[Bioperl-l] Re: More unresolved issues with Bio::AnnotatableI
Aaron J. Mackey
amackey at pcbi.upenn.edu
Wed Jun 22 20:45:08 EDT 2005
I think Graph::Directed comes with Graph (since Graph is just a wrapper
for Graph::Directed and Graph::Undirected)
Allen Day wrote:
> 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
>>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?
More information about the Bioperl-l