Package loci.common

Class NIOFileHandle

java.lang.Object

loci.common.AbstractNIOHandle

loci.common.NIOFileHandle

All Implemented Interfaces:

DataInput, DataOutput, IRandomAccess

public class NIOFileHandle
extends AbstractNIOHandle

A wrapper for buffered NIO logic that implements the IRandomAccess interface.

Author:

Chris Allan (callan at blackcat dot ca)

See Also:

IRandomAccess, RandomAccessFile

Field Summary

Fields

Modifier and Type	Field	Description
protected ByteBuffer	buffer	The buffer itself.
protected int	bufferSize	The buffer size.
protected long	bufferStartPosition	The absolute position of the start of the buffer.
protected NIOByteBufferProvider	byteBufferProvider	Provider class for NIO byte buffers, allocated or memory mapped.
protected FileChannel	channel	The file channel backed by the random access file.
protected static int	defaultBufferSize	Default NIO buffer size to facilitate buffered I/O.
protected static int	defaultRWBufferSize	Default NIO buffer size to facilitate buffered I/O for read/write streams.
protected boolean	isReadWrite	Whether or not the file is opened read/write.
protected FileChannel.MapMode	mapMode	The default map mode for the file.
protected ByteOrder	order	The buffer's byte ordering.
protected long	position	The absolute position within the file.
protected RandomAccessFile	raf	The random access file object backing this FileHandle.

Fields inherited from class loci.common.AbstractNIOHandle

EOF_ERROR_MSG

Constructor Summary

Constructors

Constructor	Description
NIOFileHandle(File file, String mode)	Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(File file, String mode, int bufferSize)	Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.
NIOFileHandle(String name, String mode)	Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes this random access stream and releases any system resources associated with the stream.
int	getBufferSize()
FileChannel	getFileChannel()
long	getFilePointer()	Returns the current offset in this stream.
ByteOrder	getOrder()	Returns the current order (endianness) of the stream.
RandomAccessFile	getRandomAccessFile()
long	length()	Returns the length of this stream.
int	read(byte[] b)	Reads up to b.length bytes of data from this stream into an array of bytes.
int	read(byte[] b, int off, int len)	Reads up to len bytes of data from this stream into an array of bytes.
int	read(ByteBuffer buf)	Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.
int	read(ByteBuffer buf, int off, int len)	Reads up to len bytes of data from this stream into a ByteBuffer.
boolean	readBoolean()
byte	readByte()
char	readChar()
double	readDouble()
float	readFloat()
void	readFully(byte[] b)
void	readFully(byte[] b, int off, int len)
int	readInt()
String	readLine()
long	readLong()
short	readShort()
int	readUnsignedByte()
int	readUnsignedShort()
String	readUTF()
void	seek(long pos)	Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.
static void	setDefaultBufferSize(int size)	Set the default buffer size for read-only files.
static void	setDefaultReadWriteBufferSize(int size)	Set the default buffer size for read/write files.
void	setLength(long length)	Sets the new length of the handle.
void	setOrder(ByteOrder order)	Sets the byte order (endianness) of the stream.
int	skipBytes(int n)
long	skipBytes(long n)	A long variant of DataInput.skipBytes(int).
void	write(byte[] b)
void	write(byte[] b, int off, int len)
void	write(int b)
void	write(ByteBuffer buf)	Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.
void	write(ByteBuffer buf, int off, int len)	Writes up to len bytes of data from the given ByteBuffer to this stream.
void	writeBoolean(boolean v)
void	writeByte(int v)
void	writeBytes(String s)
void	writeChar(int v)
void	writeChars(String s)
void	writeDouble(double v)
void	writeFloat(float v)
void	writeInt(int v)
void	writeLong(long v)
void	writeShort(int v)
void	writeUTF(String str)

Methods inherited from class loci.common.AbstractNIOHandle

exists, validateLength, validateMode

Methods inherited from class java.lang.Object

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

Field Detail

defaultBufferSize

protected static int defaultBufferSize

Default NIO buffer size to facilitate buffered I/O.

defaultRWBufferSize

protected static int defaultRWBufferSize

Default NIO buffer size to facilitate buffered I/O for read/write streams.

raf

protected RandomAccessFile raf

The random access file object backing this FileHandle.

channel

protected FileChannel channel

The file channel backed by the random access file.

position

protected long position

The absolute position within the file.

bufferStartPosition

protected long bufferStartPosition

The absolute position of the start of the buffer.

bufferSize

protected int bufferSize

The buffer size.

buffer

protected ByteBuffer buffer

The buffer itself.

isReadWrite

protected boolean isReadWrite

Whether or not the file is opened read/write.

mapMode

protected FileChannel.MapMode mapMode

The default map mode for the file.

order

protected ByteOrder order

The buffer's byte ordering.

byteBufferProvider

protected NIOByteBufferProvider byteBufferProvider

Provider class for NIO byte buffers, allocated or memory mapped.

Constructor Detail

NIOFileHandle

public NIOFileHandle(File file,
                     String mode,
                     int bufferSize)
              throws IOException

Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.

Parameters:

file - a File representing a file on disk

mode - the access mode; r (read only) and rw (read/write) are supported

bufferSize - the size of the buffer used to speed up reading and writing

Throws:

IOException - if there is an error accessing the file

NIOFileHandle

public NIOFileHandle(File file,
                     String mode)
              throws IOException

Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.

Parameters:

file - a File representing a file on disk

mode - the access mode; r (read only) and rw (read/write) are supported

Throws:

IOException - if there is an error accessing the file

NIOFileHandle

public NIOFileHandle(String name,
                     String mode)
              throws IOException

Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

Parameters:

name - the path to a file on disk

mode - the access mode; r (read only) and rw (read/write) are supported

Throws:

IOException - if there is an error accessing the file

Method Detail

setDefaultBufferSize

public static void setDefaultBufferSize(int size)

Set the default buffer size for read-only files. Subsequent uses of the NIOFileHandle(String, String) and NIOFileHandle(File, String) constructors will use this buffer size.

Parameters:

size - the new default buffer size

setDefaultReadWriteBufferSize

public static void setDefaultReadWriteBufferSize(int size)

Set the default buffer size for read/write files. Subsequent uses of the NIOFileHandle(String, String) and NIOFileHandle(File, String) constructors will use this buffer size.

Parameters:

size - the new default buffer size

getRandomAccessFile

public RandomAccessFile getRandomAccessFile()

Returns:

the random access file object backing this FileHandle.

getFileChannel

public FileChannel getFileChannel()

Returns:

the FileChannel from this FileHandle.

getBufferSize

public int getBufferSize()

Returns:

the current buffer size.

setLength

public void setLength(long length)
               throws IOException

Description copied from class: AbstractNIOHandle

Sets the new length of the handle.

Specified by:

setLength in class AbstractNIOHandle

Parameters:

length - New length.

Throws:

IOException - If there is an error changing the handle's length.

close

public void close()
           throws IOException

Description copied from interface: IRandomAccess

Closes this random access stream and releases any system resources associated with the stream.

Throws:

IOException - if the underlying stream(s) could not be closed

getFilePointer

public long getFilePointer()

Description copied from interface: IRandomAccess

Returns the current offset in this stream.

Returns:

the current byte offset within the file; expected to be non-negative and less than the value of #length()

length

public long length()
            throws IOException

Description copied from interface: IRandomAccess

Returns the length of this stream.

Returns:

the length in bytes of the stream

Throws:

IOException - if the length cannot be retrieved

getOrder

public ByteOrder getOrder()

Description copied from interface: IRandomAccess

Returns the current order (endianness) of the stream.

Returns:

See above.

setOrder

public void setOrder(ByteOrder order)

Description copied from interface: IRandomAccess

Sets the byte order (endianness) of the stream.

Parameters:

order - Order to set.

read

public int read(byte[] b)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to b.length bytes of data from this stream into an array of bytes.

Parameters:

b - the array to fill from this stream

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

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

Description copied from interface: IRandomAccess

Reads up to len bytes of data from this stream into an array of bytes.

Parameters:

b - the array to fill from this stream

off - the offset in b from which to start filling; expected to be non-negative and no greater than b.length - len

len - the number of bytes to read; expected to be positive and no greater than b.length - offset

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

public int read(ByteBuffer buf)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to buffer.capacity() bytes of data from this stream into a ByteBuffer.

Parameters:

buf - the ByteBuffer to fill from this stream

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

read

public int read(ByteBuffer buf,
                int off,
                int len)
         throws IOException

Description copied from interface: IRandomAccess

Reads up to len bytes of data from this stream into a ByteBuffer.

Parameters:

buf - the ByteBuffer to fill from this stream

off - the offset in b from which to start filling; expected to be non-negative and no greater than buffer.capacity() - len

len - the number of bytes to read; expected to be positive and no greater than buffer.capacity() - offset

Returns:

the total number of bytes read into the buffer.

Throws:

IOException - if reading is not possible

seek

public void seek(long pos)
          throws IOException

Description copied from interface: IRandomAccess

Sets the stream pointer offset, measured from the beginning of this stream, at which the next read or write occurs.

Parameters:

pos - new byte offset (pointer) in the current stream. Unless otherwise noted, may be larger or smaller than the current pointer, but must be non-negative and less than the value of #length()

Throws:

IOException - if pos is invalid or the seek fails

See Also:

IRandomAccess.getFilePointer()

readBoolean

public boolean readBoolean()
                    throws IOException

Throws:

IOException

readByte

public byte readByte()
              throws IOException

Throws:

IOException

readChar

public char readChar()
              throws IOException

Throws:

IOException

readDouble

public double readDouble()
                  throws IOException

Throws:

IOException

readFloat

public float readFloat()
                throws IOException

Throws:

IOException

readFully

public void readFully(byte[] b)
               throws IOException

Throws:

IOException

readFully

public void readFully(byte[] b,
                      int off,
                      int len)
               throws IOException

Throws:

IOException

readInt

public int readInt()
            throws IOException

Throws:

IOException

readLine

public String readLine()
                throws IOException

Throws:

IOException

readLong

public long readLong()
              throws IOException

Throws:

IOException

readShort

public short readShort()
                throws IOException

Throws:

IOException

readUnsignedByte

public int readUnsignedByte()
                     throws IOException

Throws:

IOException

readUnsignedShort

public int readUnsignedShort()
                      throws IOException

Throws:

IOException

readUTF

public String readUTF()
               throws IOException

Throws:

IOException

skipBytes

public int skipBytes(int n)
              throws IOException

Throws:

IOException

skipBytes

public long skipBytes(long n)
               throws IOException

Description copied from interface: IRandomAccess

A long variant of DataInput.skipBytes(int).

Parameters:

n - the number of bytes to skip

Returns:

the number of bytes skipped

Throws:

IOException - if the operation failed

write

public void write(byte[] b)
           throws IOException

Throws:

IOException

write

public void write(byte[] b,
                  int off,
                  int len)
           throws IOException

Throws:

IOException

write

public void write(ByteBuffer buf)
           throws IOException

Description copied from interface: IRandomAccess

Writes up to buffer.capacity() bytes of data from the given ByteBuffer to this stream.

Parameters:

buf - the ByteBuffer containing bytes to write to this stream

Throws:

IOException - if writing is not possible

write

public void write(ByteBuffer buf,
                  int off,
                  int len)
           throws IOException

Description copied from interface: IRandomAccess

Writes up to len bytes of data from the given ByteBuffer to this stream.

Parameters:

buf - the ByteBuffer containing bytes to write to this stream

off - the offset in b from which to start writing; expected to be non-negative and no greater than buf.capacity() - len

len - the number of bytes to write; expected to be positive and no greater than buf.capacity() - offset

Throws:

IOException - if writing is not possible

write

public void write(int b)
           throws IOException

Throws:

IOException

writeBoolean

public void writeBoolean(boolean v)
                  throws IOException

Throws:

IOException

writeByte

public void writeByte(int v)
               throws IOException

Throws:

IOException

writeBytes

public void writeBytes(String s)
                throws IOException

Throws:

IOException

writeChar

public void writeChar(int v)
               throws IOException

Throws:

IOException

writeChars

public void writeChars(String s)
                throws IOException

Throws:

IOException

writeDouble

public void writeDouble(double v)
                 throws IOException

Throws:

IOException

writeFloat

public void writeFloat(float v)
                throws IOException

Throws:

IOException

writeInt

public void writeInt(int v)
              throws IOException

Throws:

IOException

writeLong

public void writeLong(long v)
               throws IOException

Throws:

IOException

writeShort

public void writeShort(int v)
                throws IOException

Throws:

IOException

writeUTF

public void writeUTF(String str)
              throws IOException

Throws:

IOException