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; }