// ----------------------------------------------------------------------------
bool CGffRecord::AssignStop(
const CSeq_feat& feature )
// ----------------------------------------------------------------------------
{
if ( feature.CanGetLocation() ) {
const CSeq_loc& location = feature.GetLocation();
unsigned int uEnd = location.GetStop( eExtreme_Positional ) + 1;
m_strEnd = NStr::UIntToString( uEnd );
}
return true;
}
// ----------------------------------------------------------------------------
bool CGffRecord::AssignSeqId(
const CSeq_feat& feature )
// ----------------------------------------------------------------------------
{
m_strSeqId = "<unknown>";
if ( feature.CanGetLocation() ) {
const CSeq_loc& location = feature.GetLocation();
const CSeq_id* pId = location.GetId();
switch ( pId->Which() ) {
case CSeq_id::e_Local:
if ( pId->GetLocal().IsId() ) {
m_strSeqId = NStr::UIntToString( pId->GetLocal().GetId() );
}
else {
m_strSeqId = pId->GetLocal().GetStr();
}
break;
case CSeq_id::e_Gi:
m_strSeqId = NStr::IntToString( pId->GetGi() );
break;
case CSeq_id::e_Other:
if ( pId->GetOther().CanGetAccession() ) {
m_strSeqId = pId->GetOther().GetAccession();
if ( pId->GetOther().CanGetVersion() ) {
m_strSeqId += ".";
m_strSeqId += NStr::UIntToString(
pId->GetOther().GetVersion() );
}
}
break;
default:
break;
}
}
return true;
}
// ----------------------------------------------------------------------------
bool CGffRecord::AssignStrand(
const CSeq_feat& feature )
// ----------------------------------------------------------------------------
{
m_strStrand = ".";
if ( feature.CanGetLocation() ) {
const CSeq_loc& location = feature.GetLocation();
ENa_strand strand = location.GetStrand();
switch( strand ) {
default:
break;
case eNa_strand_plus:
m_strStrand = "+";
break;
case eNa_strand_minus:
m_strStrand = "-";
break;
}
}
return true;
}
