Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.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/pal/tree/UPGMAAligningTree.java (modified) (6 diffs)

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

@@ -18 +18 @@
 import java.util.logging.Level;
 
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
@@ -221 +222 @@
                         //Align 2 sequences
                         if(seqCount1 == 1 && seqCount2 == 1) {
-                                alignment = (alignments.get(node1.getNumber(), node2.getNumber())).getAlignment();
+                                AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                aa.align(node1.getSequence(0).getSequence(), node2.getSequence(0).getSequence(), submat, 5);
+                                alignment = aa.getAlignment();
                                 
                         }
@@ -231 +234 @@
                                 double maxScore = 0.0;
                                 int maxIndex = 0;
-                                for(int i=0;i<seqCount1;i++) {
-                                        tempStorage.set(i, 1, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5));
+                                for(int i=0;i<seqCount1;i++){
+                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                        aa.align(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5);
+                                        tempStorage.set(i, 1, aa);
+                                        
                                         if(maxScore < tempStorage.get(i, 1).getAlignmentScore()) {
                                                 maxScore = tempStorage.get(i, 1).getAlignmentScore();
@@ -249 +255 @@
                                 int maxIndex = 0;
                                 for(int i=0;i<seqCount2;i++) {
-                                        tempStorage.set(1, i, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5));
+                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                        aa.align(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5);
+                                        tempStorage.set(1, i, aa);
                                         if(maxScore < tempStorage.get(1, i).getAlignmentScore()) {
                                                 maxScore = tempStorage.get(1, i).getAlignmentScore();
@@ -269 +277 @@
                                         for(int i=0;i<seqCount1;i++) {
                                                 for(int j=0;j<seqCount2;j++) {
-                                                        tempStorage1.set(j, 0, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5));
+                                                        AlignmentAlgorithm aa =AlignmentAlgorithmFactory.create();
+                                                        aa.align(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5);
+                                                        tempStorage1.set(j, 0, aa);
                                                         if(maxScore1 < tempStorage1.get(j, 0).getAlignmentScore()) {
                                                                 maxScore1 = tempStorage1.get(j, 0).getAlignmentScore();
@@ -280 +290 @@
                                         for(int i=0; i<seqCount2;i++) {
                                                 for (int j=0;j<seqCount1;j++) {
-                                                        tempStorage2.set(j, 0, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5));
+                                                        AlignmentAlgorithm aa =AlignmentAlgorithmFactory.create();
+                                                        aa.align(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5);
+                                                        tempStorage2.set(j, 0, aa);
                                                         if(maxScore2 < tempStorage2.get(j, 0).getAlignmentScore()) {
                                                                 maxScore2 = tempStorage2.get(j, 0).getAlignmentScore();