Example usage for java.util Arrays copyOfRange

List of usage examples for java.util Arrays copyOfRange

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Introduction

In this page you can find the example usage for java.util Arrays copyOfRange.

Prototype

public static boolean[] copyOfRange(boolean[] original, int from, int to)

Source Link

Document

Copies the specified range of the specified array into a new array.

Usage

From source file:com.asakusafw.runtime.io.text.directio.AbstractTextStreamFormatTest.java

/**
 * input - w/ splitter./*from  w w  w.j  a  va  2 s  . c  o  m*/
 * @throws Exception if failed
 */
@Test
public void input_splitter_trim_trail() throws Exception {
    MockFormat format = format(3).withInputSplitter(InputSplitters.byLineFeed());
    String[][] data = { { "A", "B", "C", }, { "D", "E", "F", }, { "G", "H", "I", }, };
    try (ModelInput<String[]> in = format.createInput(String[].class, "dummy", input(data), 0, 6)) {
        String[][] result = collect(3, in);
        assertThat(result, is(Arrays.copyOfRange(data, 0, 2)));
    }
}

From source file:eu.stratosphere.myriad.driver.MyriadDriverFrontend.java

/**
 * @param args//from  w ww . jav a2  s  .c o  m
 * @return
 */
private ParsedOptions parseOptions(String[] args) throws ParseException {
    ParsedOptions parsedOptions = new ParsedOptions();

    if (args.length < 1) {
        throw new ParseException("Missing dgen-install-dir argument");
    }

    parsedOptions.setFile("dgen-install-dir", new File(args[0]));

    // parse the command line arguments
    CommandLineParser parser = new PosixParser();
    CommandLine line = parser.parse(this.options, Arrays.copyOfRange(args, 1, args.length));

    if (line.hasOption('x')) {
        parsedOptions.setStringArray("execute-stage", line.getOptionValues('x'));
    } else {
        parsedOptions.setErrorMessage("execute-stage",
                "You should provide at least one data generator stage to be executed");
    }

    try {
        parsedOptions.setFloat("scaling-factor", Float.parseFloat(line.getOptionValue('s', "1.0")));
    } catch (NumberFormatException e) {
        parsedOptions.setErrorMessage("scaling-factor", e.getMessage());
    }

    try {
        parsedOptions.setShort("node-count", Short.parseShort(line.getOptionValue('N', "1")));
    } catch (NumberFormatException e) {
        parsedOptions.setErrorMessage("node-count", e.getMessage());
    }

    parsedOptions.setString("dataset-id", line.getOptionValue('m', "default-dataset"));
    parsedOptions.setFile("output-base", new File(line.getOptionValue('o', "/tmp")));

    return parsedOptions;
}

From source file:dk.au.cs.karibu.backend.standard.StandardServerRequestHandler.java

@Override
public boolean receive(byte[] bytes) {
    // result of the processing - assumed to succeed
    boolean processingSuccess = true;

    // Retrieve producer code 
    producerCode = new String(Arrays.copyOfRange(bytes, 0, PRODUCER_CODE_LENGTH));
    // assume that the collectionName will be identical to the producer code
    collectionName = producerCode;/*w  w  w .  j  a  v  a  2s  .  co m*/

    byte payload[] = Arrays.copyOfRange(bytes, PRODUCER_CODE_LENGTH, bytes.length);

    // Collect statistics
    statisticHandler.notifyReceive(producerCode, bytes.length);

    Deserializer deserializer = null;
    // Get the deserializer, optimize by caching the reference 
    deserializer = mapCode2Deserializer.get(producerCode);
    if (deserializer == null) {
        deserializer = factory.createDeserializer(producerCode);
        if (deserializer != null) {
            mapCode2Deserializer.put(producerCode, deserializer);
            log.info("Caching the deserializer (" + deserializer + ")");
        }
    }

    BasicDBObject dbo = null;
    // If the deserializer is null, then we have encountered 
    // an unknown producer - store the raw payload in 
    // a collection named DEADLETTER_CODE and suffixed with
    // the producer code.
    if (deserializer == null) {
        collectionName = StandardServerRequestHandler.DEADLETTER_COLLECTION_NAME_PREFIX + producerCode;
        log.info("DeadLetter: Unknown producer code (" + producerCode + ")," + " stored binary in collection "
                + collectionName);
        deserializer = new DeadLetterDeserializer();
    }

    // Try to create the DBO. Our Mongo JSON parser may throw 
    // a runtime exception if the format is wrong! If the 
    // format is wrong we will store the message in a 
    // special collection 
    try {
        dbo = deserializer.buildDocumentFromByteArray(payload);
    } catch (com.mongodb.util.JSONParseException parseException) {
        String theTrace = ExceptionUtils.getStackTrace(parseException);
        collectionName = WRONG_FORMAT_COLLECTION_NAME_PREFIX + producerCode;
        log.info("Illformed JSON received from producer " + producerCode + ", will store in collection "
                + collectionName + ". " + theTrace);
        // we can reuse the serializer used for dead letters 
        deserializer = new DeadLetterDeserializer();
        dbo = deserializer.buildDocumentFromByteArray(payload);
    } catch (RuntimeException otherException) {
        String theTrace = ExceptionUtils.getStackTrace(otherException);
        log.error("Unhandled runtime exception during deserialization. " + theTrace);
    }

    // if another runtime exception happened, the dbo may still be null 
    if (dbo != null) {
        try {
            storage.process(collectionName, dbo);
        } catch (MongoInternalException mie) {
            processingSuccess = false;
            String theTrace = ExceptionUtils.getStackTrace(mie);
            String theMessage = mie.getMessage();
            if (theMessage != null && theMessage.contains("is over Max BSON size")) {
                log.error("Mongo Internal exception during storage on producer code: " + producerCode
                        + " / Message size is over MongoDB limit - the message will be dropped!");
                processingSuccess = true;
            } else {
                log.error("Mongo Internal exception during storage on producer code: " + producerCode + " / "
                        + theTrace);
            }
        } catch (MongoException mongoexc) {
            processingSuccess = false;
            String theTrace = ExceptionUtils.getStackTrace(mongoexc);
            log.error("Mongo exception during storage on producer code: " + producerCode + " / " + theTrace);

        } catch (Exception me) {
            processingSuccess = false;
            String theTrace = ExceptionUtils.getStackTrace(me);
            log.error("Unhandled runtime exception during storage on producer code: " + producerCode + " / "
                    + theTrace);
        }
    } else { // dbo == null thus deserialization failed...
        // WHY SETTTING IT TO TRUE?
        processingSuccess = true;
        // EXPLANATION: Otherwise the message will not
        // be acknowledged to the MQ and thus pushed back 
        // which means we end in an infinte loop trying
        // to process it...

        // If deserialization fails it is programmers mistake
        // that must be caught during early testing, not caught
        // in production!
    }

    return processingSuccess;
}

From source file:de.mylifesucks.oss.ncsimulator.protocol.SerialComm.java

/**
 *
 * @param event//from www .  ja v  a  2s. c  o m
 * @see http://www.mikrokopter.de/ucwiki/en/SerialProtocol
 */
public void serialEvent(SerialPortEvent event) {

    //"0x1B,0x1B,0x55,0xAA,0x00"
    byte[] pattern = new byte[] { 27, 27, 85, (byte) 170, 0 };

    switch (event.getEventType()) {
    case SerialPortEvent.BI:
    case SerialPortEvent.OE:
    case SerialPortEvent.FE:
    case SerialPortEvent.PE:
    case SerialPortEvent.CD:
    case SerialPortEvent.CTS:
    case SerialPortEvent.DSR:
    case SerialPortEvent.RI:
    case SerialPortEvent.OUTPUT_BUFFER_EMPTY:
        break;
    case SerialPortEvent.DATA_AVAILABLE:
        try {
            while (inputStream.available() > 0) {

                Arrays.fill(readBuffer, (byte) 0);
                int numBytes = inputStream.read(readBuffer);
                byte[] data = Arrays.copyOfRange(readBuffer, 0, numBytes);
                //        System.out.println(Hex.encodeHexString(readBuffer));
                //        System.out.println(Hex.encodeHexString(data));

                HandleInputData(data);
            }
        } catch (IOException ex) {
        }
        break;
    }
}

From source file:com.thinkbiganalytics.spark.datavalidator.Validator.java

static CommandLineParams parseRemainingParameters(String[] args, int from) {
    CommandLineParams params = new CommandLineParams();
    new JCommander(params, Arrays.copyOfRange(args, from, args.length));
    return params;
}

From source file:alluxio.cli.AlluxioShell.java

/**
 * Handles the specified shell command request, displaying usage if the command format is invalid.
 *
 * @param argv [] Array of arguments given by the user's input from the terminal
 * @return 0 if command is successful, -1 if an error occurred
 *//*from  w  ww  . j  a  v  a2  s.  c om*/
public int run(String... argv) {
    if (argv.length == 0) {
        printUsage();
        return -1;
    }

    // Sanity check on the number of arguments
    String cmd = argv[0];
    ShellCommand command = mCommands.get(cmd);

    if (command == null) { // Unknown command (we didn't find the cmd in our dict)
        String[] replacementCmd = getReplacementCmd(cmd);
        if (replacementCmd == null) {
            System.out.println(cmd + " is an unknown command.\n");
            printUsage();
            return -1;
        }
        // Handle command alias, and print out WARNING message for deprecated cmd.
        String deprecatedMsg = "WARNING: " + cmd + " is deprecated. Please use "
                + StringUtils.join(replacementCmd, " ") + " instead.";
        System.out.println(deprecatedMsg);
        LOG.warn(deprecatedMsg);

        String[] replacementArgv = (String[]) ArrayUtils.addAll(replacementCmd,
                ArrayUtils.subarray(argv, 1, argv.length));
        return run(replacementArgv);
    }

    String[] args = Arrays.copyOfRange(argv, 1, argv.length);
    CommandLine cmdline = command.parseAndValidateArgs(args);
    if (cmdline == null) {
        printUsage();
        return -1;
    }

    // Handle the command
    try {
        return command.run(cmdline);
    } catch (Exception e) {
        System.out.println(e.getMessage());
        LOG.error("Error running " + StringUtils.join(argv, " "), e);
        return -1;
    }
}

From source file:com.monitor.baseservice.utils.XCodeUtil.java

/**
 * 1?xcode?//w ww.  j a  v a 2s  .  c o m
 * 2?base64?
 * 3?????CRCCRC?8
 * 4?CRC
 * 5??????JSON
 * 
 * @param xCode
 * @return
 * @throws LogicalException 
 */
@SuppressWarnings("unchecked")
public static Map<String, Object> xDecode(String xCode) throws LogicalException {
    // 1
    String real = xCode.substring(PREFIX_LENGTH);
    byte[] rst = Base64.decodeBase64(real);

    byte[] data = Arrays.copyOf(rst, rst.length - (Long.SIZE / Byte.SIZE));
    byte[] crc = Arrays.copyOfRange(rst, data.length, rst.length);
    // 4
    long value = byteArrayToLong(crc);
    byte[] realCrc = crcUnsigned(data, CRC_KEY.getBytes());
    long realValue = byteArrayToLong(realCrc);
    if (!(value == realValue)) {
        System.out.println("license verify failed.");
        throw new LogicalException(RetStat.ERR_BAD_PARAMS, null);
    }

    xorCode(data, XOR_KEY);

    String info = new String(data);

    return JSONObject.parseObject(info, Map.class);
}

From source file:my.adam.smo.common.SymmetricEncryptionBox.java

public byte[] getMessageWithoutSeed(byte[] cryptogram) {
    return Arrays.copyOfRange(cryptogram, seedLength, cryptogram.length);
}

From source file:uk.ac.ebi.eva.pipeline.io.writers.VepAnnotationMongoWriterTest.java

/**
 * Test that every VariantAnnotation gets written, even if the same variant receives different annotation from
 * different batches./*from w ww .j a va 2s.  com*/
 * @throws Exception if the annotationWriter.write fails, or the DBs cleaning fails
 */
@Test
public void shouldWriteAllFieldsIntoMongoDbMultipleSetsAnnotations() throws Exception {
    String dbName = jobOptions.getDbName();
    String dbCollectionVariantsName = jobOptions.getPipelineOptions().getString("db.collections.variants.name");
    JobTestUtils.cleanDBs(dbName);

    List<VariantAnnotation> annotations = new ArrayList<>();
    for (String annotLine : vepOutputContent.split("\n")) {
        annotations.add(AnnotationLineMapper.mapLine(annotLine, 0));
    }
    DBCollection variants = mongoClient.getDB(dbName).getCollection(dbCollectionVariantsName);

    // first do a mock of a "variants" collection, with just the _id
    writeIdsIntoMongo(annotations, variants);

    //prepare annotation sets
    List<VariantAnnotation> annotationSet1 = new ArrayList<>();
    List<VariantAnnotation> annotationSet2 = new ArrayList<>();
    List<VariantAnnotation> annotationSet3 = new ArrayList<>();

    String[] vepOutputLines = vepOutputContent.split("\n");

    for (String annotLine : Arrays.copyOfRange(vepOutputLines, 0, 2)) {
        annotationSet1.add(AnnotationLineMapper.mapLine(annotLine, 0));
    }

    for (String annotLine : Arrays.copyOfRange(vepOutputLines, 2, 4)) {
        annotationSet2.add(AnnotationLineMapper.mapLine(annotLine, 0));
    }

    for (String annotLine : Arrays.copyOfRange(vepOutputLines, 4, 7)) {
        annotationSet3.add(AnnotationLineMapper.mapLine(annotLine, 0));
    }

    // now, load the annotation
    String collections = jobOptions.getPipelineOptions().getString("db.collections.variants.name");
    annotationWriter = new VepAnnotationMongoWriter(mongoOperations, collections);

    annotationWriter.write(annotationSet1);
    annotationWriter.write(annotationSet2);
    annotationWriter.write(annotationSet3);

    // and finally check that documents in DB have the correct number of annotation
    DBCursor cursor = variants.find();

    while (cursor.hasNext()) {
        DBObject dbObject = cursor.next();
        String id = dbObject.get("_id").toString();

        VariantAnnotation annot = converter.convertToDataModelType((DBObject) dbObject.get("annot"));

        if (id.equals("20_63360_C_T") || id.equals("20_63399_G_A") || id.equals("20_63426_G_T")) {
            assertEquals(2, annot.getConsequenceTypes().size());
            assertEquals(4, annot.getXrefs().size());
        }

    }
}

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

public static String trimMetaSeq(String seq, int trimStart, int trimStop) {
    int modelPos = 0;
    char[] bases = seq.toCharArray();
    int start = 0, stop = 0;
    char b;/*from ww w.j a v  a  2 s  .c  om*/

    for (int index = 0; index < bases.length; index++) {
        b = bases[index];

        if (b == '.' || b == '~') {
            continue;
        }

        if (modelPos == trimStart) {
            start = index;
        }

        if (modelPos == trimStop) {
            stop = index;
        }

        modelPos++;
    }

    if (stop == 0) {
        stop = bases.length;
    }

    return new String(Arrays.copyOfRange(bases, start, stop));
}