def parse(self, values_are_confidence=False, rooted=False):
"""Parse the text stream this object was initialized with."""
nexml_doc = ElementTree.iterparse(self.handle, events=('end', ))
for event, node in nexml_doc:
if node.tag == qUri('nex:tree'):
node_dict = {}
node_children = {}
root = None
child_tags = node.getchildren()
nodes = []
edges = []
for child in child_tags:
if child.tag == qUri('nex:node'):
nodes.append(child)
if child.tag == qUri('nex:edge'):
edges.append(child)
for node in nodes:
node_id = node.attrib['id']
this_node = node_dict[node_id] = {}
if 'otu' in node.attrib and node.attrib['otu']:
this_node['name'] = node.attrib['otu']
if 'root' in node.attrib and node.attrib['root'] == 'true':
root = node_id
for child in node.getchildren():
if child.tag == qUri('nex:meta'):
self.add_annotation(node_dict[node_id], child)
srcs = set()
tars = set()
for edge in edges:
src, tar = edge.attrib['source'], edge.attrib['target']
srcs.add(src)
tars.add(tar)
if src not in node_children:
node_children[src] = set()
node_children[src].add(tar)
if 'length' in edge.attrib:
node_dict[tar]['branch_length'] = float(
edge.attrib['length'])
if 'property' in edge.attrib and edge.attrib[
'property'] in matches('cdao:has_Support_Value'):
node_dict[tar]['confidence'] = float(
edge.attrib['content'])
for child in edge.getchildren():
if child.tag == qUri('nex:meta'):
self.add_annotation(node_dict[tar], child)
if root is None:
# if no root specified, start the recursive tree creation function
# with the first node that's not a child of any other nodes
rooted = False
possible_roots = (node.attrib['id'] for node in nodes
if node.attrib['id'] in srcs
and node.attrib['id'] not in tars)
root = next(possible_roots)
else:
rooted = True
yield NeXML.Tree(root=self._make_tree(root, node_dict,
node_children),
rooted=rooted)
def parse(self, values_are_confidence=False, rooted=False):
"""Parse the text stream this object was initialized with."""
nexml_doc = ElementTree.iterparse(self.handle, events=("end",))
for event, node in nexml_doc:
if node.tag == qUri("nex:tree"):
node_dict = {}
node_children = {}
root = None
child_tags = node.getchildren()
nodes = []
edges = []
for child in child_tags:
if child.tag == qUri("nex:node"):
nodes.append(child)
if child.tag == qUri("nex:edge"):
edges.append(child)
for node in nodes:
node_id = node.attrib["id"]
this_node = node_dict[node_id] = {}
if "otu" in node.attrib and node.attrib["otu"]:
this_node["name"] = node.attrib["otu"]
if "root" in node.attrib and node.attrib["root"] == "true":
root = node_id
for child in node.getchildren():
if child.tag == qUri("nex:meta"):
self.add_annotation(node_dict[node_id], child)
srcs = set()
tars = set()
for edge in edges:
src, tar = edge.attrib["source"], edge.attrib["target"]
srcs.add(src)
tars.add(tar)
if src not in node_children:
node_children[src] = set()
node_children[src].add(tar)
if "length" in edge.attrib:
node_dict[tar]["branch_length"] = float(edge.attrib["length"])
if "property" in edge.attrib and edge.attrib["property"] in matches("cdao:has_Support_Value"):
node_dict[tar]["confidence"] = float(edge.attrib["content"])
for child in edge.getchildren():
if child.tag == qUri("nex:meta"):
self.add_annotation(node_dict[tar], child)
if root is None:
# if no root specified, start the recursive tree creation function
# with the first node that's not a child of any other nodes
rooted = False
possible_roots = (node.attrib["id"] for node in nodes
if node.attrib["id"] in srcs and
node.attrib["id"] not in tars)
root = next(possible_roots)
else:
rooted = True
yield NeXML.Tree(root=self._make_tree(root, node_dict, node_children), rooted=rooted)