Changeset 1558 for branches/ralph/src/main/java/de/ugoe

Timestamp:

05/29/14 22:43:07 (11 years ago)

Author:

rkrimmel

Message:

new Smith waterman variant

Location:

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/algorithms/MatrixEntry.java (added)
• alignment/algorithms/NumberSequence.java (modified) (1 diff)
• alignment/algorithms/SmithWaterman.java (modified) (3 diffs)
• alignment/algorithms/SmithWatermanRepeated.java (added)
• alignment/substitution/ObjectDistanceSubstitionMatrix.java (modified) (4 diffs)
• alignment/substitution/TriangleMatrix.java (modified) (1 diff)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (3 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java

@@ -25 +25 @@
                 this.signature = signature;
         }
+        
+        public void printSequence()
+        {       
+                for (int i = 0; i < sequence.length; i++) {
+                        System.out.format("%4d", sequence[i]);
+                }
+                System.out.println();
+        }
 
 }

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java

@@ -162 +162 @@
          * Get the maximum value in the score matrix.
          */
-        private double getMaxScore() {
+        public double getMaxScore() {
                 double maxScore = 0;
 
@@ -184 +184 @@
         }
 
+        
+        
         /**
          * TODO: Iterative Version!!! Output the local alignments ending in the (i,
@@ -272 +274 @@
                         }
                 }
-                // Note: empty alignments are not printed.
         }
 

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java

@@ -30 +30 @@
         
         public ObjectDistanceSubstitionMatrix(
-                        SymbolMap<ITaskInstance, ITask> uniqueTasks) {
+                        SymbolMap<ITaskInstance, ITask> uniqueTasks,float positiveThreshold) {
                 this.uniqueTasks = uniqueTasks;
+                this.positiveThreshold = positiveThreshold;
                 idmapping = new HashMap<Integer, Integer>();
                 matrix = new TriangleMatrix(uniqueTasks.size()+1);
                 gapPenalty = -10;
-                //Todo: Calculate this value (the mean distance between every element) before
-                positiveThreshold =7;
+                
         }
 
@@ -47 +47 @@
         public void generate() {
                 int index = 0;
-                float meandistance = 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<ITaskInstance> it = uniqueTasks.getSymbols().iterator(); it
                                 .hasNext();) {
@@ -87 +90 @@
                                         tempindex2 = idmapping.get(eti2.getTask().getId());
                                 }
-                                float distance = AlignmentHelpers.distanceBetween(first, second);
-                                meandistance += distance;
+                                float distance = -1*AlignmentHelpers.distanceBetween(first, second);
+                                //meandistance += distance;
                         
-                                if (distance > positiveThreshold) {
-                                        distance = -1*distance;
+                                if(distance > maxDistance){
+                                        maxDistance = distance;
                                 }
+                                
+                                distance += 5;
+                                
+                                //if (distance < positiveThreshold) {
+                                //      distance = -1*distance;
+                                //}
+                                
                                 matrix.set(tempindex1, tempindex2,distance);
                                 
                         }
                 }
-                System.out.println(meandistance/(uniqueTasks.size()*uniqueTasks.size()));
+                //System.out.println("ObjectDistanceMatrix: MaxDistance: " + maxDistance);
+                //System.out.println(meandistance/(uniqueTasks.size()*uniqueTasks.size()));
                 //System.out.println(idmapping.toString());
                 //System.out.println(matrix.toString());
@@ -104 +115 @@
                 
         }
+        
+        public String toString(){
+                return matrix.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));
         }

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/TriangleMatrix.java

@@ -33 +33 @@
                         for(int j = 0; j< size; j++) {
                                 if(i<j) {
-                                        result = result + (this.get(i,j) + " ");
+                                        result = result + String.format("%+4.1f",this.get(i,j));
                                 }
                                 else {
-                                        result = result + ("    ");
+                                        result = result + ("      ");
                                 }
                         }

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -28 +28 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWaterman;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
 import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
@@ -145 +146 @@
         
         
-        
         // this is the real rule application. Loop while something is replaced.
         SymbolMap<ITaskInstance, ITask> uniqueTasks = harmonizeEventTaskInstancesModel(appData);
-        ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(uniqueTasks);  
+        ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(uniqueTasks,20);
         submat.generate();
-        
-        SmithWaterman sw = new SmithWaterman(numberseqs.get(1).getSequence(), numberseqs.get(1).getSequence(), submat);
-        
+      
+       
+        
+        System.out.print("Sequence 1: ");
+        NumberSequence ns1 = numberseqs.get(7);
+        NumberSequence ns2 = numberseqs.get(8);
+        ns1.printSequence();
+        System.out.print("Sequence 2: ");
+        ns2.printSequence();
+        //SmithWatermanRepeated sw = new SmithWatermanRepeated(numberseqs.get(20).getSequence(), numberseqs.get(24).getSequence(), submat,10);
+        SmithWatermanRepeated sw = new SmithWatermanRepeated(ns1.getSequence(), ns2.getSequence(), submat,15);
+        System.out.println("Max Scrore: " + sw.getMaxScore());
+        
+        sw.printDPMatrix();
    
         
         
-      
-        
-        
-        //Hier mein kram hin
+
         do {
             System.out.println();
@@ -165 +173 @@
             
             
-            appData.getStopWatch().start("whole loop");
-            detectAndReplaceIterations(appData);
-
-            appData.getStopWatch().start("task replacement");
-            detectAndReplaceTasks(appData);
-            appData.getStopWatch().stop("task replacement");
-            appData.getStopWatch().stop("whole loop");
-            
-            
-            appData.getStopWatch().dumpStatistics(System.out);
-            appData.getStopWatch().reset();
+            //appData.getStopWatch().start("whole loop");
+            //detectAndReplaceIterations(appData);
+
+            //appData.getStopWatch().start("task replacement");
+            //detectAndReplaceTasks(appData);
+            //appData.getStopWatch().stop("task replacement");
+            //appData.getStopWatch().stop("whole loop");
+            
+            
+            //appData.getStopWatch().dumpStatistics(System.out);
+            //appData.getStopWatch().reset();
             
         }