[Bioperl-l] Annotation proposal

Ewan Birney birney@ebi.ac.uk
Tue, 10 Apr 2001 19:06:05 +0100 (BST)

On Tue, 10 Apr 2001, Matthew Pocock wrote:

> Ewan Birney wrote:
> >     Bio::Seq and Bio::SeqFeature::Gene should *be* Bio::AnnotationContainerI's
> > not *have-a* annotation. This is closer to both OMG and BioJava things, which
> > I think is nice.
> Not quite so close - Annotatable defines the method getAnnotation which 
> returns an Annotation instance. Sequences, Features and other things 
> extend Annotatable so have an Annotation.

Aha. Ok. This means that Bioperl and Biojava are in sync anyway now, so
... perhaps I should leave it the way it is ;).

Re: your frame stuff/code snippets.

Frankly it just *scares me* what you can do with Perl AUTOLOAD, a
little bit of closure/anonymous subroutines and a hash. Is this sane?

But basically you are right - I think we do want some type-safe system but
run-time resolved mix-in something-or-other, aka Frames aka whatever other
buzzword you want to put in it. What is the best way to allow this to
happen? How constrained should it be by compile time language constraints?

Re: Annotation. The database (bioperl-db) stuff for sequences went
really well because we have interfaces. For annotations it was a little
bit of  Interfaces. For Bioperl-0.8 (the
far, distant future...) I want to
have a goal of Interface definition for nearly everything. Yup - I know -
we are turning Perl into Java piece-by-piece. There is some sort of weird
moral here.