org.biojava.utils.io

Class RandomAccessReader

java.lang.Object

java.io.Reader

org.biojava.utils.io.RandomAccessReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, java.lang.Readable

public class RandomAccessReader
extends java.io.Reader

RandomAccessReader extends Reader to provide a means to create buffered Readers from RandomAccessFiles.

Since:

1.2

Author:

Keith James

Field Summary

Fields inherited from class java.io.Reader

lock

Constructor Summary

Constructors

Constructor and Description
RandomAccessReader(java.io.RandomAccessFile raf) Creates a new RandomAccessReader wrapping the RandomAccessFile and using a default-sized buffer (8192 bytes).
RandomAccessReader(java.io.RandomAccessFile raf, int sz) Creates a new RandomAccessReader wrapping the RandomAccessFile and using a buffer of the specified size.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() close closes the underlying RandomAccessFile.
long	getFilePointer() getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.
long	length() length returns the length of the underlying RandomAccessFile.
int	read() read reads one byte from the underlying RandomAccessFile.
int	read(char[] cbuf, int off, int len) read reads from the underlying RandomAccessFile into an array.
void	seek(long pos) seek moves the pointer to the specified position.

Methods inherited from class java.io.Reader

mark, markSupported, read, read, ready, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomAccessReader

public RandomAccessReader(java.io.RandomAccessFile raf)
                   throws java.io.IOException

Creates a new RandomAccessReader wrapping the RandomAccessFile and using a default-sized buffer (8192 bytes).

Parameters:

raf - a RandomAccessFile to wrap.

Throws:

java.io.IOException - if an error occurs.

RandomAccessReader

public RandomAccessReader(java.io.RandomAccessFile raf,
                  int sz)
                   throws java.io.IOException

Creates a new RandomAccessReader wrapping the RandomAccessFile and using a buffer of the specified size.

Parameters:

raf - a RandomAccessFile to wrap.

sz - an int buffer size.

Throws:

java.io.IOException

Method Detail

close

public void close()
           throws java.io.IOException

close closes the underlying RandomAccessFile.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class java.io.Reader

Throws:

java.io.IOException - if an error occurs.

length

public long length()
            throws java.io.IOException

length returns the length of the underlying RandomAccessFile.

Returns:

a long.

Throws:

java.io.IOException - if an error occurs.

read

public final int read()
               throws java.io.IOException

read reads one byte from the underlying RandomAccessFile.

Overrides:

read in class java.io.Reader

Returns:

an int, -1 if the end of the stream has been reached.

Throws:

java.io.IOException - if an error occurs.

read

public int read(char[] cbuf,
       int off,
       int len)
         throws java.io.IOException

read reads from the underlying RandomAccessFile into an array.

Specified by:

read in class java.io.Reader

Parameters:

cbuf - a char [] array to read into.

off - an int offset in the array at which to start storing chars.

len - an int maximum number of char to read.

Returns:

an int number of chars read, or -1 if the end of the stream has been reached.

Throws:

java.io.IOException - if an error occurs.

getFilePointer

public long getFilePointer()
                    throws java.io.IOException

getFilePointer returns the effective position of the pointer in the underlying RandomAccessFile.

Returns:

a long offset.

Throws:

java.io.IOException - if an error occurs.

seek

public void seek(long pos)
          throws java.io.IOException

seek moves the pointer to the specified position.

Parameters:

pos - a long offset.

Throws:

java.io.IOException - if an error occurs.