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 1575)
+++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java	(revision 1576)
@@ -15,7 +15,5 @@
 package de.ugoe.cs.autoquest.tasktrees.temporalrelation;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintWriter;
+
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -28,9 +26,8 @@
 import java.util.logging.Level;
 
-import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.FengDoolittle;
+
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.TriangleMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree.UPGMATree;
@@ -171,6 +168,4 @@
 		for (int i = 0; i < numberseqs.size(); i++) {
 			NumberSequence ns1 = numberseqs.get(i);
-			//System.out.print("Sequence " + i + ": ");
-			//ns1.printSequence();
 			for (int j = 0; j < numberseqs.size(); j++) {
 				NumberSequence ns2 = numberseqs.get(j);
@@ -208,37 +203,14 @@
 					
 					if(!Double.isInfinite(distance) && !Double.isNaN(distance)) {
-						//System.out.println("Score: " + String.format("%5.1f", score) + " sRand: " + String.format("%5.1f", sRand) + " sMax: " + String.format("%6.1f", sMax)  + " distance: " + String.format("%2.3f",distance));
 						if(distance < sequenceDistances.get(i, j)) {	
 							sequenceDistances.set(i,j,distance );
 						}
 					}
-
-					if (score > 0) {
-						/*
-						 * System.out.println(
-						 * "=================================================");
-						 * System.out.println("| Sequence " +
-						 * String.format("%3d", i) +" Sequence " +
-						 * String.format("%3d", j) + "                     |");
-						 * System.out.println(
-						 * "=================================================");
-						 * System.out.print("Sequence " + i + ": ");
-						 * ns1.printSequence(); System.out.print("Sequence " + j
-						 * + ": "); ns2.printSequence(); System.out.println();
-						 * //System.out.println("Max Scrore: " +
-						 * sw.getMaxScore());
-						 * System.out.println("Alignment Score: " +
-						 * sw.getAlignmentScore()); //sw.printDPMatrix();
-						 * sw.traceback(); System.out.println();
-						 * System.out.println();
-						 */
-					}
-				}
-			}
-		}
-		System.out.println(sequenceDistances.toString());
+				}
+			}
+		}
 		UPGMATree guidetree = new UPGMATree(numberseqs, sequenceDistances);
-		System.out.println(guidetree.toString());
 		
+		/*
 		do {
 			System.out.println();
@@ -256,5 +228,5 @@
 			// appData.getStopWatch().reset();
 
-		} while (appData.detectedAndReplacedTasks());
+		} while (appData.detectedAndReplacedTasks()); */
 
 		Console.println("created "