Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1698) @@ -3,4 +3,9 @@ */ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.HashSet; +import java.util.LinkedList; + +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; @@ -50,7 +55,9 @@ @Override - public void generate() { - // TODO Auto-generated method stub - + public void generate(HashSet uniqueTasks) { + } + + @Override + public void update(LinkedList newlyGeneratedTasks) { } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java (revision 1698) @@ -1,3 +1,8 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.HashSet; +import java.util.LinkedList; + +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; public class DummySubstitutionMatrix implements SubstitutionMatrix { @@ -19,6 +24,13 @@ @Override - public void generate() { + public void generate(HashSet uniqueTasks) { } + @Override + public void update(LinkedList newlyGeneratedTasks) { + // TODO Auto-generated method stub + + } + + } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1698) @@ -3,4 +3,9 @@ */ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.HashSet; +import java.util.LinkedList; + +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; /** @@ -40,8 +45,11 @@ + @Override - public void generate() { - // TODO Auto-generated method stub - + public void generate(HashSet uniqueTasks) { + } + + @Override + public void update(LinkedList newlyGeneratedTasks) { } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1698) @@ -28,12 +28,11 @@ private double positiveThreshold; - public ObjectDistanceSubstitionMatrix(HashSet uniqueTasks, + public ObjectDistanceSubstitionMatrix( float positiveThreshold, int gapPenalty, boolean calculateNonTaskInstances) { - this.uniqueTasks = uniqueTasks; + this.positiveThreshold = positiveThreshold; idmapping = new HashMap(); etisOfTasks = new HashMap>(); - matrix = new TriangleMatrix(uniqueTasks.size() + 1); this.gapPenalty = gapPenalty; this.calculateNonTaskInstances = calculateNonTaskInstances; @@ -65,18 +64,17 @@ } - - public void generate() { - if (this.calculateNonTaskInstances) { - Console.traceln(Level.INFO, " searching EventTasks in Tasks"); + + //Just Calculate the distance between the new tasks and the matrix. + public void update(LinkedList newTasks) { + matrix.increaseSize(newTasks.size()); + if (this.calculateNonTaskInstances) { + Console.traceln(Level.INFO, "searching EventTasks in Tasks"); searchEventTaskInstances(); } - Console.traceln(Level.INFO, " calculating distances"); - int index1 = -1; - int index2 = -1; - float distance = 0; - int count = 0; - for (Iterator it = uniqueTasks.iterator(); it.hasNext();) { - count++; - + + for(Iterator it = newTasks.iterator();it.hasNext();) { + int index1 = -1; + int index2 = -1; + float distance = 0; ITask task1 = it.next(); for (Iterator jt = uniqueTasks.iterator(); jt.hasNext();) { @@ -130,4 +128,71 @@ } } + + public void generate(HashSet uniqueTasks) { + this.uniqueTasks = uniqueTasks; + matrix = new TriangleMatrix(uniqueTasks.size() + 1); + matrix.initialize(0); + if (this.calculateNonTaskInstances) { + Console.traceln(Level.INFO, "searching EventTasks in Tasks"); + searchEventTaskInstances(); + } + Console.traceln(Level.INFO, "calculating distances"); + int index1 = -1; + int index2 = -1; + float distance = 0; + for (Iterator it = uniqueTasks.iterator(); it.hasNext();) { + ITask task1 = it.next(); + for (Iterator jt = uniqueTasks.iterator(); jt.hasNext();) { + ITask task2 = jt.next(); + ITaskInstance ti1 = null; + ITaskInstance ti2 = null; + // We just need to the first instance here + if (task1.getInstances().size() > 0) { + ti1 = (ITaskInstance) task1.getInstances().iterator() + .next(); + } + if (task2.getInstances().size() > 0) { + ti2 = (ITaskInstance) task2.getInstances().iterator() + .next(); + } + IEventTaskInstance eti1 = null; + IEventTaskInstance eti2 = null; + + if (ti1 instanceof IEventTaskInstance + && ti2 instanceof IEventTaskInstance) { + eti1 = (IEventTaskInstance) ti1; + index1 = getIndex(eti1); + eti2 = (IEventTaskInstance) ti2; + index2 = getIndex(eti2); + distance = distanceBetweenInstances(eti1, eti2); + } else if (ti1 instanceof IEventTaskInstance + && !(ti2 instanceof IEventTaskInstance)) { + task1 = ((ITaskInstance) ti1).getTask(); + index2 = getIndex(task2); + eti1 = (IEventTaskInstance) ti1; + index1 = getIndex(eti1); + distance = distanceBetweenTaskAndInstance(task2, eti1); + } else if (!(ti1 instanceof IEventTaskInstance) + && ti2 instanceof IEventTaskInstance) { + index1 = getIndex(task1); + eti2 = (IEventTaskInstance) ti2; + index2 = getIndex(eti2); + distance = distanceBetweenTaskAndInstance(task1, eti2); + } else if (!(ti1 instanceof IEventTaskInstance) + && !(ti2 instanceof IEventTaskInstance)) { + index1 = getIndex(task1); + index2 = getIndex(task2); + distance = distanceBetweenTasks(task1, task2); + } else { + System.out.println("Unknown error"); + } + + matrix.set(index1, index2, distance); + + } + } + } + + private float distanceBetweenTaskAndInstance(ITask task1, @@ -157,5 +222,6 @@ public boolean scoreExists(int id, int id2) { - return idmapping.containsKey(id) && idmapping.containsKey(id2); + //return idmapping.containsKey(id) && idmapping.containsKey(id2); + return false; } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1698) @@ -1,3 +1,8 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.HashSet; +import java.util.LinkedList; + +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; @@ -10,5 +15,7 @@ public double getGapPenalty(); - public void generate(); + public void generate(HashSet uniqueTasks); + + public void update(LinkedList newlyGeneratedTasks); Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/TriangleMatrix.java (revision 1698) @@ -1,20 +1,37 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; +import java.util.ArrayList; + +//Must be initialized! public class TriangleMatrix { - private float[] matrix; + private ArrayList matrix; protected int size; + private float initalizationValue; + //Increases the size + public void increaseSize(int count) { + int oldsize = size; + this.size += count; + matrix.ensureCapacity(size*(size+1/2)); + for(int i=0;i<(oldsize*count)+(count*(count+1)/2);i++) { + matrix.add(this.initalizationValue); + } + } + + public TriangleMatrix(int size) { this.size = size; - matrix = new float [size*(size+1)/2]; + matrix = new ArrayList(); + matrix.ensureCapacity(size*(size+1/2)); } + public float 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))]; + return matrix.get(row*size-(row*(row+1)/2 - (size-col))); } @@ -23,10 +40,12 @@ int row = Math.min(first, second); int col = Math.max(first, second); - matrix[row*size-(row*(row+1)/2 - (size-col))] = value; + matrix.set(row*size-(row*(row+1)/2 - (size-col)),value); } public void initialize(float value) { - for (int i=0; i < matrix.length; i++) { - matrix[i] = value; + this.initalizationValue = value; + matrix.clear(); + for (int i=0; i < this.size*(this.size+1)/2; i++) { + matrix.add(value); } } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1697) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1698) @@ -68,5 +68,5 @@ class SequenceForTaskDetectionRuleAlignment implements ISessionScopeRule { - private int iteration = 0; + //private int iteration = 0; /** *

@@ -139,6 +139,10 @@ harmonizeEventTaskInstancesModel(appData); + // Generate a substitution matrix between all occurring events. + Console.traceln(Level.INFO, "generating substitution matrix"); + appData.getSubmat().generate(appData.getUniqueTasks()); + do { - iteration++; + //iteration++; appData.detectedAndReplacedTasks = false; @@ -146,4 +150,5 @@ detectAndReplaceIterations(appData); appData.getStopWatch().start("task replacement"); + appData.updateSubstitutionMatrix(); detectAndReplaceTasks(appData); // appData.getStopWatch().stop("task replacement"); @@ -168,4 +173,5 @@ return appData.getResult(); } + private ArrayList createNumberSequences( @@ -322,6 +328,5 @@ IIteration iteration = taskFactory.createNewIteration(); - appData.getUniqueTasks().add(iteration); - appData.getNumber2Task().put(iteration.getId(), iteration); + appData.newTaskCreated(iteration); iterations.put(iteratedTask, iteration); iterationInstances.put(iteration, @@ -445,6 +450,5 @@ public ISequence matchAsSequence(RuleApplicationData appData, Match m) { ISequence sequence = taskFactory.createNewSequence(); - appData.uniqueTasks.add(sequence); - appData.number2task.put(sequence.getId(), sequence); + appData.newTaskCreated(sequence); int[] first = m.getFirstSequence().getSequence(); @@ -469,6 +473,5 @@ else if (first[i] == -1 && second[i] != -1) { IOptional optional = taskFactory.createNewOptional(); - appData.uniqueTasks.add(optional); - appData.number2task.put(optional.getId(), optional); + appData.newTaskCreated(optional); taskBuilder.setMarkedTask(optional, appData.getNumber2Task() .get(second[i])); @@ -479,6 +482,5 @@ else if (first[i] != -1 && second[i] == -1) { IOptional optional = taskFactory.createNewOptional(); - appData.uniqueTasks.add(optional); - appData.number2task.put(optional.getId(), optional); + appData.newTaskCreated(optional); taskBuilder.setMarkedTask(optional, appData.getNumber2Task() .get(first[i])); @@ -494,6 +496,5 @@ ISelection selection = taskFactory.createNewSelection(); - appData.getUniqueTasks().add(selection); - appData.number2task.put(selection.getId(), selection); + appData.newTaskCreated(selection); taskBuilder.addChild(selection, appData.getNumber2Task() .get(first[i])); @@ -504,14 +505,11 @@ boolean selectionfound = true; ISelection selection = taskFactory.createNewSelection(); - appData.getUniqueTasks().add(selection); - appData.number2task.put(selection.getId(), selection); + appData.newTaskCreated(selection); ISequence subsequence1 = taskFactory.createNewSequence(); - appData.uniqueTasks.add(subsequence1); - appData.number2task.put(subsequence1.getId(), subsequence1); + appData.newTaskCreated(subsequence1); ISequence subsequence2 = taskFactory.createNewSequence(); - appData.uniqueTasks.add(subsequence2); - appData.number2task.put(subsequence2.getId(), subsequence2); + appData.newTaskCreated(subsequence2); taskBuilder.addChild(selection, subsequence1); @@ -542,6 +540,5 @@ ISelection selection = taskFactory.createNewSelection(); - appData.getUniqueTasks().add(selection); - appData.number2task.put(selection.getId(), selection); + appData.newTaskCreated(selection); taskBuilder.addChild(selection, appData.getNumber2Task() .get(first[i])); @@ -568,16 +565,10 @@ // Create NumberSequences appData.setNumberSequences(this.createNumberSequences(appData)); - - // Generate a substitution matrix between all occurring events. - Console.traceln(Level.INFO, "generating substitution matrix"); - ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix( - appData.getUniqueTasks(), 6, -3,true); - submat.generate(); - + // Generate pairwise alignments Console.traceln(Level.INFO, "generating pairwise alignments"); LinkedList matchseqs = new LinkedList(); PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator - .generate(appData.getNumberSequences(), submat, 9); + .generate(appData.getNumberSequences(), appData.getSubmat(), 9); // Retrieve all matches reached a specific threshold @@ -729,5 +720,4 @@ alignments = null; matchseqs = null; - submat = null; appData.getStopWatch().stop("replacing tasks"); } @@ -740,9 +730,14 @@ private HashMap number2task; - // TODO: We Actually just need number2task here + // TODO: We Actually just need number2task here, this structure can be removed in the future. private HashSet uniqueTasks; - + + ObjectDistanceSubstitionMatrix submat; + + private ArrayList numberseqs; + private LinkedList newTasks; + /** * @@ -775,4 +770,20 @@ stopWatch = new StopWatch(); result = new RuleApplicationResult(); + submat= new ObjectDistanceSubstitionMatrix(6,-3,true); + newTasks = new LinkedList(); + } + + private ObjectDistanceSubstitionMatrix getSubmat() { + return submat; + } + + private void resetNewlyCreatedTasks() { + uniqueTasks.addAll(newTasks); + newTasks.clear(); + } + + private void newTaskCreated(ITask task) { + number2task.put(task.getId(), task); + newTasks.add(task); } @@ -788,8 +799,4 @@ } - // private void setUniqueTasks(SymbolMap ut) { - // this.uniqueTasks = ut; - // } - private void setNumberSequences(ArrayList numberseqs) { this.numberseqs = numberseqs; @@ -800,4 +807,10 @@ } + private void updateSubstitutionMatrix() { + submat.update(getNewTasks()); + resetNewlyCreatedTasks(); + } + + /** * @@ -814,4 +827,8 @@ } + public LinkedList getNewTasks() { + return newTasks; + } + /** * @return the stopWatch