List of usage examples for org.apache.commons.cli OptionBuilder hasArg
public static OptionBuilder hasArg(boolean hasArg)
hasArg is true. From source file:com.milaboratory.mitcr.cli.Main.java
public static void main(String[] args) { int o = 0;//from w w w . j av a2s . c o m 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:edu.vt.cs.cnd2xsd.Cnd2XsdConverter.java
/** * Usage: Cnd2Xsd [path to source cnd] [path to write the xsd] * @param args/*from w ww .j ava 2 s. c o m*/ * @throws LoginException * @throws RepositoryException * @throws IOException * @throws JAXBException */ @SuppressWarnings("static-access") public static void main(String[] args) throws LoginException, RepositoryException, IOException, JAXBException, org.apache.commons.cli.ParseException { Session session = null; Cnd2XsdConverter converter = new Cnd2XsdConverter(); try { Options opt = new Options(); opt.addOption(OptionBuilder.hasArg(true).isRequired(false) .withDescription("Path for the input cnd file").create("fc")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false).withDescription("Path for properties map.") .create("fp")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false) .withDescription("Path for generating XML schema.").create("fx")); opt.addOption(OptionBuilder.hasArg(false).isRequired(false).withDescription("Prints this list.") .create("help")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false).withDescription("The namespace for the XSD.") .create("ns")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false).withDescription("The namespace prefix.") .create("nsp")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false) .withDescription("The root element in the XSD.").create("r")); opt.addOption(OptionBuilder.hasArg(true).isRequired(false).withDescription("The root element type.") .create("rtype")); //create the basic parser BasicParser parser = new BasicParser(); CommandLine cl = parser.parse(opt, args); HelpFormatter f = new HelpFormatter(); //check if we have any leftover args if (cl.getArgs().length != 0 || args.length == 0) { f.printHelp(MAINCLI, opt); return; } if (cl.hasOption("help")) { f.printHelp(MAINCLI, opt); return; } String cndFilePath = cl.getOptionValue("fc"); String xsdFilePath = cl.getOptionValue("fx"); String propmapPath = cl.getOptionValue("fp"); String ns = cl.getOptionValue("ns"); String nsPrefix = cl.getOptionValue("nsp"); String rt = cl.getOptionValue("r"); String rtype = cl.getOptionValue("rtype"); converter.init(cndFilePath, propmapPath, ns, nsPrefix, rt, rtype); FileOutputStream fout = new FileOutputStream(xsdFilePath); converter.convert(fout); } finally { if (session != null) { session.save(); session.logout(); } } }
From source file:ctrus.pa.bow.en.EnBOWOptions.java
@Override @SuppressWarnings("static-access") public void defineOptions() { super.defineDefaultOptions(); Option o1 = OptionBuilder.hasArg(false).withDescription("Split camel cased terms").create(SPLIT_CAMELCASE); addOption(o1);//from w ww . j av a 2 s. com }
From source file:gov.nasa.jpl.mudrod.ontology.process.LocalOntology.java
public static void main(String[] args) throws Exception { // boolean options Option helpOpt = new Option("h", "help", false, "show this help message"); // argument options Option ontDirOpt = OptionBuilder.hasArg(true).withArgName(ONT_DIR) .withDescription("A directory containing .owl files.").isRequired(false).create(); // create the options Options options = new Options(); options.addOption(helpOpt);//from ww w. ja v a 2 s . co m options.addOption(ontDirOpt); String ontDir; CommandLineParser parser = new GnuParser(); try { CommandLine line = parser.parse(options, args); if (line.hasOption(ONT_DIR)) { ontDir = line.getOptionValue(ONT_DIR).replace("\\", "/"); } else { ontDir = LocalOntology.class.getClassLoader().getResource("ontology").getFile(); } if (!ontDir.endsWith("/")) { ontDir += "/"; } } catch (Exception e) { LOG.error("Error whilst processing main method of LocalOntology.", e); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("LocalOntology: 'ontDir' argument is mandatory. ", options, true); return; } File fileDir = new File(ontDir); //Fail if the input is not a directory. if (fileDir.isDirectory()) { List<String> owlFiles = new ArrayList<>(); for (File owlFile : fileDir.listFiles()) { owlFiles.add(owlFile.toString()); } MudrodEngine mEngine = new MudrodEngine(); Properties props = mEngine.loadConfig(); Ontology ontology = new OntologyFactory(props).getOntology(); //convert to correct iput for ontology loading. String[] owlArray = new String[owlFiles.size()]; owlArray = owlFiles.toArray(owlArray); ontology.load(owlArray); String[] terms = new String[] { "Glacier ice" }; //Demonstrate that we can do basic ontology heirarchy navigation and log output. for (Iterator<OntClass> i = getParser().rootClasses(getModel()); i.hasNext();) { //print Ontology Class Hierarchy OntClass c = i.next(); renderHierarchy(System.out, c, new LinkedList<>(), 0); for (Iterator<OntClass> subClass = c.listSubClasses(true); subClass.hasNext();) { OntClass sub = subClass.next(); //This means that the search term is present as an OntClass if (terms[0].equalsIgnoreCase(sub.getLabel(null))) { //Add the search term(s) above to the term cache. for (int j = 0; j < terms.length; j++) { addSearchTerm(terms[j], sub); } //Query the ontology and return subclasses of the search term(s) for (int k = 0; k < terms.length; k++) { Iterator<String> iter = ontology.subclasses(terms[k]); while (iter.hasNext()) { LOG.info("Subclasses >> " + iter.next()); } } //print any synonymic relationships to demonstrate that we can //undertake synonym-based query expansion for (int l = 0; l < terms.length; l++) { Iterator<String> iter = ontology.synonyms(terms[l]); while (iter.hasNext()) { LOG.info("Synonym >> " + iter.next()); } } } } } mEngine.end(); } }
From source file:gov.nasa.jpl.mudrod.main.MudrodEngine.java
/** * Main program invocation. Accepts one argument denoting location (on disk) * to a log file which is to be ingested. Help will be provided if invoked * with incorrect parameters.// ww w . j a v a2 s. c o m * * @param args * {@link java.lang.String} array contaning correct parameters. */ public static void main(String[] args) { // boolean options Option helpOpt = new Option("h", "help", false, "show this help message"); // log ingest (preprocessing + processing) Option logIngestOpt = new Option("l", LOG_INGEST, false, "begin log ingest"); // metadata ingest (preprocessing + processing) Option metaIngestOpt = new Option("m", META_INGEST, false, "begin metadata ingest"); // ingest both log and metadata Option fullIngestOpt = new Option("f", FULL_INGEST, false, "begin full ingest Mudrod workflow"); // processing only, assuming that preprocessing results is in dataDir Option processingOpt = new Option("p", PROCESSING, false, "begin processing with preprocessing results"); // argument options Option dataDirOpt = OptionBuilder.hasArg(true).withArgName("/path/to/data/directory").hasArgs(1) .withDescription("the data directory to be processed by Mudrod").withLongOpt("dataDirectory") .isRequired().create(DATA_DIR); Option esHostOpt = OptionBuilder.hasArg(true).withArgName("host_name").hasArgs(1) .withDescription("elasticsearch cluster unicast host").withLongOpt("elasticSearchHost") .isRequired(false).create(ES_HOST); Option esTCPPortOpt = OptionBuilder.hasArg(true).withArgName("port_num").hasArgs(1) .withDescription("elasticsearch transport TCP port").withLongOpt("elasticSearchTransportTCPPort") .isRequired(false).create(ES_TCP_PORT); Option esPortOpt = OptionBuilder.hasArg(true).withArgName("port_num").hasArgs(1) .withDescription("elasticsearch HTTP/REST port").withLongOpt("elasticSearchHTTPPort") .isRequired(false).create(ES_HTTP_PORT); // create the options Options options = new Options(); options.addOption(helpOpt); options.addOption(logIngestOpt); options.addOption(metaIngestOpt); options.addOption(fullIngestOpt); options.addOption(processingOpt); options.addOption(dataDirOpt); options.addOption(esHostOpt); options.addOption(esTCPPortOpt); options.addOption(esPortOpt); CommandLineParser parser = new GnuParser(); try { CommandLine line = parser.parse(options, args); String processingType = null; if (line.hasOption(LOG_INGEST)) { processingType = LOG_INGEST; } else if (line.hasOption(PROCESSING)) { processingType = PROCESSING; } else if (line.hasOption(META_INGEST)) { processingType = META_INGEST; } else if (line.hasOption(FULL_INGEST)) { processingType = FULL_INGEST; } String dataDir = line.getOptionValue(DATA_DIR).replace("\\", "/"); if (!dataDir.endsWith("/")) { dataDir += "/"; } MudrodEngine me = new MudrodEngine(); me.loadConfig(); me.props.put(DATA_DIR, dataDir); if (line.hasOption(ES_HOST)) { String esHost = line.getOptionValue(ES_HOST); me.props.put(MudrodConstants.ES_UNICAST_HOSTS, esHost); } if (line.hasOption(ES_TCP_PORT)) { String esTcpPort = line.getOptionValue(ES_TCP_PORT); me.props.put(MudrodConstants.ES_TRANSPORT_TCP_PORT, esTcpPort); } if (line.hasOption(ES_HTTP_PORT)) { String esHttpPort = line.getOptionValue(ES_HTTP_PORT); me.props.put(MudrodConstants.ES_HTTP_PORT, esHttpPort); } me.es = new ESDriver(me.getConfig()); me.spark = new SparkDriver(me.getConfig()); loadFullConfig(me, dataDir); if (processingType != null) { switch (processingType) { case PROCESSING: me.startProcessing(); break; case LOG_INGEST: me.startLogIngest(); break; case META_INGEST: me.startMetaIngest(); break; case FULL_INGEST: me.startFullIngest(); break; default: break; } } me.end(); } catch (Exception e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp( "MudrodEngine: 'dataDir' argument is mandatory. " + "User must also provide an ingest method.", options, true); LOG.error("Error whilst parsing command line.", e); } }
From source file:ctrus.pa.bow.java.JavaBOWOptions.java
@SuppressWarnings("static-access") @Override// ww w . j a va 2s.co m public void defineOptions() { super.defineDefaultOptions(); Option o1 = OptionBuilder.hasArg(false).withDescription("Split camel cased terms").create(SPLIT_CAMELCASE); addOption(o1); Option o3 = OptionBuilder.hasArg(false) .withDescription("Consider terms from copyright notice in source files").create(CONSIDER_COPYRIGHT); addOption(o3); Option o4 = OptionBuilder.hasArg(false).withDescription("Ignore comments in source files") .create(IGNORE_COMMENTS); addOption(o4); Option o6 = OptionBuilder.hasArg(false).withDescription("Create BOW model per method, default is per class") .create(METHOD_CHUNKING); addOption(o6); /* Option o7 = OptionBuilder.hasArg(false) .withDescription("Retain compound terms (eg.camel cased) in the model") .create(RETAIN_COMPOUND_WORDS); addOption(o7); */ Option o8 = OptionBuilder.hasArg(false).withDescription("Create BOW model for state analysis") .create(STATE_ANALYSIS); addOption(o8); Option o9 = OptionBuilder.hasArg(false) .withDescription("Create multiple Bag of Words based on Java code structure") .create(STRUCTURE_MULTI_BOW); addOption(o9); }
From source file:net.nicholaswilliams.java.licensing.licensor.interfaces.cli.spi.CliOptionsBuilder.java
public CliOptionsBuilder hasArg(boolean hasArg) { OptionBuilder.hasArg(hasArg); return this; }
From source file:edu.uga.cs.fluxbuster.FluxbusterCLI.java
@SuppressWarnings("static-access") private static Options initializeOptions() { Options retval = new Options(); retval.addOption(OptionBuilder.isRequired(false).withDescription("Print help message.").withLongOpt("help") .create("?")) .addOption(OptionBuilder.hasArg(false).isRequired(false) .withDescription("Generate clusters. (Optional)").withLongOpt("generate-clusters") .create("g")) .addOption(OptionBuilder.hasArg(false).isRequired(false) .withDescription("Calculate cluster features. (Optional)").withLongOpt("calc-features") .create("f")) .addOption(OptionBuilder.hasArg(false).isRequired(false) .withDescription("Calculate cluster similarities. (Optional)") .withLongOpt("calc-similarity").create("s")) .addOption(OptionBuilder.hasArg(false).isRequired(false) .withDescription("Classify clusters. (Optional)").withLongOpt("classify-clusters") .create("c")) .addOption(OptionBuilder.hasArg().isRequired(true) .withDescription("The start date of the input data. " + "Should be in yyyyMMdd format.") .withLongOpt("start-date").create("d")) .addOption(OptionBuilder.hasArg().isRequired(true) .withDescription("The end date of the input data. " + "Should be in yyyyMMdd format.") .withLongOpt("end-date").create("e")); return retval; }
From source file:carmen.utils.Utils.java
public static void registerOption(List<Option> options, String option_name, String arg_name, boolean has_arg, String description) {//ww w . ja v a 2s . c o m OptionBuilder.withArgName(arg_name); OptionBuilder.hasArg(has_arg); OptionBuilder.withDescription(description); Option option = OptionBuilder.create(option_name); options.add(option); }
From source file:ctrus.pa.bow.DefaultOptions.java
@SuppressWarnings("static-access") public void defineDefaultOptions() { Option o1 = OptionBuilder.hasArg(false).withDescription("Use weights for words").create(USE_WEIGHT); addOption(o1);//from w w w .ja va2 s . c om Option o2 = OptionBuilder.hasArg(false).withDescription("Stem the words extracted").create(USE_STEMMING); addOption(o2); Option o3 = OptionBuilder.hasArg(false).withDescription("Retain the capital characters in the term") .create(CASE_SENSITIVE); addOption(o3); Option o4 = OptionBuilder.hasArg(false).withDescription("Retain the numerals").create(RETAIN_NUMERAL); addOption(o4); Option o5 = OptionBuilder.hasArg(true).withDescription("Minimum word length to consider, default is 3") .create(MIN_WORD_LENGTH); addOption(o5); Option o6 = OptionBuilder.hasArg(true).withDescription("Stemming algorithm to use").create(STEMMING_ALGO); addOption(o6); Option o7 = OptionBuilder.hasArg(true).withDescription("Directory containing input documents").isRequired() .create(SOURCE_DIR); addOption(o7); Option o8 = OptionBuilder.hasArg(true) .withDescription("Output single file with each line corresponding to an input source file") .create(OUTPUT_SINGLE_FILE); addOption(o8); Option o9 = OptionBuilder.hasArg(true).withDescription("Stop words file").create(STOP_WORDS_FILE); addOption(o9); Option o10 = OptionBuilder.hasArg(true).withDescription("Directory to write output").isRequired() .create(OUTPUT_DIR); addOption(o10); Option o11 = OptionBuilder.hasArg(true).withDescription("Replace jargon words with full words") .create(REPLACE_JARGONS); addOption(o11); Option o12 = OptionBuilder.hasArg(true).withDescription("Chunk characters eg. ;,_:") .create(TERM_CHUNK_CHARS); addOption(o12); Option o13 = OptionBuilder.hasArg(false).withDescription("Output debug log").create(DEBUG_LOG); addOption(o13); Option o14 = OptionBuilder.hasArg(false).withDescription("Print this help").create(PRINT_HELP); addOption(o14); Option o15 = OptionBuilder.hasArg(false).withDescription("Print the vocabulary to a file 'voc.txt'") .create(PRINT_VOCABULARY); addOption(o15); Option o16 = OptionBuilder.hasArg(true).withDescription("Hash the term if its length exceeds <arg>") .create(HASH_TERMS); addOption(o16); Option o17 = OptionBuilder.hasArg(true).withDescription("Special characters to ignore eg. _$") .create(IGNORE_SPECIAL_CHARS); addOption(o17); Option o18 = OptionBuilder.hasArg(false).withDescription("Each line is a document in the input file(s)") .create(DOCUMENT_PER_LINE); addOption(o18); Option o19 = OptionBuilder.hasArg(false).withDescription("Do not stem the terms").create(NO_STEMMING); addOption(o19); Option o20 = OptionBuilder.hasArg(true) .withDescription("Term left to delimiter is considered document Id, default is space") .create(DOCUMENT_ID_DELIMITER); addOption(o20); Option o21 = OptionBuilder.hasArg(false).withDescription("Retain the document ids from input") .create(PRESERVE_DOC_ID); addOption(o21); }