[Bioperl-l] TreeFunctionsI::findnode_by_id ?

Heikki Lehvaslaiho heikki at sanbi.ac.za
Sun Aug 17 03:02:31 EDT 2008


Done.

findnode_by_id() was not and is not used anywhere in BioPerl core code.

Thanks for input,

   -Heikki

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.
>
> -jason
>
> 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
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>
> Jason Stajich
> jason at bioperl.org
>
>
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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
___ _/_/_/_/_/________________________________________________________


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