[Bioperl-l] GFF and LocatableSeq refactoring

[Mark A. Jensen]

Yes, I'd say the Nexml support exceeds the 'complicated' test.
There are no modifications to existing modules (except for
the addition of annotation attributes to members of the
Bio::PopGen model, which are don't-cares to anything out
there currently). The manifest of a NeXML drop-in would look like

Bio/NexmlIO.pm
Bio/Nexml/Factory.pm
Bio/SeqIO/nexml.pm
Bio/AlignIO/nexml.pm
Bio/TreeIO/nexml.pm

and, if I get it completed, support for arbitrary characters
via Bio::PopGen

Bio/PopGen/IO/nexml.pm

(all based on hacks of Chase's code, btw; we thought
 it would round out the package nicely...)

Of course, the big dependency that not everyone will need or
want is Rutger's Bio::Phylo, so the Nexml support will have
to be optional even in 1.7, I think. I am adding run-time checks
for Bio::Phylo in the modules so they die relatively gracefully and
informatively, rather than just barf. Also, the tests will have
appropriate skip blocks.

I do want to get the code into bioperl-live, however, unless
there's a gotcha there I'm not seeing--

cheers 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 4:09 PM
Subject: Re: [Bioperl-l] GFF and LocatableSeq refactoring


>
> On Aug 14, 2009, at 7:45 PM, Mark A. Jensen wrote:
>
>> I'm planning to move Chase Miller's excellent NeXML read/write 
>> implementation into the trunk, complete with tests. If we can get it  to pass 
>> the test suite, is there room in the point release for it?
>
>
> We've in the past stayed away from adding new features to stable  branches 
> with the exception of new methods in existing classes and  that didn't do 
> anything complicated.
>
> I'm not sure I remember everything but I think the NeXML support does  exceed 
> that level, doesn't it? Can it be rolled into its own pre- release that is a 
> drop-in to an existing 1.6.x installation for those  who want to go there?
>
> -hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>