diff -u -r1.1 -r1.2
--- CheckSkeletonsForMultipleTracks.java	16 May 2007 20:58:13 -0000	1.1
+++ CheckSkeletonsForMultipleTracks.java	21 Sep 2007 01:01:18 -0000	1.2
@@ -10,6 +10,7 @@

 import org.lcsim.event.util.*;
 import org.lcsim.recon.cluster.structural.likelihood.*;
 import org.lcsim.recon.cluster.util.BasicCluster;

+import org.lcsim.recon.pfa.identifier.TrackClusterMatcher;

 
 public class CheckSkeletonsForMultipleTracks extends Driver {
 

@@ -20,13 +21,15 @@

     protected String m_mipsListName;
     protected String m_clumpsListName;
     protected LikelihoodEvaluator m_eval = null;

-    public CheckSkeletonsForMultipleTracks(LikelihoodEvaluator eval, String inputTrackList, String inputSkeletonClusterList, String outputSkeletonClusterList, String mips, String clumps) {

+    protected TrackClusterMatcher m_clusterMatcher = null;
+    public CheckSkeletonsForMultipleTracks(LikelihoodEvaluator eval, String inputTrackList, String inputSkeletonClusterList, String outputSkeletonClusterList, String mips, String clumps, TrackClusterMatcher clusterMatcher) {

 	m_eval = eval;
 	m_inputSkeletonClusterListName = inputSkeletonClusterList;
 	m_outputSkeletonClusterListName = outputSkeletonClusterList;
 	m_inputTrackListName = inputTrackList;
 	m_mipsListName = mips;
 	m_clumpsListName = clumps;

+	m_clusterMatcher = clusterMatcher;

     }
 
     public void process(EventHeader event) {

@@ -44,11 +47,8 @@

 	// and we don't want to be confused by a nearby track that shouldn't be
 	// hooked up to any of these.
 	Map<Cluster,List<Track>> map = new HashMap<Cluster,List<Track>> ();

-	LocalHelixExtrapolationTrackClusterMatcher tmpExtrap = new LocalHelixExtrapolationTrackClusterMatcher();
-	tmpExtrap.process(event);
-	tmpExtrap.setCutSeparation(14.0); // about two cells

 	for (Track tr : inputTracks) {

-	    Cluster matchedCluster = tmpExtrap.matchTrackToCluster(tr, inputSkeletons);

+	    Cluster matchedCluster = m_clusterMatcher.matchTrackToCluster(tr, inputSkeletons);

 	    if (map.get(matchedCluster) == null) { map.put(matchedCluster, new Vector<Track>()); }
 	    map.get(matchedCluster).add(tr);
 	}

@@ -69,16 +69,16 @@

 		// Check for pathological case where >1 track hits the same subcluster
 		List<Link> confirmedLinks = new Vector<Link>(); // empty
 		List<Cluster> initialSkeletonList = assembleClusters(confirmedLinks, vClumpsAndMIPs);

-		boolean testInitiallyOK = checkUniqueTrackAssignments(tmpExtrap, initialSkeletonList, tracksForThisCluster);

+		boolean testInitiallyOK = checkUniqueTrackAssignments(m_clusterMatcher, initialSkeletonList, tracksForThisCluster);

 		while (!testInitiallyOK) { 
 		    // Pathological case. Only way out is to drop 1 (or more) tracks...
 		    if (m_debug) { System.out.println("Warning! In initial pass > 1 track already matched to a cluster segment. Trying to fix..."); }

-		    Track trackToRemove = findMultiplyAssignedTrack(tmpExtrap, initialSkeletonList, tracksForThisCluster);

+		    Track trackToRemove = findMultiplyAssignedTrack(m_clusterMatcher, initialSkeletonList, tracksForThisCluster);

 		    List<Track> newTracksForThisCluster = new Vector<Track>();
 		    newTracksForThisCluster.addAll(tracksForThisCluster);
 		    newTracksForThisCluster.remove(trackToRemove);
 		    tracksForThisCluster = newTracksForThisCluster;

-		    testInitiallyOK = checkUniqueTrackAssignments(tmpExtrap, initialSkeletonList, tracksForThisCluster);

+		    testInitiallyOK = checkUniqueTrackAssignments(m_clusterMatcher, initialSkeletonList, tracksForThisCluster);

 		}
 
 		// Compute likelihood of each pairwise link

@@ -157,15 +157,19 @@

 		    }
 		    // Assemble clusters with old link set (sanity check)
 		    List<Cluster> previousSkeletonList = assembleClusters(confirmedLinks, vClumpsAndMIPs);

-		    boolean testPreviousOK = checkUniqueTrackAssignments(tmpExtrap, previousSkeletonList, tracksForThisCluster);
-		    if (!testPreviousOK) { throw new AssertionError("Internal consistency failure"); }

+		    boolean testPreviousOK = checkUniqueTrackAssignments(m_clusterMatcher, previousSkeletonList, tracksForThisCluster);
+		    if (!testPreviousOK) { 
+			// This can happen if the track-matching behaviour depends on
+			// the other clusters present.
+			System.out.println("WARNING: Internal consistency failure"); 
+		    }

 		    // Assemble clusters with new link added
 		    List<Link> testLinkList = new Vector<Link>();
 		    testLinkList.addAll(confirmedLinks);
 		    testLinkList.add(bestLink);
 		    List<Cluster> updatedSkeletonList = assembleClusters(testLinkList, vClumpsAndMIPs);
 		    // Verify no double tracks

-		    boolean verified = checkUniqueTrackAssignments(tmpExtrap, updatedSkeletonList, tracksForThisCluster);

+		    boolean verified = checkUniqueTrackAssignments(m_clusterMatcher, updatedSkeletonList, tracksForThisCluster);

 		    if (verified) {
 			confirmedLinks.add(bestLink);
 			potentialTrackToTrackLinks.remove(bestLink);

@@ -185,7 +189,7 @@

 		    Map<Cluster, List<Track>> mapClustersToTracks = new HashMap<Cluster, List<Track>>();
 		    for (Track tr : tracksForThisCluster) {
 			if (tr == null) { throw new AssertionError("Null track!"); }

-			Cluster matchedCluster = tmpExtrap.matchTrackToCluster(tr, updatedSkeletonList);

+			Cluster matchedCluster = m_clusterMatcher.matchTrackToCluster(tr, updatedSkeletonList);

 			if (mapClustersToTracks.get(matchedCluster) == null) { mapClustersToTracks.put(matchedCluster, new Vector<Track>()); }
 			mapClustersToTracks.get(matchedCluster).add(tr);
 		    }

@@ -255,7 +259,7 @@

 	}
     }
 

-    boolean checkUniqueTrackAssignments(LocalHelixExtrapolationTrackClusterMatcher extrap, List<Cluster> clusters, List<Track> tracks) {

+    boolean checkUniqueTrackAssignments(TrackClusterMatcher extrap, List<Cluster> clusters, List<Track> tracks) {

 	Track duplicateTrack = findMultiplyAssignedTrack(extrap, clusters, tracks);
 	return (duplicateTrack == null);
     }

@@ -321,7 +325,7 @@

     }
 
     // Kind of hackish

-    Track findMultiplyAssignedTrack(LocalHelixExtrapolationTrackClusterMatcher extrap, List<Cluster> clusters, List<Track> tracks) {

+    Track findMultiplyAssignedTrack(TrackClusterMatcher extrap, List<Cluster> clusters, List<Track> tracks) {

 	Map<Cluster, List<Track>> mapClustersToTracks = new HashMap<Cluster, List<Track>>();
 	for (Track tr : tracks) {
 	    if (tr == null) { throw new AssertionError("Null track!"); }