[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Allen Day]

On Tue, 23 Nov 2004, Jason Stajich wrote:

> 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.

that fails for me too, in addition to spewing out lots of diagnotistics.  
however, if you run 'make test_Unflattener2', it passes.  strange.

-allen

> 
> -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/
> 
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