[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

[Chris Fields]

Hilmar Lapp wrote:
> 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.

Sorry Brian, what I meant was, based on CVS history, the various *tag*
methods in AnnotatableI were added all at once, with deprecations already
present in the commit.  So the methods weren't there to begin with, then
added only to be deprecated later?  Hence the confusion...

I think Hilmar's right; the CVS history indicates these were added just
prior to rel. 1.5 by Allen and seem to be related to SeqFeatureI.  I'm sure
the intent was good, but they contradict methods in the Feature/Annotation
HOWTO on retrieving Annotation objects via the Annotation::Collection
object.  I think that agrees with your point about the various Annotation*
method names being the more appropriate ones.  

Does everybody agree we should just remove them?

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