[Bioperl-l] Database Retrieval
hlapp at gmx.net
Tue Aug 8 09:42:06 EDT 2006
On Aug 8, 2006, at 9:26 AM, Chris Fields wrote:
>> would it be possible to return standard bioperl objects, like
>> Bio:SeqI objects, or Bio::Annotation::Reference, Bio::LocationI, etc?
> '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.
> If someone really wants references, they could build a class to get
> them into the appropriate objects using your DB class as the
> 'backend' to get the raw data.
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 ...
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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