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Searched refs:m_cds (Results 1 – 6 of 6) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/
H A Dobjcoords.cpp99 bool IsValid() { return m_mrna || m_cds; } in IsValid()
111 CConstRef<CSeq_feat> m_cds; /// CDS feature on main sequence member in CReportEntry
532 if (!m_cds && !m_rna_cds) return; in x_GetCCoordinate()
564 } else if (m_cds) { // This condition is trivially true, but stays here to denote the case in x_GetCCoordinate()
569 (m_cds->GetLocation(), in x_GetCCoordinate()
601 } else if (m_cds) { in x_GetPCoordinate()
602 if (!x_MapPos(*x_GetCdsMapper(scope, *m_cds), *m_main_id, pos, mapped_pos)) in x_GetPCoordinate()
640 m_cds.Reset(&cds); in SetCds()
742 if (!m_cds) { in SetAlignment()
770 TSeqPos cds_start_on_dna = m_cds->GetLocation().GetStart(eExtreme_Biological); in SetAlignment()
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H A Dhgvs_parser2.cpp362 this->m_cds = other.m_cds; in CContext()
381 if(m_cds.IsNull()) { in GetCDS()
384 return *m_cds; in GetCDS()
413 if(m_cds.IsNull()) { in SetId()
414 m_cds.Reset(new CSeq_feat()); in SetId()
415 m_cds->Assign(mf.GetMappedFeature()); in SetId()
421 if(m_cds.IsNull()) { in SetId()
H A Dhgvs_parser.cpp198 if(m_cds.IsNull()) { in GetCDS()
201 return *m_cds; in GetCDS()
232 if(m_cds.IsNull()) { in SetId()
233 m_cds.Reset(new CSeq_feat()); in SetId()
234 m_cds->Assign(mf.GetMappedFeature()); in SetId()
240 if(m_cds.IsNull()) { in SetId()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/misc/hgvs/
H A Dhgvs_parser.hpp274 m_cds.Reset(); in Clear()
333 CRef<CSeq_feat> m_cds; member in variation_ref::CHgvsParser::CContext
H A Dhgvs_parser2.hpp270 m_cds.Reset(); in Clear()
326 CRef<CSeq_feat> m_cds; member in variation::CHgvsParser::CContext
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dchainer.cpp257 int m_type, m_left_cds, m_right_cds, m_cds; member
1830 if(max(ap->m_cds,bp->m_cds) >= 300 && ap->m_cds != bp->m_cds) // only long cdses count in operator ()()
1831 return (ap->m_cds > bp->m_cds); in operator ()()
2592 delta_cds = mi.m_cds-cds_overlap; in LRCanChainItoJ()
2623 mi.m_cds += START_BONUS; in LRIinit()
2642 mi.m_left_cds = mi.m_cds; in LRIinit()
2729 mi.m_right_cds = mi.m_cds; in RightLeft()
2833 int delta_cds = mi.m_cds-cds_overlap; in RightLeft()
3143 mi.m_cds = mi.m_left_cds+mi.m_right_cds-mi.m_cds; in MakeChains()
3270 mi.m_cds = mi.m_left_cds+mi.m_right_cds-mi.m_cds; in MakeChains()
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