// ----------------------------------------------------------------------------
bool CGtfReader::x_MergeFeatureLocationSingleInterval(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
const CSeq_interval& gene_int = pFeature->GetLocation().GetInt();
if ( gene_int.GetFrom() > record.SeqStart() -1 ) {
pFeature->SetLocation().SetInt().SetFrom( record.SeqStart() );
}
if ( gene_int.GetTo() < record.SeqStop() - 1 ) {
pFeature->SetLocation().SetInt().SetTo( record.SeqStop() );
}
if (record.Type() == "CDS" && pFeature->GetData().IsCdregion()) {
return x_FeatureTrimQualifiers(record, pFeature);
}
return true;
}
CRef<CBioseq_set> CMakeCdrProds::MakeCdrProds(CRef<CSeq_annot> annot,
CBioseq_Handle handle)
{
CRef<CBioseq_set> bioseq_set(new CBioseq_set);
if (!annot->GetData().IsFtable()) {
// Is this the right thing to do?
// Could throw, or could return null CRef instead.
return bioseq_set;
}
list<CRef<CSeq_feat> >& ftable = annot->SetData().SetFtable();
NON_CONST_ITERATE (list<CRef<CSeq_feat> >, feat, ftable) {
if (!(*feat)->GetData().IsCdregion()) {
// not interested if not a Cdregion
continue;
}
if ((*feat)->IsSetProduct()) {
// already has a product; don't make new one
continue;
}
string prot;
CSeqTranslator::Translate(**feat, handle.GetScope(), prot);
CRef<CSeq_data> seq_data(new CSeq_data(prot,
CSeq_data::e_Iupacaa));
CRef<CSeq_inst> seq_inst(new CSeq_inst);
seq_inst->SetSeq_data(*seq_data);
seq_inst->SetRepr(CSeq_inst_Base::eRepr_raw);
seq_inst->SetMol(CSeq_inst_Base::eMol_aa);
seq_inst->SetLength(prot.size());
CRef<CBioseq> bio_seq(new CBioseq);
string num = NStr::NumericToString(sm_Counter.Add(1));
// pad to five digits
if (num.size() < 5) {
num.insert(SIZE_TYPE(0), 5 - num.size(), '0');
}
string acc = "tp" + num;
string full_acc = "lcl|" + acc;
CRef<CSeq_id> id(new CSeq_id(full_acc));
bio_seq->SetId().push_back(id);
// a title
CRef<CSeqdesc> title(new CSeqdesc);
title->SetTitle(string("Translation product ") + acc);
bio_seq->SetDescr().Set().push_back(title);
// Mol_type
CRef<CSeqdesc> mol_type(new CSeqdesc);
mol_type->SetMol_type( eGIBB_mol_peptide);
bio_seq->SetDescr().Set().push_back(mol_type);
// set the instance
bio_seq->SetInst(*seq_inst);
// wrap this Bio_seq in an entry
CRef<CSeq_entry> seq_entry(new CSeq_entry);
seq_entry->SetSeq(*bio_seq);
// add this entry to our Bioseq_set
bioseq_set->SetSeq_set().push_back(seq_entry);
// record it as product in the annot we're handed
CRef<CSeq_loc> prod_loc(new CSeq_loc);
prod_loc->SetWhole(*id);
(*feat)->SetProduct(*prod_loc);
}
return bioseq_set;
}