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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

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This commit is contained in:
Eric Coissac
2016-08-03 10:13:47 +02:00
parent 1e6d6e32e0 26b8e1f215
commit 465ea81c77
27 changed files with 1970 additions and 490 deletions
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2
python/obitools3/obidms/_obidms.cfiles
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@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

6
python/obitools3/obidms/_obidms.pxd
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@ -18,7 +18,6 @@ cdef class OBIDMS_column:
cdef index_t nb_elements_per_line
cdef list elements_names
cpdef update_pointer(self)
cpdef list get_elements_names(self)
cpdef str get_data_type(self)
cpdef index_t get_nb_lines_used(self)
@ -52,14 +51,19 @@ cdef class OBIView:
cpdef add_column(self,
str column_name,
obiversion_t version_number=*,
str alias=*,
str type=*,
index_t nb_lines=*,
index_t nb_elements_per_line=*,
list elements_names=*,
str indexer_name=*,
str associated_column_name=*,
obiversion_t associated_column_version=*,
str comments=*,
bint create=*
)
cpdef change_column_alias(self, str current_alias, str new_alias)
cpdef update_column_pointers(self)
cpdef select_line(self, index_t line_nb)
cpdef select_lines(self, list line_selection)
cpdef save_and_close(self)

88
python/obitools3/obidms/_obidms.pyx
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@ -55,7 +55,7 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
from .capi.obiview cimport Obiview_p, \
Obiview_infos_p, \
Column_reference_p, \
Alias_column_pair_p, \
obi_new_view_nuc_seqs, \
obi_new_view, \
obi_new_view_cloned_from_name, \
@ -65,7 +65,7 @@ from .capi.obiview cimport Obiview_p, \
obi_open_view, \
obi_view_delete_column, \
obi_view_add_column, \
obi_view_get_column, \
obi_view_create_column_alias, \
obi_view_get_column, \
obi_view_get_pointer_on_column_in_view, \
obi_select_line, \
@ -124,9 +124,6 @@ cdef class OBIDMS_column :
for line_nb in range(lines_used):
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.pointer, str2bytes(self.column_name))
cpdef list get_elements_names(self):
return self.elements_names
@ -297,58 +294,57 @@ cdef class OBIView :
for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
col_name = bytes2str(view.infos.column_references[i].alias)
subclass = OBIDMS_column.get_subclass_type(column_p)
self.columns[col_name] = subclass(self, col_name)
def __repr__(self) :
cdef str s
s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.infos.line_count) + " lines\n"
s = str(self.name) + "\n" + str(self.comments) + "\n" + str(self.pointer.infos.line_count) + " lines\n"
for column_name in self.columns :
s = s + self.columns[column_name].__repr__() + '\n'
s = s + column_name + ": " + self.columns[column_name].__repr__() + '\n'
return s
cpdef delete_column(self, str column_name) :
cdef int i
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
view = self.pointer
if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
if obi_view_delete_column(self.pointer, str2bytes(column_name)) < 0 :
raise Exception("Problem deleting a column from a view")
# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
# Update the dictionary of column objects:
(self.columns).pop(column_name)
for column_n in self.columns :
(self.columns[column_n]).update_pointer()
self.update_column_pointers()
cpdef add_column(self,
str column_name,
obiversion_t version_number=-1,
str alias='',
str type='',
index_t nb_lines=0,
index_t nb_elements_per_line=1,
list elements_names=None,
str indexer_name="",
str associated_column_name="",
obiversion_t associated_column_version=-1,
str comments="",
bint create=True
) :
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef bytes column_name_b
cdef bytes elements_names_b
cdef object subclass
cdef OBIDMS_column_p column_p
column_name_b = str2bytes(column_name)
if alias == '' :
alias = column_name
alias_b = column_name_b
else :
alias_b = str2bytes(alias)
if nb_elements_per_line > 1 :
elements_names_b = str2bytes(';'.join(elements_names))
@ -372,20 +368,37 @@ cdef class OBIView :
data_type = OBI_SEQ
else :
raise Exception("Invalid provided data type")
if (obi_view_add_column(self.pointer, column_name_b, version_number, # TODO should return pointer on column?
if (obi_view_add_column(self.pointer, column_name_b, version_number, alias_b, # TODO should return pointer on column?
data_type, nb_lines, nb_elements_per_line,
elements_names_b, str2bytes(indexer_name),
str2bytes(associated_column_name), associated_column_version,
str2bytes(comments), create) < 0) :
raise Exception("Problem adding a column in a view")
# Get the column pointer
column_p = obi_view_get_column(self.pointer, column_name_b)
column_p = obi_view_get_column(self.pointer, alias_b)
# Open and store the subclass
subclass = OBIDMS_column.get_subclass_type(column_p)
(self.columns)[column_name] = subclass(self, column_name)
(self.columns)[alias] = subclass(self, alias)
cpdef change_column_alias(self, str current_alias, str new_alias):
if (obi_view_create_column_alias(self.pointer, str2bytes(current_alias), str2bytes(new_alias)) < 0) :
raise Exception("Problem changing a column alias")
# Update the dictionaries of column column objects
self.columns[new_alias] = self.columns[current_alias]
(self.columns).pop(current_alias)
cpdef update_column_pointers(self):
cdef str column_n
cdef OBIDMS_column column
for column_n in self.columns :
column = self.columns[column_n]
column.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.pointer, str2bytes(column_n))
cpdef save_and_close(self) :
if (obi_save_and_close_view(self.pointer) < 0) :
@ -493,7 +506,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
for i in range(view.infos.column_count) :
column_p = <OBIDMS_column_p> (view.columns)[i]
header = (column_p).header
col_name = bytes2str(header.name)
col_name = bytes2str(view.infos.column_references[i].alias)
subclass = OBIDMS_column.get_subclass_type(column_p)
self.columns[col_name] = subclass(self, col_name)
@ -553,7 +566,7 @@ cdef class OBIView_line :
(((self.view).columns)[column_name]).set_line(self.index, value)
def __contains__(self, str column_name):
return (column_name in self.view)
return (column_name in self.view.columns)
def __repr__(self):
cdef dict line
@ -623,7 +636,7 @@ cdef class OBIDMS :
cdef Obiview_infos_p view_infos_p
cdef dict view_infos_d
cdef Column_reference_p column_refs
cdef Alias_column_pair_p column_refs
cdef int i, j
cdef str column_name
@ -643,11 +656,12 @@ cdef class OBIDMS :
view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
view_infos_d["column_references"] = {}
column_refs = view_infos_p.column_references
column_references = view_infos_p.column_references
for j in range(view_infos_d["column_count"]) :
column_name = bytes2str((column_refs[j]).column_name)
column_name = bytes2str((column_references[j]).alias)
view_infos_d["column_references"][column_name] = {}
view_infos_d["column_references"][column_name]["version"] = column_refs[j].version
view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
obi_view_unmap_file(self.pointer, view_infos_p)

2
python/obitools3/obidms/_obidmscolumn_bool.cfiles
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@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

18
python/obitools3/obidms/_obidmscolumn_bool.pyx
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@ -1,9 +1,9 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obibool_with_elt_name_in_view, \
obi_column_get_obibool_with_elt_idx_in_view, \
obi_column_set_obibool_with_elt_name_in_view, \
obi_column_set_obibool_with_elt_idx_in_view
from .capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIBool_NA, obibool_t
@ -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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_bool_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
if obi_set_bool_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_bool_with_elt_name_and_col_p_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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_bool_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
if obi_set_bool_with_elt_name_and_col_p_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")

2
python/obitools3/obidms/_obidmscolumn_char.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

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

@ -1,9 +1,9 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obichar_with_elt_name_in_view, \
obi_column_get_obichar_with_elt_idx_in_view, \
obi_column_set_obichar_with_elt_name_in_view, \
obi_column_set_obichar_with_elt_idx_in_view
from .capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIChar_NA, obichar_t
@ -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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_char_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
if obi_set_char_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_char_with_elt_name_and_col_p_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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_char_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
if obi_set_char_with_elt_name_and_col_p_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")

2
python/obitools3/obidms/_obidmscolumn_float.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

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

@ -1,9 +1,9 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obifloat_with_elt_name_in_view, \
obi_column_get_obifloat_with_elt_idx_in_view, \
obi_column_set_obifloat_with_elt_name_in_view, \
obi_column_set_obifloat_with_elt_idx_in_view
from .capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIFloat_NA, obifloat_t
@ -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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_float_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
if obi_set_float_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_float_with_elt_name_and_col_p_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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_float_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
if obi_set_float_with_elt_name_and_col_p_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")

2
python/obitools3/obidms/_obidmscolumn_int.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

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

@ -1,9 +1,9 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obiint_with_elt_name_in_view, \
obi_column_get_obiint_with_elt_idx_in_view, \
obi_column_set_obiint_with_elt_name_in_view, \
obi_column_set_obiint_with_elt_idx_in_view
from .capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIInt_NA, obiint_t
@ -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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_int_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
if obi_set_int_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_int_with_elt_name_and_col_p_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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_int_with_elt_idx_and_col_p_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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
if obi_set_int_with_elt_name_and_col_p_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")

2
python/obitools3/obidms/_obidmscolumn_qual.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

44
python/obitools3/obidms/_obidmscolumn_qual.pyx
View File

@ -1,13 +1,13 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obiqual_char_with_elt_name_in_view, \
obi_column_get_obiqual_char_with_elt_idx_in_view, \
obi_column_set_obiqual_char_with_elt_name_in_view, \
obi_column_set_obiqual_char_with_elt_idx_in_view, \
obi_column_get_obiqual_int_with_elt_name_in_view, \
obi_column_get_obiqual_int_with_elt_idx_in_view, \
obi_column_set_obiqual_int_with_elt_name_in_view, \
obi_column_set_obiqual_int_with_elt_idx_in_view
from .capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
obi_set_qual_char_with_elt_name_and_col_p_in_view, \
obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
obi_get_qual_int_with_elt_name_and_col_p_in_view, \
obi_get_qual_int_with_elt_idx_and_col_p_in_view, \
obi_set_qual_int_with_elt_name_and_col_p_in_view, \
obi_set_qual_int_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIQual_char_NA, OBIQual_int_NA, const_char_p
@ -29,7 +29,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
cdef int value_length
cdef object result
cdef int i
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length)
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
@ -44,7 +44,7 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
cdef char* value
cdef object result
cdef int i
value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
@ -58,23 +58,23 @@ cdef class OBIDMS_column_qual(OBIDMS_column):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
if obi_set_qual_int_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_line(self, index_t line_nb, object value):
if value is None :
if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], 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)[0], line_nb, 0, OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_set_qual_char_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
@ -85,7 +85,7 @@ cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
cdef int value_length
cdef object result
cdef int i
value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
value = obi_get_qual_int_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
if value == OBIQual_int_NA :
@ -99,7 +99,7 @@ cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
cpdef object get_str_item(self, index_t line_nb, str element_name):
cdef char* value
cdef object result
value = obi_column_get_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_qual_char_with_elt_name_and_col_p_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 == OBIQual_char_NA :
@ -120,7 +120,7 @@ cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i, &value_length)
value = obi_get_qual_int_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, i, &value_length)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_int_NA :
@ -145,7 +145,7 @@ cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :
value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_qual_char_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIQual_char_NA :
@ -164,21 +164,21 @@ cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
cdef uint8_t* value_b
cdef int value_length
if value is None :
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
raise Exception("Problem setting a value in a column")
else :
value_length = len(value)
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
for i in range(value_length) :
value_b[i] = <uint8_t>value[i]
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
if obi_set_qual_int_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
raise Exception("Problem setting a value in a column")
free(value_b)
cpdef set_str_item(self, index_t line_nb, str element_name, object value):
if value is None :
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
if obi_set_qual_char_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")

2
python/obitools3/obidms/_obidmscolumn_seq.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

20
python/obitools3/obidms/_obidmscolumn_seq.pyx
View File

@ -1,9 +1,9 @@
#cython: language_level=3
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.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_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
@ -20,7 +20,7 @@ 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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
@ -32,10 +32,10 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
# TODO choose alignment type (lcs or other) with supplementary argument
@ -56,7 +56,7 @@ 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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_seq_with_elt_name_and_col_p_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 == OBISeq_NA :
@ -75,7 +75,7 @@ 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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBISeq_NA :
@ -102,7 +102,7 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
else:
raise TypeError('Sequence value must be of type Bytes, Str or None')
if obi_column_set_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
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:
raise Exception("Problem setting a value in a column")
# cpdef align(self, ): # TODO

2
python/obitools3/obidms/_obidmscolumn_str.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

20
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -1,9 +1,9 @@
#cython: language_level=3
from .capi.obiview cimport obi_column_get_obistr_with_elt_name_in_view, \
obi_column_get_obistr_with_elt_idx_in_view, \
obi_column_set_obistr_with_elt_name_in_view, \
obi_column_set_obistr_with_elt_idx_in_view
from .capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view
from .capi.obierrno cimport obi_errno
from .capi.obitypes cimport OBIStr_NA, const_char_p
@ -15,7 +15,7 @@ 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.pointer, (self.pointer)[0], line_nb, 0)
value = obi_get_str_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
@ -27,10 +27,10 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cpdef set_line(self, index_t line_nb, object value):
if value is None :
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIStr_NA) < 0:
if obi_set_str_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIStr_NA) < 0:
raise Exception("Problem setting a value in a column")
else :
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
if obi_set_str_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
raise Exception("Problem setting a value in a column")
@ -39,7 +39,7 @@ 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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
value = obi_get_str_with_elt_name_and_col_p_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 == OBIStr_NA :
@ -58,7 +58,7 @@ 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.pointer, (self.pointer)[0], line_nb, i)
value = obi_get_str_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
if obi_errno > 0 :
raise IndexError(line_nb)
if value == OBIStr_NA :
@ -79,6 +79,6 @@ 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.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
if obi_set_str_with_elt_name_and_col_p_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")

2
python/obitools3/obidms/_obiseq.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

2
python/obitools3/obidms/_obitaxo.cfiles
View File

@ -8,6 +8,8 @@
../../../src/dna_seq_indexer.c
../../../src/encode.h
../../../src/encode.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obi_align.h

37
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -16,21 +16,28 @@ from libc.stdint cimport uint8_t
cdef extern from "obidmscolumn.h" nogil:
struct Column_reference_t :
const_char_p column_name
obiversion_t version
ctypedef Column_reference_t* Column_reference_p
struct OBIDMS_column_header_t:
size_t header_size
size_t data_size
index_t line_count
index_t lines_used
index_t nb_elements_per_line
const_char_p elements_names
OBIType_t returned_data_type
OBIType_t stored_data_type
time_t creation_date
obiversion_t version
obiversion_t cloned_from
const_char_p name
const_char_p indexer_name
const_char_p comments
size_t header_size
size_t data_size
index_t line_count
index_t lines_used
index_t nb_elements_per_line
const_char_p elements_names
OBIType_t returned_data_type
OBIType_t stored_data_type
time_t creation_date
obiversion_t version
obiversion_t cloned_from
const_char_p name
const_char_p indexer_name
Column_reference_t associated_column
const_char_p comments
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
@ -48,6 +55,8 @@ cdef extern from "obidmscolumn.h" nogil:
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p indexer_name,
const_char_p associated_colum_name,
obiversion_t associated_colum_version,
const_char_p comments)
OBIDMS_column_p obi_open_column(OBIDMS_p dms,

165
python/obitools3/obidms/capi/obiview.pxd
View File

@ -10,7 +10,9 @@ from .obitypes cimport const_char_p, \
index_t, \
time_t
from ..capi.obidms cimport OBIDMS_p
from ..capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidmscolumn cimport OBIDMS_column_p, \
Column_reference_t, \
Column_reference_p
from libc.stdint cimport uint8_t
@ -24,11 +26,11 @@ cdef extern from "obiview.h" nogil:
extern const_char_p QUALITY_COLUMN
struct Column_reference_t :
const_char_p column_name
obiversion_t version
struct Alias_column_pair_t :
Column_reference_t column_refs
const_char_p alias
ctypedef Column_reference_t* Column_reference_p
ctypedef Alias_column_pair_t* Alias_column_pair_p
struct Obiview_infos_t :
@ -40,7 +42,7 @@ cdef extern from "obiview.h" nogil:
Column_reference_t line_selection
index_t line_count
int column_count
Column_reference_p column_references
Alias_column_pair_p column_references
const_char_p comments
ctypedef Obiview_infos_t* Obiview_infos_p
@ -53,7 +55,9 @@ cdef extern from "obiview.h" nogil:
OBIDMS_column_p line_selection
OBIDMS_column_p new_line_selection
OBIDMS_column_p columns
int nb_predicates
# TODO declarations for column dictionary and predicate function array?
ctypedef Obiview_t* Obiview_p
@ -74,11 +78,14 @@ cdef extern from "obiview.h" nogil:
int obi_view_add_column(Obiview_p view,
const_char_p column_name,
obiversion_t version_number,
const_char_p alias,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p indexer_name,
const_char_p associated_column_name,
obiversion_t associated_column_version,
const_char_p comments,
bint create)
@ -92,189 +99,205 @@ cdef extern from "obiview.h" nogil:
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)
int obi_save_view(Obiview_p view)
int obi_close_view(Obiview_p view)
int obi_save_and_close_view(Obiview_p view)
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_INT
int obi_set_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obiint_t value)
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obiint_t value)
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
obiint_t obi_get_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
obiint_t obi_get_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_BOOL
int obi_set_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obibool_t value)
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obibool_t value)
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
obibool_t obi_get_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
obibool_t obi_get_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_CHAR
int obi_set_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obichar_t value)
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obichar_t value)
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
obichar_t obi_get_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
obichar_t obi_get_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_FLOAT
int obi_set_float_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
obifloat_t obi_get_float_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
obifloat_t obi_get_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiqual_char_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_QUAL
int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const char* value)
int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const uint8_t* value,
int value_length)
char* obi_column_get_obiqual_char_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
const uint8_t* obi_column_get_obiqual_int_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
int* value_length)
int obi_column_set_obiqual_char_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
const char* value)
int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
const uint8_t* value,
int value_length)
char* obi_column_get_obiqual_char_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name)
const uint8_t* obi_column_get_obiqual_int_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const char* element_name,
int* value_length)
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_STR
int obi_set_str_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const_char_p value)
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
const_char_p obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
const_char_p obi_get_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
# OBI_SEQ
int obi_set_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name,
const_char_p value)
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
int obi_set_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx,
const_char_p value)
char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
char* obi_get_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
const_char_p element_name)
char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
char* obi_get_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
OBIDMS_column_p column_p,
index_t line_nb,
index_t element_idx)