[Biojava-dev] [Bug 2177] Unclosed streams in org.biojava.bio.program.scf.SCF

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2177





------- Comment #1 from andyyatz at gmail.com  2007-01-05 05:42 -------
(In reply to comment #0)
> Hi,
> 
> There are problems in the following methods where the input streams have not
> been closed.  This can cause a 'too many open files' os error when working
> rapidly over large data sets.
> 
> org.biojava.bio.program.scf.SCF.load(File f)
> - FileInputStream fin;
> 
> org.biojava.bio.program.scf.SCF.ParserFactory.parse(InputStream in, SCF out,
> long initOffset)
>  - DataInputStream din
> 

After a quick look at the source:

1). Yes SCF.load(File f) needs to be changed to:

protected void load(File f) throws IOException,
  UnsupportedChromatogramFormatException {
  FileInputStream fin = new FileInputStream(f);
  try {
    load(fin, 0);
  }
  finally {
    fin.close();
  }
}

Since this method opens the InputStream to the SCF file it has to be
responsible for closing the stream.

2). I don't think that parse(InputStream in, SCF out, long initOffset) should
be closing streams since it does not create them. It should be creating
method's responsibility to close these streams.


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