Switch to version 3.0.0-beta14

taxids

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0-beta13'
+serial= '0-beta14'
 
 version ="%d.%02d.%s" % (major,minor,serial)

src/obidms_taxonomy.c

@@ -2376,9 +2376,10 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
 				// and the deleted taxids with no current reference. An element of the list is composed of the taxid, and the index
 				// of the taxon in the taxa structure, or -1 for deleted taxids.
 				// Creating the merged list requires to merge the 3 ordered lists into one.
-				while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) || ((nD >= 0) && (delnodes[nD] < old_taxid)))
+				while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) ||
+						((nD >= 0) && (delnodes[nD] < old_taxid)))
 				{
-					if ((tax->taxa)->taxon[nT].taxid < delnodes[nD])
+					if ((nT < (tax->taxa)->count) && (tax->taxa)->taxon[nT].taxid < delnodes[nD])
 					{ // Add element from taxa list
 						// Enlarge structure if needed
 						if (n == buffer_size)
@@ -2401,7 +2402,7 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
 						nT++;
 						n++;
 					}
-					else if (delnodes[nD] < (tax->taxa)->taxon[nT].taxid)
+					else
 					{ // Add element from deleted taxids list
 						// Enlarge structure if needed
 						if (n == buffer_size)
@@ -3036,12 +3037,12 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
 
 	strcpy(tax->tax_name, taxonomy_name);
 
-	buffer_size = 2048;
-
 	taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
 	if (taxonomy_path == NULL)
 		return NULL;
 
+	buffer_size = strlen(taxonomy_path) + strlen(taxonomy_name) + 6;
+
 	// Read ranks
 	ranks_file_name = (char*) malloc(buffer_size*sizeof(char));
 	if (ranks_file_name == NULL)

src/obidmscolumn.c

@@ -1973,7 +1973,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 
 	// Calculate the new file size
 	old_line_count = (column->header)->line_count;
-	new_line_count = old_line_count * COLUMN_GROWTH_FACTOR;
+	new_line_count = ceil((double) old_line_count * (double) COLUMN_GROWTH_FACTOR);
 
 	if (new_line_count > MAXIMUM_LINE_COUNT)
 	{
@@ -2381,6 +2381,54 @@ char* obi_get_elements_names(OBIDMS_column_p column)
 }
 
 
+char* obi_get_formatted_elements_names(OBIDMS_column_p column)
+{
+	char* elements_names;
+	int   i, j;
+	int   elt_idx;
+	int   len;
+
+	elements_names = (char*) malloc(((column->header)->elements_names_length + (column->header)->nb_elements_per_line) * sizeof(char));
+	if (elements_names == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for elements names");
+		return NULL;
+	}
+
+	j = 0;
+	for (i=0; i < (column->header)->nb_elements_per_line; i++)
+	{
+		elt_idx = ((column->header)->elements_names_idx)[i];
+		len = strlen(((column->header)->elements_names)+elt_idx);
+		memcpy(elements_names+j, ((column->header)->elements_names)+elt_idx, len*sizeof(char));
+		j = j + len;
+		elements_names[j] = ';';
+		j++;
+		elements_names[j] = ' ';
+		j++;
+	}
+
+	elements_names[j - 1] = '\0';
+
+	return elements_names;
+}
+
+
+char* obi_column_formatted_infos(OBIDMS_column_p column)
+{
+	char* column_infos;
+	char* elt_names;
+
+	column_infos = malloc(1024 * sizeof(char));
+
+	elt_names = obi_get_formatted_elements_names(column);
+
+
+	free(elt_names);
+	return column_infos;
+}
+
 
 int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb, index_t elt_idx)
 {

src/obidmscolumn.h

@@ -34,7 +34,7 @@
 #define NB_ELTS_MAX_IF_DEFAULT_NAME (1000000) 	/**< The maximum number of elements per line if the default element names
 										   	   	 *   are used ("0\01\02\0...\0n"), considering ELEMENTS_NAMES_MAX.  // TODO not up to date
 										   	   	 */
-#define COLUMN_GROWTH_FACTOR (2)	 	  		/**< The growth factor when a column is enlarged.
+#define COLUMN_GROWTH_FACTOR (1.3)	 	  		/**< The growth factor when a column is enlarged.
                                 	   	   	   	 */
 #define MAXIMUM_LINE_COUNT (1000000000)   		/**< The maximum line count for the data of a column (1E9). //TODO
                                 	       	   	 */
@@ -505,6 +505,14 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
 char* obi_get_elements_names(OBIDMS_column_p column);
 
 
+// TODO
+//char* obi_get_formatted_elements_names(OBIDMS_column_p column);
+
+
+// TODO
+//char* obi_column_formatted_infos(OBIDMS_column_p column);
+
+
 /**
  * @brief Prepares a column to set a value.
  *