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

Files and functions for columns with the data type OBIChar_t, working

Browse Source 
but using char* (needs to be changed)
This commit is contained in:
Celine Mercier
2015-08-26 10:31:56 +02:00
parent 9ad31fddff
commit 611699252e
7 changed files with 159 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx
View File

@ -4,7 +4,7 @@ from .capidmscolumn cimport *
from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int import OBIDMS_column_int
from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float import OBIDMS_column_float
from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool import OBIDMS_column_bool
#from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char import OBIDMS_column_char
from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char import OBIDMS_column_char
from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx import OBIDMS_column_idx
@ -112,12 +112,12 @@ cdef class OBIDMS_column:
nb_elements, nb_elements_per_line,
elements_names)
# elif type == 4 :
# column = OBIDMS_column_char(dms_name, column_name,
# create, clone, clone_data,
# version_number, type,
# nb_elements, nb_elements_per_line,
# elements_names)
elif type == 4 :
column = OBIDMS_column_char(dms_name, column_name,
create, clone, clone_data,
version_number, type,
nb_elements, nb_elements_per_line,
elements_names)
elif type == 5 :
column = OBIDMS_column_idx(dms_name, column_name,

0
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/__init__.py Normal file
View File

16
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.cfiles Normal file
View File

@ -0,0 +1,16 @@
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/obilittlebigman.h
../../../../../src/obilittlebigman.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/private_at_functions.h
../../../../../src/private_at_functions.c

7
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pxd Normal file
View File

@ -0,0 +1,7 @@
from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
cdef extern from "obidmscolumn_char.h" nogil:
int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
obichar_t* obi_column_get_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx)

30
python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx Normal file
View File

@ -0,0 +1,30 @@
#cython: language_level=3
from .capidmscolumn_char cimport *
cdef class OBIDMS_column_char(OBIDMS_column) :
def set_item(self, line_nb, element_name, value):
if element_name != "" :
element_idx = self.get_element_index_from_name(element_name)
else :
if obi_column_get_nb_elements_per_line(self.pointer) == 1 :
element_idx = 0
else :
print("An element name must be specified")
return -1
return obi_column_set_char(self.pointer, line_nb, element_idx, value)
def get_item(self, line_nb, element_name):
if element_name != "" :
element_idx = self.get_element_index_from_name(element_name)
else :
if obi_column_get_nb_elements_per_line(self.pointer) == 1 :
element_idx = 0
else :
print("An element name must be specified")
return -1
return (obi_column_get_char(self.pointer, line_nb, element_idx)).decode(encoding='UTF-8')[:1] #not ideal...

40
src/obidmscolumn_char.c Normal file
View File

@ -0,0 +1,40 @@
/****************************************************************************
* OBIDMS_column_char functions *
****************************************************************************/
/**
* @file obidsmcolumn_char.c
* @author Celine Mercier
* @date August 10th 2015
* @brief Functions handling OBIColumns containing data with the OBIType OBI_CHAR.
*/
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
#include "obierrno.h"
#include "obidebug.h"
/**********************************************************************
*
* 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
*
**********************************************************************/
int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
{
// when/where check if can write?
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value[0];
return 0;
}
obichar_t* obi_column_get_char(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;
}

59
src/obidmscolumn_char.h Normal file
View File

@ -0,0 +1,59 @@
/****************************************************************************
* OBIDMS_column_char header file *
****************************************************************************/
/**
* @file obidsmcolumn_char.h
* @author Celine Mercier
* @date August 10th 2015
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_CHAR.
*/
#include <stdlib.h>
#include <stdio.h>
#include "obidmscolumn.h"
#include "obitypes.h"
/**
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR.
*
* @param column a pointer as returned by obi_create_column()
* @warning Pointers returned by obi_open_column() don't allow writing.
*
* @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
*
* @return an integer value indicating the success of the operation.
*
* @retvalue 0 on success
* @retvalue -1 on failure and the `obi_errno` variable is set.
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_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
*
* @return the recovered value
*
* @since August 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
obichar_t* obi_column_get_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx);