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 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1542)
@@ -15,5 +15,4 @@
 package de.ugoe.cs.autoquest.plugin.alignment.commands;
 
-
 import java.util.Collection;
 import java.util.LinkedList;
@@ -22,4 +21,5 @@
 import de.ugoe.cs.autoquest.eventcore.Event;
 import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SequenceGenerator;
 import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
 import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
@@ -46,10 +46,12 @@
 	@SuppressWarnings("unchecked")
 	public void run(List<Object> parameters) {
-		String sequencesName = "sequences";
-		String algorithm;
+		String sequencesName = "numberSequences";
+		String substitutionName = "substitutionMatrix";
+		String algorithm = "smithwaterman";
 		try {
 			sequencesName = (String) parameters.get(0);
-			if (parameters.size() > 1) {
-				algorithm = (String) parameters.get(1);
+			substitutionName = (String) parameters.get(1);
+			if (parameters.size() > 2) {
+				algorithm = (String) parameters.get(2);
 			}
 		} catch (Exception e) {
@@ -57,32 +59,33 @@
 		}
 
-		Collection<List<Event>> sequences = new LinkedList<List<Event>>();
+		SimpleSequenceGenerator gen;
 		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
-		if(obj != null) {
-			
-			if(obj.getClass().equals(sequences.getClass())) {
-				sequences = (Collection<List<Event>>) obj;
-			}
-		 
+		if (obj != null) {
+			if (obj.getClass().equals(SimpleSequenceGenerator.class)) {
+				gen = (SimpleSequenceGenerator) obj;
+				Console.println("Number of sequences: " + gen.sequenceCount());
+
+				int[] seq1 = gen.get(0).getSequence();
+				int[] seq2 = gen.get(0).getSequence();
 				
-					Console.println("Number of sequences: " + sequences.size());
+				ObjectDistanceSubstitionMatrix submat = new
+				ObjectDistanceSubstitionMatrix();
+				submat.generate(sequences);
+				// SmithWaterman sw = new SmithWaterman(seq1, seq2,
+				// new NearbySubstitutionMatrix(seq1, seq2, 10));
+				// sw.printDPMatrix();
+				// System.out.println();
+				// sw.printAlignments();
+				// sw.getMatches();
+				System.out.println("foo");
 
-					SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
-					gen.generate(sequences);
-					int[] seq1 = gen.get(0).getSequence();
-					int[] seq2 = gen.get(0).getSequence();
-					//ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
-					//submat.generate(sequences);
-					//SmithWaterman sw = new SmithWaterman(seq1, seq2,
-					//		new NearbySubstitutionMatrix(seq1, seq2, 10));
-
-				//sw.printDPMatrix();
-				//System.out.println();
-				//sw.printAlignments();
-				// sw.getMatches();
-					System.out.println("foo");
-				}
+			} else {
+				Console.printerr("No number sequences generated. Please run the generateNumberSequences before.");
+				
 			}
 
+					}
+
+	}
 
 	/*
@@ -93,5 +96,5 @@
 	@Override
 	public String help() {
-		return "binaryAlignment <sequencesName> {<algorithm>}";
+		return "binaryAlignment <sequencesName> <substitutionMatrixname> {<algorithm>}";
 	}
 
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java	(revision 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java	(revision 1542)
@@ -83,5 +83,5 @@
 	@Override
 	public String help() {
-		return "binaryAlignment <sequencesName> {<algorithm>}";
+		return "generateNumberSequences <equencesName> {<algorithm>}";
 	}
 
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java	(revision 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java	(revision 1542)
@@ -1,7 +1,8 @@
 package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 
-public class NumberSequence {
+public class NumberSequence implements Serializable {
 	private int[] sequence;
 	private int signature;
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java	(revision 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java	(revision 1542)
@@ -37,3 +37,9 @@
 		return null;
 	}
+
+	@Override
+	public int sequenceCount() {
+		return count;
+	}
+	
 }
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java	(revision 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java	(revision 1542)
@@ -10,4 +10,5 @@
 	public void generate(Collection<List<Event>> eventList);
 	public NumberSequence get(int index);
+	public int 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 1541)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1542)
@@ -2,4 +2,5 @@
 
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -20,5 +21,5 @@
 
 
-public class SimpleSequenceGenerator implements SequenceGenerator {
+public class SimpleSequenceGenerator implements SequenceGenerator, Serializable {
 
 	private ArrayList<NumberSequence> numberseqs;
@@ -42,7 +43,7 @@
 		if (sequences != null) {
 			TaskTreeManager ttm = new TaskTreeManager();
-			Console.println("Creating the task model");
+			
 			ttm.createTaskModel(sequences);
-			Console.println("Finished creating the task model");
+			
 			TaskHandlingStrategy preparationTaskHandlingStrategy  = new TaskHandlingStrategy(TaskEquality.SEMANTICALLY_EQUAL);
 			SymbolMap<ITaskInstance, ITask> uniqueTasks = preparationTaskHandlingStrategy
@@ -84,9 +85,13 @@
 
 
-	@Override
 	public NumberSequence get(int index) {
 		return numberseqs.get(index);
 	}
 
+
+	public int sequenceCount() {
+		return numberseqs.size();
+	}
+
 }