Example usage for java.util Arrays copyOf

Introduction

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

Prototype

public static boolean[] copyOf(boolean[] original, int newLength) 

Source Link

Document

Copies the specified array, truncating or padding with false (if necessary) so the copy has the specified length.

Usage

From source file:Main.java

public static void main(String[] args) {

    // intializing an array arr1
    float[] arr1 = new float[] { 10f, 20f, 25f };

    System.out.println(Arrays.toString(arr1));

    // copying array arr1 to arr2 with newlength as 5
    float[] arr2 = Arrays.copyOf(arr1, 5);
    arr2[3] = 30f;/*from   w  w w  .  j ava  2  s  .  c om*/
    arr2[4] = 40f;

    System.out.println(Arrays.toString(arr2));
}

---

From source file:Main.java

public static void main(String[] args) {

    // intializing an array arr1
    double[] arr1 = new double[] { 1.5, 2.5, 3.5 };

    System.out.println(Arrays.toString(arr1));

    // copying array arr1 to arr2 with newlength as 5
    double[] arr2 = Arrays.copyOf(arr1, 5);
    arr2[3] = 0.44;/*  ww  w  .  j  a  va 2 s  .  co  m*/
    arr2[4] = 0.55;

    System.out.println(Arrays.toString(arr2));
}

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From source file:eu.stratosphere.yarn.YarnTaskManagerRunner.java

public static void main(final String[] args) throws IOException {
    Map<String, String> envs = System.getenv();
    final String yarnClientUsername = envs.get(Client.ENV_CLIENT_USERNAME);
    final String localDirs = envs.get(Environment.LOCAL_DIRS.key());

    // configure local directory
    final String[] newArgs = Arrays.copyOf(args, args.length + 2);
    newArgs[newArgs.length - 2] = "-" + TaskManager.ARG_CONF_DIR;
    newArgs[newArgs.length - 1] = localDirs;
    LOG.info("Setting log path " + localDirs);
    LOG.info("YARN daemon runs as '" + UserGroupInformation.getCurrentUser().getShortUserName() + "' setting"
            + " user to execute Stratosphere TaskManager to '" + yarnClientUsername + "'");
    UserGroupInformation ugi = UserGroupInformation.createRemoteUser(yarnClientUsername);
    for (Token<? extends TokenIdentifier> toks : UserGroupInformation.getCurrentUser().getTokens()) {
        ugi.addToken(toks);/*  w ww  .j  a va 2s. c o m*/
    }
    ugi.doAs(new PrivilegedAction<Object>() {
        @Override
        public Object run() {
            try {
                TaskManager.main(newArgs);
            } catch (Exception e) {
                e.printStackTrace();
            }
            return null;
        }
    });
}

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From source file:mase.deprecated.SelectionBenchmark.java

public static void main(String[] args) {

    int L = 100, N = 10000;
    double[] truncationP = new double[] { 0.25, 0.50, 0.75 };
    int[] tournamentP = new int[] { 2, 5, 7, 10 };

    DescriptiveStatistics[] truncationStat = new DescriptiveStatistics[truncationP.length];
    for (int i = 0; i < truncationStat.length; i++) {
        truncationStat[i] = new DescriptiveStatistics();
    }//  w w w  . ja va2s .c  o m
    DescriptiveStatistics[] tournamentStat = new DescriptiveStatistics[tournamentP.length];
    DescriptiveStatistics[] tournamentStat2 = new DescriptiveStatistics[tournamentP.length];
    for (int i = 0; i < tournamentStat.length; i++) {
        tournamentStat[i] = new DescriptiveStatistics();
        tournamentStat2[i] = new DescriptiveStatistics();
    }
    DescriptiveStatistics rouletteStat = new DescriptiveStatistics();
    DescriptiveStatistics rouletteStat2 = new DescriptiveStatistics();
    DescriptiveStatistics baseStat = new DescriptiveStatistics();

    for (int i = 0; i < N; i++) {
        // generate test vector
        double[] test = new double[L];
        for (int j = 0; j < L; j++) {
            test[j] = Math.random();
        }

        // truncation
        for (int p = 0; p < truncationP.length; p++) {
            double[] v = Arrays.copyOf(test, test.length);
            Arrays.sort(v);
            int nElites = (int) Math.ceil(truncationP[p] * test.length);
            double cutoff = v[test.length - nElites];
            double[] weights = new double[test.length];
            for (int k = 0; k < test.length; k++) {
                weights[k] = test[k] >= cutoff ? test[k] * (1 / truncationP[p]) : 0;
            }
            truncationStat[p].addValue(sum(weights));
        }

        // tournament
        for (int p = 0; p < tournamentP.length; p++) {
            double[] weights = new double[test.length];
            HashSet<Integer> added = new HashSet<Integer>();
            for (int k = 0; k < test.length; k++) {
                int idx = makeTournament(test, tournamentP[p]);
                weights[idx] += test[idx];
                added.add(idx);
            }
            tournamentStat2[p].addValue(added.size());
            tournamentStat[p].addValue(sum(weights));
        }

        // roulette
        double[] weights = new double[test.length];
        HashSet<Integer> added = new HashSet<Integer>();
        for (int k = 0; k < test.length; k++) {
            int idx = roulette(test);
            weights[idx] += test[idx];
            added.add(idx);
        }
        rouletteStat.addValue(sum(weights));
        rouletteStat2.addValue(added.size());

        // base
        baseStat.addValue(sum(test));
    }

    for (int p = 0; p < truncationP.length; p++) {
        System.out.println("Truncation\t" + truncationP[p] + "\t" + truncationStat[p].getMean() + "\t"
                + truncationStat[p].getStandardDeviation() + "\t" + ((int) Math.ceil(L * truncationP[p]))
                + "\t 0");
    }
    for (int p = 0; p < tournamentP.length; p++) {
        System.out.println("Tournament\t" + tournamentP[p] + "\t" + tournamentStat[p].getMean() + "\t"
                + tournamentStat[p].getStandardDeviation() + "\t" + tournamentStat2[p].getMean() + "\t"
                + tournamentStat2[p].getStandardDeviation());
    }
    System.out.println("Roulette\t\t" + rouletteStat.getMean() + "\t" + rouletteStat.getStandardDeviation()
            + "\t" + rouletteStat2.getMean() + "\t" + rouletteStat2.getStandardDeviation());
    System.out.println(
            "Base    \t\t" + baseStat.getMean() + "\t" + baseStat.getStandardDeviation() + "\t " + L + "\t0");
}

---

From source file:GrowBufferedReader.java

public static void main(String... args) {
    try {// ww  w.  j a  va 2s .  co  m
        BufferedReader br = new BufferedReader(car);

        Class<?> c = br.getClass();
        Field f = c.getDeclaredField("cb");

        // cb is a private field
        f.setAccessible(true);
        char[] cbVal = char[].class.cast(f.get(br));

        char[] newVal = Arrays.copyOf(cbVal, cbVal.length * 2);
        if (args.length > 0 && args[0].equals("grow"))
            f.set(br, newVal);

        for (int i = 0; i < srcBufSize; i++)
            br.read();

        // see if the new backing array is being used
        if (newVal[srcBufSize - 1] == src[srcBufSize - 1])
            out.format("Using new backing array, size=%d%n", newVal.length);
        else
            out.format("Using original backing array, size=%d%n", cbVal.length);

        // production code should handle these exceptions more gracefully
    } catch (FileNotFoundException x) {
        x.printStackTrace();
    } catch (NoSuchFieldException x) {
        x.printStackTrace();
    } catch (IllegalAccessException x) {
        x.printStackTrace();
    } catch (IOException x) {
        x.printStackTrace();
    }
}

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From source file:com.linkedin.pinot.perf.MultiValueReaderWriterBenchmark.java

public static void main(String[] args) throws Exception {
    List<String> lines = IOUtils.readLines(new FileReader(new File(args[0])));
    int totalDocs = lines.size();
    int max = Integer.MIN_VALUE;
    int maxNumberOfMultiValues = Integer.MIN_VALUE;
    int totalNumValues = 0;
    int data[][] = new int[totalDocs][];
    for (int i = 0; i < lines.size(); i++) {
        String line = lines.get(i);
        String[] split = line.split(",");
        totalNumValues = totalNumValues + split.length;
        if (split.length > maxNumberOfMultiValues) {
            maxNumberOfMultiValues = split.length;
        }/*from   w ww  .  jav  a2s . c  o m*/
        data[i] = new int[split.length];
        for (int j = 0; j < split.length; j++) {
            String token = split[j];
            int val = Integer.parseInt(token);
            data[i][j] = val;
            if (val > max) {
                max = val;
            }
        }
    }
    int maxBitsNeeded = (int) Math.ceil(Math.log(max) / Math.log(2));
    int size = 2048;
    int[] offsets = new int[size];
    int bitMapSize = 0;
    File outputFile = new File("output.mv.fwd");

    FixedBitSkipListSCMVWriter fixedBitSkipListSCMVWriter = new FixedBitSkipListSCMVWriter(outputFile,
            totalDocs, totalNumValues, maxBitsNeeded);

    for (int i = 0; i < totalDocs; i++) {
        fixedBitSkipListSCMVWriter.setIntArray(i, data[i]);
        if (i % size == size - 1) {
            MutableRoaringBitmap rr1 = MutableRoaringBitmap.bitmapOf(offsets);
            ByteArrayOutputStream bos = new ByteArrayOutputStream();
            DataOutputStream dos = new DataOutputStream(bos);
            rr1.serialize(dos);
            dos.close();
            //System.out.println("Chunk " + i / size + " bitmap size:" + bos.size());
            bitMapSize += bos.size();
        } else if (i == totalDocs - 1) {
            MutableRoaringBitmap rr1 = MutableRoaringBitmap.bitmapOf(Arrays.copyOf(offsets, i % size));
            ByteArrayOutputStream bos = new ByteArrayOutputStream();
            DataOutputStream dos = new DataOutputStream(bos);
            rr1.serialize(dos);
            dos.close();
            //System.out.println("Chunk " + i / size + " bitmap size:" + bos.size());
            bitMapSize += bos.size();
        }
    }
    fixedBitSkipListSCMVWriter.close();
    System.out.println("Output file size:" + outputFile.length());
    System.out.println("totalNumberOfDoc\t\t\t:" + totalDocs);
    System.out.println("totalNumberOfValues\t\t\t:" + totalNumValues);
    System.out.println("chunk size\t\t\t\t:" + size);
    System.out.println("Num chunks\t\t\t\t:" + totalDocs / size);
    int numChunks = totalDocs / size + 1;
    int totalBits = (totalNumValues * maxBitsNeeded);
    int dataSizeinBytes = (totalBits + 7) / 8;

    System.out.println("Raw data size with fixed bit encoding\t:" + dataSizeinBytes);
    System.out.println("\nPer encoding size");
    System.out.println();
    System.out.println("size (offset + length)\t\t\t:" + ((totalDocs * (4 + 4)) + dataSizeinBytes));
    System.out.println();
    System.out.println("size (offset only)\t\t\t:" + ((totalDocs * (4)) + dataSizeinBytes));
    System.out.println();
    System.out.println("bitMapSize\t\t\t\t:" + bitMapSize);
    System.out.println("size (with bitmap)\t\t\t:" + (bitMapSize + (numChunks * 4) + dataSizeinBytes));

    System.out.println();
    System.out.println("Custom Bitset\t\t\t\t:" + (totalNumValues + 7) / 8);
    System.out.println("size (with custom bitset)\t\t\t:"
            + (((totalNumValues + 7) / 8) + (numChunks * 4) + dataSizeinBytes));

}

---

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

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file");
    options.addOption("l", "less-than", false, "Trim at <= instead of strictly =");
    options.addOption("i", "illumina", false, "Illumina trimming mode");

    FastqWriter fastqOut = null;/* w  w w  . j a v  a 2s .c o m*/
    FastaWriter fastaOut = null;

    byte qualTrim = -1;

    boolean writeFasta = true;
    boolean trimle = false;
    boolean illumina = false;

    List<SeqReader> readers = new ArrayList();
    List<File> seqFiles = new ArrayList();

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("fastq-out")) {
            writeFasta = false;
        }

        if (line.hasOption("less-than")) {
            trimle = true;
        }
        if (line.hasOption("illumina")) {
            illumina = true;
        }

        args = line.getArgs();

        if (args.length < 2) {
            throw new Exception("Unexpected number of arguments");
        }

        if (args[0].length() != 1) {
            throw new Exception("Expected single character quality score");
        }

        qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0));

        for (int index = 1; index < args.length; index++) {
            File seqFile = new File(args[index]);
            SeqReader reader;
            if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) {
                if (index + 1 == args.length) {
                    throw new Exception("Fasta files must be immediately followed by their quality file");
                }

                File qualFile = new File(args[index + 1]);
                if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) {
                    throw new Exception(seqFile + " was not followed by a fasta quality file");
                }

                reader = new QSeqReader(seqFile, qualFile);
                index++;
            } else {
                if (seqFile.getName().endsWith(".gz")) {
                    reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile)));
                } else {
                    reader = new SequenceReader(seqFile);
                }
            }

            readers.add(reader);
            seqFiles.add(seqFile);
        }
    } catch (Exception e) {
        new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] <ascii_score> <seq_file> [qual_file]",
                options, true);
        System.err.println("Error: " + e.getMessage());
        System.exit(1);
    }

    for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) {
        File seqFile = seqFiles.get(readerIndex);
        String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf("."));
        if (writeFasta) {
            fastaOut = new FastaWriter(outStem + ".fasta");
        } else {
            fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction);
        }

        int[] lengthHisto = new int[200];

        SeqReader reader = readers.get(readerIndex);

        QSequence qseq;

        long totalLength = 0;
        int totalSeqs = 0;
        long trimmedLength = 0;
        int trimmedSeqs = 0;

        int zeroLengthAfterTrimming = 0;

        long startTime = System.currentTimeMillis();

        while ((qseq = (QSequence) reader.readNextSequence()) != null) {
            char[] bases = qseq.getSeqString().toCharArray();
            byte[] qual = qseq.getQuality();

            if (bases.length != qual.length) {
                System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq");
                continue;
            }

            totalSeqs++;
            totalLength += bases.length;

            int trimIndex = -1;
            if (illumina && qual[bases.length - 1] == qualTrim) {
                trimIndex = bases.length - 1;
                while (trimIndex >= 0 && qual[trimIndex] == qualTrim) {
                    trimIndex--;
                }

                trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base
            } else if (!illumina) {
                for (int index = 0; index < bases.length; index++) {
                    if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) {
                        trimIndex = index;
                        break;
                    }
                }
            }

            String outSeq;
            byte[] outQual;
            if (trimIndex == -1) {
                outSeq = qseq.getSeqString();
                outQual = qseq.getQuality();
            } else {
                outSeq = new String(bases, 0, trimIndex);
                outQual = Arrays.copyOfRange(qual, 0, trimIndex);
                trimmedSeqs++;
            }
            int len = outSeq.length();
            trimmedLength += len;

            if (len >= lengthHisto.length) {
                lengthHisto = Arrays.copyOf(lengthHisto, len + 1);
            }
            lengthHisto[len]++;

            if (outSeq.length() == 0) {
                //System.err.println(qseq.getSeqName() + ": length 0 after trimming");
                zeroLengthAfterTrimming++;
                continue;
            }

            if (writeFasta) {
                fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq);
            } else {
                fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual);
            }
        }

        reader.close();

        if (writeFasta) {
            fastaOut.close();
        } else {
            fastqOut.close();
        }

        System.out.println(
                "Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s");
        System.out.println("Before trimming:");
        System.out.println("Total Sequences:           " + totalSeqs);
        System.out.println("Total Sequence Data:       " + totalLength);
        System.out.println("Average sequence length:   " + ((float) totalLength / totalSeqs));
        System.out.println();
        System.out.println("After trimming:");
        System.out.println("Total Sequences:           " + (totalSeqs - zeroLengthAfterTrimming));
        System.out.println("Sequences Trimmed:         " + trimmedSeqs);
        System.out.println("Total Sequence Data:       " + trimmedLength);
        System.out.println("Average sequence length:   "
                + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming)));
        System.out.println();

        System.out.println("Length\tCount");
        for (int index = 0; index < lengthHisto.length; index++) {
            if (lengthHisto[index] == 0) {
                continue;
            }

            System.out.println(index + "\t" + lengthHisto[index]);
        }

        System.out.println();
        System.out.println();
        System.out.println();
    }
}

---

From source file:Main.java

public static String[] copyArray(String[] arr) {
    String[] arrNew = Arrays.copyOf(arr, arr.length);
    return arrNew;
}

---

From source file:Main.java

public static <T> T[] concatArrays(T[] a, T[] b) {
    T[] result = Arrays.copyOf(a, a.length + b.length);
    System.arraycopy(b, 0, result, a.length, b.length);
    return result;
}

---

From source file:Main.java

public static <T> T[] concat(T[] first, T[] second) {
    T[] result = Arrays.copyOf(first, first.length + second.length);
    System.arraycopy(second, 0, result, first.length, second.length);
    return result;
}

---

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