static int md5_to_seqid(GtGenomeNode *gn, GtRegionMapping *region_mapping,
GtError *err)
{
GtStr *seqid;
int had_err = 0;
gt_error_check(err);
gt_assert(gn && region_mapping);
seqid = gt_genome_node_get_seqid(gn);
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
/* seqid is a MD5 seqid -> change id */
GtStr *desc = gt_str_new();
had_err = gt_region_mapping_get_description(region_mapping, desc, seqid,
err);
if (!had_err) {
GtStr *new_seqid = gt_str_new();
gt_regular_seqid_save(new_seqid, desc);
if (gt_feature_node_try_cast(gn)) {
M2IChangeSeqidInfo info;
info.new_seqid = new_seqid;
info.region_mapping = region_mapping;
had_err = gt_feature_node_traverse_children((GtFeatureNode*) gn, &info,
m2i_change_seqid, true,
err);
}
else
gt_genome_node_change_seqid(gn, new_seqid);
gt_str_delete(new_seqid);
}
gt_str_delete(desc);
}
return had_err;
}
static int gff3_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn,
GtError *err)
{
GtGFF3Visitor *gff3_visitor;
int had_err;
gt_error_check(err);
gff3_visitor = gff3_visitor_cast(nv);
gff3_version_string(nv);
had_err = gt_feature_node_traverse_children(fn, gff3_visitor, store_ids, true,
err);
if (!had_err) {
if (gt_feature_node_is_tree(fn)) {
had_err = gt_feature_node_traverse_children(fn, gff3_visitor,
gff3_show_feature_node, true,
err);
}
else {
/* got a DAG -> traverse in topologically sorted depth first fashion to
make sure that the 'Parent' attributes are shown in correct order */
had_err =
gt_feature_node_traverse_children_top(fn, gff3_visitor,
gff3_show_feature_node, err);
}
}
/* reset hashmaps */
gt_hashmap_reset(gff3_visitor->feature_node_to_id_array);
gt_hashmap_reset(gff3_visitor->feature_node_to_unique_id_str);
/* show terminator, if the feature has children (otherwise it is clear that
the feature is complete, because no ID attribute has been shown) */
if (gt_feature_node_has_children(fn) ||
(gff3_visitor->retain_ids && gt_feature_node_get_attribute(fn, "ID"))) {
if (!gff3_visitor->outstr)
gt_file_xprintf(gff3_visitor->outfp, "%s\n", GT_GFF_TERMINATOR);
else {
gt_str_append_cstr(gff3_visitor->outstr, GT_GFF_TERMINATOR);
gt_str_append_char(gff3_visitor->outstr, '\n');
}
}
return had_err;
}
static int inter_feature_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn, GtError *err)
{
GtInterFeatureVisitor *v;
gt_error_check(err);
v = gt_inter_feature_visitor_cast(nv);
return gt_feature_node_traverse_children(fn, v, inter_feature_if_necessary,
false, err);
}
static int stat_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn,
GtError *err)
{
GtStatVisitor *sv;
gt_error_check(err);
sv = stat_visitor_cast(nv);
return gt_feature_node_traverse_children(fn, sv, compute_statistics, false,
err);
}
static int gtf_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn,
GtError *err)
{
GtGTFVisitor *gtf_visitor;
int had_err;
gt_error_check(err);
gtf_visitor = gtf_visitor_cast(nv);
had_err = gt_feature_node_traverse_children(fn, gtf_visitor,
gtf_show_feature_node, false,
err);
return had_err;
}
