[Bioperl-l] Re: [BioSQL-l] seqfeature.display_id

[Heikki Lehvaslaiho]

I am always confused bby dispaly_id/dispaly_name, so I welcome anything
that could make the distinction clearer.

On Tue, 2002-10-01 at 18:11, Hilmar Lapp wrote:
> I agree with this. That's why I proposed to
> 
> 1) make the meaning absolutely clear and rename display_id to 
> display_name (but keep an undocumented alias)
> 
> 2) fix the implementation in SeqFeature::Generic to refer to its own 
> attribute instead of being an alias for seqname()

I wonder how many ids there are in seqfeatures?

I've used heavily seq_id(), which is defined in Bio::LocationI,
in Bio::Coodinate modules. 

Hilmar, before changeing anything, could you have look if there is some
overlap between Bio::LocationI and Bio::SeqFeatureI that could be pruned
out.


	-Heikki

> Can I take your responses as agreement with me making these changes?
> 
> Jason/Heikki, any comment or feeling on this?
> 
> 	-hilmar
> 
> On Tuesday, October 1, 2002, at 05:25 AM, Ewan Birney wrote:
> 
> > On Tue, 1 Oct 2002, Lincoln Stein wrote:
> >
> >> Was there any further discussion on this?  I do use display_id() 
> >> in the
> >> Bio::Graphics module, and am confused about the distinction between
> >> display_id() and seqname().
> >
> > IMNSHO
> >
> > display_id() == thing to be displayed for this object to a user
> >
> > seqname() == name of sequence attached - possibly better called 
> > seq_id or
> > seq_accession_number() or something more obviously "real id like".
> >
> >
> >
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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