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

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

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From source file:eu.edisonproject.classification.main.BatchMain.java

public static void main(String[] args) throws Exception {
    try {/*from   w w w  . ja v  a 2s .com*/
        //            args = new String[1];
        //            args[0] = "..";
        //            TestDataFlow.execute(args);
        //            System.exit(0);
        //            TestTFIDF.execute(args);

        Options options = new Options();

        Option operation = new Option("op", "operation", true, "type of operation to perform. "
                + "To convert txt to avro 'a'.\n" + "For running clasification on avro documents 'c'");
        operation.setRequired(true);
        options.addOption(operation);

        Option input = new Option("i", "input", true, "input path");
        input.setRequired(false);
        options.addOption(input);

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

        Option competencesVector = new Option("c", "competences-vector", true, "competences vectors");
        competencesVector.setRequired(false);
        options.addOption(competencesVector);

        Option v1 = new Option("v1", "vector1", true, "");
        v1.setRequired(false);
        options.addOption(v1);

        Option v2 = new Option("v2", "vector2", true, "");
        v2.setRequired(false);
        options.addOption(v2);

        Option popertiesFile = new Option("p", "properties", true, "path for a properties file");
        popertiesFile.setRequired(false);
        options.addOption(popertiesFile);

        CommandLineParser parser = new BasicParser();
        CommandLine cmd = parser.parse(options, args);
        String propPath = cmd.getOptionValue("properties");
        MyProperties prop;
        if (propPath == null) {
            prop = ConfigHelper
                    .getProperties(".." + File.separator + "etc" + File.separator + "configure.properties");
        } else {
            prop = ConfigHelper.getProperties(propPath);
        }

        switch (cmd.getOptionValue("operation")) {
        case "a":
            text2Avro(cmd.getOptionValue("input"), cmd.getOptionValue("output"), prop);
            break;
        case "c":
            calculateTFIDF(cmd.getOptionValue("input"), cmd.getOptionValue("output"),
                    cmd.getOptionValue("competences-vector"), prop);
            break;
        case "p":
            //                    -op p -v2 $HOME/Downloads/msc.csv -v1 $HOME/Downloads/job.csv -p $HOME/workspace/E-CO-2/etc/classification.properties
            profile(cmd.getOptionValue("v1"), cmd.getOptionValue("v2"), cmd.getOptionValue("output"));
            break;
        }

    } catch (IllegalArgumentException | ParseException | IOException ex) {
        Logger.getLogger(BatchMain.class.getName()).log(Level.SEVERE, null, ex);
    }

}

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 .ja v  a2  s  . co  m
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

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

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

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary 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: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  ww  w .j ava  2 s .  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:SequentialPersonalizedPageRank.java

@SuppressWarnings({ "static-access" })
public static void main(String[] args) throws IOException {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(/*from   w  w w .  j  ava2s . co  m*/
            OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
    options.addOption(OptionBuilder.withArgName("node").hasArg()
            .withDescription("source node (i.e., destination of the random jump)").create(SOURCE));

    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();

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

    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(SOURCE)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }

    String infile = cmdline.getOptionValue(INPUT);
    final String source = cmdline.getOptionValue(SOURCE);
    float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;

    int edgeCnt = 0;
    DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();

    BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));

    String line;
    while ((line = data.readLine()) != null) {
        line.trim();
        String[] arr = line.split("\\t");

        for (int i = 1; i < arr.length; i++) {
            graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
        }
    }

    data.close();

    if (!graph.containsVertex(source)) {
        System.err.println("Error: source node not found in the graph!");
        System.exit(-1);
    }

    WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();

    Set<Set<String>> components = clusterer.transform(graph);
    int numComponents = components.size();
    System.out.println("Number of components: " + numComponents);
    System.out.println("Number of edges: " + graph.getEdgeCount());
    System.out.println("Number of nodes: " + graph.getVertexCount());
    System.out.println("Random jump factor: " + alpha);

    // Compute personalized PageRank.
    PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph,
            new Transformer<String, Double>() {
                @Override
                public Double transform(String vertex) {
                    return vertex.equals(source) ? 1.0 : 0;
                }
            }, alpha);

    ranker.evaluate();

    // Use priority queue to sort vertices by PageRank values.
    PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
    int i = 0;
    for (String pmid : graph.getVertices()) {
        q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
    }

    // Print PageRank values.
    System.out.println("\nPageRank of nodes, in descending order:");
    Ranking<String> r = null;
    while ((r = q.poll()) != null) {
        System.out.println(r.rankScore + "\t" + r.getRanked());
    }
}

From source file:executables.Align.java

@SuppressWarnings("static-access")
public static void main(String[] args) throws IOException {
    Options options = new Options()
            .addOption(OptionBuilder.withArgName("f1").withDescription("Fasta file 1").hasArg().create("f1"))
            .addOption(OptionBuilder.withArgName("f2").withDescription("Fasta file 2").hasArg().create("f2"))
            .addOption(OptionBuilder.withArgName("s1").withDescription("sequence 1").hasArg().create("s1"))
            .addOption(OptionBuilder.withArgName("s2").withDescription("sequence 2").hasArg().create("s2"))
            .addOption(OptionBuilder.withArgName("gap-linear").withDescription("Linear gap cost").hasArg()
                    .create("gl"))
            .addOption(OptionBuilder.withArgName("gap-open").withDescription("Affine gap open cost").hasArg()
                    .create("go"))
            .addOption(OptionBuilder.withArgName("gap-extend").withDescription("Affine gap extend cost")
                    .hasArg().create("ge"))
            .addOption(OptionBuilder.withArgName("gap-function").withDescription("Gap function file").hasArg()
                    .create("gf"))
            .addOption(/*from w ww .  ja  va 2s.co  m*/
                    OptionBuilder.withArgName("gapless").withDescription("Gapless alignment").create("gapless"))
            .addOption(OptionBuilder.withArgName("mode")
                    .withDescription("Alignment mode: global,local,freeshift (Default: freeshift)").hasArg()
                    .create('m'))
            .addOption(OptionBuilder.withArgName("match").withDescription("Match score").hasArg().create("ma"))
            .addOption(OptionBuilder.withArgName("mismatch").withDescription("Mismatch score").hasArg()
                    .create("mi"))
            .addOption(OptionBuilder.withDescription("Do not append unaligned flanking sequences")
                    .create("noflank"))
            .addOption(OptionBuilder.withArgName("check").withDescription("Calculate checkscore").create('c'))
            .addOption(OptionBuilder.withArgName("format").withDescription(
                    "Output format, see String.format, parameters are: id1,id2,score,alignment (alignment only, if -f is specified); (default: '%s %s %.4f' w/o -f and '%s %s %.4f\n%s' w/ -f)")
                    .hasArg().create("format"))
            .addOption(OptionBuilder.withArgName("matrix")
                    .withDescription("Output dynamic programming matrix as well").create("matrix"))
            .addOption(OptionBuilder.withArgName("quasar-format")
                    .withDescription("Scoring matrix in quasar format").hasArg().create('q'))
            .addOption(
                    OptionBuilder.withArgName("pairs").withDescription("Pairs file").hasArg().create("pairs"))
            .addOption(OptionBuilder.withArgName("output").withDescription("Output").hasArg().create('o'))
            .addOption(OptionBuilder.withArgName("seqlib").withDescription("Seqlib file").hasArg()
                    .create("seqlib"))
            .addOption(OptionBuilder.withArgName("full").withDescription("Full output").create('f'));

    CommandLineParser parser = new PosixParser();
    try {
        CommandLine cmd = parser.parse(options, args);

        LongScoring<CharSequence> scoring = createScoring(cmd);
        AlignmentMode mode = createMode(cmd);
        if (mode == null)
            throw new ParseException("Mode unknown: " + cmd.getOptionValue('m'));

        Iterator<MutablePair<String, String>> idIterator = createSequences(scoring, cmd);

        GapCostFunction gap = createGapFunction(cmd);
        String format = getFormat(cmd);

        LongAligner<CharSequence> aligner;
        if (gap instanceof AffineGapCostFunction)
            aligner = new LongAligner<CharSequence>(scoring, ((AffineGapCostFunction) gap).getGapOpen(),
                    ((AffineGapCostFunction) gap).getGapExtend(), mode);
        else if (gap instanceof LinearGapCostFunction)
            aligner = new LongAligner<CharSequence>(scoring, ((LinearGapCostFunction) gap).getGap(), mode);
        else if (gap instanceof InfiniteGapCostFunction)
            aligner = new LongAligner<CharSequence>(scoring, mode);
        else
            throw new RuntimeException("Gap cost function " + gap.toString() + " currently not supported!");

        SimpleAlignmentFormatter formatter = cmd.hasOption('f')
                ? new SimpleAlignmentFormatter().setAppendUnaligned(!cmd.hasOption("noflank"))
                : null;

        CheckScore checkscore = cmd.hasOption('c') ? new CheckScore() : null;
        Alignment alignment = checkscore != null || formatter != null ? new Alignment() : null;

        float score;
        String ali;
        LineOrientedFile out = new LineOrientedFile(
                cmd.hasOption('o') ? cmd.getOptionValue('o') : LineOrientedFile.STDOUT);
        Writer wr = out.startWriting();

        while (idIterator.hasNext()) {
            MutablePair<String, String> ids = idIterator.next();

            score = alignment == null ? aligner.alignCache(ids.Item1, ids.Item2)
                    : aligner.alignCache(ids.Item1, ids.Item2, alignment);
            ali = formatter != null ? formatter.format(alignment, scoring, gap, mode,
                    scoring.getCachedSubject(ids.Item1), scoring.getCachedSubject(ids.Item2)) : "";
            out.writeLine(String.format(Locale.US, format, ids.Item1, ids.Item2, score, ali));

            if (cmd.hasOption("matrix")) {
                aligner.writeMatrix(wr,
                        aligner.getScoring().getCachedSubject(ids.Item1).toString().toCharArray(),
                        aligner.getScoring().getCachedSubject(ids.Item2).toString().toCharArray());
            }

            if (checkscore != null)
                checkscore.checkScore(aligner, scoring.getCachedSubject(ids.Item1).length(),
                        scoring.getCachedSubject(ids.Item2).length(), alignment, score);

        }

        out.finishWriting();

    } catch (ParseException e) {
        e.printStackTrace();
        HelpFormatter f = new HelpFormatter();
        f.printHelp("Align", options);
    }
}

From source file:Jimbo.Cheerlights.TweetListener.java

/**
 * @param args the command line arguments
 * @throws twitter4j.TwitterException//from  w  ww .  ja v  a2 s  . co m
 * @throws java.io.IOException
 * @throws org.apache.commons.cli.ParseException In case of command line error
 */
public static void main(String[] args) throws TwitterException, IOException, ParseException {
    // Set up simpler logging to stdout
    Jimbo.Logging.Logging.useStdout();

    LOG.log(Level.INFO, "Starting twitter listener");

    Options options = new Options();

    options.addOption("b", Listener.MQTT_BROKER_KEY, true, "URL of the broker")
            .addOption("c", Listener.MQTT_CLIENT_KEY, true, "The MQTT client name to use")
            .addOption("t", Listener.MQTT_TOPIC_KEY, true, "The MQTT topic to use");

    CommandLineParser parser = new DefaultParser();
    CommandLine command = parser.parse(options, args);

    MQTTClient mqtt = null;
    String mqtt_topic = Listener.DEFAULT_MQTT_TOPIC;

    if (command.hasOption(Listener.MQTT_BROKER_KEY)) {
        if (!command.hasOption(Listener.MQTT_CLIENT_KEY))
            throw new ParseException("MQTT without client name");

        if (command.hasOption(Listener.MQTT_TOPIC_KEY))
            mqtt_topic = command.getOptionValue(Listener.MQTT_TOPIC_KEY);

        try {
            mqtt = new MQTTClient(command.getOptionValue(Listener.MQTT_BROKER_KEY),
                    command.getOptionValue(Listener.MQTT_CLIENT_KEY));
            mqtt.run();
        }

        catch (MqttException e) {
            LOG.log(Level.WARNING, "Failed to create MQTT client: {0}", e.toString());
        }
    } else {
        if (command.hasOption(Listener.MQTT_TOPIC_KEY))
            LOG.warning("MQTT topic supplied but no broker");

        if (command.hasOption(Listener.MQTT_CLIENT_KEY))
            LOG.warning("MQTT client name but no broker");
    }

    Twitter twitter = new TwitterFactory().getInstance();
    StatusListener listener = new listener("224.1.1.1", (short) 5123, mqtt, mqtt_topic);
    FilterQuery fq = new FilterQuery();

    String keywords[] = { "#cheerlights" };

    fq.track(keywords);

    TwitterStream twitterStream = new TwitterStreamFactory().getInstance();
    twitterStream.addListener(listener);
    twitterStream.filter(fq);

    LOG.log(Level.INFO, "Up and running....");
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosGraphCreator.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);/*from   w  w  w .ja  va2 s .co  m*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output directory");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(optFileOpt);

    CommandLineParser parser = new PosixParser();

    try {

        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(OUT)));

        Class<?> inClazz = KyanosGraphCreator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();

        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource sourceResource = resourceSet.createResource(sourceUri);
        Map<String, Object> loadOpts = new HashMap<String, Object>();
        if ("zxmi".equals(sourceUri.fileExtension())) {
            loadOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        }

        Runtime.getRuntime().gc();
        long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory before loading: {0}",
                MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
        LOG.log(Level.INFO, "Loading source resource");
        sourceResource.load(loadOpts);
        LOG.log(Level.INFO, "Source resource loaded");
        Runtime.getRuntime().gc();
        long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory after loading: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
        LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));

        Resource targetResource = resourceSet.createResource(targetUri);

        Map<String, Object> saveOpts = new HashMap<String, Object>();

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                saveOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        storeOptions.add(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        saveOpts.put(BlueprintsResourceOptions.STORE_OPTIONS, storeOptions);
        targetResource.save(saveOpts);

        LOG.log(Level.INFO, "Start moving elements");
        targetResource.getContents().clear();
        targetResource.getContents().addAll(sourceResource.getContents());
        LOG.log(Level.INFO, "End moving elements");
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saved");

        if (targetResource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) targetResource);
        } else {
            targetResource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

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

public static void main(String[] args) {
    // @formatter:off
    Options options = new Options();
    OptionHelper.add(options, OPTION_CONFIG, true, false, "path", "config file");
    // @formatter:on

    CommandLineParser clp = new GnuParser();

    CommandLine line = null;//from w  w w.  j a  v a 2s. c  o m
    try {
        line = clp.parse(options, args);
    } catch (ParseException e) {
        System.err.println("Parsing command line failed: " + e.getMessage());
        new HelpFormatter().printHelp(HELP_MESSAGE, options);
        System.exit(1);
    }

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

    Configuration configuration = PreferenceManager.getConfiguration();
    String lookAndFeel = configuration.getSelectedLookAndFeel();
    if (lookAndFeel == null) {
        lookAndFeel = UIManager.getSystemLookAndFeelClassName();
    }
    try {
        UIManager.setLookAndFeel(lookAndFeel);
    } catch (Exception e) {
        logger.error("error while setting look and feel '" + lookAndFeel + "': " + e.getClass().getSimpleName()
                + ", message: " + e.getMessage());
    }

    Content content = null;
    String filename = "res/presets/Startup.geom";

    String[] extra = line.getArgs();
    if (extra.length > 0) {
        filename = extra[0];
    }

    ContentReader reader = new ContentReader();
    InputStream input = Thread.currentThread().getContextClassLoader().getResourceAsStream(filename);
    try {
        content = reader.read(input);
    } catch (Exception e) {
        logger.info("unable to load startup geometry file", e);
        logger.info("Exception: " + e.getClass().getSimpleName());
        logger.info("Message: " + e.getMessage());
    }

    final LiveCG runner = new LiveCG();
    final Content c = content;

    SwingUtilities.invokeLater(new Runnable() {
        @Override
        public void run() {
            runner.setup(true, c);
        }
    });
    SwingUtilities.invokeLater(new Runnable() {
        @Override
        public void run() {
            runner.frame.requestFocus();
        }
    });
}

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.");
    }/*  www .  jav  a2 s.  c o  m*/

    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;

    }

}