Finished adding all the functions to directly set and get indices in

columns containing indices referring to any type of data.

src/obidmscolumn_idx.c

@@ -24,27 +24,18 @@
  **********************************************************************/
 
 
-int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
+int obi_column_set_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value)
 {
 	if (obi_column_prepare_to_set_value(column, line_nb) < 0)
 		return -1;
 
 	// Set the value
-	*(((index_t*) (column->data)) + line_nb) = value;
+	*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
 
 	return 0;
 }
 
 
-index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
-{
-	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
-		return OBIIdx_NA;
-
-	return *(((index_t*) (column->data)) + line_nb);
-}
-
-
 index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
 {
 	if (obi_column_prepare_to_get_value(column, line_nb) < 0)
@@ -54,6 +45,16 @@ index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_n
 }
 
 
+int obi_column_set_index_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, index_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_index_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
 index_t obi_column_get_index_with_elt_name(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);

src/obidmscolumn_idx.h

@@ -6,10 +6,10 @@
  * @file obidsmcolumn_idx.h
  * @author Celine Mercier
  * @date February 14th 2016
- * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
+ * @brief Header file for the functions handling OBIColumns containing indices (stored data type: OBI_IDX).
  *
- * Note: OBI_IDX columns contain indices referring to data stored elsewhere
+ * Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
- *		 (for example lines in other columns) and contain only one element (index) per line.
+ *	     or data stored in indexers.
  */
 
 
@@ -25,47 +25,40 @@
 
 
 /**
- * @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX.
+ * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
+ *        using the index of the element in the line.
  *
- *	Note: OBI_IDX columns contain indices referring to data stored elsewhere
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
- *		  (for example lines in other columns) and contain only one element (index) per line.
+ *	      or data stored in indexers.
+ *
+ * In the case of columns referring to values stored in indexers, this allows to directly set already-known
+ * indices without going through the time-consuming step of indexing the value.
  *
  * @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 value The value that should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The index 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
+ * @since November 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
+int obi_column_set_index_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value);
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
+ * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
+ *        using the index of the element in the line.
  *
- *	Note: OBI_IDX columns contain indices referring to data stored elsewhere
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
- *		  (for example lines in other columns) and contain only one element (index) per line.
+ *	      or data stored in indexers.
  *
- * @param column A pointer as returned by obi_create_column() or obi_clone_column().
+ * The value recovered is the index itself and not the data it is referring to.
- * @param line_nb The number of the line where the value should be recovered.
- *
- * @returns The recovered value.
- * @retval OBIIdx_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)
- */
-index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
-
-
-/**
- * @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.
@@ -81,9 +74,41 @@ index_t obi_column_get_index_with_elt_idx(OBIDMS_column_p column, index_t line_n
 
 
 /**
- * @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX,
+ * @brief Sets a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
+ *        using the index of the element in the line.
+ *
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
+ *	      or data stored in indexers.
+ *
+ * In the case of columns referring to values stored in indexers, this allows to directly set already-known
+ * indices without going through the time-consuming step of indexing the value.
+ *
+ * @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 index 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 November 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_index_with_elt_name(OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing indices (stored data type: OBI_IDX),
  *        using the name of the element in the line.
  *
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
+ *	      or data stored in indexers.
+ *
+ * The value recovered is the index itself and not the data it is referring to.
+ *
  * @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.

src/obiview.c

@@ -1263,9 +1263,9 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 				}
 
 				if (view_to_clone->line_selection != NULL)
-					line_nb = obi_column_get_index(view_to_clone->line_selection, line_nb);
+					line_nb = obi_column_get_index_with_elt_idx(view_to_clone->line_selection, line_nb, 0);
 
-				if (obi_column_set_index(view->line_selection, ((view->line_selection)->header)->lines_used, line_nb) < 0)
+				if (obi_column_set_index_with_elt_idx(view->line_selection, ((view->line_selection)->header)->lines_used, 0, line_nb) < 0)
 				{
 					obi_close_column(view->line_selection);
 					obi_view_unmap_file(view->dms, view->infos);
@@ -2724,6 +2724,15 @@ const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const
 
 /*********** FOR COLUMNS WITH INDEXED VALUES ***********/
 
+
+int obi_set_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, index_t value)
+{
+	if (prepare_to_set_value_in_column(view, &column, &line_nb) < 0)
+		return -1;
+	return obi_column_set_index_with_elt_idx(column, line_nb, element_idx, value);
+}
+
+
 index_t obi_get_index_with_elt_idx_and_col_p_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, &line_nb) < 0)
@@ -2732,6 +2741,15 @@ index_t obi_get_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colu
 }
 
 
+int obi_set_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, index_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_set_index_with_elt_idx_and_col_p_in_view(view, column, line_nb, element_idx, value);
+}
+
+
 index_t obi_get_index_with_elt_name_and_col_p_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);
@@ -2741,6 +2759,26 @@ index_t obi_get_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_col
 }
 
 
+int obi_set_index_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, index_t value)
+{
+	OBIDMS_column_p column_p;
+	column_p = obi_view_get_column(view, column_name);
+	if (column_p == NULL)
+		return -1;
+	return obi_set_index_with_elt_name_and_col_p_in_view(view, column_p, line_nb, element_name, value);
+}
+
+
+int obi_set_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, index_t value)
+{
+	OBIDMS_column_p column_p;
+	column_p = obi_view_get_column(view, column_name);
+	if (column_p == NULL)
+		return -1;
+	return obi_set_index_with_elt_idx_and_col_p_in_view(view, column_p, line_nb, element_idx, value);
+}
+
+
 index_t obi_get_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx)
 {
 	OBIDMS_column_p column_p;

src/obiview.h

@@ -1314,6 +1314,38 @@ const char* obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_c
 const char* obi_get_str_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing indices, using the index of the element in the line,
+ *        in the context of a view.
+ *
+ *  Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned.
+ *
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
+ *	      or data stored in indexers.
+ *
+ * In the case of columns referring to values stored in indexers, this allows to directly set already-known
+ * indices without going through the time-consuming step of indexing the value.
+ *
+ * @param view A pointer on the opened writable view.
+ * @param column A pointer on the column.
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_idx The index of the element that should be set in the line.
+ * @param value The value that should be set.
+ *
+ * @returns An integer value indicating the success of the operation.
+ * @retval 0 on success.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_set_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, index_t element_idx, index_t value);
+
+
+// TODO
+int obi_set_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx, index_t value);
+
+
 /**
  * @brief Recovers a value in an OBIDMS column containing indexes, in the context of a view.
  *
@@ -1338,6 +1370,38 @@ index_t obi_get_index_with_elt_idx_and_col_p_in_view(Obiview_p view, OBIDMS_colu
 index_t obi_get_index_with_elt_idx_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, index_t element_idx);
 
 
+/**
+ * @brief Sets a value in an OBIDMS column containing indices, using the index of the element in the line,
+ *        in the context of a view.
+ *
+ *  Note: If the column is read-only or if there is a line selection associated with the view (making columns non-writable), it is cloned.
+ *
+ *	Note: Columns containing indices refer to data stored elsewhere, for example lines in other columns,
+ *	      or data stored in indexers.
+ *
+ * In the case of columns referring to values stored in indexers, this allows to directly set already-known
+ * indices without going through the time-consuming step of indexing the value.
+ *
+ * @param view A pointer on the opened writable view.
+ * @param column A pointer on the column.
+ * @param line_nb The number of the line where the value should be set.
+ * @param element_name The name of the element that should be recovered 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 November 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_set_index_with_elt_name_and_col_p_in_view(Obiview_p view, OBIDMS_column_p column_p, index_t line_nb, const char* element_name, index_t value);
+
+
+// TODO
+int obi_set_index_with_elt_name_and_col_name_in_view(Obiview_p view, const char* column_name, index_t line_nb, const char* element_name, index_t value);
+
+
 /**
  * @brief Recovers a value in an OBIDMS column containing indexes,
  *        using the name of the element in the line, in the context of a view.