Changeset 1588 for branches

Timestamp:

07/08/14 21:38:11 (10 years ago)

Author:

rkrimmel

Message:

Fixed Needleman Wunsch Algorithm

Location:

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/algorithms/AlignmentAlgorithmFactory.java (modified) (1 diff)
• alignment/algorithms/NeedlemanWunsch.java (modified) (4 diffs)
• alignment/pal/tree/UPGMAAligningTree.java (modified) (2 diffs)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (2 diffs)

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

@@ -8 +8 @@
         public static AlignmentAlgorithm create(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) {
                 
-                //return new NeedlemanWunsch(input1,input2,submat,threshold);
+                //return new SmithWaterman(input1,input2,submat,threshold);
                 return new NeedlemanWunsch(input1,input2,submat,threshold);
                 //return new SmithWatermanRepeated(input1,input2,submat,threshold);

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

@@ -2 +2 @@
 
 import java.util.ArrayList;
-import java.util.logging.Level;
+import java.util.Iterator;
+import java.util.LinkedList;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants;
-import de.ugoe.cs.util.console.Console;
+
 
 public class NeedlemanWunsch implements AlignmentAlgorithm {
@@ -116 +117 @@
 
                                 matrix[i][j].setScore(Math.max(diagScore,
-                                                Math.max(upScore, Math.max(leftScore, 0))));
+                                                Math.max(upScore, leftScore)));
 
                                 // find the directions that give the maximum scores.
@@ -175 +176 @@
         public void traceback() {
                 MatrixEntry tmp = matrix[length1][length2];
-                int aligned1[] = new int[length1 + length2 + 2];
-                int aligned2[] = new int[length1 + 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 (length1 + 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; 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();
                 }
 
@@ -216 +218 @@
                 int count = 0;
                 do {
+                        System.out.println(tmp);
                         String append1 = "";
                         String append2 = "";

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

@@ -217 +217 @@
                         int seqCount2 = node2.getSequences().size();
                         
+                        /*
                         for(int i = 0; i < seqCount1; i++) {
                                 for(int j = 0; j < seqCount2; j++) {
@@ -223 +224 @@
                                 }
                         }
+                        */
                         
                         Console.traceln(Level.INFO,"Merging node " + node1.getIdentifier() + " with " + node2.getIdentifier());

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -29 +29 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
-import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree.UPGMAAligningTree;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
@@ -211 +209 @@
                 //alignments.get(20, 47).printAlignment();
                 
-                System.out.println(alignments.getDistanceMatrix().toString());
+                System.out.println(alignments.getDistanceMatrix());
                 UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
-                //System.out.println("Number of sequences in root node: " + guidetree.getRoot().getSequences().size());
+                System.out.println("Number of sequences in root node: " + guidetree.getRoot().getSequences().size());
                 for (Iterator<NumberSequence> it =  guidetree.getRoot().getSequences().iterator(); it.hasNext();) {
                         NumberSequence tmp  = it.next();