[Biojava-dev] CATH parser

[Andreas Prlic]

Hi Daniel, this is great, Can you bundle your .java files and send
them to me off list?

Thanks,

Andreas



On Sat, Jun 23, 2012 at 8:39 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Andreas,
> I've made significant progress on the CATH parser. I essentially followed
> the paradigm of the SCOP package, using new classes CathDatabase
> (interface), CathInstallation, CathDescription, CathDomain, CathNode and
> CathSegment. All are direct analogs of SCOP classes except for CathSegment
> (which represents sub-domain divisions in CATH).
>
> I believe I have reached a point where some further guidance on the
> implementation (read: code review) is warranted. May I share my classes with
> the list? Also, how should I do so?
>
> Best,
> -da
>
>
> On Sun, Jun 3, 2012 at 10:37 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> Hi Daniel,
>>
>> That would be great! It is probably best to try to model this in a
>> similar way to SCOP.
>>
>> The central interface for this is ScopDatabase. This is supported by
>> three different implementations, one that downloads and (re-)uses a
>> local copy of SCOP, one that fetches SCOP data via remote web services
>> and a third class that provides access for the Berkeley version of
>> SCOP.
>>
>> As such, a start would be to define such an interface for CATH and
>> then come up with an initial implementation for this.
>>
>> Cheers,
>> Andreas
>>
>>
>>
>>
>> On Sat, Jun 2, 2012 at 9:52 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
>> > Hello BioJava devs,
>> >
>> > I recently noticed that a CATH parser is listed among the features
>> > requested for BioJava3. It happens that I have a CATH parser implemented
>> > in
>> > one of my projects, so it should be relatively easy for me to
>> > re-implement
>> > according to BioJava style and extend with any particular features I
>> > might
>> > have left out.
>> >
>> > I would like to know, (1) is this still a desired feature, (2) what
>> > functionality is needed and (3) what patterns should be used (and
>> > whether
>> > any existing classes provide a suitable paradigm).
>> >
>> > Best,
>> > -da
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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