Changeset 1555 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment

Timestamp:

05/25/14 16:51:10 (10 years ago)

Author:

rkrimmel

Message:

Smith waterman working again

Location:

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

Files:

• algorithms/SmithWaterman.java (modified) (4 diffs)
• substitution/ObjectDistanceSubstitionMatrix.java (modified) (4 diffs)
• substitution/TriangleMatrix.java (modified) (2 diffs)

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

@@ -69 +69 @@
                 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 +90 @@
         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 +97 @@
                 // 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 +279 @@
          */
         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();

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

@@ -26 +26 @@
         private TriangleMatrix matrix;
         private SymbolMap<ITaskInstance, ITask> uniqueTasks;
-
+        private float gapPenalty; 
+        private float positiveThreshold;
+        
         public ObjectDistanceSubstitionMatrix(
                         SymbolMap<ITaskInstance, ITask> uniqueTasks) {
@@ -32 +34 @@
                 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;
         }
 
         @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<ITaskInstance> it = uniqueTasks.getSymbols().iterator(); it
                                 .hasNext();) {
@@ -50 +55 @@
                                 eti1 = (IEventTaskInstance) obj1;
                         }
-                        int j = 0;
+                
                         for (Iterator<ITaskInstance> jt = uniqueTasks.getSymbols()
                                         .iterator(); jt.hasNext();) {
@@ -60 +65 @@
                                 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));
         }

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

@@ -8 +8 @@
         public TriangleMatrix(int size) {
                 this.size = size;
-                matrix = new float[size*(size+1)/2];
+                matrix = new float [size*(size+1)/2];
         }
         
@@ -24 +24 @@
         }
 
+        
+        
         
         //Note: String just looks good for small. testing matrices