org.biojava.utils.io

Class CachingInputStream

java.lang.Object

java.io.InputStream

org.biojava.utils.io.CachingInputStream

All Implemented Interfaces:

Closeable, AutoCloseable, Seekable

public class CachingInputStream
extends InputStream
implements Seekable

A wrapper around InputStream that provides in-memory caching of the input data. This allows it to provide a seek(long) method, which lets the user use an InputStream like a RandomAccessFile (with appropriate caveats about memory footprint, security, and performance).

This class has not been tested with very long input streams. It might choke.

Author:

Rhett Sutphin (UI CBCB)

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	cache The byte cache itself.
protected InputStream	in The underlying input stream whose data we're caching
protected int	ptr The 0-based index into cache of the _next_ byte to return.
protected int	validLen A count of the number of bytes in cache that contain data read from the stream.

Constructor Summary

Constructors

Constructor and Description
CachingInputStream(InputStream in)

Method Summary

Modifier and Type	Method and Description
protected void	expandCache(int additionalBytes) Expands the cache to hold some number of additionalBytes.
int	read()
int	read(byte[] b, int start, int len)
void	seek(long pos) Moves the pointer in the inputstream such that the byte starting at pos are returned by the next read.
long	skip(long num)

Methods inherited from class java.io.InputStream

available, close, mark, markSupported, read, reset

Methods inherited from class java.lang.Object

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

Field Detail

cache

protected byte[] cache

The byte cache itself.

ptr

protected int ptr

The 0-based index into cache of the _next_ byte to return. If ptr == validLen, data must be read from the stream into the cache.

validLen

protected int validLen

A count of the number of bytes in cache that contain data read from the stream.

in

protected InputStream in

The underlying input stream whose data we're caching

Constructor Detail

CachingInputStream

public CachingInputStream(InputStream in)

Method Detail

seek

public void seek(long pos)
          throws IOException

Description copied from interface: Seekable

Moves the pointer in the inputstream such that the byte starting at pos are returned by the next read.

Specified by:

seek in interface Seekable

Parameters:

pos - the position to which to seek

Throws:

IOException - when there's an I/O problem

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

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

Overrides:

read in class InputStream

Throws:

IOException

skip

public long skip(long num)
          throws IOException

Overrides:

skip in class InputStream

Throws:

IOException

expandCache

protected void expandCache(int additionalBytes)

Expands the cache to hold some number of additionalBytes. Expansion is done multiplicatively for efficiency. Immediately after calling this method, you must fill the additional bytes from the stream because this method also updates validLen.