Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java

Timestamp:

07/14/14 23:27:01 (10 years ago)

Author:

rkrimmel

Message:

Removed parameters from alignmentalgorihm factory constructor and changed interface by adding a new align() method, which now gets all the data via parameter

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java (modified) (2 diffs)

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

@@ -21 +21 @@
                                 if (i != j) {
                                         int smithWatermanThreshold = 10;
-
-                                        alignments.set(i, j,AlignmentAlgorithmFactory.create(
-                                                        ns1.getSequence(), ns2.getSequence(), submat,
-                                                        smithWatermanThreshold));
+                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                        aa.align(ns1.getSequence(), ns2.getSequence(), submat,
+                                                        smithWatermanThreshold);
+                                        alignments.set(i,j,aa);
+                                
                                         
-                                        AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory.create(
+                                        AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory.create();
+                                                        sameSequence1.align(
                                                         ns1.getSequence(), ns1.getSequence(), submat,
                                                         smithWatermanThreshold);
-                                        AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory.create(
-                                                        ns2.getSequence(), ns2.getSequence(), submat,
+                                        AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory.create();
+                                                        sameSequence2.align(ns2.getSequence(), ns2.getSequence(), submat,
                                                         smithWatermanThreshold);
-                                        AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory.create(
-                                                        ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
+                                        AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory.create();
+                                                        randomSequence.align(ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
                                         
                                         // Score of the aligmnment
                                         double score = alignments.get(i,j).getAlignmentScore();
+                                        /*
                                         if(score > 0) {
                                                 System.out.println("Alignment: " + i + " " + j);
@@ -52 +55 @@
                                                 System.out.println();
                                         }
+                                        */
                                         // Scores of the sequence being aligned to itself (maximum score)
                                         double sSelf1 = sameSequence1.getAlignmentScore();