diff -u -r1.2 -r1.3
--- HPSNearestNeighborRMS.java	24 Apr 2012 14:09:14 -0000	1.2
+++ HPSNearestNeighborRMS.java	24 Apr 2012 17:46:01 -0000	1.3
@@ -1,13 +1,10 @@

-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */

 package org.lcsim.hps.recon.tracking;
 
 import java.util.*;
 import org.lcsim.detector.identifier.IIdentifier;
 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.detector.tracker.silicon.SiTrackerIdentifierHelper;

+import org.lcsim.event.RawTrackerHit;

 
 
 /**

@@ -119,7 +116,7 @@

      * @return list of clusters, with a cluster being a list of RawTrackerHits
      */
     @Override

-    public List<List<HPSTrackerHit>> findClusters(List<HPSTrackerHit> base_hits) {

+    public List<List<HPSFittedRawTrackerHit>> findClusters(List<HPSFittedRawTrackerHit> base_hits) {

 
         //  Check that the seed threshold is at least as large as  the neighbor threshold
         if (_seed_threshold < _neighbor_threshold) {

@@ -129,20 +126,20 @@

         //  Create maps that show the channel status and relate the channel number to the raw hit and vice versa
         int mapsize = 2 * base_hits.size();
         Map<Integer, Boolean> clusterable = new HashMap<Integer, Boolean>(mapsize);

-        Map<HPSTrackerHit, Integer> hit_to_channel = new HashMap<HPSTrackerHit, Integer>(mapsize);
-        Map<Integer, HPSTrackerHit> channel_to_hit = new HashMap<Integer, HPSTrackerHit>(mapsize);

+        Map<HPSFittedRawTrackerHit, Integer> hit_to_channel = new HashMap<HPSFittedRawTrackerHit, Integer>(mapsize);
+        Map<Integer, HPSFittedRawTrackerHit> channel_to_hit = new HashMap<Integer, HPSFittedRawTrackerHit>(mapsize);

 
         //  Create list of channel numbers to be used as cluster seeds
         List<Integer> cluster_seeds = new ArrayList<Integer>();
 
         //  Loop over the raw hits and construct the maps used to relate cells and hits, initialize the
         //  clustering status map, and create a list of possible cluster seeds

-        for (HPSTrackerHit base_hit : base_hits) {

+        for (HPSFittedRawTrackerHit base_hit : base_hits) {

-            

+            RawTrackerHit rth=base_hit.getRawTrackerHit();

             // get the channel number for this hit

-            SiTrackerIdentifierHelper sid_helper = (SiTrackerIdentifierHelper) base_hit.getIdentifierHelper();
-            IIdentifier id = base_hit.getIdentifier();

+            SiTrackerIdentifierHelper sid_helper = (SiTrackerIdentifierHelper) rth.getIdentifierHelper();
+            IIdentifier id = rth.getIdentifier();

             int channel_number = sid_helper.getElectrodeValue(id);
 
             //  Check for duplicate RawTrackerHit

@@ -161,7 +158,7 @@

 
             //  Get the signal from the readout chip
             double signal = base_hit.getAmp();

-            double noiseRMS = HPSSVTCalibrationConstants.getNoise((SiSensor)base_hit.getDetectorElement(),channel_number);

+            double noiseRMS = HPSSVTCalibrationConstants.getNoise((SiSensor)rth.getDetectorElement(),channel_number);

 
             //  Mark this hit as available for clustering if it is above the neighbor threshold
             clusterable.put(channel_number, signal/noiseRMS >= _neighbor_threshold);

@@ -173,7 +170,7 @@

         }
 
         //  Create a list of clusters

-        List<List<HPSTrackerHit>> cluster_list = new ArrayList<List<HPSTrackerHit>>();

+        List<List<HPSFittedRawTrackerHit>> cluster_list = new ArrayList<List<HPSFittedRawTrackerHit>>();

 
         //  Now loop over the cluster seeds to form clusters
         for (int seed_channel : cluster_seeds) {

@@ -182,7 +179,7 @@

             if (!clusterable.get(seed_channel)) continue;
 
             //  Create a new cluster

-            List<HPSTrackerHit> cluster = new ArrayList<HPSTrackerHit>();

+            List<HPSFittedRawTrackerHit> cluster = new ArrayList<HPSFittedRawTrackerHit>();

             double cluster_signal = 0.;
             double cluster_noise_squared = 0.;
 

@@ -200,7 +197,7 @@

                 int clustered_cell = unchecked.removeFirst();
                 cluster.add(channel_to_hit.get(clustered_cell));
                 cluster_signal += channel_to_hit.get(clustered_cell).getAmp();

-                cluster_noise_squared += Math.pow(HPSSVTCalibrationConstants.getNoise((SiSensor)(channel_to_hit.get(clustered_cell)).getDetectorElement(),clustered_cell),2);

+                cluster_noise_squared += Math.pow(HPSSVTCalibrationConstants.getNoise((SiSensor)(channel_to_hit.get(clustered_cell)).getRawTrackerHit().getDetectorElement(),clustered_cell),2);

 //                cluster_noise_squared +=0;  //need to get the noise from the calib. const. class
                 //  Get the neigbor channels
 //                Set<Integer> neighbor_channels = electrodes.getNearestNeighborCells(clustered_cell);