[Bioperl-l] Database Retrieval
cjfields at uiuc.edu
Tue Aug 8 10:16:20 EDT 2006
On Aug 8, 2006, at 8:42 AM, Hilmar Lapp wrote:
>> 'Front-end' classes that return appropriate objects (SeqI, LocationI,
>> etc) could be built around the DB class; the key is the consistent
>> interface. So we would need a RandomAccessI-like interface for
>> LocationI, Annotation::References, etc.
> Sounds like a good idea. Do you feel like coding up prototypes?
> That'd be great.
I could work on that. RandomAccessI is a pretty simple interface
class with a few abstract methods:
Other RandomAccessI-implementing modules add 'get_Stream*' methods,
Using that, we could have get_Location(s)*, get_Ref(s)*, get_Taxon/
Taxa*, etc. Most of these would only use a unique ID or query, though.
Would we want to lump all these together in one non-specific
interface class or split them up into several specific interfaces?
Many of the latter will likely have only a few methods, but at least
they would be consistent, so I think the latter.
> Yes, sure - but: one should keep in mind that bioperl as a library
> and as a project offers certain promises in return of the hassle to
> install and learn it, one of which is to offer implementations of
> common tasks as reusable code in well-defined and consistent APIs.
> Just keep that in mind as the long term picture ...
Agreed. The only caveat: I think the 'backend' DB-specific class
would, by necessity, have to use a DB-specific interface that allowed
maximum access to the database. The 'front-end' class which gets the
raw data into Bioperlish objects must have a consistent Bioperl
interface; this is something we really need to enforce.
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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