First version for the association of one column to another. Closes #55

src/obidmscolumn.c

@@ -534,6 +534,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 								  index_t      nb_elements_per_line,
 								  const char*  elements_names,
 								  const char*  indexer_name,
+								  const char*  associated_column_name,
+								  obiversion_t associated_column_version,
 								  const char*  comments
 								 )
 {
@@ -750,6 +752,30 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	if (comments != NULL)
 		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
 
+	// Store the associated column reference if needed // TODO discuss cases
+	if (data_type == OBI_QUAL)
+	{
+		if (associated_column_name == NULL)
+		{
+			obidebug(1, "\nError: The name of the associated column when creating a new column is NULL");
+			munmap(new_column->header, header_size);
+			close(column_file_descriptor);
+			free(new_column);
+			return NULL;
+		}
+		strcpy((header->associated_column).column_name, associated_column_name);
+
+		if (associated_column_version == -1)
+		{
+			obidebug(1, "\nError: The version of the associated column when creating a new column is not defined");
+			munmap(new_column->header, header_size);
+			close(column_file_descriptor);
+			free(new_column);
+			return NULL;
+		}
+		(header->associated_column).version = associated_column_version;
+	}
+
 	// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
 	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
 	{
@@ -964,6 +990,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   nb_elements_per_line,
 								   (column_to_clone->header)->elements_names,
 								   (column_to_clone->header)->indexer_name,
+								   ((column_to_clone->header)->associated_column).column_name,
+								   ((column_to_clone->header)->associated_column).version,
 								   (column_to_clone->header)->comments
 								  );
 

src/obidmscolumn.h

@@ -38,6 +38,17 @@
  	 	 	 	 	 	 	 	 	     */
 
 
+/**
+ * @brief Structure referencing a column by its name and its version.
+ */
+typedef struct Column_reference {
+	char 	   	 column_name[OBIDMS_COLUMN_MAX_NAME+1];    /**< Name of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+	obiversion_t version;				   		    	   /**< Version of the column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
+} Column_reference_t, *Column_reference_p;
+
+
 /**
  * @brief OBIDMS column header structure.
  */
@@ -73,6 +84,8 @@ typedef struct OBIDMS_column_header {
 	                                             	 	 	 	 */
 	char            	indexer_name[INDEXER_MAX_NAME+1]; 		/**< If there is one, the indexer name as a NULL terminated string.
 	                                             	 	 	 	 */
+	Column_reference_t 	associated_column;						/**< If there is one, the reference to the associated column.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	char 				comments[COMMENTS_MAX_LENGTH+1];		/**< Comments stored as a classical zero end C string.
 												 	 	 	 	 */
 } OBIDMS_column_header_t, *OBIDMS_column_header_p;
@@ -168,13 +181,15 @@ size_t obi_get_platform_header_size();
  * @param nb_elements_per_line The number of elements per line.								// TODO talk about default values
  * @param elements_names The names of the elements with ';' as separator.
  * @param indexer_name The name of the indexer if there is one associated with the column.
+ * @param associated_column_name The name of the associated column if there is one.
+ * @param associated_column_version The version of the associated column if there is one.
  * @param comments Optional comments associated with the column.
  *
  * @returns A pointer on the newly created column structure.
  * @retval NULL if an error occurred.
  *
  * @since May 2015
- * @author Eric Coissac (eric.coissac@metabarcoding.org)
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
 OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 		                          const char* column_name,
@@ -183,6 +198,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 								  index_t nb_elements_per_line,
 								  const char* elements_names,
 								  const char* indexer_name,
+								  const char*  associated_column_name,
+								  obiversion_t associated_column_version,
 								  const char* comments
 								 );
 

src/obiview.c

@@ -582,7 +582,11 @@ bool view_check_quality_matches_seq_column(Obiview_p view)	// TODO Print error i
 	if (qual_column == NULL)
 		return false;
 
-	seq_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);	// TODO Get associated nuc column
+	seq_column = obi_view_get_column(view, ((qual_column->header)->associated_column).column_name);
+	//seq_column = obi_open_column(view->dms, ((qual_column->header)->associated_column).column_name, ((qual_column->header)->associated_column).version);
+	// TODO discuss the fact that it's opened outside of the context of the view or not
+	// TODO if outside of view, make function that opens a column from a column reference structure?
+
 	if (seq_column == NULL)
 		return false;
 
@@ -608,6 +612,9 @@ bool view_check_quality_matches_seq_column(Obiview_p view)	// TODO Print error i
 				return false;
 		}
 	}
+
+	//obi_close_column(seq_column);
+
 	return true;
 }
 
@@ -714,7 +721,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		// If there is a new line selection, build it by combining it with the one from the view to clone if there is one
 		else if (line_selection != NULL)
 		{
-			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
 			if ((view->line_selection) == NULL)
 			{
 				obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -837,6 +844,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
 Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p view_to_clone, index_t* line_selection, const char* comments)
 {
 	Obiview_p 		view;
+	OBIDMS_column_p associated_nuc_column;
 
 	if (view_to_clone != NULL)
 	{ // Check that the view to clone is already a NUC_SEQS view (TODO discuss possibility of transforming type of a view)
@@ -857,25 +865,26 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 	if (view_to_clone == NULL)
 	{
 		// Adding sequence column
-		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", "Nucleotide sequences", true) < 0)
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding id column
-		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", "Ids", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding definition column
-		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", "Definitions", true) < 0)
+		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
 		}
 		// Adding quality column
-		if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", "Sequence qualities", true) < 0)
+		associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
+		if (obi_view_add_column(view, QUALITY_COLUMN, -1, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0)		// TODO discuss automatic association
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -1062,6 +1071,8 @@ int obi_view_add_column(Obiview_p view,
 						index_t nb_elements_per_line,
 						const char* elements_names,
 						const char* indexer_name,
+						const char* associated_column_name,
+						obiversion_t associated_column_version,
 						const char* comments,
 						bool create)	// all infos for creation or open
 {
@@ -1131,7 +1142,7 @@ int obi_view_add_column(Obiview_p view,
 	// Open or create the column
 	if (create)
 	{	// Create column
-		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, comments);
+		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments);
 	}
 	else
 	{ // Open column
@@ -1241,7 +1252,7 @@ int obi_select_line(Obiview_p view, index_t line_nb)
 	// If the column for line selection doesn't already exists, create it and store its informations
 	if ((view->new_line_selection) == NULL)
 	{
-		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
 		if ((view->new_line_selection) == NULL)
 		{
 			obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -1276,7 +1287,7 @@ int obi_select_lines(Obiview_p view, index_t* line_nbs)
 	// If column for line selection doesn't already exists, create it and store its informations
 	if ((view->new_line_selection) == NULL)
 	{
-		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL);
+		view->new_line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, LINES_COLUMN_NAME, NULL, NULL, -1, NULL);
 		if ((view->new_line_selection) == NULL)
 		{
 			obidebug(1, "\nError creating a column corresponding to a line selection");

src/obiview.h

@@ -54,17 +54,6 @@
                                 	 	  	  	 */
 
 
-/**
- * @brief Structure referencing a column by its name and its version.
- */
-typedef struct Column_reference {
-	char 	   	 column_name[OBIDMS_COLUMN_MAX_NAME+1];    /**< Name of the column.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
-	obiversion_t version;				   		    	   /**< Version of the column.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	    */
-} Column_reference_t, *Column_reference_p;
-
-
 /**
  * @brief Structure for a closed view stored in the view file.
  * 		  Views are identified by their name.
@@ -333,6 +322,8 @@ int obi_view_add_column(Obiview_p view,
 						index_t nb_elements_per_line,
 						const char* elements_names,
 						const char* indexer_name,
+						const char* associated_column_name,
+						obiversion_t associated_column_version,
 						const char* comments,
 						bool create);