[Bioperl-l] 'virtual' seqs

[Lincoln Stein]

I think it's important that we be able to perform manipulations on feature 
tables and annotations even when the underlying sequence is completely 
unavailable (not even a guarantee that you can fetch the sequence if you wait 
long enough).  Laziness is a great feature, but it's more of an 
implementation issue than something that should be exposed to the API.

As Ewan suggests, it's probably better to return a string of N's rather than 
an undef sequence; otherwise lots of programs will break.  However I think 
that EmptySequence has the wrong connotation.  I prefer VirtualSequence, or 
possibly UnknownSequence.

Lincoln

On Wednesday 26 June 2002 06:59 pm, Hilmar Lapp wrote:
> I like LazySeq best -- it means the absence of the sequence is not written
> in stone, fetching is just expensive and can take a while.
>
> Also, one should be able to write these sequences to transport the
> annotation and feature table (without potentially expensive sequence
> transport, too). In this case a parser's write_seq() method asking the
> object for the sequence should get an empty string instead of triggering
> the actual sequence fetch. At least as an option.
>
> I'm wondering how this should be implemented ... not sure what's the right
> thing to do.
>
> 	-hilmar
>
> > -----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.  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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================