Changeset 1589 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

07/09/14 12:13:13 (10 years ago)

Author:

rkrimmel

Message:

Refactoring and code cleanup

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

@@ -29 +29 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentGenerator;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree.UPGMAAligningTree;
@@ -158 +159 @@
                 submat.generate();
 
+                
+                PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat);
         
-                BinaryAlignmentStorage alignments = new BinaryAlignmentStorage(numberseqs.size(),numberseqs.size());
-
-
-                for (int i = 0; i < numberseqs.size(); i++) {
-                        NumberSequence ns1 = numberseqs.get(i);
-                        for (int j = 0; j < numberseqs.size(); j++) {
-                                NumberSequence ns2 = numberseqs.get(j);
-
-                                if (i != j) {
-                                        int smithWatermanThreshold = 10;
-
-                                        alignments.set(i, j,AlignmentAlgorithmFactory.create(
-                                                        ns1.getSequence(), ns2.getSequence(), submat,
-                                                        smithWatermanThreshold));
-                                        AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory.create(
-                                                        ns1.getSequence(), ns1.getSequence(), submat,
-                                                        smithWatermanThreshold);
-                                        AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory.create(
-                                                        ns2.getSequence(), ns2.getSequence(), submat,
-                                                        smithWatermanThreshold);
-                                        AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory.create(
-                                                        ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
-                                        
-                                        // Score of the aligmnment
-                                        double score = alignments.get(i,j).getAlignmentScore();
-                                        // Scores of the sequence being aligned to itself (maximum score)
-                                        double sSelf1 = sameSequence1.getAlignmentScore();
-                                        double sSelf2 = sameSequence2.getAlignmentScore();
-                                        // Score of sequences shuffled before aligned  
-                                        double sRand = randomSequence.getAlignmentScore();
-
-                                        double sMax = (sSelf1 + sSelf2) / 2;
-                                        double sEff = (score - sRand)/ (sMax - sRand);
-                                        if(sEff < 0) {
-                                                sEff = 0;
-                                        }
-                                        double distance = -Math.log(sEff);
-                                        
-                                        
-                                        if(!Double.isInfinite(distance) && !Double.isNaN(distance)) {
-                                                if(distance < alignments.getDistance(i, j)) {   
-                                                        alignments.setDistance(i,j,distance );
-                                                }
-                                        }
-                                }
-                        }
-                }
-                //alignments.get(20, 47).printDPMatrix();
-                //alignments.get(20, 47).printAlignment();
                 
                 System.out.println(alignments.getDistanceMatrix());
-                UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
-                System.out.println("Number of sequences in root node: " + guidetree.getRoot().getSequences().size());
-                for (Iterator<NumberSequence> it =  guidetree.getRoot().getSequences().iterator(); it.hasNext();) {
-                        NumberSequence tmp  = it.next();
-                        tmp.printSequence();
-                }
+                //UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
+                
+