[Bioperl-l] deprecated modules

[Jason Stajich]

Not yet - it needs to be done.

On Wed, 14 Aug 2002, Hilmar Lapp wrote:

> I haven't followed too closely the SearchIO::Blast implementation,
> hence my question: Does that re-implement HSP tiling? (The
> Tools::Blast code does, and I found it to be an essential feature for
> certain purposes)
>
> 	-hilmar
>
> > -----Original Message-----
> > From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> > Sent: Wednesday, August 14, 2002 11:22 AM
> > To: Bioperl
> > Subject: [Bioperl-l] deprecated modules
> >
> >
> > Bio::Tools::Blast has been deprecated for a while - I'd like
> > to remove it
> > from the trunk.  Additionally I'd like to remove Bio::UnivAln
> > as it too
> > has been deprecated.  Steve and I have agreed that
> > Bio::SearchIO::psiblast, Bio::Search::HSP::BlastHSP
> > Bio::Search::Hit::BlastHit, and
> > Bio::Search::Result::BlastResult will be
> > deprecated in 1.2 assuming we get all the functionality moved
> > over to the
> > SearchIO::blast and XX::GenericXX objects.
> >
> > I can create a DEPRECATED file to list module history like this:
> >
> > # These are modules which are deprecated and later removed from the
> > toolkit
> >
> > Deprecated Modules     Version Deprecated   Version Removed
> > --------------------------------------------------------------
> > Bio::Tools::Blast            1.0	          1.1
> > Bio::Tools::Blast::HSP       1.0		  1.1
> > Bio::Tools::Blast::HTML      1.0		  1.1
> > Bio::Tools::Blast::Sbjct     1.0		  1.1
> >
> > Bio::Tools::WWW		     1.1
> >
> > Bio::UnivAln		     1.0		  1.1
> >
> >
> > My feeling is that BPlite currently still serves a purpose
> > and should stay
> > on the trunk, but it might need some maintence/testing at some point.
> >
> > Shout if you don't want to see this happen.
> >
> > -jason
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu