[Bioperl-l] TreeFunctionsI::findnode_by_id ?

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Aug 14 09:14:48 EDT 2008

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 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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