htsjdk.samtools.seekablestream.SeekableBufferedStream Maven / Gradle / Ivy

Go to download
/*
 * The MIT License
 *
 * Copyright (c) 2009 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.seekablestream;

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

/**
 * A wrapper class to provide buffered read access to a SeekableStream.  Just wrapping such a stream with
 * a BufferedInputStream will not work as it does not support seeking.  In this implementation a
 * seek call is delegated to the wrapped stream, and the buffer reset.
 */
public class SeekableBufferedStream extends SeekableStream {

    /** Little extension to buffered input stream to give access to the available bytes in the buffer. */
    private class ExtBufferedInputStream extends BufferedInputStream {
        private ExtBufferedInputStream(final InputStream inputStream, final int i) {
            super(inputStream, i);
        }

        /** Returns the number of bytes that can be read from the buffer without reading more into the buffer. */
        int getBytesInBufferAvailable() {
            return this.count - this.pos;
        }

        /** Return true if the position can be changed by the given delta and remain in the buffer. */
        boolean canChangePos(long delta) {
            long newPos = this.pos + delta;
            return newPos >= 0 && newPos < this.count;
        }

        /** Changes the position in the buffer by a given delta. */
        void changePos(int delta) {
            int newPos = this.pos + delta;
            if (newPos < 0 || newPos >= this.count) {
                throw new IllegalArgumentException("New position not in buffer pos=" + this.pos + ", delta=" + delta);
            }
            this.pos = newPos;
        }
    }


    public static final int DEFAULT_BUFFER_SIZE = 512000;

    final private int bufferSize;
    final SeekableStream wrappedStream;
    ExtBufferedInputStream bufferedStream;
    long position;

    public SeekableBufferedStream(final SeekableStream stream, final int bufferSize) {
        this.bufferSize = bufferSize;
        this.wrappedStream = stream;
        this.position = 0;
        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
    }

    public SeekableBufferedStream(final SeekableStream stream) {
        this(stream, DEFAULT_BUFFER_SIZE);
    }

    @Override
    public long length() {
        return wrappedStream.length();
    }

    @Override
    public long skip(final long skipLength) throws IOException {
        if (skipLength < this.bufferedStream.getBytesInBufferAvailable()) {
            final long retval = this.bufferedStream.skip(skipLength);
            this.position += retval;
            return retval;
        } else {
            final long position = this.position + skipLength;
            seekInternal(position);
            return skipLength;
        }
    }

    @Override
    public void seek(final long position) throws IOException {
        if (this.position == position) {
            return;
        }
        // check if the seek is within the buffer
        long delta = position - this.position;
        if (this.bufferedStream.canChangePos(delta)) {
            // casting to an int is safe since the buffer is less than the size of an int
            this.bufferedStream.changePos((int) delta);
            this.position = position;
        } else {
            seekInternal(position);
        }
    }

    private void seekInternal(final long position) throws IOException {
        wrappedStream.seek(position);
        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
        this.position = position;
    }

    @Override
    public int read() throws IOException {
        int b = bufferedStream.read();
        position++;
        return b;
    }

    @Override
    public int read(final byte[] buffer, final int offset, final int length) throws IOException {
        int nBytesRead = bufferedStream.read(buffer, offset, length);
        if (nBytesRead > 0) {
            //if we can't read as many bytes as we are asking for then attempt another read to reset the buffer.
            if (nBytesRead < length) {
                final int additionalBytesRead = bufferedStream.read(buffer, nBytesRead + offset, length - nBytesRead);
                //if there were additional bytes read then update nBytesRead
                if (additionalBytesRead > 0) {
                    nBytesRead += additionalBytesRead;
                }
            }
            position += nBytesRead;
        }
        return nBytesRead;
    }

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

    @Override
    public boolean eof() throws IOException {
        return position >= wrappedStream.length();
    }

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

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