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/*
* Copyright (c) 2013-2017, Centre for Genomic Regulation (CRG).
* Copyright (c) 2013-2017, Paolo Di Tommaso and the respective authors.
*
* This file is part of 'Nextflow'.
*
* Nextflow is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Nextflow is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Nextflow. If not, see ByteArrayInputStream contains
* an internal buffer that contains bytes that
* may be read from the stream. An internal
* counter keeps track of the next byte to
* be supplied by the read method.
*
* Closing a ByteArrayInputStream has no effect. The methods in
* this class can be called after the stream has been closed without
* generating an IOException.
*
* @author Arthur van Hoff
* @see java.io.StringBufferInputStream
* @since JDK1.0
*/
public class FastByteArrayInputStream extends InputStream {
/**
* An array of bytes that was provided
* by the creator of the stream. Elements buf[0]
* through buf[count-1] are the
* only bytes that can ever be read from the
* stream; element buf[pos] is
* the next byte to be read.
*/
protected byte buf[];
/**
* The index of the next character to read from the input stream buffer.
* This value should always be nonnegative
* and not larger than the value of count.
* The next byte to be read from the input stream buffer
* will be buf[pos].
*/
protected int pos;
/**
* The currently marked position in the stream.
* ByteArrayInputStream objects are marked at position zero by
* default when constructed. They may be marked at another
* position within the buffer by the mark() method.
* The current buffer position is set to this point by the
* reset() method.
*
* If no mark has been set, then the value of mark is the offset
* passed to the constructor (or 0 if the offset was not supplied).
*
* @since JDK1.1
*/
protected int mark = 0;
/**
* The index one greater than the last valid character in the input
* stream buffer.
* This value should always be nonnegative
* and not larger than the length of buf.
* It is one greater than the position of
* the last byte within buf that
* can ever be read from the input stream buffer.
*/
protected int count;
/**
* Creates a ByteArrayInputStream
* so that it uses buf as its
* buffer array.
* The buffer array is not copied.
* The initial value of pos
* is 0 and the initial value
* of count is the length of
* buf.
*
* @param buf the input buffer.
*/
public FastByteArrayInputStream(byte buf[]) {
this.buf = buf;
this.pos = 0;
this.count = buf.length;
}
/**
* Creates ByteArrayInputStream
* that uses buf as its
* buffer array. The initial value of pos
* is offset and the initial value
* of count is the minimum of offset+length
* and buf.length.
* The buffer array is not copied. The buffer's mark is
* set to the specified offset.
*
* @param buf the input buffer.
* @param offset the offset in the buffer of the first byte to read.
* @param length the maximum number of bytes to read from the buffer.
*/
public FastByteArrayInputStream(byte buf[], int offset, int length) {
this.buf = buf;
this.pos = offset;
this.count = Math.min(offset + length, buf.length);
this.mark = offset;
}
/**
* Reads the next byte of data from this input stream. The value
* byte is returned as an int in the range
* 0 to 255. If no byte is available
* because the end of the stream has been reached, the value
* -1 is returned.
*
* This read method
* cannot block.
*
* @return the next byte of data, or -1 if the end of the
* stream has been reached.
*/
public int read() {
return (pos < count) ? (buf[pos++] & 0xff) : -1;
}
/**
* Reads up to len bytes of data into an array of bytes
* from this input stream.
* If pos equals count,
* then -1 is returned to indicate
* end of file. Otherwise, the number k
* of bytes read is equal to the smaller of
* len and count-pos.
* If k is positive, then bytes
* buf[pos] through buf[pos+k-1]
* are copied into b[off] through
* b[off+k-1] in the manner performed
* by System.arraycopy. The
* value k is added into pos
* and k is returned.
*
* This read method cannot block.
*
* @param b the buffer into which the data is read.
* @param off the start offset in the destination array b
* @param len the maximum number of bytes read.
* @return the total number of bytes read into the buffer, or
* -1 if there is no more data because the end of
* the stream has been reached.
* @exception NullPointerException If b is null.
* @exception IndexOutOfBoundsException If off is negative,
* len is negative, or len is greater than
* b.length - off
*/
public int read(byte b[], int off, int len) {
if (b == null) {
throw new NullPointerException();
} else if (off < 0 || len < 0 || len > b.length - off) {
throw new IndexOutOfBoundsException();
}
if (pos >= count) {
return -1;
}
int avail = count - pos;
if (len > avail) {
len = avail;
}
if (len <= 0) {
return 0;
}
System.arraycopy(buf, pos, b, off, len);
pos += len;
return len;
}
/**
* Skips n bytes of input from this input stream. Fewer
* bytes might be skipped if the end of the input stream is reached.
* The actual number k
* of bytes to be skipped is equal to the smaller
* of n and count-pos.
* The value k is added into pos
* and k is returned.
*
* @param n the number of bytes to be skipped.
* @return the actual number of bytes skipped.
*/
public long skip(long n) {
long k = count - pos;
if (n < k) {
k = n < 0 ? 0 : n;
}
pos += k;
return k;
}
/**
* Returns the number of remaining bytes that can be read (or skipped over)
* from this input stream.
*
* The value returned is count - pos,
* which is the number of bytes remaining to be read from the input buffer.
*
* @return the number of remaining bytes that can be read (or skipped
* over) from this input stream without blocking.
*/
public int available() {
return count - pos;
}
/**
* Tests if this InputStream supports mark/reset. The
* markSupported method of ByteArrayInputStream
* always returns true.
*
* @since JDK1.1
*/
public boolean markSupported() {
return true;
}
/**
* Set the current marked position in the stream.
* ByteArrayInputStream objects are marked at position zero by
* default when constructed. They may be marked at another
* position within the buffer by this method.
*
* If no mark has been set, then the value of the mark is the
* offset passed to the constructor (or 0 if the offset was not
* supplied).
*
*
Note: The readAheadLimit for this class
* has no meaning.
*
* @since JDK1.1
*/
public void mark(int readAheadLimit) {
mark = pos;
}
/**
* Resets the buffer to the marked position. The marked position
* is 0 unless another position was marked or an offset was specified
* in the constructor.
*/
public void reset() {
pos = mark;
}
/**
* Closing a ByteArrayInputStream has no effect. The methods in
* this class can be called after the stream has been closed without
* generating an IOException.
*
*/
public void close() throws IOException {
}
}