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 gunzip(File inFile, File outFile) {
    System.out.println("Expanding " + inFile.getAbsolutePath() + " to " + outFile.getAbsolutePath());

    FileOutputStream out = null;/*from  w w  w. jav  a2s . co m*/
    GZIPInputStream zIn = null;
    FileInputStream fis = null;
    try {
        out = new FileOutputStream(outFile);
        fis = new FileInputStream(inFile);
        zIn = new GZIPInputStream(fis);
        byte[] buffer = new byte[8 * 1024];
        int count = 0;
        do {
            out.write(buffer, 0, count);
            count = zIn.read(buffer, 0, buffer.length);
        } while (count != -1);
    } catch (IOException ioe) {
        ioe.printStackTrace();
    }
}

From source file:Main.java

public static File ungzip(File gzip, File toDir) throws IOException {
    toDir.mkdirs();/*  w  w w .ja v  a2s  . c o m*/
    File out = new File(toDir, gzip.getName());
    GZIPInputStream gin = null;
    FileOutputStream fout = null;
    try {
        FileInputStream fin = new FileInputStream(gzip);
        gin = new GZIPInputStream(fin);
        fout = new FileOutputStream(out);
        copy(gin, fout);
        gin.close();
        fout.close();
    } finally {
        closeQuietly(gin);
        closeQuietly(fout);
    }
    return out;
}

From source file:Main.java

public static String uncompress(InputStream inputStream) throws IOException {
    if (inputStream == null) {
        return null;
    }// w  ww .ja va  2  s  .c o m
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    GZIPInputStream gunzip = new GZIPInputStream(inputStream);
    byte[] buffer = new byte[256];
    int n;
    while ((n = gunzip.read(buffer)) >= 0) {
        out.write(buffer, 0, n);
    }
    return out.toString();
}

From source file:Main.java

/**
 * Degzips <strong>all</strong> of the datain the specified {@link ByteBuffer}.
 *
 * @param compressed The compressed buffer.
 * @return The decompressed array.//from   w  ww.  j  a  v a  2 s .com
 * @throws IOException If there is an error decompressing the buffer.
 */
public static byte[] degzip(byte[] compressed) throws IOException {
    try (InputStream is = new GZIPInputStream(new ByteArrayInputStream(compressed));
            ByteArrayOutputStream out = new ByteArrayOutputStream()) {
        byte[] buffer = new byte[1024];

        while (true) {
            int read = is.read(buffer, 0, buffer.length);
            if (read == -1) {
                break;
            }

            out.write(buffer, 0, read);
        }

        return out.toByteArray();
    }
}

From source file:Main.java

/**
 * Descomprime uma string utilizando o GZIP
 * //  ww  w. j  a v  a2  s. c om
 * @param str
 * @param encoding
 * @return
 */
public static String gzipDecompressString(String str, String encoding) {
    String decompressedString = "";

    try {
        byte[] bytes = Base64.decodeBase64(str.getBytes(encoding));
        ByteArrayInputStream bais = new ByteArrayInputStream(bytes);
        GZIPInputStream gzip = new GZIPInputStream(bais);
        Reader reader = new InputStreamReader(gzip, encoding);
        StringBuffer sbuf = new StringBuffer();
        char[] buffer = new char[32 * 1024];
        int nread;
        while ((nread = reader.read(buffer)) >= 0) {
            sbuf.append(buffer, 0, nread);
        }
        decompressedString = sbuf.toString();
        reader.close();
    } catch (Exception e) {
        e.printStackTrace();
    }

    return decompressedString;
}

From source file:Main.java

/**
 * Degzips the compressed array and places the results into the decompressed array.
 *
 * @param compressed The compressed array.
 * @param decompressed The decompressed array.
 * @throws IOException If an I/O error occurs.
 *///from  ww w .  ja  v a  2s . c  o m
public static void degzip(byte[] compressed, byte[] decompressed) throws IOException {
    try (DataInputStream is = new DataInputStream(new GZIPInputStream(new ByteArrayInputStream(compressed)))) {
        is.readFully(decompressed);
    }
}

From source file:Main.java

/**
 * Uncompress gzipped files/*from   w w w . ja  v a  2s.c om*/
 * @param gzippedFile The file to uncompress
 * @param destinationFile The resulting file
 * @throws java.io.IOException thrown if there is a problem finding or writing the files
 */
public static void gunzip(File gzippedFile, File destinationFile) throws IOException {
    int buffer = 2048;

    FileInputStream in = new FileInputStream(gzippedFile);
    GZIPInputStream zipin = new GZIPInputStream(in);

    byte[] data = new byte[buffer];

    // decompress the file
    FileOutputStream out = new FileOutputStream(destinationFile);
    try {
        int length;
        while ((length = zipin.read(data, 0, buffer)) != -1)
            out.write(data, 0, length);
    } finally {
        out.close();

        zipin.close();
        in.close();
    }

}

From source file:edu.cornell.med.icb.goby.reads.ColorSpaceConverter.java

public static void main(final String[] args) throws JSAPException, IOException {
    final JSAP jsap = new JSAP();

    final FlaggedOption sequenceOption = new FlaggedOption("input");
    sequenceOption.setRequired(true);/*from www.j  ava  2 s .c o m*/
    sequenceOption.setLongFlag("input");
    sequenceOption.setShortFlag('i');
    sequenceOption.setStringParser(FileStringParser.getParser().setMustBeFile(true).setMustExist(true));
    sequenceOption.setHelp("The input file (in Fasta format) to convert");
    jsap.registerParameter(sequenceOption);

    final FlaggedOption outputOption = new FlaggedOption("output");
    outputOption.setRequired(false);
    outputOption.setLongFlag("output");
    outputOption.setShortFlag('o');
    outputOption.setStringParser(FileStringParser.getParser().setMustBeFile(true));
    outputOption.setHelp("The output file to write to (default = stdout)");
    jsap.registerParameter(outputOption);

    final FlaggedOption titleOption = new FlaggedOption("title");
    titleOption.setRequired(false);
    titleOption.setLongFlag("title");
    titleOption.setShortFlag('t');
    titleOption.setHelp("Title for this conversion");
    jsap.registerParameter(titleOption);

    final Switch verboseOption = new Switch("verbose");
    verboseOption.setLongFlag("verbose");
    verboseOption.setShortFlag('v');
    verboseOption.setHelp("Verbose output");
    jsap.registerParameter(verboseOption);

    final Switch helpOption = new Switch("help");
    helpOption.setLongFlag("help");
    helpOption.setShortFlag('h');
    helpOption.setHelp("Print this message");
    jsap.registerParameter(helpOption);

    jsap.setUsage("Usage: " + ColorSpaceConverter.class.getName() + " " + jsap.getUsage());

    final JSAPResult result = jsap.parse(args);

    if (result.getBoolean("help")) {
        System.out.println(jsap.getHelp());
        System.exit(0);
    }

    if (!result.success()) {
        final Iterator<String> errors = result.getErrorMessageIterator();
        while (errors.hasNext()) {
            System.err.println(errors.next());
        }
        System.err.println(jsap.getUsage());
        System.exit(1);
    }

    final boolean verbose = result.getBoolean("verbose");

    final File sequenceFile = result.getFile("input");
    if (verbose) {
        System.out.println("Reading sequence from: " + sequenceFile);
    }

    // extract the title to use for the output header
    final String title;
    if (result.contains("title")) {
        title = result.getString("title");
    } else {
        title = sequenceFile.getName();
    }

    Reader inputReader = null;
    PrintWriter outputWriter = null;

    try {
        if ("gz".equals(FilenameUtils.getExtension(sequenceFile.getName()))) {
            inputReader = new InputStreamReader(new GZIPInputStream(FileUtils.openInputStream(sequenceFile)));
        } else {
            inputReader = new FileReader(sequenceFile);
        }
        final FastaParser fastaParser = new FastaParser(inputReader);

        final File outputFile = result.getFile("output");
        final OutputStream outputStream;
        if (outputFile != null) {
            outputStream = FileUtils.openOutputStream(outputFile);
            if (verbose) {
                System.out.println("Writing sequence : " + outputFile);
            }
        } else {
            outputStream = System.out;
        }
        outputWriter = new PrintWriter(outputStream);

        // write the header portion of the output
        outputWriter.print("# ");
        outputWriter.print(new Date());
        outputWriter.print(' ');
        outputWriter.print(ColorSpaceConverter.class.getName());
        for (final String arg : args) {
            outputWriter.print(' ');
            outputWriter.print(arg);
        }
        outputWriter.println();
        outputWriter.print("# Cwd: ");
        outputWriter.println(new File(".").getCanonicalPath());
        outputWriter.print("# Title: ");
        outputWriter.println(title);

        // now parse the input sequence
        long sequenceCount = 0;
        final MutableString descriptionLine = new MutableString();
        final MutableString sequence = new MutableString();
        final MutableString colorSpaceSequence = new MutableString();

        while (fastaParser.hasNext()) {
            fastaParser.next(descriptionLine, sequence);
            outputWriter.print('>');
            outputWriter.println(descriptionLine);

            convert(sequence, colorSpaceSequence);
            CompactToFastaMode.writeSequence(outputWriter, colorSpaceSequence);

            sequenceCount++;
            if (verbose && sequenceCount % 10000 == 0) {
                System.out.println("Converted " + sequenceCount + " entries");
            }
        }

        if (verbose) {
            System.out.println("Conversion complete!");
        }
    } finally {
        IOUtils.closeQuietly(inputReader);
        IOUtils.closeQuietly(outputWriter);
    }
}

From source file:net.es.nsi.common.util.ContentType.java

public static InputStream decode(String contentType, InputStream is) throws IOException {
    if (XGZIP.equalsIgnoreCase(contentType)) {
        return new GZIPInputStream(is);
    } else {//from   w  ww  .  j  ava2 s.c  o m
        return is;
    }
}

From source file:Main.java

public static byte[] readCompressedData(ByteArrayInputStream bais) {
    int uncompressedLength = getLength(bais);
    byte[] output = new byte[uncompressedLength];
    byte[] compressed = readData(bais);
    GZIPInputStream gs;// w w  w . j  a v  a  2  s  .  com
    try {
        gs = new GZIPInputStream(new ByteArrayInputStream(compressed));
        for (int i = 0; i < uncompressedLength; ++i) {
            output[i] = (byte) gs.read();
        }
    } catch (IOException e) {
        throw new RuntimeException("Cannot decompress", e);
    }

    return output;
}