[Bioperl-l] GFF and LocatableSeq refactoring

[Hilmar Lapp]

Great! Two suggestions:

> • deprecate the get_Annotations(Str) method in favor of  
> get_annotation(Str), which adheres better to standard perl method  
> naming

Yes, but also is then inconsistent with existing BioPerl naming, with  
the method name indicating what type of object you get back  
(Bio::AnnotationI in this case; see also e.g., get_SeqFeatures() in  
Bio::SeqI).

> • finally, split Bio::FeatureIO modules off into their own CPAN  
> distribution

Wouldn't one start with this?

	-hilmar

On Aug 14, 2009, at 7:50 PM, Robert Buels wrote:

> Chris Fields wrote:
>> 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?).
>
> Sure, I'll head up the gff_refactor branch work.  If you're  
> interested in what changes are being planned for Bio::SeqFeature::*,  
> Bio::Annotat*, and/or Bio::FeatureIO*, have a look at the  
> implementation plan Chris and I developed just now on IRC, which is at
>
> http://www.bioperl.org/wiki/GFF_Refactor#Implementation_Plan
>
> Now soliciting suggestions, comments, and assistance.
>
> Rob
>
>
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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