 * and overlay this with my bins in x and y.  
-	 * @param arg
-	 * @throws FileNotFoundException 
-	 */
-	public static void main(String arg[]) throws FileNotFoundException{
-		JFrame frame = new JFrame();
-		frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-		frame.add(new ShowCustomBinning(new File(arg[0])));
-		frame.setSize(800, 800);
-		frame.setVisible(true);
-		
-	}
-	public void paint(Graphics g){
-		drawEcalOutline(g);
-		drawFidEcalOutline(g);
-		drawCustomBinRectangles(g);
-	}
-	
-	void drawFidEcalOutline(Graphics g){
-		g.setColor(Color.GRAY);
-		double x_edge_low = -262.74;
-		double x_edge_high = 347.7;
-		double y_edge_low = 33.54;
-		double y_edge_high = 75.18;
-
-		double x_gap_low = -106.66;
-		double x_gap_high = 42.17;
-		double y_gap_high = 47.18;
-		double x1,y1, x2, y2;
-		double nPoints = 500;
-		for(int i = 0; i< nPoints-1; i++){
-			x1 = x_gap_high+i/nPoints*(x_edge_high-x_gap_high);
-			x2 = x_gap_high+(i+1)/nPoints*(x_edge_high-x_gap_high);
-			y1 = y_edge_low;
-			y2 = y1;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			
-			x1 = x_edge_low+i/nPoints*(x_gap_low-x_edge_low);
-			x2 = x_edge_low+(i+1)/nPoints*(x_gap_low-x_edge_low);
-			y1 = y2 = y_edge_low;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			
-			
-			x1 = x_gap_low+i/nPoints*(x_gap_high-x_gap_low);
-			x2 = x_gap_low+(i+1)/nPoints*(x_gap_high-x_gap_low);
-			y1 = y2 = y_gap_high;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			x1 = x_edge_low+i/nPoints*(x_edge_high-x_edge_low);
-			x2 = x_edge_low+(i+1)/nPoints*(x_edge_high-x_edge_low);
-			y1 = y2 = y_edge_high;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-		}
-		drawEcalFaceLine(g, x_gap_low, y_edge_low, x_gap_low, y_gap_high);
-		drawEcalFaceLine(g, x_gap_high, y_edge_low, x_gap_high, y_gap_high);
-
-		drawEcalFaceLine(g, x_edge_low, y_edge_low, x_edge_low, y_edge_high);
-		drawEcalFaceLine(g, x_edge_high, y_edge_low, x_edge_high, y_edge_high);
-		
-
-		drawEcalFaceLine(g, x_gap_low, -y_edge_low, x_gap_low, -y_gap_high);
-		drawEcalFaceLine(g, x_gap_high, -y_edge_low, x_gap_high, -y_gap_high);
-
-		drawEcalFaceLine(g, x_edge_low, -y_edge_low, x_edge_low, -y_edge_high);
-		drawEcalFaceLine(g, x_edge_high, -y_edge_low, x_edge_high, -y_edge_high);
-	
-	}
-	
-	void drawEcalOutline(Graphics g){
-		g.setColor(Color.BLACK);
-		double x_edge_low = -276.50;
-		double x_edge_high = 361.55;
-		double y_edge_low = 20.17;
-		double y_edge_high = 89;
-
-		double x_gap_low = -93.30;
-		double x_gap_high = 28.93;
-		double y_gap_high = 33.12;
-		double x1,y1, x2, y2;
-		double nPoints = 500;
-		for(int i = 0; i< nPoints-1; i++){
-			x1 = x_gap_high+i/nPoints*(x_edge_high-x_gap_high);
-			x2 = x_gap_high+(i+1)/nPoints*(x_edge_high-x_gap_high);
-			y1 = y_edge_low;
-			y2 = y1;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			
-			x1 = x_edge_low+i/nPoints*(x_gap_low-x_edge_low);
-			x2 = x_edge_low+(i+1)/nPoints*(x_gap_low-x_edge_low);
-			y1 = y2 = y_edge_low;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			
-			
-			x1 = x_gap_low+i/nPoints*(x_gap_high-x_gap_low);
-			x2 = x_gap_low+(i+1)/nPoints*(x_gap_high-x_gap_low);
-			y1 = y2 = y_gap_high;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-			
-			x1 = x_edge_low+i/nPoints*(x_edge_high-x_edge_low);
-			x2 = x_edge_low+(i+1)/nPoints*(x_edge_high-x_edge_low);
-			y1 = y2 = y_edge_high;
-			drawEcalFaceLine(g, x1, y1, x2, y2);
-			drawEcalFaceLine(g, x1, -y1, x2, -y2);
-		}
-		drawEcalFaceLine(g, x_gap_low, y_edge_low, x_gap_low, y_gap_high);
-		drawEcalFaceLine(g, x_gap_high, y_edge_low, x_gap_high, y_gap_high);
-
-		drawEcalFaceLine(g, x_edge_low, y_edge_low, x_edge_low, y_edge_high);
-		drawEcalFaceLine(g, x_edge_high, y_edge_low, x_edge_high, y_edge_high);
-		
-
-		drawEcalFaceLine(g, x_gap_low, -y_edge_low, x_gap_low, -y_gap_high);
-		drawEcalFaceLine(g, x_gap_high, -y_edge_low, x_gap_high, -y_gap_high);
-
-		drawEcalFaceLine(g, x_edge_low, -y_edge_low, x_edge_low, -y_edge_high);
-		drawEcalFaceLine(g, x_edge_high, -y_edge_low, x_edge_high, -y_edge_high);
-	}
-	
-	CustomBinning binning;
-	
-	ShowCustomBinning(File file) throws FileNotFoundException{
-		this.binning = new CustomBinning(file);
-		print(this.binning);
-	}
-	Color altBin1 = new Color(0, 0, 128);
-	Color altBin2 = new Color(0,128,0);
-	void drawCustomBinRectangles(Graphics g){
-		for(int i = 0; i<binning.nTheta; i++){
-			g.setColor(i%2 == 0 ? altBin1 : altBin2);
-			for(int j = 0; j<binning.phiMax[i].length; j++){
-				double phi1 = binning.phiMax[i][j];
-				double phi2 = binning.phiMin[i][j];
-				double theta1 = binning.thetaMin[i];
-				double theta2 = binning.thetaMax[i];
-				
-				int x =getX(theta1)+1, y = getY(phi1), w =  getX(theta2)-getX(theta1), h = getY(phi2)-getY(phi1);
-				g.drawRect(x, y, w, h);
-				 x =getX(theta1)+1; y = getY(-phi2); w =  getX(theta2)-getX(theta1); h = getY(-phi1)-getY(-phi2);
-
-				g.drawRect(x, y, w, h);
-				
-				
-			}
-		}
-	}
-	
-	
-	void drawEcalFaceLine(Graphics g, double x1, double y1, double x2, double y2){
-
-		double[] polar1 = EcalUtil.getThetaPhiSpherical(x1, y1);
-		double[] polar2 = EcalUtil.getThetaPhiSpherical(x2, y2);
-		g.drawLine(getX(polar1[0]), getY(polar1[1]), getX(polar2[0]), getY(polar2[1]));
-		
-	}
-	int getX(double theta){
-		return (int)(this.getWidth()*theta/.3);
-	}
-	int getY(double phi){
-		return (int)(this.getHeight()*(3.2-phi)/6.4);
-	}
-	static void print(CustomBinning binning){
-		System.out.println("  Bin \\# &	$\\theta_{\\textrm{min}}$ &	$\\theta_{\\textrm{max}}$ & $\\phi_{\\textrm{min 1}}$ &	$\\phi_{\\textrm{max 1}}$ & $\\phi_{\\textrm{min 2}}$ & $\\phi_{\\textrm{max 2}}$ & Solid angle  \\\\");
-		for(int i = 0; i<binning.nTheta; i++){
-			if(binning.phiMax[i].length == 1)
-				System.out.printf("%d & %.0f & %.0f & %.0f & %.0f & -- & -- & %.0f \\\\\n",
-					i+1,
-					binning.thetaMin[i]*1000,
-					binning.thetaMax[i]*1000,
-					binning.phiMin[i][0]*1000,
-					binning.phiMax[i][0]*1000.,
-					binning.getSteradians(i)*1e6);
-			if(binning.phiMax[i].length == 2)
-				System.out.printf("%d & %.0f & %.0f & %.0f & %.0f & %.0f & %.0f & %.0f \\\\\n",
-					i+1,
-					binning.thetaMin[i]*1000,
-					binning.thetaMax[i]*1000,
-					binning.phiMin[i][0]*1000,
-					binning.phiMax[i][0]*1000,
-					binning.phiMin[i][1]*1000,
-					binning.phiMax[i][1]*1000,
-					binning.getSteradians(i)*1e6);
-		}
-		System.out.println("total " + binning.getTotSteradians()*1e6 + " microsteradians");
-	} 
+    /**
+     * show Rafo's fiducial cuts translated into rotated theta and phi, 
+     * and overlay this with my bins in x and y.  
+     * @param arg
+     * @throws FileNotFoundException 
+     */
+    public static void main(String arg[]) throws FileNotFoundException{
+        JFrame frame = new JFrame();
+        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        Canvas c = new ShowCustomBinning(new File(arg[0]));
+        String outdir = arg[1];
+        frame.add(c);
+        frame.setSize(1200, 800);
+        frame.setVisible(true);
+        
+        
+        try {
+            BufferedImage im = new BufferedImage(c.getWidth(), c.getHeight(), BufferedImage.TYPE_INT_ARGB);
+            c.paint(im.getGraphics());
+            ImageIO.write(im, "PNG", new File(outdir +"/bins.png"));
+        } catch (IOException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
+        
+        frame = new JFrame();
+        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        c = new ShowCustomBinningXY(new File(arg[0]));
+        frame.add(c);
+        frame.setSize(1200, 615);
+        frame.setVisible(true);
+        
+        try {
+            BufferedImage im = new BufferedImage(c.getWidth(), c.getHeight(), BufferedImage.TYPE_INT_ARGB);
+            c.paint(im.getGraphics());
+            ImageIO.write(im, "PNG", new File(outdir + "/bins_xy.png"));
+        } catch (IOException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        }
+    }
+    public void paint(Graphics g){
+        g.setFont(new Font(Font.DIALOG, Font.PLAIN, 24));
+        
+        drawEcalOutline(g);
+        drawFidEcalOutline(g);
+        drawCustomBinRectangles(g);
+        g.setColor(Color.BLACK);
+        drawXAxis(g);
+        drawYAxis(g);
+    }
+    
+    void drawFidEcalOutline(Graphics g){
+        g.setColor(Color.GRAY);
+        double x_edge_low = -262.74;
+        double x_edge_high = 347.7;
+        double y_edge_low = 33.54;
+        double y_edge_high = 75.18;
+
+        double x_gap_low = -106.66;
+        double x_gap_high = 42.17;
+        double y_gap_high = 47.18;
+        double x1,y1, x2, y2;
+        double nPoints = 500;
+        for(int i = 0; i< nPoints-1; i++){
+            x1 = x_gap_high+i/nPoints*(x_edge_high-x_gap_high);
+            x2 = x_gap_high+(i+1)/nPoints*(x_edge_high-x_gap_high);
+            y1 = y_edge_low;
+            y2 = y1;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            
+            x1 = x_edge_low+i/nPoints*(x_gap_low-x_edge_low);
+            x2 = x_edge_low+(i+1)/nPoints*(x_gap_low-x_edge_low);
+            y1 = y2 = y_edge_low;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            
+            
+            x1 = x_gap_low+i/nPoints*(x_gap_high-x_gap_low);
+            x2 = x_gap_low+(i+1)/nPoints*(x_gap_high-x_gap_low);
+            y1 = y2 = y_gap_high;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            x1 = x_edge_low+i/nPoints*(x_edge_high-x_edge_low);
+            x2 = x_edge_low+(i+1)/nPoints*(x_edge_high-x_edge_low);
+            y1 = y2 = y_edge_high;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+        }
+        drawEcalFaceLine(g, x_gap_low, y_edge_low, x_gap_low, y_gap_high);
+        drawEcalFaceLine(g, x_gap_high, y_edge_low, x_gap_high, y_gap_high);
+
+        drawEcalFaceLine(g, x_edge_low, y_edge_low, x_edge_low, y_edge_high);
+        drawEcalFaceLine(g, x_edge_high, y_edge_low, x_edge_high, y_edge_high);
+        
+
+        drawEcalFaceLine(g, x_gap_low, -y_edge_low, x_gap_low, -y_gap_high);
+        drawEcalFaceLine(g, x_gap_high, -y_edge_low, x_gap_high, -y_gap_high);
+
+        drawEcalFaceLine(g, x_edge_low, -y_edge_low, x_edge_low, -y_edge_high);
+        drawEcalFaceLine(g, x_edge_high, -y_edge_low, x_edge_high, -y_edge_high);
+    
+    }
+    
+    void drawEcalOutline(Graphics g){
+        /*double x_edge_low = -262.74;
+        double x_edge_high = 347.7;
+        double y_edge_low = 33.54;
+        double y_edge_high = 75.18;
+
+        double x_gap_low = -106.66;
+        double x_gap_high = 42.17;
+        double y_gap_high = 47.18;*/
+        
+        g.setColor(Color.BLACK);
+        double x_edge_low = -269.56;
+        double x_edge_high = 354.52;
+        double y_edge_low = 26.72;
+        double y_edge_high = 82;
+
+        double x_gap_low = -99.84;
+        double x_gap_high = 33.35;
+        double y_gap_high = 40.36;
+        double x1,y1, x2, y2;
+        double nPoints = 500;
+        for(int i = 0; i< nPoints-1; i++){
+            x1 = x_gap_high+i/nPoints*(x_edge_high-x_gap_high);
+            x2 = x_gap_high+(i+1)/nPoints*(x_edge_high-x_gap_high);
+            y1 = y_edge_low;
+            y2 = y1;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            
+            x1 = x_edge_low+i/nPoints*(x_gap_low-x_edge_low);
+            x2 = x_edge_low+(i+1)/nPoints*(x_gap_low-x_edge_low);
+            y1 = y2 = y_edge_low;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            
+            
+            x1 = x_gap_low+i/nPoints*(x_gap_high-x_gap_low);
+            x2 = x_gap_low+(i+1)/nPoints*(x_gap_high-x_gap_low);
+            y1 = y2 = y_gap_high;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+            
+            x1 = x_edge_low+i/nPoints*(x_edge_high-x_edge_low);
+            x2 = x_edge_low+(i+1)/nPoints*(x_edge_high-x_edge_low);
+            y1 = y2 = y_edge_high;
+            drawEcalFaceLine(g, x1, y1, x2, y2);
+            drawEcalFaceLine(g, x1, -y1, x2, -y2);
+        }
+        drawEcalFaceLine(g, x_gap_low, y_edge_low, x_gap_low, y_gap_high);
+        drawEcalFaceLine(g, x_gap_high, y_edge_low, x_gap_high, y_gap_high);
+
+        drawEcalFaceLine(g, x_edge_low, y_edge_low, x_edge_low, y_edge_high);
+        drawEcalFaceLine(g, x_edge_high, y_edge_low, x_edge_high, y_edge_high);
+        
+
+        drawEcalFaceLine(g, x_gap_low, -y_edge_low, x_gap_low, -y_gap_high);
+        drawEcalFaceLine(g, x_gap_high, -y_edge_low, x_gap_high, -y_gap_high);
+
+        drawEcalFaceLine(g, x_edge_low, -y_edge_low, x_edge_low, -y_edge_high);
+        drawEcalFaceLine(g, x_edge_high, -y_edge_low, x_edge_high, -y_edge_high);
+    }
+    
+    CustomBinning binning;
+    
+    ShowCustomBinning(File file) throws FileNotFoundException{
+        this.binning = new CustomBinning(file);
+        print(this.binning);
+    }
+    Color altBin1 = new Color(0, 0, 128);
+    Color altBin2 = new Color(0,128,0);
+    Color fillBin1 = new Color(196, 196, 255);
+    Color fillBin2 = new Color(196,255,196);
+    void drawCustomBinRectangles(Graphics g){
+        for(int i = 0; i<binning.nTheta; i++){
+            g.setColor(i%2 == 0 ? altBin1 : altBin2);
+            for(int j = 0; j<binning.phiMax[i].length; j++){
+                double phi1 = binning.phiMax[i][j];
+                double phi2 = binning.phiMin[i][j];
+                double theta1 = binning.thetaMin[i];
+                double theta2 = binning.thetaMax[i];
+                
+                int x =getX(theta1)+1, y = getY(phi1), w =  getX(theta2)-getX(theta1), h = getY(phi2)-getY(phi1);
+
+                g.setColor(i%2 == 0 ? fillBin1 : fillBin2);
+                g.fillRect(x, y, w, h);
+                g.setColor(i%2 == 0 ? altBin1 : altBin2);
+                g.drawRect(x, y, w, h);
+                 x =getX(theta1)+1; y = getY(-phi2); w =  getX(theta2)-getX(theta1); h = getY(-phi1)-getY(-phi2);
+                 g.setColor(i%2 == 0 ? fillBin1 : fillBin2);
+                    g.fillRect(x, y, w, h);
+                    g.setColor(i%2 == 0 ? altBin1 : altBin2);
+                    g.drawRect(x, y, w, h);
+            }
+            
+        }
+    }
+    void drawXAxis(Graphics g){
+        //x axis
+        g.drawString("θ", getX(.28), getY(0) - 40);
+        g.drawLine(getX(0), getY(0), getX(.28), getY(0));
+        for(int i = 0; i< 28; i++){
+            if(i%5 == 0 && i != 0){
+                g.drawString(i/100.+"", getX(i/100.)-15, getY(0)-20);
+                g.drawLine(getX(i/100.), getY(0), getX(i/100.), getY(0)-15);
+            }
+            g.drawLine(getX(i/100.), getY(0), getX(i/100.), getY(0)-5);
+        }
+    }
+    void drawYAxis(Graphics g){
+        g.drawString("φ", getX(0)+70, getY(3));
+        g.drawLine(getX(0), getY(-3), getX(0), getY(3));
+        for(int i = -30; i<= 30; i++){
+            if(i%5 == 0 && i != 0){
+                g.drawString(i/10.+"", getX(0)+20, getY(i/10.) + 5);
+
+                g.drawLine(getX(0), getY(i/10.), getX(0) + 15, getY(i/10.));
+            }
+            if(i == 0){
+                //g.drawString(i/10.+"", getX(0)+10, getY(i/10.) - 15);
+            }
+            g.drawLine(getX(0), getY(i/10.), getX(0) + 5, getY(i/10.));
+        }
+    }
+    
+    
+    void drawEcalFaceLine(Graphics g, double x1, double y1, double x2, double y2){
+
+        double[] polar1 = EcalUtil.getThetaPhiSpherical(x1, y1);
+        double[] polar2 = EcalUtil.getThetaPhiSpherical(x2, y2);
+        g.drawLine(getX(polar1[0]), getY(polar1[1]), getX(polar2[0]), getY(polar2[1]));
+        
+    }
+    int getX(double theta){
+        return (int)(this.getWidth()*theta/.3)+left_margin;
+    }
+    int left_margin = 20;
+    int getY(double phi){
+        return (int)(this.getHeight()*(3.2-phi)/6.4);
+    }
+    static void print(CustomBinning binning){
+        System.out.println("  Bin \\# & $\\theta_{\\textrm{min}}$ & $\\theta_{\\textrm{max}}$ & $\\phi_{\\textrm{min 1}}$ & $\\phi_{\\textrm{max 1}}$ & $\\phi_{\\textrm{min 2}}$ & $\\phi_{\\textrm{max 2}}$ & Solid angle  \\\\");
+        for(int i = 0; i<binning.nTheta; i++){
+            if(binning.phiMax[i].length == 1)
+                System.out.printf("%d & %.0f & %.0f & %.0f & %.0f & -- & -- & %.0f \\\\\n",
+                    i+1,
+                    binning.thetaMin[i]*1000,
+                    binning.thetaMax[i]*1000,
+                    binning.phiMin[i][0]*1000,
+                    binning.phiMax[i][0]*1000.,
+                    binning.getSteradians(i)*1e6);
+            if(binning.phiMax[i].length == 2)
+                System.out.printf("%d & %.0f & %.0f & %.0f & %.0f & %.0f & %.0f & %.0f \\\\\n",
+                    i+1,
+                    binning.thetaMin[i]*1000,
+                    binning.thetaMax[i]*1000,
+                    binning.phiMin[i][0]*1000,
+                    binning.phiMax[i][0]*1000,
+                    binning.phiMin[i][1]*1000,
+                    binning.phiMax[i][1]*1000,
+                    binning.getSteradians(i)*1e6);
+        }
+        System.out.println("total " + binning.getTotSteradians()*1e6 + " microsteradians");
+    } 
 }

Modified: java/branches/HPSJAVA-409/util/pom.xml
 =============================================================================
--- java/branches/HPSJAVA-409/util/pom.xml	(original)
+++ java/branches/HPSJAVA-409/util/pom.xml	Wed Apr 27 11:11:32 2016
@@ -7,7 +7,7 @@
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>
-        <version>3.4.2-SNAPSHOT</version>
+        <version>3.9-SNAPSHOT</version>
     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/util/</url>

Modified: java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/CalculateAcceptanceFromMadGraph.java
 =============================================================================
--- java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/CalculateAcceptanceFromMadGraph.java	(original)
+++ java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/CalculateAcceptanceFromMadGraph.java	Wed Apr 27 11:11:32 2016
@@ -21,7 +21,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.lcsim.fit.helicaltrack.HelixParamCalculator;
 
 public class CalculateAcceptanceFromMadGraph {
@@ -165,7 +165,7 @@
         // Set up command line parsing.
         Options options = createCommandLineOptions();
 
-        CommandLineParser parser = new DefaultParser();
+        CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         CommandLine cl = null;

Modified: java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/ConvertToStdhep.java
 =============================================================================
--- java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/ConvertToStdhep.java	(original)
+++ java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/ConvertToStdhep.java	Wed Apr 27 11:11:32 2016
@@ -15,7 +15,6 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import hep.io.stdhep.StdhepBeginRun;
 import hep.io.stdhep.StdhepEndRun;
 import hep.io.stdhep.StdhepEvent;
 import hep.io.stdhep.StdhepWriter;
@@ -31,7 +30,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.lcsim.detector.IRotation3D;
 import org.lcsim.detector.RotationGeant;
 
@@ -95,7 +94,7 @@
         // Set up command line parsing.
         Options options = createCommandLineOptions();
 
-        CommandLineParser parser = new DefaultParser();
+        CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         CommandLine cl = null;
@@ -502,10 +501,10 @@
     }*/
 
     static private double getDecayLength(double gamma){
-    	Random generator = new Random();
-    	double a = generator.nextDouble();
-    	double l = -gamma*_declength*Math.log(1-a);
-    	return l; 
+        Random generator = new Random();
+        double a = generator.nextDouble();
+        double l = -gamma*_declength*Math.log(1-a);
+        return l; 
     }
     
     /*
@@ -724,7 +723,7 @@
                     double gamma = ApEnergy / ApMass;
                     if (expDecay) {
                         decLen = getDecayLength(gamma);
-                    	// decLen = getDecayLength(maxWght, gamma);
+                        // decLen = getDecayLength(maxWght, gamma);
                     }
                     if (flatDecay) {
                         decLen = generator.nextDouble() * maxLen;

Modified: java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/DumpLHEEventsToASCII.java
 =============================================================================
--- java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/DumpLHEEventsToASCII.java	(original)
+++ java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/DumpLHEEventsToASCII.java	Wed Apr 27 11:11:32 2016
@@ -26,7 +26,7 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 import org.lcsim.detector.IRotation3D;
 import org.lcsim.detector.RotationGeant;
 
@@ -89,7 +89,7 @@
         // Set up command line parsing.
         Options options = createCommandLineOptions();
 
-        CommandLineParser parser = new DefaultParser();
+        CommandLineParser parser = new PosixParser();
 
         // Parse command line arguments.
         CommandLine cl = null;
@@ -108,7 +108,7 @@
         String sigyString = String.valueOf(sigy);
         eptString = convertDecimal(eptString);
         if (cl.hasOption("t")) {
-	    trident=true;
+        trident=true;
         }
         if (cl.hasOption("m")) {
             massString = cl.getOptionValue("m");
@@ -475,7 +475,7 @@
             throw new RuntimeException("Unexpected entry for number of particles");
         }
         int nhep = nums.get(0).intValue();
-	//        System.out.println("Number of particles for event " + nevhep + ": " + nhep);
+    //        System.out.println("Number of particles for event " + nevhep + ": " + nhep);
 
         double decLen = 0;
         double maxWght = 0;
@@ -503,14 +503,14 @@
             if (vals.size() != 13) {
                 throw new RuntimeException("Unexpected entry for a particle");
             }
-	    idhepTmp = vals.get(0).intValue();
-//	    System.out.println(idhepTmp);
+        idhepTmp = vals.get(0).intValue();
+//      System.out.println(idhepTmp);
             if (vals.get(1).intValue() == 9) {//apparently, vertices aren't counted in nhep
-		nhep++;
-	    }
+        nhep++;
+        }
 
             if (vals.get(1).intValue() == 1) {//ignore initial  & intermediate state particles
-		//		System.out.println("Ok...good"+idhepTmp);
+        //      System.out.println("Ok...good"+idhepTmp);
 
 
 
@@ -523,8 +523,8 @@
                         phepRec[j] = vals.get(j + 6);
                     if (idhepTmp == -623){
                         phepNuc[j] = vals.get(j + 6);
-			//			System.out.println("Found the recoil nucleus");
-		    }
+            //          System.out.println("Found the recoil nucleus");
+            }
                 }
 
 

Modified: java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/LCIOFilterDriver.java
 =============================================================================
--- java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/LCIOFilterDriver.java	(original)
+++ java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/LCIOFilterDriver.java	Wed Apr 27 11:11:32 2016
@@ -5,7 +5,6 @@
 package org.hps.util;
 import java.io.IOException;
 import org.lcsim.event.EventHeader;
-import org.lcsim.event.Track;
 import org.lcsim.util.Driver;
 import org.lcsim.lcio.LCIOWriter;
 

Modified: java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/MergeBunches.java
 =============================================================================
--- java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/MergeBunches.java	(original)
+++ java/branches/HPSJAVA-409/util/src/main/java/org/hps/util/MergeBunches.java	Wed Apr 27 11:11:32 2016
@@ -34,7 +34,6 @@
 import org.lcsim.lcio.LCIOUtil;
 import org.lcsim.lcio.LCIOWriter;
 import org.lcsim.lcio.SIOMCParticle;
-import org.lcsim.util.loop.LCIODriver;
 
 public class MergeBunches extends Driver {
 
@@ -455,7 +454,6 @@
      * Copies an mc particle and stores it together with  the copy in a map.
      * Adds it to the list of mc particles as well as the overlay mc particles.
      * Also copies and keeps all ancestors.
-     * @param event
      * @param particle
      */
     protected void addOverlayMcParticle(MCParticle particle) {