List of usage examples for java.util TreeSet contains
public boolean contains(Object o)
From source file:DecorateMutationsSNP.java
/** * The procedure creates a .txt file containing the information about the SNP mutations in the extant units * The first row represents the position of each mutation that is a double value in the interval (0,1) * The other rows represent the leave nodes as a matrix of 0 and 1 indicating the absence/presence of the corresponding mutation * @param wholePath path of the directory where the output file is stored * @param arg instance of the class PopulationARG that represents the ARG of a single population (in this case and actual population) * @see PopulationARG/*from w w w . j a va2s. com*/ */ public static void createSNP_TxtFile(String wholePath, PopulationARG arg) { Writer writer = null; File file = new File("" + wholePath); try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file), "utf-8")); TreeSet<Double> posMutations = GenerateAdmixturePopulations.getAllMutations(); //System.out.println("Creating file SNPs for population "+arg.getId_pop()); //System.out.println("# of all mutations in all populations "+posMutations.size()); writer.write("Population " + arg.getId_pop() + "\n"); writer.write("Number of extant units (rows): " + arg.getExtantUnits() + "\n"); writer.write("Number of SNPs for each extant unit (columns): " + posMutations.size() + "\n\n"); Iterator<Double> it_posMuts = posMutations.iterator(); Double position; while (it_posMuts.hasNext()) { position = it_posMuts.next(); String troncato = String.format("%.4f", position); writer.write(troncato + " "); } writer.write("\n\n"); //For each leave print a row representing the absence or presence of SNP mutations for (int i = 0; i < arg.getExtantUnits(); i++) { it_posMuts = posMutations.iterator(); while (it_posMuts.hasNext()) { position = it_posMuts.next(); //check if the arg has the mutation if (arg.getMutationSet().containsKey(position)) { //if yes then check if the leaf has the mutation //Mutation mut = arg.getMutationSet().get(position); TreeSet<Double> muts_set = arg.getNodeSet().get(i).getMutation_set(); if (muts_set.contains(position)) writer.write("1 "); else writer.write("0 "); } else writer.write("0 "); } writer.write("\n"); } writer.close(); } //fine try catch (IOException ex) { // report } }
From source file:org.ariadne.oai.utils.HarvesterUtils.java
public static ReposProperties addRepository(ReposProperties repoProps) throws Exception { OAIRepository repository = new OAIRepository(); String fallBackReposId = repoProps.getBaseURL().replaceFirst("http.?://", "").split("/", 2)[0].split(":", 2)[0];/*from w ww . j av a 2s.c om*/ String internalId = fallBackReposId.replaceAll("\\.", "_"); Hashtable ids = PropertiesManager.getInstance().getPropertyStartingWith(internalId); TreeSet<String> allIds = new TreeSet<String>(); for (Object o : ids.keySet()) { allIds.add(((String) o).split("\\.")[0]); } int i = 1; while (allIds.contains(internalId)) { internalId = internalId.split("_u_")[0] + "_u_" + i++; } String urlString = repoProps.getBaseURL() + "?verb=Identify"; try { URL u = new URL(urlString); HttpURLConnection http = (HttpURLConnection) u.openConnection(); if (http.getResponseCode() == 200) { repository.setBaseURL(repoProps.getBaseURL()); String url = repository.getBaseURL(); } else { throw new IOException(Integer.toString(http.getResponseCode())); } } catch (IOException ex) { throw new Exception("The given Url isn't a valid OAI Repository (Could not connect to Url \"" + urlString + "\". ErrorMsg was : " + ex.getMessage() + ") "); } catch (OAIException e) { throw new Exception( "The given Url \"" + urlString + "\" isn't a valid OAI Repository (" + e.getMessage() + ")."); } catch (IllegalStateException e) { try { throw new Exception( "The baseUrl of the OAI Repository is not correct (found url in Identify verb : " + repository.getBaseURL() + ")"); } catch (OAIException e1) { throw new Exception( "The baseUrl of the OAI Repository is not correct (Error : " + e1.getMessage() + ")"); } } catch (Exception e) { throw new Exception( "The following error occured : (" + e.getClass().getName() + ") " + e.getMessage() + "."); } return addTarget(repoProps, repository, fallBackReposId, internalId); }
From source file:at.alladin.rmbt.qos.QoSUtil.java
/** * //from w w w. j a v a 2 s.c om * @param settings * @param conn * @param answer * @param lang * @param errorList * @throws SQLException * @throws JSONException * @throws HstoreParseException * @throws IllegalAccessException * @throws IllegalArgumentException */ public static void evaluate(final ResourceBundle settings, final Connection conn, final TestUuid uuid, final JSONObject answer, String lang, final ErrorList errorList) throws SQLException, HstoreParseException, JSONException, IllegalArgumentException, IllegalAccessException { // Load Language Files for Client final List<String> langs = Arrays.asList(settings.getString("RMBT_SUPPORTED_LANGUAGES").split(",\\s*")); if (langs.contains(lang)) { errorList.setLanguage(lang); } else { lang = settings.getString("RMBT_DEFAULT_LANGUAGE"); } if (conn != null) { final Client client = new Client(conn); final Test test = new Test(conn); boolean necessaryDataAvailable = false; if (uuid != null && uuid.getType() != null && uuid.getUuid() != null) { switch (uuid.getType()) { case OPEN_TEST_UUID: if (test.getTestByOpenTestUuid(UUID.fromString(uuid.getUuid())) > 0 && client.getClientByUid(test.getField("client_id").intValue())) { necessaryDataAvailable = true; } break; case TEST_UUID: if (test.getTestByUuid(UUID.fromString(uuid.getUuid())) > 0 && client.getClientByUid(test.getField("client_id").intValue())) { necessaryDataAvailable = true; } break; } } final long timeStampFullEval = System.currentTimeMillis(); if (necessaryDataAvailable) { final Locale locale = new Locale(lang); final ResultOptions resultOptions = new ResultOptions(locale); final JSONArray resultList = new JSONArray(); QoSTestResultDao resultDao = new QoSTestResultDao(conn); List<QoSTestResult> testResultList = resultDao.getByTestUid(test.getUid()); if (testResultList == null || testResultList.isEmpty()) { throw new UnsupportedOperationException("test " + test + " has no result list"); } //map that contains all test types and their result descriptions determined by the test result <-> test objectives comparison Map<TestType, TreeSet<ResultDesc>> resultKeys = new HashMap<>(); //test description set: Set<String> testDescSet = new TreeSet<>(); //test summary set: Set<String> testSummarySet = new TreeSet<>(); //Staring timestamp for evaluation time measurement final long timeStampEval = System.currentTimeMillis(); //iterate through all result entries for (final QoSTestResult testResult : testResultList) { //reset test counters testResult.setFailureCounter(0); testResult.setSuccessCounter(0); //get the correct class of the result; TestType testType = null; try { testType = TestType.valueOf(testResult.getTestType().toUpperCase(Locale.US)); } catch (IllegalArgumentException e) { final String errorMessage = "WARNING: QoS TestType '" + testResult.getTestType().toUpperCase(Locale.US) + "' not supported by ControlServer. Test with UID: " + testResult.getUid() + " skipped."; System.out.println(errorMessage); errorList.addErrorString(errorMessage); testType = null; } if (testType == null) { continue; } Class<? extends AbstractResult<?>> clazz = testType.getClazz(); //parse hstore data final JSONObject resultJson = new JSONObject(testResult.getResults()); AbstractResult<?> result = QoSUtil.HSTORE_PARSER.fromJSON(resultJson, clazz); result.setResultJson(resultJson); if (result != null) { //add each test description key to the testDescSet (to fetch it later from the db) if (testResult.getTestDescription() != null) { testDescSet.add(testResult.getTestDescription()); } if (testResult.getTestSummary() != null) { testSummarySet.add(testResult.getTestSummary()); } testResult.setResult(result); } //compare test results compareTestResults(testResult, result, resultKeys, testType, resultOptions); //resultList.put(testResult.toJson()); //save all test results after the success and failure counters have been set //resultDao.updateCounter(testResult); } //ending timestamp for evaluation time measurement final long timeStampEvalEnd = System.currentTimeMillis(); //------------------------------------------------------------- //fetch all result strings from the db QoSTestDescDao descDao = new QoSTestDescDao(conn, locale); //FIRST: get all test descriptions Set<String> testDescToFetchSet = testDescSet; testDescToFetchSet.addAll(testSummarySet); Map<String, String> testDescMap = descDao.getAllByKeyToMap(testDescToFetchSet); for (QoSTestResult testResult : testResultList) { //and set the test results + put each one to the result list json array String preParsedDesc = testDescMap.get(testResult.getTestDescription()); if (preParsedDesc != null) { String description = String.valueOf( TestScriptInterpreter.interprete(testDescMap.get(testResult.getTestDescription()), QoSUtil.HSTORE_PARSER, testResult.getResult(), true, resultOptions)); testResult.setTestDescription(description); } //do the same for the test summary: String preParsedSummary = testDescMap.get(testResult.getTestSummary()); if (preParsedSummary != null) { String description = String.valueOf( TestScriptInterpreter.interprete(testDescMap.get(testResult.getTestSummary()), QoSUtil.HSTORE_PARSER, testResult.getResult(), true, resultOptions)); testResult.setTestSummary(description); } resultList.put(testResult.toJson(uuid.getType())); } //finally put results to json answer.put("testresultdetail", resultList); JSONArray resultDescArray = new JSONArray(); //SECOND: fetch all test result descriptions for (TestType testType : resultKeys.keySet()) { TreeSet<ResultDesc> descSet = resultKeys.get(testType); //fetch results to same object descDao.loadToTestDesc(descSet); //another tree set for duplicate entries: //TODO: there must be a better solution //(the issue is: compareTo() method returns differnt values depending on the .value attribute (if it's set or not)) TreeSet<ResultDesc> descSetNew = new TreeSet<>(); //add fetched results to json for (ResultDesc desc : descSet) { if (!descSetNew.contains(desc)) { descSetNew.add(desc); } else { for (ResultDesc d : descSetNew) { if (d.compareTo(desc) == 0) { d.getTestResultUidList().addAll(desc.getTestResultUidList()); } } } } for (ResultDesc desc : descSetNew) { if (desc.getValue() != null) { resultDescArray.put(desc.toJson()); } } } //System.out.println(resultDescArray); //put result descriptions to json answer.put("testresultdetail_desc", resultDescArray); QoSTestTypeDescDao testTypeDao = new QoSTestTypeDescDao(conn, locale); JSONArray testTypeDescArray = new JSONArray(); for (QoSTestTypeDesc desc : testTypeDao.getAll()) { final JSONObject testTypeDesc = desc.toJson(); if (testTypeDesc != null) { testTypeDescArray.put(testTypeDesc); } } //put result descriptions to json answer.put("testresultdetail_testdesc", testTypeDescArray); JSONObject evalTimes = new JSONObject(); evalTimes.put("eval", (timeStampEvalEnd - timeStampEval)); evalTimes.put("full", (System.currentTimeMillis() - timeStampFullEval)); answer.put("eval_times", evalTimes); //System.out.println(answer); } else errorList.addError("ERROR_REQUEST_TEST_RESULT_DETAIL_NO_UUID"); } else errorList.addError("ERROR_DB_CONNECTION"); }
From source file:org.apache.hadoop.hdfs.server.namenode.JspHelper.java
public static DatanodeInfo bestNode(LocatedBlock blk) throws IOException { TreeSet<DatanodeInfo> deadNodes = new TreeSet<DatanodeInfo>(); DatanodeInfo chosenNode = null;/*from ww w .j a v a 2 s . co m*/ int failures = 0; Socket s = null; DatanodeInfo[] nodes = blk.getLocations(); if (nodes == null || nodes.length == 0) { throw new IOException("No nodes contain this block"); } while (s == null) { if (chosenNode == null) { do { chosenNode = nodes[rand.nextInt(nodes.length)]; } while (deadNodes.contains(chosenNode)); } int index = rand.nextInt(nodes.length); chosenNode = nodes[index]; //just ping to check whether the node is alive InetSocketAddress targetAddr = NetUtils .createSocketAddr(chosenNode.getHost() + ":" + chosenNode.getInfoPort()); try { s = new Socket(); s.connect(targetAddr, HdfsConstants.READ_TIMEOUT); s.setSoTimeout(HdfsConstants.READ_TIMEOUT); } catch (IOException e) { deadNodes.add(chosenNode); s.close(); s = null; failures++; } if (failures == nodes.length) throw new IOException("Could not reach the block containing the data. Please try again"); } s.close(); return chosenNode; }
From source file:com.opendoorlogistics.core.utils.strings.Strings.java
public static String getFiltered(String s, char... acceptChars) { TreeSet<Character> set = new TreeSet<>(); for (char c : acceptChars) { set.add(c);/*from w ww. java2 s. c o m*/ } StringBuilder ret = new StringBuilder(); for (int i = 0; i < s.length(); i++) { if (set.contains(s.charAt(i))) { ret.append(s.charAt(i)); } } return ret.toString(); }
From source file:net.spfbl.core.Reverse.java
public static String getListedIP(String ip, String server, Collection<String> valueSet) { String host = Reverse.getHostReverse(ip, server); if (host == null) { return null; } else {/*from ww w . j av a 2 s . c om*/ try { TreeSet<String> IPv4Set = null; TreeSet<String> IPv6Set = null; for (String value : valueSet) { if (SubnetIPv4.isValidIPv4(value)) { if (IPv4Set == null) { IPv4Set = getIPv4Set(host); } if (IPv4Set.contains(value)) { return value; } } else if (SubnetIPv6.isValidIPv6(value)) { if (IPv6Set == null) { IPv6Set = getIPv6Set(host); } if (IPv6Set.contains(value)) { return value; } } } return null; } catch (CommunicationException ex) { Server.logDebug("DNS service '" + server + "' unreachable."); return null; } catch (ServiceUnavailableException ex) { Server.logDebug("DNS service '" + server + "' unavailable."); return null; } catch (NameNotFoundException ex) { // No listado. return null; } catch (NamingException ex) { Server.logError(ex); return null; } } }
From source file:net.spfbl.core.Reverse.java
public static String getListedHost(String host, String zone, Collection<String> valueSet) { host = Domain.normalizeHostname(host, false); if (host == null) { return null; } else {// www . j av a2 s .c om try { host = host + '.' + zone; TreeSet<String> IPv4Set = null; TreeSet<String> IPv6Set = null; for (String value : valueSet) { if (SubnetIPv4.isValidIPv4(value)) { if (IPv4Set == null) { IPv4Set = getIPv4Set(host); } if (IPv4Set.contains(value)) { return value; } } else if (SubnetIPv6.isValidIPv6(value)) { if (IPv6Set == null) { IPv6Set = getIPv6Set(host); } if (IPv6Set.contains(value)) { return value; } } } return null; } catch (CommunicationException ex) { Server.logDebug("DNS service '" + zone + "' unreachable."); return null; } catch (ServiceUnavailableException ex) { Server.logDebug("DNS service '" + zone + "' unavailable."); return null; } catch (NameNotFoundException ex) { // No listado. return null; } catch (NamingException ex) { Server.logError(ex); return null; } } }
From source file:desmoj.extensions.visualization2d.engine.modelGrafic.StatisticGrafic.java
/** * get all views (viewId's) with Statistic * @return//from www .j a va2 s . co m */ public static String[] getViews(Model model) { TreeSet<String> views = new TreeSet<String>(); String[] ids = model.getStatistics().getAllIds(); for (int i = 0; i < ids.length; i++) { Statistic statistic = model.getStatistics().get(ids[i]); StatisticGrafic statisticGrafic = (StatisticGrafic) statistic.getGrafic(); if (statisticGrafic != null) { String viewId = statisticGrafic.getViewId(); if (!views.contains(viewId)) views.add(viewId); } } String[] out = new String[views.size()]; int i = 0; for (Iterator<String> it = views.iterator(); it.hasNext();) { out[i] = it.next(); i++; } return out; }
From source file:org.opendatakit.aggregate.odktables.impl.api.RealizedTableServiceImpl.java
@Override public Response deleteTable() throws ODKDatastoreException, ODKTaskLockException, PermissionDeniedException { TreeSet<GrantedAuthorityName> ui = SecurityServiceUtil.getCurrentUserSecurityInfo(cc); if (!ui.contains(GrantedAuthorityName.ROLE_ADMINISTER_TABLES)) { throw new PermissionDeniedException("User does not belong to the 'Administer Tables' group"); }/*from www . ja v a 2s .co m*/ tm.deleteTable(tableId); logger.info("tableId: " + tableId); Datastore ds = cc.getDatastore(); if (ds instanceof DatastoreImpl) { ((DatastoreImpl) ds).getDam().logUsage(); } return Response.ok().header(ApiConstants.OPEN_DATA_KIT_VERSION_HEADER, ApiConstants.OPEN_DATA_KIT_VERSION) .header("Access-Control-Allow-Origin", "*").header("Access-Control-Allow-Credentials", "true") .build(); }
From source file:org.opendatakit.aggregate.servlet.GetUsersAndPermissionsServlet.java
@Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { if (req.getScheme().equals("http")) { logger.warn("Retrieving users and capabilities over http"); }/*from w w w . j a v a 2 s .c om*/ CallingContext cc = ContextFactory.getCallingContext(this, req); ArrayList<UserSecurityInfo> allUsers; try { allUsers = SecurityServiceUtil.getAllUsers(true, cc); } catch (DatastoreFailureException e) { logger.error("Retrieving users and capabilities .csv persistence error: " + e.toString()); e.printStackTrace(); resp.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR, ErrorConsts.PERSISTENCE_LAYER_PROBLEM + "\n" + e.toString()); return; } catch (AccessDeniedException e) { logger.error("Retrieving users and capabilities .csv access denied error: " + e.toString()); e.printStackTrace(); resp.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR, e.toString()); return; } StringWriter buffer = new StringWriter(); RFC4180CsvWriter writer = new RFC4180CsvWriter(buffer); String[] columnContent = new String[10]; columnContent[0] = "Username"; columnContent[1] = "Full Name"; columnContent[2] = "Account Type"; columnContent[3] = "Data Collector"; columnContent[4] = "Data Viewer"; columnContent[5] = "Form Manager"; columnContent[6] = "Synchronize Tables"; columnContent[7] = "Tables Super-user"; columnContent[8] = "Administer Tables"; columnContent[9] = "Site Administrator"; writer.writeNext(columnContent); for (UserSecurityInfo i : allUsers) { if (i.getType() == UserType.REGISTERED) { if (i.getEmail() != null) { columnContent[0] = i.getEmail().substring(EmailParser.K_MAILTO.length()); columnContent[2] = "Google"; } else { columnContent[0] = i.getUsername(); columnContent[2] = "ODK"; } columnContent[1] = i.getFullName(); } else { columnContent[0] = User.ANONYMOUS_USER; columnContent[1] = User.ANONYMOUS_USER_NICKNAME; columnContent[2] = null; } TreeSet<GrantedAuthorityName> grants = i.getAssignedUserGroups(); columnContent[3] = grants.contains(GrantedAuthorityName.GROUP_DATA_COLLECTORS) ? "X" : null; columnContent[4] = grants.contains(GrantedAuthorityName.GROUP_DATA_VIEWERS) ? "X" : null; columnContent[5] = grants.contains(GrantedAuthorityName.GROUP_FORM_MANAGERS) ? "X" : null; columnContent[6] = grants.contains(GrantedAuthorityName.GROUP_SYNCHRONIZE_TABLES) ? "X" : null; columnContent[7] = grants.contains(GrantedAuthorityName.GROUP_SUPER_USER_TABLES) ? "X" : null; columnContent[8] = grants.contains(GrantedAuthorityName.GROUP_ADMINISTER_TABLES) ? "X" : null; columnContent[9] = grants.contains(GrantedAuthorityName.GROUP_SITE_ADMINS) ? "X" : null; writer.writeNext(columnContent); } writer.close(); // do not cache... resp.setHeader("Cache-Control:", "no-cache, no-store, must-revalidate"); resp.setHeader("Pragma:", "no-cache"); resp.setHeader("Expires:", "0"); resp.setHeader("Last-Modified:", WebUtils.rfc1123Date(new Date())); resp.setContentType(HtmlConsts.RESP_TYPE_CSV); resp.addHeader(HtmlConsts.CONTENT_DISPOSITION, "attachment; filename=\"UsersAndCapabilities.csv\""); resp.setStatus(HttpServletResponse.SC_OK); resp.getOutputStream().write(buffer.getBuffer().toString().getBytes(CharEncoding.UTF_8)); }