[Bioperl-l] GFF and LocatableSeq refactoring

Mark A. Jensen maj at fortinbras.us
Sat Aug 15 20:36:47 UTC 2009


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 :
> ===========================================================
>
>
>
>
> 




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