[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
allenday at ucla.edu
Tue Nov 23 16:47:26 EST 2004
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.
> 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
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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