diff -u -r1.4 -r1.5
--- McTruthLinker.java	16 Feb 2012 13:06:52 -0000	1.4
+++ McTruthLinker.java	16 Feb 2012 16:14:04 -0000	1.5
@@ -32,7 +32,8 @@

  * objects and their true mc particles.
  * <p>
  * By default three LCRelations are created

- * <ul><li><b>Tracks to MCParticles:</b><br>

+ * <ul>
+ * <li><b>Tracks to MCParticles:</b><br>

  * This requires the name of the track collection and an LCRelation between
  * TrackerHits and MCParticles.</li>
  * <li><b>Clusters to MCParticles:</b><br>

@@ -40,37 +41,38 @@

  * CalorimeterHits and SimCalorimeterHits.</li>
  * <li><b>PFOs to MCParticles:</b><br>
  * This requires the name of the PFO collection and the creation of both

- * LCRelations described above.</li></ul>

+ * LCRelations described above.</li>
+ * </ul>

  * Putting any of these into the event can be prevented by setting the
  * respective name to an empty String.
  * <p>

- * The weights of these relations are based on fractions contributed by
- * the mc particle. For the track relation it is based on the fraction of hits
- * and for clusters it is based on the fraction of energy. Non-charged PFOs
- * use the weight of the clusters, while charged PFOs use a combined weight
- * of the tracks and the clusters, based on a global track to cluster weight.
- * As a default only the track relations are used for charged PFOs.

+ * The weights of these relations are based on fractions contributed by the mc
+ * particle. For the track relation it is based on the fraction of hits and for
+ * clusters it is based on the fraction of energy. Non-charged PFOs use the
+ * weight of the clusters, while charged PFOs use a combined weight of the
+ * tracks and the clusters, based on a global track to cluster weight. As a
+ * default only the track relations are used for charged PFOs.

  * <p>

- * Instead of the simple fraction-based weights described above a weight
- * based on a Tanimoto metric can be used. Then also the hits produced by
- * a mc particle which are not part of the reconstructed object are taken
- * into account. This leads to a lower weight for missed hits.

+ * Instead of the simple fraction-based weights described above a weight based
+ * on a Tanimoto metric can be used. Then also the hits produced by a mc
+ * particle which are not part of the reconstructed object are taken into
+ * account. This leads to a lower weight for missed hits.

  * <p>
  * For all objects, only the relation to the MCParticle which has the highest
  * weight is kept. Setting the fullRecoRelation switch to true will keep all
  * relations instead.
  * <p>
  * By default a reduced set of MCParticles is created. This skimmed list

- * contains only those MCParticles created by the generator (intermediate
- * and final state particles) and emitted bremsstrahlung photons. In addition
- * all particles which are of a pre-defined set of particle types and which
- * decay in flight in the tracking system and their intermediate daughters
- * are kept. By default these particle types are gamma, pi0 and K0s. There is
- * also an energy cut applied to which of these daughter particles are kept.
- * All relations which would point to an MCParticle not contained in this
- * reduced list point to their closest ancestor which is in this list instead.
- * Again, this behavior can be switched off, by setting the name of the 
- * skimmed mc particle collection to an empty String.

+ * contains only those MCParticles created by the generator (intermediate and
+ * final state particles) and emitted bremsstrahlung photons. In addition all
+ * particles which are of a pre-defined set of particle types and which decay in
+ * flight in the tracking system and their intermediate daughters are kept. By
+ * default these particle types are gamma, pi0 and K0s. There is also an energy
+ * cut applied to which of these daughter particles are kept. All relations
+ * which would point to an MCParticle not contained in this reduced list point
+ * to their closest ancestor which is in this list instead. Again, this behavior
+ * can be switched off, by setting the name of the skimmed mc particle
+ * collection to an empty String.

  * 
  * @author <a href="mailto:[log in to unmask]">Christian Grefe</a>
  */

@@ -95,221 +97,247 @@

 	protected List<Integer> keepDaughtersPDGID = new ArrayList<Integer>();
 	protected Map<MCParticle, MCParticle> mcParticleToSkimmed;
 	protected double daughterEnergyCut = 0.01;

-	

+

 	// -------------------- Constructors --------------------

-	

+

 	public McTruthLinker() {

-		keepDaughtersPDGID.add(22);  // gamma

+		keepDaughtersPDGID.add(22); // gamma

 		keepDaughtersPDGID.add(111); // pi0
 		keepDaughtersPDGID.add(310); // K0s
 	}

-	
-	
-	

+

 	// -------------------- Driver Interface Methods --------------------

-	

+

 	@Override
 	protected void startOfData() {
 		if (mcParticlesSkimmedName.equals("")) {
 			this.useSkimmedMcParticles = false;
 		}
 	}

-	

+

 	@Override
 	protected void process(EventHeader event) {

-		

+

 		List<LCRelation> trackMcRelation = null;
 		List<LCRelation> caloHitMcRelation = null;
 		List<LCRelation> clusterMcRelation = null;
 		List<LCRelation> pfoMcRelation = null;
 		mcParticlesSkimmed = null;
 		mcParticleToSkimmed = null;

-		

+

 		// skimmed mc particles
 		if (useSkimmedMcParticles) {
 			try {

-				List<MCParticle> mcParticles = event.get(MCParticle.class, mcParticleCollectionName);

+				List<MCParticle> mcParticles = event.get(MCParticle.class,
+						mcParticleCollectionName);

 				mcParticlesSkimmed = createSkimmedMcParticleList(mcParticles);

-				mcParticleToSkimmed = fillMcParticleToSkimmedMap(mcParticles, mcParticlesSkimmed);

+				mcParticleToSkimmed = fillMcParticleToSkimmedMap(mcParticles,
+						mcParticlesSkimmed);

 				int flags = event.getMetaData(mcParticles).getFlags();

-				flags = LCIOUtil.bitSet(flags, LCIOConstants.BITSubset, true );
-				event.put(mcParticlesSkimmedName, mcParticlesSkimmed, MCParticle.class, flags);
-				print(HLEVEL_NORMAL, "Added skimmed mc particles \""+mcParticlesSkimmedName+"\" to the event.");

+				flags = LCIOUtil.bitSet(flags, LCIOConstants.BITSubset, true);
+				event.put(mcParticlesSkimmedName, mcParticlesSkimmed,
+						MCParticle.class, flags);
+				print(HLEVEL_NORMAL, "Added skimmed mc particles \""
+						+ mcParticlesSkimmedName + "\" to the event.");

 			} catch (IllegalArgumentException e) {
 				print(HLEVEL_DEFAULT,

-						"WARNING: no skimmed mc particle collection created.\n" +
-						"e.getMessage()",
-						true);

+						"WARNING: no skimmed mc particle collection created.\n"
+								+ "e.getMessage()", true);

 			}
 		}

-		

+

 		// track to mc particle relation

-		if (!trackHitMcRelationName.equals("") && !trackCollectionName.equals("")) {

+		if (!trackHitMcRelationName.equals("")
+				&& !trackCollectionName.equals("")) {

 			try {

-				List<Track> tracks = event.get(Track.class, trackCollectionName);
-				List<LCRelation> trackHitMcRelation = event.get(LCRelation.class, trackHitMcRelationName);
-				trackMcRelation = createTrackMcRelation(tracks, trackHitMcRelation);

+				List<Track> tracks = event
+						.get(Track.class, trackCollectionName);
+				List<LCRelation> trackHitMcRelation = event.get(
+						LCRelation.class, trackHitMcRelationName);
+				trackMcRelation = createTrackMcRelation(tracks,
+						trackHitMcRelation);

 				if (!trackMcRelationName.equals("")) {
 					int flags = 0;

-					flags = LCIOUtil.bitSet(flags, LCIOConstants.LCREL_WEIGHTED, true);
-					event.put(trackMcRelationName, trackMcRelation, LCRelation.class, flags);
-					print(HLEVEL_NORMAL, "Added track to mc particle relations \""+trackMcRelationName+"\" to the event.");

+					flags = LCIOUtil.bitSet(flags,
+							LCIOConstants.LCREL_WEIGHTED, true);
+					event.put(trackMcRelationName, trackMcRelation,
+							LCRelation.class, flags);
+					print(HLEVEL_NORMAL,
+							"Added track to mc particle relations \""
+									+ trackMcRelationName + "\" to the event.");

 				}
 			} catch (IllegalArgumentException e) {
 				print(HLEVEL_DEFAULT,

-						"WARNING: no track to mc particle relation created.\n" +
-						"e.getMessage()",
-						true);

+						"WARNING: no track to mc particle relation created.\n"
+								+ "e.getMessage()", true);

 			}
 		}

-		

+

 		// calorimeter hit to mc particle relation

-		if (!caloHitSimHitRelationName.equals("")) { 

+		if (!caloHitSimHitRelationName.equals("")) {

 			try {

-				caloHitMcRelation = createCaloHitMcRelation(event.get(LCRelation.class, caloHitSimHitRelationName));

+				caloHitMcRelation = createCaloHitMcRelation(event.get(
+						LCRelation.class, caloHitSimHitRelationName));

 			} catch (IllegalArgumentException e) {
 				print(HLEVEL_DEFAULT,

-						"WARNING: no calorimeter hit to mc particle relation created.\n" +
-						"e.getMessage()",
-						true);

+						"WARNING: no calorimeter hit to mc particle relation created.\n"
+								+ "e.getMessage()", true);

 			}
 		}

-		

+

 		// cluster to mc particle relation
 		if (!clusterCollectionName.equals("")) {
 			try {

-				List<Cluster> clusters = event.get(Cluster.class, clusterCollectionName);
-				clusterMcRelation = createClusterMcRelation(clusters, caloHitMcRelation);

+				List<Cluster> clusters = event.get(Cluster.class,
+						clusterCollectionName);
+				clusterMcRelation = createClusterMcRelation(clusters,
+						caloHitMcRelation);

 				if (!clusterMcRelationName.equals("")) {
 					int flags = 0;

-					flags = LCIOUtil.bitSet(flags, LCIOConstants.LCREL_WEIGHTED, true);
-					event.put(clusterMcRelationName, clusterMcRelation, LCRelation.class, flags);
-					print(HLEVEL_NORMAL, "Added cluster to mc particle relations \""+clusterMcRelationName+"\" to the event.");

+					flags = LCIOUtil.bitSet(flags,
+							LCIOConstants.LCREL_WEIGHTED, true);
+					event.put(clusterMcRelationName, clusterMcRelation,
+							LCRelation.class, flags);
+					print(HLEVEL_NORMAL,
+							"Added cluster to mc particle relations \""
+									+ clusterMcRelationName
+									+ "\" to the event.");

 				}
 			} catch (IllegalArgumentException e) {
 				print(HLEVEL_DEFAULT,

-						"WARNING: no cluster to mc particle relation created.\n" +
-						"e.getMessage()",
-						true);

+						"WARNING: no cluster to mc particle relation created.\n"
+								+ "e.getMessage()", true);

 			}
 		}

-		

+

 		// PFO to mc particle relation
 		if (!pfoCollectionName.equals("")) {
 			try {

-				List<ReconstructedParticle> PFOs = event.get(ReconstructedParticle.class, pfoCollectionName);
-				pfoMcRelation = createPfoMcRelation(PFOs, trackMcRelation, clusterMcRelation);

+				List<ReconstructedParticle> PFOs = event.get(
+						ReconstructedParticle.class, pfoCollectionName);
+				pfoMcRelation = createPfoMcRelation(PFOs, trackMcRelation,
+						clusterMcRelation);

 				if (!pfoMcRelationName.equals("")) {
 					int flags = 0;

-					flags = LCIOUtil.bitSet(flags, LCIOConstants.LCREL_WEIGHTED, true);
-					event.put(pfoMcRelationName, pfoMcRelation, LCRelation.class, flags);
-					print(HLEVEL_NORMAL, "Added PFO to mc particle relations \""+pfoMcRelationName+"\" to the event.");

+					flags = LCIOUtil.bitSet(flags,
+							LCIOConstants.LCREL_WEIGHTED, true);
+					event.put(pfoMcRelationName, pfoMcRelation,
+							LCRelation.class, flags);
+					print(HLEVEL_NORMAL,
+							"Added PFO to mc particle relations \""
+									+ pfoMcRelationName + "\" to the event.");

 				}
 			} catch (IllegalArgumentException e) {
 				print(HLEVEL_DEFAULT,

-						"WARNING: no PFO to mc particle relation created.\n" +
-						"e.getMessage()",
-						true);

+						"WARNING: no PFO to mc particle relation created.\n"
+								+ "e.getMessage()", true);

 			}
 		}
 	}

-	
-	
-	

+

 	// -------------------- Setter Methods --------------------

-	

+

 	public void setFullRecoRelation(boolean fullRecoRelation) {
 		this.fullRecoRelation = fullRecoRelation;
 	}

-	

+

 	public void setUseTanimotoDistance(boolean useTanimotoDistance) {
 		this.useTanimotoDistance = useTanimotoDistance;
 	}

-	
-	public void setPfoTrackWeight(double pfoTrackWeight) throws IllegalArgumentException {
-		if (pfoTrackWeight < 0) throw new IllegalArgumentException("PFO track weight can not be negative.");

+
+	public void setPfoTrackWeight(double pfoTrackWeight)
+			throws IllegalArgumentException {
+		if (pfoTrackWeight < 0)
+			throw new IllegalArgumentException(
+					"PFO track weight can not be negative.");

 		this.pfoTrackWeight = pfoTrackWeight;
 	}

-	
-	public void setPfoClusterWeight(double pfoClusterWeight) throws IllegalArgumentException {
-		if (pfoTrackWeight < 0) throw new IllegalArgumentException("PFO cluster weight can not be negative.");

+
+	public void setPfoClusterWeight(double pfoClusterWeight)
+			throws IllegalArgumentException {
+		if (pfoTrackWeight < 0)
+			throw new IllegalArgumentException(
+					"PFO cluster weight can not be negative.");

 		this.pfoClusterWeight = pfoClusterWeight;
 	}

-	

+

 	public void setTrackHitMcRelationName(String trackHitMcRelationName) {
 		this.trackHitMcRelationName = trackHitMcRelationName;
 	}

-	

+

 	public void setTrackCollectionName(String trackCollectionName) {
 		this.trackCollectionName = trackCollectionName;
 	}

-	

+

 	public void setTrackMcRelationName(String trackMcRelationName) {
 		this.trackMcRelationName = trackMcRelationName;
 	}

-	

+

 	public void setCaloHitSimHitRelationName(String caloHitSimHitRelationName) {
 		this.caloHitSimHitRelationName = caloHitSimHitRelationName;
 	}

-	

+

 	public void setClusterCollectionName(String clusterCollectionName) {
 		this.clusterCollectionName = clusterCollectionName;
 	}

-	

+

 	public void setClusterMcRelationName(String clusterMcRelationName) {
 		this.clusterMcRelationName = clusterMcRelationName;
 	}

-	

+

 	public void setPfoCollectionName(String pfoCollectionName) {
 		this.pfoCollectionName = pfoCollectionName;
 	}

-	

+

 	public void setPfoMcRelationName(String pfoMcRelationName) {
 		this.pfoMcRelationName = pfoMcRelationName;
 	}

-	

+

 	public void setMcParticleCollectionName(String mcParticleCollectionName) {
 		this.mcParticleCollectionName = mcParticleCollectionName;
 	}

-	

+

 	public void setMcParticlesSkimmedName(String mcParticlesSkimmedName) {
 		this.mcParticlesSkimmedName = mcParticlesSkimmedName;
 	}

-	

+

 	public void setKeepDaughtersPDGID(int[] keepDaughtersPDGID) {
 		this.keepDaughtersPDGID.clear();
 		for (int pdgid : keepDaughtersPDGID) {
 			this.keepDaughtersPDGID.add(pdgid);
 		}
 	}

-	

+

 	public void setDaughterEnergyCut(double daughterEnergyCut) {
 		this.daughterEnergyCut = daughterEnergyCut;
 	}

-	
-	
-	

+

 	// -------------------- Protected Methods --------------------

-	

+

 	/**

-	 * Creates a list of skimmed mc particles which are kept together
-	 * with all their ancestors. First of all, all the particles that
-	 * are created by the generator (IntermediateState or FinalState)
-	 * are kept. In addition bremsstrahlung photons created by these
-	 * particles are kept. Finally all the particles from a given list
-	 * (default: gamma, pi0, K0s) are kept together with their direct
-	 * daughters.

+	 * Creates a list of skimmed mc particles which are kept together with all
+	 * their ancestors. First of all, all the particles that are created by the
+	 * generator (IntermediateState, Documentation or FinalState) are kept. In
+	 * addition bremsstrahlung photons created by these particles are kept.
+	 * Finally all the particles from a given list (default: gamma, pi0, K0s)
+	 * are kept together with their direct daughters.

 	 */

-	protected List<MCParticle> createSkimmedMcParticleList(List<MCParticle> mcParticles) {
-		

+	protected List<MCParticle> createSkimmedMcParticleList(
+			List<MCParticle> mcParticles) {
+

 		List<MCParticle> skimmedMcParticles = new ArrayList<MCParticle>();

-		

+

 		for (MCParticle mcParticle : mcParticles) {
 			SimulatorStatus simStatus = mcParticle.getSimulatorStatus();

-			if (mcParticle.getGeneratorStatus() == MCParticle.INTERMEDIATE ) {

+			if (mcParticle.getGeneratorStatus() == MCParticle.INTERMEDIATE) {

 				// first add all intermediate particles
 				addMcParticleWithParents(mcParticle, skimmedMcParticles);
 			}

+			if (mcParticle.getGeneratorStatus() == MCParticle.DOCUMENTATION) {
+				// add all documentation particles, needed for Mokka which
+				// stores the initial particles like that
+				addMcParticleWithParents(mcParticle, skimmedMcParticles);
+			}

 			if (mcParticle.getGeneratorStatus() == MCParticle.FINAL_STATE) {
 				// add all mc particles created by the generator
 				addMcParticleWithParents(mcParticle, skimmedMcParticles);

@@ -317,91 +345,129 @@

 				if (simStatus.isDecayedInCalorimeter()) {
 					// keep bremsstrahlung
 					for (MCParticle daughter : mcParticle.getDaughters()) {

-						if (daughter.getPDGID() == 22 && daughter.getEnergy() > daughterEnergyCut && !daughter.getSimulatorStatus().isBackscatter()) {
-							addMcParticleWithParents(daughter, skimmedMcParticles);

+						if (daughter.getPDGID() == 22
+								&& daughter.getEnergy() > daughterEnergyCut
+								&& !daughter.getSimulatorStatus()
+										.isBackscatter()) {
+							addMcParticleWithParents(daughter,
+									skimmedMcParticles);

 						}
 					}
 				}
 				//
 			} else if (mcParticle.getSimulatorStatus().isDecayedInTracker()) {

-				// now add all daughters of the particles that decayed in flight and should be kept

+				// now add all daughters of the particles that decayed in flight
+				// and should be kept

 				if (keepDaughtersPDGID.contains(mcParticle.getPDGID())) {
 					for (MCParticle daughter : mcParticle.getDaughters()) {

-						if (daughter.getEnergy() > daughterEnergyCut && !daughter.getSimulatorStatus().isBackscatter()) {
-							addMcParticleWithParents(daughter, skimmedMcParticles);

+						if (daughter.getEnergy() > daughterEnergyCut
+								&& !daughter.getSimulatorStatus()
+										.isBackscatter()) {
+							addMcParticleWithParents(daughter,
+									skimmedMcParticles);

 						}
 					}
 				}

-				

+

 			}
 		}

-		
-		print(HLEVEL_NORMAL, "Keeping "+skimmedMcParticles.size()+" of "+mcParticles.size()+" mc particles in skimmed list.");
-		

+
+		print(HLEVEL_NORMAL, "Keeping " + skimmedMcParticles.size() + " of "
+				+ mcParticles.size() + " mc particles in skimmed list.");
+

 		return skimmedMcParticles;
 	}

-	

+

 	/**

-	 * Fills a map connecting an mc particle with its closest ancestor
-	 * that is present in the skimmed mc particle list.
-	 * If no suitable ancestor is found the map is filled with null for
-	 * that mc particle.
-	 * @param mcParticles The list of all mc particles
-	 * @param skimmedMcParticles A subset of the mc particles
-	 * @return A mapping between all mc particles and their closest ancestor present in the skimmed mc particles

+	 * Fills a map connecting an mc particle with its closest ancestor that is
+	 * present in the skimmed mc particle list. If no suitable ancestor is found
+	 * the map is filled with null for that mc particle.
+	 * 
+	 * @param mcParticles
+	 *            The list of all mc particles
+	 * @param skimmedMcParticles
+	 *            A subset of the mc particles
+	 * @return A mapping between all mc particles and their closest ancestor
+	 *         present in the skimmed mc particles

 	 */

-	protected Map<MCParticle, MCParticle> fillMcParticleToSkimmedMap(List<MCParticle> mcParticles, List<MCParticle> skimmedMcParticles) {
-		

+	protected Map<MCParticle, MCParticle> fillMcParticleToSkimmedMap(
+			List<MCParticle> mcParticles, List<MCParticle> skimmedMcParticles) {
+

 		Map<MCParticle, MCParticle> mcParticleToSkimmedMap = new HashMap<MCParticle, MCParticle>();

-		

+

 		for (MCParticle mcParticle : mcParticles) {

-			MCParticle ancestor = findMcParticleAncestor(mcParticle, skimmedMcParticles);

+			MCParticle ancestor = findMcParticleAncestor(mcParticle,
+					skimmedMcParticles);

 			mcParticleToSkimmedMap.put(mcParticle, ancestor);
 			if (mcParticle != ancestor) {

-				print(HLEVEL_FULL,
-						"Warning: Rejecting mc particle." +
-						"\tEnergy: "+mcParticle.getEnergy()+"\n" +
-						"\tCharge: "+mcParticle.getCharge()+"\n" +
-						"\tPDGID: "+mcParticle.getPDGID()+"\n" +
-						"\tGenStatus: "+mcParticle.getGeneratorStatus()+"\n" +
-						"\tCreated in simulation: "+mcParticle.getSimulatorStatus().isCreatedInSimulation()+"\n" +
-						"\tBackscatter: "+mcParticle.getSimulatorStatus().isBackscatter()+"\n" +
-						"\tDecay in calorimeter: "+mcParticle.getSimulatorStatus().isDecayedInCalorimeter()+"\n" +
-						"\tDecay in tracker: "+mcParticle.getSimulatorStatus().isDecayedInTracker()+"\n" +
-						"\tStopped: "+mcParticle.getSimulatorStatus().isStopped()+"\n" +
-						"\tMother: "+mcParticle.getParents().get(0).getPDGID(),
-						true);

+				print(HLEVEL_FULL, "Warning: Rejecting mc particle."
+						+ "\tEnergy: "
+						+ mcParticle.getEnergy()
+						+ "\n"
+						+ "\tCharge: "
+						+ mcParticle.getCharge()
+						+ "\n"
+						+ "\tPDGID: "
+						+ mcParticle.getPDGID()
+						+ "\n"
+						+ "\tGenStatus: "
+						+ mcParticle.getGeneratorStatus()
+						+ "\n"
+						+ "\tCreated in simulation: "
+						+ mcParticle.getSimulatorStatus()
+								.isCreatedInSimulation()
+						+ "\n"
+						+ "\tBackscatter: "
+						+ mcParticle.getSimulatorStatus().isBackscatter()
+						+ "\n"
+						+ "\tDecay in calorimeter: "
+						+ mcParticle.getSimulatorStatus()
+								.isDecayedInCalorimeter()
+						+ "\n"
+						+ "\tDecay in tracker: "
+						+ mcParticle.getSimulatorStatus().isDecayedInTracker()
+						+ "\n"
+						+ "\tStopped: "
+						+ mcParticle.getSimulatorStatus().isStopped()
+						+ "\n"
+						+ "\tMother: "
+						+ mcParticle.getParents().get(0).getPDGID(), true);

 			}
 		}
 		return mcParticleToSkimmedMap;
 	}

-	

+

 	/**

-	 * Creates the relations from tracks to mc particles by using a list
-	 * of LCRelations from hits to mc particles.
-	 * In case of a skimmed mc particle list the relations are pointing
-	 * to the closest ancestor present in the skimmed list.

+	 * Creates the relations from tracks to mc particles by using a list of
+	 * LCRelations from hits to mc particles. In case of a skimmed mc particle
+	 * list the relations are pointing to the closest ancestor present in the
+	 * skimmed list.

 	 * <p>

-	 * The relations are weighted by the fraction of hits belonging to
-	 * a certain mc particle (N_{match}/N_{track}).

+	 * The relations are weighted by the fraction of hits belonging to a certain
+	 * mc particle (N_{match}/N_{track}).

 	 * <p>

-	 * In case of Tanimoto distance also the total number of hits produced
-	 * by the mc particle are taken into account. It gives less weight to
-	 * tracks that miss true hits. The weight is then calculated as
-	 * 1 - (N_{track}+N_{mc}-2*N_{match})/(N_{track}+N_{mc}-N_{match).
-	 * @param tracks The list of tracks to be truth linked
-	 * @param trackHitMcRelation The LCRelations between track hits and mc particles

+	 * In case of Tanimoto distance also the total number of hits produced by
+	 * the mc particle are taken into account. It gives less weight to tracks
+	 * that miss true hits. The weight is then calculated as 1 -
+	 * (N_{track}+N_{mc}-2*N_{match})/(N_{track}+N_{mc}-N_{match).
+	 * 
+	 * @param tracks
+	 *            The list of tracks to be truth linked
+	 * @param trackHitMcRelation
+	 *            The LCRelations between track hits and mc particles

 	 * @return The weighted LCRelations between tracks and mc particles
 	 */

-	protected List<LCRelation> createTrackMcRelation(List<Track> tracks, List<LCRelation> trackHitMcRelation) {
-		

+	protected List<LCRelation> createTrackMcRelation(List<Track> tracks,
+			List<LCRelation> trackHitMcRelation) {
+

 		if (trackHitMcRelation == null) {

-			throw new IllegalArgumentException("No tracker hit to mc relations given.");

+			throw new IllegalArgumentException(
+					"No tracker hit to mc relations given.");

 		}

-		

+

 		RelationalTable<TrackerHit, MCParticle> trackHitMcRelationTable = createRelationalTable(trackHitMcRelation);
 		List<LCRelation> trackMcRelation = new ArrayList<LCRelation>();

-		

+

 		for (Track track : tracks) {
 			// Store number of hits contributed by each mc particle
 			Map<MCParticle, Integer> mcParticleContribution = new HashMap<MCParticle, Integer>();

@@ -409,10 +475,13 @@

 			double trackHits = trackHitsList.size();
 			double sumOfWeights = 0;
 			for (TrackerHit trackHit : trackHitsList) {

-				for (MCParticle mcParticle : trackHitMcRelationTable.allFrom(trackHit)) {
-					if (useSkimmedMcParticles) mcParticle = mcParticleToSkimmed.get(mcParticle);

+				for (MCParticle mcParticle : trackHitMcRelationTable
+						.allFrom(trackHit)) {
+					if (useSkimmedMcParticles)
+						mcParticle = mcParticleToSkimmed.get(mcParticle);

 					if (mcParticleContribution.containsKey(mcParticle)) {

-						mcParticleContribution.put(mcParticle, mcParticleContribution.get(mcParticle)+1);

+						mcParticleContribution.put(mcParticle,
+								mcParticleContribution.get(mcParticle) + 1);

 					} else {
 						mcParticleContribution.put(mcParticle, 1);
 					}

@@ -423,94 +492,117 @@

 				double weight = 0.0;
 				double recoHits = mcParticleContribution.get(mcParticle);
 				if (useTanimotoDistance) {

-					double trueHits = trackHitMcRelationTable.allTo(mcParticle).size();
-					weight = 1 - (trackHits+trueHits-2*recoHits)/(trackHits+trueHits-recoHits);

+					double trueHits = trackHitMcRelationTable.allTo(mcParticle)
+							.size();
+					weight = 1 - (trackHits + trueHits - 2 * recoHits)
+							/ (trackHits + trueHits - recoHits);

 				} else {

-					weight = recoHits/trackHits;

+					weight = recoHits / trackHits;

 				}
 				sumOfWeights += weight;

-				trackMcRelation.add(new BaseLCRelation(track, mcParticle, weight));
-				print(HLEVEL_FULL, "Added a track to mc particle relation with weight "+weight+".");
-				if (!fullRecoRelation) break;
-			}
-			print(HLEVEL_HIGH, "Total weight of track contributions is "+sumOfWeights+".");
-		}
-		
-		print(HLEVEL_NORMAL, "Created "+trackMcRelation.size()+" track to mc particle relations.");
-		

+				trackMcRelation.add(new BaseLCRelation(track, mcParticle,
+						weight));
+				print(HLEVEL_FULL,
+						"Added a track to mc particle relation with weight "
+								+ weight + ".");
+				if (!fullRecoRelation)
+					break;
+			}
+			print(HLEVEL_HIGH, "Total weight of track contributions is "
+					+ sumOfWeights + ".");
+		}
+
+		print(HLEVEL_NORMAL, "Created " + trackMcRelation.size()
+				+ " track to mc particle relations.");
+

 		return trackMcRelation;
 	}

-	

+

 	/**

-	 * Creates the relations from calorimeter hits to mc particles
-	 * by using a list of LCRelations from CalorimeterHits to
-	 * SimCalorimeterHits and the intrinsic link to mc particles of
-	 * the sim hits.

+	 * Creates the relations from calorimeter hits to mc particles by using a
+	 * list of LCRelations from CalorimeterHits to SimCalorimeterHits and the
+	 * intrinsic link to mc particles of the sim hits.

 	 * <p>

-	 * The produced relations are weighted by the energy fraction
-	 * contributed by the mc particle to the SimCalorimeterHit
-	 * (E_{MC,Hit}/E_{Hit})
-	 * @param caloHitSimHitRelation The relations between CalorimeterHits and SimCalorimeterHits

+	 * The produced relations are weighted by the energy fraction contributed by
+	 * the mc particle to the SimCalorimeterHit (E_{MC,Hit}/E_{Hit})
+	 * 
+	 * @param caloHitSimHitRelation
+	 *            The relations between CalorimeterHits and SimCalorimeterHits

 	 * @return The weighted LCRelations between CalorimeterHits and MCParticles
 	 */

-	protected List<LCRelation> createCaloHitMcRelation(List<LCRelation> caloHitSimHitRelation) {
-		

+	protected List<LCRelation> createCaloHitMcRelation(
+			List<LCRelation> caloHitSimHitRelation) {
+

 		List<LCRelation> caloHitMcRelation = new ArrayList<LCRelation>();

-		

+

 		for (LCRelation relation : caloHitSimHitRelation) {
 			CalorimeterHit digiHit = (CalorimeterHit) relation.getFrom();
 			SimCalorimeterHit simHit = (SimCalorimeterHit) relation.getTo();
 			double hitEnergy = simHit.getRawEnergy();
 			double sumOfWeights = 0;
 			for (int i = 0; i < simHit.getMCParticleCount(); i++) {

-				double weight = simHit.getContributedEnergy(i)/hitEnergy;

+				double weight = simHit.getContributedEnergy(i) / hitEnergy;

 				sumOfWeights += weight;

-				caloHitMcRelation.add(new BaseLCRelation(digiHit, simHit.getMCParticle(i), weight));
-				print(HLEVEL_FULL, "Added a calorimeter hit to mc particle relation with weight "+weight+".");

+				caloHitMcRelation.add(new BaseLCRelation(digiHit, simHit
+						.getMCParticle(i), weight));
+				print(HLEVEL_FULL,
+						"Added a calorimeter hit to mc particle relation with weight "
+								+ weight + ".");

 			}

-			print(HLEVEL_FULL, "Total weight of calorimeter hit contributions is "+sumOfWeights+".");

+			print(HLEVEL_FULL,
+					"Total weight of calorimeter hit contributions is "
+							+ sumOfWeights + ".");

 		}

-		
-		print(HLEVEL_NORMAL, "Created "+caloHitMcRelation.size()+" calorimeter hit to mc particle relations.");
-		

+
+		print(HLEVEL_NORMAL, "Created " + caloHitMcRelation.size()
+				+ " calorimeter hit to mc particle relations.");
+

 		return caloHitMcRelation;
 	}

-	

+

 	/**

-	 * Creates the relations from Clusters to MCParticles by using
-	 * a list of LCRelations from CalorimeterHits to MCParticles.

+	 * Creates the relations from Clusters to MCParticles by using a list of
+	 * LCRelations from CalorimeterHits to MCParticles.

 	 * <p>

-	 * The produced relations are weighted by the energy fraction
-	 * contributed by the MCParticle to the Cluster
-	 * (E_{MC,Cluster}/E_{Cluster})
-	 * @param clusters The list of clusters to be truth linked
-	 * @param caloHitMcRelation The relations between CalorimeterHits and MCParticles

+	 * The produced relations are weighted by the energy fraction contributed by
+	 * the MCParticle to the Cluster (E_{MC,Cluster}/E_{Cluster})
+	 * 
+	 * @param clusters
+	 *            The list of clusters to be truth linked
+	 * @param caloHitMcRelation
+	 *            The relations between CalorimeterHits and MCParticles

 	 * @return The weighted LCRelations between Clusters and MCParticles
 	 * @throws IllegalArgumentException
 	 */

-	protected List<LCRelation> createClusterMcRelation(List<Cluster> clusters, List<LCRelation> caloHitMcRelation) throws IllegalArgumentException {
-		

+	protected List<LCRelation> createClusterMcRelation(List<Cluster> clusters,
+			List<LCRelation> caloHitMcRelation) throws IllegalArgumentException {
+

 		if (caloHitMcRelation == null) {

-			throw new IllegalArgumentException("No calorimeter hit to mc relations given.");

+			throw new IllegalArgumentException(
+					"No calorimeter hit to mc relations given.");

 		}

-		

+

 		RelationalTable<CalorimeterHit, MCParticle> caloHitMcRelationTable = createRelationalTable(caloHitMcRelation);
 		List<LCRelation> clusterMcRelation = new ArrayList<LCRelation>();

-		

+

 		for (Cluster cluster : clusters) {
 			double sumOfWeights = 0;
 			double clusterEnergy = cluster.getEnergy();

-			Map<MCParticle,Double> mcParticlesWeight = new HashMap<MCParticle, Double>();

+			Map<MCParticle, Double> mcParticlesWeight = new HashMap<MCParticle, Double>();

 			for (CalorimeterHit hit : cluster.getCalorimeterHits()) {
 				double hitEnergy = hit.getCorrectedEnergy();

-				double hitWeight = hitEnergy/clusterEnergy;
-				Map<MCParticle,Double> hitMcParticlesWeight = caloHitMcRelationTable.allFromWithWeights(hit);

+				double hitWeight = hitEnergy / clusterEnergy;
+				Map<MCParticle, Double> hitMcParticlesWeight = caloHitMcRelationTable
+						.allFromWithWeights(hit);

 				for (MCParticle mcParticle : hitMcParticlesWeight.keySet()) {

-					// TODO implement optional use of Tanimoto distance 
-					double weight = hitWeight*hitMcParticlesWeight.get(mcParticle);
-					if (useSkimmedMcParticles) mcParticle = mcParticleToSkimmed.get(mcParticle);