Changeset 1586 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

Timestamp:

06/30/14 08:51:09 (10 years ago)

Author:

rkrimmel

Message:

Adding simple smith waterman and changing alignment algorithm creation to factory pattern

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (modified) (8 diffs)

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

@@ -15 +15 @@
 
 import java.util.ArrayList;
-import java.util.Iterator;
 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;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
@@ -228 +229 @@
                                 int maxIndex = 0;
                                 for(int i=0;i<seqCount1;i++) {
-                                        tempStorage.set(i, 1, new SmithWatermanRepeated(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5));
+                                        tempStorage.set(i, 1, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5));
                                         if(maxScore < tempStorage.get(i, 1).getAlignmentScore()) {
                                                 maxScore = tempStorage.get(i, 1).getAlignmentScore();
@@ -234 +235 @@
                                         }
                                 }
+                                //if(maxScore > 0)
                                 alignment.add(tempStorage.get(maxIndex, 1).getAlignment().get(1));
                         }
@@ -243 +245 @@
                                 int maxIndex = 0;
                                 for(int i=0;i<seqCount2;i++) {
-                                        tempStorage.set(1, i, new SmithWatermanRepeated(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5));
+                                        tempStorage.set(1, i, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5));
                                         if(maxScore < tempStorage.get(1, i).getAlignmentScore()) {
                                                 maxScore = tempStorage.get(1, i).getAlignmentScore();
@@ -249 +251 @@
                                         }
                                 }
+                                //if(maxScore > 0)
                                 alignment.add(tempStorage.get(1,maxIndex).getAlignment().get(1));
                         }
@@ -261 +264 @@
                                         for(int i=0;i<seqCount1;i++) {
                                                 for(int j=0;j<seqCount2;j++) {
-                                                        tempStorage1.set(j, 0, new SmithWatermanRepeated(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5));
+                                                        tempStorage1.set(j, 0, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5));
                                                         if(maxScore1 < tempStorage1.get(j, 0).getAlignmentScore()) {
                                                                 maxScore1 = tempStorage1.get(j, 0).getAlignmentScore();
@@ -267 +270 @@
                                                         }
                                                 }
+                                                //if(maxScore1 > 0)
                                                 alignment.add(tempStorage1.get(maxIndex1,0).getAlignment().get(0));
                                         }
                                         for(int i=0; i<seqCount2;i++) {
                                                 for (int j=0;j<seqCount1;j++) {
-                                                        tempStorage2.set(j, 0, new SmithWatermanRepeated(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5));
+                                                        tempStorage2.set(j, 0, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5));
                                                         if(maxScore2 < tempStorage2.get(j, 0).getAlignmentScore()) {
                                                                 maxScore2 = tempStorage2.get(j, 0).getAlignmentScore();
@@ -277 +281 @@
                                                         }
                                                 }
+                                                //if(maxScore2 > 0)
                                                 alignment.add(tempStorage2.get(maxIndex2,0).getAlignment().get(0));
                                         }