Basis for OBIDMS columns with the type OBI_IDX

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.cfiles

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+../../../../../src/obidmscolumn_idx.c
+../../../../../src/obidmscolumn_idx.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

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pxd

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+from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
+
+
+cdef extern from "obidmscolumn_idx.h" nogil:
+
+    int obi_column_set_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
+    obiidx_t obi_column_get_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx

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+#cython: language_level=3
+
+from .capidmscolumn_idx cimport *
+
+
+cdef class OBIDMS_column_idx(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_idx(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_idx(self.pointer, line_nb, element_idx)
+        
+    

src/obidmscolumn_idx.c

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+/****************************************************************************
+ * OBIDMS_column_idx functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_idx.c
+ * @author Celine Mercier
+ * @date August 10th 2015
+ * @brief Functions handling OBIColumns containing data with the OBIType OBI_IDX.
+ */
+
+
+#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_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
+{
+	// when/where check if can write?
+	*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+	return 0;
+}
+
+
+obiidx_t obi_column_get_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+{
+	return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
+}
+

src/obidmscolumn_idx.h

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+/****************************************************************************
+ * OBIDMS_column_idx header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_idx.h
+ * @author Celine Mercier
+ * @date August 10th 2015
+ * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
+ */
+
+
+#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_IDX.
+ *
+ * @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_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
+ *
+ * @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)
+ */
+obiidx_t obi_column_get_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+
+