Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java (revision 1620) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java (revision 1621) @@ -2,13 +2,13 @@ import java.util.ArrayList; +import java.util.Iterator; import java.util.LinkedList; public class Match { private ArrayList matchseqs; - - private LinkedList occurences; - - - Match(){ + + private LinkedList occurences; + + Match() { matchseqs = new ArrayList(2); occurences = new LinkedList(); @@ -16,28 +16,52 @@ matchseqs.add(null); } - + public NumberSequence getFirstSequence() { return matchseqs.get(0); } - + public NumberSequence getSecondSequence() { return matchseqs.get(1); } - + public void setFirstSequence(NumberSequence seq) { matchseqs.set(0, seq); } - + public void setSecondSequence(NumberSequence seq) { matchseqs.set(1, seq); } - + public void addOccurence(MatchOccurence occurence) { occurences.add(occurence); } - + public int occurenceCount() { return occurences.size(); - } + } + + public boolean equals(Match m) { + if ((m.getFirstSequence().equals(this.getFirstSequence()) || m + .getFirstSequence().equals(this.getSecondSequence())) + && (m.getSecondSequence().equals(this.getFirstSequence()) || m + .getSecondSequence().equals(this.getSecondSequence()))) { + return true; + } + return false; + } + + public LinkedList getOccurences() { + return occurences; + } + + public void setOccurences(LinkedList occurences) { + this.occurences = occurences; + } + + + public void addOccurencesOf(Match m) { + LinkedList occ = m.getOccurences(); + occurences.addAll(occ); + } } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1620) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1621) @@ -2,4 +2,5 @@ import java.util.ArrayList; +import java.util.LinkedList; import java.util.Random; @@ -61,8 +62,8 @@ } - - public int containsPattern(Match pattern) { + //Searching occurences of + public LinkedList containsPattern(Match pattern) { + LinkedList result = new LinkedList(); int i = 0; - int count = 0; int[] pat1 = pattern.getFirstSequence().getSequence(); int[] pat2 = pattern.getSecondSequence().getSequence(); @@ -88,9 +89,9 @@ ipat2++; } - count++; + result.add(i); } i++; } - return count; + return result; } @@ -119,3 +120,18 @@ this.id = id; } + + public boolean equals(NumberSequence n) { + int[] seq = n.getSequence(); + if(n.size() !=this.size()) { + return false; + } + for (int i=0; i uniqueTasks = harmonizeEventTaskInstancesModel(appData); - Console.traceln(Level.INFO,"generating substitution matrix"); + // Generate a substitution matrix between all occuring events. + Console.traceln(Level.INFO, "generating substitution matrix"); ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix( - uniqueTasks, 6,-3); + uniqueTasks, 6, -3); submat.generate(); - Console.traceln(Level.INFO,"generating pairwise alignments"); - ArrayList matchseqs = new ArrayList(); - PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat,9); - - Console.traceln(Level.INFO,"retrieving significant sequence pieces"); - for (int i=0; i< numberseqs.size();i++) { - Console.traceln(Level.FINEST,"retrieving significant sequence pieces: " + Math.round((float)i/(float)numberseqs.size()*100) + "%"); - for(int j=0; j< numberseqs.size();j++) { - if(i != j) { + // Generate pairwise alignments + Console.traceln(Level.INFO, "generating pairwise alignments"); + LinkedList matchseqs = new LinkedList(); + PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator + .generate(numberseqs, submat, 9); + + // Retrieve all matches reached a specific threshold + Console.traceln(Level.INFO, "retrieving significant sequence pieces"); + for (int i = 0; i < numberseqs.size(); i++) { + Console.traceln( + Level.FINEST, + "retrieving significant sequence pieces: " + + Math.round((float) i / (float) numberseqs.size() + * 100) + "%"); + for (int j = 0; j < numberseqs.size(); j++) { + if (i != j) { matchseqs.addAll(alignments.get(i, j).getMatches()); - } - } - } - Console.traceln(Level.FINEST,"retrieving significant sequence pieces: 100%"); - + } + } + } + Console.traceln(Level.FINEST, + "retrieving significant sequence pieces: 100%"); Console.traceln(Level.INFO, "searching for patterns occuring most"); - //search this match in every other sequence - for(int i=0; i < matchseqs.size();i++) { + // search each match in every other sequence + for (Iterator it = matchseqs.iterator(); it.hasNext();) { int sequencecount = 0; int totalcount = 0; - Match pattern = matchseqs.get(i); + Match pattern = it.next(); + + // Skip sequences with more 0 events (scrolls) than other events. + // Both of the pattern sequences are equally long, so the added 0 + // counts + // just need to be smaller than the length of one sequence + if (pattern.getFirstSequence().eventCount(0) + + pattern.getSecondSequence().eventCount(0) + 1 > pattern + .getFirstSequence().size()) + continue; + + for (int j = 0; j < numberseqs.size(); j++) { + LinkedList startpositions = numberseqs.get(j) + .containsPattern(pattern); + if (startpositions.size() > 0) { + sequencecount++; + totalcount += startpositions.size(); + for (Iterator jt = startpositions.iterator(); jt + .hasNext();) { + pattern.addOccurence( + new MatchOccurence(jt.next(), j)); + } + + } + } + } + + Console.traceln(Level.INFO, "sorting results"); + // Sort results to get the most occuring results + Comparator comparator = new Comparator() { + public int compare(Match m1, Match m2) { + return m2.occurenceCount() - m1.occurenceCount(); // use your + // logic + } + }; + Collections.sort(matchseqs, comparator); + + + + + // Harmonize matches: finding double matches and merge them + /* + Console.traceln(Level.INFO, "harmonizing matches"); + int i=0; + + while(i pattern.getFirstSequence().size()) - continue; - Console.traceln(Level.FINEST, "searching for patterns occuring most: " + Math.round((float)i/(float)matchseqs.size()*100) + "%"); - for(int j=0; j < numberseqs.size();j++) { - int tmpcount = numberseqs.get(j).containsPattern(pattern); - if(tmpcount > 0) { - sequencecount++; - totalcount+=tmpcount; - } - } - - if(totalcount > 1) { - matchseqs.get(i).getFirstSequence().printSequence(); + + + + // Just printing the results out + for (int i = 0; i < matchseqs.size(); i++) { + // Every pattern consists of 2 sequences, therefore the minimum + // occurences here is 2. + // We just need the sequences also occuring in other sequences as + // well + if (matchseqs.get(i).occurenceCount() > 2) { matchseqs.get(i).getFirstSequence().printSequence(); - System.out.println("Found pattern in " + sequencecount +"/" + numberseqs.size() + " sequences, total of " + totalcount + " occurences"); + matchseqs.get(i).getSecondSequence().printSequence(); + System.out.println("Found pattern " + + matchseqs.get(i).occurenceCount() + " times"); System.out.println(); } } + + 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 it = guidetree.getRoot().getSequences().iterator();it.hasNext();) { - // NumberSequence tmp = (NumberSequence) it.next(); - // tmp.printSequence(); - //} - - + /* - do { - - // appData.getStopWatch().start("whole loop"); - // detectAndReplaceIterations(appData); - - // appData.getStopWatch().start("task replacement"); - // detectAndReplaceTasks(appData); - // appData.getStopWatch().stop("task replacement"); - // appData.getStopWatch().stop("whole loop"); - - // appData.getStopWatch().dumpStatistics(System.out); - // appData.getStopWatch().reset(); - - } while (appData.detectedAndReplacedTasks()); */ + * do { + * + * // appData.getStopWatch().start("whole loop"); // + * detectAndReplaceIterations(appData); + * + * // appData.getStopWatch().start("task replacement"); // + * detectAndReplaceTasks(appData); // + * appData.getStopWatch().stop("task replacement"); // + * appData.getStopWatch().stop("whole loop"); + * + * // appData.getStopWatch().dumpStatistics(System.out); // + * appData.getStopWatch().reset(); + * + * } while (appData.detectedAndReplacedTasks()); + */ Console.println("created "