def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.id = "node_%s" % hash(self)
self.nexml_edge.id = "edge_%s" % hash(self)
self.nexml_project = None
self._nexml_support = LiteralMeta(datatype="float",
property="branch_support",
content=1.0)
self.nexml_edge.length = 0.0
self.nexml_edge.add_meta(self._nexml_support)
# Initialize empty PhyloTree
super(NexmlTree, self).__init__()
self._children = Children()
self._children.node = self
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
read_newick(newick, root_node=self, format=format)
self.set_species_naming_function(sp_naming_function)
def build(self, node):
self.nexml_tree = FloatTree()
tree = self.nexml_tree
tree.build(node)
# This detects the outgroup of the tree even if the root tag
# is not set in any node
rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge])
nodeid2node = {rootid.pop(): self}
for xmledge in tree.edge:
child = nodeid2node.setdefault(xmledge.target, self.__class__() )
parent = nodeid2node.setdefault(xmledge.source, self.__class__() )
child.name = xmledge.target
parent.name = xmledge.source
child.nexml_edge = xmledge
if xmledge.length is not None:
child.dist = float(xmledge.length)
parent.add_child(child)
for xmlnode in tree.node:
# just a warning. I don't know if this can occur
if xmlnode.id not in nodeid2node:
print >>sys.stderr, "unused node", xmlnode.id
continue
ete_node = nodeid2node[xmlnode.id]
ete_node.nexml_node = xmlnode
if xmlnode.id is not None:
ete_node.name = xmlnode.id
