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:apps.quantification.LearnQuantificationSVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_learn> <path to svm_light_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);//  ww  w  . j a v  a 2  s.com
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_light (default 1)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("k");
    OptionBuilder.withDescription("Kernel type (default 0: linear, 1: polynomial, 2: RBF, 3: sigmoid)");
    OptionBuilder.withLongOpt("k");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    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_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightLearnerCustomizer classificationLearnerCustomizer = null;
    SvmLightClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

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

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmLightLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmLightClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("k")) {
            System.out.println("Kernel type: " + line.getOptionValue("k"));
            classificationLearnerCustomizer.setKernelType(Integer.parseInt(line.getOptionValue("k")));
        }

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmLightOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.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);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmLightLearner classificationLearner = new SvmLightLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmLightLearnPath());
    IDataManager classifierDataManager = new SvmLightDataManager(new SvmLightClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_light_classify"));
    String description = "_SVMLight_C-" + classificationLearnerCustomizer.getC() + "_K-"
            + classificationLearnerCustomizer.getKernelType();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:apps.quantification.QuantifySVMLight.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = QuantifySVMLight.class.getName()
            + " [OPTIONS] <path to svm_light_classify> <testIndexDirectory> <quantificationModelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);/*from  w w  w  .ja va2s  .c  o 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 files in svm_light format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmLightClassifierCustomizer customizer = null;

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

        remainingArgs = line.getArgs();

        customizer = new SvmLightClassifierCustomizer(remainingArgs[0]);

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

        if (line.hasOption("s")) {
            System.out.println("Keeping temporary files.");
            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 indexFile = remainingArgs[1];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String quantifierFilename = remainingArgs[2];

    FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false);
    indexFssm.open();

    IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    indexFssm.close();

    FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false);
    quantifierFssm.open();

    SvmLightDataManager classifierDataManager = new SvmLightDataManager(customizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false);
    fssm.open();

    IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager,
            ClassificationMode.PER_CATEGORY);
    fssm.close();

    quantifierFssm.close();

    Quantification ccQuantification = quantifiers[0].quantify(test);
    Quantification paQuantification = quantifiers[1].quantify(test);
    Quantification accQuantification = quantifiers[2].quantify(test);
    Quantification maxQuantification = quantifiers[3].quantify(test);
    Quantification sccQuantification = quantifiers[4].quantify(test);
    Quantification spaQuantification = quantifiers[5].quantify(test);
    Quantification trueQuantification = new Quantification("True", test.getClassificationDB());

    File quantifierFile = new File(quantifierFilename);

    String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_"
            + quantifierFile.getName() + ".txt";

    BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName));
    IShortIterator iterator = test.getCategoryDB().getCategories();
    while (iterator.hasNext()) {
        short category = iterator.next();
        String prefix = quantifierFile.getName() + "\t" + indexName + "\t"
                + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t"
                + trueQuantification.getQuantification(category) + "\t";

        writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category)
                + "\n");
    }
    writer.close();

    BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator()
            + indexName + "_" + quantifierFile.getName() + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs();
    TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleTPRs();
    TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs();

    ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet();
    ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3])
            .getInternalQuantifier()).getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = test.getCategoryDB().getCategoryName(cat);
        ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat);
        ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double maxTPR = maxTPRs.get(cat);
        double maxFPR = maxFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat
                + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t"
                + simpleFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t"
                + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn()
                + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t"
                + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t"
                + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:apps.quantification.QuantifySVMPerf.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = QuantifySVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <quantificationModelDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("d");
    OptionBuilder.withDescription("Dump confidences file");
    OptionBuilder.withLongOpt("d");
    OptionBuilder.isRequired(false);//from ww  w .j  a va  2  s  . com
    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 files 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("v"))
            customizer.printSvmPerfOutput(true);

        if (line.hasOption("s")) {
            System.out.println("Keeping temporary files.");
            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 indexFile = remainingArgs[1];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String quantifierFilename = remainingArgs[2];

    FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false);
    indexFssm.open();

    IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    indexFssm.close();

    FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false);
    quantifierFssm.open();

    SvmPerfDataManager classifierDataManager = new SvmPerfDataManager(customizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false);
    fssm.open();

    IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager,
            ClassificationMode.PER_CATEGORY);
    fssm.close();

    quantifierFssm.close();

    Quantification ccQuantification = quantifiers[0].quantify(test);
    Quantification paQuantification = quantifiers[1].quantify(test);
    Quantification accQuantification = quantifiers[2].quantify(test);
    Quantification maxQuantification = quantifiers[3].quantify(test);
    Quantification sccQuantification = quantifiers[4].quantify(test);
    Quantification spaQuantification = quantifiers[5].quantify(test);
    Quantification trueQuantification = new Quantification("True", test.getClassificationDB());

    File quantifierFile = new File(quantifierFilename);

    String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_"
            + quantifierFile.getName() + ".txt";

    BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName));
    IShortIterator iterator = test.getCategoryDB().getCategories();
    while (iterator.hasNext()) {
        short category = iterator.next();
        String prefix = quantifierFile.getName() + "\t" + indexName + "\t"
                + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t"
                + trueQuantification.getQuantification(category) + "\t";

        writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category)
                + "\n");
        writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category)
                + "\n");
    }
    writer.close();

    BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator()
            + indexName + "_" + quantifierFile.getName() + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs();
    TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleTPRs();
    TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier())
            .getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs();

    ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet();
    ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3])
            .getInternalQuantifier()).getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = test.getCategoryDB().getCategoryName(cat);
        ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat);
        ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double maxTPR = maxTPRs.get(cat);
        double maxFPR = maxFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat
                + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t"
                + simpleFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t"
                + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn()
                + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n";
        bfs.write(line);
        line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t"
                + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t"
                + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t"
                + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:co.paralleluniverse.photon.Photon.java

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

    final Options options = new Options();
    options.addOption("rate", true, "Requests per second (default " + rateDefault + ")");
    options.addOption("duration", true,
            "Minimum test duration in seconds: will wait for <duration> * <rate> requests to terminate or, if progress check enabled, no progress after <duration> (default "
                    + durationDefault + ")");
    options.addOption("maxconnections", true,
            "Maximum number of open connections (default " + maxConnectionsDefault + ")");
    options.addOption("timeout", true,
            "Connection and read timeout in millis (default " + timeoutDefault + ")");
    options.addOption("print", true,
            "Print cycle in millis, 0 to disable intermediate statistics (default " + printCycleDefault + ")");
    options.addOption("check", true,
            "Progress check cycle in millis, 0 to disable progress check (default " + checkCycleDefault + ")");
    options.addOption("stats", false, "Print full statistics when finish (default false)");
    options.addOption("minmax", false, "Print min/mean/stddev/max stats when finish (default false)");
    options.addOption("name", true, "Test name to print in the statistics (default '" + testNameDefault + "')");
    options.addOption("help", false, "Print help");

    try {/*from  w  w  w  .j  a v  a  2  s.c  om*/
        final CommandLine cmd = new BasicParser().parse(options, args);
        final String[] ar = cmd.getArgs();
        if (cmd.hasOption("help") || ar.length != 1)
            printUsageAndExit(options);

        final String url = ar[0];

        final int timeout = Integer.parseInt(cmd.getOptionValue("timeout", timeoutDefault));
        final int maxConnections = Integer
                .parseInt(cmd.getOptionValue("maxconnections", maxConnectionsDefault));
        final int duration = Integer.parseInt(cmd.getOptionValue("duration", durationDefault));
        final int printCycle = Integer.parseInt(cmd.getOptionValue("print", printCycleDefault));
        final int checkCycle = Integer.parseInt(cmd.getOptionValue("check", checkCycleDefault));
        final String testName = cmd.getOptionValue("name", testNameDefault);
        final int rate = Integer.parseInt(cmd.getOptionValue("rate", rateDefault));

        final MetricRegistry metrics = new MetricRegistry();
        final Meter requestMeter = metrics.meter("request");
        final Meter responseMeter = metrics.meter("response");
        final Meter errorsMeter = metrics.meter("errors");
        final Logger log = LoggerFactory.getLogger(Photon.class);
        final ConcurrentHashMap<String, AtomicInteger> errors = new ConcurrentHashMap<>();
        final HttpGet request = new HttpGet(url);
        final StripedTimeSeries<Long> sts = new StripedTimeSeries<>(30000, false);
        final StripedHistogram sh = new StripedHistogram(60000, 5);

        log.info("name: " + testName + " url:" + url + " rate:" + rate + " duration:" + duration
                + " maxconnections:" + maxConnections + ", " + "timeout:" + timeout);
        final DefaultConnectingIOReactor ioreactor = new DefaultConnectingIOReactor(IOReactorConfig.custom()
                .setConnectTimeout(timeout).setIoThreadCount(10).setSoTimeout(timeout).build());

        Runtime.getRuntime().addShutdownHook(new Thread(() -> {
            final List<ExceptionEvent> events = ioreactor.getAuditLog();
            if (events != null)
                events.stream().filter(event -> event != null).forEach(event -> {
                    System.err.println(
                            "Apache Async HTTP Client I/O Reactor Error Time: " + event.getTimestamp());
                    //noinspection ThrowableResultOfMethodCallIgnored
                    if (event.getCause() != null)
                        //noinspection ThrowableResultOfMethodCallIgnored
                        event.getCause().printStackTrace();
                });
            if (cmd.hasOption("stats"))
                printFinishStatistics(errorsMeter, sts, sh, testName);
            if (!errors.keySet().isEmpty())
                errors.entrySet().stream()
                        .forEach(p -> log.info(testName + " " + p.getKey() + " " + p.getValue() + "ms"));
            System.out.println(
                    testName + " responseTime(90%): " + sh.getHistogramData().getValueAtPercentile(90) + "ms");
            if (cmd.hasOption("minmax")) {
                final HistogramData hd = sh.getHistogramData();
                System.out.format("%s %8s%8s%8s%8s\n", testName, "min", "mean", "sd", "max");
                System.out.format("%s %8d%8.2f%8.2f%8d\n", testName, hd.getMinValue(), hd.getMean(),
                        hd.getStdDeviation(), hd.getMaxValue());
            }
        }));

        final PoolingNHttpClientConnectionManager mngr = new PoolingNHttpClientConnectionManager(ioreactor);
        mngr.setDefaultMaxPerRoute(maxConnections);
        mngr.setMaxTotal(maxConnections);
        final CloseableHttpAsyncClient ahc = HttpAsyncClientBuilder.create().setConnectionManager(mngr)
                .setDefaultRequestConfig(RequestConfig.custom().setLocalAddress(null).build()).build();
        try (final CloseableHttpClient client = new FiberHttpClient(ahc)) {
            final int num = duration * rate;

            final CountDownLatch cdl = new CountDownLatch(num);
            final Semaphore sem = new Semaphore(maxConnections);
            final RateLimiter rl = RateLimiter.create(rate);

            spawnStatisticsThread(printCycle, cdl, log, requestMeter, responseMeter, errorsMeter, testName);

            for (int i = 0; i < num; i++) {
                rl.acquire();
                if (sem.availablePermits() == 0)
                    log.debug("Maximum connections count reached, waiting...");
                sem.acquireUninterruptibly();

                new Fiber<Void>(() -> {
                    requestMeter.mark();
                    final long start = System.nanoTime();
                    try {
                        try (final CloseableHttpResponse ignored = client.execute(request)) {
                            responseMeter.mark();
                        } catch (final Throwable t) {
                            markError(errorsMeter, errors, t);
                        }
                    } catch (final Throwable t) {
                        markError(errorsMeter, errors, t);
                    } finally {
                        final long now = System.nanoTime();
                        final long millis = TimeUnit.NANOSECONDS.toMillis(now - start);
                        sts.record(start, millis);
                        sh.recordValue(millis);
                        sem.release();
                        cdl.countDown();
                    }
                }).start();
            }
            spawnProgressCheckThread(log, duration, checkCycle, cdl);
            cdl.await();
        }
    } catch (final ParseException ex) {
        System.err.println("Parsing failed.  Reason: " + ex.getMessage());
    }
}

From source file:client.MultiplexingClient.java

public static void main(String[] args) throws Exception {
    // Prepare to parse the command line
    Options options = new Options();
    Option sslOpt = new Option("s", "ssl", false, "Use SSL");
    Option debugOpt = new Option("d", true,
            "Debug level (NONE, FINER, FINE, CONFIG, INFO, WARNING, SEVERE. Default INFO.");
    Option numConnectionsOpt = new Option("n", true, "Number of connections to establish. [Default: 1]");
    Option numPcktOpt = new Option("p", true, "Number of packets to send in each connection. [Default: 20]");
    Option pcktMaxSizeOpt = new Option("m", true, "Maximum size of packets. [Default: 4096]");
    Option help = new Option("h", "print this message");

    options.addOption(help);//  w  w w.  j  ava2 s  .co  m
    options.addOption(debugOpt);
    options.addOption(numConnectionsOpt);
    options.addOption(numPcktOpt);
    options.addOption(pcktMaxSizeOpt);
    options.addOption(sslOpt);
    CommandLineParser parser = new PosixParser();
    // parse the command line arguments
    CommandLine line = parser.parse(options, args);

    if (line.hasOption(help.getOpt()) || line.getArgs().length < 1) {
        showUsage(options);
        return;
    }

    if (line.hasOption(sslOpt.getOpt())) {
        channelFactory = new SSLChannelFactory(true, TRUSTSTORE, TRUSTSTORE_PASSWORD);
    } else {
        channelFactory = new PlainChannelFactory();
    }

    if (line.hasOption(numConnectionsOpt.getOpt())) {
        connectionCount = Integer.parseInt(line.getOptionValue(numConnectionsOpt.getOpt()));
    } else {
        connectionCount = 1;
    }

    if (line.hasOption(numPcktOpt.getOpt())) {
        packetsToSend = Integer.parseInt(line.getOptionValue(numPcktOpt.getOpt()));
    } else {
        packetsToSend = 20;
    }

    if (line.hasOption(pcktMaxSizeOpt.getOpt())) {
        maxPcktSize = Integer.parseInt(line.getOptionValue(pcktMaxSizeOpt.getOpt()));
    } else {
        maxPcktSize = 4096;
    }

    InetSocketAddress remotePoint;
    try {
        String host = line.getArgs()[0];
        int colonIndex = host.indexOf(':');
        remotePoint = new InetSocketAddress(host.substring(0, colonIndex),
                Integer.parseInt(host.substring(colonIndex + 1)));
    } catch (Exception e) {
        showUsage(options);
        return;
    }

    // Setups the logging context for Log4j
    //     NDC.push(Thread.currentThread().getName());

    st = new SelectorThread();
    for (int i = 0; i < connectionCount; i++) {
        new MultiplexingClient(remotePoint);
        // Must sleep for a while between opening connections in order
        // to give the remote host enough time to handle them. Otherwise,
        // the remote host backlog will get full and the connection
        // attemps will start to be refused.
        Thread.sleep(100);
    }
}

From source file:com.genentech.retrival.tabExport.TABExporter.java

public static void main(String[] args) throws ParseException, JDOMException, IOException {
    long start = System.currentTimeMillis();
    int nStruct = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("sqlFile", true, "sql-xml file");
    opt.setRequired(true);//from w  ww  . j av a  2  s . c om
    options.addOption(opt);

    opt = new Option("sqlName", true, "name of SQL element in xml file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("o", true, "output file");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("newLineReplacement", true,
            "If given newlines in fields will be replaced by this string.");
    options.addOption(opt);

    opt = new Option("noHeader", false, "Do not output header line");
    options.addOption(opt);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    String outFile = cmd.getOptionValue("o");
    String sqlFile = cmd.getOptionValue("sqlFile");
    String sqlName = cmd.getOptionValue("sqlName");
    String newLineReplacement = cmd.getOptionValue("newLineReplacement");

    args = cmd.getArgs();

    try {
        PrintStream out = System.out;
        if (outFile != null)
            out = new PrintStream(outFile);

        SQLStatement stmt = SQLStatement.createFromFile(new File(sqlFile), sqlName);
        Object[] sqlArgs = args;
        if (stmt.getParamTypes().length != args.length) {
            System.err.printf(
                    "\nWarining sql statement needs %d parameters but got only %d. Filling up with NULLs.\n",
                    stmt.getParamTypes().length, args.length);
            sqlArgs = new Object[stmt.getParamTypes().length];
            System.arraycopy(args, 0, sqlArgs, 0, args.length);
        }

        Selecter sel = Selecter.factory(stmt);
        if (!sel.select(sqlArgs)) {
            System.err.println("No rows returned!");
            System.exit(0);
        }

        String[] fieldNames = sel.getFieldNames();
        if (fieldNames.length == 0) {
            System.err.println("Query did not return any columns");
            exitWithHelp(options);
        }

        if (!cmd.hasOption("noHeader")) {
            StringBuilder sb = new StringBuilder(200);
            for (String f : fieldNames)
                sb.append(f).append('\t');
            if (sb.length() > 1)
                sb.setLength(sb.length() - 1); // chop last \t
            String header = sb.toString();

            out.println(header);
        }

        StringBuilder sb = new StringBuilder(200);
        while (sel.hasNext()) {
            Record sqlRec = sel.next();
            sb.setLength(0);

            for (int i = 0; i < fieldNames.length; i++) {
                String fld = sqlRec.getStrg(i);
                if (newLineReplacement != null)
                    fld = NEWLinePattern.matcher(fld).replaceAll(newLineReplacement);

                sb.append(fld).append('\t');
            }

            if (sb.length() > 1)
                sb.setLength(sb.length() - 1); // chop last \t
            String row = sb.toString();

            out.println(row);

            nStruct++;
        }

    } catch (Exception e) {
        throw new Error(e);
    } finally {
        System.err.printf("TABExporter: Exported %d records in %dsec\n", nStruct,
                (System.currentTimeMillis() - start) / 1000);
    }
}

From source file:com.aerospike.examples.Main.java

/**
 * Main entry point.//from w  ww .j a va2 s  .c  om
 */
public static void main(String[] args) {

    try {
        Options options = new Options();
        options.addOption("h", "host", true, "Server hostname (default: localhost)");
        options.addOption("p", "port", true, "Server port (default: 3000)");
        options.addOption("U", "user", true, "User name");
        options.addOption("P", "password", true, "Password");
        options.addOption("n", "namespace", true, "Namespace (default: test)");
        options.addOption("s", "set", true, "Set name. Use 'empty' for empty set (default: demoset)");
        options.addOption("g", "gui", false, "Invoke GUI to selectively run tests.");
        options.addOption("d", "debug", false, "Run in debug mode.");
        options.addOption("u", "usage", false, "Print usage.");

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

        if (args.length == 0 || cl.hasOption("u")) {
            logUsage(options);
            return;
        }
        Parameters params = parseParameters(cl);
        String[] exampleNames = cl.getArgs();

        if ((exampleNames.length == 0) && (!cl.hasOption("g"))) {
            logUsage(options);
            return;
        }

        // Check for all.
        for (String exampleName : exampleNames) {
            if (exampleName.equalsIgnoreCase("all")) {
                exampleNames = ExampleNames;
                break;
            }
        }

        if (cl.hasOption("d")) {
            Log.setLevel(Level.DEBUG);
        }

        if (cl.hasOption("g")) {
            GuiDisplay.startGui(params);
        } else {
            Console console = new Console();
            runExamples(console, params, exampleNames);
        }
    } catch (Exception ex) {
        System.out.println(ex.getMessage());
        ex.printStackTrace();
    }
}

From source file:microbiosima.Microbiosima.java

/**
 * @param args//from w w  w  .j ava 2  s . c o m
 *            the command line arguments
 * @throws java.io.FileNotFoundException
 * @throws java.io.UnsupportedEncodingException
 */
public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException {
    //Init with default values
    int populationSize = 500;
    int microSize = 1000;
    int numberOfSpecies = 150;
    int numberOfGeneration = 10000;
    int numberOfObservation = 100;
    int numberOfReplication = 1;
    double pctEnv = 0;
    double pctPool = 0;

    Options options = new Options();

    Option help = new Option("h", "help", false, "print this message");
    Option version = new Option("v", "version", false, "print the version information and exit");
    options.addOption(help);
    options.addOption(version);

    options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS")
            .desc("Number generation for observation [default: 100]").build());
    options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP")
            .desc("Number of replication [default: 1]").build());

    Builder C = Option.builder("c").longOpt("config").numberOfArgs(4).argName("Pop Micro Spec Gen")
            .desc("Four Parameters in the following orders: "
                    + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation"
                    + " [default: 500 1000 150 10000]");
    options.addOption(C.build());

    HelpFormatter formatter = new HelpFormatter();
    String syntax = "microbiosima pctEnv pctPool";
    String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n"
            + "required arguments:\n" + "  pctEnv             Percentage of environmental acquisition\n"
            + "  pctPool            Percentage of pooled environmental component\n" + "\noptional arguments:\n";
    String footer = "\n";

    formatter.setWidth(80);

    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = null;

    try {
        cmd = parser.parse(options, args);
        String[] pct_config = cmd.getArgs();

        if (cmd.hasOption("h") || args.length == 0) {
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(0);
        }
        if (cmd.hasOption("v")) {
            System.out.println("Microbiosima " + VERSION);
            System.exit(0);
        }
        if (pct_config.length != 2) {
            System.out.println("ERROR! Required exactly two argumennts for pct_env and pct_pool. It got "
                    + pct_config.length + ": " + Arrays.toString(pct_config));
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(3);
        } else {
            pctEnv = Double.parseDouble(pct_config[0]);
            pctPool = Double.parseDouble(pct_config[1]);
            if (pctEnv < 0 || pctEnv > 1) {
                System.out.println(
                        "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv="
                                + pctEnv + ")! EXIT");
                System.exit(3);
            }
            if (pctPool < 0 || pctPool > 1) {
                System.out.println(
                        "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool="
                                + pctPool + ")! EXIT");
                System.exit(3);
            }

        }
        if (cmd.hasOption("config")) {
            String[] configs = cmd.getOptionValues("config");
            populationSize = Integer.parseInt(configs[0]);
            microSize = Integer.parseInt(configs[1]);
            numberOfSpecies = Integer.parseInt(configs[2]);
            numberOfGeneration = Integer.parseInt(configs[3]);
        }
        if (cmd.hasOption("obs")) {
            numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs"));
        }
        if (cmd.hasOption("rep")) {
            numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep"));
        }

    } catch (ParseException e) {
        e.printStackTrace();
        System.exit(3);
    }

    StringBuilder sb = new StringBuilder();
    sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize)
            .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ")
            .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration)
            .append("\n\tNumber generation for observation: ").append(numberOfObservation)
            .append("\n\tNumber of replication: ").append(numberOfReplication).append("\n");
    System.out.println(sb.toString());

    //      System.exit(3);
    // LogNormalDistribution lgd=new LogNormalDistribution(0,1);
    // environment=lgd.sample(150);
    // double environment_sum=0;
    // for (int i=0;i<No;i++){
    // environment_sum+=environment[i];
    // }
    // for (int i=0;i<No;i++){
    // environment[i]/=environment_sum;
    // }

    double[] environment = new double[numberOfSpecies];
    for (int i = 0; i < numberOfSpecies; i++) {
        environment[i] = 1 / (double) numberOfSpecies;
    }

    for (int rep = 0; rep < numberOfReplication; rep++) {
        String prefix = "" + (rep + 1) + "_";
        String sufix = "_E" + pctEnv + "_P" + pctPool + ".txt";

        System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix);
        try {

            PrintWriter file1 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix)));
            PrintWriter file2 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix)));
            PrintWriter file3 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix)));
            PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix)));
            PrintWriter file5 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix)));
            PrintWriter file6 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix)));

            Population population = new Population(microSize, environment, populationSize, pctEnv, pctPool, 0,
                    0);

            while (population.getNumberOfGeneration() < numberOfGeneration) {
                population.sumSpecies();
                if (population.getNumberOfGeneration() % numberOfObservation == 0) {
                    file1.println(population.gammaDiversity(true));
                    file2.println(population.alphaDiversity(true));
                    file3.print(population.betaDiversity(true));
                    file3.print("\t");
                    file3.println(population.BrayCurtis(true));
                    file4.println(population.printOut());
                    file5.println(population.interGenerationDistance());
                    file6.println(population.environmentPopulationDistance());
                }
                population.getNextGen();
            }
            file1.close();
            file2.close();
            file3.close();
            file4.close();
            file5.close();
            file6.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:androidimporter.AndroidImporter.java

public static void main(String[] args) throws ParseException {
    //"/usr/local/apache-ant/bin/ant"
    String antPath = System.getProperty("ANT_PATH", System.getenv("ANT_PATH"));
    if (antPath == null || !new File(antPath).exists()) {
        throw new RuntimeException("Cannot find ant at " + antPath
                + ".  Please specify location to ant via the ANT_PATH environment variable or java system property.");
    }/*w w  w. ja  va  2 s  .  com*/

    Options opts = new Options()
            .addOption("i", "android-resource-dir", true, "Android project res directory path")
            .addOption("o", "cn1-project-dir", true, "Path to the CN1 output project directory.")
            .addOption("r", "cn1-resource-file", false,
                    "Path to CN1 output .res file.  Defaults to theme.res in project dir")
            .addOption("p", "package", true, "Java package to place GUI forms in.")
            .addOption("h", "help", false, "Usage instructions");

    CommandLineParser parser = new DefaultParser();

    CommandLine line = parser.parse(opts, args);

    if (line.hasOption("help")) {
        showHelp(opts);
        System.exit(0);
    }
    args = line.getArgs();

    if (args.length < 1) {
        System.out.println("No command provided.");
        showHelp(opts);
        System.exit(0);
    }

    switch (args[0]) {
    case "import-project": {

        if (!line.hasOption("android-resource-dir") || !line.hasOption("cn1-project-dir")
                || !line.hasOption("package")) {
            System.out.println("Please provide android-resource-dir, package, and cn1-project-dir options");
            showHelp(opts);
            System.exit(1);
        }
        File resDir = findResDir(new File(line.getOptionValue("android-resource-dir")));
        if (resDir == null || !resDir.isDirectory()) {
            System.out.println("Failed to find android resource directory from provided value");
            showHelp(opts);
            System.exit(1);
        }

        File projDir = new File(line.getOptionValue("cn1-project-dir"));
        File resFile = new File(projDir, "src" + File.separator + "theme.res");
        if (line.hasOption("cn1-resource-file")) {
            resFile = new File(line.getOptionValue("cn1-resource-file"));
        }

        JavaSEPort.setShowEDTViolationStacks(false);
        JavaSEPort.setShowEDTWarnings(false);
        JFrame frm = new JFrame("Placeholder");
        frm.setVisible(false);
        Display.init(frm.getContentPane());
        JavaSEPort.setBaseResourceDir(resFile.getParentFile());
        try {
            System.out.println("About to import project at " + resDir.getAbsolutePath());
            System.out.println("Codename One Output Project: " + projDir.getAbsolutePath());
            System.out.println("Resource file: " + resFile.getAbsolutePath());
            System.out.println("Java Package: " + line.getOptionValue("package"));
            AndroidProjectImporter.importProject(resDir, projDir, resFile, line.getOptionValue("package"));
            Runtime.getRuntime().exec(new String[] { antPath, "init" }, new String[] {},
                    resFile.getParentFile().getParentFile());
            //runAnt(new File(resFile.getParentFile().getParentFile(), "build.xml"), "init");
            System.exit(0);
        } catch (Exception ex) {
            ex.printStackTrace();
        } finally {
            System.exit(0);
        }
        break;
    }

    default:
        System.out.println("Unknown command " + args[0]);
        showHelp(opts);
        break;

    }

}

From source file:com.genentech.chemistry.openEye.apps.SDFTopologicalIndexer.java

/**
 * @param args/*ww  w. ja  v a2 s . c  o m*/
 */
public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option(OPT_INFILE, true,
            "input file oe-supported Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    opt.setArgName("fn");
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    opt.setArgName("fn");
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    if (args.length == 0) {
        System.err.println("Specify at least one index type");
        exitWithHelp(options);
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    Set<String> selectedIndexes = new HashSet<String>(args.length);
    if (args.length == 1 && "all".equalsIgnoreCase(args[0]))
        selectedIndexes = AVAILIndexes;
    else
        selectedIndexes.addAll(Arrays.asList(args));

    if (!AVAILIndexes.containsAll(selectedIndexes)) {
        selectedIndexes.removeAll(AVAILIndexes);
        StringBuilder err = new StringBuilder("Unknown Index types: ");
        for (String it : selectedIndexes)
            err.append(it).append(" ");
        System.err.println(err);
        exitWithHelp(options);
    }

    SDFTopologicalIndexer sdfIndexer = new SDFTopologicalIndexer(outFile, selectedIndexes);

    sdfIndexer.run(inFile);
    sdfIndexer.close();
}