Changeset 1620 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java

Timestamp:

07/23/14 18:18:11 (10 years ago)

Author:

rkrimmel

Message:

More intelligent match finding and creation

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java (modified) (3 diffs)

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

@@ -14 +14 @@
         public static PairwiseAlignmentStorage generate(
                         ArrayList<NumberSequence> numberseqs,
-                        ObjectDistanceSubstitionMatrix submat) {
+                        ObjectDistanceSubstitionMatrix submat, 
+                        int threshold) {
                 PairwiseAlignmentStorage alignments = new PairwiseAlignmentStorage(
                                 numberseqs.size(), numberseqs.size());
+                int smithWatermanThreshold = threshold;
 
                 for (int i = 0; i < numberseqs.size(); i++) {
@@ -25 +27 @@
                                 if (i != j) {
                                         Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
-                                        int smithWatermanThreshold = 10;
+                                
                                         AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-                                        aa.align(ns1.getSequence(), ns2.getSequence(), submat,
+                                        aa.align(ns1, ns2, submat,
                                                         smithWatermanThreshold);
                                         alignments.set(i, j, aa);
@@ -33 +35 @@
                                         AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory
                                                         .create();
-                                        sameSequence1.align(ns1.getSequence(), ns1.getSequence(),
+                                        sameSequence1.align(ns1, ns1,
                                                         submat, smithWatermanThreshold);
                                         AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory
                                                         .create();
-                                        sameSequence2.align(ns2.getSequence(), ns2.getSequence(),
+                                        sameSequence2.align(ns2, ns2,
                                                         submat, smithWatermanThreshold);
                                         AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory
                                                         .create();
-                                        randomSequence.align(ns1.shuffle().getSequence(), ns2
-                                                        .shuffle().getSequence(), submat,
+                                        randomSequence.align(ns1.shuffle(), ns2
+                                                        .shuffle(), submat,
                                                         smithWatermanThreshold);