[Biojava-l] Homologene parser update?

[Gary Bader]

Hi,
	I just wrote a homologene parser that includes unit tests.  NCBI split 
homologene into simple + complex file formats - I only parse the simple 
format.  Should I send you the code?  I doubt you would want to 
integrate it now, since I can imagine a few more useful methods, but, 
with design pointers, I could extend the code to be more useful.  Should 
we take this discussion off the list?

Cheers,
Gary

mark.schreiber at novartis.com wrote:
> 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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>>
>>
>>
> 
> 
> 
>