Index: trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java
===================================================================
--- trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1306)
+++ trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1307)
@@ -18,4 +18,5 @@
 import java.io.FilenameFilter;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
@@ -24,4 +25,7 @@
 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.DifferenceSubstitutionMatrix;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -36,5 +40,5 @@
  * @version 1.0
  */
-public class CMDbinaryAligment implements Command {
+public class CMDbinaryAlignment implements Command {
 
 	/*
@@ -56,7 +60,24 @@
 		}
 
-		
 		Collection<List<Event>> sequences = new LinkedList<List<Event>>();
-		
+		sequences = (Collection<List<Event>>) GlobalDataContainer.getInstance()
+				.getData(sequencesName);
+		Console.println("Number of sequences: " + sequences.size());
+		for (Iterator<List<Event>> it = sequences.iterator(); it.hasNext();) {
+			List<Event> ev = it.next();
+			RandomSequenceGenerator randgen = new RandomSequenceGenerator(1,
+					80, 10);
+			int[] seq1 = randgen.generate(ev);
+			int[] seq2 = randgen.generate(ev);
+			SmithWaterman sw = new SmithWaterman(seq1, seq2,
+					new DifferenceSubstitutionMatrix(seq1, seq2));
+
+			sw.printDPMatrix();
+			Console.println("Number of events in sequence: " + ev.size());
+			for (Iterator<Event> foo = ev.iterator(); foo.hasNext();) {
+				Event blubb = foo.next();
+				// Console.println(blubb.toString());
+			}
+		}
 
 	}