[Bioperl-l] GFF and LocatableSeq refactoring

[Mark A. Jensen]

I'm all for an attempt to split out phylogenetic stuff, it
seems natural, and think in terms of a phylo package
dependent upon a sequence package, and if necessary
vice versa -- although if the Bio::Species - Bio::Tree::Node
connection is relatively loose, perhaps we can refactor to
make some attributes/methods optional features that carp
when the phylo package is not installed. (Roles, anyone?)

However, probably 1.6.x doesn't sound like the place to
do that! I myself wouldn't have any problem waiting till
1.7 for 'official' Nexml support--but I hope Chase will chime
in on that. What does Chris think?
MAJ
----- Original Message ----- 
From: "Hilmar Lapp" <hlapp at gmx.net>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "Chris Fields" <cjfields at illinois.edu>; "BioPerl List" 
<bioperl-l at lists.open-bio.org>
Sent: Saturday, August 15, 2009 4:49 PM
Subject: Re: [Bioperl-l] GFF and LocatableSeq refactoring


>
> On Aug 15, 2009, at 4:36 PM, Mark A. Jensen wrote:
>
>> I do want to get the code into bioperl-live, however, unless there's  a 
>> gotcha there I'm not seeing--
>
>
> That sounds great to me, though it may make some of Chris' hair stand  on end 
> if he wants this to go into a separate module from the start :)  Maybe a 
> phylogenetics module can be carved out that this would become  part of? Though 
> I recall someone saying recently that Bio::Species and  by extension 
> Bio::SeqIO is dependent on Bio::Tree::Node, so maybe  that's not realistic to 
> split out.
>
> -hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
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