[Bioperl-l] Genquire

[David Block]

On Tue, 6 Nov 2001, Elia Stupka wrote:

> > Ewan - I took your criticism to heart and installed an adaptor layer.  
> > Theoretically, the adaptor layer makes Genquire data-source independent.
> 
> In short, read your mail, will get into the code, it's clear now that we
> should keep bioperl-db GUIless and get Genquire adaptors working for it
> soon. It would help if you had the in memory business object approach
> working, so we could also just use all bioperl parsers, create in memory
> objects, show them on Genquire, but that is a second step.
> 
> Elia
> 
> 
My Sequence object, GQ::Server::Sequence, 'isa' Bio::UpdateableSeqI, which 
'isa' Bio::SeqI, and it implements most or all of Bio::Seq.  I'm just not 
sure about the creation routine.  That might be all that needs fixing.  
Since Bio::Tk::SeqCanvas works on arbitrary Bio::SeqI objects, 
GQ::Server::Sequence had to be basically a Bio::SeqI object, with a few 
extras added for GUI and DB functionality.  So, we should be able to reuse 
bioperl parsers, and maybe create a bridge from an arbitrary Bio::Seq 
object to a full-on GQ::Server::Sequence, and we're set.

However, implementation of all of this probably depends on individual 
needs for persistence, write access, and near vs. distant storage.

Hopefully Genquire will be flexible enough to be a GUI for all of these 
cases.

Dave

(time to think up a good .sig file)