[Bioperl-l] 'virtual' seqs

[Jason Stajich]

On Thu, 20 Jun 2002, David Block wrote:

> 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 guess so - if someone can use it would be happy to have the
implementation - you comfortable with that?  Isn't the laziness an
implementation issue or do you have to explicitly tell the object when you
want it to retrieve the full data rather than just on the first seq()
call?


> 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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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu