When closing a view, it is now automatically checked that all OBI_QUAL

columns correspond to their associated OBI_SEQ column

src/obiview.c

@@ -368,7 +368,7 @@ char* view_has_definition_column(Obiview_p view);
 
 
 /**
- * @brief Internal function checking that the quality column of a view and the sequence column associated to it
+ * @brief Internal function checking that all the quality columns of a view and their associated sequence columns
  * 		  correspond properly:
  * 		  	- when a line is defined for either column, it must also be defined for the other column
  * 		  	- when a line is defined, the lengths of the sequence and of the quality must be equal
@@ -381,7 +381,7 @@ char* view_has_definition_column(Obiview_p view);
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* view_check_quality_matches_seq_column(Obiview_p view);
+char* view_check_qual_match_seqs(Obiview_p view);
 
 
 /**
@@ -960,9 +960,9 @@ char* view_has_definition_column(Obiview_p view)
 }
 
 
-char* view_check_quality_matches_seq_column(Obiview_p view)	// TODO Print error if there is one?
+char* view_check_qual_match_seqs(Obiview_p view)
 {
-	index_t 		i, j;
+	index_t 		i, j, k;
 	index_t			nb_elements_per_line;
 	int	    		qual_len;
 	const uint8_t*	qual;
@@ -970,69 +970,85 @@ char* view_check_quality_matches_seq_column(Obiview_p view)	// TODO Print error
 	OBIDMS_column_p qual_column;
 	OBIDMS_column_p seq_column;
 	char* 			predicate;
+	bool			at_least_one_qual_col;
 
-	predicate = (char*) malloc((strlen("The sequences and sequence quality arrays match.") + 1) * sizeof(char));
-	if (predicate == NULL)
+	// Go through all columns in the view and check the predicate for all quality columns
+	at_least_one_qual_col = false;
+	for (i=0; i < ((view->infos)->column_count); i++)
 	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for predicate character string.");
-		return NULL;
-	}
-
-	strcpy(predicate, "The sequences and sequence quality arrays match.");
+		// Check if it's a quality column
+		if ((((view->columns)[i])->header)->returned_data_type == OBI_QUAL)
+		{
+			at_least_one_qual_col = true;
+			// Check that the quality arrays match the sequences of the associated column
+			qual_column = (view->columns)[i];
+			seq_column = obi_open_column(view->dms, ((qual_column->header)->associated_column).column_name, ((qual_column->header)->associated_column).version);
+			if (seq_column == NULL)
+			{
+				obidebug(1, "\nError checking the predicate: The sequences and sequence quality arrays match.");
+				return NULL;
+			}
 
-	qual_column = obi_view_get_column(view, QUALITY_COLUMN);
-	if (qual_column == NULL)
-	{
-		obidebug(1, "\nError checking the predicate: %s", predicate);
-		return NULL;
-	}
+			nb_elements_per_line = (qual_column->header)->nb_elements_per_line;
+			// Check that the quality and the sequence columns have the same number of elements per line
+			if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line)
+			{
+				obidebug(1, "\nError checking the predicate: The sequences and sequence quality arrays match.");
+				return NULL;
+			}
 
-	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 -> problem if alias. Open from full refs maybe
-	// TODO if outside of view, make function that opens a column from a column reference structure?
+			// Check each sequence and its sequence
+			for (j=0; j < (view->infos)->line_count; j++)
+			{
+				for (k=0; k < nb_elements_per_line; k++)
+				{
+					qual = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view, qual_column, j, k, &qual_len);
+					seq = obi_get_seq_with_elt_idx_and_col_p_in_view(view, seq_column, j, k);
+					if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA))
+					{
+						// Test that the lengths of the quality and the sequence are equal
+						if (qual_len != (int)strlen(seq))
+						{
+							obidebug(1, "\nError checking the predicate: The sequences and sequence quality arrays match.");
+							return NULL;
+						}
+					}
+					// Test if one value is NA and not the other
+					else if (((qual == OBIQual_int_NA) && (seq != OBISeq_NA)) || ((qual != OBIQual_int_NA) && (seq == OBISeq_NA)))
+					{
+						obidebug(1, "\nError checking the predicate: The sequences and sequence quality arrays match.");
+						return NULL;
+					}
+				}
+			}
 
-	if (seq_column == NULL)
-	{
-		obidebug(1, "\nError checking the predicate: %s", predicate);
-		return NULL;
+			obi_close_column(seq_column);
+		}
 	}
 
-	nb_elements_per_line = (qual_column->header)->nb_elements_per_line;
-	// Check that the quality and the sequence columns have the same number of elements per line
-	if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line)
+	if (at_least_one_qual_col)
 	{
-		obidebug(1, "\nError checking the predicate: %s", predicate);
-		return NULL;
+		predicate = (char*) malloc((strlen("The sequences and sequence quality arrays match.") + 1) * sizeof(char));
+		if (predicate == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for predicate character string.");
+			return NULL;
+		}
+		strcpy(predicate, "The sequences and sequence quality arrays match.");
 	}
-
-	for (i=0; i < (view->infos)->line_count; i++)
+	else
 	{
-		for (j=0; j < nb_elements_per_line; j++)
+		predicate = (char*) malloc(1 * sizeof(char));
+		if (predicate == NULL)
 		{
-			qual = obi_column_get_obiqual_int_with_elt_idx(qual_column, i, j, &qual_len);
-			seq = obi_column_get_obiseq_with_elt_idx(seq_column, i, j);
-			if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA))
-			{
-				// Test that the lengths of the quality and the sequence are equal
-				if (qual_len != (int)strlen(seq))
-				{
-					obidebug(1, "\nError checking the predicate: %s", predicate);
-					return NULL;
-				}
-			}
-			// Test if one value is NA and not the other
-			else if (((qual == OBIQual_int_NA) && (seq != OBISeq_NA)) || ((qual != OBIQual_int_NA) && (seq == OBISeq_NA)))
-			{
-				obidebug(1, "\nError checking the predicate: %s", predicate);
-				return NULL;
-			}
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for predicate character string.");
+			return NULL;
 		}
+		strcpy(predicate, "");
 	}
 
-	//obi_close_column(seq_column);
-
 	return predicate;
 }
 
@@ -1051,11 +1067,11 @@ char* view_check_all_predicates(Obiview_p view)
 	char*  all_predicates_string = NULL;
 	char** all_predicates = NULL;
 
-	if (view->nb_predicates == 0)	// TODO or no error? discuss
+	if (view->nb_predicates == 0)
 	{
-		obi_set_errno(OBIVIEW_ERROR);
-		obidebug(1, "\nError trying to check predicates of a view with no predicates.");
-		return NULL;
+		all_predicates_string = (char*) malloc(1*sizeof(char));
+		strcpy(all_predicates_string, "");
+		return all_predicates_string;
 	}
 
 	size_to_allocate = 0;
@@ -1073,7 +1089,6 @@ char* view_check_all_predicates(Obiview_p view)
 	{
 		// Initialize predicate in predicate array
 		all_predicates[i] = NULL;
-
 		// Check the predicate
 		predicate = view_check_one_predicate(view, (view->predicate_functions)[i]);
 		if (predicate == NULL)
@@ -1105,7 +1120,8 @@ char* view_check_all_predicates(Obiview_p view)
 	strcpy(all_predicates_string, all_predicates[0]);
 	for (i=1; i < view->nb_predicates; i++)
 	{
-		strcat(all_predicates_string, "\n");
+		if (strlen(all_predicates_string))	// First predicate not empty
+			strcat(all_predicates_string, "\n");
 		strcat(all_predicates_string, all_predicates[i]);
 	}
 
@@ -1271,16 +1287,6 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		// Fill informations
 		strcpy((view->infos)->view_type, (view_to_clone->infos)->view_type);
 		strcpy((view->infos)->created_from, (view_to_clone->infos)->name);
-		// Copy predicates
-		view->nb_predicates = view_to_clone->nb_predicates;
-		if (view->nb_predicates > 0)
-		{
-			view->predicate_functions = malloc((view->nb_predicates) * sizeof(char* (*) (Obiview_p)));
-			for (i=0; i<(view->nb_predicates); i++)
-				(view->predicate_functions)[i] = (view_to_clone->predicate_functions)[i];
-		}
-		else
-			view->predicate_functions = NULL;
 
 		// Write comment specifying the name of the cloned view
 		clone_comment = (char*) malloc((strlen((view_to_clone->infos)->name) + 15)*sizeof(char));
@@ -1313,8 +1319,6 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		view->line_selection     		  = NULL;
 		((view->infos)->created_from)[0]  = '\0';
 		((view->infos)->view_type)[0]     = '\0';
-		view->nb_predicates 			  = 0;
-		view->predicate_functions 		  = NULL;
 		//view->columns          = NULL;  // TODO
 	}
 
@@ -1322,6 +1326,18 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	strcpy((view->infos)->name, view_name);
 	(view->infos)->creation_date = time(NULL);
 
+	// Fill automatic predicate functions
+	view->nb_predicates = 1;
+	view->predicate_functions = malloc((view->nb_predicates) * sizeof(char* (*) (Obiview_p)));
+	if (view->predicate_functions == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for view predicates");
+		return NULL;
+	}
+	(view->predicate_functions)[0] = view_check_qual_match_seqs;
+
+	// Write comments
 	if (write_comments_to_view_file(view, comments) < 0)
 	{
 		obidebug(1, "\nError writing comments when creating a view");
@@ -1403,9 +1419,10 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 {
 	Obiview_p 		view;
 	OBIDMS_column_p associated_nuc_column;
+	int				nb_predicates;
 
 	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)
+	{ // Check that the view to clone is already a NUC_SEQS view
 		if (strcmp((view_to_clone->infos)->view_type, VIEW_TYPE_NUC_SEQS))
 		{
 			obi_set_errno(OBIVIEW_ERROR);
@@ -1452,25 +1469,34 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 		}
 	}
 
-	// Add predicate functions of the view type
+	// Add predicate functions specific to the view type
 	// TODO macros?
 
 	if (quality_column)
-		view->nb_predicates = 5;
+		nb_predicates = view->nb_predicates + 4;
 	else
-		view->nb_predicates = 3;
+		nb_predicates = view->nb_predicates + 3;
 
-	view->predicate_functions = malloc((view->nb_predicates) * sizeof(char* (*) (Obiview_p)));
+	if (view->nb_predicates == 0)
+		view->predicate_functions = malloc(nb_predicates * sizeof(char* (*) (Obiview_p)));
+	else
+		view->predicate_functions = realloc(view->predicate_functions, nb_predicates * sizeof(char* (*) (Obiview_p)));
 
-	(view->predicate_functions)[0] = view_has_nuc_sequence_column;
-	(view->predicate_functions)[1] = view_has_id_column;
-	(view->predicate_functions)[2] = view_has_definition_column;
-	if (quality_column)
+	if (view->predicate_functions == NULL)
 	{
-		(view->predicate_functions)[3] = view_has_quality_column;
-		(view->predicate_functions)[4] = view_check_quality_matches_seq_column;
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for view predicates");
+		return NULL;
 	}
 
+	(view->predicate_functions)[(view->nb_predicates)] = view_has_nuc_sequence_column;
+	(view->predicate_functions)[(view->nb_predicates) + 1] = view_has_id_column;
+	(view->predicate_functions)[(view->nb_predicates) + 2] = view_has_definition_column;
+	if (quality_column)
+		(view->predicate_functions)[(view->nb_predicates) + 3] = view_has_quality_column;
+
+	view->nb_predicates = nb_predicates;
+
 	return view;
 }
 
@@ -1825,8 +1851,6 @@ int obi_view_delete_column(Obiview_p view, const char* column_name)
 	int  i;
 	bool found;
 
-	// TODO check that not deleting an obligatory column?
-
 	// Check that the view is not read-only
 	if (view->read_only)
 	{
@@ -2020,19 +2044,16 @@ int obi_save_and_close_view(Obiview_p view)
 
 	if (!(view->read_only))
 	{
-		if (view->nb_predicates > 0)
+		predicates = view_check_all_predicates(view);
+		if (predicates == NULL)
 		{
-			predicates = view_check_all_predicates(view);
-			if (predicates == NULL)
-			{
-				obidebug(1, "\nView predicates not respected");
-				return -1;	// TODO reverse view (delete files)
-			}
-			else
-			{
-				write_comments_to_view_file(view, predicates);
-				free(predicates);
-			}
+			obidebug(1, "\nView predicates not respected");
+			return -1;	// TODO reverse view (delete files)
+		}
+		else
+		{
+			write_comments_to_view_file(view, predicates);
+			free(predicates);
 		}
 		if (obi_save_view(view) < 0)
 			return -1;

src/obiview.h

@@ -464,7 +464,7 @@ int obi_save_view(Obiview_p view);
 /**
  * @brief Closes an opened view.
  *
- * @warning Use obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
+ * @warning Uses obi_save_and_close_view() to automatically save the view if it's not already saved in the view file.
  *
  * @param view A pointer on the view.
  *
@@ -481,6 +481,9 @@ int obi_close_view(Obiview_p view);
 /**
  * @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
  *
+ * The predicates associated with the view are checked before saving it, and -1 is returned if at
+ * least one predicate is not respected.
+ *
  * @param view A pointer on the view.
  *
  * @returns A value indicating the success of the operation.