Changeset 1584

Timestamp:

06/27/14 15:25:25 (11 years ago)

Author:

rkrimmel

Message:

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

Location:

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/matrix/BinaryAlignmentStorage.java (modified) (1 diff)
• alignment/pal/tree/UPGMAAligningTree.java (modified) (4 diffs)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (6 diffs)

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

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
+
+
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
 
 public class BinaryAlignmentStorage {
 
+    private SmithWatermanRepeated[][] alignments;
+    UPGMAMatrix sequenceDistances;
+   
+    public BinaryAlignmentStorage(int size) {
+        alignments = new SmithWatermanRepeated[size][size];
+        sequenceDistances = new UPGMAMatrix(size);
+        sequenceDistances.initialize(Double.POSITIVE_INFINITY);
+    }
+    
+    public void set(int i,int j,SmithWatermanRepeated sw) {
+        alignments[i][j] = sw;
+    }
+    
+    public SmithWatermanRepeated get(int i,int j) {
+        return alignments[i][j];
+    }
+    
+    public void setDistance(int i,int j,double distance) {
+        sequenceDistances.set(i, j, distance);
+    }
+    
+    public double getDistance(int i,int j) {
+        return sequenceDistances.get(i,j);
+    }
+    
+    public UPGMAMatrix getDistanceMatrix() {
+        return sequenceDistances;
+    }
 }
+

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

@@ -17 +17 @@
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier;
@@ -41 +42 @@
          * @param m distance matrix
          */
-        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, UPGMAMatrix m)
-        {
-                if (m.size() < 2)
+        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, BinaryAlignmentStorage alignments)
+        {
+                if (alignments.getDistanceMatrix().size() < 2)
                 {
                         new IllegalArgumentException("LESS THAN 2 TAXA IN DISTANCE MATRIX");
@@ -49 +50 @@
         
                 this.numberseqs = numberseqs;
-                init(m);
+                this.alignments = alignments;
+                init(alignments.getDistanceMatrix());
 
                 while (true)
@@ -73 +75 @@
         //
         private ArrayList<NumberSequence> numberseqs;
+        private BinaryAlignmentStorage alignments;
         private int numClusters;
         private int besti, abi;

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);