Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java	(revision 1447)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java	(revision 1447)
@@ -0,0 +1,97 @@
+//   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.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.logging.Level;
+
+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 CMDdeleteShortSequences 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";
+		int delcount = 0;
+		int limit = 10;
+		try {
+			sequencesName = (String) parameters.get(0);
+			if (parameters.size() > 1) {
+				try {
+					limit = Integer.parseInt((String) parameters.get(1));
+					}
+				catch (NumberFormatException e)
+				{
+					Console.traceln(Level.WARNING,"Parameter not an integer. Using the default value.");
+				}
+			}
+		} catch (Exception e) {
+			throw new IllegalArgumentException();
+		}
+
+		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 (sequences != null) {
+			Console.println("Number of sequences: " + sequences.size());
+			Iterator<List<Event>> iter = sequences.iterator();
+			while(iter.hasNext()) {
+			    if (iter.next().size() < limit) {
+			    	iter.remove();
+			    	delcount++;
+			    }
+			}
+			
+			Console.traceln(Level.INFO, "Deleted "+ delcount + " short sequences from " + sequencesName);
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see de.ugoe.cs.util.console.Command#help()
+	 */
+	@Override
+	public String help() {
+		return "deleteShortSequences <sequence name>";
+	}
+
+}