/*
* The MIT License
*
* Copyright (c) 2013 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.tribble.readers;
import java.io.IOException;
import java.io.Reader;
/**
* A variant of {@link java.io.BufferedReader} with improved performance reading files with long lines.
*
* This class is almost identical to BufferedReader, but it retains a single line buffer for accumulating characters in a line, and allows
* its size to grow. Conversely, {@link java.io.BufferedReader} assumes each new line will be approximately 80 characters and its
* performance suffers when that is not the case.
*
* Unlike {@link java.io.BufferedReader}, this class is not thread safe.
*
* @author mccowan
*/
public class LongLineBufferedReader extends Reader {
private Reader in;
private char cb[];
private int nChars, nextChar;
private static final int INVALIDATED = -2;
private static final int UNMARKED = -1;
private int markedChar = UNMARKED;
private int readAheadLimit = 0; /* Valid only when markedChar > 0 */
/**
* If the next character is a line feed, skip it
*/
private boolean skipLF = false;
/**
* The skipLF flag when the mark was set
*/
private boolean markedSkipLF = false;
private static final int DEFAULT_CHAR_BUFFER_SIZE = 8192;
private static final int DEFAULT_EXPECTED_LINE_LENGTH = 80;
private StringBuilder lineBuffer = new StringBuilder(DEFAULT_EXPECTED_LINE_LENGTH);
/**
* Creates a buffering character-input stream that uses an input buffer of
* the specified size.
*
* @param in A Reader
* @param sz Input-buffer size
* @throws IllegalArgumentException If sz is <= 0
*/
public LongLineBufferedReader(Reader in, int sz) {
super(in);
if (sz <= 0)
throw new IllegalArgumentException("Buffer size <= 0");
this.in = in;
cb = new char[sz];
nextChar = nChars = 0;
}
/**
* Creates a buffering character-input stream that uses a default-sized
* input buffer.
*
* @param in A Reader
*/
public LongLineBufferedReader(Reader in) {
this(in, DEFAULT_CHAR_BUFFER_SIZE);
}
/**
* Checks to make sure that the stream has not been closed
*/
private void ensureOpen() throws IOException {
if (in == null)
throw new IOException("Stream closed");
}
/**
* Fills the input buffer, taking the mark into account if it is valid.
*/
private void fill() throws IOException {
int dst;
if (markedChar <= UNMARKED) {
/* No mark */
dst = 0;
} else {
/* Marked */
int delta = nextChar - markedChar;
if (delta >= readAheadLimit) {
/* Gone past read-ahead limit: Invalidate mark */
markedChar = INVALIDATED;
readAheadLimit = 0;
dst = 0;
} else {
if (readAheadLimit <= cb.length) {
/* Shuffle in the current buffer */
System.arraycopy(cb, markedChar, cb, 0, delta);
markedChar = 0;
dst = delta;
} else {
/* Reallocate buffer to accommodate read-ahead limit */
char ncb[] = new char[readAheadLimit];
System.arraycopy(cb, markedChar, ncb, 0, delta);
cb = ncb;
markedChar = 0;
dst = delta;
}
nextChar = nChars = delta;
}
}
int n;
do {
n = in.read(cb, dst, cb.length - dst);
} while (n == 0);
if (n > 0) {
nChars = dst + n;
nextChar = dst;
}
}
/**
* Reads a single character.
*
* @return The character read, as an integer in the range
* 0 to 65535 (<tt>0x00-0xffff</tt>), or -1 if the
* end of the stream has been reached
* @throws IOException If an I/O error occurs
*/
public int read() throws IOException {
synchronized (lock) {
ensureOpen();
for (; ; ) {
if (nextChar >= nChars) {
fill();
if (nextChar >= nChars)
return -1;
}
if (skipLF) {
skipLF = false;
if (cb[nextChar] == '\n') {
nextChar++;
continue;
}
}
return cb[nextChar++];
}
}
}
/**
* Reads characters into a portion of an array, reading from the underlying
* stream if necessary.
*/
private int read1(char[] cbuf, int off, int len) throws IOException {
if (nextChar >= nChars) {
/* If the requested length is at least as large as the buffer, and
if there is no mark/reset activity, and if line feeds are not
being skipped, do not bother to copy the characters into the
local buffer. In this way buffered streams will cascade
harmlessly. */
if (len >= cb.length && markedChar <= UNMARKED && !skipLF) {
return in.read(cbuf, off, len);
}
fill();
}
if (nextChar >= nChars) return -1;
if (skipLF) {
skipLF = false;
if (cb[nextChar] == '\n') {
nextChar++;
if (nextChar >= nChars)
fill();
if (nextChar >= nChars)
return -1;
}
}
int n = Math.min(len, nChars - nextChar);
System.arraycopy(cb, nextChar, cbuf, off, n);
nextChar += n;
return n;
}
/**
* Reads characters into a portion of an array.
* <p/>
* <p> This method implements the general contract of the corresponding
* <code>{@link Reader#read(char[], int, int) read}</code> method of the
* <code>{@link Reader}</code> class. As an additional convenience, it
* attempts to read as many characters as possible by repeatedly invoking
* the <code>read</code> method of the underlying stream. This iterated
* <code>read</code> continues until one of the following conditions becomes
* true: <ul>
* <p/>
* <li> The specified number of characters have been read,
* <p/>
* <li> The <code>read</code> method of the underlying stream returns
* <code>-1</code>, indicating end-of-file, or
* <p/>
* <li> The <code>ready</code> method of the underlying stream
* returns <code>false</code>, indicating that further input requests
* would block.
* <p/>
* </ul> If the first <code>read</code> on the underlying stream returns
* <code>-1</code> to indicate end-of-file then this method returns
* <code>-1</code>. Otherwise this method returns the number of characters
* actually read.
* <p/>
* <p> Subclasses of this class are encouraged, but not required, to
* attempt to read as many characters as possible in the same fashion.
* <p/>
* <p> Ordinarily this method takes characters from this stream's character
* buffer, filling it from the underlying stream as necessary. If,
* however, the buffer is empty, the mark is not valid, and the requested
* length is at least as large as the buffer, then this method will read
* characters directly from the underlying stream into the given array.
* Thus redundant <code>BufferedReaderTwo</code>s will not copy data
* unnecessarily.
*
* @param cbuf Destination buffer
* @param off Offset at which to start storing characters
* @param len Maximum number of characters to read
* @return The number of characters read, or -1 if the end of the
* stream has been reached
* @throws IOException If an I/O error occurs
*/
public int read(char cbuf[], int off, int len) throws IOException {
synchronized (lock) {
ensureOpen();
if ((off < 0) || (off > cbuf.length) || (len < 0) ||
((off + len) > cbuf.length) || ((off + len) < 0)) {
throw new IndexOutOfBoundsException();
} else if (len == 0) {
return 0;
}
int n = read1(cbuf, off, len);
if (n <= 0) return n;
while ((n < len) && in.ready()) {
int n1 = read1(cbuf, off + n, len - n);
if (n1 <= 0) break;
n += n1;
}
return n;
}
}
/**
* Reads a line of text. A line is considered to be terminated by any one
* of a line feed ('\n'), a carriage return ('\r'), or a carriage return
* followed immediately by a linefeed.
*
* @param ignoreLF If true, the next '\n' will be skipped
* @return A String containing the contents of the line, not including
* any line-termination characters, or null if the end of the
* stream has been reached
* @throws IOException If an I/O error occurs
* @see java.io.LineNumberReader#readLine()
*/
String readLine(boolean ignoreLF) throws IOException {
int startChar;
lineBuffer.setLength(0);
synchronized (lock) {
ensureOpen();
boolean omitLF = ignoreLF || skipLF;
bufferLoop:
for (; ; ) {
if (nextChar >= nChars)
fill();
if (nextChar >= nChars) { /* EOF */
if (lineBuffer != null && lineBuffer.length() > 0)
return lineBuffer.toString();
else
return null;
}
boolean eol = false;
char c = 0;
int i;
/* Skip a leftover '\n', if necessary */
if (omitLF && (cb[nextChar] == '\n'))
nextChar++;
skipLF = false;
omitLF = false;
charLoop:
for (i = nextChar; i < nChars; i++) {
c = cb[i];
if ((c == '\n') || (c == '\r')) {
eol = true;
break charLoop;
}
}
startChar = nextChar;
nextChar = i;
if (eol) {
String str;
lineBuffer.append(cb, startChar, i - startChar);
str = lineBuffer.toString();
nextChar++;
if (c == '\r') {
skipLF = true;
}
return str;
}
lineBuffer.append(cb, startChar, i - startChar);
}
}
}
/**
* Reads a line of text. A line is considered to be terminated by any one
* of a line feed ('\n'), a carriage return ('\r'), or a carriage return
* followed immediately by a linefeed.
*
* @return A String containing the contents of the line, not including
* any line-termination characters, or null if the end of the
* stream has been reached
* @throws IOException If an I/O error occurs
*/
public String readLine() throws IOException {
return readLine(false);
}
/**
* Skips characters.
*
* @param n The number of characters to skip
* @return The number of characters actually skipped
* @throws IllegalArgumentException If <code>n</code> is negative.
* @throws IOException If an I/O error occurs
*/
public long skip(long n) throws IOException {
if (n < 0L) {
throw new IllegalArgumentException("skip value is negative");
}
synchronized (lock) {
ensureOpen();
long r = n;
while (r > 0) {
if (nextChar >= nChars)
fill();
if (nextChar >= nChars) /* EOF */
break;
if (skipLF) {
skipLF = false;
if (cb[nextChar] == '\n') {
nextChar++;
}
}
long d = nChars - nextChar;
if (r <= d) {
nextChar += r;
r = 0;
break;
} else {
r -= d;
nextChar = nChars;
}
}
return n - r;
}
}
/**
* Tells whether this stream is ready to be read. A buffered character
* stream is ready if the buffer is not empty, or if the underlying
* character stream is ready.
*
* @throws IOException If an I/O error occurs
*/
public boolean ready() throws IOException {
synchronized (lock) {
ensureOpen();
/*
* If newline needs to be skipped and the next char to be read
* is a newline character, then just skip it right away.
*/
if (skipLF) {
/* Note that in.ready() will return true if and only if the next
* read on the stream will not block.
*/
if (nextChar >= nChars && in.ready()) {
fill();
}
if (nextChar < nChars) {
if (cb[nextChar] == '\n')
nextChar++;
skipLF = false;
}
}
return (nextChar < nChars) || in.ready();
}
}
/**
* Tells whether this stream supports the mark() operation, which it does.
*/
public boolean markSupported() {
return true;
}
/**
* Marks the present position in the stream. Subsequent calls to reset()
* will attempt to reposition the stream to this point.
*
* @param readAheadLimit Limit on the number of characters that may be
* read while still preserving the mark. An attempt
* to reset the stream after reading characters
* up to this limit or beyond may fail.
* A limit value larger than the size of the input
* buffer will cause a new buffer to be allocated
* whose size is no smaller than limit.
* Therefore large values should be used with care.
* @throws IllegalArgumentException If readAheadLimit is < 0
* @throws IOException If an I/O error occurs
*/
public void mark(int readAheadLimit) throws IOException {
if (readAheadLimit < 0) {
throw new IllegalArgumentException("Read-ahead limit < 0");
}
synchronized (lock) {
ensureOpen();
this.readAheadLimit = readAheadLimit;
markedChar = nextChar;
markedSkipLF = skipLF;
}
}
/**
* Resets the stream to the most recent mark.
*
* @throws IOException If the stream has never been marked,
* or if the mark has been invalidated
*/
public void reset() throws IOException {
synchronized (lock) {
ensureOpen();
if (markedChar < 0)
throw new IOException((markedChar == INVALIDATED)
? "Mark invalid"
: "Stream not marked");
nextChar = markedChar;
skipLF = markedSkipLF;
}
}
public void close() throws IOException {
synchronized (lock) {
if (in == null)
return;
in.close();
in = null;
cb = null;
}
}
}