[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Jason Stajich jason.stajich at duke.edu
Tue Nov 23 15:11:11 EST 2004

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.

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

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