Example usage for java.io PrintStream PrintStream

List of usage examples for java.io PrintStream PrintStream

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Introduction

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

Prototype

public PrintStream(File file) throws FileNotFoundException

Source Link

Document

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

Usage

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

public static void readData(String inFile, File outdir, String xAxisLabel, String yAxisLabel)
        throws IOException {
    XYSeriesCollection dataset = new XYSeriesCollection();
    DefaultBoxAndWhiskerCategoryDataset scatterDataset = new DefaultBoxAndWhiskerCategoryDataset();

    BufferedReader reader = new BufferedReader(new FileReader(inFile));
    String line = reader.readLine();

    while ((line = reader.readLine()) != null) {
        String[] values = line.split("\\t");
        XYSeries series = new XYSeries(values[2]);
        dataset.addSeries(series);//from www  . j a va  2  s.  c o  m

        double average = Double.parseDouble(values[4]);
        int Q1 = Integer.parseInt(values[6]);
        ;
        int median = Integer.parseInt(values[7]);
        int Q3 = Integer.parseInt(values[8]);
        int pct_98 = Integer.parseInt(values[9]);
        int pct_2 = Integer.parseInt(values[10]);
        int minOutlier = 0; // we don't care about the outliers
        int maxOutlier = 0; //

        BoxAndWhiskerItem item = new BoxAndWhiskerItem(average, median, Q1, Q3, pct_2, pct_98, minOutlier,
                maxOutlier, new ArrayList());
        scatterDataset.add(item, values[2], "");
    }

    String title = new File(inFile).getName();
    int index = title.indexOf(".");
    if (index != -1) {
        title = title.substring(0, index);
    }

    Font lableFont = new Font("Helvetica", Font.BOLD, 28);
    createBoxplot(scatterDataset, new PrintStream(new File(outdir, title + ".boxchart.png")), title, xAxisLabel,
            yAxisLabel, lableFont);

}

From source file:jp.terasoluna.fw.util.ExceptionUtil.java

/**
 * ?????/*from   ww w  . j a va 2  s .co  m*/
 * 
 * <p>
 *  ??????????????
 *  ????????
 *  ???getRootCause()????????ServletException??
 * </p>
 *
 * @param throwable 
 * @return ???
 */
public static String getStackTrace(Throwable throwable) {
    StringBuilder sb = new StringBuilder();
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    while (throwable != null) {
        baos.reset();
        throwable.printStackTrace(new PrintStream(baos));
        sb.append(baos.toString());

        //throwable?Class??
        Class<? extends Throwable> throwableClass = throwable.getClass();

        // ServletException ?? getRootCause ?
        if (SERVLET_EXCEPTION_NAME.equals(throwableClass.getName())) {
            try {
                //throwable = ((ServletException) throwable).getRootCause()
                //Class??????
                Method method = throwableClass.getMethod(GET_ROOT_CAUSE);
                throwable = (Throwable) method.invoke(throwable);
            } catch (NoSuchMethodException e) {
                //???????
                log.error(e.getMessage());
                throwable = null;
            } catch (IllegalAccessException e) {
                //?????????
                log.error(e.getMessage());
                throwable = null;
            } catch (InvocationTargetException e) {
                //?????
                log.error(e.getMessage());
                throwable = null;
            }

        } else {
            throwable = throwable.getCause();
        }
    }
    return sb.toString();
}

From source file:de.langmi.spring.batch.examples.basics.purejava.jobruns.PureJavaJobRunTest.java

@Before
public void setup() throws Exception {
    // catch and set new system out
    oldSysOut = System.out;//w w  w  .  j av  a2  s  . com
    System.setOut(new PrintStream(newSysOut));

    setupBatchInfrastructure();
}

From source file:CraftAPI.java

/**
 * Construct the object./*from  w w w  .  j  a va 2s . com*/
 */
public CraftAPI() {
    eventDispatcher = new EventDispatcher();
    listener = new CraftAPIListener(eventDispatcher);

    try {
        System.setOut(new PrintStream(new CopyingEventOuputStream(System.out, eventDispatcher)));
        System.setErr(new PrintStream(new CopyingEventOuputStream(System.err, eventDispatcher)));
        // Logger.GLOBAL_LOGGER_NAME doesn't seem to work
        Logger.getLogger("Minecraft").addHandler(new LoggingEventHandler(eventDispatcher, new LogFormat()));
    } catch (Throwable t) {
        logger.log(Level.WARNING, "CraftAPI: Could not redirect stdout/stderr");
        t.printStackTrace();
    }
}

From source file:de.ifgi.fmt.web.filter.RuntimeExceptionMapper.java

/**
 * //from   ww  w .ja v a  2 s  .  com
 * @param t
 * @return
 */
@Override
public Response toResponse(Throwable t) {
    if (t instanceof WebApplicationException) {
        log.warn("Mapping Exception", t);
        return ((WebApplicationException) t).getResponse();
    }

    Throwable e = t;
    while (e != null) {
        if (e instanceof ServiceError) {
            return new ServiceErrorMapper().toResponse((ServiceError) e);
        }
        e = e.getCause();
    }

    log.info("Mapping Exception", t);
    ByteArrayOutputStream out = null;
    try {
        out = new ByteArrayOutputStream();
        t.printStackTrace(new PrintStream(out));
        return Response.serverError().entity(new String(out.toByteArray())).type(MediaType.TEXT_PLAIN).build();
    } catch (Throwable t2) {
        throw new RuntimeException(t);
    } finally {
        IOUtils.closeQuietly(out);
    }
}

From source file:com.liferay.ide.project.core.modules.BladeCLI.java

public static String[] execute(String args) throws BladeCLIException {
    IPath bladeCLIPath = getBladeCLIPath();

    if (FileUtil.notExists(bladeCLIPath)) {
        throw new BladeCLIException("Could not get blade cli jar.");
    }//from   w w w . ja v a2s  .  c o m

    Project project = new Project();
    Java javaTask = new Java();

    javaTask.setProject(project);
    javaTask.setFork(true);
    javaTask.setFailonerror(true);
    javaTask.setJar(bladeCLIPath.toFile());
    javaTask.setArgs(args);

    DefaultLogger logger = new DefaultLogger();

    project.addBuildListener(logger);
    List<String> lines = new ArrayList<>();
    int returnCode = 0;

    try (StringBufferOutputStream out = new StringBufferOutputStream();
            PrintStream printStream = new PrintStream(out)) {
        logger.setOutputPrintStream(printStream);

        logger.setMessageOutputLevel(Project.MSG_INFO);

        returnCode = javaTask.executeJava();

        try (Scanner scanner = new Scanner(out.toString())) {
            while (scanner.hasNextLine()) {
                lines.add(scanner.nextLine().replaceAll(".*\\[null\\] ", ""));
            }
        }

        boolean hasErrors = false;

        StringBuilder errors = new StringBuilder();

        for (String line : lines) {
            if (line.startsWith("Error")) {
                hasErrors = true;
            } else if (hasErrors) {
                errors.append(line);
            }
        }

        if ((returnCode != 0) || hasErrors) {
            throw new BladeCLIException(errors.toString());
        }

    } catch (IOException e) {
        throw new BladeCLIException(e.getMessage(), e);
    }
    return lines.toArray(new String[0]);
}

From source file:dk.netarkivet.common.utils.warc.WARCUtils.java

/**
 * Create new WARCWriter, writing to warcfile newFile.
 * @param newFile the WARCfile, that the WARCWriter writes to.
 * @return new WARCWriter, writing to warcfile newFile.
 *//*from www.j  av a2 s.  c o m*/
public static WARCWriter createWARCWriter(File newFile) {
    WARCWriter writer;
    PrintStream ps = null;
    try {
        ps = new PrintStream(new FileOutputStream(newFile));
        writer = new WARCWriterNAS(new AtomicInteger(), ps,
                //This name is used for the first (file metadata) record
                newFile, false, //Don't compress
                //Use current time
                ArchiveDateConverter.getWarcDateFormat().format(new Date()), null //No particular file metadata to add
        );
    } catch (IOException e) {
        if (ps != null) {
            ps.close();
        }
        String message = "Could not create WARCWriter to file '" + newFile + "'.\n";
        log.warn(message);
        throw new IOFailure(message, e);
    }
    return writer;
}

From source file:com.findcomputerstuff.nips.DefaultSecurityModule.java

private String processMessage(String message, MessageAction action) {
    String outStr = null;//from   ww  w .j a  va 2 s.  com
    SSMLib ssm = new nfp.ssm.core.SSMLib(publicKeyFile, privateKeyFile);
    try (ByteArrayOutputStream os = new ByteArrayOutputStream()) {
        PrintStream console = System.out;
        try (PrintStream ps = new PrintStream(os)) {
            System.setOut(ps); /* redirect stdout */
        }
        switch (action) {
        case DECRYPT:
            outStr = ssm.decryptFile(message, privateKeyPassword);
            break;
        case ENCRYPT:
            outStr = ssm.encryptMessage(message);
            break;
        }

        System.out.flush();
        System.setOut(console); /* restore stdout */
        if (StringUtils.isBlank(outStr))
            throw new SsmEncryptionException(os.toString());
    } catch (IOException e) {
        e.printStackTrace();
    }
    return outStr;
}

From source file:edu.msu.cme.rdp.kmer.cli.KmerCoverage.java

/**
 * This program maps the kmers from reads to kmers on each contig,
 * writes the mean, median coverage of each contig to a file
 * writes the kmer abundance to a file/*from  ww w  .  j a  v  a 2s .c  o m*/
 * @param args
 * @throws IOException 
 */
public static void main(String[] args) throws IOException, InterruptedException {
    int kmerSize = 45;
    final int maxThreads;
    final int maxTasks = 1000;
    final PrintStream match_reads_out;
    try {
        CommandLine cmdLine = new PosixParser().parse(options, args);
        args = cmdLine.getArgs();
        if (args.length < 5) {
            throw new Exception("Unexpected number of arguments");
        }
        kmerSize = Integer.parseInt(args[0]);
        if (kmerSize > Kmer.max_nucl_kmer_size) {
            throw new Exception("kmerSize should be less than " + Kmer.max_nucl_kmer_size);
        }
        if (cmdLine.hasOption("match_reads_out")) {
            match_reads_out = new PrintStream(cmdLine.getOptionValue("match_reads_out"));
        } else {
            match_reads_out = null;
        }
        if (cmdLine.hasOption("threads")) {
            maxThreads = Integer.valueOf(cmdLine.getOptionValue("threads"));
            if (maxThreads >= Runtime.getRuntime().availableProcessors()) {
                System.err.println(" Runtime.getRuntime().availableProcessors() "
                        + Runtime.getRuntime().availableProcessors());
            }

        } else {
            maxThreads = 1;
        }

        final KmerCoverage kmerCoverage = new KmerCoverage(kmerSize, new SequenceReader(new File(args[1])));

        final AtomicInteger outstandingTasks = new AtomicInteger();
        ExecutorService service = Executors.newFixedThreadPool(maxThreads);

        Sequence seq;

        // parse one file at a time
        for (int index = 4; index < args.length; index++) {

            SequenceReader reader = new SequenceReader(new File(args[index]));
            while ((seq = reader.readNextSequence()) != null) {
                if (seq.getSeqString().length() < kmerSize) {
                    continue;
                }
                final Sequence threadSeq = seq;

                Runnable r = new Runnable() {

                    public void run() {
                        try {
                            kmerCoverage.processReads(threadSeq, match_reads_out);
                            outstandingTasks.decrementAndGet();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                };

                outstandingTasks.incrementAndGet();
                service.submit(r);

                while (outstandingTasks.get() >= maxTasks)
                    ;

            }
            reader.close();
        }
        service.shutdown();
        service.awaitTermination(1, TimeUnit.DAYS);

        kmerCoverage.printCovereage(new FileOutputStream(new File(args[2])),
                new FileOutputStream(new File(args[3])));
        if (match_reads_out != null) {
            match_reads_out.close();
        }
    } catch (Exception e) {
        new HelpFormatter().printHelp(
                "KmerCoverage <kmerSize> <query_file> <coverage_out> <abundance_out> <reads_file> <reads_file>...\nmaximum kmerSize "
                        + Kmer.max_nucl_kmer_size,
                options);
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:com.twineworks.kettle.ruby.step.RubyStepParseErrorHelper.java

RubyStepParseErrorHelper() {

    Display display = Display.getDefault();
    errorLineColor = new Color(display, new RGB(255, 220, 220));
    container = RubyStepFactory.createScriptingContainer(false);

    // do not litter the console with potential parse errors
    container.setError(new PrintStream(new NullOutputStream()));
    container.setOutput(new PrintStream(new NullOutputStream()));

}