Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java	(revision 1747)
+++ 	(revision )
@@ -1,94 +1,0 @@
-/**
- * 
- */
-package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
-
-import java.util.HashSet;
-import java.util.LinkedList;
-
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
-
-// TODO: Auto-generated Javadoc
-/**
- * The Class DifferenceSubstitutionMatrix.
- *
- * @author Ralph Krimmel
- */
-public class DifferenceSubstitutionMatrix implements SubstitutionMatrix {
-
-	/** The input1. */
-	private final int[] input1;
-	
-	/** The input2. */
-	private final int[] input2;
-	
-	/** The max value. */
-	private final int maxValue;
-
-	/**
-	 * Instantiates a new difference substitution matrix.
-	 *
-	 * @param input1 the input1
-	 * @param input2 the input2
-	 */
-	public DifferenceSubstitutionMatrix(int[] input1, int[] input2) {
-		this.input1 = input1;
-		this.input2 = input2;
-		this.maxValue = getMaxValue();
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#generate(java.util.HashSet)
-	 */
-	@Override
-	public void generate(HashSet<ITask> uniqueTasks) {
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#getGapPenalty()
-	 */
-	@Override
-	public float getGapPenalty() {
-		return -maxValue;
-	}
-
-	/**
-	 * Gets the max value.
-	 *
-	 * @return the max value
-	 */
-	private int getMaxValue() {
-		int max = input1[0];
-		for (int i = 0; i < input1.length; i++) {
-			if (input1[i] > max) {
-				max = input1[i];
-			}
-		}
-		for (int j = 0; j < input2.length; j++) {
-			if (input2[j] > max) {
-				max = input2[j];
-			}
-		}
-		return max;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int,
-	 * int)
-	 */
-	@Override
-	public float getScore(int pos1, int pos2) {
-		return maxValue - (input1[pos1] - input2[pos2]);
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#update(java.util.LinkedList)
-	 */
-	@Override
-	public void update(LinkedList<ITask> newlyGeneratedTasks) {
-	}
-
-}
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java	(revision 1747)
+++ 	(revision )
@@ -1,53 +1,0 @@
-/*
- * 
- */
-package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
-
-import java.util.HashSet;
-import java.util.LinkedList;
-
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
-
-// TODO: Auto-generated Javadoc
-/**
- * The Class DummySubstitutionMatrix.
- */
-public class DummySubstitutionMatrix implements SubstitutionMatrix {
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#generate(java.util.HashSet)
-	 */
-	@Override
-	public void generate(HashSet<ITask> uniqueTasks) {
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#getGapPenalty()
-	 */
-	@Override
-	public float getGapPenalty() {
-		return -1;
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#getScore(int, int)
-	 */
-	@Override
-	public float getScore(int pos1, int pos2) {
-		if (pos1 == pos2) {
-			return 1;
-		} else {
-			return 0;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#update(java.util.LinkedList)
-	 */
-	@Override
-	public void update(LinkedList<ITask> newlyGeneratedTasks) {
-		// TODO Auto-generated method stub
-
-	}
-
-}
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java	(revision 1747)
+++ 	(revision )
@@ -1,80 +1,0 @@
-/**
- * 
- */
-package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
-
-import java.util.HashSet;
-import java.util.LinkedList;
-
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
-
-// TODO: Auto-generated Javadoc
-/**
- * The Class NearbySubstitutionMatrix.
- *
- * @author Ralph Krimmel
- */
-public class NearbySubstitutionMatrix implements SubstitutionMatrix {
-
-	/** The input1. */
-	private final int[] input1;
-	
-	/** The input2. */
-	private final int[] input2;
-	
-	/** The range. */
-	private final int range;
-
-	/**
-	 * Instantiates a new nearby substitution matrix.
-	 *
-	 * @param input1 the input1
-	 * @param input2 the input2
-	 * @param range the range
-	 */
-	public NearbySubstitutionMatrix(int[] input1, int[] input2, int range) {
-		this.input1 = input1;
-		this.input2 = input2;
-		this.range = range;
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#generate(java.util.HashSet)
-	 */
-	@Override
-	public void generate(HashSet<ITask> uniqueTasks) {
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#getGapPenalty()
-	 */
-	@Override
-	public float getGapPenalty() {
-		return -range - 1;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int,
-	 * int)
-	 */
-	@Override
-	public float getScore(int pos1, int pos2) {
-		final int difference = Math.abs(input1[pos1] - input2[pos2]);
-		if (difference < range) {
-			return range - difference;
-		} else {
-			return -range;
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix#update(java.util.LinkedList)
-	 */
-	@Override
-	public void update(LinkedList<ITask> newlyGeneratedTasks) {
-	}
-
-}
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java	(revision 1747)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java	(revision 1748)
@@ -5,4 +5,5 @@
 
 import java.io.Serializable;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -37,5 +38,5 @@
 	
 	/** The unique tasks. */
-	private HashSet<ITask> uniqueTasks;
+	private Collection<ITask> uniqueTasks;
 	
 	/** The gap penalty. */
@@ -209,5 +210,5 @@
 	 */
 	@Override
-	public void generate(HashSet<ITask> uniqueTasks) {
+	public void generate(Collection<ITask> uniqueTasks) {
 		this.uniqueTasks = uniqueTasks;
 		if (this.calculateNonEventTaskInstances) {
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PreallocatedDynamicTriangleMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PreallocatedDynamicTriangleMatrix.java	(revision 1747)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PreallocatedDynamicTriangleMatrix.java	(revision 1748)
@@ -54,5 +54,5 @@
             this.size += count;
             if(size>actualsize) {
-                int newElements = ((oldsize * count) + ((count * (count + 1)) / 2));
+                //int newElements = ((oldsize * count) + ((count * (count + 1)) / 2));
                 actualsize*=2;
                 float[] newmatrix = new float[actualsize];
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java	(revision 1747)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java	(revision 1748)
@@ -4,5 +4,5 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
 
-import java.util.HashSet;
+import java.util.Collection;
 import java.util.LinkedList;
 
@@ -20,5 +20,5 @@
 	 * @param uniqueTasks the unique tasks
 	 */
-	public void generate(HashSet<ITask> uniqueTasks);
+	public void generate(Collection<ITask> uniqueTasks);
 
 	/**