Changeset 1570

Timestamp:

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

Author:

rkrimmel

Message:

Adding FitchMargaliash? Class

Location:

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

Files:

• alignment/substitution/FitchMargoliashMatrix.java (added)
• alignment/substitution/ObjectDistanceSubstitionMatrix.java (modified) (3 diffs)
• alignment/substitution/SubstitutionMatrix.java (modified) (1 diff)
• alignment/substitution/TriangleMatrix.java (modified) (1 diff)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (5 diffs)

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

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.substitution;
 
-import java.util.ArrayList;
-import java.util.Collection;
+
 import java.util.HashMap;
 import java.util.Iterator;
 
-import de.ugoe.cs.autoquest.eventcore.guimodel.GUIModel;
+
 import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement;
-
-import java.util.List;
-
-import de.ugoe.cs.autoquest.eventcore.Event;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentHelpers;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IEventTaskInstance;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
 import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
-import de.ugoe.cs.util.console.GlobalDataContainer;
+
 
 public class ObjectDistanceSubstitionMatrix implements SubstitutionMatrix {
@@ -92 +86 @@
                                 }
                                 float distance = -1*AlignmentHelpers.distanceBetween(first, second);
-                                //meandistance += distance;
+                        
                         
                                 if(distance > maxDistance){
@@ -98 +92 @@
                                 }
                                 
-                                distance += 5;
+                                distance += positiveThreshold;
                                 
-                                //if (distance < positiveThreshold) {
-                                //      distance = -1*distance;
-                                //}
+
                                 
                                 matrix.set(tempindex1, tempindex2,distance);

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

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.substitution;
 
-import java.util.Collection;
-import java.util.List;
-
-import de.ugoe.cs.autoquest.eventcore.Event;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
 
 

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

@@ -5 +5 @@
         private double[] matrix;
         private int size;
+        
+        
         
         public TriangleMatrix(int size) {

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");