def property(self, elem):
return PX.Property(elem.text.strip(),
elem.get('ref'),
elem.get('applies_to'),
elem.get('datatype'),
unit=elem.get('unit'),
id_ref=elem.get('id_ref'))
def property(self, elem):
"""Create properties from external resources."""
return PX.Property(elem.text.strip(),
elem.get('ref'),
elem.get('applies_to'),
elem.get('datatype'),
unit=elem.get('unit'),
id_ref=elem.get('id_ref'))
def property(self, elem):
"""Create properties from external resources."""
return PX.Property(elem.text.strip(),
elem.get("ref"),
elem.get("applies_to"),
elem.get("datatype"),
unit=elem.get("unit"),
id_ref=elem.get("id_ref"))
def output_xml(coloured_trees, path, colour_branches):
# adding font as a property of each tip clade, to show colour
coloured_trees = [ PhyloXML.Phylogeny.from_tree(tree) for tree in coloured_trees ]# convert to PhyloNexus
for tree in coloured_trees:
for clade in tree.get_terminals():
value = BranchColor.to_hex(clade.color) # value of the property (ie the colour)
clade.properties = [PhyloXML.Property(value, "style:font_color", "node", "xsd:token")]
if not colour_branches:
for clade in tree.get_nonterminals() + tree.get_terminals():
clade.color = None
Phylo.write(coloured_trees, path, "phyloxml")
