[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Jason Stajich]

I think if we just don't issue deprecation warnings it will be fine by 
me -- even if we are just calling the new subroutine under the hood.  
Tests seem to pass although Unflattner.t is falling over today not sure 
what is problem.

-jason
On Nov 23, 2004, at 2:28 PM, Aaron J. Mackey wrote:

>
>> On Friday, November 19, 2004, at 02:50  PM, Allen Day wrote:
>>
>>> * Bio::SeqFeatureI now ISA Bio::AnnotationCollectionI
>>> * All Bio::SeqFeatureI *_tag_* methods have been moved to
>>>   Bio::AnnotationCollectionI, marked as deprecated, and mapped to 
>>> their
>>>   analogous and mostly pre-existing Bio::AnnotationCollectionI 
>>> methods.
>>>
>>>   Methods which were not in Bio::AnnotationCollectionI, but were i
>>>   Bio::Annotation::Collection and were necessary for *_tag_* method
>>>   remapping were created in Bio::AnnotationCollecitonI.
>
> I've been paying some attention to this, but thought that the changes 
> were only those required to get Bio::FeatureIO working (i.e. 
> recapitulate GFF3 logic) without hampering object usage; do our tests 
> pass with these changes in place?
>
> On Nov 23, 2004, at 2:12 PM, Jason Stajich wrote:
>
>> it has not been tagged yet.  I think Aaron is just really busy on 
>> this front.
>
> I did tag the HEAD at RC1, so we could branch from there if we needed 
> to; if this is really the big bug-bear that Hilmar and Jason are 
> claiming, then I'd ask Allen to retract his patches that alter 
> interface definitions, and branch.
>
> And I was so hoping to get RC2 packaged up later today ...
>
> -Aaron
>
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/