Index: anches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Alignment.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Alignment.java (revision 1571) +++ (revision ) @@ -1,8 +1,0 @@ -package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; - -import java.util.List; - -public interface Alignment { - public List getMatches(); - -} Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/FengDoolittle.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/FengDoolittle.java (revision 1571) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/FengDoolittle.java (revision 1572) @@ -1,5 +1,5 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; -import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.TriangleMatrix; +import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.TriangleMatrix; public class FengDoolittle { Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1571) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1572) @@ -4,7 +4,7 @@ import java.util.List; -import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.SubstitutionMatrix; - -public class SmithWaterman implements Alignment { +import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; + +public class SmithWaterman { /** Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1571) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1572) @@ -2,9 +2,11 @@ import java.util.ArrayList; +import java.util.Iterator; +import java.util.LinkedList; import java.util.List; -import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.SubstitutionMatrix; - -public class SmithWatermanRepeated implements Alignment { +import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; + +public class SmithWatermanRepeated { /** @@ -29,5 +31,6 @@ private MatrixEntry[][] matrix; - + + private List alignment; private float scoreThreshold; @@ -50,4 +53,5 @@ matrix = new MatrixEntry[length1+2][length2+1]; + alignment = new ArrayList(); for (int i = 0; i <= length1+1; i++) { @@ -218,5 +222,42 @@ } - public List traceback() { + + public void traceback() { + MatrixEntry tmp = matrix[length1+1][0]; + + int aligned1[] = new int[length1+length2]; + int aligned2[] = new int[length1+length2]; + int count = 0; + do + { + if(count != 0) + { + aligned1[count] = tmp.getXvalue(); + aligned2[count] = tmp.getYvalue(); + } + + tmp = tmp.getPrevious(); + count++; + + } while(tmp != null); + + //reverse order + int reversed1[] = new int[count]; + int reversed2[] = new int[count]; + + for(int i = count; count > 0; count ++) { + + } + + NumberSequence ns1 = new NumberSequence(reversed1.length); + NumberSequence ns2 = new NumberSequence(reversed2.length); + ns1.setSequence(reversed1); + ns2.setSequence(reversed2); + + alignment.add(ns1); + alignment.add(ns2); + } + + public void printAlignment() { MatrixEntry tmp = matrix[length1+1][0]; String aligned1 = ""; @@ -259,5 +300,4 @@ System.out.println(aligned1); System.out.println(aligned2); - return null; } @@ -321,4 +361,13 @@ return matchList; } + + + public List getAlignment() { + return alignment; + } + + public void setAlignment(List alignment) { + this.alignment = alignment; + } } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1572) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1572) @@ -0,0 +1,62 @@ +/** + * + */ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; + +/** + * @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 void generate() { + // TODO Auto-generated method stub + + } + +} Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1572) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1572) @@ -0,0 +1,56 @@ +/** + * + */ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; + +/** + * @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 void generate() { + // TODO Auto-generated method stub + + } + + + +} Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1572) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1572) @@ -0,0 +1,122 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + + +import java.util.HashMap; +import java.util.Iterator; + + +import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement; +import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentHelpers; +import de.ugoe.cs.autoquest.tasktrees.treeifc.IEventTaskInstance; +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance; +import de.ugoe.cs.autoquest.usageprofiles.SymbolMap; + + +public class ObjectDistanceSubstitionMatrix implements SubstitutionMatrix { + + // private ArrayList matrix; + HashMap idmapping; + private TriangleMatrix matrix; + private SymbolMap uniqueTasks; + private double gapPenalty; + private double positiveThreshold; + + public ObjectDistanceSubstitionMatrix( + SymbolMap uniqueTasks,float positiveThreshold) { + this.uniqueTasks = uniqueTasks; + this.positiveThreshold = positiveThreshold; + idmapping = new HashMap(); + matrix = new TriangleMatrix(uniqueTasks.size()+1); + gapPenalty = -5; + + } + + @Override + public double getGapPenalty() { + return gapPenalty; + } + + @Override + public void generate() { + int index = 0; + //TODO We need to determine this parameter before generating the matrix.. + //float meandistance = 18; + //TODO We need to determine this parameter before generating the matrix.. + float maxDistance =34; + for (Iterator it = uniqueTasks.getSymbols().iterator(); it + .hasNext();) { + Object obj1 = it.next(); + IEventTaskInstance eti1 = null; + if (obj1 instanceof IEventTaskInstance) { + eti1 = (IEventTaskInstance) obj1; + } + //System.out.println(eti1.getTask().toString()); + + for (Iterator jt = uniqueTasks.getSymbols() + .iterator(); jt.hasNext();) { + IEventTaskInstance eti2 = null; + Object obj2 = jt.next(); + if (obj2 instanceof IEventTaskInstance) { + eti2 = (IEventTaskInstance) obj2; + } + IGUIElement first = (IGUIElement) eti1.getEvent().getTarget(); + IGUIElement second = (IGUIElement) eti2.getEvent().getTarget(); + int tempindex1 = -1; + int tempindex2 = -1; + if(!idmapping.containsKey(eti1.getTask().getId())) + { + idmapping.put(eti1.getTask().getId(), index); + tempindex1 = index; + index++; + } + else + { + tempindex1 = idmapping.get(eti1.getTask().getId()); + } + if(!idmapping.containsKey(eti2.getTask().getId())) + { + idmapping.put(eti2.getTask().getId(), index); + tempindex2 = index; + index++; + } + else + { + tempindex2 = idmapping.get(eti2.getTask().getId()); + } + float distance = -1*AlignmentHelpers.distanceBetween(first, second); + + + if(distance > maxDistance){ + maxDistance = distance; + } + + distance += positiveThreshold; + + + + matrix.set(tempindex1, tempindex2,distance); + + } + } + //System.out.println("ObjectDistanceMatrix: MaxDistance: " + maxDistance); + //System.out.println(meandistance/(uniqueTasks.size()*uniqueTasks.size())); + //System.out.println(idmapping.toString()); + //System.out.println(matrix.toString()); + //System.out.println(idmapping.keySet().toString()); + //System.out.println(idmapping.values().toString()); + + } + + public String toString(){ + return matrix.toString(); + } + + @Override + public double getDistance(int taskId1, int taskId2) { + //System.out.println("Taskid1: " + taskId1 + " Taskid2: " + taskId2 + " Idmapping1: " + idmapping.get(taskId1) + " Idmapping2: " + idmapping.get(taskId2)); + return matrix.get(idmapping.get(taskId1),idmapping.get(taskId2)); + } + +} + Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1572) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1572) @@ -0,0 +1,15 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + + + +public interface SubstitutionMatrix { + + + public double getDistance(int pos1, int pos2); + + public double getGapPenalty(); + + public void generate(); + + +} Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java (revision 1572) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java (revision 1572) @@ -0,0 +1,55 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +public class TriangleMatrix { + + private double[] matrix; + protected int size; + + + + public TriangleMatrix(int size) { + this.size = size; + matrix = new double [size*(size+1)/2]; + } + + public double get(int first, int second) { + int row = Math.min(first, second); + int col = Math.max(first, second); + return matrix[row*size-(row*(row+1)/2 - (size-col))]; + + } + + public void set(int first, int second, double value) { + int row = Math.min(first, second); + int col = Math.max(first, second); + matrix[row*size-(row*(row+1)/2 - (size-col))] = value; + } + + public void initialize(double value) { + for (int i=0; i < matrix.length; i++) { + matrix[i] = value; + } + } + + + public String toString() { + String result = ""; + for (int i = 0; i < size; i++) { + for(int j = 0; j< size; j++) { + if(i