// ----------------------------------------------------------------------------
bool CSoMap::xFeatureMakeMiscRna(
const string& so_type,
CSeq_feat& feature)
// ----------------------------------------------------------------------------
{
feature.SetData().SetImp().SetKey("misc_RNA");
if (so_type=="pseudogenic_transcript") {
feature.SetPseudo(true);
}
return true;
}
// ----------------------------------------------------------------------------
bool CSoMap::xFeatureMakeCds(
const string& so_type,
CSeq_feat& feature)
// ----------------------------------------------------------------------------
{
feature.SetData().SetCdregion();
if (so_type=="pseudogenic_CDS") {
feature.SetPseudo(true);
}
return true;
}
// ----------------------------------------------------------------------------
bool CSoMap::xFeatureMakeGene(
const string& so_type,
CSeq_feat& feature)
// ----------------------------------------------------------------------------
{
feature.SetData().SetGene();
if (so_type == "pseudogene") {
feature.SetPseudo(true);
}
return true;
}
// ----------------------------------------------------------------------------
bool CSoMap::xFeatureMakeRna(
const string& so_type,
CSeq_feat& feature)
// ----------------------------------------------------------------------------
{
static const map<string, CRNA_ref::EType, CompareNoCase> mTypeToRna = {
{"mRNA", CRNA_ref::eType_mRNA},
{"rRNA", CRNA_ref::eType_rRNA},
{"pseudogenic_rRNA", CRNA_ref::eType_rRNA},
{"tRNA", CRNA_ref::eType_tRNA},
{"pseudogenic_tRNA", CRNA_ref::eType_tRNA},
{"tmRNA", CRNA_ref::eType_tmRNA},
};
auto it = mTypeToRna.find(so_type);
feature.SetData().SetRna().SetType(it->second);
if(NStr::StartsWith(so_type, "pseudogenic_")) {
feature.SetPseudo(true);
}
return true;
}