[Bioperl-l] Bio::FeatureHolderI interface confusion

Ewan Birney birney at ebi.ac.uk
Thu Jun 19 10:06:58 EDT 2003

On Wed, 18 Jun 2003, Chris Mungall wrote:

> Ok, here's a constructive suggestion
> (1) add mutability operations to the SeqFeatureI interface, as Hilmar
> suggests.

I *really* dislike mutability to interfaces. Certain implementations just
can't do it. Mutability is an implementation specific case. Or we need to
split into immutable and mutable interfaces.

> (2) do something about this rather confusing inheritance structure
> SeqFeatureI   FeatureHolderI
>     ^           ^      ^
>     +--------+  |      +-----------+
>              |  |                  |
>              SF::Generic          SeqI
> If I'd drawn this out earlier it might have helped clarify things in my
> mind, or at least shine some light on my lack of clarity.
> This seems like a weird structure to me. Either FeatureHolderI is
> something that applies to features or it isn't. If it applies, then
> shouldn't SeqFeatureI inherit from it? If not then it seems like a
> superfluous interface that could be folded into SeqI
> Hilmar's point about criticism vs contribution is well taken. It's very
> easy to moan from the sidelines and not come up with an actual solution.
> However, whilst I'm all for collaborative coding, I'm not really in favour
> of committee based design. Besides, my own cranky ideas about design are
> so polar opposite to what is in bioperl right now I feel that my
> contributions would be detrimental here. I actually think I'm more
> constructive moaning from the sidelines. Except when major chaos and
> confusion ensues and propagates, like now.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list