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

[Lincoln Stein]

Hi Marc,

Can you take the responsibility for keeping the "horrible hack" 
section of the bugfixes branch up to date in CVS?  I don't want to 
start colliding with you.

Lincoln

On Wednesday 02 February 2005 09:54 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-REGION
>-PROTEIN (beware, it is a slow computer and a slow connection)
>
> Cheers,
> Marc
>
>
>
>
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
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