Package org.biojava.utils.io

Class LargeBuffer

java.lang.Object

org.biojava.utils.io.LargeBuffer

public class LargeBuffer
extends Object

Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs.

Author:

Matthews Pocock

Constructor Summary

Constructors

Constructor	Description
LargeBuffer(FileChannel channel, FileChannel.MapMode mode, long pos, long size)

Method Summary

Modifier and Type	Method	Description
void	force()
byte	get()
byte	get(long pos)
char	getChar()
char	getChar(long pos)
double	getDouble()
double	getDouble(long pos)
float	getFloat()
float	getFloat(long pos)
int	getInt()
int	getInt(long pos)
long	getLong()
long	getLong(long pos)
short	getShort()
short	getShort(long pos)
long	position()
void	position(long pos)
void	put(byte val)
void	put(long pos, byte b)
void	putChar(char val)
void	putChar(long pos, char c)
void	putDouble(double val)
void	putDouble(long pos, double d)
void	putFloat(float val)
void	putFloat(long pos, float f)
void	putInt(int val)
void	putInt(long pos, int i)
void	putLong(long val)
void	putLong(long pos, long l)
void	putShort(long pos, short s)
void	putShort(short val)

Methods inherited from class java.lang.Object

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

Constructor Detail

LargeBuffer

public LargeBuffer(FileChannel channel,
                   FileChannel.MapMode mode,
                   long pos,
                   long size)
            throws IOException

Throws:

IOException

Method Detail

get

public byte get(long pos)
         throws IndexOutOfBoundsException,
                IOException

Throws:

IndexOutOfBoundsException

IOException

get

public byte get()
         throws IndexOutOfBoundsException,
                IOException

Throws:

IndexOutOfBoundsException

IOException

put

public void put(long pos,
                byte b)
         throws IndexOutOfBoundsException,
                IOException

Throws:

IndexOutOfBoundsException

IOException

put

public void put(byte val)
         throws IndexOutOfBoundsException,
                IOException

Throws:

IndexOutOfBoundsException

IOException

getChar

public char getChar(long pos)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

getChar

public char getChar()
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

putChar

public void putChar(long pos,
                    char c)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

putChar

public void putChar(char val)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

getDouble

public double getDouble(long pos)
                 throws IndexOutOfBoundsException,
                        IOException

Throws:

IndexOutOfBoundsException

IOException

getDouble

public double getDouble()
                 throws IndexOutOfBoundsException,
                        IOException

Throws:

IndexOutOfBoundsException

IOException

putDouble

public void putDouble(long pos,
                      double d)
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

putDouble

public void putDouble(double val)
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

getFloat

public float getFloat(long pos)
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

getFloat

public float getFloat()
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

putFloat

public void putFloat(long pos,
                     float f)
              throws IndexOutOfBoundsException,
                     IOException

Throws:

IndexOutOfBoundsException

IOException

putFloat

public void putFloat(float val)
              throws IndexOutOfBoundsException,
                     IOException

Throws:

IndexOutOfBoundsException

IOException

getInt

public int getInt(long pos)
           throws IndexOutOfBoundsException,
                  IOException

Throws:

IndexOutOfBoundsException

IOException

getInt

public int getInt()
           throws IndexOutOfBoundsException,
                  IOException

Throws:

IndexOutOfBoundsException

IOException

putInt

public void putInt(long pos,
                   int i)
            throws IndexOutOfBoundsException,
                   IOException

Throws:

IndexOutOfBoundsException

IOException

putInt

public void putInt(int val)
            throws IndexOutOfBoundsException,
                   IOException

Throws:

IndexOutOfBoundsException

IOException

getLong

public long getLong(long pos)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

getLong

public long getLong()
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

putLong

public void putLong(long pos,
                    long l)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

putLong

public void putLong(long val)
             throws IndexOutOfBoundsException,
                    IOException

Throws:

IndexOutOfBoundsException

IOException

getShort

public short getShort(long pos)
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

getShort

public short getShort()
               throws IndexOutOfBoundsException,
                      IOException

Throws:

IndexOutOfBoundsException

IOException

putShort

public void putShort(long pos,
                     short s)
              throws IndexOutOfBoundsException,
                     IOException

Throws:

IndexOutOfBoundsException

IOException

putShort

public void putShort(short val)
              throws IndexOutOfBoundsException,
                     IOException

Throws:

IndexOutOfBoundsException

IOException

position

public long position()

position

public void position(long pos)

force

public void force()