[Biojava-dev] CATH parser

[Daniel Asarnow]

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
> > _______________________________________________
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> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>