Index: branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java	(revision 1654)
@@ -24,4 +24,6 @@
 		AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
 				.create();
+		
+		assertNotNull(testalignment1);
 		testalignment1.align(ns1, ns2,submat,5);
 
@@ -44,4 +46,5 @@
 		AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
 				.create();
+		assertNotNull(testalignment1);
 		testalignment1.align(ns1, ns2,submat,5);
 		assertTrue(testalignment1.getAlignmentScore()==5);
@@ -63,4 +66,5 @@
 		AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
 				.create();
+		assertNotNull(testalignment1);
 		testalignment1.align(ns1, ns2,submat,4);
 		testalignment1.printDPMatrix();
@@ -90,6 +94,7 @@
 		AlignmentAlgorithm testalignment1 = AlignmentAlgorithmFactory
 				.create();
+		assertNotNull(testalignment1);
 		testalignment1.align(ns1, ns2,submat,3);
-		//assertTrue(testalignment1.getAlignmentScore()==7);
+		assertTrue(testalignment1.getAlignmentScore()==1.0);
 		
 		}
Index: branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignmentTest.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignmentTest.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignmentTest.java	(revision 1654)
@@ -97,5 +97,5 @@
             "}";
 
-        applySessionScopeRule(SequenceForTaskDetectionRule.class, input, output);
+        applySessionScopeRule(SequenceForTaskDetectionRuleAlignment.class, input, output);
     }
 
@@ -171,5 +171,5 @@
             "}";
 
-        applySessionScopeRule(SequenceForTaskDetectionRule.class, input, output);
+        applySessionScopeRule(SequenceForTaskDetectionRuleAlignment.class, input, output);
     }
 
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java	(revision 1654)
@@ -60,9 +60,10 @@
 	}
 
-	
+	/*
 	public void addOccurencesOf(Match m) {
 		LinkedList<MatchOccurence> occ = m.getOccurences();
 		occurences.addAll(occ);
 	}
+	*/
 	
    
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java	(revision 1654)
@@ -227,4 +227,5 @@
 		}
 
+		
 		NumberSequence ns1 = new NumberSequence(reversed1.length);
 		NumberSequence ns2 = new NumberSequence(reversed2.length);
@@ -304,6 +305,6 @@
 				tmpal.setFirstSequence(tmpns1);
 				tmpal.setSecondSequence(tmpns2);
-				tmpal.addOccurence(new MatchOccurence(start,alignment.get(0).getId()));
-				tmpal.addOccurence(new MatchOccurence(start,alignment.get(1).getId()));
+				//tmpal.addOccurence(new MatchOccurence(start,alignment.get(0).getId()));
+				//tmpal.addOccurence(new MatchOccurence(start,alignment.get(1).getId()));
 				result.add(tmpal);
 			}
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java	(revision 1654)
@@ -14,4 +14,6 @@
 
 package de.ugoe.cs.autoquest.tasktrees.temporalrelation;
+
+import java.util.Iterator;
 
 import de.ugoe.cs.autoquest.tasktrees.treeifc.ISequence;
@@ -93,9 +95,10 @@
         ISequenceInstance subsequence = taskFactory.createNewTaskInstance(model);
         
-       
+       for (Iterator<ITaskInstance> it = subsequence.iterator();it.hasNext();) {
+    	   ITaskInstance foo =  it.next();
+    	   System.out.println(foo);
+       }
         
         System.out.println("Got model: " + model.toString());
-        
-       
         
        
Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java
===================================================================
--- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1653)
+++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1654)
@@ -203,14 +203,17 @@
 				if (startpositions.size() > 0) {
 					NumberSequence tempns = appData.getNumberSequences().get(j);
-					for(int k=0;k<tempns.getSequence().length;k++) {
-						System.out.println(k + ": " + tempns.getSequence()[k]);
-					}
+					
 					for (Iterator<Integer> jt = startpositions.iterator(); jt
 							.hasNext();) {
 						int start = jt.next();
+						//TODO: Debug Output
 						System.out.println("Found match ");
 						pattern.getFirstSequence().printSequence();
 						pattern.getSecondSequence().printSequence(); 
 						System.out.println("in sequence " + (j+1) + " at position " + start);
+						for(int k=0;k<tempns.getSequence().length;k++) {
+							System.out.print(k + ": " + tempns.getSequence()[k] + " ");
+							System.out.println(appData.getNumber2Task().get(tempns.getSequence()[k]));
+						}
 						pattern.addOccurence(
 								new MatchOccurence(start, j));
@@ -225,9 +228,9 @@
 		Comparator<Match> comparator = new Comparator<Match>() {
 			public int compare(Match m1, Match m2) {
-				return m2.occurenceCount() - m1.occurenceCount(); // use your
-																	// logic
+				return m2.occurenceCount() - m1.occurenceCount(); 
+																	
 			}
 		};
-		Collections.sort(matchseqs, comparator);
+		//Collections.sort(matchseqs, comparator);
 		
 
@@ -276,5 +279,5 @@
 					matchseqs.get(i).getFirstSequence().printSequence();
 					matchseqs.get(i).getSecondSequence().printSequence();
-					System.out.println(" in session number: " + (oc.getSequenceId()+1) + " at position " + oc.getStartindex() + "-" + (oc.getStartindex()+matchseqs.get(i).getFirstSequence().size()));
+					System.out.println(" in session number: " + (oc.getSequenceId()+1) + " at position " + (oc.getStartindex()) + "-" + (oc.getStartindex()+matchseqs.get(i).getFirstSequence().size()));
 					System.out.println("Printing session: ");
 					for(int j=0;j<sessions.get(oc.getSequenceId()).size();j++) {
@@ -356,8 +359,7 @@
 		ITask task;
 		List<IUserSession> sessions = appData.getSessions();
-		int sessionNo = 0;
-		for (IUserSession session : sessions) {
-			Console.traceln(Level.FINE, "handling " + (++sessionNo) + ". "
-					+ session);
+		for (int j = 0; j< sessions.size();j++) {
+			IUserSession session = sessions.get(j);
+	
 			NumberSequence templist = new NumberSequence(session.size());
 
@@ -380,5 +382,5 @@
 			}
 			//Each NumberSequence is identified by its id, beginning to count at zero
-			templist.setId(sessionNo-1);
+			templist.setId(j);
 			appData.getNumberSequences().add(templist);
 			comparator.clearBuffers();
@@ -562,4 +564,6 @@
 	    		}
 	    	}
+	    	
+	    	//TODO: Debug output
 	    	for (int i =0;i<sequence.getChildren().size();i++) {
 	    		System.out.println(sequence.getChildren().get(i));