NCBI C++ ToolKit
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Classes | |
class | CVariantPlacement |
CVariantPlacement –. More... | |
class | CVariantPlacement_Base |
CVariantPlacement_Base –. More... | |
class | CVariation_Base |
CVariation_Base –. More... | |
class | CVariation_Base::C_Data |
C_Data –. More... | |
class | CVariation_Base::C_Data::C_Set |
Set of related Variations. More... | |
class | CVariation_Base::C_E_Consequence |
C_E_Consequence –. More... | |
class | CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity |
C_Loss_of_heterozygosity –. More... | |
class | CVariation_Base::C_Frameshift |
Frameshift-related info. More... | |
class | CVariation_Base::C_E_Somatic_origin |
C_E_Somatic_origin –. More... | |
class | CVariation_Base::C_E_Somatic_origin::C_Condition |
condition related to this origin's type More... | |
class | CVariationException |
CVariationException –. More... | |
class | CVariationException_Base |
CVariationException_Base –. More... | |
class | CVariationMethod |
CVariationMethod –. More... | |
class | CVariationMethod_Base |
CVariationMethod_Base –. More... | |
typedef C_E_Consequence CVariation_Base::C_E |
Definition at line 1229 of file Variation_.hpp.
Definition at line 127 of file VariantPlacement_.hpp.
Definition at line 1227 of file Variation_.hpp.
typedef int CVariationException_Base::TCode |
Definition at line 109 of file VariationException_.hpp.
Definition at line 129 of file VariantPlacement_.hpp.
Definition at line 1111 of file Variation_.hpp.
typedef list< CRef< C_E_Consequence > > CVariation_Base::TConsequence |
Definition at line 1230 of file Variation_.hpp.
typedef C_Data CVariation_Base::TData |
Definition at line 1228 of file Variation_.hpp.
typedef list< CRef< CDbtag > > CVariantPlacement_Base::TDbxrefs |
Definition at line 131 of file VariantPlacement_.hpp.
Definition at line 1011 of file Variation_.hpp.
typedef string CVariation_Base::TDescription |
Definition at line 1220 of file Variation_.hpp.
typedef list< CRef< CVariationException > > CVariantPlacement_Base::TExceptions |
Definition at line 130 of file VariantPlacement_.hpp.
typedef list< CRef< CVariationException > > CVariation_Base::TExceptions |
Definition at line 1234 of file Variation_.hpp.
typedef list< CRef< CUser_object > > CVariantPlacement_Base::TExt |
Definition at line 132 of file VariantPlacement_.hpp.
typedef list< CRef< CUser_object > > CVariation_Base::TExt |
Definition at line 1232 of file Variation_.hpp.
typedef int CVariantPlacement_Base::TFrame |
Definition at line 125 of file VariantPlacement_.hpp.
Definition at line 1231 of file Variation_.hpp.
Definition at line 133 of file VariantPlacement_.hpp.
Definition at line 128 of file VariantPlacement_.hpp.
Definition at line 134 of file VariantPlacement_.hpp.
typedef CDbtag CVariation_Base::TId |
Definition at line 1214 of file Variation_.hpp.
Definition at line 360 of file Variation_.hpp.
typedef CSeq_loc CVariantPlacement_Base::TLoc |
Definition at line 118 of file VariantPlacement_.hpp.
Definition at line 730 of file Variation_.hpp.
Definition at line 161 of file VariantPlacement_.hpp.
Definition at line 168 of file Variation_.hpp.
typedef Tparent::CMemberIndex<E_memberIndex, 3> CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::TmemberIndex |
Definition at line 566 of file Variation_.hpp.
Definition at line 882 of file Variation_.hpp.
typedef Tparent::CMemberIndex<E_memberIndex, 3> CVariation_Base::C_E_Somatic_origin::C_Condition::TmemberIndex |
Definition at line 1020 of file Variation_.hpp.
Definition at line 1119 of file Variation_.hpp.
Definition at line 1262 of file Variation_.hpp.
Definition at line 118 of file VariationException_.hpp.
Definition at line 132 of file VariationMethod_.hpp.
Definition at line 110 of file VariationException_.hpp.
Definition at line 1223 of file Variation_.hpp.
typedef list< int > CVariationMethod_Base::TMethod |
Definition at line 123 of file VariationMethod_.hpp.
typedef int CVariantPlacement_Base::TMol |
Definition at line 119 of file VariantPlacement_.hpp.
Definition at line 159 of file Variation_.hpp.
typedef string CVariation_Base::TName |
Definition at line 1218 of file Variation_.hpp.
typedef string CVariation_Base::C_Data::TNote |
Definition at line 359 of file Variation_.hpp.
Definition at line 728 of file Variation_.hpp.
typedef list< CRef< CDbtag > > CVariation_Base::C_E_Somatic_origin::C_Condition::TObject_id |
Definition at line 1012 of file Variation_.hpp.
typedef list< CRef< CDbtag > > CVariation_Base::TOther_ids |
Definition at line 1217 of file Variation_.hpp.
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Definition at line 67 of file VariantPlacement.hpp.
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Definition at line 85 of file VariantPlacement_.hpp.
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Definition at line 92 of file Variation_.hpp.
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Definition at line 109 of file Variation_.hpp.
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Definition at line 128 of file Variation_.hpp.
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Definition at line 529 of file Variation_.hpp.
Definition at line 546 of file Variation_.hpp.
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Definition at line 862 of file Variation_.hpp.
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Definition at line 982 of file Variation_.hpp.
Definition at line 1000 of file Variation_.hpp.
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Definition at line 67 of file VariationException.hpp.
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Definition at line 74 of file VariationException_.hpp.
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Definition at line 67 of file VariationMethod.hpp.
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Definition at line 78 of file VariationMethod_.hpp.
Definition at line 135 of file VariantPlacement_.hpp.
typedef CDbtag CVariation_Base::TParent_id |
Definition at line 1215 of file Variation_.hpp.
Definition at line 873 of file Variation_.hpp.
typedef list< CRef< CPhenotype > > CVariation_Base::TPhenotype |
Definition at line 1222 of file Variation_.hpp.
Definition at line 120 of file VariantPlacement_.hpp.
typedef list< CRef< CVariantPlacement > > CVariation_Base::TPlacements |
Definition at line 1221 of file Variation_.hpp.
typedef list< CRef< CPopulation_data > > CVariation_Base::TPopulation_data |
Definition at line 1224 of file Variation_.hpp.
typedef CPub_set CVariation_Base::TPub |
Definition at line 1226 of file Variation_.hpp.
Definition at line 557 of file Variation_.hpp.
Definition at line 124 of file VariationMethod_.hpp.
typedef list< CRef< CObject_id > > CVariation_Base::TSample_id |
Definition at line 1216 of file Variation_.hpp.
Definition at line 126 of file VariantPlacement_.hpp.
typedef CBioseq CVariation_Base::C_Data::TSeq |
Definition at line 362 of file Variation_.hpp.
typedef C_Set CVariation_Base::C_Data::TSet |
Definition at line 361 of file Variation_.hpp.
typedef list< int > CVariantPlacement_Base::TSo_terms |
Definition at line 136 of file VariantPlacement_.hpp.
typedef list< int > CVariation_Base::TSo_terms |
Definition at line 1235 of file Variation_.hpp.
typedef list< CRef< C_E_Somatic_origin > > CVariation_Base::TSomatic_origin |
Definition at line 1233 of file Variation_.hpp.
Definition at line 1110 of file Variation_.hpp.
Definition at line 121 of file VariantPlacement_.hpp.
Definition at line 122 of file VariantPlacement_.hpp.
Definition at line 123 of file VariantPlacement_.hpp.
Definition at line 124 of file VariantPlacement_.hpp.
typedef list< string > CVariation_Base::TSynonyms |
Definition at line 1219 of file Variation_.hpp.
Definition at line 558 of file Variation_.hpp.
Definition at line 157 of file Variation_.hpp.
Definition at line 1225 of file Variation_.hpp.
Definition at line 729 of file Variation_.hpp.
typedef list< CRef< CVariation > > CVariation_Base::C_Data::C_Set::TVariations |
Definition at line 158 of file Variation_.hpp.
Definition at line 874 of file Variation_.hpp.
Choice variants.
Definition at line 296 of file Variation_.hpp.
Choice variants.
Definition at line 667 of file Variation_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Seq+1 |
Definition at line 307 of file Variation_.hpp.
Maximum+1 value of the choice variant enumerator.
Enumerator | |
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e_MaxChoice | == e_Loss_of_heterozygosity+1 |
Definition at line 676 of file Variation_.hpp.
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strong |
Definition at line 139 of file VariantPlacement_.hpp.
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Enumerator | |
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e__allMandatory | |
e_type | |
e_variations | |
e_name |
Definition at line 162 of file Variation_.hpp.
Enumerator | |
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e__allMandatory | |
e_reference | |
e_test |
Definition at line 561 of file Variation_.hpp.
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Enumerator | |
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e__allMandatory | |
e_phase | |
e_x_length |
Definition at line 877 of file Variation_.hpp.
Enumerator | |
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e__allMandatory | |
e_description | |
e_object_id |
Definition at line 1015 of file Variation_.hpp.
Enumerator | |
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e__allMandatory | |
e_source | |
e_condition |
Definition at line 1114 of file Variation_.hpp.
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Definition at line 1238 of file Variation_.hpp.
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Enumerator | |
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e__allMandatory | |
e_code | |
e_message |
Definition at line 113 of file VariationException_.hpp.
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Enumerator | |
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e__allMandatory | |
e_method | |
e_reference_location |
Definition at line 127 of file VariationMethod_.hpp.
Definition at line 84 of file VariationException_.hpp.
Definition at line 138 of file Variation_.hpp.
Definition at line 88 of file VariationMethod_.hpp.
Definition at line 95 of file VariantPlacement_.hpp.
location flags
Enumerator | |
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ePlacement_method_projected | |
ePlacement_method_asserted | |
ePlacement_method_aligned |
Definition at line 108 of file VariantPlacement_.hpp.
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END_CLASS_INFO CVariation_Base::C_E_Somatic_origin::C_Condition::C_Condition | ( | void | ) |
Definition at line 539 of file Variation_.cpp.
References CVariation_Base::m_set_State.
END_CHOICE_INFO CVariation_Base::C_Data::C_Data | ( | void | ) |
Definition at line 284 of file Variation_.cpp.
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END_CHOICE_INFO CVariation_Base::C_E_Consequence::C_E_Consequence | ( | void | ) |
Definition at line 465 of file Variation_.cpp.
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END_CLASS_INFO CVariation_Base::C_E_Somatic_origin::C_E_Somatic_origin | ( | void | ) |
Definition at line 603 of file Variation_.cpp.
References CVariation_Base::m_set_State.
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END_CLASS_INFO CVariation_Base::C_Frameshift::C_Frameshift | ( | void | ) |
Definition at line 496 of file Variation_.cpp.
References CVariation_Base::C_Frameshift::m_set_State.
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END_CLASS_INFO CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::C_Loss_of_heterozygosity | ( | void | ) |
Definition at line 327 of file Variation_.cpp.
References CVariation_Base::m_set_State.
END_CLASS_INFO CVariation_Base::C_Data::C_Set::C_Set | ( | void | ) |
Definition at line 115 of file Variation_.cpp.
References CVariation_Base::C_Data::C_Set::m_set_State.
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Check if it is safe to call GetAssembly method.
Definition at line 1236 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetAssembly().
Referenced by CVariantPlacement_Base::GetAssembly(), and CSNPSearchJob::x_DoSearch().
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Check if it is safe to call GetClinical_test method.
Definition at line 3015 of file Variation_.hpp.
References CVariation_Base::IsSetClinical_test().
Referenced by CVariation_Base::GetClinical_test().
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Check if it is safe to call GetCode method.
Definition at line 229 of file VariationException_.hpp.
References CVariationException_Base::IsSetCode().
Referenced by CVariationException_Base::GetCode().
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Check if it is safe to call GetComment method.
Definition at line 1304 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetComment().
Referenced by CVariantPlacement_Base::GetComment().
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Check if it is safe to call GetCondition method.
Definition at line 2645 of file Variation_.hpp.
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Check if it is safe to call GetConsequence method.
Definition at line 3066 of file Variation_.hpp.
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Check if it is safe to call GetData method.
Definition at line 3036 of file Variation_.hpp.
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Check if it is safe to call GetDbxrefs method.
Definition at line 1376 of file VariantPlacement_.hpp.
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Check if it is safe to call GetDescription method.
Definition at line 2552 of file Variation_.hpp.
References CVariation_Base::IsSetDescription().
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Check if it is safe to call GetDescription method.
Definition at line 2830 of file Variation_.hpp.
References CVariation_Base::IsSetDescription().
Referenced by CVariation_Base::C_E_Somatic_origin::C_Condition::GetDescription(), CVariation_Base::GetDescription(), and CVariationHandler::GetLabel().
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Check if it is safe to call GetExceptions method.
Definition at line 1351 of file VariantPlacement_.hpp.
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Check if it is safe to call GetExceptions method.
Definition at line 3162 of file Variation_.hpp.
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Check if it is safe to call GetExt method.
Definition at line 1401 of file VariantPlacement_.hpp.
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Check if it is safe to call GetExt method.
Definition at line 3112 of file Variation_.hpp.
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Check if it is safe to call GetFrame method.
Definition at line 1168 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetFrame().
Referenced by CVariantPlacement_Base::GetFrame().
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Check if it is safe to call GetFrameshift method.
Definition at line 3091 of file Variation_.hpp.
References CVariation_Base::IsSetFrameshift().
Referenced by CVariation_Base::GetFrameshift().
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Check if it is safe to call GetGene_location method.
Definition at line 1426 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetGene_location().
Referenced by CVariantPlacement_Base::GetGene_location().
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Check if it is safe to call GetHgvs_name method.
Definition at line 1257 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetHgvs_name().
Referenced by CVariantPlacement_Base::GetHgvs_name().
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Check if it is safe to call GetId method.
Definition at line 1473 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetId().
Referenced by CVariantPlacement_Base::GetId().
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Check if it is safe to call GetId method.
Definition at line 2666 of file Variation_.hpp.
References CVariation_Base::IsSetId().
Referenced by CVariation_Base::GetId(), and CVariationHandler::GetLabel().
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Check if it is safe to call GetLoc method.
Definition at line 908 of file VariantPlacement_.hpp.
Referenced by CTestBMApp::Run().
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Check if it is safe to call GetMessage method.
Definition at line 276 of file VariationException_.hpp.
References CVariationException_Base::IsSetMessage().
Referenced by CVariationException_Base::GetMessage().
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Check if it is safe to call GetMethod method.
Definition at line 2927 of file Variation_.hpp.
References CVariation_Base::IsSetMethod().
Referenced by CVariation_Base::GetMethod().
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Check if it is safe to call GetMethod method.
Definition at line 238 of file VariationMethod_.hpp.
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Check if it is safe to call GetMol method.
Definition at line 938 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetMol().
Referenced by CVariantPlacement_Base::GetMol().
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Check if it is safe to call GetName method.
Definition at line 2129 of file Variation_.hpp.
References CVariation_Base::IsSetName().
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Check if it is safe to call GetName method.
Definition at line 2758 of file Variation_.hpp.
References CVariation_Base::IsSetName().
Referenced by CVariation_Base::C_Data::C_Set::GetName(), and CVariation_Base::GetName().
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Check if it is safe to call GetObject_id method.
Definition at line 2599 of file Variation_.hpp.
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Check if it is safe to call GetOther_ids method.
Definition at line 2733 of file Variation_.hpp.
Referenced by CVariationHandler::GetLabel().
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Check if it is safe to call GetParent_id method.
Definition at line 1494 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetParent_id().
Referenced by CVariantPlacement_Base::GetParent_id().
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Check if it is safe to call GetParent_id method.
Definition at line 2687 of file Variation_.hpp.
References CVariation_Base::IsSetParent_id().
Referenced by CVariation_Base::GetParent_id().
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Check if it is safe to call GetPhase method.
Definition at line 2458 of file Variation_.hpp.
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Check if it is safe to call GetPhenotype method.
Definition at line 2902 of file Variation_.hpp.
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Check if it is safe to call GetPlacement_method method.
Definition at line 985 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetPlacement_method().
Referenced by CVariantPlacement_Base::GetPlacement_method().
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Check if it is safe to call GetPlacements method.
Definition at line 2877 of file Variation_.hpp.
Referenced by CSNPTableModel::GetExtraValueAt().
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Check if it is safe to call GetPopulation_data method.
Definition at line 2948 of file Variation_.hpp.
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Check if it is safe to call GetPub method.
Definition at line 2994 of file Variation_.hpp.
References CVariation_Base::IsSetPub().
Referenced by CVariation_Base::GetPub().
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Check if it is safe to call GetReference method.
Definition at line 2279 of file Variation_.hpp.
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Check if it is safe to call GetReference_location method.
Definition at line 263 of file VariationMethod_.hpp.
References CVariationMethod_Base::IsSetReference_location().
Referenced by CVariationMethod_Base::GetReference_location().
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Check if it is safe to call GetSample_id method.
Definition at line 2708 of file Variation_.hpp.
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Check if it is safe to call GetSeq method.
Definition at line 1215 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetSeq().
Referenced by CVariantPlacement_Base::GetSeq().
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Check if it is safe to call GetSo_terms method.
Definition at line 1515 of file VariantPlacement_.hpp.
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Check if it is safe to call GetSo_terms method.
Definition at line 3187 of file Variation_.hpp.
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Check if it is safe to call GetSomatic_origin method.
Definition at line 3137 of file Variation_.hpp.
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Check if it is safe to call GetSource method.
Definition at line 2624 of file Variation_.hpp.
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Check if it is safe to call GetStart_offset method.
Definition at line 1032 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStart_offset().
Referenced by CVariantPlacement_Base::GetStart_offset().
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Check if it is safe to call GetStart_offset_fuzz method.
Definition at line 1079 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStart_offset_fuzz().
Referenced by CVariantPlacement_Base::GetStart_offset_fuzz().
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Check if it is safe to call GetStop_offset method.
Definition at line 1100 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStop_offset().
Referenced by CVariantPlacement_Base::GetStop_offset().
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Check if it is safe to call GetStop_offset_fuzz method.
Definition at line 1147 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStop_offset_fuzz().
Referenced by CVariantPlacement_Base::GetStop_offset_fuzz().
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Check if it is safe to call GetSynonyms method.
Definition at line 2805 of file Variation_.hpp.
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Check if it is safe to call GetTest method.
Definition at line 2326 of file Variation_.hpp.
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Check if it is safe to call GetType method.
Definition at line 2057 of file Variation_.hpp.
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Check if it is safe to call GetVariant_prop method.
Definition at line 2973 of file Variation_.hpp.
References CVariation_Base::IsSetVariant_prop().
Referenced by CVariation_Base::GetVariant_prop().
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Check if it is safe to call GetVariations method.
Definition at line 2104 of file Variation_.hpp.
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Check if it is safe to call GetX_length method.
Definition at line 2505 of file Variation_.hpp.
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 2176 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice, and CVariation_Base::C_Data::ThrowInvalidSelection().
Referenced by CVariation_Base::C_Data::GetInstance(), CVariation_Base::C_Data::GetNote(), CVariation_Base::C_E_Consequence::GetNote(), CVariation_Base::C_Data::GetSeq(), and CVariation_Base::C_Data::GetSet().
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Verify selection, throw exception if it differs from the expected.
index | Expected selection. |
Definition at line 2373 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice, and CVariation_Base::C_Data::ThrowInvalidSelection().
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Definition at line 86 of file VariantPlacement.hpp.
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END_CLASS_INFO CVariantPlacement_Base::CVariantPlacement_Base | ( | void | ) |
Definition at line 284 of file VariantPlacement_.cpp.
References CObject::IsAllocatedInPool(), CVariantPlacement_Base::m_set_State, and CVariantPlacement_Base::ResetLoc().
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END_CLASS_INFO CVariation_Base::CVariation_Base | ( | void | ) |
Definition at line 881 of file Variation_.cpp.
References CObject::IsAllocatedInPool(), CVariation_Base::m_set_State, and CVariation_Base::ResetData().
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Definition at line 86 of file VariationException.hpp.
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END_CLASS_INFO CVariationException_Base::CVariationException_Base | ( | void | ) |
Definition at line 99 of file VariationException_.cpp.
References CVariationException_Base::m_set_State.
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Definition at line 86 of file VariationMethod.hpp.
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END_CLASS_INFO CVariationMethod_Base::CVariationMethod_Base | ( | void | ) |
Definition at line 127 of file VariationMethod_.cpp.
References CVariationMethod_Base::m_set_State.
CVariantPlacement_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_Data::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_Data::C_Set::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_E_Consequence::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_Frameshift::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_E_Somatic_origin::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariation_Base::C_E_Somatic_origin::C_Condition::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariationException_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
CVariationMethod_Base::DECLARE_INTERNAL_TYPE_INFO | ( | ) |
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Definition at line 150 of file Variation_.cpp.
References CObject::AddReference(), CVariation_Base::C_Data::e_Instance, CVariation_Base::C_Data::e_Note, CVariation_Base::C_Data::e_Seq, CVariation_Base::C_Data::e_Set, CVariation_Base::C_Data::m_choice, CVariation_Base::C_Data::m_object, and CVariation_Base::C_Data::m_string.
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Definition at line 360 of file Variation_.cpp.
References CObject::AddReference().
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Access to ECode's attributes (values, names) as defined in spec.
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Access to EData_set_type's attributes (values, names) as defined in spec.
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Access to EMethod_E's attributes (values, names) as defined in spec.
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Access to EMol's attributes (values, names) as defined in spec.
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Access to EPlacement_method's attributes (values, names) as defined in spec.
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Get the Assembly member data.
Definition at line 1242 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetAssembly(), CVariantPlacement_Base::m_Assembly, and CSerialObject::ThrowUnassigned().
Referenced by CGuiObjectInfoVariation::GetToolTip(), s_AddTopLevelGenomicLinks(), and CSNPSearchJob::x_DoSearch().
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Get the Clinical_test member data.
Definition at line 3021 of file Variation_.hpp.
References CVariation_Base::CanGetClinical_test(), CVariation_Base::m_Clinical_test, and CSerialObject::ThrowUnassigned().
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Get the Code member data.
Definition at line 242 of file VariationException_.hpp.
References CVariationException_Base::CanGetCode(), CVariationException_Base::m_Code, and CSerialObject::ThrowUnassigned().
Referenced by CHgvsReader::ReadSeqAnnot().
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Get the Comment member data.
Definition at line 1310 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetComment(), CVariantPlacement_Base::m_Comment, and CSerialObject::ThrowUnassigned().
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Get the Condition member data.
Definition at line 2651 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
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Get the Consequence member data.
Definition at line 3072 of file Variation_.hpp.
References CVariation_Base::m_Consequence.
Referenced by variation::CVariationUtil::s_FindConsequenceForPlacement(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Data member data.
Definition at line 3042 of file Variation_.hpp.
References CVariation_Base::m_Data, and CVariation_Base::ResetData().
Referenced by variation::CVariationUtil::AsVariation_feats(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), variation::CVariationUtil::FlipStrand(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), CVariation::Index(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::RepackageAssertedSequence(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FactorOutPlacements(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::s_FindConsequenceForPlacement(), variation::CVariationUtil::s_IsInstStrandFlippable(), variation::CVariationUtil::x_AsVariation_ref(), variation::CHgvsParser::x_FindAssertedSequence(), CVariationUtilities::x_FixAlleles(), variation::CVariationUtil::x_InferNAfromAA(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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Get the Dbxrefs member data.
Definition at line 1382 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Dbxrefs.
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Get the Description member data.
Definition at line 2558 of file Variation_.hpp.
References CVariation_Base::CanGetDescription(), CVariation_Base::m_Description, and CSerialObject::ThrowUnassigned().
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Get the Description member data.
Definition at line 2836 of file Variation_.hpp.
References CVariation_Base::CanGetDescription(), CVariation_Base::m_Description, and CSerialObject::ThrowUnassigned().
Referenced by CVariationHandler::GetLabel(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Exceptions member data.
Definition at line 1357 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Exceptions.
Referenced by CHgvsReader::ReadSeqAnnot().
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Get the Exceptions member data.
Definition at line 3168 of file Variation_.hpp.
References CVariation_Base::m_Exceptions.
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Get the Ext member data.
Definition at line 1407 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Ext.
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Get the Ext member data.
Definition at line 3118 of file Variation_.hpp.
References CVariation_Base::m_Ext.
Referenced by variation::CVariationUtil::AsVariation_feats(), CVariationNormalization::isFullyShifted(), and CVariationNormalization_base< T >::ResetFullyShifted().
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Get the Frame member data.
Definition at line 1181 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetFrame(), CVariantPlacement_Base::m_Frame, and CSerialObject::ThrowUnassigned().
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Get the Frameshift member data.
Definition at line 3097 of file Variation_.hpp.
References CVariation_Base::CanGetFrameshift(), CVariation_Base::m_Frameshift, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Gene_location member data.
Definition at line 1439 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetGene_location(), CVariantPlacement_Base::m_Gene_location, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::SetVariantProperties(), and variation::CVariationUtil::x_SetVariantPropertiesForIntronic().
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Get the Hgvs_name member data.
Definition at line 1263 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetHgvs_name(), CVariantPlacement_Base::m_Hgvs_name, and CSerialObject::ThrowUnassigned().
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Get the Id member data.
Definition at line 1479 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetId(), CVariantPlacement_Base::m_Id, and CSerialObject::ThrowUnassigned().
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Get the Id member data.
Definition at line 2672 of file Variation_.hpp.
References CVariation_Base::CanGetId(), CVariation_Base::m_Id, and CSerialObject::ThrowUnassigned().
Referenced by CVariationHandler::GetLabel(), variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
const CVariation_Base::C_Data::TInstance & CVariation_Base::C_Data::GetInstance | ( | void | ) | const |
Get the variant data.
Definition at line 198 of file Variation_.cpp.
References CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_Data::e_Instance, and CVariation_Base::C_Data::m_object.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::s_IsInstStrandFlippable(), variation::CVariationUtil::x_AsVariation_ref(), and variation::CVariationUtil::x_InferNAfromAA().
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Get the Loc member data.
Definition at line 914 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Loc, and CVariantPlacement_Base::ResetLoc().
Referenced by variation::AdjustMoltype(), variation::CVariationUtil::AsVariation(), variation::CVariationUtil::AsVariation_feats(), variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckPlacement(), variation::CreateUnknownProtConsequenceVariation(), NSearchFeatPanel::GatherFeatures(), CSNPTableModel::GetExtraValueAt(), variation::CVariationUtil::Remap(), variation::CVariationUtil::RemapToAnnotatedTarget(), CTestBMApp::Run(), variation::CVariationUtil::s_AddIntronicOffsets(), s_AddTopLevelGenomicLinks(), variation::CVariationUtil::s_FindConsequenceForPlacement(), variation::CVariationUtil::s_GetLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CHgvsParser::s_SeqIdToHgvsStr(), variation::CVariationUtil::SetPlacementProperties(), variation::CHgvsParser::sx_AppendMoltypeExceptions(), variation::CVariationUtil::TranslateNAtoAA(), variation::ValidExonTerminals(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CHgvsParser::x_AsHgvsExpression(), variation::CHgvsParser::x_AsHgvsInstExpression(), CSNPSearchJob::x_DoSearch(), variation::CVariationUtil::x_FindOrCreateLiteral(), CVariationUtilities::x_GetRefAlleleFromVP(), variation::CVariationUtil::x_InferNAfromAA(), variation::CHgvsParser::x_location(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), variation::CHgvsParser::x_seq_loc(), variation::CHgvsParser::x_seq_ref(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_ssr().
const CVariation_Base::C_E_Consequence::TLoss_of_heterozygosity & CVariation_Base::C_E_Consequence::GetLoss_of_heterozygosity | ( | void | ) | const |
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Get the Message member data.
Definition at line 282 of file VariationException_.hpp.
References CVariationException_Base::CanGetMessage(), CVariationException_Base::m_Message, and CSerialObject::ThrowUnassigned().
Referenced by CHgvsReader::ReadSeqAnnot().
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Get the Method member data.
Definition at line 2933 of file Variation_.hpp.
References CVariation_Base::CanGetMethod(), CVariation_Base::m_Method, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Method member data.
Definition at line 244 of file VariationMethod_.hpp.
References CVariationMethod_Base::m_Method.
Referenced by variation::SetComputational(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Mol member data.
Definition at line 951 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetMol(), CVariantPlacement_Base::m_Mol, and CSerialObject::ThrowUnassigned().
Referenced by variation::AdjustMoltype(), variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::CheckExonBoundary(), variation::CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::Remap(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CHgvsParser::s_SeqIdToHgvsStr(), variation::CVariationUtil::SetPlacementProperties(), variation::CHgvsParser::sx_AppendMoltypeExceptions(), variation::CVariationUtil::TranslateNAtoAA(), variation::CHgvsParser::x_abs_pos(), variation::CHgvsParser::x_general_pos(), variation::CVariationUtil::x_InferNAfromAA(), variation::CHgvsParser::x_location(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_prot_fs(), variation::CHgvsParser::x_prot_missense(), variation::CHgvsParser::x_prot_pos(), variation::CHgvsParser::x_range(), variation::CHgvsParser::x_raw_seq(), and variation::CVariationUtil::x_Remap().
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Get the Name member data.
Definition at line 2135 of file Variation_.hpp.
References CVariation_Base::CanGetName(), CVariation_Base::m_Name, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Name member data.
Definition at line 2764 of file Variation_.hpp.
References CVariation_Base::CanGetName(), CVariation_Base::m_Name, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the variant data.
Definition at line 2217 of file Variation_.hpp.
References CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_Data::e_Note, and CVariation_Base::C_Data::m_string.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the variant data.
Definition at line 2426 of file Variation_.hpp.
References CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_Data::e_Note, and CVariation_Base::C_Data::m_string.
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Get the Object_id member data.
Definition at line 2605 of file Variation_.hpp.
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Get the Other_ids member data.
Definition at line 2739 of file Variation_.hpp.
References CVariation_Base::m_Other_ids.
Referenced by CVariationHandler::GetLabel(), variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Parent_id member data.
Definition at line 1500 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetParent_id(), CVariantPlacement_Base::m_Parent_id, and CSerialObject::ThrowUnassigned().
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Get the Parent_id member data.
Definition at line 2693 of file Variation_.hpp.
References CVariation_Base::CanGetParent_id(), CVariation_Base::m_Parent_id, and CSerialObject::ThrowUnassigned().
Referenced by variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Phase member data.
Definition at line 2471 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Phenotype member data.
Definition at line 2908 of file Variation_.hpp.
References CVariation_Base::m_Phenotype.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Placement_method member data.
Definition at line 998 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetPlacement_method(), CVariantPlacement_Base::m_Placement_method, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::Remap().
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Get the Placements member data.
Definition at line 2883 of file Variation_.hpp.
References CVariation_Base::m_Placements.
Referenced by variation::CVariationUtil::AsVariation_feats(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), CSNPTableModel::GetExtraValueAt(), CVariationUtilities::IsIntronicVariation(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CVariationUtil::s_GetPlacements(), and variation::CVariationUtil::x_AdjustDelinsToInterval().
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Get the Population_data member data.
Definition at line 2954 of file Variation_.hpp.
References CVariation_Base::m_Population_data.
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Get the Pub member data.
Definition at line 3000 of file Variation_.hpp.
References CVariation_Base::CanGetPub(), CVariation_Base::m_Pub, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::AsVariation_feats().
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Get the Reference member data.
Definition at line 2285 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
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Get the Reference_location member data.
Definition at line 269 of file VariationMethod_.hpp.
References CVariationMethod_Base::CanGetReference_location(), CVariationMethod_Base::m_Reference_location, and CSerialObject::ThrowUnassigned().
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Get the Sample_id member data.
Definition at line 2714 of file Variation_.hpp.
References CVariation_Base::m_Sample_id.
Referenced by variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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Get the Seq member data.
Definition at line 1221 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetSeq(), CVariantPlacement_Base::m_Seq, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_FindFirstLiteral(), variation::CHgvsParser::x_AsHgvsInstExpression(), variation::CHgvsParser::x_no_change(), and variation::CHgvsParser::x_PlacementCoordsToStr().
const CVariation_Base::C_Data::TSeq & CVariation_Base::C_Data::GetSeq | ( | void | ) | const |
Get the variant data.
Definition at line 242 of file Variation_.cpp.
References CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_Data::e_Seq, and CVariation_Base::C_Data::m_object.
const CVariation_Base::C_Data::TSet & CVariation_Base::C_Data::GetSet | ( | void | ) | const |
Get the variant data.
Definition at line 220 of file Variation_.cpp.
References CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_Data::e_Set, and CVariation_Base::C_Data::m_object.
Referenced by variation::CVariationUtil::AsVariation_feats(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::s_FindConsequenceForPlacement(), variation::CVariationUtil::x_AsVariation_ref(), variation::CHgvsParser::x_FindAssertedSequence(), variation::CVariationUtil::x_InferNAfromAA(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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Get the So_terms member data.
Definition at line 1521 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_So_terms.
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Get the So_terms member data.
Definition at line 3193 of file Variation_.hpp.
References CVariation_Base::m_So_terms.
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Get the Somatic_origin member data.
Definition at line 3143 of file Variation_.hpp.
References CVariation_Base::m_Somatic_origin.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Source member data.
Definition at line 2630 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
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Get the Start_offset member data.
Definition at line 1045 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetStart_offset(), CVariantPlacement_Base::m_Start_offset, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckPlacement(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_GetLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::SetPlacementProperties(), variation::ValidExonTerminals(), CVariationUtilities::x_GetRefAlleleFromVP(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), and variation::CHgvsParser::x_ssr().
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Get the Start_offset_fuzz member data.
Definition at line 1085 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetStart_offset_fuzz(), CVariantPlacement_Base::m_Start_offset_fuzz, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::ValidExonTerminals(), variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CVariationUtil::x_Remap().
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Get the Stop_offset member data.
Definition at line 1113 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetStop_offset(), CVariantPlacement_Base::m_Stop_offset, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckPlacement(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_GetLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::SetPlacementProperties(), variation::ValidExonTerminals(), CVariationUtilities::x_GetRefAlleleFromVP(), variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CVariationUtil::x_Remap().
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Get the Stop_offset_fuzz member data.
Definition at line 1153 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::CanGetStop_offset_fuzz(), CVariantPlacement_Base::m_Stop_offset_fuzz, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::ValidExonTerminals(), variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CVariationUtil::x_Remap().
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Get the Synonyms member data.
Definition at line 2811 of file Variation_.hpp.
References CVariation_Base::m_Synonyms.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Get the Test member data.
Definition at line 2332 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
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Get the Type member data.
Definition at line 2070 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
Referenced by variation::CHgvsParser::x_AsHgvsExpression(), variation::CVariationUtil::x_AsVariation_ref(), variation::CHgvsParser::x_FindAssertedSequence(), and variation::CHgvsParser::x_list().
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Get the Variant_prop member data.
Definition at line 2979 of file Variation_.hpp.
References CVariation_Base::CanGetVariant_prop(), CVariation_Base::m_Variant_prop, and CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
const CVariation_Base::C_E_Consequence::TVariation & CVariation_Base::C_E_Consequence::GetVariation | ( | void | ) | const |
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Get the Variations member data.
Definition at line 2110 of file Variation_.hpp.
Referenced by variation::CVariationUtil::AsVariation_feats(), CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::s_FindConsequenceForPlacement(), variation::CHgvsParser::x_AsHgvsExpression(), variation::CVariationUtil::x_AsVariation_ref(), variation::CHgvsParser::x_FindAssertedSequence(), variation::CVariationUtil::x_InferNAfromAA(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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Get the X_length member data.
Definition at line 2518 of file Variation_.hpp.
References CSerialObject::ThrowUnassigned().
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Complex is selected.
Definition at line 2255 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Complex, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Instance is selected.
Instance type is defined as 'typedef CVariation_inst TInstance'.
Definition at line 2243 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Instance, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), CVariationUtilities::GetVariationRefAlt(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::x_AsVariation_ref(), CVariationUtilities::x_FixAlleles(), variation::CVariationUtil::x_InferNAfromAA(), and CVariationNormalization_base< T >::x_Shift().
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Check if variant Loss_of_heterozygosity is selected.
Loss_of_heterozygosity type is defined as 'typedef C_Loss_of_heterozygosity TLoss_of_heterozygosity'.
Definition at line 2446 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice.
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Check if variant Note is selected.
Note type is defined as 'typedef string TNote'.
Definition at line 2211 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Note, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Note is selected.
Note type is defined as 'typedef string TNote'.
Definition at line 2420 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Note, and CVariation_Base::C_Data::m_choice.
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Check if variant Seq is selected.
Seq type is defined as 'typedef CBioseq TSeq'.
Definition at line 2267 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Seq, and CVariation_Base::C_Data::m_choice.
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Check if variant Set is selected.
Set type is defined as 'typedef C_Set TSet'.
Definition at line 2249 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Set, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::AsVariation_feats(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::RepackageAssertedSequence(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FactorOutPlacements(), variation::CVariationUtil::s_FindAssertedLiteral(), variation::CVariationUtil::s_FindConsequenceForPlacement(), variation::CVariationUtil::x_AsVariation_ref(), variation::CHgvsParser::x_FindAssertedSequence(), variation::CVariationUtil::x_InferNAfromAA(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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reference to the assembly (GenColl ID) for this location Check if a value has been assigned to Assembly data member.
Data member Assembly is optional; its type is defined as 'typedef CDbtag TAssembly'
Definition at line 1230 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Assembly.
Referenced by CVariantPlacement_Base::CanGetAssembly().
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References to external Check if a value has been assigned to Clinical_test data member.
Data member Clinical_test is optional; its type is defined as 'typedef CDbtag TClinical_test'
Definition at line 3009 of file Variation_.hpp.
References CVariation_Base::m_Clinical_test.
Referenced by CVariation_Base::CanGetClinical_test().
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Check if a value has been assigned to Code data member.
Data member Code is optional; its type is defined as 'typedef int TCode'
Definition at line 223 of file VariationException_.hpp.
References CVariationException_Base::m_set_State.
Referenced by CVariationException_Base::CanGetCode(), CHgvsReader::ReadSeqAnnot(), and CVariationException_Base::SetCode().
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the reference location for this variant Check if a value has been assigned to Comment data member.
Data member Comment is optional; its type is defined as 'typedef string TComment'
Definition at line 1298 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::CanGetComment(), and CVariantPlacement_Base::SetComment().
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Check if a value has been assigned to Condition data member.
Data member Condition is optional; its type is defined as 'typedef C_Condition TCondition'
Definition at line 2639 of file Variation_.hpp.
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Check if a value has been assigned to Consequence data member.
Data member Consequence is optional; its type is defined as 'typedef list< CRef< C_E_Consequence > > TConsequence'
Definition at line 3060 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by CVariation::Index(), variation::CVariationUtil::s_FindConsequenceForPlacement(), and variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Data data member.
Data member Data is mandatory; its type is defined as 'typedef C_Data TData'
Definition at line 3030 of file Variation_.hpp.
References CVariation_Base::m_Data, and CRef< C, Locker >::NotEmpty().
Referenced by CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), CVariation::Index(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), CVariationUtilities::x_FixAlleles(), and CVariationNormalization_base< T >::x_Shift().
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e.g.
rs#, that are placement-specific Check if a value has been assigned to Dbxrefs data member.
Data member Dbxrefs is optional; its type is defined as 'typedef list< CRef< CDbtag > > TDbxrefs'
Definition at line 1370 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
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Check if a value has been assigned to Description data member.
Data member Description is optional; its type is defined as 'typedef string TDescription'
Definition at line 2546 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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tag for comment and descriptions Check if a value has been assigned to Description data member.
Data member Description is optional; its type is defined as 'typedef string TDescription'
Definition at line 2824 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by CVariation_Base::C_E_Somatic_origin::C_Condition::CanGetDescription(), CVariation_Base::CanGetDescription(), CVariation_Base::C_E_Somatic_origin::C_Condition::SetDescription(), CVariation_Base::SetDescription(), and variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Exceptions data member.
Data member Exceptions is optional; its type is defined as 'typedef list< CRef< CVariationException > > TExceptions'
Definition at line 1345 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CHgvsReader::ReadSeqAnnot().
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Check if a value has been assigned to Exceptions data member.
Data member Exceptions is optional; its type is defined as 'typedef list< CRef< CVariationException > > TExceptions'
Definition at line 3156 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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for process-specific placement tags/labels Check if a value has been assigned to Ext data member.
Data member Ext is optional; its type is defined as 'typedef list< CRef< CUser_object > > TExt'
Definition at line 1395 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
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Additional undescribed extensions Check if a value has been assigned to Ext data member.
Data member Ext is optional; its type is defined as 'typedef list< CRef< CUser_object > > TExt'
Definition at line 3106 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::AsVariation_feats(), and CVariationNormalization::isFullyShifted().
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0-based position of bio-start relative to containing codon Check if a value has been assigned to Frame data member.
Data member Frame is optional; its type is defined as 'typedef int TFrame'
Definition at line 1162 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::CanGetFrame(), and CVariantPlacement_Base::SetFrame().
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Check if a value has been assigned to Frameshift data member.
Data member Frameshift is optional; its type is defined as 'typedef C_Frameshift TFrameshift'
Definition at line 3085 of file Variation_.hpp.
References CVariation_Base::m_Frameshift.
Referenced by CVariation_Base::CanGetFrameshift(), variation::CVariationUtil::x_AsVariation_ref(), and variation::CVariationUtil::x_InferNAfromAA().
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Same semantics as VariantProperties.gene-location, except placement-specific Check if a value has been assigned to Gene_location data member.
Data member Gene_location is optional; its type is defined as 'typedef int TGene_location'
Definition at line 1420 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::CanGetGene_location(), CVariantPlacement_Base::SetGene_location(), variation::CVariationUtil::SetPlacementProperties(), and variation::CVariationUtil::x_SetVariantPropertiesForIntronic().
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Check if a value has been assigned to Hgvs_name data member.
Data member Hgvs_name is optional; its type is defined as 'typedef string THgvs_name'
Definition at line 1251 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::CanGetHgvs_name(), and CVariantPlacement_Base::SetHgvs_name().
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Check if a value has been assigned to Id data member.
Data member Id is optional; its type is defined as 'typedef CObject_id TId'
Definition at line 1467 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Id.
Referenced by CVariantPlacement_Base::CanGetId().
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ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334', 'dbSNP|ss12345', 'dbVar|nsv1'
we relate three kinds of IDs here:
Data member Id is optional; its type is defined as 'typedef CDbtag TId'
Definition at line 2660 of file Variation_.hpp.
References CVariation_Base::m_Id.
Referenced by CVariation_Base::CanGetId(), variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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actual concrete placement we are considering Check if a value has been assigned to Loc data member.
Data member Loc is mandatory; its type is defined as 'typedef CSeq_loc TLoc'
Definition at line 902 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Loc.
Referenced by NSearchFeatPanel::GatherFeatures().
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Check if a value has been assigned to Message data member.
Data member Message is mandatory; its type is defined as 'typedef string TMessage'
Definition at line 270 of file VariationException_.hpp.
References CVariationException_Base::m_set_State.
Referenced by CVariationException_Base::CanGetMessage(), CHgvsReader::ReadSeqAnnot(), and CVariationException_Base::SetMessage().
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sequencing / acuisition method Check if a value has been assigned to Method data member.
Data member Method is optional; its type is defined as 'typedef CVariationMethod TMethod'
Definition at line 2921 of file Variation_.hpp.
References CVariation_Base::m_Method.
Referenced by CVariation_Base::CanGetMethod(), and variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Method data member.
Data member Method is mandatory; its type is defined as 'typedef list< int > TMethod'
Definition at line 232 of file VariationMethod_.hpp.
References CVariationMethod_Base::m_set_State.
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Check if a value has been assigned to Mol data member.
Data member Mol is mandatory; its type is defined as 'typedef int TMol'
Definition at line 932 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by variation::AdjustMoltype(), CVariantPlacement_Base::CanGetMol(), variation::CVariationUtil::CheckExonBoundary(), CVariantPlacement_Base::SetMol(), variation::CVariationUtil::SetPlacementProperties(), and variation::CVariationUtil::x_InferNAfromAA().
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Check if a value has been assigned to Name data member.
Data member Name is optional; its type is defined as 'typedef string TName'
Definition at line 2123 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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names and synonyms some variants have well-known canonical names and possible accepted synonyms Check if a value has been assigned to Name data member.
Data member Name is optional; its type is defined as 'typedef string TName'
Definition at line 2752 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by CVariation_Base::C_Data::C_Set::CanGetName(), CVariation_Base::CanGetName(), CVariation_Base::C_Data::C_Set::SetName(), CVariation_Base::SetName(), and variation::CVariationUtil::x_AsVariation_ref().
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reference to BioTerm / other descriptive database Check if a value has been assigned to Object_id data member.
Data member Object_id is optional; its type is defined as 'typedef list< CRef< CDbtag > > TObject_id'
Definition at line 2593 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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Check if a value has been assigned to Other_ids data member.
Data member Other_ids is optional; its type is defined as 'typedef list< CRef< CDbtag > > TOther_ids'
Definition at line 2727 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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id of the placement from which this one was derived Check if a value has been assigned to Parent_id data member.
Data member Parent_id is optional; its type is defined as 'typedef CObject_id TParent_id'
Definition at line 1488 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Parent_id.
Referenced by CVariantPlacement_Base::CanGetParent_id().
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Check if a value has been assigned to Parent_id data member.
Data member Parent_id is optional; its type is defined as 'typedef CDbtag TParent_id'
Definition at line 2681 of file Variation_.hpp.
References CVariation_Base::m_Parent_id.
Referenced by CVariation_Base::CanGetParent_id(), variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Phase data member.
Data member Phase is optional; its type is defined as 'typedef int TPhase'
Definition at line 2452 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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phenotype Check if a value has been assigned to Phenotype data member.
Data member Phenotype is optional; its type is defined as 'typedef list< CRef< CPhenotype > > TPhenotype'
Definition at line 2896 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Placement_method data member.
Data member Placement_method is optional; its type is defined as 'typedef int TPlacement_method'
Definition at line 979 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::CanGetPlacement_method(), variation::CVariationUtil::Remap(), and CVariantPlacement_Base::SetPlacement_method().
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where this beast is seen note that this is a set of locations, and there are no restrictions to the contents to this set.
Check if a value has been assigned to Placements data member.
Data member Placements is optional; its type is defined as 'typedef list< CRef< CVariantPlacement > > TPlacements'
Definition at line 2871 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::AsVariation_feats(), variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), variation::CVariationUtil::FlipStrand(), CVariationUtilities::IsIntronicVariation(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::RepackageAssertedSequence(), variation::CVariationUtil::s_GetPlacements(), variation::CVariationUtil::x_AdjustDelinsToInterval(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The case of multiple alleles for a SNP would be described by parent-feature of type Variation-set.diff-alleles, where the child features of type Variation-inst, all at the same location, would describe individual alleles.
population data Check if a value has been assigned to Population_data data member.
Data member Population_data is optional; its type is defined as 'typedef list< CRef< CPopulation_data > > TPopulation_data'
Definition at line 2942 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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publication support; same type as in seq-feat Check if a value has been assigned to Pub data member.
Data member Pub is optional; its type is defined as 'typedef CPub_set TPub'
Definition at line 2988 of file Variation_.hpp.
References CVariation_Base::m_Pub.
Referenced by variation::CVariationUtil::AsVariation_feats(), and CVariation_Base::CanGetPub().
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In germline comparison, it will be reference genome assembly (default) or reference/normal population.
In somatic mutation, it will be a name of the normal tissue. Check if a value has been assigned to Reference data member.
Data member Reference is optional; its type is defined as 'typedef string TReference'
Definition at line 2273 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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if sequence-based validation methods are used, what reference sequence location validated the presence of this? Check if a value has been assigned to Reference_location data member.
Data member Reference_location is optional; its type is defined as 'typedef CSeq_loc TReference_location'
Definition at line 257 of file VariationMethod_.hpp.
References CVariationMethod_Base::m_Reference_location.
Referenced by CVariationMethod_Base::CanGetReference_location().
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Check if a value has been assigned to Sample_id data member.
Data member Sample_id is optional; its type is defined as 'typedef list< CRef< CObject_id > > TSample_id'
Definition at line 2702 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::InheritParentAttributes(), and variation::CVariationUtil::x_AsVariation_ref().
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for situations in which a raw location isn't sufficient Check if a value has been assigned to Seq data member.
Data member Seq is optional; its type is defined as 'typedef CSeq_literal TSeq'
Definition at line 1209 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Seq.
Referenced by variation::CHgvsParser::AsHgvsExpression(), CVariantPlacement_Base::CanGetSeq(), variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_FindFirstLiteral(), variation::CHgvsParser::x_no_change(), and variation::CHgvsParser::x_PlacementCoordsToStr().
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Sequence Ontology terms for this placement Check if a value has been assigned to So_terms data member.
Data member So_terms is optional; its type is defined as 'typedef list< int > TSo_terms'
Definition at line 1509 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
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Check if a value has been assigned to So_terms data member.
Data member So_terms is optional; its type is defined as 'typedef list< int > TSo_terms'
Definition at line 3181 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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Check if a value has been assigned to Somatic_origin data member.
Data member Somatic_origin is optional; its type is defined as 'typedef list< CRef< C_E_Somatic_origin > > TSomatic_origin'
Definition at line 3131 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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description of the somatic origin itself Check if a value has been assigned to Source data member.
Data member Source is optional; its type is defined as 'typedef CSubSource TSource'
Definition at line 2618 of file Variation_.hpp.
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location refinements, describing offsets into introns from product coordinates.
Biological semantics: start-offset/stop-offset apply to bio-start/bio-stop respectively. positive = downstream; negative = upstream. Check if a value has been assigned to Start_offset data member.
Data member Start_offset is optional; its type is defined as 'typedef int TStart_offset'
Definition at line 1026 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), CVariantPlacement_Base::CanGetStart_offset(), variation::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckPlacement(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_GetLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::SetPlacementProperties(), CVariantPlacement_Base::SetStart_offset(), variation::CVariationUtil::TranslateNAtoAA(), variation::ValidExonTerminals(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CVariationUtil::x_FindOrCreateLiteral(), CVariationUtilities::x_GetRefAlleleFromVP(), variation::CVariationUtil::x_InferNAfromAA(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), variation::CHgvsParser::x_seq_loc(), variation::CHgvsParser::x_seq_ref(), and variation::CHgvsParser::x_ssr().
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Check if a value has been assigned to Start_offset_fuzz data member.
Data member Start_offset_fuzz is optional; its type is defined as 'typedef CInt_fuzz TStart_offset_fuzz'
Definition at line 1073 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Start_offset_fuzz.
Referenced by CVariantPlacement_Base::CanGetStart_offset_fuzz(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::ValidExonTerminals(), variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CVariationUtil::x_Remap().
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Check if a value has been assigned to Stop_offset data member.
Data member Stop_offset is optional; its type is defined as 'typedef int TStop_offset'
Definition at line 1094 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), CVariantPlacement_Base::CanGetStop_offset(), variation::CVariationUtil::CheckExonBoundary(), variation::CVariationUtil::CheckPlacement(), variation::CVariationUtil::Remap(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_GetLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::SetPlacementProperties(), CVariantPlacement_Base::SetStop_offset(), variation::CVariationUtil::TranslateNAtoAA(), variation::ValidExonTerminals(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CVariationUtil::x_FindOrCreateLiteral(), CVariationUtilities::x_GetRefAlleleFromVP(), variation::CVariationUtil::x_InferNAfromAA(), variation::CHgvsParser::x_PlacementCoordsToStr(), variation::CVariationUtil::x_Remap(), variation::CHgvsParser::x_seq_loc(), variation::CHgvsParser::x_seq_ref(), and variation::CHgvsParser::x_ssr().
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Check if a value has been assigned to Stop_offset_fuzz data member.
Data member Stop_offset_fuzz is optional; its type is defined as 'typedef CInt_fuzz TStop_offset_fuzz'
Definition at line 1141 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Stop_offset_fuzz.
Referenced by CVariantPlacement_Base::CanGetStop_offset_fuzz(), variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::ValidExonTerminals(), variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CVariationUtil::x_Remap().
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Check if a value has been assigned to Synonyms data member.
Data member Synonyms is optional; its type is defined as 'typedef list< string > TSynonyms'
Definition at line 2799 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Name of the testing subject type or the testing tissue.
Check if a value has been assigned to Test data member.
Data member Test is optional; its type is defined as 'typedef string TTest'
Definition at line 2320 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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Check if a value has been assigned to Type data member.
Data member Type is mandatory; its type is defined as 'typedef int TType'
Definition at line 2051 of file Variation_.hpp.
References CVariation_Base::C_Data::C_Set::m_set_State.
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variant properties bit fields Check if a value has been assigned to Variant_prop data member.
Data member Variant_prop is optional; its type is defined as 'typedef CVariantProperties TVariant_prop'
Definition at line 2967 of file Variation_.hpp.
References CVariation_Base::m_Variant_prop.
Referenced by CVariation_Base::CanGetVariant_prop(), and variation::CVariationUtil::x_AsVariation_ref().
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Check if a value has been assigned to Variations data member.
Data member Variations is mandatory; its type is defined as 'typedef list< CRef< CVariation > > TVariations'
Definition at line 2098 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by CVariationUtilities::GetVariationType().
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Check if a value has been assigned to X_length data member.
Data member X_length is optional; its type is defined as 'typedef int TX_length'
Definition at line 2499 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Splicing is selected.
Definition at line 2408 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice.
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Check if variant Uniparental_disomy is selected.
Definition at line 2231 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Uniparental_disomy, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Unknown is selected.
Definition at line 2199 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Unknown, and CVariation_Base::C_Data::m_choice.
Referenced by variation::CVariationUtil::x_AsVariation_ref().
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Check if variant Unknown is selected.
Definition at line 2396 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Unknown, and CVariation_Base::C_Data::m_choice.
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Check if variant Variation is selected.
Variation type is defined as 'typedef CVariation TVariation'.
Definition at line 2440 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice.
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Reset the whole object.
Definition at line 232 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::ResetAssembly(), CVariantPlacement_Base::ResetComment(), CVariantPlacement_Base::ResetDbxrefs(), CVariantPlacement_Base::ResetExceptions(), CVariantPlacement_Base::ResetExt(), CVariantPlacement_Base::ResetFrame(), CVariantPlacement_Base::ResetGene_location(), CVariantPlacement_Base::ResetHgvs_name(), CVariantPlacement_Base::ResetId(), CVariantPlacement_Base::ResetLoc(), CVariantPlacement_Base::ResetMol(), CVariantPlacement_Base::ResetParent_id(), CVariantPlacement_Base::ResetPlacement_method(), CVariantPlacement_Base::ResetSeq(), CVariantPlacement_Base::ResetSo_terms(), CVariantPlacement_Base::ResetStart_offset(), CVariantPlacement_Base::ResetStart_offset_fuzz(), CVariantPlacement_Base::ResetStop_offset(), and CVariantPlacement_Base::ResetStop_offset_fuzz().
Referenced by variation::CHgvsParser::CContext::SetPlacement().
void CVariation_Base::C_Data::C_Set::Reset | ( | void | ) |
Reset the whole object.
Definition at line 94 of file Variation_.cpp.
References CVariation_Base::ResetName().
void CVariation_Base::C_Data::Reset | ( | void | ) |
Reset the whole object.
Definition at line 127 of file Variation_.cpp.
References CVariation_Base::C_Data::e_not_set, CVariation_Base::C_Data::m_choice, and CVariation_Base::C_Data::ResetSelection().
void CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::Reset | ( | void | ) |
Reset the whole object.
Definition at line 308 of file Variation_.cpp.
void CVariation_Base::C_E_Consequence::Reset | ( | void | ) |
void CVariation_Base::C_Frameshift::Reset | ( | void | ) |
Reset the whole object.
Definition at line 477 of file Variation_.cpp.
void CVariation_Base::C_E_Somatic_origin::C_Condition::Reset | ( | void | ) |
Reset the whole object.
Definition at line 520 of file Variation_.cpp.
References CVariation_Base::ResetDescription().
Referenced by CVariation_Base::C_E_Somatic_origin::SetCondition().
void CVariation_Base::C_E_Somatic_origin::Reset | ( | void | ) |
Reset the whole object.
Definition at line 584 of file Variation_.cpp.
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Reset the whole object.
Definition at line 825 of file Variation_.cpp.
References CVariation_Base::ResetClinical_test(), CVariation_Base::ResetConsequence(), CVariation_Base::ResetData(), CVariation_Base::ResetDescription(), CVariation_Base::ResetExceptions(), CVariation_Base::ResetExt(), CVariation_Base::ResetFrameshift(), CVariation_Base::ResetId(), CVariation_Base::ResetMethod(), CVariation_Base::ResetName(), CVariation_Base::ResetOther_ids(), CVariation_Base::ResetParent_id(), CVariation_Base::ResetPhenotype(), CVariation_Base::ResetPlacements(), CVariation_Base::ResetPopulation_data(), CVariation_Base::ResetPub(), CVariation_Base::ResetSample_id(), CVariation_Base::ResetSo_terms(), CVariation_Base::ResetSomatic_origin(), CVariation_Base::ResetSynonyms(), and CVariation_Base::ResetVariant_prop().
Referenced by CVariation_Base::C_Data::~C_Data(), and CVariation_Base::C_E_Consequence::~C_E_Consequence().
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Reset the whole object.
Definition at line 81 of file VariationException_.cpp.
References CVariationException_Base::ResetCode(), and CVariationException_Base::ResetMessage().
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Reset the whole object.
Definition at line 109 of file VariationMethod_.cpp.
References CVariationMethod_Base::ResetMethod(), and CVariationMethod_Base::ResetReference_location().
void CVariantPlacement_Base::ResetAssembly | ( | void | ) |
Reset Assembly data member.
Definition at line 145 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Assembly.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetClinical_test | ( | void | ) |
Reset Clinical_test data member.
Definition at line 747 of file Variation_.cpp.
References CVariation_Base::m_Clinical_test.
Referenced by CVariation_Base::Reset().
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Reset Code data member.
Definition at line 235 of file VariationException_.hpp.
References CVariationException_Base::m_Code, and CVariationException_Base::m_set_State.
Referenced by CVariationException_Base::Reset().
void CVariantPlacement_Base::ResetComment | ( | void | ) |
Reset Comment data member.
Definition at line 168 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Comment, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::C_E_Somatic_origin::ResetCondition | ( | void | ) |
Reset Condition data member.
Definition at line 567 of file Variation_.cpp.
void CVariation_Base::ResetConsequence | ( | void | ) |
Reset Consequence data member.
Definition at line 778 of file Variation_.cpp.
References CVariation_Base::m_Consequence, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
void CVariation_Base::ResetData | ( | void | ) |
Reset Data data member.
Definition at line 764 of file Variation_.cpp.
References CVariation_Base::m_Data, and CRef< C, Locker >::Reset().
Referenced by CVariation_Base::CVariation_Base(), CVariation_Base::GetData(), CVariation_Base::Reset(), and CVariation_Base::SetData().
void CVariantPlacement_Base::ResetDbxrefs | ( | void | ) |
Reset Dbxrefs data member.
Definition at line 180 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Dbxrefs, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::C_E_Somatic_origin::C_Condition::ResetDescription | ( | void | ) |
Reset Description data member.
Definition at line 508 of file Variation_.cpp.
References CVariation_Base::m_Description, and CVariation_Base::m_set_State.
void CVariation_Base::ResetDescription | ( | void | ) |
Reset Description data member.
Definition at line 672 of file Variation_.cpp.
References CVariation_Base::m_Description, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::C_E_Somatic_origin::C_Condition::Reset(), and CVariation_Base::Reset().
void CVariantPlacement_Base::ResetExceptions | ( | void | ) |
Reset Exceptions data member.
Definition at line 174 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Exceptions, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset(), and variation::CHgvsParser::x_no_change().
void CVariation_Base::ResetExceptions | ( | void | ) |
Reset Exceptions data member.
Definition at line 813 of file Variation_.cpp.
References CVariation_Base::m_Exceptions, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
void CVariantPlacement_Base::ResetExt | ( | void | ) |
Reset Ext data member.
Definition at line 186 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Ext, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetExt | ( | void | ) |
Reset Ext data member.
Definition at line 801 of file Variation_.cpp.
References CVariation_Base::m_Ext, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset(), and CVariationNormalization_base< T >::ResetFullyShifted().
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inline |
Reset Frame data member.
Definition at line 1174 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Frame, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetFrameshift | ( | void | ) |
Reset Frameshift data member.
Definition at line 784 of file Variation_.cpp.
References CVariation_Base::m_Frameshift.
Referenced by CVariation_Base::Reset().
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inline |
Reset Gene_location data member.
Definition at line 1432 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Gene_location, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset(), and variation::CVariationUtil::x_SetVariantPropertiesForIntronic().
void CVariantPlacement_Base::ResetHgvs_name | ( | void | ) |
Reset Hgvs_name data member.
Definition at line 162 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Hgvs_name, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariantPlacement_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 192 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Id.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetId | ( | void | ) |
Reset Id data member.
Definition at line 614 of file Variation_.cpp.
References CVariation_Base::m_Id.
Referenced by CVariation_Base::Reset().
END_ENUM_INFO void CVariantPlacement_Base::ResetLoc | ( | void | ) |
Reset Loc data member.
Definition at line 80 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Loc.
Referenced by CVariantPlacement_Base::CVariantPlacement_Base(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::Reset(), and CVariantPlacement_Base::SetLoc().
END_ENUM_INFO void CVariationException_Base::ResetMessage | ( | void | ) |
Reset Message data member.
Definition at line 75 of file VariationException_.cpp.
References CVariationException_Base::m_Message, and CVariationException_Base::m_set_State.
Referenced by CVariationException_Base::Reset().
void CVariation_Base::ResetMethod | ( | void | ) |
Reset Method data member.
Definition at line 690 of file Variation_.cpp.
References CVariation_Base::m_Method.
Referenced by CVariation_Base::Reset().
END_ENUM_INFO void CVariationMethod_Base::ResetMethod | ( | void | ) |
Reset Method data member.
Definition at line 86 of file VariationMethod_.cpp.
References CVariationMethod_Base::m_Method, and CVariationMethod_Base::m_set_State.
Referenced by CVariationMethod_Base::Reset().
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Reset Mol data member.
Definition at line 944 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Mol, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::C_Data::C_Set::ResetName | ( | void | ) |
Reset Name data member.
Definition at line 88 of file Variation_.cpp.
References CVariation_Base::m_Name, and CVariation_Base::m_set_State.
void CVariation_Base::ResetName | ( | void | ) |
Reset Name data member.
Definition at line 660 of file Variation_.cpp.
References CVariation_Base::m_Name, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::C_Data::C_Set::Reset(), and CVariation_Base::Reset().
void CVariation_Base::C_E_Somatic_origin::C_Condition::ResetObject_id | ( | void | ) |
Reset Object_id data member.
Definition at line 514 of file Variation_.cpp.
References CVariation_Base::m_set_State.
void CVariation_Base::ResetOther_ids | ( | void | ) |
Reset Other_ids data member.
Definition at line 654 of file Variation_.cpp.
References CVariation_Base::m_Other_ids, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
void CVariantPlacement_Base::ResetParent_id | ( | void | ) |
Reset Parent_id data member.
Definition at line 209 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Parent_id.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetParent_id | ( | void | ) |
Reset Parent_id data member.
Definition at line 631 of file Variation_.cpp.
References CVariation_Base::m_Parent_id.
Referenced by CVariation_Base::Reset().
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Reset Phase data member.
Definition at line 2464 of file Variation_.hpp.
References CVariation_Base::m_set_State.
void CVariation_Base::ResetPhenotype | ( | void | ) |
Reset Phenotype data member.
Definition at line 684 of file Variation_.cpp.
References CVariation_Base::m_Phenotype, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
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Reset Placement_method data member.
Definition at line 991 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Placement_method, and CVariantPlacement_Base::m_set_State.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetPlacements | ( | void | ) |
Reset Placements data member.
Definition at line 678 of file Variation_.cpp.
References CVariation_Base::m_Placements, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset(), and variation::CVariationUtil::x_InferNAfromAA().
void CVariation_Base::ResetPopulation_data | ( | void | ) |
Reset Population_data data member.
Definition at line 707 of file Variation_.cpp.
References CVariation_Base::m_Population_data, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
void CVariation_Base::ResetPub | ( | void | ) |
Reset Pub data member.
Definition at line 730 of file Variation_.cpp.
References CVariation_Base::m_Pub.
Referenced by CVariation_Base::Reset().
void CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::ResetReference | ( | void | ) |
Reset Reference data member.
Definition at line 296 of file Variation_.cpp.
References CVariation_Base::m_set_State.
void CVariationMethod_Base::ResetReference_location | ( | void | ) |
Reset Reference_location data member.
Definition at line 92 of file VariationMethod_.cpp.
References CVariationMethod_Base::m_Reference_location.
Referenced by CVariationMethod_Base::Reset().
void CVariation_Base::ResetSample_id | ( | void | ) |
Reset Sample_id data member.
Definition at line 648 of file Variation_.cpp.
References CVariation_Base::m_Sample_id, and CVariation_Base::m_set_State.
Referenced by CVariation_Base::Reset().
void CVariation_Base::C_Data::ResetSelection | ( | void | ) |
Reset the selection (set it to e_not_set).
Definition at line 133 of file Variation_.cpp.
References CVariation_Base::C_Data::e_Instance, CVariation_Base::C_Data::e_not_set, CVariation_Base::C_Data::e_Note, CVariation_Base::C_Data::e_Seq, CVariation_Base::C_Data::e_Set, CVariation_Base::C_Data::m_choice, CVariation_Base::C_Data::m_object, and CVariation_Base::C_Data::m_string.
Referenced by CVariation_Base::C_Data::Reset(), CVariation_Base::C_Data::SetInstance(), CVariation_Base::C_Data::SetSeq(), and CVariation_Base::C_Data::SetSet().
void CVariation_Base::C_E_Consequence::ResetSelection | ( | void | ) |
Reset the selection (set it to e_not_set).
Definition at line 344 of file Variation_.cpp.
References e_not_set.
void CVariantPlacement_Base::ResetSeq | ( | void | ) |
Reset Seq data member.
Definition at line 128 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Seq.
Referenced by variation::CVariationUtil::AttachSeq(), variation::RepackageAssertedSequence(), CVariantPlacement_Base::Reset(), and variation::CVariationUtil::TranslateNAtoAA().
void CVariantPlacement_Base::ResetSo_terms | ( | void | ) |
Reset So_terms data member.
Definition at line 226 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_set_State, and CVariantPlacement_Base::m_So_terms.
Referenced by CVariantPlacement_Base::Reset().
void CVariation_Base::ResetSo_terms | ( | void | ) |
Reset So_terms data member.
Definition at line 819 of file Variation_.cpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_So_terms.
Referenced by CVariation_Base::Reset().
void CVariation_Base::ResetSomatic_origin | ( | void | ) |
Reset Somatic_origin data member.
Definition at line 807 of file Variation_.cpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_Somatic_origin.
Referenced by CVariation_Base::Reset().
void CVariation_Base::C_E_Somatic_origin::ResetSource | ( | void | ) |
Reset Source data member.
Definition at line 550 of file Variation_.cpp.
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Reset Start_offset data member.
Definition at line 1038 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State, and CVariantPlacement_Base::m_Start_offset.
Referenced by variation::CVariationUtil::FlipStrand(), CVariantPlacement_Base::Reset(), variation::CVariationUtil::s_ResolveIntronicOffsets(), and variation::CHgvsParser::s_SetStartOffset().
void CVariantPlacement_Base::ResetStart_offset_fuzz | ( | void | ) |
Reset Start_offset_fuzz data member.
Definition at line 94 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Start_offset_fuzz.
Referenced by variation::CVariationUtil::FlipStrand(), CVariantPlacement_Base::Reset(), variation::CVariationUtil::s_ResolveIntronicOffsets(), and variation::CHgvsParser::s_SetStartOffset().
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Reset Stop_offset data member.
Definition at line 1106 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State, and CVariantPlacement_Base::m_Stop_offset.
Referenced by variation::CVariationUtil::FlipStrand(), CVariantPlacement_Base::Reset(), variation::CVariationUtil::s_ResolveIntronicOffsets(), and variation::CHgvsParser::s_SetStopOffset().
void CVariantPlacement_Base::ResetStop_offset_fuzz | ( | void | ) |
Reset Stop_offset_fuzz data member.
Definition at line 111 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Stop_offset_fuzz.
Referenced by variation::CVariationUtil::FlipStrand(), CVariantPlacement_Base::Reset(), variation::CVariationUtil::s_ResolveIntronicOffsets(), and variation::CHgvsParser::s_SetStopOffset().
void CVariation_Base::ResetSynonyms | ( | void | ) |
Reset Synonyms data member.
Definition at line 666 of file Variation_.cpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_Synonyms.
Referenced by CVariation_Base::Reset().
void CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::ResetTest | ( | void | ) |
Reset Test data member.
Definition at line 302 of file Variation_.cpp.
References CVariation_Base::m_set_State.
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Reset Type data member.
Definition at line 2063 of file Variation_.hpp.
References CVariation_Base::m_set_State.
void CVariation_Base::ResetVariant_prop | ( | void | ) |
Reset Variant_prop data member.
Definition at line 713 of file Variation_.cpp.
References CVariation_Base::m_Variant_prop.
Referenced by CVariation_Base::Reset().
END_ENUM_INFO void CVariation_Base::C_Data::C_Set::ResetVariations | ( | void | ) |
Reset Variations data member.
Definition at line 82 of file Variation_.cpp.
References CVariation_Base::C_Data::C_Set::m_set_State, and CVariation_Base::C_Data::C_Set::m_Variations.
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Reset X_length data member.
Definition at line 2511 of file Variation_.hpp.
References CVariation_Base::m_set_State.
void CVariation_Base::C_Data::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CVariation_Base::C_E_Consequence::Select | ( | E_Choice | index, |
EResetVariant | reset, | ||
CObjectMemoryPool * | pool | ||
) |
Select the requested variant if needed, allocating CObject variants from memory pool.
void CVariation_Base::C_Data::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
Referenced by CVariation_Base::C_Data::SetComplex(), CVariation_Base::C_Data::SetInstance(), CVariation_Base::C_Data::SetNote(), CVariation_Base::C_E_Consequence::SetNote(), CVariation_Base::C_Data::SetSeq(), CVariation_Base::C_Data::SetSet(), CVariation_Base::C_E_Consequence::SetSplicing(), CVariation_Base::C_Data::SetUniparental_disomy(), CVariation_Base::C_Data::SetUnknown(), and CVariation_Base::C_E_Consequence::SetUnknown().
void CVariation_Base::C_E_Consequence::Select | ( | E_Choice | index, |
EResetVariant | reset = eDoResetVariant |
||
) |
Select the requested variant if needed.
index | New selection state. |
reset | Flag that defines the resetting of the variant data. The data will be reset if either the current selection differs from the new one, or the flag is set to eDoResetVariant. |
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static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 182 of file Variation_.cpp.
References CVariation_Base::C_Data::sm_SelectionNames.
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static |
Retrieve selection name (for diagnostic purposes).
index | One of possible selection states. |
Definition at line 387 of file Variation_.cpp.
void CVariantPlacement_Base::SetAssembly | ( | CVariantPlacement_Base::TAssembly & | value | ) |
Assign a value to Assembly data member.
value | Reference to value. |
Definition at line 150 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Assembly, and value.
CVariantPlacement_Base::TAssembly & CVariantPlacement_Base::SetAssembly | ( | void | ) |
Assign a value to Assembly data member.
Definition at line 155 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Assembly.
void CVariation_Base::SetClinical_test | ( | CVariation_Base::TClinical_test & | value | ) |
Assign a value to Clinical_test data member.
value | Reference to value. |
Definition at line 752 of file Variation_.cpp.
References CVariation_Base::m_Clinical_test, and value.
CVariation_Base::TClinical_test & CVariation_Base::SetClinical_test | ( | void | ) |
Assign a value to Clinical_test data member.
Definition at line 757 of file Variation_.cpp.
References CVariation_Base::m_Clinical_test.
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Assign a value to Code data member.
value | Value to assign |
Definition at line 251 of file VariationException_.hpp.
References CVariationException_Base::m_Code, CVariationException_Base::m_set_State, and value.
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Assign a value to Code data member.
Definition at line 258 of file VariationException_.hpp.
References CVariationException_Base::IsSetCode(), CVariationException_Base::m_Code, CVariationException_Base::m_set_State, and CSerialObject::UnassignedByte().
Assign a value to Comment data member.
value | Value to assign |
Definition at line 1319 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Comment, CVariantPlacement_Base::m_set_State, and value.
|
inline |
Definition at line 1326 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Comment, CVariantPlacement_Base::m_set_State, and value.
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inline |
Assign a value to Comment data member.
Definition at line 1333 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetComment(), CVariantPlacement_Base::m_Comment, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedString().
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inline |
Select the variant.
Definition at line 2261 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Complex, eDoNotResetVariant, and CVariation_Base::C_Data::Select().
void CVariation_Base::C_E_Somatic_origin::SetCondition | ( | TCondition & | value | ) |
Assign a value to Condition data member.
value | Reference to value. |
Definition at line 572 of file Variation_.cpp.
References CVariation_Base::C_E_Somatic_origin::C_Condition::Reset(), and value.
CVariation_Base::C_E_Somatic_origin::TCondition & CVariation_Base::C_E_Somatic_origin::SetCondition | ( | void | ) |
Assign a value to Condition data member.
Definition at line 577 of file Variation_.cpp.
References CVariation_Base::C_E_Somatic_origin::C_Condition::Reset().
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inline |
Assign a value to Consequence data member.
Definition at line 3078 of file Variation_.hpp.
References CVariation_Base::m_Consequence, and CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), and CVariation::Index().
void CVariation_Base::SetData | ( | CVariation_Base::TData & | value | ) |
Assign a value to Data data member.
value | Reference to value. |
Definition at line 773 of file Variation_.cpp.
References CVariation_Base::m_Data, CRef< C, Locker >::Reset(), and value.
Referenced by variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), variation::CVariationUtil::FlipStrand(), variation::RepackageAssertedSequence(), CVariationNormalization_base< CVariationNormalizationRight >::ResetFullyShifted(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_FactorOutPlacements(), CVariationUtilities::x_FixAlleles(), variation::CVariationUtil::x_InferNAfromAA(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
|
inline |
Assign a value to Data data member.
Definition at line 3051 of file Variation_.hpp.
References CVariation_Base::m_Data, and CVariation_Base::ResetData().
Referenced by CVariation::Index().
|
inline |
Assign a value to Dbxrefs data member.
Definition at line 1388 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Dbxrefs, and CVariantPlacement_Base::m_set_State.
Referenced by variation::CVariationUtil::s_AttachGeneIDdbxref().
|
inline |
Assign a value to Description data member.
value | Value to assign |
Definition at line 2567 of file Variation_.hpp.
References CVariation_Base::m_Description, CVariation_Base::m_set_State, and value.
|
inline |
Assign a value to Description data member.
value | Value to assign |
Definition at line 2845 of file Variation_.hpp.
References CVariation_Base::m_Description, CVariation_Base::m_set_State, and value.
|
inline |
Definition at line 2574 of file Variation_.hpp.
References CVariation_Base::m_Description, CVariation_Base::m_set_State, and value.
|
inline |
Definition at line 2852 of file Variation_.hpp.
References CVariation_Base::m_Description, CVariation_Base::m_set_State, and value.
|
inline |
Assign a value to Description data member.
Definition at line 2581 of file Variation_.hpp.
References CVariation_Base::IsSetDescription(), CVariation_Base::m_Description, CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
|
inline |
Assign a value to Description data member.
Definition at line 2859 of file Variation_.hpp.
References CVariation_Base::IsSetDescription(), CVariation_Base::m_Description, CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
|
inline |
Assign a value to Exceptions data member.
Definition at line 1363 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Exceptions, and CVariantPlacement_Base::m_set_State.
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckPlacement(), variation::CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::Remap(), variation::CHgvsParser::sx_AppendMoltypeExceptions(), variation::CHgvsParser::x_deletion(), variation::CHgvsParser::x_delins(), variation::CHgvsParser::x_location(), and variation::CVariationUtil::x_Remap().
|
inline |
Assign a value to Exceptions data member.
Definition at line 3174 of file Variation_.hpp.
References CVariation_Base::m_Exceptions, and CVariation_Base::m_set_State.
|
inline |
Assign a value to Ext data member.
Definition at line 1413 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Ext, and CVariantPlacement_Base::m_set_State.
|
inline |
Assign a value to Ext data member.
Definition at line 3124 of file Variation_.hpp.
References CVariation_Base::m_Ext, and CVariation_Base::m_set_State.
Referenced by NSNPVariationHelper::ConvertFeat(), CVariationNormalization_base< T >::ResetFullyShifted(), CVariationUtilities::x_AddRefAlleleFixFlag(), and CVariationNormalization_base< T >::x_SetShiftFlag().
|
inline |
Assign a value to Frame data member.
value | Value to assign |
Definition at line 1190 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Frame, CVariantPlacement_Base::m_set_State, and value.
Referenced by variation::CVariationUtil::TranslateNAtoAA().
|
inline |
Assign a value to Frame data member.
Definition at line 1197 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetFrame(), CVariantPlacement_Base::m_Frame, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedByte().
void CVariation_Base::SetFrameshift | ( | CVariation_Base::TFrameshift & | value | ) |
Assign a value to Frameshift data member.
value | Reference to value. |
Definition at line 789 of file Variation_.cpp.
References CVariation_Base::m_Frameshift, and value.
Referenced by variation::CVariationUtil::x_AsVariation().
CVariation_Base::TFrameshift & CVariation_Base::SetFrameshift | ( | void | ) |
Assign a value to Frameshift data member.
Definition at line 794 of file Variation_.cpp.
References CVariation_Base::m_Frameshift.
|
inline |
Assign a value to Gene_location data member.
value | Value to assign |
Definition at line 1448 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Gene_location, CVariantPlacement_Base::m_set_State, and value.
Referenced by variation::CVariationUtil::SetPlacementProperties(), and variation::CVariationUtil::x_SetVariantPropertiesForIntronic().
|
inline |
Assign a value to Gene_location data member.
Definition at line 1455 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetGene_location(), CVariantPlacement_Base::m_Gene_location, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedByte().
|
inline |
Assign a value to Hgvs_name data member.
value | Value to assign |
Definition at line 1272 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Hgvs_name, CVariantPlacement_Base::m_set_State, and value.
Referenced by variation::CHgvsParser::AttachHgvs().
|
inline |
Definition at line 1279 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Hgvs_name, CVariantPlacement_Base::m_set_State, and value.
|
inline |
Assign a value to Hgvs_name data member.
Definition at line 1286 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetHgvs_name(), CVariantPlacement_Base::m_Hgvs_name, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedString().
void CVariantPlacement_Base::SetId | ( | CVariantPlacement_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 197 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Id, and value.
void CVariation_Base::SetId | ( | CVariation_Base::TId & | value | ) |
Assign a value to Id data member.
value | Reference to value. |
Definition at line 619 of file Variation_.cpp.
References CVariation_Base::m_Id, and value.
CVariantPlacement_Base::TId & CVariantPlacement_Base::SetId | ( | void | ) |
Assign a value to Id data member.
Definition at line 202 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Id.
CVariation_Base::TId & CVariation_Base::SetId | ( | void | ) |
Assign a value to Id data member.
Definition at line 624 of file Variation_.cpp.
References CVariation_Base::m_Id.
void CVariation_Base::C_Data::SetInstance | ( | TInstance & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 210 of file Variation_.cpp.
References CObject::AddReference(), CVariation_Base::C_Data::e_Instance, CVariation_Base::C_Data::m_choice, CVariation_Base::C_Data::m_object, CVariation_Base::C_Data::ResetSelection(), and value.
CVariation_Base::C_Data::TInstance & CVariation_Base::C_Data::SetInstance | ( | void | ) |
Select the variant.
Definition at line 204 of file Variation_.cpp.
References CVariation_Base::C_Data::e_Instance, eDoNotResetVariant, CVariation_Base::C_Data::m_object, and CVariation_Base::C_Data::Select().
void CVariantPlacement_Base::SetLoc | ( | CVariantPlacement_Base::TLoc & | value | ) |
Assign a value to Loc data member.
value | Reference to value. |
Definition at line 89 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Loc, and value.
Referenced by variation::CVariationUtil::AsVariation(), NSNPVariationHelper::ConvertFeat(), variation::CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CVariationUtil::TranslateNAtoAA(), variation::CHgvsParser::x_AdjustPlacementForHgvs(), variation::CHgvsParser::x_AsHgvsInstExpression(), CGBankLoadingJob::x_CreateProjectItems(), variation::CVariationUtil::x_CreateUnknownVariation(), variation::CHgvsParser::x_expr2(), variation::CVariationUtil::x_InferNAfromAA(), variation::CHgvsParser::x_location(), variation::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_range(), variation::CVariationUtil::x_Remap(), variation::CHgvsParser::x_seq_loc(), CVariationNormalization_base< T >::x_Shift(), variation::CHgvsParser::x_ssr(), and variation::CHgvsParser::x_translocation().
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Assign a value to Loc data member.
Definition at line 923 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Loc, and CVariantPlacement_Base::ResetLoc().
void CVariation_Base::C_E_Consequence::SetLoss_of_heterozygosity | ( | TLoss_of_heterozygosity & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 437 of file Variation_.cpp.
References CObject::AddReference(), and value.
CVariation_Base::C_E_Consequence::TLoss_of_heterozygosity & CVariation_Base::C_E_Consequence::SetLoss_of_heterozygosity | ( | void | ) |
Select the variant.
Definition at line 431 of file Variation_.cpp.
References eDoNotResetVariant.
Assign a value to Message data member.
value | Value to assign |
Definition at line 291 of file VariationException_.hpp.
References CVariationException_Base::m_Message, CVariationException_Base::m_set_State, and value.
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Definition at line 298 of file VariationException_.hpp.
References CVariationException_Base::m_Message, CVariationException_Base::m_set_State, and value.
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Assign a value to Message data member.
Definition at line 305 of file VariationException_.hpp.
References CVariationException_Base::IsSetMessage(), CVariationException_Base::m_Message, CVariationException_Base::m_set_State, and CSerialObject::UnassignedString().
void CVariation_Base::SetMethod | ( | CVariation_Base::TMethod & | value | ) |
Assign a value to Method data member.
value | Reference to value. |
Definition at line 695 of file Variation_.cpp.
References CVariation_Base::m_Method, and value.
CVariation_Base::TMethod & CVariation_Base::SetMethod | ( | void | ) |
Assign a value to Method data member.
Definition at line 700 of file Variation_.cpp.
References CVariation_Base::m_Method.
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Assign a value to Method data member.
Definition at line 250 of file VariationMethod_.hpp.
References CVariationMethod_Base::m_Method, and CVariationMethod_Base::m_set_State.
Referenced by variation::CreateUnknownProtConsequenceVariation(), and variation::SetComputational().
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Assign a value to Mol data member.
value | Value to assign |
Definition at line 960 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Mol, CVariantPlacement_Base::m_set_State, and value.
Referenced by variation::AdjustMoltype(), variation::CVariationUtil::AsVariation(), variation::CreateUnknownProtConsequenceVariation(), variation::CHgvsParser::sx_AppendMoltypeExceptions(), variation::CVariationUtil::TranslateNAtoAA(), variation::CHgvsParser::x_AsHgvsInstExpression(), variation::CVariationUtil::x_CreateUnknownVariation(), variation::CVariationUtil::x_InferNAfromAA(), variation::CVariationUtil::x_Remap(), and variation::CHgvsParser::x_translocation().
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Assign a value to Mol data member.
Definition at line 967 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetMol(), CVariantPlacement_Base::m_Mol, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedByte().
Assign a value to Name data member.
value | Value to assign |
Definition at line 2144 of file Variation_.hpp.
References CVariation_Base::m_Name, CVariation_Base::m_set_State, and value.
Referenced by variation::CVariationUtil::x_AsVariation().
Assign a value to Name data member.
value | Value to assign |
Definition at line 2773 of file Variation_.hpp.
References CVariation_Base::m_Name, CVariation_Base::m_set_State, and value.
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Definition at line 2151 of file Variation_.hpp.
References CVariation_Base::m_Name, CVariation_Base::m_set_State, and value.
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Definition at line 2780 of file Variation_.hpp.
References CVariation_Base::m_Name, CVariation_Base::m_set_State, and value.
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Assign a value to Name data member.
Definition at line 2158 of file Variation_.hpp.
References CVariation_Base::IsSetName(), CVariation_Base::m_Name, CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
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Assign a value to Name data member.
Definition at line 2787 of file Variation_.hpp.
References CVariation_Base::IsSetName(), CVariation_Base::m_Name, CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
Select the variant and set its data.
value | Variant data. |
Definition at line 192 of file Variation_.cpp.
References CVariation_Base::C_Data::e_Note, eDoNotResetVariant, CVariation_Base::C_Data::m_string, CVariation_Base::C_Data::Select(), and value.
Select the variant and set its data.
value | Variant data. |
Definition at line 397 of file Variation_.cpp.
References eDoNotResetVariant, and value.
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Select the variant.
Definition at line 2224 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Note, eDoNotResetVariant, CVariation_Base::C_Data::m_string, and CVariation_Base::C_Data::Select().
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Select the variant.
Definition at line 2433 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Note, eDoNotResetVariant, CVariation_Base::C_Data::m_string, and CVariation_Base::C_Data::Select().
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Assign a value to Object_id data member.
Definition at line 2611 of file Variation_.hpp.
References CVariation_Base::m_set_State.
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Assign a value to Other_ids data member.
Definition at line 2745 of file Variation_.hpp.
References CVariation_Base::m_Other_ids, and CVariation_Base::m_set_State.
void CVariantPlacement_Base::SetParent_id | ( | CVariantPlacement_Base::TParent_id & | value | ) |
Assign a value to Parent_id data member.
value | Reference to value. |
Definition at line 214 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Parent_id, and value.
void CVariation_Base::SetParent_id | ( | CVariation_Base::TParent_id & | value | ) |
Assign a value to Parent_id data member.
value | Reference to value. |
Definition at line 636 of file Variation_.cpp.
References CVariation_Base::m_Parent_id, and value.
CVariantPlacement_Base::TParent_id & CVariantPlacement_Base::SetParent_id | ( | void | ) |
Assign a value to Parent_id data member.
Definition at line 219 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Parent_id.
CVariation_Base::TParent_id & CVariation_Base::SetParent_id | ( | void | ) |
Assign a value to Parent_id data member.
Definition at line 641 of file Variation_.cpp.
References CVariation_Base::m_Parent_id.
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Assign a value to Phase data member.
value | Value to assign |
Definition at line 2480 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Assign a value to Phase data member.
Definition at line 2487 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Phenotype data member.
Definition at line 2914 of file Variation_.hpp.
References CVariation_Base::m_Phenotype, and CVariation_Base::m_set_State.
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Assign a value to Placement_method data member.
value | Value to assign |
Definition at line 1007 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_Placement_method, CVariantPlacement_Base::m_set_State, and value.
Referenced by variation::CVariationUtil::x_Remap().
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Assign a value to Placement_method data member.
Definition at line 1014 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetPlacement_method(), CVariantPlacement_Base::m_Placement_method, CVariantPlacement_Base::m_set_State, and CSerialObject::UnassignedByte().
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Assign a value to Placements data member.
Definition at line 2889 of file Variation_.hpp.
References CVariation_Base::m_Placements, and CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), NSNPVariationHelper::ConvertFeat(), variation::CVariationUtil::FlipStrand(), variation::RepackageAssertedSequence(), variation::CVariationUtil::s_FactorOutPlacements(), variation::SetFirstPlacement(), variation::CVariationUtil::x_AdjustDelinsToInterval(), CVariationNormalization_base< T >::x_Shift(), and variation::CHgvsParser::x_unwrap_iff_singleton().
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Assign a value to Population_data data member.
Definition at line 2960 of file Variation_.hpp.
References CVariation_Base::m_Population_data, and CVariation_Base::m_set_State.
void CVariation_Base::SetPub | ( | CVariation_Base::TPub & | value | ) |
Assign a value to Pub data member.
value | Reference to value. |
Definition at line 735 of file Variation_.cpp.
References CVariation_Base::m_Pub, and value.
CVariation_Base::TPub & CVariation_Base::SetPub | ( | void | ) |
Assign a value to Pub data member.
Definition at line 740 of file Variation_.cpp.
References CVariation_Base::m_Pub.
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Assign a value to Reference data member.
value | Value to assign |
Definition at line 2294 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Definition at line 2301 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Assign a value to Reference data member.
Definition at line 2308 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
void CVariationMethod_Base::SetReference_location | ( | CVariationMethod_Base::TReference_location & | value | ) |
Assign a value to Reference_location data member.
value | Reference to value. |
Definition at line 97 of file VariationMethod_.cpp.
References CVariationMethod_Base::m_Reference_location, and value.
CVariationMethod_Base::TReference_location & CVariationMethod_Base::SetReference_location | ( | void | ) |
Assign a value to Reference_location data member.
Definition at line 102 of file VariationMethod_.cpp.
References CVariationMethod_Base::m_Reference_location.
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Assign a value to Sample_id data member.
Definition at line 2720 of file Variation_.hpp.
References CVariation_Base::m_Sample_id, and CVariation_Base::m_set_State.
void CVariantPlacement_Base::SetSeq | ( | CVariantPlacement_Base::TSeq & | value | ) |
Assign a value to Seq data member.
value | Reference to value. |
Definition at line 133 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Seq, and value.
Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::TranslateNAtoAA(), variation::CHgvsParser::x_deletion(), variation::CHgvsParser::x_duplication(), variation::CHgvsParser::x_location(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_nuc_subst(), and variation::CHgvsParser::x_range().
void CVariation_Base::C_Data::SetSeq | ( | TSeq & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 254 of file Variation_.cpp.
References CObject::AddReference(), CVariation_Base::C_Data::e_Seq, CVariation_Base::C_Data::m_choice, CVariation_Base::C_Data::m_object, CVariation_Base::C_Data::ResetSelection(), and value.
CVariantPlacement_Base::TSeq & CVariantPlacement_Base::SetSeq | ( | void | ) |
Assign a value to Seq data member.
Definition at line 138 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Seq.
CVariation_Base::C_Data::TSeq & CVariation_Base::C_Data::SetSeq | ( | void | ) |
Select the variant.
Definition at line 248 of file Variation_.cpp.
References CVariation_Base::C_Data::e_Seq, eDoNotResetVariant, CVariation_Base::C_Data::m_object, and CVariation_Base::C_Data::Select().
void CVariation_Base::C_Data::SetSet | ( | TSet & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 232 of file Variation_.cpp.
References CObject::AddReference(), CVariation_Base::C_Data::e_Set, CVariation_Base::C_Data::m_choice, CVariation_Base::C_Data::m_object, CVariation_Base::C_Data::ResetSelection(), and value.
CVariation_Base::C_Data::TSet & CVariation_Base::C_Data::SetSet | ( | void | ) |
Select the variant.
Definition at line 226 of file Variation_.cpp.
References CVariation_Base::C_Data::e_Set, eDoNotResetVariant, CVariation_Base::C_Data::m_object, and CVariation_Base::C_Data::Select().
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Assign a value to So_terms data member.
Definition at line 1527 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State, and CVariantPlacement_Base::m_So_terms.
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Assign a value to So_terms data member.
Definition at line 3199 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_So_terms.
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Assign a value to Somatic_origin data member.
Definition at line 3149 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_Somatic_origin.
void CVariation_Base::C_E_Somatic_origin::SetSource | ( | TSource & | value | ) |
Assign a value to Source data member.
value | Reference to value. |
Definition at line 555 of file Variation_.cpp.
References CSubSource_Base::Reset(), and value.
CVariation_Base::C_E_Somatic_origin::TSource & CVariation_Base::C_E_Somatic_origin::SetSource | ( | void | ) |
Assign a value to Source data member.
Definition at line 560 of file Variation_.cpp.
References CSubSource_Base::Reset().
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Select the variant.
Definition at line 2414 of file Variation_.hpp.
References eDoNotResetVariant, and CVariation_Base::C_Data::Select().
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Assign a value to Start_offset data member.
value | Value to assign |
Definition at line 1054 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State, CVariantPlacement_Base::m_Start_offset, and value.
Referenced by variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CHgvsParser::s_SetStartOffset(), and variation::CVariationUtil::x_Remap().
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Assign a value to Start_offset data member.
Definition at line 1061 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::m_set_State, CVariantPlacement_Base::m_Start_offset, and CSerialObject::UnassignedByte().
void CVariantPlacement_Base::SetStart_offset_fuzz | ( | CVariantPlacement_Base::TStart_offset_fuzz & | value | ) |
Assign a value to Start_offset_fuzz data member.
value | Reference to value. |
Definition at line 99 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Start_offset_fuzz, and value.
Referenced by variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CHgvsParser::s_SetStartOffset(), and variation::CVariationUtil::x_Remap().
CVariantPlacement_Base::TStart_offset_fuzz & CVariantPlacement_Base::SetStart_offset_fuzz | ( | void | ) |
Assign a value to Start_offset_fuzz data member.
Definition at line 104 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Start_offset_fuzz.
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Assign a value to Stop_offset data member.
value | Value to assign |
Definition at line 1122 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::m_set_State, CVariantPlacement_Base::m_Stop_offset, and value.
Referenced by variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::s_AddIntronicOffsets(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CVariationUtil::s_ResolveIntronicOffsets(), variation::CHgvsParser::s_SetStopOffset(), variation::CVariationUtil::x_Remap(), and variation::CHgvsParser::x_ssr().
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Assign a value to Stop_offset data member.
Definition at line 1129 of file VariantPlacement_.hpp.
References CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::m_set_State, CVariantPlacement_Base::m_Stop_offset, and CSerialObject::UnassignedByte().
void CVariantPlacement_Base::SetStop_offset_fuzz | ( | CVariantPlacement_Base::TStop_offset_fuzz & | value | ) |
Assign a value to Stop_offset_fuzz data member.
value | Reference to value. |
Definition at line 116 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Stop_offset_fuzz, and value.
Referenced by variation::CVariationUtil::FlipStrand(), variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets(), variation::CHgvsParser::s_SetStopOffset(), and variation::CVariationUtil::x_Remap().
CVariantPlacement_Base::TStop_offset_fuzz & CVariantPlacement_Base::SetStop_offset_fuzz | ( | void | ) |
Assign a value to Stop_offset_fuzz data member.
Definition at line 121 of file VariantPlacement_.cpp.
References CVariantPlacement_Base::m_Stop_offset_fuzz.
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Assign a value to Synonyms data member.
Definition at line 2817 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CVariation_Base::m_Synonyms.
Referenced by variation::CHgvsParser::AttachHgvs().
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Assign a value to Test data member.
value | Value to assign |
Definition at line 2341 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Definition at line 2348 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Assign a value to Test data member.
Definition at line 2355 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CSerialObject::UnassignedString().
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Assign a value to Type data member.
value | Value to assign |
Definition at line 2079 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
Referenced by variation::CVariationUtil::x_AsVariation(), and variation::CHgvsParser::x_list().
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Assign a value to Type data member.
Definition at line 2086 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CSerialObject::UnassignedByte().
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Select the variant.
Definition at line 2237 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Uniparental_disomy, eDoNotResetVariant, and CVariation_Base::C_Data::Select().
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Select the variant.
Definition at line 2205 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Unknown, eDoNotResetVariant, and CVariation_Base::C_Data::Select().
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Select the variant.
Definition at line 2402 of file Variation_.hpp.
References CVariation_Base::C_Data::e_Unknown, eDoNotResetVariant, and CVariation_Base::C_Data::Select().
void CVariation_Base::SetVariant_prop | ( | CVariation_Base::TVariant_prop & | value | ) |
Assign a value to Variant_prop data member.
value | Reference to value. |
Definition at line 718 of file Variation_.cpp.
References CVariation_Base::m_Variant_prop, and value.
CVariation_Base::TVariant_prop & CVariation_Base::SetVariant_prop | ( | void | ) |
Assign a value to Variant_prop data member.
Definition at line 723 of file Variation_.cpp.
References CVariation_Base::m_Variant_prop.
void CVariation_Base::C_E_Consequence::SetVariation | ( | TVariation & | value | ) |
Select the variant and set its data.
value | Reference to the data. |
Definition at line 415 of file Variation_.cpp.
References CObject::AddReference(), and value.
CVariation_Base::C_E_Consequence::TVariation & CVariation_Base::C_E_Consequence::SetVariation | ( | void | ) |
Select the variant.
Definition at line 409 of file Variation_.cpp.
References eDoNotResetVariant.
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Assign a value to Variations data member.
Definition at line 2116 of file Variation_.hpp.
References CVariation_Base::m_set_State.
Referenced by variation::CVariationUtil::x_AsVariation(), and variation::CHgvsParser::x_list().
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Assign a value to X_length data member.
value | Value to assign |
Definition at line 2527 of file Variation_.hpp.
References CVariation_Base::m_set_State, and value.
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Assign a value to X_length data member.
Definition at line 2534 of file Variation_.hpp.
References CVariation_Base::m_set_State, and CSerialObject::UnassignedByte().
void CVariation_Base::C_Data::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 187 of file Variation_.cpp.
References DIAG_COMPILE_INFO, CVariation_Base::C_Data::m_choice, and CVariation_Base::C_Data::sm_SelectionNames.
Referenced by CVariation_Base::C_Data::CheckSelected(), and CVariation_Base::C_E_Consequence::CheckSelected().
void CVariation_Base::C_E_Consequence::ThrowInvalidSelection | ( | E_Choice | index | ) | const |
Throw 'InvalidSelection' exception.
index | Expected selection. |
Definition at line 392 of file Variation_.cpp.
References DIAG_COMPILE_INFO.
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Which variant is currently selected.
Definition at line 2170 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice.
Referenced by CVariationUtilities::GetVariationRefAlt(), CVariationUtilities::GetVariationType(), and CVariationNormalization_base< T >::x_Shift().
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Which variant is currently selected.
Definition at line 2367 of file Variation_.hpp.
References CVariation_Base::C_Data::m_choice.
CVariation_Base::C_E_Somatic_origin::C_Condition::~C_Condition | ( | void | ) |
Definition at line 545 of file Variation_.cpp.
CVariation_Base::C_Data::~C_Data | ( | void | ) |
Definition at line 290 of file Variation_.cpp.
References CVariation_Base::Reset().
CVariation_Base::C_E_Consequence::~C_E_Consequence | ( | void | ) |
Definition at line 471 of file Variation_.cpp.
References CVariation_Base::Reset().
CVariation_Base::C_E_Somatic_origin::~C_E_Somatic_origin | ( | void | ) |
Definition at line 609 of file Variation_.cpp.
CVariation_Base::C_Frameshift::~C_Frameshift | ( | void | ) |
Definition at line 503 of file Variation_.cpp.
CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::~C_Loss_of_heterozygosity | ( | void | ) |
Definition at line 333 of file Variation_.cpp.
CVariation_Base::C_Data::C_Set::~C_Set | ( | void | ) |
Definition at line 122 of file Variation_.cpp.
CVariantPlacement::~CVariantPlacement | ( | void | ) |
Definition at line 50 of file VariantPlacement.cpp.
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Definition at line 294 of file VariantPlacement_.cpp.
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virtual |
Definition at line 890 of file Variation_.cpp.
CVariationException::~CVariationException | ( | void | ) |
Definition at line 50 of file VariationException.cpp.
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virtual |
Definition at line 106 of file VariationException_.cpp.
CVariationMethod::~CVariationMethod | ( | void | ) |
Definition at line 50 of file VariationMethod.cpp.
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virtual |
Definition at line 133 of file VariationMethod_.cpp.
union { ... } |
union { ... } |
Definition at line 880 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetAssembly(), CVariantPlacement_Base::IsSetAssembly(), CVariantPlacement_Base::ResetAssembly(), and CVariantPlacement_Base::SetAssembly().
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Definition at line 511 of file Variation_.hpp.
Referenced by CVariation_Base::C_Data::CheckSelected(), CVariation_Base::C_E_Consequence::CheckSelected(), CVariation_Base::C_Data::DoSelect(), CVariation_Base::C_Data::IsComplex(), CVariation_Base::C_Data::IsInstance(), CVariation_Base::C_E_Consequence::IsLoss_of_heterozygosity(), CVariation_Base::C_Data::IsNote(), CVariation_Base::C_E_Consequence::IsNote(), CVariation_Base::C_Data::IsSeq(), CVariation_Base::C_Data::IsSet(), CVariation_Base::C_E_Consequence::IsSplicing(), CVariation_Base::C_Data::IsUniparental_disomy(), CVariation_Base::C_Data::IsUnknown(), CVariation_Base::C_E_Consequence::IsUnknown(), CVariation_Base::C_E_Consequence::IsVariation(), CVariation_Base::C_Data::Reset(), CVariation_Base::C_Data::ResetSelection(), CVariation_Base::C_Data::SetInstance(), CVariation_Base::C_Data::SetSeq(), CVariation_Base::C_Data::SetSet(), CVariation_Base::C_Data::ThrowInvalidSelection(), CVariation_Base::C_Data::Which(), and CVariation_Base::C_E_Consequence::Which().
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Definition at line 842 of file Variation_.hpp.
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private |
Definition at line 2031 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetClinical_test(), CVariation_Base::IsSetClinical_test(), CVariation_Base::ResetClinical_test(), and CVariation_Base::SetClinical_test().
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Definition at line 209 of file VariationException_.hpp.
Referenced by CVariationException_Base::GetCode(), CVariationException_Base::ResetCode(), and CVariationException_Base::SetCode().
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Definition at line 882 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetComment(), CVariantPlacement_Base::ResetComment(), and CVariantPlacement_Base::SetComment().
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Definition at line 1211 of file Variation_.hpp.
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Definition at line 2033 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetConsequence(), CVariation_Base::ResetConsequence(), and CVariation_Base::SetConsequence().
Definition at line 2032 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetData(), CVariation_Base::IsSetData(), CVariation_Base::ResetData(), and CVariation_Base::SetData().
Definition at line 884 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetDbxrefs(), CVariantPlacement_Base::ResetDbxrefs(), and CVariantPlacement_Base::SetDbxrefs().
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Definition at line 1106 of file Variation_.hpp.
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Definition at line 2024 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), BEGIN_NAMED_CLASS_INFO(), CVariation_Base::C_E_Somatic_origin::C_Condition::GetDescription(), CVariation_Base::GetDescription(), CVariation_Base::C_E_Somatic_origin::C_Condition::ResetDescription(), CVariation_Base::ResetDescription(), CVariation_Base::C_E_Somatic_origin::C_Condition::SetDescription(), and CVariation_Base::SetDescription().
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Definition at line 883 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetExceptions(), CVariantPlacement_Base::ResetExceptions(), and CVariantPlacement_Base::SetExceptions().
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Definition at line 2037 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetExceptions(), CVariation_Base::ResetExceptions(), and CVariation_Base::SetExceptions().
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Definition at line 885 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetExt(), CVariantPlacement_Base::ResetExt(), and CVariantPlacement_Base::SetExt().
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Definition at line 2035 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetExt(), CVariation_Base::ResetExt(), and CVariation_Base::SetExt().
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Definition at line 878 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetFrame(), CVariantPlacement_Base::ResetFrame(), and CVariantPlacement_Base::SetFrame().
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Definition at line 2034 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetFrameshift(), CVariation_Base::IsSetFrameshift(), CVariation_Base::ResetFrameshift(), and CVariation_Base::SetFrameshift().
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Definition at line 886 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetGene_location(), CVariantPlacement_Base::ResetGene_location(), and CVariantPlacement_Base::SetGene_location().
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Definition at line 881 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetHgvs_name(), CVariantPlacement_Base::ResetHgvs_name(), and CVariantPlacement_Base::SetHgvs_name().
Definition at line 887 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetId(), CVariantPlacement_Base::IsSetId(), CVariantPlacement_Base::ResetId(), and CVariantPlacement_Base::SetId().
Definition at line 2018 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetId(), CVariation_Base::IsSetId(), CVariation_Base::ResetId(), and CVariation_Base::SetId().
Definition at line 871 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::IsSetLoc(), CVariantPlacement_Base::ResetLoc(), and CVariantPlacement_Base::SetLoc().
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Definition at line 210 of file VariationException_.hpp.
Referenced by CVariationException_Base::GetMessage(), CVariationException_Base::ResetMessage(), and CVariationException_Base::SetMessage().
Definition at line 2027 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetMethod(), CVariation_Base::IsSetMethod(), CVariation_Base::ResetMethod(), and CVariation_Base::SetMethod().
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Definition at line 218 of file VariationMethod_.hpp.
Referenced by CVariationMethod_Base::GetMethod(), CVariationMethod_Base::ResetMethod(), and CVariationMethod_Base::SetMethod().
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Definition at line 872 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetMol(), CVariantPlacement_Base::ResetMol(), and CVariantPlacement_Base::SetMol().
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Definition at line 292 of file Variation_.hpp.
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Definition at line 2022 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), BEGIN_NAMED_CLASS_INFO(), CVariation_Base::C_Data::C_Set::GetName(), CVariation_Base::GetName(), CVariation_Base::C_Data::C_Set::ResetName(), CVariation_Base::ResetName(), CVariation_Base::C_Data::C_Set::SetName(), and CVariation_Base::SetName().
NCBI_NS_NCBI::CSerialObject* CVariation_Base::C_Data::m_object |
Definition at line 519 of file Variation_.hpp.
Referenced by BEGIN_NAMED_CHOICE_INFO(), CVariation_Base::C_Data::DoSelect(), CVariation_Base::C_Data::GetInstance(), CVariation_Base::C_Data::GetSeq(), CVariation_Base::C_Data::GetSet(), CVariation_Base::C_Data::ResetSelection(), CVariation_Base::C_Data::SetInstance(), CVariation_Base::C_Data::SetSeq(), and CVariation_Base::C_Data::SetSet().
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 519 of file Variation_.hpp.
NCBI_NS_NCBI::CSerialObject* CVariation_Base::C_E_Consequence::m_object |
Definition at line 850 of file Variation_.hpp.
NCBI_NS_NCBI::CSerialObject* { ... } ::m_object |
Definition at line 850 of file Variation_.hpp.
Definition at line 1107 of file Variation_.hpp.
Definition at line 2021 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetOther_ids(), CVariation_Base::ResetOther_ids(), and CVariation_Base::SetOther_ids().
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Definition at line 888 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetParent_id(), CVariantPlacement_Base::IsSetParent_id(), CVariantPlacement_Base::ResetParent_id(), and CVariantPlacement_Base::SetParent_id().
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Definition at line 2019 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetParent_id(), CVariation_Base::IsSetParent_id(), CVariation_Base::ResetParent_id(), and CVariation_Base::SetParent_id().
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Definition at line 972 of file Variation_.hpp.
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Definition at line 2026 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetPhenotype(), CVariation_Base::ResetPhenotype(), and CVariation_Base::SetPhenotype().
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Definition at line 873 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetPlacement_method(), CVariantPlacement_Base::ResetPlacement_method(), and CVariantPlacement_Base::SetPlacement_method().
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Definition at line 2025 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetPlacements(), CVariation_Base::ResetPlacements(), and CVariation_Base::SetPlacements().
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Definition at line 2028 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetPopulation_data(), CVariation_Base::ResetPopulation_data(), and CVariation_Base::SetPopulation_data().
Definition at line 2030 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetPub(), CVariation_Base::IsSetPub(), CVariation_Base::ResetPub(), and CVariation_Base::SetPub().
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Definition at line 662 of file Variation_.hpp.
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Definition at line 219 of file VariationMethod_.hpp.
Referenced by CVariationMethod_Base::GetReference_location(), CVariationMethod_Base::IsSetReference_location(), CVariationMethod_Base::ResetReference_location(), and CVariationMethod_Base::SetReference_location().
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Definition at line 2020 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetSample_id(), CVariation_Base::ResetSample_id(), and CVariation_Base::SetSample_id().
Definition at line 879 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetSeq(), CVariantPlacement_Base::IsSetSeq(), CVariantPlacement_Base::ResetSeq(), and CVariantPlacement_Base::SetSeq().
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Definition at line 289 of file Variation_.hpp.
Referenced by CVariation_Base::C_Data::C_Set::C_Set(), CVariation_Base::C_Data::C_Set::IsSetType(), and CVariation_Base::C_Data::C_Set::ResetVariations().
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Definition at line 661 of file Variation_.hpp.
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Definition at line 971 of file Variation_.hpp.
Referenced by CVariation_Base::C_Frameshift::C_Frameshift().
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Definition at line 1105 of file Variation_.hpp.
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Definition at line 1209 of file Variation_.hpp.
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Definition at line 208 of file VariationException_.hpp.
Referenced by CVariationException_Base::CVariationException_Base(), CVariationException_Base::IsSetCode(), CVariationException_Base::IsSetMessage(), CVariationException_Base::ResetCode(), CVariationException_Base::ResetMessage(), CVariationException_Base::SetCode(), and CVariationException_Base::SetMessage().
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Definition at line 217 of file VariationMethod_.hpp.
Referenced by CVariationMethod_Base::CVariationMethod_Base(), CVariationMethod_Base::IsSetMethod(), CVariationMethod_Base::ResetMethod(), and CVariationMethod_Base::SetMethod().
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Definition at line 870 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::CVariantPlacement_Base(), CVariantPlacement_Base::IsSetComment(), CVariantPlacement_Base::IsSetDbxrefs(), CVariantPlacement_Base::IsSetExceptions(), CVariantPlacement_Base::IsSetExt(), CVariantPlacement_Base::IsSetFrame(), CVariantPlacement_Base::IsSetGene_location(), CVariantPlacement_Base::IsSetHgvs_name(), CVariantPlacement_Base::IsSetMol(), CVariantPlacement_Base::IsSetPlacement_method(), CVariantPlacement_Base::IsSetSo_terms(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::ResetComment(), CVariantPlacement_Base::ResetDbxrefs(), CVariantPlacement_Base::ResetExceptions(), CVariantPlacement_Base::ResetExt(), CVariantPlacement_Base::ResetFrame(), CVariantPlacement_Base::ResetGene_location(), CVariantPlacement_Base::ResetHgvs_name(), CVariantPlacement_Base::ResetMol(), CVariantPlacement_Base::ResetPlacement_method(), CVariantPlacement_Base::ResetSo_terms(), CVariantPlacement_Base::ResetStart_offset(), CVariantPlacement_Base::ResetStop_offset(), CVariantPlacement_Base::SetComment(), CVariantPlacement_Base::SetDbxrefs(), CVariantPlacement_Base::SetExceptions(), CVariantPlacement_Base::SetExt(), CVariantPlacement_Base::SetFrame(), CVariantPlacement_Base::SetGene_location(), CVariantPlacement_Base::SetHgvs_name(), CVariantPlacement_Base::SetMol(), CVariantPlacement_Base::SetPlacement_method(), CVariantPlacement_Base::SetSo_terms(), CVariantPlacement_Base::SetStart_offset(), and CVariantPlacement_Base::SetStop_offset().
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Definition at line 2017 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), BEGIN_NAMED_CLASS_INFO(), CVariation_Base::C_E_Somatic_origin::C_Condition::C_Condition(), CVariation_Base::C_E_Somatic_origin::C_E_Somatic_origin(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::C_Loss_of_heterozygosity(), CVariation_Base::CVariation_Base(), CVariation_Base::IsSetConsequence(), CVariation_Base::C_E_Somatic_origin::C_Condition::IsSetDescription(), CVariation_Base::IsSetDescription(), CVariation_Base::IsSetExceptions(), CVariation_Base::IsSetExt(), CVariation_Base::C_Data::C_Set::IsSetName(), CVariation_Base::IsSetName(), CVariation_Base::C_E_Somatic_origin::C_Condition::IsSetObject_id(), CVariation_Base::IsSetOther_ids(), CVariation_Base::C_Frameshift::IsSetPhase(), CVariation_Base::IsSetPhenotype(), CVariation_Base::IsSetPlacements(), CVariation_Base::IsSetPopulation_data(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::IsSetReference(), CVariation_Base::IsSetSample_id(), CVariation_Base::IsSetSo_terms(), CVariation_Base::IsSetSomatic_origin(), CVariation_Base::IsSetSynonyms(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::IsSetTest(), CVariation_Base::C_Data::C_Set::IsSetVariations(), CVariation_Base::C_Frameshift::IsSetX_length(), CVariation_Base::ResetConsequence(), CVariation_Base::C_E_Somatic_origin::C_Condition::ResetDescription(), CVariation_Base::ResetDescription(), CVariation_Base::ResetExceptions(), CVariation_Base::ResetExt(), CVariation_Base::C_Data::C_Set::ResetName(), CVariation_Base::ResetName(), CVariation_Base::C_E_Somatic_origin::C_Condition::ResetObject_id(), CVariation_Base::ResetOther_ids(), CVariation_Base::C_Frameshift::ResetPhase(), CVariation_Base::ResetPhenotype(), CVariation_Base::ResetPlacements(), CVariation_Base::ResetPopulation_data(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::ResetReference(), CVariation_Base::ResetSample_id(), CVariation_Base::ResetSo_terms(), CVariation_Base::ResetSomatic_origin(), CVariation_Base::ResetSynonyms(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::ResetTest(), CVariation_Base::C_Data::C_Set::ResetType(), CVariation_Base::C_Frameshift::ResetX_length(), CVariation_Base::SetConsequence(), CVariation_Base::C_E_Somatic_origin::C_Condition::SetDescription(), CVariation_Base::SetDescription(), CVariation_Base::SetExceptions(), CVariation_Base::SetExt(), CVariation_Base::C_Data::C_Set::SetName(), CVariation_Base::SetName(), CVariation_Base::C_E_Somatic_origin::C_Condition::SetObject_id(), CVariation_Base::SetOther_ids(), CVariation_Base::C_Frameshift::SetPhase(), CVariation_Base::SetPhenotype(), CVariation_Base::SetPlacements(), CVariation_Base::SetPopulation_data(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetReference(), CVariation_Base::SetSample_id(), CVariation_Base::SetSo_terms(), CVariation_Base::SetSomatic_origin(), CVariation_Base::SetSynonyms(), CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::SetTest(), CVariation_Base::C_Data::C_Set::SetType(), CVariation_Base::C_Data::C_Set::SetVariations(), and CVariation_Base::C_Frameshift::SetX_length().
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Definition at line 889 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetSo_terms(), CVariantPlacement_Base::ResetSo_terms(), and CVariantPlacement_Base::SetSo_terms().
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Definition at line 2038 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetSo_terms(), CVariation_Base::ResetSo_terms(), and CVariation_Base::SetSo_terms().
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Definition at line 2036 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetSomatic_origin(), CVariation_Base::ResetSomatic_origin(), and CVariation_Base::SetSomatic_origin().
Definition at line 1210 of file Variation_.hpp.
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Definition at line 874 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetStart_offset(), CVariantPlacement_Base::ResetStart_offset(), and CVariantPlacement_Base::SetStart_offset().
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Definition at line 875 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetStart_offset_fuzz(), CVariantPlacement_Base::IsSetStart_offset_fuzz(), CVariantPlacement_Base::ResetStart_offset_fuzz(), and CVariantPlacement_Base::SetStart_offset_fuzz().
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Definition at line 876 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetStop_offset(), CVariantPlacement_Base::ResetStop_offset(), and CVariantPlacement_Base::SetStop_offset().
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Definition at line 877 of file VariantPlacement_.hpp.
Referenced by CVariantPlacement_Base::GetStop_offset_fuzz(), CVariantPlacement_Base::IsSetStop_offset_fuzz(), CVariantPlacement_Base::ResetStop_offset_fuzz(), and CVariantPlacement_Base::SetStop_offset_fuzz().
NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> CVariation_Base::C_Data::m_string |
Definition at line 518 of file Variation_.hpp.
Referenced by BEGIN_NAMED_CHOICE_INFO(), CVariation_Base::C_Data::DoSelect(), CVariation_Base::C_Data::GetNote(), CVariation_Base::C_E_Consequence::GetNote(), CVariation_Base::C_Data::ResetSelection(), CVariation_Base::C_Data::SetNote(), and CVariation_Base::C_E_Consequence::SetNote().
NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> { ... } ::m_string |
Definition at line 518 of file Variation_.hpp.
NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> { ... } ::m_string |
Definition at line 849 of file Variation_.hpp.
NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string> CVariation_Base::C_E_Consequence::m_string |
Definition at line 849 of file Variation_.hpp.
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Definition at line 2023 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetSynonyms(), CVariation_Base::ResetSynonyms(), and CVariation_Base::SetSynonyms().
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Definition at line 663 of file Variation_.hpp.
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Definition at line 290 of file Variation_.hpp.
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Definition at line 2029 of file Variation_.hpp.
Referenced by BEGIN_NAMED_BASE_CLASS_INFO(), CVariation_Base::GetVariant_prop(), CVariation_Base::IsSetVariant_prop(), CVariation_Base::ResetVariant_prop(), and CVariation_Base::SetVariant_prop().
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Definition at line 291 of file Variation_.hpp.
Referenced by CVariation_Base::C_Data::C_Set::ResetVariations().
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Definition at line 973 of file Variation_.hpp.
Definition at line 515 of file Variation_.hpp.
Referenced by CVariation_Base::C_Data::SelectionName(), and CVariation_Base::C_Data::ThrowInvalidSelection().
Definition at line 846 of file Variation_.hpp.