Example usage for org.apache.commons.cli OptionBuilder withLongOpt

List of usage examples for org.apache.commons.cli OptionBuilder withLongOpt

Introduction

In this page you can find the example usage for org.apache.commons.cli OptionBuilder withLongOpt.

Prototype

public static OptionBuilder withLongOpt(String newLongopt) 

Source Link

Document

The next Option created will have the following long option value.

Usage

From source file:edu.buffalo.fusim.Fusim.java

@SuppressWarnings("static-access")
private void buildOptions() {
    options = new Options();

    options.addOption(OptionBuilder.withLongOpt("help").withDescription("print usage info").create("h"));
    options.addOption(OptionBuilder.withLongOpt("gene-model")
            .withDescription("Path to gene model file in refFlat format").hasArg().create("g"));
    options.addOption(OptionBuilder.withLongOpt("reference")
            .withDescription("Path to indexed reference genome fasta file (.fai)").hasArg().create("r"));
    options.addOption(OptionBuilder.withLongOpt("background-reads").withDescription(
            "Path to BAM file containing background reads. Genes will be selected for fusions according to the read profile of the background reads.")
            .hasArg().create("b"));
    options.addOption(OptionBuilder.withLongOpt("fusions")
            .withDescription("Number of fusions to generate using two randomly selected genes").hasArg()
            .create("n"));
    options.addOption(OptionBuilder.withLongOpt("text-output").withDescription("File name of text output")
            .hasArg().create("t"));
    options.addOption(OptionBuilder.withLongOpt("fasta-output").withDescription("File name of FASTA output")
            .hasArg().create("f"));
    options.addOption(//  www  .  j a  va 2  s .  c o m
            OptionBuilder.withLongOpt("cds-only").withDescription("Only include CDS exons").create("c"));
    options.addOption(OptionBuilder.withLongOpt("read-through")
            .withDescription("Number of read through fusions").hasArg().create("x"));
    options.addOption(OptionBuilder.withLongOpt("tri-fusion")
            .withDescription("Number of fusions with three genes").hasArg().create("j"));
    options.addOption(OptionBuilder.withLongOpt("self-fusion")
            .withDescription("Number of self-fusions (fusions with single gene)").hasArg().create("s"));
    options.addOption(OptionBuilder.withLongOpt("intra-chrom")
            .withDescription("Number of intra-chromosome fusions (fusions within single chrom)").hasArg()
            .create("y"));
    options.addOption(OptionBuilder.withLongOpt("rpkm-cutoff")
            .withDescription(
                    "RPKM cutoff when using background BAM file. Genes below the cutoff will be ignored")
            .hasArg().create("k"));
    options.addOption(OptionBuilder.withLongOpt("threads")
            .withDescription("Number of threads to spawn when processing background BAM file").hasArg()
            .create("p"));
    options.addOption(OptionBuilder.withLongOpt("convert")
            .withDescription("Convert GTF/GFF to refFlat (genePred) format").create("z"));
    options.addOption(OptionBuilder.withLongOpt("gtf").withDescription("Input GTF file for conversion").hasArg()
            .create("i"));
    options.addOption(OptionBuilder.withLongOpt("output").withDescription("Output refFlat file for conversion")
            .hasArg().create("o"));
    options.addOption(OptionBuilder.withLongOpt("gene-selection-method").withDescription(
            "Method to use when selecting genes for fusions: uniform|binned|empirical|empirical-sturges")
            .hasArg().create("m"));
    options.addOption(OptionBuilder.withLongOpt("auto-correct-orientation")
            .withDescription(
                    "Auto correct orientation of fusion sequence if genes are located on different strands")
            .create("a"));
    options.addOption(OptionBuilder.withLongOpt("out-of-frame")
            .withDescription(
                    "Allow fusions outside of reading frames. By default the reading frame is preserved")
            .create("d"));
    options.addOption(OptionBuilder.withLongOpt("keep-exon-boundary")
            .withDescription("Generate fusion breaks on exon boundaries only").create("e"));
    options.addOption(OptionBuilder.withLongOpt("limit")
            .withDescription("Limit all fusions to specific geneId, transcriptId, or chrom").hasArg()
            .create("l"));
    options.addOption(
            OptionBuilder.withLongOpt("gene1").withDescription("Filter for gene1").hasArg().create("1"));
    options.addOption(
            OptionBuilder.withLongOpt("gene2").withDescription("Filter for gene2").hasArg().create("2"));
    options.addOption(
            OptionBuilder.withLongOpt("gene3").withDescription("Filter for gene3").hasArg().create("3"));
    options.addOption(OptionBuilder.withLongOpt("foreign-insertion-length")
            .withDescription(
                    "Maxium length of randomly generated sequence to insert between fusion breakpoints")
            .hasArg().create("u"));
    options.addOption(OptionBuilder.withLongOpt("foreign-insertion-perecent")
            .withDescription("Percent of fusions to insert foreign sequence between fusion breakpoints")
            .hasArg().create("w"));
    options.addOption(OptionBuilder.withLongOpt("version").withDescription("Display version info").create("v"));
}

From source file:com.aliyun.odps.ship.common.OptionsBuilder.java

public static Options getUploadOptions() {
    Options opts = getGlobalOptions();//from ww w. j  ava 2s .co m
    opts.addOption(OptionBuilder.withLongOpt(Constants.DISCARD_BAD_RECORDS).withDescription(
            "specify discard bad records action(true|false), default " + Constants.DEFAULT_DISCARD_BAD_RECORDS)
            .hasArg().withArgName("ARG").create("dbr"));
    opts.addOption(OptionBuilder.withLongOpt(Constants.SCAN)
            .withDescription("specify scan file action(true|false|only), default " + Constants.DEFAULT_SCAN)
            .hasArg().withArgName("ARG").create("s"));
    opts.addOption(OptionBuilder.withLongOpt(Constants.BLOCK_SIZE)
            .withDescription("block size in MiB, default " + Constants.DEFAULT_BLOCK_SIZE).hasArg()
            .withArgName("ARG").create("bs"));
    opts.addOption(OptionBuilder.withLongOpt(Constants.MAX_BAD_RECORDS)
            .withDescription("max bad records, default " + Constants.DEFAULT_BAD_RECORDS).hasArg()
            .withArgName("ARG").create("mbr"));
    return opts;
}

From source file:mod.org.dcm4che2.tool.DcmSnd.java

private static CommandLine parse(String[] args) {
    Options opts = new Options();

    OptionBuilder.withArgName("name");
    OptionBuilder.hasArg();//from   w w  w.  j  av  a2s.  co m
    OptionBuilder.withDescription("set device name, use DCMSND by default");
    opts.addOption(OptionBuilder.create("device"));

    OptionBuilder.withArgName("aet[@host][:port]");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("set AET, local address and listening port of local "
            + "Application Entity, use device name and pick up any valid "
            + "local address to bind the socket by default");
    opts.addOption(OptionBuilder.create("L"));

    opts.addOption("ts1", false,
            "offer Default Transfer Syntax in " + "separate Presentation Context. By default offered with "
                    + "Explicit VR Little Endian TS in one PC.");

    opts.addOption("fileref", false,
            "send objects without pixel data, but with a reference to "
                    + "the DICOM file using DCM4CHE URI Referenced Transfer Syntax "
                    + "to import DICOM objects on a given file system to a DCM4CHEE " + "archive.");

    OptionBuilder.withArgName("username");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "enable User Identity Negotiation with specified username and " + " optional passcode");
    opts.addOption(OptionBuilder.create("username"));

    OptionBuilder.withArgName("passcode");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription(
            "optional passcode for User Identity Negotiation, " + "only effective with option -username");
    opts.addOption(OptionBuilder.create("passcode"));

    opts.addOption("uidnegrsp", false,
            "request positive User Identity Negotation response, " + "only effective with option -username");

    OptionBuilder.withArgName("NULL|3DES|AES");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("enable TLS connection without, 3DES or AES encryption");
    opts.addOption(OptionBuilder.create("tls"));

    OptionGroup tlsProtocol = new OptionGroup();
    tlsProtocol.addOption(new Option("tls1", "disable the use of SSLv3 and SSLv2 for TLS connections"));
    tlsProtocol.addOption(new Option("ssl3", "disable the use of TLSv1 and SSLv2 for TLS connections"));
    tlsProtocol.addOption(new Option("no_tls1", "disable the use of TLSv1 for TLS connections"));
    tlsProtocol.addOption(new Option("no_ssl3", "disable the use of SSLv3 for TLS connections"));
    tlsProtocol.addOption(new Option("no_ssl2", "disable the use of SSLv2 for TLS connections"));
    opts.addOptionGroup(tlsProtocol);

    opts.addOption("noclientauth", false, "disable client authentification for TLS");

    OptionBuilder.withArgName("file|url");
    OptionBuilder.hasArg();
    OptionBuilder
            .withDescription("file path or URL of P12 or JKS keystore, resource:tls/test_sys_2.p12 by default");
    opts.addOption(OptionBuilder.create("keystore"));

    OptionBuilder.withArgName("password");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("password for keystore file, 'secret' by default");
    opts.addOption(OptionBuilder.create("keystorepw"));

    OptionBuilder.withArgName("password");
    OptionBuilder.hasArg();
    OptionBuilder
            .withDescription("password for accessing the key in the keystore, keystore password by default");
    opts.addOption(OptionBuilder.create("keypw"));

    OptionBuilder.withArgName("file|url");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("file path or URL of JKS truststore, resource:tls/mesa_certs.jks by default");
    opts.addOption(OptionBuilder.create("truststore"));

    OptionBuilder.withArgName("password");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("password for truststore file, 'secret' by default");
    opts.addOption(OptionBuilder.create("truststorepw"));

    OptionBuilder.withArgName("aet@host:port");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("request storage commitment of (successfully) sent objects "
            + "afterwards in new association to specified remote " + "Application Entity");
    opts.addOption(OptionBuilder.create("stgcmtae"));

    opts.addOption("stgcmt", false,
            "request storage commitment of (successfully) sent objects " + "afterwards in same association");

    OptionBuilder.withArgName("attr=value");
    OptionBuilder.hasArgs();
    OptionBuilder.withValueSeparator('=');
    OptionBuilder.withDescription("Replace value of specified attribute "
            + "with specified value in transmitted objects. attr can be "
            + "specified by name or tag value (in hex), e.g. PatientName " + "or 00100010.");
    opts.addOption(OptionBuilder.create("set"));

    OptionBuilder.withArgName("salt");
    OptionBuilder.hasArgs();
    OptionBuilder.withDescription(
            "Anonymize the files.  Set to 0 for a random anonymization (not repeatable) or 1 for a daily anonymization or another"
                    + " value for a specific salt for reproducible anonymization (useful for allowing studies to be sent at a later date and still correctly named/associated)");
    OptionBuilder.withLongOpt("anonymize");
    opts.addOption(OptionBuilder.create("a"));

    OptionBuilder.withArgName("sx1[:sx2[:sx3]");
    OptionBuilder.hasArgs();
    OptionBuilder.withValueSeparator(':');
    OptionBuilder.withDescription(
            "Suffix SOP [,Series [,Study]] " + "Instance UID with specified value[s] in transmitted objects.");
    opts.addOption(OptionBuilder.create("setuid"));

    OptionBuilder.withArgName("maxops");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("maximum number of outstanding operations it may invoke "
            + "asynchronously, unlimited by default.");
    opts.addOption(OptionBuilder.create("async"));

    opts.addOption("pdv1", false, "send only one PDV in one P-Data-TF PDU, "
            + "pack command and data PDV in one P-DATA-TF PDU by default.");
    opts.addOption("tcpdelay", false, "set TCP_NODELAY socket option to false, true by default");

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("timeout in ms for TCP connect, no timeout by default");
    opts.addOption(OptionBuilder.create("connectTO"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("delay in ms for Socket close after sending A-ABORT, " + "50ms by default");
    opts.addOption(OptionBuilder.create("soclosedelay"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("delay in ms for closing the listening socket, " + "1000ms by default");
    opts.addOption(OptionBuilder.create("shutdowndelay"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("period in ms to check for outstanding DIMSE-RSP, " + "10s by default");
    opts.addOption(OptionBuilder.create("reaper"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("timeout in ms for receiving DIMSE-RSP, 10s by default");
    opts.addOption(OptionBuilder.create("rspTO"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("timeout in ms for receiving A-ASSOCIATE-AC, 5s by default");
    opts.addOption(OptionBuilder.create("acceptTO"));

    OptionBuilder.withArgName("ms");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("timeout in ms for receiving A-RELEASE-RP, 5s by default");
    opts.addOption(OptionBuilder.create("releaseTO"));

    OptionBuilder.withArgName("KB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("maximal length in KB of received P-DATA-TF PDUs, 16KB by default");
    opts.addOption(OptionBuilder.create("rcvpdulen"));

    OptionBuilder.withArgName("KB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("maximal length in KB of sent P-DATA-TF PDUs, 16KB by default");
    opts.addOption(OptionBuilder.create("sndpdulen"));

    OptionBuilder.withArgName("KB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("set SO_RCVBUF socket option to specified value in KB");
    opts.addOption(OptionBuilder.create("sorcvbuf"));

    OptionBuilder.withArgName("KB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("set SO_SNDBUF socket option to specified value in KB");
    opts.addOption(OptionBuilder.create("sosndbuf"));

    OptionBuilder.withArgName("KB");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("transcoder buffer size in KB, 1KB by default");
    opts.addOption(OptionBuilder.create("bufsize"));

    OptionBuilder.withArgName("count");
    OptionBuilder.hasArg();
    OptionBuilder.withDescription("Batch size - Number of files to be sent in each batch, "
            + "where a storage commit is done between batches ");
    opts.addOption(OptionBuilder.create("batchsize"));

    opts.addOption("lowprior", false, "LOW priority of the C-STORE operation, MEDIUM by default");
    opts.addOption("highprior", false, "HIGH priority of the C-STORE operation, MEDIUM by default");
    opts.addOption("h", "help", false, "print this message");
    opts.addOption("V", "version", false, "print the version information and exit");
    CommandLine cl = null;
    try {
        cl = new GnuParser().parse(opts, args);
    } catch (ParseException e) {
        exit("dcmsnd: " + e.getMessage());
        throw new RuntimeException("unreachable");
    }
    if (cl.hasOption('V')) {
        Package p = DcmSnd.class.getPackage();
        System.out.println("dcmsnd v" + p.getImplementationVersion());
        System.exit(0);
    }
    if (cl.hasOption('h') || cl.getArgList().size() < 2) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE);
        System.exit(0);
    }
    return cl;
}

From source file:com.facebook.presto.accumulo.tools.RewriteIndex.java

@SuppressWarnings("static-access")
@Override/*from ww  w .  ja v  a2s.c  o m*/
public Options getOptions() {
    Options opts = new Options();
    opts.addOption(OptionBuilder.withLongOpt("authorizations").withDescription(
            "List of scan authorizations.  Default is to get user authorizations for the user in the configuration.")
            .hasArgs().create(AUTHORIZATIONS_OPT));
    opts.addOption(OptionBuilder.withLongOpt("schema").withDescription("Presto schema name").hasArg()
            .isRequired().create(SCHEMA_OPT));
    opts.addOption(OptionBuilder.withLongOpt("table").withDescription("Presto table name").hasArg().isRequired()
            .create(TABLE_OPT));
    opts.addOption(OptionBuilder.withLongOpt(FORCE_OPT)
            .withDescription("Force deleting of entries. Default is a dry run").create());
    opts.addOption(OptionBuilder.withLongOpt(ADD_ONLY_OPT).withDescription(
            "Only add index entries, do not delete them or run the rewrite metrics tool.  Requires --force to do anything.  Default is to add and delete.")
            .create());
    return opts;
}

From source file:net.sf.freecol.FreeCol.java

/**
 * Processes the command-line arguments and takes appropriate
 * actions for each of them./*w  w w. j ava  2 s. c om*/
 *
 * @param args The command-line arguments.
 */
private static void handleArgs(String[] args) {
    Options options = new Options();
    final String help = Messages.message("cli.help");
    final File dummy = new File("dummy");
    final String argDirectory = Messages.message("cli.arg.directory");

    // Help options.
    options.addOption(OptionBuilder.withLongOpt("usage").withDescription(help).create());
    options.addOption(OptionBuilder.withLongOpt("help").withDescription(help).create());

    // Special options handled early.
    options.addOption(OptionBuilder.withLongOpt("freecol-data")
            .withDescription(Messages.message("cli.freecol-data")).withArgName(argDirectory).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("default-locale").withDescription(Messages.message("cli.default-locale"))
                    .withArgName(Messages.message("cli.arg.locale")).hasArg().create());

    // Ordinary options, handled here.
    options.addOption(OptionBuilder.withLongOpt("advantages")
            .withDescription(Messages.message(
                    StringTemplate.template("cli.advantages").addName("%advantages%", getValidAdvantages())))
            .withArgName(Messages.message("cli.arg.advantages")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("check-savegame").withDescription(Messages.message("cli.check-savegame"))
                    .withArgName(Messages.message("cli.arg.file")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("clientOptions").withDescription(Messages.message("cli.clientOptions"))
                    .withArgName(Messages.message("cli.arg.clientOptions")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("debug")
            .withDescription(Messages.message(
                    StringTemplate.template("cli.debug").addName("%modes%", FreeColDebugger.getDebugModes())))
            .withArgName(Messages.message("cli.arg.debug")).hasOptionalArg().create());
    options.addOption(OptionBuilder.withLongOpt("debug-run").withDescription(Messages.message("cli.debug-run"))
            .withArgName(Messages.message("cli.arg.debugRun")).hasOptionalArg().create());
    options.addOption(OptionBuilder.withLongOpt("debug-start")
            .withDescription(Messages.message("cli.debug-start")).create());
    options.addOption(
            OptionBuilder.withLongOpt("difficulty").withDescription(Messages.message("cli.difficulty"))
                    .withArgName(Messages.message("cli.arg.difficulty")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("europeans").withDescription(Messages.message("cli.european-count"))
                    .withArgName(Messages.message("cli.arg.europeans")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("fast").withDescription(Messages.message("cli.fast")).create());
    options.addOption(OptionBuilder.withLongOpt("font").withDescription(Messages.message("cli.font"))
            .withArgName(Messages.message("cli.arg.font")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("full-screen")
            .withDescription(Messages.message("cli.full-screen")).create());
    options.addOption(OptionBuilder.withLongOpt("gui-scale")
            .withDescription(Messages
                    .message(StringTemplate.template("cli.gui-scale").addName("%scales%", getValidGUIScales())))
            .withArgName(Messages.message("cli.arg.gui-scale")).hasOptionalArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("headless").withDescription(Messages.message("cli.headless")).create());
    options.addOption(
            OptionBuilder.withLongOpt("load-savegame").withDescription(Messages.message("cli.load-savegame"))
                    .withArgName(Messages.message("cli.arg.file")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("log-console")
            .withDescription(Messages.message("cli.log-console")).create());
    options.addOption(OptionBuilder.withLongOpt("log-file").withDescription(Messages.message("cli.log-file"))
            .withArgName(Messages.message("cli.arg.name")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("log-level").withDescription(Messages.message("cli.log-level"))
            .withArgName(Messages.message("cli.arg.loglevel")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("name").withDescription(Messages.message("cli.name"))
            .withArgName(Messages.message("cli.arg.name")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("no-intro").withDescription(Messages.message("cli.no-intro")).create());
    options.addOption(OptionBuilder.withLongOpt("no-java-check")
            .withDescription(Messages.message("cli.no-java-check")).create());
    options.addOption(OptionBuilder.withLongOpt("no-memory-check")
            .withDescription(Messages.message("cli.no-memory-check")).create());
    options.addOption(
            OptionBuilder.withLongOpt("no-sound").withDescription(Messages.message("cli.no-sound")).create());
    options.addOption(
            OptionBuilder.withLongOpt("no-splash").withDescription(Messages.message("cli.no-splash")).create());
    options.addOption(
            OptionBuilder.withLongOpt("private").withDescription(Messages.message("cli.private")).create());
    options.addOption(OptionBuilder.withLongOpt("seed").withDescription(Messages.message("cli.seed"))
            .withArgName(Messages.message("cli.arg.seed")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("server").withDescription(Messages.message("cli.server")).create());
    options.addOption(
            OptionBuilder.withLongOpt("server-name").withDescription(Messages.message("cli.server-name"))
                    .withArgName(Messages.message("cli.arg.name")).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("server-port").withDescription(Messages.message("cli.server-port"))
                    .withArgName(Messages.message("cli.arg.port")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("splash").withDescription(Messages.message("cli.splash"))
            .withArgName(Messages.message("cli.arg.file")).hasOptionalArg().create());
    options.addOption(OptionBuilder.withLongOpt("tc").withDescription(Messages.message("cli.tc"))
            .withArgName(Messages.message("cli.arg.name")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("timeout").withDescription(Messages.message("cli.timeout"))
            .withArgName(Messages.message("cli.arg.timeout")).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("user-cache-directory")
            .withDescription(Messages.message("cli.user-cache-directory")).withArgName(argDirectory)
            .withType(dummy).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("user-config-directory")
            .withDescription(Messages.message("cli.user-config-directory")).withArgName(argDirectory)
            .withType(dummy).hasArg().create());
    options.addOption(OptionBuilder.withLongOpt("user-data-directory")
            .withDescription(Messages.message("cli.user-data-directory")).withArgName(argDirectory)
            .withType(dummy).hasArg().create());
    options.addOption(
            OptionBuilder.withLongOpt("version").withDescription(Messages.message("cli.version")).create());
    options.addOption(OptionBuilder.withLongOpt("windowed").withDescription(Messages.message("cli.windowed"))
            .withArgName(Messages.message("cli.arg.dimensions")).hasOptionalArg().create());

    CommandLineParser parser = new PosixParser();
    boolean usageError = false;
    try {
        CommandLine line = parser.parse(options, args);
        if (line.hasOption("help") || line.hasOption("usage")) {
            printUsage(options, 0);
        }

        if (line.hasOption("default-locale")) {
            ; // Do nothing, already handled in main().
        }
        if (line.hasOption("freecol-data")) {
            ; // Do nothing, already handled in main().
        }

        if (line.hasOption("advantages")) {
            String arg = line.getOptionValue("advantages");
            Advantages a = selectAdvantages(arg);
            if (a == null) {
                fatal(StringTemplate.template("cli.error.advantages")
                        .addName("%advantages%", getValidAdvantages()).addName("%arg%", arg));
            }
        }

        if (line.hasOption("check-savegame")) {
            String arg = line.getOptionValue("check-savegame");
            if (!FreeColDirectories.setSavegameFile(arg)) {
                fatal(StringTemplate.template("cli.err.save").addName("%string%", arg));
            }
            checkIntegrity = true;
            standAloneServer = true;
        }

        if (line.hasOption("clientOptions")) {
            String fileName = line.getOptionValue("clientOptions");
            if (!FreeColDirectories.setClientOptionsFile(fileName)) {
                // Not fatal.
                gripe(StringTemplate.template("cli.error.clientOptions").addName("%string%", fileName));
            }
        }

        if (line.hasOption("debug")) {
            // If the optional argument is supplied use limited mode.
            String arg = line.getOptionValue("debug");
            if (arg == null || arg.isEmpty()) {
                // Let empty argument default to menus functionality.
                arg = FreeColDebugger.DebugMode.MENUS.toString();
            }
            if (!FreeColDebugger.setDebugModes(arg)) { // Not fatal.
                gripe(StringTemplate.template("cli.error.debug").addName("%modes%",
                        FreeColDebugger.getDebugModes()));
            }
            // user set log level has precedence
            if (!line.hasOption("log-level"))
                logLevel = Level.FINEST;
        }
        if (line.hasOption("debug-run")) {
            FreeColDebugger.enableDebugMode(FreeColDebugger.DebugMode.MENUS);
            FreeColDebugger.configureDebugRun(line.getOptionValue("debug-run"));
        }
        if (line.hasOption("debug-start")) {
            debugStart = true;
            FreeColDebugger.enableDebugMode(FreeColDebugger.DebugMode.MENUS);
        }

        if (line.hasOption("difficulty")) {
            String arg = line.getOptionValue("difficulty");
            String difficulty = selectDifficulty(arg);
            if (difficulty == null) {
                fatal(StringTemplate.template("cli.error.difficulties")
                        .addName("%difficulties%", getValidDifficulties()).addName("%arg%", arg));
            }
        }

        if (line.hasOption("europeans")) {
            int e = selectEuropeanCount(line.getOptionValue("europeans"));
            if (e < 0) {
                gripe(StringTemplate.template("cli.error.europeans").addAmount("%min%", EUROPEANS_MIN));
            }
        }

        if (line.hasOption("fast")) {
            fastStart = true;
            introVideo = false;
        }

        if (line.hasOption("font")) {
            fontName = line.getOptionValue("font");
        }

        if (line.hasOption("full-screen")) {
            windowSize = null;
        }

        if (line.hasOption("gui-scale")) {
            String arg = line.getOptionValue("gui-scale");
            if (!setGUIScale(arg)) {
                gripe(StringTemplate.template("cli.error.gui-scale").addName("%scales%", getValidGUIScales())
                        .addName("%arg%", arg));
            }
        }

        if (line.hasOption("headless")) {
            headless = true;
        }

        if (line.hasOption("load-savegame")) {
            String arg = line.getOptionValue("load-savegame");
            if (!FreeColDirectories.setSavegameFile(arg)) {
                fatal(StringTemplate.template("cli.error.save").addName("%string%", arg));
            }
        }

        if (line.hasOption("log-console")) {
            consoleLogging = true;
        }
        if (line.hasOption("log-file")) {
            FreeColDirectories.setLogFilePath(line.getOptionValue("log-file"));
        }
        if (line.hasOption("log-level")) {
            setLogLevel(line.getOptionValue("log-level"));
        }

        if (line.hasOption("name")) {
            setName(line.getOptionValue("name"));
        }

        if (line.hasOption("no-intro")) {
            introVideo = false;
        }
        if (line.hasOption("no-java-check")) {
            javaCheck = false;
        }
        if (line.hasOption("no-memory-check")) {
            memoryCheck = false;
        }
        if (line.hasOption("no-sound")) {
            sound = false;
        }
        if (line.hasOption("no-splash")) {
            splashStream = null;
        }

        if (line.hasOption("private")) {
            publicServer = false;
        }

        if (line.hasOption("server")) {
            standAloneServer = true;
        }
        if (line.hasOption("server-name")) {
            serverName = line.getOptionValue("server-name");
        }
        if (line.hasOption("server-port")) {
            String arg = line.getOptionValue("server-port");
            if (!setServerPort(arg)) {
                fatal(StringTemplate.template("cli.error.serverPort").addName("%string%", arg));
            }
        }

        if (line.hasOption("seed")) {
            FreeColSeed.setFreeColSeed(line.getOptionValue("seed"));
        }

        if (line.hasOption("splash")) {
            String splash = line.getOptionValue("splash");
            try {
                FileInputStream fis = new FileInputStream(splash);
                splashStream = fis;
            } catch (FileNotFoundException fnfe) {
                gripe(StringTemplate.template("cli.error.splash").addName("%name%", splash));
            }
        }

        if (line.hasOption("tc")) {
            setTC(line.getOptionValue("tc")); // Failure is deferred.
        }

        if (line.hasOption("timeout")) {
            String arg = line.getOptionValue("timeout");
            if (!setTimeout(arg)) { // Not fatal
                gripe(StringTemplate.template("cli.error.timeout").addName("%string%", arg).addName("%minimum%",
                        Integer.toString(TIMEOUT_MIN)));
            }
        }

        if (line.hasOption("user-cache-directory")) {
            String arg = line.getOptionValue("user-cache-directory");
            String errMsg = FreeColDirectories.setUserCacheDirectory(arg);
            if (errMsg != null) { // Not fatal.
                gripe(StringTemplate.template(errMsg).addName("%string%", arg));
            }
        }

        if (line.hasOption("user-config-directory")) {
            String arg = line.getOptionValue("user-config-directory");
            String errMsg = FreeColDirectories.setUserConfigDirectory(arg);
            if (errMsg != null) { // Not fatal.
                gripe(StringTemplate.template(errMsg).addName("%string%", arg));
            }
        }

        if (line.hasOption("user-data-directory")) {
            String arg = line.getOptionValue("user-data-directory");
            String errMsg = FreeColDirectories.setUserDataDirectory(arg);
            if (errMsg != null) { // Fatal, unable to save.
                fatal(StringTemplate.template(errMsg).addName("%string%", arg));
            }
        }

        if (line.hasOption("version")) {
            System.out.println("FreeCol " + getVersion());
            System.exit(0);
        }

        if (line.hasOption("windowed")) {
            String arg = line.getOptionValue("windowed");
            setWindowSize(arg); // Does not fail
        }

    } catch (ParseException e) {
        System.err.println("\n" + e.getMessage() + "\n");
        usageError = true;
    }
    if (usageError)
        printUsage(options, 1);
}

From source file:iDynoOptimizer.MOEAFramework26.src.org.moeaframework.analysis.sensitivity.SobolAnalysis.java

@SuppressWarnings("static-access")
@Override//from www  .  j ava  2 s .  c  o m
public Options getOptions() {
    Options options = super.getOptions();

    options.addOption(
            OptionBuilder.withLongOpt("parameterFile").hasArg().withArgName("file").isRequired().create('p'));
    options.addOption(OptionBuilder.withLongOpt("input").hasArg().withArgName("file").isRequired().create('i'));
    options.addOption(
            OptionBuilder.withLongOpt("metric").hasArg().withArgName("value").isRequired().create('m'));
    options.addOption(OptionBuilder.withLongOpt("simple").create('s'));
    options.addOption(OptionBuilder.withLongOpt("output").hasArg().withArgName("file").create('o'));
    options.addOption(OptionBuilder.withLongOpt("resamples").hasArg().withArgName("number").create('r'));

    return options;
}

From source file:com.facebook.presto.accumulo.tools.RewriteMetricsTask.java

@SuppressWarnings("static-access")
@Override//from   w w  w .  j a v  a 2 s .c o m
public Options getOptions() {
    Options opts = new Options();
    opts.addOption(OptionBuilder.withLongOpt("authorizations").withDescription(
            "List of scan authorizations.  Default is to get user authorizations for the user in the configuration.")
            .hasArgs().create(AUTHORIZATIONS_OPT));
    opts.addOption(OptionBuilder.withLongOpt("schema").withDescription("Presto schema name").hasArg()
            .isRequired().create(SCHEMA_OPT));
    opts.addOption(OptionBuilder.withLongOpt("table").withDescription("Presto table name").hasArg().isRequired()
            .create(TABLE_OPT));
    opts.addOption(OptionBuilder.withLongOpt(FORCE_OPT)
            .withDescription("Force deleting of entries. Default is a dry run").create());
    return opts;
}

From source file:com.aliyun.odps.ship.common.OptionsBuilder.java

public static Options getDownloadOptions() {
    Options opts = getGlobalOptions();/* w ww .  j a va  2  s .  com*/
    opts.addOption(OptionBuilder.withLongOpt(Constants.LIMIT)
            .withDescription("specify the number of records to download").hasArg().withArgName("ARG").create());
    return opts;
}

From source file:com.aliyun.odps.ship.common.OptionsBuilder.java

public static Options getResumeOptions() {
    Options opts = getGlobalOptions();//from  w  w  w. jav  a2s. c om
    opts.addOption(OptionBuilder.withLongOpt("force").withDescription("force resume").create("f"));
    return opts;
}

From source file:com.aliyun.odps.ship.common.OptionsBuilder.java

public static Options getShowOptions() {
    Options opts = getGlobalOptions();/*from   w  ww.  j  a  v a 2  s.  co m*/
    opts.addOption(OptionBuilder.withLongOpt("number").withDescription("lines").hasArg().withArgName("ARG")
            .create("n"));
    return opts;
}