def newick_to_RBN(s):
"""
@param s: newick string
@return: directed topology, branch lengths, vertex name map
"""
tree = NewickIO.parse_simple(s, _IO_Tree())
Ftree.RB_assert_branch_lengths(tree.R, tree.B)
return tree.R, tree.B, tree.v_to_name
def newick_to_TN(s):
"""
Everything to do with branch lengths is ignored.
@param s: newick string
@return: undirected topology, vertex name map
"""
tree = NewickIO.parse_simple(s, _IO_Tree())
return Ftree.R_to_T(tree.R), tree.v_to_name
def newick_to_TBN(s):
"""
@param s: newick string
@return: undirected topology, branch lengths, vertex name map
"""
tree = NewickIO.parse_simple(s, _IO_Tree())
T = Ftree.R_to_T(tree.R)
Ftree.TB_assert_branch_lengths(T, tree.B)
return T, tree.B, tree.v_to_name
def newick_to_R(s, name_type=None):
tree = NewickIO.parse_simple(s, _IO_Tree())
N = get_validated_name_map(tree.v_to_name, name_type)
return set((N[a], N[b]) for a, b in tree.R)
