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/*
* Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
* All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
* is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
* ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
* OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
* RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
* ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
* DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
* BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
* FOREGOING.
*/
package htsjdk.tribble.readers;
import htsjdk.tribble.TribbleException;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
/**
* A wrapper around an {@code InputStream} which performs it's own buffering, and keeps track of the position.
*
* TODO: This class implements Positional, which in turn extends LocationAware, which requires preservation of
* virtual file pointers on BGZF inputs. However, if the inputStream wrapped by this class is a BlockCompressedInputStream,
* it violates that contract by wrapping the stream and returning positional file offsets instead.
*
* @author depristo
*/
public final class PositionalBufferedStream extends InputStream implements Positional {
final InputStream is;
final byte[] buffer;
int nextChar;
int nChars;
long position;
public PositionalBufferedStream(final InputStream is) {
this(is, 512000);
}
public PositionalBufferedStream(final InputStream is, final int bufferSize) {
this.is = is;
buffer = new byte[bufferSize];
nextChar = nChars = 0;
}
@Override
public final long getPosition() {
return position;
}
@Override
public final int read() throws IOException {
final int c = peek();
if ( c >= 0 ) {
// update position and buffer offset if peek says we aren't yet done
position++;
nextChar++;
}
return c;
}
@Override
public final int read(final byte[] bytes, final int start, final int len) throws IOException {
if ( len == 0 ) // If len is zero, then no bytes are read and 0 is returned
return 0;
if (nChars < 0) // If no byte is available because the stream is at end of file, the value -1 is returned
return -1;
else {
int nRead = 0;
int remaining = len;
while ( remaining > 0 ) {
// Try to Refill buffer if at the end of current buffer
if ( nChars == nextChar )
if ( fill() < 0 ) { // EOF
break;
}
// we copy as many bytes from the buffer as possible, up to the number of need
final int nCharsToCopy = Math.min(nChars - nextChar, remaining);
System.arraycopy(buffer, nextChar, bytes, start + nRead, nCharsToCopy);
// update nextChar (pointer into buffer) and keep track of nRead and remaining
nextChar += nCharsToCopy;
nRead += nCharsToCopy;
remaining -= nCharsToCopy;
}
// make sure we update our position tracker to reflect having advanced by nRead bytes
position += nRead;
/** Conform to {@link InputStream#read(byte[], int, int)} contract by returning -1 if EOF and no data was read. */
return nRead == 0 ? -1 : nRead;
}
}
@Override
public final int read(final byte[] bytes) throws IOException {
return read(bytes, 0, bytes.length);
}
@Override
public final boolean isDone() throws IOException {
return nChars == -1 || peek() == -1;
}
@Override
public final int peek() throws IOException {
// Check for EOF
if (nChars < 0) {
return -1;
} else if (nextChar == nChars){
//Try to Refill buffer if at the end of current buffer
if ( fill() < 0 ){
return -1;
}
}
return byteToInt(buffer[nextChar]);
}
private final int fill() throws IOException {
nChars = is.read(buffer);
nextChar = 0;
return nChars;
}
@Override
public final long skip(final long nBytes) throws IOException {
long remainingToSkip = nBytes;
// because we have this buffer, that may be shorter than nBytes
// we loop while there are bytes to skip, filling the buffer
// When the buffer contains enough data that we have less than
// its less left to skip we increase nextChar by the remaining
// amount
while ( remainingToSkip > 0 && ! isDone() ) {
final long bytesLeftInBuffer = nChars - nextChar;
if ( remainingToSkip > bytesLeftInBuffer ) {
// we need to refill the buffer and continue our skipping
remainingToSkip -= bytesLeftInBuffer;
fill();
} else {
// there are enough bytes in the buffer to not read again
// we just push forward the pointer nextChar
nextChar += remainingToSkip;
remainingToSkip = 0;
}
}
final long actuallySkipped = nBytes - remainingToSkip;
position += actuallySkipped;
return actuallySkipped;
}
@Override
public final void close() {
try {
is.close();
} catch (IOException ex) {
throw new TribbleException("Failed to close PositionalBufferedStream", ex);
}
}
private final static int byteToInt(byte b) {
return b & 0xFF;
}
public static void main(String[] args) throws Exception {
final File testFile = new File(args[0]);
final int iterations = Integer.parseInt(args[1]);
final boolean includeInputStream = Boolean.valueOf(args[2]);
final boolean doReadFileInChunks = Boolean.valueOf(args[3]);
System.out.printf("Testing %s%n", args[0]);
for (int i = 0; i < iterations; i++) {
if ( includeInputStream ) {
final InputStream is = new FileInputStream(testFile);
if ( doReadFileInChunks )
readFileInChunks("InputStream", is);
else
readFileByLine("InputStream", is);
is.close();
}
final PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(testFile));
if ( doReadFileInChunks )
readFileInChunks("PositionalBufferedStream", pbs);
else
readFileByLine("PositionalBufferedStream", pbs);
pbs.close();
}
}
private static void readFileByLine(final String name, final InputStream is) throws IOException {
final BufferedReader reader2 = new BufferedReader(new InputStreamReader(is));
final long t0 = System.currentTimeMillis();
long lineCount = 0;
while (reader2.readLine() != null) {
lineCount++;
}
final long dt = System.currentTimeMillis() - t0;
final double rate = ((double) lineCount) / dt;
printStatus(name, lineCount, rate, dt);
reader2.close();
}
private static void readFileInChunks(final String name, final InputStream is) throws IOException {
final long t0 = System.currentTimeMillis();
long chunk = 0;
final byte[] bytes = new byte[4096];
while (is.read(bytes) != -1) {
chunk++;
}
final long dt = System.currentTimeMillis() - t0;
final double rate = ((double) chunk) / dt;
printStatus(name, chunk, rate, dt);
is.close();
}
private static final void printStatus(final String name, long lineCount, double rate, long dt) {
System.out.printf("%30s: %d lines read. Rate = %.2e lines per second. DT = %d%n", name, lineCount, rate, dt);
System.out.flush();
}
}
