[Bioperl-l] TreeFunctionsI::findnode_by_id ?
heikki at sanbi.ac.za
Sun Aug 17 03:02:31 EDT 2008
findnode_by_id() was not and is not used anywhere in BioPerl core code.
Thanks for input,
On Saturday 16 August 2008 01:00:04 Jason Stajich wrote:
> I think D.
> There should probably only be one find_node function.
> findnode_by_id was written by Ramiro for the re-rooting code and I
> guess it wasn't checked to reduce unneeded functions. I don't have
> any problems removing/deprecating it but will need to update the code
> that depends on it to use find_node properly.
> On Aug 14, 2008, at 6:14 AM, Heikki Lehvaslaiho wrote:
> > A generic method for retrieving nodes from a Bio::Tree::TreeI
> > objects is
> > Bio::Tree::TreeFunctionsI::find_node. It defaults to searching the
> > 'id'
> > attribute unless a field is given. I can retrieve nodes based on
> > internal id
> > like this:
> > $tree->find_node(-internal_id => $internal_id);
> > I now found Bio::Tree::TreeFunctionsI::findnode_by_id() that
> > retrieves by id.
> > However, the POD documentation claims that it retrieves by internal
> > id.
> > What needs to be done?
> > A. Fix the doc to speak about id
> > B. Fix to code to retrieve by internal_id
> > C. Fix the doc and create findnode_by_internal_id()
> > C. Remove findnode_by_id() as redundant and confusing
> > D. Deprecate findnode_by_id() as redundant and confusing
> > There are no tests for findnode_by_id() which to me tilts selection
> > to D and A
> > for now.
> > Any other opinions?
> > -Heikki
> > --
> > ______ _/ _/_____________________________________________________
> > _/ _/
> > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
> > _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
> > _/ _/ _/ SANBI, South African National Bioinformatics Institute
> > _/ _/ _/ University of Western Cape, South Africa
> > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> Jason Stajich
> jason at bioperl.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
______ _/ _/_____________________________________________________
_/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za
_/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of Western Cape, South Africa
_/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
More information about the Bioperl-l