org.biojava.utils.io

Class LargeBuffer

java.lang.Object

org.biojava.utils.io.LargeBuffer

public class LargeBuffer
extends java.lang.Object

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

Author:

Matthews Pocock

Constructor Summary

Constructors

Constructor and Description
LargeBuffer(java.nio.channels.FileChannel channel, java.nio.channels.FileChannel.MapMode mode, long pos, long size)

Method Summary

Modifier and Type	Method and 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(java.nio.channels.FileChannel channel,
                   java.nio.channels.FileChannel.MapMode mode,
                   long pos,
                   long size)
            throws java.io.IOException

Throws:

java.io.IOException

Method Detail

get

public byte get(long pos)
         throws java.lang.IndexOutOfBoundsException,
                java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

get

public byte get()
         throws java.lang.IndexOutOfBoundsException,
                java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

put

public void put(long pos,
                byte b)
         throws java.lang.IndexOutOfBoundsException,
                java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

put

public void put(byte val)
         throws java.lang.IndexOutOfBoundsException,
                java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getChar

public char getChar(long pos)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getChar

public char getChar()
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putChar

public void putChar(long pos,
                    char c)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putChar

public void putChar(char val)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getDouble

public double getDouble(long pos)
                 throws java.lang.IndexOutOfBoundsException,
                        java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getDouble

public double getDouble()
                 throws java.lang.IndexOutOfBoundsException,
                        java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putDouble

public void putDouble(long pos,
                      double d)
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putDouble

public void putDouble(double val)
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getFloat

public float getFloat(long pos)
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getFloat

public float getFloat()
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putFloat

public void putFloat(long pos,
                     float f)
              throws java.lang.IndexOutOfBoundsException,
                     java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putFloat

public void putFloat(float val)
              throws java.lang.IndexOutOfBoundsException,
                     java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getInt

public int getInt(long pos)
           throws java.lang.IndexOutOfBoundsException,
                  java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getInt

public int getInt()
           throws java.lang.IndexOutOfBoundsException,
                  java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putInt

public void putInt(long pos,
                   int i)
            throws java.lang.IndexOutOfBoundsException,
                   java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putInt

public void putInt(int val)
            throws java.lang.IndexOutOfBoundsException,
                   java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getLong

public long getLong(long pos)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getLong

public long getLong()
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putLong

public void putLong(long pos,
                    long l)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putLong

public void putLong(long val)
             throws java.lang.IndexOutOfBoundsException,
                    java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getShort

public short getShort(long pos)
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

getShort

public short getShort()
               throws java.lang.IndexOutOfBoundsException,
                      java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putShort

public void putShort(long pos,
                     short s)
              throws java.lang.IndexOutOfBoundsException,
                     java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

putShort

public void putShort(short val)
              throws java.lang.IndexOutOfBoundsException,
                     java.io.IOException

Throws:

java.lang.IndexOutOfBoundsException

java.io.IOException

position

public long position()

position

public void position(long pos)

force

public void force()