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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)

72
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
@ -297,48 +294,42 @@ 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
) :
@ -349,6 +340,11 @@ cdef class OBIView :
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))
@ -373,18 +369,35 @@ cdef class OBIView :
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) :
@ -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

9
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -16,6 +16,12 @@ 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
@ -30,6 +36,7 @@ cdef extern from "obidmscolumn.h" nogil:
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,

163
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
@ -53,6 +55,8 @@ 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)

197
src/hashtable.c Normal file
View File

@ -0,0 +1,197 @@
/****************************************************************************
* Hash table source file *
****************************************************************************/
/**
* @file hashtable.c
* @author Celine Mercier
* @date July 26th 2016
* @brief Source file for hash table functions.
*/
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include "string.h"
#include "murmurhash2.h"
#include "hashtable.h"
// Create a new hashtable
hashtable_p ht_create(size_t size)
{
hashtable_p hashtable = NULL;
size_t i;
// Allocate the table
hashtable = malloc(sizeof(hashtable_t));
if (hashtable == NULL)
return NULL;
// Allocate the head nodes
hashtable->table = malloc(size * sizeof(entry_p));
if (hashtable->table == NULL)
return NULL;
// Initialize the head nodes
for (i=0; i<size; i++)
hashtable->table[i] = NULL;
hashtable->size = size;
return hashtable;
}
// Create an entry
entry_p ht_new_entry(const char* key, void* value)
{
entry_p new_entry;
new_entry = malloc(sizeof(entry_t));
if (new_entry == NULL)
return NULL;
new_entry->key = strdup(key);
if (new_entry->key == NULL)
return NULL;
new_entry->value = value;
new_entry->next = NULL;
return new_entry;
}
// Delete an entry
int ht_delete_entry(hashtable_p hashtable, const char* key)
{
entry_p last = NULL;
entry_p entry = NULL;
size_t bin = 0;
bin = murmurhash2(key, strlen(key), SEED);
bin = bin % hashtable->size;
// Step through the bin looking for the value
entry = hashtable->table[bin];
while ((entry != NULL) && (strcmp(key, entry->key ) != 0))
{
last = entry;
entry = entry->next;
}
if (entry == NULL) // key not found
return -1;
// Link the entries before and after the entry
if (last != NULL) // If not head node
last->next = entry->next;
else // If head node
hashtable->table[bin] = entry->next;
// Free the entry
free(entry->key);
free(entry->value);
free(entry);
return 0;
}
// Set a new entry in the hash table. If the key is already in the table, the value is replaced by the new one
int ht_set(hashtable_p hashtable, const char* key, void* value)
{
size_t bin = 0;
entry_p new_entry = NULL;
entry_p next = NULL;
entry_p last = NULL;
if ((key == NULL) || (value == NULL))
return -1;
bin = murmurhash2(key, strlen(key), SEED);
bin = bin % hashtable->size;
next = hashtable->table[bin];
while ((next != NULL) && (strcmp(key, next->key) != 0))
{
last = next;
next = next->next;
}
// If the key is already in the table, the value is replaced
if ((next != NULL) && (strcmp(key, next->key) == 0))
new_entry->value = value;
// Else, create the new entry and link it at the end of the list
else
{
// Create the new entry
new_entry = ht_new_entry(key, value);
if (new_entry == NULL)
return -1;
// If it is the first entry of that bin, we're at the head node of the list, and we replace it with the new entry
if (last == NULL)
hashtable->table[bin] = new_entry;
// Else link the new entry at the end of the list
else
last->next = new_entry;
}
return 0;
}
// Retrieve a value from a hash table
void* ht_get(hashtable_p hashtable, const char* key)
{
size_t bin = 0;
entry_p entry;
bin = murmurhash2(key, strlen(key), SEED);
bin = bin % hashtable->size;
// Step through the bin looking for the value
entry = hashtable->table[bin];
while ((entry != NULL) && (strcmp(key, entry->key ) != 0))
entry = entry->next;
if (entry == NULL)
return NULL;
else
return entry->value;
}
// Free the hash table
void ht_free(hashtable_p hashtable)
{
size_t i;
entry_p entry;
entry_p next;
for (i=0; i < hashtable->size; i++)
{
next = hashtable->table[i];
while (next != NULL)
{
entry = next;
free(entry->key);
next = entry->next;
free(entry);
}
}
free(hashtable->table);
free(hashtable);
}

123
src/hashtable.h Normal file
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@ -0,0 +1,123 @@
/****************************************************************************
* Hash table header file *
****************************************************************************/
/**
* @file hashtable.h
* @author Celine Mercier
* @date July 26th 2016
* @brief Header file for hash table functions.
*/
#ifndef HASHTABLE_H_
#define HASHTABLE_H_
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#define SEED (0x9747b28c) /**< The seed used by the hash function.
*/
/**
* @brief Structure for an entry.
*/
typedef struct entry_s {
char* key; /**< Key used to refer to the entry.
*/
void* value; /**< Pointer on the value to be stored.
*/
struct entry_s* next; /**< Pointer on the next entry in the bin.
*/
} entry_t, *entry_p;
/**
* @brief Structure for a hash table.
*/
typedef struct hashtable {
size_t size; /**< Number of bins in the table.
*/
entry_p* table; /**< Table of bins.
*/
} hashtable_t, *hashtable_p;
/**
* @brief Creates a new hashtable.
*
* @param size The number of bins in the hash table.
*
* @returns A pointer to the newly created hash table.
* @retval NULL if an error occurred.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
hashtable_p ht_create(size_t size);
/**
* @brief Inserts a new entry in the hash table.
* If the key is already in the table, the value is replaced by the new one.
*
* @param hashtable A pointer on the hash table structure.
* @param key The key.
* @param value A pointer on the value associated with the key.
*
* @retval 0 if the entry was correctly set.
* @retval -1 if an error occurred.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int ht_set(hashtable_p hashtable, const char* key, void* value);
/**
* @brief Retrieves a value from a hash table.
*
* @param hashtable A pointer on the hash table structure.
* @param key The key.
*
* @returns A pointer on the value associated with the key.
* @retval NULL if the key was not found.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void* ht_get(hashtable_p hashtable, const char* key);
/**
* @brief Deletes an entry.
*
* @param hashtable A pointer on the hash table structure.
* @param key The key.
*
* @retval 0 if the entry was correctly deleted.
* @retval -1 if an error occurred.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int ht_delete_entry(hashtable_p hashtable, const char* key);
/**
* @brief Frees a hash table.
*
* @param hashtable A pointer on the hash table structure.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void ht_free(hashtable_p hashtable);
#endif /* HASHTABLE_H_ */

28
src/obidmscolumn.c
View File

@ -534,6 +534,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments
)
{
@ -750,6 +752,30 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
if (comments != NULL)
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
// Store the associated column reference if needed // TODO discuss cases
if (data_type == OBI_QUAL)
{
if (associated_column_name == NULL)
{
obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(new_column);
return NULL;
}
strcpy((header->associated_column).column_name, associated_column_name);
if (associated_column_version == -1)
{
obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
munmap(new_column->header, header_size);
close(column_file_descriptor);
free(new_column);
return NULL;
}
(header->associated_column).version = associated_column_version;
}
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
{
@ -964,6 +990,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line,
(column_to_clone->header)->elements_names,
(column_to_clone->header)->indexer_name,
((column_to_clone->header)->associated_column).column_name,
((column_to_clone->header)->associated_column).version,
(column_to_clone->header)->comments
);

19
src/obidmscolumn.h
View File

@ -38,6 +38,17 @@
*/
/**
* @brief Structure referencing a column by its name and its version.
*/
typedef struct Column_reference {
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
*/
obiversion_t version; /**< Version of the column.
*/
} Column_reference_t, *Column_reference_p;
/**
* @brief OBIDMS column header structure.
*/
@ -73,6 +84,8 @@ typedef struct OBIDMS_column_header {
*/
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
*/
Column_reference_t associated_column; /**< If there is one, the reference to the associated column.
*/
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
*/
} OBIDMS_column_header_t, *OBIDMS_column_header_p;
@ -168,13 +181,15 @@ size_t obi_get_platform_header_size();
* @param nb_elements_per_line The number of elements per line. // TODO talk about default values
* @param elements_names The names of the elements with ';' as separator.
* @param indexer_name The name of the indexer if there is one associated with the column.
* @param associated_column_name The name of the associated column if there is one.
* @param associated_column_version The version of the associated column if there is one.
* @param comments Optional comments associated with the column.
*
* @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred.
*
* @since May 2015
* @author Eric Coissac (eric.coissac@metabarcoding.org)
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* column_name,
@ -183,6 +198,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments
);

1189
src/obiview.c
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File diff suppressed because it is too large Load Diff

302
src/obiview.h
View File

@ -25,6 +25,7 @@
#include "obidms.h"
#include "obidmscolumn.h"
#include "obierrno.h"
#include "hashtable.h"
#define OBIVIEW_NAME_MAX_LENGTH (1000) /**< The maximum length of an OBIDMS view name.
@ -55,14 +56,15 @@
/**
* @brief Structure referencing a column by its name and its version.
* @brief Structure for column aliases.
* Column aliases are alternative names used to identify a column in the context of a view.
*/
typedef struct Column_reference {
char column_name[OBIDMS_COLUMN_MAX_NAME+1]; /**< Name of the column.
typedef struct Alias_column_pair {
Column_reference_t column_refs; /**< References (name and version) of the column.
*/
obiversion_t version; /**< Version of the column.
char alias[OBIDMS_COLUMN_MAX_NAME+1]; /**< Alias of the column in the context of a view.
*/
} Column_reference_t, *Column_reference_p;
} Alias_column_pair_t, *Alias_column_pair_p;
/**
@ -82,13 +84,13 @@ typedef struct Obiview_infos {
*/
bool all_lines; /**< Whether there is a line selection associated with the view.
*/
Column_reference_t line_selection; /**< Whether there is a line selection associated with the view.
Column_reference_t line_selection; /**< The references of the line selection associated with the view if there is one.
*/
index_t line_count; /**< The number of lines in the view.
*/
int column_count; /**< The number of columns in the view.
*/
Column_reference_t column_references[MAX_NB_OPENED_COLUMNS]; /**< References (name and version) for all the columns in the view.
Alias_column_pair_t column_references[MAX_NB_OPENED_COLUMNS]; /**< References (name, version and alias) for all the columns in the view.
*/
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
*/
@ -117,33 +119,16 @@ typedef struct Obiview {
*/
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
*/
hashtable_p column_dict; /**< Hash table storing the pairs of column names or aliases with the associated
* column pointers.
*/
int nb_predicates; /**< Number of predicates to test when closing the view.
*/
char* (**predicate_functions)(struct Obiview* view); /**< Array of pointers on all predicate functions to test when closing the view.
*/
} Obiview_t, *Obiview_p;
/**
* @brief Structure for the header of view files.
*/
typedef struct Obiviews_header {
size_t header_size; /**< Size of the header in bytes.
*/
size_t views_size; /**< Size of the views in bytes.
*/
int view_count; /**< Number of views saved.
*/
} Obiviews_header_t, *Obiviews_header_p;
/**
* @brief Structure for the information stored in view files.
*/
typedef struct Obiviews_infos_all {
Obiviews_header_p header; /**< Pointer on the header of the view file.
*/
Obiview_infos_p view_infos; /**< Pointer on the beginning (first view) of the informations on views.
*/
} Obiviews_infos_all_t, *Obiviews_infos_all_p;
/**
* @brief Creates a new view.
*
@ -306,6 +291,7 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
* @param view A pointer on the view.
* @param column_name The name of the column.
* @param version_number The version of the column if it should be opened and not created (if -1, the latest version is retrieved).
* @param alias The unique name used to identify the column in the context of this view.
* @param data_type The OBIType code of the data.
* @param nb_lines The number of lines to be stored.
* @param nb_elements_per_line The number of elements per line.
@ -324,11 +310,14 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
int obi_view_add_column(Obiview_p view,
const char* column_name,
obiversion_t version_number,
const char* alias,
OBIType_t data_type,
index_t nb_lines,
index_t nb_elements_per_line,
const char* elements_names,
const char* indexer_name,
const char* associated_column_name,
obiversion_t associated_column_version,
const char* comments,
bool create);
@ -383,6 +372,27 @@ OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name);
/**
* @brief Changes the name that identifies a column in the context of a view.
*
* In the context of a view, each column is identified by a name that is unique in this view.
*
* @warning The view must be writable.
*
* @param view A pointer on the view.
* @param current_name The current name that identifies the column in this view.
* @param alias The new name that should be used to identify the column in this view.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since July 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias);
/**
* @brief Selects a line in the context of a view.
*
@ -479,38 +489,6 @@ int obi_close_view(Obiview_p view);
int obi_save_and_close_view(Obiview_p view);
/**
* @brief Opens the structure containing all the informations written in the view file.
*
* @param dms A pointer on the OBIDMS to which the view file belongs.
*
* @returns A pointer on the view informations structure.
* @retval NULL if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms);
/**
* @brief Closes the structure containing all the informations written in the view file.
*
* @param views A pointer on the view informations structure.
*
* @returns A value indicating the success of the operation.
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_close_view_infos(Obiviews_infos_all_p views);
// TODO in following functions would it be better to use column names instead of column pointers?
// check if it would be a gain or loss of time
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line,
* in the context of a view.
@ -518,7 +496,7 @@ int obi_close_view_infos(Obiviews_infos_all_p views);
* Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned.
*
* @param view A pointer on the opened writable view.
* @param column A pointer on the column.
* @param column_p A pointer on the column.
* @param line_nb The number of the line where the value should be set.
* @param element_idx The index of the element that should be set in the line.
* @param value The value that should be set.
@ -530,14 +508,17 @@ int obi_close_view_infos(Obiviews_infos_all_p views);
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
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);
// TODO
int obi_set_bool_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obibool_t value);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column A pointer on the column.
* @param column_p A pointer on the column.
* @param line_nb The number of the line where the value should be recovered.
* @param element_idx The index of the element that should be recovered in the line.
*
@ -547,7 +528,10 @@ int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
obibool_t obi_get_bool_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -555,7 +539,7 @@ obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_col
* using the name of the element in the line, in the context of a view.
*
* @param view A pointer on the opened writable view.
* @param column A pointer on the column.
* @param column_p A pointer on the column.
* @param line_nb The number of the line where the value should be set.
* @param element_name The name of the element that should be set in the line.
* @param value The value that should be set.
@ -567,7 +551,11 @@ obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_col
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
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* element_name, obibool_t value);
// TODO
int obi_set_bool_with_elt_name_and_column_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obibool_t value);
/**
@ -575,7 +563,7 @@ int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* using the name of the element in the line, in the context of a view.
*
* @param view A pointer on the opened view.
* @param column A pointer on the column.
* @param column_p A pointer on the column.
* @param line_nb The number of the line where the value should be recovered.
* @param element_name The name of the element that should be recovered in the line.
*
@ -585,7 +573,11 @@ int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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* element_name);
// TODO
obibool_t obi_get_bool_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -607,7 +599,11 @@ obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_co
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
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);
// TODO
int obi_set_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obichar_t value);
/**
@ -624,7 +620,11 @@ int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
obichar_t obi_get_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -644,7 +644,11 @@ obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_col
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
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* element_name, obichar_t value);
// TODO
int obi_set_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obichar_t value);
/**
@ -662,7 +666,11 @@ int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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* element_name);
// TODO
obichar_t obi_get_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -684,7 +692,11 @@ obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_co
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
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);
// TODO
int obi_set_float_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obifloat_t value);
/**
@ -701,7 +713,11 @@ int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
obifloat_t obi_get_float_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -721,7 +737,11 @@ obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_c
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
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* element_name, obifloat_t value);
// TODO
int obi_set_float_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obifloat_t value);
/**
@ -739,7 +759,11 @@ int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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* element_name);
// TODO
obifloat_t obi_get_float_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -761,7 +785,11 @@ obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
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);
// TODO
int obi_set_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, obiint_t value);
/**
@ -778,7 +806,11 @@ int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
obiint_t obi_get_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -798,7 +830,11 @@ obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_colum
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
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* element_name, obiint_t value);
// TODO
int obi_set_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, obiint_t value);
/**
@ -816,7 +852,11 @@ int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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* element_name);
// TODO
obiint_t obi_get_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -841,7 +881,11 @@ obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_colu
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
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);
// TODO
int obi_set_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value);
/**
@ -867,7 +911,11 @@ int obi_column_set_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_colu
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length);
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);
// TODO
int obi_set_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length);
/**
@ -888,7 +936,11 @@ int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_colum
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
char* obi_get_qual_char_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -910,7 +962,11 @@ char* obi_column_get_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_co
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const uint8_t* obi_column_get_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length);
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);
// TODO
const uint8_t* obi_get_qual_int_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, int* value_length);
/**
@ -935,7 +991,11 @@ const uint8_t* obi_column_get_obiqual_int_with_elt_idx_in_view(Obiview_p view, O
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
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);
// TODO
int obi_set_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value);
/**
@ -961,7 +1021,11 @@ int obi_column_set_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_col
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length);
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);
// TODO
int obi_set_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const uint8_t* value, int value_length);
/**
@ -982,7 +1046,11 @@ int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_colu
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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);
// TODO
char* obi_get_qual_char_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -1004,7 +1072,11 @@ char* obi_column_get_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_c
* @since May 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const uint8_t* obi_column_get_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length);
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);
// TODO
const uint8_t* obi_get_qual_int_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, int* value_length);
/**
@ -1026,7 +1098,11 @@ const uint8_t* obi_column_get_obiqual_int_with_elt_name_in_view(Obiview_p view,
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
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* value);
// TODO
int obi_set_seq_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value);
/**
@ -1043,7 +1119,11 @@ int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
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);
// TODO
char* obi_get_seq_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -1063,7 +1143,11 @@ char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
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* element_name, const char* value);
// TODO
int obi_set_seq_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value);
/**
@ -1081,7 +1165,11 @@ int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
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* element_name);
// TODO
char* obi_get_seq_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
/**
@ -1103,7 +1191,11 @@ char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
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* value);
// TODO
int obi_set_str_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, const char* value);
/**
@ -1120,7 +1212,11 @@ int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p c
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
const char* 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);
// TODO
const char* obi_get_str_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
/**
@ -1140,7 +1236,11 @@ const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_co
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
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* element_name, const char* value);
// TODO
int obi_set_str_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, const char* value);
/**
@ -1158,7 +1258,11 @@ int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
const char* 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* element_name);
// TODO
const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
#endif /* OBIVIEW_H_ */