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Refactored and relocated the set and get functions of all column types,

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both within and out of the context of a view
This commit is contained in:
Celine Mercier
2016-04-13 15:10:24 +02:00
parent 5ec2d8842e
commit 9d042f7bd0
28 changed files with 1079 additions and 1320 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
python/obitools3/obidms/_obidms.cfiles
View File

@ -37,3 +37,15 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h

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

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obibool_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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

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

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obichar_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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

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

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
obi_column_get_obifloat_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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

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

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obiint_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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

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

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obiseq_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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

22
python/obitools3/obidms/_obidmscolumn_str.pyx
View File

@ -1,7 +1,7 @@
#cython: language_level=3
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
obi_column_get_obistr_with_elt_name_in_view, \
from .capi.obidmscolumn cimport obi_truncate_and_close_column
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
@ -16,8 +16,8 @@ from libc.string cimport strcmp
cdef class OBIDMS_column_str(OBIDMS_column):
cpdef object get_line(self, index_t line_nb):
cdef char* value
cdef object result
cdef const_char_p value
cdef object result
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
if obi_errno > 0 :
raise IndexError(line_nb)
@ -41,8 +41,8 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
cpdef object get_item(self, index_t line_nb, str element_name):
cdef char* value
cdef object result
cdef const_char_p value
cdef object result
value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
if obi_errno > 0 :
raise IndexError(line_nb, element_name)
@ -54,11 +54,11 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
return result
cpdef object get_line(self, index_t line_nb) :
cdef char* value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
cdef const_char_p value
cdef object value_in_result
cdef dict result
cdef index_t i
cdef bint all_NA
result = {}
all_NA = True
for i in range(self.nb_elements_per_line) :

177
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -76,30 +76,7 @@ cdef extern from "obidmscolumn.h" nogil:
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
from ..capi.obiview cimport Obiview_p # TODO
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
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,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
@ -121,28 +98,6 @@ cdef extern from "obidmscolumn_int.h" nogil:
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
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,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
@ -163,28 +118,6 @@ cdef extern from "obidmscolumn_bool.h" nogil:
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
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,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
@ -205,83 +138,39 @@ cdef extern from "obidmscolumn_char.h" nogil:
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
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,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
obifloat_t value)
index_t line_nb,
const_char_p element_name,
obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
obifloat_t value)
index_t line_nb,
index_t element_idx,
obifloat_t value)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
index_t line_nb,
const_char_p element_name)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
index_t line_nb,
index_t element_idx)
cdef extern from "obidmscolumn_str.h" nogil:
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
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,
char* value)
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
const_char_p value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p value)
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
char* element_name)
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
@ -289,43 +178,21 @@ cdef extern from "obidmscolumn_str.h" nogil:
cdef extern from "obidmscolumn_seq.h" nogil:
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
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,
char* value)
const_char_p obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name,
char* value)
const_char_p value)
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx,
char* value)
const_char_p value)
const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
char* element_name)
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
index_t line_nb,
const_char_p element_name)
const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
index_t line_nb,
index_t element_idx)

136
python/obitools3/obidms/capi/obiview.pxd
View File

@ -3,6 +3,10 @@
from .obitypes cimport const_char_p, \
OBIType_t, \
obiversion_t, \
obiint_t, \
obibool_t, \
obichar_t, \
obifloat_t, \
index_t, \
time_t
from ..capi.obidms cimport OBIDMS_p
@ -111,4 +115,136 @@ cdef extern from "obiview.h" nogil:
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
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,
index_t line_nb,
index_t element_idx)
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
OBIDMS_column_p column,
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,
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,
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,
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,
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,
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,
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,
index_t line_nb,
index_t element_idx)

48
python/obitools3/obiimport.py
View File

@ -26,16 +26,16 @@ if __name__ == '__main__':
view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
for i in range(35000000) :
if (not (i%500000)) :
print(str(time.time())+'\t'+str(i))
id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
view[i].set_id(id)
if id != view[i]["ID"] :
print("nope", id, view[i]["ID"])
# for i in range(35000000) :
# if (not (i%500000)) :
# print(str(time.time())+'\t'+str(i))
# id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
# view[i].set_id(id)
# if id != view[i]["ID"] :
# print("nope", id, view[i]["ID"])
# input_file = open(args.input_file, 'r')
# input_file_buffered = bufferedRead(input_file)
input_file = open(args.input_file, 'r')
input_file_buffered = bufferedRead(input_file)
#
# if args.input_file[-1:] == "a" :
@ -113,32 +113,32 @@ if __name__ == '__main__':
# l = 0
# next = False
#
# l=0
# i=0
l=0
i=0
# while (True):
# l+=1
# line = input_file.readline()
# if line=="":
# break
# for line in input_file_buffered :
for line in input_file_buffered :
#
# #if i > 1E7 :
#if i > 1E7 :
# # print('hmm?')
#
# if i == 6000000 :
# break
#
# if l%4 == 0 :
if l%4 == 0 :
#
# if (not (i%500000)) :
# print(str(time.time())+'\t'+str(i))
if (not (i%500000)) :
print(str(time.time())+'\t'+str(i))
# #
# # #print("header", line)
# #
# id = line.split(" ", 1)[0][1:]
id = line.split(" ", 1)[0][1:]
# print(id)
# # #rest = (line[:-1].split(" ", 1)[1]).split(";")
# view[i].set_id(id)
view[i].set_id(id)
# print(view[i]["ID"])
#
# i+=1
@ -178,17 +178,17 @@ if __name__ == '__main__':
# # description = description.strip()
# # view[i].set_description(description)
#
# # elif l%4 == 1 :
elif l%4 == 1 :
# #
# # seq = line[:-1]
seq = line[:-1]
# #print("seq", seq)
# # view[i].set_sequence(seq)
# # i+=1
view[i].set_sequence(seq)
i+=1
#
# l+=1
l+=1
#
#
# input_file.close()
input_file.close()
#print(view)
print(view.__repr__())

48
src/obidmscolumn.c
View File

@ -1418,7 +1418,53 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
}
char* obi_column_format_date(time_t date)
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
{
// Check if the column is read-only
if (!(column->writable))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value in a read-only column");
return -1;
}
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
return 0;
}
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
return -1;
}
return 0;
}
char* obi_column_format_date(time_t date) // TODO put in utils.c
{
char* formatted_time;
struct tm* tmp;

10
src/obidmscolumn.h
View File

@ -344,7 +344,15 @@ int obi_unmap_header(OBIDMS_column_header_p header);
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
/**
// TODO doc
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb);
// TODO doc
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb);
/** TODO put in utils.c
* @brief Formats a date in a way that is easy to read.
*
* @warning The pointer returned must be freed by the caller.

112
src/obidmscolumn_bool.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -32,25 +31,8 @@
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@ -59,111 +41,31 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
}
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)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable)))
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
if (obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value) < 0)
return -1;
return 0;
}
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIBool_NA;
}
return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
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)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBIBool_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
return 0;
return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
}
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIBool_NA;
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIBool_NA;
return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

75
src/obidmscolumn_bool.h
View File

@ -19,7 +19,6 @@
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obiview.h"
/**
@ -96,79 +95,5 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIDMSCOLUMN_BOOL_H_ */

113
src/obidmscolumn_char.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -32,25 +31,8 @@
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@ -59,111 +41,30 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
}
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)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable)))
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
if (obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value) < 0)
return -1;
return 0;
}
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIChar_NA;
}
return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
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)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBIChar_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
return 0;
return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
}
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIChar_NA;
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIChar_NA;
return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

75
src/obidmscolumn_char.h
View File

@ -19,7 +19,6 @@
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obiview.h"
/**
@ -96,79 +95,5 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIDMSCOLUMN_CHAR_H_ */

112
src/obidmscolumn_float.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -31,25 +30,8 @@
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@ -58,111 +40,31 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
}
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)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable)))
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
if (obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value) < 0)
return -1;
return 0;
}
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIFloat_NA;
}
return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
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)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBIFloat_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
return 0;
return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
}
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIFloat_NA;
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIFloat_NA;
return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

75
src/obidmscolumn_float.h
View File

@ -19,7 +19,6 @@
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obiview.h"
/**
@ -96,79 +95,5 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIDMSCOLUMN_FLOAT_H_ */

27
src/obidmscolumn_idx.c
View File

@ -31,25 +31,8 @@
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((index_t*) (column->data)) + line_nb) = value;
@ -60,12 +43,8 @@ int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIIdx_NA;
}
return *(((index_t*) (column->data)) + line_nb);
}

1
src/obidmscolumn_idx.h
View File

@ -20,6 +20,7 @@
#include "obidmscolumn.h"
#include "obitypes.h"
// TODO doc
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);

114
src/obidmscolumn_int.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -29,28 +28,10 @@
*
**********************************************************************/
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
{
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Set the value
*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
@ -59,112 +40,31 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
}
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)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable)))
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
if (obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value) < 0)
return -1;
return 0;
}
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBIInt_NA;
}
return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
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)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBIInt_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
return 0;
return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
}
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIInt_NA;
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIInt_NA;
return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

75
src/obidmscolumn_int.h
View File

@ -19,7 +19,6 @@
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obiview.h"
/**
@ -96,79 +95,5 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb,
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIDMSCOLUMN_INT_H_ */

118
src/obidmscolumn_seq.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -30,31 +29,14 @@
*
**********************************************************************/
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
{
index_t idx;
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Add the value in the indexer
idx = obi_index_dna_seq(column->indexer, value);
if (idx == -1)
return -1;
@ -66,50 +48,12 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
}
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, char* value)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable)))
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
}
const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
index_t idx;
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBISeq_NA;
}
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
@ -121,60 +65,22 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
}
const 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)
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBISeq_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
}
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, char* value)
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBISeq_NA;
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
}
const 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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBISeq_NA;
return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

84
src/obidmscolumn_seq.h
View File

@ -40,7 +40,7 @@
* @since November 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
/**
@ -57,7 +57,7 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
* @since November 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
/**
@ -78,7 +78,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
* @since November 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
/**
@ -95,83 +95,7 @@ int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb,
* @since November 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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, char* value);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the index of the element in the line.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const 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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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, char* value);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @since February 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
const 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_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
#endif /* OBIDMSCOLUMN_SEQ_H_ */

120
src/obidmscolumn_str.c
View File

@ -14,7 +14,6 @@
#include <stdio.h>
#include "obidmscolumn.h"
#include "obiview.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
@ -30,31 +29,14 @@
*
**********************************************************************/
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
{
index_t idx;
index_t idx;
// Check that the line number is not greater than the maximum allowed
if (line_nb >= MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
return -1;
}
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
return -1;
// Check if the file needs to be enlarged
while ((line_nb+1) > (column->header)->line_count)
{
// Enlarge the file
if (obi_enlarge_column(column) < 0)
return -1;
}
// Update lines used
if ((line_nb+1) > (column->header)->lines_used)
(column->header)->lines_used = line_nb+1;
// Add in the indexer
// Add the value in the indexer
idx = obi_index_char_str(column->indexer, value);
if (idx == -1)
return -1;
@ -66,50 +48,12 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
}
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, char* value)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
if ((view->line_selection != NULL) || (!(column->writable))) // TODO why check here writable?
{
// Get the right line number
if (column->writable)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
column = obi_view_clone_column(view, (column->header)->name);
if (column == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if ((line_nb+1) > view->line_count)
{
if (obi_view_update_lines(view, (line_nb+1)) < 0)
return -1;
}
return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
}
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
{
index_t idx;
index_t idx;
if ((line_nb+1) > ((column->header)->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
return OBIStr_NA;
}
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
return OBISeq_NA;
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
@ -121,60 +65,22 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
}
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)
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
{
if ((line_nb+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return OBIStr_NA;
}
if (view->line_selection)
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
}
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
}
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, char* value)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIStr_NA;
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx;
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIStr_NA;
return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
}

80
src/obidmscolumn_str.h
View File

@ -40,7 +40,7 @@
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
/**
@ -78,7 +78,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
* @since October 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
/**
@ -98,81 +98,5 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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, char* value);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the index of the element in the line.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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, char* value);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIDMSCOLUMN_STR_H_ */

294
src/obiview.c
View File

@ -25,6 +25,12 @@
#include "utils.h"
#include "obilittlebigman.h"
#include "obidmscolumn_idx.h"
#include "obidmscolumn_bool.h"
#include "obidmscolumn_char.h"
#include "obidmscolumn_float.h"
#include "obidmscolumn_int.h"
#include "obidmscolumn_seq.h"
#include "obidmscolumn_str.h"
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
@ -73,6 +79,14 @@ static char* build_obiview_file_name();
int create_obiview_file(int dms_file_descriptor);
// TODO doc
int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p);
// TODO doc
int prepare_to_get_value_in_column(Obiview_p view, OBIDMS_column_p column, index_t* line_nb_p);
/************************************************************************
*
* D E F I N I T I O N O F T H E P R I V A T E F U N C T I O N S
@ -203,6 +217,58 @@ int create_obiview_file(int dms_file_descriptor)
}
int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, index_t* line_nb_p)
{
// Check that the view is not read-only
if (view->read_only)
{
obi_set_errno(OBIVIEW_ERROR);
obidebug(1, "\nError trying to set a value in a column in a read-only view");
return -1;
}
// If there is a line selection associated with the view or if the column
// is read-only, all columns or this column respectively must be cloned
if ((view->line_selection != NULL) || (!((*column_pp)->writable)))
{
// Get the right line number
if (view->line_selection != NULL)
(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));
(*column_pp) = obi_view_clone_column(view, ((*column_pp)->header)->name);
if ((*column_pp) == NULL)
{
obidebug(1, "\nError trying to clone a column to modify it");
return -1;
}
}
if (((*line_nb_p)+1) > view->line_count)
{
if (obi_view_update_lines(view, ((*line_nb_p)+1)) < 0)
return -1;
}
return 0;
}
int prepare_to_get_value_from_column(Obiview_p view, OBIDMS_column_p column, index_t* line_nb_p)
{
if (((*line_nb_p)+1) > (view->line_count))
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
return -1;
}
if (view->line_selection)
(*line_nb_p) = *(((index_t*) ((view->line_selection)->data)) + (*line_nb_p));
return 0;
}
/**********************************************************************
*
* D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S
@ -1148,3 +1214,231 @@ int obi_save_and_close_view(Obiview_p view)
return 0;
}
/*********** FOR BOOL COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBIBool_NA;
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIBool_NA;
return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/
/*********** FOR CHAR COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBIChar_NA;
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIChar_NA;
return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/
/*********** FOR FLOAT COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBIFloat_NA;
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIFloat_NA;
return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/
/*********** FOR INT COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBIInt_NA;
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIInt_NA;
return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/
/*********** FOR SEQ COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBISeq_NA;
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBISeq_NA;
return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/
/*********** FOR STR COLUMNS ***********/
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)
{
if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
return -1;
return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
}
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)
{
if (prepare_to_get_value_from_column(view, column, &line_nb) < 0)
return OBIStr_NA;
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return -1;
return obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
}
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)
{
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == OBIIdx_NA)
return OBIStr_NA;
return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
}
/****************************************/

451
src/obiview.h
View File

@ -186,4 +186,455 @@ int obi_close_view(Obiview_p view);
int obi_save_and_close_view(Obiview_p view);
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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
* using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the index of the element in the line.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to DNA sequences handled by an indexer, using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the index of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the index of the element in the line.
*
* @param column A pointer as returned by obi_create_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
/**
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the name of the element in the line.
*
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns An integer value indicating the success of the operation.
* @retval 0 on success.
* @retval -1 if an error occurred.
*
* @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);
/**
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
* to character strings handled by an indexer, using the name of the element in the line.
*
* @param column A pointer as returned by obi_create_column() or obi_clone_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.
*
* @returns The recovered value.
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
*
* @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);
#endif /* OBIVIEW_H_ */