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# ctypedef struct ailist_t: | |
# int64_t nr, mr # Number of regions | |
# interval_t *interval_list # Regions data | |
# uint32_t first, last # Record range of intervals | |
# int nc, lenC[10], idxC[10] | |
# uint32_t *maxE | |
# ... | |
# uint32_t binary_search(interval_t* As, uint32_t idxS, uint32_t idxE, uint32_t qe) nogil | |
@cython.boundscheck(False) | |
@cython.wraparound(False) | |
@cython.initializedcheck(False) | |
def ifa(self, const long[::1] starts, const long[::1] ends, const long[::1] index): | |
# Check if object is still open | |
if self.is_closed: | |
raise NameError("AIList object has been closed.") | |
if self.is_constructed == False: | |
self.construct() | |
cdef int length = len(starts) | |
cdef int nfound = 0 | |
output_arr = np.ones(length, dtype=np.int64) * -1 | |
output_arr_other = np.ones(length, dtype=np.int64) * -1 | |
cdef int64_t [::1] output | |
cdef int64_t [::1] output_other | |
output = output_arr | |
output_other = output_arr_other | |
cdef int i = 0 | |
cdef int k = 0 | |
cdef int t = 0 | |
cdef int32_t qs, qe, qx, cs, ce | |
cdef ailist_t *ail = self.interval_list | |
for i in range(len(starts)): | |
qs, qe, qx = starts[i], ends[i], index[i] | |
# print("-----" * 5) | |
# print("qs, qe, qx", qs, qe, qx) | |
for k in range(ail.nc): | |
# print(" k", k) | |
cs = ail.idxC[k] | |
ce = cs + ail.lenC[k] | |
if ail.lenC[k] > 15: | |
# print(" if") | |
t = binary_search(ail.interval_list, cs, ce, qe) | |
while (t >= cs and ail.maxE[t] > qs): | |
# print(" t", t) | |
if (ail.interval_list[t].end > qs): | |
# print(" ail.interval_list[t].end", ail.interval_list[t].end) | |
if nfound >= length: | |
length = (length + 1) * 2 | |
output_arr = np.resize(output_arr, length) | |
output_arr_other = np.resize(output_arr_other, length) | |
output = output_arr | |
output_other = output_arr_other | |
output[nfound] = i | |
output_other[nfound] = ail.interval_list[t].index | |
nfound += 1 | |
# print(" nfound", nfound) | |
# print(" output_arr", output_arr) | |
# print(" output_arr_other", output_arr_other) | |
t -= 1 | |
else: | |
# print(" else") | |
for t in range(cs, ce): | |
# print(" t", t) | |
# print(" ail.interval_list[t].start", ail.interval_list[t].start) | |
# print(" ail.interval_list[t].end", ail.interval_list[t].end) | |
if (ail.interval_list[t].start < qe and ail.interval_list[t].end > qs): | |
if nfound >= length: | |
length = (length + 1) * 2 | |
output_arr = np.resize(output_arr, length) | |
output_arr_other = np.resize(output_arr_other, length) | |
output = output_arr | |
output_other = output_arr_other | |
output[nfound] = i | |
output_other[nfound] = ail.interval_list[t].index | |
# print(" nfound", nfound) | |
# print(" output_arr", output_arr) | |
# print(" output_arr_other", output_arr_other) | |
nfound += 1 | |
return output_arr[:nfound], output_arr_other[:nfound] | |
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