[Bioperl-l] Performance of Bio::Species

Chris Fields cjfields at uiuc.edu
Sat Nov 25 08:32:43 EST 2006


On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote:
...

> I think the Tree actually only keeps a ref to its root Node, which  
> means
> Nodes in general must keep hard refs to their Descendants. With that
> constraint, I haven't been able to break the deadlock and get these
> things to clean up.
>
> Hopefully I'm missing something obvious; please look into it.

I'm curious to see if this affects sequence parsing (i.e. SwissProt  
DB parsing).  Does anyone know?  It sounds pretty serious.

Sendu, could you commit a bug report for this?  I don't think this  
should hold up rel 1.5.2 (it's a dev release) but it would be nice to  
get it fixed.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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