[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:

> Hi,
> 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?
> -Allen
> 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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