111 lines
4.3 KiB
Cython
111 lines
4.3 KiB
Cython
#cython: language_level=3
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from .capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
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obi_get_seq_with_elt_idx_and_col_p_in_view, \
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obi_set_seq_with_elt_name_and_col_p_in_view, \
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obi_set_seq_with_elt_idx_and_col_p_in_view
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from .capi.obialign cimport obi_align_one_column
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from .capi.obierrno cimport obi_errno
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from .capi.obitypes cimport OBISeq_NA, const_char_p
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from ._obidms cimport OBIView
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from obitools3.utils cimport str2bytes, bytes2str
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from libc.stdlib cimport free
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cdef class OBIDMS_column_seq(OBIDMS_column):
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cpdef object get_line(self, index_t line_nb):
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cdef char* value
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cdef object result
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value = obi_get_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
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if obi_errno > 0 :
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raise IndexError(line_nb)
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if value == OBISeq_NA :
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result = None
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else :
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result = bytes2str(value)
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free(value)
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return result
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cpdef set_line(self, index_t line_nb, object value):
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if value is None :
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if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
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raise Exception("Problem setting a value in a column")
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else :
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if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
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raise Exception("Problem setting a value in a column")
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# TODO choose alignment type (lcs or other) with supplementary argument
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cpdef align(self,
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OBIView score_view,
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OBIDMS_column score_column,
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double threshold = 0.0,
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bint normalize = True,
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int reference = 0, # TODO
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bint similarity_mode = True):
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if (obi_align_one_column(self.view.pointer, (self.pointer)[0], score_view.pointer, (score_column.pointer)[0], threshold, normalize, reference, similarity_mode) < 0) :
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raise Exception("An error occurred while aligning sequences")
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cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
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cpdef object get_item(self, index_t line_nb, str element_name):
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cdef char* value
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cdef object result
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value = obi_get_seq_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
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if obi_errno > 0 :
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raise IndexError(line_nb, element_name)
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if value == OBISeq_NA :
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result = None
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else :
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result = bytes2str(value)
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free(value)
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return result
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cpdef object get_line(self, index_t line_nb) :
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cdef char* value
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cdef object value_in_result
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cdef dict result
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cdef index_t i
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cdef bint all_NA
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result = {}
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all_NA = True
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for i in range(self.nb_elements_per_line) :
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value = obi_get_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
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if obi_errno > 0 :
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raise IndexError(line_nb)
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if value == OBISeq_NA :
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value_in_result = None
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else :
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value_in_result = bytes2str(value)
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free(value)
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result[self.elements_names[i]] = value_in_result
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if all_NA and (value_in_result is not None) :
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all_NA = False
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if all_NA :
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result = None
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return result
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cpdef set_item(self, index_t line_nb, str element_name, object value):
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cdef bytes value_b
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if value is None :
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value_b = OBISeq_NA
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elif isinstance(value, bytes) :
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value_b = value
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elif isinstance(value, str) :
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value_b = str2bytes(value)
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else:
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raise TypeError('Sequence value must be of type Bytes, Str or None')
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if obi_set_seq_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
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raise Exception("Problem setting a value in a column")
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# cpdef align(self, ): # TODO
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# raise Exception("Columns with multiple sequences per line can't be aligned") # TODO discuss
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