bool CPacked_seqpnt::x_IsMinusStrand(void) const
{
ENa_strand strand = eNa_strand_unknown;
if ( IsSetStrand() ) {
strand = GetStrand();
}
return (strand == eNa_strand_minus) || (strand == eNa_strand_both_rev);
}
bool CLocation_constraint :: x_DoesStrandMatchConstraint(const CSeq_loc& loc) const
{
if (loc.Which() == CSeq_loc::e_not_set) {
return false;
}
if (GetStrand() == eStrand_constraint_any) {
return true;
}
if (loc.GetStrand() == eNa_strand_minus) {
if (GetStrand() == eStrand_constraint_minus) {
return true;
}
else return false;
}
else {
if (GetStrand() == eStrand_constraint_plus) {
return true;
}
else return false;
}
};
bool CLocation_constraint :: x_IsLocationConstraintEmpty() const
{
if (GetStrand() != eStrand_constraint_any
|| GetSeq_type() != eSeqtype_constraint_any
|| GetPartial5() != ePartial_constraint_either
|| GetPartial3() != ePartial_constraint_either
|| GetLocation_type() != eLocation_type_constraint_any
|| (CanGetEnd5()
&& GetEnd5().Which() != CLocation_pos_constraint::e_not_set)
|| (CanGetEnd3()
&& GetEnd3().Which() != CLocation_pos_constraint::e_not_set)) {
return false;
}
return true;
};
bool CLocation_constraint :: Match(const CSeq_feat& feat, CConstRef <CSeq_feat> feat_to, CConstRef <CBioseq> feat_bioseq) const
{
if (x_IsLocationConstraintEmpty()) {
return true;
}
const CSeq_loc& feat_loc = feat.GetLocation();
if (GetStrand() != eStrand_constraint_any) {
if (feat_bioseq.Empty()) {
return false;
}
else if (feat_bioseq->IsAa()) {
if (feat_to.Empty()) { // when feat is product, feat_to points to cds
return false;
}
else if (!x_DoesStrandMatchConstraint (feat_to->GetLocation())) {
return false;
}
}
else if (!x_DoesStrandMatchConstraint (feat_loc)) {
return false;
}
}
if (!x_DoesBioseqMatchSequenceType(feat_bioseq, GetSeq_type())) {
return false;
}
if (!x_DoesLocationMatchPartialnessConstraint (feat_loc)) {
return false;
}
if (!x_DoesLocationMatchTypeConstraint (feat_loc)) {
return false;
}
if (!x_DoesLocationMatchDistanceConstraint(feat_bioseq, feat_loc)) {
return false;
}
return true;
};
void CPacked_seqpnt::FlipStrand(void)
{
if (IsSetStrand()) {
SetStrand(Reverse(GetStrand()));
}
}
bool CSeq_interval::x_IsMinusStrand(void) const
{
return IsSetStrand() && IsReverse(GetStrand());
}
void CSeq_interval::FlipStrand(void)
{
if (IsSetStrand()) {
SetStrand(Reverse(GetStrand()));
}
}
