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 1554) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1555) @@ -69,6 +69,6 @@ this.submat = submat; - System.out.println("Starting SmithWaterman algorithm with a " - + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName()); + //System.out.println("Starting SmithWaterman algorithm with a " + // + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName()); scoreThreshold = 20; score = new double[length1 + 1][length2 + 1]; @@ -90,5 +90,5 @@ private double similarity(int i, int j) { if (i == 0 || j == 0) { - // it's a gap (indel) + // it's a gap return submat.getGapPenalty(); } @@ -97,5 +97,5 @@ // return (input1[i - 1] == input2[j - 1]) ? MATCH_SCORE : // MISMATCH_SCORE; - return submat.getDistance(i - 1, j - 1); + return submat.getDistance(input1[i - 1], input2[j - 1]); } @@ -279,15 +279,16 @@ */ public void printDPMatrix() { - System.out.print(" "); + System.out.print(" "); for (int j = 1; j <= length2; j++) - System.out.print(" " + input2[j - 1]); + System.out.format("%5d", input2[j - 1]); System.out.println(); for (int i = 0; i <= length1; i++) { if (i > 0) - System.out.print(input1[i - 1] + " "); - else - System.out.print(" "); + System.out.format("%5d ",input1[i - 1]); + else{ + System.out.print(" "); + } for (int j = 0; j <= length2; j++) { - System.out.print(score[i][j] + " "); + System.out.format("%4.1f ",score[i][j]); } System.out.println(); Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java (revision 1554) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java (revision 1555) @@ -26,5 +26,7 @@ private TriangleMatrix matrix; private SymbolMap uniqueTasks; - + private float gapPenalty; + private float positiveThreshold; + public ObjectDistanceSubstitionMatrix( SymbolMap uniqueTasks) { @@ -32,15 +34,18 @@ idmapping = new HashMap(); matrix = new TriangleMatrix(uniqueTasks.size()+1); + gapPenalty = -10; + //Todo: Calculate this value (the mean distance between every element) before + positiveThreshold =7; } @Override public float getGapPenalty() { - // TODO Auto-generated method stub - return 0; + return gapPenalty; } @Override public void generate() { - int i = 0; + int index = 0; + float meandistance = 0; for (Iterator it = uniqueTasks.getSymbols().iterator(); it .hasNext();) { @@ -50,5 +55,5 @@ eti1 = (IEventTaskInstance) obj1; } - int j = 0; + for (Iterator jt = uniqueTasks.getSymbols() .iterator(); jt.hasNext();) { @@ -60,15 +65,48 @@ IGUIElement first = (IGUIElement) eti1.getEvent().getTarget(); IGUIElement second = (IGUIElement) eti2.getEvent().getTarget(); - idmapping.put(eti1.getTask().getId(), i); - idmapping.put(eti2.getTask().getId(), j); - matrix.set(i, j, AlignmentHelpers.distanceBetween(first, second)); - j++; + 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 = AlignmentHelpers.distanceBetween(first, second); + meandistance += distance; + + if (distance > positiveThreshold) { + distance = -1*distance; + } + matrix.set(tempindex1, tempindex2,distance); + } - i++; } + 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()); + } @Override public float 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/substitution/TriangleMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/TriangleMatrix.java (revision 1554) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/TriangleMatrix.java (revision 1555) @@ -8,5 +8,5 @@ public TriangleMatrix(int size) { this.size = size; - matrix = new float[size*(size+1)/2]; + matrix = new float [size*(size+1)/2]; } @@ -24,4 +24,6 @@ } + + //Note: String just looks good for small. testing matrices Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1554) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1555) @@ -123,4 +123,5 @@ this.preparationTaskHandlingStrategy = new TaskHandlingStrategy(minimalTaskEquality); this.identityTaskHandlingStrategy = new TaskHandlingStrategy(TaskEquality.IDENTICAL); + numberseqs = new ArrayList(); } @@ -140,15 +141,14 @@ public RuleApplicationResult apply(List sessions) { RuleApplicationData appData = new RuleApplicationData(sessions); - numberseqs = new ArrayList(); + // this is the real rule application. Loop while something is replaced. - SymbolMap uniqueTasks = harmonizeEventTaskInstancesModel(appData,numberseqs); + SymbolMap uniqueTasks = harmonizeEventTaskInstancesModel(appData); ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(uniqueTasks); submat.generate(); - - SmithWaterman sm = new SmithWaterman(numberseqs.get(0).getSequence(), numberseqs.get(0).getSequence(), submat); + SmithWaterman sm = new SmithWaterman(numberseqs.get(1).getSequence(), numberseqs.get(1).getSequence(), submat); sm.printDPMatrix(); @@ -201,5 +201,5 @@ * @return Returns the unique tasks symbol map */ - private SymbolMap harmonizeEventTaskInstancesModel(RuleApplicationData appData, ArrayList numberseqs) { + private SymbolMap harmonizeEventTaskInstancesModel(RuleApplicationData appData) { Console.traceln(Level.INFO, "harmonizing task model of event task instances"); appData.getStopWatch().start("harmonizing event tasks");