[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

[Brian Osborne]

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.