[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Chris Mungall]

Unflattener.t is failing because someone has messed up get_tagset_values()
- this is a convenience method I originally added to SeqFeatureI. I'm not
familiar enough with the new changes and AnnotationCollections to fix
this.

Surely the onus has always been on the person making changes to make sure
the test suite passes before committing their changes? In which case, how
did these changes make it in in the first place?

On Tue, 23 Nov 2004, Jason Stajich wrote:

>
> On Nov 23, 2004, at 4:47 PM, Allen Day wrote:
>
> > 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.
> >
> no it is Unflattner not Unflattner2
>
> % make test_Unflattener
> [SNIP OUT SOME STUFF]
>
> -------------------- WARNING ---------------------
> MSG: get_tagset_values() is deprecated.  use get_Annotations()
> ---------------------------------------------------
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Abstract method "Bio::AnnotationCollectionI::get_Annotations" is
> not implemented by package Bio::SeqFeature::Generic.
>
>
> > -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/
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
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> >>
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> >
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
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