[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Allen Day]

Fixed.  Here is a summary of what I did to make this happen.  I went ahead 
and did the work necessary to make Bio::SeqFeatureI AnnotatableI instead 
of being itself an AnnotationCollectionI.

. Bio::SeqFeatureI inherits Bio::AnnotatableI NOT 
  Bio::AnnotationCollectionI
. *_tag_* methods are in Bio::AnnotatableI, and internally defer to
  Bio::AnnotatableI->annotation->some_analagous_mapped_function()
  . method behavior is now more similar to original *_tag_* method
    behavior ; tag "values" are now instantiated as 
    Bio::Annotation::SimpleValue objects by default, unless their name
    indicates they should be otherwise (e.g. tag name "comment" or 
    "dblink")
. deprecation warnings commented until 1.6
. Bio::AnnotatableI now keeps a tag->annotation_type registry to allow
  new tags to be created (see Bio::SeqFeature::AnnotationAdaptor).
  . Bio::SeqFeature::AnnotationAdaptor is now not very useful, as *_tag_*
    methods map directly onto Bio::AnnotationI's 
    Bio::AnnotationCollectionI instance.
. Unflattener and Unflattener2 tests pass with no changes.
. All tests pass.

-Allen


On Tue, 23 Nov 2004, Chris Mungall wrote:

> 
> 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
> > >> Bioperl-l at portal.open-bio.org
> > >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >>
> > > _______________________________________________
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> > >
> > >
> > --
> > Jason Stajich
> > jason.stajich at duke.edu
> > http://www.duke.edu/~jes12/
> >
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> >
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