Commit in hps-java/src/main/java/org/lcsim/hps/conditions on MAIN
ecal/EcalChannel.java+351.1 -> 1.2
    /EcalChannelConverter.java+131.1 -> 1.2
    /EcalConditions.java+53-61.1 -> 1.2
    /EcalConditionsLoader.java+13-11.1 -> 1.2
    /EcalGain.java+28-31.1 -> 1.2
    /EcalGainCollection.java+1-31.1 -> 1.2
    /EcalGainConverter.java+13-111.1 -> 1.2
svt/SvtConditions.java+6-11.5 -> 1.6
   /SvtConditionsLoader.java+10-21.3 -> 1.4
+172-27
9 modified files
add doc

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalChannel.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalChannel.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalChannel.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -4,6 +4,9 @@
  * This class encapsulates all the information about a single ECal channel, e.g. one crystal.
  * This includes the ID from the conditions database; the crate, slot, and channel numbers
  * from the DAQ hardware; and the physical x and y values of the geometric crystal volumes. 
+ * Each of these three pieces of data specifies a unique channel, so the information is in 
+ * some sense redundant.  This class allows all these values to be associated by channel 
+ * in the same place.
  * @author Jeremy McCormick <[log in to unmask]>
  */
 public class EcalChannel {
@@ -32,30 +35,58 @@
         this.y = y;
     }
 
+    /**
+     * Get the crate number.
+     * @return The crate number.
+     */
     public int getCrate() {
         return crate;
     }
     
+    /**
+     * Get the slot number.
+     * @return The slot number.
+     */
     public int getSlot() {
         return slot;
     }
     
+    /**
+     * Get the channel number.
+     * @return The channel number.
+     */
     public int getChannel() {
         return channel;
     }
     
+    /**
+     * Get the x value.
+     * @return The x value.
+     */
     public int getX() {
         return x;
     }
     
+    /**
+     * Get the y value.
+     * @return The y value.
+     */
     public int getY() {
         return y;
     }
 
+    /**
+     * Get the ID.
+     * @return The ID of the channel.
+     */
     public int getId() {
         return id;
     }
     
+    /**
+     * Implementation of equals.
+     * @return True if objects are equal; false if not.
+     */
     public boolean equals(Object o) {
         if (o == null) {
             return false;
@@ -75,6 +106,10 @@
                 && c.getY() == y;
     }
     
+    /**
+     * Implement of string conversion.
+     * @return The string representation of this channel data.
+     */
     public String toString() {
         return "id: " + id 
                 + ", crate: " + crate 

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalChannelConverter.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalChannelConverter.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalChannelConverter.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -11,8 +11,17 @@
 import org.lcsim.hps.conditions.ConnectionManager;
 import org.lcsim.hps.conditions.DatabaseConditionsConverter;
 
+/**
+ * This class creates the {@link EcalChannelMap} from the conditions table containing the channel data.
+ * @author Jeremy McCormick <[log in to unmask]>
+ */
 public class EcalChannelConverter extends DatabaseConditionsConverter<EcalChannelMap> {
 
+    /**
+     * Load the data from the conditions database.
+     * @param manager The conditions manager.
+     * @param name The name of the conditions set. 
+     */
      public EcalChannelMap getData(ConditionsManager manager, String name) {
                   
          // Collection to be returned to caller.
@@ -72,6 +81,10 @@
          return channels;
     }
 
+     /**
+      * Get the type that this converter handles.
+      * @return The type handled by this converter.
+      */
     public Class<EcalChannelMap> getType() {
         return EcalChannelMap.class;
     }

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalConditions.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalConditions.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalConditions.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -1,11 +1,16 @@
 package org.lcsim.hps.conditions.ecal;
 
-import java.io.PrintStream;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
 
+/**
+ * This class allows accses to all ECal conditions from the database,
+ * including gain, pedestal and bad channel settings per crystal. 
+ * 
+ * @author Jeremy McCormick <[log in to unmask]>
+ */
 public class EcalConditions {
     
     EcalChannelMap channels = new EcalChannelMap();
@@ -13,56 +18,98 @@
     Map<EcalChannel, Double> gains = new HashMap<EcalChannel, Double>();
     Map<EcalChannel, Double> pedestals = new HashMap<EcalChannel, Double>();
     Set<EcalChannel> badChannels = new HashSet<EcalChannel>();
-    
-    PrintStream ps = System.out;
-    
+        
     /**
      * Class constructor, which is package protected.
      */
     EcalConditions() {        
     }
     
+    /**
+     * Get the gain value by channel.  
+     * This value is multiplied by an ADC count to get an energy value.
+     * @param channel The channel.
+     * @return The gain for this channel.
+     */
     public Double getGain(EcalChannel channel) {
         return gains.get(channel);
     } 
     
+    /**
+     * Get the pedestal by channel.
+     * @param channel The channel.
+     * @return The pedestal value for this channel.
+     */
     public Double getPedestal(EcalChannel channel) {
         return pedestals.get(channel);
     }
     
+    /**
+     * Get whether or not the given channel is "bad" in some way, 
+     * meaning it should not be used for reconstruction, etc.
+     * @param channel The channel.
+     * @return True if channel is bad; false if not.
+     */
     public boolean isDeadChannel(EcalChannel channel) {        
         return badChannels.contains(channel);
     }
     
+    /**
+     * Get the map between database IDs and <code>EcalChannel</code> objects.
+     * @return The channel map.
+     */
     public EcalChannelMap getChannelMap() {
         return channels;
     }
     
+    /**
+     * Set the gain for the channel.
+     * @param channel The channel.
+     * @param gain The gain.
+     */
     void setGain(EcalChannel channel, double gain) {
         gains.put(channel, gain);
     }
     
+    /**
+     * Set the pedestal for the channel.
+     * @param channel The channel. 
+     * @param pedestal The pedestal.
+     */
     void setPedestal(EcalChannel channel, double pedestal) {
         pedestals.put(channel, pedestal);
     } 
     
+    /**
+     * Flag a channel as bad.
+     * @param channel The channel.
+     */
     void addDeadChannel(EcalChannel channel) {
         badChannels.add(channel);
     }
     
+    /**
+     * Set the channel map.
+     * @param channels The channel map.
+     */
     void setChannelMap(EcalChannelMap channels) {
         this.channels = channels;
     }
     
+    /**
+     * Convert this object to a string.
+     * @return A string representation of this object.
+     */
     public String toString() {
         StringBuffer buff = new StringBuffer();
         for (EcalChannel channel : channels.values()) {
             boolean badChannel = badChannels.contains(channel);
             Double gain = getGain(channel);
             Double pedestal = getPedestal(channel);
-            ps.println(channel + ", gain: " + (gain == null ? "NONE" : gain)
+            buff.append(channel 
+                    + ", gain: " + (gain == null ? "NONE" : gain)
                     + ", pedestal: " + (pedestal == null ? "NONE" : pedestal)
-                    + ", badChannel: " + badChannel);
+                    + ", badChannel: " + badChannel + '\n');
         }
         return buff.toString();
     }

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalConditionsLoader.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalConditionsLoader.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalConditionsLoader.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -6,10 +6,18 @@
 
 import org.lcsim.conditions.ConditionsManager;
 
+/**
+ * This class loads all ecal conditions into an {@link EcalConditions} objects.
+ * @author Jeremy McCormick <[log in to unmask]>
+ */
 public class EcalConditionsLoader {
-    
+   
+    /** The conditions object that will be constructed. */
     private EcalConditions conditions = null;
     
+    /**
+     * Load ECal conditions into the <code>conditions</code> instance variable.
+     */
     public void load() {
         
         // Reset conditions object.
@@ -31,6 +39,10 @@
         }
     }
     
+    /**
+     * Get the ecal conditions object that was loaded.
+     * @return The ecal conditions object or null if not loaded yet.
+     */
     public EcalConditions getEcalConditions() {
         return conditions;
     }

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalGain.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalGain.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalGain.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -1,19 +1,44 @@
 package org.lcsim.hps.conditions.ecal;
 
-public class EcalGain {
-    
+/**
+ * This class is a simplistic representation of gain values from the ecal
+ * conditions database.  The assigned channels can be looked up by using the
+ * {@link EcalChannelMap} for the event.  This class is used as input for 
+ * setting up gains within an {@link EcalConditions} object by the
+ * {@link EcalConditionsLoader}.  
+ * 
+ * @author Jeremy McCormick <[log in to unmask]>
+ */
+class EcalGain {
+   
+    /** The database ID. */
     private int id;
+    
+    /** The gain value. */
     private double gain;
     
-    public EcalGain(int id, double gain) {
+    /**
+     * Fully qualified class constructor.
+     * @param id
+     * @param gain
+     */
+    EcalGain(int id, double gain) {
         this.id = id;
         this.gain = gain;
     }
     
+    /**
+     * Get the database ID.
+     * @return The database ID.
+     */
     public int getId() {
         return id;
     }
     
+    /**
+     * Get the gain value.
+     * @return The gain value.
+     */
     public double getGain() {
         return gain;
     }       

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalGainCollection.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalGainCollection.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalGainCollection.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -4,8 +4,6 @@
 
 /**
  * This class maps integer IDs from the database to ECal gain parameters.
- * The EcalChannelMap data structure can be used to retrieve the channel
- * data from the ID.
  */
-public class EcalGainCollection extends LinkedHashMap<Integer,EcalGain> {
+class EcalGainCollection extends LinkedHashMap<Integer,EcalGain> {
 }

hps-java/src/main/java/org/lcsim/hps/conditions/ecal
EcalGainConverter.java 1.1 -> 1.2
diff -u -r1.1 -r1.2
--- EcalGainConverter.java	25 Sep 2013 22:14:24 -0000	1.1
+++ EcalGainConverter.java	25 Sep 2013 22:36:52 -0000	1.2
@@ -10,8 +10,16 @@
 import org.lcsim.hps.conditions.ConnectionManager;
 import org.lcsim.hps.conditions.DatabaseConditionsConverter;
 
+/**
+ * This class creates an {@link EcalGainCollection} from the appropriate conditions database information.
+ */
 public class EcalGainConverter extends DatabaseConditionsConverter<EcalGainCollection> {
     
+    /**
+     * Create the collection from the conditions database.
+     * @param manager The conditions manager.
+     * @param name The name of the conditions set.
+     */
     public EcalGainCollection getData(ConditionsManager manager, String name) {
         
         // Collection to be returned to caller.
@@ -38,21 +46,11 @@
             // Get the name of the current database being used.
             String database = ConnectionManager.getConnectionParameters().getDatabase();
             
-            /*
-            String query = "SELECT ecal_channel_id, crate, slot, channel, gain FROM "  
-                    + database + "." + tableName + ", " 
-                    + database + "." + ECAL_CHANNELS 
-                    + "WHERE " + fieldName + " = " + fieldValue 
-                    + " AND " + tableName + ".ecal_channel_id = ecal_channels.id " 
-                    + " ORDER BY " + ECAL_CHANNELS + ".id ASC";
-                    */
             String query = "SELECT ecal_channel_id, gain FROM "  
                     + database + "." + tableName   
                     + " WHERE " + fieldName + " = " + fieldValue  
                     + " ORDER BY id ASC";
-            
-            //System.out.println(query);
-                        
+                                   
             // Execute the query and get the results.
             statement = connection.createStatement();
             resultSet = statement.executeQuery(query);
@@ -87,6 +85,10 @@
         return gains;
     }
 
+    /**
+     * Get the type handled by this converter.
+     * @return The type handled by this converter.
+     */
     public Class<EcalGainCollection> getType() {
         return EcalGainCollection.class;
     }

hps-java/src/main/java/org/lcsim/hps/conditions/svt
SvtConditions.java 1.5 -> 1.6
diff -u -r1.5 -r1.6
--- SvtConditions.java	24 Sep 2013 02:51:35 -0000	1.5
+++ SvtConditions.java	25 Sep 2013 22:36:53 -0000	1.6
@@ -6,13 +6,18 @@
 import org.lcsim.detector.tracker.silicon.SiSensor;
 
 /**
+ * This class models all available SVT conditions data, including 
+ * noise, pedestal, shaping time, and time shift by channel.
  * 
  * @author Omar Moreno <[log in to unmask]>
  * @author Jeremy McCormick <[log in to unmask]>
- * @version $Id: SvtConditions.java,v 1.5 2013/09/24 02:51:35 jeremy Exp $
+ * @version $Id: SvtConditions.java,v 1.6 2013/09/25 22:36:53 jeremy Exp $
  */
 public class SvtConditions {
 
+    /**
+     * Data maps for SVT conditions. 
+     */
     private Map<SiSensor, double[]> noiseMap = new HashMap<SiSensor, double[]>();
     private Map<SiSensor, double[]> pedestalMap = new HashMap<SiSensor, double[]>();
     private Map<SiSensor, double[]> tpMap = new HashMap<SiSensor, double[]>();

hps-java/src/main/java/org/lcsim/hps/conditions/svt
SvtConditionsLoader.java 1.3 -> 1.4
diff -u -r1.3 -r1.4
--- SvtConditionsLoader.java	25 Sep 2013 22:14:24 -0000	1.3
+++ SvtConditionsLoader.java	25 Sep 2013 22:36:53 -0000	1.4
@@ -11,12 +11,16 @@
 import static org.lcsim.hps.conditions.ConditionsConstants.SVT_CALIBRATIONS;
 
 /**
- * 
+ * This class creates an {@link SvtConditions} object from the conditions database.
  */
 public class SvtConditionsLoader {
         
+    // Object to be returned to caller.
     private SvtConditions conditions = null;
-              
+             
+    /**
+     * Load the SVT conditions.
+     */
     public void load() {
                         
         // Get the default conditions manager.  This needs to be setup beforehand with the detector.        
@@ -56,6 +60,10 @@
         }                         
     }
     
+    /**
+     * Get the SVT conditions.
+     * @return The SVT conditions or null if not loaded yet.
+     */
     public SvtConditions getSvtConditions() {
         return conditions;
     }
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