Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java	(revision 1615)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java	(revision 1616)
@@ -1,8 +1,4 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
 
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
 
 public class AlignmentAlgorithmFactory {
@@ -25,5 +21,4 @@
 			
 		} catch (ClassNotFoundException | SecurityException | InstantiationException | IllegalAccessException | IllegalArgumentException e) {
-			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java
===================================================================
--- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java	(revision 1615)
+++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java	(revision 1616)
@@ -187,38 +187,5 @@
 	}
 
-	public void printAlignment() {
-		MatrixEntry tmp = matrix[length1][length2];
-		String aligned1 = "";
-		String aligned2 = "";
-		int count = 0;
-		do {
-			System.out.println(tmp);
-			String append1 = "";
-			String append2 = "";
-
-			if (tmp.getXvalue() == Constants.GAP_SYMBOL) {
-				append1 = "  ___";
-			} else {
-				append1 = String.format("%5d", tmp.getXvalue());
-			}
-
-			if (tmp.getYvalue() == Constants.GAP_SYMBOL) {
-				append2 = "  ___";
-			} else {
-				append2 = String.format("%5d", tmp.getYvalue());
-			}
-			if (count != 0) {
-				aligned1 = append1 + aligned1;
-				aligned2 = append2 + aligned2;
-			}
-
-			tmp = tmp.getPrevious();
-			count++;
-
-		} while (tmp != null);
-		System.out.println(aligned1);
-		System.out.println(aligned2);
-	}
-
+	
 	/**
 	 * print the dynmaic programming matrix
@@ -241,4 +208,38 @@
 		}
 	}
+	
+	public void printAlignment() {
+		int[] tmp1 = alignment.get(0).getSequence();
+		int[] tmp2 = alignment.get(1).getSequence();
+		for (int i=0; i< tmp1.length;i++) {
+			if(tmp1[i] == Constants.GAP_SYMBOL) {
+				System.out.print("  ___");
+			}
+			else if(tmp1[i] == Constants.UNMATCHED_SYMBOL) {
+				System.out.print("  ...");
+			}
+			else {
+				System.out.format("%5d", tmp1[i]);
+			}
+			
+		}
+		System.out.println();
+		for (int i=0; i< tmp2.length;i++) {
+			if(tmp2[i] == Constants.GAP_SYMBOL) {
+				System.out.print("  ___");
+			}
+			else if(tmp2[i] == Constants.UNMATCHED_SYMBOL) {
+				System.out.print("  ...");
+			}
+			else {
+				System.out.format("%5d", tmp2[i]);
+			}
+			
+		}
+		System.out.println();
+		
+		
+	
+	}
 
 	/*