diff -u -r1.21 -r1.22
--- ReclusterDTreeDriver.java	29 Oct 2008 17:29:03 -0000	1.21
+++ ReclusterDTreeDriver.java	7 Feb 2009 05:06:57 -0000	1.22
@@ -1,6 +1,7 @@

 package org.lcsim.recon.pfa.structural;
 
 import java.util.*; 

+import java.util.Arrays;

 import java.io.IOException; 
 import hep.physics.vec.*;
 import hep.physics.particle.properties.*;

@@ -35,7 +36,7 @@

   * in this package, which uses the implementation in
   * org.lcsim.recon.cluster.directedtree developed by NIU).
   *

-  * @version $Id: ReclusterDTreeDriver.java,v 1.21 2008/10/29 17:29:03 mcharles Exp $

+  * @version $Id: ReclusterDTreeDriver.java,v 1.22 2009/02/07 05:06:57 tjkim Exp $

   * @author Mat Charles <[log in to unmask]>
   */
 

@@ -59,7 +60,6 @@

     protected boolean m_oldMipFinderCrossesTrees = true;
     protected boolean m_useNewMipFinder = true;
     protected boolean m_useOldMipFinder = true;

-    protected boolean m_removePoorQualityMips = false; // DANGER: STILL USED

     protected boolean m_clusterAsJets = true;
     protected boolean m_ignorePunchThroughTracksForJets = true;
     protected boolean m_useTracksThatDontReachCalorimeter = true;

@@ -93,21 +93,36 @@

 
     protected boolean m_debugSeedSplitting = false;
 

-    protected boolean m_useMucalBarrel = false;
-    protected boolean m_useMucalEndcap = true;
-    protected boolean m_useFcal = false;
-

     protected List<String> m_inputMips = new Vector<String>();
     protected List<String> m_inputClumps = new Vector<String>();
     protected List<String> m_inputBlocks = new Vector<String>();
     protected List<String> m_inputLeftoverHits = new Vector<String>();
     protected List<String> m_inputTrackClusterMaps = new Vector<String>();

+

     public void addInputMips(String name) { m_inputMips.add(name); }
     public void addInputClumps(String name) { m_inputClumps.add(name); }
     public void addInputBlocks(String name) { m_inputBlocks.add(name); }
     public void addInputLeftoverHits(String name) { m_inputLeftoverHits.add(name); }
     public void addTrackToClusterMap(String name) { m_inputTrackClusterMaps.add(name); }

-

+  
+    public void setAddInputMips(String [] inputMips) { m_inputMips.addAll(Arrays.asList(inputMips)); }
+    public void setAddInputClumps(String [] inputClumps) {m_inputClumps.addAll(Arrays.asList(inputClumps)); }
+    public void setAddInputBlocks(String [] inputBlocks) {m_inputBlocks.addAll(Arrays.asList(inputBlocks)); }
+    public void setAddInputLeftoverHits(String [] inputLeftoverHits) {m_inputLeftoverHits.addAll(Arrays.asList(inputLeftoverHits)); }
+    public void setAddTrackToClusterMap(String [] inputTrackClusterMaps) {m_inputTrackClusterMaps.addAll(Arrays.asList(inputTrackClusterMaps)); } 
+
+    public void setJetScoreThreshold(double jetScoreThreshold){m_jetScoreThreshold = jetScoreThreshold;}
+    public void setJetTolerance(double jetTolerance){m_jetTolerance =jetTolerance;}
+    public void setMinScoreForReassignment(double minScoreForReassignment){m_minScoreForReassignment = minScoreForReassignment;}
+    public void setUseMucalBarrel(boolean useMucalBarrel){boolean m_useMucalBarrel = useMucalBarrel;}
+    public void setUseMucalEndcap(boolean useMucalEndcap){boolean m_useMucalEndcap = useMucalEndcap;}
+
+    public void setDTreeClusterList(String dTreeClusterList)  { m_dTreeClusterListName = dTreeClusterList;}
+    public void setTrackList(String trackList) { m_inputTrackList = trackList;}
+    public void setMcList(String mcList) { m_mcList = mcList;}
+    public void setMuonTrackClusterMap(String muonTrackClusterMap) { m_muonTrackClusterMapName = muonTrackClusterMap;}
+    public void setOutputParticleListName(String outputParticleListName) { m_outputParticleListName = outputParticleListName;}
+    

     public void writeExtraEventOutput(boolean writeExtra) {
 	m_writeExtraEventOutput = writeExtra;
     }

@@ -132,7 +147,6 @@

     public void process(EventHeader event) {
 	super.debugProcess(event);
 	m_event = event;

-

 	// Some likelihood selectors need per-event info
 	supplyEventToLikelihoodSelectors();
 

@@ -1483,33 +1497,33 @@

 	    Set<Cluster> clusters = newMapTrackToShowerComponents.get(tr);
 	    Cluster sharedHitClus = makeClusterOfSharedHits(clusters, allSharedClusters);
 	    if (sharedHitClus.getCalorimeterHits().size()>0) { clusters.add(sharedHitClus); }

-	    // Remember to handle case where >1 physical track is bundled into one logical track:

+            // Remember to handle case where >1 physical track is bundled into one logical track:

 	    Set<Track> finalStateTracks = new HashSet<Track>();

-	    if (tr instanceof MultipleTrackTrack) {
-		finalStateTracks.addAll(tr.getTracks());
-	    } else {
-		finalStateTracks.add(tr);
-	    }
-	    // Loop over final-state track(s) and make particles.
-	    // Only the first one gets clusters (to avoid double-counting).
-	    boolean firstTrack = true;
-	    for (Track subTr : finalStateTracks) {
-		// Assign clusters to first track.
-		Set<Cluster> clustersForThisTrack = new HashSet<Cluster>();
-		if (firstTrack) {
-		    clustersForThisTrack.addAll(clusters);
-		    firstTrack = false;
-		}
-		// Make particle (assume pion)
-		ReconstructedParticle part = null;
-		if (subTr.getCharge() > 0) {
-		    part = makeSingleChargedParticle(subTr, clustersForThisTrack, pdg_piplus);
-		} else {
-		    part = makeSingleChargedParticle(subTr, clustersForThisTrack, pdg_piminus);
-		}
-		outputParticleList.add(part);
-	    }
-	}

+    	    if (tr instanceof MultipleTrackTrack) {
+                finalStateTracks.addAll(tr.getTracks());
+            } else {
+                finalStateTracks.add(tr);
+            }
+            // Loop over final-state track(s) and make particles.
+            // Only the first one gets clusters (to avoid double-counting).
+            boolean firstTrack = true;
+            for (Track subTr : finalStateTracks) {
+                // Assign clusters to first track.
+                Set<Cluster> clustersForThisTrack = new HashSet<Cluster>();
+                if (firstTrack) {
+                    clustersForThisTrack.addAll(clusters);
+                    firstTrack = false;
+                }
+                // Make particle (assume pion)
+                ReconstructedParticle part = null;
+                if (subTr.getCharge() > 0) {
+                    part = makeSingleChargedParticle(subTr, clustersForThisTrack, pdg_piplus);
+                } else {
+                    part = makeSingleChargedParticle(subTr, clustersForThisTrack, pdg_piminus);
+                }
+                outputParticleList.add(part);
+            }
+        }

 	return outputParticleList;
     }
 

@@ -1518,29 +1532,29 @@

 	int pdg_piminus = -211;
 	List<ReconstructedParticle> outputParticleList = new Vector<ReconstructedParticle>();
 	for (Set<Track> jet : newMapJetToShowerComponents.keySet()) {

-	    // Remember to handle case where >1 physical track is bundled into one logical track:
-	    Set<Track> finalStateTracks = new HashSet<Track>();
-	    for (Track tr : jet) {
-		if (tr instanceof MultipleTrackTrack) {
-		    finalStateTracks.addAll(tr.getTracks());
-		} else {
-		    finalStateTracks.add(tr);
-		}
-	    }
-	    // Loop over final-state tracks and make particles:

+            // Remember to handle case where >1 physical track is bundled into one logical track:
+            Set<Track> finalStateTracks = new HashSet<Track>();
+            for (Track tr : jet) {
+                if (tr instanceof MultipleTrackTrack) {
+                    finalStateTracks.addAll(tr.getTracks());
+                } else {
+                    finalStateTracks.add(tr);
+                }
+            }
+            // Loop over final-state tracks and make particles:

 	    boolean firstTrackInJet = true;
 	    for (Track tr : finalStateTracks) {

-		Set<Cluster> clusters = null;

+                Set<Cluster> clusters = null;

 		if (firstTrackInJet) {

-		    // Assign all clusters to first track in jet
-		    clusters = newMapJetToShowerComponents.get(jet);
-		    Cluster sharedHitClus = makeClusterOfSharedHits(clusters, allSharedClusters);
-		    if (sharedHitClus.getCalorimeterHits().size()>0) { clusters.add(sharedHitClus); }
-		    firstTrackInJet = false;
-		} else {
-		    // Other tracks get none
-		    clusters = new HashSet<Cluster>();
-		}

+                    // Assign all clusters to first track in jet
+                    clusters = newMapJetToShowerComponents.get(jet);
+                    Cluster sharedHitClus = makeClusterOfSharedHits(clusters, allSharedClusters);
+                    if (sharedHitClus.getCalorimeterHits().size()>0) { clusters.add(sharedHitClus); }
+                    firstTrackInJet = false;
+                } else {
+                    // Other tracks get none
+                    clusters = new HashSet<Cluster>();
+                }

 		ReconstructedParticle part = null;
 		if (tr.getCharge() > 0) {
 		    part = makeSingleChargedParticle(tr, clusters, pdg_piplus);

diff -u -r1.18 -r1.19
--- ReclusterDriver.java	12 Dec 2008 22:27:59 -0000	1.18
+++ ReclusterDriver.java	7 Feb 2009 05:06:57 -0000	1.19
@@ -41,7 +41,7 @@

   * This version is superseded by ReclusterDTreeDriver,
   * which derives from it.
   *

-  * @version $Id: ReclusterDriver.java,v 1.18 2008/12/12 22:27:59 jeremy Exp $

+  * @version $Id: ReclusterDriver.java,v 1.19 2009/02/07 05:06:57 tjkim Exp $

   * @author Mat Charles <[log in to unmask]>
   */
 

@@ -88,7 +88,10 @@

     protected int m_punchThroughLayers = 5;
     protected int m_punchThroughHitMinimum = 4;
     protected boolean m_checkSharedHitsForPunchThrough = true;

-    protected boolean m_allowLateralPunchThrough = false; // Set to FALSE for mucal enabled

+    protected boolean m_useMucalBarrel = false;
+    protected boolean m_useMucalEndcap = true;
+    protected boolean m_useFcal = false;
+

 
     protected HelixExtrapolator m_findCluster = null;
 

@@ -3343,7 +3346,7 @@

 	    clusterToCheckForPunchThrough = makeCombinedCluster(showerComponents);
 	}
 

-	if (!m_allowLateralPunchThrough) {

+	if (m_useMucalEndcap) {

 	    // Ignore punch-through at the sides, since we can easily pick it up in the endcap muon system
 	    // So we'll remove endcap hits from consideration.
 	    BasicCluster newCluster = new BasicCluster();

@@ -3362,7 +3365,7 @@

 
 	// Optionally, also check for tracks that punch through the sides of the barrel
 	boolean lateralPunchThrough = false;

-	if (m_allowLateralPunchThrough) {

+	if (!m_useMucalEndcap) {

 	    int barrelEdgeHitCount = countHitsInSideEdgesOfHcal(clusterToCheckForPunchThrough, m_punchThroughLayers);
 	    lateralPunchThrough = (barrelEdgeHitCount >= m_punchThroughHitMinimum);
 	}