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.exjello.mail.ExchangeConnection.java

private void findInbox() throws Exception {
    inbox = null;//  ww w .j  av a  2 s.  c o m
    drafts = null;
    submissionUri = null;
    sentitems = null;
    outbox = null;
    HttpClient client = getClient();
    ExchangeMethod op = new ExchangeMethod(PROPFIND_METHOD, server + "/exchange/" + mailbox);
    op.setHeader("Content-Type", XML_CONTENT_TYPE);
    op.setHeader("Depth", "0");
    op.setHeader("Brief", "t");
    op.setRequestEntity(createFindInboxEntity());
    InputStream stream = null;
    try {
        int status = client.executeMethod(op);
        stream = op.getResponseBodyAsStream();
        if (status >= 300) {
            throw new IllegalStateException("Unable to obtain inbox.");
        }
        SAXParserFactory spf = SAXParserFactory.newInstance();
        spf.setNamespaceAware(true);
        SAXParser parser = spf.newSAXParser();
        parser.parse(stream, new DefaultHandler() {
            private final StringBuilder content = new StringBuilder();

            public void startElement(String uri, String localName, String qName, Attributes attributes)
                    throws SAXException {
                content.setLength(0);
            }

            public void characters(char[] ch, int start, int length) throws SAXException {
                content.append(ch, start, length);
            }

            public void endElement(String uri, String localName, String qName) throws SAXException {
                if (!HTTPMAIL_NAMESPACE.equals(uri))
                    return;
                if ("inbox".equals(localName)) {
                    ExchangeConnection.this.inbox = content.toString();
                } else if ("drafts".equals(localName)) {
                    ExchangeConnection.this.drafts = content.toString();
                } else if ("sentitems".equals(localName)) {
                    ExchangeConnection.this.sentitems = content.toString();
                } else if ("outbox".equals(localName)) {
                    ExchangeConnection.this.outbox = content.toString();
                } else if ("sendmsg".equals(localName)) {
                    ExchangeConnection.this.submissionUri = content.toString();
                }
            }
        });
        stream.close();
        stream = null;
    } finally {
        try {
            if (stream != null) {
                byte[] buf = new byte[65536];
                try {
                    if (session.getDebug()) {
                        PrintStream log = session.getDebugOut();
                        log.println("Response Body:");
                        int count;
                        while ((count = stream.read(buf, 0, 65536)) != -1) {
                            log.write(buf, 0, count);
                        }
                        log.flush();
                        log.println();
                    } else {
                        while (stream.read(buf, 0, 65536) != -1)
                            ;
                    }
                } catch (Exception ignore) {
                } finally {
                    try {
                        stream.close();
                    } catch (Exception ignore2) {
                    }
                }
            }
        } finally {
            op.releaseConnection();
        }
    }
}

From source file:org.exjello.mail.Exchange2003Connection.java

public InputStream getInputStream(ExchangeMessage message) throws Exception {
    synchronized (this) {
        if (!isConnected()) {
            throw new IllegalStateException("Not connected.");
        }//from  w w  w  . j  a  v a  2  s . c o  m
        HttpClient client = getClient();
        GetMethod op = new GetMethod(escape(message.getUrl()));
        op.setRequestHeader("Translate", "F");
        InputStream stream = null;
        try {
            int status = client.executeMethod(op);
            stream = op.getResponseBodyAsStream();
            if (status >= 300) {
                throw new IllegalStateException("Unable to obtain inbox: " + status);
            }
            final File tempFile = File.createTempFile("exmail", null, null);
            tempFile.deleteOnExit();
            OutputStream output = new FileOutputStream(tempFile);
            byte[] buf = new byte[65536];
            int count;
            while ((count = stream.read(buf, 0, 65536)) != -1) {
                output.write(buf, 0, count);
            }
            output.flush();
            output.close();
            stream.close();
            stream = null;
            return new CachedMessageStream(tempFile, (ExchangeFolder) message.getFolder());
        } finally {
            try {
                if (stream != null) {
                    byte[] buf = new byte[65536];
                    try {
                        if (session.getDebug()) {
                            PrintStream log = session.getDebugOut();
                            log.println("Response Body:");
                            int count;
                            while ((count = stream.read(buf, 0, 65536)) != -1) {
                                log.write(buf, 0, count);
                            }
                            log.flush();
                            log.println();
                        } else {
                            while (stream.read(buf, 0, 65536) != -1)
                                ;
                        }
                    } catch (Exception ignore) {
                    } finally {
                        try {
                            stream.close();
                        } catch (Exception ignore2) {
                        }
                    }
                }
            } finally {
                op.releaseConnection();
            }
        }
    }
}

From source file:org.exjello.mail.Exchange2003Connection.java

private void listFolder(DefaultHandler handler, String folder) throws Exception {
    synchronized (this) {
        if (!isConnected()) {
            throw new IllegalStateException("Not connected.");
        }//from   w  w w .ja  v  a 2  s.co m
        HttpClient client = getClient();
        ExchangeMethod op = new ExchangeMethod(SEARCH_METHOD, folder);
        op.setHeader("Content-Type", XML_CONTENT_TYPE);
        if (limit > 0)
            op.setHeader("Range", "rows=0-" + limit);
        op.setHeader("Brief", "t");

        /* Mirco: Manage of custom query */
        if ((filterLastCheck == null || "".equals(filterLastCheck))
                && (filterFrom == null || "".equals(filterFrom))
                && (filterNotFrom == null || "".equals(filterNotFrom))
                && (filterTo == null || "".equals(filterTo))) {
            op.setRequestEntity(unfiltered ? createAllInboxEntity() : createUnreadInboxEntity());
        } else {
            op.setRequestEntity(
                    createCustomInboxEntity(unfiltered, filterLastCheck, filterFrom, filterNotFrom, filterTo));
        }
        InputStream stream = null;
        try {
            int status = client.executeMethod(op);
            stream = op.getResponseBodyAsStream();
            if (status >= 300) {
                throw new IllegalStateException("Unable to obtain " + folder + ".");
            }
            SAXParserFactory spf = SAXParserFactory.newInstance();
            spf.setNamespaceAware(true);
            SAXParser parser = spf.newSAXParser();
            parser.parse(stream, handler);
            stream.close();
            stream = null;
        } finally {
            try {
                if (stream != null) {
                    byte[] buf = new byte[65536];
                    try {
                        if (session.getDebug()) {
                            PrintStream log = session.getDebugOut();
                            log.println("Response Body:");
                            int count;
                            while ((count = stream.read(buf, 0, 65536)) != -1) {
                                log.write(buf, 0, count);
                            }
                            log.flush();
                            log.println();
                        } else {
                            while (stream.read(buf, 0, 65536) != -1)
                                ;
                        }
                    } catch (Exception ignore) {
                    } finally {
                        try {
                            stream.close();
                        } catch (Exception ignore2) {
                        }
                    }
                }
            } finally {
                op.releaseConnection();
            }
        }
    }
}

From source file:com.act.lcms.MS2Simple.java

private void plot(List<Pair<MS2Collected, Integer>> ms2Spectra, Double mz, List<Double> ms2SearchMZs,
        String outPrefix, String fmt) throws IOException {
    String outPDF = outPrefix + "." + fmt;
    String outDATA = outPrefix + ".data";

    // Write data output to outfile
    PrintStream out = new PrintStream(new FileOutputStream(outDATA));

    List<String> plotID = new ArrayList<>(ms2Spectra.size());
    for (Pair<MS2Collected, Integer> pair : ms2Spectra) {
        MS2Collected yzSlice = pair.getLeft();
        String caption;//from ww  w .  java  2 s  . c o  m
        if (ms2SearchMZs != null && ms2SearchMZs.size() > 0) {
            caption = String.format("target: %.4f, time: %.4f, volts: %.4f, %d / %d matches",
                    yzSlice.triggerMass, yzSlice.triggerTime, yzSlice.voltage,
                    pair.getRight() == null ? 0 : pair.getRight(), ms2SearchMZs.size());
        } else {
            caption = String.format("target: %.4f, time: %.4f, volts: %.4f", yzSlice.triggerMass,
                    yzSlice.triggerTime, yzSlice.voltage);
        }
        plotID.add(caption);
        // Compute the total intensity on the fly so we can plot on a percentage scale.
        double maxIntensity = 0.0;
        for (YZ yz : yzSlice.ms2) {
            if (yz.intensity > maxIntensity) {
                maxIntensity = yz.intensity;
            }
        }
        // print out the spectra to outDATA
        for (YZ yz : yzSlice.ms2) {
            out.format("%.4f\t%.4f\n", yz.mz, 100.0 * yz.intensity / maxIntensity);
            out.flush();
        }
        // delimit this dataset from the rest
        out.print("\n\n");
    }

    // close the .data
    out.close();

    // render outDATA to outPDF using gnuplot
    // 105.0 here means 105% for the y-range of a [0%:100%] plot. We want to leave some buffer space at
    // at the top, and hence we go a little outside of the 100% max range.
    /* We intend to plot the fragmentation pattern, and so do not expect to see fragments that are bigger than the
     * original selected molecule.  We truncate the x-range to the specified m/z but since that will make values close
     * to the max hard to see we add a buffer and truncate the plot in the x-range to m/z + 50.0. */
    new Gnuplotter().plot2DImpulsesWithLabels(outDATA, outPDF, plotID.toArray(new String[plotID.size()]),
            mz + 50.0, "mz", 105.0, "intensity (%)", fmt);
}

From source file:se.sics.kompics.p2p.experiment.dsl.SimulationScenario.java

/**
 * Save simulation command line./* w  ww  . jav a 2 s . co m*/
 * 
 * @param args
 *            the args
 */
private void saveSimulationCommandLine(final LinkedList<String> args) {
    File file = null;
    try {
        // Windows batch file
        file = new File(directory + "run-simulation.bat");
        PrintStream ps = new PrintStream(file);

        for (String arg : args) {
            ps.println(arg.replaceAll(directory, "") + "\t^");
            // ps.println(arg + "\t^");
        }
        ps.println(";");

        ps.flush();
        ps.close();

        // Linux/Unix Bash script
        file = new File(directory + "run-simulation.sh");
        ps = new PrintStream(file);
        ps.println("#!/bin/bash");
        ps.println();

        for (String arg : args) {
            ps.println(arg.replaceAll(directory, "") + "\t\\");
            // ps.println(arg + "\t\\");
        }
        ps.println(";");

        ps.flush();
        ps.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:com.vonglasow.michael.satstat.ui.MainActivity.java

@Override
protected void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);

    defaultUEH = Thread.getDefaultUncaughtExceptionHandler();

    Thread.setDefaultUncaughtExceptionHandler(new UncaughtExceptionHandler() {
        public void uncaughtException(Thread t, Throwable e) {
            Context c = getApplicationContext();
            File dumpDir = c.getExternalFilesDir(null);
            DateFormat fmt = new SimpleDateFormat("yyyy-MM-dd-HH-mm-ss", Locale.ROOT);
            fmt.setTimeZone(TimeZone.getTimeZone("UTC"));
            String fileName = String.format("satstat-%s.log", fmt.format(new Date(System.currentTimeMillis())));

            File dumpFile = new File(dumpDir, fileName);
            PrintStream s;
            try {
                InputStream buildInStream = getResources().openRawResource(R.raw.build);
                s = new PrintStream(dumpFile);
                s.append("SatStat build: ");

                int i;
                try {
                    i = buildInStream.read();
                    while (i != -1) {
                        s.write(i);/*from   ww w  .  j  ava2  s. c  o  m*/
                        i = buildInStream.read();
                    }
                    buildInStream.close();
                } catch (IOException e1) {
                    e1.printStackTrace();
                }

                s.append("\n\n");
                e.printStackTrace(s);
                s.flush();
                s.close();

                Intent mediaScanIntent = new Intent(Intent.ACTION_MEDIA_SCANNER_SCAN_FILE);
                Uri contentUri = Uri.fromFile(dumpFile);
                mediaScanIntent.setData(contentUri);
                c.sendBroadcast(mediaScanIntent);
            } catch (FileNotFoundException e2) {
                e2.printStackTrace();
            }
            defaultUEH.uncaughtException(t, e);
        }
    });

    mSharedPreferences = PreferenceManager.getDefaultSharedPreferences(this);
    mSharedPreferences.registerOnSharedPreferenceChangeListener(this);
    prefUnitType = mSharedPreferences.getBoolean(Const.KEY_PREF_UNIT_TYPE, prefUnitType);
    prefKnots = mSharedPreferences.getBoolean(Const.KEY_PREF_KNOTS, prefKnots);
    prefCoord = Integer
            .valueOf(mSharedPreferences.getString(Const.KEY_PREF_COORD, Integer.toString(prefCoord)));
    prefUtc = mSharedPreferences.getBoolean(Const.KEY_PREF_UTC, prefUtc);
    prefCid = mSharedPreferences.getBoolean(Const.KEY_PREF_CID, prefCid);
    prefCid2 = mSharedPreferences.getBoolean(Const.KEY_PREF_CID2, prefCid2);
    prefWifiSort = Integer
            .valueOf(mSharedPreferences.getString(Const.KEY_PREF_WIFI_SORT, Integer.toString(prefWifiSort)));
    prefMapOffline = mSharedPreferences.getBoolean(Const.KEY_PREF_MAP_OFFLINE, prefMapOffline);
    prefMapPath = mSharedPreferences.getString(Const.KEY_PREF_MAP_PATH, prefMapPath);

    ActionBar actionBar = getSupportActionBar();

    setContentView(R.layout.activity_main);

    // Find out default screen orientation
    Configuration config = getResources().getConfiguration();
    WindowManager wm = (WindowManager) getSystemService(Context.WINDOW_SERVICE);
    int rot = wm.getDefaultDisplay().getRotation();
    isWideScreen = (config.orientation == Configuration.ORIENTATION_LANDSCAPE
            && (rot == Surface.ROTATION_0 || rot == Surface.ROTATION_180)
            || config.orientation == Configuration.ORIENTATION_PORTRAIT
                    && (rot == Surface.ROTATION_90 || rot == Surface.ROTATION_270));
    Log.d(TAG, "isWideScreen=" + Boolean.toString(isWideScreen));

    // Create the adapter that will return a fragment for each of the
    // primary sections of the app.
    mSectionsPagerAdapter = new SectionsPagerAdapter(getSupportFragmentManager());

    // Set up the ViewPager with the sections adapter.
    mViewPager = (ViewPager) findViewById(R.id.pager);
    mViewPager.setAdapter(mSectionsPagerAdapter);

    Context ctx = new ContextThemeWrapper(getApplication(), R.style.AppTheme);
    mTabLayout = new TabLayout(ctx);
    LinearLayout.LayoutParams mTabLayoutParams = new LinearLayout.LayoutParams(LayoutParams.MATCH_PARENT,
            LayoutParams.WRAP_CONTENT);
    mTabLayout.setLayoutParams(mTabLayoutParams);

    for (int i = 0; i < mSectionsPagerAdapter.getCount(); i++) {
        TabLayout.Tab newTab = mTabLayout.newTab();
        newTab.setIcon(mSectionsPagerAdapter.getPageIcon(i));
        mTabLayout.addTab(newTab);
    }

    actionBar.setDisplayShowCustomEnabled(true);
    actionBar.setCustomView(mTabLayout);

    mTabLayout.setOnTabSelectedListener(new TabLayout.ViewPagerOnTabSelectedListener(mViewPager));
    mViewPager.addOnPageChangeListener(new TabLayout.TabLayoutOnPageChangeListener(mTabLayout));

    // This is needed by the mapsforge library.
    AndroidGraphicFactory.createInstance(this.getApplication());

    // Get system services for event delivery
    locationManager = (LocationManager) this.getSystemService(Context.LOCATION_SERVICE);
    sensorManager = (SensorManager) getSystemService(Context.SENSOR_SERVICE);
    mOrSensor = sensorManager.getDefaultSensor(Sensor.TYPE_ORIENTATION);
    mAccSensor = sensorManager.getDefaultSensor(Sensor.TYPE_ACCELEROMETER);
    mGyroSensor = sensorManager.getDefaultSensor(Sensor.TYPE_GYROSCOPE);
    mMagSensor = sensorManager.getDefaultSensor(Sensor.TYPE_MAGNETIC_FIELD);
    mLightSensor = sensorManager.getDefaultSensor(Sensor.TYPE_LIGHT);
    mProximitySensor = sensorManager.getDefaultSensor(Sensor.TYPE_PROXIMITY);
    mPressureSensor = sensorManager.getDefaultSensor(Sensor.TYPE_PRESSURE);
    mHumiditySensor = sensorManager.getDefaultSensor(Sensor.TYPE_RELATIVE_HUMIDITY);
    mTempSensor = sensorManager.getDefaultSensor(Sensor.TYPE_AMBIENT_TEMPERATURE);
    telephonyManager = (TelephonyManager) getSystemService(Context.TELEPHONY_SERVICE);
    connectivityManager = (ConnectivityManager) getSystemService(Context.CONNECTIVITY_SERVICE);
    wifiManager = (WifiManager) getSystemService(Context.WIFI_SERVICE);
}

From source file:org.exjello.mail.Exchange2003Connection.java

public void send(MimeMessage message) throws Exception {
    Address[] bccRecipients = message.getRecipients(Message.RecipientType.BCC);
    if (bccRecipients == null || bccRecipients.length == 0) {
        bccRecipients = null;//from w  w  w  .  j  ava  2 s  . c  o m
    }
    message.setRecipients(Message.RecipientType.BCC, (Address[]) null);
    synchronized (this) {
        if (!isConnected()) {
            throw new IllegalStateException("Not connected.");
        }
        if (!canSend()) {
            throw new IllegalStateException("Unable to access outbox.");
        }
        HttpClient client = getClient();
        String path = drafts;
        if (!path.endsWith("/"))
            path += "/";
        String messageName = generateMessageName();
        path += escape(messageName + ".eml");
        PutMethod op = new PutMethod(path);
        op.setRequestHeader("Content-Type", MESSAGE_CONTENT_TYPE);
        op.setRequestEntity(createMessageEntity(message));
        InputStream stream = null;
        try {
            int status = client.executeMethod(op);
            stream = op.getResponseBodyAsStream();
            if (status >= 300) {
                throw new IllegalStateException("Unable to post message to draft folder.");
            }
        } finally {
            try {
                if (stream != null) {
                    byte[] buf = new byte[65536];
                    try {
                        if (session.getDebug()) {
                            PrintStream log = session.getDebugOut();
                            log.println("Response Body:");
                            int count;
                            while ((count = stream.read(buf, 0, 65536)) != -1) {
                                log.write(buf, 0, count);
                            }
                            log.flush();
                            log.println();
                        } else {
                            while (stream.read(buf, 0, 65536) != -1)
                                ;
                        }
                    } catch (Exception ignore) {
                    } finally {
                        try {
                            stream.close();
                        } catch (Exception ignore2) {
                        }
                    }
                }
            } finally {
                op.releaseConnection();
            }
        }
        if (bccRecipients != null) {
            ExchangeMethod patch = new ExchangeMethod(PROPPATCH_METHOD, path);
            patch.setHeader("Content-Type", XML_CONTENT_TYPE);
            patch.addHeader("Depth", "0");
            patch.addHeader("Translate", "f");
            patch.addHeader("Brief", "t");
            patch.setRequestEntity(createAddBccEntity(bccRecipients));
            stream = null;
            try {
                int status = client.executeMethod(patch);
                stream = patch.getResponseBodyAsStream();
                if (status >= 300) {
                    throw new IllegalStateException("Unable to add BCC recipients. Status: " + status);
                }
            } finally {
                try {
                    if (stream != null) {
                        byte[] buf = new byte[65536];
                        try {
                            if (session.getDebug()) {
                                PrintStream log = session.getDebugOut();
                                log.println("Response Body:");
                                int count;
                                while ((count = stream.read(buf, 0, 65536)) != -1) {
                                    log.write(buf, 0, count);
                                }
                                log.flush();
                                log.println();
                            } else {
                                while (stream.read(buf, 0, 65536) != -1)
                                    ;
                            }
                        } catch (Exception ignore) {
                        } finally {
                            try {
                                stream.close();
                            } catch (Exception ignore2) {
                            }
                        }
                    }
                } finally {
                    patch.releaseConnection();
                }
            }
        }
        ExchangeMethod move = new ExchangeMethod(MOVE_METHOD, path);
        String destination = submissionUri;
        if (!destination.endsWith("/"))
            destination += "/";
        move.setHeader("Destination", destination);
        stream = null;
        try {
            int status = client.executeMethod(move);
            stream = move.getResponseBodyAsStream();
            if (status >= 300) {
                throw new IllegalStateException("Unable to move message to outbox: Status " + status);
            }
        } finally {
            try {
                if (stream != null) {
                    byte[] buf = new byte[65536];
                    try {
                        if (session.getDebug()) {
                            PrintStream log = session.getDebugOut();
                            log.println("Response Body:");
                            int count;
                            while ((count = stream.read(buf, 0, 65536)) != -1) {
                                log.write(buf, 0, count);
                            }
                            log.flush();
                            log.println();
                        } else {
                            while (stream.read(buf, 0, 65536) != -1)
                                ;
                        }
                    } catch (Exception ignore) {
                    } finally {
                        try {
                            stream.close();
                        } catch (Exception ignore2) {
                        }
                    }
                }
            } finally {
                move.releaseConnection();
            }
        }
        if (session.getDebug()) {
            session.getDebugOut().println("Sent successfully.");
        }
    }
}

From source file:cpcc.vvrte.services.js.JavascriptServiceTest.java

@Test
public void shouldHandleVvRte() throws IOException, InterruptedException {
    MyBuiltInFunctions functions = new MyBuiltInFunctions();
    JavascriptService jss = new JavascriptServiceImpl(logger, serviceResources, functions);
    jss.addAllowedClassRegex("cpcc.vvrte.services.js.JavascriptServiceTest\\$MyBuiltInFunctions");

    ByteArrayOutputStream out = new ByteArrayOutputStream();
    PrintStream stdOut = new PrintStream(out, true);
    VvRteFunctions.setStdOut(stdOut);/*  w  w w.ja v a2 s  . c o  m*/

    InputStream scriptStream = this.getClass().getResourceAsStream("simple-vv.js");
    String script = IOUtils.toString(scriptStream, "UTF-8");
    assertThat(script).isNotNull().isNotEmpty();

    VirtualVehicle vv = new VirtualVehicle();
    vv.setId(123);
    vv.setCode(script);
    vv.setApiVersion(1);
    vv.setUuid("599c6710-a042-11e5-a0fb-83f9ea30f21e");

    functions.setMigrate(true);
    JavascriptWorker sut = jss.createWorker(vv, false);
    sut.run();

    // System.out.println("shouldHandleVvRte() result1: '" + sut.getResult() + "'");
    // System.out.println("shouldHandleVvRte() output1: '" + out.toString("UTF-8") + "'");
    assertThat(sut.getWorkerState()).isNotNull().isEqualTo(VirtualVehicleState.INTERRUPTED);
    InputStream resultStream = this.getClass().getResourceAsStream("simple-vv-expected-result-1.txt");
    String expectedResult = IOUtils.toString(resultStream, "UTF-8");
    assertThat(out.toString("UTF-8")).isNotNull().isEqualTo(expectedResult);

    functions.setMigrate(false);
    byte[] snapshot = sut.getSnapshot();
    vv.setContinuation(snapshot);
    sut = jss.createWorker(vv, true);
    sut.run();
    stdOut.flush();
    assertThat(sut.getWorkerState()).isNotNull().isEqualTo(VirtualVehicleState.FINISHED);

    // System.out.println("shouldHandleVvRte() result2: '" + x.getResult() + "'");
    // System.out.println("shouldHandleVvRte() output2: '" + out.toString("UTF-8") + "'");
    resultStream = this.getClass().getResourceAsStream("simple-vv-expected-result-2.txt");
    expectedResult = IOUtils.toString(resultStream, "UTF-8");
    assertThat(out.toString("UTF-8")).isNotNull().isEqualTo(expectedResult);

    verify(sessionManager, times(6)).commit();
    verify(perthreadManager, times(2)).cleanup();
}

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

/**
 * Returns true if the application is launched.
 * //from   w  w w  .  j  a v  a 2 s  . co m
 * @return true, if the server is ready.
 */
private boolean isLaunched() {
    try {
        Socket client = getSocket();
        LOGGER.info("Is server ready for " + testName + "?");
        PrintStream os = new PrintStream(client.getOutputStream(), false, CHARSET_UTF_8);
        os.println("isLaunched");
        os.flush();
        BufferedReader in = new BufferedReader(new InputStreamReader(client.getInputStream(), CHARSET_UTF_8));
        String s = in.readLine();
        LOGGER.info(s);
        client.close();
        return Boolean.valueOf(s);
    } catch (UnknownHostException e) {
        LOGGER.error("isLaunched UnknownHostException: ", e);
    } catch (ConnectException e) {
        LOGGER.trace("Server not available.");
    } catch (IOException e) {
        LOGGER.error("isLaunched IOException: ", e);
    }
    return false;
}

From source file:org.broad.igv.tools.IgvTools.java

private void GFFToBed(String ifile, String ofile) throws FileNotFoundException {
    IGVBEDCodec outCodec = new IGVBEDCodec();
    GFFParser parser = new GFFParser();
    GFFCodec codec = null;/* ww  w  .ja va  2s .  c  o m*/
    try {
        codec = (GFFCodec) CodecFactory.getCodec(ifile, null);
    } catch (Exception e) {
        throw new IllegalArgumentException("Input file is not recognized as a GFF");
    }
    BufferedReader reader = null;
    PrintStream outStream = System.out;
    if (!ofile.equals(STDOUT_FILE_STR)) {
        outStream = new PrintStream(new FileOutputStream(ofile));
    }
    try {
        reader = ParsingUtils.openBufferedReader(ifile);
        List<Feature> features = parser.loadFeatures(reader, null, codec);
        for (Feature feat : features) {
            String encoded = outCodec.encode(feat);
            outStream.print(encoded);
            outStream.print('\n');
        }
    } catch (IOException e) {
        log.error(e.getMessage(), e);
    } finally {
        if (reader != null) {
            try {
                reader.close();
            } catch (IOException e) {
                log.error(e.getMessage(), e);
            }
        }
        if (outStream != null) {
            outStream.flush();
            outStream.close();
        }
    }
}