diff -u -r1.2 -r1.3
--- PerfectPFA.java	3 Jan 2006 19:34:15 -0000	1.2
+++ PerfectPFA.java	6 Jan 2006 22:59:47 -0000	1.3
@@ -33,7 +33,7 @@

 /**
  * A perfect PFA
  *

- * @version $Id: PerfectPFA.java,v 1.2 2006/01/03 19:34:15 mcharles Exp $

+ * @version $Id: PerfectPFA.java,v 1.3 2006/01/06 22:59:47 mcharles Exp $

  */
 
 public class PerfectPFA extends Driver

@@ -52,6 +52,7 @@

     ICloud1D m_hTotalEnergyPrimaryRonAllNeutrinos;
     ICloud1D m_hTotalEnergyPrimaryCheat;
     ICloud1D m_hTotalEnergyPrimaryCheatNoNeutrinos;

+    ICloud1D m_hTotalEnergyPrimaryCheatSomeNeutrinos;

     ICloud1D m_hTotalEnergyPrimaryCheatAllNeutrinos;
     ICloud1D m_hTotalEnergyPrimaryCheatCheat;
     EventHeader m_event;

@@ -73,6 +74,7 @@

 	    m_hTotalEnergyPrimaryRonAllNeutrinos = m_histoFactory.createCloud1D("hTotalEnergyPrimaryRonAllNeutrinos");
 	    m_hTotalEnergyCheat = m_histoFactory.createCloud1D("hTotalEnergyCheat");
 	    m_hTotalEnergyPrimaryCheatNoNeutrinos = m_histoFactory.createCloud1D("hTotalEnergyPrimaryCheatNoNeutrinos");

+	    m_hTotalEnergyPrimaryCheatSomeNeutrinos = m_histoFactory.createCloud1D("hTotalEnergyPrimaryCheatSomeNeutrinos");

 	    m_hTotalEnergyPrimaryCheatAllNeutrinos = m_histoFactory.createCloud1D("hTotalEnergyPrimaryCheatAllNeutrinos");
 	    m_hTotalEnergyPrimaryCheat = m_histoFactory.createCloud1D("hTotalEnergyPrimaryCheat");
 	    m_hTotalEnergyPrimaryCheatCheat = m_histoFactory.createCloud1D("hTotalEnergyPrimaryCheatCheat");

@@ -122,7 +124,7 @@

 	// Now, for each charged MC particle, build a TrackExtrapolationInfo object...
 	Map<TrackExtrapolationInfo, Cluster> mapHelixToCluster = new HashMap<TrackExtrapolationInfo, Cluster>();
 	Map<Cluster, List<TrackExtrapolationInfo>> mapClusterToHelix = new HashMap<Cluster, List<TrackExtrapolationInfo>>();

-	Set<MCParticle> particleSet = mapParticlesToClusters.keySet();

+	Set<MCParticle> particleSet = mapParticlesToClusters.keySet(); // <- particleSet is the set of particles contributing to clusters

 	for (MCParticle part : particleSet) {
 	    if (Math.abs(part.getCharge()) > 0.5) {
 		// Charged particle

@@ -165,8 +167,9 @@

 
 	for (MCParticle part : particleSet) {
 	    BasicCluster clus = mapParticlesToClusters.get(part);

-	    List<MCParticle> primaries = mapParticleToPrimary.get(part);

+	    List<MCParticle> primaries = mapParticleToPrimary.get(part); // <-- primaries from this particle (which contributes to one or more clusters)

 	    if (clus != null && clus.getCalorimeterHits().size()>0) {

+		// Found something with calorimeter hits...

 		if (Math.abs(part.getCharge()) > 0.5) {
 		    // Charged particle
 		    pfaEnergySumRon += part.getEnergy();

@@ -186,7 +189,7 @@

 	    cheatEnergySum += part.getEnergy();
 	    for (MCParticle primary : primaries) {
 		if (!usedPrimaryAll.contains(primary)) {

-		    cheatEnergySumPrimary += primary.getEnergy();

+		    cheatEnergySumPrimary += primary.getEnergy(); // <-- count energy of each primary

 		    usedPrimaryAll.add(primary);
 		}
 	    }

@@ -214,13 +217,21 @@

             if (pdg==12 || pdg==14 || pdg==16 || pdg==18 || pdg==-12 || pdg==-14 || pdg==-16 || pdg==-18) {
                 truthNeutrinoEnergySum += p.getEnergy();
 	        List<MCParticle> primaries = mapParticleToPrimary.get(p);

+		boolean flagUsedPrimaryAll = false;
+		boolean flagUsedPrimaryCharged = false;

 		for (MCParticle primary : primaries) {

-		    if (!usedPrimaryAll.contains(p)) {
-			truthNeutrinoEnergySumForPrimaryAll += p.getEnergy();

+		    if (usedPrimaryAll.contains(primary)) {
+			flagUsedPrimaryAll = true;
+		    }
+		    if (usedPrimaryCharged.contains(primary)) {
+			flagUsedPrimaryCharged = true;

 		    }

-		    if (!usedPrimaryCharged.contains(p)) {
-			truthNeutrinoEnergySumForPrimaryCharged += p.getEnergy();
-		    }		

+		}
+		if (!flagUsedPrimaryAll) {
+		    truthNeutrinoEnergySumForPrimaryAll += p.getEnergy();
+		}
+		if (!flagUsedPrimaryCharged) {
+		    truthNeutrinoEnergySumForPrimaryCharged += p.getEnergy();

 		}
             }
         }

@@ -233,6 +244,7 @@

 
 	m_hTotalEnergyPrimaryRonNoNeutrinos.fill(pfaEnergySumRonPrimary);
 	m_hTotalEnergyPrimaryCheatNoNeutrinos.fill(cheatEnergySumPrimary);

+	m_hTotalEnergyPrimaryCheatSomeNeutrinos.fill(cheatEnergySumPrimary+truthNeutrinoEnergySumForPrimaryAll);

 	m_hTotalEnergyPrimaryRonAllNeutrinos.fill(pfaEnergySumRonPrimary+truthNeutrinoEnergySum);
 	m_hTotalEnergyPrimaryCheatAllNeutrinos.fill(cheatEnergySumPrimary+truthNeutrinoEnergySum);