Example usage for org.apache.commons.cli CommandLine getArgs

List of usage examples for org.apache.commons.cli CommandLine getArgs

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Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLine getArgs.

Prototype

public String[] getArgs()

Source Link

Document

Retrieve any left-over non-recognized options and arguments

Usage

From source file:bboss.org.artofsolving.jodconverter.cli.Convert.java

public static void main(String[] arguments) throws ParseException, JSONException, IOException {
    CommandLineParser commandLineParser = new PosixParser();
    CommandLine commandLine = commandLineParser.parse(OPTIONS, arguments);

    String outputFormat = null;/*from   w w  w  .j av  a2s  .c o m*/
    if (commandLine.hasOption(OPTION_OUTPUT_FORMAT.getOpt())) {
        outputFormat = commandLine.getOptionValue(OPTION_OUTPUT_FORMAT.getOpt());
    }

    int port = DEFAULT_OFFICE_PORT;
    if (commandLine.hasOption(OPTION_PORT.getOpt())) {
        port = Integer.parseInt(commandLine.getOptionValue(OPTION_PORT.getOpt()));
    }

    String[] fileNames = commandLine.getArgs();
    if ((outputFormat == null && fileNames.length != 2) || fileNames.length < 1) {
        String syntax = "java -jar jodconverter-core.jar [options] input-file output-file\n"
                + "or [options] -o output-format input-file [input-file...]";
        HelpFormatter helpFormatter = new HelpFormatter();
        helpFormatter.printHelp(syntax, OPTIONS);
        System.exit(STATUS_INVALID_ARGUMENTS);
    }

    DocumentFormatRegistry registry;
    if (commandLine.hasOption(OPTION_REGISTRY.getOpt())) {
        File registryFile = new File(commandLine.getOptionValue(OPTION_REGISTRY.getOpt()));
        registry = new JsonDocumentFormatRegistry(FileUtils.readFileToString(registryFile));
    } else {
        registry = new DefaultDocumentFormatRegistry();
    }

    DefaultOfficeManagerConfiguration configuration = new DefaultOfficeManagerConfiguration();
    configuration.setPortNumber(port);
    if (commandLine.hasOption(OPTION_TIMEOUT.getOpt())) {
        int timeout = Integer.parseInt(commandLine.getOptionValue(OPTION_TIMEOUT.getOpt()));
        configuration.setTaskExecutionTimeout(timeout * 1000);
    }
    if (commandLine.hasOption(OPTION_USER_PROFILE.getOpt())) {
        String templateProfileDir = commandLine.getOptionValue(OPTION_USER_PROFILE.getOpt());
        configuration.setTemplateProfileDir(new File(templateProfileDir));
    }

    OfficeManager officeManager = configuration.buildOfficeManager();
    officeManager.start();
    OfficeDocumentConverter converter = new OfficeDocumentConverter(officeManager, registry);
    try {
        if (outputFormat == null) {
            File inputFile = new File(fileNames[0]);
            File outputFile = new File(fileNames[1]);
            converter.convert(inputFile, outputFile);
        } else {
            for (int i = 0; i < fileNames.length; i++) {
                File inputFile = new File(fileNames[i]);
                String outputName = FilenameUtils.getBaseName(fileNames[i]) + "." + outputFormat;
                File outputFile = new File(FilenameUtils.getFullPath(fileNames[i]) + outputName);
                converter.convert(inputFile, outputFile);
            }
        }
    } finally {
        officeManager.stop();
    }
}

From source file:com.aestel.chemistry.openEye.fp.Fingerprinter.java

public static void main(String... args) throws IOException {
    long start = System.currentTimeMillis();
    long iCounter = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);/* ww  w  .j  a v  a  2  s .c  o  m*/
    options.addOption(opt);

    opt = new Option("out", true, "output file .tsv or oe-supported");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("idTag", true, "field with ID (default title)");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("fpType", true, "fingerPrintType: maccs|linear7|linear7*4|HashLinear7*4\n"
            + "   maccs: generate maccs keys\n"
            + "   linear7 generate 7 bonds long linear fingerprints (210k known rest hashed)\n"
            + "   linear7*4 linear 7 bonds if more than 4 atoms code atoms as * (5.1k known rest hashed)\n"
            + "   HashLinear7*4: as linear7*4 but hashed to 16k");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("format", true,
            "folded512|folded2048|bitList|fragList|none\n" + "   folded512/2048: hex encoded 512/2048 bits\n"
                    + "   bitList: list of bitpositions\n" + "   none: no fp output for use with writeCodeMap");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("writeCodeMap", false, "Overwrite the codeMap file at the end of processing");
    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 idTag = null;
    if (cmd.hasOption("idTag"))
        idTag = cmd.getOptionValue("idTag");

    String outformat = cmd.getOptionValue("format").toLowerCase().intern();
    if (args.length != 0) {
        exitWithHelp(options);
    }

    String type = cmd.getOptionValue("fpType");
    boolean updateDictionaryFile = cmd.hasOption("writeCodeMap");
    boolean hashUnknownFrag = true;
    if (type.equals("HashLinear7*4"))
        hashUnknownFrag = false;
    if (type.equals("maccs"))
        hashUnknownFrag = false;
    if (updateDictionaryFile)
        hashUnknownFrag = false;
    Fingerprinter fprinter = createFingerprinter(type, updateDictionaryFile, hashUnknownFrag);
    OEMolBase mol = new OEGraphMol();

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    oemolistream ifs = new oemolistream(inFile);

    Runtime rt = Runtime.getRuntime();
    Outputter out;
    if (outFile.endsWith(".txt") || outFile.endsWith(".tab"))
        out = new TabOutputter(fprinter.getMapper(), outFile, outformat);
    else
        out = new OEOutputter(fprinter.getMapper(), outFile, type, outformat);

    while (oechem.OEReadMolecule(ifs, mol)) {
        iCounter++;
        Fingerprint fp = fprinter.getFingerprint(mol);

        String id;
        if (idTag == null)
            id = mol.GetTitle();
        else
            id = oechem.OEGetSDData(mol, idTag);

        if (iCounter % 100 == 0)
            System.err.print(".");
        if (iCounter % 4000 == 0) {
            System.err.printf(" %d %dsec\tt=%d f=%d u=%d m=%d tf=%d\n", iCounter,
                    (System.currentTimeMillis() - start) / 1000, rt.totalMemory() / 1024,
                    rt.freeMemory() / 1024, (rt.totalMemory() - rt.freeMemory()) / 1024, rt.maxMemory() / 1024,
                    (rt.freeMemory() + (rt.maxMemory() - rt.totalMemory())) / 1024);
        }

        out.output(id, mol, fp);
    }

    System.err.printf("Fingerprinter: Read %d structures in %d sec\n", iCounter,
            (System.currentTimeMillis() - start) / 1000);

    if (updateDictionaryFile)
        fprinter.writeDictionary();
    out.close();
    fprinter.close();
}

From source file:com.chip8java.emulator.Runner.java

/**
 * Runs the emulator with the specified command line options.
 * //from   ww  w.jav  a  2  s .  c  om
 * @param argv
 *            The set of options passed to the emulator
 */
public static void main(String[] argv) {
    CommandLine commandLine = parseCommandLineOptions(argv);
    Emulator.Builder emulatorBuilder = new Emulator.Builder();

    if (commandLine.hasOption(HELP_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("emulator", generateOptions());
        System.exit(0);
    }

    if (commandLine.hasOption(SCALE_OPTION)) {
        int scale = Integer.parseInt(commandLine.getOptionValue(SCALE_OPTION));
        emulatorBuilder.setScale(scale);
    }

    String[] args = commandLine.getArgs();
    if (args.length != 0) {
        emulatorBuilder.setRom(args[0]);
    }

    if (commandLine.hasOption(TRACE_OPTION)) {
        emulatorBuilder.setTrace();
    }

    if (commandLine.hasOption(DELAY_OPTION)) {
        int delay = Integer.parseInt(commandLine.getOptionValue(DELAY_OPTION));
        emulatorBuilder.setCycleTime((long) delay);
    }

    Emulator emulator = emulatorBuilder.build();
    emulator.start();
}

From source file:net.sf.jsignpdf.verify.SignatureCounter.java

/**
 * Main program.//w w  w . ja  va 2  s. c o m
 * 
 * @param args
 */
public static void main(String[] args) {

    // create the Options
    final Option optHelp = new Option("h", "help", false, "print this message");
    final Option optDebug = new Option("d", "debug", false, "enables debug output");
    final Option optNames = new Option("n", "names", false,
            "print comma separated signature names instead of the count");
    final Option optPasswd = new Option("p", "password", true, "set password for opening PDF");
    optPasswd.setArgName("password");

    final Options options = new Options();
    options.addOption(optHelp);
    options.addOption(optDebug);
    options.addOption(optNames);
    options.addOption(optPasswd);

    CommandLine line = null;
    try {
        // create the command line parser
        CommandLineParser parser = new PosixParser();
        // parse the command line arguments
        line = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Unable to parse command line (Use -h for the help)\n" + exp.getMessage());
        System.exit(Constants.EXIT_CODE_PARSE_ERR);
    }

    final String[] tmpArgs = line.getArgs();
    if (line.hasOption("h") || args == null || args.length == 0) {
        // automatically generate the help statement
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(70, "java -jar SignatureCounter.jar [file1.pdf [file2.pdf ...]]",
                "JSignPdf SignatureCounter is a command line tool which prints count of signatures in given PDF document.",
                options, null, true);
    } else {
        byte[] tmpPasswd = null;
        if (line.hasOption("p")) {
            tmpPasswd = line.getOptionValue("p").getBytes();
        }
        final boolean debug = line.hasOption("d");
        final boolean names = line.hasOption("n");

        for (String tmpFilePath : tmpArgs) {
            if (debug) {
                System.out.print("Counting signatures in " + tmpFilePath + ": ");
            }
            final File tmpFile = new File(tmpFilePath);
            if (!tmpFile.canRead()) {
                System.err.println("Couldn't read the file. Check the path and permissions: " + tmpFilePath);
                System.exit(Constants.EXIT_CODE_CANT_READ_FILE);
            }
            try {
                final PdfReader pdfReader = PdfUtils.getPdfReader(tmpFilePath, tmpPasswd);
                @SuppressWarnings("unchecked")
                final List<String> sigNames = pdfReader.getAcroFields().getSignatureNames();
                if (names) {
                    //print comma-separated names
                    boolean isNotFirst = false;
                    for (String sig : sigNames) {
                        if (isNotFirst) {
                            System.out.println(",");
                        } else {
                            isNotFirst = true;
                        }
                        System.out.println(sig);
                    }
                } else {
                    //normal processing print only count of signatures
                    System.out.println(sigNames.size());
                    if (debug) {
                        System.out.println("Signature names: " + sigNames);
                    }
                }
            } catch (IOException e) {
                e.printStackTrace();
                System.exit(Constants.EXIT_CODE_COMMON_ERROR);
            }
        }
    }
}

From source file:io.github.azige.whitespace.Cli.java

public static void main(String[] args) {
    Options options = new Options().addOption("h", "help", false, "??")
            .addOptionGroup(new OptionGroup()
                    .addOption(new Option("p",
                            "????????"))
                    .addOption(new Option("c", "?????")))
            .addOption(null, "szm", false,
                    "????")
            .addOption("e", "encoding", true, "??" + DEFAULT_ENCODING);

    try {//from  w  ww .j a v a  2  s. c om
        CommandLineParser parser = new BasicParser();
        CommandLine cl = parser.parse(options, args);

        if (cl.hasOption('h')) {
            printHelp(System.out, options);
            return;
        }

        if (cl.hasOption('e')) {
            encoding = Charset.forName(cl.getOptionValue('e'));
        } else {
            encoding = Charset.forName(DEFAULT_ENCODING);
        }

        if (cl.hasOption("szm")) {
            useSzm = true;
        }

        String[] fileArgs = cl.getArgs();
        if (fileArgs.length != 1) {
            printHelp(System.err, options);
            return;
        }

        try (InputStream input = Files.newInputStream(Paths.get(fileArgs[0]))) {
            if (cl.hasOption('p')) {
                printPseudoCode(input);
            } else if (cl.hasOption('c')) {
                compile(input, fileArgs[0]);
            } else {
                execute(input, fileArgs[0]);
            }
        }
    } catch (ParseException ex) {
        ex.printStackTrace();
        printHelp(System.err, options);
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

From source file:com.anjlab.sat3.Program.java

public static void main(String[] args) throws Exception {
    System.out.println("Reference Implementation of Romanov's Polynomial Algorithm for 3-SAT Problem"
            + "\nCopyright (c) 2010 AnjLab" + "\nThis program comes with ABSOLUTELY NO WARRANTY."
            + "\nThis is free software, and you are welcome to redistribute it under certain conditions."
            + "\nSee LICENSE.txt file or visit <http://www.gnu.org/copyleft/lesser.html> for details.");

    LOGGER.debug("Reading version number from manifest");
    String implementationVersion = Helper.getImplementationVersionFromManifest("3-SAT Core RI");
    System.out.println("Version: " + implementationVersion + "\n");

    Options options = getCommandLineOptions();

    CommandLineParser parser = new PosixParser();
    CommandLine commandLine = parser.parse(options, args);

    if (commandLine.getArgs().length != 1 || commandLine.hasOption(HELP_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Program.class.getName() + " [OPTIONS] <input-file-name>"
                + "\nWhere <input-file-name> is a path to file containing k-SAT formula instance in DIMACS CNF or Romanov SKT file format.",
                options);//from w w  w.jav a  2 s  .c  o m
        System.exit(0);
    }

    String formulaFile = commandLine.getArgs()[0];

    Helper.UsePrettyPrint = commandLine.hasOption(USE_PRETTY_PRINT_OPTION);
    Helper.EnableAssertions = !commandLine.hasOption(DISABLE_ASSERTIONS_OPTION);
    Helper.UseUniversalVarNames = !commandLine.hasOption(USE_ABC_VAR_NAMES_OPTION);

    Properties statistics = new Properties();
    StopWatch stopWatch = new StopWatch();

    try {
        statistics.put(Helper.IMPLEMENTATION_VERSION, implementationVersion);

        stopWatch.start("Load formula");
        ITabularFormula formula = Helper.loadFromFile(formulaFile);
        long timeElapsed = stopWatch.stop();

        statistics.put(Helper.INITIAL_FORMULA_LOAD_TIME, String.valueOf(timeElapsed));

        if (commandLine.hasOption(GENERATE_3SAT_OPTION)) {
            String generated3SatFilename = formulaFile + "-3sat.cnf";

            LOGGER.info("Saving 3-SAT formula to {}...", generated3SatFilename);
            Helper.saveToDIMACSFileFormat(formula, generated3SatFilename);
        }

        if (formula.getVarCount() > 26) {
            LOGGER.info("Variables count > 26 => force using universal names for variables.");
            Helper.UseUniversalVarNames = true;
        }

        statistics.put(Helper.INITIAL_FORMULA_VAR_COUNT, String.valueOf(formula.getVarCount()));
        statistics.put(Helper.INITIAL_FORMULA_CLAUSES_COUNT, String.valueOf(formula.getClausesCount()));

        Helper.prettyPrint(formula);
        stopWatch.printElapsed();

        if (commandLine.hasOption(FIND_HSS_ROUTE_OPTION)) {
            String hssPath = commandLine.getOptionValue(FIND_HSS_ROUTE_OPTION);

            stopWatch.start("Load HSS from " + hssPath);
            ObjectArrayList hss = Helper.loadHSS(hssPath);
            stopWatch.stop();
            stopWatch.printElapsed();

            findHSSRoute(commandLine, formulaFile, statistics, stopWatch, formula, null, null, hss, hssPath);

            return;
        }

        if (commandLine.hasOption(EVALUATE_OPTION)) {
            String resultsFilename = commandLine.getOptionValue(EVALUATE_OPTION);
            boolean satisfiable = evaluateFormula(stopWatch, formula, resultsFilename);
            if (satisfiable) {
                System.out.println("Formula evaluated as SAT");
            } else {
                System.out.println("Formula evaluated as UNSAT");
            }
            //  Only evaluate formula value
            return;
        }

        //  Find if formula is SAT

        //  Clone initial formula to verify formula satisfiability later
        ITabularFormula formulaClone = null;
        if (Helper.EnableAssertions) {
            stopWatch.start("Clone initial formula");
            formulaClone = formula.clone();
            stopWatch.stop();
            stopWatch.printElapsed();
        }

        stopWatch.start("Create CTF");
        ObjectArrayList ct = Helper.createCTF(formula);
        timeElapsed = stopWatch.stop();
        printFormulas(ct);
        stopWatch.printElapsed();

        statistics.put(Helper.CTF_CREATION_TIME, String.valueOf(timeElapsed));
        statistics.put(Helper.CTF_COUNT, String.valueOf(ct.size()));

        LOGGER.info("CTF count: {}", ct.size());

        if (Helper.EnableAssertions) {
            assertNoTripletsLost(formula, ct);
        }

        //  Clone CTF to verify formula satisfiability against it later
        ObjectArrayList ctfClone = null;

        if (Helper.EnableAssertions) {
            ctfClone = Helper.cloneStructures(ct);
        }

        stopWatch.start("Create CTS");
        Helper.completeToCTS(ct, formula.getPermutation());
        timeElapsed = stopWatch.stop();
        printFormulas(ct);
        stopWatch.printElapsed();

        statistics.put(Helper.CTS_CREATION_TIME, String.valueOf(timeElapsed));

        if (commandLine.hasOption(CREATE_SKT_OPTION)) {
            String sktFilename = formulaFile + ".skt";
            stopWatch.start("Convert CTS to " + sktFilename);
            Helper.convertCTStructuresToRomanovSKTFileFormat(ct, sktFilename);
            stopWatch.stop();
            stopWatch.printElapsed();

            return;
        }

        ObjectArrayList hss = unifyAndCreateHSS(statistics, stopWatch, ct);

        String hssPath = formulaFile + "-hss";
        stopWatch.start("Save HSS to " + hssPath + "...");
        Helper.saveHSS(hssPath, hss);
        stopWatch.stop();
        stopWatch.printElapsed();

        findHSSRoute(commandLine, formulaFile, statistics, stopWatch, formula, formulaClone, ctfClone, hss,
                hssPath);
    } catch (EmptyStructureException e) {
        stopWatch.stop();
        stopWatch.printElapsed();

        LOGGER.info("One of the structures was built empty", e);

        String resultsFilename = getResultsFilename(commandLine, formulaFile);
        stopWatch.start("Saving current statictics of calculations to " + resultsFilename);
        writeUnsatToFile(resultsFilename, statistics);
        stopWatch.stop();
        stopWatch.printElapsed();

        System.out.println("Formula not satisfiable");
    } finally {
        System.out.println("Program completed");
    }
}

From source file:jlite.cli.JobMatch.java

public static void main(String[] args) {
    System.out.println(); // extra line
    CommandLineParser parser = new GnuParser();
    Options options = setupOptions();/*from  w  w  w.  j a v  a  2  s .  c om*/
    HelpFormatter helpFormatter = new HelpFormatter();
    helpFormatter.setSyntaxPrefix("Usage: ");
    CommandLine line = null;
    try {
        line = parser.parse(options, args);
        if (line.hasOption("help")) {
            helpFormatter.printHelp(100, COMMAND, "\noptions:", options, "\n" + CLI.FOOTER, false);
            System.out.println(); // extra line
            System.exit(0);
        } else {
            if (line.hasOption("xml")) {
                System.out.println("<output>");
            }
            String[] remArgs = line.getArgs();
            if (remArgs.length == 1) {
                run(remArgs[0], line);
            } else if (remArgs.length == 0) {
                throw new MissingArgumentException("Missing required argument: <jdl_file>");
            } else {
                throw new UnrecognizedOptionException("Unrecognized extra arguments");
            }
        }
    } catch (ParseException e) {
        System.err.println(e.getMessage() + "\n");
        helpFormatter.printHelp(100, COMMAND, "\noptions:", options, "\n" + CLI.FOOTER, false);
        System.out.println(); // extra line
        System.exit(-1);
    } catch (Exception e) {
        if (line.hasOption("xml")) {
            System.out.println("<error>" + e.getMessage() + "</error>");
        } else {
            System.err.println(e.getMessage());
        }
    } finally {
        if (line.hasOption("xml")) {
            System.out.println("</output>");
        }
    }
    System.out.println(); // extra line
}

From source file:com.zimbra.common.util.RandomPassword.java

public static void main(String args[]) {
    CommandLineParser parser = new GnuParser();
    Options options = new Options();
    options.addOption("l", "localpart", false, "generated string does not contain dot(.)");

    CommandLine cl = null;
    boolean err = false;

    try {/*from   w  w w.ja va 2s.c o m*/
        cl = parser.parse(options, args, true);
    } catch (ParseException pe) {
        System.err.println("error: " + pe.getMessage());
        err = true;
    }

    if (err || cl.hasOption('h')) {
        usage();
    }

    boolean localpart = false;
    int minLength = DEFAULT_MIN_LENGTH;
    int maxLength = DEFAULT_MAX_LENGTH;

    if (cl.hasOption('l'))
        localpart = true;

    args = cl.getArgs();

    if (args.length != 0) {
        if (args.length != 2) {
            usage();
        }
        try {
            minLength = Integer.valueOf(args[0]).intValue();
            maxLength = Integer.valueOf(args[1]).intValue();
        } catch (Exception e) {
            System.err.println(e);
            e.printStackTrace();
        }
    }

    System.out.println(generate(minLength, maxLength, localpart));
}

From source file:name.martingeisse.ecotools.simulator.ui.Main.java

/**
 * The main method./* w  w w  .j  av a 2s.co m*/
 * @param args command-line arguments
 * @throws Exception Any exceptions are passed to the environment.
 */
public static void main(String[] args) throws Exception {

    /** define command-line options **/
    Options options = new Options();
    options.addOption("i", false, "interactive mode (do not start simulation automatically)");
    options.addOption("l", true, "load program");
    options.addOption("r", true, "load ROM contents");
    options.addOption("d", true, "enable disk simulation with the specified disk image file");
    options.addOption("t", true, "enable terminal simulation with the specified number of terminals (0..2)");
    options.addOption("g", false, "enable graphics controller simulation");
    options.addOption("c", false, "enable console simulation");
    options.addOption("C", false, "enable block console simulation");
    options.addOption("o", true, "enable output device simulation and write output to the specified file");
    options.addOption("s", false, "enable null sound device");

    /** print help for the empty command line **/
    if (args.length == 0) {
        showUsgeAndExit(options);
    }

    /** parse the command line **/
    CommandLineParser commandLineParser = new PosixParser();
    CommandLine commandLine;
    try {
        commandLine = commandLineParser.parse(options, args);
    } catch (UnrecognizedOptionException e) {
        System.out.println("unrecognized option: " + e.getOption());
        showUsgeAndExit(options);
        return;
    }

    /** build the simulator configuration **/
    SimulatorConfiguration configuration = new SimulatorConfiguration();

    /** load configuration files **/
    for (String arg : commandLine.getArgs()) {
        configuration.loadConfigurationFile(arg);
    }

    /** interpret the options **/

    if (commandLine.hasOption("l")) {
        configuration.setProgramFilename(commandLine.getOptionValue("l"));
    }

    if (commandLine.hasOption("r")) {
        configuration.setRomFilename(commandLine.getOptionValue("r"));
    }

    if (commandLine.hasOption("d")) {
        configuration.setDiskFilename(commandLine.getOptionValue("d"));
    }

    if (commandLine.hasOption("t")) {
        String terminalCountSpecification = commandLine.getOptionValue("t");
        try {
            configuration.setTerminalCount(
                    (terminalCountSpecification == null) ? 0 : Integer.parseInt(terminalCountSpecification));
        } catch (NumberFormatException e) {
            System.out.println("number format error in number of terminals: " + terminalCountSpecification);
        }
    }

    if (commandLine.hasOption("i")) {
        configuration.setInteractive(true);
    }

    if (commandLine.hasOption("g")) {
        configuration.setGraphics(true);
    }

    if (commandLine.hasOption("c")) {
        configuration.setConsole(true);
    }

    if (commandLine.hasOption("C")) {
        configuration.setBlockConsole(true);
    }

    if (commandLine.hasOption("o")) {
        configuration.setOutputFilename(commandLine.getOptionValue("o"));
    }

    if (commandLine.hasOption("s")) {
        configuration.setSound(true);
    }

    configuration.checkConsistency();
    configuration.deriveSettings();

    /** setup simulation framework and run **/
    EcoSimulatorFramework framework = new EcoSimulatorFramework();
    configuration.applyPreCreate(framework);
    framework.create();
    configuration.applyPostCreate(framework);
    framework.open();
    framework.mainLoop();
    framework.dispose();
    framework.exit();

}

From source file:edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance.java

/**
* This program does the pairwise alignment between each pair of sequences, 
* reports a summary of the average distances and the stdev at each rank.
* @param args//from   ww  w .j a  va2  s.co m
* @throws Exception 
*/
public static void main(String[] args) throws Exception {

    String trainseqFile = null;
    String taxFile = null;
    PrintStream outStream = null;
    AlignmentMode mode = AlignmentMode.overlap;
    boolean show_alignment = false;

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

        if (line.hasOption("show_alignment")) {
            show_alignment = true;
        }
        if (line.hasOption("alignment-mode")) {
            String m = line.getOptionValue("alignment-mode").toLowerCase();
            mode = AlignmentMode.valueOf(m);

        }

        if (args.length != 3) {
            throw new Exception("wrong arguments");
        }
        args = line.getArgs();
        trainseqFile = args[0];
        taxFile = args[1];
        outStream = new PrintStream(new File(args[2]));
    } catch (Exception e) {
        System.err.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(80, " [options] trainseqFile taxonFile outFile", "", options, "");
        return;
    }

    PairwiseSeqDistance theObj = new PairwiseSeqDistance(trainseqFile, taxFile, mode, show_alignment);

    theObj.printSummary(outStream);
}