[Bioperl-l] bioperl-db: rich queries implementation

[Chris Mungall]

On Mon, 11 Jun 2001, Elia Stupka wrote:

> Wow, this sounds excellent. 
> 
> Since I am playing often and writing bioperl-db stuff, I would be very
> interested in seeing the code committed, and contributing to it. I was
> helping a team in Singapore with ensembl and incidentally we are also
> building there a very juicy bioperl-db, which they were going to use both
> for EnsEMBL and as a stand-alone db to query viaa the web, so that will be
> a perfect test case!

yup, it should be fairly easy to knock up a CGI that builds up a BioQuery
object allowing the user to progressively combine more constraints with
ands/ors/nots.

Ok, code committed.

See what you think, especially wrt clarity of the code. I really don't
want to go complicating the rather lovely bioperl-db.

the basic idea is pretty simple; the BaseAdaptor takes care of combining
the the query constraints into the SQL statement(s). It asks the
individual adaptors (so far just SeqAdaptor) how to resolve the individual
constraint elements, what tables and joins are reuiqred etc.

if this all seems like a reasonable direction to go in, I'll add
constraint resolvers for fetching features. 

> Elia
> 
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