[Bioperl-l] SeqI interface

[Ewan Birney]

On Thu, 8 Feb 2001, Jason Stajich wrote:

> On Thu, 8 Feb 2001, Ewan Birney wrote:
> 
> > On Thu, 8 Feb 2001, Jason Stajich wrote:
> > 
> > > Shouldn't methods like primary_seq, annotation, add_SeqFeature be part of
> > > the SeqI interface?  They are part of Seq.pm.  
> > > I'm trying to be sure that I provide a complete implementation of
> > > Bio::SeqI in Bio::CorbaClient::Seq.
> > 
> > primary_seq and annotation - yes
> okay I'll include them in the SeqI definition.
> > 
> > add_SeqFeature - no (in my view). Adding a SeqFeature forces all SeqI
> > objects to become mutable (bad)
> 
> oh right, makes sense. same argument holds true in SplitLocationI with
> adding a sublocation which is what Hilmar was trying to get me to
> understand... now I do.
> 
> saw 2 more potential methods to include in the interface-
> species, feature_count

I am good for both of those being in.


> 
> objections to making them part of the interface?  I species I can live
> without, but feature_count seems logical to include.
> 
> >  
> > 
> > > 
> > > Thanks.
> > > 
> > > Jason Stajich
> > > jason@chg.mc.duke.edu
> > > Center for Human Genetics
> > > Duke University Medical Center 
> > > http://www.chg.duke.edu/ 
> > > 
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------