Changeset 1587 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java

Timestamp:

07/04/14 00:38:41 (10 years ago)

Author:

rkrimmel

Message:

Adding needleman wunsch

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (modified) (6 diffs)

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

@@ -32 +32 @@
 
         private ArrayList<NumberSequence> alignment;
-
-        private float scoreThreshold;
 
         /**
@@ -51 +49 @@
                 // + submat.getClass() + " Substitution Matrix: " +
                 // submat.getClass().getCanonicalName());
-                this.scoreThreshold = threshold;
 
                 matrix = new MatrixEntry[length1 + 1][length2 + 1];
@@ -93 +90 @@
 
                 // the first column
-                for (int j = 1; j < length2+1; j++) {
+                for (int j = 1; j < length2; j++) {
                         matrix[0][j].setScore(0);
                         matrix[0][j].setPrevious(matrix[0][j - 1]);
@@ -101 +98 @@
                 // the first row
 
-                for (int j = 1; j < length1+1; j++) {
+                for (int j = 1; j < length1; j++) {
                         matrix[j][0].setScore(0);
                         matrix[j][0].setPrevious(matrix[j - 1][0]);
@@ -262 +259 @@
                         System.out.format("%5d", input1[i - 1]);
                 System.out.println();
-                for (int j = 0; j < length2; j++) {
+                for (int j = 0; j <= length2; j++) {
                         if (j > 0)
                                 System.out.format("%5d ", input2[j - 1]);
@@ -268 +265 @@
                                 System.out.print("      ");
                         }
-                        for (int i = 0; i < length1; i++) {
+                        for (int i = 0; i <= length1; i++) {
                                         System.out.format("%4.1f ", matrix[i][j].getScore());
                         }