Changeset 1649 for branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

08/03/14 22:53:27 (10 years ago)

Author:

rkrimmel

Message:

Adding tests to some classes.

File:

• branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (4 diffs)

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

@@ -102 +102 @@
                                 //position of the maximal score of the previous row
                                 
-                                for(int j = 2; j < length2;j++) {
+                                for(int j = 2; j <= length2;j++) {
                                         if(matrix[i-1][j].getScore() > tempMax) {
                                                 tempMax = matrix[i-1][j].getScore();
@@ -122 +122 @@
                         
                         //The last additional score is not related to a character in the input sequence, it's the total score. Therefore we don't need to save something for it
-                        if(i<length1+1) 
-                        {
+                        //and can end here
+                        if(i<length1+1) {
                                 matrix[i][0].setXvalue(input1[i-1]);
                                 matrix[i][0].setYvalue(Constants.UNMATCHED_SYMBOL);
                         }
-                        else { 
-                        //End after we calculated final score
+                        else {
                                 return;
                         }
-                        
-                        
-                        for (int j = 1; j < length2; j++) {
+                 
+                        
+                        
+                        for (int j = 1; j <= length2; j++) {
                                 double diagScore = matrix[i - 1][j - 1].getScore() + similarity(i, j);
                                 double upScore = matrix[i][j - 1].getScore() + submat.getGapPenalty();
@@ -181 +181 @@
                 // skip the first row and column
                 for (int i = 1; i <= length1; i++) {
-                        for (int j = 1; j < length2; j++) {
+                        for (int j = 1; j <= length2; j++) {
                                 if (matrix[i][j].getScore() > maxScore) {
                                         maxScore = matrix[i][j].getScore();
@@ -373 +373 @@
                 
                 for (int i = 0; i <= length1+1; i++) {
-                        for(int j = 0; j< length2; j++) {
+                        for(int j = 0; j<= length2; j++) {
                                 matrix[i][j] = new MatrixEntry();
                         }