List of usage examples for java.util HashSet iterator
public Iterator<E> iterator()
From source file:org.intermine.bio.dataconversion.XenmineConverter.java
/** * //from www .j a va 2 s . c o m * @param reader * @throws Exception * @throws ObjectStoreException */ private void processInteractionsFile(Reader preader) throws Exception, ObjectStoreException { /* Xenbase gene ID * gene symbol * interactant ID:interactant symbol:co-citation occurrence */ System.out.println("Processing Interactants file...."); Iterator<?> tsvIter; try { tsvIter = FormattedTextParser.parseTabDelimitedReader(preader); } catch (Exception e) { throw new Exception("cannot parse file: " + preader.toString(), e); } while (tsvIter.hasNext()) { String[] line = (String[]) tsvIter.next(); if (line.length < 3) { LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length); continue; } String genePageId = line[0].trim().substring(12); String symbol = line[1].trim(); String interactants = line[2].trim(); //genePageId-PMID:symbol:someNumber if (interactants == null || interactants.length() == 0 || interactants.equals("")) { continue; } String[] interactingGenes = interactants.split(","); //System.out.println("Gene Page.."+ genePageId + " Length of inG.." + interactingGenes.length); HashSet geneIds = genesPageName.get(genePageId); Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene = genes.get(geneId); if (interactingGenes.length != 0) { for (int i = 0; i < interactingGenes.length; i++) { String gpid[] = interactingGenes[i].split("\\:"); String genePageIdInteractant = gpid[0]; //System.out.println("gene interactant.." + genePageIdInteractant); HashSet interactingGeneIds = genesPageName.get(genePageIdInteractant); if (interactingGeneIds == null) { continue; } Iterator itt = interactingGeneIds.iterator(); while (itt.hasNext()) { String interactingGeneId = (String) itt.next(); Item interactingGene = genes.get(interactingGeneId); if (gene != null && interactingGene != null) { getInteraction(gene.getIdentifier(), interactingGene.getIdentifier()); } } } } } } preader.close(); }
From source file:org.intermine.bio.dataconversion.XenmineConverter.java
/** * /*from ww w . ja va 2 s . c o m*/ * @param reader * @throws Exception * @throws ObjectStoreException */ private void processNonEntrezOrthologFile(Reader preader) throws Exception, ObjectStoreException { /* Xenbase * OMIM * MGI * ZFIN */ System.out.println("Processing Non Entrze Orthologs.. XenbaseGeneNonEntrezOrthologMapping.txt file...."); Iterator<?> tsvIter; try { tsvIter = FormattedTextParser.parseTabDelimitedReader(preader); } catch (Exception e) { throw new Exception("cannot parse file: " + preader.toString(), e); } String prevXenopusId = ""; while (tsvIter.hasNext()) { String[] line = (String[]) tsvIter.next(); if (line.length < 4) { LOG.error("Couldn't process line. Expected 4 cols, but was " + line.length); continue; } System.out.println(line[0].trim()); String xenopusId = line[0].trim().substring(8); //it doesn;t say GENEPAGE!! String omimId = line[1].trim(); String mgiId = line[2].trim(); String zfinId = line[3].trim(); String chickenId = line[4].trim(); if (prevXenopusId == xenopusId) { HashSet geneIds = genesPageName.get(xenopusId); Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene0 = genes.get(geneId); if (gene0 != null) { if (!StringUtils.isEmpty(zfinId)) { String gene3 = getGene(zfinId, "7955"); if (gene3 != null) processHomologues(gene0.getIdentifier(), gene3); } } } } else { HashSet geneIds = genesPageName.get(xenopusId); Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene0 = genes.get(geneId); if (gene0 != null) { if (!StringUtils.isEmpty(omimId)) { String gene1 = getGene(omimId, "9606"); if (gene1 != null) processHomologues(gene0.getIdentifier(), gene1); } if (!StringUtils.isEmpty(mgiId)) { String gene2 = getGene(mgiId, "10090"); if (gene2 != null) processHomologues(gene0.getIdentifier(), gene2); } if (!StringUtils.isEmpty(zfinId)) { String gene3 = getGene(zfinId, "7955"); if (gene3 != null) processHomologues(gene0.getIdentifier(), gene3); } if (!StringUtils.isEmpty(chickenId)) { String gene4 = getGene(chickenId, "9031"); if (gene4 != null) processHomologues(gene0.getIdentifier(), gene4); } } } } prevXenopusId = xenopusId; } preader.close(); }
From source file:org.unitime.timetable.model.Solution.java
public void removeDivSecNumbers(org.hibernate.Session hibSession) { HashSet classes = new HashSet(); for (Iterator i = getAssignments().iterator(); i.hasNext();) { Assignment assignment = (Assignment) i.next(); Class_ clazz = assignment.getClazz(); if (clazz == null || clazz.getClassSuffix() == null) continue; classes.add(clazz);//from w w w .ja va2 s .c om } HashSet subparts2fix = new HashSet(); for (Iterator i = classes.iterator(); i.hasNext();) { Class_ clazz = (Class_) i.next(); clazz.setClassSuffix(null); subparts2fix.add(clazz.getSchedulingSubpart()); hibSession.update(clazz); } List otherClasses = new SolutionDAO().getSession() .createQuery("select distinct c from Class_ c, Solution s inner join s.owner.departments d " + "where s.uniqueId = :solutionId and c.managingDept=d and " + "c.uniqueId not in (select a.clazz.uniqueId from s.assignments a)") .setLong("solutionId", getUniqueId().longValue()).list(); for (Iterator i = otherClasses.iterator(); i.hasNext();) { Class_ clazz = (Class_) i.next(); if (clazz.getClassSuffix() == null) continue; clazz.setClassSuffix(null); subparts2fix.add(clazz.getSchedulingSubpart()); hibSession.update(clazz); } for (Iterator i = subparts2fix.iterator(); i.hasNext();) { SchedulingSubpart subpart = (SchedulingSubpart) i.next(); TreeSet takenDivNums = new TreeSet(takenDivisionNumbers(subpart)); int dec = 0, lastDiv = 0; for (Iterator j = takenDivNums.iterator(); j.hasNext();) { int div = ((Integer) j.next()).intValue(); dec += (div - lastDiv - 1); lastDiv = div; if (dec > 0) { sLog.debug(subpart.getSchedulingSubpartLabel() + ": " + div + "->" + (div - dec)); InstructionalOffering offering = subpart.getInstrOfferingConfig().getInstructionalOffering(); ItypeDesc itype = subpart.getItype(); for (Iterator i1 = offering.getInstrOfferingConfigs().iterator(); i1.hasNext();) { InstrOfferingConfig cfg = (InstrOfferingConfig) i1.next(); for (Iterator i2 = cfg.getSchedulingSubparts().iterator(); i2.hasNext();) { SchedulingSubpart s = (SchedulingSubpart) i2.next(); if (!s.getItype().equals(itype)) continue; for (Iterator i3 = s.getClasses().iterator(); i3.hasNext();) { Class_ clazz = (Class_) i3.next(); if (clazz.getClassSuffix() == null || clazz.getClassSuffix().length() != 6) continue; int clazzDivNum = Integer.parseInt(clazz.getClassSuffix().substring(0, 3)); int clazzSecNum = Integer.parseInt(clazz.getClassSuffix().substring(3, 6)); if (clazzDivNum == div) { clazz.setClassSuffix(sSufixFormat.format(clazzDivNum - dec) + sSufixFormat.format(clazzSecNum)); hibSession.update(clazz); } } } } } } } }
From source file:org.intermine.bio.dataconversion.XenmineConverter.java
/** * /*from ww w. j av a 2s .com*/ * @param reader * @throws Exception * @throws ObjectStoreException */ private void processAnatomyMappingFile(Reader preader) throws Exception, ObjectStoreException { /* Xenbase Gene ID * gene symbol * start stage * end stage * tissues * XB-GENEPAGE-478053 trnt1 XAO:1000031 NF stage 10.5 XAO:1000009 frog * XAO:0000001 ectoderm,XAO:0003024 head,XAO:0000129 intestine,XAO:0000133 liver,XAO:0000256 oocyte, * XAO:0000258 ovary,XAO:0000157 testis,XAO:0003004 whole organism */ System.out.println("Processing Anatomy Mapping file...."); Iterator<?> tsvIter; try { tsvIter = FormattedTextParser.parseTabDelimitedReader(preader); } catch (Exception e) { throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile() } while (tsvIter.hasNext()) { String[] line = (String[]) tsvIter.next(); String xenbaseGeneId = line[0].trim().substring(12); String symbol = line[1].trim(); String startStageFull = line[2].trim(); //XAO:1000049 NF stage 35 and 36 String[] t = startStageFull.split("\\s"); String startStage = t[0]; String endStageFull = line[3].trim(); String[] te = endStageFull.split("\\s"); String endStage = te[0]; String anatomicalTissue = line[4].trim(); System.out.println(xenbaseGeneId); HashSet geneIds = genesPageName.get(xenbaseGeneId); //check this stuff with what is in genes..a thorough once over Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene = genes.get(geneId); if (gene != null) { //figure out how to store this stuff Item anatomy = createItem("AnatomyMapping"); Item sterm = getTerm(startStage); Item eterm = getTerm(endStage); anatomy.setReference("startStage", sterm.getIdentifier()); anatomy.setReference("endStage", eterm.getIdentifier()); setAnatomicalTissues(anatomy, anatomicalTissue, "tissues"); anatomy.setReference("gene", gene.getIdentifier()); store(anatomy); //don't store all other items created if there is no gene to associate with..? } } } preader.close(); }
From source file:org.intermine.bio.dataconversion.XenmineConverter.java
/** * /* w w w .j a v a 2 s . co m*/ * @param reader * @throws Exception * @throws ObjectStoreException */ private void processLiteratureFile(Reader preader) throws Exception, ObjectStoreException { /* Xenbase Literature ID * PMID * Xenbase genePage IDs associated with the PMID above */ System.out.println("Processing Literature file...."); Iterator<?> tsvIter; try { tsvIter = FormattedTextParser.parseTabDelimitedReader(preader); } catch (Exception e) { throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile() } while (tsvIter.hasNext()) { String[] line = (String[]) tsvIter.next(); if (line.length < 3) { LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length); continue; } String literatureId = line[0].trim().substring(7); String pmid = line[1].trim(); String litGenes = line[2].trim(); //XB-GENEPAGE-491748 elavl2,XB-GENEPAGE-481418 gdf1,XB-GENEPAGE-481799 elavl1 if (litGenes.isEmpty() || litGenes == null) { System.out.println("empty 3rd column."); continue; } String storedRefId = getPub(pmid, literatureId); String[] gids = litGenes.split(","); if (gids.length != 0) { for (int i = 0; i < gids.length; i++) { String gpid[] = gids[i].split("\\s"); String genePageId = gpid[0].substring(12); HashSet geneIds = genesPageName.get(genePageId); //check this stuff with what is in genes..a thorough once over Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene = genes.get(geneId); if (gene != null) { gene.addToCollection("publications", storedRefId); } } } } else { String gpid[] = litGenes.split("\\s"); String genePageId = gpid[0].substring(12); HashSet geneIds = genesPageName.get(genePageId); //check this stuff with what is in genes..a thorough once over Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene = genes.get(geneId); if (gene != null) { gene.addToCollection("publications", storedRefId); } } } } preader.close(); }
From source file:services.SimulationService.java
public boolean remove(SWGObject object, float x, float z, boolean notifyObservers) { if (object == null || !object.isInQuadtree()) { return false; }//from ww w .j a va2 s. c o m boolean success = quadTrees.get(object.getPlanet().getName()).remove(x, z, object); object.setIsInQuadtree(success); if (success && notifyObservers) { HashSet<Client> oldObservers = new HashSet<Client>(object.getObservers()); for (Iterator<Client> it = oldObservers.iterator(); it.hasNext();) { Client observerClient = it.next(); if (observerClient.getParent() != null) { observerClient.getParent().makeUnaware(object); // Experimental until engine fixed if (observerClient.getParent().getAwareObjects().contains(object)) { object.viewChildren(observerClient.getParent(), false, false, new Traverser() { @Override public void process(SWGObject object) { if (object == null) return; if (object.getClient() != null) object.makeUnaware(observerClient.getParent()); observerClient.getParent().makeUnaware(object); } }); if (!object.isInSnapshot()) object.sendDestroy(observerClient); object.removeObserver(observerClient.getParent()); observerClient.getParent().getAwareObjects().remove(object); } // Experimental until engine fixed } } } return success; }
From source file:org.lockss.scheduler.TaskRunner.java
boolean cleanupSchedule(Scheduler scheduler, boolean doDrop) { if (currentSchedule == null) { log.debug("cleanupSchedule(): currentSchedule = null"); return false; }/* w w w . ja va2 s .co m*/ // don't do this too often if (TimeBase.msSince(lastCleanup) < minCleanupInterval) { return false; } lastCleanup = TimeBase.nowMs(); List unexpired = getUnexpiredTasks(); if (scheduler.createSchedule(unexpired)) { // no cleanup necessary, nothing pruned log.debug("cleanupSchedule(): no cleanup necessary"); return false; } HashSet remainingTasks = new HashSet(unexpired); HashSet dropped = new HashSet(); for (int ix = maxDrop; ix > 0; ix--) { SchedulableTask droppable = findDroppableTask(dropped); if (droppable == null) { log.error("Failed to cleanup schedule: " + currentSchedule + " after dropping " + dropped); return false; } if (log.isDebug3()) log.debug3("Considering dropping: " + droppable); remainingTasks.remove(droppable); dropped.add(droppable); if (scheduler.createSchedule(remainingTasks)) { log.debug3("succeeded"); if (doDrop) { for (Iterator iter = dropped.iterator(); iter.hasNext();) { SchedulableTask task = (SchedulableTask) iter.next(); log.warning("Dropped " + task); task.setDropped(); decrStats(task, STAT_WAITING); addOverrunner(task, STAT_DROPPED); } } return true; } } return false; }
From source file:pl.edu.icm.coansys.source.ReduceDocsWithSameSourceId.java
@Override protected void reduce(Writable key, Iterable<BytesWritable> values, Context context) throws IOException, InterruptedException { ArrayList<String> docIds = new ArrayList<String>(); HashSet<String> issns = new HashSet<String>(); HashSet<String> isbns = new HashSet<String>(); HashSet<String> titles = new HashSet<String>(); for (BytesWritable value : values) { DocumentProtos.DocumentWrapper docWrapper = DocumentProtos.DocumentWrapper.parseFrom(value.copyBytes()); docIds.add(docWrapper.getRowId()); String issn = null;// w w w. ja v a2 s . co m String isbn = null; if (docWrapper.hasDocumentMetadata() && docWrapper.getDocumentMetadata().hasBasicMetadata()) { DocumentProtos.BasicMetadataOrBuilder bm = docWrapper.getDocumentMetadata() .getBasicMetadataOrBuilder(); if (bm.hasIssn()) { issn = bm.getIssn(); } if (bm.hasIsbn()) { isbn = bm.getIsbn(); } if (StringUtils.isNotBlank(isbn)) { isbn = isbn.trim().toUpperCase(); isbns.add(isbn); } if (StringUtils.isNotBlank(issn)) { issn = issn.trim().toUpperCase(); issns.add(issn); } if (bm.hasJournal()) { String title = bm.getJournal().trim(); if (StringUtils.isNotBlank(title)) { titles.add(title); } } } } String issn = null; String isbn = null; ArrayList<String> titleA = new ArrayList<String>(titles); Collections.sort(titleA, new Comparator<String>() { @Override public int compare(String o1, String o2) { //najdusze naprzd return o2.length() - o1.length(); } }); if (issns.size() > 0) { issn = issns.iterator().next(); } if (isbns.size() > 0) { isbn = isbns.iterator().next(); } String id = "http://comac.ceon.pl/source-"; if (issn != null) { id += ("issn-" + issn); if (isbn != null) { id += "-"; } } if (isbn != null) { id += ("isbn-" + isbn); } for (String docId : docIds) { ParentModelProtos.ParentDisambiguationOut.Builder parent = ParentModelProtos.ParentDisambiguationOut .newBuilder(); parent.setDocId(docId); parent.setParentId(id); parent.addAllParentName(titles); if (isbn != null) { parent.setType(DocumentProtos.BasicMetadata.ParentType.BOOK); } else { parent.setType(DocumentProtos.BasicMetadata.ParentType.JOURNAL); } context.write(new Text(docId), new BytesWritable(parent.build().toByteArray())); } }
From source file:org.intermine.bio.dataconversion.XenmineConverter.java
/** * // w w w . j a va 2 s . c o m * @param reader * @throws Exception * @throws ObjectStoreException */ private void processGoFile(Reader preader) throws Exception, ObjectStoreException { /* Xenbase genepage ID * gene symbol * GO Ids (comma separated) */ System.out.println("Processing GO file...."); Iterator<?> tsvIter; try { tsvIter = FormattedTextParser.parseTabDelimitedReader(preader); } catch (Exception e) { throw new Exception("cannot parse file: " + preader.toString(), e); //getCurrentFile() } while (tsvIter.hasNext()) { String[] line = (String[]) tsvIter.next(); if (line.length < 3) { LOG.error("Couldn't process line. Expected 3 cols, but was " + line.length); continue; } String genePageId = line[0].trim().substring(12); String symbol = line[1].trim(); String goids = line[2].trim(); //GO:0005525,GO:0007264,GO:0015031 HashSet geneIds = genesPageName.get(genePageId); if (geneIds == null) { System.out.println("genePageId: null for genes.."); continue; } Iterator it = geneIds.iterator(); while (it.hasNext()) { String geneId = (String) it.next(); Item gene = genes.get(geneId); //System.out.println("genePageId: " + genePageId + " geneId " + geneId); String[] gids = goids.split(","); for (int i = 0; i < gids.length; i++) { String goTermIdentifier = gids[i]; if (gene != null) { createGoAnnotation(gene.getIdentifier(), gene, goTermIdentifier, "XenBase", "XenBase"); } } } } preader.close(); }
From source file:org.processmining.analysis.petrinet.cpnexport.HLToCPNTranslator.java
/** * Gets for the given transitions all the other transitions that are * involved in the same choice based on frequencies. * /*from w w w . j a va2s . c o m*/ * @param transitionsFreqDep * HashSet. A hashset in which we only have one transition and * for which we want to obtain all the other transitions that are * involved in the same choice based on frequencies. */ private void getTransitionsForChoiceOnFrequencies(HashSet<ColoredTransition> transitionsFreqDep) { int oldSizeTransitions = transitionsFreqDep.size(); HashSet<ColoredPlace> places = new HashSet<ColoredPlace>(); Iterator<ColoredTransition> transitionsFreqDepIt = transitionsFreqDep.iterator(); while (transitionsFreqDepIt.hasNext()) { ColoredTransition transition = transitionsFreqDepIt.next(); places.addAll(transition.getPredecessors()); } // get the outgoing transitions for each place in places Iterator<ColoredPlace> placesIt = places.iterator(); while (placesIt.hasNext()) { ColoredPlace place = placesIt.next(); transitionsFreqDep.addAll(place.getSuccessors()); } if (transitionsFreqDep.size() > oldSizeTransitions) { getTransitionsForChoiceOnFrequencies(transitionsFreqDep); } }