Changeset 1667 for branches/autoquest-core-tasktrees-alignment

Timestamp:

08/12/14 22:40:30 (10 years ago)

Author:

rkrimmel

Message:

Removed unused code (bohoo, all the time i needed to write it)

Location:

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment

Files:

• algorithms/GenerateTask.java (deleted)
• algorithms/MatchOccurence.java (modified) (1 diff)
• matrix/PairwiseAlignmentGenerator.java (modified) (1 diff)
• pal (deleted)

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurence.java

@@ -20 +20 @@
         }
 
-
         public int getStartindex() {
                 return startindex;

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java

@@ -31 +31 @@
                                                         smithWatermanThreshold);
                                         alignments.set(i, j, aa);
-                                        //TODO: This is old code used for generating pairwise distances between alignments (to build
-                                        // a guide tree
-                                        /*
-                                        AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory
-                                                        .create();
-                                        sameSequence1.align(ns1, ns1,
-                                                        submat, smithWatermanThreshold);
-                                        AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory
-                                                        .create();
-                                        sameSequence2.align(ns2, ns2,
-                                                        submat, smithWatermanThreshold);
-                                        AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory
-                                                        .create();
-                                        randomSequence.align(ns1.shuffle(), ns2
-                                                        .shuffle(), 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);
-                                                }
-                                        }
-                                        */
                                 }
                         }