Changeset 1570 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

06/18/14 21:24:30 (10 years ago)

Author:

rkrimmel

Message:

Adding FitchMargaliash? Class

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (5 diffs)

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

@@ -27 +27 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.FengDoolittle;
 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;
@@ -163 +162 @@
 
                 TriangleMatrix sequenceDistances = new TriangleMatrix(numberseqs.size());
+                sequenceDistances.initialize(Double.POSITIVE_INFINITY);
 
                 for (int i = 0; i < numberseqs.size(); i++) {
@@ -190 +190 @@
                                         
                                         double score = twoSequences.getAlignmentScore();
-                                        // Scores of the sequence beeing aligned to itself
+                                        // Scores of the sequence being aligned to itself
                                         double sSelf1 = sameSequence1.getAlignmentScore();
                                         double sSelf2 = sameSequence2.getAlignmentScore();
@@ -198 +198 @@
                                         double sMax = (sSelf1 + sSelf2) / 2;
                                         double sEff = (score - sRand)/ (sMax - sRand);
+                                        if(sEff < 0) {
+                                                sEff = 0;
+                                        }
                                         double distance = -Math.log(sEff);
-                                
-                                        System.out.println("Score: " + score + " sRand: " + sRand + " sMax: " + sMax + " sEff: " + sEff + " distance: " + distance);
                                         
-                                        sequenceDistances.set(i,j,distance );
+                                        
+                                        if(!Double.isInfinite(distance) && !Double.isNaN(distance)) {
+                                                //System.out.println("Score: " + String.format("%5.1f", score) + " sRand: " + String.format("%5.1f", sRand) + " sMax: " + String.format("%6.1f", sMax)  + " distance: " + String.format("%2.3f",distance));
+                                                if(distance < sequenceDistances.get(i, j)) {    
+                                                        sequenceDistances.set(i,j,distance );
+                                                }
+                                        }
 
                                         if (score > 0) {
@@ -227 +234 @@
                         }
                 }
-                //System.out.println(sequenceDistances.toString());
+                System.out.println(sequenceDistances.toString());
                 
                 do {
                         System.out.println();
-                        FengDoolittle fd = new FengDoolittle();
+                        //FengDoolittle fd = new FengDoolittle();
 
                         // appData.getStopWatch().start("whole loop");