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)