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Code generated by DATATOOL from 'seqset.asn' (module 'NCBI-Seqset')

Choice variants.

No variant selected.

Definition at line 87 of file Seq_entry_.hpp.

Maximum+1 value of the choice variant enumerator.

== e_Set+1

Definition at line 93 of file Seq_entry_.hpp.

Definition at line 140 of file Bioseq_set_.hpp.

nuc acid and coded proteins

segmented sequence + parts

constructed sequence + parts

parts for 2 or 3

geninfo backbone

geninfo

converted genbank

converted pir

all the seqs from a single publication

a set of equivalent maps or seqs

converted SWISSPROT

a complete PDB entry

set of mutations

population study

phylogenetic study

ecological sample study

genomic products, chrom+mRNA+protein

whole genome shotgun project

named annotation set

with instantiated mRNA+protein

set from a single read

paired sequences within a read-set

viral segments or mitochondrial minicircles

Definition at line 97 of file Bioseq_set_.hpp.

Check if it is safe to call GetSeq_set method.

Returns

• true, if the data member is getatable.
• false, otherwise.

Definition at line 750 of file Bioseq_set_.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), FlattenBioseqSet(), get_parent_seqset(), CDiscrepancyContext::ParseObject(), CWithdrawSequences::PopulateSet(), CReorderSequencesDlg::PopulateSet(), CSegregateSetsBase::PopulateSet(), ReplaceWellknownSeqs(), CSegregateSetsBase::TakeFromSet(), CFlatGatherer::x_GatherCDSReferences(), CRemoteBlast::x_InitQueries(), and CExportStrategy::x_Process_Query().

Access to EClass's attributes (values, names) as defined in spec.

Get the Class member data.

Returns

Copy of the member data.

Definition at line 630 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Class.

Referenced by CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CSourceModParser::ApplyAllMods(), CTable2AsnContext::ApplyComments(), CTable2AsnContext::ApplyCreateUpdateDates(), seqsubmit_split::CSeqEntryHelper::BuildObject(), CConvertSetTypeDlg::ChangeNotify(), CValidError_bioseqset::CheckForInconsistentBiomols(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), sequpd::FixCollidingIDs_Bioseq(), CFlatFileGenerator::Generate(), CEditObjectSet::GetEditCommand(), CBioseq_set::GetGenomicFromGenProdSet(), CBioseq_setHandler::GetLabel(), CBioseq_set::GetLabel(), CBioseq_set::GetMasterFromSegSet(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CGuiObjectInfoBioseq_set::GetSubtype(), CDeflineProcess::IndexedProcess(), CValidError_imp::IsHugeSet(), CSegregateSetsBase::MoveDescrToEntries(), CBioseq_set::NeedsDocsumTitle(), seqsubmit_split::NeedToProcess(), CConvertSetTypeDlg::OnTreebookSelChanged(), CDiscrepancyContext::ParseObject(), CReorderSequencesDlg::ReadBioseq(), CRemoveSet::remove_sets_from_set(), CRemoveSet::RemoveOneSet(), RevComp(), s_CountTopSetSiblings(), s_GetBioseq_setContent(), s_GetBioseq_setType(), s_GetGenProdContent(), s_GetIdLabel(), s_GetNucProtContent(), s_GetSegsetContent(), s_GetSeqFromSet(), s_HasUnprocessedCdregions(), s_IsValidNPSubset(), s_SetDBLinkDesc(), sApplyDescriptors(), CNewCleanup_imp::SeqsetBC(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CBioseq_set_Info::sx_ShallowCopy(), CSegregateSetsBase::TakeFromSet(), TrimEntry(), CDeflineProcess::UnindexedProcess(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CNewCleanup_imp::x_ChangePopToPhy(), CTopLevelSeqEntryContext::x_InitSeqs(), CNewCleanup_imp::x_MovePopPhyMutPub(), CCleanupApp::x_ProcessHugeFileBlob(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), CFeatureTableReader::xCheckIfNeedConversion(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), and CFeatureTableReader::xParseCdregions().

Get the Descr member data.

Returns

Reference to the member data.

Definition at line 735 of file Bioseq_set_.hpp.

References CBioseq_set_Base::CanGetDescr(), CBioseq_set_Base::m_Descr, and CSerialObject::ThrowUnassigned().

Referenced by CDiscrepancyContext::AutofixBioseq_set(), BOOST_AUTO_TEST_CASE(), BuildProtBioseqSet(), CollectDescriptors(), CBlobSplitterImpl::CopySkeleton(), FixDupDates(), FixEmblUpdateDates(), GetDescrPointer(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::GetOrgName(), GetPDBBlockFromSeqEntry(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), MoveSourceDescrToTop(), CDiscrepancyContext::PopulateSeqSet(), CDUpdater::reformatBioseq(), CSequenceEditingEventHandler::SaveDescriptors(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CValidError_bioseqset::ShouldHaveNoDblink(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidateSetTitle(), CNewCleanup_imp::x_ClearEmptyDescr(), CNewCleanup_imp::x_CollapseSet(), CSeqMasterIndex::x_InitSeqs(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MoveNpDBlinks(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CValidError_bioseqset::x_ValidateSetDescriptors(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().

Get the variant data.

Returns

Reference to the data.

Definition at line 102 of file Seq_entry_.cpp.

References CSeq_entry_Base::CheckSelected(), CSeq_entry_Base::e_Seq, and CSeq_entry_Base::m_object.

Referenced by AddChromosomeNoLocation(), AddFeat(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CFeatureTableReader::AddProteins(), AddProtFeat(), AddToDeltaSeq(), CAlignmentAssistant::AdjustBioseq(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CClearKeywords::ApplyToCSeq_entry(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), BOOST_AUTO_TEST_CASE(), BuildGoodByteGraph(), CheckAdjustStart(), CheckAdjustStop(), CheckMiscPartialErrors(), CheckOneSpecificHost(), CollectDescriptors(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CMolInfoEditDlg::CreateNewMolInfo(), CGuiObjectInfoSeq_entry::CreateObject(), CCmdAddSeqEntry::Execute(), ExtractBioseq(), FindNucInSeqEntry(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), CDiscrepancyPanel::GetAccessionForObject(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), CSeq_entry::GetAnnot(), GetBioseqWithType(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), AlignmentCollection::GetDefline(), CSeq_entry::GetDescr(), GetDescrPointer(), GetGoodSeqEntryWithFeatureIds(), CSeq_entryHandler::GetLabel(), CSeq_entry::GetLabel(), CWGSDb_Impl::GetMasterDescrEntry(), CWGSDb_Impl::GetMasterGi(), CWithdrawSequences::GetNames(), GetNcbieaaString(), CFastaBioseqSource::GetNext(), CMaskFastaReader::GetNextSequence(), CBioseq_set::GetNucFromNucProtSet(), CDUpdater::GetOneBioseqFromSeqEntry(), GetPDBBlockFromSeqEntry(), CPssm::GetQueryLength(), CPssm::GetQuerySequenceData(), GetResidueAtPosition(), GetSeqLength(), GetSeqsStatus(), TaxTreeData::GetTaxIDForSequence(), HasRepairedIDs(), HasSeqIdOfType(), CViewGraphic::InitView(), CVcfTableView::InitView(), CDiscrepancyPanel::InvalidObject(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CReadBlastApp::less_seq(), CFastaObjectLoader::LoadFromStream(), CTblastnNode::Main(), MakeEntryForDeltaConversion(), CSequesterSets::OnAccept(), CEditSequence::OnAccept(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CTbl2AsnApp::ProcessHugeFile(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CFastaReaderEx::ReadDeltaFasta(), ReplaceWellknownSeqs(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CLocalFinderApp::Run(), CWinMaskDemoApplication::Run(), CAgpconvertApplication::Run(), CVDBTblastnApp::Run(), s_AddCDS(), s_AddSeqDataToPssm(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CreateQueryMap(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_ReadAndTestQueryFromString_CFastaReader(), s_RemoveAnnotsFromEntry(), PssmScorer::score(), SetCompleteness(), CNewCleanup_imp::SetGlobalFlags(), CValidErrorSuppress::SetSuppressedCodes(), ShowOrgRef(), CSegregateSetsBase::TakeFromSet(), TestCds(), TestCdsFromLastBioseq(), TestCdsFromLastBioseqOutsideAlign(), TestCdsFromLastBioseqWithCodeBreak(), TestCdsWithCodeBreak(), TestCircularTopology(), TestDoNotExtendOverGap(), TestDoNotFuseAbuttingIntervals(), TestExtendOverGap(), TestFuseAbuttingIntervals(), TestOneGapSeq(), TestOrderedLoc(), TestPartialWhenCutLastInterval(), TestPartialWhenCutLastIntervalDoNotExtend(), TestPartialWhenCutStart(), TestPartialWhenCutStartDoNotExtend(), TestPartialWhenCutStop(), TestPartialWhenCutStopDoNotExtend(), TestPointLocInside(), TestPointLocOutside(), TestTrnaAnticodon(), TestTrnaAnticodonFromLastBioseq(), TestTwoIntCdsFromLastBioseqOutsideAlign(), TestTwoIntCdsOnMinusStrand(), TestUTRPair(), TrimEntry(), SequenceSet::UnpackSeqEntry(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_imp::ValidateBioSource(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CConversionApp::Write(), CFastaOstream::Write(), CSequenceUpdater::x_AdjustProteinFeature(), CCountryFixup::x_ApplyToDescriptors(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CBlastFastaInputSource::x_FastaToSeqLoc(), CAsnCacheTestApplication::x_FindAnnotated(), CSraInputSource::x_GetNextSeq_loc(), x_InferenceInSeqs(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CBamRefSeqInfo::x_LoadRangesCov(), CMakeProfileDBApp::x_MakeVol(), CBioseq_Info::x_ParentAttach(), CLDS2_Manager::x_ParseFile(), CPrimeCacheApplication::x_Process_Fasta(), CSplignApp::x_ReadFastaSetId(), CASN1InputSourceOMF::x_ReadOneSeq(), CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs(), CNgAlignApp::x_RecurseSeqEntry(), CTblastnApp::x_RunMTBySplitDB(), CAgpConverter::x_SetChromosomeNameInSourceSubtype(), CCDSTranslationPanel::x_SetProtein(), CPrimeCacheApplication::x_StripSeqEntry(), CMakeProfileDBApp::x_UpdateCobalt(), CSequenceUpdater::x_UpdateProteinID(), CAgpConverter::x_VerifyComponents(), CFeatureTableReader::xAddProteinToSeqEntry(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xMergeCDSFeatures_impl().

Get the Seq_set member data.

Returns

Reference to the member data.

Definition at line 756 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Seq_set.

Referenced by CFeatureTableReader::AddProteins(), CDiscrepancyContext::AutofixBioseq_set(), BioseqSetDescriptorPropagateUp(), CSequesterSets::BioseqSetDescriptorPropagateUp(), BOOST_AUTO_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGoodEcoSetWithAlign(), CConvertSetTypeDlg::ChangeNotify(), Check3Extend(), Check5Extend(), CValidError_bioseqset::CheckForImproperlyNestedSets(), CollectDescriptors(), CCdCore::CopyBioseqForSeqId(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), DeleteProteinAndRenormalizeNucProtSet(), CCdCore::EraseSequences(), CCmdInsertBioseqSet::Execute(), ExtractBioseq(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), FlattenBioseqSet(), CScore_CdsInternalStops::Get(), CDUpdater::GetAllIdsFromSeqEntry(), CCdCore::GetBioseqWithSeqId(), CCdCore::GetDefline(), CBioseq_set::GetGenomicFromGenProdSet(), CCdCore::GetGIFromSequenceList(), CBioseq_set::GetLabel(), CBioseq_set::GetMasterFromSegSet(), CCdCore::GetMmdbId(), CBlastInputOMF::GetNextSeqBatch(), CBioseq_set::GetNucFromNucProtSet(), CBlast4_queries::GetNumQueries(), CFastaIOWrapper::GetNumRead(), CDUpdater::GetOneBioseqFromSeqEntry(), GetPDBBlockFromSeqEntry(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CCdCore::GetSeqEntryForIndex(), CCdCore::GetSeqEntryForRow(), CCdCore::GetSeqIDForIndex(), CCdCore::GetSeqIDs(), CCdCore::GetSeqIndex(), GetSourceDescriptors(), CSraRun::GetSpotEntry(), HasRepairedIDs(), HasSeqIdOfType(), CValidError_bioseqset::IsCDSProductInGPS(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CMagicBlastThread::Main(), SBlobInserter::operator()(), CDiscrepancyContext::ParseObject(), CReorderSequencesDlg::PopulateSet(), CTabularFormatter_StopCodonChanges::Print(), CBiosampleChkApp::ProcessSet(), CTLSHandler::ProcessSet(), PropagateDescriptor(), CConversionApp::Read(), CFastaReader::ReadAlignedSet(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CCleanup::RenormalizeNucProtSets(), RevComp(), s_BuildBadEcNumberEntry(), s_CollectSeqIds(), s_CountTopSetSiblings(), s_CreateQueryMap(), s_DescriptorPropagateDown(), s_GetBioseq_setContent(), s_GetIdLabel(), s_GetJustNucSeqEntry(), s_GetSeqFromSet(), s_GetSourceDescriptors(), s_HasTopSetSiblings(), s_ImportQueries(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_ScanWhilePossibleNPSet(), CAgpConverter::SetComponentsBioseqSet(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), TestCollidingAccessionFixes(), TestFeatInsideGap(), CSplitCacheApp::TestSplitBioseq(), TrimEntry(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CCmdInsertBioseqSet::Unexecute(), SequenceSet::UnpackSeqSet(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseqset::ValidateSetElements(), CFastaOstream::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_CollapseSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CFlatGatherer::x_GatherCDSReferences(), x_InferenceInSeqs(), CRemoteBlast::x_InitQueries(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), x_IsEmptyCDD(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MovePopPhyMutPub(), CExportStrategy::x_Process_Query(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveNestedGenBankSet(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CPrimeCacheApplication::x_StripSeqEntry(), CCmdInsertBioseqSet::x_TransferSeqSet(), CFormatGuessEx::x_TryFasta(), and CMultiReader::xApplyTemplate().

Get the variant data.

Returns

Reference to the data.

Definition at line 124 of file Seq_entry_.cpp.

References CSeq_entry_Base::CheckSelected(), CSeq_entry_Base::e_Set, and CSeq_entry_Base::m_object.

Referenced by CAddStructuredCommentKeyword::add_to_existing_genbank(), CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CFeatureTableReader::AddProteins(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CTable2AsnContext::ApplyCreateUpdateDates(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), CClearKeywords::ApplyToCSeq_entry(), CRemoveBankitComment::ApplyToCSeq_entry(), CRemoveGenomeProjectsDB::ApplyToCSeq_entry(), CRemoveStructuredComment::ApplyToCSeq_entry(), CRemoveSeqAnnot::ApplyToCSeq_entry(), CConvertComment::ApplyToCSeq_entry(), CModifyStructuredComment::ApplyToCSeq_entry(), CRemoveUnverified::ApplyToCSeq_entry(), CRemoveStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), CAttachedHandles::Attach(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), CMacroBioData_SeqSetIter::BuildEditedObject(), BuildGoodEcoSetWithAlign(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildSetAlign(), BuildSetDendiagAlign(), Check3Extend(), Check5Extend(), CollectDescriptors(), Convert_Seq_entry_Bioseq_set(), Convert_Seq_id_Bioseq_set(), CFeatureTableReader::ConvertNucSetToSet(), CSequenceEditingEventHandler::ConvertSetType(), CCdCore::CopyBioseqForSeqId(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CreateEditorForObject(), CGuiObjectInfoSeq_entry::CreateObject(), CCdCore::EraseSequences(), CStrainRequest::ExploreStrainsByTaxname(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), ExtractBioseq(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), sequpd::FixCollidingIDs_Bioseq(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), CValidError_imp::GatherTentativeName(), get_parent_seqset(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), CValidError_imp::GetAncestor(), CSeq_entry::GetAnnot(), CCdCore::GetBioseqWithSeqId(), CCdCore::GetDefline(), CExportTableDlg::GetDesc(), CUnculTaxTool::GetDesc(), CAddFluComments::GetDesc(), CSeq_entry::GetDescr(), GetDescrPointer(), CCdCore::GetGIFromSequenceList(), CSeq_entryHandler::GetLabel(), CSeq_entry::GetLabel(), CCdCore::GetMmdbId(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CFastaIOWrapper::GetNumRead(), CDUpdater::GetOneBioseqFromSeqEntry(), CTable2AsnContext::GetOrgName(), CBioseq::GetParentSet(), CBioseq_set::GetParentSet(), GetPDBBlockFromSeqEntry(), CMacroBioData_SeqSetIter::GetScopedObject(), CCdCore::GetSeqEntryForIndex(), CCdCore::GetSeqEntryForRow(), CCdCore::GetSeqIDForIndex(), CCdCore::GetSeqIDs(), CCdCore::GetSeqIndex(), GetSourceDescriptors(), HasRepairedIDs(), HasSeqIdOfType(), CBioseqEditor::IsEditable(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), seqsubmit_split::NeedToProcess(), CSequesterSets::OnAccept(), SBlobInserter::operator()(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CTbl2AsnApp::ProcessAlignmentFile(), CTbl2AsnApp::ProcessHugeFile(), CFastaReader::ReadAlignedSet(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CDUpdater::reformatBioseq(), CCleanup::RemoveNcbiCleanupObject(), RemoveTitlesSeqEntry(), RemoveUserObjectType(), CCleanup::RenormalizeNucProtSets(), RevComp(), CMacroBioData_SeqSetIter::RunDeleteCommand(), CMacroBioData_SeqSetIter::RunEditCommand(), s_BuildBadEcNumberEntry(), s_CollectCollidingIDs_Entry(), s_CollectPubDescriptorLabels(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSourceDescriptors(), s_HasUnprocessedCdregions(), s_IsHtgInSep(), s_RemoveAnnotsFromEntry(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), CNewCleanup_imp::SetGlobalFlags(), CValidErrorSuppress::SetSuppressedCodes(), ShowOrgRef(), sx_ComesBefore(), CSegregateSetsBase::TakeFromSet(), TestCollidingAccessionFixes(), TestFeatInsideGap(), CSplitCacheApp::TestSplitBioseq(), TrimEntry(), CCmdAddSeqEntry::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CDeflineProcess::UnindexedProcess(), SequenceSet::UnpackSeqEntry(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CConversionApp::Write(), CFastaOstream::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CAppendModToOrg::x_ApplyToDescriptors(), CApplyGCode::x_ApplyToDescriptors(), CCountryConflict::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToDescriptors(), CLatLonTool::x_ApplyToDescriptors(), IModifyBiosourceQuals::x_ApplyToDescriptors(), IPubDescEditor::x_ApplyToDescriptors(), IRemovePubs::x_ApplyToDescriptors(), CRemoveUnreviewed::x_ApplyToSeq_entry(), CRemoveDescDlg::x_ApplyToSeq_entry(), CStrainRequest::x_CollectStrainsForRecord(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CTaxValidationAndCleanup::x_GatherSources(), x_InferenceInSeqs(), CGC_Assembly_Parser::x_InitSeq_entry(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), x_IsEmptyCDD(), CAgpconvertApplication::x_LoadTemplate(), CBioseq_set_Info::x_ParentAttach(), CStrainSerotypeInfluenza::x_ParseDescriptors(), CCleanupApp::x_ProcessHugeFileBlob(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveDupBioSource(), CMacroBioData_SeqSetIter::x_SetDefaultObjectInfo(), CStrainSerotypeInfluenza::x_TestEntryForParsing(), CFormatGuessEx::x_TryFasta(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xCheckIfNeedConversion(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), and CTbl2AsnApp::xProcessOneFile().

Check if variant Seq is selected.

Seq type is defined as 'typedef CBioseq TSeq'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 257 of file Seq_entry_.hpp.

References CSeq_entry_Base::e_Seq, and CSeq_entry_Base::m_choice.

Referenced by CTbl2AsnApp::AddAnnots(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CFeatureTableReader::AddProteins(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), AddSource(), AddTitle(), AdjustProtFeatForNucProtSet(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CClearKeywords::ApplyToCSeq_entry(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), BOOST_AUTO_TEST_CASE(), ChangeId(), ClearFocus(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CopyBioseqWithType(), CopySeqIdsOfType(), CBlobSplitterImpl::CopySkeleton(), CMolInfoEditDlg::CreateNewMolInfo(), CGuiObjectInfoSeq_entry::CreateObject(), CCmdAddSeqEntry::Execute(), FetchSequenceViaHTTP(), FindNucInSeqEntry(), FlattenBioseqSet(), fta_get_user_object(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), get_parent_seqset(), CDiscrepancyPanel::GetAccessionForObject(), GetAccessionFromObjects(), CDUpdater::GetAllIdsFromSeqEntry(), GetBioseqWithType(), AlignmentCollection::GetDefline(), GetDescrPointer(), CWGSDb_Impl::GetMasterDescrEntry(), CWithdrawSequences::GetNames(), GetNcbieaaString(), CFastaBioseqSource::GetNext(), CMaskFastaReader::GetNextSequence(), CBioseq_set::GetNucFromNucProtSet(), CDUpdater::GetOneBioseqFromSeqEntry(), CTable2AsnContext::GetOrgName(), GetPDBBlockFromSeqEntry(), GetResidueAtPosition(), GetSeqsStatus(), TaxTreeData::GetTaxIDForSequence(), HasRepairedIDs(), HasSeqIdOfType(), IdFromEntry(), CViewGraphic::InitView(), CVcfTableView::InitView(), CDiscrepancyPanel::InvalidObject(), CViewGraphicFactory::IsCompatibleWith(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), CFastaObjectLoader::LoadFromStream(), CTblastnNode::Main(), CTable2AsnContext::MergeSeqDescr(), CTable2AsnContext::MergeWithTemplate(), MoveSourceDescrToTop(), seqsubmit_split::NeedToProcess(), CSequesterSets::OnAccept(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), SBlobInserter::operator()(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CPubmedUpdater::PostProcessPubs(), CTbl2AsnApp::ProcessHugeFile(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CFastaReaderEx::ReadDeltaFasta(), CBasicFastaWrapper::ReadFile(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CCachedSequence::RegisterIds(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), ResetOrgname(), RevComp(), CPsiBlastApp::Run(), CVDBTblastnApp::Run(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), s_FastaStringToBioseq(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_MoveProteinSpecificFeats(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), ScanFastaFile(), SeqEntryFromSeqSubmit(), SetChromosome(), SetCommon(), SetCompleteness(), SetDbxref(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), CNewCleanup_imp::SetGlobalFlags(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), CValidErrorSuppress::SetSuppressedCodes(), SetTaxname(), SetTaxon(), SetTransgenic(), ShowOrgRef(), SimplifySeqEntryForCD(), CSegregateSetsBase::TakeFromSet(), SequenceSet::UnpackSeqEntry(), UnpackSeqEntry(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_imp::ValidateBioSource(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CDescPlacementPanel::x_AddToStrings(), CCountryFixup::x_ApplyToDescriptors(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CSequenceUpdater::x_FixIDInNewEntry(), x_InferenceInSeqs(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CSplitDataLoader::x_LoadData(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MoveNpDBlinks(), CLDS2_Manager::x_ParseFile(), CSequenceUpdater::x_PrepareNewEntry(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemovePub(), CTblastnApp::x_RunMTBySplitDB(), CHugeFileDemoApp::x_ShowSeqSizes(), CPrimeCacheApplication::x_StripSeqEntry(), CMakeProfileDBApp::x_UpdateCobalt(), CCdregionValidator::x_ValidateTrans(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Check if variant Set is selected.

Set type is defined as 'typedef CBioseq_set TSet'.

Returns

• true, if the variant is selected.
• false, otherwise.

Definition at line 263 of file Seq_entry_.hpp.

References CSeq_entry_Base::e_Set, and CSeq_entry_Base::m_choice.

Referenced by CAddStructuredCommentKeyword::add_to_existing_genbank(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), CSetGlobalRefGeneStatus::ApplyToCSeq_entry(), CClearKeywords::ApplyToCSeq_entry(), CRemoveBankitComment::ApplyToCSeq_entry(), CRemoveGenomeProjectsDB::ApplyToCSeq_entry(), CRemoveStructuredComment::ApplyToCSeq_entry(), CRemoveSeqAnnot::ApplyToCSeq_entry(), CConvertComment::ApplyToCSeq_entry(), CModifyStructuredComment::ApplyToCSeq_entry(), CRemoveUnverified::ApplyToCSeq_entry(), CRemoveStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CMolInfoEditDlg::ApplyToInst(), CMolInfoEditDlg::ApplyToMolInfo(), CAttachedHandles::Attach(), BOOST_AUTO_TEST_CASE(), CMacroBioData_SeqSetIter::BuildEditedObject(), ChangeId(), ChangeNucId(), ChangeProtId(), ClearFocus(), CollectDescriptors(), Convert_Seq_entry_Bioseq_set(), Convert_Seq_id_Bioseq_set(), CFeatureTableReader::ConvertNucSetToSet(), CopyBioseqWithType(), CopySeqIdsOfType(), CreateEditorForObject(), CGuiObjectInfoSeq_entry::CreateObject(), CStrainRequest::ExploreStrainsByTaxname(), ExtractBioseq(), FetchSequenceViaHTTP(), CCdsToMatPeptide::FindAnnot(), FindCd(), FindNucInSeqEntry(), sequpd::FixCollidingIDs_Bioseq(), FlattenBioseqSet(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), CValidError_imp::GatherTentativeName(), CFlatFileGenerator::Generate(), get_parent_seqset(), GetAccessionFromObjects(), CValidError_imp::GetAncestor(), GetBioseqWithType(), CExportTableDlg::GetDesc(), CUnculTaxTool::GetDesc(), CAddFluComments::GetDesc(), CSeq_entryHandler::GetLabel(), CWithdrawSequences::GetNames(), CBioseq_set::GetNucFromNucProtSet(), CFastaIOWrapper::GetNumRead(), CTable2AsnContext::GetOrgName(), CBioseq::GetParentSet(), CBioseq_set::GetParentSet(), CMacroBioData_SeqSetIter::GetScopedObject(), GetSeqLength(), GetSourceDescriptors(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), HasRepairedIDs(), HasSeqIdOfType(), IdFromEntry(), CBioseqEditor::IsEditable(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CReadBlastApp::less_seq(), CTable2AsnContext::MergeWithTemplate(), CDUpdater::modifySeqAlignSeqEntry(), CFeatureTableReader::MoveRegionsToProteins(), CReadBlastApp::NormalizeSeqentry(), CDiscrepancyContext::ParseObject(), CValidError_imp::PostErr(), CForeignContaminationScreenReportReader::PostProcess(), CPubmedUpdater::PostProcessPubs(), CTbl2AsnApp::ProcessAlignmentFile(), CPhrapReader::Read(), CFastaReader::ReadAlignedSet(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CDUpdater::reformatBioseq(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CCdsToMatPeptide::RemoveProteins(), RemoveTitlesSeqEntry(), RemoveUserObjectType(), ResetOrgname(), RevComp(), CMacroBioData_SeqSetIter::RunDeleteCommand(), CMacroBioData_SeqSetIter::RunEditCommand(), s_CollectCollidingIDs_Entry(), s_CollectPubDescriptorLabels(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSourceDescriptors(), s_HasUnprocessedCdregions(), s_IsHtgInSep(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), SetChromosome(), SetCommon(), SetDbxref(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), CNewCleanup_imp::SetGlobalFlags(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), CValidErrorSuppress::SetSuppressedCodes(), SetTaxname(), SetTaxon(), SetTransgenic(), ShowOrgRef(), SimplifySeqEntryForCD(), SortSeqDescr(), CSegregateSetsBase::TakeFromSet(), TrimEntry(), CCmdAddSeqEntry::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CDeflineProcess::UnindexedProcess(), CValidError_imp::Validate(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CConversionApp::Write(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CDescPlacementPanel::x_AddToStrings(), CSequenceUpdater::x_AdjustProteinFeature(), CAppendModToOrg::x_ApplyToDescriptors(), CApplyGCode::x_ApplyToDescriptors(), CCountryConflict::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToDescriptors(), CLatLonTool::x_ApplyToDescriptors(), IModifyBiosourceQuals::x_ApplyToDescriptors(), IPubDescEditor::x_ApplyToDescriptors(), IRemovePubs::x_ApplyToDescriptors(), CRemoveUnreviewed::x_ApplyToSeq_entry(), CRemoveDescDlg::x_ApplyToSeq_entry(), CStrainRequest::x_CollectStrainsForRecord(), CDesktopDataBuilder::x_CreateSet(), CPrimeCacheApplication::x_ExtractAndIndex(), CSubmissionWizard::x_ExtractDescriptorsFromSeqEntry(), CRemoteBlast::x_ExtractQueryIds(), CAsnCacheTestApplication::x_FindAnnotated(), CTaxValidationAndCleanup::x_GatherSources(), SWGSCreateInfo::x_GetProtSet(), x_InferenceInSeqs(), CTopLevelSeqEntryContext::x_InitSeqs(), CSeqMasterIndex::x_InitSeqs(), CAgpconvertApplication::x_LoadTemplate(), CFeatTableViewFactory::x_NeedsConversion(), CViewGraphicFactory::x_NeedsConversion(), CBioseq_set_Info::x_ParentAttach(), CStrainSerotypeInfluenza::x_ParseDescriptors(), CCleanupApp::x_ProcessTraditionally(), CNgAlignApp::x_RecurseSeqEntry(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemovePub(), CMacroBioData_SeqSetIter::x_SetDefaultObjectInfo(), CPrimeCacheApplication::x_StripSeqEntry(), CStrainSerotypeInfluenza::x_TestEntryForParsing(), CFormatGuessEx::x_TryFasta(), CSequenceUpdater::x_UpdateProteinID(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xCheckIfNeedConversion(), CFeatureTableReader::xParseCdregions(), CTbl2AsnApp::xProcessOneFile(), seqsubmit_split::CSeqSubSplitter::xTryProcessSeqEntry(), CPubmedUpdater::xUpdatePubReferences(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Check if a value has been assigned to Annot data member.

Data member Annot is optional; its type is defined as 'typedef list< CRef< CSeq_annot > > TAnnot'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 769 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_set_State.

Referenced by AddFeat(), CDiscrepancyContext::AutofixBioseq_set(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), ChangeId(), ChangeNucId(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), CDiscrepancyContext::PopulateSeqSet(), CReadBlastApp::RemoveProblems(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateGenProdSet(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_CollapseSet(), CAsnCacheTestApplication::x_FindAnnotated(), x_InferenceInSeqs(), CSeqMasterIndex::x_InitSeqs(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), CBioseq_set_Info::x_SetObject(), CSplitDataLoader::x_SplitSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Check if a value has been assigned to Class data member.

Data member Class is optional with default eClass_not_set; its type is defined as 'typedef EClass TClass'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 605 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_set_State.

Referenced by CTbl2AsnApp::AddAnnots(), AddSeqdescToSeqEntryRecursively(), AddTitle(), CSourceModParser::ApplyAllMods(), CTable2AsnContext::ApplyComments(), CTable2AsnContext::ApplyCreateUpdateDates(), CValidError_bioseqset::CheckForInconsistentBiomols(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CBlobSplitterImpl::CopySkeleton(), CBioseq_set::GetLabel(), CDeflineProcess::IndexedProcess(), CValidError_imp::IsHugeSet(), CSegregateSetsBase::MoveDescrToEntries(), CBioseq_set::NeedsDocsumTitle(), seqsubmit_split::NeedToProcess(), CConvertSetTypeDlg::OnTreebookSelChanged(), CDiscrepancyContext::ParseObject(), CRemoveSet::remove_sets_from_set(), CRemoveSet::RemoveOneSet(), RevComp(), s_CountTopSetSiblings(), s_HasUnprocessedCdregions(), s_IsValidNPSubset(), sApplyDescriptors(), CNewCleanup_imp::SeqsetBC(), CBioseq_set_Base::SetClass(), CBioseq_set_Info::sx_ShallowCopy(), CDeflineProcess::UnindexedProcess(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CNewCleanup_imp::x_ChangePopToPhy(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), CFeatureTableReader::xCheckIfNeedConversion(), and CFeatureTableReader::xMergeCDSFeatures_impl().

Check if a value has been assigned to Descr data member.

Data member Descr is optional; its type is defined as 'typedef CSeq_descr TDescr'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 723 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Descr.

Referenced by CAutogeneratedCleanup::BasicCleanupBioseqSet(), CBioseq_set_Base::CanGetDescr(), CollectDescriptors(), CBlobSplitterImpl::CopySkeleton(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), fta_remove_cleanup_user_object(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::GetOrgName(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), CSequenceEditingEventHandler::SaveDescriptors(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CValidError_bioseqset::ShouldHaveNoDblink(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), TrimEntry(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidateSetTitle(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_ClearEmptyDescr(), CNewCleanup_imp::x_CollapseSet(), CSeqMasterIndex::x_InitSeqs(), CNewCleanup_imp::x_MoveNpDBlinks(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CSplitDataLoader::x_SplitSet(), CValidError_bioseqset::x_ValidateSetDescriptors(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().

Check if a value has been assigned to Seq_set data member.

Data member Seq_set is mandatory; its type is defined as 'typedef list< CRef< CSeq_entry > > TSeq_set'

Returns

• true, if a value has been assigned.
• false, otherwise.

Definition at line 744 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_set_State.

Referenced by CTbl2AsnApp::AddAnnots(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CFeatureTableReader::AddProteins(), AddSeqdescToSeqEntryRecursively(), subfuse::CSubmissionCollector::AdjustLocalIds(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), CConvertSetTypeDlg::ChangeNotify(), CValidError_bioseqset::CheckForImproperlyNestedSets(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), CBioseq_set::GetLabel(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), GetSourceDescriptors(), HasRepairedIDs(), CValidError_bioseqset::IsCDSProductInGPS(), CValidError_bioseq::IsWGS(), CValidError_bioseq::IsWGSMaster(), CMagicBlastThread::Main(), CBiosampleChkApp::ProcessSet(), CTLSHandler::ProcessSet(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), CCleanup::RenormalizeNucProtSets(), s_CollectCollidingIDs_Entry(), s_CollectSeqIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_CountTopSetSiblings(), s_DescriptorPropagateDown(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetJustNucSeqEntry(), s_GetSeqFromSet(), s_GetSourceDescriptors(), s_HasTopSetSiblings(), s_ScanWhilePossibleNPSet(), s_UpdateFeatureIds(), ShowOrgRef(), CBioseq_set_Info::sx_ShallowCopy(), CSplitCacheApp::TestSplitBioseq(), CCmdInsertBioseqSet::Unexecute(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidateSegSet(), CValidError_bioseqset::ValidateSetElements(), CNewCleanup_imp::x_AddNcbiCleanupObject(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_CollapseSet(), CCreateGeneModelTask::x_GetCommand(), CNewCleanup_imp::x_MovePopPhyMutPub(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemoveNestedGenBankSet(), CNewCleanup_imp::x_RemoveNestedNucProtSet(), CBioseq_set_Info::x_SetObject(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Reset Descr data member.

Definition at line 145 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Descr.

Referenced by BOOST_AUTO_TEST_CASE(), BuildProtBioseqSet(), CEditObjectSet::GetEditCommand(), CTable2AsnContext::MergeSeqDescr(), CRemoveSet::MoveDescrToEntries(), CSegregateSetsBase::MoveDescrToEntries(), CCleanup::RemoveNcbiCleanupObject(), CBioseq_set_Base::Reset(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CNewCleanup_imp::x_ClearEmptyDescr(), CSplitDataLoader::x_SplitSet(), and CPrimeCacheApplication::x_StripSeqEntry().

Select the requested variant if needed, allocating CObject variants from memory pool.

Assign a value to Annot data member.

Returns

Reference to the data value.

Definition at line 787 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Annot, and CBioseq_set_Base::m_set_State.

Referenced by CObjectManager::AcquireSharedSeq_annot(), AddFeat(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGoodEcoSetWithAlign(), BuildProtBioseqSet(), ChangeId(), ChangeNucId(), Check3Extend(), Check5Extend(), Check5Policy(), CheckPropagatedCDSLocation(), Convert_Seq_annot_Seq_entry(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAnnotationASN1::CImplementationData::DumpEvidence(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), GetCDSFromGoodNucProtSet(), CSNPDbSeqIterator::GetEntry(), GetGoodSeqEntryWithFeatureIds(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CBamRefSeqInfo::LoadMainEntry(), CCSRAFileInfo::LoadReadsBlob(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CFastaReaderEx::ReadAlignedSet(), CFastaReader::ReadAlignedSet(), CFeature_table_reader::ReadSequinFeatureTables(), CReadBlastApp::RemoveProblems(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), RevComp(), s_AddCDS(), s_UpdateFeatureIds(), TestFeatInsideGap(), TrimEntry(), TruncateTransSplicedCDSForExtension(), SWGSCreateInfo::x_AddFeaturesDirect(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), CPhrap_Contig::x_CreateAlignPairs(), CID2SNPProcessor_Impl::x_LoadBlob(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), CSplitDataLoader::x_SplitSet(), CFeatureTableReader::xParseCdregions(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Assign a value to Class data member.

Parameters

Definition at line 636 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Class, CBioseq_set_Base::m_set_State, and rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodGenProdSet(), BuildGoodSegSet(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildProtBioseqSet(), BuildSmallGenomeSet(), CConvertSetTypeDlg::ChangeNotify(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), CPhrap_Contig::CreateContig(), CCmdInsertBioseqSet::Execute(), CEditObjectSet::GetEditCommand(), CSraRun::GetSpotEntry(), MakeBioseqSet(), CInfluenzaSet::MakeSet(), s_MakeGroupsForUniqueValues(), SeqEntryFromSeqSubmit(), CNewCleanup_imp::SeqsetBC(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), TrimEntry(), CNewCleanup_imp::x_ChangePopToPhy(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), SWGSCreateInfo::x_GetProtSet(), CGC_Assembly_Parser::x_InitSeq_entry(), CCleanupApp::x_ProcessHugeFileBlob(), CFeatureTableReader::xConvertSeqIntoSeqSet(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().

Assign a value to Descr data member.

Parameters

value Reference to value.

Definition at line 150 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Descr, and rapidjson::value.

Referenced by AddGoodPub(), AddGoodSource(), AddRefGeneTrackingUserObject(), AddSource(), AddTitle(), CSegregateSetsBase::AddUserObject(), CTable2AsnContext::ApplyComments(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BuildGoodEcoSet(), BuildProtBioseqSet(), ClearFocus(), CBlobSplitterImpl::CopySkeleton(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FixDupDates(), FixEmblUpdateDates(), fta_get_user_object(), fta_remove_cleanup_user_object(), CEditObjectSet::GetEditCommand(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), RemoveDbxref(), ResetOrgname(), sApplyDescriptors(), SetChromosome(), SetCommon(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), SetSubSource(), SetTaxname(), SetTaxon(), SetTransgenic(), TrimEntry(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CPhrapReader::x_CreateDesc(), CNewCleanup_imp::x_MoveNpPub(), CNewCleanup_imp::x_MovePopPhyMutPub(), CGFFReader::x_ParseDateComment(), CSplitDataLoader::x_SplitSet(), and seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry().

Assign a value to Id data member.

Parameters

value Reference to value.

Definition at line 93 of file Bioseq_set_.cpp.

References CBioseq_set_Base::m_Id, and rapidjson::value.

Referenced by CBlobSplitterImpl::CopySkeleton(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), TrimEntry(), SWGSCreateInfo::x_GetProtSet(), CID2SNPProcessor_Impl::x_LoadBlob(), and CSplitDataLoader::x_SplitSet().

Select the variant.

Returns

Reference to the variant data.

Definition at line 108 of file Seq_entry_.cpp.

References CSeq_entry_Base::e_Seq, eDoNotResetVariant, CSeq_entry_Base::m_object, and CSeq_entry_Base::Select().

Referenced by CObjectManager::AcquireSharedBioseq(), CTbl2AsnApp::AddAnnots(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGenbankKeyword(), AddGoodImpFeat(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CObjectLoadingTask::AddObjects(), CGBProjectHelper::AddProjectItemsFromRID(), CCleanup::AddProtein(), AddProtRefSeqEntry(), AddRefGeneTrackingUserObject(), AddSentinelRNASeq(), AddSeqdescToSeqEntryRecursively(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), AddToDeltaSeq(), AddTpaAssemblyUserObject(), AdjustProtFeatForNucProtSet(), AgpRead(), CForeignContaminationScreenReportReader::AnnotateOrRemove(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), CDUpdater::blast(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildBigGoodNucProtSet(), BuildGapFuzz100DeltaSeq(), BuildGenProdSetWithBigProduct(), BuildGoodDeltaSeq(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), BuildGoodProtSeq(), BuildGoodSegSet(), BuildGoodSeq(), BuildGoodSpliceNucProtSet(), BuildNucProtSet(), BuildSegSetPart(), BuildSequence(), ChangeGoodNucProtSetIdToGenbankName(), ChangeId(), ChangeNucId(), ChangeNucProtSetNucId(), ChangeNucProtSetProteinId(), ChangeProtId(), CheckLocalId(), CkInitMetSP(), CkNonTerSP(), ClearFocus(), Convert_Bioseq_Seq_entry(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CGapsEditor::ConvertNs2Gaps(), CCopyHook_Bioseq::CopyObject(), CBlobSplitterImpl::CopySkeleton(), CCreateProteinId::create_protein_ids(), CAlnVecMultiDataSource::CreateConsensus(), CAlnVec::CreateConsensus(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CPhrap_Read::CreateRead(), CMytestApplication::DoProcessFeatureGeneOverlap(), CDiscrepancyContext::Extend(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), FetchSequenceViaHTTP(), CFeatureTableReader::FindOpenReadingFrame(), StructureSet::FindOrCreateSequence(), CDUpdater::findSeq(), SequenceTable::findSequence(), fta_get_user_object(), fta_remove_cleanup_user_object(), CFlatFileGenerator::Generate(), GetBioseqWithType(), GetCDSFromGenProdSet(), CModifySeqId::GetCommand(), GetGoodSeqEntryWithFeatureIds(), CWGSDb_Impl::GetMasterSeq_entry(), GetmRNAFromGenProdSet(), CMaskBDBReader::GetNextSequence(), CDUpdater::GetOneBioseqFromSeqEntry(), GetProtFeatFromGoodNucProtSet(), CMytestApplication::GetSeqEntry(), CSeqSetPresenter::GetSeqEntry(), GetSPAnnot(), CSraRun::GetSpotEntry(), TaxTreeData::GetTaxIDForSequence(), PssmMaker::getTrunctMaster(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), IdFromEntry(), CwxDemoAlignTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadAccession(), CTSE_Default_Assigner::LoadChunkBioseqs(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), CFastaObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CCSRAFileInfo::LoadReadsBlob(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CMultiReader::LoadTemplate(), CMakeCdrProds::MakeCdrProds(), MakeEntryForDeltaConversion(), MakeNucProtSet3Partial(), MakeProteinForGoodNucProtSet(), MakeProteinForNucProtSet(), CBam2Seq_graph::MakeSeq_entry(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeSeqDescr(), CDUpdater::modifySeqAlignSeqEntry(), CSequenceIStreamBlastDB::next(), CReadBlastApp::NormalizeSeqentry(), CSequesterSets::OnAccept(), CDesktopViewContext::OnPasteSelection(), CPrimeCacheApplication::CCacheBioseq::operator()(), CAgpConverter::OutputBioseqs(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CPubmedUpdater::PostProcessPubs(), PSSMWrapper::PSSMWrapper(), CGlimmerReader::Read(), CConversionApp::Read(), CHugeFileProcess::Read(), CFastaReaderEx::ReadDeltaFasta(), CBlastInputReader::ReadOneSeq(), CFastaReader::ReadOneSeq(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CCachedSequence::RegisterIds(), RemoveDbxref(), RemoveDeltaSeqGaps(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), ResetOrgname(), RetranslateCdsForNucProtSet(), RevComp(), CLocalFinderApp::Run(), CAgpconvertApplication::Run(), s_AddSeqDataToPssm(), s_AddSeqTitleToPssm(), s_ArePrimersUnique(), s_CollectCollidingIDs_Entry(), s_CollidedIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), s_FastaStringToBioseq(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_GetQueryBioseq(), s_MakeNewMasterSeq(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_QueryVectorToBioseqSet(), s_RemoveAnnotsFromEntry(), s_SetSeqdescUser(), s_TSeqLocVectorToBioseqSet(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), CSeq_entry::SetAnnot(), SetBiomol(), SetChromosome(), SetCommon(), SetCompleteness(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), SetTaxname(), SetTaxon(), SetTech(), SetTitle(), SetTransgenic(), CValidError_imp::Setup(), SimplifySeqEntryForCD(), SPFeatProtRef(), CCachedSequence::SplitSeqData(), TestCircularTopology(), TestFeatInsideGap(), TestNewAccessionOnNuc(), TestNewAccessionOnStandaloneProt(), TestOneGapSeq(), TestOneGeneralSeqId(), TestOneLongGeneral(), TestOneMiscPartial(), TestOneOtherAcc(), TestOneReplicon(), TestOneStrain(), TestOneStrainNew(), TestStartGapSeg(), TranslateCDSCommand(), TryMiscWithNs(), UnpackSeqEntry(), CDUpdater::update(), CGC_Assembly_Parser::x_AddBioseq(), CCachedSequence::x_AddFullSeq_data(), SWGSCreateInfo::x_AddProducts(), CSequenceUpdater::x_AdjustProteinFeature(), x_BioseqSetFromBioseq(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), CImportFeatTable::x_DoImportCDS(), CAgpToSeqEntry::x_FinishedBioseq(), CSequenceUpdater::x_FixIDInNewEntry(), CBamAlignIterator::x_GetMatchEntry(), CCSraAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSeqMasterIndex::x_Initialize(), CAgpConverter::x_InitializeAndCheckCopyOfTemplate(), CAgpConverter::x_InitializeCopyOfTemplate(), CBuffer_DataLoader::x_LoadData(), CSplitDataLoader::x_LoadData(), CAgpconvertApplication::x_LoadTemplate(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MoveNpDBlinks(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CPrimeCacheApplication::x_Process_Fasta(), CCleanupApp::x_ProcessHugeFile(), CCleanupApp::x_ProcessTraditionally(), CShortReadFastaInputSource::x_ReadFastaOneSeq(), CGFFReader::x_ReadFastaSequences(), CShortReadFastaInputSource::x_ReadFastc(), CShortReadFastaInputSource::x_ReadFastqOneSeq(), CGapStatsApplication::x_ReadFileOrAccn(), CASN1InputSourceOMF::x_ReadFromSingleFile(), CASN1InputSourceOMF::x_ReadFromTwoFiles(), CSraInputSource::x_ReadOneSeq(), CSraInputSource::x_ReadPairs(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CNewCleanup_imp::x_RemovePub(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CNetBlastSubmittingJob::x_Run(), CBioseq_set_Info::x_SetChunkBioseqs2(), CAgpConverter::x_SetCreateAndUpdateDatesToToday(), CCDSTranslationPanel::x_SetLocationForProtein(), CSeq_entry_Info::x_SetObject(), CCDSTranslationPanel::x_SetProtein(), CPrimeCacheApplication::x_StripSeqEntry(), CSequenceUpdater::x_UpdateProteinID(), CFeatureTableReader::xAddProteinToSeqEntry(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatTableEdit::xGenerate_mRNA_Product(), CMultiReader::xReadASN1Text(), CFeatureTableReader::xTranslateProtein(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

Assign a value to Seq_set data member.

Returns

Reference to the data value.

Definition at line 762 of file Bioseq_set_.hpp.

References CBioseq_set_Base::m_Seq_set, and CBioseq_set_Base::m_set_State.

Referenced by CObjectManager::AcquireSharedSeq_annot(), CTbl2AsnApp::AddAnnots(), AddCdregionToSmallGenomeSet(), AddCDSAndProtForBigGoodNucProtSet(), AddChromosomeNoLocation(), AddFeatAnnotToSeqEntry(), AddLocalIdUserObjects(), CGBProjectHelper::AddProjectItemsFromRID(), AddSeqdescToSeqEntryRecursively(), CCdCore::AddSequence(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), AgpRead(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CTable2AsnContext::ApplyCreateUpdateDates(), CAutogeneratedCleanup::BasicCleanupBioseqSet(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodEcoSetWithAlign(), BuildGoodGenProdSet(), BuildGoodSegSet(), BuildGoodSpliceNucProtSet(), BuildProtBioseqSet(), BuildSmallGenomeSet(), ChangeId(), CConvertSetTypeDlg::ChangeNotify(), ChangeNucId(), ChangeProtId(), Check3Policy(), CCdCore::Clear(), Convert_Seq_annot_Seq_entry(), Convert_Seq_entry_Bioseq_set(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CGapsEditor::ConvertNs2Gaps(), CFeatureTableReader::ConvertNucSetToSet(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CMytestApplication::DoProcessFeatureGeneOverlap(), CCdCore::EraseSequence(), CAutogeneratedExtendedCleanup::ExtendedCleanupBioseqSet(), FetchSequenceViaHTTP(), CFeatureTableReader::FindOpenReadingFrame(), FixDupDates(), FixEmblUpdateDates(), get_parent_seqset(), CCdCore::GetBioseqForIndex(), GetBioseqWithType(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), CSNPDbSeqIterator::GetEntry(), GetGenomicFromGenProdSet(), GetGoodSeqEntryWithFeatureIds(), seqsubmit_split::CSeqEntryHelper::GetListOfEntries(), CBlastInputOMF::GetNextSeqBatch(), GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), GetProteinSequenceFromGoodNucProtSet(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CSraRun::GetSpotEntry(), IdFromEntry(), CCdFromFasta::ImportAlignmentData(), CFastaObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CCSRAFileInfo::LoadReadsBlob(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), MakeBioseqSet(), CMakeCdrProds::MakeCdrProds(), MakeMultiSeqCDS(), MakeNucProtSet3Partial(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeWithTemplate(), CReadBlastApp::NormalizeSeqentry(), OneTerminalTranslationExceptionTest(), CWithdrawSequences::PopulateSet(), CReorderSequencesDlg::PopulateSet(), CSegregateSetsBase::PopulateSet(), CForeignContaminationScreenReportReader::PostProcess(), CPubmedUpdater::PostProcessPubs(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CBasicFastaWrapper::ReadFile(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFastaReader::ReadSet(), CCleanup::RemoveNcbiCleanupObject(), CRemoveSet::RemoveOneSet(), CReadBlastApp::RemoveProblems(), RemoveUserObjectType(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), RevComp(), s_AddCDS(), s_CollectCollidingIDs_Entry(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_QueryVectorToBioseqSet(), s_RemoveAnnotsFromEntry(), s_TSeqLocVectorToBioseqSet(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), SetNucProtSetProductName(), CTable2AsnContext::SetSeqId(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), SimplifySeqEntryForCD(), SortSeqDescr(), CReadBlastApp::SortSeqs(), CSegregateSetsBase::TakeFromSet(), TestCollidingAccessionFixes(), TestFeatInsideGap(), TestGoodNucId(), TrimEntry(), TruncateTransSplicedCDSForExtension(), CConversionApp::Write(), CGC_Assembly_Parser::x_AddBioseq(), SWGSCreateInfo::x_AddProducts(), CAutogeneratedCleanup::x_BasicCleanupSeqEntry_set(), x_BioseqSetFromBioseq(), CNewCleanup_imp::x_BioseqSetGenBankEC(), CPhrapReader::x_ConvertContig(), x_CreateEmptyLocalCDDEntry(), CFeatureGenerator::SImplementation::x_CreateMrnaBioseq(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CSequenceUpdater::x_FixIDInNewEntry(), CCreateGeneModelTask::x_GetCommand(), CBamAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CGC_Assembly_Parser::x_InitSeq_entry(), CID2SNPProcessor_Impl::x_LoadBlob(), CBamRefSeqInfo::x_LoadRangesEstimated(), CScope_Impl::x_MakeDummyTSE(), CNewCleanup_imp::x_MovePopPhyMutPub(), CBioseq_set_Info::x_ParentAttach(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CCleanupApp::x_ProcessHugeFileBlob(), CShortReadFastaInputSource::x_ReadFastaOrFastq(), CGFFReader::x_ReadFastaSequences(), CShortReadFastaInputSource::x_ReadFastc(), CASN1InputSourceOMF::x_ReadFromSingleFile(), CASN1InputSourceOMF::x_ReadFromTwoFiles(), CShortReadFastaInputSource::x_ReadFromTwoFiles(), CSraInputSource::x_ReadOneSeq(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_ReadSeqEntriesFromFile(), CPsiBlastTestFixture::x_ReadSeqEntriesFromFile(), CFastaReader::x_ReadSeqsToAlign(), CNewCleanup_imp::x_RemoveDupBioSource(), CNetBlastSubmittingJob::x_Run(), CPSGS_CDDProcessor::x_SendAnnot(), CBioseq_set_Info::x_SetObject(), CSplitDataLoader::x_SplitSet(), CPrimeCacheApplication::x_StripSeqEntry(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), CMultiReader::xReadASN1Text(), CPubmedUpdater::xUpdatePubReferences(), CNewCleanup_imp::xUpdateSeqfeatCitPub(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().

Select the variant.

Returns

Reference to the variant data.

Definition at line 130 of file Seq_entry_.cpp.

References CSeq_entry_Base::e_Set, eDoNotResetVariant, CSeq_entry_Base::m_object, and CSeq_entry_Base::Select().

Referenced by CObjectManager::AcquireSharedSeq_annot(), CTbl2AsnApp::AddAnnots(), AddCdregionToSmallGenomeSet(), AddCDSAndProtForBigGoodNucProtSet(), AddChromosomeNoLocation(), AddFeat(), AddFeatAnnotToSeqEntry(), AddGoodPub(), AddGoodSource(), AddLocalIdUserObjects(), CAnnotationASN1::CImplementationData::AddModel(), CObjectLoadingTask::AddObjects(), AddRefGeneTrackingUserObject(), AddSeqdescToSeqEntryRecursively(), CCdCore::AddSequence(), CDRefresher::addSequences(), SequenceTable::addSequences(), AddSource(), AddTitle(), subfuse::CSubmissionCollector::AdjustLocalIds(), AdjustProtFeatForNucProtSet(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CTable2AsnContext::ApplyCreateUpdateDates(), CAttachedHandles::Attach(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildBigGoodNucProtSet(), BuildGenProdSetWithBigProduct(), BuildGoodEcoSet(), BuildGoodEcoSetWithAlign(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), BuildGoodSegSet(), BuildGoodSpliceNucProtSet(), BuildNucProtSet(), seqsubmit_split::CSeqEntryHelper::BuildObject(), BuildProtBioseqSet(), BuildSmallGenomeSet(), ChangeId(), ChangeNucId(), ChangeProtId(), Check3Extend(), Check3Policy(), Check5Extend(), Check5Policy(), CheckPropagatedCDSLocation(), CCdCore::Clear(), ClearFocus(), Convert_Bioseq_set_Seq_entry(), Convert_Seq_annot_Seq_entry(), CGapsEditor::ConvertNs2Gaps(), CFeatureTableReader::ConvertNucSetToSet(), CCopyHook_Bioseq_set::CopyObject(), CBlobSplitterImpl::CopySkeleton(), CreateBioseqsAndAlign(), CPhrap_Contig::CreateContig(), CreateMimeFromBiostruc(), CAnnotationASN1::CImplementationData::CreateModelProducts(), CSeqEntrySource::CSeqEntrySource(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAnnotationASN1::CImplementationData::DumpEvidence(), CCdCore::EraseSequence(), CCmdInsertBioseqSet::Execute(), CGBFlatFileObjectLoader::Execute(), CDiscrepancyContext::Extend(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), FetchSequenceViaHTTP(), CCdsToMatPeptide::FindAnnot(), CFeatureTableReader::FindOpenReadingFrame(), fta_get_user_object(), fta_remove_cleanup_user_object(), g_ApplyDescriptors(), CFlatFileGenerator::Generate(), get_parent_seqset(), CCdCore::GetBioseqForIndex(), GetBioseqWithType(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), GetCDSFromGoodNucProtSet(), CSegregateSets::GetCommand(), CWithdrawSequences::GetCommand(), CSNPDbSeqIterator::GetEntry(), GetGenomicFromGenProdSet(), GetGoodSeqEntryWithFeatureIds(), seqsubmit_split::CSeqEntryHelper::GetListOfEntries(), GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), GetProteinSequenceFromGoodNucProtSet(), CMytestApplication::GetSeqEntry(), CSeqSetPresenter::GetSeqEntry(), CSraRun::GetSpotEntry(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), IdFromEntry(), CCdFromFasta::ImportAlignmentData(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CFastaObjectLoader::LoadFromStream(), CAsnObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CCSRAFileInfo::LoadReadsBlob(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), MakeMultiSeqCDS(), MakeNucProtSet3Partial(), CInfluenzaSet::MakeSet(), CCdsToMatPeptide::MergeConvert(), CTable2AsnContext::MergeSeqDescr(), CTable2AsnContext::MergeWithTemplate(), CFeatureTableReader::MoveRegionsToProteins(), MoveSourceDescrToTop(), CReadBlastApp::NormalizeSeqentry(), CAsn2FastaApp::ObtainSeqEntryFromBioseqSet(), CAsn2FlatApp::ObtainSeqEntryFromBioseqSet(), CSequesterSets::OnAccept(), OneTerminalTranslationExceptionTest(), CDesktopViewContext::OnPasteSelection(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), CSegregateSetsBase::PopulateSet(), CForeignContaminationScreenReportReader::PostProcess(), CPubmedUpdater::PostProcessPubs(), CBam2GraphApp::ProcessFile(), CBam2GraphApp::ProcessSrz(), CGlimmerReader::Read(), CConversionApp::Read(), CPhrapReader::Read(), CFastaReaderEx::ReadAlignedSet(), CFastaReader::ReadAlignedSet(), CBasicFastaWrapper::ReadFile(), CGff2Reader::ReadSeqEntry(), UpdateViewer::ReadSequencesFromFile(), CFeature_table_reader::ReadSequinFeatureTables(), CFastaReader::ReadSet(), RemoveDbxref(), CCdsToMatPeptide::RemoveFeature(), CCleanup::RemoveNcbiCleanupObject(), CReadBlastApp::RemoveProblems(), CCdsToMatPeptide::RemoveProteins(), RemoveUserObjectType(), ReplaceWellknownSeqs(), CAnnotationASN1::CImplementationData::ResetASN1(), ResetOrgname(), RevComp(), s_AddCDS(), s_CollectCollidingIDs_Entry(), s_CollidedIds(), CUpdateSeq_Input::s_ConvertDeltaToRawEntry(), CUpdateSeq_Input::s_FixCollidingIDs_Entry(), s_MakeGroupsForUniqueValues(), s_MoveProteinSpecificFeats(), s_RemoveAnnotsFromEntry(), s_UpdateFeatureIds(), SeqEntryFromSeqSubmit(), CSeq_entry::SetAnnot(), SetChromosome(), SetCommon(), SetDbxref(), CSeq_entry::SetDescr(), SetDiv(), SetFocus(), SetGcode(), SetGenome(), SetLineage(), SetMGcode(), SetNucProtSetProductName(), SetOrgMod(), SetOrigin(), SetPGcode(), SetRefGeneTrackingStatus(), CTable2AsnContext::SetSeqId(), SetSubSource(), SetTaxname(), SetTaxon(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), SetTransgenic(), SimplifySeqEntryForCD(), SortSeqDescr(), CReadBlastApp::SortSeqs(), sUpdateCase(), TestCollidingAccessionFixes(), TestFeatInsideGap(), TestGoodNucId(), TrimEntry(), TruncateTransSplicedCDSForExtension(), UnpackSeqEntry(), CGC_Assembly_Parser::x_AddBioseq(), SWGSCreateInfo::x_AddProducts(), CPhrapReader::x_ConvertContig(), x_CreateEmptyLocalCDDEntry(), CSequenceUpdater::x_FixIDInNewEntry(), CCreateGeneModelTask::x_GetCommand(), CBamAlignIterator::x_GetMatchEntry(), SWGSCreateInfo::x_GetProtSet(), CSeqMasterIndex::x_Initialize(), CGC_Assembly_Parser::x_InitSeq_entry(), CSplitDataLoader::x_LoadData(), CBamRefSeqInfo::x_LoadRangesEstimated(), CScope_Impl::x_MakeDummyTSE(), CBioseq_set_Info::x_ParentAttach(), CGFFReader::x_ParseDateComment(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), CGFFReader::x_PlaceSeq(), CSequenceUpdater::x_PrepareNewEntry(), CCleanupApp::x_ProcessHugeFile(), CCleanupApp::x_ProcessHugeFileBlob(), CCleanupApp::x_ProcessTraditionally(), CGFFReader::x_ReadFastaSequences(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_ReadSeqEntriesFromFile(), CPsiBlastTestFixture::x_ReadSeqEntriesFromFile(), CFastaReader::x_ReadSeqsToAlign(), CNewCleanup_imp::x_RemoveDupBioSource(), CNewCleanup_imp::x_RemovePub(), CPSGS_CDDProcessor::x_SendAnnot(), CSeq_entry_Info::x_SetObject(), CPrimeCacheApplication::x_StripSeqEntry(), CMultiReader::xApplyTemplate(), CFeatureTableReader::xConvertSeqIntoSeqSet(), seqsubmit_split::CSeqSubSplitter::xFlattenSeqEntry(), CFeatureTableReader::xMergeCDSFeatures_impl(), CFeatureTableReader::xParseCdregions(), CAnnotWriterApp::xProcessInputObject(), CMultiReader::xReadASN1Text(), CPubmedUpdater::xUpdatePubReferences(), CNewCleanup_imp::xUpdateSeqfeatCitPub(), and seqsubmit_split::CSeqSubSplitter::xWrapSeqEntries().

Which variant is currently selected.

Returns

Choice state enumerator.

Definition at line 228 of file Seq_entry_.hpp.

References CSeq_entry_Base::m_choice.

Referenced by CTable2AsnContext::ApplyCreateUpdateDates(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), CGapsEditor::ConvertNs2Gaps(), CBlobSplitterImpl::CopySkeleton(), CMytestApplication::DoProcessFeatureGeneOverlap(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), CFeatureTableReader::FindOpenReadingFrame(), CSeq_entry::GetAnnot(), CSeq_entry::GetDescr(), CSeq_entry::GetLabel(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CAsn2FastaApp::ObtainSeqEntryFromSeqEntry(), CAsn2FlatApp::ObtainSeqEntryFromSeqEntry(), CSeq_entry::Parentize(), CSeq_entry::ParentizeOneLevel(), SegMaskerApplication::Run(), CWinMaskApplication::Run(), CSeq_entry::SetAnnot(), CSeq_entry::SetDescr(), CFastaOstream::Write(), CSeq_entry_Info::x_SetObject(), and CFeatureTableReader::xMergeCDSFeatures_impl().

Definition at line 213 of file Bioseq_set_.cpp.

Definition at line 494 of file Bioseq_set_.hpp.

Referenced by CBioseq_set_Base::CBioseq_set_Base(), CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::IsSetLevel(), CBioseq_set_Base::IsSetRelease(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_set_Base::ResetAnnot(), CBioseq_set_Base::ResetClass(), CBioseq_set_Base::ResetLevel(), CBioseq_set_Base::ResetRelease(), CBioseq_set_Base::ResetSeq_set(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetLevel(), CBioseq_set_Base::SetRelease(), and CBioseq_set_Base::SetSeq_set().

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