82     m_Handle(seq),  in CBioseqContext()
144     m_Handle(seq),  in CBioseqContext()
215         sequence::GetId(id, m_Handle.GetScope(), sequence::eGetId_Best);  in GetPreferredSynonym()
281         CSeq_id_Handle idh1 = CSeq_id_Handle::GetHandle(*m_Handle.GetSeqId());  in x_SetLocation()
282         CSeq_id_Handle idh2 = sequence::GetIdHandle(*user_loc, &m_Handle.GetScope());  in x_SetLocation()
283         if ( !sequence::IsSameBioseq(idh1, idh2, &m_Handle.GetScope()) ) {  in x_SetLocation()
284             CSeq_loc_Mapper mapper(m_Handle, CSeq_loc_Mapper::eSeqMap_Up);  in x_SetLocation()
296 …IsReverse(loc->GetStrand()) && range.GetFrom() == 0 && range.GetTo() == m_Handle.GetInst_Length() …  in x_SetLocation()
317     _ASSERT(GetBioseqFromSeqLoc(loc, GetScope()) == m_Handle);  in x_SetMapper()
338     CFeat_CI gene_ci( m_Handle, sel );  in x_SetHasMultiIntervalGenes()
362         CRef<CBioseqIndex> bsx = idx->GetBioseqIndex (m_Handle);  in HasMultiIntervalGenes()
377     CSeqdesc_CI desc_ci( m_Handle, CSeqdesc::e_Source );  in x_SetTaxname()
429     CFeat_CI biosrc_ci( m_Handle, sel );  in x_SetTaxname()
452             CRef<CBioseqIndex> bsx = idx->GetBioseqIndex (m_Handle);  in GetTaxname()
471             CRef<CBioseqIndex> bsx = idx->GetBioseqIndex (m_Handle);  in IsCrossKingdom()
557         ! FIELD_IS_SET_AND_IS(m_Handle, Inst_Ext, Map) )  in x_SetOpticalMapPoints()
562     const CMap_ext & map_ext = m_Handle.GetInst_Ext().GetMap();  in x_SetOpticalMapPoints()
615     for (CSeqdesc_CI it(m_Handle, CSeqdesc::e_User);  it;  ++it) {  in x_SetDataFromUserObjects()
694     CAnnot_CI annot_ci(m_Handle, sel);  in x_CheckForShowComments()
741     return CFeat_CI(m_Handle.GetScope(),  in x_HasOperon()
752         CRef<CBioseqIndex> bsx = idx->GetBioseqIndex (m_Handle);  in HasOperon()
766         m_Handle, sequence::eGetId_Best).GetSeqId());  in x_SetId()
775     for (CSeqdesc_CI it(m_Handle, CSeqdesc::e_User);  it;  ++it) {  in x_SetId()
790     ITERATE (CBioseq::TId, id_iter, m_Handle.GetBioseqCore()->GetId()) {  in x_SetId()
946     return m_Handle.IsSetInst_Repr() ?  in x_GetRepr()
947         m_Handle.GetInst_Repr() : CSeq_inst::eRepr_not_set;  in x_GetRepr()
953     CSeqdesc_CI desc(m_Handle, CSeqdesc::e_Molinfo);  in x_GetMolInfo()
965          CSeq_entry_Handle eh = m_Handle.GetParentEntry();  in x_IsPart()
988         m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_segset);  in x_HasParts()
997             if ( it->IsSeq()  &&  it->GetSeq() == m_Handle ) {  in x_HasParts()
1025     if ( m_Handle.IsSetInst_Ext() ) {  in x_IsDeltaLitOnly()
1026         const CBioseq_Handle::TInst_Ext& ext = m_Handle.GetInst_Ext();  in x_IsDeltaLitOnly()
1043     return m_Master ? m_Master->GetPartNumber(m_Handle) : 0;  in x_GetPartNumber()
1050         m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_small_genome_set);  in x_IsInSGS()
1058         m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_gen_prod_set);  in x_IsInGPS()
1066         m_Handle.GetExactComplexityLevel(CBioseq_set::eClass_nuc_prot);  in x_IsInNucProt()
1103     m_Handle(seq)  in CMasterContext()
1123     CScope& scope = m_Handle.GetScope();  in GetPartNumber()
1126     ITERATE (CSeg_ext::Tdata, it, m_Handle.GetInst_Ext().GetSeg().Get()) {  in GetPartNumber()
1130         const CSeq_id& id = GetId(**it, &m_Handle.GetScope());  in GetPartNumber()
1131         CBioseq_Handle bsh = scope.GetBioseqHandleFromTSE(id, m_Handle);  in GetPartNumber()
1148     CScope& scope = m_Handle.GetScope();  in x_SetNumParts()
1152     ITERATE (CSeg_ext::Tdata, it, m_Handle.GetInst_Ext().GetSeg().Get()) {  in x_SetNumParts()
1159         CBioseq_Handle part = scope.GetBioseqHandleFromTSE(id, m_Handle);  in x_SetNumParts()
1196     s_GetNameForBioseq(m_Handle, parent_name);  in x_SetBaseName()
1210     CScope* scope = &m_Handle.GetScope();  in x_SetBaseName()
1212     const CSeqMap& seqmap = m_Handle.GetSeqMap();  in x_SetBaseName()
1219         segment = scope->GetBioseqHandleFromTSE(id, m_Handle);  in x_SetBaseName()