[Bioperl-l] GFF and LocatableSeq refactoring

[Chris Fields]

Mark,

re: NeXML, yes, of course.  There'll be an alpha release or two prior  
to core 1.6.1 (I need to test the Build.PL/Bio::Root::Build changes  
Sendu added in).

chris

On Aug 14, 2009, at 6:45 PM, Mark A. Jensen wrote:

> Hey Chris et al, I'm there on LocatableSeq, definitely. I do have  
> one project to finish this weekend before I move to that: 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?
> MAJ
> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
> >
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Friday, August 14, 2009 7:29 PM
> Subject: [Bioperl-l] GFF and LocatableSeq refactoring
>
>
>> As we have pretty much everything in place for another point  
>> release  (which I will start merging over this weekend into the 1.6  
>> branch), I  have gone ahead and made two branches for refactoring  
>> some of the more  important pieces of bioperl code.  Both refactors  
>> may require API  changes; if so these will be part of a 1.7 release.
>> 1) GFF - entail refactoring bioperl code to better handle GFF2/3.
>> This is a large section of code, so small incremental changes may  
>> be  merged to trunk over time (and thus may involve several  
>> branches).   Included is refactoring of feature typing to be more  
>> consistent and  lightweight, and will initially involve  
>> Bio::FeatureIO and  Bio::SeqFeature::Annotated (which may be  
>> deprecated in the process).   See the following for additional  
>> details:
>> http://www.bioperl.org/wiki/GFF_Refactor
>> 2) Align/LocatableSeq - dealing with inconsistencies in  
>> Bio::AlignI  (SimpleAlign) and LocatableSeq.  This is primarily to  
>> address  significant bugs but will also entail cleaning up  
>> SimpleAlign methods  (factoring out more utility-like methods into  
>> Bio::Align::AlignUtils  or similar).  This also may involve several  
>> branches.  See the  following for additional details:
>> http://www.bioperl.org/wiki/Align_Refactor
>> Any help/suggestions for the above two would be greatly  
>> appreciated!   Robert Buels may be heading up the initial FeatureIO  
>> work; I will  likely start on LocatableSeq/Align (Mark, wanna help?).
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>