ArtPoon/BelleJS

XML fails to run

Closed this issue · 4 comments

Attempting YFV FASTA file with tip dates and UCLN clock.

Read alignment: alignment
  Sequences = 71
      Sites = 654
   Datatype = nucleotide
Site patterns 'patterns' created from positions 1-654 of alignment 'alignment'
  unique pattern count = 280
Mar 29, 2021 11:30:52 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, test.xml:
Object with idref=taxa must not have other content or attributes (or perhaps it was not intended to be a reference?).

Error thrown at: dr.xml.XMLParser.convert(Unknown Source)

Same exception thrown with no modifications to analysis options (JC, strict clock..)

I think this is the problem:

	<coalescentSimulator id="startingTree">
	<taxa xmlns="http://www.w3.org/1999/xhtml" idref="taxa"></taxa>
	<constantSize idref="constant"/>
	</coalescentSimulator>

Manually edited the XML file. The problem is this bit: xmlns="http://www.w3.org/1999/xhtml"

Changing this from createElement fixed the problem:

taxa = document.createElementNS("", "taxa"),