Changeset 1711 for branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation
- Timestamp:
- 09/02/14 13:19:33 (10 years ago)
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java
r1710 r1711 34 34 35 35 import de.ugoe.cs.autoquest.CommandHelpers; 36 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm; 37 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory; 36 38 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Match; 37 39 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.MatchOccurence; 38 40 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; 39 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentGenerator;40 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentStorage;41 41 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix; 42 42 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; … … 203 203 } 204 204 else { 205 Console.traceln(Level.INFO,"loading substitution matrixfrom file");205 Console.traceln(Level.INFO,"loading harmonized sessions from file"); 206 206 appData = loadAppData("harmonized"); 207 207 } 208 208 System.out.println(SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix); 209 209 if(!SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix) { 210 210 Console.traceln(Level.INFO, "generating substitution matrix from " + appData.getUniqueTasks().size() + " unique tasks"); … … 216 216 } 217 217 else { 218 Console.traceln(Level.INFO,"loading substitution matrix from file"); 218 219 appData = loadAppData("substitution"); 219 220 } … … 649 650 650 651 // Generate pairwise alignments 652 int size = appData.getNumberSequences().size(); 651 653 Console.traceln(Level.INFO, "generating pairwise alignments"); 652 654 LinkedList<Match> matchseqs = new LinkedList<Match>(); 653 PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator 654 .generate(appData.getNumberSequences(), appData.getSubmat(), 9); 655 656 // Retrieve all matches reached a specific threshold 657 Console.traceln(Level.INFO, "retrieving significant sequence pieces"); 655 int count = 0; 656 658 657 for (int i = 0; i < appData.getNumberSequences().size(); i++) { 658 NumberSequence ns1 = appData.getNumberSequences().get(i); 659 count++; 660 if((count%(size/100)==0)) { 661 Console.traceln(Level.INFO,(Math.round((float) count/size*100))+ "%"); 662 } 659 663 for (int j = 0; j < appData.getNumberSequences().size(); j++) { 664 NumberSequence ns2 = appData.getNumberSequences().get(j); 660 665 if (i != j) { 661 matchseqs.addAll(alignments.get(i, j).getMatches()); 666 667 Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j); 668 AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); 669 aa.align(ns1, ns2, appData.getSubmat(),9); 670 matchseqs.addAll(aa.getMatches()); 662 671 } 663 672 } … … 799 808 } 800 809 } 801 802 alignments = null;803 810 matchseqs = null; 804 811 appData.getStopWatch().stop("replacing tasks");
Note: See TracChangeset
for help on using the changeset viewer.