Changeset 1655 for branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment

Timestamp:

08/09/14 17:40:11 (10 years ago)

Author:

rkrimmel

Message:

Commit before making dramatic changes. (Not really)

Location:

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

Files:

• algorithms/Match.java (modified) (1 diff)
• matrix/PairwiseAlignmentGenerator.java (modified) (3 diffs)

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

@@ -60 +60 @@
         }
 
-        /*
+        
         public void addOccurencesOf(Match m) {
-                LinkedList<MatchOccurence> occ = m.getOccurences();
-                occurences.addAll(occ);
+                occurences.addAll(m.getOccurences());
         }
-        */
+        
         
    

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();
@@ -45 +47 @@
                                                         .shuffle(), submat,
                                                         smithWatermanThreshold);
-
+                                        
                                         // Score of the aligmnment
                                         double score = alignments.get(i, j).getAlignmentScore();
@@ -69 +71 @@
                                                 }
                                         }
+                                        */
                                 }
                         }