[Bioperl-l] Database Retrieval

Chris Fields cjfields at uiuc.edu
Tue Aug 8 12:53:28 EDT 2006


Sounds good.  I guess first things first.  We should get the basic  
UCSC DB backend up and running first, then implement RandomAccessI  
for simple sequence retrieval.  I'll try getting interfaces for  
Location, Refs, others along the way, which can be implemented as  
needed.  This will be pretty simple

So, we'll probably have something along the lines of

Bio::DB::RandomAccessI - Bio::SeqI retrieval interface
Bio::DB::LocationI - Bio::LocationI retrieval interface
Bio::DB::ReferenceI - Bio::Annotation::Reference (or similar)  
retrieval interface
Bio::DB::ClusterI - Bio::ClusterI retrieval interface (SNP)
....and so on

Should Sean get an CVS account or should we just pass everything via  
a proxy, Sendu maybe?  Might be easier to give him CVS access so  
Sendu can focus on Taxonomy, I can focus on the interfaces and  
getting through my benchwork (?!?), and Hilmar can focus on $job.

Chris

On Aug 8, 2006, at 10:21 AM, Hilmar Lapp wrote:

>
> On Aug 8, 2006, at 10:16 AM, Chris Fields wrote:
>
>> 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.
>
> Right. It is easy for an implementation class to implement multiple
> interfaces, but it is messy to split up interfaces later that were
> lumped together earlier without a clear need to do so.
>
> "do one task only but do it well" - that's the motto for the
> interface, where doing it well also means to keep it as simple as
> possible.
>
> thanks for taking a stab.
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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