static void infer_cds_visitor_check_cds_phase(AgnInferCDSVisitor *v)
{
unsigned long num_cds_feats = gt_array_size(v->cds);
if(num_cds_feats == 0)
return;
GtFeatureNode *cdsf1 = *(GtFeatureNode **)gt_array_get(v->cds, 0);
GtStrand strand = gt_feature_node_get_strand(cdsf1);
if(strand == GT_STRAND_REVERSE)
cdsf1 = *(GtFeatureNode **)gt_array_get(v->cds, num_cds_feats - 1);
gt_feature_node_set_phase(cdsf1, GT_PHASE_ZERO);
if(num_cds_feats == 1)
return;
unsigned long cds_length = gt_genome_node_get_length((GtGenomeNode *)cdsf1);
int i;
if(strand == GT_STRAND_REVERSE)
{
for(i = num_cds_feats - 2; i >= 0; i--)
{
GtFeatureNode *cds = *(GtFeatureNode **)gt_array_get(v->cds, i);
int phasenum = cds_length % 3;
GtPhase phase = GT_PHASE_ZERO;
if(phasenum == 1)
phase = GT_PHASE_TWO;
else if(phasenum == 2)
phase = GT_PHASE_ONE;
gt_feature_node_set_phase(cds, phase);
cds_length += gt_genome_node_get_length((GtGenomeNode *)cds);
}
}
else
{
for(i = 1; i < num_cds_feats; i++)
{
GtFeatureNode *cds = *(GtFeatureNode **)gt_array_get(v->cds, i);
int phasenum = cds_length % 3;
GtPhase phase = GT_PHASE_ZERO;
if(phasenum == 1)
phase = GT_PHASE_TWO;
else if(phasenum == 2)
phase = GT_PHASE_ONE;
gt_feature_node_set_phase(cds, phase);
cds_length += gt_genome_node_get_length((GtGenomeNode *)cds);
}
}
}
static int check_cds_phases(GtArray *cds_features, GtCDSCheckVisitor *v,
bool is_multi, bool second_pass, GtError *err)
{
GtPhase current_phase, correct_phase = GT_PHASE_ZERO;
GtFeatureNode *fn;
GtStrand strand;
unsigned long i, current_length;
int had_err = 0;
gt_error_check(err);
gt_assert(cds_features);
gt_assert(gt_array_size(cds_features));
fn = *(GtFeatureNode**) gt_array_get_first(cds_features);
strand = gt_feature_node_get_strand(fn);
if (strand == GT_STRAND_REVERSE)
gt_array_reverse(cds_features);
for (i = 0; !had_err && i < gt_array_size(cds_features); i++) {
fn = *(GtFeatureNode**) gt_array_get(cds_features, i);
/* the first phase can be anything (except being undefined), because the
GFF3 spec says:
NOTE 4 - CDS features MUST have have a defined phase field. Otherwise it
is not possible to infer the correct polypeptides corresponding to
partially annotated genes. */
if ((!i && gt_feature_node_get_phase(fn) == GT_PHASE_UNDEFINED) ||
(i && gt_feature_node_get_phase(fn) != correct_phase)) {
if (gt_hashmap_get(v->cds_features, fn)) {
if (v->tidy && !is_multi && !gt_feature_node_has_children(fn)) {
/* we can split the feature */
gt_warning("%s feature on line %u in file \"%s\" has multiple "
"parents which require different phases; split feature",
gt_ft_CDS,
gt_genome_node_get_line_number((GtGenomeNode*) fn),
gt_genome_node_get_filename((GtGenomeNode*) fn));
gt_hashmap_add(v->cds_features_to_split, fn, fn);
v->splitting_is_necessary = true; /* split later */
}
else {
gt_error_set(err, "%s feature on line %u in file \"%s\" has multiple "
"parents which require different phases",
gt_ft_CDS,
gt_genome_node_get_line_number((GtGenomeNode*) fn),
gt_genome_node_get_filename((GtGenomeNode*) fn));
had_err = -1;
}
}
else {
if (v->tidy) {
if (!second_pass) {
gt_warning("%s feature on line %u in file \"%s\" has the wrong "
"phase %c -> correcting it to %c", gt_ft_CDS,
gt_genome_node_get_line_number((GtGenomeNode*) fn),
gt_genome_node_get_filename((GtGenomeNode*) fn),
GT_PHASE_CHARS[gt_feature_node_get_phase(fn)],
GT_PHASE_CHARS[correct_phase]);
}
gt_feature_node_set_phase(fn, correct_phase);
}
else {
gt_error_set(err, "%s feature on line %u in file \"%s\" has the "
"wrong phase %c (should be %c)", gt_ft_CDS,
gt_genome_node_get_line_number((GtGenomeNode*) fn),
gt_genome_node_get_filename((GtGenomeNode*) fn),
GT_PHASE_CHARS[gt_feature_node_get_phase(fn)],
GT_PHASE_CHARS[correct_phase]);
had_err = -1;
}
}
}
if (!had_err) {
current_phase = gt_feature_node_get_phase(fn);
current_length = gt_genome_node_get_length((GtGenomeNode*) fn);
correct_phase = (3 - (current_length - current_phase) % 3) % 3;
gt_hashmap_add(v->cds_features, fn, fn); /* record CDS feature */
}
}
return had_err;
}
