Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1343)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1446)
@@ -45,5 +45,5 @@
 	 */
 	public void run(List<Object> parameters) {
-		String sequencesName;
+		String sequencesName = "sequences";
 		String algorithm;
 		try {
@@ -71,6 +71,6 @@
 					SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
 					gen.generate(sequences);
-					int[] seq1 = gen.get(0);
-					int[] seq2 = gen.get(0);
+					int[] seq1 = gen.get(0).getSequence();
+					int[] seq2 = gen.get(0).getSequence();
 					ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
 					submat.generate(sequences);
@@ -80,5 +80,5 @@
 				sw.printDPMatrix();
 				System.out.println();
-				//sw.printAlignments();
+				sw.printAlignments();
 				// sw.getMatches();
 				}