Changeset 1589 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

07/09/14 12:13:13 (10 years ago)

Author:

rkrimmel

Message:

Refactoring and code cleanup

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (2 diffs)

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

@@ -2 +2 @@
 
 import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.logging.Level;
 
@@ -216 +218 @@
         }
 
-        
-        
         public void traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
-                int aligned1[] = new int[length1+1+length2+2];
-                int aligned2[] = new int[length1+1+length2+2];
+                LinkedList<Integer> aligned1 = new LinkedList<Integer>();
+                LinkedList<Integer> aligned2 = new LinkedList<Integer>();
+                do {
+                        
+                        aligned1.add(new Integer(tmp.getXvalue()));
+                        aligned2.add(new Integer(tmp.getYvalue()));
+
+                        tmp = tmp.getPrevious();
+
+                } while (tmp != null);
+                
+                // reverse order of the alignment
+                int reversed1[] = new int[aligned1.size()];
+                int reversed2[] = new int[aligned2.size()];
+
                 int count = 0;
-                do
-                {       
-                        if(count != 0)
-                        {
-                                if (length1+1+length2+2 == count) {     
-                                        Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
-                                        break;
-                                }
-                                aligned1[count] = tmp.getXvalue();
-                                aligned2[count] = tmp.getYvalue();
-                        }
-                        
-                        tmp = tmp.getPrevious();
+                for (Iterator<Integer> it = aligned1.descendingIterator(); it.hasNext();) {
                         count++;
-                
-                } while(tmp != null);
-                count--;
-                //reverse order of the alignment
-                int reversed1[] = new int[count];
-                int reversed2[] = new int[count];
-                
-                
-                for(int i = count-1; i > 0; i--) {
-                        reversed1[reversed1.length-i]= aligned1[i];
-                        reversed2[reversed2.length-i]= aligned2[i];
-                }
-                
+                        reversed1[reversed1.length - count] = it.next();
+                        
+                }
+                count = 0;
+                for (Iterator<Integer> it = aligned2.descendingIterator(); it.hasNext();) {
+                        count++;
+                        reversed2[reversed2.length - count] = it.next();
+                }
+
                 NumberSequence ns1 = new NumberSequence(reversed1.length);
                 NumberSequence ns2 = new NumberSequence(reversed2.length);
                 ns1.setSequence(reversed1);
                 ns2.setSequence(reversed2);
-                
+
                 alignment.add(ns1);
                 alignment.add(ns2);
         }
+        
+
         
         public void printAlignment() {