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

[Allen Day]

On Wed, 2 Feb 2005, 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.

There was such a method, but I moved it to Bio/AnnotationI.  All the
*_tag_* methods now live there, and are inherited by Bio::SeqFeatureI,
with Bio::SeqFeature::* inheriting from that.

> 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-REGION-PROTEIN
> (beware, it is a slow computer and a slow connection)
> 
> Cheers,
> Marc
> 
> 
> 
> 
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