[Bioperl-l] Unigene proposal and basic implementation

[Lincoln Stein]

Personally I don't mind creating two new top level directories for each new 
class, but whatever the convention is, it should be consistent across the 
entire project.

Here's another style to discuss:

	Bio::Seq
		::IO
		::IO/Interface.pm
		::IO/embl.pm
		::Interface.pm
	Bio::Seq::RichSeq.pm

That is, instead of having a Bio::SeqI and a Bio::SeqIO, we have a 
Bio::Seq::Interface and a Bio::Seq::IO::Interface

Yes, this will break everything, but we can create faux packages to smooth 
over the differences.

Lincoln

On Tuesday 16 April 2002 08:18, Jason Stajich wrote:
> On Tue, 16 Apr 2002, Kris Boulez wrote:
> > We have
> >
> > Bio::AlignIO
> >      AnnSeqIO
> >      MapIO
> >      SearchIO
> >      SeqIO
> >      TreeIO
> >
> > but also
> >
> > Bio::LiveSeq::IO
> >      Variation::IO
> >      Structure::IO
> >      Biblio::IO
> >
> >
> > What do people think about Bio::IO ?
>
> No - this AlignIO -> LiveSeq::IO transition was designed so we
> don't create 2 top level directories for each new for data system.  But
> it is not part of the unwritten bioperl best practices document.  I'm
> pretty much okay with mixing the two for now but I definitely agree that
> it would be better to use a single paradigm when naming.
>
> I don't think Bio::IO would be a good way to group though, I really prefer
> that the parser stay closer to the data objects wrt to namespace.
>
> Just my opinion though...  Counter arguments welcomed.
>
> -j
>
> > Kris,
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l