Example usage for org.apache.commons.cli HelpFormatter HelpFormatter

List of usage examples for org.apache.commons.cli HelpFormatter HelpFormatter

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HelpFormatter

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From source file:com.linkedin.restli.tools.idlgen.RestLiResourceModelExporterCmdLineApp.java

/**
 * @param args restliexporter -sourcepath sourcepath -resourcepackages packagenames [-name api_name] [-outdir outdir]
 *//*from w w w  .  java2s. com*/
public static void main(String[] args) {
    //    args = new String[] {"-name", "groups",
    //                         "-resourcepackages", "com.linkedin.groups.server.rest1.impl com.linkedin.groups.server.rest2.impl ",
    //                         "-resourceclasses", "com.linkedin.groups.server.restX.impl.FooResource",
    //                         "-sourcepath", "src/main/java",
    //                         "-outdir", "src/codegen/idl",
    //                         "-split"};

    CommandLine cl = null;
    try {
        final CommandLineParser parser = new GnuParser();
        cl = parser.parse(OPTIONS, args);
    } catch (ParseException e) {
        System.err.println("Invalid arguments: " + e.getMessage());
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(
                "restliexporter -sourcepath sourcepath [-resourcepackages packagenames] [-resourceclasses classnames]"
                        + "[-name api_name] [-outdir outdir]",
                OPTIONS);
        System.exit(0);
    }

    try {
        new RestLiResourceModelExporter().export(cl.getOptionValue("name"), null,
                cl.getOptionValues("sourcepath"), cl.getOptionValues("resourcepackages"),
                cl.getOptionValues("resourceclasses"), cl.getOptionValue("outdir", "."),
                AdditionalDocProvidersUtil.findDocProviders(log, cl.hasOption("loadAdditionalDocProviders")));
    } catch (Throwable e) {
        log.error("Error writing IDL files", e);
        System.exit(1);
    }
}

From source file:de.huberlin.cuneiform.main.Main.java

public static void main(String[] args)
        throws ParseException, IOException, NotDerivableException, InterruptedException, JSONException {

    GnuParser gnuParser;/*from w w  w.  j  a v  a 2 s.c o m*/
    CommandLine cmdline;
    Options opt;
    String value;
    int platform;
    File outputDir;
    String[] fileList;
    StringBuffer buf;
    String line;
    String dagid;
    File logFile;

    opt = new Options();

    opt.addOption("p", "platform", true, "The platform to perform the Cuneiform script's interpretation. "
            + "Possible platforms are: 'dot', 'local', and 'debug'. Default is 'local'.");

    opt.addOption("d", "directory", true,
            "The output directory, to put the interpretation intermediate and output result as well as the default location to store the log.");

    opt.addOption("c", "clean", false,
            "If set, the execution engine ignores all cached results and starts a clean workflow run.");

    opt.addOption("r", "runid", true,
            "If set, a custom id is set for this workflow run. By default a UUID string is used.");

    opt.addOption("f", "file", true,
            "Override the default location of the log file and use the specified filename instead. If the platform is 'dot', this option sets the name of the output dot-file.");

    opt.addOption("h", "help", false, "Print help text.");

    gnuParser = new GnuParser();
    cmdline = gnuParser.parse(opt, args);

    if (cmdline.hasOption("help")) {

        System.out.println("CUNEIFORM - A Functional Workflow Language\n" + LABEL_VERSION);
        new HelpFormatter().printHelp("java -jar cuneiform.jar [OPTION]*", opt);

        return;
    }

    if (cmdline.hasOption("platform")) {

        value = cmdline.getOptionValue("platform");

        if (value.equals("dot"))
            platform = PLATFORM_DOT;
        else if (value.equals("local"))
            platform = PLATFORM_LOCAL;
        else if (value.equals("debug"))
            platform = PLATFORM_DEBUG;
        else
            throw new RuntimeException("Specified platform '" + value + "' not recognized.");

    } else
        platform = PLATFORM_LOCAL;

    if (cmdline.hasOption('d')) {

        value = cmdline.getOptionValue('d');
    } else
        value = "build";

    outputDir = new File(value);

    if (outputDir.exists()) {

        if (!outputDir.isDirectory())
            throw new IOException(
                    "Output directory '" + outputDir.getAbsolutePath() + "' exists but is not a directory.");

        else if (cmdline.hasOption('c')) {

            FileUtils.deleteDirectory(outputDir);

            if (!outputDir.mkdirs())
                throw new IOException(
                        "Could not create output directory '" + outputDir.getAbsolutePath() + "'");
        }
    } else if (!outputDir.mkdirs())
        throw new IOException("Could not create output directory '" + outputDir.getAbsolutePath() + "'");

    if (cmdline.hasOption('r'))
        dagid = cmdline.getOptionValue('r');
    else
        dagid = UUID.randomUUID().toString();

    if (cmdline.hasOption('f'))
        logFile = new File(cmdline.getOptionValue('f'));
    else
        logFile = null;

    fileList = cmdline.getArgs();
    buf = new StringBuffer();
    if (fileList.length == 0) {

        try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) {

            while ((line = reader.readLine()) != null)
                buf.append(line).append('\n');
        }

        switch (platform) {

        case PLATFORM_DOT:
            createDot(buf.toString(), outputDir, logFile);
            break;
        case PLATFORM_LOCAL:
            runLocal(buf.toString(), outputDir, logFile, dagid);
            break;
        case PLATFORM_DEBUG:
            runDebug(buf.toString(), outputDir, logFile, dagid);
            break;
        default:
            throw new RuntimeException("Platform not recognized.");
        }
    } else

        switch (platform) {

        case PLATFORM_DOT:
            createDot(fileList, outputDir, logFile);
            break;
        case PLATFORM_LOCAL:
            runLocal(fileList, outputDir, logFile, dagid);
            break;
        case PLATFORM_DEBUG:
            runDebug(fileList, outputDir, logFile, dagid);
            break;
        default:
            throw new RuntimeException("Platform not recognized.");
        }

}

From source file:com.blackducksoftware.integration.hubdiff.HubDiff.java

public static void main(String[] args) throws IOException, IllegalArgumentException, EncryptionException,
        HubIntegrationException, JSONException {
    Options options = new Options();
    Option optUrl1 = new Option("h1", "hub-url-1", true,
            "the base url to the hub. Example: http://int-hub01.dc1.lan:8080");
    Option optUsername1 = new Option("u1", "username-1", true, "the username for your hub instance");
    Option optPassword1 = new Option("p1", "password-1", true,
            "the password for your hub instance and username");
    Option optUrl2 = new Option("h2", "hub-url-2", true,
            "the base url to the hub. Example: http://int-auto.dc1.lan:9000");
    Option optUsername2 = new Option("u2", "username-2", true, "the username for your hub instance");
    Option optPassword2 = new Option("p2", "password-2", true,
            "the password for your hub instance and username");
    Option optOutputFile = new Option("o", "output", true, "the file path to your output file");

    optUrl1.setRequired(true);/*  w  w  w  . j a v a 2s  .  c o m*/
    optUsername1.setRequired(true);
    optPassword1.setRequired(true);
    optUsername2.setRequired(true);
    optUrl1.setRequired(true);
    optPassword2.setRequired(true);
    optOutputFile.setRequired(false);

    // Add options to collection
    options.addOption(optUrl1);
    options.addOption(optUsername1);
    options.addOption(optPassword1);
    options.addOption(optUrl2);
    options.addOption(optUsername2);
    options.addOption(optPassword2);
    options.addOption(optOutputFile);

    // Parse the arguments array for the options
    CommandLineParser cliParser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine optionParser;
    try {
        optionParser = cliParser.parse(options, args);
    } catch (ParseException e) {
        formatter.printHelp("hub-model-generator", options);
        log.error(e.getMessage());
        System.exit(1);
        return;
    }

    // Read arguments
    String url1 = optionParser.getOptionValue("hub-url-1");
    String username1 = optionParser.getOptionValue("username-1");
    String password1 = optionParser.getOptionValue("password-1");
    String url2 = optionParser.getOptionValue("hub-url-2");
    String username2 = optionParser.getOptionValue("username-2");
    String password2 = optionParser.getOptionValue("password-2");
    String outputFilePath = optionParser.getOptionValue("output");

    HubServerConfigBuilder configBuilder = new HubServerConfigBuilder();
    configBuilder.setHubUrl(url1);
    configBuilder.setUsername(username1);
    configBuilder.setPassword(password1);
    HubServerConfig config1 = configBuilder.build();

    HubServerConfigBuilder configBuilder2 = new HubServerConfigBuilder();
    configBuilder2.setHubUrl(url2);
    configBuilder2.setUsername(username2);
    configBuilder2.setPassword(password2);
    HubServerConfig config2 = configBuilder2.build();

    HubDiff hubDiff = new HubDiff(config1, config2);
    hubDiff.printDiff(System.out);

    if (outputFilePath != null) {
        File outputFile = new File(outputFilePath);
        hubDiff.writeDiffAsCSV(outputFile);
    }
}

From source file:escada.tpc.common.clients.jmx.ClientEmulationStartup.java

public static void main(String args[]) {
    // create Options object
    Options options = new Options();
    // add clients option
    options.addOption("clients", true, "Number of clients concurrently accessing the database.");
    options.addOption("frag", true, "It shifts the clients in order to access different warehouses.");
    options.addOption("hostId", true, "Host identifier, allow to have statistics per host.");
    options.addOption("dbConnectionString", true, "Database JDBC url.");
    try {//from   w  w w. j  a  v  a2s  . co  m
        CommandLineParser parser = new PosixParser();
        CommandLine cmd = parser.parse(options, args);

        ClientEmulationStartup c = new ClientEmulationStartup();
        String clients = cmd.getOptionValue("clients");
        if (clients != null) {
            c.getWorkloadResources().setClients(new Integer(clients));
        }
        String frag = cmd.getOptionValue("frag");
        if (frag != null) {
            c.getWorkloadResources().setFrag(new Integer(frag));
        }
        String hostId = cmd.getOptionValue("hostId");
        if (hostId != null) {
            c.getWorkloadResources().setHostId(new Integer(hostId));
        }
        String dbConnectionString = cmd.getOptionValue("dbConnectionString");
        if (dbConnectionString != null) {
            c.getDatabaseResources().setConnectionString(dbConnectionString);
        }
        c.start(true);
    } catch (ParseException e) {
        System.err.println("Parsing failed.  Reason: " + e.getMessage());
        // automatically generate the help statement
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("ClientEmulationStartup", options);
    } catch (NumberFormatException e) {
        System.err.println("Parsing failed.  Reason: " + e.getMessage());
        // automatically generate the help statement
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("ClientEmulationStartup", options);
    } catch (Exception ex) {
        Thread.dumpStack();
        System.exit(-1);
    }
}

From source file:de.prozesskraft.pkraft.Waitinstance.java

public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException {

    /*----------------------------
      get options from ini-file/* w ww .  j  a  v  a2  s  . c  om*/
    ----------------------------*/
    java.io.File inifile = new java.io.File(WhereAmI.getInstallDirectoryAbsolutePath(Waitinstance.class) + "/"
            + "../etc/pkraft-waitinstance.ini");

    if (inifile.exists()) {
        try {
            ini = new Ini(inifile);
        } catch (InvalidFileFormatException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        } catch (IOException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
    } else {
        System.err.println("ini file does not exist: " + inifile.getAbsolutePath());
        System.exit(1);
    }

    /*----------------------------
      create boolean options
    ----------------------------*/
    Option ohelp = new Option("help", "print this message");
    Option ov = new Option("v", "prints version and build-date");

    /*----------------------------
      create argument options
    ----------------------------*/
    Option oinstance = OptionBuilder.withArgName("FILE").hasArg().withDescription(
            "[mandatory if no -scandir] instance file (process.pmb) that this program will wait till its status is 'error' or 'finished'")
            //            .isRequired()
            .create("instance");

    Option oscandir = OptionBuilder.withArgName("DIR").hasArg().withDescription(
            "[mandatory if no -instance] directory tree with instances (process.pmb). the first instance found will be tracked.")
            //            .isRequired()
            .create("scandir");

    Option omaxrun = OptionBuilder.withArgName("INTEGER").hasArg().withDescription(
            "[optional, default: 4320] time period (in minutes, default: 3 days) this program waits till it aborts further waiting.")
            //            .isRequired()
            .create("maxrun");

    /*----------------------------
      create options object
    ----------------------------*/
    Options options = new Options();

    options.addOption(ohelp);
    options.addOption(ov);
    options.addOption(oinstance);
    options.addOption(oscandir);
    options.addOption(omaxrun);

    /*----------------------------
      create the parser
    ----------------------------*/
    CommandLineParser parser = new GnuParser();
    // parse the command line arguments
    commandline = parser.parse(options, args);

    /*----------------------------
      usage/help
    ----------------------------*/
    if (commandline.hasOption("help")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("waitinstance", options);
        System.exit(0);
    }

    if (commandline.hasOption("v")) {
        System.out.println("author:  alexander.vogel@caegroup.de");
        System.out.println("version: [% version %]");
        System.out.println("date:    [% date %]");
        System.exit(0);
    }
    /*----------------------------
      ueberpruefen ob eine schlechte kombination von parametern angegeben wurde
    ----------------------------*/
    Integer maxrun = new Integer(4320);
    String pathInstance = null;
    String pathScandir = null;

    // instance & scandir
    if (!(commandline.hasOption("instance")) && !(commandline.hasOption("scandir"))) {
        System.err.println("one of the options -instance/-scandir is mandatory");
        exiter();
    } else if ((commandline.hasOption("instance")) && (commandline.hasOption("scandir"))) {
        System.err.println("both options -instance/-scandir are not allowed");
        exiter();
    } else if (commandline.hasOption("instance")) {
        pathInstance = commandline.getOptionValue("instance");
    } else if (commandline.hasOption("scandir")) {
        pathScandir = commandline.getOptionValue("scandir");
    }

    // maxrun
    if (commandline.hasOption("maxrun")) {
        maxrun = new Integer(commandline.getOptionValue("maxrun"));
    }
    /*----------------------------
      die lizenz ueberpruefen und ggf abbrechen
    ----------------------------*/

    // check for valid license
    ArrayList<String> allPortAtHost = new ArrayList<String>();
    allPortAtHost.add(ini.get("license-server", "license-server-1"));
    allPortAtHost.add(ini.get("license-server", "license-server-2"));
    allPortAtHost.add(ini.get("license-server", "license-server-3"));

    MyLicense lic = new MyLicense(allPortAtHost, "1", "user-edition", "0.1");

    // lizenz-logging ausgeben
    for (String actLine : (ArrayList<String>) lic.getLog()) {
        System.err.println(actLine);
    }

    // abbruch, wenn lizenz nicht valide
    if (!lic.isValid()) {
        System.exit(1);
    }

    /*----------------------------
      die eigentliche business logic
    ----------------------------*/

    // scannen nach dem ersten process.pmb 
    if ((pathScandir != null) && (pathInstance == null)) {
        String[] allBinariesOfScanDir = getProcessBinaries(pathScandir);

        if (allBinariesOfScanDir.length == 0) {
            System.err.println("no instance (process.pmb) found in directory tree " + pathScandir);
            exiter();
        } else {
            pathInstance = allBinariesOfScanDir[0];
            System.err.println("found instance: " + pathInstance);
        }
    }

    // ueberpruefen ob instance file existiert
    java.io.File fileInstance = new java.io.File(pathInstance);

    if (!fileInstance.exists()) {
        System.err.println("instance file does not exist: " + fileInstance.getAbsolutePath());
        exiter();
    }

    if (!fileInstance.isFile()) {
        System.err.println("instance file is not a file: " + fileInstance.getAbsolutePath());
        exiter();
    }

    // zeitpunkt wenn spaetestens beendet werden soll
    long runTill = System.currentTimeMillis() + (maxrun * 60 * 1000);

    // logging
    System.err.println("waiting for instance: " + fileInstance.getAbsolutePath());
    System.err.println("checking its status every 5 minutes");
    System.err.println("now is: " + new Timestamp(startInMillis).toString());
    System.err.println("maxrun till: " + new Timestamp(runTill).toString());

    // instanz einlesen
    Process p1 = new Process();
    p1.setInfilebinary(fileInstance.getAbsolutePath());
    Process p2 = p1.readBinary();

    // schleife, die prozess einliest und ueberprueft ob er noch laeuft
    while (!(p2.getStatus().equals("error") || p2.getStatus().equals("finished"))) {
        // logging
        System.err.println(new Timestamp(System.currentTimeMillis()) + " instance status: " + p2.getStatus());

        // 5 minuten schlafen: 300000 millis
        try {
            Thread.sleep(300000);
        } catch (InterruptedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

        // ist die maximale laufzeit von this erreicht, dann soll beendet werden (3 tage)
        if (System.currentTimeMillis() > runTill) {
            System.err
                    .println("exiting because of maxrun. now is: " + new Timestamp(System.currentTimeMillis()));
            System.exit(2);
        }

        // den prozess frisch einlesen
        p2 = p1.readBinary();
    }

    System.err.println("exiting because instance status is: " + p2.getStatus());
    System.err.println("now is: " + new Timestamp(System.currentTimeMillis()).toString());
    System.exit(0);

}

From source file:cc.wikitools.lucene.IndexWikipediaDump.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("bz2 Wikipedia XML dump file")
            .create(INPUT_OPTION));/*from   w ww  . java  2 s  . c  o m*/
    options.addOption(
            OptionBuilder.withArgName("dir").hasArg().withDescription("index location").create(INDEX_OPTION));
    options.addOption(OptionBuilder.withArgName("num").hasArg()
            .withDescription("maximum number of documents to index").create(MAX_OPTION));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of indexing threads")
            .create(THREADS_OPTION));

    options.addOption(new Option(OPTIMIZE_OPTION, "merge indexes into a single segment"));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }

    if (!cmdline.hasOption(INPUT_OPTION) || !cmdline.hasOption(INDEX_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(IndexWikipediaDump.class.getCanonicalName(), options);
        System.exit(-1);
    }

    String indexPath = cmdline.getOptionValue(INDEX_OPTION);
    int maxdocs = cmdline.hasOption(MAX_OPTION) ? Integer.parseInt(cmdline.getOptionValue(MAX_OPTION))
            : Integer.MAX_VALUE;
    int threads = cmdline.hasOption(THREADS_OPTION) ? Integer.parseInt(cmdline.getOptionValue(THREADS_OPTION))
            : DEFAULT_NUM_THREADS;

    long startTime = System.currentTimeMillis();

    String path = cmdline.getOptionValue(INPUT_OPTION);
    PrintStream out = new PrintStream(System.out, true, "UTF-8");
    WikiClean cleaner = new WikiCleanBuilder().withTitle(true).build();

    Directory dir = FSDirectory.open(new File(indexPath));
    IndexWriterConfig config = new IndexWriterConfig(Version.LUCENE_43, ANALYZER);
    config.setOpenMode(OpenMode.CREATE);

    IndexWriter writer = new IndexWriter(dir, config);
    LOG.info("Creating index at " + indexPath);
    LOG.info("Indexing with " + threads + " threads");

    try {
        WikipediaBz2DumpInputStream stream = new WikipediaBz2DumpInputStream(path);

        ExecutorService executor = Executors.newFixedThreadPool(threads);
        int cnt = 0;
        String page;
        while ((page = stream.readNext()) != null) {
            String title = cleaner.getTitle(page);

            // These are heuristic specifically for filtering out non-articles in enwiki-20120104.
            if (title.startsWith("Wikipedia:") || title.startsWith("Portal:") || title.startsWith("File:")) {
                continue;
            }

            if (page.contains("#REDIRECT") || page.contains("#redirect") || page.contains("#Redirect")) {
                continue;
            }

            Runnable worker = new AddDocumentRunnable(writer, cleaner, page);
            executor.execute(worker);

            cnt++;
            if (cnt % 10000 == 0) {
                LOG.info(cnt + " articles added");
            }
            if (cnt >= maxdocs) {
                break;
            }
        }

        executor.shutdown();
        // Wait until all threads are finish
        while (!executor.isTerminated()) {
        }

        LOG.info("Total of " + cnt + " articles indexed.");

        if (cmdline.hasOption(OPTIMIZE_OPTION)) {
            LOG.info("Merging segments...");
            writer.forceMerge(1);
            LOG.info("Done!");
        }

        LOG.info("Total elapsed time: " + (System.currentTimeMillis() - startTime) + "ms");
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        writer.close();
        dir.close();
        out.close();
    }
}

From source file:apps.classification.ClassifySVMPerf.java

public static void main(String[] args) throws IOException {

    boolean dumpConfidences = false;

    String cmdLineSyntax = ClassifySVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <modelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);/*from w ww .j  av a2s.  co  m*/
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmPerfClassifierCustomizer customizer = null;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        customizer = new SvmPerfClassifierCustomizer(remainingArgs[0]);

        if (line.hasOption("d"))
            dumpConfidences = true;

        if (line.hasOption("v"))
            customizer.printSvmPerfOutput(true);

        if (line.hasOption("s")) {
            customizer.setDeleteTestFiles(false);
            customizer.setDeletePredictionsFiles(false);
        }

        if (line.hasOption("t"))
            customizer.setTempPath(line.getOptionValue("t"));

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    if (remainingArgs.length != 3) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String testFile = remainingArgs[1];

    File file = new File(testFile);

    String testName = file.getName();
    String testPath = file.getParent();

    String classifierFile = remainingArgs[2];

    file = new File(classifierFile);

    String classifierName = file.getName();
    String classifierPath = file.getParent();
    FileSystemStorageManager storageManager = new FileSystemStorageManager(testPath, false);
    storageManager.open();
    IIndex test = TroveReadWriteHelper.readIndex(storageManager, testName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);
    storageManager.close();

    SvmPerfDataManager dataManager = new SvmPerfDataManager(customizer);
    storageManager = new FileSystemStorageManager(classifierPath, false);
    storageManager.open();
    SvmPerfClassifier classifier = (SvmPerfClassifier) dataManager.read(storageManager, classifierName);
    storageManager.close();

    classifier.setRuntimeCustomizer(customizer);

    // CLASSIFICATION
    String classificationName = testName + "_" + classifierName;

    Classifier classifierModule = new Classifier(test, classifier, dumpConfidences);
    classifierModule.setClassificationMode(ClassificationMode.PER_CATEGORY);
    classifierModule.exec();

    IClassificationDB testClassification = classifierModule.getClassificationDB();

    storageManager = new FileSystemStorageManager(testPath, false);
    storageManager.open();
    TroveReadWriteHelper.writeClassification(storageManager, testClassification, classificationName + ".cla",
            true);
    storageManager.close();

    if (dumpConfidences) {
        ClassificationScoreDB confidences = classifierModule.getConfidences();
        ClassificationScoreDB.write(testPath + Os.pathSeparator() + classificationName + ".confidences",
                confidences);
    }
}

From source file:ca.cutterslade.match.scheduler.Main.java

public static void main(final String[] args) throws InterruptedException {
    final CommandLineParser parser = new PosixParser();
    try {// w w w.  j  ava 2  s  .  c  o m
        final CommandLine line = parser.parse(OPTIONS, args);
        final int teams = Integer.parseInt(line.getOptionValue('t'));
        final int tiers = Integer.parseInt(line.getOptionValue('r'));
        final int gyms = Integer.parseInt(line.getOptionValue('g'));
        final int courts = Integer.parseInt(line.getOptionValue('c'));
        final int times = Integer.parseInt(line.getOptionValue('m'));
        final int days = Integer.parseInt(line.getOptionValue('d'));
        final int size = Integer.parseInt(line.getOptionValue('z'));
        final Configuration config;
        if (line.hasOption("random"))
            config = Configuration.RANDOM_CONFIGURATION;
        else
            config = new Configuration(ImmutableMap.<SadFaceFactor, Integer>of(),
                    line.hasOption("randomMatches"), line.hasOption("randomSlots"),
                    line.hasOption("randomDays"));
        final Scheduler s = new Scheduler(config, teams, tiers, gyms, courts, times, days, size);
        System.out.println(summary(s));
    } catch (final ParseException e) {
        final HelpFormatter f = new HelpFormatter();
        final PrintWriter pw = new PrintWriter(System.err);
        f.printHelp(pw, 80, "match-scheduler", null, OPTIONS, 2, 2, null, true);
        pw.println(
                "For example: match-scheduler -t 48 -r 3 -d 12 -m 2 -g 3 -c 2 -z 4 --randomMatches --randomSlots");
        pw.close();
    }
}

From source file:edu.msu.cme.rdp.kmer.KmerSearch.java

public static void main(String[] args) throws IOException {
    KmerTrie kmerTrie = null;/*from   w ww.ja  v a  2s  .  c om*/
    SeqReader queryReader = null;
    SequenceType querySeqType = SequenceType.Unknown;
    FastaWriter out = null;
    boolean exhaustive = true;
    boolean translQuery = false;
    int wordSize = -1;
    int translTable = 11;

    try {
        CommandLine cmdLine = new PosixParser().parse(options, args);
        args = cmdLine.getArgs();

        if (args.length != 3) {
            throw new Exception("Unexpected number of arguments");
        }

        if (cmdLine.hasOption("out")) {
            out = new FastaWriter(cmdLine.getOptionValue("out"));
        } else {
            out = new FastaWriter(System.out);
        }

        if (cmdLine.hasOption("correct")) {
            exhaustive = false;
        } else {
            exhaustive = true;
        }

        if (cmdLine.hasOption("transl-table")) {
            translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table"));
        }

        File trainingFile = new File(args[0]);
        wordSize = Integer.valueOf(args[1]);
        File queryFile = new File(args[2]);

        querySeqType = SeqUtils.guessSequenceType(queryFile);
        queryReader = new SequenceReader(new File(args[2]));

        kmerTrie = KmerTrie.buildTrie(new SequenceReader(trainingFile), wordSize);

        if (querySeqType == SequenceType.Protein && kmerTrie.getTreeSeqType() == SequenceType.Nucleotide) {
            throw new Exception("Trie is made of nucleotide sequences but the query sequences are protein");
        }

        if (querySeqType == SequenceType.Nucleotide && kmerTrie.getTreeSeqType() == SequenceType.Protein) {
            translQuery = true;
            System.err.println(
                    "Query sequences are nucleotide but trie is in protein space, query sequences will be translated");
        }

        if (querySeqType == SequenceType.Protein && exhaustive) {
            System.err.println("Cannot do an exaustive search with protein sequences, disabling");
            exhaustive = false;
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("KmerSearch <ref_file> <word_size> <query_file>", options);
        System.err.println(e.getMessage());
        System.exit(1);
    }

    long startTime = System.currentTimeMillis();
    long seqCount = 0, passedCount = 0;

    Sequence querySeq;

    while ((querySeq = queryReader.readNextSequence()) != null) {
        seqCount++;

        List<Sequence> testSequences;

        if (!exhaustive) {
            if (translQuery) {
                testSequences = Arrays.asList(new Sequence(querySeq.getSeqName(), "", ProteinUtils.getInstance()
                        .translateToProtein(querySeq.getSeqString(), true, translTable)));
            } else {
                testSequences = Arrays.asList(querySeq);
            }
        } else {
            if (translQuery) {
                testSequences = ProteinUtils.getInstance().allTranslate(querySeq);
            } else {
                testSequences = Arrays.asList(querySeq, new Sequence(querySeq.getSeqName(), "",
                        IUBUtilities.reverseComplement(querySeq.getSeqString())));
            }
        }

        boolean passed = false;
        for (Sequence seq : testSequences) {
            for (char[] kmer : KmerGenerator.getKmers(seq.getSeqString(), wordSize)) {
                if (kmerTrie.contains(kmer) != null) {
                    passed = true;
                    break;
                }
            }

            if (passed) {
                out.writeSeq(seq);
                passedCount++;
                break;
            }
        }
    }
    System.err.println("Processed: " + seqCount);
    System.err.println("Passed: " + passedCount);
    System.err.println("Failed: " + (seqCount - passedCount));
    System.err.println("Time: " + (System.currentTimeMillis() - startTime) + " ms");
}

From source file:de.topobyte.livecg.ShowVisualization.java

public static void main(String[] args) {
    EnumNameLookup<Visualization> visualizationSwitch = new EnumNameLookup<Visualization>(Visualization.class,
            true);//w  w w  .j  av  a 2s  . c  om

    // @formatter:off
    Options options = new Options();
    OptionHelper.add(options, OPTION_CONFIG, true, false, "path", "config file");
    OptionHelper.add(options, OPTION_VISUALIZATION, true, true, "type",
            "type of visualization. one of <" + VisualizationUtil.getListOfAvailableVisualizations() + ">");
    OptionHelper.add(options, OPTION_STATUS, true, false,
            "status to " + "set the algorithm to. The format depends on the algorithm");
    // @formatter:on

    Option propertyOption = new Option(OPTION_PROPERTIES, "set a special property");
    propertyOption.setArgName("property=value");
    propertyOption.setArgs(2);
    propertyOption.setValueSeparator('=');
    options.addOption(propertyOption);

    CommandLineParser clp = new GnuParser();

    CommandLine line = null;
    try {
        line = clp.parse(options, args);
    } catch (ParseException e) {
        System.err.println("Parsing command line failed: " + e.getMessage());
        new HelpFormatter().printHelp(HELP_MESSAGE, options);
        System.exit(1);
    }

    String[] extra = line.getArgs();
    if (extra.length == 0) {
        System.out.println("Missing file argument");
        new HelpFormatter().printHelp(HELP_MESSAGE, options);
        System.exit(1);
    }
    String input = extra[0];

    StringOption argConfig = ArgumentHelper.getString(line, OPTION_CONFIG);
    if (argConfig.hasValue()) {
        String configPath = argConfig.getValue();
        LiveConfig.setPath(configPath);
    }

    StringOption argVisualization = ArgumentHelper.getString(line, OPTION_VISUALIZATION);
    StringOption argStatus = ArgumentHelper.getString(line, OPTION_STATUS);

    Visualization visualization = visualizationSwitch.find(argVisualization.getValue());
    if (visualization == null) {
        System.err.println("Unsupported visualization '" + argVisualization.getValue() + "'");
        System.exit(1);
    }

    System.out.println("Visualization: " + visualization);

    ContentReader contentReader = new ContentReader();
    Content content = null;
    try {
        content = contentReader.read(new File(input));
    } catch (Exception e) {
        System.out.println("Error while reading input file '" + input + "'. Exception type: "
                + e.getClass().getSimpleName() + ", message: " + e.getMessage());
        System.exit(1);
    }

    Properties properties = line.getOptionProperties(OPTION_PROPERTIES);

    ContentLauncher launcher = null;

    switch (visualization) {
    case GEOMETRY: {
        launcher = new ContentDisplayLauncher();
        break;
    }
    case DCEL: {
        launcher = new DcelLauncher();
        break;
    }
    case FREESPACE: {
        launcher = new FreeSpaceChainsLauncher();
        break;
    }
    case DISTANCETERRAIN: {
        launcher = new DistanceTerrainChainsLauncher();
        break;
    }
    case CHAN: {
        launcher = new ChanLauncher();
        break;
    }
    case FORTUNE: {
        launcher = new FortunesSweepLauncher();
        break;
    }
    case MONOTONE_PIECES: {
        launcher = new MonotonePiecesLauncher();
        break;
    }
    case MONOTONE_TRIANGULATION: {
        launcher = new MonotoneTriangulationLauncher();
        break;
    }
    case TRIANGULATION: {
        launcher = new MonotonePiecesTriangulationLauncher();
        break;
    }
    case SPIP: {
        launcher = new ShortestPathInPolygonLauncher();
        break;
    }
    case BUFFER: {
        launcher = new PolygonBufferLauncher();
        break;
    }
    }

    try {
        launcher.launch(content, true);
    } catch (LaunchException e) {
        System.err.println("Unable to start visualization");
        System.err.println("Error message: " + e.getMessage());
        System.exit(1);
    }
}