Changeset 1584 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/BinaryAlignmentStorage.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/alignment/matrix/BinaryAlignmentStorage.java (modified) (1 diff)

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;
+    }
 }
+