Changeset 1592 for branches/ralph/src/main/java/de/ugoe/cs/autoquest

Timestamp:

07/09/14 22:49:39 (10 years ago)

Author:

rkrimmel

Message:

Trying new approach

Location:

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

Files:

• algorithms/AlignmentAlgorithm.java (modified) (1 diff)
• algorithms/NeedlemanWunsch.java (modified) (1 diff)
• algorithms/NumberSequence.java (modified) (1 diff)
• algorithms/SmithWaterman.java (modified) (1 diff)
• algorithms/SmithWatermanRepeated.java (modified) (5 diffs)
• matrix/PairwiseAlignmentGenerator.java (modified) (2 diffs)

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

@@ -16 +16 @@
         public abstract void printAlignment();
 
+        public abstract ArrayList<ArrayList<NumberSequence>> getMatches();
+
 }

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

@@ -283 +283 @@
         }
 
+        @Override
+        public ArrayList<ArrayList<NumberSequence>> getMatches() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
 
 

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

@@ -49 +49 @@
         }
 
+        public int size() {
+                return sequence.length;
+        }
 }

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

@@ -288 +288 @@
         }
 
+        @Override
+        public ArrayList<ArrayList<NumberSequence>> getMatches() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
 }

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

@@ -93 +93 @@
                 matrix[0][0].setScore(0);
                 matrix[0][0].setPrevious(null); // starting point
+                matrix[0][0].setXvalue(Constants.UNMATCHED_SYMBOL);
+                matrix[0][0].setYvalue(Constants.UNMATCHED_SYMBOL);
 
                 // the first column
@@ -132 +134 @@
                         tempMax -= scoreThreshold;
                         matrix[i][0].setScore(Math.max(firstRowLeftScore, tempMax));
-                        if(tempMax ==matrix[i][0].getScore()){
+                        if(tempMax == matrix[i][0].getScore()){
                                 matrix[i][0].setPrevious(matrix[i-1][maxRowIndex]);
                         }
@@ -222 +224 @@
                 LinkedList<Integer> aligned1 = new LinkedList<Integer>();
                 LinkedList<Integer> aligned2 = new LinkedList<Integer>();
-                do {
+                while (tmp.getPrevious() != null) {
                         
                         aligned1.add(new Integer(tmp.getXvalue()));
@@ -228 +230 @@
 
                         tmp = tmp.getPrevious();
-
-                } while (tmp != null);
+                } 
                 
                 // reverse order of the alignment
@@ -296 +297 @@
                         count++;
                         
-                } while(tmp != null);
+                } while(tmp.getPrevious() != null);
                 System.out.println(aligned1);
                 System.out.println(aligned2);
         }
         
-
+        public ArrayList<ArrayList<NumberSequence>> getMatches() {
+                ArrayList<ArrayList<NumberSequence>> result = new ArrayList<ArrayList<NumberSequence>>();
+                
+                //both alignment sequences should be equally long
+                int i = 0;
+                int[] seq1 = alignment.get(0).getSequence();
+                int[] seq2 = alignment.get(1).getSequence();
+                int start = 0;
+                while (i < seq1.length){
+                        if(seq2[i] != Constants.UNMATCHED_SYMBOL) {
+                                start = i;
+                                int count = 0;
+                                while(i < seq2.length && seq2[i] != Constants.UNMATCHED_SYMBOL) {
+                                        i++;
+                                        count++;
+                                }
+                                //I am really missing memcpy here 
+                                int[] tmp1 = new int[count];
+                                int[] tmp2 = new int[count];
+                                for (int j = 0; j<count;j++) {
+                                        tmp1[j] = seq1[start+j];
+                                        tmp2[j] = seq2[start+j];
+                                }
+                                NumberSequence tmpns1 = new NumberSequence(count);
+                                NumberSequence tmpns2 = new NumberSequence(count);
+                                tmpns1.setSequence(tmp1);
+                                tmpns2.setSequence(tmp2);
+                                ArrayList<NumberSequence> tmpal = new ArrayList<NumberSequence>();
+                                tmpal.add(tmpns1);
+                                tmpal.add(tmpns2);
+                                result.add(tmpal);
+                        }
+                        i++;
+                }
+                
+                
+                
+                
+                
+                
+                return result;
+                
+        }
         
         /**

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

@@ -2 +2 @@
 
 import java.util.ArrayList;
+import java.util.Iterator;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
@@ -38 +39 @@
                                         if(score > 0) {
                                                 System.out.println();
-                                                alignments.get(i, j).printAlignment();
+                                                //alignments.get(i, j).printAlignment();
+                                                ArrayList<ArrayList<NumberSequence>> matches = alignments.get(i, j).getMatches();
+                                                for(Iterator<ArrayList<NumberSequence>> it = matches.iterator();it.hasNext();) {
+                                                        ArrayList<NumberSequence> tmp = it.next();
+                                                        tmp.get(0).printSequence();
+                                                        tmp.get(1).printSequence();
+                                                }
                                                 System.out.println();
                                         }