The default element names for columns with multiple elements per line

are now "O;1;2;...;n"

python/obitools3/obidms/_obidms.pyx

@@ -379,10 +379,10 @@ cdef class OBIView :
         else :
             alias_b = str2bytes(alias)
         
-        if nb_elements_per_line > 1 :
+        if elements_names is None :
+            elements_names_b = str2bytes("")
+        else :
             elements_names_b = str2bytes(';'.join(elements_names))
-        elif nb_elements_per_line == 1 :
-            elements_names_b = column_name_b
     
         if type :                       # TODO make C function that does that
             if type == 'OBI_INT' :
@@ -528,61 +528,44 @@ cdef class OBIView_NUC_SEQS(OBIView):
     # TODO discuss
     cpdef align(self, OBIView oview, OBIView iview2=None,
                 double threshold=0.0, bint normalize=True, int reference=0, bint similarity_mode=True) :
-                
-        cdef OBIView iview1
-
-        cdef Obiview_p iview1_p
-        cdef Obiview_p iview2_p
-        cdef Obiview_p oview_p
-        
-        cdef OBIDMS_column icol1
-        cdef OBIDMS_column_p icol1_p
-        cdef OBIDMS_column_p* icol1_pp
-        
-        cdef OBIDMS_column id1_col
-        cdef OBIDMS_column_p id1_col_p
-        cdef OBIDMS_column_p* id1_col_pp
-
-        cdef OBIDMS_column id2_col
-        cdef OBIDMS_column_p id2_col_p
-        cdef OBIDMS_column_p* id2_col_pp
-
-        cdef OBIDMS_column ocol
-        cdef OBIDMS_column_p ocol_p
-        cdef OBIDMS_column_p* ocol_pp
-        
-        cdef str id1_col_name
-        cdef str id2_col_name
-        cdef str score_col_name
-        
-        id1_col_name = "ID1"        # TODO discuss names, aliases
-        id2_col_name = "ID2"
-        score_col_name = "score"
-        
-        iview1= self
-        iview1_p = iview1._pointer
-        icol1 = iview1[bytes2str(NUC_SEQUENCE_COLUMN)]
-        icol1_pp = icol1._pointer
-        icol1_p = icol1_pp[0]
-
-        oview.add_column(id1_col_name, type='OBI_STR', create=True)
-        oview.add_column(id2_col_name, type='OBI_STR', create=True)       
-        oview.add_column(score_col_name, type='OBI_FLOAT', create=True)
-
-        oview_p = oview._pointer        
-        ocol = oview[score_col_name]
-        ocol_pp = ocol._pointer
-        ocol_p = ocol_pp[0]
-        
-        id1_col = oview[id1_col_name]
-        id2_col = oview[id2_col_name]
-        id1_col_pp = id1_col._pointer
-        id2_col_pp = id2_col._pointer
-        id1_col_p = id1_col_pp[0]
-        id2_col_p = id2_col_pp[0]
-
-        if obi_align_one_column(iview1_p, icol1_p, NULL, oview_p, id1_col_p, id2_col_p, ocol_p, threshold, normalize, reference, similarity_mode) < 0 :
-            raise Exception("Error aligning sequences")
+        pass
+#                 
+#         cdef OBIView iview1
+# 
+#         cdef Obiview_p iview1_p
+#         cdef Obiview_p iview2_p
+#         cdef Obiview_p oview_p
+#         
+#         cdef OBIDMS_column icol1
+#         cdef OBIDMS_column_p icol1_p
+#         cdef OBIDMS_column_p* icol1_pp
+#         
+#         cdef OBIDMS_column id1_col
+#         cdef OBIDMS_column_p id1_col_p
+#         cdef OBIDMS_column_p* id1_col_pp
+# 
+#         cdef OBIDMS_column id2_col
+#         cdef OBIDMS_column_p id2_col_p
+#         cdef OBIDMS_column_p* id2_col_pp
+# 
+#         cdef OBIDMS_column ocol
+#         cdef OBIDMS_column_p ocol_p
+#         cdef OBIDMS_column_p* ocol_pp
+#         
+#         cdef str id1_col_name
+#         cdef str id2_col_name
+#         cdef str score_col_name
+# 
+#         score_col_name = "score"
+#         
+#         iview1= self
+#         iview1_p = iview1._pointer
+#         icol1 = iview1[bytes2str(NUC_SEQUENCE_COLUMN)]
+#         icol1_pp = icol1._pointer
+#         icol1_p = icol1_pp[0]
+# 
+#         if obi_align_one_column(iview1_p, icol1_p, threshold, normalize, reference, similarity_mode) < 0 :
+#             raise Exception("Error aligning sequences")
         
 
 ######################################################################################################

src/obidmscolumn.c

@@ -422,10 +422,18 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
 
 int obi_column_set_elements_names(OBIDMS_column_p column, const char* elements_names)
 {
+	if (strlen(elements_names) > ELEMENTS_NAMES_MAX)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError: element names too long (max: %d)", ELEMENTS_NAMES_MAX);
+		return -1;
+	}
+
 	strcpy((column->header)->elements_names, elements_names);
 	return 0;
 }
 
+
 index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
 {
 	return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
@@ -543,6 +551,37 @@ size_t obi_get_platform_header_size()
 }
 
 
+// TODO
+char* build_default_elements_names(index_t nb_elements_per_line)
+{
+	char* elements_names;
+	int   i;
+
+	elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char));
+	if (elements_names == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for elements names");
+		return NULL;
+	}
+
+	if (nb_elements_per_line > NB_ELTS_MAX_IF_DEFAULT_NAME)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError: too many elements per line to use the default names (max = %d elements)", NB_ELTS_MAX_IF_DEFAULT_NAME);
+		return NULL;
+	}
+
+	for (i= 0; i < nb_elements_per_line; i++)
+		sprintf(elements_names, "%d", i);
+
+	// Terminal character
+	elements_names[strlen(elements_names)] = '\0';
+
+	return elements_names;
+}
+
+
 OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 		                          const char*  column_name,
 								  OBIType_t    data_type,
@@ -574,16 +613,19 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	// Check that the informations given are not NULL/invalid/greater than the allowed sizes
 	if (dms == NULL)
 	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nCan't create column because of invalid DMS");
 		return NULL;
 	}
 	if (column_name == NULL)
 	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nCan't create column because of empty column name");
 		return NULL;
 	}
 	if ((data_type < 1) || (data_type > 8))		// TODO check in more robust way
 	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
 		obidebug(1, "\nCan't create column because of invalid data type");
 		return NULL;
 	}
@@ -637,14 +679,15 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	else if (nb_lines < minimum_line_count)
 		nb_lines = minimum_line_count;
 
-	// The number of elements names should be equal to the number of elements per line
-	if ((elements_names == NULL) && (nb_elements_per_line > 1))
+	// Check and build if needed the element names
+	if ((elements_names == NULL) || (strcmp(elements_names, "") == 0))	// Build the default element names: str of the element index
 	{
-		obidebug(1, "\nCan't create column because no elements names were given for a number of elements per line greater than 1");
-		return NULL;
+		elements_names = build_default_elements_names(nb_elements_per_line);
+		if (elements_names == NULL)
+			return NULL;
 	}
-	else if ((elements_names != NULL) && (nb_elements_per_line > 1))
-	{
+	else if (((elements_names == NULL) || (strcmp(elements_names, "") != 0)) && (nb_elements_per_line > 1))
+	{ // The number of elements names should be equal to the number of elements per line
 		char* token;
 		index_t n = 0;
 		token = strdup(elements_names);
@@ -660,11 +703,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 			return NULL;
 		}
 	}
-	else if ((nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))		// TODO Discuss, maybe just make it the column name
-	{
-		obidebug(1, "\nCan't create column because the element name does not match the column name");
-		return NULL;
-	}
+	// TODO what if 1 element and name specified? doc
 
 	// Calculate the size needed
 	header_size = obi_get_platform_header_size();
@@ -1060,7 +1099,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 		for (i=0; i<((line_selection->header)->lines_used); i++)
 		{
 			// Get the index in the line selection column
-			index = obi_column_get_index(line_selection, i);
+			index = obi_column_get_index_with_elt_idx(line_selection, i, 0);
 			// Copy the line at the index in the column to clone to the new column
 			memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
 		}
@@ -1590,7 +1629,7 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
 }
 
 
-int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)	// TODO problem with some columns in a view being empty or shorter and triggering an error because they've been truncated when the view was closed. Fixed with obiview.c in update_lines() for now
+int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
 {
 	if ((line_nb+1) > ((column->header)->line_count))
 	{

src/obidmscolumn.h

@@ -28,14 +28,17 @@
 #include "obiblob_indexer.h"
 
 
-#define ELEMENTS_NAMES_MAX (2048)     	/**< The maximum length of the list of elements names.	// TODO Discuss
-                                	     */
-#define COLUMN_GROWTH_FACTOR (2)	 	/**< The growth factor when a column is enlarged.
-                                	   	 */
-#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO
-                                	     */
-#define COMMENTS_MAX_LENGTH (2048)      /**< The maximum length for comments.
- 	 	 	 	 	 	 	 	 	     */
+#define ELEMENTS_NAMES_MAX (2048)     	  /**< The maximum length of the list of elements names.	// TODO Discuss
+                                	       */
+#define NB_ELTS_MAX_IF_DEFAULT_NAME (539) /**< The maximum number of elements per line if the default element names
+										   *   are used ("0;1;2;...;n"), considering ELEMENTS_NAMES_MAX.
+                                	   	   */
+#define COLUMN_GROWTH_FACTOR (2)	 	  /**< The growth factor when a column is enlarged.
+                                	   	   */
+#define MAXIMUM_LINE_COUNT (1000000000)   /**< The maximum line count for the data of a column. //TODO
+                                	       */
+#define COMMENTS_MAX_LENGTH (2048)        /**< The maximum length for comments.
+ 	 	 	 	 	 	 	 	 	       */
 
 
 /**
@@ -64,7 +67,8 @@ typedef struct OBIDMS_column_header {
 	index_t				nb_elements_per_line;   			   	/**< Number of elements per line.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	char				elements_names[ELEMENTS_NAMES_MAX+1];	/**< Names of the line elements with ';' as separator
-															 	 *	 (should be the column name if one element per line).
+																 *   (no terminal ';').
+															 	 *	 (default are the indices: "0;1;2;...;n").
 															 	 */
 	OBIType_t			returned_data_type;		    			/**< Type of the data that is returned when getting an
 															 	 *   element from the column.
@@ -179,7 +183,8 @@ size_t obi_get_platform_header_size();
  * @param data_type The OBIType code of the data.
  * @param nb_lines The number of lines to be stored.
  * @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 elements_names The names of the elements with ';' as separator (no terminal ';'),
+ *                       NULL or "" if the default names are to be used ("0;1;2;...;n").
  * @param indexer_name The name of the indexer if there is one associated with the column.
  *                     If NULL or "", the indexer name is set as the column name.
  * @param associated_column_name The name of the associated column if there is one.

src/obiview.c

@@ -1236,7 +1236,7 @@ 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, -1, NULL);
+			view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, NULL, NULL, -1, NULL);
 			if ((view->line_selection) == NULL)
 			{
 				obidebug(1, "\nError creating a column corresponding to a line selection");
@@ -1440,19 +1440,19 @@ 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, NUC_SEQUENCE_COLUMN, OBI_SEQ, 0, 1, NUC_SEQUENCE_COLUMN, "", NULL, -1, "Nucleotide sequences", true) < 0)
+		if (obi_view_add_column(view, NUC_SEQUENCE_COLUMN, -1, NUC_SEQUENCE_COLUMN, OBI_SEQ, 0, 1, NULL, "", 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, ID_COLUMN, OBI_STR, 0, 1, ID_COLUMN, "", NULL, -1, "Ids", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, ID_COLUMN, OBI_STR, 0, 1, NULL, "", 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, DEFINITION_COLUMN, OBI_STR, 0, 1, DEFINITION_COLUMN, "", NULL, -1, "Definitions", true) < 0)
+		if (obi_view_add_column(view, DEFINITION_COLUMN, -1, DEFINITION_COLUMN, OBI_STR, 0, 1, NULL, "", NULL, -1, "Definitions", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -1461,7 +1461,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 		if (quality_column)
 		{
 			associated_nuc_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);
-			if (obi_view_add_column(view, QUALITY_COLUMN, -1, QUALITY_COLUMN, OBI_QUAL, 0, 1, QUALITY_COLUMN, "", (associated_nuc_column->header)->name, (associated_nuc_column->header)->version, "Sequence qualities", true) < 0)		// TODO discuss automatic association
+			if (obi_view_add_column(view, QUALITY_COLUMN, -1, QUALITY_COLUMN, OBI_QUAL, 0, 1, NULL, "", (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;

src/obiview.h

@@ -299,8 +299,10 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name);
  * @param data_type The OBIType code of the data.
  * @param nb_lines The number of lines to be stored.
  * @param nb_elements_per_line The number of elements per line.
- * @param elements_names The names of the elements with ';' as separator.
+ * @param elements_names The names of the elements with ';' as separator (no terminal ';'),
+ *                       NULL or "" if the default names are to be used ("0;1;2;...;n").
  * @param indexer_name The name of the indexer if there is one associated with the column.
+ *                     If NULL or "", the indexer name is set as the column name.
  * @param comments Optional comments associated with the column.
  * @param create Whether the column should be created (create == true) or opened (create == false).
  *