Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java	(revision 1617)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java	(revision 1618)
@@ -1,31 +1,33 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
 
-
+import java.util.ArrayList;
 import java.util.Random;
 
-public class NumberSequence  {
+public class NumberSequence {
 	private int[] sequence;
 	private int signature;
-	
+
 	public NumberSequence(int size) {
-		
+
 		sequence = new int[size];
 	}
-	
+
 	public int[] getSequence() {
 		return sequence;
 	}
+
 	public void setSequence(int[] sequence) {
 		this.sequence = sequence;
 	}
+
 	public int getSignature() {
 		return signature;
 	}
+
 	public void setSignature(int signature) {
 		this.signature = signature;
 	}
-	
-	public void printSequence()
-	{	
+
+	public void printSequence() {
 		for (int i = 0; i < sequence.length; i++) {
 			System.out.format("%5d", sequence[i]);
@@ -33,18 +35,39 @@
 		System.out.println();
 	}
-	
-	public NumberSequence shuffle(){
+
+	public NumberSequence shuffle() {
 		NumberSequence result = new NumberSequence(sequence.length);
 		result.setSequence(this.sequence);
 		Random rgen = new Random();
-		
-		for (int i=0; i<result.sequence.length; i++) {
-		    int randomPosition = rgen.nextInt(result.sequence.length);
-		    int temp = result.sequence[i];
-		    result.sequence[i] = result.sequence[randomPosition];
-		    result.sequence[randomPosition] = temp;
+
+		for (int i = 0; i < result.sequence.length; i++) {
+			int randomPosition = rgen.nextInt(result.sequence.length);
+			int temp = result.sequence[i];
+			result.sequence[i] = result.sequence[randomPosition];
+			result.sequence[randomPosition] = temp;
 		}
 		return result;
-		
+
+	}
+
+	// TODO: This can be done faster
+	public int containsPattern(ArrayList<NumberSequence> pattern) {
+		int i = 0;
+		int count = 0;
+		int[] pat1 = pattern.get(0).getSequence();
+		int[] pat2 = pattern.get(1).getSequence();
+		notmatched: while (i < sequence.length - pat1.length) {
+			if (sequence[i] == pat1[0] || sequence[i] == pat2[0]) {
+				for (int j = 0; j < pat1.length; j++) {
+					if (sequence[i + j] != pat1[j]
+							&& sequence[i + j] != pat2[j]) {
+						continue notmatched;
+					}
+				}
+				count++;
+			}
+			i++;
+		}
+		return count;
 	}
 
Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1617)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1618)
@@ -375,6 +375,7 @@
 		}
 	
-
+		//Console.traceln(Level.INFO,"Generating DP Matrix");
 		buildMatrix();
+		//Console.traceln(Level.INFO,"Doing traceback");
 		traceback();
 	}
Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java	(revision 1617)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java	(revision 1618)
@@ -3,8 +3,10 @@
 import java.util.ArrayList;
 import java.util.Iterator;
+import java.util.logging.Level;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
+import de.ugoe.cs.util.console.Console;
 
 public class PairwiseAlignmentGenerator {
@@ -22,4 +24,5 @@
 
 				if (i != j) {
+					Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
 					int smithWatermanThreshold = 10;
 					AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1617)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1618)
@@ -153,42 +153,50 @@
 		SymbolMap<ITaskInstance, ITask> uniqueTasks = harmonizeEventTaskInstancesModel(appData);
 
+		Console.traceln(Level.INFO,"generating substitution matrix");
 		ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(
 				uniqueTasks, 5);
 		submat.generate();
 
-		ArrayList<NumberSequence> matchseqs = new ArrayList<NumberSequence>();
+		Console.traceln(Level.INFO,"generating pairwise alignments");
+		ArrayList<ArrayList<NumberSequence>> matchseqs = new ArrayList<ArrayList<NumberSequence>>();
 		PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat);
 		
+		Console.traceln(Level.INFO,"retrieving significant sequence pieces");
 		for (int i=0; i< numberseqs.size();i++) {
 			for(int j=0; j< numberseqs.size();j++) {
 				if(i != j) {
 					ArrayList<ArrayList<NumberSequence>> tmp = alignments.get(i, j).getMatches();
-					int count = 0;
-					for(Iterator<ArrayList<NumberSequence>> it = tmp.iterator();it.hasNext();) {
-						System.out.println("Match number " + count);
-						ArrayList<NumberSequence> tmp2 = it.next();
-						tmp2.get(0).printSequence();
-						tmp2.get(1).printSequence();
-						System.out.println();
-						count++;
-						matchseqs.addAll(tmp2);
+					matchseqs.addAll(tmp);
+				}   
+			}
+		}
+		
+		Console.traceln(Level.INFO, "searching for patterns occuring most");
+		//search this match in every other sequence
+		for(int i=0; i < matchseqs.size();i++) {
+			for(int j=0; j < matchseqs.size();j++) {
+				if(i>j) {
+					if(matchseqs.get(j).get(0).containsPattern(matchseqs.get(i)) > 0 || matchseqs.get(j).get(1).containsPattern(matchseqs.get(i)) > 0) {
+						System.out.println("Found something!");
 					}
-					System.out.println();
-				}
-			}
-		}
-		
-		AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+				}
+			}
+				
+		}
 		
 		
-		PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(numberseqs, submat);
-		UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);
-		System.out.println(alignments.getDistanceMatrix());
-		//UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
 		
-		for(Iterator<NumberSequence> it = guidetree.getRoot().getSequences().iterator();it.hasNext();) {
-			NumberSequence tmp = (NumberSequence) it.next();
-			tmp.printSequence();
-		}
+		alignments = null;
+		
+		//
+		//AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+		//PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(matchseqs, submat);
+		//UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);
+		//System.out.println(alignments.getDistanceMatrix());
+		
+		//for(Iterator<NumberSequence> it = guidetree.getRoot().getSequences().iterator();it.hasNext();) {
+		//	NumberSequence tmp = (NumberSequence) it.next();
+		//	tmp.printSequence();
+		//}