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 1542)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1543)
@@ -62,5 +62,5 @@
 		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
 		if (obj != null) {
-			if (obj.getClass().equals(SimpleSequenceGenerator.class)) {
+			if (obj instanceof SimpleSequenceGenerator) {
 				gen = (SimpleSequenceGenerator) obj;
 				Console.println("Number of sequences: " + gen.sequenceCount());
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1542)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1543)
@@ -66,4 +66,5 @@
 						uniqueTasks.addSymbol(taskInstance,
 								taskInstance.getTask());
+				
 								templist.getSequence()[i]=taskInstance.getTask().getId();
 								
@@ -75,5 +76,5 @@
 					
 				}
-
+				
 				comparator.clearBuffers();
 				numberseqs.add(templist);