[Bioperl-l] All done with Bio::DB::Query

[Lincoln Stein]

get_stream_by_batch does use the new code; the method still works and is 
documented, but is marked as deprecated.  get_Stream_by_batch() was 
originally an optimized form of get_Stream_by_id().  Now that it doesn't 
contribute any performance improvement, I think we should deprecate it.

Sorry about the module name clash.  Perhaps we should rename as 
Bio::DB::SimpleQuery?

Lincoln

On Sunday 24 November 2002 04:46 pm, Hilmar Lapp wrote:
> Cool Lincoln.
>
> Can't get_stream_by_batch rewritten to use the new code? Sorry if
> the answer is obvious.
>
> I should have said that Bio::DB::Query is the namespace that I also
> use in bioperl-db for object-relational query modules. There's no
> clash yet of module names, and the chance for one is probably fairly
> low; I just thought I mention this here. If you or anyone else feels
> we need to better protect from possible future clashes, we need to
> rename either in bioperl-live or bioperl-db.
>
> 	-hilmar
>
> On Friday, November 22, 2002, at 08:24 AM, Lincoln Stein wrote:
> > Hi,
> >
> > I'm all done with the following modules:
> >
> > 	Bio::DB::QueryI
> > 	Bio::DB::Query::WebDBQuery  # web utilities
> > 	Bio::DB::Query::GenBank   # the only "real" one
> >
> > I have tested on a variety of Unix systems, but I need a Windows
> > tester.  I
> > used fork() in a couple of places in order to make SeqIO streaming
> > pipelineable (otherwise it has to download the whole set of records
> > before it
> > can start processing the first one).  The code should detect that
> > it is not
> > on a platform that supports fork-and-pipe and automatically fall
> > back to the
> > old way of doing things, but I'm not 100% certain it will work as
> > advertised.
> >
> > I've also done a touch up here and there on the Bio::DB:: modules,
> > mostly to
> > deprecate Aaron Mackey's get_Stream_by_batch() methods, which are
> > superseded
> > by the eutils interface.
> >
> > Let us all be glad that NCBI has committed to maintain eutils as
> > its official
> > interface.
> >
> > Lincoln
> >
> > --
> > Lincoln Stein
> > lstein@cshl.org
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.org