[Bioperl-l] deprecated modules

[Hilmar Lapp]

Then please don't remove those modules yet ... I wonder how people would 
derive meaningful %id and % matched without HSP tiling ... basically, 
you'd need to iterate over all HSPs and do it yourself. I doubt many 
people go through this, but maybe I'm missing something.

SteveC, any chance you port your HSP tiling code over to SearchIO?

	-hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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On Wed, 14 Aug 2002, Jason Stajich wrote:

> 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
> > >
> > >
> > > _______________________________________________
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> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> 
>