[Bioperl-l] Interest in Bio::Community modules

Fields, Christopher J cjfields at illinois.edu
Tue Nov 29 14:11:11 EST 2011

On Nov 28, 2011, at 6:59 PM, Florent Angly wrote:

> Hi Chris,
> On 29/11/11 05:47, Fields, Christopher J wrote:
> ...
>> Re: using Moose and BioPerl, from experience it's a little tricky integrating the two as BioPerl uses perl's simple OO system while Moose allows much more (though it has it's own issues, memory and speed being the top two).  Specifying inheritance from a BioPerl module is a bit trickier, you'll have to wrap the module via MooseX::NonMoose.  Beyond that, I think if you stick with using is-a/has-a based relations for the time being when defining interactions with other BioPerl modules you'll be fine.
> Beyond Bio::RootI, I cannot imagine that any of the Bio::Community::* modules would need to inherit from any other BioPerl modules. Considering this and the performance aspects of Moose, do you think that using Moose is a wise design decision?

Moose can actually help in some circumstances; flattening the inheritance hierarchy by using roles seems to help.  And it never hurts to learn something new like Moose and other modern perl niceties.

> Best,
> Florent


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