[Bioperl-l] SeqI interface

[Jason Stajich]

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

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/ 
> > 
> > 
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> > 
> 
> -----------------------------------------------------------------
> 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/