[Bioperl-l] PrimarySeqI and IdentifiableI

[Ewan Birney]

On Thu, 5 Sep 2002, Hilmar Lapp wrote:

> I apologize for my ignorance if this has all been thrashed out and I 
> just forgot.
> 
> Right now PrimarySeqI is-a IdentifiableI, which means every 
> Bio::PrimarySeqI compliant object is, in fact must be, 
> Bio::IdentifiableI compliant at the same time.
> 
> Bio::Seq as an example theoretically is but practically is not 
> because it doesn't implement a number of methods from IdentifiableI.
> 
> There are at least 4 methods to implement.
> 
> This prompted me to wonder whether we should really mandate that 
> every implementor of PrimarySeqI needs to implement IdentifiableI at 
> the same time. Alternatively, they go separate, and a particular 
> implementation can choose whether it implements IdentifiableI too or 
> not. Analogous for DescribableI.
> 
> I'm actually leaning towards separating them. Someone may want to 
> have a very bare-bones sequence object that isn't even Identifiable 
> nor Describable. This may not be LSID compatible though (anyone got 
> thoughts on that?).
> 
> Please voice your opinion if you want to weigh in. Core people?
> 
> I'll have to fix Bio::Seq anyway (I guess there's little doubt it 
> should be Identifiable), but if we decide to separate IdentifiableI 
> (and DescribableI) from PrimarySeqI, I'll fix that right away, too.

It is a good question - I would say that they should implement the methods
but could easily pass back "" strings. What is the other solution - A
composition solution? Then clients have to test whether

$seq->identifier() is undef?




> 
> 	-hilmar
> 
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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