[Bioperl-l] treexml

Jason Stajich JASON_STAJICH at BERKELEY.EDU
Wed Jun 11 16:50:34 EDT 2008


Hey Mira -

Looks like things are going well. I just wanted to check and see if  
it is totally necessary to create new classes or if you can use the  
get/set tag/value pair interface that already exists?

These are the functions that are present in Bio::Tree::TreeI and  
Bio::Tree::NodeI :
  add_tag_value
  remove_tag
  get_all_tags
  get_tag_values
  has_tag

These are the same functions we use in SeqFeatureI interface as  
well.  It is just possible to re-use these rather than making a new  
function for every data type - this way we don't have to change the  
interface for different richness of data.

BTW (and this may be me who did it, but maybe Sendu remembers) - I am  
not sure why Bio::Tree::TreeI ISA Bio::Tree::NodeI.  Does anyone  
know? Trees are containers around a set of Nodes which are linked  
together to form a tree and the Tree object holds a pointer to the  
root node.

-jason
--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org



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