def bipartition_by_edge(self, e):
"""Prunes the subtree that attached to the head_node of edge e and returns them as a separate tree."""
t = self._tree
nr = e.head_node
assert e.tail_node is not None
assert e.head_node is not None
assert nr.parent_node is e.tail_node
is_valid_tree(t)
n = self.n_leaves
potentially_deleted_nd = e.tail_node
grandparent_nd = potentially_deleted_nd.parent_node
e.tail_node.remove_child(nr, suppress_deg_two=True)
nr.edge.length = None
nr.parent_node = None
convert_node_to_root_polytomy(nr)
t1 = PhylogeneticTree(Tree(seed_node=nr))
n1 = t1.n_leaves # temp we could speed this up, by telling the Phylogenetic tree how many leaves it has
if hasattr(e, "num_leaves_below"):
if grandparent_nd is None:
old_root = potentially_deleted_nd
if old_root.edge:
old_root.edge.num_leaves_below -= n1
else:
if potentially_deleted_nd in grandparent_nd.child_nodes():
potentially_deleted_nd.edge.num_leaves_below -= n1
old_root = grandparent_nd
if old_root.edge:
old_root.edge.num_leaves_below -= n1
while old_root.parent_node:
old_root = old_root.parent_node
if old_root.edge:
old_root.edge.num_leaves_below -= n1
else:
old_root = grandparent_nd or potentially_deleted_nd
while old_root.parent_node:
old_root = old_root.parent_node
t2 = PhylogeneticTree(Tree(seed_node=old_root))
is_valid_tree(t1._tree)
is_valid_tree(t2._tree)
return t1, t2
def bipartition_by_edge(self, e):
"""Prunes the subtree that attached to the head_node of edge e and returns them as a separate tree."""
t = self._tree
nr = e.head_node
assert e.tail_node is not None
assert e.head_node is not None
assert nr.parent_node is e.tail_node
is_valid_tree(t)
n = self.n_leaves
potentially_deleted_nd = e.tail_node
grandparent_nd = potentially_deleted_nd.parent_node
e.tail_node.remove_child(nr, suppress_deg_two=True)
nr.edge.length = None
nr.parent_node = None
convert_node_to_root_polytomy(nr)
t1 = PhylogeneticTree(Tree(seed_node=nr))
n1 = t1.n_leaves # temp we could speed this up, by telling the Phylogenetic tree how many leaves it has
if hasattr(e, "num_leaves_below"):
if grandparent_nd is None:
old_root = potentially_deleted_nd
if old_root.edge:
old_root.edge.num_leaves_below -= n1
else:
if potentially_deleted_nd in grandparent_nd.child_nodes():
potentially_deleted_nd.edge.num_leaves_below -= n1
old_root = grandparent_nd
if old_root.edge:
old_root.edge.num_leaves_below -= n1
while old_root.parent_node:
old_root = old_root.parent_node
if old_root.edge:
old_root.edge.num_leaves_below -= n1
else:
old_root = grandparent_nd or potentially_deleted_nd
while old_root.parent_node:
old_root = old_root.parent_node
t2 = PhylogeneticTree(Tree(seed_node=old_root))
is_valid_tree(t1._tree)
is_valid_tree(t2._tree)
return t1, t2