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 1329)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1330)
@@ -15,29 +15,14 @@
 package de.ugoe.cs.autoquest.plugin.alignment.commands;
 
-import java.io.File;
-import java.io.FilenameFilter;
+
 import java.util.Collection;
-import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
-import java.util.logging.Level;
 
-import de.ugoe.cs.autoquest.CommandHelpers;
 import de.ugoe.cs.autoquest.eventcore.Event;
 import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
-import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator;
 import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
-import de.ugoe.cs.autoquest.plugin.alignment.substitution.DifferenceSubstitutionMatrix;
 import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
-import de.ugoe.cs.autoquest.tasktrees.manager.TaskTreeManager;
-import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
-import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskInstanceComparator;
-import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskHandlingStrategy;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
-import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder;
-import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -49,5 +34,5 @@
  * </p>
  * 
- * @author Steffen Herbold
+ * @author Ralph Krimmel
  * @version 1.0
  */
@@ -72,6 +57,13 @@
 
 		Collection<List<Event>> sequences = new LinkedList<List<Event>>();
-		sequences = (Collection<List<Event>>) GlobalDataContainer.getInstance()
-				.getData(sequencesName);
+		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
+		if(obj.getClass().equals(sequences.getClass())) {
+			sequences = (Collection<List<Event>>) obj;
+		}
+		 
+	
+		
+		
+
 				if(sequences != null) {
 					Console.println("Number of sequences: " + sequences.size());
@@ -81,10 +73,12 @@
 					int[] seq1 = gen.get(0);
 					int[] seq2 = gen.get(0);
+					ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
+					submat.generate(sequences);
 					SmithWaterman sw = new SmithWaterman(seq1, seq2,
 							new NearbySubstitutionMatrix(seq1, seq2, 10));
 
-				//printDPMatrix();
+				sw.printDPMatrix();
 				System.out.println();
-				sw.printAlignments();
+				//sw.printAlignments();
 				// sw.getMatches();
 				}
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 1329)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1330)
@@ -36,5 +36,5 @@
 			TaskTreeManager ttm = new TaskTreeManager();
 			ttm.createTaskModel(sequences);
-
+			
 			TaskHandlingStrategy preparationTaskHandlingStrategy  = new TaskHandlingStrategy(TaskEquality.SEMANTICALLY_EQUAL);
 			SymbolMap<ITaskInstance, ITask> uniqueTasks = preparationTaskHandlingStrategy
@@ -42,9 +42,9 @@
 			TaskInstanceComparator comparator = preparationTaskHandlingStrategy
 					.getTaskComparator();
-			int unifiedTasks = 0;
 			ITask task;
 			ITaskBuilder taskBuilder = new TaskBuilder();
 
 			List<IUserSession> sessions = ttm.getTaskModel().getUserSessions();
+			
 			for (IUserSession session : sessions) {
 				//Creating a new sequence that just consists of integers
@@ -58,7 +58,7 @@
 								taskInstance.getTask());
 								templist[i]=taskInstance.getTask().getId();
+								
 					} else {
 						taskBuilder.setTask(taskInstance, task);
-						unifiedTasks++;
 						templist[i]=task.getId();