// ----------------------------------------------------------------------------
bool CGtfRecord::MakeChildRecord(
const CGtfRecord& parent,
const CSeq_interval& location,
unsigned int uExonNumber )
// ----------------------------------------------------------------------------
{
if ( ! location.CanGetFrom() || ! location.CanGetTo() ) {
return false;
}
m_strId = parent.m_strId;
m_strSource = parent.m_strSource;
m_strType = parent.m_strType;
m_strGeneId = parent.GeneId();
m_strTranscriptId = parent.TranscriptId();
m_uSeqStart = location.GetFrom();
m_uSeqStop = location.GetTo();
if ( parent.m_pdScore ) {
m_pdScore = new double( *(parent.m_pdScore) );
}
if ( parent.m_peStrand ) {
m_peStrand = new ENa_strand( *(parent.m_peStrand) );
}
m_Attributes.insert( parent.m_Attributes.begin(), parent.m_Attributes.end() );
if ( 0 != uExonNumber ) {
SetAttribute("exon_number", NStr::UIntToString(uExonNumber));
}
return true;
};
// ----------------------------------------------------------------------------
void CGffFeatureRecord::SetLocation(
const CSeq_interval& interval)
// ----------------------------------------------------------------------------
{
m_pLoc.Reset(new CSeq_loc());
m_pLoc->SetInt().Assign(interval);
if ( interval.CanGetFrom() ) {
mSeqStart = interval.GetFrom();
}
if ( interval.CanGetTo() ) {
mSeqStop = interval.GetTo();
}
unsigned int seqStart = Location().GetStart(eExtreme_Positional);
unsigned int seqStop = Location().GetStop(eExtreme_Positional);
string min = NStr::IntToString(seqStart + 1);
string max = NStr::IntToString(seqStop + 1);
if (Location().IsPartialStart(eExtreme_Biological)) {
if (Location().GetStrand() == eNa_strand_minus) {
SetAttribute("end_range", max + string(",."));
}
else {
SetAttribute("start_range", string(".,") + min);
}
}
if (Location().IsPartialStop(eExtreme_Biological)) {
if (Location().GetStrand() == eNa_strand_minus) {
SetAttribute("start_range", string(".,") + min);
}
else {
SetAttribute("end_range", max + string(",."));
}
}
if ( interval.IsSetStrand() ) {
SetStrand(interval.GetStrand());
}
}