def _add_leaf(node: Node, target: str, leaf: str):
if PhyTree._is_group(node.name):
if node.name == target:
node.add_descendant(Node(f"{{{leaf}}}"))
else:
if PhyTree._is_group(target):
expected_leaves = set(PhyTree._get_group_leaves(target))
else:
expected_leaves = {target}
for child in node.descendants:
if PhyTree._is_group(child.name):
child_leaves = set(
PhyTree._get_group_leaves(child.name))
if expected_leaves <= child_leaves:
PhyTree._add_leaf(child, target, leaf)
break
elif PhyTree._is_leaf(child.name):
if child.name in expected_leaves:
PhyTree._add_leaf(child, target, leaf)
else:
raise ValueError(f"Couldn't find {target}")
elif PhyTree._is_leaf(node.name):
if node.name == target:
if node.name != '{}':
node.add_descendant(Node(node.name))
node.add_descendant(Node(f"{{{leaf}}}"))
else:
node.name = f"{{{leaf}}}"
return
else:
raise ValueError(f"Unexpected leaf: {node.name}")
else:
raise ValueError(f"Couldn't recognize {leaf} as a leaf or a group")
node.name = node.name.replace("}", f" {leaf}}}")
def rename_none_node(node_to_rename: newick.Node, counter):
"""
Renaming node with no name to differ from other not named node.
:param node_to_rename: node to be checked
:param counter: int; counter for none nodes
:return: (Node, int)
"""
if node_to_rename.name is None:
node_to_rename.name = str(node_to_rename.name) + "_" + str(counter)
counter += 1
return node_to_rename, counter
def test_node_parameters_changeability(self):
test_obj = Node(name="A")
self.assertEqual("A", test_obj.name)
test_obj.name = "B"
self.assertEqual("B", test_obj.name)
def test_node_parameters_changeability(self):
test_obj = Node(name="A")
self.assertEqual("A", test_obj.name)
test_obj.name = "B"
self.assertEqual("B", test_obj.name)