[Bioperl-l] treexml

Chris Fields cjfields at uiuc.edu
Wed Jun 11 17:01:10 EDT 2008


On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:

> 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.

I agree; it simplifies the interface, even if it sacrifices small  
conveniences.

> 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.

Not sure myself; maybe this was part of Sendu's Taxonomy overhaul a  
while back?

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

-c

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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