Changeset 1568 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution

Timestamp:

06/18/14 08:59:41 (10 years ago)

Author:

rkrimmel

Message:

Building distance matrix between sequences

Location:

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

Files:

• DifferenceSubstitutionMatrix.java (modified) (2 diffs)
• NearbySubstitutionMatrix.java (modified) (2 diffs)
• ObjectDistanceSubstitionMatrix.java (modified) (5 diffs)
• SubstitutionMatrix.java (modified) (1 diff)
• TriangleMatrix.java (modified) (2 diffs)

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

@@ -29 +29 @@
          * @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 +49 @@
 
         @Override
-        public float getGapPenalty() {
+        public double getGapPenalty() {
                 return -maxValue;
         }

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

@@ -29 +29 @@
          * @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 +41 @@
 
         @Override
-        public float getGapPenalty() {
+        public double getGapPenalty() {
                 return -range-1;
         }

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;
+        private double gapPenalty; 
+        private double positiveThreshold;
         
         public ObjectDistanceSubstitionMatrix(
@@ -40 +40 @@
 
         @Override
-        public float getGapPenalty() {
+        public double getGapPenalty() {
                 return gapPenalty;
         }
@@ -48 +48 @@
                 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 +58 @@
                                 eti1 = (IEventTaskInstance) obj1;
                         }
+                        //System.out.println(eti1.getTask().toString());
                 
                         for (Iterator<ITaskInstance> jt = uniqueTasks.getSymbols()
@@ -121 +122 @@
 
         @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));

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

@@ -11 +11 @@
         
 
-        public float getDistance(int pos1, int pos2);
+        public double getDistance(int pos1, int pos2);
 
-        public float getGapPenalty();
+        public double getGapPenalty();
 
         public void generate();

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

@@ -3 +3 @@
 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 +18 @@
         }
         
-        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);