Changeset 1620 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.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/pal/tree/UPGMAAligningTree.java (modified) (5 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

@@ -223 +223 @@
                         if(seqCount1 == 1 && seqCount2 == 1) {
                                 AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-                                aa.align(node1.getSequence(0).getSequence(), node2.getSequence(0).getSequence(), submat, 5);
+                                aa.align(node1.getSequence(0), node2.getSequence(0), submat, 5);
                                 alignment = aa.getAlignment();
                                 
@@ -236 +236 @@
                                 for(int i=0;i<seqCount1;i++){
                                         AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-                                        aa.align(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5);
+                                        aa.align(node1.getSequence(i), node2.getSequence(0) , submat, 5);
                                         tempStorage.set(i, 1, aa);
                                         
@@ -256 +256 @@
                                 for(int i=0;i<seqCount2;i++) {
                                         AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-                                        aa.align(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5);
+                                        aa.align(node2.getSequence(i), node1.getSequence(0) , submat, 5);
                                         tempStorage.set(1, i, aa);
                                         if(maxScore < tempStorage.get(1, i).getAlignmentScore()) {
@@ -278 +278 @@
                                                 for(int j=0;j<seqCount2;j++) {
                                                         AlignmentAlgorithm aa =AlignmentAlgorithmFactory.create();
-                                                        aa.align(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5);
+                                                        aa.align(node1.getSequence(i), node2.getSequence(j), submat, 5);
                                                         tempStorage1.set(j, 0, aa);
                                                         if(maxScore1 < tempStorage1.get(j, 0).getAlignmentScore()) {
@@ -291 +291 @@
                                                 for (int j=0;j<seqCount1;j++) {
                                                         AlignmentAlgorithm aa =AlignmentAlgorithmFactory.create();
-                                                        aa.align(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5);
+                                                        aa.align(node2.getSequence(i),node1.getSequence(j),submat,5);
                                                         tempStorage2.set(j, 0, aa);
                                                         if(maxScore2 < tempStorage2.get(j, 0).getAlignmentScore()) {