[Bioperl-l] Bio::DB::DBFetch Bio::DB::BioFetch

[Heikki Lehvaslaiho]

Jason Stajich wrote:
> 
> Heikki and Lincoln - can you guys explain what are the differences between
> these modules - I realize BioFetch uses the registry.  Afraid that we
> might have some duplication here?


To some extent, yes, but I think we have to live it for the time being. 

I'll explain. When I wrote dbfetch script the generic classes in Bio::DB
were WebDBSeqI and NCBIHelper; the latter adding NCBI Entrez server
peculiarities so that instantiable GenBank and GenPept modules would be
easier to maintain. So I wrote DBFetch which has a same function as
NCBIHelper and on top of that Bio::DB::EMBL. 

Licoln wrote the first version of Bio::DB::Fetch so that it inherited
directly from WebDBSeqI. 

The way these two approaches differ from each other is that DBFetch is meant
to subclassed to add new databases, where as BioFetch needs to ammended
internally. 


We can not expect BioFetch to be valid for all possible databases, so I
guess we need subclassable objects as well. If someone has a clear vision
how these modules could be reogranized, I'd be interested to hear that.

	-Heikki



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