[Bioperl-l] Identifiable and Describable

[Ewan Birney]

On Tue, 23 Jul 2002, Hilmar Lapp wrote:

> > 
> > I still don't think LSID/MOBY/Ensembl's are different 
> > implemetnations -
> > they use the same slots in semantically identical ways and it is more
> > encoding things...
> > 
> 
> They do, right. But the LSID string would be an encoding, wouldn't it?
> And another one might encode the same information in a different way,
> right? So, the method lsid_string() returns an encoding, and the name
> implies that it's a specific encoding.

Yup.

> 
> One could rename to say id_string() in the interface, and an
> implemention using the LSID encoding then returns an LSID-compliant
> string ... Does that make sense?

I don't think this would be sensible because ... say, in your case, ...
bioperl-db attaches a Bio::Identifiable::Yadda implementation with Yadda
encoding, but then you want to get out a LSID encoding - the client would
have to artificially build an LSID module.


Three real solutions here in my view:


(a) just keep adding new encodings to Bio::IdenitifiableI interface (lsid,
moby, whatever). Encodings should be cheap and easy functions to add, and
I see no problem in adding their *implementation* at the interface level
in this "decorated interface" idea that we use

(b) something like a visitor pattern which would be:

   Bio::Identifier::EncodingVisitorI
                  ::EncodingVisitor::LSID
                  ::EncodingVisitor::Moby

   and then it would be

   $encoding = $bio_identifiable_obj->encoding($encoding_visitor);


(c) sort of like the above, but via a string, and with a proposed
implementation


    $encoding = $bio_identifiable_obj->encoding('lsid');




Preferences?



> 
> 	-hilmar
> -- 
> -------------------------------------------------------------
> GNF Genome Informatics: We like beer, not whine.
> -------------------------------------------------------------
> 

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