Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

07/14/14 23:27:01 (10 years ago)

Author:

rkrimmel

Message:

Removed parameters from alignmentalgorihm factory constructor and changed interface by adding a new align() method, which now gets all the data via parameter

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (2 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

@@ -43 +43 @@
         private SubstitutionMatrix submat;
 
-        public SmithWatermanRepeated(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) {
-                this.input1 = input1;
-                this.input2 = input2;
-                length1 = input1.length;
-                length2 = input2.length;
-                this.submat = submat;
-
-                //System.out.println("Starting SmithWaterman algorithm with a "
-                //              + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
-                this.scoreThreshold = threshold;
-                
-                matrix = new MatrixEntry[length1+2][length2+1];
-                alignment = new ArrayList<NumberSequence>();
-                
-                for (int i = 0; i <= length1+1; i++) {
-                        for(int j = 0; j< length2; j++) {
-                                matrix[i][j] = new MatrixEntry();
-                        }
-                }
-        
-
-                buildMatrix();
-                traceback();
+        public SmithWatermanRepeated() {
+        
         }
 
@@ -374 +353 @@
         }
 
+        @Override
+        public void align(int[] input1, int[] input2, SubstitutionMatrix submat,
+                        float threshold) {
+                this.input1 = input1;
+                this.input2 = input2;
+                length1 = input1.length;
+                length2 = input2.length;
+                this.submat = submat;
+
+                //System.out.println("Starting SmithWaterman algorithm with a "
+                //              + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
+                this.scoreThreshold = threshold;
+                
+                matrix = new MatrixEntry[length1+2][length2+1];
+                alignment = new ArrayList<NumberSequence>();
+                
+                for (int i = 0; i <= length1+1; i++) {
+                        for(int j = 0; j< length2; j++) {
+                                matrix[i][j] = new MatrixEntry();
+                        }
+                }
+        
+
+                buildMatrix();
+                traceback();
+        }
+
 }