Changeset 1711 for branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

09/02/14 13:19:33 (10 years ago)

Author:

rkrimmel

Message:

Removing useless code.

File:

• branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (5 diffs)

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

@@ -34 +34 @@
 
 import de.ugoe.cs.autoquest.CommandHelpers;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Match;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.MatchOccurence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentGenerator;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
@@ -203 +203 @@
                 }
                 else {
-                        Console.traceln(Level.INFO,"loading substitution matrix from file");
+                        Console.traceln(Level.INFO,"loading harmonized sessions from file");
                         appData = loadAppData("harmonized");
                 }
-        
+                System.out.println(SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix);
                 if(!SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix) {       
                         Console.traceln(Level.INFO, "generating substitution matrix from " + appData.getUniqueTasks().size() + " unique tasks");
@@ -216 +216 @@
                 }
                 else {
+                        Console.traceln(Level.INFO,"loading substitution matrix from file");
                         appData = loadAppData("substitution");
                 }
@@ -649 +650 @@
                 
                 // Generate pairwise alignments
+                int size = appData.getNumberSequences().size();
                 Console.traceln(Level.INFO, "generating pairwise alignments");
                 LinkedList<Match> matchseqs = new LinkedList<Match>();
-                PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator
-                                .generate(appData.getNumberSequences(), appData.getSubmat(), 9);
-
-                // Retrieve all matches reached a specific threshold
-                Console.traceln(Level.INFO, "retrieving significant sequence pieces");
+                int count = 0;
+                
                 for (int i = 0; i < appData.getNumberSequences().size(); i++) {
+                        NumberSequence ns1 = appData.getNumberSequences().get(i);
+                        count++;
+                        if((count%(size/100)==0)) {
+                                Console.traceln(Level.INFO,(Math.round((float) count/size*100))+ "%");
+                        }
                         for (int j = 0; j < appData.getNumberSequences().size(); j++) {
+                                NumberSequence ns2 = appData.getNumberSequences().get(j);
                                 if (i != j) {
-                                        matchseqs.addAll(alignments.get(i, j).getMatches());
+                                        
+                                        Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
+                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                        aa.align(ns1, ns2, appData.getSubmat(),9);
+                                        matchseqs.addAll(aa.getMatches());
                                 }
                         }
@@ -799 +808 @@
                         }
                 }
-
-                alignments = null;
                 matchseqs = null;
                 appData.getStopWatch().stop("replacing tasks");