// ----------------------------------------------------------------------------
bool CGtfReader::x_CreateFeatureLocation(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
CRef<CSeq_id> pId = CReadUtil::AsSeqId(
record.Id(), m_iFlags & fAllIdsAsLocal);
CSeq_interval& location = pFeature->SetLocation().SetInt();
location.SetId( *pId );
location.SetFrom( record.SeqStart() );
if (record.Type() != "mRNA") {
location.SetTo(record.SeqStop());
}
else {
// place holder
// actual location will be computed from the exons and CDSs living on
// this feature.
location.SetTo(record.SeqStart());
}
if ( record.IsSetStrand() ) {
location.SetStrand( record.Strand() );
}
return true;
}
// ----------------------------------------------------------------------------
bool CGtfReader::x_MergeFeatureLocationMultiInterval(
const CGff2Record& record,
CRef< CSeq_feat > pFeature )
// ----------------------------------------------------------------------------
{
CRef<CSeq_id> pId = CReadUtil::AsSeqId(
record.Id(), m_iFlags & fAllIdsAsLocal);
CRef< CSeq_loc > pLocation( new CSeq_loc );
pLocation->SetInt().SetId( *pId );
pLocation->SetInt().SetFrom( record.SeqStart() );
pLocation->SetInt().SetTo( record.SeqStop() );
if ( record.IsSetStrand() ) {
pLocation->SetInt().SetStrand( record.Strand() );
}
pLocation = pLocation->Add(
pFeature->SetLocation(), CSeq_loc::fSortAndMerge_All, 0 );
pFeature->SetLocation( *pLocation );
return true;
}
