Changeset 1575 for branches/ralph/src/main/java/de/ugoe/cs/autoquest

Timestamp:

06/25/14 16:12:05 (10 years ago)

Author:

rkrimmel

Message:

Fixed wrong initialization of the first column in dynamic programming matrix.

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

@@ -5 +5 @@
 import java.util.LinkedList;
 import java.util.List;
+import java.util.logging.Level;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
+import de.ugoe.cs.util.console.Console;
 
 public class SmithWatermanRepeated {
@@ -95 +97 @@
                 for (int j = 1; j < length2; j++) {
                         matrix[0][j].setScore(0);
-                        matrix[0][j].setPrevious(matrix[0][j-1]);
-                        
+                        //We don't need to go back to [0][0] if we reached matrix[0][x], so just end here
+                        //matrix[0][j].setPrevious(matrix[0][j-1]);
+                        matrix[0][j].setPrevious(null); 
                 }
                 
@@ -219 +222 @@
         public void traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
-                //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 aligned1[] = new int[length1+length2+2];
+                int aligned2[] = new int[length1+length2+2];
                 int count = 0;
                 do
@@ -234 +235 @@
                         tmp = tmp.getPrevious();
                         count++;
-                        System.out.println(count);
+                if (length1+length2+2 == count) {       
+                        Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
+                        break;
+                }
                         
                 } while(tmp != null);
-
-                //reverse order
+                count--;
+                //reverse order of the alignment
                 int reversed1[] = new int[count];
                 int reversed2[] = new int[count];