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78 lines
2.1 KiB
Cython
78 lines
2.1 KiB
Cython
from typing import List
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import numpy
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from ..errors import Errors
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from libc.stdint cimport int32_t
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cdef class AlignmentArray:
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"""AlignmentArray is similar to Thinc's Ragged with two simplfications:
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indexing returns numpy arrays and this type can only be used for CPU arrays.
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However, these changes make AlignmentArray more efficient for indexing in a
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tight loop."""
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__slots__ = []
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def __init__(self, alignment: List[List[int]]):
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cdef int data_len = 0
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cdef int outer_len
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cdef int idx
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self._starts_ends = numpy.zeros(len(alignment) + 1, dtype='int32')
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cdef int32_t* starts_ends_ptr = <int32_t*>self._starts_ends.data
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for idx, outer in enumerate(alignment):
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outer_len = len(outer)
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starts_ends_ptr[idx + 1] = starts_ends_ptr[idx] + outer_len
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data_len += outer_len
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self._lengths = None
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self._data = numpy.empty(data_len, dtype="int32")
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idx = 0
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cdef int32_t* data_ptr = <int32_t*>self._data.data
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for outer in alignment:
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for inner in outer:
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data_ptr[idx] = inner
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idx += 1
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def __getitem__(self, idx):
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starts = self._starts_ends[:-1]
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ends = self._starts_ends[1:]
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if isinstance(idx, int):
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start = starts[idx]
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end = ends[idx]
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elif isinstance(idx, slice):
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if not (idx.step is None or idx.step == 1):
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raise ValueError(Errors.E1027)
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start = starts[idx]
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if len(start) == 0:
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return self._data[0:0]
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start = start[0]
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end = ends[idx][-1]
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else:
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raise ValueError(Errors.E1028)
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return self._data[start:end]
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@property
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def data(self):
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return self._data
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@property
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def lengths(self):
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if self._lengths is None:
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self._lengths = self.ends - self.starts
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return self._lengths
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@property
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def ends(self):
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return self._starts_ends[1:]
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@property
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def starts(self):
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return self._starts_ends[:-1]
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