[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

Hilmar Lapp hlapp at gmx.net
Tue Oct 31 12:44:58 EST 2006


Well isn't this a result of conflating some of the SeqFeatureI  
methods into the annotation collection?

If I'm not mistaken on this then those methods were introduced in  
1.5.0 and hence can go away without deprecation.

	-hilmar

On Oct 31, 2006, at 11:37 AM, Brian Osborne wrote:

> Chris,
>
> I don't think the intent was to remove the methods, rather we'd  
> just call
> deprecated(). Example from AnnotatableI:
>
> sub remove_tag {
>   my ($self, at args) = @_;
>
>   #uncomment in 1.6
>   #$self->deprecated('remove_tag() is deprecated, use
> remove_Annotations()');
>
>   return $self->annotation->remove_Annotations(@args);
> }
>
> With regards to "why", I can't reconstruct the entire rationale  
> myself but I
> can say that the newer names make more sense. Take that example  
> above - it's
> function is to remove entire Annotations not just to remove tags, so
> remove_Annotations is a better name.
>
> Brian O.
>
>
> On 10/31/06 1:08 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
>
>> A bit OT: were we planning on getting rid of the various *_tag_*  
>> methods in
>> AnnotatableI at some point?  I'm a bit confused as to why they  
>> were added.
>
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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