Example usage for java.io ObjectOutputStream close

Introduction

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

Prototype

public void close() throws IOException 

Source Link

Document

Closes the stream.

Usage

From source file:fi.aalto.seqpig.io.BamStorer.java

@Override
public void checkSchema(ResourceSchema s) throws IOException {

    selectedBAMAttributes = new HashMap<String, Integer>();
    allBAMFieldNames = new HashMap<String, Integer>();
    String[] fieldNames = s.fieldNames();

    for (int i = 0; i < fieldNames.length; i++) {
        System.out.println("field: " + fieldNames[i]);
        allBAMFieldNames.put(fieldNames[i], new Integer(i));

        if (fieldNames[i].equalsIgnoreCase("RG") || fieldNames[i].equalsIgnoreCase("LB")
                || fieldNames[i].equalsIgnoreCase("PU") || fieldNames[i].equalsIgnoreCase("PG")
                || fieldNames[i].equalsIgnoreCase("AS") || fieldNames[i].equalsIgnoreCase("SQ")
                || fieldNames[i].equalsIgnoreCase("MQ") || fieldNames[i].equalsIgnoreCase("NM")
                || fieldNames[i].equalsIgnoreCase("H0") || fieldNames[i].equalsIgnoreCase("H1")
                || fieldNames[i].equalsIgnoreCase("H2") || fieldNames[i].equalsIgnoreCase("UQ")
                || fieldNames[i].equalsIgnoreCase("PQ") || fieldNames[i].equalsIgnoreCase("NH")
                || fieldNames[i].equalsIgnoreCase("IH") || fieldNames[i].equalsIgnoreCase("HI")
                || fieldNames[i].equalsIgnoreCase("MD") || fieldNames[i].equalsIgnoreCase("CS")
                || fieldNames[i].equalsIgnoreCase("CQ") || fieldNames[i].equalsIgnoreCase("CM")
                || fieldNames[i].equalsIgnoreCase("R2") || fieldNames[i].equalsIgnoreCase("Q2")
                || fieldNames[i].equalsIgnoreCase("S2") || fieldNames[i].equalsIgnoreCase("CC")
                || fieldNames[i].equalsIgnoreCase("CP") || fieldNames[i].equalsIgnoreCase("SM")
                || fieldNames[i].equalsIgnoreCase("AM") || fieldNames[i].equalsIgnoreCase("MF")
                || fieldNames[i].equalsIgnoreCase("E2") || fieldNames[i].equalsIgnoreCase("U2")
                || fieldNames[i].equalsIgnoreCase("OQ")) {

            System.out.println("selected attribute: " + fieldNames[i] + " i: " + i);
            selectedBAMAttributes.put(fieldNames[i], new Integer(i));
        }//from  ww w.  j  av a  2  s  .co  m
    }

    if (!(allBAMFieldNames.containsKey("name") && allBAMFieldNames.containsKey("start")
            && allBAMFieldNames.containsKey("end") && allBAMFieldNames.containsKey("read")
            && allBAMFieldNames.containsKey("cigar") && allBAMFieldNames.containsKey("basequal")
            && allBAMFieldNames.containsKey("flags") && allBAMFieldNames.containsKey("insertsize")
            && allBAMFieldNames.containsKey("mapqual") && allBAMFieldNames.containsKey("matestart")
            && allBAMFieldNames.containsKey("materefindex") && allBAMFieldNames.containsKey("refindex")))
        throw new IOException("Error: Incorrect BAM tuple-field name or compulsory field missing");

    Base64 codec = new Base64();
    Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
    String datastr;

    ByteArrayOutputStream bstream = new ByteArrayOutputStream();
    ObjectOutputStream ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(selectedBAMAttributes);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("selectedBAMAttributes", datastr);

    bstream = new ByteArrayOutputStream();
    ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(allBAMFieldNames);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("allBAMFieldNames", datastr);
}

---

From source file:fi.aalto.seqpig.io.SamStorer.java

public SamStorer(String samfileheaderfilename) {

    String str = "";
    this.samfileheader = "";

    try {// w  w w.ja  va 2 s. c o  m
        Configuration conf = UDFContext.getUDFContext().getJobConf();

        // see https://issues.apache.org/jira/browse/PIG-2576
        if (conf == null || conf.get("mapred.task.id") == null) {
            // we are running on the frontend
            decodeSAMFileHeader();
            return;
        }

        URI uri = new URI(samfileheaderfilename);
        FileSystem fs = FileSystem.get(uri, conf);

        BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(samfileheaderfilename))));

        while (true) {
            str = in.readLine();

            if (str == null)
                break;
            else
                this.samfileheader += str + "\n";
        }

        in.close();
    } catch (Exception e) {
        System.out.println("ERROR: could not read SAM header from file " + samfileheaderfilename);
        System.out.println("exception was: " + e.toString());
    }

    try {
        Base64 codec = new Base64();
        Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());

        ByteArrayOutputStream bstream = new ByteArrayOutputStream();
        ObjectOutputStream ostream = new ObjectOutputStream(bstream);
        ostream.writeObject(this.samfileheader);
        ostream.close();

        String datastr = codec.encodeBase64String(bstream.toByteArray());
        p.setProperty("samfileheader", datastr);
    } catch (Exception e) {
        System.out.println("ERROR: Unable to store SAMFileHeader in BamStorer!");
    }

    this.samfileheader_decoded = getSAMFileHeader();
}

---

From source file:fi.aalto.seqpig.io.SamStorer.java

@Override
public void checkSchema(ResourceSchema s) throws IOException {

    selectedSAMAttributes = new HashMap<String, Integer>();
    allSAMFieldNames = new HashMap<String, Integer>();
    String[] fieldNames = s.fieldNames();

    for (int i = 0; i < fieldNames.length; i++) {
        System.out.println("field: " + fieldNames[i]);
        allSAMFieldNames.put(fieldNames[i], new Integer(i));

        if (fieldNames[i].equalsIgnoreCase("RG") || fieldNames[i].equalsIgnoreCase("LB")
                || fieldNames[i].equalsIgnoreCase("PU") || fieldNames[i].equalsIgnoreCase("PG")
                || fieldNames[i].equalsIgnoreCase("AS") || fieldNames[i].equalsIgnoreCase("SQ")
                || fieldNames[i].equalsIgnoreCase("MQ") || fieldNames[i].equalsIgnoreCase("NM")
                || fieldNames[i].equalsIgnoreCase("H0") || fieldNames[i].equalsIgnoreCase("H1")
                || fieldNames[i].equalsIgnoreCase("H2") || fieldNames[i].equalsIgnoreCase("UQ")
                || fieldNames[i].equalsIgnoreCase("PQ") || fieldNames[i].equalsIgnoreCase("NH")
                || fieldNames[i].equalsIgnoreCase("IH") || fieldNames[i].equalsIgnoreCase("HI")
                || fieldNames[i].equalsIgnoreCase("MD") || fieldNames[i].equalsIgnoreCase("CS")
                || fieldNames[i].equalsIgnoreCase("CQ") || fieldNames[i].equalsIgnoreCase("CM")
                || fieldNames[i].equalsIgnoreCase("R2") || fieldNames[i].equalsIgnoreCase("Q2")
                || fieldNames[i].equalsIgnoreCase("S2") || fieldNames[i].equalsIgnoreCase("CC")
                || fieldNames[i].equalsIgnoreCase("CP") || fieldNames[i].equalsIgnoreCase("SM")
                || fieldNames[i].equalsIgnoreCase("AM") || fieldNames[i].equalsIgnoreCase("MF")
                || fieldNames[i].equalsIgnoreCase("E2") || fieldNames[i].equalsIgnoreCase("U2")
                || fieldNames[i].equalsIgnoreCase("OQ")) {

            System.out.println("selected attribute: " + fieldNames[i] + " i: " + i);
            selectedSAMAttributes.put(fieldNames[i], new Integer(i));
        }//from ww  w.ja v a 2  s. c  om
    }

    if (!(allSAMFieldNames.containsKey("name") && allSAMFieldNames.containsKey("start")
            && allSAMFieldNames.containsKey("end") && allSAMFieldNames.containsKey("read")
            && allSAMFieldNames.containsKey("cigar") && allSAMFieldNames.containsKey("basequal")
            && allSAMFieldNames.containsKey("flags") && allSAMFieldNames.containsKey("insertsize")
            && allSAMFieldNames.containsKey("mapqual") && allSAMFieldNames.containsKey("matestart")
            && allSAMFieldNames.containsKey("materefindex") && allSAMFieldNames.containsKey("refindex")))
        throw new IOException("Error: Incorrect SAM tuple-field name or compulsory field missing");

    Base64 codec = new Base64();
    Properties p = UDFContext.getUDFContext().getUDFProperties(this.getClass());
    String datastr;

    ByteArrayOutputStream bstream = new ByteArrayOutputStream();
    ObjectOutputStream ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(selectedSAMAttributes);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("selectedSAMAttributes", datastr);

    bstream = new ByteArrayOutputStream();
    ostream = new ObjectOutputStream(bstream);
    ostream.writeObject(allSAMFieldNames);
    ostream.close();
    datastr = codec.encodeBase64String(bstream.toByteArray());
    p.setProperty("allSAMFieldNames", datastr);
}

---

From source file:com.mongodb.hadoop.mapred.input.MongoInputSplit.java

/**
 * Serialize the Split instance//from  w ww . jav a2  s .c  o  m
 */

public void write(DataOutput out) throws IOException {
    final ObjectOutputStream objOut = new ObjectOutputStream((OutputStream) out);
    // TODO - Use object outputstream instead of going to <-> from string?
    out.writeUTF(_mongoURI.toString());

    out.writeUTF(JSON.serialize(_querySpec));
    out.writeUTF(JSON.serialize(_fieldSpec));
    out.writeUTF(JSON.serialize(_sortSpec));
    out.writeInt(_limit);
    out.writeInt(_skip);
    objOut.close();
}

---

From source file:com.all.dht.util.DhtFileUtils.java

public void persistObjectToFile(Serializable object, String routeTableFile) throws IOException {
    ObjectOutputStream out = new ObjectOutputStream(
            new BufferedOutputStream(new SecureOutputStream(new FileOutputStream(routeTableFile))));
    out.writeObject(object);/*  w  w w.  j ava  2s.co  m*/
    out.flush();
    out.close();
}

---

From source file:deepschema.ExtractingTool.java

/**
 * Caches classes and subclasses to file.
 * //  ww w  .  j  a  v a2 s. c o  m
 * @param operation : "read" or "write"
 */
@SuppressWarnings("unchecked")
void cache(String action) {
    final String cacheFile = ".cache";
    try {
        switch (action) {
        case "read": {
            ObjectInputStream objectInputStream = new ObjectInputStream(new FileInputStream(cacheFile));
            classes = (Map<Integer, WikidataClassProperties>) ((ObjectInputStream) objectInputStream)
                    .readObject();
            instances = (Map<Integer, WikidataInstanceProperties>) ((ObjectInputStream) objectInputStream)
                    .readObject();
            objectInputStream.close();
        }
        case "write": {
            ObjectOutputStream objectOutputStream = new ObjectOutputStream(new FileOutputStream(cacheFile));
            objectOutputStream.writeObject(classes);
            objectOutputStream.writeObject(instances);
            objectOutputStream.flush();
            objectOutputStream.close();
        }
        }
    } catch (ClassNotFoundException | IOException e) {
        System.err.println("Problem while reading/writing from/to cache.");
        e.printStackTrace();
    }
}

---

From source file:com.vmware.identity.openidconnect.sample.RelyingPartyInstaller.java

private void writeObject(String file, Object object) throws IOException {
    FileOutputStream fos = null;/*  w ww.j  av  a2  s .com*/
    ObjectOutputStream oos = null;
    try {
        fos = new FileOutputStream(file.toString());
        oos = new ObjectOutputStream(fos);
        oos.writeObject(object);
    } finally {
        if (oos != null) {
            oos.close();
        }
    }
}

---

From source file:org.eclipse.thym.core.internal.util.BundleHttpCacheStorage.java

@Override
public void putEntry(String key, HttpCacheEntry entry) throws IOException {
    ByteArrayOutputStream byteArrayOS = null;
    ObjectOutputStream objectOut = null;

    try {//  www .j  av a2s . c o m
        File f = getCacheFile(key);
        byteArrayOS = new ByteArrayOutputStream();
        objectOut = new ObjectOutputStream(byteArrayOS);
        objectOut.writeObject(entry);
        objectOut.flush();
        FileUtils.writeByteArrayToFile(f, byteArrayOS.toByteArray());
    } finally {
        if (objectOut != null)
            objectOut.close();
        if (byteArrayOS != null)
            byteArrayOS.close();
    }
}

---

From source file:com.offbynull.coroutines.instrumenter.InstrumenterTest.java

@Test
public void mustProperlySuspendWithSerialization() throws Exception {
    try (URLClassLoader classLoader = loadClassesInZipResourceAndInstrument(
            SERIALIZABLE_INVOKE_TEST + ".zip")) {
        Class<Coroutine> cls = (Class<Coroutine>) classLoader.loadClass(SERIALIZABLE_INVOKE_TEST);
        Coroutine coroutine = ConstructorUtils.invokeConstructor(cls, new StringBuilder());

        // Create and run original for a few cycles
        CoroutineRunner originalRunner = new CoroutineRunner(coroutine);

        Assert.assertTrue(originalRunner.execute());
        Assert.assertTrue(originalRunner.execute());
        Assert.assertTrue(originalRunner.execute());
        Assert.assertTrue(originalRunner.execute());
        Assert.assertTrue(originalRunner.execute());
        Assert.assertTrue(originalRunner.execute());

        // Serialize
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        ObjectOutputStream oos = new ObjectOutputStream(baos);
        oos.writeObject(originalRunner);
        oos.close();
        baos.close();/*from   w  w  w . j a  v  a 2  s .c  om*/
        byte[] serializedCoroutine = baos.toByteArray();

        // Deserialize
        ByteArrayInputStream bais = new ByteArrayInputStream(serializedCoroutine);
        ObjectInputStream ois = new ObjectInputStream(bais) {

            @Override
            protected Class<?> resolveClass(ObjectStreamClass desc) throws IOException, ClassNotFoundException {
                try {
                    return super.resolveClass(desc);
                } catch (ClassNotFoundException cnfe) {
                    return classLoader.loadClass(desc.getName());
                }
            }

        };
        CoroutineRunner deserializedRunner = (CoroutineRunner) ois.readObject();

        // Continue running deserialized
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertFalse(deserializedRunner.execute()); // coroutine finished executing here
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertTrue(deserializedRunner.execute());
        Assert.assertTrue(deserializedRunner.execute());

        // Assert everything continued fine with deserialized version
        Object deserializedCoroutine = FieldUtils.readField(deserializedRunner, "coroutine", true);
        StringBuilder deserializedBuilder = (StringBuilder) FieldUtils.readField(deserializedCoroutine,
                "builder", true);

        Assert.assertEquals("started\n" + "0\n" + "1\n" + "2\n" + "3\n" + "4\n" + "5\n" + "6\n" + "7\n" + "8\n"
                + "9\n" + "started\n" + "0\n" + "1\n" + "2\n", deserializedBuilder.toString());
    }
}

---

From source file:models.TopicModel.java

public TopicModel(String name, int numTopics, double alpha, double beta, Reader dataReader) throws Exception {
    this.name = name;
    this.alpha = alpha;
    this.beta = beta;
    this.numTopics = numTopics;

    TopicModel named_model = TopicModel.find.where().eq("name", name).findUnique();

    if (named_model != null) {
        // TODO: a better exception. Also, handle concurrency
        throw new Exception("A model of that name already exists");
    }/*  w  w w.j a v a2  s. c  o  m*/

    // convert input to vectors
    Pipe instancePipe = getStandardPipes();
    InstanceList instances = new InstanceList(instancePipe);
    instances.addThruPipe(
            new CsvIterator(dataReader, Pattern.compile("^(\\S*)[\\s,]*(\\S*)[\\s,]*(.*)$"), 3, 2, 1));

    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    ObjectOutputStream oos = new ObjectOutputStream(baos);
    oos.writeObject(instances);
    oos.close();
    this.featureSequence = baos.toByteArray();

    Configuration config = Play.application().configuration();
    // train model
    malletTopicModel = new PersistentParallelTopicModel(this.numTopics, this.alpha, this.beta);
    malletTopicModel.addInstances(instances);
    malletTopicModel.setNumIterations(config.getInt("smarts.topicModel.numIterations"));
    malletTopicModel.setOptimizeInterval(config.getInt("smarts.topicModel.optimizeIntervals"));
    malletTopicModel.setBurninPeriod(config.getInt("smarts.topicModel.burnInPeriod"));
    malletTopicModel.setSymmetricAlpha(config.getBoolean("smarts.topicModel.symmetricAlpha"));
    malletTopicModel.setNumThreads(config.getInt("smarts.topicModel.numThreads"));

    malletTopicModel.estimate();
}

---

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