Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java (revision 1740) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java (revision 1741) @@ -6,4 +6,5 @@ import java.io.Serializable; import java.util.ArrayList; +import java.util.Iterator; import java.util.LinkedList; @@ -12,5 +13,5 @@ * The Class Match. */ -public class Match implements Serializable { +public class Match implements Comparable,Serializable { /** The Constant serialVersionUID. */ @@ -21,5 +22,5 @@ /** The occurences. */ - private LinkedList occurences; + private LinkedList occurrences; /** @@ -28,8 +29,8 @@ public Match() { matchseqs = new ArrayList(2); - occurences = new LinkedList(); + occurrences = new LinkedList(); matchseqs.add(null); matchseqs.add(null); - } + } // TODO Auto-generated method stub /** @@ -38,15 +39,15 @@ * @param occurence the occurence */ - public void addOccurence(MatchOccurence occurence) { - occurences.add(occurence); + public void addOccurence(MatchOccurrence occurence) { + occurrences.add(occurence); } /** - * Adds the occurences of. + * Adds the occurrences of given match to this match . * - * @param m the m + * @param m the match the occurrences should be merged with this one */ public void addOccurencesOf(Match m) { - occurences.addAll(m.getOccurences()); + occurrences.addAll(m.getOccurences()); } @@ -54,6 +55,6 @@ * Equals. * - * @param m the m - * @return true, if successful + * @param m the Match the equality should be checked against + * @return true, if both Matches are equal */ public boolean equals(Match m) { @@ -77,10 +78,10 @@ /** - * Gets the occurences. + * Gets the occurrences. * - * @return the occurences + * @return the occurrences */ - public LinkedList getOccurences() { - return occurences; + public LinkedList getOccurences() { + return occurrences; } @@ -95,10 +96,10 @@ /** - * Occurence count. + * Occurrence count. * - * @return the int + * @return the number of occurrences of this match */ public int occurenceCount() { - return occurences.size(); + return occurrences.size(); } @@ -113,10 +114,10 @@ /** - * Sets the occurences. + * Sets the occurrences. * - * @param occurences the new occurences + * @param occurences the new occurrences */ - public void setOccurences(LinkedList occurences) { - this.occurences = occurences; + public void setOccurences(LinkedList occurences) { + this.occurrences = occurences; } @@ -130,8 +131,45 @@ } + + /** + * Ocurrence id sum. Used for comparing and sorting matches + * + * @return th + */ + public int ocurrenceIDSum() { + int sum = 0; + for(Iterator it = occurrences.iterator();it.hasNext();) { + MatchOccurrence mo = it.next(); + sum+=mo.getSequenceId(); + } + return sum; + } + + /** + * Task id sum. Used for comparing and sorting matches + * + * @return + */ + public int taskIdSum() { + int sum = 0; + int[] first = this.getFirstSequence().getSequence(); + int[] second = this.getSecondSequence().getSequence(); + for(int i = 0;i < this.getFirstSequence().size();i++) { + sum= first[i]+second[i]; + } + return sum; + } + + public Match cloneWithoutOccurences() throws CloneNotSupportedException { + Match result; + result = (Match) this.clone(); + result.occurrences.clear(); + return result; + } + /** * Size. * - * @return the int + * @return the size (number of aligned tasks) */ public int size() { @@ -140,3 +178,12 @@ } + /* (non-Javadoc) + * @see java.lang.Comparable#compareTo(java.lang.Object) + */ + @Override + public int compareTo(Match arg0) { + + return 0; + } + } Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurence.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurence.java (revision 1740) +++ (revision ) @@ -1,92 +1,0 @@ -/* - * - */ -package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; - -import java.io.Serializable; - -// TODO: Auto-generated Javadoc -/** - * The Class MatchOccurence. - */ -public class MatchOccurence implements Serializable { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = 6186633243145293781L; - - /** The startindex. */ - private int startindex; - - /** The endindex. */ - private int endindex; - - /** The sequence id. */ - private int sequenceId; - - /** - * Instantiates a new match occurence. - * - * @param startindex the startindex - * @param endindex the endindex - * @param sequenceId the sequence id - */ - public MatchOccurence(int startindex, int endindex, int sequenceId) { - this.startindex = startindex; - this.endindex = endindex; - this.sequenceId = sequenceId; - } - - /** - * Gets the endindex. - * - * @return the endindex - */ - public int getEndindex() { - return endindex; - } - - /** - * Gets the sequence id. - * - * @return the sequence id - */ - public int getSequenceId() { - return sequenceId; - } - - /** - * Gets the startindex. - * - * @return the startindex - */ - public int getStartindex() { - return startindex; - } - - /** - * Sets the endindex. - * - * @param endindex the new endindex - */ - public void setEndindex(int endindex) { - this.endindex = endindex; - } - - /** - * Sets the sequence id. - * - * @param sequenceId the new sequence id - */ - public void setSequenceId(int sequenceId) { - this.sequenceId = sequenceId; - } - - /** - * Sets the startindex. - * - * @param startindex the new startindex - */ - public void setStartindex(int startindex) { - this.startindex = startindex; - } -} Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurrence.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurrence.java (revision 1741) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/MatchOccurrence.java (revision 1741) @@ -0,0 +1,92 @@ +/* + * + */ +package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; + +import java.io.Serializable; + +// TODO: Auto-generated Javadoc +/** + * The Class MatchOccurence. + */ +public class MatchOccurrence implements Serializable { + + /** The Constant serialVersionUID. */ + private static final long serialVersionUID = 6186633243145293781L; + + /** The startindex. */ + private int startindex; + + /** The endindex. */ + private int endindex; + + /** The sequence id. */ + private int sequenceId; + + /** + * Instantiates a new match occurence. + * + * @param startindex the startindex + * @param endindex the endindex + * @param sequenceId the sequence id + */ + public MatchOccurrence(int startindex, int endindex, int sequenceId) { + this.startindex = startindex; + this.endindex = endindex; + this.sequenceId = sequenceId; + } + + /** + * Gets the endindex. + * + * @return the endindex + */ + public int getEndindex() { + return endindex; + } + + /** + * Gets the sequence id. + * + * @return the sequence id + */ + public int getSequenceId() { + return sequenceId; + } + + /** + * Gets the startindex. + * + * @return the startindex + */ + public int getStartindex() { + return startindex; + } + + /** + * Sets the endindex. + * + * @param endindex the new endindex + */ + public void setEndindex(int endindex) { + this.endindex = endindex; + } + + /** + * Sets the sequence id. + * + * @param sequenceId the new sequence id + */ + public void setSequenceId(int sequenceId) { + this.sequenceId = sequenceId; + } + + /** + * Sets the startindex. + * + * @param startindex the new startindex + */ + public void setStartindex(int startindex) { + this.startindex = startindex; + } +} Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1740) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1741) @@ -262,8 +262,4 @@ tmpal.setFirstSequence(tmpns1); tmpal.setSecondSequence(tmpns2); - // tmpal.addOccurence(new - // MatchOccurence(start,alignment.get(0).getId())); - // tmpal.addOccurence(new - // MatchOccurence(start,alignment.get(1).getId())); result.add(tmpal); } Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1740) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1741) @@ -220,13 +220,13 @@ matrix.initialize(0); - int count = 0; - final int size = uniqueTasks.size(); + //int count = 0; + //final int size = uniqueTasks.size(); for (final Iterator it = uniqueTasks.iterator(); it.hasNext();) { final ITask task1 = it.next(); - count++; - if (((count % (size / 100)) == 0)) { - Console.traceln(Level.INFO, - (Math.round(((float) count / size) * 100)) + "%"); - } + //count++; + //if (((count % (size / 100)) == 0)) { + // Console.traceln(Level.INFO, + // (Math.round(((float) count / size) * 100)) + "%"); + //} for (final Iterator jt = uniqueTasks.iterator(); jt .hasNext();) { Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java (revision 1740) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java (revision 1741) @@ -64,5 +64,6 @@ final ISequenceInstance subsequence = taskFactory .createNewTaskInstance(model); - @SuppressWarnings("unused") + // TODO: Debugging output + /* int modelid = model.getId(); if(modelid == 5412) { @@ -77,5 +78,5 @@ } - } + }*/ // TODO: This is dirty, return this in addition with the sequence // instance instead @@ -125,8 +126,8 @@ } else if ((parent.get(startIndex).getTask().equals(tmpSel.getChildren().get(0).getId())) || (parent.get(startIndex).getTask().equals(tmpSel.getChildren().get(1).getId()))) { - //taskBuilder.setChild(selection, parent.get(startIndex)); - //taskBuilder.addChild(subsequence, selection); - //taskBuilder.removeTaskInstance(parent, startIndex); - //modelindex++; + taskBuilder.setChild(selection, parent.get(startIndex)); + taskBuilder.addChild(subsequence, selection); + taskBuilder.removeTaskInstance(parent, startIndex); + modelindex++; continue; @@ -226,7 +227,7 @@ // Thread.currentThread().getName() + ": " + Math.round((float) // count/size*100))+ "%"); - // System.out.println(message + " in thread" - // + Thread.currentThread().getName() + ": " - // + Math.round(((float) count / size) * 100) + "%"); + System.out.println(message + " in thread " + + Thread.currentThread().getName() + ": " + + Math.round(((float) count / size) * 100) + "%"); } } else { @@ -234,7 +235,7 @@ // Thread.currentThread().getName() + ": " +Math.round((float) // count/size*100))+ "%"); - // System.out.println(message + " in thread" - // + Thread.currentThread().getName() + ": " - // + Math.round(((float) count / size) * 100) + "%"); + System.out.println(message + " in thread " + + Thread.currentThread().getName() + ": " + + Math.round(((float) count / size) * 100) + "%"); } Index: branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1740) +++ branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1741) @@ -25,4 +25,6 @@ import java.util.List; import java.util.Map; +import java.util.PriorityQueue; +import java.util.Queue; import java.util.Set; import java.util.concurrent.ExecutorService; @@ -34,5 +36,5 @@ 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.MatchOccurrence; import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix; @@ -72,229 +74,5 @@ public class SequenceForTaskDetectionRuleAlignment implements ISessionScopeRule { - /** - * The Class RuleApplicationData. - */ - private static class RuleApplicationData implements Serializable { - - /** The Constant serialVersionUID. */ - private static final long serialVersionUID = -7559657686755522960L; - - /** - * The number2task HashMap. Since we align the tasks just by their - * integer id, we need this to convert them back to Tasks again - */ - private final HashMap number2task; - - /** - * The unique tasks, keeps track about all unique tasks TODO: We - * Actually just need number2task here, this structure can be removed in - * the future. - */ - private final HashSet uniqueTasks; - - /** - * The substitution matrix used by the alignment algorithm to be able to - * compare distances of tasks - */ - private final ObjectDistanceSubstitionMatrix submat; - - /** - * HashMap for keeping track in which sequence which replacement has - * been performed. Neccessary for updating the indices of other - * occurrences accordingly - */ - private HashMap> replacedOccurences; - - /** The list of all found matches */ - private LinkedList matchseqs; - - /** - * The generated NumberSequences. This is the integer representation of - * the user sessions - */ - private ArrayList numberseqs; - - /** The list of newly created tasks (of one iteration). */ - private final LinkedList newTasks; - - /** The user sessions containing all EventTasks/Instances */ - private final List sessions; - - /** True if we replaced something in the user sessions in one iteration. */ - private boolean detectedAndReplacedTasks; - - /** The result we give autoquest back */ - private final RuleApplicationResult result; - - /** Stop Watch to measure performance */ - private final StopWatch stopWatch; - - /** - * Instantiates a new rule application data. - * - * @param sessions - * The user sessions - */ - private RuleApplicationData(List sessions) { - this.sessions = sessions; - numberseqs = new ArrayList(); - uniqueTasks = new HashSet(); - number2task = new HashMap(); - stopWatch = new StopWatch(); - result = new RuleApplicationResult(); - submat = new ObjectDistanceSubstitionMatrix(6, -3, false); - newTasks = new LinkedList(); - this.detectedAndReplacedTasks = true; - } - - /** - * Detected and replaced tasks. - * - * @return true, if successful - */ - private boolean detectedAndReplacedTasks() { - return detectedAndReplacedTasks; - } - - /** - * Gets the matchseqs. - * - * @return the matchseqs - */ - public LinkedList getMatchseqs() { - return matchseqs; - } - - /** - * Gets the new tasks. - * - * @return the new tasks - */ - public LinkedList getNewTasks() { - return newTasks; - } - - /** - * Gets the number2task. - * - * @return the number2task HashMap - */ - private HashMap getNumber2Task() { - return number2task; - } - - /** - * Gets the number sequences. - * - * @return the number sequences - */ - private ArrayList getNumberSequences() { - return numberseqs; - } - - /** - * Gets the replaced occurrences. - * - * @return the replaced occurences - */ - public HashMap> getReplacedOccurrences() { - return replacedOccurences; - } - - /** - * Gets the result. - * - * @return the result - */ - private RuleApplicationResult getResult() { - return result; - } - - /** - * Gets the sessions. - * - * @return the UserSessions as List. - */ - private List getSessions() { - return sessions; - } - - /** - * Gets the stop watch. - * - * @return the stopWatch - */ - private StopWatch getStopWatch() { - return stopWatch; - } - - /** - * Gets the submat. - * - * @return the submat - */ - private ObjectDistanceSubstitionMatrix getSubmat() { - return submat; - } - - /** - * Gets the unique tasks. - * - * @return the unique tasks - */ - private HashSet getUniqueTasks() { - return uniqueTasks; - } - - /** - * New task created. - * - * @param task - * the task - */ - private void newTaskCreated(ITask task) { - number2task.put(task.getId(), task); - newTasks.add(task); - } - - /** - * Reset newly created tasks. - */ - synchronized private void resetNewlyCreatedTasks() { - uniqueTasks.addAll(newTasks); - newTasks.clear(); - } - - /** - * Sets the number sequences. - * - * @param numberseqs - * the new number sequences - */ - private void setNumberSequences(ArrayList numberseqs) { - this.numberseqs = numberseqs; - } - - /** - * Sets the replaced occurences. - * - * @param replacedOccurences - * the replaced occurences - */ - public void setReplacedOccurences( - HashMap> replacedOccurences) { - this.replacedOccurences = replacedOccurences; - } - - /** - * Update substitution matrix. - */ - private void updateSubstitutionMatrix() { - submat.update(getNewTasks()); - resetNewlyCreatedTasks(); - } - - } - + /** The n threads. */ public static int nThreads = Runtime.getRuntime().availableProcessors() - 1; @@ -380,9 +158,10 @@ detectAndReplaceIterations(appData); appData.getStopWatch().start("task replacement"); + //Just does anything if the substitution matrix is created with the option to do so appData.updateSubstitutionMatrix(); detectAndReplaceTasks(appData); // appData.getStopWatch().stop("task replacement"); appData.getStopWatch().stop("whole loop"); - appData.getStopWatch().dumpStatistics(System.out); + //appData.getStopWatch().dumpStatistics(System.out); appData.getStopWatch().reset(); @@ -400,5 +179,5 @@ RuleApplicationStatus.FINISHED); } - new TaskTreeValidator().validate(appData.getSessions()); + //new TaskTreeValidator().validate(appData.getSessions()); return appData.getResult(); } @@ -488,10 +267,32 @@ @Override public int compare(Match m1, Match m2) { - return m2.occurenceCount() - m1.occurenceCount(); - + int cmp = m2.occurenceCount() - m1.occurenceCount(); + if(cmp != 0) { + return cmp; + } + else { + cmp = m2.size()-m1.size(); + if(cmp != 0) { + return cmp; + } + else { + //This should rarely happen + cmp = m2.ocurrenceIDSum()-m1.ocurrenceIDSum(); + if(cmp !=0) { + return cmp; + } + else { + cmp = m2.taskIdSum()-m1.taskIdSum(); + + return cmp; + } + } + } } }; + Collections.sort(appData.getMatchseqs(), comparator); appData.getStopWatch().stop("detecting tasks"); + // Replace matches in the sessions @@ -502,49 +303,26 @@ } - /** - * Generate pairwise alignments. - * - * @param appData - * the app data - */ - private void generatePairwiseAlignments(RuleApplicationData appData) { - final int numberSeqSize = appData.getNumberSequences().size(); - appData.matchseqs = new LinkedList(); - Console.traceln(Level.INFO, "generating pairwise alignments from " - + numberSeqSize + " sessions with " + nThreads + " threads"); - - int newThreads = nThreads; - if (numberSeqSize < nThreads) { - newThreads = numberSeqSize; - } - - final ExecutorService executor = Executors - .newFixedThreadPool(newThreads); - final int interval = numberSeqSize / newThreads; - int rest = numberSeqSize % newThreads; - Console.traceln(Level.FINE, "Interval: " + interval + " Rest: " + rest); - for (int i = 0; i <= (numberSeqSize - interval); i += interval) { - int offset = 0; - if (rest != 0) { - offset = 1; - rest--; - } - - final int from = i; - final int to = i + interval+offset-1; - Console.traceln(Level.FINER, "Aligning: Creating thread for sessions " + from + " till " + to); - final ParallelPairwiseAligner aligner = new ParallelPairwiseAligner( - appData, from, to); - executor.execute(aligner); - i+=offset; - } - executor.shutdown(); - try { - executor.awaitTermination(2, TimeUnit.HOURS); - } catch (final InterruptedException e) { - e.printStackTrace(); - } - } - + + //TODO: DEBUG METHOD + @SuppressWarnings("unused") + private void printMatches(RuleApplicationData appData) { + LinkedList matchseqs = appData.getMatchseqs(); + if(iteration>1) { + System.out.println("PRINTING MATCHES"); + for (Iterator it = matchseqs.iterator(); it.hasNext();) { + Match m = it.next(); + m.getFirstSequence().printSequence(); + m.getSecondSequence().printSequence(); + for(Iterator jt = m.getOccurences().iterator();jt.hasNext();) { + MatchOccurrence mo = jt.next(); + System.out.print(mo.getSequenceId() + " "); + } + System.out.println(); + System.out.println(); + } + } + } + + /** *

@@ -879,4 +657,27 @@ } + private void prepareReplacements(RuleApplicationData appData) { + appData.initializeQueues(appData.getSessions().size()); + final int matchSeqSize = appData.getMatchseqs().size(); + int count = 0; + for (Iterator it = appData.getMatchseqs().iterator(); it.hasNext();) { + Match m = it.next(); + for(Iterator jt=m.getOccurences().iterator();jt.hasNext();) { + MatchOccurrence mo = jt.next(); + + Match emptyMatch = null; + try { + emptyMatch = m.cloneWithoutOccurences(); + } catch (CloneNotSupportedException e) { + e.printStackTrace(); + } + emptyMatch.addOccurence(mo); + appData.getPlannedReplacements()[mo.getSequenceId()].add(m); + } + count++; + + } + } + /** * Replace matches. @@ -886,22 +687,23 @@ */ private void replaceMatches(RuleApplicationData appData) { - appData.setReplacedOccurences(new HashMap>()); + appData.setReplacedOccurences(new HashMap>()); final int matchSeqSize = appData.getMatchseqs().size(); - + int count = 0; for (int i = 0; i < matchSeqSize; i++) { - + count++; // Every pattern consists of 2 sequences, therefore the minimum // occurrences here is 2. // We just need the sequences also occurring in other sequences // as well + RuleUtils.printProgressPercentage("Replacement progress", count, matchSeqSize); if (appData.getMatchseqs().get(i).occurenceCount() > 2) { final ISequence task = matchAsSequence(appData, appData .getMatchseqs().get(i)); - invalidOccurence: for (final Iterator it = appData + invalidOccurence: for (final Iterator it = appData .getMatchseqs().get(i).getOccurences().iterator(); it .hasNext();) { - final MatchOccurence oc = it.next(); + final MatchOccurrence oc = it.next(); // Check if nothing has been replaced in the sequence we @@ -911,5 +713,5 @@ appData.getReplacedOccurrences().put( oc.getSequenceId(), - new LinkedList()); + new LinkedList()); } else { // check if we have any replaced occurence with @@ -928,9 +730,9 @@ // harmonized. - for (final Iterator jt = appData + for (final Iterator jt = appData .getReplacedOccurrences() .get(oc.getSequenceId()).iterator(); jt .hasNext();) { - final MatchOccurence tmpOC = jt.next(); + final MatchOccurrence tmpOC = jt.next(); if ((oc.getStartindex() >= tmpOC.getStartindex()) @@ -1004,4 +806,52 @@ /** + * Generate pairwise alignments. + * + * @param appData + * the app data + */ + private void generatePairwiseAlignments(RuleApplicationData appData) { + final int numberSeqSize = appData.getNumberSequences().size(); + appData.matchseqs = new LinkedList(); + Console.traceln(Level.INFO, "generating pairwise alignments from " + + numberSeqSize + " sessions with " + nThreads + " threads"); + + int newThreads = nThreads; + if (numberSeqSize < nThreads) { + newThreads = numberSeqSize; + } + + final ExecutorService executor = Executors + .newFixedThreadPool(newThreads); + final int interval = numberSeqSize / newThreads; + int rest = numberSeqSize % newThreads; + Console.traceln(Level.FINE, "Interval: " + interval + " Rest: " + rest); + for (int i = 0; i <= (numberSeqSize - interval); i += interval) { + int offset = 0; + if (rest != 0) { + offset = 1; + rest--; + } + + final int from = i; + final int to = i + interval+offset-1; + Console.traceln(Level.FINER, "Aligning: Creating thread for sessions " + from + " till " + to); + final ParallelPairwiseAligner aligner = new ParallelPairwiseAligner( + appData, from, to); + executor.execute(aligner); + i+=offset; + } + executor.shutdown(); + try { + executor.awaitTermination(2, TimeUnit.HOURS); + } catch (final InterruptedException e) { + e.printStackTrace(); + } + } + + + + + /** * Search matches in all sessions. * @@ -1089,5 +939,4 @@ this.to = to; } - /* * (non-Javadoc) @@ -1124,5 +973,5 @@ .iterator(); jt.hasNext();) { final int start = jt.next(); - pattern.addOccurence(new MatchOccurence(start, + pattern.addOccurence(new MatchOccurrence(start, start + pattern.size(), j)); } @@ -1132,4 +981,6 @@ } } + + /** @@ -1193,4 +1044,251 @@ } } + + /** + * The Class RuleApplicationData. + */ + private static class RuleApplicationData implements Serializable { + + /** The Constant serialVersionUID. */ + private static final long serialVersionUID = -7559657686755522960L; + + /** + * The number2task HashMap. Since we align the tasks just by their + * integer id, we need this to convert them back to Tasks again + */ + private final HashMap number2task; + + /** + * The unique tasks, keeps track about all unique tasks TODO: We + * Actually just need number2task here, this structure can be removed in + * the future. + */ + private final HashSet uniqueTasks; + + /** + * The substitution matrix used by the alignment algorithm to be able to + * compare distances of tasks + */ + private final ObjectDistanceSubstitionMatrix submat; + + /** + * HashMap for keeping track in which sequence which replacement has + * been performed. Neccessary for updating the indices of other + * occurrences accordingly + */ + private HashMap> replacedOccurences; + + private Queue[] plannedReplacements; + + + /** The list of all found matches */ + private LinkedList matchseqs; + + /** + * The generated NumberSequences. This is the integer representation of + * the user sessions + */ + private ArrayList numberseqs; + + /** The list of newly created tasks (of one iteration). */ + private final LinkedList newTasks; + + /** The user sessions containing all EventTasks/Instances */ + private final List sessions; + + /** True if we replaced something in the user sessions in one iteration. */ + private boolean detectedAndReplacedTasks; + + /** The result we return from this rule */ + private final RuleApplicationResult result; + + /** Stop Watch to measure performance */ + private final StopWatch stopWatch; + + + + /** + * Instantiates a new rule application data. + * + * @param sessions + * The user sessions + */ + private RuleApplicationData(List sessions) { + this.sessions = sessions; + numberseqs = new ArrayList(); + uniqueTasks = new HashSet(); + number2task = new HashMap(); + stopWatch = new StopWatch(); + result = new RuleApplicationResult(); + submat = new ObjectDistanceSubstitionMatrix(6, -3, false); + newTasks = new LinkedList(); + this.detectedAndReplacedTasks = true; + } + + private void initializeQueues(int size) { + plannedReplacements = new Queue[size]; + for(int i=0;i(); + } + } + + public Queue[] getPlannedReplacements() { + return plannedReplacements; + } + + public void setPlannedReplacements(Queue[] plannedReplacements) { + this.plannedReplacements = plannedReplacements; + } + + /** + * Detected and replaced tasks. + * + * @return true, if successful + */ + private boolean detectedAndReplacedTasks() { + return detectedAndReplacedTasks; + } + + /** + * Gets the matchseqs. + * + * @return the matchseqs + */ + public LinkedList getMatchseqs() { + return matchseqs; + } + + /** + * Gets the new tasks. + * + * @return the new tasks + */ + public LinkedList getNewTasks() { + return newTasks; + } + + /** + * Gets the number2task. + * + * @return the number2task HashMap + */ + private HashMap getNumber2Task() { + return number2task; + } + + /** + * Gets the number sequences. + * + * @return the number sequences + */ + private ArrayList getNumberSequences() { + return numberseqs; + } + + /** + * Gets the replaced occurrences. + * + * @return the replaced occurences + */ + public HashMap> getReplacedOccurrences() { + return replacedOccurences; + } + + /** + * Gets the result. + * + * @return the result + */ + private RuleApplicationResult getResult() { + return result; + } + + /** + * Gets the sessions. + * + * @return the UserSessions as List. + */ + private List getSessions() { + return sessions; + } + + /** + * Gets the stop watch. + * + * @return the stopWatch + */ + private StopWatch getStopWatch() { + return stopWatch; + } + + /** + * Gets the submat. + * + * @return the submat + */ + private ObjectDistanceSubstitionMatrix getSubmat() { + return submat; + } + + /** + * Gets the unique tasks. + * + * @return the unique tasks + */ + private HashSet getUniqueTasks() { + return uniqueTasks; + } + + /** + * New task created. + * + * @param task + * can be called when new tasks are created to keep track of all newly created tasks + */ + private void newTaskCreated(ITask task) { + number2task.put(task.getId(), task); + newTasks.add(task); + } + + /** + * Reset newly created tasks. + */ + synchronized private void resetNewlyCreatedTasks() { + uniqueTasks.addAll(newTasks); + newTasks.clear(); + } + + /** + * Sets the number sequences. + * + * @param numberseqs + * the new number sequences + */ + private void setNumberSequences(ArrayList numberseqs) { + this.numberseqs = numberseqs; + } + + /** + * Sets the replaced occurences. + * + * @param replacedOccurences + * the replaced occurences + */ + public void setReplacedOccurences( + HashMap> replacedOccurences) { + this.replacedOccurences = replacedOccurences; + } + + /** + * Update substitution matrix. + */ + private void updateSubstitutionMatrix() { + submat.update(getNewTasks()); + resetNewlyCreatedTasks(); + } + + } + + }