[Bioperl-l] AnnotatableI tag methods, was Rfam/Pfam annotations and SimpleAlign

Chris Fields cjfields at uiuc.edu
Tue Oct 31 22:41:17 UTC 2006

> On Oct 31, 2006, at 1:44 PM, Chris Fields wrote:
> > Does everybody agree we should just remove them?
> I wish you could but I'm afraid that would break stuff? 
> Otherwise why were they added in the first place? I thought 
> Bio::SeqFeature::Annotated needs them maybe?
> 	-hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

Yep, removing them clobbers a ton of tests, including anything that requires
SeqIO::FTHelper.  Looks like SeqFeature::Generic and a few others use them.

I could understand if these were meant to be permanent methods, but why add
these in if they were to be deprecated in 1.6?  Something that was meant to
be a transition but wasn't finished?  That seems to be indicated in the
commented out lines for all the *tag* methods:

  #uncomment in 1.6
  #$self->deprecated('remove_tag() is deprecated, use

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


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