// ----------------------------------------------------------------------------
bool CSoMap::xMapRna(
const CSeq_feat& feature,
string& so_type)
// ----------------------------------------------------------------------------
{
static const map<CSeqFeatData::ESubtype, string> mapSubtypeStraight = {
{CSeqFeatData::eSubtype_misc_RNA, "transcript"},
{CSeqFeatData::eSubtype_rRNA, "rRNA"},
{CSeqFeatData::eSubtype_tRNA, "tRNA"},
};
static const map<CSeqFeatData::ESubtype, string> mapSubtypePseudo = {
{CSeqFeatData::eSubtype_misc_RNA, "pseudogenic_transcript"},
{CSeqFeatData::eSubtype_rRNA, "pseudogenic_rRNA"},
{CSeqFeatData::eSubtype_tRNA, "pseudogenic_tRNA"},
};
auto subtype = feature.GetData().GetSubtype();
if (feature.IsSetPseudo() && feature.GetPseudo()) {
auto cit = mapSubtypePseudo.find(subtype);
if (cit == mapSubtypePseudo.end()) {
return false;
}
so_type = cit->second;
return true;
}
if (feature.IsSetPseudo() && !feature.GetPseudo()) {
auto cit = mapSubtypeStraight.find(subtype);
if (cit == mapSubtypeStraight.end()) {
return false;
}
so_type = cit->second;
return true;
}
for (auto qual: feature.GetQual()) {
if (qual->GetQual() == "pseudo" || qual->GetQual() == "pseudogene") {
auto cit = mapSubtypePseudo.find(subtype);
if (cit == mapSubtypePseudo.end()) {
return false;
}
so_type = cit->second;
return true;
}
}
auto cit = mapSubtypeStraight.find(subtype);
if (cit == mapSubtypeStraight.end()) {
return false;
}
so_type = cit->second;
return true;
}
// ----------------------------------------------------------------------------
bool CSoMap::xMapGene(
const CSeq_feat& feature,
string& so_type)
// ----------------------------------------------------------------------------
{
if (feature.IsSetPseudo() && feature.GetPseudo()) {
so_type = "pseudogene";
return true;
}
for (auto qual: feature.GetQual()) {
if (qual->GetQual() == "pseudo" || qual->GetQual() == "pseudogene") {
so_type = "pseudogene";
return true;
}
}
so_type = "gene";
return true;
}