Index: /branches/autoquest-core-tasktrees-alignment-test/MatchTest.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment-test/MatchTest.java	(revision 1648)
+++ /branches/autoquest-core-tasktrees-alignment-test/MatchTest.java	(revision 1648)
@@ -0,0 +1,14 @@
+package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class MatchTest {
+
+	@Test
+	public void testEqualsMatch() {
+		fail("Not yet implemented");
+	}
+
+}
Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java	(revision 1648)
+++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequenceTest.java	(revision 1648)
@@ -0,0 +1,109 @@
+package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class NumberSequenceTest {
+
+	@Test
+	public void testContainsPattern() {
+		int[] seq = new int[10];
+		for (int i=0; i<10; i++) {
+			seq[i] = i;
+		}
+		
+		int[] pat1 = new int[]{2,3,4};
+		int[] pat2 = new int[]{2,3,4};
+		
+		int[] pat3 = new int[]{5,-1,7};
+		int[] pat4 = new int[]{1,2,3};
+		
+		int[] pat5 = new int[]{-1,-1,-1};
+		int[] pat6 = new int[]{10,11,12};
+		
+		
+		NumberSequence ns = new NumberSequence(10);
+		ns.setSequence(seq);
+		
+		NumberSequence firstpattern = new NumberSequence(3);
+		NumberSequence secondpattern = new NumberSequence(3);
+		firstpattern.setSequence(pat1);
+		secondpattern.setSequence(pat2);
+		
+		Match pattern = new Match();
+		pattern.setFirstSequence(firstpattern);
+		pattern.setSecondSequence(secondpattern);
+		
+		assertEquals(Integer.valueOf(2),ns.containsPattern(pattern).get(0));
+		
+		firstpattern.setSequence(pat3);
+		secondpattern.setSequence(pat4);
+		
+		assertEquals(Integer.valueOf(1),ns.containsPattern(pattern).get(0));
+		assertEquals(Integer.valueOf(5),ns.containsPattern(pattern).get(1));
+	
+		firstpattern.setSequence(pat5);
+		secondpattern.setSequence(pat5);
+		
+		assertEquals(0,ns.containsPattern(pattern).size());
+		
+		firstpattern.setSequence(pat6);
+		secondpattern.setSequence(pat6);
+		
+		assertEquals(0,ns.containsPattern(pattern).size());
+	}
+
+	@Test
+	public void testEventCount() {
+		int[] seq = new int[10];
+		for (int i=0; i<10; i++) {
+			seq[i] = i;
+		}
+		NumberSequence ns = new NumberSequence(10);
+		ns.setSequence(seq);
+		
+		int[] pat2 = new int[]{-1,-1,-1};
+		int[] pat3 = new int[]{0,1,2,3,0,2};
+		
+		assertEquals(1,ns.eventCount(5));
+		
+		ns.setSequence(pat2);
+		assertEquals(3,ns.eventCount(-1));
+		
+		ns.setSequence(pat3);
+		assertEquals(2,ns.eventCount(0));
+		assertEquals(2,ns.eventCount(2));
+		assertEquals(0,ns.eventCount(5));
+	}
+
+	@Test
+	public void testEqualsNumberSequence() {
+		int[] seq1 = new int[10];
+		for (int i=0; i<10; i++) {
+			seq1[i] = i;
+		}
+		NumberSequence ns1 = new NumberSequence(10);
+		ns1.setSequence(seq1);
+		
+		int[] seq2 = new int[10];
+		for (int i=0; i<10; i++) {
+			seq2[i] = i;
+		}
+		NumberSequence ns2 = new NumberSequence(10);
+		ns2.setSequence(seq2);
+		
+		int[] seq3 = new int[10];
+		for (int i=0; i<10; i++) {
+			seq3[i] = 2*i;
+		}
+		NumberSequence ns3 = new NumberSequence(10);
+		ns3.setSequence(seq3);
+		
+		assertTrue(ns1.equals(ns2));
+		assertFalse(ns1.equals(ns3));
+		assertFalse(ns2.equals(ns3));
+		
+	}
+
+}
Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java	(revision 1648)
+++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeatedTest.java	(revision 1648)
@@ -0,0 +1,34 @@
+package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class SmithWatermanRepeatedTest {
+
+	@Test
+	public void testGetMaxScore() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testGetAlignmentScore() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testGetMatches() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testGetAlignment() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testAlign() {
+		fail("Not yet implemented");
+	}
+
+}
Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrixTest.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrixTest.java	(revision 1648)
+++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrixTest.java	(revision 1648)
@@ -0,0 +1,19 @@
+package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class ObjectDistanceSubstitionMatrixTest {
+
+	@Test
+	public void testGenerate() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testGetScore() {
+		fail("Not yet implemented");
+	}
+
+}
Index: /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrixTest.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrixTest.java	(revision 1648)
+++ /branches/autoquest-core-tasktrees-alignment-test/src/test/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrixTest.java	(revision 1648)
@@ -0,0 +1,19 @@
+package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class TriangleMatrixTest {
+
+	@Test
+	public void testGet() {
+		fail("Not yet implemented");
+	}
+
+	@Test
+	public void testSet() {
+		fail("Not yet implemented");
+	}
+
+}
Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java
===================================================================
--- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java	(revision 1647)
+++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java	(revision 1648)
@@ -9,18 +9,4 @@
 	private int id;
 
-	public ArrayList<Match> getMatches() {
-		return matches;
-	}
-
-
-	public void setMatches(ArrayList<Match> matches) {
-		this.matches = matches;
-	}
-	
-	public void addMatches(ArrayList<Match> matches) {
-		this.matches.addAll(matches);
-	}
-
-	private ArrayList<Match> matches;
 
 	public NumberSequence(int size) {