[Bioperl-l] RE: [Gmod-gbrowse] features not displaying

Jason Stajich jason.stajich at duke.edu
Wed Feb 2 13:16:07 EST 2005

I think we really need to unify the attributes / get_tag_values,  
name/seq_id/display_name Bio::SeqFeatureI,Bio::AnnotableI,  
Bio::Das::SegmentI functions.  This seems to be the crux of the  

If we can document what is expected can we not update the interfaces  
and push the method aliases down to the primary objects.  I don't know  
that we ever expected Bio::SeqFeature::Generic objects to have the  
'attributes' method - is this a Das/Bioperl method naming conflict?


Jason Stajich
jason.stajich at duke.edu

On Feb 2, 2005, at 9:54 AM, Marc Logghe wrote:

>> 3) Bio::SeqFeature::Generic::get_tag_values does not exist
>> anymore: Bio::SeqFeature::Geneneric does not inherit from
>> Bio::AnnotatableI which implements that method, which is bad
>> (can it pass the tests, then ?). I don't know what the
>> situation is in bioperl-live HEAD.
> Correction: get_tag_values is inherited from Bio::AnnotatableI via  
> Bio::SeqFeatureI.
> So, this error could be fixed by changing (in the 'horrible patch  
> section' of package Bio::DB::Das::BioSQL bugfix-release)
> *Bio::SeqFeature::Generic::attributes =  
> \&Bio::SeqFeature::Generic::get_tag_values;
> to:
> *Bio::SeqFeature::Generic::attributes =  
> \&Bio::AnnotatableI::get_tag_values;
> Making it even more horrible ;-)
> But it works.
> It seems that in older bioperl-live releases there actually *was* a  
> Bio::SeqFeature::Generic::get_tag_values sub making the original hack  
> work. In release 1.5.0 this sub was gone, breaking the hack.
> Now, I'll try to tackle the double features problem. Status can be  
> followed at
> http://biologghe.homelinux.org:4380/cgi-bin/gbrowse/biosql? 
> name=NP_491141%3A1..629;source=biosql;width=800;version=100;label=CDS- 
> (beware, it is a slow computer and a slow connection)
> Cheers,
> Marc
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
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