def add_init(self, beastxml):
"""
Add the <init> element for the tree.
"""
# If a starting tree is specified, use it...
if beastxml.config.languages.starting_tree:
beastxml.init = xml.init(
beastxml.run,
estimate="false",
id="startingTree",
initial="@Tree.t:beastlingTree",
spec="beast.util.TreeParser",
IsLabelledNewick="true",
newick=beastxml.config.languages.starting_tree)
# ...if not, use the simplest random tree initialiser possible
else:
# If we have non-trivial monophyly constraints, use ConstrainedRandomTree
if beastxml.config.languages.monophyly and len(
beastxml.config.languages.languages) > 2:
self.add_constrainedrandomtree_init(beastxml)
# If we have hard-bound calibrations, use SimpleRandomTree
elif any([
c.dist == "uniform"
for c in beastxml.config.calibrations.values()
]):
self.add_simplerandomtree_init(beastxml)
# Otherwise, just use RandomTree
else:
self.add_randomtree_init(beastxml)
def add_constrainedrandomtree_init(self, beastxml):
attribs = {"estimate":"false", "id":"startingTree", "initial":"@Tree.t:beastlingTree", "taxonset":"@taxa", "spec":"beast.evolution.tree.ConstrainedRandomTree", "constraints":"@constraints"}
if self.birthrate_estimate is not None:
attribs["rootHeight"] = str(self.treeheight_estimate)
beastxml.init = xml.init(beastxml.run, attrib=attribs)
popmod = xml.populationModel(beastxml.init, spec="ConstantPopulation")
xml.popSize(popmod, spec="parameter.RealParameter", value="1")
def add_simplerandomtree_init(self, beastxml):
attribs = {
"estimate": "false",
"id": "startingTree",
"initial": "@Tree.t:beastlingTree",
"taxonset": "@taxa",
"spec": "beast.evolution.tree.SimpleRandomTree"
}
if self.birthrate_estimate is not None:
attribs["rootHeight"] = str(self.treeheight_estimate)
beastxml.init = xml.init(beastxml.run, attrib=attribs)