obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

First version of alignment functions (imported from suma* programs)

Browse Source
This commit is contained in:
Celine Mercier
2016-05-11 16:36:23 +02:00
parent 3567681339
commit b3c47809da
27 changed files with 1991 additions and 43 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
python/obitools3/obidms/_obidms.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

3
python/obitools3/obidms/_obidms.pxd
View File

@ -6,11 +6,12 @@ from .capi.obiview cimport Obiview_p
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
from ._obitaxo cimport OBI_Taxonomy
cdef class OBIDMS_column:
cdef OBIDMS_column_p* pointer
cdef OBIDMS dms
cdef Obiview_p view
cdef OBIView view
cdef str data_type
cdef str dms_name
cdef str column_name

18
python/obitools3/obidms/_obidms.pyx
View File

@ -63,6 +63,7 @@ from .capi.obiview cimport Obiview_p, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_get_column, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_select_line, \
obi_select_lines, \
@ -90,7 +91,7 @@ cdef class OBIDMS_column :
# Fill structure
self.pointer = column_pp
self.dms = view.dms
self.view = view.pointer
self.view = view
self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
self.column_name = bytes2str((column_p.header).name)
self.nb_elements_per_line = (column_p.header).nb_elements_per_line
@ -120,7 +121,7 @@ cdef class OBIDMS_column :
yield self.get_line(line_nb)
cpdef update_pointer(self):
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view.pointer, str2bytes(self.column_name))
cpdef list get_elements_names(self):
return self.elements_names
@ -336,7 +337,6 @@ cdef class OBIView :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p* column_pp
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
@ -369,10 +369,9 @@ cdef class OBIView :
raise Exception("Problem adding a column in a view")
# Get the column pointer
column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
column_p = obi_view_get_column(self.pointer, column_name_b)
# Open and store the subclass
column_p = column_pp[0] # TODO ugly cython dereferencing
subclass = OBIDMS_column.get_subclass_type(column_p)
(self.columns)[column_name] = subclass(self, column_name)
@ -495,18 +494,15 @@ cdef class OBIView_NUC_SEQS(OBIView):
cpdef delete_column(self, str column_name) :
cdef int i
cdef Obiview_p view
cdef Obiview_p view_p
cdef OBIDMS_column column
cdef OBIDMS_column_p column_p
cdef OBIDMS_column_header_p header
cdef str column_n
if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DEFINITION_COLUMN))) :
raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
view = self.pointer
view_p = self.pointer
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Remove instance from the dictionary

4
python/obitools3/obidms/_obidmscolumn_bool.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_bool.pyx
View File

@ -17,7 +17,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
@ -29,7 +29,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
if obi_column_set_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -38,7 +38,7 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obibool_t value
cdef object result
value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obibool_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIBool_NA :
@ -56,7 +56,7 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIBool_NA :
@ -73,5 +73,5 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIBool_NA
if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
if obi_column_set_obibool_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
raise Exception("Problem setting a value in a column")

4
python/obitools3/obidms/_obidmscolumn_char.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_char.pyx
View File

@ -15,7 +15,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
@ -27,7 +27,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
if obi_column_set_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")
@ -36,7 +36,7 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obichar_t value
cdef object result
value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obichar_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIChar_NA :
@ -54,7 +54,7 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIChar_NA :
@ -71,6 +71,6 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIChar_NA
if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
if obi_column_set_obichar_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
raise Exception("Problem setting a value in a column")

4
python/obitools3/obidms/_obidmscolumn_float.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_float.pyx
View File

@ -15,7 +15,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
@ -27,7 +27,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIFloat_NA
if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
if obi_column_set_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -36,7 +36,7 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obifloat_t value
cdef object result
value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obifloat_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIFloat_NA :
@ -54,7 +54,7 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIFloat_NA :
@ -71,6 +71,6 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIFloat_NA
if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
if obi_column_set_obifloat_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
raise Exception("Problem setting a value in a column")

4
python/obitools3/obidms/_obidmscolumn_int.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_int.pyx
View File

@ -17,7 +17,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
@ -29,7 +29,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
value = OBIInt_NA
if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
if obi_column_set_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")
@ -38,7 +38,7 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef obiint_t value
cdef object result
value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obiint_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIInt_NA :
@ -56,7 +56,7 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIInt_NA :
@ -73,6 +73,6 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
cpdef set_item(self, index_t line_nb, str element_name, object value):
if value is None :
value = OBIInt_NA
if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
if obi_column_set_obiint_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
raise Exception("Problem setting a value in a column")

4
python/obitools3/obidms/_obidmscolumn_seq.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_seq.pxd
View File

@ -1,12 +1,20 @@
#cython: language_level=3
from .capi.obitypes cimport index_t
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
from ._obidms cimport OBIView, OBIDMS_column, OBIDMS_column_multi_elts
cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef object get_line(self, index_t line_nb)
cpdef set_line(self, index_t line_nb, object value)
cpdef align(self,
OBIView score_view,
OBIDMS_column score_column,
double threshold = *,
bint normalize = *,
int reference = *,
bint similarity_mode = *)
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name)

28
python/obitools3/obidms/_obidmscolumn_seq.pyx
View File

@ -4,9 +4,12 @@ from .capi.obiview cimport obi_column_get_obiseq_with_elt_name_in_view, \
obi_column_get_obiseq_with_elt_idx_in_view, \
obi_column_set_obiseq_with_elt_name_in_view, \
obi_column_set_obiseq_with_elt_idx_in_view
from .capi.obialign cimport obi_align_one_column
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBISeq_NA, const_char_p
from ._obidms cimport OBIView
from obitools3.utils cimport str2bytes, bytes2str
from libc.stdlib cimport free
@ -18,7 +21,7 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if strcmp(value, OBISeq_NA) == 0 :
@ -34,16 +37,28 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
value_b = OBISeq_NA
else :
value_b = str2bytes(value)
if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
# TODO choose alignment type (lcs or other) with supplementary argument
cpdef align(self,
OBIView score_view,
OBIDMS_column score_column,
double threshold = 0.0,
bint normalize = True,
int reference = 0, # TODO
bint similarity_mode = True):
if (obi_align_one_column(self.view.pointer, (self.pointer)[0], score_view.pointer, (score_column.pointer)[0], threshold, normalize, reference, similarity_mode) < 0) :
raise Exception("An error occurred while aligning sequences")
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef char* value
cdef object result
value = obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if strcmp(value, OBISeq_NA) == 0 :
@ -62,7 +77,7 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if strcmp(value, OBISeq_NA) == 0 :
@ -83,6 +98,9 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
value_b = OBISeq_NA
else :
value_b = str2bytes(value)
if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
if obi_column_set_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")
# cpdef align(self, ): # TODO
# raise Exception("Columns with multiple sequences per line can't be aligned") # TODO discuss

4
python/obitools3/obidms/_obidmscolumn_str.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -17,7 +17,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef const_char_p value
cdef object result
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if strcmp(value, OBIStr_NA) == 0 :
@ -33,7 +33,7 @@ cdef class OBIDMS_column_str(OBIDMS_column):
value_b = OBIStr_NA
else :
value_b = str2bytes(value)
if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
raise Exception("Problem setting a value in a column")
@ -42,7 +42,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef const_char_p value
cdef object result
value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_column_get_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if strcmp(value, OBIStr_NA) == 0 :
@ -61,7 +61,7 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if strcmp(value, OBIStr_NA) == 0 :
@ -82,6 +82,6 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
value_b = OBIStr_NA
else :
value_b = str2bytes(value)
if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
if obi_column_set_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
raise Exception("Problem setting a value in a column")

4
python/obitools3/obidms/_obiseq.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

4
python/obitools3/obidms/_obitaxo.cfiles
View File

@ -10,6 +10,8 @@
../../../src/encode.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h
../../../src/obi_align.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/obiblob_indexer.h
@ -37,6 +39,8 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c

10
python/obitools3/obidms/capi/obialign.pxd Normal file
View File

@ -0,0 +1,10 @@
#cython: language_level=3
from ..capi.obiview cimport Obiview_p
from ..capi.obidmscolumn cimport OBIDMS_column_p
cdef extern from "obi_align.h" nogil:
int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bint normalize, int reference, bint similarity_mode)