Changeset 1649 for branches/autoquest-core-tasktrees-alignment/src/main/java

Timestamp:

08/03/14 22:53:27 (10 years ago)

Author:

rkrimmel

Message:

Adding tests to some classes.

Location:

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/algorithms/AlignmentAlgorithm.java (modified) (1 diff)
• alignment/algorithms/SmithWatermanRepeated.java (modified) (4 diffs)
• alignment/matrix/DummySubstitutionMatrix.java (added)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (4 diffs)

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

@@ -19 +19 @@
 
         public abstract ArrayList<Match> getMatches();
+        
+        public double getMaxScore();
 
         void align(NumberSequence input1, NumberSequence input2,

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

@@ -102 +102 @@
                                 //position of the maximal score of the previous row
                                 
-                                for(int j = 2; j < length2;j++) {
+                                for(int j = 2; j <= length2;j++) {
                                         if(matrix[i-1][j].getScore() > tempMax) {
                                                 tempMax = matrix[i-1][j].getScore();
@@ -122 +122 @@
                         
                         //The last additional score is not related to a character in the input sequence, it's the total score. Therefore we don't need to save something for it
-                        if(i<length1+1) 
-                        {
+                        //and can end here
+                        if(i<length1+1) {
                                 matrix[i][0].setXvalue(input1[i-1]);
                                 matrix[i][0].setYvalue(Constants.UNMATCHED_SYMBOL);
                         }
-                        else { 
-                        //End after we calculated final score
+                        else {
                                 return;
                         }
-                        
-                        
-                        for (int j = 1; j < length2; j++) {
+                 
+                        
+                        
+                        for (int j = 1; j <= length2; j++) {
                                 double diagScore = matrix[i - 1][j - 1].getScore() + similarity(i, j);
                                 double upScore = matrix[i][j - 1].getScore() + submat.getGapPenalty();
@@ -181 +181 @@
                 // skip the first row and column
                 for (int i = 1; i <= length1; i++) {
-                        for (int j = 1; j < length2; j++) {
+                        for (int j = 1; j <= length2; j++) {
                                 if (matrix[i][j].getScore() > maxScore) {
                                         maxScore = matrix[i][j].getScore();
@@ -373 +373 @@
                 
                 for (int i = 0; i <= length1+1; i++) {
-                        for(int j = 0; j< length2; j++) {
+                        for(int j = 0; j<= length2; j++) {
                                 matrix[i][j] = new MatrixEntry();
                         }

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -166 +166 @@
                                 .generate(appData.getNumberSequences(), submat, 9);
 
+                
+                
                 // Retrieve all matches reached a specific threshold
                 Console.traceln(Level.INFO, "retrieving significant sequence pieces");
@@ -203 +205 @@
                                         for (Iterator<Integer> jt = startpositions.iterator(); jt
                                                         .hasNext();) {
+                                                int start = jt.next();
+                                                System.out.println("Found match ");
+                                                pattern.getFirstSequence().printSequence();
+                                                pattern.getSecondSequence().printSequence(); 
+                                                System.out.println("in sequence " + (j+1) + " at position " + start);
                                                 pattern.addOccurence(
-                                                                new MatchOccurence(jt.next(), j));
+                                                                new MatchOccurence(start, j));
                                         }
 
@@ -366 +373 @@
                                 }
                                 appData.getNumber2Task().put(templist.getSequence()[i], taskInstance.getTask());
+                                
+                                //System.out.println("TaskID: " + taskInstance.getTask().getId()+ " Numbersequence: " + templist.getSequence()[i]);
                         }
                         //Each NumberSequence is identified by its id, beginning to count at zero
-                        templist.setId(appData.getNumberSequences().size());
+                        templist.setId(sessionNo-1);
                         appData.getNumberSequences().add(templist);
                         comparator.clearBuffers();
@@ -550 +559 @@
                         }
                 }
+                for (int i =0;i<sequence.getChildren().size();i++) {
+                        System.out.println(sequence.getChildren().get(i));
+                
+                        if(sequence.getChildren().get(i).getType() == "selection") {
+                                for(int j=0; j< ((ISelection) sequence.getChildren().get(i)).getChildren().size();j++) {
+                                        System.out.println("\t" +((ISelection) sequence.getChildren().get(i)).getChildren().get(j));
+                                }
+                        }
+                }
                         return sequence;
                 }