Example usage for java.util.zip GZIPInputStream GZIPInputStream

Introduction

In this page you can find the example usage for java.util.zip GZIPInputStream GZIPInputStream.

Prototype

public GZIPInputStream(InputStream in) throws IOException 

Source Link

Document

Creates a new input stream with a default buffer size.

Usage

From source file:Main.java

public static void main(String[] args) throws Exception {
    String inName = "a.pack.gz";
    String outName = "a.unpacked";
    Pack200.Unpacker unpacker = Pack200.newUnpacker();
    JarOutputStream out = new JarOutputStream(new FileOutputStream(outName));
    InputStream in = new FileInputStream(inName);
    in = new GZIPInputStream(in);
    unpacker.unpack(in, out);//from  w ww  . j a v  a 2 s. c om
    out.close();
}

---

From source file:Main.java

public static void main(String[] args) throws Exception {

    String inName = "abc.pack.gz";
    String outName = "abc";

    Pack200.Unpacker unpacker = Pack200.newUnpacker();
    JarOutputStream out = new JarOutputStream(new FileOutputStream(outName));
    InputStream in = new FileInputStream(inName);
    if (inName.endsWith(".gz")) {
        in = new GZIPInputStream(in);
    }//from ww  w  .  j a v  a2s.  c o m

    unpacker.unpack(in, out);
    out.close();
}

---

From source file:MainClass.java

public static void main(String[] args) throws Exception {

    String inName = args[0];// w  w  w .ja v a 2  s .c  om
    String outName;
    if (inName.endsWith(".pack.gz")) {
        outName = inName.substring(0, inName.length() - 8);
    } else if (inName.endsWith(".pack")) {
        outName = inName.substring(0, inName.length() - 5);
    } else {
        outName = inName + ".unpacked";
    }

    JarOutputStream out = null;
    InputStream in = null;

    Pack200.Unpacker unpacker = Pack200.newUnpacker();
    out = new JarOutputStream(new FileOutputStream(outName));
    in = new FileInputStream(inName);
    if (inName.endsWith(".gz"))
        in = new GZIPInputStream(in);
    unpacker.unpack(in, out);
    out.close();
}

---

From source file:GZIPcompress.java

public static void main(String[] args) throws IOException {
    if (args.length == 0) {
        System.out.println("Usage: \nGZIPcompress file\n" + "\tUses GZIP compression to compress "
                + "the file to test.gz");
        System.exit(1);//ww w.  ja  v a2  s.co m
    }
    BufferedReader in = new BufferedReader(new FileReader(args[0]));
    BufferedOutputStream out = new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream("test.gz")));
    System.out.println("Writing file");
    int c;
    while ((c = in.read()) != -1)
        out.write(c);
    in.close();
    out.close();
    System.out.println("Reading file");
    BufferedReader in2 = new BufferedReader(
            new InputStreamReader(new GZIPInputStream(new FileInputStream("test.gz"))));
    String s;
    while ((s = in2.readLine()) != null)
        System.out.println(s);
}

---

From source file:CommandsFromZipFile.java

/**
 *  Sample test to retrieve command value using zip file
 * @param args/* w ww .  j a va 2s .c  o m*/
 */
public static void main(String[] args) {
    //by default it sets to Ctrl+D
    System.setProperty("jline.shutdownhook", "true");
    try {
        ConsoleReader consoleReader = new ConsoleReader();
        consoleReader.setPrompt("carbon>");
        consoleReader.addCompleter(new StringsCompleter(IOUtils.readLines(
                new GZIPInputStream(CommandsFromZipFile.class.getResourceAsStream("commandList.txt.gz")))));
        consoleReader.addCompleter(new FileNameCompleter());
        String line = "";
        String colored = "";

        while ((line = consoleReader.readLine()) != null) {
            if ("clear".equals(line.trim())) {
                System.out.print("\33[2J");
                System.out.flush();
                System.out.print("\33[1;1H");
                System.out.flush();
            } else if ("aback".equals(line.trim())) {
                colored = Ansi.ansi().fg(Ansi.Color.RED).a("Entered command : ")
                        .a(Ansi.Attribute.INTENSITY_BOLD).a(line).a(Ansi.Attribute.INTENSITY_BOLD_OFF)
                        .fg(Ansi.Color.DEFAULT).toString();
                consoleReader.println(colored);
            } else {
                consoleReader.println(line);
            }
        }
    } catch (IOException exception) {
        LOGGER.error(" Unable to load commands from the zip file ", exception);
    } finally {
        try {
            jline.TerminalFactory.get().restore();
        } catch (Exception exception) {
            LOGGER.error(" Unable to restore the terminal ", exception);
        }
    }
}

---

From source file:com.javacreed.examples.sql.Example2.java

public static void main(final String[] args) throws Exception {
    try (BasicDataSource dataSource = DatabaseUtils.createDataSource();
            Connection connection = dataSource.getConnection()) {
        final ExampleTest test = new ExampleTest(connection, "compressed_table", "compressed") {
            @Override//  w ww.j  a  v a  2s. c  o m
            protected String parseRow(final ResultSet resultSet) throws Exception {
                try (GZIPInputStream in = new GZIPInputStream(resultSet.getBinaryStream("compressed"))) {
                    return IOUtils.toString(in, "UTF-8");
                }
            }

            @Override
            protected void setPreparedStatement(final String data, final PreparedStatement statement)
                    throws Exception {
                // Compress the data before inserting it. We need to compress before inserting the data to make this process
                // as realistic as possible.
                final ByteArrayOutputStream baos = new ByteArrayOutputStream(data.length());
                try (OutputStream out = new GZIPOutputStream(baos, data.length())) {
                    out.write(data.getBytes("UTF-8"));
                }
                statement.setBinaryStream(1, new ByteArrayInputStream(baos.toByteArray()));
            }
        };
        test.runTest();
    }
    Example2.LOGGER.debug("Done");
}

---

From source file:ReadGZIP.java

public static void main(String[] argv) throws IOException {
    String FILENAME = "file.txt.gz";

    // Since there are 4 constructor calls here, I wrote them out in full.
    // In real life you would probably nest these constructor calls.
    FileInputStream fin = new FileInputStream(FILENAME);
    GZIPInputStream gzis = new GZIPInputStream(fin);
    InputStreamReader xover = new InputStreamReader(gzis);
    BufferedReader is = new BufferedReader(xover);

    String line;/*ww  w.j a va2 s  . c  o m*/
    // Now read lines of text: the BufferedReader puts them in lines,
    // the InputStreamReader does Unicode conversion, and the
    // GZipInputStream "gunzip"s the data from the FileInputStream.
    while ((line = is.readLine()) != null)
        System.out.println("Read: " + line);
}

---

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;//from w ww  . j  a  va 2  s .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:de.hpi.fgis.hdrs.tools.Loader.java

public static void main(String[] args) throws IOException {

    if (2 > args.length) {
        System.out.println(usage);
        System.out.println(options);
        System.exit(1);//from   w w  w . ja va  2  s .  c  o  m
    }

    if (0 > args[0].indexOf(':')) {
        args[0] += ":" + Configuration.DEFAULT_RPC_PORT;
    }
    Configuration conf = Configuration.create();
    Client client = new Client(conf, args[0]);

    File[] files;
    String options = "";
    if (args[1].startsWith("-")) {
        options = args[1];
        if (3 > args.length) {
            System.out.println(usage);
            System.exit(1);
        }
        if (0 < options.indexOf('d')) {
            File dir = new File(args[2]);
            if (!dir.isDirectory()) {
                throw new IOException("Directory does not exist.");
            }
            files = dir.listFiles();
        } else {
            files = new File[] { new File(args[2]) };
        }
    } else {
        files = new File[] { new File(args[1]) };
    }

    boolean quiet = 0 < options.indexOf('q');
    boolean context = 0 < options.indexOf('c');

    boolean bench = 0 < options.indexOf('b');
    List<BenchSample> benchSamples = null;
    if (bench) {
        benchSamples = new ArrayList<BenchSample>();
    }

    long timeStalled = 0;
    long timeRouterUpdate = 0;
    long abortedTransactions = 0;

    long nBytesTotal = 0;
    long nTriplesTotal = 0;
    long timeTotal = 0;

    for (int i = 0; i < files.length; ++i) {
        Closeable source = null;
        TripleScanner scanner = null;

        try {
            if (0 < options.indexOf('t')) {
                TripleFileReader reader = new TripleFileReader(files[i]);
                reader.open();
                scanner = reader.getScanner();
                source = reader;
            } else if (0 < options.indexOf('z')) {
                GZIPInputStream stream = new GZIPInputStream(new FileInputStream(files[i]));
                BTCParser parser = new BTCParser();
                parser.setSkipContext(!context);
                scanner = new StreamScanner(stream, parser);
                source = stream;
            } else {
                BTCParser parser = new BTCParser();
                parser.setSkipContext(!context);
                FileSource file = new FileSource(files[i], parser);
                scanner = file.getScanner();
                source = file;
            }
        } catch (IOException ioe) {
            System.out.println("Error: Couldn't open " + files[i] + ". See log for details.");
            LOG.error("Error: Couldn't open " + files[i] + ":", ioe);
            continue;
        }

        long nBytes = 0;
        long nTriples = 0;
        long time = System.currentTimeMillis();

        TripleOutputStream out = client.getOutputStream();

        while (scanner.next()) {
            Triple t = scanner.pop();
            out.add(t);
            nBytes += t.serializedSize();
            nTriples++;

            if (!quiet && 0 == (nTriples % (16 * 1024))) {
                System.out.print(String.format("\rloading... %d triples (%.2f MB, %.2f MB/s)", nTriples,
                        LogFormatUtil.MB(nBytes),
                        LogFormatUtil.MBperSec(nBytes, System.currentTimeMillis() - time)));
            }
        }
        out.close();

        time = System.currentTimeMillis() - time;

        scanner.close();
        source.close();

        if (!quiet) {
            System.out.print("\r");
        }
        System.out.println(String.format("%s: %d triples (%.2f MB) loaded " + "in %.2f seconds (%.2f MB/s)",
                files[i], nTriples, LogFormatUtil.MB(nBytes), time / 1000.0,
                LogFormatUtil.MBperSec(nBytes, time)));

        nBytesTotal += nBytes;
        nTriplesTotal += nTriples;
        timeTotal += time;

        timeStalled += out.getTimeStalled();
        timeRouterUpdate += out.getTimeRouterUpdate();
        abortedTransactions += out.getAbortedTransactions();

        if (bench) {
            benchSamples.add(new BenchSample(time, nTriples, nBytes));
        }
    }

    client.close();

    if (0 == nTriplesTotal) {
        System.out.println("No triples loaded.");
        return;
    }

    System.out.println(
            String.format("Done loading.  Totals: %d triples (%.2f MB) loaded " + "in %.2f seconds (%.2f MB/s)",
                    nTriplesTotal, LogFormatUtil.MB(nBytesTotal), timeTotal / 1000.0,
                    LogFormatUtil.MBperSec(nBytesTotal, timeTotal)));

    System.out.println(String.format(
            "  Client stats.  Stalled: %.2f s  RouterUpdate: %.2f s" + "  AbortedTransactions: %d",
            timeStalled / 1000.0, timeRouterUpdate / 1000.0, abortedTransactions));

    if (bench) {
        System.out.println();
        System.out.println("Benchmark Samples:");
        System.out.println("time\tsum T\tsum MB\tMB/s");
        System.out.println(String.format("%.2f\t%d\t%.2f\t%.2f", 0f, 0, 0f, 0f));
        long time = 0, nTriples = 0, nBytes = 0;
        for (BenchSample sample : benchSamples) {
            time += sample.time;
            nTriples += sample.nTriples;
            nBytes += sample.nBytes;
            System.out.println(String.format("%.2f\t%d\t%.2f\t%.2f", time / 1000.0, nTriples,
                    LogFormatUtil.MB(nBytes), LogFormatUtil.MBperSec(sample.nBytes, sample.time)));
        }
    }
}

---

From source file:Main.java

public static byte[] decompressGZIP(byte bytes[]) throws IOException {
    ByteArrayInputStream is = new ByteArrayInputStream(bytes);
    GZIPInputStream gzipis = new GZIPInputStream(is);
    ByteArrayOutputStream os = new ByteArrayOutputStream();
    int i;/*from w w w  .j a  va 2s .  co m*/
    while ((i = gzipis.read()) != -1) {
        os.write(i);
    }
    gzipis.close();
    os.close();
    return os.toByteArray();
}

---

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