Changeset 1583 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

06/26/14 23:34:58 (10 years ago)

Author:

rkrimmel

Message:

Small fixes and comments.

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (3 diffs)

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

@@ -160 +160 @@
                 UPGMAMatrix sequenceDistances = new UPGMAMatrix(numberseqs.size());
                 sequenceDistances.initialize(Double.POSITIVE_INFINITY);
+                
+                //Save the alignments so we do not need to recalculate those when aligning them again in feng doolittle algorithm
+                SmithWatermanRepeated[][] alignments = new SmithWatermanRepeated[numberseqs.size()][numberseqs.size()]; 
 
                 for (int i = 0; i < numberseqs.size(); i++) {
@@ -169 +172 @@
                                         int smithWatermanThreshold = 10;
 
-                                        SmithWatermanRepeated twoSequences = new SmithWatermanRepeated(
+                                        alignments[i][j] = new SmithWatermanRepeated(
                                                         ns1.getSequence(), ns2.getSequence(), submat,
                                                         smithWatermanThreshold);
@@ -182 +185 @@
                                         
                                         // Score of the aligmnment
-                                        double score = twoSequences.getAlignmentScore();
+                                        double score = alignments[i][j].getAlignmentScore();
                                         // Scores of the sequence being aligned to itself (maximum score)
                                         double sSelf1 = sameSequence1.getAlignmentScore();