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Newick files with comma-delimited labels load incorrectly #170

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arendsee opened this issue Apr 15, 2021 · 3 comments
Open

Newick files with comma-delimited labels load incorrectly #170

arendsee opened this issue Apr 15, 2021 · 3 comments
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@arendsee
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For the tree

(('A','B')[&label=1,!color=#73ffff],'C');`

I would expect a 3-tip tree with the (A,B) subtree containing the label 1 and color #73ffff. But the comma in the label seems to be interpreted as an additional leaf.

See screen shot below:

Screen Shot 2021-04-15 at 5 12 54 PM

I'm using FigTree v1.4.2

@rambaut
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rambaut commented Apr 19, 2021

Comments (in [, ]) and 'metacomments' are only defined by the Nexus format. Surround the tree by:

#NEXUS
begin trees;
   tree TREE = (('A','B')[&label=1,!color=#73ffff],'C');
end;

@arendsee
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Then perhaps either an error should be raised or the comments should be entirely ignored. Single field comments, like [&label=1] do work in the Newick inputs. So there is partial support, but commas aren't handled.

@rambaut
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rambaut commented Aug 18, 2022

I agree - it should either complain or parse them.

@rambaut rambaut added this to the 1.4.5 milestone Aug 18, 2022
@rambaut rambaut added the bug label Aug 18, 2022
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