Example usage for java.io PrintStream flush

List of usage examples for java.io PrintStream flush

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Introduction

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

Prototype

public void flush()

Source Link

Document

Flushes the stream.

Usage

From source file:org.testeditor.fixture.swt.SwtBotFixture.java

/**
 * @param message//from  w w w  . jav  a 2  s .c  om
 *            the message as a string, that should send.
 * @return the result of the call
 * @throws UnknownHostException
 * @throws IOException
 */
private boolean sendMessage(String message) {

    StringBuilder result = new StringBuilder();

    try {
        Socket client = getSocket();

        PrintStream os = new PrintStream(client.getOutputStream(), false, CHARSET_UTF_8);
        os.println(message);
        LOGGER.info("Send message to AUT:" + message);
        os.flush();
        BufferedReader in = new BufferedReader(new InputStreamReader(client.getInputStream(), CHARSET_UTF_8));

        int c;
        while ((c = in.read()) != -1) {
            result.append((char) c);
        }
        String myMessage = result.toString();
        if (myMessage.indexOf("ERROR ") > -1) {
            LOGGER.error("Fails: " + myMessage);
            throw new RuntimeException("Message: " + message + " fails with: " + myMessage);
        }

        client.close();

    } catch (UnknownHostException e) {
        LOGGER.error("SendMessage Host not Found", e);
    } catch (IOException e) {
        LOGGER.error("Send Message IOException ", e);
    }
    if (result.toString().startsWith("true")) {
        return true;
    }
    return false;
}

From source file:com.isentropy.accumulo.collections.AccumuloSortedMap.java

public void dump(PrintStream ps, int max_values_per_key) {
    K prev = null;/*from  w w w  . jav a 2 s  . c  om*/
    int valuesShown = 0;
    for (Iterator<Entry<K, V>> it = multiEntryIterator(); it.hasNext();) {
        Entry<K, V> e = it.next();
        K k = e.getKey();
        if (prev == null || !k.equals(prev)) {
            valuesShown = 0;
        }
        if (max_values_per_key < 0 || valuesShown++ < max_values_per_key) {
            ps.println(formatDumpLine(e));
        }
    }
    ps.flush();
}

From source file:edu.cornell.med.icb.goby.modes.SequenceVariationStatsMode.java

/**
 * Display sequence variations./*ww  w  .  jav a2s  .c om*/
 *
 * @throws java.io.IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    PrintStream stream = null;
    try {
        stream = outputFilename == null ? System.out : new PrintStream(new FileOutputStream(outputFilename));
        switch (outputFormat) {
        case TAB_DELIMITED:
        case TSV:
            stream.println(
                    "basename\tread-index\tcount-variation-bases\tbases-at-index/all-variations-bases\tbases-at-index/all-reference-bases\tcount-reference-bases");
            break;
        }

        for (final String basename : basenames) {
            alignmentIterator.resetTallies();
            final String[] singleBasename = { basename };
            // Iterate through each alignment and write sequence variations to output file:
            alignmentIterator.iterate(singleBasename);

            final Long2LongMap readIndexTallies = alignmentIterator.getReadIndexVariationTally();
            final double totalNumberOfVariationBases = sum(readIndexTallies.values());
            final double numberOfAlignmentEntries = alignmentIterator.getNumAlignmentEntries();

            final long countReferenceBases = alignmentIterator.getReferenceBaseCount();
            for (final long readIndex : readIndexTallies.keySet()) {
                final long countVariationBasesAtReadIndex = readIndexTallies.get(readIndex);
                final double frequency = ((double) countVariationBasesAtReadIndex)
                        / totalNumberOfVariationBases;
                final double alignFrequency = ((double) countVariationBasesAtReadIndex) / countReferenceBases;

                stream.printf("%s\t%d\t%d\t%s\t%f\t%d%n", FilenameUtils.getBaseName(basename), readIndex,
                        countVariationBasesAtReadIndex, frequency, alignFrequency, countReferenceBases);
            }
            stream.flush();
        }
    } finally {
        if (stream != System.out) {
            IOUtils.closeQuietly(stream);
        }
    }
}

From source file:com.act.lcms.plotter.WriteAndPlotMS1Results.java

public List<Pair<String, String>> writeMS1Values(Map<String, List<XZ>> ms1s, Double maxIntensity,
        Map<String, Double> metlinMzs, OutputStream os, boolean heatmap, boolean applyThreshold,
        Set<String> ionsToWrite) throws IOException {
    // Write data output to outfile
    PrintStream out = new PrintStream(os);

    List<Pair<String, String>> plotID = new ArrayList<>(ms1s.size());
    for (Map.Entry<String, List<XZ>> ms1ForIon : ms1s.entrySet()) {
        String ion = ms1ForIon.getKey();
        // Skip ions not in the ionsToWrite set if that set is defined.
        if (ionsToWrite != null && !ionsToWrite.contains(ion)) {
            continue;
        }//from  ww  w  .ja  v  a 2 s  . c  om

        List<XZ> ms1 = ms1ForIon.getValue();
        String plotName = String.format("ion: %s, mz: %.5f", ion, metlinMzs.get(ion));
        plotID.add(Pair.of(ion, plotName));
        // print out the spectra to outDATA
        for (XZ xz : ms1) {
            if (heatmap) {
                /*
                * When we are building heatmaps, we use gnuplots pm3d package
                * along with `dgrid3d 2000,2` (which averages data into grids
                * that are 2000 on the time axis and 2 in the y axis), and
                * `view map` that flattens a 3D graphs into a 2D view.
                * We want time to be on the x-axis and intensity on the z-axis
                * (because that is the one that is mapped to heat colors)
                * but then we need an artificial y-axis. We create proxy y=1
                * and y=2 datapoints, and then dgrid3d averaging over 2 creates
                * a vertical "strip".
                */
                out.format("%.4f\t1\t%.4f\n", xz.getTime(), xz.getIntensity());
                out.format("%.4f\t2\t%.4f\n", xz.getTime(), xz.getIntensity());
            } else {
                out.format("%.4f\t%.4f\n", xz.getTime(), xz.getIntensity());
            }
            out.flush();
        }
        // delimit this dataset from the rest
        out.print("\n\n");
    }

    return plotID;
}

From source file:Main.java

protected static void print(PrintStream out, Node node) {
    if (node == null)
        return;// w  ww.  j  a  v a2 s . c o  m
    short type = node.getNodeType();
    switch (type) {
    case Node.DOCUMENT_NODE: {
        out.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
        //out.println("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
        NodeList nodelist = node.getChildNodes();
        int size = nodelist.getLength();
        for (int i = 0; i < size; i++)
            print(out, nodelist.item(i));
        break;
    }

    case Node.DOCUMENT_TYPE_NODE: {
        DocumentType docType = (DocumentType) node;
        out.print("<!DOCTYPE " + getDocumentTypeData(docType) + ">\n");
        break;
    }

    case Node.ELEMENT_NODE: {
        out.print('<');
        out.print(node.getNodeName());
        NamedNodeMap map = node.getAttributes();
        if (map != null) {
            int size = map.getLength();
            for (int i = 0; i < size; i++) {
                Attr attr = (Attr) map.item(i);
                out.print(' ');
                out.print(attr.getNodeName());
                out.print("=\"");
                out.print(normalize(attr.getNodeValue()));
                out.print('"');
            }
        }

        if (!node.hasChildNodes())
            out.print("/>");
        else {
            out.print('>');
            NodeList nodelist = node.getChildNodes();
            int numChildren = nodelist.getLength();
            for (int i = 0; i < numChildren; i++)
                print(out, nodelist.item(i));

            out.print("</");
            out.print(node.getNodeName());
            out.print('>');
        }
        break;
    }

    case Node.ENTITY_REFERENCE_NODE: {
        NodeList nodelist = node.getChildNodes();
        if (nodelist != null) {
            int size = nodelist.getLength();
            for (int i = 0; i < size; i++)
                print(out, nodelist.item(i));

        }
        break;
    }

    case Node.CDATA_SECTION_NODE: {
        out.print(normalize(node.getNodeValue()));
        break;
    }

    case Node.TEXT_NODE: {
        out.print(normalize(node.getNodeValue()));
        break;
    }

    case Node.PROCESSING_INSTRUCTION_NODE: {
        out.print("<?");
        out.print(node.getNodeName());
        String s = node.getNodeValue();
        if (s != null && s.length() > 0) {
            out.print(' ');
            out.print(s);
        }
        out.print("?>");
        break;
    }

    case Node.COMMENT_NODE: {
        out.print("<!--");
        out.print(node.getNodeValue());
        out.print("-->");
        break;
    }

    default: {
        out.print(normalize(node.getNodeValue()));
        break;
    }
    }
    out.flush();
}

From source file:Main.java

protected static void print(PrintStream out, Node node) {
    if (node == null)
        return;/*  w ww.j  av  a 2  s  .co  m*/
    short type = node.getNodeType();
    switch (type) {
    case Node.DOCUMENT_NODE: {
        out.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
        // out.println("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n");
        NodeList nodelist = node.getChildNodes();
        int size = nodelist.getLength();
        for (int i = 0; i < size; i++)
            print(out, nodelist.item(i));
        break;
    }

    case Node.DOCUMENT_TYPE_NODE: {
        DocumentType docType = (DocumentType) node;
        out.print("<!DOCTYPE " + getDocumentTypeData(docType) + ">\n");
        break;
    }

    case Node.ELEMENT_NODE: {
        out.print('<');
        out.print(node.getNodeName());
        NamedNodeMap map = node.getAttributes();
        if (map != null) {
            int size = map.getLength();
            for (int i = 0; i < size; i++) {
                Attr attr = (Attr) map.item(i);
                out.print(' ');
                out.print(attr.getNodeName());
                out.print("=\"");
                out.print(normalize(attr.getNodeValue()));
                out.print('"');
            }
        }

        if (!node.hasChildNodes())
            out.print("/>");
        else {
            out.print('>');
            NodeList nodelist = node.getChildNodes();
            int numChildren = nodelist.getLength();
            for (int i = 0; i < numChildren; i++)
                print(out, nodelist.item(i));

            out.print("</");
            out.print(node.getNodeName());
            out.print('>');
        }
        break;
    }

    case Node.ENTITY_REFERENCE_NODE: {
        NodeList nodelist = node.getChildNodes();
        if (nodelist != null) {
            int size = nodelist.getLength();
            for (int i = 0; i < size; i++)
                print(out, nodelist.item(i));

        }
        break;
    }

    case Node.CDATA_SECTION_NODE: {
        out.print(normalize(node.getNodeValue()));
        break;
    }

    case Node.TEXT_NODE: {
        out.print(normalize(node.getNodeValue()));
        break;
    }

    case Node.PROCESSING_INSTRUCTION_NODE: {
        out.print("<?");
        out.print(node.getNodeName());
        String s = node.getNodeValue();
        if (s != null && s.length() > 0) {
            out.print(' ');
            out.print(s);
        }
        out.print("?>");
        break;
    }

    case Node.COMMENT_NODE: {
        out.print("<!--");
        out.print(node.getNodeValue());
        out.print("-->");
        break;
    }

    default: {
        out.print(normalize(node.getNodeValue()));
        break;
    }
    }
    out.flush();
}

From source file:com.tremolosecurity.provisioning.core.ProvisioningEngineImpl.java

@Override
public void initScheduler() throws ProvisioningException {
    if (this.cfgMgr.getCfg().getProvisioning() == null
            || this.cfgMgr.getCfg().getProvisioning().getScheduler() == null) {
        logger.warn("Scheduler not defined");
        return;/* w  ww  .  j  a v a  2s. c  o m*/
    }

    SchedulingType sct = this.cfgMgr.getCfg().getProvisioning().getScheduler();

    Properties scheduleProps = new Properties();

    scheduleProps.setProperty("org.quartz.scheduler.instanceName", sct.getInstanceLabel());

    String instanceLabel = null;
    try {
        Enumeration<NetworkInterface> enumer = NetworkInterface.getNetworkInterfaces();
        while (enumer.hasMoreElements()) {
            NetworkInterface ni = enumer.nextElement();
            Enumeration<InetAddress> enumeri = ni.getInetAddresses();
            while (enumeri.hasMoreElements()) {
                InetAddress addr = enumeri.nextElement();
                if (addr.getHostAddress().startsWith(sct.getInstanceIPMask())) {
                    instanceLabel = addr.getHostAddress();
                }
            }
        }
    } catch (SocketException e) {
        throw new ProvisioningException("Could not read network addresses", e);
    }

    if (instanceLabel == null) {
        logger.warn("No IP starts with '" + sct.getInstanceIPMask() + "'");
        instanceLabel = "AUTO";
    }

    scheduleProps.setProperty("org.quartz.scheduler.instanceId", instanceLabel);
    scheduleProps.setProperty("org.quartz.threadPool.threadCount", Integer.toString(sct.getThreadCount()));

    if (sct.isUseDB()) {
        scheduleProps.setProperty("org.quartz.jobStore.class", "org.quartz.impl.jdbcjobstore.JobStoreTX");
        scheduleProps.setProperty("org.quartz.jobStore.driverDelegateClass",
                sct.getScheduleDB().getDelegateClassName());
        scheduleProps.setProperty("org.quartz.jobStore.dataSource", "scheduleDB");
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.driver", sct.getScheduleDB().getDriver());
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.URL", sct.getScheduleDB().getUrl());
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.user", sct.getScheduleDB().getUser());
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.password",
                sct.getScheduleDB().getPassword());
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.maxConnections",
                Integer.toString(sct.getScheduleDB().getMaxConnections()));
        scheduleProps.setProperty("org.quartz.dataSource.scheduleDB.validationQuery",
                sct.getScheduleDB().getValidationQuery());
        scheduleProps.setProperty("org.quartz.jobStore.useProperties", "true");
        scheduleProps.setProperty("org.quartz.jobStore.isClustered", "true");
    } else {
        scheduleProps.setProperty("org.quartz.jobStore.class", "org.quartz.simpl.RAMJobStore");
    }

    try {

        /*String classpath = System.getProperty("java.class.path");
        String[] classpathEntries = classpath.split(File.pathSeparator);
        for (String cp : classpathEntries) {
           System.out.println(cp);
        }*/

        PrintStream out = new PrintStream(new FileOutputStream(
                System.getProperty(OpenUnisonConstants.UNISON_CONFIG_QUARTZDIR) + "/quartz.properties"));
        scheduleProps.store(out, "Unison internal scheduler properties");
        out.flush();
        out.close();
    } catch (IOException e) {
        throw new ProvisioningException("Could not write to quartz.properties", e);
    }

    try {
        this.scheduler = StdSchedulerFactory.getDefaultScheduler();
        this.scheduler.start();
        this.cfgMgr.addThread(new StopScheduler(this.scheduler));
        HashSet<String> jobKeys = new HashSet<String>();

        for (JobType jobType : sct.getJob()) {
            jobKeys.add(jobType.getName() + "-" + jobType.getGroup());
            JobKey jk = new JobKey(jobType.getName(), jobType.getGroup());
            JobDetail jd = this.scheduler.getJobDetail(jk);
            if (jd == null) {
                logger.info("Adding new job '" + jobType.getName() + "' / '" + jobType.getGroup() + "'");
                try {
                    addJob(jobType, jk);

                } catch (ClassNotFoundException e) {
                    throw new ProvisioningException("Could not initialize job", e);
                }

            } else {
                //check to see if we need to modify
                StringBuffer cron = new StringBuffer();
                cron.append(jobType.getCronSchedule().getSeconds()).append(' ')
                        .append(jobType.getCronSchedule().getMinutes()).append(' ')
                        .append(jobType.getCronSchedule().getHours()).append(' ')
                        .append(jobType.getCronSchedule().getDayOfMonth()).append(' ')
                        .append(jobType.getCronSchedule().getMonth()).append(' ')
                        .append(jobType.getCronSchedule().getDayOfWeek()).append(' ')
                        .append(jobType.getCronSchedule().getYear());

                Properties configProps = new Properties();
                for (ParamType pt : jobType.getParam()) {
                    configProps.setProperty(pt.getName(), pt.getValue());
                }

                Properties jobProps = new Properties();
                for (String key : jd.getJobDataMap().getKeys()) {
                    jobProps.setProperty(key, (String) jd.getJobDataMap().getString(key));
                }

                List<Trigger> triggers = (List<Trigger>) scheduler.getTriggersOfJob(jd.getKey());
                CronTrigger trigger = (CronTrigger) triggers.get(0);

                if (!jobType.getClassName().equals(jd.getJobClass().getName())) {
                    logger.info("Reloading job '" + jobType.getName() + "' / '" + jobType.getGroup()
                            + "' - change in class name");
                    reloadJob(jobType, jd);
                } else if (!cron.toString().equalsIgnoreCase(trigger.getCronExpression())) {
                    logger.info("Reloading job '" + jobType.getName() + "' / '" + jobType.getGroup()
                            + "' - change in schedule");
                    reloadJob(jobType, jd);
                } else if (!configProps.equals(jobProps)) {
                    logger.info("Reloading job '" + jobType.getName() + "' / '" + jobType.getGroup()
                            + "' - change in properties");
                    reloadJob(jobType, jd);
                }
            }
        }

        for (String groupName : scheduler.getJobGroupNames()) {

            for (JobKey jobKey : scheduler.getJobKeys(GroupMatcher.jobGroupEquals(groupName))) {

                String jobName = jobKey.getName();
                String jobGroup = jobKey.getGroup();

                //get job's trigger
                List<Trigger> triggers = (List<Trigger>) scheduler.getTriggersOfJob(jobKey);

                if (!jobKeys.contains(jobName + "-" + jobGroup)) {
                    logger.info("Removing jab '" + jobName + "' / '" + jobGroup + "'");
                    scheduler.deleteJob(jobKey);
                }

            }

        }

    } catch (SchedulerException e) {
        throw new ProvisioningException("Could not initialize scheduler", e);
    } catch (ClassNotFoundException e) {
        throw new ProvisioningException("Could not initialize scheduler", e);
    }

}

From source file:org.apache.streams.instagram.test.data.InstagramUserInfoDataConverterIT.java

@Test
public void InstagramUserInfoDataConverterIT() throws Exception {
    InputStream is = InstagramUserInfoDataConverterIT.class.getResourceAsStream("/testUserInfoData.txt");
    InputStreamReader isr = new InputStreamReader(is);
    BufferedReader br = new BufferedReader(isr);

    PrintStream outStream = new PrintStream(new BufferedOutputStream(
            new FileOutputStream("target/test-classes/InstagramUserInfoDataConverterIT.txt")));

    try {//  w ww  .j  a  va 2s.co m
        while (br.ready()) {
            String line = br.readLine();
            if (!StringUtils.isEmpty(line)) {

                LOGGER.info("raw: {}", line);

                UserInfoData userInfoData = gson.fromJson(line, UserInfoData.class);

                ActivityObjectConverter<UserInfoData> converter = new InstagramUserInfoDataConverter();

                ActivityObject activityObject = converter.toActivityObject(userInfoData);

                LOGGER.info("activityObject: {}", activityObject.toString());

                assertThat(activityObject, is(not(nullValue())));

                assertThat(activityObject.getId(), is(not(nullValue())));
                assertThat(activityObject.getImage(), is(not(nullValue())));
                assertThat(activityObject.getDisplayName(), is(not(nullValue())));
                assertThat(activityObject.getSummary(), is(not(nullValue())));

                Map<String, Object> extensions = (Map<String, Object>) activityObject.getAdditionalProperties()
                        .get("extensions");
                assertThat(extensions, is(not(nullValue())));
                assertThat(extensions.get("following"), is(not(nullValue())));
                assertThat(extensions.get("followers"), is(not(nullValue())));
                assertThat(extensions.get("screenName"), is(not(nullValue())));
                assertThat(extensions.get("posts"), is(not(nullValue())));

                assertThat(activityObject.getAdditionalProperties().get("handle"), is(not(nullValue())));
                assertThat(activityObject.getId(), is(not(nullValue())));
                assertThat(activityObject.getUrl(), is(not(nullValue())));

                assertThat(activityObject.getAdditionalProperties().get("provider"), is(not(nullValue())));

                outStream.println(mapper.writeValueAsString(activityObject));

            }
        }
        outStream.flush();

    } catch (Exception ex) {
        LOGGER.error("Exception: ", ex);
        outStream.flush();
        Assert.fail();
    }
}

From source file:com.github.lindenb.jvarkit.tools.misc.AlleleFrequencyCalculator.java

@Override
protected Collection<Throwable> call(String inputName) throws Exception {
    PrintStream out = null;
    VcfIterator in = null;/*w w  w.  j av a  2 s .c om*/
    try {
        final List<String> args = this.getInputFiles();
        if (inputName == null) {
            LOG.info("reading stdin");
            in = new VcfIteratorImpl(stdin());
        } else {
            LOG.info("reading " + args.get(0));
            in = VCFUtils.createVcfIterator(inputName);
        }

        out = openFileOrStdoutAsPrintStream();

        out.println("CHR\tPOS\tID\tREF\tALT\tTOTAL_CNT\tALT_CNT\tFRQ");
        while (in.hasNext() && !out.checkError()) {

            VariantContext ctx = in.next();
            Allele ref = ctx.getReference();
            if (ref == null)
                continue;
            if (ctx.getNSamples() == 0 || ctx.getAlternateAlleles().isEmpty())
                continue;
            Allele alt = ctx.getAltAlleleWithHighestAlleleCount();
            if (alt == null)
                continue;

            GenotypesContext genotypes = ctx.getGenotypes();
            if (genotypes == null)
                continue;
            int total_ctn = 0;
            int alt_ctn = 0;
            for (int i = 0; i < genotypes.size(); ++i) {
                Genotype g = genotypes.get(i);
                for (Allele allele : g.getAlleles()) {
                    if (allele.equals(ref)) {
                        total_ctn++;
                    } else if (allele.equals(alt)) {
                        total_ctn++;
                        alt_ctn++;
                    }
                }

            }

            out.print(ctx.getContig());
            out.print("\t");
            out.print(ctx.getStart());
            out.print("\t");
            out.print(ctx.hasID() ? ctx.getID() : ".");
            out.print("\t");
            out.print(ref.getBaseString());
            out.print("\t");
            out.print(alt.getBaseString());
            out.print("\t");
            out.print(total_ctn);
            out.print("\t");
            out.print(alt_ctn);
            out.print("\t");
            out.print(alt_ctn / (float) total_ctn);
            out.println();
        }
        out.flush();

        return RETURN_OK;
    } catch (Exception err) {
        return wrapException(err);
    } finally {
        CloserUtil.close(out);
        CloserUtil.close(in);
    }
}