[Bioperl-l] Auto-method caller proposal

Sendu Bala bix at sendu.me.uk
Tue Jan 9 16:50:52 UTC 2007

Nathan (Nat) Goodman wrote:
>> Sendu Bala wrote:
>> As a generally useful thing I'd like to see all Bioperl modules have
>> easy access to this functionality, just as they can currently call
>> _rearrange(). So yes, we would impose AutoClass on everyone. This may
>> not be a major burden since it is already an optional
>> pre-requisite. So, before I investigate using Class::AutoClass instead
>> of my own proposed method, does anyone feel there are good benefits of
>> Class::AutoClass over my proposed method (considering I already added
>> a -synonym option to it), and do those benefits outweigh having
>> Class::AutoClass as a Bioperl installation requirement?
> Just to be clear.  Based on my understanding of your requirements, I appears
> you don't really want the full-blown auto-generation and auto-initialization
> capabilities of AutoClass.  My suggestion is that you look at the code in
> AutoClass and its companion Args handler, and extract any pieces that are
> relevant to what you're trying to do.  I'd be happy to help with this. 

As far as I know, my proposed method already does everything I want it 
to do, so there wouldn't be any need to 'extract any pieces' from 

> If I've mis-understood your requirements and you do want the full AutoClass
> capabilities, I'd be happy to assist with adapting it to fit the BioPerl
> framework. 
> A lot depends on whether you need the initialization to include things like
> default values and to work correctly in the presence of inheritance.  These
> requirements really complicate the picture.

...So yes, if AutoClass were to be used it would be to take advantage of 
the whole thing. My current question is simply, "does AutoClass offer 
things we want and 'should' take advantage of, that my proposed method 
does not offer"?

My preference at the moment is to use my proposed method, if only 
because I'm lazy. I want someone to tell me there is significant value 
in using AutoClass before I spend time on it. Alternatively Nat, if you 
could provide AutoClass-using code that does what my method does but in 
a better way or with more features, in a form that I can commit to the 
Bioperl repository and immediately start taking advantage of in new 
Bioperl modules, please do so.

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