- Timestamp:
- 09/04/14 17:08:05 (10 years ago)
- File:
-
- 1 edited
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branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java
r1721 r1723 23 23 import java.io.Serializable; 24 24 import java.util.ArrayList; 25 import java.util.Collection;26 25 import java.util.Collections; 27 26 import java.util.Comparator; … … 33 32 import java.util.Map; 34 33 import java.util.Set; 35 import java.util.concurrent.Callable;36 34 import java.util.concurrent.ExecutorService; 37 35 import java.util.concurrent.Executors; … … 656 654 657 655 // Generate pairwise alignments 658 int numberSeqSize = appData.getNumberSequences().size(); 659 Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions"); 660 int count = 0; 661 662 //Checking if i have an already calculated file result of this action in the working directory 663 File aligned = new File("aligned" + iteration + ".dat"); 664 if(!(aligned.exists() && !aligned.isDirectory())) { 665 appData.matchseqs = new LinkedList<Match>(); 666 for (int i = 0; i < appData.getNumberSequences().size(); i++) { 667 NumberSequence ns1 = appData.getNumberSequences().get(i); 668 count++; 669 printProgressPercentage(count,numberSeqSize); 670 for (int j = 0; j < appData.getNumberSequences().size(); j++) { 671 NumberSequence ns2 = appData.getNumberSequences().get(j); 672 if (i != j) { 673 //Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j); 674 AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); 675 aa.align(ns1, ns2, appData.getSubmat(),9); 676 appData.getMatchseqs().addAll(aa.getMatches()); 677 } 678 } 679 } 680 GlobalDataContainer.getInstance().addData("aligned" + iteration, appData); 681 saveAppData("aligned" + iteration); 682 } 683 else { 684 Console.traceln(Level.INFO,"loading matches from file"); 685 appData = loadAppData("aligned"+iteration); 686 } 687 688 689 Console.traceln(Level.INFO, "searching for patterns occuring most with " + nThreads + " threads"); 690 691 //Prepare parallel search of matchseqs 692 ExecutorService executor = Executors.newFixedThreadPool(nThreads); 693 int matchSeqSize=appData.getMatchseqs().size(); 694 int interval = Math.round(matchSeqSize/nThreads); 695 int rest = matchSeqSize % nThreads; 696 697 for(int i =0;i<matchSeqSize-interval;i+=interval) { 698 int offset =0; 699 if(rest!=0) { 700 offset=1; 701 rest--; 702 } 703 int from = i; 704 int to = i+interval+offset; 705 System.out.println("Creating thread with matches from " + from + " to " + to); 706 // search each match in every other sequence 707 ParallelMatchOcurrencesFinder finder = new ParallelMatchOcurrencesFinder(appData,from,to); 708 executor.execute(finder); 709 } 710 executor.shutdown(); 711 try { 712 executor.awaitTermination(2, TimeUnit.HOURS); 713 } catch (InterruptedException e) { 714 // TODO Auto-generated catch block 715 e.printStackTrace(); 716 } 717 718 719 Console.traceln(Level.INFO, "sorting results"); 656 appData.setMatchseqs(generatePairwiseAlignments(appData)); 657 658 //Searching each match in all other sessions, counting its occurences 659 searchMatchesInAllSessions(appData); 660 720 661 // Sort results to get the most occurring results 662 Console.traceln(Level.INFO, "sorting " + appData.getMatchseqs().size() + " results"); 721 663 Comparator<Match> comparator = new Comparator<Match>() { 722 664 public int compare(Match m1, Match m2) { … … 725 667 } 726 668 }; 669 727 670 Collections.sort(appData.getMatchseqs(), comparator); 728 671 appData.getStopWatch().stop("detecting tasks"); 729 672 673 // Replace matches in the sessions 674 Console.traceln(Level.INFO, "Replacing matches in sessions"); 730 675 appData.getStopWatch().start("replacing tasks"); 731 676 HashMap<Integer, List<MatchOccurence>> replacedOccurences = new HashMap<Integer, List<MatchOccurence>>(); 732 // Replace matches in the sessions733 677 for (int i = 0; i < appData.getMatchseqs().size(); i++) { 734 678 … … 744 688 MatchOccurence oc = it.next(); 745 689 746 /*747 if (iteration > 0) {748 749 System.out.println("Trying to replace sequence: ");750 appData.getMatchseqs().get(i).getFirstSequence().printSequence();751 appData.getMatchseqs().get(i).getSecondSequence().printSequence();752 System.out.println(" in session number: "753 + (oc.getSequenceId() + 1) + " at position "754 + (oc.getStartindex()) + "-" + oc.getEndindex());755 System.out.println();756 757 System.out.println("Printing session: ");758 for (int j = 0; j < appData.getSessions()759 .get(oc.getSequenceId()).size(); j++) {760 System.out.println(j761 + ": "762 + appData.getSessions().get(oc.getSequenceId())763 .get(j));764 }765 }*/766 690 767 691 // Check if nothing has been replaced in the sequence we … … 808 732 } 809 733 } 734 System.out.println("Replacing"); 810 735 ISequenceInstance sequenceInstances = RuleUtils 811 736 .createNewSubSequenceInRange(appData.getSessions() … … 827 752 828 753 754 755 756 private void searchMatchesInAllSessions(RuleApplicationData appData) { 757 Console.traceln(Level.INFO, "searching for patterns occuring most with " + nThreads + " threads"); 758 //Prepare parallel search of matchseqs 759 ExecutorService executor = Executors.newFixedThreadPool(nThreads); 760 int matchSeqSize=appData.getMatchseqs().size(); 761 int interval = Math.round(matchSeqSize/nThreads); 762 int rest = matchSeqSize % nThreads; 763 764 for(int i =0;i<matchSeqSize-interval;i+=interval) { 765 int offset =0; 766 if(rest!=0) { 767 offset=1; 768 rest--; 769 } 770 int from = i; 771 int to = i+interval+offset; 772 System.out.println("Creating thread with matches from " + from + " to " + to); 773 // search each match in every other sequence 774 ParallelMatchOcurrencesFinder finder = new ParallelMatchOcurrencesFinder(appData,from,to); 775 executor.execute(finder); 776 } 777 executor.shutdown(); 778 try { 779 executor.awaitTermination(2, TimeUnit.HOURS); 780 } catch (InterruptedException e) { 781 // TODO Auto-generated catch block 782 e.printStackTrace(); 783 } 784 785 } 786 829 787 //Print out the progress 830 788 private static void printProgressPercentage(int count, int size) { 831 832 789 if(size>100) { 833 790 if((count%(size/100)==0)) { 834 Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100))+ "%"); 791 //Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100))+ "%"); 792 System.out.println("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100)+ "%"); 835 793 } 836 794 } 837 795 else { 838 Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100))+ "%"); 796 //Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100))+ "%"); 797 System.out.println("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100)+ "%"); 798 839 799 } 840 800 } … … 857 817 int count = 0; 858 818 int size=to-from; 859 Console.traceln(Level.INFO, "Pattern count is " + size);860 for (int i=from; i<to;i++) { {819 820 for (int i=from; i<to;i++) { 861 821 Match pattern = appData.getMatchseqs().get(i); 862 822 count++; … … 880 840 + pattern.size(), j)); 881 841 } 882 883 842 } 884 843 } 885 844 } 845 } 846 } 847 848 849 private class ParallelPairwiseAligner implements Runnable { 850 private final RuleApplicationData appData; 851 private final int from; 852 private final int to; 853 ParallelPairwiseAligner(RuleApplicationData appData, int from, int to) { 854 this.appData = appData; 855 this.from = from; 856 this.to = to; 857 } 858 859 @Override 860 public void run() { 861 int count = 0; 862 int size=to-from; 863 864 for (int i=from; i<to;i++) { 865 NumberSequence ns1 = appData.getNumberSequences().get(i); 866 count++; 867 printProgressPercentage(count,size); 868 for (int j = 0; j < appData.getNumberSequences().size(); j++) { 869 NumberSequence ns2 = appData.getNumberSequences().get(j); 870 if (i != j) { 871 AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); 872 aa.align(ns1, ns2, appData.getSubmat(),9); 873 synchronized(appData.getMatchseqs()) { 874 appData.getMatchseqs().addAll(aa.getMatches()); 875 } 876 } 877 } 878 } 886 879 } 887 } 888 } 889 890 891 880 } 881 882 private LinkedList<Match> generatePairwiseAlignments(RuleApplicationData appData) { 883 int numberSeqSize = appData.getNumberSequences().size(); 884 LinkedList<Match> result; 885 //Checking if i have an already calculated file result of this action in the working directory 886 File aligned = new File("aligned" + iteration + ".dat"); 887 if(!(aligned.exists() && !aligned.isDirectory())) { 888 Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions"); 889 result = new LinkedList<Match>(); 890 891 ExecutorService executor = Executors.newFixedThreadPool(nThreads); 892 int interval = Math.round(numberSeqSize/nThreads); 893 int rest = numberSeqSize % nThreads; 894 895 for (int i = 0; i < numberSeqSize-interval; i+=interval) { 896 int offset = 0; 897 if(rest!=0) { 898 offset=1; 899 rest--; 900 } 901 int from = i; 902 int to = i+interval+offset; 903 System.out.println("Creating thread with matches from " + from + " to " + to); 904 ParallelPairwiseAligner aligner = new ParallelPairwiseAligner(appData,from,to); 905 executor.execute(aligner); 906 } 907 executor.shutdown(); 908 try { 909 executor.awaitTermination(10, TimeUnit.MINUTES); 910 } catch (InterruptedException e) { 911 // TODO Auto-generated catch block 912 e.printStackTrace(); 913 } 914 915 GlobalDataContainer.getInstance().addData("aligned" + iteration, appData); 916 saveAppData("aligned" + iteration); 917 return result; 918 } 919 else { 920 Console.traceln(Level.INFO,"loading matches from file"); 921 appData = loadAppData("aligned"+iteration); 922 return appData.getMatchseqs(); 923 } 924 } 925 892 926 893 927 /** … … 947 981 newTasks = new LinkedList<ITask>(); 948 982 949 //this.detectedAndReplacedTasks = true;983 this.detectedAndReplacedTasks = true; 950 984 } 951 985
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