[Bioperl-l] Database Retrieval

Hilmar Lapp 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
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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