[Bioperl-l] Re: More unresolved issues with Bio::AnnotatableI
allenday at ucla.edu
Wed Jun 22 20:43:44 EDT 2005
Where is the dependency on Graph::Directed introduced? A grep through
Bio/* in bioperl-live on HEAD reveals several references in the POD to
Graph.pm, but I don't see it anywhere in the code.
I don't know if Chris Mungall's GO-Perl API removes the dependency on
Graph::Directed, but it is certainly easier to use than Bio::OntologyIO as
a means to access the OBO ontologies. I'm willing to look into converting
Bio::Annotation::OntologyTerm to use GO::Model::* instead of
Bio::Ontology::Term, but it may interfere with other projects using the
class (e.g. bioperl-db).
Hilmar, I know you were looking at the GO-Perl codebase recently, can you
comment on any of the above?
On Wed, 22 Jun 2005, Aaron J. Mackey wrote:
> Because AnnotatableI has implementations for add_tag and get_tag that
> invoke Bio::Annotation::OntologyTerm, and therefore Graph::Directed,
> which relies on Scalar::Util::weaken(), therefore I cannot even use
> basic Bio::Seq functionality on any perl that doesn't have weak
> references (oddly, this cropped up in a 5.8.0 install via an RPM that
> was evidently compiled without support for weak references, so this
> isn't just an "ancient perl" problem).
> This is something of a showstopper for any 1.6; in effect, we'd need
> to disable Annotation::OntologyTerm use for any Perl without weak
> reference support.
> We've said it before, and we need to say it again: the changes made
> to the feature/annotation object model are seriously impeding our
> ability to move forward to a release (and frighteningly, the GBrowse
> distribution now includes those parts of 1.5 that it relies on, so a
> user's BioPerl install could be a hodge-podge of 1.4/1.5 code). This
> seems important to all GMOD projects, so why hasn't there been any
> work on it?
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