Changeset 1574

Timestamp:

06/23/14 08:38:03 (10 years ago)

Author:

rkrimmel

Message:

Improvements to smith waterman

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (5 diffs)

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

@@ -63 +63 @@
 
                 buildMatrix();
+                traceback();
         }
 
@@ -216 +217 @@
         
         
-        private int[] traceback(int i, int j) {
-                
-                        
-                return null;
-        }
-        
-        
         public void traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
-                
-                int aligned1[] = new int[length1+length2];
-                int aligned2[] = new int[length1+length2];
+                //TODO: Why do we need such long arrays, also, add a check if we reach the limit?
+                int aligned1[] = new int[2*length1+2*length2];
+                int aligned2[] = new int[2*length1+2*length2];
+                System.out.println("Aligned length: " + aligned1.length);
                 int count = 0;
                 do
@@ -239 +234 @@
                         tmp = tmp.getPrevious();
                         count++;
+                        System.out.println(count);
                         
                 } while(tmp != null);
@@ -246 +242 @@
                 int reversed2[] = new int[count];
                 
-                for(int i = count; count > 0; count ++) {
-                        
+                
+                for(int i = count-1; i > 0; i--) {
+                        reversed1[reversed1.length-i]= aligned1[i];
+                        reversed2[reversed2.length-i]= aligned2[i];
                 }
                 
@@ -328 +326 @@
         }
 
-        /**
-         * Return a set of Matches identified in Dynamic programming matrix. A match
-         * is a pair of subsequences whose score is higher than the preset
-         * scoreThreshold
-         **/
-        public List<Match> getMatches() {
-                ArrayList<Match> matchList = new ArrayList();
-                int fA = 0, fB = 0;
-                // skip the first row and column, find the next maxScore after
-                // prevmaxScore
-                for (int i = 1; i <= length1; i++) {
-                        for (int j = 1; j <= length2; j++) {
-                                if (matrix[i][j].getScore() > scoreThreshold
-                                                && matrix[i][j].getScore() > matrix[i - 1][j - 1].getScore()
-                                                && matrix[i][j].getScore() > matrix[i - 1][j].getScore()
-                                                && matrix[i][j].getScore() > matrix[i][j - 1].getScore()) {
-                                        if (i == length1 || j == length2
-                                                        || matrix[i][j].getScore() > matrix[i + 1][j + 1].getScore()) {
-                                                // should be lesser than prev maxScore
-                                                fA = i;
-                                                fB = j;
-                                                int[] f = traceback(fA, fB); // sets the x, y to
-                                                                                                                // startAlignment
-                                                                                                                // coordinates
-                                                System.out.println(f[0] + " " + i + " " + f[1] + " "
-                                                                + j + " " + matrix[i][j].getScore());
-                                                // TODO Add matches to matchList
-                                        }
-                                }
-                        }
-                }
-                return matchList;
-        }
-        
 
         public List<NumberSequence> getAlignment() {