[Biojava-l] Homologene parser update?

[mark.schreiber at novartis.com]

Hello -

The best way to proove the code is worthy is to provide JUnit tests with 
the code that provide good coverage of the functionality. If the tests 
pass the code is worthy. Other more esoteric things like good API design 
and efficiency are also nice but if the unit tests don't pass it doesn't 
work.

Let us know what you plan to do.

- Mark





Gary Bader <bader at cbio.mskcc.org>
06/09/2005 05:53 AM

 
        To:     Mark Schreiber/GP/Novartis at PH
        cc:     biojava-l at biojava.org, smh1008 at cus.cam.ac.uk
        Subject:        Re: [Biojava-l] Homologene parser update?


Hi Mark,
                 Thanks.  The changes that NCBI made to their file formats 
are large, so 
I could write another builder/parser for the new file format, but it 
would not map completely to the existing parser (which is now broken 
because of NCBI format changes to even the deprecated file format).  If 
I want to contribute code, who decides that the code is worthy (e.g. 
does a design review)?  Ideally, this would happen before I start coding.
                 I haven't figured out if I am going to use the existing 
framework for 
my current project, since the file format has become simpler, but I 
would like to contribute if possible.

Thanks,
Gary

mark.schreiber at novartis.com wrote:
> Hello -
> 
> It seems most of this was contributed by David Huen. I'm not sure if he 
> plans an update. If the changes are not large then you might want to 
> consider contributing the changes yourself.
> 
> Best of Luck
> 
> - Mark
> 
> 
> 
> 
> 
> Gary Bader <bader at cbio.mskcc.org>
> Sent by: biojava-l-bounces at portal.open-bio.org
> 06/08/2005 08:22 AM
> 
> 
>         To:     biojava-l at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] Homologene parser update?
> 
> 
> Hi,
>                  I just tried the Homologene parser in biojava 1.4pre1 
and 
> noticed that 
> it only supports the deprecated Homologene file format and throws a 
> number of exceptions parsing that file (likely because of updates to the 

> old file format).  Is there an update for this parser available 
> anywhere?  I think it would be very useful.
> 
> Thanks,
> Gary
> 
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