LISTSERV mailing list manager LISTSERV 16.5

Help for HPS-SVN Archives


HPS-SVN Archives

HPS-SVN Archives


HPS-SVN@LISTSERV.SLAC.STANFORD.EDU


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

HPS-SVN Home

HPS-SVN Home

HPS-SVN  November 2014

HPS-SVN November 2014

Subject:

r1466 - in /java/trunk/conditions/src: main/java/org/hps/conditions/ main/java/org/hps/conditions/cli/ main/java/org/hps/conditions/deprecated/ main/java/org/hps/conditions/ecal/ main/java/org/hps/conditions/svt/ test/java/org/hps/conditions/ test/java/org/hps/conditions/beam/ test/java/org/hps/conditions/ecal/ test/java/org/hps/conditions/svt/

From:

[log in to unmask]

Reply-To:

Notification of commits to the hps svn repository <[log in to unmask]>

Date:

Mon, 10 Nov 2014 08:16:55 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (7167 lines)

Author: [log in to unmask]
Date: Mon Nov 10 00:16:49 2014
New Revision: 1466

Log:
Format all source code in conditions module.

Modified:
    java/trunk/conditions/src/main/java/org/hps/conditions/AbstractConditionsDriver.java
    java/trunk/conditions/src/main/java/org/hps/conditions/AbstractIdentifier.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObject.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectCollection.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectException.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectUtil.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecordConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeries.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeriesConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ConnectionParameters.java
    java/trunk/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java
    java/trunk/conditions/src/main/java/org/hps/conditions/QueryBuilder.java
    java/trunk/conditions/src/main/java/org/hps/conditions/TableConstants.java
    java/trunk/conditions/src/main/java/org/hps/conditions/TableMetaData.java
    java/trunk/conditions/src/main/java/org/hps/conditions/TestRunConditionsDriver.java
    java/trunk/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java
    java/trunk/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamSpot.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamlineConstants.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/CalibrationDriver.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/EcalConditions.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/FieldMap.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTCalibrationConstants.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTConstants.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTSensorSetup.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/QuietBaseLCSimEvent.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/StereoPair.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/SvtUtils.java
    java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/TestRunConditionsReader.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalBadChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalCalibration.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsUtil.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalDetectorSetup.java
    java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalLed.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditions.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditionsConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtT0Shift.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtBadChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtCalibration.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditions.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConfiguration.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConverterRegistry.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDetectorSetup.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtShapeFitParameters.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditionsConverter.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDaqMapping.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDetectorSetup.java
    java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java
    java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsDriverTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/beam/BeamCurrentTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalDetectorSetupTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtBadChannelTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtConfigurationTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDaqMappingTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDetectorSetupTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtConditionsConverterTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDaqMappingTest.java
    java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDetectorSetupTest.java

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/AbstractConditionsDriver.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/AbstractConditionsDriver.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/AbstractConditionsDriver.java	Mon Nov 10 00:16:49 2014
@@ -8,10 +8,9 @@
 import org.lcsim.util.Driver;
 
 /**
- * This abstract {@link org.lcsim.util.Driver} contains the 
- * general methods used to set up {@link DatabaseConditionsManager} 
- * and load the conditions onto a detector.  The connection
- * parameters are set by subclasses.
+ * This abstract {@link org.lcsim.util.Driver} contains the general methods used
+ * to set up {@link DatabaseConditionsManager} and load the conditions onto a
+ * detector. The connection parameters are set by subclasses.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -22,19 +21,18 @@
 
     private String ecalSubdetectorName = "Ecal";
     protected String svtSubdetectorName = "Tracker";
-    
+
     boolean loadSvtConditions = true;
     boolean loadEcalConditions = true;
-
 
     public void setLoadSvtConditions(boolean loadSvtConditions) {
         this.loadSvtConditions = loadSvtConditions;
     }
-    
+
     public void setLoadEcalConditions(boolean loadEcaltConditions) {
         this.loadEcalConditions = loadSvtConditions;
     }
-    
+
     public void setEcalSubdetectorName(String ecalSubdetectorName) {
         this.ecalSubdetectorName = ecalSubdetectorName;
     }
@@ -42,7 +40,7 @@
     public void setSvtSubdetectorName(String svtSubdetectorName) {
         this.svtSubdetectorName = svtSubdetectorName;
     }
-       
+
     /**
      * This method updates a new detector with SVT and ECal conditions data.
      */

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/AbstractIdentifier.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/AbstractIdentifier.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/AbstractIdentifier.java	Mon Nov 10 00:16:49 2014
@@ -1,8 +1,8 @@
 package org.hps.conditions;
 
 /**
- * This class is a simplistic representation of a packaged identifier for use in the
- * conditions system.
+ * This class is a simplistic representation of a packaged identifier for use in
+ * the conditions system.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsDriver.java	Mon Nov 10 00:16:49 2014
@@ -6,6 +6,7 @@
 import org.hps.conditions.svt.SvtDetectorSetup;
 import org.lcsim.conditions.ConditionsManager;
 import org.lcsim.geometry.Detector;
+
 /**
  * This {@link org.lcsim.util.Driver} is a subclass of
  * {@link AbstractConditionsDriver} and specifies the database connection
@@ -18,13 +19,13 @@
 
     public ConditionsDriver() {
         if (ConditionsManager.defaultInstance() instanceof DatabaseConditionsManager) {
-        	getLogger().config("ConditionsDriver found existing DatabaseConditionsManager.");
+            getLogger().config("ConditionsDriver found existing DatabaseConditionsManager.");
             manager = (DatabaseConditionsManager) ConditionsManager.defaultInstance();
         } else {
             manager = new DatabaseConditionsManager();
         }
     }
-      
+
     /**
      * Load the {@link SvtConditions} set onto <code>HpsSiSensor</code>.
      * @param detector The detector to update.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObject.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObject.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObject.java	Mon Nov 10 00:16:49 2014
@@ -3,9 +3,9 @@
 import java.util.LinkedHashMap;
 
 /**
- * This is an ORM interface for accessing conditions database information by row. It can
- * handle new or existing records. The ID values for new records are -1 which indicates
- * they are not in the database yet.
+ * This is an ORM interface for accessing conditions database information by
+ * row. It can handle new or existing records. The ID values for new records are
+ * -1 which indicates they are not in the database yet.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public interface ConditionsObject {
@@ -44,7 +44,8 @@
     void insert() throws ConditionsObjectException;
 
     /**
-     * Select data into this object from the database using a SQL SELECT statement.
+     * Select data into this object from the database using a SQL SELECT
+     * statement.
      */
     void select() throws ConditionsObjectException;
 
@@ -55,19 +56,22 @@
     boolean isReadOnly();
 
     /**
-     * Return true if this object is new and hasn't been inserted into the database yet.
+     * Return true if this object is new and hasn't been inserted into the
+     * database yet.
      * @return True if object is new.
      */
     boolean isNew();
 
     /**
-     * Return true if this object's data has been modified without a database update.
+     * Return true if this object's data has been modified without a database
+     * update.
      * @return True if object is dirty.
      */
     boolean isDirty();
 
     /**
-     * Generic set method for field values. This will set the object to the 'dirty' state.
+     * Generic set method for field values. This will set the object to the
+     * 'dirty' state.
      * @param fieldName The name of the field.
      * @param fieldValue The field value.
      */
@@ -75,7 +79,8 @@
 
     /**
      * Set all of the field values on this object.
-     * @param fieldValues The FieldValueMap containing pairs of names and values.
+     * @param fieldValues The FieldValueMap containing pairs of names and
+     *            values.
      */
     void setFieldValues(FieldValueMap fieldValues);
 
@@ -94,35 +99,38 @@
     public <T> T getFieldValue(String field);
 
     /**
-     * Set the ConditionsTableMetaData of this object. This cannot be reset once set.
+     * Set the ConditionsTableMetaData of this object. This cannot be reset once
+     * set.
      * @param tableMetaData The ConditionsTableMetaData.
      * @throws ConditionsObjectException if already set
      */
     void setTableMetaData(TableMetaData tableMetaData) throws ConditionsObjectException;
 
     /**
-     * Set the collection ID of this object. This cannot be reset once set to a valid ID
-     * (e.g. not -1).
+     * Set the collection ID of this object. This cannot be reset once set to a
+     * valid ID (e.g. not -1).
      * @param collectionId The collection ID.
      * @throws ConditionsObjectException if already set
      */
     void setCollectionId(int collectionId) throws ConditionsObjectException;
 
     /**
-     * Set the row ID of this object. This cannot be reset once set to a valid ID (e.g.
-     * not -1).
+     * Set the row ID of this object. This cannot be reset once set to a valid
+     * ID (e.g. not -1).
      * @param rowId The object's row ID.
      * @throws ConditionsObjectException if already set
      */
     public void setRowId(int rowId) throws ConditionsObjectException;
 
     /**
-     * Set the object to read only mode. This cannot be changed back once it is set.
+     * Set the object to read only mode. This cannot be changed back once it is
+     * set.
      */
     void setIsReadOnly();
 
     /**
-     * Simple class extending <code>java.lang.Map</code> that maps field names to values.
+     * Simple class extending <code>java.lang.Map</code> that maps field names
+     * to values.
      */
     public static final class FieldValueMap extends LinkedHashMap<String, Object> {
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectCollection.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectCollection.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectCollection.java	Mon Nov 10 00:16:49 2014
@@ -18,7 +18,7 @@
 
     protected ConditionsObjectCollection() {
     }
-        
+
     public ConditionsObjectCollection(TableMetaData tableMetaData, int collectionId, boolean isReadOnly) {
         this.tableMetaData = tableMetaData;
         this.collectionId = collectionId;
@@ -27,7 +27,7 @@
             this.isNew = true;
         }
     }
-    
+
     public ConditionsRecord getConditionsRecord() {
         return conditionsRecord;
     }
@@ -44,8 +44,10 @@
         return getObjects().contains(object);
     }
 
-    // TODO: Should check here if object has an existing collection ID that is different
-    // from this collection's, in which case this collection becomes "mixed" and it should
+    // TODO: Should check here if object has an existing collection ID that is
+    // different
+    // from this collection's, in which case this collection becomes "mixed" and
+    // it should
     // be
     // flagged as read only.
     public void add(ObjectType object) throws ConditionsObjectException {
@@ -53,7 +55,8 @@
             throw new IllegalArgumentException("Collection already contains this object.");
         }
         try {
-            // Only assign a collection ID to the object if this collection has a valid ID
+            // Only assign a collection ID to the object if this collection has
+            // a valid ID
             // and the object does not have one already.
             if (getCollectionId() != -1)
                 object.setCollectionId(getCollectionId());
@@ -85,7 +88,8 @@
         setIsDirty(false);
     }
 
-    // TODO: This does not need to loop. It should just call delete on the collection ID
+    // TODO: This does not need to loop. It should just call delete on the
+    // collection ID
     // value.
     public void delete() throws ConditionsObjectException {
         if (isReadOnly()) {
@@ -96,7 +100,8 @@
         }
     }
 
-    // TODO: This should not loop. It should select all the objects with a matching
+    // TODO: This should not loop. It should select all the objects with a
+    // matching
     // collection ID
     // from the database.
     public void select() throws ConditionsObjectException, SQLException {
@@ -105,7 +110,8 @@
         }
     }
 
-    // TODO: This method needs to get the next collection ID from the conditions manager.
+    // TODO: This method needs to get the next collection ID from the conditions
+    // manager.
     // TODO: This operation should lock the table.
     public void insert() throws ConditionsObjectException, SQLException {
         if (!isNew()) {
@@ -131,7 +137,8 @@
         this.isDirty = isDirty;
     }
 
-    // TODO: This can probably just check if collection ID is not valid e.g. equals -1.
+    // TODO: This can probably just check if collection ID is not valid e.g.
+    // equals -1.
     public boolean isNew() {
         return isNew;
     }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java	Mon Nov 10 00:16:49 2014
@@ -9,8 +9,8 @@
 
 /**
  * <p>
- * Implementation of default conversion from database tables to a {@link ConditionsObject}
- * class.
+ * Implementation of default conversion from database tables to a
+ * {@link ConditionsObject} class.
  * </p>
  * <p>
  * This class actually returns collections and not individual objects.
@@ -21,16 +21,18 @@
  * @param <T> The type of the returned data which should be a class extending
  *            {@link ConditionsObjectCollection}.
  */
-// FIXME: This class should only allow one collection to be returned and not mix the database records together.
-// TODO: This class can probably be removed in favor of using the ConditionsSeriesConverter in all cases.
+// FIXME: This class should only allow one collection to be returned and not mix
+// the database records together.
+// TODO: This class can probably be removed in favor of using the
+// ConditionsSeriesConverter in all cases.
 public abstract class ConditionsObjectConverter<T> implements ConditionsConverter<T> {
 
     public ConditionsObjectConverter() {
     }
 
     /**
-     * Classes that extend this must define this method to specify what type the converter
-     * is able to handle.
+     * Classes that extend this must define this method to specify what type the
+     * converter is able to handle.
      * @return The Class that this converter handles.
      */
     public abstract Class getType();
@@ -40,7 +42,8 @@
 
         // System.out.println("finding conditions for key " + name + " ...");
 
-        // Get the DatabaseConditionsManager which is required for using this converter.
+        // Get the DatabaseConditionsManager which is required for using this
+        // converter.
         DatabaseConditionsManager databaseConditionsManager = DatabaseConditionsManager.castFrom(conditionsManager);
 
         // Get the table meta data from the key given by the caller.
@@ -50,8 +53,9 @@
 
         // Create a collection to return.
         ConditionsObjectCollection collection = ConditionsObjectUtil.createCollection(tableMetaData);
-        
-        // Get the ConditionsRecord with the meta-data, which will use the current run
+
+        // Get the ConditionsRecord with the meta-data, which will use the
+        // current run
         // number from the manager.
         ConditionsRecordCollection conditionsRecords = databaseConditionsManager.findConditionsRecords(name);
 
@@ -61,11 +65,13 @@
         } else if (conditionsRecords.getObjects().size() > 1) {
             // There were multiple records returned.
             if (!allowMultipleCollections())
-                // If there are multiple records returned but this is not allowed by the
+                // If there are multiple records returned but this is not
+                // allowed by the
                 // converter, then this is a fatal error.
                 throw new RuntimeException("Multiple conditions records returned but this is not allowed.");
         } else {
-            // There was a single conditions record so the collection information can be
+            // There was a single conditions record so the collection
+            // information can be
             // set meaningfully.
             try {
                 collection.setCollectionId(conditionsRecords.get(0).getCollectionId());
@@ -109,7 +115,7 @@
         // Return new collection.
         return (T) collection;
     }
-   
+
     public boolean allowMultipleCollections() {
         return true;
     }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectException.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectException.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectException.java	Mon Nov 10 00:16:49 2014
@@ -1,8 +1,8 @@
 package org.hps.conditions;
 
 /**
- * Generic Exception type throw by methods of {@link ConditionsObject} or other associated
- * classes such as converters and collections.
+ * Generic Exception type throw by methods of {@link ConditionsObject} or other
+ * associated classes such as converters and collections.
  */
 @SuppressWarnings("serial")
 public final class ConditionsObjectException extends Exception {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectUtil.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectUtil.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsObjectUtil.java	Mon Nov 10 00:16:49 2014
@@ -7,12 +7,13 @@
 import org.hps.conditions.ConditionsObject.FieldValueMap;
 
 /**
- * Some static utility methods for <tt>ConditionsObject</tt> and related classes.
+ * Some static utility methods for <tt>ConditionsObject</tt> and related
+ * classes.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 final class ConditionsObjectUtil {
-    
+
     private ConditionsObjectUtil() {
     }
 
@@ -42,8 +43,8 @@
         }
         newObject.setFieldValues(fieldValues);
         return newObject;
-    }    
-    
+    }
+
     static final ConditionsObjectCollection createCollection(TableMetaData tableMetaData) {
         ConditionsObjectCollection collection;
         try {
@@ -53,5 +54,5 @@
         }
         return collection;
     }
-    
+
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java	Mon Nov 10 00:16:49 2014
@@ -3,13 +3,15 @@
 import java.util.Date;
 
 /**
- * This class represents a single record from the primary conditions data table, which
- * defines the validity range for a specific collection of conditions objects.
+ * This class represents a single record from the primary conditions data table,
+ * which defines the validity range for a specific collection of conditions
+ * objects.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 // TODO: Check behavior of select, delete, update and insert operations.
-// TODO: Override default behavior of methods in super class that don't make sense.
+// TODO: Override default behavior of methods in super class that don't make
+// sense.
 public final class ConditionsRecord extends AbstractConditionsObject {
 
     /**
@@ -17,15 +19,16 @@
      */
     public static class ConditionsRecordCollection extends ConditionsObjectCollection<ConditionsRecord> {
         /**
-         * Since ConditionsRecord collections are always "mixed", meaning the collection
-         * ID values are usually all going to be different, the default behavior of the
-         * super class is overridden.
+         * Since ConditionsRecord collections are always "mixed", meaning the
+         * collection ID values are usually all going to be different, the
+         * default behavior of the super class is overridden.
          */
         public void add(ConditionsRecord record) {
             objects.add(record);
         }
 
-        // FIXME: Should probably override more methods here that don't make sense for
+        // FIXME: Should probably override more methods here that don't make
+        // sense for
         // this type!
     }
 
@@ -81,8 +84,9 @@
     }
 
     /**
-     * Get the name of these conditions, which should be unique by run number. This is
-     * called the "key" in the table meta data to distinguish it from "table name".
+     * Get the name of these conditions, which should be unique by run number.
+     * This is called the "key" in the table meta data to distinguish it from
+     * "table name".
      * @return The name of the conditions.
      */
     public String getName() {
@@ -104,7 +108,7 @@
     public int getCollectionId() {
         return getFieldValue("collection_id");
     }
-    
+
     /**
      * Get the string tag associated with these conditions.
      * @return The string tag.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecordConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecordConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsRecordConverter.java	Mon Nov 10 00:16:49 2014
@@ -9,7 +9,8 @@
 /**
  * Read ConditionsRecord objects from the conditions database.
  * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: ConditionsRecordConverter.java,v 1.5 2013/10/15 23:24:47 jeremy Exp $
+ * @version $Id: ConditionsRecordConverter.java,v 1.5 2013/10/15 23:24:47 jeremy
+ *          Exp $
  */
 class ConditionsRecordConverter extends ConditionsObjectConverter<ConditionsRecordCollection> {
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeries.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeries.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeries.java	Mon Nov 10 00:16:49 2014
@@ -5,33 +5,34 @@
 import java.util.List;
 
 /**
- * This class represents a series of collections containing <tt>ConditionsObjects</tt>.  It 
- * is used to conditions collections when there are multiple ones with the same key that
- * are valid for the current run. 
- *  
+ * This class represents a series of collections containing
+ * <tt>ConditionsObjects</tt>. It is used to conditions collections when there
+ * are multiple ones with the same key that are valid for the current run.
+ * 
  * @author Jeremy McCormick <[log in to unmask]>
  *
- * @param <CollectionType> The specific type of the <tt>ConditionsObjectCollection</tt> the series contains.
+ * @param <CollectionType> The specific type of the
+ *            <tt>ConditionsObjectCollection</tt> the series contains.
  */
 public class ConditionsSeries<CollectionType extends ConditionsObjectCollection> implements Iterable<CollectionType> {
-    
+
     List<CollectionType> collections = new ArrayList<CollectionType>();
-    
+
     CollectionType getCollection(int series) {
         return collections.get(series);
     }
-        
+
     int addCollection(CollectionType collection) {
         if (collections.contains(collection))
             throw new IllegalArgumentException("The collection is already registered with this object.");
         collections.add(collection);
         return collections.indexOf(collection);
     }
-    
+
     int getNumberOfCollections() {
         return collections.size();
     }
-    
+
     CollectionType findCollection(ConditionsRecord record) {
         for (CollectionType collection : collections) {
             if (collection.conditionsRecord == record)
@@ -39,7 +40,7 @@
         }
         return null;
     }
-    
+
     public Iterator<CollectionType> iterator() {
         return collections.iterator();
     }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeriesConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeriesConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConditionsSeriesConverter.java	Mon Nov 10 00:16:49 2014
@@ -7,14 +7,16 @@
 
 /**
  * <p>
- * This converter creates a <tt>ConditionsSeries</tt> which is a set of <tt>ConditionsObjectCollection</tt>
- * objects with the same type.  This can be used to retrieve sets of conditions that may overlap in 
- * time validity, such as sets of bad channels .
+ * This converter creates a <tt>ConditionsSeries</tt> which is a set of
+ * <tt>ConditionsObjectCollection</tt> objects with the same type. This can be
+ * used to retrieve sets of conditions that may overlap in time validity, such
+ * as sets of bad channels .
  * </p>
  * <p>
- * Since type inference from the target variable is used in the {@link #createSeries(String)} method
- * signature, there only needs to be one of these converters per {@link DatabaseConditionsManager}.
- * The creation of the specific types is also done automatically, so each type of conditions object
+ * Since type inference from the target variable is used in the
+ * {@link #createSeries(String)} method signature, there only needs to be one of
+ * these converters per {@link DatabaseConditionsManager}. The creation of the
+ * specific types is also done automatically, so each type of conditions object
  * does not need its own converter class.
  * </p>
  * 
@@ -23,20 +25,24 @@
 class ConditionsSeriesConverter {
 
     DatabaseConditionsManager conditionsManager = null;
-    
+
     ConditionsSeriesConverter(DatabaseConditionsManager conditionsManager) {
         if (conditionsManager == null)
             throw new RuntimeException("The conditionsManager is null.");
         this.conditionsManager = conditionsManager;
     }
-        
+
     /**
-     * Create a <tt>ConditionsSeries</tt> which is a series of <tt>ConditionsObjectCollections</tt> of the same type,
-     * each of which have their own <tt>ConditionsRecord</tt>.  This should be used for overlapping conditions, such as
-     * sets of bad channels that are combined together as in the test run.
+     * Create a <tt>ConditionsSeries</tt> which is a series of
+     * <tt>ConditionsObjectCollections</tt> of the same type, each of which have
+     * their own <tt>ConditionsRecord</tt>. This should be used for overlapping
+     * conditions, such as sets of bad channels that are combined together as in
+     * the test run.
      * 
-     * @param conditionsKey The name of the conditions key to retrieve from the conditions table.
-     * @return The <tt>ConditionsSeries</tt> matching <tt>conditionsKey</tt> which type inferred from target variable.
+     * @param conditionsKey The name of the conditions key to retrieve from the
+     *            conditions table.
+     * @return The <tt>ConditionsSeries</tt> matching <tt>conditionsKey</tt>
+     *         which type inferred from target variable.
      */
     @SuppressWarnings({ "unchecked", "rawtypes" })
     public <CollectionType extends ConditionsObjectCollection> ConditionsSeries<CollectionType> createSeries(String conditionsKey) {
@@ -48,13 +54,14 @@
 
         ConditionsSeries<CollectionType> series = new ConditionsSeries<CollectionType>();
 
-        // Get the ConditionsRecord with the meta-data, which will use the current run
+        // Get the ConditionsRecord with the meta-data, which will use the
+        // current run
         // number from the manager.
         ConditionsRecordCollection conditionsRecords = conditionsManager.findConditionsRecords(conditionsKey);
 
         // Loop over conditions records. This will usually just be one record.
         for (ConditionsRecord conditionsRecord : conditionsRecords.getObjects()) {
-            
+
             ConditionsObjectCollection collection = ConditionsObjectUtil.createCollection(tableMetaData);
 
             try {
@@ -85,13 +92,13 @@
 
                     // Add new object to collection, which will also assign it a
                     // collection ID if applicable.
-                    collection.add(newObject);                                       
+                    collection.add(newObject);
                 }
             } catch (SQLException | ConditionsObjectException e) {
                 throw new RuntimeException(e);
             }
-            
-            series.addCollection((CollectionType)collection);
+
+            series.addCollection((CollectionType) collection);
         }
 
         // Return new collection.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ConnectionParameters.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ConnectionParameters.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ConnectionParameters.java	Mon Nov 10 00:16:49 2014
@@ -11,11 +11,12 @@
 import java.util.Properties;
 
 /**
- * This class encapsulates the parameters for connecting to a database, including
- * hostname, port, user and password. It can also create and return a Connection object
- * based on these parameters.
+ * This class encapsulates the parameters for connecting to a database,
+ * including hostname, port, user and password. It can also create and return a
+ * Connection object based on these parameters.
  * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: ConnectionParameters.java,v 1.8 2013/10/04 01:54:16 jeremy Exp $
+ * @version $Id: ConnectionParameters.java,v 1.8 2013/10/04 01:54:16 jeremy Exp
+ *          $
  */
 public class ConnectionParameters {
 
@@ -27,10 +28,10 @@
 
     /**
      * Protected constructor for sub-classes.
-     */	
+     */
     protected ConnectionParameters() {
     }
-    
+
     /**
      * Fully qualified constructor.
      * @param user The user name.
@@ -39,7 +40,7 @@
      * @param port The port number.
      * @param conditionsTable The table containing conditions validity data.
      */
-   public  ConnectionParameters(String user, String password, String database, String hostname, int port) {
+    public ConnectionParameters(String user, String password, String database, String hostname, int port) {
         this.user = user;
         this.password = password;
         this.database = database;
@@ -47,7 +48,7 @@
         this.port = port;
     }
 
-   /**
+    /**
      * Get Properties object for this connection.
      * @return The Properties for this connection.
      */
@@ -105,11 +106,11 @@
     }
 
     /**
-     * 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 Connection object.
      */
-    public Connection createConnection() {               
+    public Connection createConnection() {
         Properties connectionProperties = getConnectionProperties();
         Connection connection = null;
         try {
@@ -137,8 +138,8 @@
     }
 
     /**
-     * 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 String The resource path.
      * @return The connection parameters.
      */
@@ -147,7 +148,8 @@
     }
 
     /**
-     * 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.
      * @throws RuntimeException if the InputStream is invalid

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java	Mon Nov 10 00:16:49 2014
@@ -33,8 +33,8 @@
 
 /**
  * <p>
- * This class should be used as the top-level ConditionsManager for database access to
- * conditions data.
+ * This class should be used as the top-level ConditionsManager for database
+ * access to conditions data.
  * </p>
  * <p>
  * In general, this will be overriding the
@@ -59,7 +59,7 @@
     protected boolean isConnected = false;
     protected ConditionsSeriesConverter conditionsSeriesConverter = new ConditionsSeriesConverter(this);
     protected static final String DEFAULT_CONFIG = "/org/hps/conditions/config/conditions_dev.xml";
-    
+
     /**
      * Simple log formatter for this class.
      */
@@ -71,7 +71,7 @@
             return sb.toString();
         }
     }
-    
+
     /**
      * Setup the logger for this class, with initial level of ALL.
      */
@@ -85,27 +85,27 @@
         logger.addHandler(handler);
         logger.config("logger initialized with level " + handler.getLevel());
     }
-    
+
     /**
      * Default connection parameters.
      */
     static class DefaultConnectionParameters extends ConnectionParameters {
-    	DefaultConnectionParameters() {
-    		this.port = 3306;
-    		try {
-				if (InetAddress.getLocalHost().getHostName().contains("jlab.org")) {
-					this.hostname = "jmysql.jlab.org";
-					this.database = "hps_conditions";
-				} else {
-					this.hostname = "ppa-jeremym-l.slac.stanford.edu";
-					this.database = "hps_conditions_dev";
-				}
-			} catch (UnknownHostException e) {
-				throw new RuntimeException(e);
-			}
-    		this.user = "hpsuser";
-    		this.password = "darkphoton";
-    	}
+        DefaultConnectionParameters() {
+            this.port = 3306;
+            try {
+                if (InetAddress.getLocalHost().getHostName().contains("jlab.org")) {
+                    this.hostname = "jmysql.jlab.org";
+                    this.database = "hps_conditions";
+                } else {
+                    this.hostname = "ppa-jeremym-l.slac.stanford.edu";
+                    this.database = "hps_conditions_dev";
+                }
+            } catch (UnknownHostException e) {
+                throw new RuntimeException(e);
+            }
+            this.user = "hpsuser";
+            this.password = "darkphoton";
+        }
     }
 
     /**
@@ -115,7 +115,7 @@
         registerConditionsConverter(new DetectorConditionsConverter());
         setupConnectionFromSystemProperty();
         configure(DEFAULT_CONFIG);
-        register();        
+        register();
     }
 
     /**
@@ -126,8 +126,8 @@
     }
 
     /**
-     * Get the static instance of this class, which must have been registered first from a
-     * call to {@link #register()}.
+     * Get the static instance of this class, which must have been registered
+     * first from a call to {@link #register()}.
      * @return The static instance of the manager.
      */
     public static DatabaseConditionsManager getInstance() {
@@ -146,11 +146,11 @@
 
         return (DatabaseConditionsManager) manager;
     }
-    
+
     public Connection getConnection() {
         return this.connection;
     }
-    
+
     /**
      * Open the database connection.
      */
@@ -196,33 +196,37 @@
         if (isConnected())
             closeConnection();
     }
-    
-    /**
-     * Get multiple <code>ConditionsObjectCollection</code> objects that may have overlapping time validity information.
+
+    /**
+     * Get multiple <code>ConditionsObjectCollection</code> objects that may
+     * have overlapping time validity information.
      * @param conditionsKey The conditions key.
-     * @return The <code>ConditionsSeries</code> containing the matching <code>ConditionsObjectCollection</code>. 
+     * @return The <code>ConditionsSeries</code> containing the matching
+     *         <code>ConditionsObjectCollection</code>.
      */
     public <CollectionType extends ConditionsObjectCollection> ConditionsSeries<CollectionType> getConditionsSeries(String conditionsKey) {
         return conditionsSeriesConverter.createSeries(conditionsKey);
     }
-    
-	/**
-	 * Get a given collection of the given type from the conditions database.
-	 * @param type Class type
-	 * @return A collection of objects of the given type from the conditions database
-	 */
-	public <CollectionType extends ConditionsObjectCollection> CollectionType getCollection(Class<CollectionType> type){
-		TableMetaData metaData = this.findTableMetaData(type);
-		if(metaData == null) {
-			throw new RuntimeException("Table name data for condition of type " + type.getSimpleName() + " was not found.");
-		}
-		String tableName = metaData.getTableName();
-		CollectionType conditionsCollection = this.getCachedConditions(type, tableName).getCachedData(); 
-		return conditionsCollection; 
-	}
-       
-    /**
-     * Simple utility method to cast the generic <code>ConditionsManager</code> to this class.
+
+    /**
+     * Get a given collection of the given type from the conditions database.
+     * @param type Class type
+     * @return A collection of objects of the given type from the conditions
+     *         database
+     */
+    public <CollectionType extends ConditionsObjectCollection> CollectionType getCollection(Class<CollectionType> type) {
+        TableMetaData metaData = this.findTableMetaData(type);
+        if (metaData == null) {
+            throw new RuntimeException("Table name data for condition of type " + type.getSimpleName() + " was not found.");
+        }
+        String tableName = metaData.getTableName();
+        CollectionType conditionsCollection = this.getCachedConditions(type, tableName).getCachedData();
+        return conditionsCollection;
+    }
+
+    /**
+     * Simple utility method to cast the generic <code>ConditionsManager</code>
+     * to this class.
      * @param conditionsManager The <code>ConditionsManager</code>.
      * @return The <code>DatabaseConditionsManager</code> object.
      */
@@ -232,16 +236,17 @@
         } else {
             throw new RuntimeException("The conditionsManager points to an object of the wrong type: " + conditionsManager.getClass().getCanonicalName());
         }
-    }    
-
-    /**
-     * This method catches changes to the detector name and run number. 
-     * It is actually called every time an lcsim event is created, so it has internal logic 
-     * to figure out if the conditions system actually needs to be updated.
+    }
+
+    /**
+     * This method catches changes to the detector name and run number. It is
+     * actually called every time an lcsim event is created, so it has internal
+     * logic to figure out if the conditions system actually needs to be
+     * updated.
      */
     @Override
     public void setDetector(String detectorName, int runNumber) throws ConditionsNotFoundException {
-    	    	
+
         // Detector update.
         if (getDetector() == null || !getDetector().equals(detectorName)) {
             logger.config("setting new detector " + detectorName);
@@ -255,7 +260,7 @@
         }
 
         // Let the super class do whatever it think it needs to do.
-        super.setDetector(detectorName, runNumber);        
+        super.setDetector(detectorName, runNumber);
     }
 
     /**
@@ -270,7 +275,8 @@
     }
 
     /**
-     * Get the lcsim compact <code>Detector</code> object from the conditions system.
+     * Get the lcsim compact <code>Detector</code> object from the conditions
+     * system.
      * @return The detector object.
      */
     public Detector getDetectorObject() {
@@ -287,7 +293,7 @@
         logger.fine("getting conditions " + name + " of type " + type.getSimpleName());
         return getCachedConditions(type, name).getCachedData();
     }
-    
+
     /**
      * Configure this object from an XML file.
      * @param file The XML file.
@@ -356,9 +362,10 @@
         logger.fine("new collection ID " + collectionId + " created for table " + tableName);
         return collectionId;
     }
-    
-    /**
-     * This method will return true if the given collection ID already exists in the table.
+
+    /**
+     * This method will return true if the given collection ID already exists in
+     * the table.
      * @param tableName The name of the table.
      * @param collectionID The collection ID value.
      * @return True if collection exists.
@@ -411,7 +418,8 @@
      * @param type The collection class.
      * @return The table meta data.
      */
-    // FIXME: This should return a list in case of multiple conditions defined with same type.
+    // FIXME: This should return a list in case of multiple conditions defined
+    // with same type.
     public TableMetaData findTableMetaData(Class type) {
         for (TableMetaData meta : tableMetaData) {
             if (meta.getCollectionClass().equals(type)) {
@@ -475,9 +483,9 @@
     }
 
     /**
-     * Find a collection of conditions validity records by key name. The key name is
-     * distinct from the table name, but they are usually set to the same value in the XML
-     * configuration.
+     * Find a collection of conditions validity records by key name. The key
+     * name is distinct from the table name, but they are usually set to the
+     * same value in the XML configuration.
      * @param name The conditions key name.
      * @return The set of matching conditions records.
      */
@@ -513,7 +521,7 @@
     public int getRunNumber() {
         return runNumber;
     }
-                
+
     /**
      * Close a JDBC <code>Statement</code>.
      * @param statement the Statement to close
@@ -532,7 +540,8 @@
     }
 
     /**
-     * Close a JDBC <code>ResultSet</code>, or rather the Statement connected to it.
+     * Close a JDBC <code>ResultSet</code>, or rather the Statement connected to
+     * it.
      * @param resultSet the ResultSet to close
      */
     static void close(ResultSet resultSet) {
@@ -558,8 +567,8 @@
     }
 
     /**
-     * Configure this class from an <code>InputStream</code> which should point to an XML
-     * document.
+     * Configure this class from an <code>InputStream</code> which should point
+     * to an XML document.
      * @param in the InputStream which should be in XML format
      */
     private void configure(InputStream in) {
@@ -597,11 +606,12 @@
      */
     private void loadConverters(Document config) {
 
-    	if (this.converters != null) {
+        if (this.converters != null) {
             this.converters.clear();
-    	}
-    	
-        // Load the list of converters from the "converters" section of the config document.
+        }
+
+        // Load the list of converters from the "converters" section of the
+        // config document.
         loadConditionsConverters(config.getRootElement().getChild("converters"));
 
         // Register the list of converters with this manager.
@@ -616,22 +626,25 @@
      * @param config The XML document.
      */
     private void loadTableMetaData(Document config) {
-    	
+
         if (this.tableMetaData != null) {
-        	this.tableMetaData.clear();
-        }
-        	
-        // Load table meta data from the "tables" section of the config document.
+            this.tableMetaData.clear();
+        }
+
+        // Load table meta data from the "tables" section of the config
+        // document.
         loadTableMetaData(config.getRootElement().getChild("tables"));
     }
-    
-    /**
-     * Setup the database connection from a file specified by Java system property setting.
-     * This is possible overridden by subsequent API calls to {@link #setConnectionProperties(File)} or
-     * {@link #setConnectionResource(String)}, as it is called in the class's constructor.
+
+    /**
+     * Setup the database connection from a file specified by Java system
+     * property setting. This is possible overridden by subsequent API calls to
+     * {@link #setConnectionProperties(File)} or
+     * {@link #setConnectionResource(String)}, as it is called in the class's
+     * constructor.
      */
     private void setupConnectionFromSystemProperty() {
-        String systemPropertiesConnectionPath = (String)System.getProperties().get(connectionProperty);
+        String systemPropertiesConnectionPath = (String) System.getProperties().get(connectionProperty);
         if (systemPropertiesConnectionPath != null) {
             File f = new File(systemPropertiesConnectionPath);
             if (!f.exists())
@@ -639,87 +652,88 @@
             this.setConnectionProperties(f);
         }
     }
-    
-	/**
-	 * This method expects an XML element containing child "table" elements.
-	 * @param element
-	 */
-	@SuppressWarnings("unchecked")
-	void loadTableMetaData(Element element) {
-
-		tableMetaData = new ArrayList<TableMetaData>();
-
-		for (Iterator<?> iterator = element.getChildren("table").iterator(); iterator.hasNext();) {
-			Element tableElement = (Element) iterator.next();
-			String tableName = tableElement.getAttributeValue("name");
-			String key = tableElement.getAttributeValue("key");
-
-			Element classesElement = tableElement.getChild("classes");
-			Element classElement = classesElement.getChild("object");
-			Element collectionElement = classesElement.getChild("collection");
-
-			String className = classElement.getAttributeValue("class");
-			String collectionName = collectionElement.getAttributeValue("class");
-
-			Class<? extends ConditionsObject> objectClass;
-			Class<?> rawObjectClass;
-			try {
-				rawObjectClass = Class.forName(className);
-				if (!ConditionsObject.class.isAssignableFrom(rawObjectClass)) {
-					throw new RuntimeException("The class " + rawObjectClass.getSimpleName() + " does not extend ConditionsObject.");
-				}
-				objectClass = (Class<? extends ConditionsObject>) rawObjectClass;
-			} catch (ClassNotFoundException e) {
-				throw new RuntimeException(e);
-			}
-
-			Class<? extends ConditionsObjectCollection<?>> collectionClass;
-			Class<?> rawCollectionClass;
-			try {
-				rawCollectionClass = Class.forName(collectionName);
-				if (!ConditionsObjectCollection.class.isAssignableFrom(rawCollectionClass))
-					throw new RuntimeException("The class " + rawCollectionClass.getSimpleName() + " does not extend ConditionsObjectCollection.");
-				collectionClass = (Class<? extends ConditionsObjectCollection<?>>) rawCollectionClass;
-			} catch (ClassNotFoundException e) {
-				throw new RuntimeException(e);
-			}
-
-			TableMetaData tableData = new TableMetaData(key, tableName, objectClass, collectionClass);
-			Element fieldsElement = tableElement.getChild("fields");
-			for (Iterator<?> fieldsIterator = fieldsElement.getChildren("field").iterator(); fieldsIterator.hasNext();) {
-				Element fieldElement = (Element) fieldsIterator.next();
-				String fieldName = fieldElement.getAttributeValue("name");
-				tableData.addField(fieldName);
-			}
-
-			tableMetaData.add(tableData);
-		}
-	}
-
-    /**
-     * This class reads in an XML configuration specifying a list of converter classes,
-     * e.g. from the config file for the {@link DatabaseConditionsManager}.
+
+    /**
+     * This method expects an XML element containing child "table" elements.
+     * @param element
+     */
+    @SuppressWarnings("unchecked")
+    void loadTableMetaData(Element element) {
+
+        tableMetaData = new ArrayList<TableMetaData>();
+
+        for (Iterator<?> iterator = element.getChildren("table").iterator(); iterator.hasNext();) {
+            Element tableElement = (Element) iterator.next();
+            String tableName = tableElement.getAttributeValue("name");
+            String key = tableElement.getAttributeValue("key");
+
+            Element classesElement = tableElement.getChild("classes");
+            Element classElement = classesElement.getChild("object");
+            Element collectionElement = classesElement.getChild("collection");
+
+            String className = classElement.getAttributeValue("class");
+            String collectionName = collectionElement.getAttributeValue("class");
+
+            Class<? extends ConditionsObject> objectClass;
+            Class<?> rawObjectClass;
+            try {
+                rawObjectClass = Class.forName(className);
+                if (!ConditionsObject.class.isAssignableFrom(rawObjectClass)) {
+                    throw new RuntimeException("The class " + rawObjectClass.getSimpleName() + " does not extend ConditionsObject.");
+                }
+                objectClass = (Class<? extends ConditionsObject>) rawObjectClass;
+            } catch (ClassNotFoundException e) {
+                throw new RuntimeException(e);
+            }
+
+            Class<? extends ConditionsObjectCollection<?>> collectionClass;
+            Class<?> rawCollectionClass;
+            try {
+                rawCollectionClass = Class.forName(collectionName);
+                if (!ConditionsObjectCollection.class.isAssignableFrom(rawCollectionClass))
+                    throw new RuntimeException("The class " + rawCollectionClass.getSimpleName() + " does not extend ConditionsObjectCollection.");
+                collectionClass = (Class<? extends ConditionsObjectCollection<?>>) rawCollectionClass;
+            } catch (ClassNotFoundException e) {
+                throw new RuntimeException(e);
+            }
+
+            TableMetaData tableData = new TableMetaData(key, tableName, objectClass, collectionClass);
+            Element fieldsElement = tableElement.getChild("fields");
+            for (Iterator<?> fieldsIterator = fieldsElement.getChildren("field").iterator(); fieldsIterator.hasNext();) {
+                Element fieldElement = (Element) fieldsIterator.next();
+                String fieldName = fieldElement.getAttributeValue("name");
+                tableData.addField(fieldName);
+            }
+
+            tableMetaData.add(tableData);
+        }
+    }
+
+    /**
+     * This class reads in an XML configuration specifying a list of converter
+     * classes, e.g. from the config file for the
+     * {@link DatabaseConditionsManager}.
      * 
      * @author Jeremy McCormick <[log in to unmask]>
      */
-	private void loadConditionsConverters(Element element) {
-		converters = new ArrayList<ConditionsConverter>();
-		for (Iterator iterator = element.getChildren("converter").iterator(); iterator.hasNext();) {
-			Element converterElement = (Element) iterator.next();
-			try {
-				Class converterClass = Class.forName(converterElement.getAttributeValue("class"));
-				if (ConditionsConverter.class.isAssignableFrom(converterClass)) {
-					try {
-						converters.add((ConditionsConverter) converterClass.newInstance());
-					} catch (InstantiationException | IllegalAccessException e) {
-						throw new RuntimeException(e);
-					}
-				} else {
-					throw new RuntimeException("The converter class " + converterClass.getSimpleName() + " does not extend the correct base type.");
-				}
-			} catch (ClassNotFoundException e) {
-				throw new RuntimeException(e);
-			}
-		}
-	}
+    private void loadConditionsConverters(Element element) {
+        converters = new ArrayList<ConditionsConverter>();
+        for (Iterator iterator = element.getChildren("converter").iterator(); iterator.hasNext();) {
+            Element converterElement = (Element) iterator.next();
+            try {
+                Class converterClass = Class.forName(converterElement.getAttributeValue("class"));
+                if (ConditionsConverter.class.isAssignableFrom(converterClass)) {
+                    try {
+                        converters.add((ConditionsConverter) converterClass.newInstance());
+                    } catch (InstantiationException | IllegalAccessException e) {
+                        throw new RuntimeException(e);
+                    }
+                } else {
+                    throw new RuntimeException("The converter class " + converterClass.getSimpleName() + " does not extend the correct base type.");
+                }
+            } catch (ClassNotFoundException e) {
+                throw new RuntimeException(e);
+            }
+        }
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/QueryBuilder.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/QueryBuilder.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/QueryBuilder.java	Mon Nov 10 00:16:49 2014
@@ -3,7 +3,8 @@
 import java.util.List;
 
 /**
- * This is a static utility class for building SQL queries for the conditions system.
+ * This is a static utility class for building SQL queries for the conditions
+ * system.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -62,7 +63,7 @@
         buff.append(") ");
         return buff.toString();
     }
-    
+
     public static String buildInsert(String tableName, int collectionID, List<String> columnNames, List<List<String>> rows) {
         StringBuffer buff = new StringBuffer();
         buff.append("INSERT INTO " + tableName + " ( collection_id");
@@ -77,16 +78,15 @@
                 buff.append(", '" + value + "'");
             }
             buff.append("), ");
-        }        
+        }
         buff.setLength(buff.length() - 2);
         return buff.toString();
     }
-    
 
     public static String buildDelete(String tableName, int rowId) {
         if (rowId <= 0)
             throw new IllegalArgumentException("Invalid row ID: " + rowId);
         String query = "DELETE FROM " + tableName + " WHERE id = " + rowId;
         return query;
-    }        
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/TableConstants.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/TableConstants.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/TableConstants.java	Mon Nov 10 00:16:49 2014
@@ -2,17 +2,19 @@
 
 /**
  * <p>
- * This is a static set of constants defining default table names and lookup key values
- * for conditions data. The actual table names for the conditions data are defined
- * externally in an XML configuration file read by the {@link DatabaseConditionsManager}.
+ * This is a static set of constants defining default table names and lookup key
+ * values for conditions data. The actual table names for the conditions data
+ * are defined externally in an XML configuration file read by the
+ * {@link DatabaseConditionsManager}.
  * </p>
  * <p>
- * It is possible that the key and table names are defined differently in the XML
- * configuration, e.g. if the name of the key is not exactly the same as the table name,
- * but usually they are the same value.
+ * It is possible that the key and table names are defined differently in the
+ * XML configuration, e.g. if the name of the key is not exactly the same as the
+ * table name, but usually they are the same value.
  * </p>
  */
-// FIXME: This should really be called something like "ConditionsKeys" as the table names
+// FIXME: This should really be called something like "ConditionsKeys" as the
+// table names
 // are found in the XML configuration only.
 public final class TableConstants {
 
@@ -39,19 +41,19 @@
 
     /** ECAL time shifts. */
     public static final String ECAL_TIME_SHIFTS = "ecal_time_shifts";
-    
+
     /** ECAL LED setup. */
-    public static final String ECAL_LEDS = "ecal_leds";    
+    public static final String ECAL_LEDS = "ecal_leds";
 
     /** Conditions key for combined SVT conditions. */
     public static final String SVT_CONDITIONS = "svt_conditions";
-    
+
     /** Conditions key for SVT alignment data. */
     public static final String SVT_ALIGNMENTS = "svt_alignments";
 
     /** Conditions key for SVT bad channels. */
     public static final String SVT_BAD_CHANNELS = "svt_bad_channels";
-   
+
     /** Table with SVT channel data. */
     public static final String SVT_CHANNELS = "svt_channels";
 
@@ -60,7 +62,7 @@
 
     /** Conditions key for SVT calibration data. */
     public static final String SVT_CALIBRATIONS = "svt_calibrations";
-    
+
     /** Conditions key for SVT configuration files. */
     public static final String SVT_CONFIGURATIONS = "svt_configurations";
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/TableMetaData.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/TableMetaData.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/TableMetaData.java	Mon Nov 10 00:16:49 2014
@@ -5,13 +5,14 @@
 
 /**
  * <p>
- * This class provides meta data about a conditions table, including a list of conditions
- * data fields. The list of fields does not include the collection ID or row ID, which are
- * implicitly assumed to exist.
+ * This class provides meta data about a conditions table, including a list of
+ * conditions data fields. The list of fields does not include the collection ID
+ * or row ID, which are implicitly assumed to exist.
  * </p>
  * <p>
- * It also has references to the implementation classes which are used to map the data
- * onto {@link ConditionsObject} and {@link ConditionsObjectCollection}s.
+ * It also has references to the implementation classes which are used to map
+ * the data onto {@link ConditionsObject} and {@link ConditionsObjectCollection}
+ * s.
  * </p>
  * 
  * @author Jeremy McCormick <[log in to unmask]>
@@ -50,7 +51,7 @@
      * Get the type of collection this table maps onto.
      * @return
      */
-   public Class<? extends ConditionsObjectCollection<?>> getCollectionClass() {
+    public Class<? extends ConditionsObjectCollection<?>> getCollectionClass() {
         return collectionClass;
     }
 
@@ -82,8 +83,8 @@
     }
 
     /**
-     * Get the key of this conditions type. May be different from table name but is
-     * usually the same.
+     * Get the key of this conditions type. May be different from table name but
+     * is usually the same.
      * @return The key name of the conditions type.
      */
     public String getKey() {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/TestRunConditionsDriver.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/TestRunConditionsDriver.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/TestRunConditionsDriver.java	Mon Nov 10 00:16:49 2014
@@ -9,9 +9,9 @@
 import static org.hps.conditions.TableConstants.SVT_CONDITIONS;
 
 /**
- * This {@link org.lcsim.util.Driver} is a subclass of {@link AbstractConditionsDriver}
- * and specifies the database connection parameters and configuration for the
- * test run database. 
+ * This {@link org.lcsim.util.Driver} is a subclass of
+ * {@link AbstractConditionsDriver} and specifies the database connection
+ * parameters and configuration for the test run database.
  * 
  * @author Omar Moreno <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
@@ -21,10 +21,11 @@
     // Default constructor used to setup the database connection
     public TestRunConditionsDriver() {
         if (ConditionsManager.defaultInstance() instanceof DatabaseConditionsManager) {
-        	//System.out.println(this.getName()+": Found existing DatabaseConditionsManager");
-            //manager = (DatabaseConditionsManager) ConditionsManager.defaultInstance();
-        	throw new RuntimeException("ConditionsManager was already setup.");
-        } else { 
+            // System.out.println(this.getName()+": Found existing DatabaseConditionsManager");
+            // manager = (DatabaseConditionsManager)
+            // ConditionsManager.defaultInstance();
+            throw new RuntimeException("ConditionsManager was already setup.");
+        } else {
             manager = new DatabaseConditionsManager();
             manager.configure("/org/hps/conditions/config/conditions_database_testrun_2012.xml");
             manager.register();
@@ -32,7 +33,8 @@
     }
 
     /**
-     * Load the {@link TestRunSvtConditions} set onto <code>HpsTestRunSiSensor</code>.
+     * Load the {@link TestRunSvtConditions} set onto
+     * <code>HpsTestRunSiSensor</code>.
      * 
      * @param detector The detector to update.
      */

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/cli/CommandLineTool.java	Mon Nov 10 00:16:49 2014
@@ -15,17 +15,18 @@
 
 /**
  * <p>
- * This class is a command-line tool for performing commands on the conditions database.
- * It has sub-commands much like the cvs or svn clients.  The only current implemented
- * command is 'load' to import text files, but more will be added.
+ * This class is a command-line tool for performing commands on the conditions
+ * database. It has sub-commands much like the cvs or svn clients. The only
+ * current implemented command is 'load' to import text files, but more will be
+ * added.
  * <p>
- * Command line options allow a custom connection properties file or XML configuration
- * to be supplied by the user which will override the default.
+ * Command line options allow a custom connection properties file or XML
+ * configuration to be supplied by the user which will override the default.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class CommandLineTool {
-    
+
     Options options = new Options();
     Map<String, AbstractCommand> commands = new HashMap<String, AbstractCommand>();
     PosixParser parser = new PosixParser();
@@ -33,12 +34,12 @@
     static final String XML_CONFIG_RESOURCE = "/org/hps/conditions/config/conditions_dev.xml";
     DatabaseConditionsManager conditionsManager;
     boolean verbose = false;
-    
-    public static void main(String[] arguments) {        
+
+    public static void main(String[] arguments) {
         CommandLineTool.create().run(arguments);
     }
-    
-    void run(String[] arguments) {        
+
+    void run(String[] arguments) {
         try {
             if (arguments.length == 0) {
                 printUsage();
@@ -58,11 +59,11 @@
                 printUsage();
                 exit(0);
             }
-            
+
             if (commandLine.hasOption("v")) {
                 verbose = true;
             }
-            
+
             setupConditionsManager(commandLine);
 
             String commandName = commandLine.getArgs()[0];
@@ -99,7 +100,7 @@
             if (verbose)
                 System.out.println("using connection resource " + CONNECTION_PROPERTIES_RESOURCE);
             conditionsManager.setConnectionResource(CONNECTION_PROPERTIES_RESOURCE);
-        }            
+        }
         if (commandLine.hasOption("x")) {
             File xmlConfigFile = new File(commandLine.getOptionValue("x"));
             conditionsManager.configure(xmlConfigFile);
@@ -109,31 +110,31 @@
             if (verbose)
                 System.out.println("using XML config resource " + XML_CONFIG_RESOURCE);
             conditionsManager.configure(XML_CONFIG_RESOURCE);
-        }            
+        }
         conditionsManager.register();
         conditionsManager.openConnection();
     }
-    
+
     void printUsage() {
         HelpFormatter help = new HelpFormatter();
         StringBuffer s = new StringBuffer();
         for (String command : commands.keySet()) {
             s.append(command + '\n');
         }
-        help.printHelp("CommandLineTool", "Commands:\n" + s.toString(), options, "");        
+        help.printHelp("CommandLineTool", "Commands:\n" + s.toString(), options, "");
     }
-    
+
     void exit(int status) {
         System.exit(status);
     }
-    
+
     void registerCommand(AbstractCommand command) {
         if (commands.containsKey(command.getName())) {
             throw new IllegalArgumentException("There is already a command called " + command.getName());
         }
         commands.put(command.getName(), command);
     }
-    
+
     static CommandLineTool create() {
         CommandLineTool cli = new CommandLineTool();
         cli.options.addOption(new Option("h", false, "Print help and exit"));

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/cli/LoadCommand.java	Mon Nov 10 00:16:49 2014
@@ -18,12 +18,15 @@
 
 /**
  * <p>
- * This is a sub-command to add conditions data using an input text file.
- * The file should be ASCII text that is tab or space delimited and includes headers with the names of 
- * the database columns.  (These must match exactly!)  The user must supply a table name as the target 
- * for the SQL insert.  An optional collection ID can be supplied, which may not exist already in the table.  
- * Otherwise, the command will fail.  By default, the next collection ID will be found by the conditions manager.
+ * This is a sub-command to add conditions data using an input text file. The
+ * file should be ASCII text that is tab or space delimited and includes headers
+ * with the names of the database columns. (These must match exactly!) The user
+ * must supply a table name as the target for the SQL insert. An optional
+ * collection ID can be supplied, which may not exist already in the table.
+ * Otherwise, the command will fail. By default, the next collection ID will be
+ * found by the conditions manager.
  * <p>
+ * 
  * <pre>
  * java -cp hps-distribution-bin.jar org.hps.conditions.cli.CommandLineTool -p conditions_dev_local.properties \
  *     load -t scratch_svt_gains -f ./scratch_svt_gains.txt -c 1
@@ -32,59 +35,59 @@
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class LoadCommand extends AbstractCommand {
-       
+
     LoadCommand() {
         super("load", "Load a set of conditions into the database from a text file");
         this.options.addOption(new Option("t", true, "Set the name of the target table in the database"));
         this.options.addOption(new Option("c", true, "Set the collection ID of this conditions set"));
         this.options.addOption(new Option("f", true, "Set the input data file"));
-    }    
-    
+    }
+
     @Override
     public void execute(String[] arguments) {
-        CommandLine commandLine;        
+        CommandLine commandLine;
         try {
-            commandLine = parser.parse(options,  arguments);
+            commandLine = parser.parse(options, arguments);
         } catch (ParseException e) {
             throw new RuntimeException(e);
         }
-        
+
         String fileName = commandLine.getOptionValue("f");
         if (fileName == null) {
             throw new IllegalArgumentException("Missing file argument.");
         }
-        
+
         String tableName = commandLine.getOptionValue("t");
         if (tableName == null) {
             throw new IllegalArgumentException("Missing table name.");
         }
-        
+
         DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
         if (conditionsManager == null) {
             throw new RuntimeException("The DatabaseConditionsManager was not setup properly.");
         }
-        
+
         int collectionID;
         if (commandLine.getOptionValue("c") != null) {
             collectionID = Integer.parseInt(commandLine.getOptionValue("c"));
             if (conditionsManager.collectionExists(tableName, collectionID)) {
                 throw new IllegalArgumentException("The user supplied collection ID " + collectionID + " already exists in this table.");
-            }            
+            }
         } else {
-            collectionID = conditionsManager.getNextCollectionID(tableName); 
+            collectionID = conditionsManager.getNextCollectionID(tableName);
         }
-                                
+
         List<String> columnNames = new ArrayList<String>();
-        List<List<String>> rows = new ArrayList<List<String>>();        
+        List<List<String>> rows = new ArrayList<List<String>>();
         parseFile(fileName, columnNames, rows);
-                        
+
         String insertSql = QueryBuilder.buildInsert(tableName, collectionID, columnNames, rows);
         if (verbose)
             System.out.println(insertSql);
         List<Integer> IDs = conditionsManager.updateQuery(insertSql);
         System.out.println("Inserted " + IDs.size() + " new rows into table " + tableName + " with collection_id " + collectionID);
     }
-    
+
     void parseFile(String fileName, List<String> columnNames, List<List<String>> rows) {
         File inputFile = new File(fileName);
         BufferedReader reader = null;
@@ -117,6 +120,6 @@
                     e.printStackTrace();
                 }
             }
-        }        
-    }    
+        }
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamSpot.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamSpot.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamSpot.java	Mon Nov 10 00:16:49 2014
@@ -8,8 +8,7 @@
 
 /**
  * Class describing the HPS beamspot at the target (Z=0)
- * @author mgraham
- * created on 6/27/2011
+ * @author mgraham created on 6/27/2011
  */
 public class BeamSpot {
 
@@ -27,7 +26,7 @@
     }
 
     public BeamSpot(double sigX, double sigY) {
-        //  default beamspot position
+        // default beamspot position
         _position[0] = 0;
         _position[1] = 0;
         _angle[0] = 0;
@@ -65,7 +64,7 @@
 
     public SymmetricMatrix getBeamCovariance() {
         return _beamcov;
-    }  
+    }
 
     public void setBeamPosition(double[] pos) {
         _position = pos;

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamlineConstants.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamlineConstants.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/BeamlineConstants.java	Mon Nov 10 00:16:49 2014
@@ -1,12 +1,17 @@
 package org.hps.conditions.deprecated;
 
 public final class BeamlineConstants {
-	
-	private BeamlineConstants() {}
-	
-	public static final double ECAL_FACE_TESTRUN   = 1524;  // mm
-	public static final double DIPOLE_EDGE_TESTRUN = 457.2 + 457.2; // 452.2 + 462.2; //914; // mm
-	public static final double DIPOLE_EDGELOW_TESTRUN = 0.; //452.2 - 462.2; // mm
-	public static final double HARP_POSITION_TESTRUN = -674.062; // mm
+
+    private BeamlineConstants() {
+    }
+
+    public static final double ECAL_FACE_TESTRUN = 1524; // mm
+    public static final double DIPOLE_EDGE_TESTRUN = 457.2 + 457.2; // 452.2 +
+                                                                    // 462.2;
+                                                                    // //914; //
+                                                                    // mm
+    public static final double DIPOLE_EDGELOW_TESTRUN = 0.; // 452.2 - 462.2; //
+                                                            // mm
+    public static final double HARP_POSITION_TESTRUN = -674.062; // mm
 
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/CalibrationDriver.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/CalibrationDriver.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/CalibrationDriver.java	Mon Nov 10 00:16:49 2014
@@ -15,15 +15,16 @@
  */
 public class CalibrationDriver extends Driver implements ConditionsListener {
 
-    // The test run number of interest.  If it equals -1, the default calibrations
+    // The test run number of interest. If it equals -1, the default
+    // calibrations
     // are loaded
     private static int runNumber = -1;
     private boolean fixRunNumber = false;
-	private String gainFilename = "default.gain";
+    private String gainFilename = "default.gain";
 
     public CalibrationDriver() {
         add(new EcalConditions());
-        //add(new HPSSVTSensorSetup());
+        // add(new HPSSVTSensorSetup());
     }
 
     public void setRunNumber(int runNumber) {
@@ -52,13 +53,15 @@
         super.detectorChanged(detector);
 
         if (!EcalConditions.calibrationLoaded()) {
-        	EcalConditions.setGainFilename(gainFilename);
-        	EcalConditions.loadCalibration();
+            EcalConditions.setGainFilename(gainFilename);
+            EcalConditions.loadCalibration();
         }
-        /*if (fixRunNumber && (!HPSSVTCalibrationConstants.pedestalLoaded() || !HPSSVTCalibrationConstants.tpLoaded())) {
-            System.out.println("Loading calibration for set run: " + runNumber);
-            loadCalibsByRun(runNumber);
-        }*/
+        /*
+         * if (fixRunNumber && (!HPSSVTCalibrationConstants.pedestalLoaded() ||
+         * !HPSSVTCalibrationConstants.tpLoaded())) {
+         * System.out.println("Loading calibration for set run: " + runNumber);
+         * loadCalibsByRun(runNumber); }
+         */
     }
 
     @Override
@@ -76,13 +79,14 @@
     }
 
     private void loadCalibsByRun(int run) {
-        //HPSSVTCalibrationConstants.loadCalibration(run);
+        // HPSSVTCalibrationConstants.loadCalibration(run);
         FieldMap.loadFieldMap(run);
     }
 
     /**
-     * get specified conditions list, parse as a map of run numbers to calibration file paths; get the appropriate file 
-     * @param calibName 
+     * get specified conditions list, parse as a map of run numbers to
+     * calibration file paths; get the appropriate file
+     * @param calibName
      * @param run
      * @return
      */
@@ -95,7 +99,7 @@
         String filePath = null;
         for (Object key : calibSet.keySet()) {
             int keyRun = Integer.parseInt((String) key);
-//            System.out.println("Available calibration for run: " + keyRun);
+            // System.out.println("Available calibration for run: " + keyRun);
             if (keyRun > mostRecentValid && keyRun <= run) {
                 mostRecentValid = keyRun;
                 filePath = calibSet.getString((String) key);

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/EcalConditions.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/EcalConditions.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/EcalConditions.java	Mon Nov 10 00:16:49 2014
@@ -21,19 +21,19 @@
  */
 public class EcalConditions extends Driver {
 
-    //DAQ channel map
+    // DAQ channel map
     private static HashMap<Long, Long> daqToPhysicalMap = new HashMap<Long, Long>();
     private static HashMap<Long, Long> physicalToDaqMap = new HashMap<Long, Long>();
-    //pedestals
+    // pedestals
     private static HashMap<Long, Double> daqToPedestalMap = new HashMap<Long, Double>();
     private static HashMap<Long, Double> daqToNoiseMap = new HashMap<Long, Double>();
-    //set of bad channels to ignore
+    // set of bad channels to ignore
     private static HashSet<Long> badChannelsSet = new HashSet<Long>();
     private static boolean badChannelsLoaded = false;
     private static IIdentifierHelper helper = null;
-    //gain
+    // gain
     private static HashMap<Long, Double> physicalToGainMap = new HashMap<Long, Double>();
-    //subdetector name (for when this is used as a driver)
+    // subdetector name (for when this is used as a driver)
     private String subdetectorName = "Ecal";
     private static Subdetector subdetector;
     private static boolean debug = false;
@@ -72,9 +72,9 @@
         loadPedestals();
         calibrationLoaded = true;
     }
-    
+
     public static void setGainFilename(String name) {
-    	gainFilename = name;
+        gainFilename = name;
     }
 
     public void setSubdetectorName(String subdetectorName) {
@@ -139,7 +139,7 @@
                     daqToPedestalMap.put(daqid, pedestal);
                     daqToNoiseMap.put(daqid, noise);
                     if (debug) {
-                        System.out.printf("Channel %d: pede %.2f noise %.2f (crate %d slot %d channel %d)\n", daqid,pedestal,noise,crate,slot,channel);
+                        System.out.printf("Channel %d: pede %.2f noise %.2f (crate %d slot %d channel %d)\n", daqid, pedestal, noise, crate, slot, channel);
                     }
                 }
             }
@@ -186,7 +186,7 @@
                     expId.setValue(helper.getFieldIndex("iy"), y);
                     badChannelsSet.add(helper.pack(expId).getValue());
                     if (debug) {
-                        System.out.printf("Channel %d is bad (x=%d y=%d)\n", helper.pack(expId).getValue(),x,y);
+                        System.out.printf("Channel %d is bad (x=%d y=%d)\n", helper.pack(expId).getValue(), x, y);
                     }
                 }
             }
@@ -201,9 +201,9 @@
         BufferedReader bufferedReader;
         ConditionsManager conditions = ConditionsManager.defaultInstance();
         try {
-        	bufferedReader = new BufferedReader(conditions.getRawConditions("calibECal/"+EcalConditions.gainFilename).getReader());
+            bufferedReader = new BufferedReader(conditions.getRawConditions("calibECal/" + EcalConditions.gainFilename).getReader());
         } catch (IOException e) {
-            throw new RuntimeException("couldn't get gain file("+gainFilename+") ", e);
+            throw new RuntimeException("couldn't get gain file(" + gainFilename + ") ", e);
         }
 
         String line;
@@ -232,7 +232,7 @@
                     double gain = Double.valueOf(lineTok.nextToken());
                     physicalToGainMap.put(makePhysicalID(x, y), gain);
                     if (debug) {
-                        System.out.printf("Channel %d: gain %.2f (x=%d y=%d)\n", makePhysicalID(x, y),gain,x,y);
+                        System.out.printf("Channel %d: gain %.2f (x=%d y=%d)\n", makePhysicalID(x, y), gain, x, y);
                     }
                 }
             }
@@ -280,7 +280,7 @@
                 } else {
                     int x = Integer.valueOf(lineTok.nextToken());
                     int y = Integer.valueOf(lineTok.nextToken());
-//                    if (x>0 && y>0) x = 24-x;
+                    // if (x>0 && y>0) x = 24-x;
                     expId.setValue(helper.getFieldIndex("ix"), x);
                     expId.setValue(helper.getFieldIndex("iy"), y);
                     int crate = Integer.valueOf(lineTok.nextToken());

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/FieldMap.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/FieldMap.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/FieldMap.java	Mon Nov 10 00:16:49 2014
@@ -13,38 +13,35 @@
 import org.hps.util.Pair;
 
 /**
-
-@author Mathew Graham <[log in to unmask]> $Id: FieldMap.java,v 1.14
-2012/07/23 23:02:57 mgraham Exp $
+ * @author Mathew Graham <[log in to unmask]> $Id: FieldMap.java,v 1.14
+ *         2012/07/23 23:02:57 mgraham Exp $
  */
 public class FieldMap {
 
     // TODO: Change all pairs such that FPGA is the fist value
     // TODO: Change all map keys to type SiSensor?
 
-	public static Map<Pair<Integer/*
-            zbin
-             */, Integer/*
-            xbin
-             */>, Double/*
-            b_y
-             */> fieldMap = new HashMap<Pair<Integer, Integer>, Double>();
-    ;
     public static Map<Pair<Integer/*
-            zbin
-             */, Integer/*
-            zbin
-             */>, Pair<Double/*
-            zpos
-             */, Double/*
-            xpos
-             */>> fieldBins = new HashMap<Pair<Integer, Integer>, Pair<Double, Double>>();
-    ;
+                                   * zbin
+                                   */, Integer/*
+                                               * xbin
+                                               */>, Double/*
+                                                           * b_y
+                                                           */> fieldMap = new HashMap<Pair<Integer, Integer>, Double>();;
+    public static Map<Pair<Integer/*
+                                   * zbin
+                                   */, Integer/*
+                                               * zbin
+                                               */>, Pair<Double/*
+                                                                * zpos
+                                                                */, Double/*
+                                                                           * xpos
+                                                                           */>> fieldBins = new HashMap<Pair<Integer, Integer>, Pair<Double, Double>>();;
     private static boolean fieldMapLoaded = false;
     private static boolean debug = false;
 
     /**
-    Default Ctor
+     * Default Ctor
      */
     private FieldMap() {
     }
@@ -55,13 +52,15 @@
 
     public static void loadFieldMap(int run) {
         System.out.println("Loading fieldmap for run " + run);
-        //write something here to read in constants from calibration file
+        // write something here to read in constants from calibration file
         ConditionsManager conditions = ConditionsManager.defaultInstance();
 
         String filePath = null;
 
-        //TODO: if we ever have more than one field map, make a list and uncomment this
-//        filePath = HPSCalibrationListener.getCalibForRun("FieldMap/bfieldmap", run);
+        // TODO: if we ever have more than one field map, make a list and
+        // uncomment this
+        // filePath =
+        // HPSCalibrationListener.getCalibForRun("FieldMap/bfieldmap", run);
 
         if (filePath == null) {
             filePath = "FieldMap/bfieldmap.dat";
@@ -73,9 +72,6 @@
         } catch (IOException e) {
             throw new RuntimeException("couldn't get baseline file", e);
         }
-
-
-
 
     }
 
@@ -113,17 +109,20 @@
                     double val = vals.get(i);
                     if (i == 0 && val >= 0) {
                         xval = 0.0;
-                        zval = val * 10.0;//convert from cm to mm
+                        zval = val * 10.0;// convert from cm to mm
                         ix = 0;
                         iz++;
                     } else {
-                        bY = val / 10000.0 * 0.491 / 0.5;//gauss-->tesla  and normalize by our nominal bfield (file is for 0.5T)
+                        bY = val / 10000.0 * 0.491 / 0.5;// gauss-->tesla and
+                                                         // normalize by our
+                                                         // nominal bfield (file
+                                                         // is for 0.5T)
                         bY = Math.abs(bY);
                         Pair zx = new Pair(zval, xval);
                         Pair izix = new Pair(iz, ix);
-//                    System.out.println("Putting B = "+bY+" & (Z,X) = "+zval+","+xval+")");
+                        // System.out.println("Putting B = "+bY+" & (Z,X) = "+zval+","+xval+")");
                         fieldMap.put(izix, bY);
-//                    System.out.println("Making _fieldBins pair = ("+iz+","+ix+")");
+                        // System.out.println("Making _fieldBins pair = ("+iz+","+ix+")");
                         fieldBins.put(izix, zx);
                         xval += 10.0;
                         ix++;
@@ -143,10 +142,10 @@
         List<Double> nums = new ArrayList<Double>();
         while (tok.hasMoreTokens()) {
             String tokVal = tok.nextToken();
-//             System.out.println(tokVal);
+            // System.out.println(tokVal);
             nums.add(Double.valueOf(tokVal).doubleValue());
         }
-//        System.out.println("Returning list");
+        // System.out.println("Returning list");
         return nums;
     }
 
@@ -179,15 +178,15 @@
         return izix;
 
     }
-    
+
     public static void printFieldMap() {
-    	int xval = 0;
+        int xval = 0;
         System.out.printf("---- B-field ----\n");
-        System.out.printf("%5s %5s %10s\n", "z","x","B");
-    	for(int zval=-100;zval< 1400;++zval) {
-    		double bfield = FieldMap.getFieldFromMap((double)zval, (double)xval);
-            System.out.printf("%5d %5d %10.3f\n", zval,xval,bfield);
-    	}
+        System.out.printf("%5s %5s %10s\n", "z", "x", "B");
+        for (int zval = -100; zval < 1400; ++zval) {
+            double bfield = FieldMap.getFieldFromMap((double) zval, (double) xval);
+            System.out.printf("%5d %5d %10.3f\n", zval, xval, bfield);
+        }
     }
-    
+
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTCalibrationConstants.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTCalibrationConstants.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTCalibrationConstants.java	Mon Nov 10 00:16:49 2014
@@ -21,54 +21,55 @@
 /**
  *
  * @author Mathew Graham <[log in to unmask]> $Id:
- * HPSSVTCalibrationConstants.java,v 1.23 2013/02/25 22:39:26 meeg Exp $
+ *         HPSSVTCalibrationConstants.java,v 1.23 2013/02/25 22:39:26 meeg Exp $
  */
 public class HPSSVTCalibrationConstants {
 
     // TODO: Change all map keys to type SiSensor?
     // TODO: Update everything to make it compatible new version of SVT Utils
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, double[] /*
-             * constants
-             */> noiseMap = new HashMap<Pair<Integer, Integer>, double[]>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, double[] /*
+                                                                 * constants
+                                                                 */> noiseMap = new HashMap<Pair<Integer, Integer>, double[]>();
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, double[] /*
-             * constants
-             */> pedestalMap = new HashMap<Pair<Integer, Integer>, double[]>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, double[] /*
+                                                                 * constants
+                                                                 */> pedestalMap = new HashMap<Pair<Integer, Integer>, double[]>();
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, double[] /*
-             * constants
-             */> tpMap = new HashMap<Pair<Integer, Integer>, double[]>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, double[] /*
+                                                                 * constants
+                                                                 */> tpMap = new HashMap<Pair<Integer, Integer>, double[]>();
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, Set<Integer> /*
-             * Bad channels
-             */> badChannelMap = new HashMap<Pair<Integer, Integer>, Set<Integer>>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, Set<Integer> /*
+                                                                     * Bad
+                                                                     * channels
+                                                                     */> badChannelMap = new HashMap<Pair<Integer, Integer>, Set<Integer>>();
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, List<Double> /*
-             * channels
-             */> gainMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, List<Double> /*
+                                                                     * channels
+                                                                     */> gainMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
     private static Map<Pair<Integer /*
-             * FPGA
-             */, Integer /*
-             * Hybrid
-             */>, List<Double> /*
-             * channels
-             */> offsetMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
+                                     * FPGA
+                                     */, Integer /*
+                                                  * Hybrid
+                                                  */>, List<Double> /*
+                                                                     * channels
+                                                                     */> offsetMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
     private static Map<Pair<Integer, Integer>, Double> t0ShiftMap = new HashMap<Pair<Integer, Integer>, Double>();
     private static boolean pedestalLoaded = false;
     private static boolean tpLoaded = false;
@@ -88,7 +89,7 @@
     }
 
     public static void loadCalibrationConstants(int run) {
-        //write something here to read in constants from calibration file
+        // write something here to read in constants from calibration file
         ConditionsManager conditions = ConditionsManager.defaultInstance();
         String filePath = null;
 
@@ -104,7 +105,6 @@
         } catch (IOException e) {
             throw new RuntimeException("couldn't get baseline file", e);
         }
-
 
         filePath = CalibrationDriver.getCalibForRun("calibSVT/tp", run);
 
@@ -203,7 +203,24 @@
                     int channel = Integer.valueOf(lineTok.nextToken());
                     double amplitude = Double.valueOf(lineTok.nextToken());
                     double t0 = Double.valueOf(lineTok.nextToken());
-                    double tp = Double.valueOf(lineTok.nextToken()) * 24.0 / 25.0; //FIXME: this is a hack to compensate for the calibrations we have that assumed 25 ns APV clock
+                    double tp = Double.valueOf(lineTok.nextToken()) * 24.0 / 25.0; // FIXME:
+                                                                                   // this
+                                                                                   // is
+                                                                                   // a
+                                                                                   // hack
+                                                                                   // to
+                                                                                   // compensate
+                                                                                   // for
+                                                                                   // the
+                                                                                   // calibrations
+                                                                                   // we
+                                                                                   // have
+                                                                                   // that
+                                                                                   // assumed
+                                                                                   // 25
+                                                                                   // ns
+                                                                                   // APV
+                                                                                   // clock
                     double chisq = Double.valueOf(lineTok.nextToken());
 
                     Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);
@@ -261,7 +278,8 @@
             reader = new BufferedReader(conditions.getRawConditions(filePath).getReader());
             loadBadChannels(reader);
         } catch (IOException exception) {
-            // If the file isn't found, continue on with just the QA bad channels
+            // If the file isn't found, continue on with just the QA bad
+            // channels
             System.out.println("File " + filePath + " was not found! Continuing with only QA bad channels");
         }
     }
@@ -460,7 +478,7 @@
      * Checks if a channel has been tagged as bad
      *
      * @param daqPair : a FPGA/Hybrid pair defining which sensor the channels in
-     * located on
+     *            located on
      * @param channel : The channel to be checked
      * @return true if the channel is bad, false otherwise
      */
@@ -477,7 +495,8 @@
         return totalBadChannels;
     }
 
-    //class to hold calibration constants for a channel; leave fields NaN or null if not known
+    // class to hold calibration constants for a channel; leave fields NaN or
+    // null if not known
     public static class ChannelConstants {
 
         private double pedestal = Double.NaN;

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTConstants.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTConstants.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTConstants.java	Mon Nov 10 00:16:49 2014
@@ -9,33 +9,33 @@
 
 public class HPSSVTConstants {
 
-	public static final int SVT_TOTAL_FPGAS = 7;
-	public static final int TOTAL_APV25_PER_HYBRID = 5;
-	public static final int TOTAL_APV25_CHANNELS = 128;
-	public static final int TOTAL_HYBRIDS_PER_FPGA = 3;
-	public static final int TOTAL_TEMPS_PER_HYBRID = 4;
-	
-	// The Rear Transition Module gain
-	public static final double RTM_GAIN = 1.5;
-	
-	// Total number of strips per sensor
-	public static final int TOTAL_STRIPS_PER_SENSOR = 639;
-	
-	// Total number of shaper signal samples obtained
-	public static final int TOTAL_NUMBER_OF_SAMPLES = 6;
-	
-	// MASKs used to encode and decode the SVT data
+    public static final int SVT_TOTAL_FPGAS = 7;
+    public static final int TOTAL_APV25_PER_HYBRID = 5;
+    public static final int TOTAL_APV25_CHANNELS = 128;
+    public static final int TOTAL_HYBRIDS_PER_FPGA = 3;
+    public static final int TOTAL_TEMPS_PER_HYBRID = 4;
+
+    // The Rear Transition Module gain
+    public static final double RTM_GAIN = 1.5;
+
+    // Total number of strips per sensor
+    public static final int TOTAL_STRIPS_PER_SENSOR = 639;
+
+    // Total number of shaper signal samples obtained
+    public static final int TOTAL_NUMBER_OF_SAMPLES = 6;
+
+    // MASKs used to encode and decode the SVT data
     public static final int TEMP_MASK = 0xFFFF;
     public static final int HYBRID_MASK = 0x3;
     public static final int APV_MASK = 0x7;
     public static final int CHANNEL_MASK = 0x7F;
     public static final int FPGA_MASK = 0xFFFF;
     public static final int SAMPLE_MASK = 0x3FFF;
-    
-    // Temperature constants 
-    public static final double MIN_TEMP = -50; 
+
+    // Temperature constants
+    public static final double MIN_TEMP = -50;
     public static final double MAX_TEMP = 150;
-    public static final int    ADC_TEMP_COUNT = 4096;
+    public static final int ADC_TEMP_COUNT = 4096;
     public static final double TEMP_K0 = 273.15;
     public static final double CONST_A = 0.03448533;
     public static final double BETA = 3750.;
@@ -43,7 +43,7 @@
     public static final double V_REF = 2.5;
     public static final double R_DIV = 10000.;
     public static final double TEMP_INC = 0.01;
-    
+
     // Length of the APV25 analog pipeline
     public static final int ANALOG_PIPELINE_LENGTH = 192;
     // Total number of channels an APV25 ASIC contains
@@ -57,5 +57,5 @@
     public static final double MULTIPLEXER_GAIN = 1;
     // The APV25 front end gain
     public static final double FRONT_END_GAIN = 100.0; //
-    	
+
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTSensorSetup.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTSensorSetup.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/HPSSVTSensorSetup.java	Mon Nov 10 00:16:49 2014
@@ -20,7 +20,7 @@
  * Setup driver for the HPSTracker subdetector.
  *
  * @author Mathew Graham <[log in to unmask]>
- * @author Omar Moreno   <[log in to unmask]>
+ * @author Omar Moreno <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
  * @version $Id: HPSSVTSensorSetup.java,v 1.13 2013/10/29 23:28:53 jeremy Exp $
  */
@@ -29,26 +29,24 @@
     boolean debug = false;
     String subdetectorName = "Tracker";
     // Sensor Characteristics
-    private double readoutStripPitch = 0.060;    // mm
-    private double senseStripPitch = 0.030;    // mm
+    private double readoutStripPitch = 0.060; // mm
+    private double senseStripPitch = 0.030; // mm
     private double readoutStripCapacitanceIntercept = 0;
-    private double readoutStripCapacitanceSlope = 0.16;  // pf/mm
+    private double readoutStripCapacitanceSlope = 0.16; // pf/mm
     private double senseStripCapacitanceIntercept = 0;
-    private double senseStripCapacitanceSlope = 0.16;   // pf/mm
+    private double senseStripCapacitanceSlope = 0.16; // pf/mm
     private double readoutTransferEfficiency = 0.986;
     private double senseTransferEfficiency = 0.419;
     /*
-     * Adding separate strip capacitance for long detectors following
-     * S/N = mip_charge/(270e- + 36*C[pf/cm]*L[cm]
-     * e.g. for expected S/N=16 and L=20cm -> C=0.1708pf/mm
-     * e.g. for expected S/N=8 and L=20cm -> C=0.39pf/mm
-     * This should be taken into account by the noise model -> FIX THIS.
-     */
-    private double longSensorLengthThreshold = 190.0; //mm
-    private double readoutLongStripCapacitanceSlope = 0.39;  // pf/mm
-    private double senseLongStripCapacitanceSlope = 0.39;  // pf/mm
-
-    
+     * Adding separate strip capacitance for long detectors following S/N =
+     * mip_charge/(270e- + 36*C[pf/cm]*L[cm] e.g. for expected S/N=16 and L=20cm
+     * -> C=0.1708pf/mm e.g. for expected S/N=8 and L=20cm -> C=0.39pf/mm This
+     * should be taken into account by the noise model -> FIX THIS.
+     */
+    private double longSensorLengthThreshold = 190.0; // mm
+    private double readoutLongStripCapacitanceSlope = 0.39; // pf/mm
+    private double senseLongStripCapacitanceSlope = 0.39; // pf/mm
+
     // Set of sensors
     Set<SiSensor> sensors = new HashSet<SiSensor>();
 
@@ -78,16 +76,17 @@
         configureSensors(sensors);
 
         // Create DAQ Maps
-        //if (!SvtUtils.getInstance().isSetup()) {
-        SvtUtils.getInstance().reset(); // Hard reset of SvtUtils to clear previous detector state.
+        // if (!SvtUtils.getInstance().isSetup()) {
+        SvtUtils.getInstance().reset(); // Hard reset of SvtUtils to clear
+                                        // previous detector state.
         SvtUtils.getInstance().setup(detector);
-        //}
+        // }
     }
 
     /**
      * Configure the SVT sensors
      * 
-     * @param subdetector  
+     * @param subdetector
      */
     private void configureSensors(Set<SiSensor> sensors) {
         // Loop through all the sensors in the set.
@@ -110,7 +109,7 @@
             // Translate to the outside of the box in order to setup electrodes.
             ITranslation3D electrodesPosition = new Translation3D(VecOp.mult(-pSide.getDistance(), pSide.getNormal()));
 
-            // Align the strips with the edge of the sensor.        
+            // Align the strips with the edge of the sensor.
             IRotation3D electrodesRotation = new RotationPassiveXYZ(0, 0, 0);
             Transform3D electrodesTransform = new Transform3D(electrodesPosition, electrodesRotation);
 
@@ -122,28 +121,28 @@
                 System.out.println("The number of readout strips is " + readoutElectrodes.getNCells());
                 System.out.println("The number of sense strips is " + senseElectrodes.getNCells());
             }
-            
+
             double roCap = this.getStripLength(sensor) > longSensorLengthThreshold ? readoutLongStripCapacitanceSlope : readoutStripCapacitanceSlope;
             double senseCap = this.getStripLength(sensor) > longSensorLengthThreshold ? senseLongStripCapacitanceSlope : senseStripCapacitanceSlope;
-                    
+
             // Set the strip capacitance.
             readoutElectrodes.setCapacitanceIntercept(readoutStripCapacitanceIntercept);
             readoutElectrodes.setCapacitanceSlope(roCap);
             senseElectrodes.setCapacitanceIntercept(senseStripCapacitanceIntercept);
             senseElectrodes.setCapacitanceSlope(senseCap);
 
-            if(debug) {
-                System.out.printf("%s: Sensor %s has strip length %.3f\n",this.getClass().getSimpleName(),sensor.getName(),this.getStripLength(sensor));
-                System.out.printf("%s: ro electrodes capacitance %.3f (cell0 %.3f)\n",this.getClass().getSimpleName(),readoutElectrodes.getCapacitance(),readoutElectrodes.getCapacitance(0));
-                System.out.printf("%s: ro sense capacitance %.3f (cell0 %.3f)\n",this.getClass().getSimpleName(),senseElectrodes.getCapacitance(),senseElectrodes.getCapacitance(0));
-            }
-            
+            if (debug) {
+                System.out.printf("%s: Sensor %s has strip length %.3f\n", this.getClass().getSimpleName(), sensor.getName(), this.getStripLength(sensor));
+                System.out.printf("%s: ro electrodes capacitance %.3f (cell0 %.3f)\n", this.getClass().getSimpleName(), readoutElectrodes.getCapacitance(), readoutElectrodes.getCapacitance(0));
+                System.out.printf("%s: ro sense capacitance %.3f (cell0 %.3f)\n", this.getClass().getSimpleName(), senseElectrodes.getCapacitance(), senseElectrodes.getCapacitance(0));
+            }
+
             // Set sense and readout electrodes.
             sensor.setSenseElectrodes(senseElectrodes);
             sensor.setReadoutElectrodes(readoutElectrodes);
 
             // Set the charge transfer efficiency.
-            double[][] transferEfficiencies = {{readoutTransferEfficiency, senseTransferEfficiency}};
+            double[][] transferEfficiencies = { { readoutTransferEfficiency, senseTransferEfficiency } };
             sensor.setTransferEfficiencies(ChargeCarrier.HOLE, new BasicMatrix(transferEfficiencies));
 
             if (debug) {
@@ -154,32 +153,31 @@
 
     double getStripLength(SiSensor sensor) {
         /*
-         * Returns the length of the strip
-         * This is getting the face of the sensor and then getting the longest edge
-         *  VERY DANGEROUS -> FIX THIS!
+         * Returns the length of the strip This is getting the face of the
+         * sensor and then getting the longest edge VERY DANGEROUS -> FIX THIS!
          */
         double length = 0;
-        List<Polygon3D> faces = ((Box) sensor.getGeometry().getLogicalVolume().getSolid()).getFacesNormalTo(new BasicHep3Vector(0,0,1));
-        for(Polygon3D face : faces) {
-            //System.out.printf("%s: Sensor %s polygon3D %s\n",this.getClass().getSimpleName(),sensor.getName(),face.toString());
+        List<Polygon3D> faces = ((Box) sensor.getGeometry().getLogicalVolume().getSolid()).getFacesNormalTo(new BasicHep3Vector(0, 0, 1));
+        for (Polygon3D face : faces) {
+            // System.out.printf("%s: Sensor %s polygon3D %s\n",this.getClass().getSimpleName(),sensor.getName(),face.toString());
             List<LineSegment3D> edges = face.getEdges();
-            for(LineSegment3D edge : edges) {
+            for (LineSegment3D edge : edges) {
                 double l = edge.getLength();
-                if(l>length) {
+                if (l > length) {
                     length = l;
                 }
-                //System.out.printf("%s: edge %.3f \n",this.getClass().getSimpleName(),edge.getLength());
+                // System.out.printf("%s: edge %.3f \n",this.getClass().getSimpleName(),edge.getLength());
             }
         }
 
         return length;
     }
-    
+
     /**
      * Set the readout strip capacitance
      * 
      * @param intercept
-     * @param slope 
+     * @param slope
      */
     public void setReadoutStripCapacitance(double intercept, double slope) {
         readoutStripCapacitanceIntercept = intercept;
@@ -187,10 +185,10 @@
     }
 
     /**
-     * Set the sense strip capacitance 
+     * Set the sense strip capacitance
      * 
      * @param intercept
-     * @param slope 
+     * @param slope
      */
     public void setSenseStripCapacitance(double intercept, double slope) {
         senseStripCapacitanceIntercept = intercept;
@@ -218,7 +216,7 @@
     /**
      * Set readout strip transfer efficiency
      * 
-     * @param efficiency 
+     * @param efficiency
      */
     public void setReadoutTransferEfficiency(double efficiency) {
         readoutTransferEfficiency = efficiency;

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/QuietBaseLCSimEvent.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/QuietBaseLCSimEvent.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/QuietBaseLCSimEvent.java	Mon Nov 10 00:16:49 2014
@@ -1,4 +1,5 @@
 package org.hps.conditions.deprecated;
+
 import hep.physics.event.BaseEvent;
 
 import java.util.ArrayList;
@@ -28,225 +29,197 @@
 import org.lcsim.lcio.LCIOUtil;
 
 /**
- * Duplicates BaseLCSimEvent but doesn't call conditionsManager.setDetector in its constructor.
- * Used in TestRunTriggeredReconToLcio to avoid causing spurious detectorChanged events.
- * TODO: really should find a better way to do this, this is awful, but I don't see a clean way to do this by just extending BaseLCSimEvent.
+ * Duplicates BaseLCSimEvent but doesn't call conditionsManager.setDetector in
+ * its constructor. Used in TestRunTriggeredReconToLcio to avoid causing
+ * spurious detectorChanged events. TODO: really should find a better way to do
+ * this, this is awful, but I don't see a clean way to do this by just extending
+ * BaseLCSimEvent.
  * @author Sho Uemura
  */
-public class QuietBaseLCSimEvent extends BaseEvent implements EventHeader
-{
+public class QuietBaseLCSimEvent extends BaseEvent implements EventHeader {
     private String detectorName;
-    private final Map<List,LCMetaData> metaDataMap = new IdentityHashMap<List,LCMetaData>();
+    private final Map<List, LCMetaData> metaDataMap = new IdentityHashMap<List, LCMetaData>();
     private ConditionsManager conditionsManager = ConditionsManager.defaultInstance();
     private static final int NANO_SECONDS = 1000000;
     public static final String READOUT_NAME = "ReadoutName";
 
     /** Creates a new instance of BaseLCSimEvent */
-    public QuietBaseLCSimEvent(int run, int event, String detectorName)
-    {
-        this(run,event,detectorName,System.currentTimeMillis()*NANO_SECONDS);
-    }
-    
-    public QuietBaseLCSimEvent(int run, int event, String detectorName, long timeStamp)
-    {
-        super(run,event,timeStamp);
+    public QuietBaseLCSimEvent(int run, int event, String detectorName) {
+        this(run, event, detectorName, System.currentTimeMillis() * NANO_SECONDS);
+    }
+
+    public QuietBaseLCSimEvent(int run, int event, String detectorName, long timeStamp) {
+        super(run, event, timeStamp);
         this.detectorName = detectorName;
-//        try
-//        {
-//            conditionsManager.setDetector(detectorName,run);
-//        }
-//        catch (ConditionsNotFoundException x)
-//        {
-//            throw new RuntimeException("Please see http://confluence.slac.stanford.edu/display/ilc/Conditions+database",x);
-//        }
-    }
-    
-    //public String getInputFile()
-    //{
-    //    return (String)get("INPUT_FILE");
-    //}
-    
-    public String toString()
-    {
-        return "Run "+getRunNumber()+" Event "+getEventNumber()+" ("+new Date(getTimeStamp()/NANO_SECONDS)+") Detector: "+detectorName;
-    }
-    
-    public Detector getDetector()
-    {
-        return conditionsManager.getCachedConditions(Detector.class,"compact.xml").getCachedData();
-    }
-
-    public List<MCParticle> getMCParticles()
-    {
-        return get(MCParticle.class,MC_PARTICLES);
-    }
-
-    public List<Track> getTracks()
-    {
-        return get(Track.class,TRACKS);
-    }
-
-    public List<Cluster> getClusters()
-    {
-        return get(Cluster.class,CLUSTERS);
-    }
-
-    public List<SimCalorimeterHit> getSimCalorimeterHits(String name)
-    {
-        return get(SimCalorimeterHit.class,name);
-    }
-
-    public List<SimTrackerHit> getSimTrackerHits(String name)
-    {
-        return get(SimTrackerHit.class,name);
-    }
-
-    public <T> List<T> get(Class<T> type, String name)
-    {
+        // try
+        // {
+        // conditionsManager.setDetector(detectorName,run);
+        // }
+        // catch (ConditionsNotFoundException x)
+        // {
+        // throw new
+        // RuntimeException("Please see http://confluence.slac.stanford.edu/display/ilc/Conditions+database",x);
+        // }
+    }
+
+    // public String getInputFile()
+    // {
+    // return (String)get("INPUT_FILE");
+    // }
+
+    public String toString() {
+        return "Run " + getRunNumber() + " Event " + getEventNumber() + " (" + new Date(getTimeStamp() / NANO_SECONDS) + ") Detector: " + detectorName;
+    }
+
+    public Detector getDetector() {
+        return conditionsManager.getCachedConditions(Detector.class, "compact.xml").getCachedData();
+    }
+
+    public List<MCParticle> getMCParticles() {
+        return get(MCParticle.class, MC_PARTICLES);
+    }
+
+    public List<Track> getTracks() {
+        return get(Track.class, TRACKS);
+    }
+
+    public List<Cluster> getClusters() {
+        return get(Cluster.class, CLUSTERS);
+    }
+
+    public List<SimCalorimeterHit> getSimCalorimeterHits(String name) {
+        return get(SimCalorimeterHit.class, name);
+    }
+
+    public List<SimTrackerHit> getSimTrackerHits(String name) {
+        return get(SimTrackerHit.class, name);
+    }
+
+    public <T> List<T> get(Class<T> type, String name) {
         return (List<T>) get(name);
     }
 
-    public <T> List<List<T>> get(Class<T> type)
-    {
+    public <T> List<List<T>> get(Class<T> type) {
         List<List<T>> result = new ArrayList<List<T>>();
-        for (Map.Entry<List,LCMetaData> entry : metaDataMap.entrySet())
-        {
-            if (type.isAssignableFrom(entry.getValue().getType()))
-            {
+        for (Map.Entry<List, LCMetaData> entry : metaDataMap.entrySet()) {
+            if (type.isAssignableFrom(entry.getValue().getType())) {
                 result.add(entry.getKey());
             }
         }
         return result;
     }
-    
-    public Collection<LCMetaData> getMetaData()
-    {
-    	return metaDataMap.values();
-    }
-    
-    public Set<List> getLists()
-    {
-    	return metaDataMap.keySet();
-    }
-
-    public LCMetaData getMetaData(List x)
-    {
+
+    public Collection<LCMetaData> getMetaData() {
+        return metaDataMap.values();
+    }
+
+    public Set<List> getLists() {
+        return metaDataMap.keySet();
+    }
+
+    public LCMetaData getMetaData(List x) {
         return metaDataMap.get(x);
     }
 
-    public void put(String name, Object component)
-    {
+    public void put(String name, Object component) {
         super.put(name, component);
-        if (component instanceof List)
-        {
+        if (component instanceof List) {
             List list = (List) component;
             Class type = list.isEmpty() ? Object.class : list.get(0).getClass();
-            for (Object o : list) 
-            {
-                if (!type.isAssignableFrom(o.getClass())) type = Object.class;
-            }
-            metaDataMap.put(list,new MetaData(name,type,0,null));
-        }
-    }
-    
-    public void put(String name, List collection, Class type, int flags)
-    {
-        put(name,collection,type,flags,null);
-    }
-    
-    public void put(String name, List collection, Class type, int flags, String readoutName)
-    {
-        super.put(name,collection);
-        
+            for (Object o : list) {
+                if (!type.isAssignableFrom(o.getClass()))
+                    type = Object.class;
+            }
+            metaDataMap.put(list, new MetaData(name, type, 0, null));
+        }
+    }
+
+    public void put(String name, List collection, Class type, int flags) {
+        put(name, collection, type, flags, null);
+    }
+
+    public void put(String name, List collection, Class type, int flags, String readoutName) {
+        super.put(name, collection);
+
         LCMetaData meta = new MetaData(name, type, flags, readoutName);
-        metaDataMap.put(collection,meta);
+        metaDataMap.put(collection, meta);
 
         setCollectionMetaData(collection, type, meta);
     }
 
     private void setCollectionMetaData(List collection, Class type, LCMetaData meta) {
-        //System.out.println("setCollectionMetaData");
+        // System.out.println("setCollectionMetaData");
         // Set MetaData on collection objects.
         if (HasMetaData.class.isAssignableFrom(type)) {
             for (Object o : collection) {
                 if (o instanceof HasMetaData) {
-                    ((HasMetaData)o).setMetaData(meta);
+                    ((HasMetaData) o).setMetaData(meta);
                 }
             }
         }
     }
-    
-    protected void put(String name, List collection, Class type, int flags, Map intMap, Map floatMap, Map stringMap)
-    {
-        super.put(name,collection);
+
+    protected void put(String name, List collection, Class type, int flags, Map intMap, Map floatMap, Map stringMap) {
+        super.put(name, collection);
         LCMetaData meta = new MetaData(name, type, flags, intMap, floatMap, stringMap);
-        metaDataMap.put(collection,meta);
+        metaDataMap.put(collection, meta);
     }
 
     /**
      * Removes a collection from the event.
      */
-    public void remove(String name)
-    {
+    public void remove(String name) {
         Object collection = get(name);
-        if (collection instanceof List) metaDataMap.remove((List) collection);
+        if (collection instanceof List)
+            metaDataMap.remove((List) collection);
         super.keys().remove(name);
     }
 
-    public String getDetectorName()
-    {
+    public String getDetectorName() {
         return detectorName;
     }
 
-    public boolean hasCollection(Class type, String name)
-    {
-        if (!hasItem(name)) return false;
+    public boolean hasCollection(Class type, String name) {
+        if (!hasItem(name))
+            return false;
         Object collection = get(name);
-        if (!(collection instanceof List)) return false;
+        if (!(collection instanceof List))
+            return false;
         return type.isAssignableFrom(metaDataMap.get(collection).getType());
     }
-    
-    public boolean hasCollection(Class type)
-    {
-        for (LCMetaData meta : metaDataMap.values())
-        {
-            if (type.isAssignableFrom(meta.getType()))
-            {
+
+    public boolean hasCollection(Class type) {
+        for (LCMetaData meta : metaDataMap.values()) {
+            if (type.isAssignableFrom(meta.getType())) {
                 return true;
             }
         }
-        return false;      
-    }
-    
-    public boolean hasItem(String name)
-    {
+        return false;
+    }
+
+    public boolean hasItem(String name) {
         return super.keys().contains(name);
     }
-    
-    public Map<String, int[]> getIntegerParameters()
-    {
-        return Collections.<String, int[]>emptyMap();
-
-    }
-
-    public Map<String, float[]> getFloatParameters()
-    {
-        return Collections.<String, float[]>emptyMap();
-
-    }
-
-    public Map<String, String[]> getStringParameters()
-    {
-        return Collections.<String, String[]>emptyMap();
-    }
-    
-    public float getWeight()
-    {
+
+    public Map<String, int[]> getIntegerParameters() {
+        return Collections.<String, int[]> emptyMap();
+
+    }
+
+    public Map<String, float[]> getFloatParameters() {
+        return Collections.<String, float[]> emptyMap();
+
+    }
+
+    public Map<String, String[]> getStringParameters() {
+        return Collections.<String, String[]> emptyMap();
+    }
+
+    public float getWeight() {
         return 1.0f;
     }
 
-    private class MetaData implements LCMetaData
-    {
+    private class MetaData implements LCMetaData {
         private int flags;
         private final String name;
         private final Class type;
@@ -255,15 +228,15 @@
         private Map<String, String[]> stringMap;
         private transient IDDecoder dec;
 
-        MetaData(String name, Class type, int flags, String readoutName)
-        {
+        MetaData(String name, Class type, int flags, String readoutName) {
             this.name = name;
             this.type = type;
             this.flags = flags;
-            if (readoutName != null) getStringParameters().put(READOUT_NAME,new String[]{ readoutName });
-        }
-        MetaData(String name, Class type, int flags, Map intMap, Map floatMap, Map stringMap)
-        {
+            if (readoutName != null)
+                getStringParameters().put(READOUT_NAME, new String[] { readoutName });
+        }
+
+        MetaData(String name, Class type, int flags, Map intMap, Map floatMap, Map stringMap) {
             this.name = name;
             this.type = type;
             this.flags = flags;
@@ -272,121 +245,109 @@
             this.stringMap = stringMap;
         }
 
-        public int getFlags()
-        {
+        public int getFlags() {
             return flags;
         }
 
-        public String getName()
-        {
+        public String getName() {
             return name;
         }
 
-        public Class getType()
-        {
+        public Class getType() {
             return type;
         }
 
-        public  org.lcsim.geometry.IDDecoder getIDDecoder()
-        {
-            if (dec == null) dec = findIDDecoder();
+        public org.lcsim.geometry.IDDecoder getIDDecoder() {
+            if (dec == null)
+                dec = findIDDecoder();
             return dec;
         }
 
-        public org.lcsim.geometry.IDDecoder findIDDecoder()
-        {
-            // If the IDDecoder name is explicitly set then use it, otherwise 
+        public org.lcsim.geometry.IDDecoder findIDDecoder() {
+            // If the IDDecoder name is explicitly set then use it, otherwise
             // use the name of the collection itself.
             String readoutName = name;
-            if (stringMap != null)
-            {
+            if (stringMap != null) {
                 String[] names = stringMap.get(READOUT_NAME);
-                if (names != null && names.length >= 1) readoutName = names[0];
+                if (names != null && names.length >= 1)
+                    readoutName = names[0];
             }
 
             // Find the IDDecoder using the Detector.
-            org.lcsim.geometry.IDDecoder result=null;
+            org.lcsim.geometry.IDDecoder result = null;
             try {
                 result = getDetector().getDecoder(readoutName);
-            }
-            catch (RuntimeException x)
-            {}
-
-            // Detector lookup failed.  Attempt to use the CellIDEncoding collection parameter.
+            } catch (RuntimeException x) {
+            }
+
+            // Detector lookup failed. Attempt to use the CellIDEncoding
+            // collection parameter.
             if (result == null)
                 result = createIDDecoderFromCellIDEncoding();
 
             // If both methods failed, then there is a problem.
-            if (result == null) 
-                throw new RuntimeException("Could not find or create an IDDecoder for the collection: "+name+", readout: "+readoutName);
+            if (result == null)
+                throw new RuntimeException("Could not find or create an IDDecoder for the collection: " + name + ", readout: " + readoutName);
 
             return result;
         }
 
         /**
-         * Make an IDDecoder for this MetaData using the CellIDEncoding parameter.
+         * Make an IDDecoder for this MetaData using the CellIDEncoding
+         * parameter.
          * @return An IDDecoder made built from the CellIDEncoding.
          */
-        private IDDecoder createIDDecoderFromCellIDEncoding()
-        {
+        private IDDecoder createIDDecoderFromCellIDEncoding() {
             String[] cellIdEncoding = getStringParameters().get("CellIDEncoding");
             IDDecoder result = null;
-            if (cellIdEncoding != null)
-            {
+            if (cellIdEncoding != null) {
                 result = new BaseIDDecoder();
                 try {
                     IDDescriptor desc = new IDDescriptor(cellIdEncoding[0]);
                     result.setIDDescription(desc);
-                }
-                catch (IDDescriptor.IDException x)
-                {
+                } catch (IDDescriptor.IDException x) {
                     throw new RuntimeException(x);
                 }
-            }          
+            }
             return result;
         }
 
-        public Map<String, int[]> getIntegerParameters()
-        {
-            if (intMap == null) intMap = new HashMap<String, int[]>();
+        public Map<String, int[]> getIntegerParameters() {
+            if (intMap == null)
+                intMap = new HashMap<String, int[]>();
             return intMap;
         }
 
-        public Map<String, float[]> getFloatParameters()
-        {
-            if (floatMap == null) floatMap = new HashMap<String, float[]>();
+        public Map<String, float[]> getFloatParameters() {
+            if (floatMap == null)
+                floatMap = new HashMap<String, float[]>();
             return floatMap;
         }
 
-        public Map<String, String[]> getStringParameters()
-        {
-            if (stringMap == null) stringMap = new HashMap<String, String[]>();
+        public Map<String, String[]> getStringParameters() {
+            if (stringMap == null)
+                stringMap = new HashMap<String, String[]>();
             return stringMap;
         }
 
-        public EventHeader getEvent()
-        {
+        public EventHeader getEvent() {
             return QuietBaseLCSimEvent.this;
         }
 
-        public void setSubset(boolean isSubset)
-        {
-            flags = LCIOUtil.bitSet(flags,LCIOConstants.BITSubset,isSubset);
-        }
-
-        public boolean isSubset()
-        {
-            return LCIOUtil.bitTest(flags,LCIOConstants.BITSubset);
-        }
-
-        public void setTransient(boolean isTransient)
-        {
-            flags = LCIOUtil.bitSet(flags,LCIOConstants.BITTransient,isTransient);
-        }
-
-        public boolean isTransient()
-        {
-            return LCIOUtil.bitTest(flags,LCIOConstants.BITTransient);
+        public void setSubset(boolean isSubset) {
+            flags = LCIOUtil.bitSet(flags, LCIOConstants.BITSubset, isSubset);
+        }
+
+        public boolean isSubset() {
+            return LCIOUtil.bitTest(flags, LCIOConstants.BITSubset);
+        }
+
+        public void setTransient(boolean isTransient) {
+            flags = LCIOUtil.bitSet(flags, LCIOConstants.BITTransient, isTransient);
+        }
+
+        public boolean isTransient() {
+            return LCIOUtil.bitTest(flags, LCIOConstants.BITTransient);
         }
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/StereoPair.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/StereoPair.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/StereoPair.java	Mon Nov 10 00:16:49 2014
@@ -7,124 +7,126 @@
  * 
  * @author Per Hansson <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
- * @version $Id: StereoPair.java,v 1.3 2013/07/30 00:53:07 omoreno Exp $ 
+ * @version $Id: StereoPair.java,v 1.3 2013/07/30 00:53:07 omoreno Exp $
  */
 public class StereoPair {
 
-	
-	// Layer number to which the stereo pair belongs to
-	private int layerNumber = -1; 
-	
-	// The axial and stereo sensors
-	private SiSensor axialSensor = null; 
-	private SiSensor stereoSensor = null;
-	
-	// The detector volume in which the stereo pair resides 
-	public enum detectorVolume{ Top, Bottom }; 
-	private detectorVolume volume = detectorVolume.Top; 
-	
-	/**
-	 * Default Ctor
-	 * 
-	 * @param layerNumber : Layer number to which the stereo pair belongs to
-	 */
-	public StereoPair(int layerNumber){
-		this.layerNumber = layerNumber; 
-	}
-	
-	/**
-	 * Ctor
-	 * 
-	 * @param layerNumber : Layer number to which the stereo pair belongs to
-	 * @param volume : detector volume (detectorVolume.Top or detector Volume.Bottom) in 
-	 * 					which the stereo pair resides 
-	 * @param axialSensor 
-	 * @param stereoSensor
-	 */
-	public StereoPair(int layerNumber, detectorVolume volume, SiSensor axialSensor, SiSensor stereoSensor){
-		this.layerNumber = layerNumber; 
-		this.volume = volume; 
-		this.axialSensor = axialSensor; 
-		this.stereoSensor = stereoSensor; 
-	}
+    // Layer number to which the stereo pair belongs to
+    private int layerNumber = -1;
 
-	/**
-	 * Set the axial sensor of stereo pair
-	 * 
-	 * @param axialSensor 
-	 */
-	public void setAxialSensor(SiSensor axialSensor){
-		this.axialSensor = axialSensor;
-	}
-	
-	/**
-	 * Set the stereo sensor of the stereo pair
-	 * 
-	 * @param stereoSensor
-	 */
-	public void setStereoSensor(SiSensor stereoSensor){
-		this.stereoSensor = stereoSensor; 
-	}
-	
-	/**
-	 * Set the SVT volume in which the stereo pair resides
-	 * 
-	 * @param volume : detectorVolume.Top or detectorVolume.Bottom
-	 */
-	public void setDetectorVolume(detectorVolume volume){
-		this.volume = volume; 
-	}
-	
-	/**
-	 * Get the axial sensor of the stereo pair
-	 * 
-	 * @return Axial sensor. Returns null if it hasn't been set yet.
-	 */
-	public SiSensor getAxialSensor(){
-		return axialSensor; 
-	}
-	
-	/**
-	 * Get the stereo sensor of the stereo pair
-	 * 
-	 * @return Stereo sensor. Returns null if it hasn't been set yet.
-	 */
-	public SiSensor getStereoSensor(){
-		return stereoSensor; 
-	}
+    // The axial and stereo sensors
+    private SiSensor axialSensor = null;
+    private SiSensor stereoSensor = null;
 
-	/**
-	 * Get the layer number to which the stereo pair belongs to
-	 * 
-	 * @return layer number
-	 */
-	public int getLayerNumber(){
-		return layerNumber; 
-	}
-	
-	/**
-	 * Get the SVT volume in which the stereo pair resides
-	 * 
-	 * @return volume : detectorVolume.Top or detectorVolume.Bottom
-	 */
-	public detectorVolume getDetectorVolume(){
-		return volume; 
-	}
-	
-	/**
-	 * Return a string describing the stereo pair
-	 * 
-	 * @return stereo pair description
-	 */
-	@Override
-	public String toString(){
-		String axialName = axialSensor == null ? "None" : axialSensor.getName();
-		String stereoName = stereoSensor == null ? "None" : stereoSensor.getName();
-		String description = "Stereo Pair:\n";
-		description += "\tLayer Number: " + this.getLayerNumber();
-		description += "\t\tAxial Sensor: " + axialName;
-		description += "\t\tStereo Sensor: " + stereoName;
-		return description; 
-		
-	}
+    // The detector volume in which the stereo pair resides
+    public enum detectorVolume {
+        Top, Bottom
+    };
+
+    private detectorVolume volume = detectorVolume.Top;
+
+    /**
+     * Default Ctor
+     * 
+     * @param layerNumber : Layer number to which the stereo pair belongs to
+     */
+    public StereoPair(int layerNumber) {
+        this.layerNumber = layerNumber;
+    }
+
+    /**
+     * Ctor
+     * 
+     * @param layerNumber : Layer number to which the stereo pair belongs to
+     * @param volume : detector volume (detectorVolume.Top or detector
+     *            Volume.Bottom) in which the stereo pair resides
+     * @param axialSensor
+     * @param stereoSensor
+     */
+    public StereoPair(int layerNumber, detectorVolume volume, SiSensor axialSensor, SiSensor stereoSensor) {
+        this.layerNumber = layerNumber;
+        this.volume = volume;
+        this.axialSensor = axialSensor;
+        this.stereoSensor = stereoSensor;
+    }
+
+    /**
+     * Set the axial sensor of stereo pair
+     * 
+     * @param axialSensor
+     */
+    public void setAxialSensor(SiSensor axialSensor) {
+        this.axialSensor = axialSensor;
+    }
+
+    /**
+     * Set the stereo sensor of the stereo pair
+     * 
+     * @param stereoSensor
+     */
+    public void setStereoSensor(SiSensor stereoSensor) {
+        this.stereoSensor = stereoSensor;
+    }
+
+    /**
+     * Set the SVT volume in which the stereo pair resides
+     * 
+     * @param volume : detectorVolume.Top or detectorVolume.Bottom
+     */
+    public void setDetectorVolume(detectorVolume volume) {
+        this.volume = volume;
+    }
+
+    /**
+     * Get the axial sensor of the stereo pair
+     * 
+     * @return Axial sensor. Returns null if it hasn't been set yet.
+     */
+    public SiSensor getAxialSensor() {
+        return axialSensor;
+    }
+
+    /**
+     * Get the stereo sensor of the stereo pair
+     * 
+     * @return Stereo sensor. Returns null if it hasn't been set yet.
+     */
+    public SiSensor getStereoSensor() {
+        return stereoSensor;
+    }
+
+    /**
+     * Get the layer number to which the stereo pair belongs to
+     * 
+     * @return layer number
+     */
+    public int getLayerNumber() {
+        return layerNumber;
+    }
+
+    /**
+     * Get the SVT volume in which the stereo pair resides
+     * 
+     * @return volume : detectorVolume.Top or detectorVolume.Bottom
+     */
+    public detectorVolume getDetectorVolume() {
+        return volume;
+    }
+
+    /**
+     * Return a string describing the stereo pair
+     * 
+     * @return stereo pair description
+     */
+    @Override
+    public String toString() {
+        String axialName = axialSensor == null ? "None" : axialSensor.getName();
+        String stereoName = stereoSensor == null ? "None" : stereoSensor.getName();
+        String description = "Stereo Pair:\n";
+        description += "\tLayer Number: " + this.getLayerNumber();
+        description += "\t\tAxial Sensor: " + axialName;
+        description += "\t\tStereo Sensor: " + stereoName;
+        return description;
+
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/SvtUtils.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/SvtUtils.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/SvtUtils.java	Mon Nov 10 00:16:49 2014
@@ -24,7 +24,7 @@
 import static org.hps.conditions.deprecated.StereoPair.detectorVolume;
 
 /**
- * A class providing various utilities related to the HPS SVT. 
+ * A class providing various utilities related to the HPS SVT.
  *
  * @author Omar Moreno <[log in to unmask]>
  * @version $Id: SvtUtils.java,v 1.19 2013/11/06 20:25:37 omoreno Exp $
@@ -35,11 +35,11 @@
     // Set of sensors
     private Set<SiSensor> sensors = new HashSet<SiSensor>();
     // Set of stereo pairs
-    private Set<StereoPair> stereoPairs = new HashSet<StereoPair>(); 
+    private Set<StereoPair> stereoPairs = new HashSet<StereoPair>();
     // Map from Sensor to Hybrid/FPGA pair
     private Map<SiSensor /* sensor */, Pair<Integer /* FPGA */, Integer /* Hybrid */>> sensorToDaqPair = new HashMap<SiSensor, Pair<Integer, Integer>>();
     // Map from Hybrid/FPGA pair
-    private Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, SiSensor /* Sensor*/> daqPairToSensor = new HashMap<Pair<Integer, Integer>, SiSensor>();
+    private Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, SiSensor /* Sensor */> daqPairToSensor = new HashMap<Pair<Integer, Integer>, SiSensor>();
     // Map from SVT top layer to Hybrid/FPGA pair
     private Map<Integer /* Layer */, List<Pair<Integer /* FPGA */, Integer /* Hybrid */>>> topLayerDaqMap = new HashMap<Integer, List<Pair<Integer, Integer>>>();
     // Map from SVT bottom layer to Hybrid/FPGA pair
@@ -50,7 +50,7 @@
     private Map<SiSensor /* Sensor */, Integer /* Layer */> sensorToBottomLayer = new HashMap<SiSensor, Integer>();
     // Map sensor to descriptor
     private Map<SiSensor /* Sensor */, String /* Description */> sensorToDescriptor = new HashMap<SiSensor, String>();
-    // Map layer to top SVT sensor 
+    // Map layer to top SVT sensor
     private Map<Integer /* Layer */, List<SiSensor> /* Sensor */> topLayerToSensor = new HashMap<Integer, List<SiSensor>>();
     // Map layer to bottom SVT sensor
     private Map<Integer /* Layer */, List<SiSensor> /* Sensor */> bottomLayerToSensor = new HashMap<Integer, List<SiSensor>>();
@@ -65,7 +65,7 @@
     boolean debug = false;
 
     /*
-     * Private ctor to keep user from instantiating 
+     * Private ctor to keep user from instantiating
      */
     private SvtUtils() {
     }
@@ -90,21 +90,21 @@
     }
 
     /**
-     * Get the plane number to which the sensor belongs to. This is does not 
+     * Get the plane number to which the sensor belongs to. This is does not
      * return the SVT layer number.
      * 
      * @param sensor
      * @return The layer number
      */
-    // TODO: Change the name to clarify that what is being returned is the plane number
+    // TODO: Change the name to clarify that what is being returned is the plane
+    // number
     public int getLayerNumber(SiSensor sensor) {
         if (sensorToTopLayer.containsKey(sensor)) {
             return sensorToTopLayer.get(sensor);
         } else if (sensorToBottomLayer.containsKey(sensor)) {
             return sensorToBottomLayer.get(sensor);
         } else {
-            throw new RuntimeException("The sensor " + sensor.getName() 
-            								+ " does not have an associated plane number");
+            throw new RuntimeException("The sensor " + sensor.getName() + " does not have an associated plane number");
         }
     }
 
@@ -126,7 +126,7 @@
     /**
      * Checks if the orientation of the sensor is axial.
      * 
-     *  @return true if it is, false if it is a stereo sensor
+     * @return true if it is, false if it is a stereo sensor
      */
     public boolean isAxial(SiSensor sensor) {
         if (this.isTopLayer(sensor) && this.getLayerNumber(sensor) % 2 == 1) {
@@ -140,9 +140,9 @@
     /**
      * Get a sensor by its plane and module id. Both are zero-indexed.
      * 
-     *  @param moduleNumber : module id
-     *  @param planeNumber : plane id (typically 1 less than the layer id)
-     *  @return sensor 
+     * @param moduleNumber : module id
+     * @param planeNumber : plane id (typically 1 less than the layer id)
+     * @return sensor
      */
     public SiSensor getSensor(int moduleNumber, int planeNumber) {
         if (moduleNumber < 0 || moduleNumber > maxModuleNumber) {
@@ -156,50 +156,52 @@
     /**
      * Get a sensor by its FPGA and hybrid number.
      * 
-     *  @param daqPair : a Pair of the form Pair<FPGA number, hybrid number>
-     *  @return sensor
+     * @param daqPair : a Pair of the form Pair<FPGA number, hybrid number>
+     * @return sensor
      */
     public SiSensor getSensor(Pair<Integer, Integer> daqPair) {
         return daqPairToSensor.get(daqPair);
     }
 
     /**
-     * Get a sensor from the top SVT volume by its plane number and sensor 
+     * Get a sensor from the top SVT volume by its plane number and sensor
      * position within a plane.
      * 
-     *  @param planeNumber
-     *  @param sensorNumber : position within a plane
-     *  @return sensor or null if the sensor doesn't exist in that position
+     * @param planeNumber
+     * @param sensorNumber : position within a plane
+     * @return sensor or null if the sensor doesn't exist in that position
      */
     public SiSensor getTopSensor(int planeNumber, int sensorNumber) {
-    	if(topLayerToSensor.get(planeNumber).size() <= sensorNumber) return null;
+        if (topLayerToSensor.get(planeNumber).size() <= sensorNumber)
+            return null;
         return topLayerToSensor.get(planeNumber).get(sensorNumber);
     }
 
     /**
-     * Get a sensor from the bottom SVT volume by its plane number and sensor 
+     * Get a sensor from the bottom SVT volume by its plane number and sensor
      * position within a plane.
      * 
-     *  @param planeNumber
-     *  @param sensorNumber : position within a plane
-     *  @return sensor or null if the sensor doesn't exist in that position
+     * @param planeNumber
+     * @param sensorNumber : position within a plane
+     * @return sensor or null if the sensor doesn't exist in that position
      */
     public SiSensor getBottomSensor(int layer, int sensorNumber) {
-    	if(bottomLayerToSensor.get(layer).size() <= sensorNumber) return null;
+        if (bottomLayerToSensor.get(layer).size() <= sensorNumber)
+            return null;
         return bottomLayerToSensor.get(layer).get(sensorNumber);
     }
 
     /**
      * Get the Set of all sensors which compose the SVT.
      * 
-     *  @return set of sensors
+     * @return set of sensors
      */
     public Set<SiSensor> getSensors() {
         return sensors;
     }
 
     /**
-     * Get the Set of all FPGA numbers. 
+     * Get the Set of all FPGA numbers.
      * 
      * @return set of FPGA numbers
      */
@@ -275,14 +277,14 @@
         }
         return sensor.makeStripId(channel, sideNumber).getValue();
     }
-    
+
     /**
      * Get the set of all stereo pairs which compose the SVT.
      * 
-     *  @return Set of stereo pairs
-     */
-    public Set<StereoPair> getStereoPairs(){
-    	return stereoPairs; 
+     * @return Set of stereo pairs
+     */
+    public Set<StereoPair> getStereoPairs() {
+        return stereoPairs;
     }
 
     /**
@@ -293,15 +295,16 @@
     public void setup(Detector detector) {
 
         this.printDebug("Method: setupMaps: \n\tDetector: " + detector.getDetectorName());
-        
+
         // Load the DAQ Map from the conditions database
         this.loadSvtDaqMap();
-        
+
         // Instantiate 'sensorArray' which allows for retrieval of a SiSensor
         // by module and layer id
         sensorArray = new SiSensor[maxModuleNumber + 1][maxLayerNumber];
 
-        // Get all of the sensors composing the SVT and add them to the set of all sensors
+        // Get all of the sensors composing the SVT and add them to the set of
+        // all sensors
         IDetectorElement detectorElement = detector.getDetectorElement().findDetectorElement(subdetectorName);
         helper = detectorElement.getIdentifierHelper();
         sensors.addAll(detectorElement.findDescendants(SiSensor.class));
@@ -325,38 +328,38 @@
             sensorArray[moduleNumber][layerNumber - 1] = sensor;
             int listPosition = 0;
             switch (moduleNumber % 2) {
-                // Top Layer
-            	case 0:
-                	
-                    listPosition = moduleNumber / 2;
-                    sensorToTopLayer.put(sensor, layerNumber);
-                    sensorToDaqPair.put( sensor, topLayerDaqMap.get(layerNumber).get(listPosition));
-                    topLayerToSensor.get(layerNumber).set(listPosition, sensor);
-                    daqPairToSensor.put(topLayerDaqMap.get(layerNumber).get(listPosition), sensor);
-                    description = "Top Layer " + layerNumber + " - Sensor " + listPosition;
-                    this.printDebug("\tDescription: " + description);
-                    sensorToDescriptor.put(sensor, description);
-                    break;
-                // Bottom Layer
-                case 1:
-                
-                	listPosition = (moduleNumber - 1) / 2;
-                    sensorToBottomLayer.put(sensor, layerNumber);
-                    sensorToDaqPair.put(sensor, bottomLayerDaqMap.get(layerNumber).get(listPosition));
-                    bottomLayerToSensor.get(layerNumber).set(listPosition, sensor);
-                    daqPairToSensor.put(bottomLayerDaqMap.get(layerNumber).get(listPosition), sensor);
-                    description = "Bottom Layer " + layerNumber + " - Sensor " + listPosition;
-                    this.printDebug("\tDescription: " + description);
-                    sensorToDescriptor.put(sensor, description);
-                    break;
-                default:
-                    throw new RuntimeException("Invalid module number: " + moduleNumber);
+            // Top Layer
+            case 0:
+
+                listPosition = moduleNumber / 2;
+                sensorToTopLayer.put(sensor, layerNumber);
+                sensorToDaqPair.put(sensor, topLayerDaqMap.get(layerNumber).get(listPosition));
+                topLayerToSensor.get(layerNumber).set(listPosition, sensor);
+                daqPairToSensor.put(topLayerDaqMap.get(layerNumber).get(listPosition), sensor);
+                description = "Top Layer " + layerNumber + " - Sensor " + listPosition;
+                this.printDebug("\tDescription: " + description);
+                sensorToDescriptor.put(sensor, description);
+                break;
+            // Bottom Layer
+            case 1:
+
+                listPosition = (moduleNumber - 1) / 2;
+                sensorToBottomLayer.put(sensor, layerNumber);
+                sensorToDaqPair.put(sensor, bottomLayerDaqMap.get(layerNumber).get(listPosition));
+                bottomLayerToSensor.get(layerNumber).set(listPosition, sensor);
+                daqPairToSensor.put(bottomLayerDaqMap.get(layerNumber).get(listPosition), sensor);
+                description = "Bottom Layer " + layerNumber + " - Sensor " + listPosition;
+                this.printDebug("\tDescription: " + description);
+                sensorToDescriptor.put(sensor, description);
+                break;
+            default:
+                throw new RuntimeException("Invalid module number: " + moduleNumber);
             }
         }
-        
+
         // Create stereo pairs
         this.createStereoPairs();
-        
+
         isSetup = true;
     }
 
@@ -364,142 +367,152 @@
      * Load the SVT DAQ Map from the conditions database
      * 
      */
-    private void loadSvtDaqMap(){ 
-    	
-    	// Path to file in conditions database
+    private void loadSvtDaqMap() {
+
+        // Path to file in conditions database
         String filePath = "daqmap/svt_default.daqmap";
-        BufferedReader daqMapReader = null; 
+        BufferedReader daqMapReader = null;
         String currentLine = null;
         try {
             daqMapReader = new BufferedReader(manager.getRawConditions(filePath).getReader());
-          
-            // Continue to read lines for the DAQ map until the end of file is 
+
+            // Continue to read lines for the DAQ map until the end of file is
             // reached. The DAQ map is has the following format
             //
-            //  layer   module   fpga   hybrid
+            // layer module fpga hybrid
             // ---------------------------------
             while ((currentLine = daqMapReader.readLine()) != null) {
-                
-            	// If the line is a comment,skip it
-                if (currentLine.indexOf("#") != -1) continue;
-               
+
+                // If the line is a comment,skip it
+                if (currentLine.indexOf("#") != -1)
+                    continue;
+
                 // Split the line into tokens by whitespace
                 StringTokenizer stringTok = new StringTokenizer(currentLine);
                 int listPosition = 0;
                 while (stringTok.hasMoreTokens()) {
-                	
-                	// Parse the line
+
+                    // Parse the line
                     int layer = Integer.valueOf(stringTok.nextToken());
                     int module = Integer.valueOf(stringTok.nextToken());
                     int fpga = Integer.valueOf(stringTok.nextToken());
                     int hybrid = Integer.valueOf(stringTok.nextToken());
-                    
-                    // Find the maximum layer number and module number.  This
-                    // is used when instantiating 'sensorArray' and when creating
+
+                    // Find the maximum layer number and module number. This
+                    // is used when instantiating 'sensorArray' and when
+                    // creating
                     // stereo pairs.
                     maxModuleNumber = Math.max(maxModuleNumber, module);
                     maxLayerNumber = Math.max(maxLayerNumber, layer);
-                   
+
                     // A pair is used to relate an FPGA value to a hybrid number
                     Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);
                     fpgaNumbers.add(fpga);
-                    
+
                     // Load the maps based on module number.
                     //
-                    // Module 0 & 2 correspond to sensors which lie in the top SVT volume
-                    // Module 1 & 3 correspond to sensors which lie in the bottom SVT volume
+                    // Module 0 & 2 correspond to sensors which lie in the top
+                    // SVT volume
+                    // Module 1 & 3 correspond to sensors which lie in the
+                    // bottom SVT volume
                     //
-                    // A module number > 1 indicate that the sensor is part of a double layer.
-                    // For the test run detector, all module numbers are either 0 or 1.
+                    // A module number > 1 indicate that the sensor is part of a
+                    // double layer.
+                    // For the test run detector, all module numbers are either
+                    // 0 or 1.
                     switch (module % 2) {
-                        case 0:
-                            listPosition = module / 2;
-                            // If the top layer DAQ map doesn't contain the layer, add it
-                            if (!topLayerDaqMap.containsKey(layer)) {
-                                topLayerDaqMap.put(layer, new ArrayList<Pair<Integer, Integer>>());
-                            }
-                            this.printDebug("\tAdding FPGA: " + daqPair.getFirstElement() + ", Hybrid: " + daqPair.getSecondElement() + " to position: " + listPosition);
-                            // Add the DAQ pair to the corresponding layer
-                            topLayerDaqMap.get(layer).add(listPosition, daqPair);
-                            
-                            // If the top layer sensor map doesn't contain the layer, add it
-                            if (!topLayerToSensor.containsKey(layer)) {
-                                topLayerToSensor.put(layer, new ArrayList<SiSensor>());
-                            }
-                            // Create room within the sensor map for the sensor
-                            topLayerToSensor.get(layer).add(null);
-                            break;
-                        case 1:
-                            listPosition = (module - 1) / 2;
-                            if (!bottomLayerDaqMap.containsKey(layer)) {
-                                bottomLayerDaqMap.put(layer, new ArrayList<Pair<Integer, Integer>>());
-                            }
-                            this.printDebug("\tAdding FPGA: " + daqPair.getFirstElement() + ", Hybrid: " + daqPair.getSecondElement() + " to position: " + listPosition);
-                            bottomLayerDaqMap.get(layer).add(listPosition, daqPair);
-                            if (!bottomLayerToSensor.containsKey(layer)) {
-                                bottomLayerToSensor.put(layer, new ArrayList<SiSensor>());
-                            }
-                            bottomLayerToSensor.get(layer).add(null);
-                            break;
-                        default:
-                            throw new RuntimeException("Invalid module number: " + module);
+                    case 0:
+                        listPosition = module / 2;
+                        // If the top layer DAQ map doesn't contain the layer,
+                        // add it
+                        if (!topLayerDaqMap.containsKey(layer)) {
+                            topLayerDaqMap.put(layer, new ArrayList<Pair<Integer, Integer>>());
+                        }
+                        this.printDebug("\tAdding FPGA: " + daqPair.getFirstElement() + ", Hybrid: " + daqPair.getSecondElement() + " to position: " + listPosition);
+                        // Add the DAQ pair to the corresponding layer
+                        topLayerDaqMap.get(layer).add(listPosition, daqPair);
+
+                        // If the top layer sensor map doesn't contain the
+                        // layer, add it
+                        if (!topLayerToSensor.containsKey(layer)) {
+                            topLayerToSensor.put(layer, new ArrayList<SiSensor>());
+                        }
+                        // Create room within the sensor map for the sensor
+                        topLayerToSensor.get(layer).add(null);
+                        break;
+                    case 1:
+                        listPosition = (module - 1) / 2;
+                        if (!bottomLayerDaqMap.containsKey(layer)) {
+                            bottomLayerDaqMap.put(layer, new ArrayList<Pair<Integer, Integer>>());
+                        }
+                        this.printDebug("\tAdding FPGA: " + daqPair.getFirstElement() + ", Hybrid: " + daqPair.getSecondElement() + " to position: " + listPosition);
+                        bottomLayerDaqMap.get(layer).add(listPosition, daqPair);
+                        if (!bottomLayerToSensor.containsKey(layer)) {
+                            bottomLayerToSensor.put(layer, new ArrayList<SiSensor>());
+                        }
+                        bottomLayerToSensor.get(layer).add(null);
+                        break;
+                    default:
+                        throw new RuntimeException("Invalid module number: " + module);
                     }
                 }
             }
-            
+
         } catch (IOException exception) {
             throw new RuntimeException("Unable to load DAQ Map from " + filePath, exception);
         }
     }
-    
-    /**
-     * 
-     */
-    private void createStereoPairs(){
-    	
-    	// Loop through all the sensors in both top and bottom layers and
-    	// create stereo pairs. 
-    	SiSensor firstSensor = null;
-    	SiSensor secondSensor = null;
-    	int trackerLayer = 0; 
-    	
-    	// 
-    	for(int layerNumber = 1; layerNumber <= maxLayerNumber; layerNumber+=2 ){
-    		for(int sensorNumber = 0; sensorNumber < (maxModuleNumber+1)/2; sensorNumber++){
-    			
-    			firstSensor = this.getTopSensor(layerNumber, sensorNumber);
-    			secondSensor = this.getTopSensor(layerNumber+1, sensorNumber);
-    			
-    			if(firstSensor == null || secondSensor == null) continue;
-    			
-    			trackerLayer = (layerNumber + 1)/2; 
-    			if(this.isAxial(firstSensor)){
-    				stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Top,  firstSensor, secondSensor));
-    			} else {
-    				stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Top, secondSensor, firstSensor));
-    			}
-    			
-    			firstSensor = this.getBottomSensor(layerNumber, sensorNumber);
-    			secondSensor = this.getBottomSensor(layerNumber+1, sensorNumber);
-    			
-    			if(firstSensor == null || secondSensor == null) continue;
-    			
-    			if(this.isAxial(firstSensor)){
-    				stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Bottom, firstSensor, secondSensor));
-    			} else {
-    				stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Bottom, secondSensor, firstSensor));
-    			}
-    		}
-    	}
-    	
-    	this.printDebug("Total number of stereo pairs created: " + stereoPairs.size());
-    	for(StereoPair stereoPair : stereoPairs){
-    		this.printDebug(stereoPair.toString());
-    	}
-    }
-
-    /**
-     * Print a debug message 
+
+    /**
+     * 
+     */
+    private void createStereoPairs() {
+
+        // Loop through all the sensors in both top and bottom layers and
+        // create stereo pairs.
+        SiSensor firstSensor = null;
+        SiSensor secondSensor = null;
+        int trackerLayer = 0;
+
+        //
+        for (int layerNumber = 1; layerNumber <= maxLayerNumber; layerNumber += 2) {
+            for (int sensorNumber = 0; sensorNumber < (maxModuleNumber + 1) / 2; sensorNumber++) {
+
+                firstSensor = this.getTopSensor(layerNumber, sensorNumber);
+                secondSensor = this.getTopSensor(layerNumber + 1, sensorNumber);
+
+                if (firstSensor == null || secondSensor == null)
+                    continue;
+
+                trackerLayer = (layerNumber + 1) / 2;
+                if (this.isAxial(firstSensor)) {
+                    stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Top, firstSensor, secondSensor));
+                } else {
+                    stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Top, secondSensor, firstSensor));
+                }
+
+                firstSensor = this.getBottomSensor(layerNumber, sensorNumber);
+                secondSensor = this.getBottomSensor(layerNumber + 1, sensorNumber);
+
+                if (firstSensor == null || secondSensor == null)
+                    continue;
+
+                if (this.isAxial(firstSensor)) {
+                    stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Bottom, firstSensor, secondSensor));
+                } else {
+                    stereoPairs.add(new StereoPair(trackerLayer, detectorVolume.Bottom, secondSensor, firstSensor));
+                }
+            }
+        }
+
+        this.printDebug("Total number of stereo pairs created: " + stereoPairs.size());
+        for (StereoPair stereoPair : stereoPairs) {
+            this.printDebug(stereoPair.toString());
+        }
+    }
+
+    /**
+     * Print a debug message
      * 
      * @param debugMessage : message to be printed
      */
@@ -508,10 +521,10 @@
             System.out.println(this.getClass().getSimpleName() + ": " + debugMessage);
         }
     }
-    
+
     public void reset() {
         sensors = new HashSet<SiSensor>();
-        stereoPairs = new HashSet<StereoPair>(); 
+        stereoPairs = new HashSet<StereoPair>();
         sensorToDaqPair = new HashMap<SiSensor, Pair<Integer, Integer>>();
         daqPairToSensor = new HashMap<Pair<Integer, Integer>, SiSensor>();
         topLayerDaqMap = new HashMap<Integer, List<Pair<Integer, Integer>>>();
@@ -521,7 +534,7 @@
         sensorToDescriptor = new HashMap<SiSensor, String>();
         topLayerToSensor = new HashMap<Integer, List<SiSensor>>();
         bottomLayerToSensor = new HashMap<Integer, List<SiSensor>>();
-        sensorArray= null;
+        sensorArray = null;
         fpgaNumbers = new HashSet<Integer>();
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/TestRunConditionsReader.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/TestRunConditionsReader.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/deprecated/TestRunConditionsReader.java	Mon Nov 10 00:16:49 2014
@@ -7,13 +7,14 @@
 import org.lcsim.conditions.ConditionsReader;
 
 /**
- * This is a simple extension of {@link org.lcsim.conditions.ConditionsReader} to find
- * text file conditions data for the HPS Test Run 2012.  It basically just checks
- * two resource locations for files and fails if they do not exist.
+ * This is a simple extension of {@link org.lcsim.conditions.ConditionsReader}
+ * to find text file conditions data for the HPS Test Run 2012. It basically
+ * just checks two resource locations for files and fails if they do not exist.
  * 
  * @author Sho Uemura <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: TestRunConditionsReader.java,v 1.4 2013/10/17 23:04:19 jeremy Exp $
+ * @version $Id: TestRunConditionsReader.java,v 1.4 2013/10/17 23:04:19 jeremy
+ *          Exp $
  */
 public class TestRunConditionsReader extends ConditionsReader {
 
@@ -21,16 +22,18 @@
 
     public TestRunConditionsReader() {
     }
-    
-    // FIXME: The reader argument is never used anywhere so this ctor is not needed.
+
+    // FIXME: The reader argument is never used anywhere so this ctor is not
+    // needed.
     public TestRunConditionsReader(ConditionsReader reader) {
     }
-    
+
     public InputStream open(String name, String type) throws IOException {
-        
-        //System.out.println(this.getClass().getSimpleName() + ".open - " + name + ", " + type);
-        
-        // Check the detector base directory.        
+
+        // System.out.println(this.getClass().getSimpleName() + ".open - " +
+        // name + ", " + type);
+
+        // Check the detector base directory.
         InputStream in = getClass().getResourceAsStream("/" + detectorName + "/" + name + "." + type);
         if (in == null) {
             // Check for embedded jar resources e.g. in hps-java.
@@ -39,7 +42,7 @@
             // If these failed to find conditions, then something went wrong.
             if (in == null) {
                 throw new IOException("Conditions " + name + " for " + detectorName + " with type " + type + " were not found");
-            }       
+            }
         }
         return in;
     }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalBadChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalBadChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalBadChannel.java	Mon Nov 10 00:16:49 2014
@@ -4,8 +4,8 @@
 import org.hps.conditions.ConditionsObjectCollection;
 
 /**
- * This class represents an ECAL channel that is considered "bad" which means it should
- * not be used in reconstruction.
+ * This class represents an ECAL channel that is considered "bad" which means it
+ * should not be used in reconstruction.
  */
 public final class EcalBadChannel extends AbstractConditionsObject {
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalCalibration.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalCalibration.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalCalibration.java	Mon Nov 10 00:16:49 2014
@@ -4,11 +4,11 @@
 import org.hps.conditions.ConditionsObjectCollection;
 
 /**
- * This class is a simplistic representation of ECal pedestal and noise values from the
- * conditions database.
+ * This class is a simplistic representation of ECal pedestal and noise values
+ * from the conditions database.
  * 
- * The pedestal and noise are in units of ADC counts. They are the mean and the standard
- * deviation of the digitized pre-amp output.
+ * The pedestal and noise are in units of ADC counts. They are the mean and the
+ * standard deviation of the digitized pre-amp output.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -26,8 +26,8 @@
     }
 
     /**
-     * Get the pedestal value in units of ADC counts, which is the mean of the digitized
-     * pre-amp output.
+     * Get the pedestal value in units of ADC counts, which is the mean of the
+     * digitized pre-amp output.
      * @return The gain value.
      */
     public double getPedestal() {
@@ -35,8 +35,8 @@
     }
 
     /**
-     * Get the noise value in units of ADC counts, which is the standard deviation of the
-     * digitized pre-amp output.
+     * Get the noise value in units of ADC counts, which is the standard
+     * deviation of the digitized pre-amp output.
      * @return The noise value.
      */
     public double getNoise() {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalChannel.java	Mon Nov 10 00:16:49 2014
@@ -12,16 +12,16 @@
 import org.lcsim.detector.identifier.IIdentifierHelper;
 
 /**
- * This class encapsulates all the information about a single ECal channel, corresponding
- * to one physical crystal in the detector.
+ * This class encapsulates all the information about a single ECal channel,
+ * corresponding to one physical crystal in the detector.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public final class EcalChannel extends AbstractConditionsObject {
 
     /**
-     * The <code>DaqId</code> is the combination of crate, slot and channel that specify
-     * the channel's DAQ configuration.
+     * The <code>DaqId</code> is the combination of crate, slot and channel that
+     * specify the channel's DAQ configuration.
      */
     public static final class DaqId extends AbstractIdentifier {
 
@@ -48,8 +48,8 @@
     }
 
     /**
-     * The <code>GeometryId</code> contains the x and y indices of the crystal in the
-     * LCSIM-based geometry representation.
+     * The <code>GeometryId</code> contains the x and y indices of the crystal
+     * in the LCSIM-based geometry representation.
      */
     public static final class GeometryId extends AbstractIdentifier {
 
@@ -82,11 +82,12 @@
     }
 
     /**
-     * The <code>ChannelId</code> is a unique number identifying the channel within its
-     * conditions collection. The channels in the database are given sequential channel
-     * IDs from 1 to N in semi-arbitrary order. The channel ID is generally the number
-     * used to connect other conditions objects such as {@link EcalGain} or
-     * {@link EcalCalibration} to the appropriate crystal in the calorimeter.
+     * The <code>ChannelId</code> is a unique number identifying the channel
+     * within its conditions collection. The channels in the database are given
+     * sequential channel IDs from 1 to N in semi-arbitrary order. The channel
+     * ID is generally the number used to connect other conditions objects such
+     * as {@link EcalGain} or {@link EcalCalibration} to the appropriate crystal
+     * in the calorimeter.
      */
     public static final class ChannelId extends AbstractIdentifier {
 
@@ -130,8 +131,9 @@
         Map<Long, EcalChannel> channelMap = new HashMap<Long, EcalChannel>();
 
         /**
-         * Add an <code>EcalChannel</code> to the collection and cache its ID information.
-         * The GeometryId must be created later as it requires access to the Detector API.
+         * Add an <code>EcalChannel</code> to the collection and cache its ID
+         * information. The GeometryId must be created later as it requires
+         * access to the Detector API.
          */
         @Override
         public void add(EcalChannel channel) throws ConditionsObjectException {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditions.java	Mon Nov 10 00:16:49 2014
@@ -6,12 +6,13 @@
 import org.hps.conditions.ecal.EcalChannel.EcalChannelCollection;
 
 /**
- * This class provides access to all ECAL conditions from the database, including gain,
- * pedestal and bad channel settings, per crystal.
+ * This class provides access to all ECAL conditions from the database,
+ * including gain, pedestal and bad channel settings, per crystal.
  * 
  * Unlike most conditions data types, it does not extend
  * {@link org.hps.conditions.ConditionsObject}, because it is a composite object
- * containing data assembled from many other {@link org.hps.conditions.ConditionsObjects}.
+ * containing data assembled from many other
+ * {@link org.hps.conditions.ConditionsObjects}.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -46,12 +47,13 @@
     }
 
     /**
-     * Get the conditions constants for a specific channel. These will be created if they
-     * do not exist for the given channel, BUT only channels in the current channel map
-     * are allowed as an argument.
+     * Get the conditions constants for a specific channel. These will be
+     * created if they do not exist for the given channel, BUT only channels in
+     * the current channel map are allowed as an argument.
      * @param channel The ECAL channel.
      * @return The conditions constants for the channel.
-     * @throws IllegalArgumentException if channel does not exist in the channel map.
+     * @throws IllegalArgumentException if channel does not exist in the channel
+     *             map.
      */
     public EcalChannelConstants getChannelConstants(EcalChannel channel) {
         // This channel must come from the map.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsConverter.java	Mon Nov 10 00:16:49 2014
@@ -12,64 +12,67 @@
 import org.hps.conditions.DatabaseConditionsManager;
 
 /**
- * This class loads all ECal conditions into an {@link EcalConditions} object from the
- * database, based on the current run number known by the conditions manager.
+ * This class loads all ECal conditions into an {@link EcalConditions} object
+ * from the database, based on the current run number known by the conditions
+ * manager.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class EcalConditionsConverter implements ConditionsConverter<EcalConditions> {
 
-	
     /**
      * Create ECAL conditions object containing all data for the current run.
      */
     public EcalConditions getData(ConditionsManager manager, String name) {
 
-    	DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
+        DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
 
         // Get the ECal channel map from the conditions database
         EcalChannelCollection channels = dbConditionsManager.getCollection(EcalChannelCollection.class);
 
-    	// Create the ECal conditions object that will be used to encapsulate
+        // Create the ECal conditions object that will be used to encapsulate
         // ECal conditions collections
         EcalConditions conditions = new EcalConditions();
-        
+
         // Set the channel map.
         conditions.setChannelCollection(channels);
 
-        // Get the ECal gains from the conditions database and add them to the conditions set
+        // Get the ECal gains from the conditions database and add them to the
+        // conditions set
         EcalGainCollection gains = dbConditionsManager.getCollection(EcalGainCollection.class);
         for (EcalGain gain : gains.getObjects()) {
-            ChannelId channelId = new ChannelId(new int[] {gain.getChannelId()});
+            ChannelId channelId = new ChannelId(new int[] { gain.getChannelId() });
             EcalChannel channel = channels.findChannel(channelId);
             conditions.getChannelConstants(channel).setGain(gain);
         }
 
-        // Get the ECal bad channels and add them to the conditions set 
-        try { 
-        	EcalBadChannelCollection badChannels = dbConditionsManager.getCollection(EcalBadChannelCollection.class);
-        	for (EcalBadChannel badChannel : badChannels.getObjects()) {
-        		ChannelId channelId = new ChannelId(new int[] {badChannel.getChannelId()});
-        		EcalChannel channel = channels.findChannel(channelId);
-        		conditions.getChannelConstants(channel).setBadChannel(true);
-        	}
-        } catch(RuntimeException e){
-        	System.out.println("[ " + conditions.getClass().getSimpleName() + "]: A set of bad channels were not found!");
+        // Get the ECal bad channels and add them to the conditions set
+        try {
+            EcalBadChannelCollection badChannels = dbConditionsManager.getCollection(EcalBadChannelCollection.class);
+            for (EcalBadChannel badChannel : badChannels.getObjects()) {
+                ChannelId channelId = new ChannelId(new int[] { badChannel.getChannelId() });
+                EcalChannel channel = channels.findChannel(channelId);
+                conditions.getChannelConstants(channel).setBadChannel(true);
+            }
+        } catch (RuntimeException e) {
+            System.out.println("[ " + conditions.getClass().getSimpleName() + "]: A set of bad channels were not found!");
         }
 
-        // Get the ECal calibrations from the conditions database and add them to the conditions set.
+        // Get the ECal calibrations from the conditions database and add them
+        // to the conditions set.
         EcalCalibrationCollection calibrations = dbConditionsManager.getCollection(EcalCalibrationCollection.class);
         for (EcalCalibration calibration : calibrations.getObjects()) {
-            ChannelId channelId = new ChannelId(new int[] {calibration.getChannelId()});
+            ChannelId channelId = new ChannelId(new int[] { calibration.getChannelId() });
             EcalChannel channel = channels.findChannel(channelId);
             conditions.getChannelConstants(channel).setCalibration(calibration);
         }
 
-        // Get the ECal time shifts from the conditions database and add them to the conditions set.
+        // Get the ECal time shifts from the conditions database and add them to
+        // the conditions set.
         EcalTimeShiftCollection timeShifts = dbConditionsManager.getCollection(EcalTimeShiftCollection.class);
         for (EcalTimeShift timeShift : timeShifts.getObjects()) {
-            ChannelId channelId = new ChannelId(new int[] {timeShift.getChannelId()});
+            ChannelId channelId = new ChannelId(new int[] { timeShift.getChannelId() });
             EcalChannel channel = channels.findChannel(channelId);
             conditions.getChannelConstants(channel).setTimeShift(timeShift);
         }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsUtil.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsUtil.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConditionsUtil.java	Mon Nov 10 00:16:49 2014
@@ -8,7 +8,8 @@
 import org.lcsim.detector.identifier.Identifier;
 
 /**
- * This is a set of utility methods for the ECAL that use the database conditions system.
+ * This is a set of utility methods for the ECAL that use the database
+ * conditions system.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -25,8 +26,8 @@
     }
 
     /**
-     * Constructor which will find the ECAL conditions from the static conditions manager
-     * instance.
+     * Constructor which will find the ECAL conditions from the static
+     * conditions manager instance.
      */
     public EcalConditionsUtil() {
         conditions = DatabaseConditionsManager.getInstance().getConditionsData(EcalConditions.class, TableConstants.ECAL_CONDITIONS);
@@ -36,7 +37,8 @@
      * Find a channel object from a cell ID, e.g. from Monte Carlo data.
      * @param helper The identifier helper of the hit.
      * @param cellId The cell ID of the hit.
-     * @return The corresponding ECAL channel found from the physical ID information.
+     * @return The corresponding ECAL channel found from the physical ID
+     *         information.
      */
     EcalChannel findChannel(IIdentifierHelper helper, long cellId) {
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java	Mon Nov 10 00:16:49 2014
@@ -47,7 +47,7 @@
             return EcalTimeShiftCollection.class;
         }
     }
-    
+
     public static final class EcalLedConverter extends ConditionsObjectConverter<EcalLed> {
         public Class getType() {
             return EcalLedCollection.class;

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalDetectorSetup.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalDetectorSetup.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalDetectorSetup.java	Mon Nov 10 00:16:49 2014
@@ -9,7 +9,8 @@
 import org.lcsim.geometry.Subdetector;
 
 /**
- * Puts {@link EcalConditions} data onto <code>EcalCrystal</code> objects on the detector.
+ * Puts {@link EcalConditions} data onto <code>EcalCrystal</code> objects on the
+ * detector.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public final class EcalDetectorSetup {
@@ -39,7 +40,8 @@
         // Loop over crystals.
         for (EcalCrystal crystal : crystals) {
 
-            // System.out.println(crystal.getName() + " @ " + crystal.getX() + ", " +
+            // System.out.println(crystal.getName() + " @ " + crystal.getX() +
+            // ", " +
             // crystal.getY());
 
             // Reset in case of existing conditions data.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalLed.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalLed.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/ecal/EcalLed.java	Mon Nov 10 00:16:49 2014
@@ -4,18 +4,18 @@
 import org.hps.conditions.ConditionsObjectCollection;
 
 /**
- * A conditions class for representing the setup of the LED system
- * in the ECAL for one channel.
+ * A conditions class for representing the setup of the LED system in the ECAL
+ * for one channel.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class EcalLed extends AbstractConditionsObject {
-    
+
     /**
-     * Generic collection class for these objects.     
+     * Generic collection class for these objects.
      */
-    public static class EcalLedCollection extends ConditionsObjectCollection<EcalLed> {        
+    public static class EcalLedCollection extends ConditionsObjectCollection<EcalLed> {
     }
-    
+
     /**
      * Get the ECAL channel ID.
      * @return The ECAL channel ID.
@@ -23,7 +23,7 @@
     int getEcalChannelId() {
         return getFieldValue("ecal_channel_id");
     }
-    
+
     /**
      * Get the crate number assigned to this crystal.
      * @return The crate number.
@@ -31,7 +31,7 @@
     int getCrateNumber() {
         return getFieldValue("crate");
     }
-    
+
     /**
      * Get the LED number assigned to this crystal.
      * @return The LED number.
@@ -39,7 +39,7 @@
     int getLedNumber() {
         return getFieldValue("number");
     }
-    
+
     /**
      * Get the time delay of this channel.
      * @return The time delay.
@@ -47,7 +47,7 @@
     double getTimeDelay() {
         return getFieldValue("time_delay");
     }
-    
+
     /**
      * Get the amplitude high setting.
      * @return The amplitude high setting.
@@ -55,12 +55,12 @@
     double getAmplitudeHigh() {
         return getFieldValue("amplitude_high");
     }
-    
+
     /**
      * Get the amplitude low setting.
      * @return The amplitude low setting.
      */
     double getAmplitudeLow() {
         return getFieldValue("amplitude_low");
-    }    
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtChannel.java	Mon Nov 10 00:16:49 2014
@@ -10,64 +10,62 @@
 import org.hps.util.Pair;
 
 /**
- * This abstract class provides basic setup information for an SVT
- * sensor channel. 
+ * This abstract class provides basic setup information for an SVT sensor
+ * channel.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public class AbstractSvtChannel extends AbstractConditionsObject {
 
     // TODO: Put constants into their own class
-	public static final int MAX_NUMBER_OF_SAMPLES = 6;
-    
-	public static abstract class AbstractSvtChannelCollection<T extends AbstractSvtChannel> 
-	    extends ConditionsObjectCollection<T> {
-	    
-	    Map<Integer, T> channelMap = new HashMap<Integer, T>();
-	   
-	    /**
-	     * Add a channel of type extending {@link AbstractSvtChannel} to the
-	     * channel map
-	     * 
-	     * @param A channel of a type extending {@link AbstractSvtChannel}
-	     */
-	    public void add(T channel){
-	    
-	        // If it doesn't exist, add the channel to the channel map
-	        if(channelMap.containsKey(channel.getChannelID())){
-                throw new IllegalArgumentException("[ " + this.getClass().getSimpleName() + " ]: Channel ID already exists: "
-                										+ channel.getChannelID());
-	        }
-	        channelMap.put(channel.getChannelID(), channel);
-	    
-	        // Add to the collection
-	        try { 
-	            super.add(channel);
-	        } catch(ConditionsObjectException e){
-	            throw new RuntimeException(e);
-	        }
-	    }
-	   
-	    /**
-	     * Find a channel of type extending {@link AbstractSvtChannel} using the
-	     * channel ID
-	     * 
-	     * @param channelID
-	     * @return An SVT channel of type extending {@link AbstractSvtChannel}
-	     */
-	    public T findChannel(int channelID){
-	        return channelMap.get(channelID);
-	    }
-	    
+    public static final int MAX_NUMBER_OF_SAMPLES = 6;
+
+    public static abstract class AbstractSvtChannelCollection<T extends AbstractSvtChannel> extends ConditionsObjectCollection<T> {
+
+        Map<Integer, T> channelMap = new HashMap<Integer, T>();
+
         /**
-         * Find the collection of channels of type extending 
+         * Add a channel of type extending {@link AbstractSvtChannel} to the
+         * channel map
+         * 
+         * @param A channel of a type extending {@link AbstractSvtChannel}
+         */
+        public void add(T channel) {
+
+            // If it doesn't exist, add the channel to the channel map
+            if (channelMap.containsKey(channel.getChannelID())) {
+                throw new IllegalArgumentException("[ " + this.getClass().getSimpleName() + " ]: Channel ID already exists: " + channel.getChannelID());
+            }
+            channelMap.put(channel.getChannelID(), channel);
+
+            // Add to the collection
+            try {
+                super.add(channel);
+            } catch (ConditionsObjectException e) {
+                throw new RuntimeException(e);
+            }
+        }
+
+        /**
+         * Find a channel of type extending {@link AbstractSvtChannel} using the
+         * channel ID
+         * 
+         * @param channelID
+         * @return An SVT channel of type extending {@link AbstractSvtChannel}
+         */
+        public T findChannel(int channelID) {
+            return channelMap.get(channelID);
+        }
+
+        /**
+         * Find the collection of channels of type extending
          * {@link AbstractSvtChannel} that match a DAQ pair.
-         *  
+         * 
          * @param pair The DAQ pair.
          * @return The channels matching the DAQ pair or null if not found.
          */
         public abstract Collection<T> find(Pair<Integer, Integer> pair);
-	
+
         /**
          * Convert this object to a human readable string.
          * 
@@ -80,8 +78,8 @@
             }
             return buff.toString();
         }
-	}
-	
+    }
+
     /**
      * Get the channel ID.
      * 
@@ -99,5 +97,5 @@
     public int getChannel() {
         return getFieldValue("channel");
     }
-    
+
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditions.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditions.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditions.java	Mon Nov 10 00:16:49 2014
@@ -8,7 +8,7 @@
 import org.hps.conditions.svt.AbstractSvtT0Shift.AbstractSvtT0ShiftCollection;
 
 /**
- * Abstract class providing some of the common functionality used to define an 
+ * Abstract class providing some of the common functionality used to define an
  * SVT conditions object
  * 
  * @author Omar Moreno <[log in to unmask]>
@@ -16,24 +16,22 @@
  */
 public abstract class AbstractSvtConditions {
 
-    protected Map<AbstractSvtChannel, ChannelConstants> channelData 
-        = new HashMap<AbstractSvtChannel, ChannelConstants>(); 
+    protected Map<AbstractSvtChannel, ChannelConstants> channelData = new HashMap<AbstractSvtChannel, ChannelConstants>();
     protected AbstractSvtT0Shift.AbstractSvtT0ShiftCollection<? extends AbstractSvtT0Shift> t0Shifts = null;
     protected AbstractSvtChannel.AbstractSvtChannelCollection<? extends AbstractSvtChannel> channelMap = null;
     protected AbstractSvtDaqMapping.AbstractSvtDaqMappingCollection<? extends AbstractSvtDaqMapping> daqMap = null;
-    
-    
+
     /**
      * Get the DAQ map associated with these conditions.
      * 
      * @return The SVT DAQ map.
      */
-    public abstract AbstractSvtDaqMappingCollection<? extends AbstractSvtDaqMapping> getDaqMap(); 
-    
+    public abstract AbstractSvtDaqMappingCollection<? extends AbstractSvtDaqMapping> getDaqMap();
+
     /**
-     * Get the conditions constants for a specific channel. These will be created if they
-     * do not exist for the given channel, BUT only channels in the current channel map
-     * are allowed as an argument.
+     * Get the conditions constants for a specific channel. These will be
+     * created if they do not exist for the given channel, BUT only channels in
+     * the current channel map are allowed as an argument.
      * 
      * @param channel The SVT channel of interest
      * @return The conditions constants for the given channel
@@ -57,38 +55,38 @@
      * @return The SVT channel map.
      */
     public abstract AbstractSvtChannelCollection<? extends AbstractSvtChannel> getChannelMap();
-    
+
     /**
      * Get the t0 shifts for this conditions set.
      * 
      * @return The t0 shifts by sensor.
      */
     public abstract AbstractSvtT0ShiftCollection<? extends AbstractSvtT0Shift> getT0Shifts();
-   
+
     /**
      * Set the DAQ map for this conditions set.
      * 
      * @param daqMap DAQ map for this conditions set.
      */
-    public void setDaqMap(AbstractSvtDaqMappingCollection<? extends AbstractSvtDaqMapping> daqMap){
-    	this.daqMap = daqMap;
+    public void setDaqMap(AbstractSvtDaqMappingCollection<? extends AbstractSvtDaqMapping> daqMap) {
+        this.daqMap = daqMap;
     }
-    
+
     /**
      * Set the SVT channel map for this conditions set.
      * 
-     *  @param channelMap The SVT channel map for this conditions set.
+     * @param channelMap The SVT channel map for this conditions set.
      */
-    public void setChannelMap(AbstractSvtChannelCollection<? extends AbstractSvtChannel> channelMap){
-    	this.channelMap = channelMap;
+    public void setChannelMap(AbstractSvtChannelCollection<? extends AbstractSvtChannel> channelMap) {
+        this.channelMap = channelMap;
     }
-    
+
     /**
-     * Set the sensor t0 shifts for this conditions set. 
+     * Set the sensor t0 shifts for this conditions set.
      * 
      * @param t0Shifts for this conditions set.
      */
-    public void setT0Shifts(AbstractSvtT0ShiftCollection<? extends AbstractSvtT0Shift> t0Shifts){ 
-    	this.t0Shifts = t0Shifts; 
+    public void setT0Shifts(AbstractSvtT0ShiftCollection<? extends AbstractSvtT0Shift> t0Shifts) {
+        this.t0Shifts = t0Shifts;
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditionsConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditionsConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtConditionsConverter.java	Mon Nov 10 00:16:49 2014
@@ -9,29 +9,29 @@
 import org.hps.conditions.svt.SvtGain.SvtGainCollection;
 import org.hps.conditions.svt.SvtShapeFitParameters.SvtShapeFitParametersCollection;
 
-
 /**
- * Abstract class providing some of the common methods used in creating
- * SVT conditions objects from the database.
+ * Abstract class providing some of the common methods used in creating SVT
+ * conditions objects from the database.
  * 
  * @author Omar Moreno <[log in to unmask]>
  *
- * @param <T extends AbstractSvtConditions>  SVT conditions object type
+ * @param <T extends AbstractSvtConditions> SVT conditions object type
  */
 public abstract class AbstractSvtConditionsConverter<T extends AbstractSvtConditions> implements ConditionsConverter<T> {
-	
-	protected T conditions;
-	
+
+    protected T conditions;
+
     /**
      * Create and return the SVT conditions object.
      * @param manager The current conditions manager.
      * @param name The conditions key, which is ignored for now.
      */
-	public T getData(ConditionsManager manager, String name){
-	
-    	DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
-    
-    	// Get the SVT calibrations (baseline, noise) from the conditions database
+    public T getData(ConditionsManager manager, String name) {
+
+        DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
+
+        // Get the SVT calibrations (baseline, noise) from the conditions
+        // database
         SvtCalibrationCollection calibrations = dbConditionsManager.getCollection(SvtCalibrationCollection.class);
         for (SvtCalibration calibration : calibrations.getObjects()) {
             AbstractSvtChannel channel = conditions.getChannelMap().findChannel(calibration.getChannelID());
@@ -39,23 +39,23 @@
         }
 
         // Get the Channel pulse fit parameters from the conditions database
-        SvtShapeFitParametersCollection shapeFitParametersCollection 
-        	= dbConditionsManager.getCollection(SvtShapeFitParametersCollection.class);
+        SvtShapeFitParametersCollection shapeFitParametersCollection = dbConditionsManager.getCollection(SvtShapeFitParametersCollection.class);
         for (SvtShapeFitParameters shapeFitParameters : shapeFitParametersCollection.getObjects()) {
             AbstractSvtChannel channel = conditions.getChannelMap().findChannel(shapeFitParameters.getChannelID());
             conditions.getChannelConstants(channel).setShapeFitParameters(shapeFitParameters);
         }
-	
-        // Get the bad channels from the conditions database.  If there aren't any bad channels, 
+
+        // Get the bad channels from the conditions database. If there aren't
+        // any bad channels,
         // notify the user and move on.
-        try { 
-        	SvtBadChannelCollection badChannels = dbConditionsManager.getCollection(SvtBadChannelCollection.class);
-        	for (SvtBadChannel badChannel : badChannels.getObjects()) {
-        		AbstractSvtChannel channel = conditions.getChannelMap().findChannel(badChannel.getChannelId());
-        		conditions.getChannelConstants(channel).setBadChannel(true);
-        	}
-        } catch (RuntimeException e) { 
-        	System.out.println("[ " + conditions.getClass().getSimpleName() + "]: A set of bad channels were not found!");
+        try {
+            SvtBadChannelCollection badChannels = dbConditionsManager.getCollection(SvtBadChannelCollection.class);
+            for (SvtBadChannel badChannel : badChannels.getObjects()) {
+                AbstractSvtChannel channel = conditions.getChannelMap().findChannel(badChannel.getChannelId());
+                conditions.getChannelConstants(channel).setBadChannel(true);
+            }
+        } catch (RuntimeException e) {
+            System.out.println("[ " + conditions.getClass().getSimpleName() + "]: A set of bad channels were not found!");
         }
 
         // Get the gains and offsets from the conditions database
@@ -67,5 +67,5 @@
         }
 
         return conditions;
-	}
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtDaqMapping.java	Mon Nov 10 00:16:49 2014
@@ -6,61 +6,57 @@
 import org.hps.conditions.ConditionsObjectCollection;
 import org.hps.util.Pair;
 
-
 /**
- * This abstract class provides some of the basic functionality used to
- * access SVT DAQ map variables. 
+ * This abstract class provides some of the basic functionality used to access
+ * SVT DAQ map variables.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public abstract class AbstractSvtDaqMapping extends AbstractConditionsObject {
-        
-	public static abstract class AbstractSvtDaqMappingCollection<T extends AbstractSvtDaqMapping>
-	        extends ConditionsObjectCollection<T> {
-   
-	    /**
-		 * Flag values for top or bottom half.
-		 */
-	    public static final String TOP_HALF    = "T";
-	    public static final String BOTTOM_HALF = "B";
 
-        
-	    /**
-	     *  Flag values for axial or stereo sensors 
+    public static abstract class AbstractSvtDaqMappingCollection<T extends AbstractSvtDaqMapping> extends ConditionsObjectCollection<T> {
+
+        /**
+         * Flag values for top or bottom half.
          */
-	    public static final String AXIAL  = "A";
-	    public static final String STEREO = "S";
+        public static final String TOP_HALF = "T";
+        public static final String BOTTOM_HALF = "B";
 
-	    /**
-	     * Get a DAQ pair for the given {@link HpsSiSensor}
-	     * 
-	     * @param sensor A sensor of type {@link HpsSiSensor}
-	     * @return The DAQ pair associated with the sensor
-	     */
-	    public abstract Pair<Integer, Integer> getDaqPair(HpsSiSensor sensor);
-	    
-	    
+        /**
+         * Flag values for axial or stereo sensors
+         */
+        public static final String AXIAL = "A";
+        public static final String STEREO = "S";
+
+        /**
+         * Get a DAQ pair for the given {@link HpsSiSensor}
+         * 
+         * @param sensor A sensor of type {@link HpsSiSensor}
+         * @return The DAQ pair associated with the sensor
+         */
+        public abstract Pair<Integer, Integer> getDaqPair(HpsSiSensor sensor);
+
         /**
          * Get the orientation of a sensor.
          * 
          * @param daqPair for a given sensor
-         * @return If a daqPair is found, return an "A" if the sensor 
-         * 		   orientation is Axial, an "S" if the orientation is Stereo or
-         * 		   null if the daqPair doesn't exist.
+         * @return If a daqPair is found, return an "A" if the sensor
+         *         orientation is Axial, an "S" if the orientation is Stereo or
+         *         null if the daqPair doesn't exist.
          */
         public abstract String getOrientation(Pair<Integer, Integer> daqPair);
-	
-	}
-	
+
+    }
+
     public String getSvtHalf() {
         return getFieldValue("svt_half");
     }
-    
+
     public int getLayerNumber() {
         return getFieldValue("layer");
     }
-    
-    public String getOrientation() { 
-    	return getFieldValue("orientation");
+
+    public String getOrientation() {
+        return getFieldValue("orientation");
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtT0Shift.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtT0Shift.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/AbstractSvtT0Shift.java	Mon Nov 10 00:16:49 2014
@@ -5,28 +5,26 @@
 import org.hps.util.Pair;
 
 /**
- * Abstract class providing some of the basic functionality used to 
- * relate a t0 shift value  with either a FEB ID/FEB hybrid ID or 
- * an FPGA ID/hybrid ID.
+ * Abstract class providing some of the basic functionality used to relate a t0
+ * shift value with either a FEB ID/FEB hybrid ID or an FPGA ID/hybrid ID.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public class AbstractSvtT0Shift extends AbstractConditionsObject {
 
-    public static abstract class AbstractSvtT0ShiftCollection<T extends AbstractSvtT0Shift>
-            extends ConditionsObjectCollection<T> { 
-        
+    public static abstract class AbstractSvtT0ShiftCollection<T extends AbstractSvtT0Shift> extends ConditionsObjectCollection<T> {
+
         /**
          * Get the t0 shift associated with a given DAQ pair
          * 
          * @param DAQ pair for a given sensor
-         * @return The t0 shift associated with the DAQ pair.  If a t0 shift
-         *         for a given DAQ pair can't be found, it returns null.
+         * @return The t0 shift associated with the DAQ pair. If a t0 shift for
+         *         a given DAQ pair can't be found, it returns null.
          */
-        public abstract T getT0Shift(Pair<Integer, Integer> pair); 
-        
+        public abstract T getT0Shift(Pair<Integer, Integer> pair);
+
     }
-    
+
     /**
      * Get the t0 shift.
      * 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java	Mon Nov 10 00:16:49 2014
@@ -5,7 +5,8 @@
 
 /**
  * <p>
- * Encapsulates an SVT alignment constant, which is an encoded key plus a double value.
+ * Encapsulates an SVT alignment constant, which is an encoded key plus a double
+ * value.
  * </p>
  * <p>
  * The format of the keys is ABCDE where:<br>
@@ -18,53 +19,55 @@
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class SvtAlignmentConstant extends AbstractConditionsObject {
-    
-    public static class SvtAlignmentCollection extends ConditionsObjectCollection<SvtAlignmentConstant> {       
+
+    public static class SvtAlignmentCollection extends ConditionsObjectCollection<SvtAlignmentConstant> {
     }
-    
+
     /** Top or bottom half. */
-    public enum Half {                
-        TOP(1), 
-        BOTTOM(2);        
-        int value;        
+    public enum Half {
+        TOP(1), BOTTOM(2);
+        int value;
+
         Half(int value) {
             this.value = value;
-        }        
-        int getValue() {
-            return value;
         }
-    };    
-    
-    /** The alignment constant type which is rotation or translation. */
-    public enum AlignmentType {        
-        ROTATION(1),
-        TRANSLATION(2);
-        int value;        
-        AlignmentType(int value) {
-            this.value = value;
-        }        
+
         int getValue() {
             return value;
         }
     };
-        
+
+    /** The alignment constant type which is rotation or translation. */
+    public enum AlignmentType {
+        ROTATION(1), TRANSLATION(2);
+        int value;
+
+        AlignmentType(int value) {
+            this.value = value;
+        }
+
+        int getValue() {
+            return value;
+        }
+    };
+
     /** The unit axis. */
-    public enum UnitAxis { 
-        U(1), 
-        V(2), 
-        W(3);
+    public enum UnitAxis {
+        U(1), V(2), W(3);
         int value;
+
         UnitAxis(int value) {
             this.value = value;
         }
+
         int getValue() {
             return value;
-        }        
+        }
     };
-    
+
     /** Maximum value of module number. */
     private static final int MAX_MODULE_NUMBER = 10;
-       
+
     /**
      * Get the alignment constant's full key with the encoded information.
      * @return the alignment constant's key
@@ -72,7 +75,7 @@
     public String getParameter() {
         return getFieldValue("parameter");
     }
-    
+
     /**
      * Get the the alignment constant's value which is always a single double.
      * @return the alignment constant's value as a double
@@ -80,7 +83,7 @@
     public double getValue() {
         return getFieldValue("value");
     }
-    
+
     /**
      * Decode the Half value from the key.
      * @return the Half value from the key
@@ -93,9 +96,9 @@
             return Half.BOTTOM;
         } else {
             throw new IllegalArgumentException("Could not parse valid Half from " + getParameter());
-        }                              
+        }
     }
-    
+
     /**
      * Decode the AlignmentType value from the key.
      * @return the AlignmentType value from the key
@@ -110,7 +113,7 @@
             throw new IllegalArgumentException("Could not parse valid AlignmentType from " + getParameter());
         }
     }
-    
+
     /**
      * Decode the UnitAxis from the key.
      * @return the UnitAxis v
@@ -127,10 +130,10 @@
             throw new IllegalArgumentException("Could not parse valid UnitAxis from " + getParameter());
         }
     }
-    
+
     /**
      * Decode the module number from the key.
-     * @return the module number from the key 
+     * @return the module number from the key
      */
     public int getModuleNumber() {
         int moduleNumber = Integer.parseInt(getParameter().substring(3, 5));
@@ -139,14 +142,14 @@
         }
         return moduleNumber;
     }
-    
+
     public String toString() {
         StringBuffer buff = new StringBuffer();
         buff.append(super.toString());
         buff.append("half: ").append(getHalf().getValue()).append('\n');
         buff.append("alignment_type: ").append(getAlignmentType().getValue()).append('\n');
         buff.append("unit_axis: ").append(getUnitAxis().getValue()).append('\n');
-        buff.append("module_number: " ).append(getModuleNumber()).append('\n');
+        buff.append("module_number: ").append(getModuleNumber()).append('\n');
         return buff.toString();
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtBadChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtBadChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtBadChannel.java	Mon Nov 10 00:16:49 2014
@@ -11,9 +11,9 @@
     public int getChannelId() {
         return getFieldValue("svt_channel_id");
     }
-    
-    public int getNote(){
-    	return getFieldValue("notes");
+
+    public int getNote() {
+        return getFieldValue("notes");
     }
 
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtCalibration.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtCalibration.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtCalibration.java	Mon Nov 10 00:16:49 2014
@@ -6,14 +6,13 @@
 import static org.hps.conditions.svt.SvtChannel.MAX_NUMBER_OF_SAMPLES;
 
 /**
- * This class  encapsulates noise and pedestal measurement for an SVT channel.
+ * This class encapsulates noise and pedestal measurement for an SVT channel.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class SvtCalibration extends AbstractConditionsObject {
 
-	
     public static class SvtCalibrationCollection extends ConditionsObjectCollection<SvtCalibration> {
     }
 
@@ -30,9 +29,9 @@
      * @return The noise value.
      */
     public double getNoise(int sample) {
-    	if(sample < 0 || sample > MAX_NUMBER_OF_SAMPLES){
-    		throw new RuntimeException("Sample number is not within range.");
-    	}
+        if (sample < 0 || sample > MAX_NUMBER_OF_SAMPLES) {
+            throw new RuntimeException("Sample number is not within range.");
+        }
         return getFieldValue(Double.class, "noise_" + Integer.toString(sample));
     }
 
@@ -41,9 +40,9 @@
      * @return The pedestal value.
      */
     public double getPedestal(int sample) {
-    	if(sample < 0 || sample > MAX_NUMBER_OF_SAMPLES){
-    		throw new RuntimeException("Sample number is not within range.");
-    	}
+        if (sample < 0 || sample > MAX_NUMBER_OF_SAMPLES) {
+            throw new RuntimeException("Sample number is not within range.");
+        }
         return getFieldValue(Double.class, "pedestal_" + Integer.toString(sample));
     }
 
@@ -52,51 +51,51 @@
      * @return This object converted to a string.
      */
     public String toString() {
-    	StringBuffer buffer = new StringBuffer();
-    	buffer.append("Channel ID: " + this.getChannelID());
+        StringBuffer buffer = new StringBuffer();
+        buffer.append("Channel ID: " + this.getChannelID());
         for (int i = 0; i < 115; i++) {
             buffer.append("-");
         }
-    	buffer.append("Pedestal sample 0:");
-    	buffer.append("      ");
-    	buffer.append("Pedestal sample 1:");
-    	buffer.append("      ");
-    	buffer.append("Pedestal sample 2:");
-    	buffer.append("      ");
-    	buffer.append("Pedestal sample 3:");
-    	buffer.append("      ");
-    	buffer.append("Pedesdtal sample 4:");
-    	buffer.append("      ");
-    	buffer.append("Pedestal sample 5:");
-    	buffer.append("\n");
+        buffer.append("Pedestal sample 0:");
+        buffer.append("      ");
+        buffer.append("Pedestal sample 1:");
+        buffer.append("      ");
+        buffer.append("Pedestal sample 2:");
+        buffer.append("      ");
+        buffer.append("Pedestal sample 3:");
+        buffer.append("      ");
+        buffer.append("Pedesdtal sample 4:");
+        buffer.append("      ");
+        buffer.append("Pedestal sample 5:");
+        buffer.append("\n");
         for (int i = 0; i < 115; i++) {
             buffer.append("-");
         }
-    	buffer.append("\n");
-    	for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-    		buffer.append(this.getPedestal(sample));
-    		buffer.append("      ");
-    	}
-    	buffer.append("Noise sample 0:");
-    	buffer.append("      ");
-    	buffer.append("Noise sample 1:");
-    	buffer.append("      ");
-    	buffer.append("Noise sample 2:");
-    	buffer.append("      ");
-    	buffer.append("Noise sample 3:");
-    	buffer.append("      ");
-    	buffer.append("Noise sample 4:");
-    	buffer.append("      ");
-    	buffer.append("Noise sample 5:");
-    	buffer.append("\n");
+        buffer.append("\n");
+        for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+            buffer.append(this.getPedestal(sample));
+            buffer.append("      ");
+        }
+        buffer.append("Noise sample 0:");
+        buffer.append("      ");
+        buffer.append("Noise sample 1:");
+        buffer.append("      ");
+        buffer.append("Noise sample 2:");
+        buffer.append("      ");
+        buffer.append("Noise sample 3:");
+        buffer.append("      ");
+        buffer.append("Noise sample 4:");
+        buffer.append("      ");
+        buffer.append("Noise sample 5:");
+        buffer.append("\n");
         for (int i = 0; i < 115; i++) {
             buffer.append("-");
         }
-    	buffer.append("\n");
-    	for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-    		buffer.append(this.getNoise(sample));
-    		buffer.append("      ");
-    	}
-    	return buffer.toString();
+        buffer.append("\n");
+        for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+            buffer.append(this.getNoise(sample));
+            buffer.append("      ");
+        }
+        return buffer.toString();
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtChannel.java	Mon Nov 10 00:16:49 2014
@@ -7,24 +7,22 @@
 import org.hps.util.Pair;
 
 /**
- * This class represents SVT channel setup information, including FEB ID, 
- * FEB Hybrid ID, and channel numbers.
+ * This class represents SVT channel setup information, including FEB ID, FEB
+ * Hybrid ID, and channel numbers.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class SvtChannel extends AbstractSvtChannel {
 
-
-	public static class SvtChannelCollection 
-	    extends AbstractSvtChannel.AbstractSvtChannelCollection<SvtChannel> {
+    public static class SvtChannelCollection extends AbstractSvtChannel.AbstractSvtChannelCollection<SvtChannel> {
 
         /**
          * Find channels that match a DAQ pair (FEB ID, FEB Hybrid ID).
          * @param pair The DAQ pair.
          * @return The channels matching the DAQ pair or null if not found.
          */
-	    @Override
+        @Override
         public Collection<SvtChannel> find(Pair<Integer, Integer> pair) {
             List<SvtChannel> channels = new ArrayList<SvtChannel>();
             int febID = pair.getFirstElement();
@@ -59,10 +57,7 @@
      * @return This object as a string.
      */
     public String toString() {
-        return "channel_id: " + getChannelID() +
-               ", feb_id: " + getFebID() + 
-               ", feb_hybrid_id: " + getFebHybridID() +
-               ", channel: " + getChannel();
+        return "channel_id: " + getChannelID() + ", feb_id: " + getFebID() + ", feb_hybrid_id: " + getFebHybridID() + ", channel: " + getChannel();
     }
 
     /**
@@ -77,9 +72,6 @@
         if (o == this)
             return true;
         SvtChannel channel = (SvtChannel) o;
-        return getChannelID() == channel.getChannelID() 
-                && getFebID() == channel.getFebID() 
-                && getFebHybridID() == channel.getFebHybridID() 
-                && getChannel() == channel.getChannel();
+        return getChannelID() == channel.getChannelID() && getFebID() == channel.getFebID() && getFebHybridID() == channel.getFebHybridID() && getChannel() == channel.getChannel();
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditions.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditions.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditions.java	Mon Nov 10 00:16:49 2014
@@ -10,23 +10,22 @@
 
 /**
  * 
- * This class contains all test run SVT conditions data by readout channel. 
- * {@link SvtChannel} objects from the SVT channel map should be used to
- * lookup the conditions using the {@link #getChannelConstants(SvtChannel)}
- * method.
+ * This class contains all test run SVT conditions data by readout channel.
+ * {@link SvtChannel} objects from the SVT channel map should be used to lookup
+ * the conditions using the {@link #getChannelConstants(SvtChannel)} method.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class SvtConditions extends AbstractSvtConditions {
 
-	/**
+    /**
      * Get the {@link SvtDaqMappingCollection} associated with these conditions.
      * 
      * @return The SVT DAQ map.
      */
     @Override
-    public SvtDaqMappingCollection getDaqMap(){
+    public SvtDaqMappingCollection getDaqMap() {
         return (SvtDaqMappingCollection) daqMap;
     }
 
@@ -36,30 +35,29 @@
      * @return The SVT channel map.
      */
     @Override
-    public SvtChannelCollection getChannelMap(){
+    public SvtChannelCollection getChannelMap() {
         return (SvtChannelCollection) channelMap;
     }
-    
+
     /**
      * Get the {@link SvtT0ShiftCollection} associated with these conditions.
      * 
      * @return The {@link SvtT0ShiftCollection}
      */
     @Override
-    public SvtT0ShiftCollection getT0Shifts() { 
-    	return (SvtT0ShiftCollection) t0Shifts;
+    public SvtT0ShiftCollection getT0Shifts() {
+        return (SvtT0ShiftCollection) t0Shifts;
     }
-    
 
     /**
-     * Convert this object to a human readable string. This method prints a formatted
-     * table of channel data independently of how its member objects implement their
-     * string conversion method. For now, it does not print the time shifts by sensor as
-     * all other information is by channel.
+     * Convert this object to a human readable string. This method prints a
+     * formatted table of channel data independently of how its member objects
+     * implement their string conversion method. For now, it does not print the
+     * time shifts by sensor as all other information is by channel.
      * 
-     * @return This object converted to a string, without the DAQ map.
-     * TODO: Make this look more human readable.  At the moment, reading this
-     * 		 requires a huge terminal window.
+     * @return This object converted to a string, without the DAQ map. TODO:
+     *         Make this look more human readable. At the moment, reading this
+     *         requires a huge terminal window.
      */
     public String toString() {
         StringBuffer buff = new StringBuffer();
@@ -131,13 +129,13 @@
             buff.append(String.format("%-6d %-5d %-8d %-8d ", channel.getChannelID(), channel.getFebID(), channel.getFebHybridID(), channel.getChannel()));
 
             // Calibration.
-            for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-            	buff.append(calibration.getPedestal(sample));
-            	buff.append("      ");
+            for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+                buff.append(calibration.getPedestal(sample));
+                buff.append("      ");
             }
-            for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-            	buff.append(calibration.getNoise(sample));
-            	buff.append("      ");
+            for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+                buff.append(calibration.getNoise(sample));
+                buff.append("      ");
             }
 
             // Gain.

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConditionsConverter.java	Mon Nov 10 00:16:49 2014
@@ -7,45 +7,46 @@
 import org.hps.conditions.svt.SvtT0Shift.SvtT0ShiftCollection;
 
 /**
- * This class creates an {@link SvtConditions} object from the database, based on the
- * current run number known by the conditions manager.
+ * This class creates an {@link SvtConditions} object from the database, based
+ * on the current run number known by the conditions manager.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class SvtConditionsConverter extends AbstractSvtConditionsConverter<SvtConditions> {
 
-	public SvtConditionsConverter(){
-		this.conditions = new SvtConditions();
-	}
-	
+    public SvtConditionsConverter() {
+        this.conditions = new SvtConditions();
+    }
+
     /**
-     * Create and return an {@link SvtConditions} object 
+     * Create and return an {@link SvtConditions} object
      * 
      * @param manager The current conditions manager.
      * @param name The conditions key, which is ignored for now.
      */
     @Override
     public SvtConditions getData(ConditionsManager manager, String name) {
-    	
-    	DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
 
-    	// Get the channel map from the conditions database
-        SvtChannelCollection channels = dbConditionsManager.getCollection(SvtChannelCollection.class); 
+        DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
 
-        // Create the SVT conditions object to use to encapsulate SVT condition collections
+        // Get the channel map from the conditions database
+        SvtChannelCollection channels = dbConditionsManager.getCollection(SvtChannelCollection.class);
+
+        // Create the SVT conditions object to use to encapsulate SVT condition
+        // collections
         conditions.setChannelMap(channels);
-       
-    	// Get the DAQ map from the conditions database
-    	SvtDaqMappingCollection daqMap= dbConditionsManager.getCollection(SvtDaqMappingCollection.class);
+
+        // Get the DAQ map from the conditions database
+        SvtDaqMappingCollection daqMap = dbConditionsManager.getCollection(SvtDaqMappingCollection.class);
         conditions.setDaqMap(daqMap);
-        
+
         // Get the collection of T0 shifts from the conditions database
         SvtT0ShiftCollection t0Shifts = dbConditionsManager.getCollection(SvtT0ShiftCollection.class);
         conditions.setT0Shifts(t0Shifts);
-        
+
         conditions = super.getData(manager, name);
-        
+
         return conditions;
     }
 

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConfiguration.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConfiguration.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConfiguration.java	Mon Nov 10 00:16:49 2014
@@ -17,7 +17,7 @@
  * This is a simple class for getting an SVT XML configuration file.
  */
 public class SvtConfiguration extends AbstractConditionsObject {
-            
+
     public static class SvtConfigurationCollection extends ConditionsObjectCollection<SvtConfiguration> {
     }
 
@@ -28,11 +28,12 @@
     public String getFileName() {
         return getFieldValue("filename");
     }
-        
+
     /**
-     * Convert the raw database field value for the configuration into an XML document.
+     * Convert the raw database field value for the configuration into an XML
+     * document.
      * @return The Document created from the raw data.
-     * @throws IOException 
+     * @throws IOException
      * @throws JDOMException
      */
     public Document createDocument() throws IOException, JDOMException {
@@ -42,7 +43,7 @@
         builder.setValidation(false);
         return builder.build(inputStream);
     }
-    
+
     /**
      * Save this configuration to a local file on disk.
      * @param filename The name of the local file.
@@ -56,9 +57,10 @@
             throw new RuntimeException(e);
         }
     }
-    
+
     /**
-     * Save this configuration to a local file on disk using its name from the database.
+     * Save this configuration to a local file on disk using its name from the
+     * database.
      */
     public void writeToFile() {
         XMLOutputter out = new XMLOutputter();

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConverterRegistry.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConverterRegistry.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtConverterRegistry.java	Mon Nov 10 00:16:49 2014
@@ -15,19 +15,20 @@
 import org.hps.conditions.svt.TestRunSvtT0Shift.TestRunSvtT0ShiftCollection;
 
 /**
- * Definitions of converters from the database to SVT specific conditions classes.
+ * Definitions of converters from the database to SVT specific conditions
+ * classes.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 @SuppressWarnings({ "unchecked", "rawtypes" })
 public final class SvtConverterRegistry {
 
-    public static class SvtAlignmentConverter extends ConditionsObjectConverter<SvtAlignmentCollection> {        
+    public static class SvtAlignmentConverter extends ConditionsObjectConverter<SvtAlignmentCollection> {
         public Class getType() {
             return SvtAlignmentCollection.class;
-        }               
+        }
     }
-    
+
     public static class SvtBadChannelConverter extends ConditionsObjectConverter<SvtBadChannelCollection> {
         public Class getType() {
             return SvtBadChannelCollection.class;
@@ -45,7 +46,7 @@
             return SvtChannelCollection.class;
         }
     }
-    
+
     public static class SvtConfigurationConverter extends ConditionsObjectConverter<SvtConfigurationCollection> {
         public Class getType() {
             return SvtConfigurationCollection.class;
@@ -75,15 +76,15 @@
             return SvtT0ShiftCollection.class;
         }
     }
-    
+
     public static class TestRunSvtDaqMappingConverter extends ConditionsObjectConverter<TestRunSvtDaqMappingCollection> {
         public Class getType() {
             return TestRunSvtDaqMappingCollection.class;
         }
     }
-    
+
     public static class TestRunSvtChannelConverter extends ConditionsObjectConverter<TestRunSvtChannelCollection> {
-        public Class getType(){
+        public Class getType() {
             return TestRunSvtChannelCollection.class;
         }
     }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDaqMapping.java	Mon Nov 10 00:16:49 2014
@@ -12,49 +12,47 @@
  */
 public class SvtDaqMapping extends AbstractSvtDaqMapping {
 
-    public static class SvtDaqMappingCollection 
-            extends AbstractSvtDaqMappingCollection<SvtDaqMapping> {
+    public static class SvtDaqMappingCollection extends AbstractSvtDaqMappingCollection<SvtDaqMapping> {
 
         /**
-         * Get a DAQ pair (FEB ID, FEB Hybrid ID) for the given 
+         * Get a DAQ pair (FEB ID, FEB Hybrid ID) for the given
          * {@link HpsSiSensor}
          * 
-		 * @param  sensor A sensor of type {@link HpsSiSensor}
-		 * @return The DAQ pair associated with the sensor 
+         * @param sensor A sensor of type {@link HpsSiSensor}
+         * @return The DAQ pair associated with the sensor
          */
         public Pair<Integer, Integer> getDaqPair(HpsSiSensor sensor) {
-        	
-        	String svtHalf = sensor.isTopLayer() ? TOP_HALF : BOTTOM_HALF;
-        	for (SvtDaqMapping object : this.getObjects()) {
-        		
-        		if(svtHalf.equals(object.getSvtHalf()) 
-        				&& object.getLayerNumber() == sensor.getLayerNumber()
-        				&& object.getSide().equals(sensor.getSide())) {
-                
-        			return new Pair<Integer, Integer>(object.getFebID(), object.getFebHybridID());
-                } 
+
+            String svtHalf = sensor.isTopLayer() ? TOP_HALF : BOTTOM_HALF;
+            for (SvtDaqMapping object : this.getObjects()) {
+
+                if (svtHalf.equals(object.getSvtHalf()) && object.getLayerNumber() == sensor.getLayerNumber() && object.getSide().equals(sensor.getSide())) {
+
+                    return new Pair<Integer, Integer>(object.getFebID(), object.getFebHybridID());
+                }
             }
             return null;
         }
-        
+
         /**
          * Get the orientation of a sensor using the FEB ID and FEB Hybrid ID.
-         * If the FEB ID and FEB Hybrid ID combination is not found, return null.
+         * If the FEB ID and FEB Hybrid ID combination is not found, return
+         * null.
          * 
          * @param daqPair (Pair<FEB ID, FEB Hybrid ID>) for a given sensor
-         * @return If a daqPair is found, return an "A" if the sensor 
-         * 		   orientation is Axial, an "S" if the orientation is Stereo or
-         * 		   null if the daqPair doesn't exist.
+         * @return If a daqPair is found, return an "A" if the sensor
+         *         orientation is Axial, an "S" if the orientation is Stereo or
+         *         null if the daqPair doesn't exist.
          */
-        public String getOrientation(Pair<Integer, Integer> daqPair){
-        	
-        	for(SvtDaqMapping daqMapping : this.getObjects()){
-        		
-        		if(daqPair.getFirstElement() == daqMapping.getFebID() && daqPair.getSecondElement() == daqMapping.getFebHybridID()){
-        			return daqMapping.getOrientation(); 
-        		}
-        	}
-        	return null;
+        public String getOrientation(Pair<Integer, Integer> daqPair) {
+
+            for (SvtDaqMapping daqMapping : this.getObjects()) {
+
+                if (daqPair.getFirstElement() == daqMapping.getFebID() && daqPair.getSecondElement() == daqMapping.getFebHybridID()) {
+                    return daqMapping.getOrientation();
+                }
+            }
+            return null;
         }
 
         /**
@@ -79,9 +77,9 @@
             buff.append("----------------------");
             buff.append('\n');
             for (SvtDaqMapping object : getObjects()) {
-            	buff.append(object.getFebID());
+                buff.append(object.getFebID());
                 buff.append("    ");
-            	buff.append(object.getFebHybridID());
+                buff.append(object.getFebHybridID());
                 buff.append("    ");
                 buff.append(object.getSvtHalf());
                 buff.append("    ");
@@ -96,16 +94,16 @@
             return buff.toString();
         }
     }
-    
-    public int getFebID() { 
-    	return getFieldValue("feb_id");
+
+    public int getFebID() {
+        return getFieldValue("feb_id");
     }
-    
-    public int getFebHybridID() { 
-    	return getFieldValue("feb_hybrid_id");
+
+    public int getFebHybridID() {
+        return getFieldValue("feb_hybrid_id");
     }
-    
-    public String getSide(){
-    	return getFieldValue("side");
+
+    public String getSide() {
+        return getFieldValue("side");
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDetectorSetup.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDetectorSetup.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtDetectorSetup.java	Mon Nov 10 00:16:49 2014
@@ -12,7 +12,8 @@
 import org.hps.util.Pair;
 
 /**
- * This class puts {@link SvtConditions} data onto <code>HpsSiSensor</code> objects.
+ * This class puts {@link SvtConditions} data onto <code>HpsSiSensor</code>
+ * objects.
  *
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
@@ -22,13 +23,13 @@
     /**
      * Load conditions data onto a detector object.
      * 
-     * @param  The detector object.
+     * @param The detector object.
      * @param conditions The conditions object.
      */
     public void load(Subdetector subdetector, SvtConditions conditions) {
 
         // Find sensor objects.
-    	List<HpsSiSensor> sensors = subdetector.getDetectorElement().findDescendants(HpsSiSensor.class);
+        List<HpsSiSensor> sensors = subdetector.getDetectorElement().findDescendants(HpsSiSensor.class);
         SvtChannelCollection channelMap = conditions.getChannelMap();
         SvtDaqMappingCollection daqMap = conditions.getDaqMap();
         SvtT0ShiftCollection t0Shifts = conditions.getT0Shifts();
@@ -47,16 +48,16 @@
 
             // Set the FEB ID of the sensor
             sensor.setFebID(daqPair.getFirstElement());
-           
+
             // Set the FEB Hybrid ID of the sensor
             sensor.setFebHybridID(daqPair.getSecondElement());
-           
+
             // Set the orientation of the sensor
             String orientation = daqMap.getOrientation(daqPair);
-            if(orientation != null && orientation.contentEquals(SvtDaqMappingCollection.AXIAL)){
-            	sensor.setAxial(true);
-            } else if(orientation != null && orientation.contains(SvtDaqMappingCollection.STEREO)){
-            	sensor.setStereo(true);
+            if (orientation != null && orientation.contentEquals(SvtDaqMappingCollection.AXIAL)) {
+                sensor.setAxial(true);
+            } else if (orientation != null && orientation.contains(SvtDaqMappingCollection.STEREO)) {
+                sensor.setStereo(true);
             }
 
             // Find all the channels for this sensor.
@@ -64,35 +65,35 @@
 
             // Loop over the channels of the sensor.
             for (SvtChannel channel : channels) {
-                
-            	// Get conditions data for this channel.
+
+                // Get conditions data for this channel.
                 ChannelConstants constants = conditions.getChannelConstants(channel);
                 int channelNumber = channel.getChannel();
 
                 //
                 // Set conditions data for this channel on the sensor object:
                 //
-                
+
                 // Check if the channel was flagged as bad
                 if (constants.isBadChannel()) {
                     sensor.setBadChannel(channelNumber);
                 }
-                
-                // Set the pedestal and noise of each of the samples for the 
+
+                // Set the pedestal and noise of each of the samples for the
                 // channel
                 double[] pedestal = new double[6];
                 double[] noise = new double[6];
-                for(int sampleN = 0; sampleN < HpsSiSensor.NUMBER_OF_SAMPLES; sampleN++){
-                	pedestal[sampleN] = constants.getCalibration().getPedestal(sampleN);
-                	noise[sampleN] = constants.getCalibration().getNoise(sampleN);
+                for (int sampleN = 0; sampleN < HpsSiSensor.NUMBER_OF_SAMPLES; sampleN++) {
+                    pedestal[sampleN] = constants.getCalibration().getPedestal(sampleN);
+                    noise[sampleN] = constants.getCalibration().getNoise(sampleN);
                 }
                 sensor.setPedestal(channelNumber, pedestal);
                 sensor.setNoise(channelNumber, noise);
-               
+
                 // Set the gain and offset for the channel
                 sensor.setGain(channelNumber, constants.getGain().getGain());
                 sensor.setOffset(channelNumber, constants.getGain().getOffset());
-               
+
                 // Set the shape fit parameters
                 sensor.setShapeFitParameters(channelNumber, constants.getShapeFitParameters().toArray());
             }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtShapeFitParameters.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtShapeFitParameters.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtShapeFitParameters.java	Mon Nov 10 00:16:49 2014
@@ -39,7 +39,7 @@
     }
 
     /**
-     * Get tp. 
+     * Get tp.
      * @return tp.
      */
     double getTp() {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/SvtT0Shift.java	Mon Nov 10 00:16:49 2014
@@ -3,23 +3,22 @@
 import org.hps.util.Pair;
 
 /**
- * This class is a data holder for associating a t0 shift with a specific 
- * sensor by FEB ID and FEB hybrid ID.
+ * This class is a data holder for associating a t0 shift with a specific sensor
+ * by FEB ID and FEB hybrid ID.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class SvtT0Shift extends AbstractSvtT0Shift {
 
-    public static class SvtT0ShiftCollection 
-        extends AbstractSvtT0Shift.AbstractSvtT0ShiftCollection<SvtT0Shift> {
+    public static class SvtT0ShiftCollection extends AbstractSvtT0Shift.AbstractSvtT0ShiftCollection<SvtT0Shift> {
 
         /**
          * Get the {@link SvtT0Shift} associated with a given DAQ pair
          * 
          * @param DAQ pair for a given sensor
-         * @return The {@link SvtT0Shift} associated with the DAQ pair.  If a t0 shift
-         *         for a given DAQ pair can't be found, it returns null.
+         * @return The {@link SvtT0Shift} associated with the DAQ pair. If a t0
+         *         shift for a given DAQ pair can't be found, it returns null.
          */
         @Override
         public SvtT0Shift getT0Shift(Pair<Integer, Integer> pair) {

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtChannel.java	Mon Nov 10 00:16:49 2014
@@ -8,38 +8,37 @@
 
 public final class TestRunSvtChannel extends AbstractSvtChannel {
 
-    public static class TestRunSvtChannelCollection 
-        extends AbstractSvtChannel.AbstractSvtChannelCollection<TestRunSvtChannel> {
+    public static class TestRunSvtChannelCollection extends AbstractSvtChannel.AbstractSvtChannelCollection<TestRunSvtChannel> {
 
         @Override
         public Collection<TestRunSvtChannel> find(Pair<Integer, Integer> pair) {
             List<TestRunSvtChannel> channels = new ArrayList<TestRunSvtChannel>();
             int fpga = pair.getFirstElement();
             int hybrid = pair.getSecondElement();
-            for(TestRunSvtChannel channel : this.getObjects()){
-                if(channel.getFpgaID() == fpga && channel.getHybridID() == hybrid){
+            for (TestRunSvtChannel channel : this.getObjects()) {
+                if (channel.getFpgaID() == fpga && channel.getHybridID() == hybrid) {
                     channels.add(channel);
                 }
             }
             return channels;
         }
     }
-    
+
     /**
      * Get the FPGA ID.
      * 
      * @return The FPGA ID
      */
-    public int getFpgaID(){
+    public int getFpgaID() {
         return getFieldValue("fpga");
     }
-   
+
     /**
      * Get the hybrid ID.
      * 
      * @return The hybrid ID.
      */
-    public int getHybridID(){
+    public int getHybridID() {
         return getFieldValue("hybrid");
     }
 
@@ -48,12 +47,9 @@
      * @return This object as a string.
      */
     public String toString() {
-        return "channel_id: " + getChannelID() +
-               ", fpga: " + getFpgaID() + 
-               ", hybrid: " + getHybridID() +
-               ", channel: " + getChannel();
+        return "channel_id: " + getChannelID() + ", fpga: " + getFpgaID() + ", hybrid: " + getHybridID() + ", channel: " + getChannel();
     }
-    
+
     /**
      * Implementation of equals.
      * @return True if the object equals this one; false if not.
@@ -66,9 +62,6 @@
         if (o == this)
             return true;
         TestRunSvtChannel channel = (TestRunSvtChannel) o;
-        return getChannelID() == channel.getChannelID() 
-                && getFpgaID() == channel.getFpgaID() 
-                && getHybridID() == channel.getHybridID() 
-                && getChannel() == channel.getChannel();
+        return getChannelID() == channel.getChannelID() && getFpgaID() == channel.getFpgaID() && getHybridID() == channel.getHybridID() && getChannel() == channel.getChannel();
     }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditions.java	Mon Nov 10 00:16:49 2014
@@ -9,18 +9,19 @@
 import static org.hps.conditions.svt.SvtChannel.MAX_NUMBER_OF_SAMPLES;
 
 /**
- * This class contains all test run SVT conditions data by readout channel. 
+ * 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)}
- * method.
+ * lookup the conditions using the
+ * {@link #getChannelConstants(TestRunSvtChannel)} method.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 public class TestRunSvtConditions extends AbstractSvtConditions {
 
-	/**
-     * Get the {@link TestRunSvtDaqMappingCollection} associated with these conditions.
+    /**
+     * Get the {@link TestRunSvtDaqMappingCollection} associated with these
+     * conditions.
      * 
      * @return The SVT DAQ map.
      */
@@ -40,24 +41,25 @@
     }
 
     /**
-     * Get the {@link TestRunSvtT0ShiftCollection} associated with these conditions.
+     * Get the {@link TestRunSvtT0ShiftCollection} associated with these
+     * conditions.
      * 
      * @return The {@link TestRunSvtT0ShiftCollection}
      */
     @Override
-    public TestRunSvtT0ShiftCollection getT0Shifts() { 
-    	return (TestRunSvtT0ShiftCollection) t0Shifts;
+    public TestRunSvtT0ShiftCollection getT0Shifts() {
+        return (TestRunSvtT0ShiftCollection) t0Shifts;
     }
-    
+
     /**
-     * Convert this object to a human readable string. This method prints a formatted
-     * table of channel data independently of how its member objects implement their
-     * string conversion method. For now, it does not print the time shifts by sensor as
-     * all other information is by channel.
+     * Convert this object to a human readable string. This method prints a
+     * formatted table of channel data independently of how its member objects
+     * implement their string conversion method. For now, it does not print the
+     * time shifts by sensor as all other information is by channel.
      * 
-     * @return This object converted to a string, without the DAQ map.
-     * TODO: Make this look more human readable.  At the moment, reading this
-     * 		 requires a huge terminal window.
+     * @return This object converted to a string, without the DAQ map. TODO:
+     *         Make this look more human readable. At the moment, reading this
+     *         requires a huge terminal window.
      */
     public String toString() {
         StringBuffer buff = new StringBuffer();
@@ -120,7 +122,7 @@
         for (TestRunSvtChannel channel : this.getChannelMap().getObjects()) {
 
             System.out.println("Channel: " + channel.toString());
-            
+
             // Get the conditions for the channel.
             ChannelConstants constants = getChannelConstants(channel);
             SvtGain gain = constants.getGain();
@@ -131,13 +133,13 @@
             buff.append(String.format("%-6d %-5d %-8d %-8d ", channel.getChannelID(), channel.getFpgaID(), channel.getHybridID(), channel.getChannel()));
 
             // Calibration.
-            for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-            	buff.append(calibration.getPedestal(sample));
-            	buff.append("      ");
+            for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+                buff.append(calibration.getPedestal(sample));
+                buff.append("      ");
             }
-            for(int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++){
-            	buff.append(calibration.getNoise(sample));
-            	buff.append("      ");
+            for (int sample = 0; sample < MAX_NUMBER_OF_SAMPLES; sample++) {
+                buff.append(calibration.getNoise(sample));
+                buff.append("      ");
             }
 
             // Gain.
@@ -161,5 +163,4 @@
         return buff.toString();
     }
 
-
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditionsConverter.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditionsConverter.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtConditionsConverter.java	Mon Nov 10 00:16:49 2014
@@ -8,9 +8,8 @@
 
 public final class TestRunSvtConditionsConverter extends AbstractSvtConditionsConverter<TestRunSvtConditions> {
 
-   
-    public TestRunSvtConditionsConverter(){
-        this.conditions = new TestRunSvtConditions(); 
+    public TestRunSvtConditionsConverter() {
+        this.conditions = new TestRunSvtConditions();
     }
 
     /**
@@ -20,20 +19,21 @@
      * @param name The conditions key, which is ignored for now.
      */
     @Override
-    public TestRunSvtConditions getData(ConditionsManager manager, String name){
-        
+    public TestRunSvtConditions getData(ConditionsManager manager, String name) {
+
         DatabaseConditionsManager dbConditionsManager = (DatabaseConditionsManager) manager;
-       
-    	// Get the channel map from the conditions database
+
+        // Get the channel map from the conditions database
         TestRunSvtChannelCollection channels = dbConditionsManager.getCollection(TestRunSvtChannelCollection.class);
 
-        // Create the SVT conditions object to use to encapsulate SVT condition collections
+        // Create the SVT conditions object to use to encapsulate SVT condition
+        // collections
         conditions.setChannelMap(channels);
-        
+
         // Get the DAQ map from the conditions database
         TestRunSvtDaqMappingCollection daqMap = dbConditionsManager.getCollection(TestRunSvtDaqMappingCollection.class);
         conditions.setDaqMap(daqMap);
-        
+
         // Get the collection of T0 shifts from the conditions database
         TestRunSvtT0ShiftCollection t0Shifts = dbConditionsManager.getCollection(TestRunSvtT0ShiftCollection.class);
         conditions.setT0Shifts(t0Shifts);
@@ -42,14 +42,13 @@
 
         return conditions;
     }
-   
-   
+
     /**
      * Get the type handled by this converter.
      * @return The type handled by this converter.
      */
-	@Override
-	public Class<TestRunSvtConditions> getType() {
-		return TestRunSvtConditions.class;
-	}
+    @Override
+    public Class<TestRunSvtConditions> getType() {
+        return TestRunSvtConditions.class;
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDaqMapping.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDaqMapping.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDaqMapping.java	Mon Nov 10 00:16:49 2014
@@ -12,60 +12,55 @@
  */
 public class TestRunSvtDaqMapping extends AbstractSvtDaqMapping {
 
-	public static class TestRunSvtDaqMappingCollection 
-	    extends AbstractSvtDaqMappingCollection<TestRunSvtDaqMapping> {
-	
+    public static class TestRunSvtDaqMappingCollection extends AbstractSvtDaqMappingCollection<TestRunSvtDaqMapping> {
+
         /**
-		 * Get a test run DAQ pair (FPGA and Hybrid ID) for the given 
-		 * {@linkplain HpsTestRunSiSensor}
-		 * 
-		 * @param  sensor A sensor of type {@link HpsTestRunSiSensor}
-		 * @return The DAQ pair associated with the sensor 
-		 */
-		public Pair<Integer, Integer> getDaqPair(HpsSiSensor sensor){
-			
-			String svtHalf = sensor.isTopLayer() ? TOP_HALF : BOTTOM_HALF; 
-			for(TestRunSvtDaqMapping daqMapping : this.getObjects()){
-				
-				if(svtHalf.equals(daqMapping.getSvtHalf())
-						&& daqMapping.getLayerNumber() == sensor.getLayerNumber()){
-					
-					return new Pair<Integer, Integer>(daqMapping.getFpgaID(), 
-													  daqMapping.getHybridID());
-				}
-			}
-			return null;
-		}
-		
+         * Get a test run DAQ pair (FPGA and Hybrid ID) for the given
+         * {@linkplain HpsTestRunSiSensor}
+         * 
+         * @param sensor A sensor of type {@link HpsTestRunSiSensor}
+         * @return The DAQ pair associated with the sensor
+         */
+        public Pair<Integer, Integer> getDaqPair(HpsSiSensor sensor) {
+
+            String svtHalf = sensor.isTopLayer() ? TOP_HALF : BOTTOM_HALF;
+            for (TestRunSvtDaqMapping daqMapping : this.getObjects()) {
+
+                if (svtHalf.equals(daqMapping.getSvtHalf()) && daqMapping.getLayerNumber() == sensor.getLayerNumber()) {
+
+                    return new Pair<Integer, Integer>(daqMapping.getFpgaID(), daqMapping.getHybridID());
+                }
+            }
+            return null;
+        }
+
         /**
-         * Get the orientation of a sensor using the FPGA and Hybrid ID.
-         * If the FPGA and Hybrid ID combination is not found, return null.
+         * Get the orientation of a sensor using the FPGA and Hybrid ID. If the
+         * FPGA and Hybrid ID combination is not found, return null.
          * 
          * @param daqPair (Pair<FPGA ID, Hybrid ID>) for a given sensor
-         * @return If a daqPair is found, return an "A" if the sensor 
-         * 		   orientation is Axial, an "S" if the orientation is Stereo or
-         * 		   null if the daqPair doesn't exist.
+         * @return If a daqPair is found, return an "A" if the sensor
+         *         orientation is Axial, an "S" if the orientation is Stereo or
+         *         null if the daqPair doesn't exist.
          */
-        public String getOrientation(Pair<Integer, Integer> daqPair){
-        	
-        	for(TestRunSvtDaqMapping daqMapping : this.getObjects()){
-        		
-        		if(daqPair.getFirstElement() == ((TestRunSvtDaqMapping) daqMapping).getFpgaID()
-        				&& daqPair.getSecondElement() == ((TestRunSvtDaqMapping) daqMapping).getHybridID()){
-        			return daqMapping.getOrientation(); 
-        		}
-        	}
-        	return null;
+        public String getOrientation(Pair<Integer, Integer> daqPair) {
+
+            for (TestRunSvtDaqMapping daqMapping : this.getObjects()) {
+
+                if (daqPair.getFirstElement() == ((TestRunSvtDaqMapping) daqMapping).getFpgaID() && daqPair.getSecondElement() == ((TestRunSvtDaqMapping) daqMapping).getHybridID()) {
+                    return daqMapping.getOrientation();
+                }
+            }
+            return null;
         }
-		
-		
+
         /**
          * Convert {@link TestRunSvtDaqMapping} to a string.
          * @return This object converted to a string.
          */
         public String toString() {
-        	StringBuffer buffer = new StringBuffer(); 
-        	buffer.append("FPGA ID: ");
+            StringBuffer buffer = new StringBuffer();
+            buffer.append("FPGA ID: ");
             buffer.append(" ");
             buffer.append("Hybrid ID: ");
             buffer.append(" ");
@@ -78,11 +73,11 @@
             buffer.append('\n');
             buffer.append("----------------------");
             buffer.append('\n');
-            for (TestRunSvtDaqMapping daqMapping : getObjects()){
-            	TestRunSvtDaqMapping testRunDaqMapping = (TestRunSvtDaqMapping) daqMapping; 
-            	buffer.append(testRunDaqMapping.getFpgaID());
+            for (TestRunSvtDaqMapping daqMapping : getObjects()) {
+                TestRunSvtDaqMapping testRunDaqMapping = (TestRunSvtDaqMapping) daqMapping;
+                buffer.append(testRunDaqMapping.getFpgaID());
                 buffer.append("    ");
-            	buffer.append(testRunDaqMapping.getHybridID());
+                buffer.append(testRunDaqMapping.getHybridID());
                 buffer.append("    ");
                 buffer.append(testRunDaqMapping.getSvtHalf());
                 buffer.append("    ");
@@ -92,15 +87,15 @@
                 buffer.append("    ");
                 buffer.append('\n');
             }
-        	return buffer.toString();
+            return buffer.toString();
         }
-	}
-	
-	public int getFpgaID(){
-		return getFieldValue("fpga");
-	}
-	
-	public int getHybridID(){
-		return getFieldValue("hybrid");
-	}
+    }
+
+    public int getFpgaID() {
+        return getFieldValue("fpga");
+    }
+
+    public int getHybridID() {
+        return getFieldValue("hybrid");
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDetectorSetup.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDetectorSetup.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtDetectorSetup.java	Mon Nov 10 00:16:49 2014
@@ -12,7 +12,7 @@
 import org.hps.util.Pair;
 
 /**
- * This class puts {@link TestRunSvtConditions} data onto 
+ * This class puts {@link TestRunSvtConditions} data onto
  * <code>HpsTestRunSiSensor</code> objects.
  *
  * @author Omar Moreno <[log in to unmask]>
@@ -22,85 +22,84 @@
     /**
      * Load conditions data onto a detector object.
      * 
-     * @param  The detector object.
+     * @param The detector object.
      * @param conditions The conditions object.
      */
-	public void load(Subdetector subdetector, TestRunSvtConditions conditions){
-	
+    public void load(Subdetector subdetector, TestRunSvtConditions conditions) {
+
         // Find sensor objects.
-    	List<HpsSiSensor> sensors = subdetector.getDetectorElement().findDescendants(HpsSiSensor.class);
-    	TestRunSvtChannelCollection channelMap = conditions.getChannelMap();
+        List<HpsSiSensor> sensors = subdetector.getDetectorElement().findDescendants(HpsSiSensor.class);
+        TestRunSvtChannelCollection channelMap = conditions.getChannelMap();
         TestRunSvtDaqMappingCollection daqMap = conditions.getDaqMap();
         TestRunSvtT0ShiftCollection t0Shifts = conditions.getT0Shifts();
-		
+
         // Loop over sensors.
-        for(HpsSiSensor sensor : sensors){
-        	
+        for (HpsSiSensor sensor : sensors) {
+
             // Reset possible existing conditions data on sensor.
             sensor.reset();
-        
+
             // Get DAQ pair (FPGA ID, Hybrid ID) corresponding to this sensor
             Pair<Integer, Integer> daqPair = daqMap.getDaqPair(sensor);
             if (daqPair == null) {
                 throw new RuntimeException("Failed to find DAQ pair for sensor: " + sensor.getName());
             }
-           
+
             // Set the FPGA ID of the sensor
             ((HpsTestRunSiSensor) sensor).setFpgaID(daqPair.getFirstElement());
-        
+
             // Set the hybrid ID of the sensor
             ((HpsTestRunSiSensor) sensor).setHybridID(daqPair.getSecondElement());
-            
+
             // Set the orientation of the sensor
             String orientation = daqMap.getOrientation(daqPair);
-            if(orientation != null && orientation.contentEquals(TestRunSvtDaqMappingCollection.AXIAL)){
-            	sensor.setAxial(true);
-            } else if(orientation != null && orientation.contains(TestRunSvtDaqMappingCollection.STEREO)){
-            	sensor.setStereo(true);
+            if (orientation != null && orientation.contentEquals(TestRunSvtDaqMappingCollection.AXIAL)) {
+                sensor.setAxial(true);
+            } else if (orientation != null && orientation.contains(TestRunSvtDaqMappingCollection.STEREO)) {
+                sensor.setStereo(true);
             }
-        
+
             // Find all the channels for this sensor.
             Collection<TestRunSvtChannel> channels = channelMap.find(daqPair);
-       
-            
+
             // Loop over the channels of the sensor.
             for (TestRunSvtChannel channel : channels) {
-            
-            	// Get conditions data for this channel.
+
+                // Get conditions data for this channel.
                 ChannelConstants constants = conditions.getChannelConstants(channel);
                 int channelNumber = channel.getChannel();
-            
+
                 //
                 // Set conditions data for this channel on the sensor object:
                 //
-                
+
                 // Check if the channel was flagged as bad
                 if (constants.isBadChannel()) {
                     sensor.setBadChannel(channelNumber);
                 }
-                
-                // Set the pedestal and noise of each of the samples for the 
+
+                // Set the pedestal and noise of each of the samples for the
                 // channel
                 double[] pedestal = new double[6];
                 double[] noise = new double[6];
-                for(int sampleN = 0; sampleN < HpsTestRunSiSensor.NUMBER_OF_SAMPLES; sampleN++){
-                	pedestal[sampleN] = constants.getCalibration().getPedestal(sampleN);
-                	noise[sampleN] = constants.getCalibration().getNoise(sampleN);
+                for (int sampleN = 0; sampleN < HpsTestRunSiSensor.NUMBER_OF_SAMPLES; sampleN++) {
+                    pedestal[sampleN] = constants.getCalibration().getPedestal(sampleN);
+                    noise[sampleN] = constants.getCalibration().getNoise(sampleN);
                 }
                 sensor.setPedestal(channelNumber, pedestal);
                 sensor.setNoise(channelNumber, noise);
-               
+
                 // Set the gain and offset for the channel
                 sensor.setGain(channelNumber, constants.getGain().getGain());
                 sensor.setOffset(channelNumber, constants.getGain().getOffset());
-               
+
                 // Set the shape fit parameters
                 sensor.setShapeFitParameters(channelNumber, constants.getShapeFitParameters().toArray());
             }
-            
+
             // Set the t0 shift for the sensor.
             TestRunSvtT0Shift sensorT0Shift = t0Shifts.getT0Shift(daqPair);
             sensor.setT0Shift(sensorT0Shift.getT0Shift());
         }
-	}
+    }
 }

Modified: java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java
 =============================================================================
--- java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java	(original)
+++ java/trunk/conditions/src/main/java/org/hps/conditions/svt/TestRunSvtT0Shift.java	Mon Nov 10 00:16:49 2014
@@ -3,26 +3,26 @@
 import org.hps.util.Pair;
 
 /**
- * This class is a container that allows associating a t0 shift with a specific 
+ * This class is a container that allows associating a t0 shift with a specific
  * sensor by FPGA ID and hybrid ID.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public final class TestRunSvtT0Shift extends AbstractSvtT0Shift {
 
-	public static class TestRunSvtT0ShiftCollection
-			extends AbstractSvtT0Shift.AbstractSvtT0ShiftCollection<TestRunSvtT0Shift> {
+    public static class TestRunSvtT0ShiftCollection extends AbstractSvtT0Shift.AbstractSvtT0ShiftCollection<TestRunSvtT0Shift> {
 
         /**
          * Get the {@link TestRunSvtT0Shift} associated with a given DAQ pair
          * 
          * @param DAQ pair for a given sensor
-         * @return The {@link TestRunSvtT0Shift} associated with the DAQ pair.  If a t0 shift
-         *         for a given DAQ pair can't be found, it returns null.
+         * @return The {@link TestRunSvtT0Shift} associated with the DAQ pair.
+         *         If a t0 shift for a given DAQ pair can't be found, it returns
+         *         null.
          */
-		@Override
-		public TestRunSvtT0Shift getT0Shift(Pair<Integer, Integer> pair) {
-	
+        @Override
+        public TestRunSvtT0Shift getT0Shift(Pair<Integer, Integer> pair) {
+
             int fpgaID = pair.getFirstElement();
             int hybridID = pair.getSecondElement();
             for (TestRunSvtT0Shift t0Shift : this.getObjects()) {
@@ -31,24 +31,24 @@
                 }
             }
             return null;
-		} 
-	}
-	
-	/**
-	 * Get the FPGA ID.
-	 * 
-	 * @return The FPGA ID.
-	 */
-	int getFpgaID() { 
-		return getFieldValue("fpga");
-	}
-	
-	/**
-	 * Get the hybrid ID.
-	 * 
-	 * @return The hybrid ID. 
-	 */
-	int getHybridID() { 
-		return getFieldValue("hybrid");
-	}
+        }
+    }
+
+    /**
+     * Get the FPGA ID.
+     * 
+     * @return The FPGA ID.
+     */
+    int getFpgaID() {
+        return getFieldValue("fpga");
+    }
+
+    /**
+     * Get the hybrid ID.
+     * 
+     * @return The hybrid ID.
+     */
+    int getHybridID() {
+        return getFieldValue("hybrid");
+    }
 }

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsDriverTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsDriverTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsDriverTest.java	Mon Nov 10 00:16:49 2014
@@ -15,13 +15,15 @@
 import org.lcsim.util.loop.LCSimLoop;
 
 /**
- * This class tests that {@link org.lcsim.hps.conditions.TestRunConditionsDriver} works correctly
- * by checking the number of runs it processes.
+ * This class tests that
+ * {@link org.lcsim.hps.conditions.TestRunConditionsDriver} works correctly by
+ * checking the number of runs it processes.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class ConditionsDriverTest extends TestCase {
 
-    // This test file has a few events from each of the "good runs" of the 2012 Test Run.
+    // This test file has a few events from each of the "good runs" of the 2012
+    // Test Run.
     private static final String fileLocation = "http://www.lcsim.org/test/hps-java/ConditionsTest.slcio";
 
     // Number of runs that should be processed in the job.

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java	Mon Nov 10 00:16:49 2014
@@ -6,18 +6,19 @@
 import org.hps.conditions.svt.SvtGain.SvtGainCollection;
 
 /**
- * Test some basic operations of {@link org.hps.conditions.ConditionsObject} using the
- * {@link org.hps.conditions.svt.SvtGain} type.
+ * Test some basic operations of {@link org.hps.conditions.ConditionsObject}
+ * using the {@link org.hps.conditions.svt.SvtGain} type.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class ConditionsObjectTest extends TestCase {
 
     public void testBasicOperations() throws ConditionsObjectException {
-    	
+
         DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
 
-        // Create a new collection, setting its table meta data and collection ID.
+        // Create a new collection, setting its table meta data and collection
+        // ID.
         TableMetaData tableMetaData = conditionsManager.findTableMetaData(TableConstants.SVT_GAINS);
         int collectionId = conditionsManager.getNextCollectionID(tableMetaData.getTableName());
         SvtGainCollection collection = new SvtGainCollection();

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/beam/BeamCurrentTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/beam/BeamCurrentTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/beam/BeamCurrentTest.java	Mon Nov 10 00:16:49 2014
@@ -73,8 +73,8 @@
         int currentRun = Integer.MIN_VALUE;
 
         /**
-         * This method will check the beam current against the answer key for the first
-         * event of a new run.
+         * This method will check the beam current against the answer key for
+         * the first event of a new run.
          */
         public void process(EventHeader event) {
             if (currentRun != event.getRunNumber()) {

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java	Mon Nov 10 00:16:49 2014
@@ -12,17 +12,17 @@
 public class EcalConditionsConverterTest extends TestCase {
 
     DatabaseConditionsManager conditionsManager;
-    
-    public void setUp() {                
+
+    public void setUp() {
         conditionsManager = DatabaseConditionsManager.getInstance();
         try {
-			conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
-		} catch (ConditionsNotFoundException e) {
-			throw new RuntimeException(e);
-		}
+            conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
+        } catch (ConditionsNotFoundException e) {
+            throw new RuntimeException(e);
+        }
     }
 
-    public void test() {       
+    public void test() {
         // Test that the manager gets ECAL conditions.
         EcalConditions conditions = conditionsManager.getCachedConditions(EcalConditions.class, "ecal_conditions").getCachedData();
         assertNotNull(conditions);

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalDetectorSetupTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalDetectorSetupTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/ecal/EcalDetectorSetupTest.java	Mon Nov 10 00:16:49 2014
@@ -9,8 +9,8 @@
 import org.lcsim.geometry.Detector;
 
 /**
- * This test loads ECal conditions data onto a Test Run detector and checks some of the results
- * for basic validity.
+ * This test loads ECal conditions data onto a Test Run detector and checks some
+ * of the results for basic validity.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  */
@@ -34,7 +34,8 @@
     private static final int CRYSTAL_COUNT = 442;
 
     /**
-     * Load SVT conditions data onto the detector and perform basic checks afterwards.
+     * Load SVT conditions data onto the detector and perform basic checks
+     * afterwards.
      */
     public void testLoad() throws Exception {
 

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtBadChannelTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtBadChannelTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtBadChannelTest.java	Mon Nov 10 00:16:49 2014
@@ -19,12 +19,14 @@
 import org.lcsim.util.loop.LCSimLoop;
 
 /**
- * This class tests that the correct bad channel conditions are found for the test run.
+ * This class tests that the correct bad channel conditions are found for the
+ * test run.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class SvtBadChannelTest extends TestCase {
 
-    // This test file has a few events from each of the "good runs" of the 2012 Test Run.
+    // This test file has a few events from each of the "good runs" of the 2012
+    // Test Run.
     private static final String TEST_FILE_URL = "http://www.lcsim.org/test/hps/conditions_test.slcio";
 
     // This is the number of bad channels in the QA set across all runs.
@@ -68,7 +70,8 @@
     }
 
     /**
-     * This Driver will check the number of bad channels for a run against the answer key.
+     * This Driver will check the number of bad channels for a run against the
+     * answer key.
      * @author Jeremy McCormick <[log in to unmask]>
      */
     class SvtBadChannelChecker extends Driver {
@@ -76,8 +79,8 @@
         int _currentRun = -1;
 
         /**
-         * This method will check the number of bad channels against the answer key for
-         * the first event of a new run.
+         * This method will check the number of bad channels against the answer
+         * key for the first event of a new run.
          */
         public void process(EventHeader event) {
             int run = event.getRunNumber();

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtConfigurationTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtConfigurationTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtConfigurationTest.java	Mon Nov 10 00:16:49 2014
@@ -13,11 +13,11 @@
 public class SvtConfigurationTest extends TestCase {
 
     DatabaseConditionsManager manager;
-    
+
     public void testSvtConfiguration() {
-    	DatabaseConditionsManager manager = DatabaseConditionsManager.getInstance();
+        DatabaseConditionsManager manager = DatabaseConditionsManager.getInstance();
         SvtConfigurationCollection collection = manager.getCachedConditions(SvtConfigurationCollection.class, TableConstants.SVT_CONFIGURATIONS).getCachedData();
-        
+
         for (SvtConfiguration config : collection) {
             Document doc = null;
             try {
@@ -28,5 +28,5 @@
             System.out.println(doc.toString());
         }
     }
-    
+
 }

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDaqMappingTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDaqMappingTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDaqMappingTest.java	Mon Nov 10 00:16:49 2014
@@ -7,54 +7,52 @@
 import org.hps.conditions.svt.SvtDaqMapping.SvtDaqMappingCollection;
 
 /**
- * This test checks if the SVT DAQ map was loaded with reasonable values and
- * is being read correctly from the conditions database.
+ * This test checks if the SVT DAQ map was loaded with reasonable values and is
+ * being read correctly from the conditions database.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public class SvtDaqMappingTest extends TestCase {
-	
-	//--- Constants ---//
-	//-----------------//
-	
-	// Total number of SVT sensors
-	public static final int TOTAL_NUMBER_OF_SENSORS = 36;
-	// Min and max values of front end boad (FEB) hybrid ID's
-	public static final int MIN_FEB_HYBRID_ID = 0; 
-	public static final int MAX_FEB_HYBRID_ID = 3; 
-	
-	//-----------------//
 
+    // --- Constants ---//
+    // -----------------//
 
-	public void test() throws Exception {
-		
-		DatabaseConditionsManager conditionsManager = new DatabaseConditionsManager();
-		conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
-		
-		TableMetaData metaData = conditionsManager.findTableMetaData(SvtDaqMappingCollection.class);
-		SvtDaqMappingCollection daqMappingCollection 
-			= conditionsManager.getConditionsData(SvtDaqMappingCollection.class, metaData.getTableName());
-		
-		int totalSensors = 0; 
-		int febHybridID; 
-		this.printDebug("");
-		for(SvtDaqMapping daqMapping : daqMappingCollection){
-			
-			this.printDebug("Sensor: \n" + daqMapping.toString());
-			
-			// Check that the FEB Hybrid ID is within the allowable limits
-			febHybridID = daqMapping.getFebHybridID();
-			assertTrue("FEB Hybrid ID is out of range!.", febHybridID >= MIN_FEB_HYBRID_ID && febHybridID <= MAX_FEB_HYBRID_ID);
-			
-			totalSensors++;
-		}
-		
-		this.printDebug("Total number of sensors found: " + totalSensors);
-		assertTrue(totalSensors == TOTAL_NUMBER_OF_SENSORS);
-		
-	}
-	
-	private void printDebug(String debugMessage) {
-		System.out.println(this.getClass().getSimpleName() + ":: " + debugMessage);
-	}	
+    // Total number of SVT sensors
+    public static final int TOTAL_NUMBER_OF_SENSORS = 36;
+    // Min and max values of front end boad (FEB) hybrid ID's
+    public static final int MIN_FEB_HYBRID_ID = 0;
+    public static final int MAX_FEB_HYBRID_ID = 3;
+
+    // -----------------//
+
+    public void test() throws Exception {
+
+        DatabaseConditionsManager conditionsManager = new DatabaseConditionsManager();
+        conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
+
+        TableMetaData metaData = conditionsManager.findTableMetaData(SvtDaqMappingCollection.class);
+        SvtDaqMappingCollection daqMappingCollection = conditionsManager.getConditionsData(SvtDaqMappingCollection.class, metaData.getTableName());
+
+        int totalSensors = 0;
+        int febHybridID;
+        this.printDebug("");
+        for (SvtDaqMapping daqMapping : daqMappingCollection) {
+
+            this.printDebug("Sensor: \n" + daqMapping.toString());
+
+            // Check that the FEB Hybrid ID is within the allowable limits
+            febHybridID = daqMapping.getFebHybridID();
+            assertTrue("FEB Hybrid ID is out of range!.", febHybridID >= MIN_FEB_HYBRID_ID && febHybridID <= MAX_FEB_HYBRID_ID);
+
+            totalSensors++;
+        }
+
+        this.printDebug("Total number of sensors found: " + totalSensors);
+        assertTrue(totalSensors == TOTAL_NUMBER_OF_SENSORS);
+
+    }
+
+    private void printDebug(String debugMessage) {
+        System.out.println(this.getClass().getSimpleName() + ":: " + debugMessage);
+    }
 }

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDetectorSetupTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDetectorSetupTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/SvtDetectorSetupTest.java	Mon Nov 10 00:16:49 2014
@@ -9,39 +9,40 @@
 import org.lcsim.geometry.Detector;
 
 /**
- * This test loads {@link SvtConditions} data onto the detector and then checks that all
- * channels of each sensor have non-zero data values for applicable parameters.
+ * This test loads {@link SvtConditions} data onto the detector and then checks
+ * that all channels of each sensor have non-zero data values for applicable
+ * parameters.
  * 
  * @author Jeremy McCormick <[log in to unmask]>
  * @author Omar Moreno <[log in to unmask]>
  */
 // TODO: Update this test with more meaningful test.
 public class SvtDetectorSetupTest extends TestCase {
-	
-	
-	//--- Constants ---//
-	//-----------------//
-	// TODO: Move all of these constants to their own class
-	
-	// Total number of SVT sensors
-	public static final int TOTAL_NUMBER_OF_SENSORS = 36;	
-	// Max FEB ID 
-	public static final int MAX_FEB_ID = 9; 
-	// Max FEB Hybrid ID
-	public static final int MAX_FEB_HYBRID_ID = 3;
-	// Max channel number
-	public static final int MAX_CHANNEL_NUMBER = 639;
-	// SVT Subdetector name
-	public static final String SVT_SUBDETECTOR_NAME = "Tracker";
-	
+
+    // --- Constants ---//
+    // -----------------//
+    // TODO: Move all of these constants to their own class
+
+    // Total number of SVT sensors
+    public static final int TOTAL_NUMBER_OF_SENSORS = 36;
+    // Max FEB ID
+    public static final int MAX_FEB_ID = 9;
+    // Max FEB Hybrid ID
+    public static final int MAX_FEB_HYBRID_ID = 3;
+    // Max channel number
+    public static final int MAX_CHANNEL_NUMBER = 639;
+    // SVT Subdetector name
+    public static final String SVT_SUBDETECTOR_NAME = "Tracker";
+
     /**
-     * Load SVT conditions data onto the detector and perform basic checks afterwards.
+     * Load SVT conditions data onto the detector and perform basic checks
+     * afterwards.
      */
     public void test() throws Exception {
-    	
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
-    	
+
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.setDetector("HPS-Proposal2014-v7-2pt2", 0);
+
         // Get the detector.
         Detector detector = conditionsManager.getCachedConditions(Detector.class, "compact.xml").getCachedData();
 
@@ -54,51 +55,46 @@
 
         // Check sensor data.
         List<HpsSiSensor> sensors = detector.getSubdetector(SVT_SUBDETECTOR_NAME).getDetectorElement().findDescendants(HpsSiSensor.class);
-        
+
         // Check for correct number of sensors processed.
-		this.printDebug("Total number of sensors found: " + sensors.size());
-		assertTrue(sensors.size() == TOTAL_NUMBER_OF_SENSORS);
-        
+        this.printDebug("Total number of sensors found: " + sensors.size());
+        assertTrue(sensors.size() == TOTAL_NUMBER_OF_SENSORS);
+
         // Loop over sensors.
-        int totalSensors = 0; 
+        int totalSensors = 0;
         for (HpsSiSensor sensor : sensors) {
 
-        	int nChannels = sensor.getNumberOfChannels();
-        	assertTrue("The number of channels this sensor has is invalid", nChannels <= MAX_CHANNEL_NUMBER);
-        
-        	this.printDebug(sensor.toString());
-        	
-        	// Check that the FEB ID as within the appropriate range
+            int nChannels = sensor.getNumberOfChannels();
+            assertTrue("The number of channels this sensor has is invalid", nChannels <= MAX_CHANNEL_NUMBER);
+
+            this.printDebug(sensor.toString());
+
+            // Check that the FEB ID as within the appropriate range
             int febID = sensor.getFebID();
-            assertTrue("FEB ID is invalid.  The FEB ID should be less than " + MAX_FEB_ID,
-            		febID <= MAX_FEB_ID);
-            
+            assertTrue("FEB ID is invalid.  The FEB ID should be less than " + MAX_FEB_ID, febID <= MAX_FEB_ID);
+
             int febHybridID = sensor.getFebHybridID();
-            assertTrue("FEB Hybrid ID is invalid.  The FEB Hybrid ID should be less than " + MAX_FEB_HYBRID_ID,
-            		febHybridID <= MAX_FEB_HYBRID_ID);
-            
+            assertTrue("FEB Hybrid ID is invalid.  The FEB Hybrid ID should be less than " + MAX_FEB_HYBRID_ID, febHybridID <= MAX_FEB_HYBRID_ID);
+
             for (int channel = 0; channel < nChannels; channel++) {
-        
-            	//
+
+                //
                 // Check that channel conditions values are not zero
-            	//
-            	for(int sampleN = 0; sampleN < 6; sampleN++){
-            		assertTrue("Pedestal sample " + sampleN + " is zero.",
-            				sensor.getPedestal(channel, sampleN) != 0);
-            		assertTrue("Noise sample " + sampleN + " is zero.",
-            				sensor.getNoise(channel, sampleN) != 0);
-            	}
+                //
+                for (int sampleN = 0; sampleN < 6; sampleN++) {
+                    assertTrue("Pedestal sample " + sampleN + " is zero.", sensor.getPedestal(channel, sampleN) != 0);
+                    assertTrue("Noise sample " + sampleN + " is zero.", sensor.getNoise(channel, sampleN) != 0);
+                }
                 assertTrue("Gain is zero.", sensor.getGain(channel) != 0);
-                assertTrue("Shape fit parameters points to null.",
-                		sensor.getShapeFitParameters(channel) != null);
-                
+                assertTrue("Shape fit parameters points to null.", sensor.getShapeFitParameters(channel) != null);
+
             }
         }
-        
-        System.out.println("Successfully loaded conditions data onto " + totalSensors + " SVT sensors!"); 
+
+        System.out.println("Successfully loaded conditions data onto " + totalSensors + " SVT sensors!");
     }
 
-    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/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtConditionsConverterTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtConditionsConverterTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtConditionsConverterTest.java	Mon Nov 10 00:16:49 2014
@@ -5,17 +5,17 @@
 import org.hps.conditions.DatabaseConditionsManager;
 
 public class TestRunSvtConditionsConverterTest extends TestCase {
-   	
-	public void test() throws Exception {
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
-		conditionsManager.configure("/org/hps/conditions/config/conditions_database_testrun_2012.xml");
-		conditionsManager.setDetector("HPS-TestRun-v5", 1351);
-		
+
+    public void test() throws Exception {
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+        conditionsManager.configure("/org/hps/conditions/config/conditions_database_testrun_2012.xml");
+        conditionsManager.setDetector("HPS-TestRun-v5", 1351);
+
         TestRunSvtConditions svtConditions = conditionsManager.getCachedConditions(TestRunSvtConditions.class, "svt_conditions").getCachedData();
         assertNotNull(svtConditions);
         System.out.println("[ " + this.getClass().getSimpleName() + "]: Printing test run SVT conditions.");
         System.out.println(svtConditions);
         System.out.println("[ " + this.getClass().getSimpleName() + "]: Succussfully loaded test run SVT conditions");
-	}
-    
+    }
+
 }

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDaqMappingTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDaqMappingTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDaqMappingTest.java	Mon Nov 10 00:16:49 2014
@@ -7,69 +7,65 @@
 import org.hps.conditions.svt.TestRunSvtDaqMapping.TestRunSvtDaqMappingCollection;
 
 /**
- * This test checks if the test run SVT DAQ map was loaded with reasonable 
+ * This test checks if the test run SVT DAQ map was loaded with reasonable
  * values and is being read correctly from the conditions database.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public class TestRunSvtDaqMappingTest extends TestCase {
 
-	TableMetaData metaData = null;
-	
-	//--- Constants ---//
-	//-----------------//
-	
-	// Total number of SVT sensors
-	public static final int TOTAL_NUMBER_OF_SENSORS = 20;
-	// Min and max values of the FPGA ID's
-	public static final int MIN_FPGA_ID = 0; 
-	public static final int MAX_FPGA_ID = 6; 
-	// Min and max values of Hybrid ID's
-	public static final int MIN_HYBRID_ID = 0; 
-	public static final int MAX_HYBRID_ID = 2; 
-	// Min and max layer number values 
-	public static final int MIN_LAYER_NUMBER = 1; 
-	public static final int MAX_LAYER_NUMBER = 10; 
-		
-	public void test() throws Exception {
-		
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+    TableMetaData metaData = null;
+
+    // --- Constants ---//
+    // -----------------//
+
+    // Total number of SVT sensors
+    public static final int TOTAL_NUMBER_OF_SENSORS = 20;
+    // Min and max values of the FPGA ID's
+    public static final int MIN_FPGA_ID = 0;
+    public static final int MAX_FPGA_ID = 6;
+    // Min and max values of Hybrid ID's
+    public static final int MIN_HYBRID_ID = 0;
+    public static final int MAX_HYBRID_ID = 2;
+    // Min and max layer number values
+    public static final int MIN_LAYER_NUMBER = 1;
+    public static final int MAX_LAYER_NUMBER = 10;
+
+    public void test() throws Exception {
+
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
         conditionsManager.configure("/org/hps/conditions/config/conditions_database_testrun_2012.xml");
         conditionsManager.setDetector("HPS-TestRun-v5", 1351);
 
-		metaData = conditionsManager.findTableMetaData(TestRunSvtDaqMappingCollection.class);
-		TestRunSvtDaqMappingCollection daqMappingCollection = 
-				conditionsManager.getConditionsData(TestRunSvtDaqMappingCollection.class, metaData.getTableName());
-	
-		int totalSensors = 0; 
-		this.printDebug("");
-		for(TestRunSvtDaqMapping daqMapping : daqMappingCollection){
-			
-			this.printDebug("Sensor: \n" + daqMapping.toString());
-		
-			// Check that the FPGA ID is within the allowable limits
-			int fpgaID = daqMapping.getFpgaID();
-			assertTrue("FPGA ID " + fpgaID + " is out of range!",
-						fpgaID >= MIN_FPGA_ID && fpgaID <= MAX_FPGA_ID);
-			
-			// Check that the Hybrid ID is within the allowable limits
-			int hybridID = daqMapping.getHybridID();
-			assertTrue("Hybrid ID " + hybridID + " is out of range!",
-						hybridID >= MIN_HYBRID_ID && hybridID <= MAX_HYBRID_ID);
-			
-			// Check that the layer number is within the allowable limits
-			int layerNumber = daqMapping.getLayerNumber();
-			assertTrue("The layer number " + layerNumber + " is out of range!", 
-					layerNumber >= MIN_LAYER_NUMBER && layerNumber <= MAX_LAYER_NUMBER);
-			
-			totalSensors++;
-		}
-		
-		this.printDebug("Total number of sensors found: " + totalSensors);
-		assertTrue(totalSensors == TOTAL_NUMBER_OF_SENSORS);
-	}
+        metaData = conditionsManager.findTableMetaData(TestRunSvtDaqMappingCollection.class);
+        TestRunSvtDaqMappingCollection daqMappingCollection = conditionsManager.getConditionsData(TestRunSvtDaqMappingCollection.class, metaData.getTableName());
 
-	private void printDebug(String debugMessage) {
-		System.out.println("[ " + this.getClass().getSimpleName() + " ]: " + debugMessage);
-	}
+        int totalSensors = 0;
+        this.printDebug("");
+        for (TestRunSvtDaqMapping daqMapping : daqMappingCollection) {
+
+            this.printDebug("Sensor: \n" + daqMapping.toString());
+
+            // Check that the FPGA ID is within the allowable limits
+            int fpgaID = daqMapping.getFpgaID();
+            assertTrue("FPGA ID " + fpgaID + " is out of range!", fpgaID >= MIN_FPGA_ID && fpgaID <= MAX_FPGA_ID);
+
+            // Check that the Hybrid ID is within the allowable limits
+            int hybridID = daqMapping.getHybridID();
+            assertTrue("Hybrid ID " + hybridID + " is out of range!", hybridID >= MIN_HYBRID_ID && hybridID <= MAX_HYBRID_ID);
+
+            // Check that the layer number is within the allowable limits
+            int layerNumber = daqMapping.getLayerNumber();
+            assertTrue("The layer number " + layerNumber + " is out of range!", layerNumber >= MIN_LAYER_NUMBER && layerNumber <= MAX_LAYER_NUMBER);
+
+            totalSensors++;
+        }
+
+        this.printDebug("Total number of sensors found: " + totalSensors);
+        assertTrue(totalSensors == TOTAL_NUMBER_OF_SENSORS);
+    }
+
+    private void printDebug(String debugMessage) {
+        System.out.println("[ " + this.getClass().getSimpleName() + " ]: " + debugMessage);
+    }
 }

Modified: java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDetectorSetupTest.java
 =============================================================================
--- java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDetectorSetupTest.java	(original)
+++ java/trunk/conditions/src/test/java/org/hps/conditions/svt/TestRunSvtDetectorSetupTest.java	Mon Nov 10 00:16:49 2014
@@ -9,95 +9,91 @@
 import org.lcsim.geometry.Detector;
 
 /**
- * This test loads {@link TestRunSvtConditions} data onto the detector and then checks that all
- * channels of each sensor have non-zero data values for applicable parameters.
+ * This test loads {@link TestRunSvtConditions} data onto the detector and then
+ * checks that all channels of each sensor have non-zero data values for
+ * applicable parameters.
  * 
  * @author Omar Moreno <[log in to unmask]>
  */
 public class TestRunSvtDetectorSetupTest extends TestCase {
 
-	//--- Constants ---//
-	//-----------------//
-	// TODO: Move all of these constants to their own class
-	
-	// Total number of SVT sensors
-	public static final int TOTAL_NUMBER_OF_SENSORS = 20;	
-	// Max FEB ID 
-	public static final int MAX_FPGA_ID = 6; 
-	// Max FEB Hybrid ID
-	public static final int MAX_HYBRID_ID = 2;
-	// Max channel number
-	public static final int MAX_CHANNEL_NUMBER = 639;
-	// SVT Subdetector name
-	public static final String SVT_SUBDETECTOR_NAME = "Tracker";
-		
+    // --- Constants ---//
+    // -----------------//
+    // TODO: Move all of these constants to their own class
+
+    // Total number of SVT sensors
+    public static final int TOTAL_NUMBER_OF_SENSORS = 20;
+    // Max FEB ID
+    public static final int MAX_FPGA_ID = 6;
+    // Max FEB Hybrid ID
+    public static final int MAX_HYBRID_ID = 2;
+    // Max channel number
+    public static final int MAX_CHANNEL_NUMBER = 639;
+    // SVT Subdetector name
+    public static final String SVT_SUBDETECTOR_NAME = "Tracker";
+
     /**
-     * Load SVT conditions data onto the detector and perform basic checks afterwards.
+     * Load SVT conditions data onto the detector and perform basic checks
+     * afterwards.
      */
-	public void test() throws Exception { 
-     
-		DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
+    public void test() throws Exception {
+
+        DatabaseConditionsManager conditionsManager = DatabaseConditionsManager.getInstance();
         conditionsManager.configure("/org/hps/conditions/config/conditions_database_testrun_2012.xml");
-		conditionsManager.setDetector("HPS-TestRun-v5", 1351);
-	
+        conditionsManager.setDetector("HPS-TestRun-v5", 1351);
+
         // Get the detector.
         Detector detector = conditionsManager.getCachedConditions(Detector.class, "compact.xml").getCachedData();
-	
+
         // Get all test run SVT conditions.
         TestRunSvtConditions conditions = conditionsManager.getCachedConditions(TestRunSvtConditions.class, "svt_conditions").getCachedData();
-	
+
         // Load the test run SVT conditions onto detector.
         TestRunSvtDetectorSetup loader = new TestRunSvtDetectorSetup();
         loader.load(detector.getSubdetector(SVT_SUBDETECTOR_NAME), conditions);
-        
+
         // Check sensor data.
         List<HpsTestRunSiSensor> sensors = detector.getSubdetector(SVT_SUBDETECTOR_NAME).getDetectorElement().findDescendants(HpsTestRunSiSensor.class);
-        
+
         // Check for correct number of sensors processed.
-		this.printDebug("Total number of sensors found: " + sensors.size());
-		assertTrue(sensors.size() == TOTAL_NUMBER_OF_SENSORS);
-        
-        
+        this.printDebug("Total number of sensors found: " + sensors.size());
+        assertTrue(sensors.size() == TOTAL_NUMBER_OF_SENSORS);
+
         // Loop over sensors.
-        int totalSensors = 0; 
+        int totalSensors = 0;
         for (HpsTestRunSiSensor sensor : sensors) {
-        	
-        	int nChannels = sensor.getNumberOfChannels();
-        	assertTrue("The number of channels this sensor has is invalid", nChannels <= MAX_CHANNEL_NUMBER);
-        
-        	this.printDebug(sensor.toString());
-        	
-        	// Check that the FEB ID as within the appropriate range
+
+            int nChannels = sensor.getNumberOfChannels();
+            assertTrue("The number of channels this sensor has is invalid", nChannels <= MAX_CHANNEL_NUMBER);
+
+            this.printDebug(sensor.toString());
+
+            // Check that the FEB ID as within the appropriate range
             int fpgaID = sensor.getFpgaID();
-            assertTrue("FPGA ID is invalid.  The FPGA ID should be less than " + MAX_FPGA_ID,
-            		fpgaID <= MAX_FPGA_ID);
-            
+            assertTrue("FPGA ID is invalid.  The FPGA ID should be less than " + MAX_FPGA_ID, fpgaID <= MAX_FPGA_ID);
+
             int hybridID = sensor.getHybridID();
-            assertTrue("Hybrid ID is invalid.  The Hybrid ID should be less than " + MAX_HYBRID_ID,
-            		hybridID <= MAX_HYBRID_ID);
+            assertTrue("Hybrid ID is invalid.  The Hybrid ID should be less than " + MAX_HYBRID_ID, hybridID <= MAX_HYBRID_ID);
 
             for (int channel = 0; channel < nChannels; channel++) {
 
-            	//
+                //
                 // Check that channel conditions values are not zero
-            	//
-            	for(int sampleN = 0; sampleN < 6; sampleN++){
-            		assertTrue("Pedestal sample " + sampleN + " is zero.",
-            				sensor.getPedestal(channel, sampleN) != 0);
-            		assertTrue("Noise sample " + sampleN + " is zero.",
-            				sensor.getNoise(channel, sampleN) != 0);
-            	}
+                //
+                for (int sampleN = 0; sampleN < 6; sampleN++) {
+                    assertTrue("Pedestal sample " + sampleN + " is zero.", sensor.getPedestal(channel, sampleN) != 0);
+                    assertTrue("Noise sample " + sampleN + " is zero.", sensor.getNoise(channel, sampleN) != 0);
+                }
                 assertTrue("Gain is zero.", sensor.getGain(channel) != 0);
-                assertTrue("Shape fit parameters points to null.",
-                		sensor.getShapeFitParameters(channel) != null);
-            	
+                assertTrue("Shape fit parameters points to null.", sensor.getShapeFitParameters(channel) != null);
+
             }
         }
-        System.out.println("Successfully loaded test run conditions data onto " + totalSensors + " SVT sensors!"); 
-	}
+        System.out.println("Successfully loaded test run conditions data onto " + totalSensors + " SVT sensors!");
+    }
 
-	private void printDebug(String debugMessage){
-		System.out.println(this.getClass().getSimpleName() + ":: " + debugMessage);
-	}
-	
+    private void printDebug(String debugMessage) {
+        System.out.println(this.getClass().getSimpleName() + ":: " + debugMessage);
+    }
+
 }

Top of Message | Previous Page | Permalink

Advanced Options


Options

Log In

Log In

Get Password

Get Password


Search Archives

Search Archives


Subscribe or Unsubscribe

Subscribe or Unsubscribe


Archives

November 2017
August 2017
July 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013

ATOM RSS1 RSS2



LISTSERV.SLAC.STANFORD.EDU

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager

Privacy Notice, Security Notice and Terms of Use