fi.tkk.ics.hadoop.bam.util.WrapSeekable.java Source code

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Here is the source code for fi.tkk.ics.hadoop.bam.util.WrapSeekable.java

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// Copyright (c) 2010 Aalto University
//
// 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.

// File created: 2010-08-25 11:24:30

package fi.tkk.ics.hadoop.bam.util;

import java.io.InputStream;
import java.io.IOException;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.Seekable;

import net.sf.samtools.seekablestream.SeekableStream;

/** Wraps Hadoop's "seekable stream" abstraction so that we can give such a one
 * to BlockCompressedInputStream and retain seekability.
 *
 * <p>This is necessary because Hadoop and the SAM tools each have their own
 * "seekable stream" abstraction.</p>
 */
public class WrapSeekable<S extends InputStream & Seekable> extends SeekableStream {
    private final S stm;
    private final long len;
    private final Path path;

    public WrapSeekable(final S s, long length, Path p) {
        stm = s;
        len = length;
        path = p;
    }

    /** A helper for the common use case. */
    public static WrapSeekable<FSDataInputStream> openPath(FileSystem fs, Path p) throws IOException {
        return new WrapSeekable<FSDataInputStream>(fs.open(p), fs.getFileStatus(p).getLen(), p);
    }

    public static WrapSeekable<FSDataInputStream> openPath(Configuration conf, Path path) throws IOException {
        return openPath(path.getFileSystem(conf), path);
    }

    @Override
    public String getSource() {
        return path.toString();
    }

    @Override
    public long length() {
        return len;
    }

    @Override
    public long position() throws IOException {
        return stm.getPos();
    }

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

    @Override
    public boolean eof() throws IOException {
        return stm.getPos() == length();
    }

    @Override
    public void seek(long pos) throws IOException {
        stm.seek(pos);
    }

    @Override
    public int read() throws IOException {
        return stm.read();
    }

    @Override
    public int read(byte[] buf, int offset, int len) throws IOException {
        return stm.read(buf, offset, len);
    }
}