Changeset 1568 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

06/18/14 08:59:41 (10 years ago)

Author:

rkrimmel

Message:

Building distance matrix between sequences

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (8 diffs)

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

@@ -71 +71 @@
          * @return Cost of substitution of the character in str1 by the one in str2
          */
-        private float similarity(int i, int j) { 
+        private double similarity(int i, int j) { 
                 return submat.getDistance(input1[i - 1], input2[j - 1]);
         }
@@ -101 +101 @@
                         // F(i,0) = max { F(i-1,0), F(i-1,j)-T  j=1,...,m
                         
-                        float firstRowLeftScore = matrix[i-1][0].getScore();
+                        double firstRowLeftScore = matrix[i-1][0].getScore();
                         //for sequences of length 1
-                        float tempMax;
+                        double tempMax;
                         int maxRowIndex;
                         if(length2 == 1) {
@@ -138 +138 @@
                                 matrix[i][0].setXvalue(input1[i-1]);
                                 matrix[i][0].setYvalue(-2);
-                                
                         }
                         else { 
@@ -147 +146 @@
                         
                         for (int j = 1; j < length2; j++) {
-                                float diagScore = matrix[i - 1][j - 1].getScore() + similarity(i, j);
-                                float upScore = matrix[i][j - 1].getScore() + submat.getGapPenalty();
-                                float leftScore = matrix[i - 1][j].getScore() + submat.getGapPenalty();
+                                double diagScore = matrix[i - 1][j - 1].getScore() + similarity(i, j);
+                                double upScore = matrix[i][j - 1].getScore() + submat.getGapPenalty();
+                                double leftScore = matrix[i - 1][j].getScore() + submat.getGapPenalty();
 
                                 matrix[i][j].setScore(Math.max(diagScore,Math.max(upScore, Math.max(leftScore,matrix[i][0].getScore()))));
@@ -207 +206 @@
          * Get the alignment score between the two input strings.
          */
-        public float getAlignmentScore() {
+        public double getAlignmentScore() {
                 return matrix[length1+1][0].getScore();
         }
@@ -213 +212 @@
         
         
-        
-        /**
-         * given the bottom right corner point trace back the top left conrner. at
-         * entry: i, j hold bottom right (end of Aligment coords) at return: hold
-         * top left (start of Alignment coords)
-         */
         private int[] traceback(int i, int j) {
                 
@@ -225 +218 @@
         }
         
-        public void traceback() {
+        public List<Match> traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
                 String aligned1 = "";
@@ -266 +259 @@
                 System.out.println(aligned1);
                 System.out.println(aligned2);
+                return null;
         }