Example usage for java.io PrintWriter PrintWriter

List of usage examples for java.io PrintWriter PrintWriter

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Introduction

In this page you can find the example usage for java.io PrintWriter PrintWriter.

Prototype

public PrintWriter(File file) throws FileNotFoundException

Source Link

Document

Creates a new PrintWriter, without automatic line flushing, with the specified file.

Usage

From source file:ekb.elastic.ingest.TaxiQuery.java

public static void main(String... args) {

    Options options = new Options();
    HelpFormatter help = new HelpFormatter();

    try {// www.  j a v a 2 s  .c  o m
        Option hostOpt = new Option("h", "host", true, "ElasticSearch URL");
        hostOpt.setArgs(1);
        hostOpt.setRequired(true);
        Option portOpt = new Option("p", "port", true, "ElasticSearch URL");
        portOpt.setArgs(1);
        portOpt.setRequired(true);
        Option clusterOpt = new Option("c", "cluster", true, "Cluster");
        clusterOpt.setArgs(1);
        clusterOpt.setRequired(true);
        Option indexOpt = new Option("i", "index", true, "The index");
        indexOpt.setArgs(1);
        indexOpt.setRequired(true);

        Option pickupTimeOpt = new Option("u", "pickup", true, "The pickup time");
        pickupTimeOpt.setArgs(1);
        pickupTimeOpt.setRequired(true);
        Option dropTimeOpt = new Option("d", "dropoff", true, "The dropoff time");
        dropTimeOpt.setArgs(1);
        dropTimeOpt.setRequired(true);

        options.addOption(hostOpt);
        options.addOption(portOpt);
        options.addOption(clusterOpt);
        options.addOption(indexOpt);
        options.addOption(pickupTimeOpt);
        options.addOption(dropTimeOpt);

        GnuParser parser = new GnuParser();
        CommandLine cmd = parser.parse(options, args);

        Settings settings = ImmutableSettings.settingsBuilder().put("cluster.name", cmd.getOptionValue('c'))
                .build();
        Client client = new TransportClient(settings).addTransportAddress(new InetSocketTransportAddress(
                cmd.getOptionValue('h'), Integer.parseInt(cmd.getOptionValue('p'))));

        TaxiQuery tq = new TaxiQuery();

        TaxiStats stats = tq.getTaxiStats(client, cmd.getOptionValues("i"));

        log.info("Results:\n" + stats.toDateString());

        sdf.parse(cmd.getOptionValue("u"));
        sdf.parse(cmd.getOptionValue("d"));

        // 2013-01-01T10:10:00

        ArrayList<TaxiBucket> list = tq.getInterval(client, cmd.getOptionValues("index"),
                cmd.getOptionValue("u"), cmd.getOptionValue("d"), 60);

        log.info("List size is: " + list.size());

        client.close();

    } catch (ParseException pe) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);

        help.printUsage(pw, 80, TaxiQuery.class.getName(), options);

        log.error(sw.toString());

    } catch (TaxiQueryException e) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);
        e.printStackTrace(pw);
        log.error(sw.toString());
    } catch (java.text.ParseException e) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);
        e.printStackTrace(pw);
        log.error(sw.toString());
    }
}

From source file:edu.msu.cme.rdp.readseq.utils.SequenceTrimmer.java

public static void main(String[] args) throws IOException {
    Options options = new Options();
    options.addOption("r", "ref-seq", true,
            "Trim points are given as positions in a reference sequence from this file");
    options.addOption("i", "inclusive", false, "Trim points are inclusive");
    options.addOption("l", "length", true, "Minimum length of sequence after trimming");
    options.addOption("f", "filled-ratio", true,
            "Minimum ratio of filled model positions of sequence after trimming");
    options.addOption("o", "out", true, "Write sequences to directory (default=cwd)");
    options.addOption("s", "stats", true, "Write stats to file");

    PrintWriter statsOut = new PrintWriter(new NullWriter());
    boolean inclusive = false;
    int minLength = 0;
    int minTrimmedLength = 0;
    int maxNs = 0;
    int maxTrimNs = 0;

    int trimStart = 0;
    int trimStop = 0;
    Sequence refSeq = null;//from  w  w  w  . j  a va2s  .c o m
    float minFilledRatio = 0;

    int expectedModelPos = -1;
    String[] inputFiles = null;
    File outdir = new File(".");
    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("ref-seq")) {
            refSeq = readRefSeq(new File(line.getOptionValue("ref-seq")));
        }

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

        if (line.hasOption("length")) {
            minLength = Integer.valueOf(line.getOptionValue("length"));
        }

        if (line.hasOption("filled-ratio")) {
            minFilledRatio = Float.valueOf(line.getOptionValue("filled-ratio"));
        }

        if (line.hasOption("out")) {
            outdir = new File(line.getOptionValue("out"));
            if (!outdir.isDirectory()) {
                outdir = outdir.getParentFile();
                System.err.println("Output option is not a directory, using " + outdir + " instead");
            }
        }

        if (line.hasOption("stats")) {
            statsOut = new PrintWriter(line.getOptionValue("stats"));
        }

        args = line.getArgs();

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

        trimStart = Integer.parseInt(args[0]);
        trimStop = Integer.parseInt(args[1]);
        inputFiles = Arrays.copyOfRange(args, 2, args.length);

        if (refSeq != null) {
            expectedModelPos = SeqUtils.getMaskedBySeqString(refSeq.getSeqString()).length();
            trimStart = translateCoord(trimStart, refSeq, CoordType.seq, CoordType.model);
            trimStop = translateCoord(trimStop, refSeq, CoordType.seq, CoordType.model);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("SequenceTrimmer <trim start> <trim stop> <aligned file> ...", options);
        System.err.println("Error: " + e.getMessage());
    }

    System.err.println("Starting sequence trimmer");
    System.err.println("*  Input files:           " + Arrays.asList(inputFiles));
    System.err.println("*  Minimum Length:        " + minLength);
    System.err.println("*  Trim point inclusive?: " + inclusive);
    System.err.println("*  Trim points:           " + trimStart + "-" + trimStop);
    System.err.println("*  Min filled ratio:      " + minFilledRatio);
    System.err.println("*  refSeq:                "
            + ((refSeq == null) ? "model" : refSeq.getSeqName() + " " + refSeq.getDesc()));

    Sequence seq;
    SeqReader reader;
    TrimStats stats;

    writeStatsHeader(statsOut);

    FastaWriter seqWriter;
    File in;
    for (String infile : inputFiles) {
        in = new File(infile);
        reader = new SequenceReader(in);
        seqWriter = new FastaWriter(new File(outdir, "trimmed_" + in.getName()));

        while ((seq = reader.readNextSequence()) != null) {
            if (seq.getSeqName().startsWith("#")) {
                seqWriter.writeSeq(seq.getSeqName(), "", trimMetaSeq(seq.getSeqString(), trimStart, trimStop));
                continue;
            }

            stats = getStats(seq, trimStart, trimStop);
            boolean passed = didSeqPass(stats, minLength, minTrimmedLength, maxNs, maxTrimNs, minFilledRatio);
            writeStats(statsOut, seq.getSeqName(), stats, passed);
            if (passed) {
                seqWriter.writeSeq(seq.getSeqName(), seq.getDesc(), new String(stats.trimmedBases));
            }
        }

        reader.close();
        seqWriter.close();
    }

    statsOut.close();
}

From source file:microbiosima.SelectiveMicrobiosima.java

/**
 * @param args/*from  www.j  av a2s  .  c  o m*/
 *            the command line arguments
 * @throws java.io.FileNotFoundException
 * @throws java.io.UnsupportedEncodingException
 */

public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException {
    int populationSize = 500;//Integer.parseInt(parameters[1]);
    int microSize = 1000;//Integer.parseInt(parameters[2]);
    int numberOfSpecies = 150;//Integer.parseInt(parameters[3]);
    int numberOfGeneration = 10000;
    int Ngene = 10;
    int numberOfObservation = 100;
    int numberOfReplication = 10;
    double Ngenepm = 5;
    double pctEnv = 0;
    double pctPool = 0;
    double msCoeff = 1;
    double hsCoeff = 1;
    boolean HMS_or_TMS = true;

    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(6).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, (5) number of total traits, (6)number of traits per microbe"
                    + " [default: 500 1000 150 10000 10 5]");
    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"
            + "  msCoeff            Parameter related to microbe selection strength\n"
            + "  hsCoeff            Parameter related to host selection strength\n"
            + "  HMS_or_TMS         String HMS or TMS to specify host-mediated or trait-mediated microbe selection\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 != 5) {
            System.out.println(
                    "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. 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]);
            msCoeff = Double.parseDouble(pct_config[2]);
            hsCoeff = Double.parseDouble(pct_config[3]);
            if (pct_config[4].equals("HMS"))
                HMS_or_TMS = true;
            if (pct_config[4].equals("TMS"))
                HMS_or_TMS = false;
            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 (msCoeff < 1) {
                System.out.println(
                        "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff="
                                + msCoeff + ")! EXIT");
                System.exit(3);
            }
            if (hsCoeff < 1) {
                System.out.println(
                        "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff="
                                + hsCoeff + ")! EXIT");
                System.exit(3);
            }
            if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) {
                System.out.println(
                        "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS="
                                + pct_config[4] + ")! 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]);
            Ngene = Integer.parseInt(configs[4]);
            Ngenepm = Double.parseDouble(configs[5]);
            if (Ngenepm > Ngene) {
                System.out.println(
                        "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT");
                System.exit(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\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ")
            .append(Ngenepm).append("\n");
    System.out.println(sb.toString());

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

    for (int rep = 0; rep < numberOfReplication; rep++) {
        String prefix = "" + (rep + 1) + "_";
        String sufix;
        if (HMS_or_TMS)
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt";
        else
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".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)));
            PrintWriter file7 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix)));
            PrintWriter file8 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix)));
            PrintWriter file9 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix)));
            PrintWriter file10 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix)));
            PrintWriter file11 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix)));
            PrintWriter file12 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix)));
            for (int i = 0; i < Ngene; i++) {
                fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1;
                fitnessToHost[i] = MathUtil.getNextInt(2) - 1;
            }
            MathUtil.setSeed(rep % numberOfReplication);
            SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm,
                    msCoeff, fitnessToHost, fitnessToMicrobe);
            MathUtil.setSeed();
            SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize,
                    pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS);

            while (population.getNumberOfGeneration() < numberOfGeneration) {
                population.sumSpecies();
                if (population.getNumberOfGeneration() % numberOfObservation == 0) {
                    //file1.print(population.gammaDiversity(false));
                    //file2.print(population.alphaDiversity(false));
                    //file1.print("\t");
                    //file2.print("\t");
                    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());
                    file7.print(population.averageHostFitness());
                    file7.print("\t");
                    file7.println(population.varianceHostFitness());
                    file8.println(population.cosOfMH());
                    file9.println(population.printOutHFitness());
                    file10.println(population.printOutMFitness());
                    file11.println(population.printBacteriaContents());
                }
                population.getNextGen();
            }
            for (SelectiveIndividual host : population.getIndividuals()) {
                file12.println(host.printBacteriaContents());
            }
            file1.close();
            file2.close();
            file3.close();
            file4.close();
            file5.close();
            file6.close();
            file7.close();
            file8.close();
            file9.close();
            file10.close();
            file11.close();
            file12.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:PrintWriterDemo.java

public static void main() throws Exception {
    PrintWriter pw = new PrintWriter(new FileWriter("dice.txt"));
    for (int i = 1; i <= 1000; i++) {
        int die = (int) (1 + 6 * Math.random());
        pw.print(die);//from  w  w w . j av  a  2 s . co m
        pw.print(' ');
        if (i % 20 == 0)
            pw.println();
    }
    pw.println();
    pw.close(); // Without this, the output file may be empty
}

From source file:Counter.java

/** Main program entry point. */
public static void main(String argv[]) {

    // is there anything to do?
    if (argv.length == 0) {
        printUsage();//from   w ww  . j  a va 2  s . c o  m
        System.exit(1);
    }

    // variables
    Counter counter = new Counter();
    PrintWriter out = new PrintWriter(System.out);
    ParserWrapper parser = null;
    int repetition = DEFAULT_REPETITION;
    boolean namespaces = DEFAULT_NAMESPACES;
    boolean validation = DEFAULT_VALIDATION;
    boolean schemaValidation = DEFAULT_SCHEMA_VALIDATION;
    boolean schemaFullChecking = DEFAULT_SCHEMA_FULL_CHECKING;
    boolean honourAllSchemaLocations = DEFAULT_HONOUR_ALL_SCHEMA_LOCATIONS;
    boolean validateAnnotations = DEFAULT_VALIDATE_ANNOTATIONS;
    boolean dynamicValidation = DEFAULT_DYNAMIC_VALIDATION;
    boolean xincludeProcessing = DEFAULT_XINCLUDE;
    boolean xincludeFixupBaseURIs = DEFAULT_XINCLUDE_FIXUP_BASE_URIS;
    boolean xincludeFixupLanguage = DEFAULT_XINCLUDE_FIXUP_LANGUAGE;

    // process arguments
    for (int i = 0; i < argv.length; i++) {
        String arg = argv[i];
        if (arg.startsWith("-")) {
            String option = arg.substring(1);
            if (option.equals("p")) {
                // get parser name
                if (++i == argv.length) {
                    System.err.println("error: Missing argument to -p option.");
                }
                String parserName = argv[i];

                // create parser
                try {
                    parser = (ParserWrapper) Class.forName(parserName).newInstance();
                } catch (Exception e) {
                    parser = null;
                    System.err.println("error: Unable to instantiate parser (" + parserName + ")");
                }
                continue;
            }
            if (option.equals("x")) {
                if (++i == argv.length) {
                    System.err.println("error: Missing argument to -x option.");
                    continue;
                }
                String number = argv[i];
                try {
                    int value = Integer.parseInt(number);
                    if (value < 1) {
                        System.err.println("error: Repetition must be at least 1.");
                        continue;
                    }
                    repetition = value;
                } catch (NumberFormatException e) {
                    System.err.println("error: invalid number (" + number + ").");
                }
                continue;
            }
            if (option.equalsIgnoreCase("n")) {
                namespaces = option.equals("n");
                continue;
            }
            if (option.equalsIgnoreCase("v")) {
                validation = option.equals("v");
                continue;
            }
            if (option.equalsIgnoreCase("s")) {
                schemaValidation = option.equals("s");
                continue;
            }
            if (option.equalsIgnoreCase("f")) {
                schemaFullChecking = option.equals("f");
                continue;
            }
            if (option.equalsIgnoreCase("hs")) {
                honourAllSchemaLocations = option.equals("hs");
                continue;
            }
            if (option.equalsIgnoreCase("va")) {
                validateAnnotations = option.equals("va");
                continue;
            }
            if (option.equalsIgnoreCase("dv")) {
                dynamicValidation = option.equals("dv");
                continue;
            }
            if (option.equalsIgnoreCase("xi")) {
                xincludeProcessing = option.equals("xi");
                continue;
            }
            if (option.equalsIgnoreCase("xb")) {
                xincludeFixupBaseURIs = option.equals("xb");
                continue;
            }
            if (option.equalsIgnoreCase("xl")) {
                xincludeFixupLanguage = option.equals("xl");
                continue;
            }
            if (option.equals("h")) {
                printUsage();
                continue;
            }
        }

        // use default parser?
        if (parser == null) {

            // create parser
            try {
                parser = (ParserWrapper) Class.forName(DEFAULT_PARSER_NAME).newInstance();
            } catch (Exception e) {
                System.err.println("error: Unable to instantiate parser (" + DEFAULT_PARSER_NAME + ")");
                continue;
            }
        }

        // set parser features
        try {
            parser.setFeature(NAMESPACES_FEATURE_ID, namespaces);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + NAMESPACES_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(VALIDATION_FEATURE_ID, validation);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(SCHEMA_VALIDATION_FEATURE_ID, schemaValidation);
        } catch (SAXException e) {
            System.err
                    .println("warning: Parser does not support feature (" + SCHEMA_VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(SCHEMA_FULL_CHECKING_FEATURE_ID, schemaFullChecking);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + SCHEMA_FULL_CHECKING_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(HONOUR_ALL_SCHEMA_LOCATIONS_ID, honourAllSchemaLocations);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + HONOUR_ALL_SCHEMA_LOCATIONS_ID + ")");
        }
        try {
            parser.setFeature(VALIDATE_ANNOTATIONS_ID, validateAnnotations);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + VALIDATE_ANNOTATIONS_ID + ")");
        }
        try {
            parser.setFeature(DYNAMIC_VALIDATION_FEATURE_ID, dynamicValidation);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + DYNAMIC_VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FEATURE_ID, xincludeProcessing);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + XINCLUDE_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FIXUP_BASE_URIS_FEATURE_ID, xincludeFixupBaseURIs);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + XINCLUDE_FIXUP_BASE_URIS_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FIXUP_LANGUAGE_FEATURE_ID, xincludeFixupLanguage);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + XINCLUDE_FIXUP_LANGUAGE_FEATURE_ID + ")");
        }

        // parse file
        try {
            long beforeParse = System.currentTimeMillis();
            Document document = null;
            for (int j = 0; j < repetition; j++) {
                document = parser.parse(arg);
            }
            long afterParse = System.currentTimeMillis();
            long parse = afterParse - beforeParse;

            ParserWrapper.DocumentInfo documentInfo = parser.getDocumentInfo();
            counter.setDocumentInfo(documentInfo);

            long beforeTraverse1 = System.currentTimeMillis();
            counter.count(document);
            long afterTraverse1 = System.currentTimeMillis();
            long traverse1 = afterTraverse1 - beforeTraverse1;

            long beforeTraverse2 = System.currentTimeMillis();
            counter.count(document);
            long afterTraverse2 = System.currentTimeMillis();
            long traverse2 = afterTraverse2 - beforeTraverse2;
            counter.printResults(out, arg, parse, traverse1, traverse2, repetition);
        } catch (SAXParseException e) {
            // ignore
        } catch (Exception e) {
            System.err.println("error: Parse error occurred - " + e.getMessage());
            Exception se = e;
            if (e instanceof SAXException) {
                se = ((SAXException) e).getException();
            }
            if (se != null)
                se.printStackTrace(System.err);
            else
                e.printStackTrace(System.err);
        }
    }

}

From source file:Main.java

public static String getStackTrace(Throwable t) {
    StringWriter sw = new StringWriter();
    PrintWriter pw = new PrintWriter(sw);
    t.printStackTrace(pw);//w  w  w . j  a va 2s .  c  om
    return sw.toString();
}

From source file:Main.java

public static String getExceptionStackTrace(Exception e) {
    StringWriter sw = new StringWriter();
    e.printStackTrace(new PrintWriter(sw));
    return sw.toString();
}

From source file:it.nibbles.javacoin.BlockTool.java

public static void main(String[] args) throws Exception {
    OptionParser parser = new OptionParser();
    parser.accepts("help");
    parser.accepts("import");
    parser.accepts("export");
    parser.accepts("testnet2");
    parser.accepts("testnet3");
    parser.accepts("prodnet");
    parser.accepts("first").withRequiredArg().ofType(Integer.class);
    parser.accepts("last").withRequiredArg().ofType(Integer.class);
    parser.accepts("hash").withRequiredArg();
    parser.accepts("port").withRequiredArg().ofType(Integer.class);
    optBdbPath = parser.accepts("bdbPath").withRequiredArg().defaultsTo("data");
    //optJdbcDriver = parser.accepts("driver").withRequiredArg().defaultsTo("com.mysql.jdbc.Driver");
    optJdbcUrl = parser.accepts("url").withRequiredArg().defaultsTo("jdbc:mysql://localhost/javacoin_testnet3");
    optJdbcUser = parser.accepts("dbuser").withRequiredArg().defaultsTo("javacoin");
    optJdbcPassword = parser.accepts("dbpass").withRequiredArg().defaultsTo("pw");
    inputfile = parser.accepts("inputfile").withRequiredArg();
    outputfile = parser.accepts("outputfile").withRequiredArg();
    //    String[] args = {
    //      "--inputfile", "blocks-0-100000.txt", "--prodnet", "--load", "--url", "jdbc:mysql://localhost/javacoin_test"
    //    };/* w w  w. ja v  a  2 s.co m*/
    OptionSet options = parser.parse(args);
    if (args.length == 0 || options.hasArgument("help") || options.nonOptionArguments().size() > 0
            || (options.has("export") && options.has("import"))
            || (options.has("export") && !options.has("outputfile"))
            || (options.has("import") && !options.has("inputfile"))
            || (options.has("testnet2") && options.has("testnet3"))
            || (options.has("testnet2") && options.has("prodnet"))
            || (options.has("testnet3") && options.has("prodnet"))) {
        println(HELP_TEXT);
        return;
    }
    if (options.hasArgument("port")) {
        //listenPort = ((Integer) options.valueOf("port")).intValue();
    }
    cmdExportBlockchain = options.has("export");
    cmdImportBlockchain = options.has("import");
    isProdnet = options.has("prodnet");
    isTestNet2 = options.has("testnet2");
    isTestNet3 = options.has("testnet3");
    if (!isProdnet && !isTestNet2 && !isTestNet3)
        isTestNet3 = true;
    if (options.hasArgument("first")) {
        firstBlock = ((Integer) options.valueOf("first")).intValue();
        if (!options.hasArgument("last"))
            lastBlock = firstBlock;
    }
    if (options.hasArgument("last")) {
        lastBlock = ((Integer) options.valueOf("last")).intValue();
        if (!options.hasArgument("first"))
            firstBlock = lastBlock;
    }
    if (options.hasArgument("hash"))
        blockHash = (String) options.valueOf("hash");
    if (cmdExportBlockchain && blockHash == null && firstBlock == 0 && lastBlock == 0) {
        println("To save blocks you have to specify a range or an hash");
        return;
    }

    //println("save: " + cmdSaveBlockchain + " load: " + cmdLoadBlockchain + " prodnet: " + isProdnet + " testnet2: " + isTestNet2 + " testnet3: " + isTestNet3);
    //println("FirstBlock: " + firstBlock + " lastBlock: " + lastBlock + " inputfile: " + inputfile.value(options) + " outputfile: " + outputfile.value(options));
    BlockTool app = new BlockTool();
    app.init(options);
    if (cmdImportBlockchain) {
        //System.out.println("Press return to start import blocks to blockchain");
        //System.in.read();
        BufferedReader reader;
        if ("-".equals(inputfile.value(options)))
            reader = new BufferedReader(new InputStreamReader(System.in));
        else
            reader = new BufferedReader(new FileReader(inputfile.value(options)));
        int numBlocks = 0;
        Block block = app.readBlock(reader, false);
        while (block != null) {
            numBlocks++;
            long startTime = System.currentTimeMillis();
            blockChain.addBlock(block);
            long insertTime = System.currentTimeMillis() - startTime;
            System.out.printf(
                    "%6d Block " + BtcUtil.hexOut(block.getHash()) + " #txs: %4d insertTime(ms): %d%n",
                    block.getTransactions().size(), insertTime);
            block = app.readBlock(reader, false);
        }
        System.out.println("Numero blocchi letti: " + numBlocks);
    } else if (cmdExportBlockchain) {
        BlockChainLink blockLink;
        try (PrintWriter writer = new PrintWriter(new File(outputfile.value(options)))) {
            if (blockHash != null) {
                blockLink = storage.getLink(BtcUtil.hexIn(blockHash));
                app.writeBlock(writer, blockLink.getBlock());
            } else {
                for (int i = firstBlock; i <= lastBlock; i++) {
                    blockLink = storage.getLinkAtHeight(i);
                    app.writeBlock(writer, blockLink.getBlock());
                }
            }
        }
    }
    app.close();
}

From source file:Main.java

public static String getExceptionStackTrace(Exception e) {
    Writer writer = new StringWriter();
    PrintWriter printWriter = new PrintWriter(writer);
    e.printStackTrace(printWriter);/*w ww  . ja v a  2  s .  com*/
    return writer.toString();
}

From source file:Main.java

public static void writeToFile(String fileName, String xml) throws IOException {
    PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fileName, true), 1024));
    out.println(xml);/*www.j a  va 2  s .  c  o  m*/
    out.flush();
    out.close();
}