Example usage for org.apache.commons.compress.utils CountingOutputStream CountingOutputStream

Introduction

In this page you can find the example usage for org.apache.commons.compress.utils CountingOutputStream CountingOutputStream.

Prototype

public CountingOutputStream(final OutputStream out) 

Source Link

Usage

From source file:htsjdk.samtools.reference.FastaReferenceWriter.java

/**
 * Creates a reference FASTA file writer (private...use the builder: {@link FastaReferenceWriterBuilder}.
 * <p>/*from   ww  w  . j a  va2s .  c o  m*/
 * You can specify a specific output stream to each file: the main fasta output, its index and its dictionary.
 * You can only provide a compressed stream to the fastaOutput, and only in the case that an index isn't written.
 * <p>
 * <p>
 * </p>
 *
 * @param fastaOutput the (uncompressed) output fasta file path.
 * @param indexOutput the (uncompressed) output stream to the index file, if requested, {@code null} if none should be generated.
 * @param dictOutput  the (uncompressed) output stream to the dictFile, if requested, {@code null} if none should be generated.
 * @throws IllegalArgumentException if {@code fastaFile} is {@code null} or {@code basesPerLine} is 0 or negative.
 */
FastaReferenceWriter(final int basesPerLine, final boolean addMd5, final OutputStream fastaOutput,
        final OutputStream indexOutput, final OutputStream dictOutput) {

    try {
        this.md5Digester = addMd5 ? MessageDigest.getInstance("MD5") : null;
    } catch (NoSuchAlgorithmException e) {
        throw new RuntimeException("Couldn't get md5 algorithm!", e);
    }

    this.defaultBasePerLine = basesPerLine;
    this.fastaStream = new CountingOutputStream(fastaOutput);
    this.indexWriter = indexOutput == null ? NullWriter.NULL_WRITER
            : new OutputStreamWriter(indexOutput, CHARSET);
    this.dictWriter = dictOutput == null ? NullWriter.NULL_WRITER : new OutputStreamWriter(dictOutput, CHARSET);
    this.dictCodec = new SAMSequenceDictionaryCodec(dictWriter);
    this.dictCodec.encodeHeaderLine(false);
}

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From source file:bobs.is.compress.sevenzip.SevenZOutputFile.java

private CountingOutputStream setupFileOutputStream() throws IOException {
    if (files.isEmpty()) {
        throw new IllegalStateException("No current 7z entry");
    }//w  ww  .  j av  a2s.c  o  m

    OutputStream out = new OutputStreamWrapper();
    final ArrayList<CountingOutputStream> moreStreams = new ArrayList<CountingOutputStream>();
    boolean first = true;
    for (final SevenZMethodConfiguration m : getContentMethods(files.get(files.size() - 1))) {
        if (!first) {
            final CountingOutputStream cos = new CountingOutputStream(out);
            moreStreams.add(cos);
            out = cos;
        }
        out = Coders.addEncoder(out, m.getMethod(), m.getOptions());
        first = false;
    }
    if (!moreStreams.isEmpty()) {
        additionalCountingStreams = moreStreams.toArray(new CountingOutputStream[moreStreams.size()]);
    }
    return new CountingOutputStream(out) {
        @Override
        public void write(final int b) throws IOException {
            super.write(b);
            crc32.update(b);
        }

        @Override
        public void write(final byte[] b) throws IOException {
            super.write(b);
            crc32.update(b);
        }

        @Override
        public void write(final byte[] b, final int off, final int len) throws IOException {
            super.write(b, off, len);
            crc32.update(b, off, len);
        }
    };
}

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From source file:srebrinb.compress.sevenzip.SevenZOutputFile.java

private CountingOutputStream setupFileOutputStream() throws IOException {
    if (files.isEmpty()) {
        throw new IllegalStateException("No current 7z entry");
    }/*  w  w  w . j  a v  a2 s. c  o m*/

    OutputStream out = new OutputStreamWrapper();
    final ArrayList<CountingOutputStream> moreStreams = new ArrayList<>();
    boolean first = true;
    for (final SevenZMethodConfiguration m : getContentMethods(files.get(files.size() - 1))) {
        if (!first) {
            final CountingOutputStream cos = new CountingOutputStream(out);
            moreStreams.add(cos);
            out = cos;
        }
        out = Coders.addEncoder(out, m.getMethod(), m.getOptions());
        first = false;
    }
    if (!moreStreams.isEmpty()) {
        additionalCountingStreams = moreStreams.toArray(new CountingOutputStream[moreStreams.size()]);
    }
    return new CountingOutputStream(out) {
        @Override
        public void write(final int b) throws IOException {
            super.write(b);
            crc32.update(b);
        }

        @Override
        public void write(final byte[] b) throws IOException {
            super.write(b);
            crc32.update(b);
        }

        @Override
        public void write(final byte[] b, final int off, final int len) throws IOException {
            super.write(b, off, len);
            crc32.update(b, off, len);
        }
    };
}

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