List of usage examples for org.apache.commons.cli Option Option
public Option(String opt, boolean hasArg, String description) throws IllegalArgumentException
From source file:com.genentech.struchk.OEMDLPercieveChecker.java
public static void main(String[] args) throws ParseException, JDOMException, IOException { // create command line Options object Options options = new Options(); Option opt = new Option("i", true, "input file [.ism,.sdf,...]"); opt.setRequired(true);//from www . ja va 2 s. c om options.addOption(opt); opt = new Option("o", true, "output file"); opt.setRequired(false); options.addOption(opt); opt = new Option("d", false, "debug: wait for user to press key at startup."); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } if (args.length != 0) { exitWithHelp(options); } String inFile = cmd.getOptionValue("i"); String outFile = cmd.getOptionValue("o"); OEMDLPercieveChecker checker = null; try { checker = new OEMDLPercieveChecker(); oemolostream out = new oemolostream(outFile); oemolistream in = new oemolistream(inFile); OEGraphMol mol = new OEGraphMol(); while (oechem.OEReadMolecule(in, mol)) { if (!checker.checkMol(mol)) oechem.OEWriteMolecule(out, mol); } checker.delete(); in.close(); in.delete(); out.close(); out.delete(); } catch (Exception e) { throw new Error(e); } System.err.println("Done:"); }
From source file:gr.forth.ics.isl.preprocessfilter2.controller.Controller.java
public static void main(String[] args) throws XPathExpressionException, ParserConfigurationException, SAXException, IOException, PreprocessFilterException, TransformerException, ParseException { PropertyReader prop = new PropertyReader(); //The following block of code is executed if there are arguments from the command line if (args.length > 0) { try {// w w w. j a va 2s . co m Options options = new Options(); CommandLineParser PARSER = new PosixParser(); Option inputFile = new Option("inputFile", true, "input xml file"); Option outputFile = new Option("outputFile", true, "output xml file"); Option parentNode = new Option("parentNode", true, "output xml file"); Option newValuesFile = new Option("newValuesFile", true, "new values xml file"); Option newParentNode = new Option("newParentNode", true, "new parent node"); Option newValueTag = new Option("newValueTag", true, "new value tag"); Option oldValueTag = new Option("oldValueTag", true, "old value tag"); Option sameValueTag = new Option("sameValueTag", true, "same value tag"); Option createNewValues = new Option("createNewValues", true, "create new values option"); options.addOption(inputFile).addOption(outputFile).addOption(parentNode).addOption(newValuesFile) .addOption(newParentNode).addOption(newValueTag).addOption(oldValueTag) .addOption(sameValueTag).addOption(createNewValues); CommandLine cli = PARSER.parse(options, args); String inputFileArg = cli.getOptionValue("inputFile"); String outputFileArg = cli.getOptionValue("outputFile"); String parentNodeArg = cli.getOptionValue("parentNode"); String newValuesFileArg = cli.getOptionValue("newValuesFile"); String newParentNodeArg = cli.getOptionValue("newParentNode"); String newValueTagArg = cli.getOptionValue("newValueTag"); String oldValueTagArg = cli.getOptionValue("oldValueTag"); String sameValueTagArg = cli.getOptionValue("sameValueTag"); String createNewValuesArg = cli.getOptionValue("createNewValues"); PreprocessFilterUtilities process = new PreprocessFilterUtilities(); if (createNewValuesArg.equals("yes")) { if (process.createNewValuesFile(inputFileArg, newValuesFileArg, parentNodeArg)) { System.out.println("Succesfull PreProcessing!!!"); } } else { if (process.createOutputFile(inputFileArg, outputFileArg, parentNodeArg, newParentNodeArg, newValueTagArg, oldValueTagArg, sameValueTagArg, newValuesFileArg)) { System.out.println("Succesfull PreProcessing!!!"); } } } catch (PreprocessFilterException ex) { Logger.getLogger(Controller.class.getName()).log(Level.SEVERE, null, ex); throw new PreprocessFilterException("PreProcess Filter Exception:", ex); } } //If there are no command line arguments then the .config file is being used. else { try { String inputFilePathProp = prop.getProperty(inputFilePath); String outputFilePathProp = prop.getProperty(outputFilePath); String parentNodeProp = prop.getProperty(parentNode); String newValuesFilePathProp = prop.getProperty(newValuesFilePath); String newParentNodeProp = prop.getProperty(newParentNode); String newValueTagProp = prop.getProperty(newValueTag); String oldValueTagProp = prop.getProperty(oldValueTag); String sameValueTagProp = prop.getProperty(sameValueTag); String createNewValuesFileProp = prop.getProperty(createNewValuesFile); PreprocessFilterUtilities process = new PreprocessFilterUtilities(); //The filter's code is executed with the .config file's resources as parameters if (createNewValuesFileProp.equals("yes")) { process.createNewValuesFile(inputFilePathProp, newValuesFilePathProp, parentNodeProp); } else { process.createOutputFile(inputFilePathProp, outputFilePathProp, parentNodeProp, newParentNodeProp, newValueTagProp, oldValueTagProp, sameValueTagProp, newValuesFilePathProp); } } catch (PreprocessFilterException ex) { Logger.getLogger(Controller.class.getName()).log(Level.SEVERE, null, ex); throw new PreprocessFilterException("PreProcess Filter Exception:", ex); } } }
From source file:com.yahoo.pasc.paxos.server.PaxosServer.java
/** * @param args/*from ww w . j a v a 2s.c om*/ * @throws NoSuchFieldException * @throws SecurityException * @throws IOException * @throws MalformedURLException */ public static void main(String[] args) throws SecurityException, NoSuchFieldException, IOException { CommandLineParser parser = new PosixParser(); Options options; { Option id = new Option("i", true, "client id"); Option port = new Option("p", true, "port used by server"); Option buffer = new Option("b", true, "number of batched messages"); // Option clients = new Option("c", true, "clients (hostname:port,...)"); Option servers = new Option("s", true, "servers (hostname:port,...)"); Option maxInstances = new Option("m", true, "max number of instances"); Option anm = new Option("a", false, "protection against ANM faults"); Option udp = new Option("u", false, "use UDP"); Option cWindow = new Option("w", true, "congestion window"); Option threads = new Option("t", true, "number of threads"); Option digests = new Option("d", true, "max digests"); Option ckPeriod = new Option("k", true, "checkpointing period"); Option inlineThresh = new Option("n", true, "threshold for sending requests iNline with accepts "); Option twoStages = new Option("2", false, "2 stages"); Option digestQuorum = new Option("q", true, "digest quorum"); Option leaderReplies = new Option("r", false, "leader replies"); Option zookeeper = new Option("z", true, "zookeeper connection string"); options = new Options(); options.addOption(id).addOption(port).addOption(buffer).addOption(servers).addOption(threads) .addOption(anm).addOption(udp).addOption(maxInstances) //.addOption(leader) .addOption(cWindow).addOption(digests).addOption(ckPeriod).addOption(inlineThresh) .addOption(twoStages).addOption(digestQuorum).addOption(leaderReplies).addOption(zookeeper); } CommandLine line = null; try { line = parser.parse(options, args); String serverAddresses[] = line.hasOption('s') ? line.getOptionValue('s').split(",") : new String[] { "10.78.36.104:20548", "10.78.36.104:20748" }; // String clientAddresses[] = line.hasOption('c') ? line.getOptionValue('c').split(",") : new String[] { "localhost:9000" }; String zookeeper = line.hasOption('z') ? line.getOptionValue('z') : "localhost:2181"; int serverId = line.hasOption('i') ? Integer.parseInt(line.getOptionValue('i')) : 0; int batchSize = line.hasOption('b') ? Integer.parseInt(line.getOptionValue('b')) : 1; int port = line.hasOption('p') ? Integer.parseInt(line.getOptionValue('p')) : 20548; int maxInstances = line.hasOption('m') ? Integer.parseInt(line.getOptionValue('m')) : 16 * 1024; int congestionWindow = line.hasOption('w') ? Integer.parseInt(line.getOptionValue('w')) : 1; int digests = line.hasOption('d') ? Integer.parseInt(line.getOptionValue('d')) : 16; int inlineThreshold = line.hasOption('n') ? Integer.parseInt(line.getOptionValue('n')) : 1000; boolean protection = line.hasOption('a'); boolean udp = line.hasOption('u'); boolean twoStages = line.hasOption('2'); int quorum = serverAddresses.length / 2 + 1; int digestQuorum = line.hasOption('q') ? Integer.parseInt(line.getOptionValue('q')) : quorum; int threads = line.hasOption('t') ? Integer.parseInt(line.getOptionValue('t')) : Runtime.getRuntime().availableProcessors() * 2 + 1; if (batchSize <= 0) { throw new RuntimeException("BatchSize must be greater than 0"); } PaxosState state = new PaxosState(maxInstances, batchSize, serverId, quorum, digestQuorum, serverAddresses.length, congestionWindow, digests); if (line.hasOption('k')) state.setCheckpointPeriod(Integer.parseInt(line.getOptionValue('k'))); if (line.hasOption('r')) state.setLeaderReplies(true); state.setRequestThreshold(inlineThreshold); if (!protection) { System.out.println("PANM disabled!"); } final PascRuntime<PaxosState> runtime = new PascRuntime<PaxosState>(protection); runtime.setState(state); runtime.addHandler(Accept.class, new AcceptorAccept()); runtime.addHandler(Prepare.class, new AcceptorPrepare()); runtime.addHandler(Accepted.class, new Learner()); runtime.addHandler(Prepared.class, new ProposerPrepared()); runtime.addHandler(Request.class, new ProposerRequest()); runtime.addHandler(InlineRequest.class, new ProposerRequest()); runtime.addHandler(Digest.class, new DigestHandler()); runtime.addHandler(PreReply.class, new LearnerPreReply()); runtime.addHandler(Leader.class, new LeadershipHandler()); if (udp) { new UdpServer(runtime, serverAddresses, null, port, threads, serverId).run(); } else { new TcpServer(runtime, new EmptyStateMachine(), null, zookeeper, serverAddresses, port, threads, serverId, twoStages).run(); } } catch (Exception e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Paxos", options); System.err.println("Unexpected exception: " + e); e.printStackTrace(); System.exit(-1); } }
From source file:edu.ehu.galan.lite.Lite.java
/** * Main entry point for LiTe from the command Line use -h option for help * * @param args//from www . java 2 s. c o m */ public static void main(String[] args) { // create Options object Options options = new Options(); Option corpus = new Option("c", true, "the location (directory) of the corpus to process, containing only one document at the moment"); Option language = new Option("l", true, "the language of the corpus (lowercase ISO format, for example 'en'"); Option algorithms = new Option("a", true, "the algorithms you want to process separated by commas: \n" + "see the documentation for see the available algorithms for each language"); Option help = new Option("h", false, "print this message"); Option resources = new Option("r", true, "the location of the lite resources folder"); Option output = new Option("o", true, "The directory where the results will be stored, by default the one where the vm has been launched"); Option listAlgs = new Option("listAlgs", false, " Algorithm list names with the supported languages (remember that the cvalue will be processed chosen or not):\n" + "===================================================\n" + "tfidf => processes the TFIDF algorithm, process terms of the input document using the Wikipedia corpus as IDF (en,es)\n" + "cvalue => processes the CValue altorithm for the inputdocument, CValue is processed whether is chosed or not! (en, es)\n" + "shallow => processes the shallow parsing grammar algorithm (en)\n" + "rake => processes the rake algorithm (language agnostig)\n" + "kpminer => processes the KPMiner algorithm (en)\n" + "chisquare => processes the ChiSquare using the NLTK toolkit (language agnostic)\n" + "pmi=> processes the Point Mutual Information using the NLTK toolkit (language agnostic)\n" + "likehood=> processes the Likehood Ratio using the NLTK toolkit (language agnostic)\n" + "tstudent=> processes the T-Student using the NLTK toolkit (language agnostic)\n" + "rawfreq=> processes the raw frequency algorithm using the NLTK toolkit (language agnostic)\n" + "freelingner=> processes the FreeLing ner algorithm via external call(es, en)\n"); options.addOption(resources); options.addOption(corpus); options.addOption(language); options.addOption(algorithms); options.addOption(listAlgs); options.addOption(output); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); String[] s = new String[] {}; // create the parser CommandLineParser parser = new org.apache.commons.cli.GnuParser(); try { // parse the command line arguments CommandLine line = parser.parse(options, args); if (line.hasOption('c') && line.hasOption('l') && line.hasOption('a') && line.hasOption('r')) { if (!line.getOptionValue('l').equals("en") && !line.getOptionValue("l").equals("es")) { System.out.println( "Supported languages \"en\" or \"es\", however you may use the statistical algorithms via the API"); } else { String outputDir = ""; if (line.hasOption('o')) { outputDir = line.getOptionValue('o'); } String lang = line.getOptionValue('l'); Corpus cor = new Corpus(line.getOptionValue('l')); cor.loadCorpus(line.getOptionValue('c'), Document.SourceType.wikipedia); String res = line.getOptionValue('r'); List<String> algs = Arrays.asList(line.getOptionValue('a').split(",")); System.out.println("Processing.... (it may take a while...)"); runner(lang, res + File.separator, algs, cor, outputDir); } } if (line.hasOption('c') && line.hasOption('l') && line.hasOption('r')) { if (!line.getOptionValue('l').equals("en") && !line.getOptionValue("l").equals("es")) { System.out.println( "Supported languages \"en\" or \"es\", however you may use the statistical algorithms via the API"); } else { String outputDir = ""; if (line.hasOption('o')) { outputDir = line.getOptionValue('o'); } System.out.println( "Processing with default algorithms (TFIDF/CValue).... (it may take a while...)"); Corpus cor = new Corpus(line.getOptionValue('l')); String res = line.getOptionValue('r'); cor.loadCorpus(line.getOptionValue('c'), Document.SourceType.wikipedia); String lang = line.getOptionValue('l'); List<String> algos = null; switch (lang) { case "es": { String[] algs = { "cvalue", "tfidf", "rake" }; algos = Arrays.asList(algs); break; } case "en": { String[] algs = { "cvalue", "tfidf", "rake" }; algos = Arrays.asList(algs); break; } } runner(lang, res + File.separator, algos, cor, outputDir); } } else if (line.hasOption("h")) { formatter.printHelp("LiTe: a language indepent term extractor", options); } else if (line.getOptions().length == 0) { formatter.printHelp("LiTe: a language indepent term extractor", options); } else { System.err.println("The 'c', 'l' and 'r' arguments are required \n"); formatter.printHelp("LiTe: a language indepent term extractor", options); } } catch (ParseException exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage() + "\n"); formatter.printHelp("LiTe: a language indepent term extractor", options); } }
From source file:com.genentech.chemistry.openEye.apps.SDFConformerSampler.java
/** * @param args//from ww w. ja v a 2 s . c o m */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_MAX_CONFS, true, "Maximum number of conformations per input."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_TORSION_FILE, true, "Optional: to overwrite torsion definition file."); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); String smartsFile = cmd.getOptionValue(OPT_TORSION_FILE); long maxConfs = Long.parseLong(cmd.getOptionValue(OPT_MAX_CONFS)); SDFConformerSampler scanner = new SDFConformerSampler(smartsFile, outFile, maxConfs); scanner.run(inFile); scanner.close(); }
From source file:com.genentech.chemistry.openEye.apps.SDFRingSystemExtractor.java
/** * @param args/*from w ww . j av a 2 s. c o m*/ */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported"); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported"); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); SDFRingSystemExtractor extractor = new SDFRingSystemExtractor(outFile); extractor.run(inFile); extractor.close(); }
From source file:com.genentech.chemistry.openEye.apps.SDFMolSeparator.java
/** * @param args//w w w . ja v a 2 s .c o m */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); SDFMolSeparator separator = new SDFMolSeparator(outFile); try { separator.run(inFile); } catch (IndexOutOfBoundsException iie) { System.err.println(iie.toString()); exitWithHelp(options); } finally { separator.close(); } }
From source file:cross.io.PropertyFileGenerator.java
/** * * @param args//from w w w . j a v a 2 s . co m */ public static void main(String[] args) { Options options = new Options(); options.addOption("f", true, "base directory for output of files"); Option provOptions = new Option("p", true, "Comma separated list of provider classes to create Properties for"); provOptions.setRequired(true); provOptions.setValueSeparator(','); options.addOption(provOptions); CommandLineParser parser = new PosixParser(); HelpFormatter hf = new HelpFormatter(); try { File basedir = null; List<String> providers = Collections.emptyList(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("f")) { basedir = new File(cmd.getOptionValue("f")); } else { hf.printHelp("java -cp maltcms.jar " + PropertyFileGenerator.class, options); } if (cmd.hasOption("p")) { String[] str = cmd.getOptionValues("p"); providers = Arrays.asList(str); } else { hf.printHelp("java -cp maltcms.jar " + PropertyFileGenerator.class, options); } for (String provider : providers) { createProperties(provider, basedir); } } catch (ParseException ex) { Logger.getLogger(PropertyFileGenerator.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:it.unipd.dei.ims.falcon.CmdLine.java
public static void main(String[] args) { // last argument is always index path Options options = new Options(); // one of these actions has to be specified OptionGroup actionGroup = new OptionGroup(); actionGroup.addOption(new Option("i", true, "perform indexing")); // if dir, all files, else only one file actionGroup.addOption(new Option("q", true, "perform a single query")); actionGroup.addOption(new Option("b", false, "perform a query batch (read from stdin)")); actionGroup.setRequired(true);/*from w ww . java 2 s. c om*/ options.addOptionGroup(actionGroup); // other options options.addOption(new Option("l", "segment-length", true, "length of a segment (# of chroma vectors)")); options.addOption( new Option("o", "segment-overlap", true, "overlap portion of a segment (# of chroma vectors)")); options.addOption(new Option("Q", "quantization-level", true, "quantization level for chroma vectors")); options.addOption(new Option("k", "min-kurtosis", true, "minimum kurtosis for indexing chroma vectors")); options.addOption(new Option("s", "sub-sampling", true, "sub-sampling of chroma features")); options.addOption(new Option("v", "verbose", false, "verbose output (including timing info)")); options.addOption(new Option("T", "transposition-estimator-strategy", true, "parametrization for the transposition estimator strategy")); options.addOption(new Option("t", "n-transp", true, "number of transposition; if not specified, no transposition is performed")); options.addOption(new Option("f", "force-transp", true, "force transposition by an amount of semitones")); options.addOption(new Option("p", "pruning", false, "enable query pruning; if -P is unspecified, use default strategy")); options.addOption(new Option("P", "pruning-custom", true, "custom query pruning strategy")); // parse HelpFormatter formatter = new HelpFormatter(); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); if (cmd.getArgs().length != 1) throw new ParseException("no index path was specified"); } catch (ParseException ex) { System.err.println("ERROR - parsing command line:"); System.err.println(ex.getMessage()); formatter.printHelp("falcon -{i,q,b} [options] index_path", options); return; } // default values final float[] DEFAULT_TRANSPOSITION_ESTIMATOR_STRATEGY = new float[] { 0.65192807f, 0.0f, 0.0f, 0.0f, 0.3532628f, 0.4997167f, 0.0f, 0.41703504f, 0.0f, 0.16297342f, 0.0f, 0.0f }; final String DEFAULT_QUERY_PRUNING_STRATEGY = "ntf:0.340765*[0.001694,0.995720];ndf:0.344143*[0.007224,0.997113];" + "ncf:0.338766*[0.001601,0.995038];nmf:0.331577*[0.002352,0.997884];"; // TODO not the final one int hashes_per_segment = Integer.parseInt(cmd.getOptionValue("l", "150")); int overlap_per_segment = Integer.parseInt(cmd.getOptionValue("o", "50")); int nranks = Integer.parseInt(cmd.getOptionValue("Q", "3")); int subsampling = Integer.parseInt(cmd.getOptionValue("s", "1")); double minkurtosis = Float.parseFloat(cmd.getOptionValue("k", "-100.")); boolean verbose = cmd.hasOption("v"); int ntransp = Integer.parseInt(cmd.getOptionValue("t", "1")); TranspositionEstimator tpe = null; if (cmd.hasOption("t")) { if (cmd.hasOption("T")) { // TODO this if branch is yet to test Pattern p = Pattern.compile("\\d\\.\\d*"); LinkedList<Double> tokens = new LinkedList<Double>(); Matcher m = p.matcher(cmd.getOptionValue("T")); while (m.find()) tokens.addLast(new Double(cmd.getOptionValue("T").substring(m.start(), m.end()))); float[] strategy = new float[tokens.size()]; if (strategy.length != 12) { System.err.println("invalid transposition estimator strategy"); System.exit(1); } for (int i = 0; i < strategy.length; i++) strategy[i] = new Float(tokens.pollFirst()); } else { tpe = new TranspositionEstimator(DEFAULT_TRANSPOSITION_ESTIMATOR_STRATEGY); } } else if (cmd.hasOption("f")) { int[] transps = parseIntArray(cmd.getOptionValue("f")); tpe = new ForcedTranspositionEstimator(transps); ntransp = transps.length; } QueryPruningStrategy qpe = null; if (cmd.hasOption("p")) { if (cmd.hasOption("P")) { qpe = new StaticQueryPruningStrategy(cmd.getOptionValue("P")); } else { qpe = new StaticQueryPruningStrategy(DEFAULT_QUERY_PRUNING_STRATEGY); } } // action if (cmd.hasOption("i")) { try { Indexing.index(new File(cmd.getOptionValue("i")), new File(cmd.getArgs()[0]), hashes_per_segment, overlap_per_segment, subsampling, nranks, minkurtosis, tpe, verbose); } catch (IndexingException ex) { Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException ex) { Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex); } } if (cmd.hasOption("q")) { String queryfilepath = cmd.getOptionValue("q"); doQuery(cmd, queryfilepath, hashes_per_segment, overlap_per_segment, nranks, subsampling, tpe, ntransp, minkurtosis, qpe, verbose); } if (cmd.hasOption("b")) { try { long starttime = System.currentTimeMillis(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String line = null; while ((line = in.readLine()) != null && !line.trim().isEmpty()) doQuery(cmd, line, hashes_per_segment, overlap_per_segment, nranks, subsampling, tpe, ntransp, minkurtosis, qpe, verbose); in.close(); long endtime = System.currentTimeMillis(); System.out.println(String.format("total time: %ds", (endtime - starttime) / 1000)); } catch (IOException ex) { Logger.getLogger(CmdLine.class.getName()).log(Level.SEVERE, null, ex); } } }
From source file:com.genentech.chemistry.openEye.apps.SDFALogP.java
/** * @param args//from ww w. j ava2s . co m */ public static void main(String... args) throws IOException { // create command line Options object Options options = new Options(); Option opt = new Option(OPT_INFILE, true, "input file oe-supported Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type."); opt.setRequired(true); options.addOption(opt); opt = new Option(OPT_SMARTS_FILE, true, "Optional: to overwrite atom type definition file."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_PRINT_COUNTS, false, "If set the count of each atom type is added to the output file."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_VALIDATE_ASSIGNMENT, false, "Print warning if no atomtype matches an atom in a candidte molecule."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_SUPRESS_ZERO, false, "If given atom type counts with count=0 will not be added."); opt.setRequired(false); options.addOption(opt); opt = new Option(OPT_NEUTRALIZE, true, "y|n to neutralize molecule if possible (default=y)"); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } String inFile = cmd.getOptionValue(OPT_INFILE); String outFile = cmd.getOptionValue(OPT_OUTFILE); String smartsFile = cmd.getOptionValue(OPT_SMARTS_FILE); boolean outputCount = cmd.hasOption(OPT_PRINT_COUNTS); boolean outputZero = !cmd.hasOption(OPT_SUPRESS_ZERO); boolean neutralize = !"n".equalsIgnoreCase(cmd.getOptionValue(OPT_NEUTRALIZE)); boolean ValidateAssignment = cmd.hasOption(OPT_VALIDATE_ASSIGNMENT); SDFALogP sdfALogP = new SDFALogP(smartsFile, outFile, outputZero, neutralize, ValidateAssignment); sdfALogP.run(inFile, outputCount); sdfALogP.close(); }