prune_taxa possible enhancement

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Yan Wong

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Sep 5, 2015, 6:45:47 AM9/5/15

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Just looking at the prune_taxa code, as I'm pruning nodes from the OpenTree (>2.5 million nodes). I wonder if wrapping 'taxa' in a set would provide a useful performance enhancement in

http://pythonhosted.org/DendroPy/_modules/dendropy/datamodel/treemodel.html#Tree.prune_taxa

Or indeed any cases where there is a loop within which list membership is tested. I'm afraid that I haven't done any performance tests, though (sorry), and it may only help in the large tree use case.

(I also see there seems to be an unused "nodes_to_remove" variable in that function).