[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Chris Mungall cjm at fruitfly.org
Mon Nov 29 16:22:56 EST 2004


On Fri, 26 Nov 2004, Hilmar Lapp wrote:

[snip]

> Beyond this, I do agree with Chris that there could be a performance
> issue with richly annotated databanks. Tag values were simple strings;
> using objects for all of them instead at feature creation and
> population time may be too heavy. Also Chris, I thought the XML idea
> sounded very interesting; did you have Data::Stag in mind to manage it?

Not necessarily - though it may borrow some ideas from Data::Stag - the
interface would have to be more bioperl-y

(The current Data::Stag implementation trades speed for convenience,
though later versions may be made more efficient)

> It would still require a working XML parser installation, no?

yes - it would require some kind of third-party XML module or modules. I
guess this may be slightly problemmatic as these are currently all
optional for bioperl, yep?

> 	-hilmar
>
> On Wednesday, November 24, 2004, at 05:58  AM, Aaron J. Mackey wrote:
>
> >
> > Allen, thanks a ton for going the extra mile.  Hilmar, does this
> > solution satisfy your worries a bit?
> >
> > Thanks again to everyone,
> >
> > -Aaron
> >
> > On Nov 23, 2004, at 9:16 PM, Allen Day wrote:
> >
> >> 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
> >>>>>>
> >>>>> _______________________________________________
> >>>>> Bioperl-l mailing list
> >>>>> Bioperl-l at portal.open-bio.org
> >>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>
> >>>>>
> >>>> --
> >>>> 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
> >>>>
> >>>
> >>
> >>
> > --
> > 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>


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