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 1722)
+++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1723)
@@ -23,5 +23,4 @@
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
@@ -33,5 +32,4 @@
 import java.util.Map;
 import java.util.Set;
-import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -656,67 +654,11 @@
 		
 		// Generate pairwise alignments
-		int numberSeqSize = appData.getNumberSequences().size();
-		Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions");
-		int count = 0;
-		
-		//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())) {
-			appData.matchseqs = new LinkedList<Match>();
-			for (int i = 0; i < appData.getNumberSequences().size(); i++) {
-				NumberSequence ns1 = appData.getNumberSequences().get(i);
-				count++;
-				printProgressPercentage(count,numberSeqSize);
-				for (int j = 0; j < appData.getNumberSequences().size(); j++) {
-					NumberSequence ns2 = appData.getNumberSequences().get(j);
-					if (i != j) {
-						//Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
-						AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-						aa.align(ns1, ns2, appData.getSubmat(),9);
-						appData.getMatchseqs().addAll(aa.getMatches());
-					}
-				}
-			}
-			GlobalDataContainer.getInstance().addData("aligned" + iteration, appData);
-			saveAppData("aligned" + iteration);
-		}
-		else {
-			Console.traceln(Level.INFO,"loading matches from file");
-			appData = loadAppData("aligned"+iteration);
-		}
-
-
-		Console.traceln(Level.INFO, "searching for patterns occuring most with " + nThreads + " threads");
-		
-		//Prepare parallel search of matchseqs
-		ExecutorService executor = Executors.newFixedThreadPool(nThreads);
-		int matchSeqSize=appData.getMatchseqs().size();
-		int interval = Math.round(matchSeqSize/nThreads);
-		int rest = matchSeqSize % nThreads;
-		
-		for(int i =0;i<matchSeqSize-interval;i+=interval) {
-			int offset =0;
-			if(rest!=0) {
-				offset=1;
-				rest--;
-			}
-			int from = i;
-			int to = i+interval+offset;
-			System.out.println("Creating thread with matches from " + from + " to " + to);
-			// search each match in every other sequence
-			ParallelMatchOcurrencesFinder finder = new ParallelMatchOcurrencesFinder(appData,from,to);
-			executor.execute(finder);
-		}
-		executor.shutdown();
-		try {
-			executor.awaitTermination(2, TimeUnit.HOURS);
-		} catch (InterruptedException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		
-		
-		Console.traceln(Level.INFO, "sorting results");
+		appData.setMatchseqs(generatePairwiseAlignments(appData));
+
+		//Searching each match in all other sessions, counting its occurences
+		searchMatchesInAllSessions(appData);
+		
 		// Sort results to get the most occurring results
+		Console.traceln(Level.INFO, "sorting " + appData.getMatchseqs().size() + " results");
 		Comparator<Match> comparator = new Comparator<Match>() {
 			public int compare(Match m1, Match m2) {
@@ -725,10 +667,12 @@
 			}
 		};
+		
 		Collections.sort(appData.getMatchseqs(), comparator);
 		appData.getStopWatch().stop("detecting tasks");
 
+		// Replace matches in the sessions
+		Console.traceln(Level.INFO, "Replacing matches in sessions");
 		appData.getStopWatch().start("replacing tasks");
 		HashMap<Integer, List<MatchOccurence>> replacedOccurences = new HashMap<Integer, List<MatchOccurence>>();
-		// Replace matches in the sessions
 		for (int i = 0; i < appData.getMatchseqs().size(); i++) {
 		
@@ -744,24 +688,4 @@
 					MatchOccurence oc = it.next();
 					
-					/*
-					if (iteration > 0) {
-					 
-					System.out.println("Trying to replace sequence: ");
-					appData.getMatchseqs().get(i).getFirstSequence().printSequence();
-					appData.getMatchseqs().get(i).getSecondSequence().printSequence();
-					System.out.println(" in session number: "
-							+ (oc.getSequenceId() + 1) + " at position "
-							+ (oc.getStartindex()) + "-" + oc.getEndindex());
-					System.out.println();
-
-					System.out.println("Printing session: ");
-					for (int j = 0; j < appData.getSessions()
-							.get(oc.getSequenceId()).size(); j++) {
-						System.out.println(j
-								+ ": "
-								+ appData.getSessions().get(oc.getSequenceId())
-										.get(j));
-					}
-					}*/
 					
 					// Check if nothing has been replaced in the sequence we
@@ -808,4 +732,5 @@
 						}
 					}
+					System.out.println("Replacing");
 					ISequenceInstance sequenceInstances = RuleUtils
 							.createNewSubSequenceInRange(appData.getSessions()
@@ -827,14 +752,49 @@
 	
 	
+	
+
+	private void searchMatchesInAllSessions(RuleApplicationData appData) {
+		Console.traceln(Level.INFO, "searching for patterns occuring most with " + nThreads + " threads");
+		//Prepare parallel search of matchseqs
+		ExecutorService executor = Executors.newFixedThreadPool(nThreads);
+		int matchSeqSize=appData.getMatchseqs().size();
+		int interval = Math.round(matchSeqSize/nThreads);
+		int rest = matchSeqSize % nThreads;
+		
+		for(int i =0;i<matchSeqSize-interval;i+=interval) {
+			int offset =0;
+			if(rest!=0) {
+				offset=1;
+				rest--;
+			}
+			int from = i;
+			int to = i+interval+offset;
+			System.out.println("Creating thread with matches from " + from + " to " + to);
+			// search each match in every other sequence
+			ParallelMatchOcurrencesFinder finder = new ParallelMatchOcurrencesFinder(appData,from,to);
+			executor.execute(finder);
+		}
+		executor.shutdown();
+		try {
+			executor.awaitTermination(2, TimeUnit.HOURS);
+		} catch (InterruptedException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+	}
+
 	//Print out the progress
 	 private static void printProgressPercentage(int count, int size) {
-		
 		if(size>100) {
 			if((count%(size/100)==0)) {	
-				Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100))+ "%");
+				//Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100))+ "%");
+				System.out.println("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100)+ "%");
 			}
 		}
 		else {
-			Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100))+ "%");
+			//Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100))+ "%");
+			System.out.println("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100)+ "%");
+			
 		}
 	}
@@ -857,6 +817,6 @@
         	int count = 0;
     		int size=to-from;
-    		Console.traceln(Level.INFO, "Pattern count is " + size);
-    		for (int i=from; i<to;i++) { {
+    		
+    		for (int i=from; i<to;i++) { 
     			Match pattern = appData.getMatchseqs().get(i);
     			count++;
@@ -880,14 +840,88 @@
     								+ pattern.size(), j));
     					}
-
     				}
     			}
     		}  
+        }
+	}
+	
+	
+	private class ParallelPairwiseAligner implements Runnable {
+        private final RuleApplicationData appData;
+        private final int from;
+        private final int to;
+            ParallelPairwiseAligner(RuleApplicationData appData, int from, int to) {
+            this.appData = appData;
+            this.from = from;
+            this.to = to;
+        }
+        
+        @Override
+        public void run() {
+        	int count = 0;
+    		int size=to-from;
+    		
+    		for (int i=from; i<to;i++) {
+    			NumberSequence ns1 = appData.getNumberSequences().get(i);
+				count++;
+				printProgressPercentage(count,size);
+				for (int j = 0; j < appData.getNumberSequences().size(); j++) {
+					NumberSequence ns2 = appData.getNumberSequences().get(j);
+					if (i != j) {
+						AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+						aa.align(ns1, ns2, appData.getSubmat(),9);
+						synchronized(appData.getMatchseqs()) {
+							appData.getMatchseqs().addAll(aa.getMatches());
+						}
+					}
+				}
+    		}  
     	}
-        }
-	}
-	
-	
-
+	}
+
+	private LinkedList<Match> generatePairwiseAlignments(RuleApplicationData appData) {
+		int numberSeqSize = appData.getNumberSequences().size();
+		LinkedList<Match> result;
+		//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>();
+			
+			ExecutorService executor = Executors.newFixedThreadPool(nThreads);
+			int interval = Math.round(numberSeqSize/nThreads);
+			int rest = numberSeqSize % nThreads;
+			
+			for (int i = 0; i < numberSeqSize-interval; i+=interval) {
+				int offset = 0;
+				if(rest!=0) {
+					offset=1;
+					rest--;
+				}
+				int from = i;
+				int to = i+interval+offset;
+				System.out.println("Creating thread with matches from " + from + " to " + to);
+				ParallelPairwiseAligner aligner = new ParallelPairwiseAligner(appData,from,to);
+				executor.execute(aligner);
+			}
+			executor.shutdown();
+			try {
+				executor.awaitTermination(10, TimeUnit.MINUTES);
+			} catch (InterruptedException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+	
+			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();
+		}
+	}
+	
 
 	/**
@@ -947,5 +981,5 @@
 			newTasks = new LinkedList<ITask>();
 			
-			//this.detectedAndReplacedTasks = true;
+			this.detectedAndReplacedTasks = true;
 		}