Definition at line 149 of file BioSource_.hpp.
◆ E_memberIndex [2/4] Enumerator e__allMandatory e_seq e_nameDefinition at line 90 of file PCRPrimer_.hpp.
◆ E_memberIndex [3/4] Enumerator e__allMandatory e_forward e_reverseDefinition at line 89 of file PCRReaction_.hpp.
◆ E_memberIndex [4/4] Enumerator e__allMandatory e_subtype e_name e_attribDefinition at line 140 of file SubSource_.hpp.
◆ EGenomebiological context
Enumerator eGenome_unknown eGenome_genomic eGenome_chloroplast eGenome_chromoplast eGenome_kinetoplast eGenome_mitochondrion eGenome_plastid eGenome_macronuclear eGenome_extrachrom eGenome_plasmid eGenome_transposon eGenome_insertion_seq eGenome_cyanelle eGenome_proviral eGenome_virion eGenome_nucleomorph eGenome_apicoplast eGenome_leucoplast eGenome_proplastid eGenome_endogenous_virus eGenome_hydrogenosome eGenome_chromosome eGenome_chromatophore eGenome_plasmid_in_mitochondrion eGenome_plasmid_in_plastidDefinition at line 97 of file BioSource_.hpp.
◆ EOrigin Enumerator eOrigin_unknown eOrigin_naturalnormal biological entity
eOrigin_natmutnaturally occurring mutant
eOrigin_mutartificially mutagenized
eOrigin_artificialartificially engineered
eOrigin_syntheticpurely synthetic
eOrigin_otherDefinition at line 128 of file BioSource_.hpp.
◆ ESubtype Enumerator eSubtype_chromosome eSubtype_map eSubtype_clone eSubtype_subclone eSubtype_haplotype eSubtype_genotype eSubtype_sex eSubtype_cell_line eSubtype_cell_type eSubtype_tissue_type eSubtype_clone_lib eSubtype_dev_stage eSubtype_frequency eSubtype_germline eSubtype_rearranged eSubtype_lab_host eSubtype_pop_variant eSubtype_tissue_lib eSubtype_plasmid_name eSubtype_transposon_name eSubtype_insertion_seq_name eSubtype_plastid_name eSubtype_country eSubtype_segment eSubtype_endogenous_virus_name eSubtype_transgenic eSubtype_environmental_sample eSubtype_isolation_source eSubtype_lat_lon+/- decimal degrees
eSubtype_collection_dateDD-MMM-YYYY format.
eSubtype_collected_byname of person who collected the sample
eSubtype_identified_byname of person who identified the sample
eSubtype_fwd_primer_seqsequence (possibly more than one; semicolon-separated)
eSubtype_rev_primer_seqsequence (possibly more than one; semicolon-separated)
eSubtype_fwd_primer_name eSubtype_rev_primer_name eSubtype_metagenomic eSubtype_mating_type eSubtype_linkage_group eSubtype_haplogroup eSubtype_whole_replicon eSubtype_phenotype eSubtype_altitude eSubtype_otherDefinition at line 84 of file SubSource_.hpp.
◆ CanGet() [1/2] bool CPCRPrimerSet_Base::CanGet ( void ) const inline ◆ CanGet() [2/2] bool CPCRReactionSet_Base::CanGet ( void ) const inline ◆ CanGetAttrib() bool CSubSource_Base::CanGetAttrib ( void ) const inline ◆ CanGetForward() bool CPCRReaction_Base::CanGetForward ( void ) const inline ◆ CanGetGenome() bool CBioSource_Base::CanGetGenome ( void ) const inline ◆ CanGetIs_focus() bool CBioSource_Base::CanGetIs_focus ( void ) const inline ◆ CanGetName() [1/2] bool CPCRPrimer_Base::CanGetName ( void ) const inline ◆ CanGetName() [2/2] bool CSubSource_Base::CanGetName ( void ) const inline ◆ CanGetOrg() bool CBioSource_Base::CanGetOrg ( void ) const inlineCheck if it is safe to call GetOrg method.
Definition at line 503 of file BioSource_.hpp.
Referenced by CheckQualsInSourceFeat(), CopyOrg(), fta_sort_biosource(), CAutoDefSourceDescription::GetAvailableModifiers(), CAutoDefSourceGroup::GetDefaultExcludeSp(), CBioSource::GetGenCode(), CAutoDefSourceDescription::IsTrickyHIV(), UpdateRawBioSource(), CValidError_imp::ValidateBioSource(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CBioseqIndex::x_InitSource(), and CSourceItem::x_SetSource().
◆ CanGetOrigin() bool CBioSource_Base::CanGetOrigin ( void ) const inline ◆ CanGetPcr_primers() bool CBioSource_Base::CanGetPcr_primers ( void ) const inline ◆ CanGetReverse() bool CPCRReaction_Base::CanGetReverse ( void ) const inline ◆ CanGetSeq() bool CPCRPrimer_Base::CanGetSeq ( void ) const inline ◆ CanGetSubtype() [1/2] bool CBioSource_Base::CanGetSubtype ( void ) const inlineCheck if it is safe to call GetSubtype method.
Definition at line 533 of file BioSource_.hpp.
Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), CAutoDefSourceDescription::GetAvailableModifiers(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), CValidError_imp::IsTransgenic(), CAutoDefSourceDescription::IsTrickyHIV(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), CAutoDefFeatureClause::x_GetDescription(), CAutoDef::x_GetFeatureClauseProductEnding(), and CSetTransgSrcDesc::x_HasTransgenicSubtype().
◆ CanGetSubtype() [2/2] bool CSubSource_Base::CanGetSubtype ( void ) const inline ◆ CBioSource_Base() [1/2] ◆ CBioSource_Base() [2/2] ◆ CPCRPrimer() [1/2] ◆ CPCRPrimer() [2/2] CPCRPrimer::CPCRPrimer ( void ) inlineDefinition at line 86 of file PCRPrimer.hpp.
◆ CPCRPrimer_Base() [1/2] ◆ CPCRPrimer_Base() [2/2] ◆ CPCRPrimerName() [1/2] ◆ CPCRPrimerName() [2/2] CPCRPrimerName::CPCRPrimerName ( void ) inlineDefinition at line 69 of file PCRPrimerName.hpp.
◆ CPCRPrimerName_Base() [1/2] ◆ CPCRPrimerName_Base() [2/2] CPCRPrimerName_Base::CPCRPrimerName_Base ( void ) inlineDefinition at line 95 of file PCRPrimerName_.hpp.
◆ CPCRPrimerSeq_Base() [1/2] ◆ CPCRPrimerSeq_Base() [2/2] CPCRPrimerSeq_Base::CPCRPrimerSeq_Base ( void ) inlineDefinition at line 95 of file PCRPrimerSeq_.hpp.
◆ CPCRPrimerSet() [1/2] ◆ CPCRPrimerSet() [2/2] CPCRPrimerSet::CPCRPrimerSet ( void ) inlineDefinition at line 86 of file PCRPrimerSet.hpp.
◆ CPCRPrimerSet_Base() [1/2] ◆ CPCRPrimerSet_Base() [2/2] ◆ CPCRReaction() [1/2] ◆ CPCRReaction() [2/2] CPCRReaction::CPCRReaction ( void ) inlineDefinition at line 86 of file PCRReaction.hpp.
◆ CPCRReaction_Base() [1/2] ◆ CPCRReaction_Base() [2/2] ◆ CPCRReactionSet() [1/2] ◆ CPCRReactionSet() [2/2] ◆ CPCRReactionSet_Base() [1/2] ◆ CPCRReactionSet_Base() [2/2] ◆ CSubSource_Base() [1/2] ◆ CSubSource_Base() [2/2] ◆ DECLARE_INTERNAL_TYPE_INFO() [1/6] CBioSource_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [2/6] CPCRPrimer_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [3/6] CPCRPrimerSet_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [4/6] CPCRReaction_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [5/6] CPCRReactionSet_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [6/6] CSubSource_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_STD_ALIAS_TYPE_INFO() [1/2] CPCRPrimerName_Base::DECLARE_STD_ALIAS_TYPE_INFO ( ) ◆ DECLARE_STD_ALIAS_TYPE_INFO() [2/2] CPCRPrimerSeq_Base::DECLARE_STD_ALIAS_TYPE_INFO ( ) ◆ EGenome()Access to EGenome's attributes (values, names) as defined in spec.
◆ EOrigin()Access to EOrigin's attributes (values, names) as defined in spec.
◆ ESubtype()Access to ESubtype's attributes (values, names) as defined in spec.
◆ Get() [1/2] ◆ Get() [2/2] ◆ GetAttrib() ◆ GetForward() ◆ GetGenome()Get the Genome member data.
Definition at line 422 of file BioSource_.hpp.
References CBioSource_Base::m_Genome.
Referenced by BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), FakeEmblBioSources(), FakeGenBankBioSources(), CBioSource::FixGenomeForQualifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), CAutoDefWithTaxonomy::GetDocsumDefLine(), CBioSource::GetGenCode(), CWriteUtil::GetGenomeString(), CSource_qual_choice::GetLimitedSourceQualFromBioSource(), variation::CVariationUtil::GetMolType(), CAutoDef::GetOneDefLine(), CBioSource::GetRepliconName(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), GetSeqTableFromSeqEntry(), CGenomeQual::GetValue(), CEditingActionBiosourceLocation::GetValue(), CSGUtils::IsChromosome(), CDiscrepancyContext::IsEukaryotic(), IsInOrganelleSmallGenomeSet(), variation::IsMitochondrion(), CSGUtils::IsMitochondrion(), IsOrganelle(), CDiscrepancyContext::IsOrganelle(), CMRnaForCDS::IsOrganelle(), CSGUtils::IsPlastid(), CCleanup::MergeDupBioSources(), CBioSourceKind::operator=(), s_GetStrictGenCode(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Relaxed(), s_IsChromosome(), s_UpdateTitleString(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateSeqFeatContext(), CSourceFeatureItem::x_AddQuals(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CApplyGCode::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutoDef::x_GetFeatureClauseProductEnding(), CDeflineGenerator::x_GetModifiers(), CValidError_bioseq::x_IgnoreEndGap(), CBioseqIndex::x_InitSource(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CDeflineGenerator::x_SetBioSrc(), CSourceItem::x_SetSource(), CValidError_bioseq::x_ValidateCompletness(), CCdregionValidator::x_ValidateGeneticCode(), CSrcWriter::xGatherGenome(), and XMLFakeBioSources().
◆ GetName() [1/2] ◆ GetName() [2/2]Get the Name member data.
Definition at line 350 of file SubSource_.hpp.
References CSubSource_Base::CanGetName(), CSubSource_Base::m_Name, and CSerialObject::ThrowUnassigned().
Referenced by CSubSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CSubSource::FixCapitalization(), CFlatSubSourceQVal::Format(), CSubSource::GetLabel(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), CEditingActionBiosourceSubSource::GetValue(), CEditingActionBiosourceAllNotes::GetValue(), IsSameSubtype(), CSubtypeEquals::operator()(), CSubSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), s_NameCloseEnough(), s_NameCloseEnoughC(), s_SubsourceEquivalent(), SetSubsource(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_PostBiosource(), CDeflineGenerator::x_SetBioSrc(), CNewCleanup_imp::x_SubSourceBC(), and CSrcWriter::xGatherSubtypeFeat().
◆ GetOrg()Get the Org member data.
Definition at line 509 of file BioSource_.hpp.
References CBioSource_Base::m_Org, and CBioSource_Base::ResetOrg().
Referenced by CUnculTaxTool::AddBioSource(), AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CBioSource::AllowMatingTypeQualifier(), CBioSource::AllowSexQualifier(), CCleanup::AreBioSourcesMergeable(), CBioSource::AutoFix(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BiosourceFeatBC(), BOOST_AUTO_TEST_CASE(), CheckMetagenome(), CheckQualsInSourceFeat(), CValidError_bioseq::CheckSourceDescriptor(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CompareDescrFeatSources(), CopyOrg(), CStrainRequest::ExploreStrainsByTaxname(), CBioSource::FixEnvironmentalSample(), FixHumanHost(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), fta_sort_biosource(), IEditingAction::GetActionCommand(), CAutoDefSourceDescription::GetAvailableModifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CAutoDefSourceDescription::GetComboDescription(), CBioSource::GetCommon(), CAutoDefSourceGroup::GetDefaultExcludeSp(), CBioSource::GetDisableStrainForwarding(), CBioSource::GetDivision(), CAutoDefWithTaxonomy::GetDocsumOrgDescription(), CSrcTableDbxrefColumn::GetFromBioSource(), GetGBBlock(), CBioSource::GetGcode(), CBioSource::GetGenCode(), GetGeneticCodeForBioseq(), CEntrezgeneHandler::GetLabel(), CBioSource::GetLineage(), CBioSource::GetMgcode(), CBioSource::GetNameValPairs(), GetOrg_refOrNull(), IAlignRowHandle::GetOrgLabel(), CBioSource::GetOrgname(), CBioSource::GetPgcode(), CUnculTaxTool::GetReply(), GetRmCultureNotesCommand(), GetSeqTableFromSeqEntry(), CAutoDefModifierCombo::GetSourceDescriptionString(), GetSourceFields(), GetSprotDescr(), GetSrcQual(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CBioseq::GetTaxId(), CBioSource::GetTaxname(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CSrcTableDbxrefColumn::GetValsFromBioSource(), CSrcTableOrgModColumn::GetValsFromBioSource(), CTaxnameQual::GetValue(), COrgModQual::GetValue(), CEditingActionBiosourceTaxname::GetValue(), CEditingActionBiosourceTaxnameAfterBinomial::GetValue(), CEditingActionBiosourceCommonName::GetValue(), CEditingActionBiosourceDivision::GetValue(), CEditingActionBiosourceLineage::GetValue(), CValidError_imp::HandleTaxonomyError(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsMissingRequiredClone(), CBioSource::IsSetCommon(), CBioSource::IsSetDivision(), CBioSource::IsSetGcode(), CBioSource::IsSetLineage(), CBioSource::IsSetMgcode(), CBioSource::IsSetOrgMod(), CBioSource::IsSetOrgname(), CBioSource::IsSetPgcode(), CBioSource::IsSetTaxname(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CEditingActionBiosourceCommonName::IsSetValue(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CAutoDefSourceDescription::IsTrickyHIV(), CBioSource::IsViral(), LoadFeat(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MakeIRDFeatsFromSourceXrefs(), MakeMailReportPostReport(), MakeMailReportPreReport(), CCleanup::MakeSmallGenomeSet(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceDbxref::Modify(), CRemoveTaxonBioSource::ModifyBioSource(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PropagateSuppliedLineage(), RemoveDbxref(), CBioSource::RemoveLineageSourceNotes(), RemoveMod(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), RemoveStrain(), RemoveTaxId(), CBioSource::RemoveUnexpectedViralQualifiers(), CPrimeCacheApplication::Run(), s_DuplicatesBiosource(), s_GetBioSourceContentLabel(), s_GetContentLabel(), s_GetDiv(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetStrictGenCode(), s_GetTaxId(), s_GetTaxid(), CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref(), CGenusSpeciesFixup::s_HasTaxId(), CUnculturedTool::s_HasTaxId(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict(), CMacroFunction_RemoveQual::s_RemoveFields(), s_ResetModSubsrcQuals(), s_SuppressMultipleEquivBioSources(), s_TitleFromSegment(), s_UpdateTitleString(), SeqEntryCheckTaxonDiv(), SetCultureCollectionFromStrain(), CBioSource::SetDisableStrainForwarding(), CCleanup::SetGeneticCodes(), SetOrgMod(), CCleanup::TaxonomyLookup(), CMacroFunction_SwapQual::TheFunction(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), UpdateBiosourceFromBiosample(), UpdateRawBioSource(), CBioSource::UpdateWithBioSample(), CSrcFeatValidator::Validate(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_imp::ValidateSubSource(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), CStrainSerotypeInfluenza::x_AddToInfluenzaNames(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CWriteDB_Impl::x_BuildDeflinesFromBioseq(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CNewCleanup_imp::x_ChangePopToPhy(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CStrainSerotypeInfluenza::x_FixupOrganismNames(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetOrgModNameValPairs(), CStrainSerotypeInfluenza::x_GetStrainSerotypeConflicts(), CDumpASNIndex::x_GetTaxId(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CBioseqIndex::x_InitSource(), CStrainSerotypeInfluenza::x_IsParsableInfluenzaVirusName(), CBioSource::x_RemoveNameElementDiffs(), CSourceItem::x_SetSource(), CBlastTabularInfo::x_SetTaxInfoAll(), CBioSource::x_ShouldIgnoreNoteForBiosample(), CStrainSerotypeInfluenza::x_TrimmingOrganismNames(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3Writer::xAssignSourceAttributesOrgMod(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), CSrcWriter::xGatherDivision(), CSrcWriter::xGatherOrgCommon(), CSrcWriter::xGatherOrgnameLineage(), CSrcWriter::xGatherTaxonId(), XMLGetGBBlock(), and CGff3Writer::xWriteSequenceHeader().
◆ GetOrigin()Get the Origin member data.
Definition at line 472 of file BioSource_.hpp.
References CBioSource_Base::m_Origin.
Referenced by CSrcTableOriginColumn::AddToBioSource(), GetBiosourceDifferences(), GetDescrEmblBlock(), CSrcTableOriginColumn::GetFromBioSource(), GetGBBlock(), CSource_qual_choice::GetLimitedSourceQualFromBioSource(), CAutoDefModifierCombo::GetSourceDescriptionString(), CEditingActionBiosourceOrigin::GetValue(), CValidError_imp::IsArtificial(), CNewCleanup_imp::IsSyntheticConstruct(), CCleanup::MergeDupBioSources(), CSourceFeatureItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CValidError_bioseq::x_ValidateCompletness(), CSrcWriter::xGatherOrigin(), XMLGetEMBLBlock(), and XMLGetGBBlock().
◆ GetPcr_primers()Get the Pcr_primers member data.
Definition at line 588 of file BioSource_.hpp.
References CBioSource_Base::CanGetPcr_primers(), CBioSource_Base::m_Pcr_primers, and CSerialObject::ThrowUnassigned().
Referenced by GetSeqTableFromSeqEntry(), CSrcTablePrimerColumn::GetValsFromBioSource(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), CValidError_imp::ValidateBioSource(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CDeflineGenerator::x_GetModifiers(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().
◆ GetReverse() ◆ GetSeq() ◆ GetSubtype() [1/2]Get the Subtype member data.
Definition at line 539 of file BioSource_.hpp.
References CBioSource_Base::m_Subtype.
Referenced by AddBioSourceToAttributes(), CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), ChangeCountryColonToComma(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), FTASubSourceAdd(), g_FindSegs(), CAutoDefSourceDescription::GetAvailableModifiers(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), GetDescrEmblBlock(), GetEmblGBBlock(), GetGBBlock(), CBioSource::GetRepliconName(), GetSeqTableFromSeqEntry(), GetSourceFields(), CGuiObjectInfoComponent::GetToolTip(), CSrcTableSubSourceColumn::GetValsFromBioSource(), CSubSrcQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), CBioSource::HasSubtype(), CAutoDefFeatureClause::IsEndogenousVirusSourceFeature(), IsMissingRequiredClone(), IsSegmentSubtype(), CUnculTaxTool::IsSpeciesSpecific(), CAutoDefSourceDescription::IsTrickyHIV(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), CTabularFormatter_SeqChrom::Print(), CTabularFormatter_SeqClone::Print(), RemoveCountryColon(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), s_GetContentLabel(), s_GetEncodeValues(), s_GetSourceSubtype(), s_HasSubSourceNote(), s_ResetModSubsrcQuals(), s_SubSourceListUniqued(), s_TitleFromSegment(), SetSubsource(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddMinicircle(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddSubsourceString(), CAutoDefModifierCombo::x_BioSourceHasSubSrc(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CUnculturedTool::x_ConvertNote(), CKeywordsItem::x_GatherInfo(), CAutoDefFeatureClause::x_GetDescription(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CAutoDef::x_GetFeatureClauseProductEnding(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetSubtypeNameValPairs(), CSetTransgSrcDesc::x_HasTransgenicSubtype(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CSubmissionWizard::x_TransferImportedSubSources(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributesSubSource(), CSrcWriter::xGatherSubtypeFeat(), and XMLGetGBBlock().
◆ GetSubtype() [2/2]Get the Subtype member data.
Definition at line 310 of file SubSource_.hpp.
References CSubSource_Base::CanGetSubtype(), CSubSource_Base::m_Subtype, and CSerialObject::ThrowUnassigned().
Referenced by CSubSource::AutoFix(), CSubSource::FixCapitalization(), CFlatSubSourceQVal::Format(), CSubSource::GetLabel(), CWriteUtil::GetSubSourceSubType(), GetSubtypeName(), CGuiObjectInfoComponent::GetToolTip(), CSubSource::IsDeprecated(), IsSameSubtype(), CValidError_imp::IsTransgenic(), CSubtypeEquals::operator()(), CBioSource::RemoveLineageSourceNotes(), s_SameSubtype(), s_SameSubtypeC(), s_SubsourceEquivalent(), s_SubSourceToSlot(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), and CSrcWriter::xGatherSubtypeFeat().
◆ IsSet() [1/2] bool CPCRPrimerSet_Base::IsSet ( void ) const inline ◆ IsSet() [2/2] bool CPCRReactionSet_Base::IsSet ( void ) const inline ◆ IsSetAttrib() bool CSubSource_Base::IsSetAttrib ( void ) const inline ◆ IsSetForward() bool CPCRReaction_Base::IsSetForward ( void ) const inline ◆ IsSetGenome() bool CBioSource_Base::IsSetGenome ( void ) const inlineCheck if a value has been assigned to Genome data member.
Data member Genome is optional with default eGenome_unknown; its type is defined as 'typedef int TGenome'
Definition at line 397 of file BioSource_.hpp.
References CBioSource_Base::m_set_State.
Referenced by BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), CBioSource::FixGenomeForQualifiers(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CAutoDefWithTaxonomy::GetDocsumDefLine(), CWriteUtil::GetGenomeString(), variation::CVariationUtil::GetMolType(), CBioSource::GetRepliconName(), GetSeqTableFromSeqEntry(), CGenomeQual::GetValue(), IsInOrganelleSmallGenomeSet(), IsOrganelle(), CDiscrepancyContext::IsOrganelle(), CMRnaForCDS::IsOrganelle(), CEditingActionBiosourceLocation::IsSetValue(), CCleanup::MergeDupBioSources(), CBioSourceKind::operator=(), s_GetStrictGenCode(), s_IsChromosome(), s_IsEmptyBioSource(), s_UpdateTitleString(), CBioSource_Base::SetGenome(), CValidError_imp::Validate(), CValidError_imp::ValidateBioSource(), CValidError_bioseq::ValidateSeqFeatContext(), CDeflineGenerator::x_AdjustProteinTitleSuffix(), CApplyGCode::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CValidError_bioseq::x_IgnoreEndGap(), CBioseqIndex::x_InitSource(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CDeflineGenerator::x_SetBioSrc(), CValidError_bioseq::x_ValidateCompletness(), and CSrcWriter::xGatherGenome().
◆ IsSetIs_focus() bool CBioSource_Base::IsSetIs_focus ( void ) const inline ◆ IsSetName() [1/2] bool CPCRPrimer_Base::IsSetName ( void ) const inline ◆ IsSetName() [2/2] bool CSubSource_Base::IsSetName ( void ) const inlineCheck if a value has been assigned to Name data member.
Data member Name is mandatory; its type is defined as 'typedef string TName'
Definition at line 338 of file SubSource_.hpp.
References CSubSource_Base::m_set_State.
Referenced by CSubSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CSubSource_Base::CanGetName(), CSubSource::FixCapitalization(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), CEditingActionBiosourceSubSource::IsSetValue(), CEditingActionBiosourceAllNotes::IsSetValue(), CSubSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), s_NameCloseEnough(), s_NameCloseEnoughC(), s_SubsourceEquivalent(), CSubSource_Base::SetName(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), CBioseqIndex::x_InitSource(), CNewCleanup_imp::x_PostBiosource(), CDeflineGenerator::x_SetBioSrc(), CDeflineGenerator::x_SetBioSrcIdx(), CNewCleanup_imp::x_SubSourceBC(), and CSrcWriter::xGatherSubtypeFeat().
◆ IsSetOrg() bool CBioSource_Base::IsSetOrg ( void ) const inlineCheck if a value has been assigned to Org data member.
Data member Org is mandatory; its type is defined as 'typedef COrg_ref TOrg'
Definition at line 497 of file BioSource_.hpp.
References CBioSource_Base::m_Org.
Referenced by CUnculTaxTool::AddBioSource(), AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), CCleanup::AddPartialToProteinTitle(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CBioSource::AllowMatingTypeQualifier(), CBioSource::AllowSexQualifier(), CCleanup::AreBioSourcesMergeable(), CBioSource::AutoFix(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BioSourceEC(), CNewCleanup_imp::BiosourceFeatBC(), CheckMetagenome(), CValidError_bioseq::CheckSourceDescriptor(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CompareDescrFeatSources(), CSourceFeatureItem::CSourceFeatureItem(), CStrainRequest::ExploreStrainsByTaxname(), CBioSource::FixEnvironmentalSample(), FixHumanHost(), fta_fix_orgref_div(), fta_get_gcode_from_biosource(), IEditingAction::GetActionCommand(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), GetBiosourceDifferences(), CLowerQuals::GetCommand(), CBioSource::GetDisableStrainForwarding(), CAutoDefWithTaxonomy::GetDocsumOrgDescription(), GetEmblDescr(), GetGBBlock(), GetGenBankDescr(), GetGeneticCodeForBioseq(), CBioSource::GetNameValPairs(), GetSeqTableFromSeqEntry(), GetSourceFields(), GetSprotDescr(), CCommentItem::GetStringForTLS(), CCommentItem::GetStringForTSA(), CCommentItem::GetStringForWGS(), CBioseq::GetTaxId(), GetTextObjectDescription(), CDiscrepancyObject::GetTextObjectDescription(), CSrcTableOrgModColumn::GetValsFromBioSource(), CTaxnameQual::GetValue(), COrgModQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), IsMissingRequiredClone(), CBioSource::IsSetCommon(), CBioSource::IsSetDivision(), CBioSource::IsSetGcode(), CBioSource::IsSetLineage(), CBioSource::IsSetMgcode(), CBioSource::IsSetOrgMod(), CBioSource::IsSetOrgname(), CBioSource::IsSetPgcode(), CBioSource::IsSetTaxname(), CEditingActionBiosourceTaxname::IsSetValue(), CEditingActionBiosourceTaxnameAfterBinomial::IsSetValue(), CEditingActionBiosourceCommonName::IsSetValue(), CEditingActionBiosourceDivision::IsSetValue(), CEditingActionBiosourceLineage::IsSetValue(), CValidError_imp::IsSyntheticConstruct(), CNewCleanup_imp::IsSyntheticConstruct(), CBioSource::IsViral(), LoadFeat(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MakeIRDFeatsFromSourceXrefs(), MakeMailReportPostReport(), MakeMailReportPreReport(), CCleanup::MakeSmallGenomeSet(), CEditingActionBiosourceDbxref::Modify(), CSrcModListPanel::PopulateModifiers(), PropagateSuppliedLineage(), RemoveDbxref(), CBioSource::RemoveLineageSourceNotes(), RemoveMod(), CBioSource::RemoveNullTerms(), CBioSource::RemoveOrgMod(), RemoveStrain(), RemoveTaxId(), CBioSource::RemoveUnexpectedViralQualifiers(), CFindASN1Dlg::ReplaceInBiosource(), s_DuplicatesBiosource(), s_GetBioSourceContentLabel(), s_GetDiv(), s_GetInstCodeFromBioSource(), s_GetSpecificHostFromBioSource(), s_GetStrictGenCode(), CMacroFunction_MakeBoldXrefs::s_HasBarcodeDbXref(), CGenusSpeciesFixup::s_HasTaxId(), CUnculturedTool::s_HasTaxId(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict(), s_IsEmptyBioSource(), CMacroFunction_RemoveQual::s_RemoveFields(), s_SuppressMultipleEquivBioSources(), SeqEntryCheckTaxonDiv(), SetCultureCollectionFromStrain(), CBioSource::SetDisableStrainForwarding(), SetOrgMod(), CCleanup::TaxonomyLookup(), CMacroFunction_SwapQual::TheFunction(), UpdateBiosourceFromBiosample(), CTaxonomyUpdater::UpdateOrgFromTaxon(), CValidError_imp::Validate(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureItem::x_AddFTableBiosrcQuals(), CAutoDefModifierCombo::x_AddHIVModifiers(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddOrgModString(), CSourceFeatureItem::x_AddQuals(), CAutoDefModifierCombo::x_AddRequiredSubSourceModifiers(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), CAutoDefModifierCombo::x_BioSourceHasOrgMod(), CNewCleanup_imp::x_CanRemoveGenbankBlockSource(), CNewCleanup_imp::x_ChangePopToPhy(), CFlatGatherer::x_CollectSourceDescriptors(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioSource(), CSourceFeatureItem::x_GatherInfo(), CKeywordsItem::x_GatherInfo(), CFlatGatherer::x_GatherSourceOrganism(), CAutoDef::x_GetFeatureClauses(), CDeflineGenerator::x_GetModifiers(), CAutoDefModifierCombo::x_HasTypeStrainComment(), CBioSource::x_RemoveNameElementDiffs(), CBioSource::x_ShouldIgnoreNoteForBiosample(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributeDbxref(), CGff3Writer::xAssignSourceAttributesOrgMod(), CGff3FlybaseWriter::xAssignTaxid(), CSrcWriter::xGatherDb(), CSrcWriter::xGatherDivision(), CSrcWriter::xGatherOrgCommon(), CSrcWriter::xGatherOrgnameLineage(), CSrcWriter::xGatherTaxonId(), XMLGetDescr(), XMLGetGBBlock(), and CGff3Writer::xWriteSequenceHeader().
◆ IsSetOrigin() bool CBioSource_Base::IsSetOrigin ( void ) const inlineCheck if a value has been assigned to Origin data member.
Data member Origin is optional with default eOrigin_unknown; its type is defined as 'typedef int TOrigin'
Definition at line 447 of file BioSource_.hpp.
References CBioSource_Base::m_set_State.
Referenced by CSrcTableOriginColumn::AddToBioSource(), GetBiosourceDifferences(), GetDescrEmblBlock(), CSrcTableOriginColumn::GetFromBioSource(), GetGBBlock(), CValidError_imp::IsArtificial(), CEditingActionBiosourceOrigin::IsSetValue(), CNewCleanup_imp::IsSyntheticConstruct(), CCleanup::MergeDupBioSources(), s_IsEmptyBioSource(), CBioSource_Base::SetOrigin(), CValidError_bioseq::x_ValidateCompletness(), CSrcWriter::xGatherOrigin(), XMLGetEMBLBlock(), and XMLGetGBBlock().
◆ IsSetPcr_primers() bool CBioSource_Base::IsSetPcr_primers ( void ) const inlineCheck if a value has been assigned to Pcr_primers data member.
Data member Pcr_primers is optional; its type is defined as 'typedef CPCRReactionSet TPcr_primers'
Definition at line 576 of file BioSource_.hpp.
References CBioSource_Base::m_Pcr_primers.
Referenced by CBioSource_Base::CanGetPcr_primers(), CSrcTableAllPrimersColumn::ClearInBioSource(), GetSeqTableFromSeqEntry(), GetSourceFields(), CSrcTablePrimerColumn::GetValsFromBioSource(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), CValidError_imp::ValidateBioSource(), CSourceFeatureItem::x_AddPcrPrimersQuals(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), CDeflineGenerator::x_GetModifiers(), CSrcTablePrimerColumn::x_GetValues(), CSrcTablePrimerColumn::x_RemoveEmptyValues(), and CSrcWriter::xGatherPcrPrimers().
◆ IsSetReverse() bool CPCRReaction_Base::IsSetReverse ( void ) const inline ◆ IsSetSeq() bool CPCRPrimer_Base::IsSetSeq ( void ) const inline ◆ IsSetSubtype() [1/2] bool CBioSource_Base::IsSetSubtype ( void ) const inlineCheck if a value has been assigned to Subtype data member.
Data member Subtype is optional; its type is defined as 'typedef list< CRef< CSubSource > > TSubtype'
Definition at line 527 of file BioSource_.hpp.
References CBioSource_Base::m_set_State.
Referenced by AddBioSourceToAttributes(), CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), ChangeCountryColonToComma(), CCleanup::CleanupCollectionDates(), CUnculTaxTool::ConvertSpeciesSpecificNote(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), fta_sort_biosource(), g_FindSegs(), GetBiosourceDifferences(), GetDescrEmblBlock(), GetEmblGBBlock(), GetGBBlock(), GetSeqTableFromSeqEntry(), GetSourceFields(), CGuiObjectInfoComponent::GetToolTip(), CSrcTableSubSourceColumn::GetValsFromBioSource(), CSubSrcQual::GetValue(), HasAmplifiedWithSpeciesSpecificPrimerNote(), CBioSource::HasSubtype(), IsMissingRequiredClone(), IsSegmentSubtype(), CUnculTaxTool::IsSpeciesSpecific(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), RemoveCountryColon(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CFindASN1Dlg::ReplaceInBiosource(), s_GetContentLabel(), s_GetSourceSubtype(), s_HasSubSourceNote(), s_IsEmptyBioSource(), s_ResetModSubsrcQuals(), s_SubSourceListUniqued(), s_TitleFromSegment(), SetChromosome(), SetSubSource(), SetTransgenic(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CAutoDefModifierCombo::x_AddMinicircle(), CAutoDefModifierCombo::x_AddSubsourceString(), CAppendModToOrg::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), CAutoDefModifierCombo::x_BioSourceHasSubSrc(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CBioSource::x_ClearCoordinatedBioSampleSubSources(), CUnculturedTool::x_ConvertNote(), CDeflineGenerator::x_GetModifiers(), CBioSource::x_GetSubtypeNameValPairs(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CSubmissionWizard::x_TransferImportedSubSources(), CValidError_bioseq::x_ValidateSourceFeatures(), CGff3Writer::xAssignSourceAttributesSubSource(), CSrcWriter::xGatherSubtypeFeat(), and XMLGetGBBlock().
◆ IsSetSubtype() [2/2] bool CSubSource_Base::IsSetSubtype ( void ) const inlineCheck if a value has been assigned to Subtype data member.
Data member Subtype is mandatory; its type is defined as 'typedef int TSubtype'
Definition at line 291 of file SubSource_.hpp.
References CSubSource_Base::m_set_State.
Referenced by CSubSource::AutoFix(), CSubSource_Base::CanGetSubtype(), CSubSource::FixCapitalization(), CWriteUtil::GetSubSourceSubType(), CGuiObjectInfoComponent::GetToolTip(), IsSameSubtype(), CBioSource::RemoveLineageSourceNotes(), s_SameSubtype(), s_SameSubtypeC(), CSubSource_Base::SetSubtype(), CValidError_imp::ValidateSubSource(), CDeflineGenerator::x_GetModifiers(), and CNewCleanup_imp::x_SubSourceBC().
◆ operator const Tdata &() [1/2] ◆ operator const Tdata &() [2/2] ◆ operator Tdata &() [1/2] ◆ operator Tdata &() [2/2] ◆ operator<<() [1/2] ◆ operator<<() [2/2] ◆ operator=() [1/10] ◆ operator=() [2/10] ◆ operator=() [3/10] ◆ operator=() [4/10] ◆ operator=() [5/10] ◆ operator=() [6/10] ◆ operator=() [7/10] ◆ operator=() [8/10] ◆ operator=() [9/10] ◆ operator=() [10/10] ◆ operator>>() [1/2] ◆ operator>>() [2/2] ◆ Reset() [1/6] void CBioSource_Base::Reset ( void ) virtual ◆ Reset() [2/6] void CPCRPrimer_Base::Reset ( void ) virtual ◆ Reset() [3/6] void CPCRPrimerSet_Base::Reset ( void ) ◆ Reset() [4/6] void CPCRReaction_Base::Reset ( void ) virtual ◆ Reset() [5/6] void CPCRReactionSet_Base::Reset ( void ) ◆ Reset() [6/6] void CSubSource_Base::Reset ( void ) virtual ◆ ResetAttrib() void CSubSource_Base::ResetAttrib ( void ) ◆ ResetForward() void CPCRReaction_Base::ResetForward ( void ) ◆ ResetGenome() void CBioSource_Base::ResetGenome ( void ) inline ◆ ResetIs_focus() void CBioSource_Base::ResetIs_focus ( void ) inline ◆ ResetName() [1/2] void CPCRPrimer_Base::ResetName ( void ) ◆ ResetName() [2/2] ◆ ResetOrg() ◆ ResetOrigin() void CBioSource_Base::ResetOrigin ( void ) inline ◆ ResetPcr_primers() void CBioSource_Base::ResetPcr_primers ( void ) ◆ ResetReverse() void CPCRReaction_Base::ResetReverse ( void ) ◆ ResetSeq() void CPCRPrimer_Base::ResetSeq ( void ) ◆ ResetSubtype() [1/2] void CBioSource_Base::ResetSubtype ( void )Reset Subtype data member.
Definition at line 113 of file BioSource_.cpp.
References CBioSource_Base::m_set_State, and CBioSource_Base::m_Subtype.
Referenced by CBioSource::AutoFix(), BOOST_AUTO_TEST_CASE(), CheckPlasmid(), CBioSource::FixSexMatingTypeInconsistencies(), CSrcModListPanel::PopulateModifiers(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CBioSource_Base::Reset(), s_ResetModSubsrcQuals(), CUnculturedTool::x_ConvertNote(), and CCulturedTool::x_RemoveIfFoundSubSourceNote().
◆ ResetSubtype() [2/2] void CSubSource_Base::ResetSubtype ( void ) inline ◆ Set() [1/2] ◆ Set() [2/2] ◆ SetAttrib() [1/3] ◆ SetAttrib() [2/3] ◆ SetAttrib() [3/3] ◆ SetDefaultGenome() void CBioSource_Base::SetDefaultGenome ( void ) inline ◆ SetDefaultOrigin() void CBioSource_Base::SetDefaultOrigin ( void ) inline ◆ SetForward() [1/2] ◆ SetForward() [2/2] ◆ SetGenome() [1/2]Assign a value to Genome data member.
Definition at line 428 of file BioSource_.hpp.
References CBioSource_Base::m_Genome, CBioSource_Base::m_set_State, and rapidjson::value.
Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BioSourceFromImpFeat(), BOOST_AUTO_TEST_CASE(), CheckBioProjectLocationVals(), GetGenomeInfo(), GetSprotDescr(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceLocation::SetValue(), UpdateRawBioSource(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), and CNewCleanup_imp::x_PostBiosource().
◆ SetGenome() [2/2] ◆ SetIs_focus() void CBioSource_Base::SetIs_focus ( void ) inline ◆ SetName() [1/5] void CPCRPrimer_Base::SetName ( const TName & value ) inline ◆ SetName() [2/5] void CSubSource_Base::SetName ( const TName & value ) inlineAssign a value to Name data member.
Definition at line 359 of file SubSource_.hpp.
References CSubSource_Base::m_Name, CSubSource_Base::m_set_State, and rapidjson::value.
Referenced by AddGoodSource(), CSetTransgSrcDesc::apply_to(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), ChangeCountryColonToComma(), CheckMetagenome(), FTASubSourceAdd(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), RemoveCountryColon(), CAgpconvertApplication::Run(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), SetSubSource(), SetSubsource(), CEditingActionBiosourceSubSource::SetValue(), CEditingActionBiosourceAllNotes::SetValue(), CBioSource::UpdateWithBioSample(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CGff2Record::xMigrateAttributes(), and CGff2Record::xMigrateAttributesSubSource().
◆ SetName() [3/5] ◆ SetName() [4/5] ◆ SetName() [5/5] ◆ SetOrg() [1/2]Assign a value to Org data member.
Definition at line 108 of file BioSource_.cpp.
References CBioSource_Base::m_Org, and rapidjson::value.
Referenced by AddGoodSource(), AddOrgmodDescriptor(), AddSource(), AddStrainDescriptor(), AddStrainDescriptorNew(), CSrcTableDbxrefColumn::AddToBioSource(), CSrcTaxnameAfterBinomialColumn::AddToBioSource(), CSrcStructuredVoucherPartColumn::AddToBioSource(), CApplyFBOL::apply(), COrgGeneralPanel::ApplyCommand(), CBarcodeTool::ApplyDbxrefs(), ApplySrcTableToSeqEntry(), CProSplign::AssignGeneticCode(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CNewCleanup_imp::BiosourceBC(), CNewCleanup_imp::BioSourceEC(), CNewCleanup_imp::BiosourceFeatBC(), BioSourceFromImpFeat(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGoodSegSet(), CachedTaxonomyLookupCommand(), CheckQualsInSourceFeat(), CheckViruses(), CSrcTaxnameAfterBinomialColumn::ClearInBioSource(), CSrcStructuredVoucherPartColumn::ClearInBioSource(), CUnculturedTool::CorrectBioSource(), CCulturedTool::CorrectBioSource(), FakeEmblBioSources(), FakeGenBankBioSources(), fta_sort_biosource(), CUnculTaxTool::GetCommandFromValuesTable(), GetEmblDescr(), GetGenBankDescr(), GetSprotDescr(), CBioSource::MakeCommon(), MakeCommonBioSource(), CCleanup::MergeDupBioSources(), CEditingActionBiosourceDbxref::Modify(), CRemoveDbXrefsBioSource::ModifyBioSource(), CRemoveTaxonBioSource::ModifyBioSource(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), RemoveDbxref(), RemoveMod(), RemoveTaxId(), CFindASN1Dlg::ReplaceInBiosource(), CEditingActionBiosourceTaxname::ResetValue(), CEditingActionBiosourceTaxnameAfterBinomial::ResetValue(), CEditingActionBiosourceCommonName::ResetValue(), CEditingActionBiosourceDivision::ResetValue(), CEditingActionBiosourceLineage::ResetValue(), CMacroFunction_AddorSetContElement::s_AddSrcOrgMod(), CMacroFunction_RemoveQual::s_RemoveFields(), s_ResetModSubsrcQuals(), s_SetBioSourceField(), SetCultureCollectionFromStrain(), SetDbxref(), SetOrgMod(), CDescrCache::SetOrgMods(), CEditingActionBiosourceTaxname::SetValue(), CEditingActionBiosourceTaxnameAfterBinomial::SetValue(), CEditingActionBiosourceCommonName::SetValue(), CEditingActionBiosourceDivision::SetValue(), CEditingActionBiosourceLineage::SetValue(), CEditingActionBiosourceOrgMod::SetValue(), CEditingActionBiosourceStructuredVoucher::SetValue(), CEditingActionBiosourceDbxref::SetValue(), SpecificHostCleanupCommand(), CCleanup::TaxonomyLookup(), TaxonomyLookupCommand(), CMacroFunction_SwapQual::TheFunction(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), CMacroFunction_MakeBoldXrefs::TheFunction(), UpdateBiosourceFromBiosample(), CTaxonomyUpdater::UpdateOrgFromTaxon(), UpdateRawBioSource(), CSrcDescEditorPanel::UpdateSeqdesc(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CStrainSerotypeInfluenza::x_AddToInfluenzaNames(), COrgGeneralPanel::x_ApplyChangesToSource(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CAppendModToOrg::x_ApplyToBioSource(), CApplyGCode::x_ApplyToBioSource(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), CFlatGatherer::x_CollectBioSources(), CNewCleanup_imp::x_CopyGBBlockDivToOrgnameDiv(), CAutogeneratedExtendedCleanup::x_ExtendedCleanupBioSource(), CStrainSerotypeInfluenza::x_FixupOrganismNames(), CFlatGatherer::x_GatherSourceOrganism(), CAgpconvertApplication::x_HandleTaxArgs(), CNewCleanup_imp::x_MoveSeqdescOrgToSourceOrg(), CCulturedTool::x_RemoveIfFoundOrgModNote(), CNewCleanup_imp::x_RemovePopPhyBioSource(), CStrainSerotypeInfluenza::x_SplittingQualifiersAtCommas(), CStrainSerotypeInfluenza::x_SplittingStructCollections(), CStrainSerotypeInfluenza::x_TrimmingOrganismNames(), CStrainSerotypeInfluenza::x_UpdateStrainSerotype(), XMLFakeBioSources(), and XMLGetDescr().
◆ SetOrg() [2/2] ◆ SetOrigin() [1/2] ◆ SetOrigin() [2/2] ◆ SetPcr_primers() [1/2]Assign a value to Pcr_primers data member.
Definition at line 124 of file BioSource_.cpp.
References CBioSource_Base::m_Pcr_primers, and rapidjson::value.
Referenced by CSrcTablePrimerColumn::AddToBioSource(), BOOST_AUTO_TEST_CASE(), CBioSource::MakeCommonExceptOrg(), CEditingActionBiosourcePrimers::Modify(), s_ArePrimersUnique(), CDescrCache::SetPCR_primers(), CEditingActionBiosourcePrimers::SetValue(), CPCRPrimerTrimJunk::x_ApplyToBioSource(), CPCRPrimerFixI::x_ApplyToBioSource(), CSwapPrimerNameSeq::x_ApplyToBioSource(), CMergePrimerSets::x_ApplyToBioSource(), CSplitPrimerSets::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), and CSrcTablePrimerColumn::x_RemoveEmptyValues().
◆ SetPcr_primers() [2/2] ◆ SetReverse() [1/2] ◆ SetReverse() [2/2] ◆ SetSeq() [1/2] void CPCRPrimer_Base::SetSeq ( const TSeq & value ) inline ◆ SetSeq() [2/2] ◆ SetSubtype() [1/3]Assign a value to Subtype data member.
Definition at line 319 of file SubSource_.hpp.
References CSubSource_Base::m_set_State, CSubSource_Base::m_Subtype, and rapidjson::value.
Referenced by AddGoodSource(), CSetTransgSrcDesc::apply_to(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), CheckMetagenome(), FTASubSourceAdd(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), CAgpconvertApplication::Run(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), CEditingActionBiosourceSubSource::SetValue(), CBioSource::UpdateWithBioSample(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CSourceModParser::x_ApplyMods(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CGff2Record::xMigrateAttributes(), and CGff2Record::xMigrateAttributesSubSource().
◆ SetSubtype() [2/3]Assign a value to Subtype data member.
Definition at line 545 of file BioSource_.hpp.
References CBioSource_Base::m_set_State, and CBioSource_Base::m_Subtype.
Referenced by AddGoodSource(), CConvertFeatToDescSource::apply(), CSetTransgSrcDesc::apply_to(), CBioSource::AutoFix(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CCleanup::BioSrcFromFeat(), BOOST_AUTO_TEST_CASE(), BuildGoodSegSet(), CheckMetagenome(), CheckPlasmid(), CCleanup::CleanupCollectionDates(), CUnculTaxTool::ConvertSpeciesSpecificNote(), CBioSource::FixEnvironmentalSample(), CBioSource::FixSexMatingTypeInconsistencies(), fta_sort_biosource(), FTASubSourceAdd(), CBioSource::MakeCommonExceptOrg(), CCleanup::MergeDupBioSources(), CCompareWithBiosample::OnClickOk(), CSrcModListPanel::PopulateModifiers(), PopulatePcrPrimers(), CBioSource::RemoveCultureNotes(), CBioSource::RemoveLineageSourceNotes(), CBioSource::RemoveNullTerms(), CBioSource::RemoveSubSource(), CFindASN1Dlg::ReplaceInBiosource(), CAgpconvertApplication::Run(), CMacroFunction_FixFormat::s_AddAltitudeToSubSourceNote(), CUnculturedTool::s_AddEnvironmentalSample(), CMacroFunction_AddorSetContElement::s_AddSrcSubSource(), s_SetBioSourceField(), s_SubSourceListUniqued(), SetChromosome(), SetEnvSampleFixAmplifiedPrimers(), SetSubSource(), SetSubsource(), CDescrCache::SetSubtype(), SetTransgenic(), CEditingActionBiosourceSubSource::SetValue(), CNewCleanup_imp::SubSourceListBC(), UpdateBiosourceFromBiosample(), CBioSource::UpdateWithBioSample(), CNewCleanup_imp::x_AddEnvSamplOrMetagenomic(), CFeatureTableReader_Imp::x_AddQualifierToBioSrc(), CGenusSpeciesFixup::x_ApplyToBioSource(), CAutogeneratedCleanup::x_BasicCleanupBiosource(), CBioSource::x_ClearCoordinatedBioSampleSubSources(), CUnculturedTool::x_ConvertNote(), CCulturedTool::x_RemoveIfFoundSubSourceNote(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), and CSubmissionWizard::x_TransferImportedSubSources().
◆ SetSubtype() [3/3] ◆ ~CBioSource_Base() CBioSource_Base::~CBioSource_Base ( void ) virtualDefinition at line 172 of file BioSource_.cpp.
◆ ~CPCRPrimer() CPCRPrimer::~CPCRPrimer ( void )Definition at line 50 of file PCRPrimer.cpp.
◆ ~CPCRPrimer_Base() CPCRPrimer_Base::~CPCRPrimer_Base ( void ) virtualDefinition at line 86 of file PCRPrimer_.cpp.
◆ ~CPCRPrimerSet() ◆ ~CPCRPrimerSet_Base() CPCRPrimerSet_Base::~CPCRPrimerSet_Base ( void ) virtualDefinition at line 74 of file PCRPrimerSet_.cpp.
◆ ~CPCRReaction() ◆ ~CPCRReaction_Base() CPCRReaction_Base::~CPCRReaction_Base ( void ) virtualDefinition at line 109 of file PCRReaction_.cpp.
◆ ~CPCRReactionSet() ◆ ~CPCRReactionSet_Base() CPCRReactionSet_Base::~CPCRReactionSet_Base ( void ) virtualDefinition at line 74 of file PCRReactionSet_.cpp.
◆ ~CSubSource_Base() CSubSource_Base::~CSubSource_Base ( void ) virtualDefinition at line 140 of file SubSource_.cpp.
◆ m_Attrib string CSubSource_Base::m_Attrib private ◆ m_data [1/2] ◆ m_data [2/2] ◆ m_Forward ◆ m_Genome int CBioSource_Base::m_Genome private ◆ m_Name [1/2] ◆ m_Name [2/2] string CSubSource_Base::m_Name private ◆ m_Org ◆ m_Origin int CBioSource_Base::m_Origin private ◆ m_Pcr_primers ◆ m_Reverse ◆ m_Seq ◆ m_set_State [1/6] Uint4 CBioSource_Base::m_set_State[1] privateDefinition at line 379 of file BioSource_.hpp.
Referenced by CBioSource_Base::CBioSource_Base(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetIs_focus(), CBioSource_Base::IsSetOrigin(), CBioSource_Base::IsSetSubtype(), CBioSource_Base::ResetGenome(), CBioSource_Base::ResetIs_focus(), CBioSource_Base::ResetOrigin(), CBioSource_Base::ResetSubtype(), CBioSource_Base::SetGenome(), CBioSource_Base::SetIs_focus(), CBioSource_Base::SetOrigin(), and CBioSource_Base::SetSubtype().
◆ m_set_State [2/6] Uint4 CPCRPrimer_Base::m_set_State[1] private ◆ m_set_State [3/6] Uint4 CPCRPrimerSet_Base::m_set_State[1] private ◆ m_set_State [4/6] Uint4 CPCRReaction_Base::m_set_State[1] private ◆ m_set_State [5/6] Uint4 CPCRReactionSet_Base::m_set_State[1] private ◆ m_set_State [6/6] Uint4 CSubSource_Base::m_set_State[1] private ◆ m_Subtype [1/2] ◆ m_Subtype [2/2] int CSubSource_Base::m_Subtype privateRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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