List of usage examples for java.util TreeSet TreeSet
public TreeSet()
From source file:org.openmrs.module.clinicalsummary.web.controller.search.AutocompleteSearchController.java
@RequestMapping(value = "/module/clinicalsummary/search/autocompleteLocation", method = RequestMethod.GET) public @ResponseBody Collection<String> searchLocation( final @RequestParam(required = true, value = "term") String nameFragment) { Collection<String> names = new TreeSet<String>(); Collection<Location> locations = Context.getLocationService().getLocations(nameFragment); for (Location location : locations) names.add(location.getName());/*from w ww.ja va 2 s. c o m*/ return names; }
From source file:Main.java
public SortedListModel() { model = new TreeSet<Object>(); ListDataListener lis = new ListDataListener() { @Override// w w w . jav a 2 s . c o m public void contentsChanged(ListDataEvent arg0) { } @Override public void intervalAdded(ListDataEvent arg0) { } @Override public void intervalRemoved(ListDataEvent arg0) { } }; super.addListDataListener(lis); super.removeListDataListener(lis); }
From source file:Main.java
public SortedListModel() { model = new TreeSet<Object>(); ListDataListener lis = new ListDataListener() { @Override//from w ww. jav a 2 s.c o m public void contentsChanged(ListDataEvent arg0) { } @Override public void intervalAdded(ListDataEvent arg0) { } @Override public void intervalRemoved(ListDataEvent arg0) { } }; super.addListDataListener(lis); ListDataListener[] ldls = getListDataListeners(); super.removeListDataListener(lis); }
From source file:Main.java
public SortedListModel() { model = new TreeSet<Object>(); ListDataListener lis = new ListDataListener() { @Override//from w w w . ja v a 2s . c o m public void contentsChanged(ListDataEvent arg0) { } @Override public void intervalAdded(ListDataEvent arg0) { } @Override public void intervalRemoved(ListDataEvent arg0) { } }; super.addListDataListener(lis); ListDataListener[] ldls = (ListDataListener[]) (getListeners(ListDataListener.class)); super.removeListDataListener(lis); }
From source file:am.ik.categolj2.domain.model.CategoryTest.java
@Test public void testInTreeSet() { Category c1 = new Category(1, 1, "Programmming"); Category c2 = new Category(1, 2, "Java"); Category c3 = new Category(1, 3, "org"); Category c4 = new Category(2, 4, "springframework"); Category c5 = new Category(1, 5, "core"); SortedSet<Category> categories = new TreeSet<Category>(); // added randomly categories.add(c3);/* w w w . j av a 2s .co m*/ categories.add(c1); categories.add(c5); categories.add(c2); categories.add(c4); Iterator<Category> iterator = categories.iterator(); assertThat(iterator.next(), is(c1)); assertThat(iterator.next(), is(c2)); assertThat(iterator.next(), is(c3)); assertThat(iterator.next(), is(c4)); assertThat(iterator.next(), is(c5)); }
From source file:com.opensourcestrategies.financials.accounts.GLAccountInTree.java
/** * Creates a new <code>GLAccountInTree</code> instance. * * @param delegator a <code>Delegator</code> value * @param glAccountId the GL account ID// ww w.j a v a 2 s . com * @param balance a <code>BigDecimal</code> value * @exception GenericEntityException if an error occurs */ public GLAccountInTree(Delegator delegator, String glAccountId, BigDecimal balance) throws GenericEntityException { super(delegator, glAccountId, balance); this.childAccounts = new TreeSet<GLAccountInTree>(); }
From source file:com.ricemap.spateDB.core.PrismNN.java
public TOPK(int k) { heap = new TreeSet<PrismNN>(); this.k = k; }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {//from www. j a v a 2s .c o m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:org.sventon.cache.direntrycache.DirEntryCacheUpdaterTest.java
@Test public void testUpdate() throws Exception { final RepositoryService serviceMock = mock(RepositoryService.class); assertEquals(0, entryCache.getSize()); final List<LogEntry> logEntries = new ArrayList<LogEntry>(); final SortedSet<ChangedPath> changedPaths1 = new TreeSet<ChangedPath>(); changedPaths1.add(new ChangedPath("/file1.java", null, -1, ChangeType.MODIFIED)); changedPaths1.add(new ChangedPath("/file2.abc", null, -1, ChangeType.ADDED)); changedPaths1.add(new ChangedPath("/trunk/file3.def", null, -1, ChangeType.REPLACED)); logEntries.add(createLogEntry(123, "author", new Date(), "Log message for revision 123.", changedPaths1)); final SortedSet<ChangedPath> changedPaths2 = new TreeSet<ChangedPath>(); changedPaths2.add(new ChangedPath("/branch", "/trunk", 123, ChangeType.ADDED)); changedPaths2.add(new ChangedPath("/trunk/file3.def", null, -1, ChangeType.DELETED)); logEntries.add(createLogEntry(124, "author", new Date(), "Log message for revision 124.", changedPaths2)); final ConfigDirectory configDirectory = TestUtils.getTestConfigDirectory(); configDirectory.setCreateDirectories(false); final MockServletContext servletContext = new MockServletContext(); servletContext.setContextPath("sventon-test"); configDirectory.setServletContext(servletContext); final Application application = new Application(configDirectory); when(serviceMock.getLatestRevision(null)).thenReturn(124L); when(serviceMock.getEntryInfo(null, "/file1.java", 123)) .thenReturn(new DirEntry("/", "file1.java", "author", new Date(), DirEntry.Kind.FILE, 123, 12345)); when(serviceMock.getEntryInfo(null, "/file2.abc", 123)) .thenReturn(new DirEntry("/", "file2.abc", "author", new Date(), DirEntry.Kind.FILE, 123, 12345)); when(serviceMock.getEntryInfo(null, "/trunk/file3.def", 123)).thenReturn( new DirEntry("/trunk", "file3.def", "author", new Date(), DirEntry.Kind.FILE, 123, 12345)); when(serviceMock.getEntryInfo(null, "/branch", 124)) .thenReturn(new DirEntry("/", "branch", "author", new Date(), DirEntry.Kind.DIR, 123, 12345)); when(serviceMock.list(null, "/branch/", 124)) .thenReturn(new DirList(Collections.<DirEntry>emptyList(), new Properties())); when(serviceMock.getEntryInfo(null, "/trunk/file3.def", 123)).thenReturn( new DirEntry("/trunk", "file3.def", "author", new Date(), DirEntry.Kind.FILE, 123, 12345)); final RepositoryName repositoryName = new RepositoryName("defaultsvn"); final RevisionUpdate revisionUpdate = new RevisionUpdate(repositoryName, logEntries, false); final DirEntryCacheUpdater cacheUpdater = new DirEntryCacheUpdater(null, application); cacheUpdater.setRepositoryService(serviceMock); cacheUpdater.updateInternal(entryCache, null, revisionUpdate); Thread.sleep(500L); // TODO: Get rid of this! assertEquals(4, entryCache.getSize()); }
From source file:com.yahoo.pulsar.broker.loadbalance.impl.DeviationShedder.java
/** * Initialize this DeviationShedder./*from www . ja v a 2s.co m*/ */ public DeviationShedder() { bundleTreeSetCache = new TreeSet<>(); metricTreeSetCache = new TreeSet<>(); }