Bioperl: Accessing sequences via Bio::DB::SeqI

[James Gilbert]

On Mon, 1 May 2000, Ewan Birney wrote:

> On Mon, 1 May 2000, Mark Dalphin wrote:
> 
> > Thanks for the reply, Ewan.  I have a further naive quetion about the use of the
> > modules:
> > 
> > Following on from my earlier letter, I see now that Bio::DB::GenBank.pm ISA
> > RandomAccessI.pm and that SeqI.pm ISA a RandomAccessI.pm. And I understand your
> > design in making SeqI.pm a superset of RandomAccessI.pm.
> > 
> > Where I am stuck is in "Why is RandomAccessI.pm ISA RootI.pm?"  One needs to
> > eventiually inherit from a concrete class, I would think.  In that case, I would
> > think that RandomAccessI.pm ISA Bio::Root::Object.pm would make more sense.  Then one
> > could write:
> 
> This is complex, so I appreciate your confusion. The RootI inheritance is
> correct. The interfaces should not mandate a particular implementation.
> The thing to keep in mind is that one might have a _radically_ different
> implementation behind an interface. The best example I know are C structs
> bound in via XS, providing hyper-fast bioperl "objects" without being
> implemented at all in Perl. It is very cute. (and works ...)

I think the BioPerl "I" modules confuse people who
are used to working with interfaces, because they
contain a lot of "decorator" methods, which
actually do things, and so are not pure abstract
interfaces.  Bio::Root::RootI implements all of
its methods, so I think it _is_ the concrete class
that Mark is looking for.

	James

James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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