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Added possibility to specify the offset for encoding and decoding

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sequence quality character strings
This commit is contained in:
Celine Mercier
2017-07-27 19:24:41 +02:00
parent 99ceed5fff
commit 15d383fa8b
6 changed files with 95 additions and 61 deletions
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18
python/obitools3/dms/column/typed_column/qual.pxd
View File

@ -3,24 +3,24 @@
from ...capi.obitypes cimport index_t
from ..column cimport Column, \
Column_multi_elts
from ..column_idx cimport Column_idx, \
Column_multi_elts_idx
cdef class Column_qual(Column) :
cdef class Column_qual(Column_idx) :
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb, int offset=*)
cpdef set_line(self, index_t line_nb, object value)
cpdef set_str_line(self, index_t line_nb, object value)
cpdef set_str_line(self, index_t line_nb, object value, int offset=*)
cdef class Column_multi_elts_qual(Column_multi_elts) :
cdef class Column_multi_elts_qual(Column_multi_elts_idx) :
cpdef object get_item(self, index_t line_nb, object elt_id)
cpdef object get_str_item(self, index_t line_nb, object elt_id)
cpdef object get_str_item(self, index_t line_nb, object elt_id, int offset=*)
cpdef object get_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb)
cpdef object get_str_line(self, index_t line_nb, int offset=*)
cpdef set_item(self, index_t line_nb, object elt_id, object value)
cpdef set_str_item(self, index_t line_nb, object elt_id, object value)
cpdef set_str_item(self, index_t line_nb, object elt_id, object value, int offset=*)

34
python/obitools3/dms/column/typed_column/qual.pyx
View File

@ -6,6 +6,8 @@ from ..column cimport register_column_class
from ...view.view cimport View
from ..column cimport Column
from obitools3.utils cimport tobytes, bytes2str, \
obi_errno_to_exception
@ -28,7 +30,9 @@ from libc.stdint cimport uint8_t
from libc.stdlib cimport malloc
cdef class Column_qual(Column):
# TODO detect type of value and call set_item_str if str or bytes
cdef class Column_qual(Column_idx):
@staticmethod
def new(View view,
@ -59,12 +63,12 @@ cdef class Column_qual(Column):
return result
cpdef object get_str_line(self, index_t line_nb):
cpdef object get_str_line(self, index_t line_nb, int offset=-1):
global obi_errno
cdef char* value
cdef object result
cdef int i
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0)
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, offset)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem getting a value from a column")
if value == OBIQual_char_NA :
result = None
@ -91,19 +95,19 @@ cdef class Column_qual(Column):
free(value_b)
cpdef set_str_line(self, index_t line_nb, object value):
cpdef set_str_line(self, index_t line_nb, object value, int offset=-1):
global obi_errno
cdef bytes value_b
if value is None :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA) < 0:
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, OBIQual_char_NA, offset) < 0:
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
else :
value_b = tobytes(value)
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b) < 0:
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, 0, value_b, offset) < 0:
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=None, error_message="Problem setting a value in a column")
cdef class Column_multi_elts_qual(Column_multi_elts):
cdef class Column_multi_elts_qual(Column_multi_elts_idx):
cpdef object get_item(self, index_t line_nb, object elt_id):
global obi_errno
@ -126,15 +130,15 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
return result
cpdef object get_str_item(self, index_t line_nb, object elt_id):
cpdef object get_str_item(self, index_t line_nb, object elt_id, int offset=-1):
global obi_errno
cdef char* value
cdef object result
if type(elt_id) == int :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id)
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, offset)
else :
elt_name = tobytes(elt_id)
value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name)
value = obi_get_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, offset)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem getting a value from a column")
if value == OBIQual_char_NA :
result = None
@ -176,7 +180,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
return result
cpdef object get_str_line(self, index_t line_nb) :
cpdef object get_str_line(self, index_t line_nb, int offset=-1) :
global obi_errno
cdef char* value
cdef object value_in_result
@ -192,7 +196,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
column_p = self.pointer()
elements_names = self.elements_names
for i in range(self.nb_elements_per_line) :
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i)
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, i, offset)
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=i, error_message="Problem getting a value from a column")
if value != OBIQual_char_NA :
value_in_result = bytes2str(value)
@ -232,7 +236,7 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
free(value_b)
cpdef set_str_item(self, index_t line_nb, object elt_id, object value):
cpdef set_str_item(self, index_t line_nb, object elt_id, object value, int offset=-1):
global obi_errno
cdef bytes value_b
cdef bytes elt_name
@ -243,11 +247,11 @@ cdef class Column_multi_elts_qual(Column_multi_elts):
value_b = tobytes(value)
if type(elt_id) == int :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b) < 0 :
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_id, value_b, offset) < 0 :
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")
else :
elt_name = tobytes(elt_id)
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b) < 0:
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self._view.pointer(), self.pointer(), line_nb, elt_name, value_b, offset) < 0:
obi_errno_to_exception(obi_errno, line_nb=line_nb, elt_id=elt_id, error_message="Problem setting a value in a column")