[Bioperl-l] small question

Ewan Birney birney@ebi.ac.uk
Sun, 30 Jul 2000 17:21:36 +0100 (GMT)

On Sun, 30 Jul 2000, L.Pollak wrote:

> > However, the rest of the "annotation" part of Bio::Seq has been
> > implemented by the fact that Bio::Seq has-a Bio::Annotation, giving us
> > DBLink objects, References etc. This is a *good thing* as we want to reuse
> > these objects elsewhere (which we certainly do). Therefore
> > 
> >    $seq->annotation->description() should be the same as
> >    $seq->desc.
> > 
> > I suspect the solution to all of this is to make the $seq->desc function
> > in set mode to set both the Bio::Annotation->description *and* the
> > primary_seq description. On get mode it should go to Bio::PrimarySeq and
> > the SeqIO packages should automatically make sure that they read in the
> > description into both the annotation and primary_seq slots.
> I think, this would be good solution. I was thinking about
> $seq->annotation->description directly calling $seq->desc (like a
> mehtod synonym), but annotation objects don't always have an 
> underlying sequence object, right? so that won't work...

Yup. Annotation objects can't "know" about Sequence objects otherwise we
have screwed something up (along with nasty memory cycles as well. Lorenz
- you should make sure you understand about memory cycles).

I hope the fix goes cleanly.

> For now i will use $seq->desc.
> > This is pretty icky though.
> I'm not rather sure what "icky" means but i think i agree. :-)

Slang English (of sorts). icky means sort of sticky-and-nasty. It is a
rather childish word.

> kind regards,
> Lorenz

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420