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 1723)
+++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1724)
@@ -195,10 +195,10 @@
 	public RuleApplicationResult apply(List<IUserSession> sessions) {
 		RuleApplicationData appData = new RuleApplicationData(sessions);
-		File harmonized = new File("harmonized.dat");
-		if(harmonized.exists() && !harmonized.isDirectory()) { 
-			Console.traceln(Level.INFO,"loading harmonized sessions from file");
-			appData = loadAppData("harmonized");
-		}
-		else {
+		//File harmonized = new File("harmonized.dat");
+		//if(harmonized.exists() && !harmonized.isDirectory()) { 
+		//	Console.traceln(Level.INFO,"loading harmonized sessions from file");
+		//	appData = loadAppData("harmonized");
+		//}
+		//else {
 			//appData.getStopWatch().start("harmonization");
 			harmonizeEventTaskInstancesModel(appData);
@@ -207,20 +207,20 @@
 			//Saving intermediate results to file
 			Console.traceln(Level.INFO,"saving substitution matrix to file");
-			saveAppData("harmonized");
-		}
-		
-		File substitution = new File("substitution.dat");
-		if(!(substitution.exists() && !substitution.isDirectory())) { 
+			//saveAppData("harmonized");
+		//}
+		
+		//File substitution = new File("substitution.dat");
+		//if(!(substitution.exists() && !substitution.isDirectory())) { 
 			Console.traceln(Level.INFO, "generating substitution matrix from " + appData.getUniqueTasks().size() + " unique tasks");
 			appData.getStopWatch().start("substitution matrix");
 			appData.getSubmat().generate(appData.getUniqueTasks());
 			appData.getStopWatch().stop("substitution matrix");
-			GlobalDataContainer.getInstance().addData("substitution", appData);
-			saveAppData("substitution");
-		}
-		else {
-			Console.traceln(Level.INFO,"loading substitution matrix from file");
-			appData = loadAppData("substitution");
-		}
+		//	GlobalDataContainer.getInstance().addData("substitution", appData);
+		//	saveAppData("substitution");
+		//}
+		//else {
+		//	Console.traceln(Level.INFO,"loading substitution matrix from file");
+		//	appData = loadAppData("substitution");
+		//}
 		
 		
@@ -229,5 +229,4 @@
 			Console.traceln(Level.INFO, "Iteration Number: " + iteration);
 			iteration++;
-	
 			appData.detectedAndReplacedTasks = false;
 			appData.getStopWatch().start("whole loop");
@@ -654,5 +653,6 @@
 		
 		// Generate pairwise alignments
-		appData.setMatchseqs(generatePairwiseAlignments(appData));
+		//appData.setMatchseqs(generatePairwiseAlignments(appData));
+		generatePairwiseAlignments(appData);
 
 		//Searching each match in all other sessions, counting its occurences
@@ -687,5 +687,4 @@
 						.get(i).getOccurences().iterator(); it.hasNext();) {
 					MatchOccurence oc = it.next();
-					
 					
 					// Check if nothing has been replaced in the sequence we
@@ -732,5 +731,5 @@
 						}
 					}
-					System.out.println("Replacing");
+					System.out.println("Replacing in sequence" + oc.getSequenceId());
 					ISequenceInstance sequenceInstances = RuleUtils
 							.createNewSubSequenceInRange(appData.getSessions()
@@ -747,5 +746,5 @@
 			}
 		}
-		appData.setMatchseqs(null);
+		//appData.setMatchseqs(null);
 		appData.getStopWatch().stop("replacing tasks");
 	}
@@ -880,13 +879,12 @@
 	}
 
-	private LinkedList<Match> generatePairwiseAlignments(RuleApplicationData appData) {
+	//private LinkedList<Match> generatePairwiseAlignments(RuleApplicationData appData) {
+	private void generatePairwiseAlignments(RuleApplicationData appData) {
 		int numberSeqSize = appData.getNumberSequences().size();
-		LinkedList<Match> result;
+		appData.matchseqs = new LinkedList<Match>();
 		//Checking if i have an already calculated file result of this action in the working directory 
-		File aligned = new File("aligned" + iteration + ".dat");
-		if(!(aligned.exists() && !aligned.isDirectory())) {
-			Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions");
-			result = new LinkedList<Match>();
-			
+		//File aligned = new File("aligned" + iteration + ".dat");
+		//if(!(aligned.exists() && !aligned.isDirectory())) {
+			Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions with " + nThreads + " threads");
 			ExecutorService executor = Executors.newFixedThreadPool(nThreads);
 			int interval = Math.round(numberSeqSize/nThreads);
@@ -901,5 +899,5 @@
 				int from = i;
 				int to = i+interval+offset;
-				System.out.println("Creating thread with matches from " + from + " to " + to);
+				System.out.println("Creating thread for sessions " + from + " till " + to);
 				ParallelPairwiseAligner aligner = new ParallelPairwiseAligner(appData,from,to);
 				executor.execute(aligner);
@@ -913,14 +911,13 @@
 			}
 	
-			GlobalDataContainer.getInstance().addData("aligned" + iteration, appData);
-			saveAppData("aligned" + iteration);
-			return result;
-		}
-		else {
-			Console.traceln(Level.INFO,"loading matches from file");
-			appData = loadAppData("aligned"+iteration);
-			return appData.getMatchseqs();
-		}
-	}
+			//GlobalDataContainer.getInstance().addData("aligned" + iteration, appData);
+			//saveAppData("aligned" + iteration);
+		//	return result;
+		}
+		//else {
+		//	Console.traceln(Level.INFO,"loading matches from file");
+		//	appData = loadAppData("aligned"+iteration);
+		//	return appData.getMatchseqs();
+		//}
 	
 
@@ -980,5 +977,4 @@
 			submat= new ObjectDistanceSubstitionMatrix(6,-3,false);
 			newTasks = new LinkedList<ITask>();
-			
 			this.detectedAndReplacedTasks = true;
 		}
@@ -988,7 +984,4 @@
 		}
 
-		public void setMatchseqs(LinkedList<Match> matchseqs) {
-			this.matchseqs = matchseqs;
-		}
 
 		private ObjectDistanceSubstitionMatrix getSubmat() {