Package org.biojava.nbio.core.util

Class UncompressInputStream

java.lang.Object
java.io.InputStream
java.io.FilterInputStream
org.biojava.nbio.core.util.UncompressInputStream
All Implemented Interfaces:
Closeable, 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
Version:
0.3-3 06/05/2001, 0.3-5 2008/01/19, 1.0 2018/01/08
Author:
Ronald Tschalar, Unidata Program Center, Richard Holland - making LZW_MAGIC package-visible., Fred Hansen (zweibieren@yahoo.com) Fixed available() and the EOF condition for mainloop. Also added some comments., Fred Hansen (zweibieren@yahoo.com) added uncompress(InputStream,OutputStream) and called it from main(String[]) and uncompress(String, FileOutputStream) normalize indentation rewrite skip method amend logging code in uncompress(String, FileOutputStream)

  • Constructor Details

    • UncompressInputStream

      public UncompressInputStream(InputStream is) throws IOException
      Parameters:
      is - the input stream to decompress
      Throws:
      IOException - if the header is malformed

  • Method Details

    • 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(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(String[] args) throws Exception
      Reads a file, uncompresses it, and sends the result to stdout. Also writes trivial statistics to stderr.
      Parameters:
      args - An array with one String element, the name of the file to read.
      Throws:
      IOException - for any failure
      Exception