Changeset 1618 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

07/16/14 18:07:05 (10 years ago)

Author:

rkrimmel

Message:

Startet implementing signigicant match detection

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (copied) (copied from branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java) (1 diff)

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

@@ -153 +153 @@
                 SymbolMap<ITaskInstance, ITask> uniqueTasks = harmonizeEventTaskInstancesModel(appData);
 
+                Console.traceln(Level.INFO,"generating substitution matrix");
                 ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(
                                 uniqueTasks, 5);
                 submat.generate();
 
-                ArrayList<NumberSequence> matchseqs = new ArrayList<NumberSequence>();
+                Console.traceln(Level.INFO,"generating pairwise alignments");
+                ArrayList<ArrayList<NumberSequence>> matchseqs = new ArrayList<ArrayList<NumberSequence>>();
                 PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat);
                 
+                Console.traceln(Level.INFO,"retrieving significant sequence pieces");
                 for (int i=0; i< numberseqs.size();i++) {
                         for(int j=0; j< numberseqs.size();j++) {
                                 if(i != j) {
                                         ArrayList<ArrayList<NumberSequence>> tmp = alignments.get(i, j).getMatches();
-                                        int count = 0;
-                                        for(Iterator<ArrayList<NumberSequence>> it = tmp.iterator();it.hasNext();) {
-                                                System.out.println("Match number " + count);
-                                                ArrayList<NumberSequence> tmp2 = it.next();
-                                                tmp2.get(0).printSequence();
-                                                tmp2.get(1).printSequence();
-                                                System.out.println();
-                                                count++;
-                                                matchseqs.addAll(tmp2);
+                                        matchseqs.addAll(tmp);
+                                }   
+                        }
+                }
+                
+                Console.traceln(Level.INFO, "searching for patterns occuring most");
+                //search this match in every other sequence
+                for(int i=0; i < matchseqs.size();i++) {
+                        for(int j=0; j < matchseqs.size();j++) {
+                                if(i>j) {
+                                        if(matchseqs.get(j).get(0).containsPattern(matchseqs.get(i)) > 0 || matchseqs.get(j).get(1).containsPattern(matchseqs.get(i)) > 0) {
+                                                System.out.println("Found something!");
                                         }
-                                        System.out.println();
-                                }
-                        }
-                }
-                
-                AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+                                }
+                        }
+                                
+                }
                 
                 
-                PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(numberseqs, submat);
-                UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);
-                System.out.println(alignments.getDistanceMatrix());
-                //UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
                 
-                for(Iterator<NumberSequence> it = guidetree.getRoot().getSequences().iterator();it.hasNext();) {
-                        NumberSequence tmp = (NumberSequence) it.next();
-                        tmp.printSequence();
-                }
+                alignments = null;
+                
+                //
+                //AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+                //PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(matchseqs, submat);
+                //UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);
+                //System.out.println(alignments.getDistanceMatrix());
+                
+                //for(Iterator<NumberSequence> it = guidetree.getRoot().getSequences().iterator();it.hasNext();) {
+                //      NumberSequence tmp = (NumberSequence) it.next();
+                //      tmp.printSequence();
+                //}