[Bioperl-l] 'virtual' seqs

[David Block]

Grrr... outlook doesn't like interspersing comments in replies...

--
David Block                    dblock@gnf.org
GNF - San Diego, CA        http://www.gnf.org     
Genome Informatics  /  Enterprise Programming

> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> Sent: Thursday, June 20, 2002 11:57 AM
> To: Bioperl
> Subject: [Bioperl-l] 'virtual' seqs
> 
> 
> We are processing datafiles - bsml,game, (agave?) documents 
> where it is
> possible to just know the length of the sequence but not have 
> any actual
> sequence data associated.  

Apollo has the concept of a LazySeqI, where it is understood that the 
sequence can be had for the asking, but it is lazily fetched.  Would that
be a helpful interface here?

I think we should have sequence 
> objects which
> can handle this - they would have a length, but seq() would warn and
> return undef.  We need one that would implement Bio::Seq::RichSeqI
> interface - call it VirtualRichSeq ? Perhaps we'll need the equivalent
> PrimaryVirtualSeq and VirtualSeq?
> 
> Can someone think of a better name, I don't want to confuse 
> with Ensembl
> VirtualXX objects?  This would be implemeted in Bio::Seq:: namespace.
> 
> -jason
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
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