Changeset 1584 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

06/27/14 15:25:25 (10 years ago)

Author:

rkrimmel

Message:

Some refactoring for storing the initial alignments so we don't need to do them again.

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (6 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -26 +26 @@
 import java.util.logging.Level;
 
-
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
@@ -158 +158 @@
                 submat.generate();
 
-                UPGMAMatrix sequenceDistances = new UPGMAMatrix(numberseqs.size());
-                sequenceDistances.initialize(Double.POSITIVE_INFINITY);
-                
-                //Save the alignments so we do not need to recalculate those when aligning them again in feng doolittle algorithm
-                SmithWatermanRepeated[][] alignments = new SmithWatermanRepeated[numberseqs.size()][numberseqs.size()]; 
+        
+                BinaryAlignmentStorage alignments = new BinaryAlignmentStorage(numberseqs.size());
+
 
                 for (int i = 0; i < numberseqs.size(); i++) {
@@ -172 +170 @@
                                         int smithWatermanThreshold = 10;
 
-                                        alignments[i][j] = new SmithWatermanRepeated(
+                                        alignments.set(i, j,new SmithWatermanRepeated(
                                                         ns1.getSequence(), ns2.getSequence(), submat,
-                                                        smithWatermanThreshold);
+                                                        smithWatermanThreshold));
                                         SmithWatermanRepeated sameSequence1 = new SmithWatermanRepeated(
                                                         ns1.getSequence(), ns1.getSequence(), submat,
@@ -185 +183 @@
                                         
                                         // Score of the aligmnment
-                                        double score = alignments[i][j].getAlignmentScore();
+                                        double score = alignments.get(i,j).getAlignmentScore();
                                         // Scores of the sequence being aligned to itself (maximum score)
                                         double sSelf1 = sameSequence1.getAlignmentScore();
@@ -201 +199 @@
                                         
                                         if(!Double.isInfinite(distance) && !Double.isNaN(distance)) {
-                                                if(distance < sequenceDistances.get(i, j)) {    
-                                                        sequenceDistances.set(i,j,distance );
+                                                if(distance < alignments.getDistance(i, j)) {   
+                                                        alignments.setDistance(i,j,distance );
                                                 }
                                         }
@@ -209 +207 @@
                 }
                 //System.out.println(sequenceDistances.toString());
-                UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, sequenceDistances);
+                UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments);