Index: trunk/autoquest-plugin-alignment/pom.xml
===================================================================
--- trunk/autoquest-plugin-alignment/pom.xml	(revision 1322)
+++ trunk/autoquest-plugin-alignment/pom.xml	(revision 1323)
@@ -23,4 +23,10 @@
     <dependencies>
         <dependency>
+            <groupId>org.apache.maven.plugins</groupId>
+            <artifactId>maven-resources-plugin</artifactId>
+            <version>2.4.3</version>
+        </dependency>
+    
+        <dependency>
             <groupId>de.ugoe.cs</groupId>
             <artifactId>java-utils</artifactId>
@@ -40,5 +46,4 @@
             <groupId>de.ugoe.cs.autoquest</groupId>
             <artifactId>autoquest-core-usageprofiles</artifactId>
-            <version>${project.parent.version}</version>
         </dependency>
         <dependency>
@@ -46,4 +51,9 @@
             <artifactId>autoquest-misc</artifactId>
             <version>${project.parent.version}</version>
+        </dependency>
+        <dependency>
+        	<groupId>de.ugoe.cs.autoquest</groupId>
+        	<artifactId>autoquest-core-tasktrees</artifactId>
+        	<version>${project.parent.version}</version>
         </dependency>
     </dependencies>
@@ -63,3 +73,12 @@
         </plugins>
     </build>
+    <dependencyManagement>
+    	<dependencies>
+    		<dependency>
+    			<groupId>de.ugoe.cs.autoquest</groupId>
+    			<artifactId>autoquest-core-usageprofiles</artifactId>
+    			<version>${project.parent.version}</version>
+    		</dependency>
+    	</dependencies>
+    </dependencyManagement>
 </project>
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/DifferenceSubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/DifferenceSubstitutionMatrix.java	(revision 1322)
+++ 	(revision )
@@ -1,54 +1,0 @@
-/**
- * 
- */
-package de.ugoe.cs.autoquest.plugin.alignment;
-
-/**
- * @author Ralph Krimmel
- *
- */
-public class DifferenceSubstitutionMatrix implements SubstitutionMatrix {
-
-	private int[] input1;
-	private int[] input2;
-	private int maxValue;
-	
-	public DifferenceSubstitutionMatrix(int[] input1,int[] input2) {
-		this.input1 = input1;
-		this.input2 = input2;
-		this.maxValue = getMaxValue();
-	}
-	
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
-	 */
-	public double getDistance(int pos1, int pos2) {
-		return maxValue - (input1[pos1] - input2[pos2]);
-	}
-	
-	private int getMaxValue() {
-		int max = input1[0];
-		for (int i=0; i < input1.length; i++) {
-			if(input1[i] > max) {
-				max = input1[i];
-			}
-		}
-		for (int j=0; j < input2.length; j++) {
-			if(input2[j] > max) {
-				max = input2[j];
-			}
-		}
-		return max;
-	}
-
-	@Override
-	public double getGapPenalty() {
-		return -maxValue;
-	}
-
-	@Override
-	public String info() {
-		return "Max Value: " + maxValue;
-	}
-
-}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/NearbySubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/NearbySubstitutionMatrix.java	(revision 1322)
+++ 	(revision )
@@ -1,46 +1,0 @@
-/**
- * 
- */
-package de.ugoe.cs.autoquest.plugin.alignment;
-
-/**
- * @author Ralph Krimmel
- *
- */
-public class NearbySubstitutionMatrix implements SubstitutionMatrix {
-
-	private int[] input1;
-	private int[] input2;
-	private int range;
-	
-	public NearbySubstitutionMatrix(int[] input1,int[] input2, int range) {
-		this.input1 = input1;
-		this.input2 = input2;
-		this.range = range;
-	}
-	
-	/* (non-Javadoc)
-	 * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
-	 */
-	public double getDistance(int pos1, int pos2) {
-		int difference = Math.abs(input1[pos1]-input2[pos2]); 
-		if(difference < range) {
-			return range-difference;
-		}
-		else {
-			return -range;
-		}
-	}
-
-
-	@Override
-	public double getGapPenalty() {
-		return -range-1;
-	}
-
-	@Override
-	public String info() {
-		return "Range: " + range;
-	}
-
-}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java	(revision 1322)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java	(revision 1323)
@@ -3,4 +3,6 @@
 import java.util.ArrayList;
 import java.util.List;
+
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.SubstitutionMatrix;
 
 public class SmithWaterman implements Alignment {
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SubstitutionMatrix.java	(revision 1322)
+++ 	(revision )
@@ -1,12 +1,0 @@
-package de.ugoe.cs.autoquest.plugin.alignment;
-
-public interface SubstitutionMatrix {
-
-	public String info();
-	
-	public double getDistance(int pos1, int pos2);
-
-	public double getGapPenalty();
-
-	
-}
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 1322)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1323)
@@ -25,8 +25,19 @@
 import de.ugoe.cs.autoquest.CommandHelpers;
 import de.ugoe.cs.autoquest.eventcore.Event;
-import de.ugoe.cs.autoquest.plugin.alignment.NearbySubstitutionMatrix;
 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.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.DifferenceSubstitutionMatrix;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
+import de.ugoe.cs.autoquest.tasktrees.manager.TaskTreeManager;
+import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
+import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskInstanceComparator;
+import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskHandlingStrategy;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
+import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder;
+import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -48,5 +59,4 @@
 	 * @see de.ugoe.cs.util.console.Command#run(java.util.List)
 	 */
-	@Override
 	public void run(List<Object> parameters) {
 		String sequencesName;
@@ -64,25 +74,21 @@
 		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 randgen1 = new RandomSequenceGenerator(1,
-					80, 3000);
-			RandomSequenceGenerator randgen2 = new RandomSequenceGenerator(1,
-					80, 3000);
-			
-			int[] seq1 = randgen1.generate(ev);
-			int[] seq2 = randgen2.generate(ev);
-			SmithWaterman sw = new SmithWaterman(seq1, seq2,
-					new NearbySubstitutionMatrix(seq1, seq2,10));
+				if(sequences != null) {
+					Console.println("Number of sequences: " + sequences.size());
 
-			//sw.printDPMatrix();
-			System.out.println();
-			//sw.printAlignments();
-			sw.getMatches();
-			Console.println("Number of events in sequence: " + ev.size());
-		}
+					SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
+					gen.generate(sequences);
+					int[] seq1 = gen.get(0);
+					int[] seq2 = gen.get(0);
+					SmithWaterman sw = new SmithWaterman(seq1, seq2,
+							new NearbySubstitutionMatrix(seq1, seq2, 10));
 
-	}
+				//printDPMatrix();
+				System.out.println();
+				sw.printAlignments();
+				// sw.getMatches();
+				}
+			}
+
 
 	/*
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 1323)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/ISequenceGenerator.java	(revision 1323)
@@ -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 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/RandomSequenceGenerator.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java	(revision 1322)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java	(revision 1323)
@@ -1,7 +1,9 @@
 package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
 import de.ugoe.cs.autoquest.eventcore.Event;
+
+import java.util.Collection;
 import java.util.List;
 
-public class RandomSequenceGenerator implements SequenceGenerator {
+public class RandomSequenceGenerator implements ISequenceGenerator{
 
 	private int min;
@@ -23,3 +25,15 @@
 		return result;
 	}
+
+	@Override
+	public void generate(Collection<List<Event>> eventList) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public int[] 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 1322)
+++ 	(revision )
@@ -1,8 +1,0 @@
-package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
-
-import java.util.List;
-import de.ugoe.cs.autoquest.eventcore.Event;
-
-public interface SequenceGenerator {
-	public int[] generate(List<Event> eventList);
-}
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 1322)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1323)
@@ -57,9 +57,12 @@
 						uniqueTasks.addSymbol(taskInstance,
 								taskInstance.getTask());
+								templist[i]=taskInstance.getTask().getId();
 					} else {
 						taskBuilder.setTask(taskInstance, task);
 						unifiedTasks++;
+						templist[i]=task.getId();
+						
 					}
-					templist[i]=task.getId();
+					
 				}
 
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java	(revision 1323)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java	(revision 1323)
@@ -0,0 +1,54 @@
+/**
+ * 
+ */
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
+
+/**
+ * @author Ralph Krimmel
+ *
+ */
+public class DifferenceSubstitutionMatrix implements SubstitutionMatrix {
+
+	private int[] input1;
+	private int[] input2;
+	private int maxValue;
+	
+	public DifferenceSubstitutionMatrix(int[] input1,int[] input2) {
+		this.input1 = input1;
+		this.input2 = input2;
+		this.maxValue = getMaxValue();
+	}
+	
+	/* (non-Javadoc)
+	 * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
+	 */
+	public double getDistance(int pos1, int pos2) {
+		return maxValue - (input1[pos1] - input2[pos2]);
+	}
+	
+	private int getMaxValue() {
+		int max = input1[0];
+		for (int i=0; i < input1.length; i++) {
+			if(input1[i] > max) {
+				max = input1[i];
+			}
+		}
+		for (int j=0; j < input2.length; j++) {
+			if(input2[j] > max) {
+				max = input2[j];
+			}
+		}
+		return max;
+	}
+
+	@Override
+	public double getGapPenalty() {
+		return -maxValue;
+	}
+
+	@Override
+	public String info() {
+		return "Max Value: " + maxValue;
+	}
+
+}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java	(revision 1323)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java	(revision 1323)
@@ -0,0 +1,46 @@
+/**
+ * 
+ */
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
+
+/**
+ * @author Ralph Krimmel
+ *
+ */
+public class NearbySubstitutionMatrix implements SubstitutionMatrix {
+
+	private int[] input1;
+	private int[] input2;
+	private int range;
+	
+	public NearbySubstitutionMatrix(int[] input1,int[] input2, int range) {
+		this.input1 = input1;
+		this.input2 = input2;
+		this.range = range;
+	}
+	
+	/* (non-Javadoc)
+	 * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
+	 */
+	public double getDistance(int pos1, int pos2) {
+		int difference = Math.abs(input1[pos1]-input2[pos2]); 
+		if(difference < range) {
+			return range-difference;
+		}
+		else {
+			return -range;
+		}
+	}
+
+
+	@Override
+	public double getGapPenalty() {
+		return -range-1;
+	}
+
+	@Override
+	public String info() {
+		return "Range: " + range;
+	}
+
+}
Index: trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java
===================================================================
--- trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java	(revision 1323)
+++ trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java	(revision 1323)
@@ -0,0 +1,12 @@
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
+
+public interface SubstitutionMatrix {
+
+	public String info();
+	
+	public double getDistance(int pos1, int pos2);
+
+	public double getGapPenalty();
+
+	
+}