Changeset 1587 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.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/SmithWatermanRepeated.java (modified) (4 diffs)

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

@@ -102 +102 @@
                 
                 
-                for (int i = 1; i <= length1 + 1; i++) {
+                for (int i = 1; i < length1 + 2; i++) {
                 
                         // Formula for first row:
@@ -220 +220 @@
         public void traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
-                int aligned1[] = new int[length1+length2+2];
-                int aligned2[] = new int[length1+length2+2];
+                int aligned1[] = new int[length1+1+length2+2];
+                int aligned2[] = new int[length1+1+length2+2];
                 int count = 0;
                 do
@@ -227 +227 @@
                         if(count != 0)
                         {
-                                if (length1+length2+2 == count) {       
+                                if (length1+1+length2+2 == count) {     
                                         Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
                                         break;
@@ -312 +312 @@
                         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]);