static int pdom_hit_attach_gff3(GtPdomModel *model, GtPdomModelHit *hit,
void *data, GT_UNUSED GtError *err)
{
unsigned long i;
GtRange rng;
GtLTRdigestStream *ls = (GtLTRdigestStream *) data;
GtStrand strand;
gt_assert(model && hit);
strand = gt_pdom_model_hit_get_best_strand(hit);
/* do not use the hits on the non-predicted strand
-- maybe identify nested elements ? */
if (strand != gt_feature_node_get_strand(ls->element.mainnode))
return 0;
for (i=0;i<gt_pdom_model_hit_best_chain_length(hit);i++)
{
GtGenomeNode *gf;
GtStr *alignmentstring,
*aastring;
GtPdomSingleHit *singlehit;
GtPhase frame;
singlehit = gt_pdom_model_hit_best_single_hit(hit, i);
alignmentstring = gt_str_new();
aastring = gt_str_new();
frame = gt_pdom_single_hit_get_phase(singlehit);
rng = gt_pdom_single_hit_get_range(singlehit);
gt_pdom_single_hit_format_alignment(singlehit, GT_ALIWIDTH,
alignmentstring);
gt_pdom_single_hit_get_aaseq(singlehit, aastring);
rng.start++; rng.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
ls->element.mainnode),
GT_PDOM_TYPE,
rng.start,
rng.end,
strand);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_alignment",
alignmentstring, (GtFree) gt_str_delete);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_aaseq",
aastring, (GtFree) gt_str_delete);
gt_feature_node_set_source((GtFeatureNode*) gf, ls->ltrdigest_tag);
gt_feature_node_set_score((GtFeatureNode*) gf,
gt_pdom_single_hit_get_evalue(singlehit));
gt_feature_node_set_phase((GtFeatureNode*) gf, frame);
if (gt_pdom_model_get_name(model)) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "name",
gt_pdom_model_get_name(model));
}
if (gt_pdom_model_get_acc(model)) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "id",
gt_pdom_model_get_acc(model));
}
gt_feature_node_add_child(ls->element.mainnode, (GtFeatureNode*) gf);
}
return 0;
}
static int gt_ltrdigest_pdom_visitor_attach_hit(GtLTRdigestPdomVisitor *lv,
GtHMMERModelHit *modelhit,
GtHMMERSingleHit *singlehit)
{
GT_UNUSED GtUword i;
GtGenomeNode *gf;
int had_err = 0;
GtRange rrng;
gt_assert(lv && singlehit);
rrng = gt_ltrdigest_pdom_visitor_coords(lv, singlehit);
if (gt_array_size(singlehit->chains) > 0 || lv->output_all_chains) {
char buf[32];
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
lv->ltr_retrotrans),
gt_ft_protein_match,
rrng.start,
rrng.end,
singlehit->strand);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_alignment",
gt_str_ref(singlehit->alignment),
(GtFree) gt_str_delete);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_aaseq",
gt_str_ref(singlehit->aastring),
(GtFree) gt_str_delete);
gt_feature_node_set_source((GtFeatureNode*) gf, lv->tag);
gt_feature_node_set_score((GtFeatureNode*) gf, (float) singlehit->evalue);
(void) snprintf(buf, (size_t) 32, "%d", (int) singlehit->frame);
gt_feature_node_add_attribute((GtFeatureNode*) gf,
"reading_frame", buf);
if (modelhit->modelname != NULL) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "name",
modelhit->modelname);
}
if (gt_array_size(singlehit->chains) > 1UL && lv->output_all_chains) {
GtStr *buffer;
GtUword j;
gt_assert(singlehit->chains != NULL);
buffer = gt_str_new();
for (j = 0UL; j < gt_array_size(singlehit->chains); j++) {
gt_str_append_cstr(buffer, modelhit->modelname);
gt_str_append_char(buffer, ':');
gt_str_append_ulong(buffer,
*(GtUword*) gt_array_get(singlehit->chains, j));
if (j != gt_array_size(singlehit->chains) - 1) {
gt_str_append_char(buffer, ',');
}
}
gt_feature_node_set_attribute((GtFeatureNode*) gf, "chains",
gt_str_get(buffer));
gt_str_delete(buffer);
}
gt_feature_node_add_child(lv->ltr_retrotrans, (GtFeatureNode*) gf);
}
gt_array_delete(singlehit->chains);
singlehit->chains = NULL;
return had_err;
}
