[Bioperl-l] Bio::FeatureHolderI

[Hilmar Lapp]

OK, so I did this and adapted Bio::Seq and Bio::SeqFeature::Generic.

Now SeqI extends (among others) FeatureHolderI and hence mandates 
that every SeqI also is-a FeatureHolderI. We could separate those, 
i.e., leave it up to SeqI implementors whether or not they want to 
implement FeatureHolderI too. To me it makes sense to leave the SeqI 
is-a FeatureHolderI in place; after all that's one of three 
extensions setting it apart from PrimarySeqI (in addition to being 
AnnotatableI and having a species). Anyone wants to voice an opinion?

Same story basically for SeqFeatureI. Here the situation is a hybrid 
one because only half of FeatureHolderI had been on that interface 
before. Furthermore, SeqFeatureI implementations without the 
possibility of having sub-features may easily make sense. So my vote 
here is to actually remove the sub-feature mandating method from 
SeqFeatureI and leave it up to implementors whether they want their 
features to be FeatureHolders as well. SeqFeatureI::Generic 
obviously does support sub-features. Anyone wants to weigh in? Any 
dissenting votes?

	-hilmar

On Sunday, November 17, 2002, at 02:27 AM, Ewan Birney wrote:

> On Sat, 16 Nov 2002, Hilmar Lapp wrote:
>
>> I'd suggest adding this alongside AnnotatableI. The benefit is not
>> new functionality, but rather imposing a more rigorous and fostering
>> a more consistent API structure on those classes that have features.
>>
>> I have the module ready to commit, and I'd adjust Bio::Seq and
>> SeqFeature::Generic to implement this (clearly not very difficult).
>> What do people thing? Core guys? This should be very similar to the
>> biojava model, but I haven't checked that for a while.
>
> I like this. We are implicitly heading closer and closer to the OMG
> LSR/BioCorba as well. Probably a good sign.
>
>
>
>
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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