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Description
As of version 1.20 (https://www.phyloxml.org/documentation/version_1.20/phyloxml.html) PhyloXML supports multiple phylogenies in the same file.
When a PhyloXML with multiple phylogenies is parsed at the following line tree_json
becomes undefined
because xml.phyloxml.phylogeny
is an array rather than an object:
phylotree.js/src/formats/phyloxml.js
Line 70 in 60aa174
tree_json = xml.phyloxml.phylogeny.clade; |
That leads to an error at the following line:
phylotree.js/src/formats/phyloxml.js
Line 71 in 60aa174
tree_json.name = "root"; |
This case should be managed in a clear way, either throwing an error stating that multiple phylogenies are not supported or choosing one of the phylogenies (e.g., the first) and giving a warning.
Ideally, it would be nice to load multi-phylogenies files as a set of Phylotree objects, but that would be an improvement rather than just fixing the bug, which is the priority in my opinion.