Changeset 1555 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms

Timestamp:

05/25/14 16:51:10 (10 years ago)

Author:

rkrimmel

Message:

Smith waterman working again

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (modified) (4 diffs)

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

@@ -69 +69 @@
                 this.submat = submat;
 
-                System.out.println("Starting SmithWaterman algorithm with a "
-                                + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
+                //System.out.println("Starting SmithWaterman algorithm with a "
+                //              + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
                 scoreThreshold = 20;
                 score = new double[length1 + 1][length2 + 1];
@@ -90 +90 @@
         private double similarity(int i, int j) {
                 if (i == 0 || j == 0) {
-                        // it's a gap (indel)
+                        // it's a gap 
                         return submat.getGapPenalty();
                 }
@@ -97 +97 @@
                 // return (input1[i - 1] == input2[j - 1]) ? MATCH_SCORE :
                 // MISMATCH_SCORE;
-                return submat.getDistance(i - 1, j - 1);
+                return submat.getDistance(input1[i - 1], input2[j - 1]);
         }
 
@@ -279 +279 @@
          */
         public void printDPMatrix() {
-                System.out.print("   ");
+                System.out.print("          ");
                 for (int j = 1; j <= length2; j++)
-                        System.out.print("   " + input2[j - 1]);
+                        System.out.format("%5d", input2[j - 1]);
                 System.out.println();
                 for (int i = 0; i <= length1; i++) {
                         if (i > 0)
-                                System.out.print(input1[i - 1] + " ");
-                        else
-                                System.out.print("  ");
+                                System.out.format("%5d ",input1[i - 1]);
+                        else{
+                                System.out.print("      ");
+                        }
                         for (int j = 0; j <= length2; j++) {
-                                System.out.print(score[i][j] + " ");
+                                System.out.format("%4.1f ",score[i][j]);
                         }
                         System.out.println();