postorder docs

[Yan Wong]

http://pythonhosted.org/DendroPy/library/treemodel.html#dendropy.datamodel.treemodel.Tree.postorder_node_iter says

postorder_node_iter(filter_fn=None)[source]

Post-order iterator over nodes of tree.

Visits nodes in self, with each node visited first followed by its children. 

Shouldn't that be "each node visited after its children"?

Yan

[Jeet Sukumaran]

Yes, it should. I will correct it. Thanks for pointing it out.

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[Yan Wong]

On thew subject of documentation, https://pythonhosted.org/DendroPy/library/treemodel.html?highlight=find_node#dendropy.datamodel.treemodel.Tree.find_node says "will return all nodes which have an attribute ‘genes’ and this value is not None.". But as I understand, this only returns the *first* node for which that is true (rather than all nodes), which is what the other parts of the documentation imply.

In fact, a function which returns (say) all nodes according to a filter would be helpful for me (I'm trying to match node labels against a regexp).

[Jeet Sukumaran]

You are right, this is another documentation issue that needs to be
corrected.

I think it would be reasonable to support a function along the lines
that you describe, called, e.g. "find_nodes()". Will add it to the
"TODO" pile as well. Thanks for the suggestion.

-- jeet

[Jeet Sukumaran]

If you need the below-described functionality immediately, something
like the following should work:

nodes = [nd for nd in tree if filter_fn(nd)]

or equivalently:

nodes = [nd for nd in tree.preorder_node_iter(filter_fn)]

Of course, if you do not need the entire collection of nodes, then
simply passing the filter function to the iterator works as well:

for nd in tree.preorder_node_iter(filter_fn):
... do stuff here ...

On 9/4/15 1:18 PM, Yan Wong wrote:

[Yan Wong]

On Saturday, 5 September 2015 02:51:40 UTC+1, Jeet Sukumaran wrote:

If you need the below-described functionality immediately, something
like the following should work:

Thanks. I actually meant to say "taxa" rather than "nodes", e.g. grep using a regexp throughout the taxon namespace. But your alternative will work find for normal trees.

Cheers

Yan