diff -u -r1.5 -r1.6
--- Apv25Full.java	17 Aug 2012 01:17:07 -0000	1.5
+++ Apv25Full.java	28 Aug 2012 07:06:53 -0000	1.6
@@ -6,6 +6,7 @@

 import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MIP;
 import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.SAMPLING_INTERVAL;
 import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MULTIPLEXER_GAIN;

+import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.CHANNELS;

 
 //--- hps-java ---//
 import org.lcsim.hps.util.ClockSingleton;

@@ -14,7 +15,7 @@

 /**
  * 
  * @author Omar Moreno <[log in to unmask]>

- * @version $Id: Apv25Full.java,v 1.5 2012/08/17 01:17:07 omoreno Exp $

+ * @version $Id: Apv25Full.java,v 1.6 2012/08/28 07:06:53 omoreno Exp $

  */
 public class Apv25Full {
     

@@ -22,22 +23,27 @@

     public static boolean readoutBit = false;
     
     // APV25 Channels; An APV25 Readout Chip contains a total of 128 channels

-    private Apv25Channel[] channels = new Apv25Channel[128];
-    

+    private Apv25Channel[] channels = new Apv25Channel[CHANNELS];
+  
+    /**
+     * Default Ctor
+     */

     public Apv25Full(){
         
         // Instantiate all APV25 channels

-        for(int channel = 0; channel < channels.length; channel++){
-            channels[channel] = new Apv25Channel();

+        for(int channelN = 0; channelN < CHANNELS; channelN++){
+            channels[channelN] = new Apv25Channel();

         }
     }
     
     /**
      * Return an instance of an APV25 channel
      * 

-     * @return an instance of Apv25Channel

+     * @param channel: APV25 channel of interest (0-127)
+     * @return an instance of an Apv25Channel

      */
     public Apv25Channel getChannel(int channel){

+        if(channel >= CHANNELS) throw new RuntimeException();

         return channels[channel];
     }
     

@@ -71,15 +77,14 @@

      */
     public Apv25AnalogData readOut(){
         

-        // TODO: Add pedestal and noise to the samples when read out
-        

         Apv25AnalogData data = new Apv25AnalogData();

-        for(int channel = 0; channel < channels.length; channel++){

+        for(int channel = 0; channel < CHANNELS; channel++){

             
             // Only readout the channel if the channel isn't bad
             if(!this.getChannel(channel).isBadChannel()){

-                double sample = (channels[channel].pipeline.readout()/FRONT_END_GAIN)*MULTIPLEXER_GAIN;
-            	data.setChannelData(channel, sample);

+                // Readout the value stored in the buffer
+                double sample = (this.getChannel(channel).getPipeline().readout()/FRONT_END_GAIN)*MULTIPLEXER_GAIN;
+                data.setChannelData(channel, sample);

             }
         }
         return data;

@@ -94,8 +99,6 @@

         private Apv25Pipeline pipeline = new Apv25Pipeline();
         
         private double shapingTime = 50; // [ns]

-        private double baseline = 0;
-        private double noise = 0;

         boolean badChannel = false;
         
         /**

@@ -116,20 +119,6 @@

         /**
          * 
          */

-        public void setBaseline(double baseline){
-            this.baseline = baseline;
-        }
-        
-        /**
-         * 
-         */
-        public void setNoise(double noise){
-            this.noise = noise;
-        }
-        
-        /**
-         * 
-         */

         public void markAsBadChannel(){
             badChannel = true;
         }

@@ -147,21 +136,7 @@

         public Apv25Pipeline getPipeline(){
         	return pipeline;
         }

-        
-        /**
-         * 
-         */
-        public double getBaseline(){
-            return this.baseline;
-        }
-        
-        /**
-         * 
-         */
-        public double getNoise(){
-            return this.noise;
-        }
-        

+                

         /**
          * Shape the injected charge
          * 

@@ -171,6 +146,9 @@

             shaperSignal = new Apv25ShaperSignal(charge);
         }
         

+        /**
+         *
+         */

         public void sampleShaperSignal(){
             
             // Obtain the beam time

@@ -188,7 +166,7 @@

                 double sample = shaperSignal.getAmplitudeAtTime(sampleTime, shapingTime);
                 
                 // Add the value to the pipeline

-                if(sample > .001) pipeline.addToCell(cell, sample);

+                pipeline.addToCell(cell, sample);

             }
         }
     }

@@ -310,4 +288,4 @@

     }
     
 

-}

\ No newline at end of file

+}