org.biojava.nbio.core.util

Class UncompressInputStream

java.lang.Object

InputStream

FilterInputStream

org.biojava.nbio.core.util.UncompressInputStream

All Implemented Interfaces:

Closeable, java.lang.AutoCloseable

public class UncompressInputStream
extends FilterInputStream

This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant). This code is based heavily on the unlzw.c code in gzip-1.2.4 (written by Peter Jannesen) and the original compress code. This version has been modified from the original 0.3-3 version by the Unidata Program Center (support@xxxxxxxxxxxxxxxx) to make the constructor public and to fix a couple of bugs. Also: - markSupported() returns false - add uncompress() static method

Field Summary

Fields inherited from class FilterInputStream

in

Constructor Summary

Constructors

Constructor and Description
UncompressInputStream(InputStream is)

Method Summary

Modifier and Type	Method and Description
int	available()
static void	main(java.lang.String[] args) Reads a file, uncompresses it, and sends the result to stdout.
boolean	markSupported() This stream does not support mark/reset on the stream.
int	read()
int	read(byte[] buf, int off, int len)
long	skip(long num)
static long	uncompress(InputStream in, OutputStream out) Read an input stream and uncompress it to an output stream.
static long	uncompress(java.lang.String fileInName, FileOutputStream out) Read a named file and uncompress it.

Methods inherited from class FilterInputStream

close, mark, read, reset

Methods inherited from class java.lang.Object

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

Constructor Detail

UncompressInputStream

public UncompressInputStream(InputStream is)
                      throws IOException

Parameters:

is - the input stream to decompress

Throws:

IOException - if the header is malformed

Method Detail

read

public int read()
         throws IOException

Overrides:

read in class FilterInputStream

Throws:

IOException

read

public int read(byte[] buf,
                int off,
                int len)
         throws IOException

Overrides:

read in class FilterInputStream

Throws:

IOException

skip

public long skip(long num)
          throws IOException

Overrides:

skip in class FilterInputStream

Throws:

IOException

available

public int available()
              throws IOException

Overrides:

available in class FilterInputStream

Throws:

IOException

markSupported

public boolean markSupported()

This stream does not support mark/reset on the stream.

Overrides:

markSupported in class FilterInputStream

Returns:

false

uncompress

public static long uncompress(java.lang.String fileInName,
                              FileOutputStream out)
                       throws IOException

Read a named file and uncompress it.

Parameters:

fileInName - Name of compressed file.

out - A destination for the result. It is closed after data is sent.

Returns:

number of bytes sent to the output stream,

Throws:

IOException - for any error

uncompress

public static long uncompress(InputStream in,
                              OutputStream out)
                       throws IOException

Read an input stream and uncompress it to an output stream.

Parameters:

in - the incoming InputStream. It is NOT closed.

out - the destination OutputStream. It is NOT closed.

Returns:

number of bytes sent to the output stream

Throws:

IOException - for any error

main

public static void main(java.lang.String[] args)
                 throws IOException

Reads a file, uncompresses it, and sends the result to stdout. Also writes trivial statistics to logger.

Parameters:

args - An array with one String element, the name of the file to read.

Throws:

IOException - for any failure