nextflow.file

Class FastBufferedInputStream

java.lang.Object

java.io.InputStream

java.io.FilterInputStream

nextflow.file.FastBufferedInputStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class FastBufferedInputStream
extends java.io.FilterInputStream

A BufferedInputStream adds functionality to another input stream-namely, the ability to buffer the input and to support the mark and reset methods. When the BufferedInputStream is created, an internal buffer array is created. As bytes from the stream are read or skipped, the internal buffer is refilled as necessary from the contained input stream, many bytes at a time. The mark operation remembers a point in the input stream and the reset operation causes all the bytes read since the most recent mark operation to be reread before new bytes are taken from the contained input stream.

Since:

JDK1.0

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	buf The internal buffer array where the data is stored.
protected int	count The index one greater than the index of the last valid byte in the buffer.
protected int	marklimit The maximum read ahead allowed after a call to the mark method before subsequent calls to the reset method fail.
protected int	markpos The value of the pos field at the time the last mark method was called.
protected int	pos The current position in the buffer.

Fields inherited from class java.io.FilterInputStream

in

Constructor Summary

Constructors

Constructor and Description
FastBufferedInputStream(java.io.InputStream in) Creates a BufferedInputStream and saves its argument, the input stream in, for later use.
FastBufferedInputStream(java.io.InputStream in, byte[] buf)
FastBufferedInputStream(java.io.InputStream in, int size) Creates a BufferedInputStream with the specified buffer size, and saves its argument, the input stream in, for later use.

Method Summary

Methods

Modifier and Type	Method and Description
int	available() Returns an estimate of the number of bytes that can be read (or skipped over) from this input stream without blocking by the next invocation of a method for this input stream.
void	close() Closes this input stream and releases any system resources associated with the stream.
void	mark(int readlimit) See the general contract of the mark method of InputStream.
boolean	markSupported() Tests if this input stream supports the mark and reset methods.
int	read() See the general contract of the read method of InputStream.
int	read(byte[] b, int off, int len) Reads bytes from this byte-input stream into the specified byte array, starting at the given offset.
void	reset() See the general contract of the reset method of InputStream.
long	skip(long n) See the general contract of the skip method of InputStream.

Methods inherited from class java.io.FilterInputStream

read

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

buf

protected volatile byte[] buf

The internal buffer array where the data is stored. When necessary, it may be replaced by another array of a different size.

count

protected int count

The index one greater than the index of the last valid byte in the buffer. This value is always in the range 0 through buf.length; elements buf[0] through buf[count-1] contain buffered input data obtained from the underlying input stream.

pos

protected int pos

The current position in the buffer. This is the index of the next character to be read from the buf array.

This value is always in the range 0 through count. If it is less than count, then buf[pos] is the next byte to be supplied as input; if it is equal to count, then the next read or skip operation will require more bytes to be read from the contained input stream.

See Also:

BufferedInputStream.buf

markpos

protected int markpos

The value of the pos field at the time the last mark method was called.

This value is always in the range -1 through pos. If there is no marked position in the input stream, this field is -1. If there is a marked position in the input stream, then buf[markpos] is the first byte to be supplied as input after a reset operation. If markpos is not -1, then all bytes from positions buf[markpos] through buf[pos-1] must remain in the buffer array (though they may be moved to another place in the buffer array, with suitable adjustments to the values of count, pos, and markpos); they may not be discarded unless and until the difference between pos and markpos exceeds marklimit.

See Also:

BufferedInputStream.mark(int), BufferedInputStream.pos

marklimit

protected int marklimit

The maximum read ahead allowed after a call to the mark method before subsequent calls to the reset method fail. Whenever the difference between pos and markpos exceeds marklimit, then the mark may be dropped by setting markpos to -1.

See Also:

BufferedInputStream.mark(int), BufferedInputStream.reset()

Constructor Detail

FastBufferedInputStream

public FastBufferedInputStream(java.io.InputStream in)

Creates a BufferedInputStream and saves its argument, the input stream in, for later use. An internal buffer array is created and stored in buf.

Parameters:

in - the underlying input stream.

FastBufferedInputStream

public FastBufferedInputStream(java.io.InputStream in,
                       int size)

Creates a BufferedInputStream with the specified buffer size, and saves its argument, the input stream in, for later use. An internal buffer array of length size is created and stored in buf.

Parameters:

in - the underlying input stream.

size - the buffer size.

Throws:

java.lang.IllegalArgumentException - if size <= 0.

FastBufferedInputStream

public FastBufferedInputStream(java.io.InputStream in,
                       byte[] buf)

Method Detail

read

public int read()
         throws java.io.IOException

See the general contract of the read method of InputStream.

Overrides:

read in class java.io.FilterInputStream

Returns:

the next byte of data, or -1 if the end of the stream is reached.

Throws:

java.io.IOException - if this input stream has been closed by invoking its close() method, or an I/O error occurs.

See Also:

FilterInputStream.in

read

public int read(byte[] b,
       int off,
       int len)
         throws java.io.IOException

Reads bytes from this byte-input stream into the specified byte array, starting at the given offset.

This method implements the general contract of the corresponding read method of the InputStream class. As an additional convenience, it attempts to read as many bytes as possible by repeatedly invoking the read method of the underlying stream. This iterated read continues until one of the following conditions becomes true:

• The specified number of bytes have been read,
• The read method of the underlying stream returns -1, indicating end-of-file, or
• The available method of the underlying stream returns zero, indicating that further input requests would block.

If the first read on the underlying stream returns -1 to indicate end-of-file then this method returns -1. Otherwise this method returns the number of bytes actually read.

Subclasses of this class are encouraged, but not required, to attempt to read as many bytes as possible in the same fashion.

Overrides:

read in class java.io.FilterInputStream

Parameters:

b - destination buffer.

off - offset at which to start storing bytes.

len - maximum number of bytes to read.

Returns:

the number of bytes read, or -1 if the end of the stream has been reached.

Throws:

java.io.IOException - if this input stream has been closed by invoking its close() method, or an I/O error occurs.

skip

public long skip(long n)
          throws java.io.IOException

See the general contract of the skip method of InputStream.

Overrides:

skip in class java.io.FilterInputStream

Throws:

java.io.IOException - if the stream does not support seek, or if this input stream has been closed by invoking its close() method, or an I/O error occurs.

available

public int available()
              throws java.io.IOException

Returns an estimate of the number of bytes that can be read (or skipped over) from this input stream without blocking by the next invocation of a method for this input stream. The next invocation might be the same thread or another thread. A single read or skip of this many bytes will not block, but may read or skip fewer bytes.

This method returns the sum of the number of bytes remaining to be read in the buffer (count - pos) and the result of calling the in.available().

Overrides:

available in class java.io.FilterInputStream

Returns:

an estimate of the number of bytes that can be read (or skipped over) from this input stream without blocking.

Throws:

java.io.IOException - if this input stream has been closed by invoking its close() method, or an I/O error occurs.

mark

public void mark(int readlimit)

See the general contract of the mark method of InputStream.

Overrides:

mark in class java.io.FilterInputStream

Parameters:

readlimit - the maximum limit of bytes that can be read before the mark position becomes invalid.

See Also:

BufferedInputStream.reset()

reset

public void reset()
           throws java.io.IOException

See the general contract of the reset method of InputStream.

If markpos is -1 (no mark has been set or the mark has been invalidated), an IOException is thrown. Otherwise, pos is set equal to markpos.

Overrides:

reset in class java.io.FilterInputStream

Throws:

java.io.IOException - if this stream has not been marked or, if the mark has been invalidated, or the stream has been closed by invoking its close() method, or an I/O error occurs.

See Also:

BufferedInputStream.mark(int)

markSupported

public boolean markSupported()

Tests if this input stream supports the mark and reset methods. The markSupported method of BufferedInputStream returns true.

Overrides:

markSupported in class java.io.FilterInputStream

Returns:

a boolean indicating if this stream type supports the mark and reset methods.

See Also:

InputStream.mark(int), InputStream.reset()

close

public void close()
           throws java.io.IOException

Closes this input stream and releases any system resources associated with the stream. Once the stream has been closed, further read(), available(), reset(), or skip() invocations will throw an IOException. Closing a previously closed stream has no effect.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.FilterInputStream

Throws:

java.io.IOException - if an I/O error occurs.