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

[Lincoln Stein]

Attributes indeed comes in via the Bio::Das interface. The concept is 
so similar to get_tag_values() that I think we can unify them via a 
bit of API glue in Bio::SeqFeatureI.

Does anyone object if I go ahead and do that?

Lincoln

On Wednesday 02 February 2005 01:16 pm, Jason Stajich wrote:
> 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
> problems.
>
> 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
>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
> 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- REGION-PROTEIN
> > (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

-- 
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
all emails regarding scheduling and other time-critical topics.
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