[Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO

[Scott Cain]

I don't know; I've spent a little time thinking about what is needed (at
least short term for me) and Bio::Location::Simple has the methods I
think I need: start,end,strand,seq_id,is_remote.  I think we just need
an object array @targets, and add_target and get_targets methods.  I
have a hard time thinking of a reason a line of GFF would have more than
one target, but I guess we should plan for it.

On Thu, 2004-10-21 at 14:09, Allen Day wrote:
> take a look at Bio::LoationI.  maybe Bio::SeqFeature::Annotated can
> inherit from this, and the interface has already set up an each_Location()
> method for you to get all the locations out.  but i don't understand the
> Bio::Location::CoordinatePolicy yet, it looks like it affects calls to 
> start() and end().
> 
> -allen
> 
> 
> On Thu, 21 Oct 2004, Scott Cain wrote:
> 
> > On Wed, 2004-10-20 at 18:47, Allen Day wrote:
> > > Target tags - Bio::SeqFeature::Annotated needs to be able to have
> > > Bio::LocatableSeq or Bio::Location::Simple attachments.  Presumably you
> > > can have multiple targets.  Do something like create methods
> > > add_location() and locations() methods.
> > > 
> > Is there a reason that you can think of that I should use
> > Bio::LocatableSeq over Bio::Location::Simple, as the latter is probably
> > more 'simple'.
> > 
> > Thanks,
> > Scott
> > 
> > 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory