Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java	(revision 1449)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java	(revision 1449)
@@ -0,0 +1,5 @@
+package de.ugoe.cs.autoquest.plugin.alignment;
+
+public class FengDoolittle {
+
+}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java	(revision 1449)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java	(revision 1449)
@@ -0,0 +1,5 @@
+package de.ugoe.cs.autoquest.plugin.alignment;
+
+public class ProgressiveMultiAlignment {
+
+}
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 1448)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1449)
@@ -44,4 +44,5 @@
 	 * @see de.ugoe.cs.util.console.Command#run(java.util.List)
 	 */
+	@SuppressWarnings("unchecked")
 	public void run(List<Object> parameters) {
 		String sequencesName = "sequences";
@@ -58,13 +59,11 @@
 		Collection<List<Event>> sequences = new LinkedList<List<Event>>();
 		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
-		if(obj.getClass().equals(sequences.getClass())) {
-			sequences = (Collection<List<Event>>) obj;
-		}
+		if(obj != null) {
+			
+			if(obj.getClass().equals(sequences.getClass())) {
+				sequences = (Collection<List<Event>>) obj;
+			}
 		 
-	
-		
-		
-
-				if(sequences != null) {
+				
 					Console.println("Number of sequences: " + sequences.size());
 
@@ -73,13 +72,14 @@
 					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));
+					//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.printDPMatrix();
+				//System.out.println();
+				//sw.printAlignments();
 				// sw.getMatches();
+					System.out.println("foo");
 				}
 			}
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 1449)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java	(revision 1449)
@@ -0,0 +1,88 @@
+//   Copyright 2012 Georg-August-Universität Göttingen, Germany
+//
+//   Licensed under the Apache License, Version 2.0 (the "License");
+//   you may not use this file except in compliance with the License.
+//   You may obtain a copy of the License at
+//
+//       http://www.apache.org/licenses/LICENSE-2.0
+//
+//   Unless required by applicable law or agreed to in writing, software
+//   distributed under the License is distributed on an "AS IS" BASIS,
+//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//   See the License for the specific language governing permissions and
+//   limitations under the License.
+
+package de.ugoe.cs.autoquest.plugin.alignment.commands;
+
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+import de.ugoe.cs.autoquest.eventcore.Event;
+import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
+import de.ugoe.cs.util.console.Command;
+import de.ugoe.cs.util.console.Console;
+import de.ugoe.cs.util.console.GlobalDataContainer;
+
+/**
+ * <p>
+ * Command to generate a binary alignment of two sequences
+ * </p>
+ * 
+ * @author Ralph Krimmel
+ * @version 1.0
+ */
+public class CMDgenerateNumberSequences implements Command {
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.util.console.Command#run(java.util.List)
+	 */
+	@SuppressWarnings("unchecked")
+	public void run(List<Object> parameters) {
+		String sequencesName = "sequences";
+		try {
+			sequencesName = (String) parameters.get(0);
+		} catch (Exception e) {
+			throw new IllegalArgumentException();
+		}
+
+		Collection<List<Event>> sequences = new LinkedList<List<Event>>();
+		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
+		if(obj != null) {
+			
+			if(obj.getClass().equals(sequences.getClass())) {
+				sequences = (Collection<List<Event>>) obj;
+			}
+		 
+				
+					Console.println("Number of sequences: " + sequences.size());
+
+					SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
+					gen.generate(sequences);
+					gen.print();
+					GlobalDataContainer.getInstance().addData("numberSequences", gen);
+				
+
+				
+				
+				}
+			}
+
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.util.console.Command#help()
+	 */
+	@Override
+	public String help() {
+		return "binaryAlignment <sequencesName> {<algorithm>}";
+	}
+
+}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/ISequenceGenerator.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/ISequenceGenerator.java	(revision 1448)
+++ 	(revision )
@@ -1,16 +1,0 @@
-package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
-
-import java.util.Collection;
-import java.util.List;
-
-import de.ugoe.cs.autoquest.eventcore.Event;
-
-public interface ISequenceGenerator {
-	
-	public void generate(Collection<List<Event>> eventList);
-	public int[] get(int index);
-	
-	
-	
-	
-}
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 1449)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java	(revision 1449)
@@ -0,0 +1,34 @@
+package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
+
+import java.util.ArrayList;
+
+public class NumberSequence {
+	private int[] sequence;
+	private int signature;
+	
+	public NumberSequence(int size) {
+		
+		sequence = new int[size];
+	}
+	
+	public String toString() {
+		return sequence.toString();
+		
+	}
+	
+	
+	
+	public int[] getSequence() {
+		return sequence;
+	}
+	public void setSequence(int[] sequence) {
+		this.sequence = sequence;
+	}
+	public int getSignature() {
+		return signature;
+	}
+	public void setSignature(int signature) {
+		this.signature = 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 1448)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java	(revision 1449)
@@ -5,5 +5,5 @@
 import java.util.List;
 
-public class RandomSequenceGenerator implements ISequenceGenerator{
+public class RandomSequenceGenerator implements SequenceGenerator{
 
 	private int min;
@@ -33,5 +33,5 @@
 
 	@Override
-	public int[] get(int index) {
+	public NumberSequence get(int index) {
 		// TODO Auto-generated method stub
 		return null;
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 1449)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java	(revision 1449)
@@ -0,0 +1,16 @@
+package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
+
+import java.util.Collection;
+import java.util.List;
+
+import de.ugoe.cs.autoquest.eventcore.Event;
+
+public interface SequenceGenerator {
+	
+	public void generate(Collection<List<Event>> eventList);
+	public NumberSequence get(int index);
+	
+	
+	
+	
+}
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 1448)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1449)
@@ -17,16 +17,23 @@
 import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder;
 import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
+import de.ugoe.cs.util.console.Console;
 
 
-public class SimpleSequenceGenerator implements ISequenceGenerator {
+public class SimpleSequenceGenerator implements SequenceGenerator {
 
-	private ArrayList<int[]> numberseqs;
+	private ArrayList<NumberSequence> numberseqs;
 
 
 	public SimpleSequenceGenerator() {
-		this.numberseqs = new ArrayList<int[]>();
+		this.numberseqs = new ArrayList<NumberSequence>();
 	
 	}
 	
+	public void print() {
+		for (NumberSequence sequence : numberseqs) {
+				System.out.println(sequence.toString());
+		}
+		
+	}
 	
 	public void generate(Collection<List<Event>> sequences) {
@@ -35,6 +42,7 @@
 		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
@@ -49,5 +57,5 @@
 			for (IUserSession session : sessions) {
 				//Creating a new sequence that just consists of integers
-				int[] templist = new int[session.size()];
+				NumberSequence templist = new NumberSequence(session.size()) ;
 				for (int i = 0; i < session.size(); i++) {
 					ITaskInstance taskInstance = session.get(i); 
@@ -57,9 +65,9 @@
 						uniqueTasks.addSymbol(taskInstance,
 								taskInstance.getTask());
-								templist[i]=taskInstance.getTask().getId();
+								templist.getSequence()[i]=taskInstance.getTask().getId();
 								
 					} else {
 						taskBuilder.setTask(taskInstance, task);
-						templist[i]=task.getId();
+						templist.getSequence()[i]=task.getId();
 						
 					}
@@ -77,5 +85,5 @@
 
 	@Override
-	public int[] get(int index) {
+	public NumberSequence get(int index) {
 		return numberseqs.get(index);
 	}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java	(revision 1448)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java	(revision 1449)
@@ -37,4 +37,10 @@
 		return matrix.get(currentSequence)[pos1][pos2];
 	}
+	
+	public double getDistance(int sequence, int pos1, int pos2) {
+		return  matrix.get(sequence)[pos1][pos2];
+		
+		
+	}
 
 	@Override
@@ -46,6 +52,4 @@
 	@Override
 	public void generate(Collection<List<Event>> eventList) {
-		GUIModel guimodel = (GUIModel) GlobalDataContainer.getInstance().getData("sequences_targets");
-		guimodel.condenseModel();
 		
 		for(Iterator<List<Event>> seqs = eventList.iterator(); seqs.hasNext();) {
Index: trunk/autoquest-plugin-alignment/target/maven-archiver/pom.properties
===================================================================
--- trunk/autoquest-plugin-alignment/target/maven-archiver/pom.properties	(revision 1449)
+++ trunk/autoquest-plugin-alignment/target/maven-archiver/pom.properties	(revision 1449)
@@ -0,0 +1,5 @@
+#Generated by Maven
+#Wed Nov 06 00:13:59 CET 2013
+version=0.0.1-SNAPSHOT
+groupId=de.ugoe.cs.autoquest
+artifactId=autoquest-plugin-alignment