[Bioperl-l] new GFF3 support methods added

Chris Mungall cjm at fruitfly.org
Tue Mar 9 20:54:30 EST 2004

On Mon, 8 Mar 2004, Hilmar Lapp wrote:

> On Monday, March 8, 2004, at 01:07  PM, Chris Mungall wrote:
> > Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler
> > class? This would contain methods
> >
> >   generate_unique_persistent_id($feat) # uses $feat->seq_id
> >   generate_unique_persistent_id($feat, $seq_id)
> >
> >   create_hierarchy_from_ParentIDs($featholder);
> >   set_ParentIDs_from_hierarchy($featholder);
> >
> > Any preference? I'm leaving them as is for now if that's ok, but I
> > have no
> > objections to moving everything to a seperate class if that's prefered.
> >
> I like your suggestion. Keeps FeatureHolderI lighter, and is easier to
> change behaviour. But maybe it's just me who likes this better.

Ok, I'll go ahead and add this

We will now have 3 classes in Bio::SeqFeature::Tools


Personally I like this pattern, whereby the object model is kept simple
and lightweight, and complex behaviour is punted to seperate classes. It
does force the question - how do we decide which methods goes in the model
class and which goes in a behaviour class? Is it just an intuitive thing?
I'm happy for the bioperl czar to weigh in (who is that these days?) and
make individual judgement calls, I just want what I'm doing to be
consistent with some overall plan.


> 	-hilmar

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