List of usage examples for java.lang Long decode
public static Long decode(String nm) throws NumberFormatException
From source file:org.jboss.dashboard.ui.config.components.sections.SectionCopyFormatter.java
public void service(HttpServletRequest request, HttpServletResponse response) throws FormatterException { try {// ww w . j av a 2 s . com WorkspaceImpl workspace = (WorkspaceImpl) getSectionsPropertiesHandler().getWorkspace(); setAttribute("sectionTitle", getLocalizedValue(workspace .getSection(Long.decode(getSectionsPropertiesHandler().getSelectedSectionId())).getTitle())); renderFragment("outputStart"); WorkspacePermission sectionPerm = WorkspacePermission.newInstance(workspace, WorkspacePermission.ACTION_CREATE_PAGE); if (UserStatus.lookup().hasPermission(sectionPerm)) { Panel[] panels = workspace .getSection(Long.decode(getSectionsPropertiesHandler().getSelectedSectionId())) .getAllPanels(); TreeSet panelInstances = new TreeSet(); for (int i = 0; i < panels.length; i++) { Panel panel = panels[i]; panelInstances.add(panel.getInstanceId()); } if (!panelInstances.isEmpty()) { setAttribute("sectionTitle", LocaleManager.lookup().localize(workspace .getSection(Long.decode(getSectionsPropertiesHandler().getSelectedSectionId())) .getTitle())); renderFragment("outputMode"); renderFragment("outputHeaders"); Iterator it = panelInstances.iterator(); int counter = 0; while (it.hasNext()) { String instanceId = it.next().toString(); PanelInstance instance = workspace.getPanelInstance(instanceId); setAttribute("instanceId", instanceId); setAttribute("group", instance.getResource(instance.getProvider().getGroup(), getLocale())); setAttribute("description", instance.getResource(instance.getProvider().getDescription(), getLocale())); setAttribute("title", getLocalizedValue(instance.getTitle())); setAttribute("counter", counter); counter++; renderFragment("outputOpt"); } renderFragment("outputOptEnd"); renderFragment("outputHeadersEnd"); } else { renderFragment("outputEmpty"); getSectionsPropertiesHandler().setDuplicateSection(Boolean.FALSE); } } renderFragment("outputEnd"); } catch (Exception e) { log.error("Error rendering section copy form: ", e); } }
From source file:org.patientview.patientview.news.NewsPreviewAction.java
public ActionForward execute(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { ActionForward actionForward;/*w ww . j a va 2 s . c o m*/ String unitcode = BeanUtils.getProperty(form, "unitcode"); boolean patient = "true".equals(BeanUtils.getProperty(form, "patient")); boolean admin = "true".equals(BeanUtils.getProperty(form, "admin")); boolean everyone = "true".equals(BeanUtils.getProperty(form, "everyone")); String headline = BeanUtils.getProperty(form, "headline"); String body = BeanUtils.getProperty(form, "body"); News news = new News(unitcode, admin, patient, everyone, headline, body); String id = BeanUtils.getProperty(form, "id"); if (!"".equals(id)) { news.setId(Long.decode(id)); } if ("Preview".equals(BeanUtils.getProperty(form, "submission"))) { request.setAttribute("news", news); actionForward = mapping.findForward("preview"); } else { LegacySpringUtils.getNewsManager().save(news); NewsUtils.putAppropriateNewsForEditInRequest(request); actionForward = mapping.findForward("add"); } return actionForward; }
From source file:org.jboss.dashboard.ui.components.ResourcesHandler.java
public CommandResponse actionDownload(CommandRequest request) throws Exception { final String dbid = request.getParameter("dbid"); final GraphicElement[] element = new GraphicElement[] { null }; if (dbid != null) { new HibernateTxFragment() { protected void txFragment(Session session) throws Exception { element[0] = (GraphicElement) session.get(GraphicElement.class, Long.decode(dbid)); }//from w w w . j a v a 2 s .c om }.execute(); if (element[0] != null) { return new SendStreamResponse(new ByteArrayInputStream(element[0].getZipFile()), "inline; filename=" + URLEncoder.encode(element[0].getId()) + ".zip;"); } } return null; }
From source file:org.patientview.patientview.aboutme.AboutmeUpdate.java
public ActionForward execute(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { User user = UserUtils.retrieveUser(request); String id = BeanUtils.getProperty(form, "id"); String aboutme = BeanUtils.getProperty(form, "aboutme"); String talkabout = BeanUtils.getProperty(form, "talkabout"); String nhsno = BeanUtils.getProperty(form, "nhsno"); Aboutme aboutMe = null;/* w w w . ja v a2s . c o m*/ if (id == null || "".equals(id)) { UserMapping userMapping = UserUtils.retrieveUserMappingsPatientEntered(user); nhsno = userMapping.getNhsno(); aboutMe = new Aboutme(nhsno, aboutme, talkabout); } else { Long idLong = Long.decode(id); aboutMe = new Aboutme(idLong, nhsno, aboutme, talkabout); } LegacySpringUtils.getAboutmeManager().save(aboutMe); request.setAttribute("user", user); request.setAttribute("aboutme", aboutMe); return LogonUtils.logonChecks(mapping, request, "success"); }
From source file:net.openhft.chronicle.queue.ChronicleReaderMain.java
private static void configureReader(final ChronicleReader chronicleReader, final CommandLine commandLine) { if (commandLine.hasOption('i')) { stream(commandLine.getOptionValues('i')).forEach(chronicleReader::withInclusionRegex); }// w w w .j av a 2s . com if (commandLine.hasOption('e')) { stream(commandLine.getOptionValues('e')).forEach(chronicleReader::withExclusionRegex); } if (commandLine.hasOption('f')) { chronicleReader.tail(); } if (commandLine.hasOption('m')) { chronicleReader.historyRecords(Long.parseLong(commandLine.getOptionValue('m'))); } if (commandLine.hasOption('n')) { chronicleReader.withStartIndex(Long.decode(commandLine.getOptionValue('n'))); } if (commandLine.hasOption('r')) { chronicleReader.asMethodReader(); } if (commandLine.hasOption('w')) { chronicleReader.withWireType(WireType.valueOf(commandLine.getOptionValue('w'))); } if (commandLine.hasOption('s')) { chronicleReader.suppressDisplayIndex(); } }
From source file:UUID.java
/** * DOCUMENT ME!/* w w w . j av a 2 s .c o m*/ * * @param s DOCUMENT ME! * * @return DOCUMENT ME! */ public static UUID fromString(String s) { String[] as = s.split("-"); if (as.length != 5) { throw new IllegalArgumentException( (new StringBuffer()).append("Invalid UUID string: ").append(s).toString()); } for (int i = 0; i < 5; i++) as[i] = (new StringBuffer()).append("0x").append(as[i]).toString(); long l = Long.decode(as[0]).longValue(); l <<= 16; l |= Long.decode(as[1]).longValue(); l <<= 16; l |= Long.decode(as[2]).longValue(); long l1 = Long.decode(as[3]).longValue(); l1 <<= 48; l1 |= Long.decode(as[4]).longValue(); return new UUID(l, l1); }
From source file:com.milaboratory.mitcr.cli.Main.java
public static void main(String[] args) { int o = 0;// www. j a v a 2s . com BuildInformation buildInformation = BuildInformationProvider.get(); final boolean isProduction = "default".equals(buildInformation.scmBranch); // buildInformation.version != null && buildInformation.version.lastIndexOf("SNAPSHOT") < 0; orderingMap.put(PARAMETERS_SET_OPTION, o++); orderingMap.put(SPECIES_OPTION, o++); orderingMap.put(GENE_OPTION, o++); orderingMap.put(ERROR_CORECTION_LEVEL_OPTION, o++); orderingMap.put(QUALITY_THRESHOLD_OPTION, o++); orderingMap.put(AVERAGE_QUALITY_OPTION, o++); orderingMap.put(LQ_OPTION, o++); orderingMap.put(CLUSTERIZATION_OPTION, o++); orderingMap.put(INCLUDE_CYS_PHE_OPTION, o++); orderingMap.put(LIMIT_OPTION, o++); orderingMap.put(EXPORT_OPTION, o++); orderingMap.put(REPORT_OPTION, o++); orderingMap.put(REPORTING_LEVEL_OPTION, o++); orderingMap.put(PHRED33_OPTION, o++); orderingMap.put(PHRED64_OPTION, o++); orderingMap.put(THREADS_OPTION, o++); orderingMap.put(COMPRESSED_OPTION, o++); orderingMap.put(PRINT_HELP_OPTION, o++); orderingMap.put(PRINT_VERSION_OPTION, o++); orderingMap.put(PRINT_DEBUG_OPTION, o++); options.addOption(OptionBuilder.withArgName("preset name").hasArg() .withDescription("preset of pipeline parameters to use").create(PARAMETERS_SET_OPTION)); options.addOption(OptionBuilder.withArgName("species").hasArg() .withDescription("overrides species ['hs' for Homo sapiens, 'mm' for us Mus musculus] " + "(default for built-in presets is 'hs')") .create(SPECIES_OPTION)); options.addOption(OptionBuilder.withArgName("gene").hasArg() .withDescription("overrides gene: TRB or TRA (default value for built-in parameter sets is TRB)") .create(GENE_OPTION)); options.addOption(OptionBuilder.withArgName("0|1|2").hasArg() .withDescription( "overrides error correction level (0 = don't correct errors, 1 = correct sequenecing " + "errors only (see -" + QUALITY_THRESHOLD_OPTION + " and -" + LQ_OPTION + " options for details), " + "2 = also correct PCR errors (see -" + CLUSTERIZATION_OPTION + " option)") .create(ERROR_CORECTION_LEVEL_OPTION)); options.addOption(OptionBuilder.withArgName("value").hasArg().withDescription( "overrides quality threshold value for segment alignment and bad quality sequences " + "correction algorithms. 0 tells the program not to process quality information. (default is 25)") .create(QUALITY_THRESHOLD_OPTION)); if (!isProduction) options.addOption(OptionBuilder.hasArg(false) .withDescription("use this option to output average instead of " + "maximal, quality for CDR3 nucleotide sequences. (Experimental option, use with caution.)") .create(AVERAGE_QUALITY_OPTION)); options.addOption(OptionBuilder.withArgName("map | drop").hasArg() .withDescription("overrides low quality CDR3s processing strategy (drop = filter off, " + "map = map onto clonotypes created from the high quality CDR3s). This option makes no difference if " + "quality threshold (-" + QUALITY_THRESHOLD_OPTION + " option) is set to 0, or error correction " + "level (-" + ERROR_CORECTION_LEVEL_OPTION + ") is 0.") .create(LQ_OPTION)); options.addOption(OptionBuilder.withArgName("smd | ete").hasArg() .withDescription("overrides the PCR error correction algorithm: smd = \"save my diversity\", " + "ete = \"eliminate these errors\". Default value for built-in parameters is ete.") .create(CLUSTERIZATION_OPTION)); options.addOption(OptionBuilder.withArgName("0|1").hasArg() .withDescription("overrides weather include bounding Cys & Phe into CDR3 sequence") .create(INCLUDE_CYS_PHE_OPTION)); options.addOption( OptionBuilder.withArgName("# of reads").hasArg() .withDescription("limits the number of input sequencing reads, use this parameter to " + "normalize several datasets or to have a glance at the data") .create(LIMIT_OPTION)); options.addOption(OptionBuilder.withArgName("new name").hasArg() .withDescription("use this option to export presets to a local xml files").create(EXPORT_OPTION)); options.addOption(OptionBuilder.withArgName("file name").hasArg() .withDescription("use this option to write analysis report (summary) to file") .create(REPORT_OPTION)); options.addOption(OptionBuilder.withArgName("1|2|3").hasArg(true) .withDescription("output detalization level (1 = simple, 2 = medium, 3 = full, this format " + "could be deserialized using mitcr API). Affects only tab-delimited output. Default value is 3.") .create(REPORTING_LEVEL_OPTION)); options.addOption(OptionBuilder.hasArg(false).withDescription( "add this option if input file is in old illumina format with 64 byte offset for quality " + "string (MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)") .create(PHRED64_OPTION)); options.addOption(OptionBuilder.hasArg(false) .withDescription("add this option if input file is in Phred+33 format for quality values " + "(MiTCR will try to automatically detect file format if one of the \"-phredXX\" options is not provided)") .create(PHRED33_OPTION)); options.addOption(OptionBuilder.withArgName("threads").hasArg() .withDescription( "specifies the number of CDR3 extraction threads (default = number of available CPU cores)") .create(THREADS_OPTION)); if (!isProduction) options.addOption(OptionBuilder.hasArg(false) .withDescription("use compressed data structures for storing individual " + "clone segments statistics (from which arises the clone segment information). This option reduces required " + "amount of memory, but introduces small stochastic errors into the algorithm which determines clone " + "segments. (Experimental option, use with caution.)") .create(COMPRESSED_OPTION)); options.addOption( OptionBuilder.hasArg(false).withDescription("print this message").create(PRINT_HELP_OPTION)); options.addOption(OptionBuilder.hasArg(false).withDescription("print version information") .create(PRINT_VERSION_OPTION)); options.addOption(OptionBuilder.hasArg(false) .withDescription("print additional information about analysis process").create(PRINT_DEBUG_OPTION)); PosixParser parser = new PosixParser(); try { long input_limit = -1; int threads = Runtime.getRuntime().availableProcessors(); int reporting_level = 3; int ec_level = 2; CommandLine cl = parser.parse(options, args, true); if (cl.hasOption(PRINT_HELP_OPTION)) { printHelp(); return; } boolean averageQuality = cl.hasOption(AVERAGE_QUALITY_OPTION), compressedAggregators = cl.hasOption(COMPRESSED_OPTION); if (cl.hasOption(PRINT_VERSION_OPTION)) { System.out.println("MiTCR by MiLaboratory, version: " + buildInformation.version); System.out.println("Branch: " + buildInformation.scmBranch); System.out.println("Built: " + buildInformation.buildDate + ", " + buildInformation.jdk + " JDK, " + "build machine: " + buildInformation.builtBy); System.out.println("SCM changeset: " + buildInformation.scmChangeset + " (" + buildInformation.scmDate.replace("\"", "") + ")"); return; } //Normal execution String paramName = cl.getOptionValue(PARAMETERS_SET_OPTION); if (paramName == null) { err.println("No parameters set is specified."); return; } Parameters params = ParametersIO.getParameters(paramName); if (params == null) { err.println("No parameters set found with name '" + paramName + "'."); return; } String value; if ((value = cl.getOptionValue(THREADS_OPTION)) != null) threads = Integer.decode(value); if ((value = cl.getOptionValue(REPORTING_LEVEL_OPTION)) != null) reporting_level = Integer.decode(value); if ((value = cl.getOptionValue(LIMIT_OPTION)) != null) input_limit = Long.decode(value); if ((value = cl.getOptionValue(GENE_OPTION)) != null) params.setGene(Gene.fromXML(value)); if ((value = cl.getOptionValue(SPECIES_OPTION)) != null) params.setSpecies(Species.getFromShortName(value)); if ((value = cl.getOptionValue(INCLUDE_CYS_PHE_OPTION)) != null) { if (value.equals("1")) params.getCDR3ExtractorParameters().setIncludeCysPhe(true); else if (value.equals("0")) params.getCDR3ExtractorParameters().setIncludeCysPhe(false); else { err.println("Illegal value for -" + INCLUDE_CYS_PHE_OPTION + " parameter."); return; } } if ((value = cl.getOptionValue(ERROR_CORECTION_LEVEL_OPTION)) != null) { int v = Integer.decode(value); ec_level = v; if (v == 0) { params.setCloneGeneratorParameters(new BasicCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.None); } else if (v == 1) { params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.None); } else if (v == 2) { params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters()); params.setClusterizationType(CloneClusterizationType.OneMismatch, .1f); } else throw new RuntimeException("This (" + v + ") error correction level is not supported."); } if ((value = cl.getOptionValue(QUALITY_THRESHOLD_OPTION)) != null) { int v = Integer.decode(value); if (v == 0) params.setQualityInterpretationStrategy(new DummyQualityInterpretationStrategy()); else params.setQualityInterpretationStrategy(new IlluminaQualityInterpretationStrategy((byte) v)); } if ((value = cl.getOptionValue(LQ_OPTION)) != null) if (ec_level > 0) switch (value) { case "map": params.setCloneGeneratorParameters(new LQMappingCloneGeneratorParameters( ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .getSegmentInformationAggregationFactor(), 3, true)); break; case "drop": params.setCloneGeneratorParameters(new LQFilteringOffCloneGeneratorParameters( ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .getSegmentInformationAggregationFactor())); break; default: throw new RuntimeException("Wrong value for -" + LQ_OPTION + " option."); } if ((value = cl.getOptionValue(CLUSTERIZATION_OPTION)) != null) if (ec_level > 1) // == 2 switch (value) { case "smd": params.setClusterizationType(CloneClusterizationType.V2D1J2T3Explicit); break; case "ete": params.setClusterizationType(CloneClusterizationType.OneMismatch); break; default: throw new RuntimeException("Wrong value for -" + CLUSTERIZATION_OPTION + " option."); } ((BasicCloneGeneratorParameters) params.getCloneGeneratorParameters()) .setAccumulatorType(AccumulatorType.get(compressedAggregators, averageQuality)); if ((value = cl.getOptionValue(EXPORT_OPTION)) != null) { //Exporting parameters ParametersIO.exportParameters(params, value); return; } String[] offArgs = cl.getArgs(); if (offArgs.length == 0) { err.println("Input file not specified."); return; } else if (offArgs.length == 1) { err.println("Output file not specified."); return; } else if (offArgs.length > 2) { err.println("Unrecognized argument."); return; } String inputFileName = offArgs[0]; String outputFileName = offArgs[1]; File input = new File(inputFileName); if (!input.exists()) { err.println("Input file not found."); return; } //TODO This also done inside SFastqReader constructor CompressionType compressionType = CompressionType.None; if (inputFileName.endsWith(".gz")) compressionType = CompressionType.GZIP; QualityFormat format = null; // If variable remains null file format will be detected automatically if (cl.hasOption(PHRED33_OPTION)) format = QualityFormat.Phred33; if (cl.hasOption(PHRED64_OPTION)) if (format == null) format = QualityFormat.Phred64; else { err.println( "Options: -" + PHRED33_OPTION + " and -" + PHRED64_OPTION + " are mutually exclusive"); return; } SFastqReader reads = format == null ? new SFastqReader(input, compressionType) : new SFastqReader(input, format, compressionType); OutputPort<SSequencingRead> inputToPipeline = reads; if (input_limit >= 0) inputToPipeline = new CountLimitingOutputPort<>(inputToPipeline, input_limit); SegmentLibrary library = DefaultSegmentLibrary.load(); AnalysisStatisticsAggregator statisticsAggregator = new AnalysisStatisticsAggregator(); FullPipeline pipeline = new FullPipeline(inputToPipeline, params, false, library); pipeline.setThreads(threads); pipeline.setAnalysisListener(statisticsAggregator); new Thread(new SmartProgressReporter(pipeline, err)).start(); // Printing status to the standard error stream pipeline.run(); if (cl.hasOption(PRINT_DEBUG_OPTION)) { err.println("Memory = " + (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())); err.println("Clusterization: " + pipeline.getQC().getReadsClusterized() + "% of reads, " + pipeline.getQC().getClonesClusterized() + " % clones"); } CloneSetClustered cloneSet = pipeline.getResult(); if ((value = cl.getOptionValue(REPORT_OPTION)) != null) { File file = new File(value); TablePrintStreamAdapter table; if (file.exists()) table = new TablePrintStreamAdapter(new FileOutputStream(file, true)); else { table = new TablePrintStreamAdapter(file); ReportExporter.printHeader(table); } //CloneSetQualityControl qc = new CloneSetQualityControl(library, params.getSpecies(), params.getGene(), cloneSet); ReportExporter.printRow(table, inputFileName, outputFileName, pipeline.getQC(), statisticsAggregator); table.close(); } if (outputFileName.endsWith(".cls")) ClsExporter.export(pipeline, outputFileName.replace(".cls", "") + " " + new Date().toString(), input.getName(), outputFileName); else { //Dry run if (outputFileName.startsWith("-")) return; ExportDetalizationLevel detalization = ExportDetalizationLevel.fromLevel(reporting_level); CompressionType compressionType1 = CompressionType.None; if (outputFileName.endsWith(".gz")) compressionType1 = CompressionType.GZIP; CloneSetIO.exportCloneSet(outputFileName, cloneSet, detalization, params, input.getAbsolutePath(), compressionType1); } } catch (ParseException | RuntimeException | IOException e) { err.println("Error occurred in the analysis pipeline."); err.println(); e.printStackTrace(); //printHelp(); } }
From source file:org.opendaylight.groupbasedpolicy.neutron.ovsdb.util.InventoryHelper.java
/** * Convert an OpenFlow Datapath ID to a Long * * @param dpid The OpenFlow Datapath ID//from ww w .j a v a 2 s . c om * @return The Long representation of the DPID */ public static Long getLongFromDpid(String dpid) { String[] addressInBytes = dpid.split(":"); Long address = (Long.decode(HEX + addressInBytes[2]) << 40) | (Long.decode(HEX + addressInBytes[3]) << 32) | (Long.decode(HEX + addressInBytes[4]) << 24) | (Long.decode(HEX + addressInBytes[5]) << 16) | (Long.decode(HEX + addressInBytes[6]) << 8) | (Long.decode(HEX + addressInBytes[7])); return address; }
From source file:org.jboss.dashboard.ui.formatters.RenderNestedSectionsFormatter.java
public void service(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws FormatterException { List visibleIds = (List) getParameter("visibleIds"); List checkedIds = (List) getParameter("checkedIds"); List selectableIds = (List) getParameter("selectableIds"); String workspaceId = (String) getParameter("workspaceId"); String rootSectionId = (String) getParameter("rootSectionId"); boolean showHiddenPages = (!(getParameter("showHiddenPages") != null && !"".equals(getParameter("showHiddenPages")))) || Boolean.valueOf((String) getParameter("showHiddenPages")).booleanValue(); Boolean checkPermissions = Boolean.valueOf((String) getParameter("checkPermissions")); try {//from w ww . j av a 2s.c o m WorkspaceImpl currentWorkspace = (WorkspaceImpl) (workspaceId != null && !"".equals(workspaceId) ? UIServices.lookup().getWorkspacesManager().getWorkspace(workspaceId) : NavigationManager.lookup().getCurrentWorkspace()); Section[] rootSections; if (StringUtils.isEmpty(rootSectionId)) { rootSections = currentWorkspace.getAllRootSections(); } else { Section parentSection = currentWorkspace.getSection(Long.decode(rootSectionId)); List<Section> children = parentSection.getChildren(); rootSections = children.toArray(new Section[children.size()]); } renderFragment("outputStart"); for (Section rootSection : rootSections) { renderSection(httpServletRequest, httpServletResponse, rootSection, visibleIds, checkedIds, selectableIds, Boolean.TRUE.equals(checkPermissions), showHiddenPages); } renderFragment("outputEnd"); } catch (Exception e) { log.error("Error rendering sections: ", e); } }
From source file:pl.nask.hsn2.normalizers.URLNormalizerUtils.java
public static String numToIPv4(StringBuilder sb, int start, int endInd) { int end = findFirstMatch(sb, ":/?", start, endInd); if (end < 0) { end = endInd;/*from w w w . j a va 2 s . co m*/ } long ip; try { ip = Long.decode(sb.substring(start, end)); if (ip <= 0xffffff) { //disallow 0.x.x.x format return null; } } catch (NumberFormatException e) { return null; } StringBuilder tmp = new StringBuilder(); for (int i = 0; i < 3; i++) { tmp.insert(0, ip & 0xff); tmp.insert(0, '.'); ip = ip >> 8; } tmp.insert(0, ip & 0xff); sb.replace(start, end, tmp.toString()); return tmp.toString(); }