Changeset 1568 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

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

Author:

rkrimmel

Message:

Building distance matrix between sequences

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (2 diffs)

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

@@ -30 +30 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
 import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.TriangleMatrix;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration;
@@ -156 +157 @@
                 // this is the real rule application. Loop while something is replaced.
                 SymbolMap<ITaskInstance, ITask> uniqueTasks = harmonizeEventTaskInstancesModel(appData);
+
                 ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(
                                 uniqueTasks, 5);
                 submat.generate();
 
-                // good tests: 7/8 20/24
+                TriangleMatrix sequenceDistances = new TriangleMatrix(numberseqs.size());
+
                 for (int i = 0; i < numberseqs.size(); i++) {
+                        NumberSequence ns1 = numberseqs.get(i);
+                        //System.out.print("Sequence " + i + ": ");
+                        //ns1.printSequence();
                         for (int j = 0; j < numberseqs.size(); j++) {
+                                NumberSequence ns2 = numberseqs.get(j);
+
+                                if (i != j) {
+                                        int smithWatermanThreshold = 10;
+
+                                        SmithWatermanRepeated twoSequences = new SmithWatermanRepeated(
+                                                        ns1.getSequence(), ns2.getSequence(), submat,
+                                                        smithWatermanThreshold);
+                                        SmithWatermanRepeated sameSequence1 = new SmithWatermanRepeated(
+                                                        ns1.getSequence(), ns1.getSequence(), submat,
+                                                        smithWatermanThreshold);
+                                        SmithWatermanRepeated sameSequence2 = new SmithWatermanRepeated(
+                                                        ns2.getSequence(), ns2.getSequence(), submat,
+                                                        smithWatermanThreshold);
+                                        
+                                        SmithWatermanRepeated randomSequence = new SmithWatermanRepeated(
+                                                        ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
+                                        //randomSequence.printDPMatrix();
+                                        //randomSequence.traceback();
+                                        
+                                        double score = twoSequences.getAlignmentScore();
+                                        // Scores of the sequence beeing aligned to itself
+                                        double sSelf1 = sameSequence1.getAlignmentScore();
+                                        double sSelf2 = sameSequence2.getAlignmentScore();
+
+                                        double sRand = randomSequence.getAlignmentScore();
+
+                                        double sMax = (sSelf1 + sSelf2) / 2;
+                                        double sEff = (score - sRand)/ (sMax - sRand);
+                                        double distance = -Math.log(sEff);
                                 
-                                NumberSequence ns1 = numberseqs.get(i);
-                                NumberSequence ns2 = numberseqs.get(j);
-                                
-                                
-                                
-                                SmithWatermanRepeated sw = new SmithWatermanRepeated(
-                                                ns1.getSequence(), ns2.getSequence(), submat, 10);
-                                
-                                if(sw.getAlignmentScore() > 0)
-                                {   
-                                        System.out.println("=================================================");
-                                        System.out.println("| Sequence " + String.format("%3d", i) +" Sequence " + String.format("%3d", j)  + "                     |");
-                                        System.out.println("=================================================");
-                                        //System.out.print("Sequence " + i + ": ");
-                                        //ns1.printSequence();
-                                        //System.out.print("Sequence " + j + ": ");
-                                        //ns2.printSequence();
-                                        //System.out.println("Max Scrore: " + sw.getMaxScore());
-                                        System.out.println("Alignment Score: " + sw.getAlignmentScore());
-                                        //sw.printDPMatrix();
-                                        sw.traceback();
-                                        System.out.println();
-                                        System.out.println();
-                                }
-                        }
-                }
-
+                                        System.out.println("Score: " + score + " sRand: " + sRand + " sMax: " + sMax + " sEff: " + sEff + " distance: " + distance);
+                                        
+                                        sequenceDistances.set(i,j,distance );
+
+                                        if (score > 0) {
+                                                /*
+                                                 * System.out.println(
+                                                 * "=================================================");
+                                                 * System.out.println("| Sequence " +
+                                                 * String.format("%3d", i) +" Sequence " +
+                                                 * String.format("%3d", j) + "                     |");
+                                                 * System.out.println(
+                                                 * "=================================================");
+                                                 * System.out.print("Sequence " + i + ": ");
+                                                 * ns1.printSequence(); System.out.print("Sequence " + j
+                                                 * + ": "); ns2.printSequence(); System.out.println();
+                                                 * //System.out.println("Max Scrore: " +
+                                                 * sw.getMaxScore());
+                                                 * System.out.println("Alignment Score: " +
+                                                 * sw.getAlignmentScore()); //sw.printDPMatrix();
+                                                 * sw.traceback(); System.out.println();
+                                                 * System.out.println();
+                                                 */
+                                        }
+                                }
+                        }
+                }
+                //System.out.println(sequenceDistances.toString());
+                
                 do {
                         System.out.println();