/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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 org.broad.igv.util.stream;
import com.google.common.primitives.Ints;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.log4j.Logger;
import java.io.IOException;
import static java.lang.System.arraycopy;
/**
* 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,
* we attempt to reuse the buffer if there is overlap between the newly requested range and where
* the buffer contains data for.
*/
public class IGVSeekableBufferedStream extends SeekableStream {
private static Logger log = Logger.getLogger(IGVSeekableBufferedStream.class);
public static final int DEFAULT_BUFFER_SIZE = 512000;
final private int maxBufferSize;
final SeekableStream wrappedStream;
long position;
/**
* Can't make the assumption that length is a valid value.
* May be -1, which means we don't know.
*/
int markpos;
int marklimit;
byte[] buffer;
long bufferStartPosition; // Position in file corresponding to start of buffer
int bufferSize;
public IGVSeekableBufferedStream(final SeekableStream stream, final int bsize) {
this.maxBufferSize = bsize;
this.wrappedStream = stream;
this.position = 0;
this.buffer = new byte[maxBufferSize];
this.bufferStartPosition = -1;
this.bufferSize = 0;
}
public IGVSeekableBufferedStream(final SeekableStream stream) {
this(stream, DEFAULT_BUFFER_SIZE);
}
public long length() {
return wrappedStream.length();
}
@Override
public long skip(final long skipLength) throws IOException {
long maxSkip = Long.MAX_VALUE;
long length = wrappedStream.length();
if (length >= 0) maxSkip = length - position - 1;
long actualSkip = Math.min(maxSkip, skipLength);
position += actualSkip;
return actualSkip;
}
@Override
public synchronized void reset() throws IOException {
if (markpos < 0) {
throw new IOException("Resetting to invalid mark");
}
position = markpos;
}
@Override
public synchronized void mark(int readlimit) {
this.markpos = (int) position;
this.marklimit = readlimit;
}
@Override
public boolean markSupported() {
return true;
}
public void seek(final long position) throws IOException {
this.position = position;
}
public void close() throws IOException {
wrappedStream.close();
}
public boolean eof() throws IOException {
long length = wrappedStream.length();
return length >= 0 && position >= length;
}
@Override
public String getSource() {
return wrappedStream.getSource();
}
@Override
public long position() throws IOException {
return position;
}
/**
* Return true iff the buffer needs to be refilled for the given
* amount of data requested
*
* @param len Number of bytes from {@code position} one plans on reading
* @return
*/
private boolean needFillBuffer(int len) {
return bufferSize == 0 || position < bufferStartPosition || (position + len) > bufferStartPosition + bufferSize;
}
public int read() throws IOException {
if (needFillBuffer(1)) {
fillBuffer();
}
int offset = (int) (position - bufferStartPosition);
int b = buffer[offset];
position++;
return (b >= 0 ? b : 256+b);
}
public int read(final byte[] b, final int off, final int len) throws IOException {
long contentLength = wrappedStream.length();
if (contentLength >= 0 && position >= contentLength) return -1;
if (len > maxBufferSize) {
// Buffering not useful here. Don't bother trying to use any (possible) overlapping buffer contents
wrappedStream.seek(position);
int nBytes = wrappedStream.read(b, off, len);
position += nBytes;
return nBytes;
} else {
long end = position + len;
long bufferEnd = bufferStartPosition + bufferSize;
if (position > bufferStartPosition && position < bufferEnd && end > bufferEnd) {
// We have part of the requested range. Return what we have, the read contract does not guarantee
// all bytes requested.
int bufferOffset = (int) (position - bufferStartPosition);
int bytesCopied = (int) (bufferEnd - position);
arraycopy(buffer, bufferOffset, b, off, bytesCopied);
position += bytesCopied;
return bytesCopied;
} else {
if (!(position >= bufferStartPosition && end <= bufferEnd)) {
fillBuffer();
}
int bufferOffset = (int) (position - bufferStartPosition);
int bytesCopied = Math.min(len, bufferSize - bufferOffset);
arraycopy(buffer, bufferOffset, b, off, bytesCopied);
position += bytesCopied;
return bytesCopied;
}
}
}
private void fillBuffer() throws IOException {
long longRem = maxBufferSize;
long length = wrappedStream.length();
if (length >= 0) longRem = Math.min((long) maxBufferSize, length - position);
//This shouldn't actually be necessary as long as maxBufferSize is
//an int, but we leave it here to stress the fact that
//we need to watch for overflow
int bytesRemaining = Ints.saturatedCast(longRem);
//Number of bytes to skip at beginning when reading from stream later
//Number of bytes known to be stored in the buffer, which are valid
int tmpBufferSize = 0;
if (bytesRemaining > 0) {
int curOffset = 0;
wrappedStream.seek(position);
while (bytesRemaining > 0) {
int count = wrappedStream.read(buffer, curOffset, bytesRemaining);
if (count < 0) {
break; // EOF.
}
curOffset += count;
bytesRemaining -= count;
tmpBufferSize += count;
}
bufferStartPosition = position;
bufferSize = tmpBufferSize;
}
}
}