[Bioperl-l] RE: [Gmod-gbrowse] features not displaying
allenday at ucla.edu
Wed Feb 2 14:22:33 EST 2005
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;
> *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
> (beware, it is a slow computer and a slow connection)
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