Example usage for java.util Arrays copyOfRange

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.itemanalysis.psychometrics.irt.model.IrmPCM.java

private double numer(double theta, double[] iparam, int category, double D) {
    double Zk = 0;
    double b = iparam[0];
    double[] s = Arrays.copyOfRange(iparam, 1, iparam.length);

    //first category
    Zk = D * (theta - b);/*w  w w. j a v  a 2s.c  om*/

    for (int k = 0; k < category; k++) {
        Zk += D * (theta - b - s[k]);
    }
    return Math.exp(Zk);
}

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From source file:nu.yona.server.messaging.entities.MessageSource.java

private PrivateKey loadPrivateKey() {
    if (privateKey == null) {
        privateKey = PublicKeyUtil/*www .jav  a2s  .  co m*/
                .privateKeyFromBytes(Arrays.copyOfRange(privateKeyBytes, 1, privateKeyBytes.length));
    }
    return privateKey;
}

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From source file:com.blockwithme.longdb.leveldb.Util.java

/** Split column ids.
 * /*from   w w  w .java  2s .  c o  m*/
 * @param theColumns
 *        the all columns
 * @return the long array list */
@CheckForNull
public static LongArrayList splitColumnIds(final byte[] theColumns) {
    if (theColumns == null || theColumns.length == 0)
        return null;
    long offset = 0;
    final LongArrayList colIds = new LongArrayList();
    while (offset + LONG_BYTES <= theColumns.length) {
        final long colId = Util
                .toLong(Arrays.copyOfRange(theColumns, (int) offset, (int) (offset + LONG_BYTES)));
        colIds.add(colId);
        offset += LONG_BYTES;
    }
    return colIds;
}

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From source file:com.netflix.bdp.s3mper.cli.S3mper.java

private String[] popArg(String[] args) {
    if (args.length == 1) {
        return new String[0];
    }//from  ww w . j  a va 2 s  .  c om

    return Arrays.copyOfRange(args, 1, args.length);
}

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From source file:com.milaboratory.core.io.sequence.fasta.FastaReaderTest.java

private static TestItem createTestData(long seed, int readsCount, boolean withWildcards) throws IOException {
    Well1024a rnd = new Well1024a(seed);

    File tempFile = File.createTempFile("temp" + seed, ".fasta");
    tempFile.deleteOnExit();//from   w  w  w  .  j a  va 2  s .  c  om
    FileOutputStream output = new FileOutputStream(tempFile);

    SingleRead[] reads = new SingleRead[readsCount];

    WildcardSymbol[] wildcards = NucleotideSequence.ALPHABET.getAllWildcards().toArray(new WildcardSymbol[0]);
    long id = 0;
    for (int i = 0; i < readsCount; ++i) {
        char[] seq = new char[50 + rnd.nextInt(100)];
        char[] seqExp = new char[seq.length];

        int qPointer = 0;
        byte[] qualityData = new byte[seq.length];
        Arrays.fill(qualityData, SequenceQuality.GOOD_QUALITY_VALUE);
        for (int j = 0; j < seq.length; ++j) {
            seq[j] = seqExp[j] = NucleotideSequence.ALPHABET.symbolFromCode((byte) rnd.nextInt(4));
            if (j != 0 && j != seq.length - 1 && ((4 * j) % seq.length == 0) && rnd.nextBoolean()) {
                //next line for sequence
                seq[j] = seqExp[j] = '\n';
                --qPointer;
            } else if (withWildcards && j % 5 == 0) {//wildcard
                WildcardSymbol wildcard = wildcards[rnd.nextInt(wildcards.length)];
                if (NucleotideSequence.ALPHABET.codeFromSymbol(wildcard.getSymbol()) == -1) {
                    seq[j] = wildcard.getSymbol();
                    seqExp[j] = NucleotideSequence.ALPHABET
                            .symbolFromCode(wildcard.getUniformlyDistributedSymbol(id ^ (j + qPointer)));//as used in FastaReader#getSequenceWithQuality(..)
                    qualityData[j + qPointer] = SequenceQuality.BAD_QUALITY_VALUE;
                }
            }
        }
        String description = ">seq" + i;
        String sequenceString = new String(seq);
        output.write(description.getBytes());
        output.write('\n');
        output.write(sequenceString.getBytes());
        output.write('\n');

        reads[i] = new SingleReadImpl(id,
                new NSequenceWithQuality(new NucleotideSequence(new String(seqExp).replace("\n", "")),
                        new SequenceQuality(Arrays.copyOfRange(qualityData, 0, seq.length + qPointer))),
                description.substring(1));
        ++id;
    }
    output.close();

    return new TestItem(tempFile, reads);
}

---

From source file:com.kakao.hbase.common.Args.java

public Args(String[] args) throws IOException {
    OptionSet optionSetTemp = createOptionParser().parse(args);

    List<?> nonOptionArguments = optionSetTemp.nonOptionArguments();
    if (nonOptionArguments.size() < 1)
        throw new IllegalArgumentException(INVALID_ARGUMENTS);

    String arg = (String) nonOptionArguments.get(0);

    if (Util.isFile(arg)) {
        String[] newArgs = (String[]) ArrayUtils.addAll(parseArgsFile(arg),
                Arrays.copyOfRange(args, 1, args.length));
        this.optionSet = createOptionParser().parse(newArgs);
        this.zookeeperQuorum = (String) optionSet.nonOptionArguments().get(0);
    } else {// w ww  .j a  v a 2s  . co m
        this.optionSet = optionSetTemp;
        this.zookeeperQuorum = arg;
    }
}

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From source file:com.yahoo.pulsar.admin.cli.PulsarAdminTool.java

boolean run(String[] args) {
    if (args.length == 0) {
        jcommander.usage();/*from  ww w .j ava2s. co  m*/
        return false;
    }

    try {
        jcommander.parse(new String[] { args[0] });
    } catch (Exception e) {
        System.err.println(e.getMessage());
        System.err.println();
        jcommander.usage();
        return false;
    }

    if (help) {
        jcommander.usage();
        return false;
    }

    if (jcommander.getParsedCommand() == null) {
        jcommander.usage();
        return false;
    } else {
        String cmd = jcommander.getParsedCommand();
        JCommander obj = jcommander.getCommands().get(cmd);
        CmdBase cmdObj = (CmdBase) obj.getObjects().get(0);

        return cmdObj.run(Arrays.copyOfRange(args, 1, args.length));
    }
}

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From source file:bb.mcmc.analysis.GewekeConvergeStat.java

@Override
protected double calculateEachStat(String key) {

    final double[] t = traceValues.get(key);

    final int length = t.length;
    final int indexStart = (int) Math.floor(length * (1 - frac2));
    final int indexEnd = (int) Math.ceil(length * frac1);
    final double[] dStart = Arrays.copyOfRange(t, 0, indexEnd);
    final double[] dEnd = Arrays.copyOfRange(t, indexStart, length);
    final double meanStart = DiscreteStatistics.mean(dStart);
    final double meanEnd = DiscreteStatistics.mean(dEnd);
    final double varStart = ConvergeStatUtils.spectrum0(dStart) / dStart.length;
    final double varEnd = ConvergeStatUtils.spectrum0(dEnd) / dEnd.length;
    final double bothVar = varStart + varEnd;

    double stat = (meanStart - meanEnd) / Math.sqrt(bothVar);

    if (Double.isNaN(stat)) { //Use two separate if to handle other NaN cases later
        if (Double.isNaN(bothVar)) {
            stat = Double.NEGATIVE_INFINITY;
            System.err.println(STATISTIC_NAME + " could not be calculated for variable with id " + key
                    + ". This is due to logged values being unchanged during the run");//. Check log file for details. ");
        }/*from w  w  w  . j a va  2 s  .co  m*/
    }
    return stat;

}

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From source file:org.psit.transwatcher.TransWatcher.java

@Override
public void run() {

    try {//from   w  ww.  j a va  2 s  .c  o  m
        while (true) {

            String cardIP = connectAndGetCardIP();
            if (cardIP != null) {
                notifyMessage("Found SD card, IP: " + cardIP);

                // handshake successful, open permanent TCP connection
                // to listen to new images
                Socket newImageListenerSocket = null;
                try {
                    newImageListenerSocket = new Socket(cardIP, 5566);
                    newImageListenerSocket.setKeepAlive(true);
                    InputStream is = newImageListenerSocket.getInputStream();
                    byte[] c = new byte[1];
                    byte[] singleMessage = new byte[255];
                    int msgPointer = 0;

                    startConnectionKeepAliveWatchDog(newImageListenerSocket);

                    startImageDownloaderQueue(cardIP);

                    setState(State.LISTENING);

                    // loop to wait for new images
                    while (newImageListenerSocket.isConnected()) {
                        if (is.read(c) == 1) {
                            if (0x3E == c[0]) { // >
                                // start of filename
                                msgPointer = 0;
                            } else if (0x00 == c[0]) {
                                // end of filename
                                String msg = new String(Arrays.copyOfRange(singleMessage, 0, msgPointer));
                                notifyMessage("Image shot: " + msg);

                                // add to download queue
                                queue.add(msg);
                            } else {
                                // single byte. add to buffer
                                singleMessage[msgPointer++] = c[0];
                            }
                        }
                    }
                    setState(State.SEARCHING_CARD);
                } catch (IOException e) {
                    notifyMessage("Error during image notification connection!");
                } finally {
                    try {
                        newImageListenerSocket.close();
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            } else {
                notifyMessage("No card found, retrying.");
            }
            Thread.sleep(2000);
        }
    } catch (InterruptedException e) {
        stopImageDownLoaderQueue();
        notifyMessage("Connection abandoned.");
    }

}

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From source file:duthientan.mmanm.com.CipherRSA.java

@Override
public void decrypt(String filePath) {
    try {/*from   w w w .j a  v a  2s .co m*/
        Cipher decipher = Cipher.getInstance("RSA");
        decipher.init(Cipher.DECRYPT_MODE, privateKey);
        Path path = Paths.get(filePath);
        String decryptFilePath = filePath.replace("RSA" + "_", "");
        byte[] data = Files.readAllBytes(path);
        byte[] textDncrypted = null;
        int chunkSize = 256;
        if (data.length < 256) {
            textDncrypted = decipher.doFinal(data);
        } else {
            for (int i = 0; i < data.length; i += chunkSize) {
                byte[] segment = Arrays.copyOfRange(data, i,
                        i + chunkSize > data.length ? data.length : i + chunkSize);
                byte[] segmentEncrypted = decipher.doFinal(segment);
                textDncrypted = ArrayUtils.addAll(textDncrypted, segmentEncrypted);
            }
        }
        FileOutputStream fos = new FileOutputStream(decryptFilePath);
        fos.write(textDncrypted);
        fos.close();
    } catch (NoSuchAlgorithmException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    } catch (NoSuchPaddingException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    } catch (InvalidKeyException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    } catch (IOException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    } catch (IllegalBlockSizeException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    } catch (BadPaddingException ex) {
        Logger.getLogger(CipherRSA.class.getName()).log(Level.SEVERE, null, ex);
    }
}

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