Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.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/SmithWaterman.java (modified) (2 diffs)

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

@@ -38 +38 @@
         private SubstitutionMatrix submat;
 
-        public SmithWaterman(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());
-
-                matrix = new MatrixEntry[length1 + 1][length2 + 1];
-                alignment = new ArrayList<NumberSequence>();
-
-                for (int i = 0; i < length1+1; i++) {
-                        for (int j = 0; j < length2+1; j++) {
-                                matrix[i][j] = new MatrixEntry();
-                        }
-                }
-
-                buildMatrix();
-                traceback();
-        }
 
         /**
@@ -294 +270 @@
         }
 
+        @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());
+
+                matrix = new MatrixEntry[length1 + 1][length2 + 1];
+                alignment = new ArrayList<NumberSequence>();
+
+                for (int i = 0; i < length1+1; i++) {
+                        for (int j = 0; j < length2+1; j++) {
+                                matrix[i][j] = new MatrixEntry();
+                        }
+                }
+
+                buildMatrix();
+                traceback();
+                
+        }
+
 }