Changeset 1586 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/BinaryAlignmentStorage.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/matrix/BinaryAlignmentStorage.java (modified) (1 diff)

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

@@ -2 +2 @@
 
 
-import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
 
 public class BinaryAlignmentStorage {
 
-    private SmithWatermanRepeated[][] alignments;
+    private AlignmentAlgorithm[][] alignments;
     UPGMAMatrix sequenceDistances;
    
     public BinaryAlignmentStorage(int sizex, int sizey) {
-        alignments = new SmithWatermanRepeated[sizex+1][sizey+1];
+        alignments = new AlignmentAlgorithm[sizex+1][sizey+1];
         sequenceDistances = new UPGMAMatrix(Math.max(sizex,sizey));
         sequenceDistances.initialize(Double.POSITIVE_INFINITY);
     }
     
-    public void set(int i,int j,SmithWatermanRepeated sw) {
+    public void set(int i,int j,AlignmentAlgorithm sw) {
         alignments[i][j] = sw;
     }
     
-    public SmithWatermanRepeated get(int i,int j) {
+    public AlignmentAlgorithm get(int i,int j) {
         return alignments[i][j];
     }