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 1701) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1702) @@ -29,5 +29,5 @@ * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) */ - public double getScore(int pos1, int pos2) { + public float getScore(int pos1, int pos2) { return maxValue - (input1[pos1] - input2[pos2]); } @@ -49,5 +49,5 @@ @Override - public double getGapPenalty() { + public float getGapPenalty() { return -maxValue; } 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 1701) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DummySubstitutionMatrix.java (revision 1702) @@ -9,5 +9,5 @@ @Override - public double getScore(int pos1, int pos2) { + public float getScore(int pos1, int pos2) { if(pos1==pos2) { return 1; @@ -19,5 +19,5 @@ @Override - public double getGapPenalty() { + public float getGapPenalty() { return -1; } Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DynamicTriangleMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DynamicTriangleMatrix.java (revision 1702) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DynamicTriangleMatrix.java (revision 1702) @@ -0,0 +1,100 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; + +import java.util.ArrayList; + +//Must be initialized! +public class DynamicTriangleMatrix implements ITriangleMatrix { + + private ArrayList matrix; + protected int size; + private float initalizationValue; + + + + //Increases the size + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ITriangleMatrix#increaseSize(int) + */ + @Override + 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 DynamicTriangleMatrix(int size) { + this.size = size; + matrix = new ArrayList(); + matrix.ensureCapacity(size*(size+1/2)); + } + + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ITriangleMatrix#get(int, int) + */ + @Override + public float get(int first, int second) { + int row = Math.min(first, second); + int col = Math.max(first, second); + return matrix.get(row*size-(row*(row+1)/2 - (size-col))); + + } + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ITriangleMatrix#set(int, int, float) + */ + @Override + public void set(int first, int second, float value) { + int row = Math.min(first, second); + int col = Math.max(first, second); + matrix.set(row*size-(row*(row+1)/2 - (size-col)),value); + } + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ITriangleMatrix#initialize(float) + */ + @Override + public void initialize(float value) { + this.initalizationValue = value; + matrix.clear(); + for (int i=0; i < this.size*(this.size+1)/2; i++) { + matrix.add(value); + } + } + + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ITriangleMatrix#toString() + */ + @Override + public String toString() { + String result = ""; + for (int i = 0; i < size; i++) { + for(int j = 0; j< size; j++) { + if(i idmapping; - private TriangleMatrix matrix; + private ITriangleMatrix matrix; private HashSet uniqueTasks; - private double gapPenalty; + private float gapPenalty; private int index = 0; private HashMap> etisOfTasks; private boolean calculateNonTaskInstances = true; + private int firstRoundMaxIndex = 0; private double positiveThreshold; public ObjectDistanceSubstitionMatrix( - float positiveThreshold, int gapPenalty, - boolean calculateNonTaskInstances) { - + float positiveThreshold, int gapPenalty, + boolean calculateNonTaskInstances) { this.positiveThreshold = positiveThreshold; idmapping = new HashMap(); @@ -40,9 +42,9 @@ } - public double getGapPenalty() { + public float getGapPenalty() { return gapPenalty; } - public void setGapPenalty(double gapPenalty) { + public void setGapPenalty(float gapPenalty) { this.gapPenalty = gapPenalty; } @@ -77,10 +79,15 @@ //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"); + try { + matrix.increaseSize(newTasks.size()); + System.out.println("Subsitution matrix size is now " + matrix.size()*(matrix.size()+1)/2); + Console.traceln(Level.INFO, "searching EventTasks in Tasks"); + } catch (Exception e) { + Console.logException(e); + } this.updateEventTaskInstances(newTasks); - } - + for(Iterator it = newTasks.iterator();it.hasNext();) { int index1 = -1; @@ -137,14 +144,18 @@ } } + } } public void generate(HashSet uniqueTasks) { this.uniqueTasks = uniqueTasks; - matrix = new TriangleMatrix(uniqueTasks.size() + 1); - matrix.initialize(0); if (this.calculateNonTaskInstances) { + matrix = new DynamicTriangleMatrix(uniqueTasks.size() + 1); Console.traceln(Level.INFO, "searching EventTasks in Tasks"); searchEventTaskInstances(); } + else{ + matrix = new StaticTriangleMatrix(uniqueTasks.size()+1); + } + matrix.initialize(0); Console.traceln(Level.INFO, "calculating distances"); int index1 = -1; @@ -197,10 +208,16 @@ System.out.println("Unknown error"); } - matrix.set(index1, index2, distance); } } - } + this.firstRoundMaxIndex=index; + } + + private void computeDistance(ITask task1, ITask task2) { + + + } + @@ -293,10 +310,14 @@ } - public double getScore(int taskId1, int taskId2) { + public float getScore(int taskId1, int taskId2) { if (taskId1 == Constants.GAP_SYMBOL || taskId1 == Constants.UNMATCHED_SYMBOL || taskId2 == Constants.GAP_SYMBOL || taskId2 == Constants.UNMATCHED_SYMBOL) { - return 0.0; + return 0; + } else if(this.calculateNonTaskInstances==false && + (taskId1>this.firstRoundMaxIndex + || taskId2>this.firstRoundMaxIndex)) { + return 0; } else { Integer first = idmapping.get(taskId1); 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 1701) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1702) @@ -11,7 +11,7 @@ - public double getScore(int pos1, int pos2); + public float getScore(int pos1, int pos2); - public double getGapPenalty(); + public float getGapPenalty(); public void generate(HashSet uniqueTasks); Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java (revision 1701) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java (revision 1702) @@ -3,5 +3,5 @@ -public class UPGMAMatrix extends TriangleMatrix { +public class UPGMAMatrix extends StaticTriangleMatrix { public UPGMAMatrix(int size) { Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java (revision 1701) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java (revision 1702) @@ -113,4 +113,5 @@ // TODO: Debug output + /* System.out.println("PRINTING MODEL: "); for (int i = 0; i < subsequence.getSequence().getChildren().size(); i++) { @@ -140,5 +141,5 @@ } System.out.println(); - + */ //TODO: This is dirty! @@ -151,10 +152,10 @@ } ITask tempTask = model.getChildren().get(modelindex); - System.out.println("Trying to add " + parent.get(startIndex) - + " to the model instance " + tempTask); + //System.out.println("Trying to add " + parent.get(startIndex) + // + " to the model instance " + tempTask); if (tempTask.getType() == "optionality") { if(((IMarkingTemporalRelationship) tempTask).getMarkedTask() == parent.get(startIndex).getTask()) { - System.out.println("Adding OptionalInstance " + parent.get(startIndex) + " to " + tempTask.getType()); + //System.out.println("Adding OptionalInstance " + parent.get(startIndex) + " to " + tempTask.getType()); IOptionalInstance optional = taskFactory.createNewTaskInstance((IOptional) tempTask); taskBuilder.setChild(optional, parent.get(startIndex)); @@ -162,5 +163,5 @@ } else { - System.out.println("Adding Empty optional, not deleting anything from the input sequence"); + //System.out.println("Adding Empty optional, not deleting anything from the input sequence"); IOptionalInstance optional = taskFactory.createNewTaskInstance((IOptional) tempTask); taskBuilder.addChild(subsequence, optional); @@ -182,16 +183,16 @@ } else if(parent.get(startIndex).getTask().getId() == tmpSel.getChildren().get(0).getId() || parent.get(startIndex).getTask().getId() == tmpSel.getChildren().get(1).getId() ) { - System.out.println("Session ID: " + parent.get(startIndex).getTask().getId() + " tmpSel(0): " + tmpSel.getChildren().get(0).getId() + " tmpSel(1): " +tmpSel.getChildren().get(1).getId() ); + //System.out.println("Session ID: " + parent.get(startIndex).getTask().getId() + " tmpSel(0): " + tmpSel.getChildren().get(0).getId() + " tmpSel(1): " +tmpSel.getChildren().get(1).getId() ); continue; } for (int k=0;k 1) { @@ -661,5 +665,5 @@ .get(j)); } - } + }*/ // Check if nothing has been replaced in the sequence we @@ -773,5 +777,5 @@ stopWatch = new StopWatch(); result = new RuleApplicationResult(); - submat= new ObjectDistanceSubstitionMatrix(6,-3,true); + submat= new ObjectDistanceSubstitionMatrix(6,-3,false); newTasks = new LinkedList(); }