[Bioperl-l] Changes to Bio::SeqI broke Bio::Graphics

[Lincoln Stein]

On Friday 08 November 2002 03:59 am, Ewan Birney wrote:
> On Thu, 7 Nov 2002, Lincoln Stein wrote:
> > Hi All,
> >
> > The recent removal of RangeI from Bio::SeqI caused all my
> > Bio::Graphics HOWTO examples to fail (about eight of them).  It also
> > broke some other scripts that I use routinely.  I was relying on the
> > object returned by Bio::SeqIO to implement start and end methods.
>
> Why? So that they looked like sequence features? I still think it is wrong
> to have Bio::SeqI inherieting from Bio::RangeI.

When rendering the features of a sequence, it looks nice to have a single 
feature that goes all the way across the whole sequence labeled with the 
display_id of the sequence.  When Bio::SeqI had start() and end() features, 
this was sufficient to pass the sequence object to the drawing code and get 
the desired effect.

Lincoln


>
> > I've fixed the HOWTOs, but the extent of the damage leads me to wonder
> > how many other people might have made the same mistake.  It occurs to
> > me that we may be breaking a *lot* of scripts out there.
>
> I wonder when we put it in. Hmmm. One to decide what to do with this for
> the 1.2 release...
>
> > Lincoln
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-- 
Lincoln Stein
lstein@cshl.org