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Unexpected warning when parsing tree with internal node labels #88

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jcoliver opened this issue Aug 6, 2019 · 0 comments
Open

Unexpected warning when parsing tree with internal node labels #88

jcoliver opened this issue Aug 6, 2019 · 0 comments

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@jcoliver
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jcoliver commented Aug 6, 2019

When reading a tree in with node support values at branch labels, this message is sometimes printed to the log:

Observed taxon 2 in ancestral position; not yet allowed by Mesquite.  Tree will not be read in properly

This occurs before the prompt for node label interpretation. This only occurs when node labels correspond to a taxon number. That is, iff a node label is a positive integer less than the total number of taxa in the linked TAXA block, this message will be shown. Node labels that are not integers defined by the set of taxon numbers (i.e. it is higher than the number of taxa or a double) do not provoke this warning.

While the warning appears, it doesn't look like there is any actual problem when reading in the tree. Node labels are treated appropriately, regardless of how the user chooses to interpret them. The code providing this warning is around line 2831 in MesquiteTree.readNamedInternal(). I think it might just be a matter of removing the conditional and warning message? An example nexus below should provoke the message when reading in tree_1, but not tree_2:

#NEXUS

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=3;
	TAXLABELS
		taxon_A taxon_B taxon_C
	;
END;

BEGIN TREES;
	Title 'Tiny trees';
	LINK Taxa = Taxa;
	TREE tree_1 = ((taxon_A:0.5, taxon_B:0.5)2:0.5, taxon_C:1.0);
	TREE tree_2 = ((taxon_A:0.5, taxon_B:0.5)5:0.5, taxon_C:1.0);
END;

This occurs with Mesquite v3.6b917

@jcoliver jcoliver changed the title Unexpected warning when parsing tree with internal branch labels Unexpected warning when parsing tree with internal node labels Aug 6, 2019
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