Changeset 1596 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

07/11/14 08:58:02 (10 years ago)

Author:

rkrimmel

Message:

Fixed printAlignment() method

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

@@ -221 +221 @@
 
         public void traceback() {
-                MatrixEntry tmp = matrix[length1+1][0];
+                MatrixEntry tmp = matrix[length1+1][0].getPrevious();
                 LinkedList<Integer> aligned1 = new LinkedList<Integer>();
                 LinkedList<Integer> aligned2 = new LinkedList<Integer>();
@@ -237 +237 @@
 
                 int count = 0;
-                for (Iterator<Integer> it = aligned1.descendingIterator(); it.hasNext();) {
+                for (Iterator<Integer> it = aligned1.iterator(); it.hasNext();) {
                         count++;
                         reversed1[reversed1.length - count] = it.next();
@@ -243 +243 @@
                 }
                 count = 0;
-                for (Iterator<Integer> it = aligned2.descendingIterator(); it.hasNext();) {
+                for (Iterator<Integer> it = aligned2.iterator(); it.hasNext();) {
                         count++;
                         reversed2[reversed2.length - count] = it.next();
@@ -260 +260 @@
         
         public void printAlignment() {
-                MatrixEntry tmp = matrix[length1+1][0];
-                String aligned1 = "";
-                String aligned2 = "";
-                int count = 0;
-                do
-                {
-                        String append1="";
-                        String append2="";
-                                        
-                        if(tmp.getXvalue() == Constants.GAP_SYMBOL) {
-                                append1 = "  ___";
-                        }
-                        else if(tmp.getXvalue() == Constants.UNMATCHED_SYMBOL) {
-                                append1 = "  ...";
+                int[] tmp1 = alignment.get(0).getSequence();
+                int[] tmp2 = alignment.get(1).getSequence();
+                for (int i=0; i< tmp1.length;i++) {
+                        if(tmp1[i] == Constants.GAP_SYMBOL) {
+                                System.out.print("  ___");
+                        }
+                        else if(tmp1[i] == Constants.UNMATCHED_SYMBOL) {
+                                System.out.print("  ...");
                         }
                         else {
-                                append1 = String.format("%5d", tmp.getXvalue());
-                        }
-
-                        if(tmp.getYvalue() == Constants.GAP_SYMBOL) {
-                                append2 = "  ___";
-                        }
-                        else if(tmp.getYvalue() == Constants.UNMATCHED_SYMBOL) {
-                                append2 = "  ...";
+                                System.out.format("%5d", tmp1[i]);
+                        }
+                        
+                }
+                System.out.println();
+                for (int i=0; i< tmp2.length;i++) {
+                        if(tmp2[i] == Constants.GAP_SYMBOL) {
+                                System.out.print("  ___");
+                        }
+                        else if(tmp2[i] == Constants.UNMATCHED_SYMBOL) {
+                                System.out.print("  ...");
                         }
                         else {
-                                append2 = String.format("%5d", tmp.getYvalue());
-                        }
-                        if(count != 0)
-                        {
-                                aligned1 = append1 + aligned1;
-                                aligned2 = append2 + aligned2;
-                        }
-                        
-                        tmp = tmp.getPrevious();
-                        count++;
-                        
-                } while(tmp.getPrevious() != null);
-                System.out.println(aligned1);
-                System.out.println(aligned2);
+                                System.out.format("%5d", tmp2[i]);
+                        }
+                        
+                }
+                System.out.println();
+                
+                
+        
         }