diff -u -r1.2 -r1.3
--- CruxConfig.java	22 Jan 2009 21:01:55 -0000	1.2
+++ CruxConfig.java	18 Feb 2009 03:29:06 -0000	1.3
@@ -45,7 +45,7 @@

  * </ul>
  *
  * @author D. Onoprienko

- * @version $Id: CruxConfig.java,v 1.2 2009/01/22 21:01:55 onoprien Exp $

+ * @version $Id: CruxConfig.java,v 1.3 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CruxConfig implements JobEventListener, CalGeometryConfig {
   

@@ -89,12 +89,12 @@

     
     // create modules
     

-    CalModule eBar = new CalModule("ECAL_BARREL", EnumSet.of(ECAL, BARREL), "EMBarrel");
-    CalModule hBar = new CalModule("HCAL_BARREL", EnumSet.of(HCAL, BARREL), "HADBarrel");
-    CalModule eSouthEnd = new CalModule("ECAL_ENDCAP_SOUTH", EnumSet.of(ECAL, ENDCAP, SOUTH), "EMEndcap");
-    CalModule eNorthEnd = new CalModule("ECAL_ENDCAP_NORTH", EnumSet.of(ECAL, ENDCAP, NORTH), "EMEndcap");
-    CalModule hSouthEnd = new CalModule("HCAL_ENDCAP_SOUTH", EnumSet.of(HCAL, ENDCAP, SOUTH), "HADEndcap");
-    CalModule hNorthEnd = new CalModule("HCAL_ENDCAP_NORTH", EnumSet.of(HCAL, ENDCAP, NORTH), "HADEndcap");

+    CalModule eBar = new CalModule("ECAL_BARREL", EnumSet.of(ECAL, BARREL, ENTRY), "EMBarrel");
+    CalModule hBar = new CalModule("HCAL_BARREL", EnumSet.of(HCAL, BARREL, EXIT), "HADBarrel");
+    CalModule eSouthEnd = new CalModule("ECAL_ENDCAP_SOUTH", EnumSet.of(ECAL, ENDCAP, SOUTH, ENTRY), "EMEndcap");
+    CalModule eNorthEnd = new CalModule("ECAL_ENDCAP_NORTH", EnumSet.of(ECAL, ENDCAP, NORTH, ENTRY), "EMEndcap");
+    CalModule hSouthEnd = new CalModule("HCAL_ENDCAP_SOUTH", EnumSet.of(HCAL, ENDCAP, SOUTH, EXIT), "HADEndcap");
+    CalModule hNorthEnd = new CalModule("HCAL_ENDCAP_NORTH", EnumSet.of(HCAL, ENDCAP, NORTH, EXIT), "HADEndcap");

     
     _modules = new ArrayList<CalModule>(6);
     Collections.addAll(_modules, eBar, hBar, eSouthEnd, eNorthEnd, hSouthEnd, hNorthEnd);

diff -u -r1.1.1.1 -r1.2
--- CruxManager.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ CruxManager.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -1,16 +1,6 @@

 package org.lcsim.contrib.onoprien.crux;
 

-import java.lang.ref.WeakReference;
-import java.util.*;
-
-import org.lcsim.conditions.ConditionsListener;
-import org.lcsim.conditions.ConditionsEvent;
-import org.lcsim.conditions.ConditionsManager;
-import org.lcsim.conditions.ConditionsManager.ConditionsSetNotFoundException;
-import org.lcsim.event.CalorimeterHit;
-import org.lcsim.event.EventHeader;
-import org.lcsim.geometry.Detector;
-import org.lcsim.util.aida.AIDA;

+import java.util.logging.Level;

 
 import org.lcsim.contrib.onoprien.util.job.Driver;
 import org.lcsim.contrib.onoprien.util.job.JobManager;

@@ -30,7 +20,7 @@

  * 
  * 
  * @author D. Onoprienko

- * @version $Id: CruxManager.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $

+ * @version $Id: CruxManager.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CruxManager extends Driver {
   

@@ -38,8 +28,8 @@

   
   private CruxManager() {
     _config = new CruxConfig();

-    _geom = new CalGeometry(_config);

     JobManager.defaultInstance().put(this, CruxManager.class);

+    log("Created CruxManager", Level.SEVERE);

   }
   
   

@@ -51,13 +41,6 @@

     return _defInstance;
   }
   

-  /**
-   * Returns <tt>CalGeometry</tt> object associated with this <tt>CruxManager</tt>.
-   */
-  public CalGeometry getGeometry() {
-    return _geom;
-  }
-  

   /** Returns <tt>CruxConfig</tt> object associated with this <tt>CruxManager</tt>. */
   public CruxConfig getConfig() {
     return _config;

@@ -81,7 +64,6 @@

   
   static private CruxManager _defInstance;
   

-  private CalGeometry _geom;

   private CruxConfig _config;
   private CruxClusterValidator _defaultClusterValidator;
 }

diff -u -r1.2 -r1.3
--- ClusteringDriver.java	12 Feb 2009 01:32:08 -0000	1.2
+++ ClusteringDriver.java	18 Feb 2009 03:29:06 -0000	1.3
@@ -2,15 +2,16 @@

 
 import java.util.*;
 import java.util.logging.Level;

-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalModule;

 
 import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;
 import org.lcsim.recon.cluster.util.Clusterer;
 
 import org.lcsim.contrib.onoprien.util.job.Driver;

+import org.lcsim.contrib.onoprien.util.job.JobManager;

+import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;
+import org.lcsim.contrib.onoprien.crux.geom.CalModule;

 import org.lcsim.contrib.onoprien.crux.infrastructure.*;
 
 /**

@@ -21,7 +22,7 @@

  * input hit map from the event, 
  *
  * @author D. Onoprienko

- * @version $Id: ClusteringDriver.java,v 1.2 2009/02/12 01:32:08 onoprien Exp $

+ * @version $Id: ClusteringDriver.java,v 1.3 2009/02/18 03:29:06 onoprien Exp $

  */
 public class ClusteringDriver extends Driver {
   

@@ -86,6 +87,7 @@

     super.process(event);
     
     CruxHitMap inMap = (CruxHitMap) event.get(_inMapName);

+    CalGeometry geom = JobManager.defaultInstance().get(CalGeometry.class);

     
     for (int out=0; out<_filters.size(); out++) {
       

@@ -96,8 +98,7 @@

         clusterList = new ArrayList<Cluster>(0);
       } else if (_splitModules) {
         clusterList = new ArrayList<Cluster>();

-        CruxManager cruxMan = CruxManager.defaultInstance();
-        List<CalModule> modules = cruxMan.getGeometry().getModules();

+        List<CalModule> modules = geom.getModules();

         for (CalModule module : modules) {
           CruxHitMap moduleMap = filteredMap.toMap(module);
           if (! moduleMap.isEmpty()) clusterList.addAll(_clusterers.get(out).createClusters(moduleMap));

diff -u -r1.1.1.1 -r1.2
--- DotAndBeadFinder.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ DotAndBeadFinder.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -1,21 +1,22 @@

 package org.lcsim.contrib.onoprien.crux.algorithms.rosary;
 
 import java.util.*;

-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalLayer;
-import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 
 import org.lcsim.event.Cluster;
 import org.lcsim.recon.cluster.nn.NearestNeighborClusterer;
 import org.lcsim.recon.cluster.util.Clusterer;
 

+import org.lcsim.contrib.onoprien.util.job.JobManager;
+
+import org.lcsim.contrib.onoprien.crux.geom.CalLayer;
+import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 import org.lcsim.contrib.onoprien.crux.infrastructure.*;
 
 /**
  * Clusterer that creates {@link Dot}s and {@link Beads} on a layer.
  *
  * @author D. Onoprienko

- * @version $Id: DotAndBeadFinder.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $

+ * @version $Id: DotAndBeadFinder.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class DotAndBeadFinder {
   

@@ -23,7 +24,7 @@

   
   public DotAndBeadFinder() {
     _clusterer = new NearestNeighborClusterer(1, 1, 0, 0, 0.);

-    _geom = CruxManager.defaultInstance().getGeometry();

+    _geom = JobManager.defaultInstance().get(CalGeometry.class);

   }
     
   

diff -u -r1.2 -r1.3
--- RosaryClusterer.java	22 Jan 2009 21:01:56 -0000	1.2
+++ RosaryClusterer.java	18 Feb 2009 03:29:06 -0000	1.3
@@ -3,16 +3,10 @@

 import java.util.*;
 import java.util.logging.Level;
 

-import hep.physics.vec.BasicHep3Vector;

 import hep.physics.vec.Hep3Vector;

-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalLayer;
-import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;
-import org.lcsim.detector.IDetectorElement;

 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.Cluster;
 import org.lcsim.event.EventHeader;

-import org.lcsim.geometry.IDDecoder;

 import org.lcsim.recon.cluster.util.Clusterer;
 
 import org.lcsim.contrib.onoprien.util.job.Driver;

@@ -21,6 +15,8 @@

 import org.lcsim.contrib.onoprien.util.job.JobManager;
 import org.lcsim.contrib.onoprien.util.swim.Trajectory;
 

+import org.lcsim.contrib.onoprien.crux.geom.CalLayer;
+import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 import org.lcsim.contrib.onoprien.crux.infrastructure.*;
 
 import static org.lcsim.contrib.onoprien.crux.algorithms.rosary.RosaryNode.Type.*;

@@ -29,7 +25,7 @@

  *
  *
  * @author D. Onoprienko

- * @version $Id: RosaryClusterer.java,v 1.2 2009/01/22 21:01:56 onoprien Exp $

+ * @version $Id: RosaryClusterer.java,v 1.3 2009/02/18 03:29:06 onoprien Exp $

  */
 public class RosaryClusterer extends Driver implements Clusterer, JobEventListener {
 

@@ -37,9 +33,9 @@

   
   public RosaryClusterer() {
     set("LOG_DEFAULT_LEVEL", Level.FINEST);

-    _cruxMan = CruxManager.defaultInstance();
-    _geom = _cruxMan.getGeometry();
-    JobManager.defaultInstance().addListener(this, _geom);

+    JobManager jobMan = JobManager.defaultInstance();
+    _geom = jobMan.get(CalGeometry.class);
+    jobMan.addListener(this, _geom);

   }
   
   public void detectorChanged(JobEvent jEvent) {

@@ -334,7 +330,6 @@

   
 // -- Private parts :  ---------------------------------------------------------
   

-  protected CruxManager _cruxMan;

   protected CalGeometry _geom;
   
   protected String _inMapName;

diff -u -r1.1 -r1.2
--- CheatClusteringDriver.java	22 Jan 2009 21:12:42 -0000	1.1
+++ CheatClusteringDriver.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -1,8 +1,6 @@

 package org.lcsim.contrib.onoprien.crux.cheat;
 
 import java.util.*;

-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.EventHeader;

@@ -11,21 +9,23 @@

 import org.lcsim.recon.cluster.util.BasicCluster;
 
 import org.lcsim.contrib.onoprien.util.job.Driver;

+import org.lcsim.contrib.onoprien.util.job.JobManager;

+import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 import org.lcsim.contrib.onoprien.crux.infrastructure.*;
 
 /**
  * Cheater that attaches hits and tracks to reconstructed particles.
  *
  * @author D. Onoprienko

- * @version $Id: CheatClusteringDriver.java,v 1.1 2009/01/22 21:12:42 onoprien Exp $

+ * @version $Id: CheatClusteringDriver.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CheatClusteringDriver extends Driver {
   
 // -- Constructors :  ----------------------------------------------------------
   
   public CheatClusteringDriver() {

-    _geom = CruxManager.defaultInstance().getGeometry();

+    _geom = JobManager.defaultInstance().get(CalGeometry.class);

   }
   
 // -- Setters :  ---------------------------------------------------------------

diff -u -r1.3 -r1.4
--- RecoDefinition.java	13 Feb 2009 20:02:18 -0000	1.3
+++ RecoDefinition.java	18 Feb 2009 03:29:06 -0000	1.4
@@ -25,12 +25,14 @@

  * the methods.
  *
  * @author D. Onoprienko

- * @version $Id: RecoDefinition.java,v 1.3 2009/02/13 20:02:18 onoprien Exp $

+ * @version $Id: RecoDefinition.java,v 1.4 2009/02/18 03:29:06 onoprien Exp $

  */
 public class RecoDefinition implements IRecoDefinition {
 
 // -- Private parts :  ---------------------------------------------------------
 

+  protected static String ERR_CNH = "Cannot handle this type of object: ";
+

   private String _name;
   protected EnumMap<RecType, CutSet> _cuts;
 

@@ -142,7 +144,7 @@

   public boolean isFindable(RecType type, MCParticle mcParticle) {
 
     CutSet cutSet = _cuts.get(type);

-    if (cutSet == null) throw new IllegalArgumentException();

+    if (cutSet == null) throw new IllegalArgumentException(ERR_CNH + type);

     
     // Charge cut
     

@@ -174,12 +176,12 @@

   }
 
   public boolean isReconstructed(RecType type, MCParticle mcParticle) {

-    if (!_cuts.containsKey(type)) throw new IllegalArgumentException();

+    if (!_cuts.containsKey(type)) throw new IllegalArgumentException(ERR_CNH + type);

     return true;
   }
   
   public boolean isFake(RecType type, Object recObject) {

-    if (!_cuts.containsKey(type)) throw new IllegalArgumentException();

+    if (!_cuts.containsKey(type)) throw new IllegalArgumentException(ERR_CNH + type);

     return true;
   }
 

diff -u -r1.1 -r1.2
--- RecoDefinitionCrux.java	13 Feb 2009 20:02:18 -0000	1.1
+++ RecoDefinitionCrux.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -30,7 +30,7 @@

  * <tt>endEvent()</tt> to clean it up once the event is processed.
  *
  * @author D. Onoprienko

- * @version $Id: RecoDefinitionCrux.java,v 1.1 2009/02/13 20:02:18 onoprien Exp $

+ * @version $Id: RecoDefinitionCrux.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class RecoDefinitionCrux extends RecoDefinition {
 

@@ -84,7 +84,7 @@

   public void setCut(RecType type, String name, Object... values) {
     try {
       super.setCut(type, name, values);

-    } catch (IllegalArgumentException x) {

+    } catch (NoSuchParameterException x) {

       CutSetCrux cutSet = _cutsCrux.get(type);
       if (cutSet == null) _cutsCrux.put(type, cutSet = new CutSetCrux());
       try {

diff -u -r1.5 -r1.6
--- ClusteringTest.java	13 Feb 2009 20:02:19 -0000	1.5
+++ ClusteringTest.java	18 Feb 2009 03:29:06 -0000	1.6
@@ -26,14 +26,16 @@

  *
  *
  * @author D. Onoprienko

- * @version $Id: ClusteringTest.java,v 1.5 2009/02/13 20:02:19 onoprien Exp $

+ * @version $Id: ClusteringTest.java,v 1.6 2009/02/18 03:29:06 onoprien Exp $

  */
 public class ClusteringTest extends Driver implements JobEventListener {
   
 // -- Constructors and initialization :  ---------------------------------------
   
   public ClusteringTest() {

-    JobManager.defaultInstance().addListener(this, CruxManager.defaultInstance().getGeometry());

+    JobManager jobMan = JobManager.defaultInstance();
+    _geom = jobMan.get(CalGeometry.class);
+    JobManager.defaultInstance().addListener(this, _geom);

   }
   
   /**

@@ -41,10 +43,7 @@

    * Called by {@link CruxManager} before processing events, and whenever detector changes.
    */
   public void detectorChanged(JobEvent jEvent) {

-    

     _aida = JobManager.defaultInstance().getAIDA();

-    
-    _geom = CruxManager.defaultInstance().getGeometry();

     _modules = _geom.getModules();
   }
   

diff -u -r1.1.1.1 -r1.2
--- CalGeometry.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ CalGeometry.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -5,7 +5,6 @@

 import hep.physics.vec.Hep3Vector;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.geometry.Detector;

-import org.lcsim.geometry.Subdetector;

 
 import org.lcsim.contrib.onoprien.util.job.JobEvent;
 import org.lcsim.contrib.onoprien.util.job.JobEventListener;

@@ -13,24 +12,34 @@

 import org.lcsim.contrib.onoprien.util.swim.Trajectory;
 
 /**

- * Singleton of this class is created by {@link CruxManager}, and provides various 
- * detector geometry related services to other classes.

+ * Provides various calorimeter geometry related services to other classes.
+ * Singleton of this class is available at run time through {@link JobManager} by
+ * calling <tt>JobManager.defaultInstance().get(CalGeometry.class)</tt>.

  * 
  * @author D. Onoprienko

- * @version $Id: CalGeometry.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $

+ * @version $Id: CalGeometry.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CalGeometry implements JobEventListener {

+
+  static public CalGeometry defaultInstance() {
+    return new CalGeometry();
+  }

   
 // -- Constructors and initialization :  ---------------------------------------
   

-  public CalGeometry(CalGeometryConfig config) {

+  private CalGeometry() {
+    JobManager.defaultInstance().addListener(this);
+  }
+
+  public void setConfig(CalGeometryConfig config) {
+    if (_config != null) throw new IllegalStateException("Geometry config has already been set.");

     _config = config;
     JobManager jobManager = JobManager.defaultInstance();
     jobManager.addListener(this, config);

-    jobManager.put(this, CalGeometry.class);

   }
 
   public void detectorChanged(JobEvent jEvent) {

+    if (_config == null) throw new IllegalStateException("Geometry config has not been set.");

     _detector = jEvent.getDetector();
     _modules = new ArrayList(_config.getModules());
   }

diff -u -r1.1.1.1 -r1.2
--- CalModule.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ CalModule.java	18 Feb 2009 03:29:06 -0000	1.2
@@ -1,7 +1,6 @@

 package org.lcsim.contrib.onoprien.crux.geom;
 
 import java.util.*;

-import org.lcsim.contrib.onoprien.crux.infrastructure.*;

 
 import org.lcsim.geometry.Subdetector;
 

@@ -9,11 +8,11 @@

  * Class to represent a part of the calorimeter.
  * 
  * @author D. Onoprienko

- * @version $Id: CalModule.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $

+ * @version $Id: CalModule.java,v 1.2 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CalModule {
   

-  public enum Attribute {ECAL, HCAL, BARREL, ENDCAP, SOUTH, NORTH}

+  public enum Attribute {ECAL, HCAL, BARREL, ENDCAP, SOUTH, NORTH, ENTRY, EXIT}

   
 // -- Constructors and initialization :  ---------------------------------------
   

@@ -69,6 +68,14 @@

   public boolean isNorth() {
     return _attributes.contains(Attribute.NORTH);
   }

+
+  public boolean isEntry() {
+    return _attributes.contains(Attribute.ENTRY);
+  }
+
+  public boolean isExit() {
+    return _attributes.contains(Attribute.EXIT);
+  }

   
   public Subdetector getSubdetector() {
     return _sd;

diff -N CruxMipStub.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ CruxMipStub.java	18 Feb 2009 03:29:07 -0000	1.1
@@ -0,0 +1,127 @@

+package org.lcsim.contrib.onoprien.crux.infrastructure;
+
+import java.util.*;
+
+import org.lcsim.event.CalorimeterHit;
+import org.lcsim.event.Cluster;
+
+import org.lcsim.contrib.onoprien.crux.geom.CalModule;
+
+/**
+ * MIP stub.
+ * Currently supports MIP stubs contained within a single calorimeter module.
+ *
+ * @author D. Onoprienko
+ * @version $Id: CruxMipStub.java,v 1.1 2009/02/18 03:29:07 onoprien Exp $
+ */
+public class CruxMipStub implements ICluster {
+
+// -- Private parts :  ---------------------------------------------------------
+
+  private final static double[] _zero3 = new double[3];
+  private final static double[] _zero6 = new double[6];
+
+  private ArrayList<CalorimeterHit> _hits;
+  private int[] _layerStartIndex;
+  private int _firstLayer, _nextLayer;
+
+  private CalModule _module;
+
+// -- Constructors :  ----------------------------------------------------------
+
+  public CruxMipStub(CalModule module, int firstLayer) {
+    _module = module;
+    _hits = new ArrayList<CalorimeterHit>();
+    _firstLayer = firstLayer;
+    _nextLayer = firstLayer;
+    _layerStartIndex = new int[module.getLayers().size()];
+  }
+
+// -- Implement ICluster :  ----------------------------------------------------
+
+  public int getType() {return 0;}
+
+  public double getEnergy() {return 0.;}
+
+  public double[] getPosition() {return _zero3;}
+
+  public double[] getPositionError() {return _zero3;}
+
+  public double getITheta() {return 0.;}
+
+  public double getIPhi() {return 0.;}
+
+  public int getSize() {return _hits.size();}
+
+  public double[] getDirectionError() {return _zero3;}
+
+  public double[] getShape() {return _zero6;}
+
+  public List<Cluster> getClusters() {return Collections.emptyList();}
+
+  public List<CalorimeterHit> getCalorimeterHits() {return Collections.unmodifiableList(_hits);}
+
+  public double[] getHitContributions() {throw new UnsupportedOperationException();}
+
+  public double[] getSubdetectorEnergies() {throw new UnsupportedOperationException();}
+
+
+// -- Additional getters :  ----------------------------------------------------
+
+  /**
+   * Returns list of calorimeter hits in the specified layer.
+   * @param layer  Ordinal layer number (layers in a {@link CalModule} are numbered from zero.
+   */
+  public List<CalorimeterHit> getHits(int layer) {
+    if (layer < _firstLayer || layer >= _nextLayer) return Collections.emptyList();
+    int fromIndex = _layerStartIndex[layer];
+    int toIndex = (layer < _nextLayer-1) ? _layerStartIndex[layer+1] : _hits.size();
+    return Collections.unmodifiableList(_hits.subList(fromIndex, toIndex));
+  }
+
+  public CalModule getModule() {
+    return _module;
+  }
+
+  public int getFirstLayer() {
+    return _firstLayer;
+  }
+
+  public int getNextLayer() {
+    return _nextLayer;
+  }
+
+  /**
+   * Returns the highest ordinal number among layers with hits. Returns -1 if this MIP stub is empty.
+   */
+  public int getLastLayer() {
+    int layer = _nextLayer;
+    while (layer-- > _firstLayer) {
+      if (!getHits(layer).isEmpty()) return layer;
+    }
+    return -1;
+  }
+
+  public List<CalorimeterHit> getLastHits() {
+    int layer = _nextLayer;
+    while (layer-- > _firstLayer) {
+      List<CalorimeterHit> out = getHits(layer);
+      if (!out.isEmpty()) return out;
+    }
+    return Collections.emptyList();
+  }
+
+
+// -- Modifiers:  --------------------------------------------------------------
+
+  public void add(List<? extends CalorimeterHit> hits) {
+    _layerStartIndex[_nextLayer++] = _hits.size();
+    _hits.addAll(hits);
+  }
+
+  public void add(CalorimeterHit hit) {
+    _layerStartIndex[_nextLayer++] = _hits.size();
+    _hits.add(hit);
+  }
+
+}

diff -u -r1.2 -r1.3
--- CatSeed.java	11 Feb 2009 23:31:40 -0000	1.2
+++ CatSeed.java	18 Feb 2009 03:29:06 -0000	1.3
@@ -5,6 +5,7 @@

 import hep.physics.vec.Hep3Vector;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.Cluster;

+import org.lcsim.event.MCParticle;

 
 import org.lcsim.contrib.onoprien.util.job.JobManager;
 import org.lcsim.contrib.onoprien.util.swim.BField;

@@ -15,16 +16,18 @@

  * Stub to prevent build from failing.
  *
  * @author D. Onoprienko

- * @version $Id: CatSeed.java,v 1.2 2009/02/11 23:31:40 onoprien Exp $

+ * @version $Id: CatSeed.java,v 1.3 2009/02/18 03:29:06 onoprien Exp $

  */
 public class CatSeed implements ICluster {
 
 // -- Private parts :  ---------------------------------------------------------
 
   private Helix _helix;

-  private ICluster _mipStub;

+  private CruxMipStub _mipStub;

   private ArrayList<ICluster> _clusters;
 

+  private MCParticle _mc;
+

   private BField _bField;
   
 // -- Constructors :  ----------------------------------------------------------

@@ -33,7 +36,7 @@

     _bField = JobManager.defaultInstance().get(BField.class);
   }
 

-  public CatSeed(Helix helix, ICluster mipStub, List<? extends ICluster> clusters) {

+  public CatSeed(Helix helix, CruxMipStub mipStub, List<? extends ICluster> clusters) {

     this();
     _helix = helix;
     _mipStub = mipStub;

@@ -115,8 +118,26 @@

    * Returns cluster of calorimeter hits that belong to the MIP-like portion of this <tt>CatSeed</tt>.
    * Hits are ordered in increasing layer number.
    */

-  public ICluster getMipStup() {

+  public CruxMipStub getMipStub() {

     return _mipStub;
   }

+
+  /**
+   * Returns <tt>MCParticle</tt> that has been associated with this CAT seed through a
+   * call to <tt>setMCParticle</tt> method. Returns <tt>null</tt> if no <tt>MCParticle</tt>
+   * has been associated.
+   */
+  public MCParticle getMCParticle() {
+    return _mc;
+  }
+
+// -- Setters :  ---------------------------------------------------------------
+
+  /**
+   * Associates <tt>MCParticle</tt> with this CAT seed.
+   */
+  public void setMCParticle(MCParticle mcParticle) {
+    _mc = mcParticle;
+  }

   
 }

diff -u -r1.2 -r1.3
--- CruxCluster.java	11 Feb 2009 23:31:40 -0000	1.2
+++ CruxCluster.java	18 Feb 2009 03:29:07 -0000	1.3
@@ -4,18 +4,22 @@

 
 import hep.physics.matrix.SymmetricMatrix;
 import hep.physics.vec.BasicHep3Vector;

-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalModule;
-import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.Cluster;
 import org.lcsim.geometry.Subdetector;
 

+import org.lcsim.contrib.onoprien.util.job.JobManager;
+
+import org.lcsim.contrib.onoprien.crux.CruxManager;
+import org.lcsim.contrib.onoprien.crux.geom.CalModule;
+import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;
+
+

 /**
  * Crux package specific implementation of {@link ICluster}.
  *
  * @author D. Onoprienko

- * @version $Id: CruxCluster.java,v 1.2 2009/02/11 23:31:40 onoprien Exp $

+ * @version $Id: CruxCluster.java,v 1.3 2009/02/18 03:29:07 onoprien Exp $

  */
 public class CruxCluster implements ICluster {
   

@@ -221,7 +225,7 @@

    * if you are planning to use this method extensively.</i>
    */
   public double[] getSubdetectorEnergies() {

-    Collection<? extends Subdetector> sdCol = CruxManager.defaultInstance().getGeometry().getDetector().getSubdetectors().values();

+    Collection<? extends Subdetector> sdCol = JobManager.defaultInstance().get(CalGeometry.class).getDetector().getSubdetectors().values();

     ArrayList<Subdetector> sdList = new ArrayList<Subdetector>(4);
     for (Subdetector sd : sdCol) {
       if (sd.isCalorimeter()) sdList.add(sd);

@@ -262,7 +266,7 @@

    * Returns a list of calorimeter modules that contain hits from this cluster.
    */
   public List<CalModule> getModules() {

-    CalGeometry geom = CruxManager.defaultInstance().getGeometry();

+    CalGeometry geom = JobManager.defaultInstance().get(CalGeometry.class);

     if (_modules == null) {
       HashSet<CalModule> moduleSet = new HashSet<CalModule>();
       if (_hits != null) {

diff -u -r1.1 -r1.2
--- RecType.java	13 Feb 2009 20:02:19 -0000	1.1
+++ RecType.java	18 Feb 2009 03:29:07 -0000	1.2
@@ -31,10 +31,16 @@

   CLUSTER(Cluster.class),
 
   /**

+   * Reconstructed particle. Unweighted.
+   */
+  PARTICLE(CruxParticle.class),
+
+  /**

    * Calorimeter assisted tracking seed. The <tt>MCParticle</tt> weight is equal to the
    * energy contributed by the <tt>MCParticle</tt> to the MIP stub portion of the seed cluster.
    */
   CAT_SEED(CatSeed.class);

+

   Class _type;
 
   RecType(Class type) {

diff -N CruxEvent.java
--- CruxEvent.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,40 +0,0 @@

-package org.lcsim.contrib.onoprien.crux.infrastructure;
-
-import org.lcsim.contrib.onoprien.crux.CruxManager;
-import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;
-import org.lcsim.geometry.Detector;
-import org.lcsim.event.EventHeader;
-
-/**
- * Class that represents an event dispatched by {@link CruxManager}.
- *
- * @author D. Onoprienko
- * @version $Id: CruxEvent.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $
- */
-public class CruxEvent {
-  
-// -- Constructors :  ----------------------------------------------------------
-  
-  public CruxEvent(CruxManager cruxMan, EventHeader event) {
-    _cruxMan = cruxMan;
-    _det = event.getDetector();
-  }
-  
-// -- Getters :  ---------------------------------------------------------------
-  
-  /** Returns <tt>CruxManager</tt> object that fired this event. */
-  public CruxManager getCruxManager() {return _cruxMan;}  
-  
-  /**
-   * Returns <tt>CalGeometry</tt> object describing the current geometry.
-   */
-  public CalGeometry getGeometry() {return _cruxMan.getGeometry();}
-  
-  /** Returns <tt>Detector</tt> object describing the current geometry. */
-  public Detector getDetector() {return _det;}
-
-// -- Private parts :  ---------------------------------------------------------
-  
-  private CruxManager _cruxMan;
-  private Detector _det;
-}

diff -N CruxEventListener.java
--- CruxEventListener.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,13 +0,0 @@

-package org.lcsim.contrib.onoprien.crux.infrastructure;
-
-/**
- * Interface to be implemented by classes listening to events dispatched by {@link CruxManager}.
- *
- * @author D. Onoprienko
- * @version $Id: CruxEventListener.java,v 1.1.1.1 2008/12/10 22:03:06 jeremy Exp $
- */
-public interface CruxEventListener {
-  
-  public void detectorChanged(CruxEvent cruxEvent);
-  
-}

diff -u -r1.4 -r1.5
--- MCTruthCrux.java	13 Feb 2009 20:02:19 -0000	1.4
+++ MCTruthCrux.java	18 Feb 2009 03:29:07 -0000	1.5
@@ -26,7 +26,7 @@

  * weights are calculated for each type of reconstructed object.
  *
  * @author D. Onoprienko

- * @version $Id: MCTruthCrux.java,v 1.4 2009/02/13 20:02:19 onoprien Exp $

+ * @version $Id: MCTruthCrux.java,v 1.5 2009/02/18 03:29:07 onoprien Exp $

  */
 public class MCTruthCrux {
   

@@ -48,6 +48,7 @@

   MCTruthCrux(MCTruthDriverCrux driver, EventHeader event) {
     _driver = driver;
     _event = event;

+    _defMaps = new EnumMap<RecType, WeightedTable>(RecType.class);

   }
 
 

@@ -273,7 +274,15 @@

    * portion of the seed cluster. The returned list is in decreasing weight order.
    */
   public WeightedList<MCParticle> findMCParticles(CatSeed seed) {

-    return findMCParticles(seed.getMipStup());

+    Cluster mipStub = seed.getMipStub();
+    MCParticle mc = seed.getMCParticle();
+    if (mc != null) {
+      WeightedList<MCParticle> out = new WeightedList<MCParticle>();
+      out.add(mc, mipStub.getSize());
+      return out;
+    } else {
+      return findMCParticles(seed.getMipStub()); // use findMCParticles(Cluster)
+    }

   }
   
 }

diff -u -r1.1 -r1.2
--- CalorimeterDriver.java	12 Feb 2009 01:32:08 -0000	1.1
+++ CalorimeterDriver.java	18 Feb 2009 03:29:07 -0000	1.2
@@ -9,7 +9,6 @@

 import org.lcsim.contrib.onoprien.util.job.JobEventListener;
 import org.lcsim.contrib.onoprien.util.job.JobManager;
 

-import org.lcsim.contrib.onoprien.crux.recon.HitMapFilterDriver;

 import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;
 import org.lcsim.contrib.onoprien.crux.geom.CalGeometryConfig;
 

@@ -20,19 +19,26 @@

  * to the event record.
  *
  * @author D. Onoprienko

- * @version $Id: CalorimeterDriver.java,v 1.1 2009/02/12 01:32:08 onoprien Exp $

+ * @version $Id: CalorimeterDriver.java,v 1.2 2009/02/18 03:29:07 onoprien Exp $

  */
 public class CalorimeterDriver extends Driver implements JobEventListener {

+
+// -- Private parts :  ---------------------------------------------------------
+
+  private String _outMapName;
+

   
 // -- Constructors and initialization :  ---------------------------------------
   
   public CalorimeterDriver() {

-    JobManager.defaultInstance().addListener(this);

+    JobManager jobMan = JobManager.defaultInstance();
+    CalGeometry geom = jobMan.get(CalGeometry.class);
+    jobMan.addListener(this, geom);

   }
 
   public void detectorChanged(JobEvent jEvent) {
     

-    if ((_outMapName == null) || (_geomConfig == null)) throw new IllegalStateException(ERR_NS);

+    if (_outMapName == null) throw new IllegalStateException(ERR_NS);

     
     //    Output of DigiSim is hit collections: "EcalBarrDigiHits", "EcalEndcapDigiHits", 
     //    "HcalBarrDigiHits", "HcalEndcapDigiHits" (added to the event).

@@ -43,13 +49,8 @@

     add(new DigiSimDriver());
     add(new SimCalorimeterHitsDriver());
     

-    // Initialize geometry
-    
-    CalGeometry geom = new CalGeometry(_geomConfig);
-    JobManager.defaultInstance().put(geom, CalGeometry.class);
-    

     // Put hits into map

-    

+

     HitMapFilterDriver mapMaker = new HitMapFilterDriver();
     mapMaker.set("INPUT", "EcalBarrDigiHits","EcalEndcapDigiHits","HcalBarrDigiHits","HcalEndcapDigiHits");
     mapMaker.set("OUTPUT", _outMapName);

@@ -82,8 +83,8 @@

       if (name.equalsIgnoreCase("OUTPUT_MAP_NAME")) {
         _outMapName = (String) value;
       } else if (name.equalsIgnoreCase("GEOMETRY_CONFIG")) {

-        _geomConfig = (CalGeometryConfig) value;
-        JobManager.defaultInstance().addListener(this, _geomConfig);

+        CalGeometryConfig geomConfig = (CalGeometryConfig) value;
+        JobManager.defaultInstance().get(CalGeometry.class).setConfig(geomConfig);

       } else {
         super.set(name, values);
       }

@@ -91,10 +92,5 @@

       throw new IllegalArgumentException(ERR_VIT, x);
     }
   }

-  
-  
-// -- Private parts :  ---------------------------------------------------------
-  
-  private String _outMapName;
-  private CalGeometryConfig _geomConfig;

+

 }

diff -u -r1.3 -r1.4
--- TestDriverRosary.java	12 Feb 2009 01:32:08 -0000	1.3
+++ TestDriverRosary.java	18 Feb 2009 03:29:07 -0000	1.4
@@ -1,6 +1,7 @@

 package org.lcsim.contrib.onoprien.crux.tests;
 
 import java.util.*;

+

 import java.util.logging.Level;
 import org.lcsim.contrib.onoprien.crux.CruxManager;
 import org.lcsim.contrib.onoprien.crux.geom.CalGeometry;

@@ -8,30 +9,26 @@

 import org.lcsim.digisim.DigiSimDriver;
 import org.lcsim.digisim.SimCalorimeterHitsDriver;
 import org.lcsim.detector.identifier.*;

-import org.lcsim.detector.solids.Tube;
-import org.lcsim.geometry.Detector;

 import org.lcsim.detector.IDetectorElement;

-import org.lcsim.event.CalorimeterHit;

 import org.lcsim.event.EventHeader;
 import org.lcsim.recon.cluster.util.CalHitMapDriver;
 
 import org.lcsim.contrib.onoprien.util.job.Driver;

+import org.lcsim.contrib.onoprien.util.job.JobManager;

 
 import org.lcsim.contrib.onoprien.crux.algorithms.TrackedParticleFinderDriver;

-import org.lcsim.contrib.onoprien.crux.algorithms.ValidationDriver;
-import org.lcsim.contrib.onoprien.crux.algorithms.Validator;

 import org.lcsim.contrib.onoprien.crux.algorithms.rosary.RosaryClusterer;

-import org.lcsim.contrib.onoprien.crux.recon.HitMapFilterDriver;

 import org.lcsim.contrib.onoprien.crux.infrastructure.*;
 import org.lcsim.contrib.onoprien.crux.mctruth.MCTruthDriverCrux;
 import org.lcsim.contrib.onoprien.crux.cheat.CheatTrackFinderDriver;
 import org.lcsim.contrib.onoprien.crux.cheat.CheatVertexFinderDriver;

+import org.lcsim.contrib.onoprien.crux.recon.HitMapFilterDriver;

 
 /**
  *
  *
  * @author D. Onoprienko

- * @version $Id: TestDriverRosary.java,v 1.3 2009/02/12 01:32:08 onoprien Exp $

+ * @version $Id: TestDriverRosary.java,v 1.4 2009/02/18 03:29:07 onoprien Exp $

  */
 public class TestDriverRosary extends Driver {
   

@@ -102,7 +99,7 @@

   public void process(EventHeader event) {
     super.process(event);
     

-    CalGeometry geom = CruxManager.defaultInstance().getGeometry();

+    CalGeometry geom = JobManager.defaultInstance().get(CalGeometry.class);

     
 //    CruxHitMap hitMap = (CruxHitMap) event.get("CalHitMap_All");
 //    Collection<CalorimeterHit> hitList = hitMap.values();