NIOFileHandle (Bio-Formats API)

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

See Also:
IRandomAccess, RandomAccessFile

Field Summary

Fields
Modifier and Type	Field and 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.
`private Long`	`defaultLength` The original length of the file.
`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.
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`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 and 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

Methods
Modifier and Type	Method and Description
`private void`	`buffer(long offset, int size)` Aligns the NIO buffer, maps it if it is not currently and sets all relevant positions and offsets.
`void`	`close()` Closes this random access stream and releases any system resources associated with the stream.
`private void`	`doWrite(int length)`
`int`	`getBufferSize()` Gets the current buffer size.
`FileChannel`	`getFileChannel()` Gets the FileChannel from this FileHandle.
`long`	`getFilePointer()` Returns the current offset in this stream.
`ByteOrder`	`getOrder()` Returns the current order of the stream.
`RandomAccessFile`	`getRandomAccessFile()` Gets the random access file object backing this FileHandle.
`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 of the stream.
`int`	`skipBytes(int n)`
`void`	`write(byte[] b)`
`void`	`write(byte[] b, int off, int len)`
`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`	`write(int b)`
`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)`
`private void`	`writeSetup(int length)`
`void`	`writeShort(int v)`
`void`	`writeUTF(String str)`

Methods inherited from class loci.common.AbstractNIOHandle
validateLength, validateMode

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
    Logger for this class.
  - 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.
  - defaultLength
```
private Long defaultLength
```
    The original length of the file.
- 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.
    
    Throws:
    
    IOException
  - 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.
    
    Throws:
    
    IOException
  - 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.
    
    Throws:
    
    IOException
- 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.
  - 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.
  - getRandomAccessFile
```
public RandomAccessFile getRandomAccessFile()
```
    Gets the random access file object backing this FileHandle.
  - getFileChannel
```
public FileChannel getFileChannel()
```
    Gets the FileChannel from this FileHandle.
  - getBufferSize
```
public int getBufferSize()
```
    Gets 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
  - getFilePointer
```
public long getFilePointer()
```
    Description copied from interface: IRandomAccess
    
    Returns the current offset in this stream.
  - length
```
public long length()
            throws IOException
```
    Description copied from interface: IRandomAccess
    
    Returns the length of this stream.
    
    Throws:
    
    IOException
  - getOrder
```
public ByteOrder getOrder()
```
    Description copied from interface: IRandomAccess
    
    Returns the current order of the stream.
    
    Returns:
    See above.
  - setOrder
```
public void setOrder(ByteOrder order)
```
    Description copied from interface: IRandomAccess
    
    Sets the byte order 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.
    
    Returns:
    the total number of bytes read into the buffer.
    
    Throws:
    
    IOException
  - 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.
    
    Returns:
    the total number of bytes read into the buffer.
    
    Throws:
    
    IOException
  - 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.
    
    Throws:
    
    IOException
  - 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.
    
    Returns:
    the total number of bytes read into the buffer.
    
    Throws:
    
    IOException
  - 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.
    
    Throws:
    
    IOException
  - 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
  - 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.
    
    Throws:
    
    IOException
  - 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.
    
    Throws:
    
    IOException
  - 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
  - buffer
```
private void buffer(long offset,
          int size)
             throws IOException
```
    Aligns the NIO buffer, maps it if it is not currently and sets all relevant positions and offsets.
    
    Parameters:
    offset - The location within the file to read from.
    size - The requested read length.
    
    Throws:
    
    IOException - If there is an issue mapping, aligning or allocating the buffer.
  - writeSetup
```
private void writeSetup(int length)
                 throws IOException
```
    Throws:
    
    IOException
  - doWrite
```
private void doWrite(int length)
              throws IOException
```
    Throws:
    
    IOException

Class NIOFileHandle

Field Summary

Fields inherited from class loci.common.AbstractNIOHandle

Constructor Summary

Method Summary

Methods inherited from class loci.common.AbstractNIOHandle

Methods inherited from class java.lang.Object

Field Detail

LOGGER

defaultBufferSize

defaultRWBufferSize

raf

channel

position

bufferStartPosition

bufferSize

buffer

isReadWrite

mapMode

order

byteBufferProvider

defaultLength

Constructor Detail

NIOFileHandle

NIOFileHandle

NIOFileHandle

Method Detail

setDefaultBufferSize

setDefaultReadWriteBufferSize

getRandomAccessFile

getFileChannel

getBufferSize

setLength

close

getFilePointer

length

getOrder

setOrder

read

read

read

read

seek

readBoolean

readByte

readChar

readDouble

readFloat

readFully

readFully

readInt

readLine

readLong

readShort

readUnsignedByte

readUnsignedShort

readUTF

skipBytes

write

write

write

write

write

writeBoolean

writeByte

writeBytes

writeChar

writeChars

writeDouble

writeFloat

writeInt

writeLong

writeShort

writeUTF

buffer

writeSetup

doWrite