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

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This commit is contained in:
Eric Coissac
2015-09-03 08:38:57 -04:00
parent f5937ec019 f2231770f1
commit 0e50fbf706
22 changed files with 417 additions and 115 deletions
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4
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pxd
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@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_bool.h" nogil:
int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pyx
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@ -6,7 +6,7 @@ from .capidmscolumn_bool cimport *
cdef class OBIDMS_column_bool(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_bool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
return obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
@ -22,7 +22,7 @@ cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_bool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
return obi_column_set_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pxd
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@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
obichar_t* obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx
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@ -6,7 +6,7 @@ from .capidmscolumn_char cimport *
cdef class OBIDMS_column_char(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return (obi_column_get_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
return (obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
cdef class OBIDMS_column_char_read(OBIDMS_column_char) :
@ -22,7 +22,7 @@ cdef class OBIDMS_column_char_read(OBIDMS_column_char) :
cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value.encode('utf-8'))
return obi_column_set_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value.encode('utf-8'))
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pxd
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@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_float.h" nogil:
int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pyx
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@ -6,7 +6,7 @@ from .capidmscolumn_float cimport *
cdef class OBIDMS_column_float(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
return obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_float_read(OBIDMS_column_float) :
@ -22,7 +22,7 @@ cdef class OBIDMS_column_float_read(OBIDMS_column_float) :
cdef class OBIDMS_column_float_writable(OBIDMS_column_float) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
return obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pxd
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@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_idx.h" nogil:
int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx
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@ -6,7 +6,7 @@ from .capidmscolumn_idx cimport *
cdef class OBIDMS_column_idx(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
return obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :
@ -22,7 +22,7 @@ cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :
cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
return obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pxd
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@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_int.h" nogil:
int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

4
python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pyx
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@ -6,7 +6,7 @@ from .capidmscolumn_int cimport *
cdef class OBIDMS_column_int(OBIDMS_column) :
def get_item(self, line_nb, element_name):
return obi_column_get_int_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
return obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
@ -22,7 +22,7 @@ cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
cdef class OBIDMS_column_int_writable(OBIDMS_column_int) :
def set_item(self, line_nb, element_name, value):
return obi_column_set_int_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
return obi_column_set_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
def close(self):
if obi_truncate_and_close_column(self.pointer) < 0 :

231
src/obidmscolumn.c
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@ -600,7 +600,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
int column_dir_file_descriptor;
size_t header_size;
size_t data_size;
size_t i, nb_elements;
new_column = NULL;
@ -732,41 +731,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
// Fill the data with NA values
nb_elements = nb_lines*nb_elements_per_line;
switch (type) {
case OBI_VOID: // TODO;
break;
case OBI_INT: for (i=0;i<nb_elements;i++)
{
*(((obiint_t*) (new_column->data)) + i) = OBIInt_NA;
}
break;
case OBI_FLOAT: for (i=0;i<nb_elements;i++)
{
*(((obifloat_t*) (new_column->data)) + i) = OBIFloat_NA;
}
break;
case OBI_BOOL: for (i=0;i<nb_elements;i++)
{
*(((obibool_t*) (new_column->data)) + i) = OBIBool_NA;
}
break;
case OBI_CHAR: for (i=0;i<nb_elements;i++)
{
*(((obichar_t*) (new_column->data)) + i) = OBIChar_NA;
}
break;
case OBI_IDX: for (i=0;i<nb_elements;i++)
{
*(((obiidx_t*) (new_column->data)) + i) = OBIIdx_NA;
}
break;
}
obi_ini_to_NA_values (new_column, 0, nb_lines);
free(column_file_name);
close(column_file_descriptor);
@ -870,7 +835,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms, const char* column_name, obiversio
// Check endianness?
// Compute data size from the informations in the header
data_size = ((column->header)->line_count) * sizeof((column->header)->data_type); // TODO line_count for tests, change to lines_used later
data_size = ((column->header)->line_count) * sizeof((column->header)->data_type);
column->data = mmap(NULL,
data_size,
@ -935,8 +900,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError creating the new column when cloning a column");
// TODO the new file should be deleted
return NULL;
// The new file is deleted
const char* column_file_name = build_column_file_name(column_name, version_number);
if (remove(column_file_name) < 0)
obidebug(1, "\nError deleting a bad cloned file");
}
(new_column->header)->cloned_from = version_number;
@ -948,7 +915,12 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
(new_column->header)->lines_used = nb_lines;
}
// close column_to_clone TODO
// close column_to_clone
if (obi_close_column(column_to_clone) < 0)
{
obidebug(1, "\nError closing a column that has been cloned");
// TODO return NULL or not?
}
return new_column;
}
@ -1006,7 +978,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
}
// Open the column file
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT);
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR);
if (column_file_descriptor < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
@ -1066,6 +1038,139 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
}
int obi_enlarge_column(OBIDMS_column_p column)
{
size_t file_size;
size_t old_data_size;
size_t new_data_size;
size_t header_size;
size_t old_line_count;
size_t new_line_count;
int column_dir_file_descriptor;
int column_file_descriptor;
char* column_file_name;
// Get the file descriptor associated to the column directory
column_dir_file_descriptor = dirfd((column->column_directory)->directory);
if (column_dir_file_descriptor < 0)
{
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor for a column directory");
return -1;
}
// Get the column file name
column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
if (column_file_name == NULL)
{
return -1;
}
// Open the column file
column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT);
if (column_file_descriptor < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError getting the file descriptor of a column file");
free(column_file_name);
return -1;
}
// Calculate the new file size
old_line_count = (column->header)->line_count;
new_line_count = old_line_count * GROWTH_FACTOR;
if (new_line_count > MAXIMUM_LINE_COUNT)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError enlarging a column file: new line count greater than the maximum allowed");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
old_data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
new_data_size = old_data_size * GROWTH_FACTOR;
header_size = (column->header)->header_size;
file_size = header_size + new_data_size;
// Unmap the data
if (munmap(column->data, old_data_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping the data of a column before enlarging");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Unmap the header
if (munmap(column->header, header_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError munmapping the header of a column before enlarging");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Enlarge the file
if (ftruncate(column_file_descriptor, file_size) < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError enlarging a column file");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Remap the header (TODO not sure if necessary??)
column->header = mmap(NULL,
header_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
column_file_descriptor,
0
);
if (column->header == MAP_FAILED)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError mmapping the header of a column after enlarging file");
close(column_file_descriptor);
free(column_file_name);
return -1;
}
// Remap the data
column->data = mmap(NULL,
new_data_size,
PROT_READ | PROT_WRITE,
MAP_SHARED,
column_file_descriptor,
(column->header)->header_size
);
if (column->data == MAP_FAILED)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError re-mmapping the data of a column after enlarging the file");
free(column_file_name);
close(column_file_descriptor);
return -1;
}
// Set new line count
(column->header)->line_count = new_line_count;
// Initialize new data lines to NA
obi_ini_to_NA_values(column, old_line_count, new_line_count - old_line_count);
free(column_file_name);
close(column_file_descriptor);
return 0;
}
int obi_truncate_and_close_column(OBIDMS_column_p column)
{
if (obi_truncate_column_to_lines_used(column) < 0)
@ -1077,6 +1182,50 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
}
void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
{
size_t i, end, nb_elements;
nb_elements = nb_lines*((column->header)->nb_elements_per_line);
end = start + nb_elements;
switch ((column->header)->data_type) {
case OBI_VOID: // TODO;
break;
case OBI_INT: for (i=start;i<end;i++)
{
*(((obiint_t*) (column->data)) + i) = OBIInt_NA;
}
break;
case OBI_FLOAT: for (i=start;i<end;i++)
{
*(((obifloat_t*) (column->data)) + i) = OBIFloat_NA;
}
break;
case OBI_BOOL: for (i=start;i<end;i++)
{
*(((obibool_t*) (column->data)) + i) = OBIBool_NA;
}
break;
case OBI_CHAR: for (i=start;i<end;i++)
{
*(((obichar_t*) (column->data)) + i) = OBIChar_NA;
}
break;
case OBI_IDX: for (i=start;i<end;i++)
{
*(((obiidx_t*) (column->data)) + i) = OBIIdx_NA;
}
break;
}
}
void obi_column_make_unwritable(OBIDMS_column_p column)
{
column->writable = false;

29
src/obidmscolumn.h
View File

@ -27,6 +27,8 @@
#define ELEMENTS_NAMES_MAX (2048)
#define INITIAL_LINE_COUNT (1000)
#define GROWTH_FACTOR (2)
#define MAXIMUM_LINE_COUNT (1000000)
typedef int32_t obiversion_t; /**< Used to store the column version number
@ -205,6 +207,20 @@ int obi_close_column(OBIDMS_column_p column);
int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
/**
* @brief Enlarges a column file.
*
* @param column a pointer on an OBIDMS column
*
* @return 0 if the operation was successfully completed
* @return -1 if an error occurred
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_enlarge_column(OBIDMS_column_p column);
/**
* @brief Truncates a column file to the number of lines used and closes it.
*
@ -219,6 +235,19 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
int obi_truncate_and_close_column(OBIDMS_column_p column);
/*
* @brief Sets the data in a column to the NA value of the data type.
*
* @param column a pointer on an OBIDMS column
* @param start the first line number of the block that should be set
* @param nb_lines the number of lines that should be set
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines);
/**
* @brief Sets the 'writable' header attribute of an OBIDMS column to False.
*

37
src/obidmscolumn_bool.c
View File

@ -28,23 +28,47 @@
*
**********************************************************************/
int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_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;
// Set the value
*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
if ((line_nb+1) > (column->header)->line_count)
{
obidebug(1, "\nError trying to get a value that is beyond the current line count");
return -1; // TODO return NA value?
}
return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
{
size_t element_idx;
@ -66,13 +90,13 @@ int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
return -1;
}
obi_column_set_bool_with_elt_idx(column, line_nb, element_idx, value);
obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
{
size_t element_idx;
@ -94,5 +118,6 @@ obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_
return -1;
}
return obi_column_get_bool_with_elt_idx(column, line_nb, element_idx);
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
}

8
src/obidmscolumn_bool.h
View File

@ -37,7 +37,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, siz
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
@ -78,7 +78,7 @@ obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_n
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
/**
@ -97,5 +97,5 @@ int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

45
src/obidmscolumn_char.c
View File

@ -28,23 +28,47 @@
*
**********************************************************************/
int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_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;
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value[0];
// Set the value
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
return ((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx;
if ((line_nb+1) > (column->header)->line_count)
{
obidebug(1, "\nError trying to get a value that is beyond the current line count");
return '\0'; // TODO return NA value?
}
return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
{
size_t element_idx;
@ -66,13 +90,13 @@ int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
return -1;
}
obi_column_set_char_with_elt_idx(column, line_nb, element_idx, value);
obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
{
size_t element_idx;
@ -84,15 +108,16 @@ obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nAn element name must be specified");
return NULL;
return '\0'; // TODO
}
}
else
{
element_idx = obi_column_get_element_index_from_name(column, element_name);
if (element_idx == -1)
return NULL;
return '\0'; // TODO
}
return obi_column_get_char_with_elt_idx(column, line_nb, element_idx);
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
}

8
src/obidmscolumn_char.h
View File

@ -37,7 +37,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
/**
@ -54,7 +54,7 @@ int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, siz
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obichar_t* obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
@ -78,7 +78,7 @@ obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value);
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value);
/**
@ -97,5 +97,5 @@ int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obichar_t* obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

37
src/obidmscolumn_float.c
View File

@ -28,23 +28,47 @@
*
**********************************************************************/
int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_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;
// Set the value
*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
if ((line_nb+1) > (column->header)->line_count)
{
obidebug(1, "\nError trying to get a value that is beyond the current line count");
return -1; // TODO return NA value?
}
return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
{
size_t element_idx;
@ -66,13 +90,13 @@ int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, c
return -1;
}
obi_column_set_float_with_elt_idx(column, line_nb, element_idx, value);
obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
{
size_t element_idx;
@ -94,5 +118,6 @@ obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t lin
return -1;
}
return obi_column_get_float_with_elt_idx(column, line_nb, element_idx);
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
}

8
src/obidmscolumn_float.h
View File

@ -37,7 +37,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, si
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
@ -78,7 +78,7 @@ obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
/**
@ -97,5 +97,5 @@ int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, c
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

37
src/obidmscolumn_idx.c
View File

@ -28,23 +28,47 @@
*
**********************************************************************/
int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_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;
// Set the value
*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
if ((line_nb+1) > (column->header)->line_count)
{
obidebug(1, "\nError trying to get a value that is beyond the current line count");
return -1; // TODO return NA value?
}
return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
{
size_t element_idx;
@ -66,13 +90,13 @@ int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
return -1;
}
obi_column_set_idx_with_elt_idx(column, line_nb, element_idx, value);
obi_column_set_obiidx_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
{
size_t element_idx;
@ -94,5 +118,6 @@ obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb
return -1;
}
return obi_column_get_idx_with_elt_idx(column, line_nb, element_idx);
return obi_column_get_obiidx_with_elt_idx(column, line_nb, element_idx);
}

8
src/obidmscolumn_idx.h
View File

@ -37,7 +37,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
@ -78,7 +78,7 @@ obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
/**
@ -97,5 +97,5 @@ int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

36
src/obidmscolumn_int.c
View File

@ -28,23 +28,47 @@
*
**********************************************************************/
int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_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;
// Set the value
*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
return 0;
}
obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
{
if ((line_nb+1) > (column->header)->line_count)
{
obidebug(1, "\nError trying to get a value that is beyond the current line count");
return -1; // TODO return NA value?
}
return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
}
int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
{
size_t element_idx;
@ -66,13 +90,13 @@ int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
return -1;
}
obi_column_set_int_with_elt_idx(column, line_nb, element_idx, value);
obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
return 0;
}
obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
{
size_t element_idx;
@ -94,6 +118,6 @@ obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb
return -1;
}
return obi_column_get_int_with_elt_idx(column, line_nb, element_idx);
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
}

8
src/obidmscolumn_int.h
View File

@ -37,7 +37,7 @@
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
/**
@ -54,7 +54,7 @@ int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size
* @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
/**
@ -78,7 +78,7 @@ obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
/**
@ -97,5 +97,5 @@ int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);