[Biojava-l] SCF parser problem

[mark.schreiber at novartis.com]

Hello -

I may have missed that patch. Can you send me the source for the corrected 
SCF parser and I will commit it to CVS so it makes the next version.

Thanks,

- Mark





Andy Yates <ady at sanger.ac.uk>
Sent by: biojava-l-bounces at portal.open-bio.org
08/25/2005 10:55 PM

 
        To:     "Zhao, Yongmei" <YZhao at tigr.org>
        cc:     biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] SCF parser problem


I also have encountered this problem before & this bug has not been 
fixed yet. I haven't had time to construct the relevant test packs for 
the distro. If you need the fix now then I can send you any src code you 
need.

Andy Y

Zhao, Yongmei wrote:
> Hello,
> 
> I parsed trace file by using the SCF parser in biojava-1.4 release, the
> output of the getTrace(AtomicSymbol nuc) method returned erroneous data,
> obviously, the data is overflow. I tested with few scf trace files and
> tried to compare the results (int[]) with the output from staden package
> io_lib, only first few sample data in the array are the same, the rest
> of the data from SCF parser does not make sense. I searched Biojava-dev
> archive, and saw a discussion talked about the bug in SCF parser, which
> was fixed and will lead to 1.4 release. I am wondering if the fix was
> included in 1.4 release or not?
> 
> 
> Thanks,
> Yongmei
> 
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