// ============================================================================
string CGtfRecord::x_MrnaToProduct(
CMappedFeat mapped_feature )
// ============================================================================
{
const CRNA_ref& rna = mapped_feature.GetData().GetRna();
if ( rna.IsSetExt() && rna.GetExt().IsName() ) {
return rna.GetExt().GetName();
}
return "";
}
// ============================================================================
string CGtfRecord::x_CdsToCode(
CMappedFeat mapped_feature )
// ============================================================================
{
const CCdregion& cdr = mapped_feature.GetData().GetCdregion();
if ( cdr.IsSetCode() ) {
return NStr::IntToString( cdr.GetCode().GetId() );
}
return "";
}
// ============================================================================
string CGtfRecord::x_GenericTranscriptId(
CMappedFeat mapped_feat )
// ============================================================================
{
static unsigned int uId = 1;
string strTranscriptId = string( "unknown_transcript_" ) +
NStr::UIntToString( uId );
if ( mapped_feat.GetData().GetSubtype() == CSeq_feat::TData::eSubtype_cdregion ) {
uId++;
}
return strTranscriptId;
}
// ============================================================================
string CGtfRecord::x_GenericGeneId(
CMappedFeat mapped_feat )
// ============================================================================
{
static unsigned int uId = 1;
string strGeneId = string( "unknown_gene_" ) +
NStr::UIntToString( uId );
if ( mapped_feat.GetData().GetSubtype() == CSeq_feat::TData::eSubtype_gene ) {
uId++;
}
return strGeneId;
}
// ============================================================================
string CGtfRecord::x_GeneToGeneId(
CMappedFeat mapped_feature )
// ============================================================================
{
const CGene_ref& gene = mapped_feature.GetData().GetGene();
if ( gene.IsSetLocus_tag() ) {
return gene.GetLocus_tag();
}
if ( gene.IsSetSyn() ) {
return gene.GetSyn().front();
}
return x_GenericGeneId( mapped_feature );
}
// ============================================================================
string CGtfRecord::x_GeneToGeneSyn(
CMappedFeat mapped_feature )
// ============================================================================
{
const CGene_ref& gene = mapped_feature.GetData().GetGene();
if ( ! gene.IsSetSyn() ) {
return "";
}
if ( gene.IsSetLocus_tag() ) {
return gene.GetSyn().front();
}
CGene_ref::TSyn::const_iterator it = gene.GetSyn().begin();
++it;
if ( it != gene.GetSyn().end() ) {
return *it;
}
return "";
}
