static int compute_statistics(GtFeatureNode *fn, void *data, GtError *err)
{
GtStatVisitor *sv;
GT_UNUSED int rval;
gt_error_check(err);
gt_assert(data);
sv = (GtStatVisitor*) data;
if (gt_feature_node_is_multi(fn) &&
gt_feature_node_get_multi_representative(fn) == fn) {
sv->number_of_multi_features++;
}
if (sv->used_sources)
compute_source_statistics(fn, sv->used_sources);
compute_type_statistics(fn, sv);
if (sv->exon_number_distribution || sv->cds_length_distribution) {
sv->exon_number_for_distri = 0;
sv->cds_length_for_distri = 0;
rval = gt_feature_node_traverse_direct_children(fn, sv,
add_exon_or_cds_number,
err);
gt_assert(!rval); /* add_exon_or_cds_number() is sane */
if (sv->exon_number_distribution && sv->exon_number_for_distri) {
gt_disc_distri_add(sv->exon_number_distribution,
sv->exon_number_for_distri);
}
if (sv->cds_length_distribution && sv->cds_length_for_distri) {
gt_disc_distri_add(sv->cds_length_distribution,
sv->cds_length_for_distri);
}
}
return 0;
}
static int visit_child(GtFeatureNode* fn, void *nti, GtError *err)
{
NodeTraverseInfo* gt_genome_node_info;
int had_err = 0;
gt_genome_node_info = (NodeTraverseInfo*) nti;
gt_error_check(err);
if (gt_feature_node_has_children(fn))
{
GtFeatureNode *oldparent = gt_genome_node_info->parent;
had_err = process_node(gt_genome_node_info->diagram, fn,
gt_genome_node_info->parent, err);
if (!had_err) {
gt_genome_node_info->parent = fn;
had_err = gt_feature_node_traverse_direct_children(fn,
gt_genome_node_info,
visit_child, err);
}
if (!had_err) {
gt_genome_node_info->parent = oldparent;
}
}
else
{
had_err = process_node(gt_genome_node_info->diagram, fn,
gt_genome_node_info->parent, err);
}
return had_err;
}
static int inter_feature_if_necessary(GtFeatureNode *fn, void *data,
GtError *err)
{
GtInterFeatureVisitor *aiv = (GtInterFeatureVisitor*) data;
gt_error_check(err);
gt_assert(fn);
aiv->parent_feature = fn;
aiv->previous_feature = NULL;
return gt_feature_node_traverse_direct_children(fn, aiv,
inter_feature_in_children,
err);
}
static int gtf_show_transcript(GtFeatureNode *feature_node,
GtGTFVisitor *gtf_visitor, GtError *err)
{
GtFeatureNode *fn;
GtUword i;
int had_err;
gt_error_check(err);
gt_assert(feature_node && gtf_visitor);
gt_array_reset(gtf_visitor->exon_features);
gt_array_reset(gtf_visitor->CDS_features);
had_err = gt_feature_node_traverse_direct_children(feature_node, gtf_visitor,
save_exon_node, err);
if (gt_array_size(gtf_visitor->exon_features)) {
/* sort exon features */
qsort(gt_array_get_space(gtf_visitor->exon_features),
gt_array_size(gtf_visitor->exon_features), sizeof (GtGenomeNode*),
(GtCompare) gt_genome_node_compare);
/* show exon features */
gtf_visitor->transcript_id++;
for (i = 0; i < gt_array_size(gtf_visitor->exon_features); i++) {
fn = *(GtFeatureNode**) gt_array_get(gtf_visitor->exon_features, i);
gt_gff3_output_leading(fn, gtf_visitor->outfp);
gt_file_xprintf(gtf_visitor->outfp, "gene_id \""GT_WU"\"; transcript_id "
"\""GT_WU"."GT_WU"\";\n", gtf_visitor->gene_id,
gtf_visitor->gene_id, gtf_visitor->transcript_id);
}
}
if (gt_array_size(gtf_visitor->CDS_features)) {
/* sort CDS features */
qsort(gt_array_get_space(gtf_visitor->CDS_features),
gt_array_size(gtf_visitor->CDS_features), sizeof (GtGenomeNode*),
(GtCompare) gt_genome_node_compare);
/* show start_codon feature */
/* fn = *(GtFeatureNode**) */ (void) gt_array_get(gtf_visitor->CDS_features,
0);
/* XXX: to be done */
/* show CDS features */
for (i = 0; i < gt_array_size(gtf_visitor->CDS_features); i++) {
fn = *(GtFeatureNode**) gt_array_get(gtf_visitor->CDS_features, i);
gt_gff3_output_leading(fn, gtf_visitor->outfp);
gt_file_xprintf(gtf_visitor->outfp, "gene_id \""GT_WU"\"; transcript_id "
"\""GT_WU"."GT_WU"\";\n", gtf_visitor->gene_id,
gtf_visitor->gene_id, gtf_visitor->transcript_id);
}
/* XXX: show stop_codon feature and shorten last CDS feature */
}
return had_err;
}
static int store_ids(GtFeatureNode *fn, void *data, GtError *err)
{
GtGFF3Visitor *gff3_visitor = (GtGFF3Visitor*) data;
AddIDInfo add_id_info;
int had_err = 0;
GtStr *id;
gt_error_check(err);
gt_assert(fn && gff3_visitor);
if (gt_feature_node_has_children(fn) || gt_feature_node_is_multi(fn) ||
(gff3_visitor->retain_ids && gt_feature_node_get_attribute(fn, "ID"))) {
if (gt_feature_node_is_multi(fn)) {
id = gt_hashmap_get(gff3_visitor->feature_node_to_unique_id_str,
gt_feature_node_get_multi_representative(fn));
if (!id) {
/* the representative does not have its own id yet -> create it */
if (gff3_visitor->retain_ids) {
id = make_id_unique(gff3_visitor,
gt_feature_node_get_multi_representative(fn));
}
else {
id = create_unique_id(gff3_visitor,
gt_feature_node_get_multi_representative(fn));
}
}
/* store id for feature, if the feature was not the representative */
if (gt_feature_node_get_multi_representative(fn) != fn) {
gt_hashmap_add(gff3_visitor->feature_node_to_unique_id_str, fn,
gt_str_ref(id));
}
}
else {
if (gff3_visitor->retain_ids)
id = make_id_unique(gff3_visitor, fn);
else
id = create_unique_id(gff3_visitor, fn);
}
/* for each child -> store the parent feature in the hash map */
add_id_info.gt_feature_node_to_id_array =
gff3_visitor->feature_node_to_id_array,
add_id_info.id = gt_str_get(id);
had_err = gt_feature_node_traverse_direct_children(fn, &add_id_info, add_id,
err);
}
return had_err;
}
/* Traverse a genome node graph with depth first search. */
static int traverse_genome_nodes(GtFeatureNode *fn, void *nti)
{
NodeTraverseInfo* gt_genome_node_info;
int had_err = 0;
gt_assert(nti);
gt_genome_node_info = (NodeTraverseInfo*) nti;
gt_genome_node_info->parent = fn;
/* handle root nodes */
had_err = process_node(gt_genome_node_info->diagram, fn, NULL,
gt_genome_node_info->err);
if (!had_err && gt_feature_node_has_children(fn)) {
had_err = gt_feature_node_traverse_direct_children(fn,
gt_genome_node_info,
visit_child,
gt_genome_node_info
->err);
}
return had_err;
}
