[Bioperl-l] treexml

Chris Fields cjfields at uiuc.edu
Thu Jun 12 08:21:31 EDT 2008


Looks like it has been there for a while:

http://code.open-bio.org/svnweb/index.cgi/bioperl/diff/bioperl-live/trunk/Bio/Tree/TreeI.pm?rev1=2900;rev2=2901

Jason was the committer, back in 2001.  Maybe (as Sendu indicates) it  
should be changed to RootI.

chris

On Jun 12, 2008, at 4:54 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Jun 11, 2008, at 3:50 PM, Jason Stajich wrote:
>>> 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?
>
> I don't think it was me. It's worth noting that if you change TreeI  
> to inherit from RootI instead of NodeI, it doesn't seem to cause any  
> problems in the obviously related test scripts.
>
> Maybe it's there as a convenience thing? I don't know.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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