Changeset 1587

Timestamp:

07/04/14 00:38:41 (10 years ago)

Author:

rkrimmel

Message:

Adding needleman wunsch

Location:

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

Files:

• alignment/algorithms/AlignmentAlgorithm.java (modified) (1 diff)
• alignment/algorithms/AlignmentAlgorithmFactory.java (modified) (1 diff)
• alignment/algorithms/NeedlemanWunsch.java (added)
• alignment/algorithms/SmithWaterman.java (modified) (6 diffs)
• alignment/algorithms/SmithWatermanRepeated.java (modified) (4 diffs)
• alignment/matrix/ObjectDistanceSubstitionMatrix.java (modified) (1 diff)
• alignment/pal/tree/UPGMAAligningTree.java (modified) (5 diffs)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (1 diff)

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

@@ -12 +12 @@
         public abstract ArrayList<NumberSequence> getAlignment();
 
+        public abstract void printDPMatrix();
+
+        public abstract void printAlignment();
+
 }

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 SmithWaterman(input1,input2,submat,threshold);
+                //return new NeedlemanWunsch(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/SmithWaterman.java

@@ -32 +32 @@
 
         private ArrayList<NumberSequence> alignment;
-
-        private float scoreThreshold;
 
         /**
@@ -51 +49 @@
                 // + submat.getClass() + " Substitution Matrix: " +
                 // submat.getClass().getCanonicalName());
-                this.scoreThreshold = threshold;
 
                 matrix = new MatrixEntry[length1 + 1][length2 + 1];
@@ -93 +90 @@
 
                 // the first column
-                for (int j = 1; j < length2+1; j++) {
+                for (int j = 1; j < length2; j++) {
                         matrix[0][j].setScore(0);
                         matrix[0][j].setPrevious(matrix[0][j - 1]);
@@ -101 +98 @@
                 // the first row
 
-                for (int j = 1; j < length1+1; j++) {
+                for (int j = 1; j < length1; j++) {
                         matrix[j][0].setScore(0);
                         matrix[j][0].setPrevious(matrix[j - 1][0]);
@@ -262 +259 @@
                         System.out.format("%5d", input1[i - 1]);
                 System.out.println();
-                for (int j = 0; j < length2; j++) {
+                for (int j = 0; j <= length2; j++) {
                         if (j > 0)
                                 System.out.format("%5d ", input2[j - 1]);
@@ -268 +265 @@
                                 System.out.print("      ");
                         }
-                        for (int i = 0; i < length1; i++) {
+                        for (int i = 0; i <= length1; i++) {
                                         System.out.format("%4.1f ", matrix[i][j].getScore());
                         }

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

@@ -102 +102 @@
                 
                 
-                for (int i = 1; i <= length1 + 1; i++) {
+                for (int i = 1; i < length1 + 2; i++) {
                 
                         // Formula for first row:
@@ -220 +220 @@
         public void traceback() {
                 MatrixEntry tmp = matrix[length1+1][0];
-                int aligned1[] = new int[length1+length2+2];
-                int aligned2[] = new int[length1+length2+2];
+                int aligned1[] = new int[length1+1+length2+2];
+                int aligned2[] = new int[length1+1+length2+2];
                 int count = 0;
                 do
@@ -227 +227 @@
                         if(count != 0)
                         {
-                                if (length1+length2+2 == count) {       
+                                if (length1+1+length2+2 == count) {     
                                         Console.traceln(Level.WARNING, "Traceback longer than both sequences summed up!");
                                         break;
@@ -312 +312 @@
                         System.out.format("%5d", input1[i - 1]);
                 System.out.println();
-                for (int j = 0; j < length2; j++) {
+                for (int j = 0; j <= length2; j++) {
                         if (j > 0)
                                 System.out.format("%5d ",input2[j - 1]);

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

@@ -29 +29 @@
                 idmapping = new HashMap<Integer, Integer>();
                 matrix = new TriangleMatrix(uniqueTasks.size()+1);
-                gapPenalty = -3;
+                gapPenalty = -2;
                 
         }

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

@@ -137 +137 @@
         private void finish()
         {
+                this.getRoot().setSequences(alignSequences(this.getRoot()));
                 distance = null;                
         }
@@ -215 +216 @@
                         int seqCount1 = node1.getSequences().size();
                         int seqCount2 = node2.getSequences().size();
+                        
+                        for(int i = 0; i < seqCount1; i++) {
+                                for(int j = 0; j < seqCount2; j++) {
+                                        node1.getSequence(i).printSequence();
+                                        node2.getSequence(j).printSequence();
+                                }
+                        }
+                        
                         Console.traceln(Level.INFO,"Merging node " + node1.getIdentifier() + " with " + node2.getIdentifier());
                         //Console.println("SeqCount1: " + seqCount1 + " seqCount2 " + seqCount2);
@@ -220 +229 @@
                         if(seqCount1 == 1 && seqCount2 == 1) {
                                 alignment = (alignments.get(node1.getNumber(), node2.getNumber())).getAlignment();
+                                
                         }
                         //Align a sequence to a group
@@ -236 +246 @@
                                 }
                                 //if(maxScore > 0)
+                                
                                 alignment.add(tempStorage.get(maxIndex, 1).getAlignment().get(1));
                         }
@@ -252 +263 @@
                                 }
                                 //if(maxScore > 0)
+                                
                                 alignment.add(tempStorage.get(1,maxIndex).getAlignment().get(1));
                         }

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

@@ -208 +208 @@
                         }
                 }
-                //System.out.println(sequenceDistances.toString());
+                //alignments.get(20, 47).printDPMatrix();
+                //alignments.get(20, 47).printAlignment();
+                
+                System.out.println(alignments.getDistanceMatrix().toString());
                 UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
-
-                for (Iterator<NumberSequence> it =  guidetree.getRoot().getChild(0).getSequences().iterator(); it.hasNext();) {
+                //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();
                         tmp.printSequence();
                 }
+                
         
                 /*