Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java	(revision 1544)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java	(revision 1544)
@@ -0,0 +1,89 @@
+//   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 CMDgenerateSubstitutionMatrix 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 = "numberSequences";
+		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 "generateSubstitutionMatrix <NumberSequencesName> {<algorithm>}";
+    }
+  
+
+}