Changeset 1615 for branches/ralph/src/main/java/de/ugoe/cs

Timestamp:

07/15/14 15:56:46 (10 years ago)

Author:

rkrimmel

Message:

Fixed bug in needlemanwunsch traceback

Location:

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

Files:

• alignment/algorithms/NeedlemanWunsch.java (modified) (4 diffs)
• alignment/matrix/ObjectDistanceSubstitionMatrix.java (modified) (2 diffs)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (1 diff)

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

@@ -154 +154 @@
                 LinkedList<Integer> aligned1 = new LinkedList<Integer>();
                 LinkedList<Integer> aligned2 = new LinkedList<Integer>();
-                do {
+                while (tmp.getPrevious() != null) {
                         
                         aligned1.add(new Integer(tmp.getXvalue()));
@@ -160 +160 @@
 
                         tmp = tmp.getPrevious();
-
-                } while (tmp != null);
+                } 
                 
                 // reverse order of the alignment
@@ -168 +167 @@
 
                 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();
@@ -174 +173 @@
                 }
                 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();

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java

@@ -21 +21 @@
         private SymbolMap<ITaskInstance, ITask> uniqueTasks;
         private double gapPenalty; 
+        
         private double positiveThreshold;
         
@@ -29 +30 @@
                 idmapping = new HashMap<Integer, Integer>();
                 matrix = new TriangleMatrix(uniqueTasks.size()+1);
-                gapPenalty = -2;
+                gapPenalty = -3;
                 
         }
 
-        @Override
+
         public double getGapPenalty() {
                 return gapPenalty;
         }
+        
+        public void setGapPenalty(double gapPenalty) {
+                this.gapPenalty = gapPenalty;
+        }
 
-        @Override
         public void generate() {
         

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

@@ -170 +170 @@
                         }
                 }
+                
                 AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+                
+                
                 PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(numberseqs, submat);
                 UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);