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cimport numpy as np
cimport cython
from bp._ba cimport BIT_ARRAY
ctypedef np.npy_intp SIZE_t
ctypedef np.npy_uint32 UINT32_t
ctypedef np.npy_int32 INT32_t
ctypedef np.npy_float64 DOUBLE_t
ctypedef np.npy_uint8 BOOL_t
cdef class mM:
cdef int b # block size
cdef int n_tip # number of tips in the binary tree
cdef int n_internal # number of internal nodes in the binary tree
cdef int n_total # total number of nodes in the binary tree
cdef int height # the height of the binary tree
cdef int m_idx # m is minimum excess
cdef int M_idx # M is maximum excess
cdef int r_idx # rank
cdef SIZE_t[:, ::1] mM
cdef SIZE_t[:] r
cdef void rmm(self, BOOL_t[:] B, int B_size) nogil
@cython.final
cdef class BP:
cdef:
public np.ndarray B
BOOL_t* _b_ptr
SIZE_t[:] _e_index
SIZE_t[:] _k_index_0
SIZE_t[:] _k_index_1
np.ndarray _names
np.ndarray _lengths
np.ndarray _edges
np.ndarray _edge_lookup
mM _rmm
SIZE_t size
cdef inline SIZE_t rank(self, SIZE_t t, SIZE_t i) nogil
cdef inline SIZE_t select(self, SIZE_t t, SIZE_t k) nogil
cdef SIZE_t _excess(self, SIZE_t i) nogil
cdef SIZE_t excess(self, SIZE_t i) nogil
cdef SIZE_t fwdsearch(self, SIZE_t i, int d) nogil
cdef SIZE_t bwdsearch(self, SIZE_t i, int d) nogil
cpdef inline SIZE_t close(self, SIZE_t i) nogil
cdef inline SIZE_t open(self, SIZE_t i) nogil
cpdef inline BOOL_t isleaf(self, SIZE_t i) nogil
cdef inline SIZE_t enclose(self, SIZE_t i) nogil
cdef BP _mask_from_self(self, BIT_ARRAY* mask, np.ndarray[DOUBLE_t, ndim=1] lengths)
cpdef SIZE_t nsibling(self, SIZE_t i) nogil
cpdef SIZE_t psibling(self, SIZE_t i) nogil
cpdef SIZE_t lchild(self, SIZE_t i) nogil
cpdef SIZE_t fchild(self, SIZE_t i) nogil
cpdef SIZE_t parent(self, SIZE_t i) nogil
cpdef SIZE_t depth(self, SIZE_t i) nogil
cpdef SIZE_t root(self) nogil
cdef int scan_block_forward(self, int i, int k, int b, int d) nogil
cdef int scan_block_backward(self, int i, int k, int b, int d) nogil
cdef void _set_edges(self, np.ndarray[INT32_t, ndim=1] edges)
# TODO: evalute down the road what methods should be cdef. There is a
# performance cost for cpdef, so for high use functions, it may make sense
# to punt down to cdef.
# http://notes-on-cython.readthedocs.io/en/latest/fibo_speed.html
cpdef inline unicode name(self, SIZE_t i)
cpdef inline DOUBLE_t length(self, SIZE_t i)
cpdef inline INT32_t edge(self, SIZE_t i)
cpdef SIZE_t edge_from_number(self, INT32_t n)
cpdef SIZE_t rmq(self, SIZE_t i, SIZE_t j) nogil
cpdef SIZE_t rMq(self, SIZE_t i, SIZE_t j) nogil
cpdef SIZE_t postorderselect(self, SIZE_t k) nogil
cpdef SIZE_t postorder(self, SIZE_t i) nogil
cpdef SIZE_t preorderselect(self, SIZE_t k) nogil
cpdef SIZE_t preorder(self, SIZE_t i) nogil
cpdef BOOL_t isancestor(self, SIZE_t i, SIZE_t j) nogil
cpdef SIZE_t levelancestor(self, SIZE_t i, SIZE_t d) nogil
cpdef SIZE_t subtree(self, SIZE_t i) nogil
cpdef BP shear(self, set tips)
cpdef BP collapse(self)
cpdef SIZE_t ntips(self) nogil
cpdef SIZE_t levelnext(self, SIZE_t i) nogil
cpdef SIZE_t height(self, SIZE_t i) nogil
cpdef SIZE_t deepestnode(self, SIZE_t i) nogil
cpdef SIZE_t lca(self, SIZE_t i, SIZE_t j) nogil
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