Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatrixEntry.java =================================================================== --- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatrixEntry.java (revision 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatrixEntry.java (revision 1568) @@ -2,5 +2,5 @@ public class MatrixEntry { - private float score; + private double score; private MatrixEntry previous; private int xvalue; @@ -15,8 +15,8 @@ } - public float getScore() { + public double getScore() { return score; } - public void setScore(float score) { + public void setScore(double score) { this.score = score; } Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java =================================================================== --- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1568) @@ -3,4 +3,5 @@ import java.io.Serializable; import java.util.ArrayList; +import java.util.Random; public class NumberSequence implements Serializable { @@ -33,4 +34,19 @@ System.out.println(); } + + public NumberSequence shuffle(){ + NumberSequence result = new NumberSequence(sequence.length); + result.setSequence(this.sequence); + Random rgen = new Random(); + + for (int i=0; i traceback() { MatrixEntry tmp = matrix[length1+1][0]; String aligned1 = ""; @@ -266,4 +259,5 @@ System.out.println(aligned1); System.out.println(aligned2); + return null; } Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/DifferenceSubstitutionMatrix.java =================================================================== --- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/DifferenceSubstitutionMatrix.java (revision 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/DifferenceSubstitutionMatrix.java (revision 1568) @@ -29,5 +29,5 @@ * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) */ - public float getDistance(int pos1, int pos2) { + public double getDistance(int pos1, int pos2) { return maxValue - (input1[pos1] - input2[pos2]); } @@ -49,5 +49,5 @@ @Override - public float getGapPenalty() { + public double getGapPenalty() { return -maxValue; } Index: branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/NearbySubstitutionMatrix.java =================================================================== --- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/NearbySubstitutionMatrix.java (revision 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/NearbySubstitutionMatrix.java (revision 1568) @@ -29,5 +29,5 @@ * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) */ - public float getDistance(int pos1, int pos2) { + public double getDistance(int pos1, int pos2) { int difference = Math.abs(input1[pos1]-input2[pos2]); if(difference < range) { @@ -41,5 +41,5 @@ @Override - public float getGapPenalty() { + public double getGapPenalty() { return -range-1; } 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 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java (revision 1568) @@ -26,6 +26,6 @@ private TriangleMatrix matrix; private SymbolMap uniqueTasks; - private float gapPenalty; - private float positiveThreshold; + private double gapPenalty; + private double positiveThreshold; public ObjectDistanceSubstitionMatrix( @@ -40,5 +40,5 @@ @Override - public float getGapPenalty() { + public double getGapPenalty() { return gapPenalty; } @@ -48,5 +48,5 @@ int index = 0; //TODO We need to determine this parameter before generating the matrix.. - float meandistance = 18; + //float meandistance = 18; //TODO We need to determine this parameter before generating the matrix.. float maxDistance =34; @@ -58,4 +58,5 @@ eti1 = (IEventTaskInstance) obj1; } + //System.out.println(eti1.getTask().toString()); for (Iterator jt = uniqueTasks.getSymbols() @@ -121,5 +122,5 @@ @Override - public float getDistance(int taskId1, int taskId2) { + 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/substitution/SubstitutionMatrix.java =================================================================== --- branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/SubstitutionMatrix.java (revision 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/SubstitutionMatrix.java (revision 1568) @@ -11,7 +11,7 @@ - public float getDistance(int pos1, int pos2); + public double getDistance(int pos1, int pos2); - public float getGapPenalty(); + public double getGapPenalty(); public void generate(); 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 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/TriangleMatrix.java (revision 1568) @@ -3,13 +3,13 @@ public class TriangleMatrix { - private float[] matrix; + private double[] matrix; private int size; public TriangleMatrix(int size) { this.size = size; - matrix = new float [size*(size+1)/2]; + matrix = new double [size*(size+1)/2]; } - public float get(int first, int second) { + public double get(int first, int second) { int row = Math.min(first, second); int col = Math.max(first, second); @@ -18,5 +18,5 @@ } - public void set(int first, int second, float value) { + public void set(int first, int second, double value) { int row = Math.min(first, second); int col = Math.max(first, second); 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 1559) +++ branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1568) @@ -30,4 +30,5 @@ import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated; import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.TriangleMatrix; import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration; @@ -156,39 +157,76 @@ // this is the real rule application. Loop while something is replaced. SymbolMap uniqueTasks = harmonizeEventTaskInstancesModel(appData); + ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix( uniqueTasks, 5); submat.generate(); - // good tests: 7/8 20/24 + TriangleMatrix sequenceDistances = new TriangleMatrix(numberseqs.size()); + for (int i = 0; i < numberseqs.size(); i++) { + NumberSequence ns1 = numberseqs.get(i); + //System.out.print("Sequence " + i + ": "); + //ns1.printSequence(); for (int j = 0; j < numberseqs.size(); j++) { + NumberSequence ns2 = numberseqs.get(j); + + if (i != j) { + int smithWatermanThreshold = 10; + + SmithWatermanRepeated twoSequences = new SmithWatermanRepeated( + ns1.getSequence(), ns2.getSequence(), submat, + smithWatermanThreshold); + SmithWatermanRepeated sameSequence1 = new SmithWatermanRepeated( + ns1.getSequence(), ns1.getSequence(), submat, + smithWatermanThreshold); + SmithWatermanRepeated sameSequence2 = new SmithWatermanRepeated( + ns2.getSequence(), ns2.getSequence(), submat, + smithWatermanThreshold); + + SmithWatermanRepeated randomSequence = new SmithWatermanRepeated( + ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold); + //randomSequence.printDPMatrix(); + //randomSequence.traceback(); + + double score = twoSequences.getAlignmentScore(); + // Scores of the sequence beeing aligned to itself + double sSelf1 = sameSequence1.getAlignmentScore(); + double sSelf2 = sameSequence2.getAlignmentScore(); + + double sRand = randomSequence.getAlignmentScore(); + + double sMax = (sSelf1 + sSelf2) / 2; + double sEff = (score - sRand)/ (sMax - sRand); + double distance = -Math.log(sEff); - NumberSequence ns1 = numberseqs.get(i); - NumberSequence ns2 = numberseqs.get(j); - - - - SmithWatermanRepeated sw = new SmithWatermanRepeated( - ns1.getSequence(), ns2.getSequence(), submat, 10); - - if(sw.getAlignmentScore() > 0) - { - System.out.println("================================================="); - System.out.println("| Sequence " + String.format("%3d", i) +" Sequence " + String.format("%3d", j) + " |"); - System.out.println("================================================="); - //System.out.print("Sequence " + i + ": "); - //ns1.printSequence(); - //System.out.print("Sequence " + j + ": "); - //ns2.printSequence(); - //System.out.println("Max Scrore: " + sw.getMaxScore()); - System.out.println("Alignment Score: " + sw.getAlignmentScore()); - //sw.printDPMatrix(); - sw.traceback(); - System.out.println(); - System.out.println(); - } - } - } - + System.out.println("Score: " + score + " sRand: " + sRand + " sMax: " + sMax + " sEff: " + sEff + " distance: " + distance); + + sequenceDistances.set(i,j,distance ); + + if (score > 0) { + /* + * System.out.println( + * "================================================="); + * System.out.println("| Sequence " + + * String.format("%3d", i) +" Sequence " + + * String.format("%3d", j) + " |"); + * System.out.println( + * "================================================="); + * System.out.print("Sequence " + i + ": "); + * ns1.printSequence(); System.out.print("Sequence " + j + * + ": "); ns2.printSequence(); System.out.println(); + * //System.out.println("Max Scrore: " + + * sw.getMaxScore()); + * System.out.println("Alignment Score: " + + * sw.getAlignmentScore()); //sw.printDPMatrix(); + * sw.traceback(); System.out.println(); + * System.out.println(); + */ + } + } + } + } + //System.out.println(sequenceDistances.toString()); + do { System.out.println();