[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Chris Mungall cjm at fruitfly.org
Tue Nov 23 17:41:10 EST 2004

On Tue, 23 Nov 2004, Allen Day wrote:


> > While it "works", I don't see why it had to be done this way; I'd
> > prefer a solution that didn't involve changing the definition of
> > Bio::SeqFeatureI (at least not yet).  Further, your "deprecations" seem
> > to indicate that you simply want Bio::SeqFeatureI to go away entirely,
> > and have us treat everything as an annotation collection (which may or
> > may not have a location on a sequence).  Is this the agreed-upon way of
> > the future?  What are you gaining, besides forcing my fingers to learn
> > get_Annotations($tag) instead of get_tag_values($tag)?
> you've got the gist of it.  i want features to be AnotatableI, not be
> AnnotationCollectionI themselves.  the main payoffs i see here are:
> [1] consistency amongst annotated objects.  why should SeqFeatureI do
> things differently?
> [2] possibility of strong annotation typing (e.g.
> Bio::Annotation::OntologyTerm instead of a plaintext string).  this is the
> main reson driving the changes.


I'm all for using ontologies for metadata and strong typing within
bioperl, but I'm concerned that this is done right, and in such a way that
it has minimal impact on the complexity and memory footprint of bioperl.

I think that if you are edging us in the direction of [2] you should come
up with a document describing your plan. I know this goes against the
bioperl extreme programming ethos of "code first, ask questions later" but
I'm quite concerned about this.


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