htsjdk.samtools.util.PositionalOutputStream Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of htsjdk Show documentation

A Java API for high-throughput sequencing data (HTS) formats

There is a newer version: 4.1.3

/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package htsjdk.samtools.util;

import java.io.IOException;
import java.io.OutputStream;

/**
 * Wraps output stream in a manner which keeps track of the position within the file and allowing writes
 * at arbitrary points
 */
public final class PositionalOutputStream extends OutputStream implements LocationAware
{
    private final OutputStream out;
    private long position = 0;

    public PositionalOutputStream(final OutputStream out) {
        this.out = out;
    }

    @Override
    public final void write(final byte[] bytes) throws IOException {
        write(bytes, 0, bytes.length);
    }

    @Override
    public final void write(final byte[] bytes, final int startIndex, final int numBytes) throws IOException {
        position += numBytes;
        out.write(bytes, startIndex, numBytes);
    }

    @Override
    public final void write(final int c)  throws IOException {
        position++;
        out.write(c);
    }

    @Override
    public final long getPosition() { return position; }

    @Override
    public void close() throws IOException {
        super.close();
        out.close();
    }
}