void gt_type_graph_add_stanza(GtTypeGraph *type_graph,
const GtOBOStanza *stanza)
{
const char *id_value, *name_value;
GtUword i, size;
GtTypeNode *node;
GtStr *buf;
gt_assert(type_graph && stanza && !type_graph->ready);
gt_assert(gt_obo_stanza_size(stanza, "id") == 1);
gt_assert(gt_obo_stanza_size(stanza, "name") == 1);
id_value = gt_symbol(gt_obo_stanza_get_value(stanza, "id", 0));
name_value = gt_symbol(gt_obo_stanza_get_value(stanza, "name", 0));
gt_assert(id_value);
gt_assert(name_value);
gt_assert(!gt_hashmap_get(type_graph->nodemap, id_value));
node = gt_type_node_new(gt_array_size(type_graph->nodes), id_value);
gt_hashmap_add(type_graph->name2id, (char*) name_value, (char*) id_value);
gt_hashmap_add(type_graph->id2name, (char*) id_value, (char*) name_value);
gt_hashmap_add(type_graph->nodemap, (char*) id_value, node);
gt_array_add(type_graph->nodes, node);
buf = gt_str_new();
/* store is_a entries in node, if necessary */
if ((size = gt_obo_stanza_size(stanza, "is_a"))) {
for (i = 0; i < size; i++) {
const char *id = gt_obo_stanza_get_value(stanza, "is_a", i);
gt_str_reset(buf);
gt_str_append_cstr_nt(buf, id, strcspn(id, " \n"));
gt_type_node_is_a_add(node, gt_symbol(gt_str_get(buf)));
}
}
/* store part_of entries in node, if necessary */
if ((size = gt_obo_stanza_size(stanza, "relationship"))) {
for (i = 0; i < size; i++) {
const char *rel = gt_obo_stanza_get_value(stanza, "relationship", i);
gt_str_reset(buf);
/* match part_of */
if (!strncmp(rel, PART_OF, strlen(PART_OF))) {
const char *part_of = rel + strlen(PART_OF) + 1;
gt_str_append_cstr_nt(buf, part_of, strcspn(part_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
continue;
}
/* match member_of */
if (!strncmp(rel, MEMBER_OF, strlen(MEMBER_OF))) {
const char *member_of = rel + strlen(MEMBER_OF) + 1;
gt_str_append_cstr_nt(buf, member_of, strcspn(member_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
continue;
}
/* match integral_part_of */
if (!strncmp(rel, INTEGRAL_PART_OF, strlen(INTEGRAL_PART_OF))) {
const char *integral_part_of = rel + strlen(INTEGRAL_PART_OF) + 1;
gt_str_append_cstr_nt(buf, integral_part_of,
strcspn(integral_part_of, " \n"));
gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf)));
}
}
}
gt_str_delete(buf);
}
const char* gt_obo_parse_tree_get_stanza_value(const GtOBOParseTree
*obo_parse_tree,
unsigned long stanza_num,
const char *stanza_key)
{
gt_assert(obo_parse_tree);
return gt_obo_stanza_get_value(*(GtOBOStanza**)
gt_array_get(obo_parse_tree->stanzas,
stanza_num), stanza_key, 0);
}
static int validate_value(const GtOBOStanza *obo_stanza, const char *value,
GtError *err)
{
gt_error_check(err);
gt_assert(obo_stanza && value);
if (!gt_obo_stanza_get_value(obo_stanza, value, 0)) {
gt_error_set(err, "%s stanza starting on line %lu in file \"%s\" lacks "
"required \"%s\" tag", gt_obo_stanza_get_type(obo_stanza),
gt_obo_stanza_line(obo_stanza),
gt_obo_stanza_filename(obo_stanza), value);
return -1;
}
return 0;
}
