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NCBI C++ ToolKit: Handles

State of bioseq handle.

Enumerator fState_none fState_suppress_temp fState_suppress_perm fState_suppress fState_dead fState_confidential fState_withdrawn fState_no_data fState_conflict fState_not_found fState_other_error

Definition at line 127 of file bioseq_handle.hpp.

◆ EFeatureFetchPolicy

Feature fetch policy describes when to look for features on sequence segments.

Enumerator eFeatureFetchPolicy_default eFeatureFetchPolicy_only_near eFeatureFetchPolicy_allow_far

Definition at line 460 of file bioseq_handle.hpp.

◆ EFindSegment

Segment search flags.

Enumerator eFindSegment_NoLimit

No limit on resolving seq-map.

eFindSegment_LimitTSE

Resolve in the parent TSE only.

Definition at line 318 of file bioseq_handle.hpp.

◆ EFlags [1/2] ◆ EFlags [2/2] ◆ ERemoveMode [1/2]

Remove current bioseq from its location.

Enumerator eRemoveSeq_entry eKeepSeq_entry

Definition at line 626 of file bioseq_handle.hpp.

◆ ERemoveMode [2/2] ◆ ESequenceClass Enumerator eSequenceClass_none eSequenceClass_INSD eSequenceClass_REFSEQ eSequenceClass_TPA

Definition at line 306 of file bioseq_handle.hpp.

◆ EVectorCoding

CSeqVector constructor flags.

Enumerator eCoding_NotSet

Use original coding - DANGEROUS! - may change.

eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

Definition at line 347 of file bioseq_handle.hpp.

◆ EVectorStrand Enumerator eStrand_Plus

Plus strand.

eStrand_Minus

Minus strand.

Definition at line 352 of file bioseq_handle.hpp.

◆ AddAlign() ◆ AddDbxref() [1/2] ◆ AddDbxref() [2/2] void CSeq_feat_EditHandle::AddDbxref ( const string & db_name, int db_key ) ◆ AddDescr() void CSeq_entry_EditHandle::AddDescr ( TDescr & v ) const ◆ AddExceptText() void CSeq_feat_EditHandle::AddExceptText ( const string & exception_text ) ◆ AddFeat()

Definition at line 308 of file seq_annot_handle.cpp.

References CCommandProcessor::run(), and CSeq_annot_Handle::x_GetScopeImpl().

Referenced by AddFeatureToBioseq(), AddIRDMiscFeature(), CApplyObject::ApplyChange(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CAddFeatChecker::Do(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdCreateFeat::Execute(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), ProcessForTrimAndSplitUpdates(), s_MoveProteinSpecificFeats(), CSeq_annot_EditHandle::TakeFeat(), CCmdDelSeq_feat::Unexecute(), CCmdCreateCDS::x_AddProteinFeatures(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CFeatTableEdit::xCreateMissingParentGene(), CFeatTableEdit::xGenerateMissingMrnaForCds(), and CGff2Writer::xGenerateMissingTranscript().

◆ AddFeatId() [1/3] ◆ AddFeatId() [2/3] void CSeq_feat_EditHandle::AddFeatId ( const string & id ) ◆ AddFeatId() [3/3] void CSeq_feat_EditHandle::AddFeatId ( int id ) ◆ AddFeatXref() [1/3] ◆ AddFeatXref() [2/3] void CSeq_feat_EditHandle::AddFeatXref ( const string & id ) ◆ AddFeatXref() [3/3] void CSeq_feat_EditHandle::AddFeatXref ( int id ) ◆ AddGraph() ◆ AddId() ◆ AddNewEntry() ◆ AddQualifier() ◆ AddSeq_descr() [1/2] void CBioseq_EditHandle::AddSeq_descr ( TDescr & v ) const ◆ AddSeq_descr() [2/2] void CBioseq_set_EditHandle::AddSeq_descr ( TDescr & v ) const ◆ AddSeqdesc() [1/3] ◆ AddSeqdesc() [2/3] bool CBioseq_set_EditHandle::AddSeqdesc ( CSeqdesc & d ) const ◆ AddSeqdesc() [3/3] bool CSeq_entry_EditHandle::AddSeqdesc ( CSeqdesc & v ) const

Definition at line 371 of file seq_entry_handle.cpp.

References CCommandProcessor::run(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by CCleanup::AddProtein(), CApplyObject::ApplyChange(), CCleanup::AutodefId(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdAddSeqEntry::Execute(), CCmdCreateDesc::Execute(), s_ActualizeUpdateDate(), s_DescriptorPropagateDown(), CCmdDelDesc::Unexecute(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), and CSequenceUpdater::x_AttachFeaturesToNewSeq().

◆ AddUsedBioseq()

Parameters

Returns: True if argument bioseq was successfully registered as 'used'. False if argument bioseq was not registered as 'used'. Possible reasons: Circular reference in 'used' tree.

Definition at line 1015 of file bioseq_handle.cpp.

References CTSE_Handle::AddUsedTSE(), and CBioseq_Handle::GetTSE_Handle().

◆ AttachAnnot() [1/5] ◆ AttachAnnot() [2/5] ◆ AttachAnnot() [3/5]

Attach an annotation.

Parameters: annot Reference to this annotation will be attached

Returns: Edit handle to the attached annotation

See also: CopyAnnot() TakeAnnot()

Definition at line 699 of file bioseq_handle.cpp.

References CSeq_entry_EditHandle::AttachAnnot(), and CBioseq_EditHandle::GetParentEntry().

Referenced by AddFeatureToBioseq(), AddIRDMiscFeature(), CAddFeatChecker::Do(), GetAnnotHandle(), CCleanup::MoveFeatToProtein(), CPromote::PromoteCdregion(), CPromote::PromoteFeatures(), CPromote::PromotePub(), CPromote::PromoteRna(), s_MoveProteinSpecificFeats(), CPromote::x_AddProtFeature(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CPromote::x_CopyCdregionToRNA(), and CSequenceUpdater::x_FuseProtFeatsForCDS().

◆ AttachAnnot() [4/5] ◆ AttachAnnot() [5/5]

Attach an annotation.

Parameters: annot Reference to this annotation will be attached

Returns: Edit handle to the attached annotation

See also: CopyAnnot() TakeAnnot()

Definition at line 448 of file seq_entry_handle.cpp.

References Ref().

Referenced by CApplyObject::ApplyChange(), CBioseq_EditHandle::AttachAnnot(), CBioseq_set_EditHandle::AttachAnnot(), CScope::AttachAnnot(), CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), BOOST_AUTO_TEST_CASE(), CSeq_entry_EditHandle::CopyAnnot(), DemoteCDSToNucSeq(), DivvyUpAlignments(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdCreateSeq_annot::Execute(), CCmdCreateAlign::Execute(), CCmdCreateFeat::Execute(), CCmdPromoteCDS::Execute(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), PromoteCDSToNucProtSet(), CScope::ReplaceAnnot(), CSeq_entry_EditHandle::TakeAnnot(), CCmdDelSeq_annot::Unexecute(), CCmdPromoteCDS::Unexecute(), and CSequenceUpdater::x_AttachFeaturesToNewSeq().

◆ AttachBioseq() [1/2] ◆ AttachBioseq() [2/2] ◆ AttachEntry() [1/5] ◆ AttachEntry() [2/5] ◆ AttachEntry() [3/5] ◆ AttachEntry() [4/5] ◆ AttachEntry() [5/5] ◆ CanGetClass() bool CBioseq_set_Handle::CanGetClass ( void ) const

Definition at line 199 of file bioseq_set_handle.cpp.

References CBioseq_set_Info::CanGetClass(), and CBioseq_set_Handle::x_GetInfo().

Referenced by CRemoveSeqId::CRemoveSeqId(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CEditSequenceEnds::GetCommand(), CAutoDef::GetMasterLocation(), CAutoDef::IsSegment(), CReorderSequencesDlg::PopulateSet(), PropagateToTarget(), CSegregateSetsBase::ReadBioseq(), CRBSubpanel::SetSubsets(), CVectorTrimPanel::x_DeleteSelected(), CFlatGatherer::x_GatherCDSReferences(), and CVectorTrimPanel::x_TrimSelected().

◆ CanGetColl() bool CBioseq_set_Handle::CanGetColl ( void ) const ◆ CanGetDate() bool CBioseq_set_Handle::CanGetDate ( void ) const ◆ CanGetDescr() [1/2] bool CBioseq_Handle::CanGetDescr ( void ) const ◆ CanGetDescr() [2/2] bool CBioseq_set_Handle::CanGetDescr ( void ) const ◆ CanGetId() [1/2] bool CBioseq_Handle::CanGetId ( void ) const ◆ CanGetId() [2/2] bool CBioseq_set_Handle::CanGetId ( void ) const ◆ CanGetInst() bool CBioseq_Handle::CanGetInst ( void ) const

Definition at line 201 of file bioseq_handle.cpp.

References CBioseq_Info::CanGetInst(), and CBioseq_Handle::x_GetInfo().

Referenced by CAutoDef::GetOneDefLine(), PackSeqPntCheckCpp(), CAsnCacheTestApplication::Run(), s_BasicValidation(), SeqIntCheckCpp(), SeqPntCheckCpp(), CUnorderedSplitter::SplitId(), CUnorderedSplitter::SplitLoc(), CGff3Writer::xWriteFeatureGeneric(), and CGff3Writer::xWriteFeatureTrna().

◆ CanGetInst_Ext() bool CBioseq_Handle::CanGetInst_Ext ( void ) const ◆ CanGetInst_Fuzz() bool CBioseq_Handle::CanGetInst_Fuzz ( void ) const ◆ CanGetInst_Hist() bool CBioseq_Handle::CanGetInst_Hist ( void ) const ◆ CanGetInst_Length() bool CBioseq_Handle::CanGetInst_Length ( void ) const ◆ CanGetInst_Mol() bool CBioseq_Handle::CanGetInst_Mol ( void ) const ◆ CanGetInst_Repr() bool CBioseq_Handle::CanGetInst_Repr ( void ) const ◆ CanGetInst_Seq_data() bool CBioseq_Handle::CanGetInst_Seq_data ( void ) const ◆ CanGetInst_Strand() bool CBioseq_Handle::CanGetInst_Strand ( void ) const ◆ CanGetInst_Topology() bool CBioseq_Handle::CanGetInst_Topology ( void ) const ◆ CanGetLevel() bool CBioseq_set_Handle::CanGetLevel ( void ) const ◆ CanGetRelease() bool CBioseq_set_Handle::CanGetRelease ( void ) const ◆ CBioseq_EditHandle() [1/4] ◆ CBioseq_EditHandle() [2/4] ◆ CBioseq_EditHandle() [3/4] ◆ CBioseq_EditHandle() [4/4] ◆ CBioseq_Handle() [1/3] ◆ CBioseq_Handle() [2/3] ◆ CBioseq_Handle() [3/3] ◆ CBioseq_set_EditHandle() [1/3] ◆ CBioseq_set_EditHandle() [2/3] ◆ CBioseq_set_EditHandle() [3/3] ◆ CBioseq_set_Handle() [1/3] ◆ CBioseq_set_Handle() [2/3] ◆ CBioseq_set_Handle() [3/3] CBioseq_set_Handle::CBioseq_set_Handle ( void ) inline ◆ CBioseq_set_ScopeInfo() ◆ ClearFeatIds() void CSeq_feat_EditHandle::ClearFeatIds ( void ) ◆ ClearFeatXrefs() void CSeq_feat_EditHandle::ClearFeatXrefs ( void ) ◆ CollapseSet() void CSeq_entry_EditHandle::CollapseSet ( void ) const

Collapse one level of Bioseq-set.

The Bioseq-set should originally contain only one sub-entry. Current Seq-entry will become the same type as sub-entry. All Seq-annot and Seq-descr objects from old Bioseq-set will be moved to new contents (sub-entry).

Definition at line 672 of file seq_entry_handle.cpp.

Referenced by CMacroFunction_RemoveSingleItemSet::s_RemoveSingleItemSet().

◆ ContainsSegment() [1/3]

Definition at line 431 of file bioseq_handle.cpp.

References CSeqMap::BeginResolved(), CBioseq_Handle::eFindSegment_LimitTSE, CSeqMap::fFindRef, CSeqMap_CI::GetRefSeqid(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSynonyms(), CBioseq_Handle::GetTopLevelEntry(), SSeqMapSelector::SetFlags(), SSeqMapSelector::SetLimitTSE(), and SSeqMapSelector::SetResolveCount().

◆ ContainsSegment() [2/3]

Check if the seq-id describes a segment of the bioseq.

Parameters: id Seq-id to be checked for being a segment of the handle. resolve_depth Depth of resolving segments. Zero allows to check only top-level segments. limit_flag Allow/prohibit resolving far references. By default all segments are resolved. If the flag is set to eFindSegment_LimitTSE, only near references are checked.

Definition at line 421 of file bioseq_handle.cpp.

References CSeq_id_Handle::GetHandle().

Referenced by GetAnchors(), and sFindAnchorRow().

◆ ContainsSegment() [3/3]

Definition at line 455 of file bioseq_handle.cpp.

References CSeqMap::BeginResolved(), CBioseq_Handle::eFindSegment_LimitTSE, CSeqMap::fFindRef, CScope::GetBioseqHandle(), CSeqMap_CI::GetRefSeqid(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSynonyms(), CBioseq_Handle::GetTopLevelEntry(), SSeqMapSelector::SetFlags(), SSeqMapSelector::SetLimitTSE(), and SSeqMapSelector::SetResolveCount().

◆ ConvertSeqToSet()

Convert the entry from Bioseq to Bioseq-set.

Old Bioseq will become the only entry of new Bioseq-set. New Bioseq-set will have the specified class. If the set_class argument is omitted, or equals to CBioseq_set::eClass_not_set, the class field of new Bioseq-set object will not be initialized. Returns new Bioseq-set handle.

Definition at line 651 of file seq_entry_handle.cpp.

References _ASSERT, CBioseq_set_EditHandle::AddNewEntry(), IScopeTransaction_Impl::Commit(), CSeq_entry_Base::e_not_set, CBioseq_Handle::IsRemoved(), CSeq_entry_Handle::IsSeq(), NCBI_THROW, CSeq_entry_EditHandle::SelectNone(), CSeq_entry_EditHandle::SelectSeq(), CSeq_entry_EditHandle::SelectSet(), CSeq_entry_EditHandle::SetSeq(), CSeq_entry_Handle::Which(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by CCleanup::AddGenBankWrapper(), CCleanup::AddProtein(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdAddSeqEntry::Execute(), s_AddBioseqToBioseq(), s_AddProtToNuc(), s_DoSmartProcessing(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CCmdDelBioseqInst::Unexecute(), and CSequenceUpdater::x_AttachFeaturesToNewSeq().

◆ ConvertSetToSeq()

Do the same as CollapseSet() when sub-entry is of type bioseq.

Throws an exception in other cases. Returns resulting Bioseq handle.

Definition at line 705 of file seq_entry_handle.cpp.

References _ASSERT, IScopeTransaction_Impl::Commit(), CSeq_entry_EditHandle::GetSingleSubEntry(), CBioseq_Handle::IsRemoved(), CSeq_entry_Handle::IsSeq(), NCBI_THROW, CSeq_entry_EditHandle::SelectNone(), CSeq_entry_EditHandle::SelectSeq(), CSeq_entry_EditHandle::SetSeq(), CSeq_entry_EditHandle::TakeAllAnnots(), CSeq_entry_EditHandle::TakeAllDescr(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by DeleteProteinAndRenormalizeNucProtSet(), CCleanup::RenormalizeNucProtSets(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CCmdAddSeqEntry::Unexecute(), and CNewCleanup_imp::x_SingleSeqSetToSeq().

◆ CopyAnnot() [1/3] ◆ CopyAnnot() [2/3] ◆ CopyAnnot() [3/3] ◆ CopyBioseq() [1/2] ◆ CopyBioseq() [2/2] ◆ CopyEntry() [1/2] ◆ CopyEntry() [2/2] ◆ CopySeq() ◆ CopySet() ◆ CopyTo() [1/2]

Copy current bioseq into seqset.

Parameters: entry Current bioseq will be inserted into seqset pointed by this handle. index Start index is 0 and -1 means end

Returns: Edit handle to inserted bioseq

Definition at line 640 of file bioseq_handle.cpp.

References CBioseq_set_EditHandle::CopyBioseq().

◆ CopyTo() [2/2]

Copy current bioseq into seq-entry.

Parameters: entry Current bioseq will be inserted into seq-entry pointed by this handle. index Start index is 0 and -1 means end

Returns: Edit handle to inserted bioseq

Definition at line 632 of file bioseq_handle.cpp.

References CSeq_entry_EditHandle::CopyBioseq().

◆ CopyToSeq()

Copy current bioseq into seq-entry and set seq-entry as bioseq.

Parameters: entry Seq-entry pointed by entry handle will be set to bioseq

Returns: Edit handle to inserted bioseq

Definition at line 648 of file bioseq_handle.cpp.

References CSeq_entry_EditHandle::CopySeq().

◆ CSeq_align_Handle() [1/2] ◆ CSeq_align_Handle() [2/2] ◆ CSeq_annot_EditHandle() [1/3] ◆ CSeq_annot_EditHandle() [2/3] ◆ CSeq_annot_EditHandle() [3/3] ◆ CSeq_annot_ftable_CI() [1/2]

Definition at line 769 of file seq_feat_handle.cpp.

References CSeq_annot_ftable_CI::fIncludeTable, CSeq_annot_Handle::IsFtable(), CSeq_feat_Handle::kNoAnnotObjectInfo, CSeq_annot_ftable_CI::m_Feat, CSeq_feat_Handle::m_FeatIndex, CSeq_annot_ftable_CI::m_Flags, CSeq_feat_Handle::m_Seq_annot, NCBI_THROW, CSeq_annot_Handle::x_GetInfo(), CSeq_annot_Info::x_HasSNP_annot_Info(), and CSeq_annot_ftable_CI::x_Settle().

◆ CSeq_annot_ftable_CI() [2/2] CSeq_annot_ftable_CI::CSeq_annot_ftable_CI ( void ) inline

Definition at line 750 of file seq_feat_handle.hpp.

◆ CSeq_annot_ftable_I() [1/2]

Definition at line 831 of file seq_feat_handle.cpp.

References CSeq_annot_ftable_I::fIncludeTable, CSeq_annot_Handle::IsFtable(), CSeq_feat_Handle::kNoAnnotObjectInfo, CSeq_annot_ftable_I::m_Feat, CSeq_feat_Handle::m_FeatIndex, CSeq_annot_ftable_I::m_Flags, CSeq_feat_Handle::m_Seq_annot, NCBI_THROW, CSeq_annot_EditHandle::x_GetInfo(), CSeq_annot_Info::x_HasSNP_annot_Info(), and CSeq_annot_ftable_I::x_Settle().

◆ CSeq_annot_ftable_I() [2/2] ◆ CSeq_annot_Handle() [1/2] ◆ CSeq_annot_Handle() [2/2] ◆ CSeq_annot_ScopeInfo() ◆ CSeq_entry_EditHandle() [1/3] ◆ CSeq_entry_EditHandle() [2/3] ◆ CSeq_entry_EditHandle() [3/3] CSeq_entry_EditHandle::CSeq_entry_EditHandle ( void ) inline ◆ CSeq_entry_Handle() [1/3] ◆ CSeq_entry_Handle() [2/3] ◆ CSeq_entry_Handle() [3/3] CSeq_entry_Handle::CSeq_entry_Handle ( void ) inline ◆ CSeq_entry_ScopeInfo() ◆ CSeq_feat_EditHandle() [1/4] ◆ CSeq_feat_EditHandle() [2/4] ◆ CSeq_feat_EditHandle() [3/4] ◆ CSeq_feat_EditHandle() [4/4] CSeq_feat_EditHandle::CSeq_feat_EditHandle ( void ) inline

Definition at line 699 of file seq_feat_handle.hpp.

◆ CSeq_feat_Handle() [1/4] ◆ CSeq_feat_Handle() [2/4] ◆ CSeq_feat_Handle() [3/4] ◆ CSeq_feat_Handle() [4/4] ◆ CSeq_graph_Handle() [1/2] ◆ CSeq_graph_Handle() [2/2] ◆ DECLARE_OPERATOR_BOOL() [1/9] ◆ DECLARE_OPERATOR_BOOL() [2/9] ◆ DECLARE_OPERATOR_BOOL() [3/9] CSeq_annot_ftable_CI::DECLARE_OPERATOR_BOOL ( m_Feat ) ◆ DECLARE_OPERATOR_BOOL() [4/9] CSeq_annot_ftable_I::DECLARE_OPERATOR_BOOL ( m_Feat ) ◆ DECLARE_OPERATOR_BOOL() [5/9] CBioseq_Handle::DECLARE_OPERATOR_BOOL ( m_Info. IsValid() )

Check if handle points to a bioseq and is not removed.

See also: operator !()

◆ DECLARE_OPERATOR_BOOL() [6/9] CBioseq_set_Handle::DECLARE_OPERATOR_BOOL ( m_Info. IsValid() )

Check if handle points to a bioseq-set.

See also: operator !()

◆ DECLARE_OPERATOR_BOOL() [7/9] CSeq_annot_Handle::DECLARE_OPERATOR_BOOL ( m_Info. IsValid() ) ◆ DECLARE_OPERATOR_BOOL() [8/9] CSeq_entry_Handle::DECLARE_OPERATOR_BOOL ( m_Info. IsValid() ) ◆ DECLARE_OPERATOR_BOOL() [9/9] CSeq_feat_Handle::DECLARE_OPERATOR_BOOL ( m_Seq_annot &&! IsRemoved() ) ◆ GetA() double CSeq_graph_Handle::GetA ( void ) const inline ◆ GetAccessSeq_id_Handle()

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's non-null.

Definition at line 939 of file bioseq_handle.cpp.

References _ASSERT, CScope::GetBioseqHandleFromTSE(), CBioseq_Handle::GetId(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeq_id_Handle(), CBioseq_Handle::GetTSE_Handle(), ITERATE, and NCBI_THROW.

Referenced by CFlatFileGenerator::Generate(), CMacroBioData_SeqIter::GetBestDescr(), sequpd::GetGoodSeqIdHandle(), CBioseq_Handle::GetRangeSeq_loc(), CBioseq_Handle::GetSeqId(), GetTaxIdForProduct(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CAnnot_Collector::x_Initialize(), CBioseqGaps_CI::x_Next(), and CHugeFileDemoApp::x_TestRW1848().

◆ GetAnnot() [1/6]

Get handle to the seq-annot.

Definition at line 148 of file seq_align_handle.hpp.

References CSeq_align_Handle::m_Annot.

Referenced by CCmdDelSeq_align::Execute(), CSeq_align_Handle::GetScope(), CAlignmentAssistant::OnValidate(), CSeq_align_Handle::Remove(), CSeq_align_Handle::Replace(), CEditsSaver::Replace(), CDesktopAlignItem::s_ContainsFarPointers(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), CSeq_align_Handle::Update(), CRawSeqToDeltaSeqByLoc::UpdateDensegAlignment(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CwxAnnotConfigDlg::x_InitAnnotList(), CSeq_align_Handle::x_RealRemove(), CSeq_align_Handle::x_RealReplace(), and CEditObjectFeaturePropagate::xInit().

◆ GetAnnot() [2/6]

Get handle to seq-annot for this feature.

Definition at line 271 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::m_Seq_annot.

Referenced by AddCodeBreak(), AdjustSingleFeature(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), CApplyObject::ApplyChange(), ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), CFeatureItemBase::CFeatureItemBase(), CFeatureGenerator::CreateMicroIntrons(), DemoteCDSToNucSeq(), CSequenceEditingEventHandler::Duplicate(), CSeq_feat_EditHandle::GetAnnot(), CSeq_annot_ftable_CI::GetAnnot(), GetBioseqForSeqFeat(), NSnp::GetCreateTime(), IEditingActionFeat::GetCurrentSeqEntryHandleFromFeatHandle(), GetDeleteAllFeaturesCommand_Ex(), CTSE_Handle::GetFeaturesWithId(), CTSE_Handle::GetFeaturesWithXref(), CTSE_Handle::GetFeatureWithId(), CTSE_Handle::GetGeneByRef(), CTSE_Handle::GetGenesByRef(), CTSE_Handle::GetGenesWithLocus(), CTSE_Handle::GetGeneWithLocus(), CSeq_feat_Handle::GetScope(), MakemRNAforCDS(), MapSeq_feat(), CCleanup::MoveFeatToProtein(), CSeq_feat_Handle::operator!=(), CSeq_feat_Handle::operator<(), CSeq_feat_Handle::operator==(), ProcessForTrimAndSplitUpdates(), CHugeFileDemoApp::ProcessHugeSeqEntry(), CPromote::PromoteCdregion(), CPromote::PromotePub(), CPromote::PromoteRna(), CSeq_annot_EditHandle::ReorderFtable(), CCleanup::RepairXrefs(), CEditsSaver::Replace(), RestoreModelFromPublicMrnaFeature(), CFeatCompareJob_Location::Run(), s_GetAnnotSelector(), s_GetRnaMappingLocs(), s_IsCDD(), s_IsDuplicateFeatures(), s_IsLocalFeature(), s_IsSameSeqAnnot(), CFeatureItem::x_AddQualSeqfeatNote(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CBioseqEditor::x_DeleteObject(), CAdjustFeaturesForGaps::x_DoOne(), CSGFeatureJob::x_Execute(), CBioseqEditor::x_GetDeleteCommand(), CSeq_feat_Handle::x_GetSeq_annot_Info(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CGff2Writer::xGenerateMissingTranscript(), CFeatTableEdit::xMakeGeneForFeature(), and CGff2Writer::xWriteFeature().

◆ GetAnnot() [3/6]

Definition at line 705 of file seq_feat_handle.hpp.

References CSeq_feat_EditHandle::CSeq_annot_EditHandle, and CSeq_feat_Handle::GetAnnot().

◆ GetAnnot() [4/6] ◆ GetAnnot() [5/6] ◆ GetAnnot() [6/6] ◆ GetB() double CSeq_graph_Handle::GetB ( void ) const inline ◆ GetBioObjectId() [1/3] ◆ GetBioObjectId() [2/3] ◆ GetBioObjectId() [3/3] ◆ GetBioseq_setCore() ◆ GetBioseqCore()

Get bioseq core structure.

Definition at line 144 of file bioseq_handle.cpp.

References CBioseq_Info::GetBioseqCore(), and CBioseq_Handle::x_GetInfo().

Referenced by CLoadSecondaryAccessions::apply(), BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CAlnVec::CalculateScore(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), ChangeSeqId(), CValidError_bioseq::CheckSourceDescriptor(), CBarcodeTool::ClickLink(), COligoSpecificityTemplate::COligoSpecificityTemplate(), Convert_Seq_id_Bioseq(), CCreateProteinId::create_protein_ids(), CChangeSeqdescTitleCommand::Execute(), CEditingActionFlatFile::Find(), CEditingActionSeqid::Find(), CHTMLFormatterEx::FormatLocation(), CVecscreenRun::CFormatter::FormatResults(), CFlatFileGenerator::Generate(), CAlignFormatUtil::GetAlignedRegionsURL(), CSGAlignmentJob::GetAlignType(), CDataTrackUtils::GetAlignType(), CConvertBadCdsAndRnaToMiscFeat::getBacterialPartialNonextendable(), CBioseqContext::GetBioseqIds(), CValidErrorFormat::GetBioseqLabel(), CAddSecondary::GetCommand(), CRemoveSeqHistAssembly::GetCommand(), CModifySeqId::GetCommand(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CAlignFormatUtil::GetDbType(), GetGIForSeqId(), CBioseq_Handle::GetLocalIdOrNull(), CBioseq_Handle::GetNonLocalIdOrNull(), CBioseq_Handle::GetObjectCore(), CEditSequence::GetSeqTitle(), CPaintAlignment::GetSeqTitle(), CDUpdater::getSequencesFromGB(), CTaxTreeDS_ObjMgr::GetTaxMap(), ListOrphanProteins(), CId1FetchApp::LookUpGI(), CEditingActionDescLocalId::Modify(), CCleanup::MoveFeatToProtein(), CSelectTargetDlg::OnSelTargetAcceptClick(), CFixForTransSplicing::PopulateListBox(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), CBlastFormat::PrintReport(), RetrievePartsOfLargeChromosome(), CBulkCDS::RowToScopedObjects(), CBulkGene::RowToScopedObjects(), CBulkMiscFeat::RowToScopedObjects(), CBulkRna::RowToScopedObjects(), SrcEditDialog::RowToScopedObjects(), CDemoApp::Run(), CSingleFeatValidator::s_BioseqHasRefSeqThatStartsWithPrefix(), s_BlastXMLAddIteration(), s_GetDisplayLabel(), s_GetQueryBioseq(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq(), CQueryDataTestFixture::s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(), s_QueryVectorToBioseqSet(), s_SetBlastXMLSearch(), s_SetCloneInfo(), CSplitCacheApp::TestSplitBlob(), CChangeSeqdescTitleCommand::Unexecute(), CValidError_bioseq::ValidateSeqId(), CId1FetchApp::WriteQualityScores(), CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableRnaQuals(), CAsn2FlatApp::x_AddSNPAnnots(), CSingleFeatValidator::x_BioseqHasNmAccession(), CSingleFeatValidator::x_CalculateLocationGaps(), CBlastFormat::x_CreateSubjectBioseq(), CDisplaySeqalign::x_DisplayBl2SeqLink(), CShowBlastDefline::x_FillDeflineAndId(), CAlnGraphic::x_GetAlnInfo(), CAutoDef::x_GetFeatureClauses(), CDisplaySeqalign::x_HTMLSeqIDLink(), CSequenceDataTester::x_Init(), CShowBlastDefline::x_InitDefline(), CSingleFeatValidator::x_IsMostlyNs(), CDisplaySeqalign::x_PrepareDynamicFeatureInfo(), CBlastFormat::x_PrintAirrRearrangement(), CDisplaySeqalign::x_PrintDefLine(), CBlastFormat::x_PrintIgTabularReport(), CBlastFormat::x_PrintTabularReport(), CBlastFormat::x_PrintTaxReport(), CBioseqContext::x_SetId(), and CValidError_bioseq::x_TranscriptIDsMatch().

◆ GetBioseqHandle() [1/2]

Get Bioseq handle from the TSE of this Seq-entry.

Definition at line 159 of file seq_entry_handle.cpp.

References CTSE_Handle::GetBioseqHandle(), and CSeq_entry_Handle::GetTSE_Handle().

Referenced by ApplySrcTableToSeqEntry(), BuildFeatureSeqTableFromSeqEntry(), CCmdAddCDS::Execute(), CCleanup::GetProteinName(), CMiscSeqTableColumn::GetRelatedApplyObjects(), GetResolveOrder(), OneRowOk(), CReorderSequencesDlg::ReadBioseq(), CSequenceUpdater::x_FormNewAlignment(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), and CFeatureTableReader::xMoveCdRegions().

◆ GetBioseqHandle() [2/2] ◆ GetBioseqLength() TSeqPos CBioseq_Handle::GetBioseqLength ( void ) const

Definition at line 267 of file bioseq_handle.cpp.

References CBioseq_Handle::GetInst_Length(), CSeqMap::GetLength(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), and CBioseq_Handle::IsSetInst_Length().

Referenced by CGapAnalysis::AddBioseqGaps(), AddIRDMiscFeature(), CFlatFileFactoryBuilder::AddItem(), AddNamedrRna(), CSAM_CIGAR_Formatter::AddRow(), CAdjustForConsensusSpliceSite::AdjustCDS(), AdjustMappedStop(), AgpWrite(), CPaintAlignment::AlignPosToSeqPos(), CAlnGraphic::AlnGraphicDisplay(), CConvertDescToFeatComment::apply(), CConvertDescToFeatSource::apply(), CConvertDescToFeatPub::apply(), CConvertDescToFeatPubConstraint::apply(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CRecomputeIntervals::apply(), CConvertGapsBySize::apply(), CExpandGaps::apply(), CCombineAdjacentGaps::apply_impl(), BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CDensityMapDS::CDensityMapDS(), CheckDuplicates(), CVisibleRange::Clamp(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CFeatureGenerator::SImplementation::ConvertMixedAlignToAnnot(), CNewCleanup_imp::ConvertSeqLocWholeToInt(), CSeq_loc_Conversion::ConvertSimpleLoc(), CreateControlRegion(), CEditSequence::CreateControls(), CreateMicrosatellite(), CSeqVector::CSeqVector(), CSequenceAmbigTrimmer::DoTrim(), EndAdded(), CMacroEngineParallel::Exec(), CGBObjectLoader::Execute(), ExtendLocationForTranslExcept(), CCleanup::ExtendToStopCodon(), CWinMaskCountsGenerator::fastalen(), CInternalStopFinder::FindStartStopRanges(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_StartStopCodon::Get(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), CExonFromCds::GetCommand(), CAddLinkageToGaps::GetCommand(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), CAlignFormatUtil::GetFrame(), CGffIdGenerator::GetGffSourceId(), GetIsLength(), CRemoveSequencesDlg::GetLabel(), CDefaultLengthGetter::GetLength(), GetLength(), CBlobSplitterImpl::GetLength(), CGuiObjectInfoSeq_align::GetLinks(), CAutoDef::GetMasterLocation(), GetOverlappingFeatures(), GetPercentN(), GetProteinName(), GetProteinString(), GetProteinWeight(), CBioseq_Handle::GetRangeSeq_loc(), CApplyRNAITSDlg::GetRNAITSList_AlignCoordFromDlg(), CApplyRNAITSDlg::GetRNAITSList_SeqCoordFromDlg(), CPaintAlignment::GetSegments(), CSeqMap::GetSeqMapForSeq_loc(), CAlnWriter::GetSeqString(), CScope_Mapper_Sequence_Info::GetSequenceLength(), GetSortedCuts(), GetStop(), HasExcludedAnnotation(), CAlnGraphic::Init(), InitSplicedsegFromPairwiseAln(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), CContigAssembly::IsAtLeastHalfDovetail(), CValidError_feat::IsIntronShort(), CValidError_annot::IsLocationUnindexed(), CRemoveUnindexedFeatures::IsLocationUnindexed(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), CCdsToMatPeptide::MergeConvert(), CBioseqEditor::OnCreateBiosourceFeat(), CBioseqEditor::OnCreateFeature(), CAlignmentAssistant::OnReverseStrand(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), PackSeqPntCheckCpp(), PatchTargetSequence(), CValidError_bioseq::PctNs(), CGlimmerReader::Read(), CDustMaskApplication::Run(), CDemoApp::Run(), CWinMaskApplication::Run(), CFeatTreeSampleApp::Run(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_CreateObjList(), s_DoNWalign(), CSequenceUpdater::s_ExtendOneEndOfSequence(), s_GetCigarString(), s_GetFrame(), s_GetNaLength(), s_GetTails(), s_GetTopology(), s_LocIntervalsSpanOrigin(), s_Render_SeqFeat(), s_RunBlast2NASeq(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToXMLHit(), s_SeqLocEndsOnBioseq(), s_SeqMapForHandle(), SeqIntCheckCpp(), SeqIntPartialCheck(), SeqLocToBioseq(), SeqPntCheckCpp(), CPaintAlignment::SeqPosToAlignPos(), CIgBlastTabularInfo::SetAirrFormatData(), CLengthSubpanel::SetClusters(), CBlastTabularInfo::SetFields(), CIgBlastTabularInfo::SetIgAnnotation(), CMacroFunction_LocationDistConstraint::TheFunction(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CAlignmentAssistant::TranslateLocations(), CReportTrim::Trim(), CCrossAlnRenderer::Update(), CIntronValidator::Validate(), CFarPointerSeq::ValidateAlignment(), CCreateSeqHistForTpa::ValidateAlignments(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateWGSMaster(), CHugeFileDemoApp::x_AddUserObjects(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), CEditObjectSeq_feat::x_AdjustCircularGene(), CIgBlast::x_AnnotateC(), CSingleFeatValidator::x_CalculateLocationGaps(), CFindITSParser::x_CreateMiscRna(), CFindITSParser::x_CreateRRna(), CImportFeatTable::x_DoImportCDS(), CComponentSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CGenbankGatherer::x_DoSingleSection(), CAlignGlyph::x_DrawAlignRowSequence(), CFastaRetrieveJob::x_DumpBioseq(), CSGSegmentMapJob::x_Execute(), CSFTranslationJob::x_Execute(), CIgBlast::x_ExtendAlign3end(), CIgBlast::x_ExtendAlign5end(), CIgBlast::x_FillJDomain(), CVectorTrimPanel::x_FindCompleteDeletions(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CAlnVecRow::x_GetAlignmentTooltip_General(), CAlnVecRow::x_GetDescrTooltip(), CAlignSeqTableModel::x_GetLength(), CUpdateSeqPanel::x_GetNameAndLength(), CScore_BlastRatio::x_GetPerfectScore(), CGuiObjectInfoSeq_feat::x_GetProductLengthRow(), CVectorTrimPanel::x_GetSortedCuts(), CMacroEngineParallel::x_GetThreadCount(), CAlignedFeatureGraph::x_GetTooltip(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CDisplaySeqalign::x_InitDefLinesHeader(), CBlastHitMatrix::x_InitPort(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CIntronValidator::x_IsIntronShort(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), COligoSpecificityCheck::x_NW_alignment(), CFindITSParser::x_ParseLine(), CValidError_imp::x_ReportInvalidFuzz(), CBlastFormat::x_ReverseQuery(), CCDSTranslationPanel::x_SetLocationForProtein(), CHitMatrixWidget::x_SetPortLimits(), CLocusItem::x_SetTopology(), CSequenceAmbigTrimmer::x_TrimToNothing(), CValidError_bioseq::x_ValidateAbuttingUTR(), CValidError_graph::x_ValidateGraphLocation(), CCdregionValidator::x_ValidateParentPartialness(), CValidError_align::x_ValidateSeqLength(), CGff3Writer::xAssignSourceEndpoints(), and CGff3Writer::xWriteSequenceHeader().

◆ GetBioseqMolType()

Get some values from core:

Definition at line 397 of file bioseq_handle.cpp.

References CBioseq_Handle::GetSequenceType().

Referenced by CHTMLFormatterEx::FormatLocation(), CScore_FrameShifts::Get(), GetProteinWeights(), GetTitle(), CValidError_bioseq::IsMrna(), CWriteUtil::IsNucleotideSequence(), CWriteUtil::IsProteinSequence(), CTabularFormatter_Indels::Print(), CTabularFormatter_StartCodonChanges::Print(), s_GetMolType(), variation_ref::CVariationUtil::SetVariantProperties(), VerifyMolType(), CHugeFileDemoApp::x_AddUserObjects(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), and variation_ref::CVariationUtil::x_SetVariantProperties().

◆ GetBlobId() ◆ GetBlobVersion() ◆ GetBounds() ◆ GetCit() ◆ GetClass()

Definition at line 205 of file bioseq_set_handle.cpp.

References CBioseq_set_Info::GetClass(), and CBioseq_set_Handle::x_GetInfo().

Referenced by AddBioseqToBioseqSet(), AddDescToSeqEntry(), CCleanup::AddGenBankWrapper(), AddOrgToDefline(), CCleanup::AddProtein(), CReportTrim::AdjustAndTranslate(), CPackageFeaturesOnParts::apply(), CRemAllProtTitles::apply(), CRemProtTitles::apply(), CApplyObject::ApplyChange(), COrgGeneralPanel::ApplyCommand(), ApplySrcTableToSeqEntry(), BOOST_AUTO_TEST_CASE(), CApplyObject::CApplyObject(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CCleanup::ConvertSrcFeatsToSrcDescs(), CountDefLineConflicts(), CNewCleanup_imp::CreateMissingMolInfo(), CRemoveSeqId::CRemoveSeqId(), CSeqsetIndex::CSeqsetIndex(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), DeleteProteinAndRenormalizeNucProtSet(), DemoteCDSToNucSeq(), CCmdAddSeqEntry::Execute(), CCmdCreateFeat::Execute(), CCmdPromoteCDS::Execute(), CValidError_base::GetAppropriateXrefParent(), CEditSequenceEnds::GetCommand(), CFarPointerSeq::GetCommand(), CSegregateSets::GetCommand(), CBioseq_Handle::GetComplexityLevel(), CBioseq_set_Handle::GetComplexityLevel(), GetDeleteSequenceCommand(), CEditObjectSeq_desc::GetEditCommand(), CBioseq_Handle::GetExactComplexityLevel(), CBioseq_set_Handle::GetExactComplexityLevel(), CAutoDef::GetMasterLocation(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CMiscSeqTableColumn::GetRelatedApplyObjects(), GetSetParent(), GetTextObjectDescription(), IsInGenProdSet(), CSGSequenceDS::IsPopSet(), CAutoDef::IsSegment(), IsSeqOrNP(), CmRNACDSLinker::LinkByProduct(), CInfluenzaSet::MakeSet(), CCleanup::MoveOneFeatToPubdesc(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CSequesterSets::OnSequester(), CMytestApplication::PlayAroundWithSuggestIntervals(), PromoteCDSToNucProtSet(), PropagateToTarget(), CSegregateSetsBase::ReadBioseq(), CSequesterSets::RecursiveCollectSets(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), CNewCleanup_imp::RemoveBadProteinTitle(), CCleanup::RenormalizeNucProtSets(), s_AddBioseqToNucProtSet(), s_AddBioseqToPartsSet(), s_DescriptorPropagateDown(), s_GetNPParent(), s_GetSeq_featAcc(), s_MakeGroupsForUniqueValues(), CMacroFunction_RemoveSingleItemSet::s_RemoveSingleItemSet(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_StandaloneProt(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), IEditingAction::SetTopSeqEntry(), CMacroFunction_ApplyPublication::TheFunction(), CCmdPromoteCDS::Unexecute(), UpdateAllDefinitionLine(), CBiosampleChkApp::UpdateBioSource(), CValidError_annot::ValidateSeqAnnotContext(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CGather_Iter::x_AddSeqEntryToStack(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CSubmissionWizard::x_ApplyUserDescriptorToRecord(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CVectorTrimPanel::x_DeleteSelected(), CAdjustFeaturesForGaps::x_DoOne(), CFlatGatherer::x_GatherCDSReferences(), CSequenceUpdater::x_GetOldBseq_EntryHandle(), CBioseqContext::x_IsPart(), CVectorTrimPanel::x_TrimSelected(), CMRNAValidator::x_ValidateCommonMRNAProduct(), and CGff2Writer::x_WriteSeqEntryHandle().

◆ GetColl() ◆ GetComment() [1/2] const string & CSeq_feat_Handle::GetComment ( void ) const inline

Definition at line 419 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetComment(), CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Handle::GetSNPComment(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CExplodeRNAFeats::apply(), CDemoApp::Run(), s_AreFeatureLabelsSame(), s_CheckQuals_conflict(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualProtNote(), CSourceFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualsSite(), CFeatureItem::x_AddRegulatoryClassQual(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CFeatureItem::x_CleanQuals(), CAutoDef::x_Is5SList(), CFeatureSearchJob::x_SearchFeatures(), CGff3Writer::xAssignFeatureAttributeNote(), and CGtfWriter::xAssignFeatureAttributeNote().

◆ GetComment() [2/2] const string & CSeq_graph_Handle::GetComment ( void ) const inline ◆ GetComp() TSeqPos CSeq_graph_Handle::GetComp ( void ) const inline ◆ GetCompleteBioseq()

Get the complete bioseq.

Definition at line 138 of file bioseq_handle.cpp.

References CBioseq_Info::GetCompleteBioseq(), and CBioseq_Handle::x_GetInfo().

◆ GetCompleteBioseq_set()

Return the complete bioseq-set object.

Any missing data will be loaded and put in the bioseq members.

Definition at line 78 of file bioseq_set_handle.cpp.

References CBioseq_set_Info::GetCompleteBioseq_set(), and CBioseq_set_Handle::x_GetInfo().

Referenced by CCleanup::AddProtein(), CEditsSaver::Attach(), CNewCleanup_imp::BasicCleanupBioseqSetHandle(), CheckDeflineMatches(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CEditsSaver::Detach(), CCmdAddSeqEntry::Execute(), GetAccessionFromObjects(), CReorderSequencesDlg::GetCommand(), CSegregateSets::GetCommand(), CWithdrawSequences::GetCommand(), CBioseq_set_Handle::GetCompleteObject(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), PropagateDescriptor(), CRemoveSet::remove_set(), CRemoveSet::remove_sets_from_set(), CReorderSequencesDlg::ReorderById(), s_DescriptorPropagateDown(), s_GetAccessionForSeqdesc(), s_HasTopSetSiblings(), s_IsBioseqInSet(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CValidError_bioseqset::ValidateNucProtSet(), CDesktopDataBuilder::x_CreateSet(), and CCmdInsertBioseqSet::x_TransferSeqSet().

◆ GetCompleteObject() [1/4] ◆ GetCompleteObject() [2/4] ◆ GetCompleteObject() [3/4] ◆ GetCompleteObject() [4/4] ◆ GetCompleteSeq_annot()

Complete and return const reference to the current seq-annot.

Definition at line 77 of file seq_annot_handle.cpp.

References CSeq_annot_Info::GetCompleteSeq_annot(), and CSeq_annot_Handle::x_GetInfo().

Referenced by CRemoveSeqAnnot::ApplyToSeqAnot(), CEditsSaver::Attach(), CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), BOOST_AUTO_TEST_CASE(), Convert_Seq_entry_Seq_annot(), Convert_Seq_loc_Seq_annot(), CCleanup::ConvertSrcFeatsToSrcDescs(), CSeq_annot_Handle::GetCompleteObject(), CNAUtils::GetNATrackInfo(), CAutoDef::GetOneFeatureClauseList(), CSeq_annot_Handle::GetSeq_annotCore(), CCleanup::MoveFeatToProtein(), CPromote::PromoteCdregion(), CPromote::PromoteFeatures(), CPromote::PromotePub(), CPromote::PromoteRna(), CEditsSaver::Remove(), CCleanup::RescueSiteRefPubs(), CTestProtProd_Cdd::RunTest(), s_DivvyUpAlignments_ProcessAnnot(), s_GetClipLoc(), s_MakeGroupsForUniqueValues(), s_SetSearchParam(), CClippedScorer::ScoreAlignments(), CValidError_imp::Setup(), CValidError_imp::Validate(), CValidator::Validate(), CValidError_annot::ValidateSeqAnnot(), CAutogeneratedCleanup::x_FallBackSeqAnnotMethod(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CAnnotGetter::x_GetCompleteSeqAnnot(), CwxAnnotConfigDlg::x_InitAnnotList(), CSGSegmentSmearJob::x_LoadFromNA(), CSGAnnotJob::x_PercentileButNotMax(), CGff2Writer::x_WriteSeqAnnotHandle(), CGff3Writer::x_WriteSeqAnnotHandle(), and CGvfWriter::x_WriteSeqAnnotHandle().

◆ GetCompleteSeq_entry()

Complete and get const reference to the seq-entry.

Definition at line 99 of file seq_entry_handle.cpp.

References CSeq_entry_Info::GetCompleteSeq_entry(), and CSeq_entry_Handle::x_GetInfo().

Referenced by CAlignmentAssistant::AdjustBioseq(), CAddSequences::apply(), CRemoveUnreviewed::Apply(), CReorderStructuredComment::apply(), CChangeStructuredCommentKeyword::apply_to_seq_and_feat(), CAddCitSubForUpdate::apply_to_seq_and_feat(), CAppendModToOrg::apply_to_seq_and_feat(), CModifyStructuredComment::apply_to_seq_and_feat(), CEditsSaver::Attach(), AutofixCommand(), AutofixCommandHugeMode(), CNewCleanup_imp::BasicCleanupSeqEntryHandle(), BOOST_AUTO_TEST_CASE(), CachedTaxonomyLookupCommand(), CCleanup::CleanupCollectionDates(), CleanupCommand(), CleanupHugeFileCommand(), CSampleEditSaver::CommitTransaction(), Convert_Seq_id_Bioseq_set(), Convert_Seq_id_Seq_entry(), CSequenceEditingEventHandler::ConvertSetType(), CSequenceEditingEventHandler::CreateSeqSubmit(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CNewCleanup_imp::ExtendedCleanupSeqEntryHandle(), CUnculTaxTool::FindBioSource(), CAddFluComments::FindBioSource(), CSequenceEditingEventHandler::FixNonReciprocalLinks(), objects::CFixSuspectProductName::FixSuspectProductNames(), COutput_SerialFormat::Format(), CFlatFileGenerator::Generate(), GetChangeStrainForwardingCommand(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), CTruncateCDS::GetCommand(), CSeq_entry_Handle::GetCompleteObject(), GetDeleteAllFeaturesCommand_Ex(), GetRmCultureNotesCommand(), CEditSequence::GetSequence(), GetTitle(), CValidator::GetTSACDSOnMinusStrandErrors(), CValidator::GetTSAConflictingBiomolTechErrors(), CValidator::GetTSANStretchErrors(), CCleanupApp::HandleSeqEntry(), CCleanupApp::HandleSeqID(), CFlatFileGenerator::HasInference(), ImportFeatTblTesting(), CMacroBioData_SeqSetIter::IsBegin(), CMacroBioData_TSEntryIter::IsBegin(), IsDeltaOrFarSeg(), CId1FetchApp::LookUpGI(), CCdsToMatPeptide::MergeConvert(), CSequesterSets::OnAccept(), CEditSequence::OnAccept(), CAlignmentAssistant::OnValidate(), SBlobInserter::operator()(), CDescPlacementPanel::PopulateLocationChoices(), CSequenceEditingEventHandler::PrepareSeqSubmit(), CSplitCacheApp::ProcessBlob(), CSplitCacheApp::ProcessEntry(), CConversionApp::Read(), CEditsSaver::Remove(), CScope_Impl::RemoveEntry(), CCleanup::RenormalizeNucProtSets(), CBulkCDS::RowToScopedObjects(), CBulkGene::RowToScopedObjects(), CBulkMiscFeat::RowToScopedObjects(), CBulkRna::RowToScopedObjects(), SrcEditDialog::RowToScopedObjects(), CDemoApp::Run(), CSampleLds2Application::Run(), s_ActualizeUpdateDate(), s_DescriptorPropagateDown(), s_DoSmartProcessing(), s_GetAccessionForSeqdesc(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CSequenceEditingEventHandler::SaveASN1File(), CSequenceEditingEventHandler::SaveSubmissionFile(), CScope_Impl::SelectNone(), CValidErrorSuppress::SetSuppressedCodes(), CValidErrorFormat::SetSuppressionRules(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CValidError_imp::SetTSE(), CValidError_imp::Setup(), SpecificHostCleanupCommand(), CCleanup::TaxonomyLookup(), TaxonomyLookupCommand(), CSplitCacheApp::TestSplitBlob(), TrimEntry(), TSeqLocVector2Bioseqs(), CCmdAddSeqEntry::Unexecute(), CValidator::Validate(), CValidError_imp::Validate(), CAsnvalThreadState::ValidateAsync(), CValidError_bioseq::ValidateBioseq(), CValidError_imp::ValidateCitations(), CValidError_annot::ValidateSeqAnnot(), CSimpleProjectView::x_ActivateTextView(), CSequenceUpdater::x_AdjustOldCDSProduct(), CValidError_bioseq::x_CheckForMultipleComments(), CCleanupJob::x_CreateProjectItems(), CTableDataValidateJob::x_FetchAll(), CCountryConflict::x_FindBioSource(), CLatLonTool::x_FindBioSource(), CSequenceUpdater::x_ImportCDSProduct(), CSeqMasterIndex::x_Initialize(), CTextPanel::x_LoadASN(), CAgpconvertApplication::x_LoadTemplate(), CSequenceUpdater::x_MakeNewEntry(), CPrimeCacheApplication::x_Process_Ids(), CHugeFileDemoApp::x_ReadAndWritePull(), CHugeFileDemoApp::x_ReadAndWritePush(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CHugeFileDemoApp::x_ShowSeqSizes(), CValidError_bioseq::x_ValidateBarcode(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CValidError_bioseq::x_ValidateMultiplePubs(), CFeatureTableReader::xAddProteinToSeqEntry(), CBsDiffApp::xLoadSeqEntry(), and CAnnotWriterApp::xTryProcessInputId().

◆ GetComplexityLevel() [1/2]

Go up to a certain complexity level (or the nearest level of the same priority if the required class is not found): level class 0 not-set (0) , 3 nuc-prot (1) , – nuc acid and coded proteins 2 segset (2) , – segmented sequence + parts 2 conset (3) , – constructed sequence + parts 1 parts (4) , – parts for 2 or 3 1 gibb (5) , – geninfo backbone 1 gi (6) , – geninfo 5 genbank (7) , – converted genbank 3 pir (8) , – converted pir 4 pub-set (9) , – all the seqs from a single publication 4 equiv (10) , – a set of equivalent maps or seqs 3 swissprot (11) , – converted SWISSPROT 3 pdb-entry (12) , – a complete PDB entry 4 mut-set (13) , – set of mutations 4 pop-set (14) , – population study 4 phy-set (15) , – phylogenetic study 4 eco-set (16) , – ecological sample study 4 gen-prod-set (17) , – genomic products, chrom+mRNa+protein 4 wgs-set (18) , – whole genome shotgun project 0 other (255)

Definition at line 578 of file bioseq_handle.cpp.

References _ASSERT, CBioseq_set_Base::eClass_other, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), last(), and CBioseq_set_Handle::sx_GetComplexityTable().

Referenced by CBioseq_Handle::GetExactComplexityLevel().

◆ GetComplexityLevel() [2/2] ◆ GetData()

Definition at line 389 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetData(), and CSeq_feat_Handle::GetSeq_feat().

◆ GetDate() ◆ GetDbxref()

Definition at line 533 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetDbxref(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by variation::GetFocusLocusIDs(), GetMrnasForGene(), HasGeneIdXref(), IsDuplicate(), CDemoApp::Run(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneID(), s_SkipFeature(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualDbXref(), CSourceFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualsGene(), CSeq_id_Resolver__LRG::x_Create(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CVcfWriter::x_WriteFeatureInfo(), CGff2Writer::xAssignFeatureAttributeDbxref(), and CGffIdGenerator::xGetGenericSuffix().

◆ GetDescr() [1/3]

Definition at line 189 of file bioseq_handle.cpp.

References CBioseq_Base_Info::GetDescr(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddPartialToProteinTitle(), CNewCleanup_imp::ClearEmptyDescr(), IAlignRowHandle::GetOrgLabel(), CBlastQuerySourceOM::GetTitle(), CWriteUtil::IsNucleotideSequence(), CWriteUtil::IsProteinSequence(), variation::IsRefSeqGene(), variation::IsRightPartial(), CNewCleanup_imp::ProtSeqBC(), CCleanup::RemoveUnseenTitles(), s_GetMolInfoAndSrcDescriptors(), s_GetTitle(), CAutogeneratedCleanup::x_BasicCleanupBioseqDescr(), CAlnVecRow::x_GetAlignmentTooltip_General(), CGffFeatureContext::xAssignSequenceHasBioSource(), and CGffFeatureContext::xAssignSequenceIsGenomicRecord().

◆ GetDescr() [2/3] ◆ GetDescr() [3/3] ◆ GetDim() ◆ GetEditHandle() [1/4]

Get 'edit' version of handle.

Definition at line 150 of file bioseq_handle.cpp.

References CScope_Impl::GetEditHandle(), and CBioseq_Handle::x_GetScopeImpl().

Referenced by AddBioseqToBioseq(), AddBioseqToBioseqSet(), AddIRDMiscFeature(), CCleanup::AddPartialToProteinTitle(), CCleanup::AddProteinTitle(), AdjustForCDSPartials(), CTrimN::apply(), CApplyObject::ApplyChange(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CNewCleanup_imp::BasicCleanupSeqIds(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::ClearEmptyDescr(), ConvertRawToDeltaByNs(), CAddIdChecker::Do(), CRemoveIdChecker::Do(), CResetIdChecker::Do(), CRemoveBioseqChecker::Do(), CRemoveFeatChecker::Do(), CAddFeatChecker::Do(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CNewCleanup_imp::FixUnsetMolFromBiomol(), GetAnnotHandle(), CCleanup::MoveFeatToProtein(), CPromote::PromoteCdregion(), CPromote::PromoteFeatures(), CPromote::PromotePub(), CPromote::PromoteRna(), CNewCleanup_imp::ProtSeqBC(), CNewCleanup_imp::RemoveSingleStrand(), RetranslateCdregion(), RetranslateCDS(), CDemoApp::Run(), s_MoveProteinSpecificFeats(), CCleanup::SetMolinfoBiomol(), CCleanup::SetMolinfoTech(), CSeq_entry_EditHandle::SetSeq(), CMacroFunction_TrimTerminalNs::TheFunction(), TrimSequenceAndAnnotation(), CBiosampleChkApp::UpdateBioSource(), CHugeFileDemoApp::x_AddUserObjects(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst(), CAutogeneratedCleanup::x_BasicCleanupBioseqDescr(), CPromote::x_CopyCdregionToRNA(), CAutodefJob::x_MakeChanges(), CPromote::x_MakeNewBioseq(), CHugeFileDemoApp::x_ReadAndWritePull(), CSequenceAmbigTrimmer::x_SliceBioseq(), CVectorTrimPanel::x_TrimSelected(), CSequenceAmbigTrimmer::x_TrimToNothing(), and CBioseqContext::~CBioseqContext().

◆ GetEditHandle() [2/4] ◆ GetEditHandle() [3/4]

Get 'edit' version of handle.

Definition at line 102 of file seq_annot_handle.cpp.

References CScope_Impl::GetEditHandle(), and CSeq_annot_Handle::x_GetScopeImpl().

Referenced by CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), DemoteCDSToNucSeq(), CAddFeatChecker::Do(), CCmdDelSeq_align::Execute(), CCmdPromoteCDS::Execute(), GetDeleteAllFeaturesCommand_Ex(), ProcessForTrimAndSplitUpdates(), CPromote::PromoteCdregion(), PromoteCDSToNucProtSet(), CPromote::PromoteFeatures(), CPromote::PromotePub(), CPromote::PromoteRna(), CCleanup::RepairXrefs(), CDemoApp::Run(), s_DetachAnnotFromScope(), CCmdPromoteCDS::Unexecute(), CSeq_align_Handle::Update(), CSeq_graph_Handle::Update(), CNewCleanup_imp::x_CollapseSet(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CAutogeneratedCleanup::x_FallBackSeqAnnotMethod(), CSeq_align_Handle::x_RealRemove(), CSeq_graph_Handle::x_RealRemove(), and CGff2Writer::xGenerateMissingTranscript().

◆ GetEditHandle() [4/4]

Get 'edit' version of handle.

Definition at line 194 of file seq_entry_handle.cpp.

References CScope::GetEditHandle(), and CSeq_entry_Handle::GetScope().

Referenced by CCleanup::AddProtein(), AdjustForCDSPartials(), CApplyObject::ApplyChange(), ApplyPolicyToFeature(), CProSplign::AssignGeneticCode(), CCleanup::AutodefId(), BioseqSetDescriptorPropagateDown(), BOOST_AUTO_TEST_CASE(), CCmdChangeSeqEntry::CCmdChangeSeqEntry(), DeleteProteinAndRenormalizeNucProtSet(), DemoteCDSToNucSeq(), DivvyUpAlignments(), CCmdAddSeqEntry::Execute(), CCmdPromoteCDS::Execute(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), CFlatFileGenerator::Generate(), CSeq_entry_EditHandle::GetSingleSubEntry(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CSequesterSets::OnAccept(), CBioseqEditor::OnDeleteBiosourceFeat(), CHugeFileDemoApp::ProcessHugeSeqEntry(), PromoteCDSToNucProtSet(), CCleanup::RenormalizeNucProtSets(), RetranslateCDS(), CDemoApp::Run(), s_ActualizeUpdateDate(), s_DescriptorPropagateDown(), s_MakeGroupsForUniqueValues(), s_PromoteSingletonSetsInSet(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CCmdAddSeqEntry::Unexecute(), CCmdDelSeq_feat::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CCmdPromoteCDS::Unexecute(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CNewCleanup_imp::x_CollapseSet(), CBioseqEditor::x_DeleteObject(), CSequenceUpdater::x_FormNewAlignment(), CBioseqEditor::x_GetDeleteCommand(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CPromote::x_PromoteRna(), CCmdChangeSeq_feat::x_Switch(), CCmdInsertBioseqSet::x_TransferSeqSet(), CFeatureTableReader::xAddProteinToSeqEntry(), and CFeatureTableReader::xMoveCdRegions().

◆ GetExactComplexityLevel() [1/2]

Return level with exact complexity, or empty handle if not found.

Definition at line 612 of file bioseq_handle.cpp.

References CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetComplexityLevel(), CSeq_entry_Handle::GetSet(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), and CSeq_entry_Handle::Reset().

Referenced by CValidError_bioseq::CdError(), GetParentForPart(), s_GetParent(), s_HasSegments(), CPromote::x_CopyCdregionToRNA(), CFlatGatherer::x_GatherReferences(), CBioseqContext::x_HasParts(), CBioseqContext::x_IsInGPS(), CBioseqContext::x_IsInNucProt(), CBioseqContext::x_IsInSGS(), CCdregionValidator::x_IsProductMisplaced(), CPromote::x_PromoteCdregion(), and CPromote::x_PromoteRna().

◆ GetExactComplexityLevel() [2/2] ◆ GetExcept() bool CSeq_feat_Handle::GetExcept ( void ) const inline ◆ GetExcept_text() const string & CSeq_feat_Handle::GetExcept_text ( void ) const inline

Definition at line 563 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetExcept_text(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by CScore_RibosomalSlippage::Get(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), CDemoApp::Run(), s_CheckQuals_cdregion(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualExceptions(), CFeatureSearchJob::x_SearchFeatures(), CSingleFeatValidator::x_ValidateGeneXRef(), CGff2Writer::xAssignFeatureAttributeException(), CGff2Writer::xAssignFeatureAttributeRibosomalSlippage(), CGtfWriter::xAssignFeaturesTranscript(), and CGff2Writer::xGenerateMissingTranscript().

◆ GetExp_ev() ◆ GetExt()

Definition at line 473 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetExt(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by CGvfWriteRecord::AssignSource(), CGvfWriteRecord::AssignType(), CWriteUtil::GetModelEvidence(), CDemoApp::Run(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualExt(), CFeatureItem::x_AddQualsRegion(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeParent(), CGvfWriteRecord::x_AssignAttributesCustom(), CGvfWriteRecord::x_AssignAttributeVarType(), CFeatureItem::x_HasMethodtRNAscanSE(), CVcfWriter::x_WriteFeatureFilter(), CVcfWriter::x_WriteFeatureGenotypeData(), CVcfWriter::x_WriteFeatureInfo(), CVcfWriter::x_WriteFeatureQual(), CGff2Writer::xAssignFeatureAttributesGoMarkup(), and CGtfWriter::xAssignFeatureMethod().

◆ GetExts() ◆ GetFeatSubtype()

Definition at line 435 of file seq_feat_handle.cpp.

References CSeqFeatData::eSubtype_variation, SAnnotTypeSelector::GetFeatSubtype(), CAnnotObject_Info::GetFeatSubtype(), CSeq_annot_Info::GetTableInfo(), CSeqTableInfo::GetType(), CSeq_feat_Handle::IsTableSNP(), CSeq_feat_Handle::x_GetAnnotObject_Info(), CSeq_feat_Handle::x_GetSeq_annot_Info(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

◆ GetFeatType()

Definition at line 421 of file seq_feat_handle.cpp.

References CSeqFeatData_Base::e_Imp, SAnnotTypeSelector::GetFeatType(), CAnnotObject_Info::GetFeatType(), CSeq_annot_Info::GetTableInfo(), CSeqTableInfo::GetType(), CSeq_feat_Handle::IsTableSNP(), CSeq_feat_Handle::x_GetAnnotObject_Info(), CSeq_feat_Handle::x_GetSeq_annot_Info(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

Referenced by IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CGeneFinder::GetAssociatedGeneInfo(), CValidator::CCacheImpl::GetFeatFromCache(), CGffIdGenerator::GetGffId(), CFeatTree::GetParent(), operator<<(), CPromote::PromoteCdregion(), CPromote::PromotePub(), CPromote::PromoteRna(), RestoreModelReadingFrame(), CDemoApp::Run(), s_SetFeatureId(), s_VerifyTree(), CSGAlignmentJob::x_LoadAlignmentFeats(), CGff2Writer::xAssignFeatureAttributeEcNumbers(), CGff2Writer::xAssignFeatureAttributeFunction(), CGff3Writer::xAssignFeatureAttributeParent(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xWriteFeature(), and CGff3Writer::xWriteNucleotideFeature().

◆ GetFeatureFetchPolicy() ◆ GetGeneXref() ◆ GetGraph() ◆ GetId() [1/3]

Definition at line 171 of file bioseq_handle.cpp.

References CBioseq_Info::GetId(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddProteinTitle(), CRemProtTitles::apply(), CApplyFBOL::apply(), CBarcodeTool::ApplyDbxrefs(), CApplyIndexerComments::ApplyToCSeq_entry(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CEditsSaver::Attach(), CNewCleanup_imp::BasicCleanupSeqIds(), CBioseqIndex::CBioseqIndex(), CheckTags(), CEditSequenceEnds::CollectLabels(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), CEditsSaver::Detach(), CRemoveBioseqChecker::Do(), CResetIds_EditCommand::Do(), CValidError_feat::DoesCDSHaveShortIntrons(), CCleanup::ExtendToStopCodon(), CHTMLFormatterEx::FormatProteinId(), CHTMLFormatterEx::FormatTranscriptId(), CBioseq_Handle::GetAccessSeq_id_Handle(), GetAnchors(), CProductColumn::GetApplyObjects(), GetBarcodeId(), GetBestBioseqLabel(), CGffIdGenerator::GetGffSourceId(), GetId(), CReorderSequencesDlg::GetIdLabel(), CValidator::CCacheImpl::GetIdToBioseq(), GetNewProtId(), GetNewProtIdFromExistingProt(), CEditSequence::GetSeqTitle(), CPaintAlignment::GetSeqTitle(), GetTitle(), variation::IsLRG(), CDLTestThread::Main(), CDLTest2Thread::Main(), CCdsToMatPeptide::MergeConvert(), CFileSubpanel::OnSelectButton(), SBlobCopier::operator()(), CAsnvalThreadState::ProcessSeqEntry(), CAsnvalThreadState::ProcessSeqSubmit(), CNewCleanup_imp::ProtSeqBC(), CAsnvalThreadState::ReadClassMember(), CNewCleanup_imp::RemoveSingleStrand(), CSeedTopApp::Run(), CMultiApplication::Run(), s_CheckQuals_cdregion(), s_FindGi(), s_FindLocalId(), s_FindSmartSeqId(), s_GetIdBase(), s_GetNameForBioseq(), s_GetProtApplyObjectsFeatures(), s_IdxGetBestIdString(), s_IsExternalRecord(), s_IsRefSeq(), s_IsSwissProt(), s_PrintIds(), s_SetIdList(), CFileSubpanel::SetClusters(), SetProteinFeature(), CIntronValidator::Validate(), CIdMapperScope::x_AddMappings(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualDbXref(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CAsnSubCacheCreateApplication::x_FetchMissingBlobs(), CVectorScreen::x_FindAccession(), CVectorScreen::x_FindLocalId(), CVectorScreen::x_FindTypeGeneral(), CDBSourceItem::x_GatherInfo(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CEditingBtnsPanel::x_GetSelectedLocations(), CCdregionValidator::x_GetShortIntrons(), CSeqMasterIndex::x_InitSeqs(), CBulkEditFeatDlg::x_IsRefSeq(), CGenericPropsPanel::x_IsRefSeq(), CFlatGatherer::x_MergeEqualBioSources(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMaster(), CFeatureGenerator::SImplementation::x_SetExceptText(), CBlastTabularInfo::x_SetSubjectIds(), CValidError_bioseq::x_SetupCommonFlags(), CHugeFileDemoApp::x_TestRW1848(), CScope_Impl::x_UpdateHandleSeq_id(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), CRNAValidator::x_ValidateTrnaType(), CGff3Writer::xAssignSourceSeqId(), CSrcWriter::xGatherBankitId(), and CSrcWriter::xGatherGi().

◆ GetId() [2/3] ◆ GetId() [3/3]

Definition at line 382 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetId(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by AddToFeatureIdColumn(), CmRNACDSLinker::AssignFeatureIds(), CAssignFeatureId::AssignHighestFeatureId(), CmRNACDSLinker::LinkSelectedFeatures(), SChildLess::operator()(), CDemoApp::Run(), s_IdXrefsAreReciprocal(), s_SetFeatureId(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CCmdAssignFeatLocalIds::x_CreateActionCmd(), CFeatTableEdit::xCreateMissingParentGene(), CFeatTableEdit::xGenerateMissingMrnaForCds(), CFeatTableEdit::xGenerateTranscriptOrProteinId(), and CFeatTableEdit::xGetIdStr().

◆ GetIds() ◆ GetInitialSeqIdOrNull() ◆ GetInst()

Definition at line 207 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddProteinTitle(), CTrimN::apply(), CConvertGapsBySize::apply(), CExpandGaps::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CCombineAdjacentGaps::apply_impl(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CValidError_bioseq::CheckSourceDescriptor(), CCleanup::ConvertDeltaSeqToRaw(), ConvertRawToDeltaByNs(), CLocationEditPolicy::Extend5(), ExtractExtraIds(), IEditingActionInst::Find(), MemetoFunctions< CBioseq_EditHandle, CSeq_inst >::Get(), CMolInfoField::GetApplyObjects(), CCorrectRNAStrandDlg::GetCommand(), CAddLinkageToGaps::GetCommand(), GetDeltaSeqForPosition(), GetNucleotideParent(), CAutoDef::GetOneDefLine(), GetRetranslateCDSCommand(), GetReverseComplimentSequenceCommand(), MakeSeqVectorForResidueCounting(), CRestoreRNAediting::OnApply(), PatchTargetSequence(), RemoteFetchLongNucleotideBioseq(), CNewCleanup_imp::RemoveSingleStrand(), RetranslateCdregion(), CRetranslateCDS::RetranslateCDSCommand(), CAddGlobalCodeBreak::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), CRevCompSequencesDlg::RevCompBioSeq(), CAsnCacheTestApplication::Run(), s_BasicValidation(), s_GetTrimCoordinates(), s_PercentBioseqMatch(), s_ProcessIntraScaffoldTail(), CSequenceUpdater::s_UpdateSeqInst(), CCleanup::SetMolinfoTech(), CUnorderedSplitter::SplitId(), CUnorderedSplitter::SplitLoc(), CMacroFunction_TrimTerminalNs::TheFunction(), TrimSequenceAndAnnotation(), TrimStopsFromCompleteCDS(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_imp::ValidateSeqLoc(), CCleanup::WGSCleanup(), CSingleFeatValidator::x_CalculateLocationGaps(), CPrimeCacheApplication::x_ExtractDelta(), x_FindLatestSequence(), CSingleFeatValidator::x_FindStartOfGap(), CVectorTrimPanel::x_GetTrimCoordinates(), CValidError_bioseq::x_IgnoreEndGap(), CValidError_bioseq::x_IsRangeGap(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), CVectorTrimPanel::x_RetranslateCDS(), CReportTrim::x_RetranslateCDS(), CSequenceAmbigTrimmer::x_SliceBioseq(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CVectorTrimPanel::x_TrimSelected(), CSequenceAmbigTrimmer::x_TrimToNothing(), CValidError_bioseq::x_ValidateAbuttingRNA(), CCdregionValidator::x_ValidateParentPartialness(), CGff3Writer::xAssignFeature(), CGff3Writer::xAssignFeatureEndpoints(), CGff3Writer::xWriteFeatureGeneric(), and CGff3Writer::xWriteFeatureTrna().

◆ GetInst_Ext()

Definition at line 363 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst_Ext(), and CBioseq_Handle::x_GetInfo().

Referenced by CBioseqIndex::CBioseqIndex(), CMasterContext::CMasterContext(), GetDeltaSeqForPosition(), GetDeltaSeqSummary(), CLocusItem::GetDivision(), CMasterContext::GetPartNumber(), s_AddPartToSegmentedBioseq(), s_IsConOrScaffold(), s_NsAreGaps(), s_SeqMapForHandle(), s_TitleFromSegment(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst(), CSeqdesc_CI::x_CheckRef(), CSingleFeatValidator::x_FindStartOfGap(), x_GetSegSeqInfoViaCDS(), CBioseqContext::x_IsDeltaLitOnly(), CDeflineGenerator::x_SetFlags(), CMasterContext::x_SetNumParts(), CBioseqContext::x_SetOpticalMapPoints(), and xf_IsDeltaLitOnly().

◆ GetInst_Fuzz() ◆ GetInst_Hist() ◆ GetInst_Length()

Definition at line 261 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst_Length(), and CBioseq_Handle::x_GetInfo().

Referenced by CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), CRecomputeIntervals::apply(), CTrimN::apply(), BOOST_AUTO_TEST_CASE(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CBioseqIndex::CBioseqIndex(), CCdsToMatPeptide::ConvertInner(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CLocationEditPolicy::Extend3(), CLocationEditPolicy::Extend5(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), variation::FindSSRLoc(), CProductColumn::GetApplyObjects(), CBioseq_Handle::GetBioseqLength(), CExtendCDSToStop::GetCommand(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CExtendPartialFeatDlg::Is3AtEndOfSeq(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), CExtendPartialFeatDlg::Is5AtStartOfSeq(), IsLocFullLength(), CTreeAlignMerger::Merge_Dist(), OverrideLenIfAccession(), CMytestApplication::PlayAroundWithSuggestIntervals(), ReverseComplementLocation(), s_AddBioseqToBioseq(), s_ConvertWholeToInt(), s_GetPolyA_genomic_priming(), s_GetProtApplyObjectsFeatures(), s_ParseTRnaFromAnticodonString(), s_PrintLocAsJavascriptArray(), CWeightedIdentityScorer::ScoreAlignments(), COverlapScorer::ScoreAlignments(), CProsplignProcess::SeqEntryProcess(), SetProteinFeature(), ShouldCheckForNsAndGap(), CMacroFunction_TrimTerminalNs::TheFunction(), TranslateCodingRegionForValidation(), CValidError_bioseq::ValidateSeqFeatContext(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), variation::CHgvsParser::x_AsHgvsInstExpression(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CCdregionValidator::x_CDS3primePartialTest(), CCdregionValidator::x_CDS5primePartialTest(), CAdjustForConsensusSpliceSite::x_ExtendStartOfExon(), CAdjustForConsensusSpliceSite::x_ExtendStopOfExon(), CFeaturePropagator::x_ExtendToStopCodon(), CSingleFeatValidator::x_FindStartOfGap(), CAutoDef::x_GetFeatureClauses(), variation::CVariationUtil::x_GetLiteralAtLoc(), CAsn2FlatApp::x_GetLocation(), CFlatFileGenerator::x_GetLocation(), CDeflineGenerator::x_GetLongestProtein(), CEditingBtnsPanel::x_GetSelectedLocations(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CSeq_loc_Mapper::x_InitGCSequence(), CValidError_bioseq::x_IsRangeGap(), CRNAValidator::x_ReportRNATranslationProblems(), CDeflineGenerator::x_SetFlags(), CBioseqContext::x_SetLocation(), CCDSTranslationPanel::x_SetLocationForProtein(), variation_ref::CVariationUtil::x_SetVariantPropertiesForIntronic(), and CGff3Writer::xAssignFeature().

◆ GetInst_Mol()

Definition at line 243 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst_Mol(), and CBioseq_Handle::x_GetInfo().

Referenced by AddBioseqToBioseq(), CCleanup::AddPartialToProteinTitle(), BOOST_AUTO_TEST_CASE(), CTestTranscript::CanTest(), CValidError_bioseq::CdError(), CValidError_bioseq::CheckSourceDescriptor(), CNewCleanup_imp::FixUnsetMolFromBiomol(), CWriteUtil::GetBiomol(), GetModelEvidance(), CBioseq_Handle::GetSequenceType(), CSeqTextDataSource::IsmRNASequence(), CMolInfoSubpanel::OnSelectButton(), CNewCleanup_imp::ProtSeqBC(), s_AddBioseqToBioseq(), s_AddBioseqToNucProtSet(), s_AddBioseqToPartsSet(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetNaLength(), s_ReplaceAllMolinfo(), CMolInfoSubpanel::SetClusters(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSeqFeatContext(), CAsn2FlatApp::x_AddSNPAnnots(), CEditSeqId::x_CollectChangedIds(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CBioseqContext::x_Init(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CLocusItem::x_SetStrand(), CValidError_bioseq::x_ValidateAbuttingUTR(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), and CFastaOstreamComp::x_Write().

◆ GetInst_Repr()

Definition at line 225 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst_Repr(), and CBioseq_Handle::x_GetInfo().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), GetDeltaSeqForPosition(), GetDeltaSeqSummary(), CLocusItem::GetDivision(), CAutoDef::GetMasterLocation(), CMasterContext::GetPartNumber(), GetTitle(), IsDeltaOrFarSeg(), CSGUtils::IsSegSet(), PatchTargetSequence(), s_AddPartToSegmentedBioseq(), s_IsConOrScaffold(), s_IsSegmented(), s_IsVirtualId(), s_ProcessIntraScaffoldTail(), s_SeqMapForHandle(), CSequenceUpdater::s_UpdateSeqInst(), CAssemblyGapValidator::Validate(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_imp::ValidateSeqLoc(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst(), CSeqdesc_CI::x_CheckRef(), CFlatGatherer::x_CollectSourceDescriptors(), CFlatGatherer::x_DoMultipleSections(), CSingleFeatValidator::x_FindStartOfGap(), CFlatGatherer::x_GatherReferences(), CBioseqContext::x_GetRepr(), CSingleFeatValidator::x_IsMostlyNs(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), CDeflineGenerator::x_SetFlags(), CMasterContext::x_SetNumParts(), CValidError_bioseq::x_SetupCommonFlags(), CUpdateSeqPanel::x_SetUpdateTypes(), and CValidError_bioseq::x_ValidateAbuttingRNA().

◆ GetInst_Seq_data() ◆ GetInst_Strand() ◆ GetInst_Topology()

Definition at line 308 of file bioseq_handle.cpp.

References CBioseq_Info::GetInst_Topology(), and CBioseq_Handle::x_GetInfo().

Referenced by BOOST_AUTO_TEST_CASE(), CBioseqIndex::CBioseqIndex(), CInternalStopFinder::FindStartStopRanges(), CScore_StartStopCodon::Get(), GetOverlappingFeatures(), CValidator::IsSeqLocCorrectlyOrdered(), CWriteUtil::IsSequenceCircular(), CMolInfoSubpanel::OnSelectButton(), CNewCleanup_imp::ProtSeqBC(), s_GetTopology(), s_IsCircularTopology(), s_ReplaceAllMolinfo(), CSeqSearch::Search(), CMolInfoSubpanel::SetClusters(), sGetWrapInfo(), ShouldCheckForNsAndGap(), CFeatureGenerator::SImplementation::TransformProteinAlignToTranscript(), CValidError_bioseq::ValidateNsAndGaps(), CAnnotObject_Less::x_GetExtremes(), CDeflineGenerator::x_GetModifiers(), CEditObjectSeq_feat::x_IsCircular(), CValidError_imp::x_ReportInvalidFuzz(), CDeflineGenerator::x_SetFlags(), CLocusItem::x_SetTopology(), and CValidError_bioseq::x_ValidateTitle().

◆ GetLevel() ◆ GetLoc() ◆ GetLocalIdOrNull() ◆ GetLocation()

Reimplemented in CMappedFeat.

Definition at line 252 of file seq_feat_handle.cpp.

References CSeq_feat_Base::GetLocation(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), AddColumnsToFeatureTable(), CStrandPanel::AddCommand(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CSplitCDSwithTooManyXs::AdjustSingleCDS(), CExplodeRNAFeats::apply(), ApplyFeatureSeqTableToSeqEntry(), ChangeFeat(), CFixForTransSplicing::CombineFeatures(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), IEditingActionFeat::FindFeatForAnotherFeat(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedFeatForAnotherFeat(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CGeneFinder::GetAssociatedGeneInfo(), CBulkEditFeatDlg::GetCommand(), CFuseFeaturesDlg::GetCommand(), CSeq_feat_Handle::GetLocationId(), CEditSequence::GetProteinFeatures(), IEditingAction::GetUpdateMRNAProductNameCmd(), IsDuplicate(), IsLocationInFrame(), CLocationConstraintMatcher::Match(), IEditingActionFeat::MatchBioseqConstraintForFeatHandle(), CCleanup::MoveFeatToProtein(), RemapOtherProtFeats(), CGeneFinder::ResolveGeneXref(), RestoreModelReadingFrame(), s_AreFullLengthCodingRegionsWithDifferentFrames(), s_AreLinkedToDifferentFeats(), s_GetFeatDesc(), s_IsDuplicateFeatures(), s_IsFarLocation(), s_IsNucLocation(), CSameConstraintMatcher::SetFeat(), IEditingActionFeat::SetFeatForAnotherFeat(), TestUpdateCDS(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CSequenceUpdater::x_ShouldRemoveFeature(), and CCdregionValidator::x_ValidateCDSPeptides().

◆ GetLocationId()

Reimplemented in CMappedFeat.

Definition at line 273 of file seq_feat_handle.cpp.

References CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_feat_Handle::GetLocation(), CSeq_feat_Handle::GetSNPSeq_id(), CSeq_feat_Handle::IsTableSNP(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

Referenced by CFeatTableEdit::GenerateLocusTags(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), CMappedFeat::GetLocationId(), CRemoveFeaturesDlg::GetProductId(), CSequenceUpdater::x_ChangeIDInFeature(), and CCreateGeneModelTask::x_GetUpdatedGeneCommand().

◆ GetLocationTotalRange() TRange CSeq_feat_Handle::GetLocationTotalRange ( void ) const inline ◆ GetName() const string & CSeq_annot_Handle::GetName ( void ) const

Definition at line 136 of file seq_annot_handle.cpp.

References CAnnotName::GetName(), CSeq_annot_Info::GetName(), and CSeq_annot_Handle::x_GetInfo().

Referenced by CGraphGlyph::CGraphGlyph(), CSGSeqGraphJob::GetSeqtableAnnots(), SAnnotCmdPreparer< type >::PrepareCmd(), CFeatCompareJob_Location::Run(), CDemoApp::Run(), CTestProtProd_Cdd::RunTest(), s_GetAnnotSelector(), s_GetClipLoc(), s_GetRnaMappingLocs(), s_IsCDD(), CClippedScorer::ScoreAlignments(), CSGAnnotJob::x_AddGraphObject(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CSGSeqGraphJob::x_LoadSeqTable(), and CEditObjectFeaturePropagate::xInit().

◆ GetNamedDbxref() ◆ GetNamedQual()

Return a named qualifier.

This will return the first item matching the qualifier name. If no such qualifier is found, an empty string is returned.

Implements ISeq_feat.

Definition at line 467 of file seq_feat_handle.cpp.

References CSeq_feat::GetNamedQual(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by CGffIdGenerator::GetGffId(), CFeatTableEdit::InstantiateProducts(), CFeatTableEdit::ProcessCodonRecognized(), s_CheckQuals_assembly_gap(), s_CheckQuals_bind(), s_CheckQuals_gap(), s_CheckQuals_mod_base(), s_CheckQuals_ncRNA(), s_CheckQuals_regulatory(), s_GetTranscriptIdFromMrna(), s_HasCompareOrCitation(), CFeatTableEdit::SubmitFixProducts(), CFeatTableEdit::xAddTranscriptAndProteinIdsToCdsAndParentMrna(), CFeatTableEdit::xAddTranscriptAndProteinIdsToMrna(), CFeatTableEdit::xAddTranscriptAndProteinIdsToUnmatchedMrna(), CGff2Writer::xAssignFeatureAttributeFunction(), CGtfWriter::xAssignFeatureAttributeGeneId(), CGff3Writer::xAssignFeatureAttributeNote(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff2Writer::xAssignFeatureAttributePseudoGene(), CGff2Writer::xAssignFeatureAttributesGoMarkup(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CFeatTableEdit::xFeatureAddProteinIdCds(), CFeatTableEdit::xFeatureAddProteinIdDefault(), CFeatTableEdit::xFeatureAddProteinIdMrna(), CFeatTableEdit::xFeatureAddTranscriptIdCds(), CFeatTableEdit::xFeatureAddTranscriptIdDefault(), CFeatTableEdit::xFeatureAddTranscriptIdMrna(), CFeatTableEdit::xFeatureSetQualifier(), CFeatTableEdit::xGenerateLocusIdsUseExisting(), CFeatTableEdit::xGenerateTranscriptOrProteinId(), CFeatTableEdit::xGetCurrentLocusTagPrefix(), CGffIdGenerator::xGetGenericId(), CGffIdGenerator::xGetIdForCds(), and CGffIdGenerator::xGetIdForRna().

◆ GetNCObjectInfo() [1/3] TObjectInfo& CBioseq_set_ScopeInfo::GetNCObjectInfo ( void ) inline ◆ GetNCObjectInfo() [2/3] TObjectInfo& CSeq_annot_ScopeInfo::GetNCObjectInfo ( void ) inline ◆ GetNCObjectInfo() [3/3] TObjectInfo& CSeq_entry_ScopeInfo::GetNCObjectInfo ( void ) inline ◆ GetNonLocalIdOrNull() ◆ GetNumval() TSeqPos CSeq_graph_Handle::GetNumval ( void ) const inline ◆ GetObjectCore() [1/4] ◆ GetObjectCore() [2/4] ◆ GetObjectCore() [3/4] ◆ GetObjectCore() [4/4] ◆ GetObjectInfo() [1/3] ◆ GetObjectInfo() [2/3] ◆ GetObjectInfo() [3/3] ◆ GetOriginalSeq_feat()

Definition at line 197 of file seq_feat_handle.cpp.

References ConstRef(), CCreatedFeat_Ref::GetOriginalFeature(), CSeq_feat_Handle::IsPlainFeat(), CSeq_feat_Handle::m_CreatedFeat, and CSeq_feat_Handle::x_GetPlainSeq_feat().

Referenced by CFeatGapInfo::AdjustForRelevantGapIntervals(), CNewCleanup_imp::BasicCleanupSeqFeatHandle(), BOOST_AUTO_TEST_CASE(), CCleanup::CleanupCollectionDates(), CFixForTransSplicing::CombineFeatures(), CmRNACDSLinker::CompleteHalfFormedXrefPairs(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), CFeatureGenerator::CreateMicroIntrons(), ExtendPartialFeatureEnds(), IEditingActionBiosource::Find(), IEditingActionFeat::Find(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), IEditingActionFeat::FindFeatForAnotherFeat(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedFeatForAnotherFeat(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), IEditingAction::GetActionCommand(), CBulkEditFeatDlg::GetCommand(), CFixForTransSplicing::GetCommand(), CFuseFeaturesDlg::GetCommand(), CEditCdsFrame::GetCommand(), CFlatFileViewContext::GetEditObject(), GetGeneForFeature(), CMappedFeat::GetLocation(), CCreatedFeat_Ref::GetMappedFeature(), CCreatedFeat_Ref::GetMappedLocation(), CFeatureSeqTableColumnBase::GetObjects(), CMappedFeat::GetOriginalFeature(), CMappedFeat::GetProduct(), IEditingAction::GetRetranslateCdsCmd(), CMappedFeat::GetSeq_feat(), CSeq_feat_Handle::GetSeq_feat(), IEditingActionFeat::GoToProtFeature(), CmRNACDSLinker::LinkByLabelAndLocation(), MapSeq_feat(), CLocationConstraintMatcher::Match(), CBioseqEditor::OnEditBiosourceFeat(), CFixForTransSplicing::OnListItemActivated(), CFixForTransSplicing::OnListItemSelected(), CFindASN1Dlg::OnReplaceButton(), CFeaturePropagator::PropagateAll(), CFeaturePropagator::PropagateAllReportFailures(), RemapOtherProtFeats(), RestoreModelAttributes(), RestoreModelFromInternalGnomonFeature(), CDemoApp::Run(), s_AreThereOtherCDSForThisProduct(), s_GetCdsByProduct(), s_GetFeatureLabel(), IEditingActionBiosource::SetFeat(), IEditingActionFeat::SetFeat(), IEditingActionFeat::SetFeatForAnotherFeat(), CCleanup::TaxonomyLookup(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddQuals(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CSGAlignmentJob::x_CreateFeatGlyph(), CAdjustFeaturesForGaps::x_DoOne(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CSortedProteins::x_GatherProteinNames(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CFeatureSearchJob::x_SearchFeatures(), CSequenceUpdater::x_ShouldImportFeature(), CValidError_bioseq::x_ValidateCDSVDJCmatch(), and CVcfWriter::x_WriteData().

◆ GetParentBioseq_set() [1/4]

Return a handle for the parent Bioseq-set, or null handle.

Definition at line 562 of file bioseq_handle.cpp.

References CSeq_entry_Info::GetParentBioseq_set_Info(), CBioseq_Handle::GetTSE_Handle(), CTSE_Info_Object::HasParent_Info(), info, and CBioseq_Handle::x_GetInfo().

Referenced by CReportTrim::AdjustAndTranslate(), CRemAllProtTitles::apply(), CRemProtTitles::apply(), CApplyObject::ApplyChange(), ApplySrcTableToSeqEntry(), BOOST_AUTO_TEST_CASE(), CApplyObject::CApplyObject(), CNewCleanup_imp::CreateMissingMolInfo(), DeleteProteinAndRenormalizeNucProtSet(), CCmdCreateFeat::Execute(), CEditSequenceEnds::GetCommand(), CFarPointerSeq::GetCommand(), GetDeleteSequenceCommand(), IsInGenProdSet(), IsInOrganelleSmallGenomeSet(), CmRNACDSLinker::LinkByProduct(), CSequesterSets::OnAccept(), ProcessForTrimAndSplitUpdates(), PropagateToTarget(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CNewCleanup_imp::RemoveBadProteinTitle(), CCleanup::RepackageProteins(), s_GetMolInfoAndSrcDescriptors(), s_GetSeq_featAcc(), s_IsBioseqInSet(), CMacroFunction_ApplyPublication::TheFunction(), CBiosampleChkApp::UpdateBioSource(), CVectorTrimPanel::x_DeleteSelected(), CFlatGatherer::x_GatherCDSReferences(), CNewCleanup_imp::x_InGpsGenomic(), CHugeFileDemoApp::x_ReadAndWritePush(), CSeq_descr_CI::x_Step(), CVectorTrimPanel::x_TrimSelected(), and CGffFeatureContext::xAssignSequenceHasBioSource().

◆ GetParentBioseq_set() [2/4]

Return a handle for the parent Bioseq-set, or null handle.

Definition at line 112 of file bioseq_set_handle.cpp.

References CBioseq_set_Handle::CBioseq_set_Handle(), CSeq_entry_Info::GetParentBioseq_set_Info(), CBioseq_set_Handle::GetTSE_Handle(), CTSE_Info_Object::HasParent_Info(), info, and CBioseq_set_Handle::x_GetInfo().

Referenced by AddDescToSeqEntry(), COrgGeneralPanel::ApplyCommand(), CApplyObject::CApplyObject(), CNewCleanup_imp::CreateMissingMolInfo(), CRemoveSeqId::CRemoveSeqId(), IsInGenProdSet(), CInfluenzaSet::MakeSet(), CReorderSequencesDlg::ReadBioseq(), CSegregateSetsBase::ReadBioseq(), CSequesterSets::RecursiveCollectSets(), CRemoveSet::remove_set(), s_GetSeq_featAcc(), s_IsBioseqInSet(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CSubmissionWizard::x_ApplyUserDescriptorToRecord(), CAdjustFeaturesForGaps::x_DoOne(), CNewCleanup_imp::x_InGpsGenomic(), and CSeq_descr_CI::x_Step().

◆ GetParentBioseq_set() [3/4]

Get parent bioseq-set handle.

Definition at line 200 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::CBioseq_set_Handle, CSeq_entry_Handle::GetTSE_Handle(), info, and CSeq_entry_Handle::x_GetInfo().

Referenced by CApplyObject::ApplyChange(), CRemoveBioseqChecker::Do(), CAddBioseqChecker::Do(), CCmdPromoteCDS::Execute(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), CMiscSeqTableColumn::GetRelatedApplyObjects(), CCdsToMatPeptide::MergeConvert(), PromoteCDSToNucProtSet(), s_GetNPParent(), and s_MakeGroupsForUniqueValues().

◆ GetParentBioseq_set() [4/4] ◆ GetParentEntry() [1/8]

Get parent Seq-entry handle.

See also: GetSeq_entry_Handle()

Definition at line 545 of file bioseq_handle.cpp.

References CBioseq_Handle::GetTSE_Handle(), and CBioseq_Handle::x_GetInfo().

Referenced by CReportTrim::AdjustAndTranslate(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CAddFluComments::Apply(), ApplySrcTableToSeqEntry(), CApplyIndexerComments::ApplyToCSeq_entry(), CApplyObject::CApplyObject(), CRemoveBioseqChecker::Check(), CSeq_annot_CI::CSeq_annot_CI(), CRemoveBioseqChecker::Do(), CAddBioseqChecker::Do(), CFlatFileGenerator::Generate(), GetAnnotHandle(), CMolInfoField::GetApplyObjects(), CWriteUtil::GetBiomol(), CBioseq_Handle::GetComplexityLevel(), CAutoDef::GetMasterLocation(), GetNucBioseq(), GetSeq_entry_Handle(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_descr_CI::GetSeq_entry_Handle(), CFlatFileGenerator::GetSeqFeatText(), GetSetParent(), CSUCDataGenerator::GetSUCResults(), GetSynchronizeProductMolInfoCommand(), CHugeFileProcess::GetTopLevelEntry(), CAsn2FlatApp::HandleTextId(), CAutoDef::IsSegment(), CNewCleanup_imp::ProtSeqBC(), CDemoApp::Run(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_IsRefSeqGene(), s_RemoveTaxnameFromProtRef(), TranslateCDSCommand(), CSampleEditSaver::UpdateSeq(), CValidError_annot::ValidateSeqAnnotContext(), CSourceModParserWrapper::x_ApplyAllMods(), CAutogeneratedCleanup::x_BasicCleanupSeqAnnots(), CValidError_bioseq::x_CheckForMultipleComments(), CFlatGatherer::x_GetAnnotDescStrucCommentFromBioseqHandle(), CBioseqContext::x_IsPart(), CValidatePanel::x_LaunchEditor(), CAgpconvertApplication::x_LoadTemplate(), CPromote::x_PromoteCdregion(), CHugeFileDemoApp::x_ReadAndWritePush(), CGapStatsApplication::x_ReadFileOrAccn(), CFlatFeatureRetrieveJob::x_Run(), CHugeFileDemoApp::x_ShowSeqSizes(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CNewCleanup_imp::xUpdateSeqfeatCitPub(), CGff3Writer::xWriteSequenceHeader(), and CGff3Writer::xWriteSource().

◆ GetParentEntry() [2/8] ◆ GetParentEntry() [3/8]

Return a handle for the parent seq-entry of the bioseq.

Definition at line 100 of file bioseq_set_handle.cpp.

References CBioseq_set_Handle::CSeq_entry_Handle, CBioseq_set_Handle::GetTSE_Handle(), info, and CBioseq_set_Handle::x_GetInfo().

Referenced by AddDescToSeqEntry(), CCleanup::AddProtein(), CReportTrim::AdjustAndTranslate(), CApplyObject::ApplyChange(), COrgGeneralPanel::ApplyCommand(), ApplySrcTableToSeqEntry(), BioseqSetDescriptorPropagateDown(), CSequesterSets::BioseqSetDescriptorPropagateDown(), BOOST_AUTO_TEST_CASE(), CApplyObject::CApplyObject(), CBioseq_CI::CBioseq_CI(), CSeq_annot_CI::CSeq_annot_CI(), DeleteProteinAndRenormalizeNucProtSet(), CCmdAddSeqEntry::Execute(), CCmdCreateFeat::Execute(), CCmdPromoteCDS::Execute(), CApplyRNAITSDlg::GetCommand(), CEditSequenceEnds::GetCommand(), CBioseq_set_Handle::GetComplexityLevel(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), GetDeleteSequenceCommand(), GetNucBioseq(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CMiscSeqTableColumn::GetRelatedApplyObjects(), GetSeq_entry_Handle(), CSeq_descr_CI::GetSeq_entry_Handle(), CSUCDataGenerator::GetSUCResults(), CInfluenzaSet::MakeSet(), CCdsToMatPeptide::MergeConvert(), CSequesterSets::OnAccept(), CReorderSequencesDlg::PopulateSet(), PromoteCDSToNucProtSet(), PropagateToTarget(), CSegregateSetsBase::ReadBioseq(), s_GetNPParent(), s_MakeGroupsForUniqueValues(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), sGetValidateObject(), CMacroFunction_ApplyPublication::TheFunction(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CSubmissionWizard::x_ApplyUserDescriptorToRecord(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CDesktopDataBuilder::x_CreateSet(), CAdjustFeaturesForGaps::x_DoOne(), CTableDataValidateJob::x_FetchAll(), CSequenceUpdater::x_GetOldBseq_EntryHandle(), CValidatePanel::x_LaunchEditor(), CNewCleanup_imp::x_SingleSeqSetToSeq(), CVectorTrimPanel::x_TrimSelected(), and CValidError_bioseqset::x_ValidateSetDescriptors().

◆ GetParentEntry() [4/8] ◆ GetParentEntry() [5/8]

Get parent Seq-entry handle.

See also: GetSeq_entry_Handle()

Definition at line 89 of file seq_annot_handle.cpp.

References CSeq_annot_Handle::GetTSE_Handle(), and CSeq_annot_Handle::x_GetInfo().

Referenced by AdjustForCDSPartials(), AdjustSingleFeature(), CPackageFeaturesOnParts::apply(), CGroupExplode::apply(), CExplodeRNAFeats::apply(), CApplyObject::ApplyChange(), ApplyPolicyToFeature(), BOOST_AUTO_TEST_CASE(), CFeatureItemBase::CFeatureItemBase(), DemoteCDSToNucSeq(), CSequenceEditingEventHandler::Duplicate(), GetAccessionFromObjects(), GetBioseqForSeqFeat(), IEditingActionFeat::GetCurrentSeqEntryHandleFromFeatHandle(), CDesktopAlignItem::GetSeqentryHandle(), CDesktopGraphItem::GetSeqentryHandle(), SAnnotCmdPreparer< type >::PrepareCmd(), CHugeFileDemoApp::ProcessHugeSeqEntry(), PromoteCDSToNucProtSet(), CEditsSaver::Remove(), RetranslateCDS(), s_DivvyUpAlignments_ProcessAnnot(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_IsLocalFeature(), CCmdPromoteCDS::Unexecute(), CRawSeqToDeltaSeqByLoc::UpdateDensegAlignment(), CValidError_annot::ValidateSeqAnnot(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CBioseqEditor::x_DeleteObject(), CAdjustFeaturesForGaps::x_DoOne(), CBioseqEditor::x_GetDeleteCommand(), CHugeFileDemoApp::x_ProcessFileTraditionally(), and CCmdChangeSeq_feat::x_Switch().

◆ GetParentEntry() [6/8]

Navigate object tree.

Definition at line 291 of file seq_annot_handle.cpp.

References CSeq_annot_EditHandle::CSeq_entry_EditHandle, CSeq_annot_Handle::GetTSE_Handle(), and CSeq_annot_EditHandle::x_GetInfo().

Referenced by CApplyObject::ApplyChange(), CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), DemoteCDSToNucSeq(), CCmdDelSeq_annot::Execute(), CHugeFileDemoApp::ProcessHugeSeqEntry(), PromoteCDSToNucProtSet(), CScope::RemoveAnnot(), CScope::ReplaceAnnot(), CHugeFileDemoApp::x_ProcessFileTraditionally(), and CCmdChangeSeq_feat::x_Switch().

◆ GetParentEntry() [7/8]

Get parent Seq-entry handle.

Definition at line 117 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::CSeq_entry_Handle(), CSeq_entry_Handle::GetTSE_Handle(), info, and CSeq_entry_Handle::x_GetInfo().

Referenced by CFeatureTableReader::AddProteins(), CPackageFeaturesOnParts::apply(), CAddFluComments::Apply(), CMolInfoEditDlg::compute_peptide_completeness(), CEditingActionFeatGeneLocus::FindRelated(), CValidError_base::GetAppropriateXrefParent(), CExonFromCds::GetCommand(), CCountryConflict::GetCommandFromValuesTable(), CLatLonTool::GetCommandFromValuesTable(), CBioseq_Handle::GetComplexityLevel(), CBioseq_set_Handle::GetComplexityLevel(), CAutoDef::GetMasterLocation(), GetNucBioseq(), GetSetParent(), CHugeFileProcess::GetTopLevelEntry(), CAutoDef::IsSegment(), CInfluenzaSet::MakeSet(), CRemoveGeneXrefs::RemoveOrphanLocus(), CRemoveGeneXrefs::RemoveOrphanLocus_tag(), CDemoApp::Run(), s_GetAccessionForSeqdesc(), s_GetParentEntry(), s_HasTopSetSiblings(), s_MakeGroupsForUniqueValues(), s_StandaloneProt(), IEditingAction::SetTopSeqEntry(), CValidError_annot::ValidateSeqAnnotContext(), CFlatGatherer::x_GetAnnotDescStrucCommentFromBioseqHandle(), CBioseqContext::x_IsPart(), and CSeq_annot_CI::x_Settle().

◆ GetParentEntry() [8/8]

Get parent seq-entry edit handle.

Definition at line 283 of file seq_entry_handle.cpp.

References CSeq_entry_EditHandle::CSeq_entry_EditHandle(), CSeq_entry_Handle::GetTSE_Handle(), info, and CSeq_entry_EditHandle::x_GetInfo().

Referenced by CSeq_entry_Remove_EditCommand::Do(), CRemoveTSE_EditCommand::Do(), CSequesterSets::OnAccept(), CSequesterSets::OnSequester(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), CSeq_entry_EditHandle::Remove(), and CScope_Impl::RemoveEntry().

◆ GetPartial() bool CSeq_feat_Handle::GetPartial ( void ) const virtual ◆ GetPlainSeq_feat() ◆ GetProduct()

Reimplemented in CMappedFeat.

Definition at line 246 of file seq_feat_handle.cpp.

References CSeq_feat_Base::GetProduct(), and CSeq_feat_Handle::GetSeq_feat().

Referenced by CExportTableDlg::AddCdsGeneMrnaTable(), AddColumnsToFeatureTable(), ApplyFeatureSeqTableToSeqEntry(), ChangeFeat(), CFixForTransSplicing::CombineFeatures(), CCreateProteinId::create_protein_ids(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CFuseFeaturesDlg::GetCommand(), GetDeleteAllFeaturesCommand_Ex(), CRemoveFeaturesDlg::GetProductId(), CSeq_feat_Handle::GetProductId(), CSeq_feat_Handle::GetProductTotalRange(), IEditingActionFeat::GoToProtFeature(), CCleanup::MoveFeatToProtein(), ProcessForTrimAndSplitUpdates(), RestoreModelFromPublicMrnaFeature(), s_AreThereOtherCDSForThisProduct(), CDesktopFeatItem::s_GetProteinName(), s_IsFarLocation(), TestUpdateCDS(), and CAdjustFeaturesForGaps::x_DoOne().

◆ GetProductId() ◆ GetProductTotalRange() ◆ GetProtXref() ◆ GetPseudo() bool CSeq_feat_Handle::GetPseudo ( void ) const inline ◆ GetQual()

Definition at line 443 of file seq_feat_handle.hpp.

References CSeq_feat_Base::GetQual(), and CSeq_feat_Handle::GetSeq_feat().

◆ GetRange() ◆ GetRangeSeq_loc()

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0, stop == 0, and strand == eNa_strand_unknown, CSeq_loc will be of type 'whole'.

Definition at line 988 of file bioseq_handle.cpp.

References eNa_strand_unknown, CBioseq_Handle::GetAccessSeq_id_Handle(), CBioseq_Handle::GetBioseqLength(), CSeq_id_Handle::GetSeqId(), CSeq_loc::SetInt(), and CSeq_loc::SetWhole().

Referenced by CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), CEditSequence::AdjustFeatureLocations(), CAlignmentAssistant::CreateFeature(), CEditSequence::CreateFeature(), CEditSequence::CreateRegulatory(), CBioseqEditor::EditSelection(), CEditingBtnsPanel::EditSequence(), CSequenceEditingEventHandler::EditSequence(), FindNewLocations(), IEditingActionFeat::FindOrCreateProtFeat(), CScoreBuilder::GetBlastScoreProtToNucl(), CFlatFileViewContext::GetEditObject(), CAlignmentAssistant::GetFeatures(), CFeatureGenerator::SImplementation::SMapper::GetRnaLoc(), LaunchBioseqEditor(), CCdsToMatPeptide::MergeConvert(), CEditSequence::OnRetranslate(), CMytestApplication::PlayAroundWithSuggestIntervals(), variation::CVariationUtil::RemapToAnnotatedTarget(), CSampleObjmgrApplication::Run(), CFarPointerSeq::RunBlast(), CCreateSeqHistForTpa::RunBlast(), CTestSingleAln_All::RunTest(), CMixedStrands::s_Blast2NASeq(), s_GetCdsSequence(), s_GetRnaMappingLocs(), s_MakeNewMasterSeq(), s_RunBlast2AASeq(), s_RunBlast2NASeq(), CProsplignProcess::SeqEntryProcess(), SeqLocToBioseq(), CAlignmentAssistant::TranslateLocations(), CEditSeqEndsWithAlign::TrimQualityScores(), CAlignmentAssistant::TrimQualityScores(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CMacroBioData::x_CreateFeatIterator(), CBioseqEditor::x_HasAlignment(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CFeaturePropagator::x_MapLocation(), and CSGAlnQualityScore::x_RetrieveQualityMap().

◆ GetRelease() ◆ GetScope() [1/9] CScope & CBioseq_Handle::GetScope ( void ) const inline

Get scope this handle belongs to.

Definition at line 791 of file bioseq_handle.hpp.

References CTSE_Handle::GetScope(), and CBioseq_Handle::GetTSE_Handle().

Referenced by CAutoDefFeatureClause::AddGene(), CBulkCDSAddPanel::AddOneCmd(), CAlignCDSAddPanel::AddOneCommand(), CAutoDefExonListClause::AddSubclause(), CAutoDefFeatureClause::AddToLocation(), CEditSeqEndsWithAlign::AdjustFeatureLocations(), CAlignmentAssistant::AdjustFeatureLocations(), AgpWrite(), CCreateLocusTagGene::apply(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CCleanup::BasicCleanup(), BuildAlignDataSource(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CheckOneFeatureType(), CAutoDefFeatureClause::CompareLocation(), CBioseq_Handle::ContainsSegment(), CRemoveFeaturesDlg::CountOrphanedProteins(), CAlignmentAssistant::CreateFeature(), ExtendPartialFeatureEnds(), CCleanup::ExtendToStopCodon(), CCleanup::ExtendToStopIfShortAndNotPartial(), CEditingActionFlatFile::Find(), GenerateTargetedLocusName(), CBioseq_Handle::GetAccessSeq_id_Handle(), GetAllSwitchPoints(), GetAnchors(), CFindRSites::GetAnnot(), CProductColumn::GetApplyObjects(), CCodonStartColumn::GetApplyObjects(), CConvertBadCdsAndRnaToMiscFeat::getBacterialPartialNonextendable(), CBioseq_Handle::GetBioseqLength(), CConvertBadCdsAndRnaToMiscFeat::getCdsOverlap(), CCorrectRNAStrandDlg::GetCommand(), CTruncateCDS::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetDeltaSeqSummary(), CGffIdGenerator::GetGffSourceId(), CSeqUtils::GetMappingInfo(), GetNewProtId(), GetNewProtIdFromExistingProt(), GetNucleotideParent(), CFeatureSeqTableColumnBase::GetObjects(), CMasterContext::GetPartNumber(), CBioseqContext::GetPreferredSynonym(), CEditSequence::GetProteinFeatures(), GetProteinWeight(), CFeatureSeqTableColumnBase::GetRelatedGeneApplyObjects(), GetReverseComplimentSequenceCommand(), CConvertBadCdsAndRnaToMiscFeat::getRnaOverlap(), CBioseqContext::GetScope(), CFlatFileLocusItem::GetSeqLoc(), GetSourceFeatForProduct(), GetSwitchPoint(), CBioseq_Handle::GetSynonyms(), GetTaxIdForProduct(), GetTitle(), variation::GetUniquePrimaryTranscriptId(), CBulkCDS::GetValuesTableFromSeqEntry(), HasExcludedAnnotation(), ListOrphanProteins(), CMakeCdrProds::MakeCdrProds(), CAutoDefFeatureClause::OkToGroupUnderByLocation(), CBioseqEditor::OnCreateBiosourceDesc(), CBioseqEditor::OnCreateDescriptor(), CBioseqEditor::OnEditBiosourceDesc(), CBioseqEditor::OnEditBiosourceFeat(), CBioseqEditor::OnPropagateAllFeatures(), CRemoveProteins::OrphanedProteins(), PromoteCDSToNucProtSet(), PropagateToTarget(), CGiCache::RecordKnown(), RemapOtherProtFeats(), CRemoveFeaturesDlg::RemoveOrphansRenormalizeNucProtSets(), RetranslateCdregion(), CRevCompSequencesDlg::RevCompBioSeq(), CBulkCDS::RowToScopedObjects(), CBulkGene::RowToScopedObjects(), CBulkMiscFeat::RowToScopedObjects(), CBulkRna::RowToScopedObjects(), SrcEditDialog::RowToScopedObjects(), CDiscrepancyReportJob::Run(), CSeedTop::Run(), CDemoApp::Run(), CFarPointerSeq::RunBlast(), CCreateSeqHistForTpa::RunBlast(), CMixedStrands::s_Blast2NASeq(), s_CheckDataStatus(), s_GetCdsSequence(), CMacroFunction_NumberOfFeatures::s_GetFeatTypeCount(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetModelEvidance(), s_GetProductFlagFromCDSProductNames(), s_GetRnaMappingLocs(), s_GetSequenceRegionId(), s_HasMobileElementForInterval(), s_IsVirtualId(), s_RunBlast2AASeq(), s_RunBlast2NASeq(), s_SeqMapForHandle(), CAutoDefExonListClause::SeqLocIntersect(), sFindAnchorRow(), sGenerateFields(), CMacroFunction_TrimTerminalNs::TheFunction(), CSeqTranslator::Translate(), CCdregion_translate::TranslateCdregion(), TrimSeqData(), CValidError_bioseq::ValidateBioseq(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CFastaOstream::WriteSequence(), CSingleFeatValidator::x_CalculateLocationGaps(), CSeqdesc_CI::x_CheckRef(), CAlnVecRow::x_CreateTrackPanel(), CImportFeatTable::x_DoImportCDS(), CFlatGatherer::x_DoMultipleSections(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CCDSTranslationProblems::x_GetCdTransErrors(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CDeflineGenerator::x_GetLongestProtein(), CAutoDefFeatureClause::x_GetProductName(), x_GetSegSeqInfoViaCDS(), x_GetSourceFeatViaCDS(), IEditingActionFeat::x_GetSublocOnBioseq(), CBioseqEditor::x_HasAlignment(), CBioseqContext::x_HasOperon(), CSequenceUpdater::x_ImportCDSProduct(), CSFTranslationJob::x_InitGeneticCode(), CSingleFeatValidator::x_IsMostlyNs(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), CPromote::x_PromoteRna(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CPromote::x_Scope(), CMasterContext::x_SetBaseName(), CBioseqContext::x_SetLocation(), CMasterContext::x_SetNumParts(), CVectorTrimPanel::x_SetSeqData(), CDeflineGenerator::x_SetTitleFromNM(), CSequenceAmbigTrimmer::x_SliceBioseq(), CVectorTrimPanel::x_TrimSelected(), CSingleFeatValidator::x_ValidateFeatPartialness(), CSingleFeatValidator::x_ValidateGeneXRef(), CGff3Writer::xAssignSourceSeqId(), and CSrcWriter::xGatherId().

◆ GetScope() [2/9] CScope & CBioseq_set_Handle::GetScope ( void ) const inline ◆ GetScope() [3/9] CScope & CSeq_align_Handle::GetScope ( void ) const inline

Get scope this handle belongs to.

Definition at line 155 of file seq_align_handle.hpp.

References CSeq_align_Handle::GetAnnot(), and CSeq_annot_Handle::GetScope().

Referenced by CPaintAlignment::AlignPosToSeqPos(), CEditSelectedGaps::apply_impl(), CAlignmentAssistant::CreateFeature(), CAlignmentAssistant::DeleteSelection(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), CAlignmentAssistant::OnPropagateFeatures(), CAlignmentAssistant::OnReverseStrand(), CAlignmentAssistant::ReportUnresolvedBioseqs(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), CPaintAlignment::SeqPosToAlignPos(), CSeq_annot_EditHandle::TakeAlign(), and CAlignmentAssistant::TranslateLocations().

◆ GetScope() [4/9] CScope & CSeq_annot_Handle::GetScope ( void ) const inline ◆ GetScope() [5/9] CScope & CSeq_entry_Handle::GetScope ( void ) const inline

Get scope this handle belongs to.

Definition at line 611 of file seq_entry_handle.hpp.

References CTSE_Handle::GetScope(), and CSeq_entry_Handle::GetTSE_Handle().

◆ GetScope() [6/9] CScope & CSeq_feat_Handle::GetScope ( void ) const inline

Get scope this handle belongs to.

Definition at line 285 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetAnnot(), and CSeq_annot_Handle::GetScope().

Referenced by CFeatTree::AddFeaturesFor(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CCreateLocusTagGene::apply(), CCleanup::BasicCleanup(), ChangeFeat(), DeleteProteinAndRenormalizeNucProtSet(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), IEditingActionFeat::FindFeatForAnotherFeat(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedFeatForAnotherFeat(), GetBestOverlappingFeat(), CBulkEditFeatDlg::GetCommand(), CRetranslateCDS::GetCommand(), CEditCdsFrame::GetCommand(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), CEditSequence::GetFeatures(), GetParentFeature(), CRemoveFeaturesDlg::GetProductId(), IEditingAction::GetRetranslateCdsCmd(), IEditingAction::GetUpdateMRNAProductNameCmd(), CEditingActionFeatTranslExcept::GetValue(), CEditingActionFeatTranslation::GetValue(), IEditingActionFeat::GoToProtFeature(), IsDuplicate(), IsLocationInFrame(), CEditingActionFeatTranslation::IsSetValue(), MapSeq_feat(), CLocationConstraintMatcher::Match(), IEditingActionFeat::MatchBioseqConstraintForFeatHandle(), CCleanup::MoveFeatToProtein(), operator<<(), ProcessForTrimAndSplitUpdates(), RemapOtherProtFeats(), RestoreModelFromInternalGnomonFeature(), RestoreModelFromPublicMrnaFeature(), s_AreFeatureLabelsSame(), s_AreFullLengthCodingRegionsWithDifferentFrames(), s_AreLinkedToDifferentFeats(), s_AreThereOtherCDSForThisProduct(), s_CollectBestOverlaps(), s_GetDbxrefFromProduct(), s_GetFeatDesc(), s_GetFeatureKeyLinkLocation(), CDesktopFeatItem::s_GetProteinName(), s_IsFarLocation(), s_IsNucLocation(), s_VerifyTree(), CSameConstraintMatcher::SetFeat(), IEditingActionFeat::SetFeatForAnotherFeat(), CSeq_annot_EditHandle::TakeFeat(), TestUpdateCDS(), CAdjustFeaturesForGaps::x_DoOne(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureMethod(), CGffIdGenerator::xExtractFarAccession(), CGff2Writer::xGenerateMissingTranscript(), and CFastaOstreamEx::xWriteFeature().

◆ GetScope() [7/9] CScope & CSeq_annot_ftable_CI::GetScope ( void ) const inline ◆ GetScope() [8/9] CScope & CSeq_annot_ftable_I::GetScope ( void ) const inline ◆ GetScope() [9/9] CScope & CSeq_graph_Handle::GetScope ( void ) const inline ◆ GetScore() ◆ GetSegs()

Definition at line 197 of file seq_align_handle.hpp.

References CSeq_align_Base::GetSegs(), and CSeq_align_Handle::x_GetSeq_align().

Referenced by CAlignmentAssistant::AdjustAlign(), CPaintAlignment::AlignPosToSeqPos(), CAlignmentAssistant::CreateFeature(), CAlignmentAssistant::DeleteSelection(), CAlignmentAssistant::GetFeatures(), CPaintAlignment::GetSegments(), CAlignmentAssistant::OnPropagateFeatures(), CAlignmentAssistant::ReportUnresolvedBioseqs(), s_DivvyUpAlignments_ProcessAnnot(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), CPaintAlignment::SeqPosToAlignPos(), and CAlignmentAssistant::TranslateLocations().

◆ GetSeq()

Definition at line 212 of file seq_entry_handle.cpp.

References CScope_Impl::GetBioseqHandle(), CSeq_entry_Handle::GetTSE_Handle(), CSeq_entry_Handle::x_GetInfo(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Add(), DescDBFunc< CSeq_entry_EditHandle >::Add(), AddOrgToDefline(), AddSeqEntryToSeqEntry(), CAlignmentAssistant::AdjustBioseq(), CEditSequence::AdjustFeatureLocations(), CApplyObject::ApplyChange(), BOOST_AUTO_TEST_CASE(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CEditSequence::CreateControls(), CreateEditorForObject(), CEditSequence::CreateFeature(), CEditSequence::CreateRegulatory(), CSeq_descr_CI::CSeq_descr_CI(), CEditingActionFeatGeneLocus::FindRelated(), GetAccessionFromObjects(), GetBioseqForSeqFeat(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), CModifySeqId::GetCommand(), GetCommandFromApplyObject(), CEditObjectSeq_desc::GetEditCommand(), CRemoveSequencesDlg::GetLabel(), CEditSequence::GetSeqTitle(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), CValidError_imp::GetTSAConflictingBiomolTechErrors(), CValidError_imp::GetTSANStretchErrors(), handler_eErr_SEQ_INST_HistoryGiCollision(), LaunchBioseqEditor(), CEditObjectSeq_desc::LocationChange(), CEditingActionDescLocalId::Modify(), CEditSequence::OnAccept(), CBioseqEditor::OnPropagateSelectedFeatures(), CEditSequence::OnRetranslate(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CWinMaskUtil::CInputBioseq_CI::operator++(), DescDBFunc< CSeq_entry_EditHandle >::Remove(), CRemoveGeneXrefs::RemoveOrphanLocus(), CRemoveGeneXrefs::RemoveOrphanLocus_tag(), RemoveSequence(), CCleanup::RenormalizeNucProtSets(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Reset(), SegMaskerApplication::Run(), s_AddBioseqToNucProtSet(), s_DoSmartProcessing(), s_GetAccession(), s_GetAccessionForSeqdesc(), s_MatchProteinById(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Set(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), UpdateAllDefinitionLine(), CDescPlacementPanel::x_AddToStrings(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CBioseq_CI::x_Settle(), and CGff2Writer::x_WriteSeqEntryHandle().

◆ GetSeq_align()

Get const reference to current seq-align.

Definition at line 75 of file seq_align_handle.cpp.

References ConstRef(), and CSeq_align_Handle::x_GetSeq_align().

Referenced by CAlignmentAssistant::AdjustAlign(), CMatePairGlyph::CMatePairGlyph(), CCmdDelSeq_align::Execute(), AnnotDataResolver< CSeq_align_Handle >::GetData(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CAlignmentAssistant::OnReverseStrand(), CEditsSaver::Replace(), CDesktopAlignItem::s_ContainsFarPointers(), s_DivvyUpAlignments_ProcessAnnot(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), CSeq_annot_EditHandle::TakeAlign(), CAlignmentAssistant::TranslateLocations(), and UpdateDensegAlignment().

◆ GetSeq_annotCore() ◆ GetSeq_entry_Handle()

Get parent Seq-entry handle.

See also: GetParentEntry()

Definition at line 556 of file bioseq_handle.cpp.

References CBioseq_Handle::GetParentEntry().

◆ GetSeq_entry_Index() ◆ GetSeq_entryCore() ◆ GetSeq_feat()

Reimplemented in CMappedFeat.

Definition at line 208 of file seq_feat_handle.cpp.

References CSeq_feat_Handle::GetOriginalSeq_feat().

◆ GetSeq_graph() ◆ GetSeq_id_Handle()

Get handle of id used to obtain this bioseq handle.

Definition at line 772 of file bioseq_handle.hpp.

References CBioseq_Handle::m_Handle_Seq_id.

Referenced by CBioseq_Handle::GetAccessSeq_id_Handle(), CSplitCacheApp::GetBioseqHandle(), CBioseq_Handle::GetInitialSeqIdOrNull(), CViewGraphic::InitView(), CVcfTableView::InitView(), CSGUtils::IsChromosome(), CSGUtils::IsmRNA(), CSGUtils::IsSegSet(), SBlobInserter::operator()(), PatchTargetSequence(), CGiCache::RecordKnown(), s_SeqMapForHandle(), VerifyMolType(), CSFTranslationJob::x_InitGeneticCode(), CAssemblyListPanel::x_UpdateSearchTerm(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), and CGff3Writer::xAssignAlignmentDensegType().

◆ GetSeq_tableNumRows() size_t CSeq_annot_Handle::GetSeq_tableNumRows ( void ) const

Definition at line 190 of file seq_annot_handle.cpp.

References CSeq_annot_Base::GetData(), CSeq_table_Base::GetNum_rows(), CSeq_annot_Base::C_Data::GetSeq_table(), and CSeq_annot_Handle::x_GetSeq_annotCore().

Referenced by NSnpBins::FindPosIndexRange(), CSeqTableReader::GetRange(), CSeqTableReader::GetValue(), CDemoApp::Run(), CEpigenomicsJob::x_Execute(), CHapmapJob::x_Load(), CSGSegmentSmearJob::x_LoadFromNA(), and CSGSeqGraphJob::x_LoadSeqTable().

◆ GetSeqId()

Get id which can be used to access this bioseq handle Throws an exception if none is available.

Definition at line 128 of file bioseq_handle.cpp.

References CBioseq_Handle::GetAccessSeq_id_Handle(), and CSeq_id_Handle::GetSeqId().

Referenced by CGapAnalysis::AddBioseqGaps(), AddIRDMiscFeature(), CConvertDescToFeatComment::apply(), CConvertDescToFeatSource::apply(), CConvertDescToFeatPub::apply(), CConvertDescToFeatPubConstraint::apply(), CRecomputeIntervals::apply(), CTrimN::apply(), BOOST_AUTO_TEST_CASE(), BuildFeatureSeqTableFromSeqEntry(), CheckDeflineMatches(), CSeq_loc_Mapper::CSeq_loc_Mapper(), NSearchFeatPanel::GatherFeatures(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), variation::CVariationUtil::GetEffectiveTranscriptLength(), CGuiObjectInfoSeq_align::GetLinks(), IAlignRowHandle::GetOrgLabel(), GetOverlappingFeatures(), CRemoveFeaturesDlg::GetProductId(), GetProteinWeights(), GetRetranslateCDSCommand(), CFlatFileLocusItem::GetSeqLoc(), GetSeqTableForSrcQualFromSeqEntry(), GetSeqTableFromSeqEntry(), IAlignRowHandle::GetTaxId(), CSGUtils::IsChromosome(), CSGUtils::IsmRNA(), CSeqUtils::MixLocToLoc(), CBioseqEditor::OnCreateBiosourceFeat(), CBioseqEditor::OnCreateFeature(), CMytestApplication::PlayAroundWithSuggestIntervals(), CApplyRNAITSDlg::Propagate_RNAITSList(), CSeedTop::Run(), s_AddPartToSegmentedBioseq(), s_CreateKmerCounts(), s_ExtendEntriesFromAlignments(), s_GetFeaturesForRange(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneIdForProduct(), s_GetLabel(), s_GetProteinName(), s_HasMobileElementForInterval(), s_RunBlast2NWSeq(), s_SetCloneInfo(), s_SetIdList(), CAgpwriteProcess::SeqEntryProcess(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), TrimSeqAlign(), CFarPointerSeq::ValidateAlignment(), CCreateSeqHistForTpa::ValidateAlignments(), CConversionApp::Write(), CFastaOstream::WriteSequence(), CPromote::x_AddProtFeature(), CHugeFileDemoApp::x_AddUserObjects(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CFeatureGraph::x_CreateMapRanges(), CFindITSParser::x_CreateMiscRna(), CTaxTreeToolJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFindITSParser::x_CreateRRna(), CAlnVecRow::x_CreateTrackPanel(), CAsn2FlatApp::x_GetLocation(), CFlatFileGenerator::x_GetLocation(), CDeflineGenerator::x_GetLongestProtein(), IEditingActionFeat::x_GetSublocOnBioseq(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CBioseqIndex::x_InitFeats(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CBlastFormat::x_ReverseQuery(), COligoSpecificityCheck::x_SavePrimerInfo(), CBLASTToolManager::x_SelectCompatibleInputObjects(), CBioseqContext::x_SetLocation(), CCDSTranslationPanel::x_SetLocationForProtein(), CPromote::x_SetSeqFeatProduct(), CBlastTabularInfo::x_SetSubjectIds(), CSrcWriter::xGatherId(), and CEditObjectFeaturePropagate::xInit().

◆ GetSeqMap()

Get sequence map.

Definition at line 415 of file bioseq_handle.cpp.

References CBioseq_Info::GetSeqMap(), and CBioseq_Handle::x_GetInfo().

Referenced by CGapInfo< CBlastTabular >::CGapInfo(), CSeqMapSwitchPoint::ChangeSwitchPoint(), CBioseq_Handle::ContainsSegment(), CBlobSplitterImpl::CopySkeleton(), CTextItemSeq_loc::CreateObject(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqMap_CI::CSeqMap_CI(), GetAllSwitchPoints(), CBioseq_Handle::GetBioseqLength(), CSeqMap::GetSeqMapForSeq_loc(), GetSwitchPoint(), LoadSequencesToScope(), CSplitCacheApp::ProcessSeqId(), CNewCleanup_imp::ProtSeqBC(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_SeqMapForHandle(), CBioseq_EditHandle::SetSeqMap(), TrimSeqData(), CFastaOstream::WriteSequence(), CAnnot_Collector::x_CollectSegments(), CFlatGatherer::x_DoMultipleSections(), CComponentSearchJob::x_DoSearch(), CAnnot_Collector::x_Initialize(), CSeqMap_CI::x_Push(), CAnnot_Collector::x_SearchSegments(), CMasterContext::x_SetBaseName(), CVectorTrimPanel::x_SetSeqData(), and CSequenceAmbigTrimmer::x_SliceBioseq().

◆ GetSequenceClass() ◆ GetSequenceType()

Definition at line 855 of file bioseq_handle.hpp.

References CBioseq_Handle::GetInst_Mol().

Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqVector::CSeqVector(), CFlatFileGenerator::Generate(), CBioseq_Handle::GetBioseqMolType(), CScoreBuilder::GetBlastScoreStd(), CSeqMap::GetSeqMapForSeq_loc(), CBioseq_Handle::IsNucleotide(), CBioseq_Handle::IsProtein(), CAlnSeqId::SetBioseqHandle(), CHugeFileDemoApp::x_AddUserObjects(), and CAsn2FastaApp::x_GetFastaOstream().

◆ GetSeqVector() [1/4] ◆ GetSeqVector() [2/4]

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

Definition at line 487 of file bioseq_handle.cpp.

Referenced by CSAM_CIGAR_Formatter::AddRow(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CConvertGapsBySize::apply(), CExpandGaps::apply(), CCombineAdjacentGaps::apply_impl(), CSplignFormatter::AsAlignmentText(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CCDSTranslationProblems::CalculateTranslationProblems(), CheckBioseqEndsForNAndGap(), CheckDuplicates(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CEditSequenceEnds::GetCommand(), CAddLinkageToGaps::GetCommand(), CObjectCoords::GetCoordinates(), GetDNASequence(), CEditSequence::GetFeatures(), GetLoc(), CAlnMixSeq::GetMinusStrandSeqVector(), GetMismatches(), CAlnMixSeq::GetPlusStrandSeqVector(), GetProteinWeight(), GetProteinWeights(), CCodingPropensity::GetScore(), CPaintAlignment::GetSegments(), CBlastSequenceSource::GetSeq(), CBlastSequenceSource::GetSeqLength(), CAlnWriter::GetSeqString(), CGuiObjectInfoSeq_align::GetSeqString(), CSparseAlignment::GetSeqString(), CSimpleOM::GetSeqVector(), CValidError_bioseq::GetTSANStretchErrors(), CBlastBioseqMaker::HasSequence(), CAlignCollapser::InitContig(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), CSeqVectorCache::PrefetchSequence(), RemoteFetchLongNucleotideBioseq(), RetrievePartsOfLargeChromosome(), CDustMaskApplication::Run(), SegMaskerApplication::Run(), CWinMaskApplication::Run(), CSampleObjmgrApplication::Run(), CTestTranscript_PolyA::RunTest(), CTestTranscript_Orfs::RunTest(), CTestTranscript_CountAmbiguities::RunTest(), s_CompareProtProdToTrans(), s_DoNWalign(), CSequenceUpdater::s_ExtendOneEndOfSequence(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_PartialAtGapOrNs(), s_PercentBioseqMatch(), s_RunBlast2NWSeq(), ScanForCpGs(), CSeqSearch::Search(), CSeqVectorProcess::SeqEntryProcess(), CIgBlastTabularInfo::SetAirrFormatData(), CMultAlign::SetGenomic(), CIgBlastTabularInfo::SetIgAnnotation(), TestStrongKozakUorfs(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), TrimStopsFromCompleteCDS(), CIntronValidator::Validate(), CAssemblyGapValidator::Validate(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateNsAndGaps(), CValidError_bioseq::ValidateRawConst(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CFastaOstream::WriteSequence(), CFeatureItem::x_AddQualTranslation(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), CSFTranslationJob::x_Execute(), CCrossPanelIR::x_GetSequence(), CAlnVec::x_GetSeqVector(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CReportTrim::x_IsThereGapNotAtTheEnd(), CSplign::x_LoadSequence(), COligoSpecificityCheck::x_NW_alignment(), CSplignApp::x_ProcessPair(), CInstancedAligner::x_RunMMGlobal(), CUnorderedSplitter::x_SplitSeqData(), CCdregionValidator::x_ValidateConflict(), and CVcfWriter::x_WriteFeature().

◆ GetSeqVector() [3/4] ◆ GetSeqVector() [4/4] ◆ GetSet()

Definition at line 219 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::CBioseq_set_Handle, CSeq_entry_Handle::GetTSE_Handle(), and CSeq_entry_Handle::x_GetInfo().

Referenced by DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Add(), DescDBFunc< CSeq_entry_EditHandle >::Add(), CCleanup::AddGenBankWrapper(), AddOrgToDefline(), CCleanup::AddProtein(), AddSeqEntryToSeqEntry(), CPackageFeaturesOnParts::apply(), CApplyObject::ApplyChange(), BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CountDefLineConflicts(), CSeq_descr_CI::CSeq_descr_CI(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), DemoteCDSToNucSeq(), CMRnaForCDS::DoesMrnaExist(), CCmdAddSeqEntry::Execute(), CCmdPromoteCDS::Execute(), GetAccessionFromObjects(), CValidError_base::GetAppropriateXrefParent(), CBioseq_Handle::GetComplexityLevel(), CBioseq_set_Handle::GetComplexityLevel(), CEditObjectSeq_desc::GetEditCommand(), CBioseq_Handle::GetExactComplexityLevel(), CBioseq_set_Handle::GetExactComplexityLevel(), CAutoDef::GetMasterLocation(), GetNucBioseq(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), GetSetParent(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CSGSequenceDS::IsPopSet(), CAutoDef::IsSegment(), IsSeqOrNP(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CSequesterSets::OnSequester(), CMytestApplication::PlayAroundWithSuggestIntervals(), CReorderSequencesDlg::PopulateSet(), PromoteCDSToNucProtSet(), PropagateDescriptor(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), DescDBFunc< CSeq_entry_EditHandle >::Remove(), CRemoveSet::remove_sets_from_set(), CCleanup::RenormalizeNucProtSets(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Reset(), s_ActualizeUpdateDate(), s_DescriptorPropagateDown(), s_GetAccessionForSeqdesc(), s_HasTopSetSiblings(), s_MakeGroupsForUniqueValues(), s_PromoteSingletonSetsInSet(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_StandaloneProt(), SegregateSetsByBioseqList(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Set(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), IEditingAction::SetTopSeqEntry(), CSplitCacheApp::TestSplitBioseq(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CCmdPromoteCDS::Unexecute(), UpdateAllDefinitionLine(), CValidError_annot::ValidateSeqAnnotContext(), CGather_Iter::x_AddSeqEntryToStack(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CBioseqEditor::x_DeleteObject(), CBioseqEditor::x_GetDeleteCommand(), CBioseqContext::x_IsPart(), CSeq_entry_CI::x_Next(), CBioseq_CI::x_PushEntry(), CCmdInsertBioseqSet::x_TransferSeqSet(), CMRNAValidator::x_ValidateCommonMRNAProduct(), and CGff2Writer::x_WriteSeqEntryHandle().

◆ GetSingleSubEntry() [1/2] ◆ GetSingleSubEntry() [2/2] ◆ GetSNPAllele() const string & CSeq_feat_Handle::GetSNPAllele ( size_t index ) const ◆ GetSNPAllelesCount() size_t CSeq_feat_Handle::GetSNPAllelesCount ( void ) const ◆ GetSNPComment() const string & CSeq_feat_Handle::GetSNPComment ( void ) const ◆ GetSNPExtra() const string & CSeq_feat_Handle::GetSNPExtra ( void ) const ◆ GetSNPGi() ◆ GetSNPId() ◆ GetSNPQualityCodeOs() void CSeq_feat_Handle::GetSNPQualityCodeOs ( vector< char > & os ) const ◆ GetSNPQualityCodeStr() const string & CSeq_feat_Handle::GetSNPQualityCodeStr ( void ) const ◆ GetSNPQualityCodeWhich() ◆ GetSNPSeq_id() const CSeq_id & CSeq_feat_Handle::GetSNPSeq_id ( void ) const ◆ GetSNPWeight() ◆ GetState()

Get state of the bioseq.

May be used with an empty bioseq handle to check why the bioseq retrieval failed.

Definition at line 95 of file bioseq_handle.cpp.

References CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_not_found, CBioseq_ScopeInfo::GetBlobState(), CTSE_Info::GetBlobState(), CScopeInfo_Base::GetTSE_Handle(), CBioseq_ScopeInfo::HasBioseq(), CBioseq_Handle::m_Info, CBioseq_Handle::x_GetScopeInfo(), and CTSE_Handle::x_GetTSE_Info().

◆ GetSynonyms() ◆ GetTitle() [1/2] const string & CSeq_feat_Handle::GetTitle ( void ) const inline ◆ GetTitle() [2/2] const string & CSeq_graph_Handle::GetTitle ( void ) const inline ◆ GetTitle_x() const string & CSeq_graph_Handle::GetTitle_x ( void ) const inline ◆ GetTitle_y() const string & CSeq_graph_Handle::GetTitle_y ( void ) const inline ◆ GetTopLevelEntry() [1/4]

Get top level Seq-entry handle.

Definition at line 539 of file bioseq_handle.cpp.

References CBioseq_Handle::GetTSE_Handle().

Referenced by CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CProSplign::AssignGeneticCode(), BOOST_AUTO_TEST_CASE(), CDesktopDataBuilder::CDesktopDataBuilder(), CBioseq_Handle::ContainsSegment(), Convert_Seq_id_Bioseq_set(), Convert_Seq_id_Seq_entry(), CHugeFileProcess::ForEachEntry(), COutput_SerialFormat::Format(), COutput_Fasta::Format(), GetBioSource(), GetDeleteSequenceCommand(), CSequenceEditingEventHandler::GetFeatureLocation(), variation::CVariationUtil::GetMolType(), GetResolveOrder(), GetSeqEntryHandle(), CFlatFileGenerator::GetSeqFeatText(), GetTitle(), GetTopSeqEntryFromScopedObject(), CAsn2FastaApp::HandleSeqID(), IsBioseqInSameSeqEntryAsAlign(), CBioseqContext::IsBioseqInSameTopLevelSeqEntry(), IsDeltaOrFarSeg(), CId1FetchApp::LookUpGI(), CAsn2FastaApp::ObtainSeqEntryFromBioseq(), CAsn2FlatApp::ObtainSeqEntryFromBioseq(), SBlobInserter::operator()(), CSplitCacheApp::ProcessBlob(), CConversionApp::Read(), CBulkCDS::RowToScopedObjects(), CBulkGene::RowToScopedObjects(), CBulkMiscFeat::RowToScopedObjects(), CBulkRna::RowToScopedObjects(), SrcEditDialog::RowToScopedObjects(), CAsnExportJob::Run(), CDemoApp::Run(), CSampleLds2Application::Run(), CSampleObjmgrApplication::Run(), CSplitCacheApp::TestSplitBlob(), TestUpdateCDS(), TranslateCDSCommand(), TrimSeqData(), TSeqLocVector2Bioseqs(), CValidError_bioseq::ValidateBioseq(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CTableViewWithTextViewNav::x_EditObject(), CTableDataValidateJob::x_FetchAll(), CFlatGatherer::x_GatherCDSReferences(), CDBSourceItem::x_GatherInfo(), CFlatGatherer::x_GatherReferences(), CCreateGeneModelTask::x_GetCommand(), CEditingBtnsPanel::x_GetSelectedLocations(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSeqMasterIndex::x_Initialize(), CValidatePanel::x_LaunchEditor(), CPrimeCacheApplication::x_Process_Ids(), CFlatFeatureRetrieveJob::x_Run(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), CSeqDesktopPanel::x_SetMaxExpansionLevel(), CVectorTrimPanel::x_SetSeqData(), CValidError_bioseq::x_ValidateCDSVDJCmatch(), CMRNAValidator::x_ValidateCommonMRNAProduct(), CCdregionValidator::x_ValidateProductPartials(), CBsDiffApp::xLoadSeqEntry(), and CAnnotWriterApp::xTryProcessInputId().

◆ GetTopLevelEntry() [2/4] ◆ GetTopLevelEntry() [3/4] ◆ GetTopLevelEntry() [4/4]

Get top level Seq-entry handle.

Definition at line 135 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::GetTSE_Handle().

Referenced by BOOST_AUTO_TEST_CASE(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), IEditingAction::DoConvertFrom(), CFlatFileGenerator::Generate(), IEditingAction::GetActionCommand(), GetDefaultTopLevelSeqEntry(), CEditObjectSeq_desc::GetEditCommand(), GetFeatureFromTableId(), CAuthorNamesPanel::GetSeqEntryHandle(), handler_eErr_SEQ_DESCR_InconsistentProteinTitle(), handler_eErr_SEQ_DESCR_MultipleStrucComms(), handler_eErr_SEQ_FEAT_GenCodeMismatch(), handler_eErr_SEQ_INST_HistAssemblyMissing(), handler_eErr_SEQ_INST_InternalNsInSeqRaw(), handler_eErr_SEQ_INST_TerminalNs(), handler_eErr_SEQ_PKG_OrphanedProtein(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CFlatFileGenerator::HasInference(), CEditObjectSeq_desc::LocationChange(), CSequenceEditingEventHandler::PrepareSeqSubmit(), RemoveSequence(), CSequenceEditingEventHandler::RmCultureNotes(), s_IsLocalFeature(), TrimTerminalNRichRegions(), CAsnvalThreadState::ValidateAsync(), CCleanup::WGSCleanup(), CSimpleProjectView::x_ActivateTextView(), CSequenceUpdater::x_FormNewAlignment(), CSeqMasterIndex::x_Initialize(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), CSubmissionWizard::x_LoadProjectItemData(), and CFeatureTableReader::xAddProteinToSeqEntry().

◆ GetTopLevelSeq_submit() ◆ GetTopLevelSubmit_block() ◆ GetTSE_Handle() [1/4]

Get CTSE_Handle of containing TSE.

Definition at line 758 of file bioseq_handle.hpp.

References CRef< C, Locker >::GetObject(), CScopeInfo_Base::GetTSE_Handle(), and CBioseq_Handle::m_Info.

Referenced by CBioseq_Handle::AddUsedBioseq(), CAnnot_Collector::CanResolveId(), CBioseq_EditHandle::CBioseq_EditHandle(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqMap_CI::CSeqMap_CI(), CBioseq_Handle::GetAccessSeq_id_Handle(), CScope::GetBioseqEditHandle(), CScope_Impl::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CScope::GetBioseqHandlesFromTSE(), CScope_Impl::GetEditHandle(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), CBioseqIndex::GetFeatureForProduct(), GetGeneForFeature(), GetLocalGeneByLocus(), GetMappedCDSForProduct(), GetmRNAforCDS(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::GetParentEntry(), CBioseq_EditHandle::GetParentEntry(), CmRNACDSLinker::GetReferencedmRNA_CDS(), CBioseq_Handle::GetScope(), CMacroBioData_FeatIterBase::GetTaxnames(), CBioseq_Handle::GetTopLevelEntry(), HasNoStop(), LoadSequencesToScope(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), CCDSTranslationPanel::OnPredictIntervalHyperlinkClicked(), CNewCleanup_imp::ProtSeqBC(), CScope::RemoveFromHistory(), CScope_Impl::RemoveTopLevelBioseq(), CDemoApp::Run(), s_AreLinkedToDifferentFeats(), s_GetBestProtFeature(), s_GetCDSformRNA(), s_GetmRNAForCDS(), CGeneOverlapProcess::SeqEntryProcess(), CGeneFeatTreeProcess::SeqEntryProcess(), CBioseq_EditHandle::SetDescr(), SAnnotSelector::SetSearchExternal(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_bioseq::ValidateSeqId(), CFastaOstream::WriteSequence(), CAnnot_Collector::x_CollectSegments(), CFlatGatherer::x_CollectSourceDescriptors(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CCreateGeneModelTask::x_GetCommand(), CSingleFeatValidator::x_GetFeatureProduct(), CBioseq_Handle::x_GetScopeImpl(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CSeqMap_CI::x_Push(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMaster(), CAnnot_Collector::x_SearchSegments(), CScope_Impl::x_UpdateHandleSeq_id(), CIdentifiersPanel::x_UpdateXrefDescriptions(), and CValidError_bioseq::x_ValidateCDSmRNAmatch().

◆ GetTSE_Handle() [2/4]

Definition at line 534 of file bioseq_set_handle.hpp.

References CScopeInfo_Base::GetTSE_Handle(), and CBioseq_set_Handle::m_Info.

Referenced by CBioseq_set_EditHandle::CBioseq_set_EditHandle(), CScope::GetBioseq_setEditHandle(), CScope_Impl::GetEditHandle(), CBioseq_set_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_set_EditHandle::GetParentEntry(), CBioseq_set_Handle::GetScope(), CBioseq_set_Handle::GetTopLevelEntry(), CScope_Impl::RemoveTopLevelBioseq_set(), CCleanup::RepackageProteins(), CBioseq_set_EditHandle::SetDescr(), CScope_Impl::x_AttachEntry(), CBioseq_set_Handle::x_GetScopeImpl(), and CSeq_entry_CI::x_SetCurrentEntry().

◆ GetTSE_Handle() [3/4]

Definition at line 297 of file seq_annot_handle.hpp.

References CScopeInfo_Base::GetTSE_Handle(), and CSeq_annot_Handle::m_Info.

Referenced by CGraphUtils::CalcGraphLevels(), CSeq_annot_EditHandle::CSeq_annot_EditHandle(), CSGAlignmentDS::GetDataLoader(), CScope_Impl::GetEditHandle(), CSeq_annot_Handle::GetParentEntry(), CSeq_annot_EditHandle::GetParentEntry(), CSeq_annot_Handle::GetScope(), CScope::GetSeq_annotEditHandle(), CSeq_annot_Handle::GetTopLevelEntry(), CSeq_annot_Handle::OrderedBefore(), CFeatIdRemapper::RemapId(), CScope_Impl::RemoveAnnot(), CScope_Impl::RemoveTopLevelAnnot(), RestoreModelFromPublicMrnaFeature(), CDemoApp::Run(), SAnnotSelector::SetLimitSeqAnnot(), CSGAlignStatJob::x_CollectAlignStats(), CSGAlignStatJob::x_Execute(), CSeq_annot_Handle::x_GetScopeImpl(), CSGAlignmentJob::x_LoadAlignments(), and CSGAlignStatJob::x_LoadAlignments().

◆ GetTSE_Handle() [4/4]

Definition at line 604 of file seq_entry_handle.hpp.

References CScopeInfo_Base::GetTSE_Handle(), and CSeq_entry_Handle::m_Info.

◆ GetType() ◆ GetXref() ◆ HasAnnots() [1/2] bool CBioseq_Handle::HasAnnots ( void ) const ◆ HasAnnots() [2/2] bool CBioseq_set_Handle::HasAnnots ( void ) const ◆ HasParentEntry() bool CSeq_entry_Handle::HasParentEntry ( void ) const

Check if current seq-entry has a parent.

Definition at line 111 of file seq_entry_handle.cpp.

References CTSE_Info_Object::HasParent_Info(), and CSeq_entry_Handle::x_GetInfo().

Referenced by CAddFluComments::Apply(), CRemoveBioseqChecker::Do(), CAddBioseqChecker::Do(), CEditingActionFeatGeneLocus::FindRelated(), CCountryConflict::GetCommandFromValuesTable(), CLatLonTool::GetCommandFromValuesTable(), CSequesterSets::OnAccept(), CSequesterSets::OnSequester(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), s_MakeGroupsForUniqueValues(), and IEditingAction::SetTopSeqEntry().

◆ IsAa() bool CBioseq_Handle::IsAa ( void ) const

Definition at line 409 of file bioseq_handle.cpp.

References CBioseq_Handle::IsProtein().

Referenced by CStrandPanel::AddCommand(), CCleanup::AddProteinTitle(), CApplyIndexerComments::ApplyToCSeq_entry(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CCDSTranslationProblems::CalculateTranslationProblems(), CBioseqIndex::CBioseqIndex(), CLocationPanel::CreateControls(), CEditingActionFeatGeneLocus::FindRelated(), CFlatFileGenerator::Generate(), CScore_SymmetricOverlap::Get(), CScore_StartStopCodon::Get(), CProductColumn::GetApplyObjects(), CConvertBadCdsAndRnaToMiscFeat::getBacterialPartialNonextendable(), GetBioSourceForBioseq(), CApplyRNAITSDlg::GetCommand(), CLocusItem::GetDivision(), GetMismatches(), CCleanup::GetNormalizableGeneQualPairs(), CFeatureSeqTableColumnBase::GetObjects(), GetOrg_refForProduct(), CGuiObjectInfoSeq_align::GetSeqString(), GetTaxIdForProduct(), HasBadProteinStart(), HasStopInProtein(), CNewCleanup_imp::ImpFeatBC(), CEditingBtnsPanel::IsLocationSelectedAa(), CLocationConstraintMatcher::Match(), CCleanup::MoveFeatToProtein(), CBioseqEditor::OnUpdateNucleotideFeat(), CBioseqEditor::OnUpdateProteinFeat(), CMytestApplication::PlayAroundWithSuggestIntervals(), CAutoDef::RegenerateDefLine(), CAutoDef::RegenerateSequenceDefLines(), RetrievePartsOfLargeChromosome(), CMacroFunction_Autodef::s_AddAutodefOptions(), CSequenceUpdater::s_ExtendOneEndOfSequence(), s_GetOriginalId(), s_MoveProteinSpecificFeats(), s_PercentBioseqMatch(), s_SequenceIsProtein(), SeqLocToBioseq(), CCleanup::SetMolinfoTech(), CMolTypeValidator::Validate(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateModifDescriptors(), CValidError_bioseq::ValidateRawConst(), CGuiObjectInfoSeq_feat::x_AddGroupLocationRows(), CGuiObjectInfoSeq_feat::x_AddLocationRows(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CURLTooltipHandler::x_DisplayUnalignedRegion(), CGenbankGatherer::x_DoSingleSection(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), CFlatGatherer::x_GatherSeqEntry(), CAlnVecRow::x_GetAlignmentTooltip_General(), CAsn2FastaApp::x_GetFastaOstream(), CGuiObjectInfoSeq_feat::x_GetProductLengthRow(), CMacroFunction_ParsedText::x_GetSpecialField(), CBioseqEditor::x_IsNa(), CReportTrim::x_IsProtLocation(), CAutodefJob::x_MakeChanges(), CProSplignTool::x_SelectCompatibleInputObjects(), CDeflineGenerator::x_SetFlags(), CUpdateSeqPanel::x_SetUpdateTypes(), variation_ref::CVariationUtil::x_SetVariantProperties(), CSingleFeatValidator::x_ValidateGeneXRef(), CValidError_bioseq::x_ValidateMolInfoForBioSource(), CSingleFeatValidator::x_ValidateReplaceQual(), CSingleFeatValidator::x_ValidateSeqFeatLoc(), and CValidError_align::x_ValidateSeqId().

◆ IsAlign() bool CSeq_annot_Handle::IsAlign ( void ) const ◆ IsEmptySeq_set() bool CBioseq_set_Handle::IsEmptySeq_set ( void ) const ◆ IsFtable() bool CSeq_annot_Handle::IsFtable ( void ) const

Definition at line 154 of file seq_annot_handle.cpp.

References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsFtable(), and CSeq_annot_Handle::x_GetSeq_annotCore().

Referenced by CAutogeneratedCleanup::BasicCleanupSeqAnnot(), CSeq_annot_ftable_CI::CSeq_annot_ftable_CI(), CSeq_annot_ftable_I::CSeq_annot_ftable_I(), GetAnnotHandle(), CNewCleanup_imp::ProtSeqBC(), s_GetClipLoc(), s_RemoveTaxnameFromProtRef(), CClippedScorer::ScoreAlignments(), CDesktopDataBuilder::x_CreateAnnot(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

◆ IsGraph() bool CSeq_annot_Handle::IsGraph ( void ) const ◆ IsIds() bool CSeq_annot_Handle::IsIds ( void ) const ◆ IsLocs() bool CSeq_annot_Handle::IsLocs ( void ) const ◆ IsNa() bool CBioseq_Handle::IsNa ( void ) const

Definition at line 403 of file bioseq_handle.cpp.

References CBioseq_Handle::IsNucleotide().

Referenced by CLinkUtils::AddBlastProductLink(), AddOrgToDefline(), CLinkUtils::AddSequenceLinks(), CAlignmentAssistant::AdjustBioseq(), CApplyIndexerComments::ApplyToCSeq_entry(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CBioseqIndex::CBioseqIndex(), CValidError_bioseq::CheckSourceDescriptor(), CFlatFileGenerator::Generate(), CApplyRNAITSDlg::GetCommand(), GetDeleteSequenceCommand(), GetDeltaSeqForPosition(), GetSynchronizeProductMolInfoCommand(), CEditingBtnsPanel::IsLocationSelectedNa(), CMytestApplication::PlayAroundWithSuggestIntervals(), s_IsNucLocation(), s_SeqAlignSetToXMLHsps(), CSequenceUpdater::s_UpdateSeqInst(), CCleanup::SetGeneticCodes(), CEditSeqEndsWithAlign::TrimBeforeAfter(), CCmdDelSeq_feat::Unexecute(), UpdateAllDefinitionLine(), CMolTypeValidator::Validate(), CValidError_bioseqset::ValidateSetElements(), CSingleFeatValidator::x_CalculateLocationGaps(), CSingleFeatValidator::x_FindStartOfGap(), CFlatGatherer::x_GatherSeqEntry(), CAlnVecRow::x_GetDescrTooltip(), CAsn2FastaApp::x_GetFastaOstream(), CSingleFeatValidator::x_IsMostlyNs(), CBLASTToolManager::x_SelectCompatibleInputObjects(), CProSplignTool::x_SelectCompatibleInputObjects(), CWindowMaskerTool::x_SelectCompatibleInputObjects(), CDeflineGenerator::x_SetFlags(), CSingleFeatValidator::x_ValidateReplaceQual(), and CValidError_align::x_ValidateSeqId().

◆ IsNamed() bool CSeq_annot_Handle::IsNamed ( void ) const

Definition at line 130 of file seq_annot_handle.cpp.

References CSeq_annot_Info::GetName(), CAnnotName::IsNamed(), and CSeq_annot_Handle::x_GetInfo().

Referenced by CGraphGlyph::CGraphGlyph(), CSGSeqGraphJob::GetSeqtableAnnots(), SAnnotCmdPreparer< type >::PrepareCmd(), CFeatCompareJob_Location::Run(), CTestProtProd_Cdd::RunTest(), s_GetAnnotSelector(), s_GetClipLoc(), s_GetRnaMappingLocs(), s_IsCDD(), CSGAnnotJob::x_AddGraphObject(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CSGSeqGraphJob::x_LoadSeqTable(), and CEditObjectFeaturePropagate::xInit().

◆ IsNucleotide() bool CBioseq_Handle::IsNucleotide ( void ) const inline

Definition at line 869 of file bioseq_handle.hpp.

References CBioseq_Handle::GetSequenceType(), and CSeq_inst::IsNa().

Referenced by CFlatFileFactoryBuilder::AddItem(), CAlnVec::CreateConsensus(), CEditSequence::CreateControls(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), CSparseMultiDataSource::GetAlignType(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CAlignmentAssistant::GetFeatures(), GetNucBioseq(), CPaintAlignment::GetSegments(), CBioseq_Handle::IsNa(), sequpd::RunBlast2Seq(), s_BasicValidation(), s_DumpSequences_wRange(), CMacroFunction_LocationSeqType::TheFunction(), TrimSeqData(), CAlnWriter::WriteAlignDenseSeg(), CAlnWriter::WriteSparseAlign(), CBLASTSeqToolJob::x_CreateProjectItems(), CVectorTrimPanel::x_DeleteSelected(), CVectorTrimPanel::x_FindCompleteDeletions(), variation::CHgvsParser::x_header(), CVectorTrimPanel::x_SetSeqData(), and CVectorTrimPanel::x_TrimSelected().

◆ IsPlainFeat() bool CSeq_feat_Handle::IsPlainFeat ( void ) const

Check if this is plain feature.

Definition at line 124 of file seq_feat_handle.cpp.

References CAnnotObject_Info::IsRegular(), CSeq_feat_Handle::x_GetAnnotObject_InfoAny(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

◆ IsProtein() bool CBioseq_Handle::IsProtein ( void ) const inline

Definition at line 862 of file bioseq_handle.hpp.

References CBioseq_Handle::GetSequenceType(), and CSeq_inst::IsAa().

Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CConvertCDSToProt::Convert(), CCdsToMatPeptide::ConvertInner(), CRemoveFeaturesDlg::CountOrphanedProteins(), CCreateProteinId::create_protein_ids(), CBlastBioseqMaker::CreateBioseqFromId(), CGuiObjectInfoSeq_id::CreateObject(), CGuiObjectInfoSeq_loc::CreateObject(), DeleteProteinAndRenormalizeNucProtSet(), CScore_SegPct::Get(), CScore_Entropy::Get(), CAlnVecGraphicDataSource::GetAlignType(), CTruncateCDS::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), CEditSequence::GetFeatures(), CGuiObjectInfoSeq_align::GetLinks(), CRemoveFeaturesDlg::GetProductId(), GetProteinName(), GetRetranslateCDSCommand(), CGuiObjectInfoSeq_align::GetToolTip(), CBulkCDS::GetValuesTableFromSeqEntry(), CAsn2FastaApp::HandleSeqEntry(), CBioseq_Handle::IsAa(), CBlastBioseqMaker::IsProtein(), ListOrphanProteins(), CRemoveProteins::OrphanedProteins(), CRemoveFeaturesDlg::RemoveOrphansRenormalizeNucProtSets(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CAddGlobalCodeBreak::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), sequpd::RunBlast2Seq(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), sGenerateFields(), CMacroFunction_LocationSeqType::TheFunction(), TrimStopsFromCompleteCDS(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CVectorTrimPanel::x_RetranslateCDS(), CReportTrim::x_RetranslateCDS(), and CVectorTrimPanel::x_TrimSelected().

◆ IsRemoved() [1/7] bool CBioseq_Handle::IsRemoved ( void ) const inline

Check if handle points to a removed bioseq.

Definition at line 765 of file bioseq_handle.hpp.

References CRef< C, Locker >::GetPointerOrNull(), CScopeInfo_Base::IsDetached(), and CBioseq_Handle::m_Info.

Referenced by CSeq_entry_EditHandle::CollapseSet(), CSeq_entry_EditHandle::ConvertSeqToSet(), CSeq_entry_EditHandle::ConvertSetToSeq(), DeleteProteinAndRenormalizeNucProtSet(), CSeq_entry_SelectNone_EditCommand::Do(), CScope_Impl::SelectSeq(), CSeq_entry_SelectNone_EditCommand::Undo(), and CScope_Impl::x_SelectSeq().

◆ IsRemoved() [2/7] bool CBioseq_set_Handle::IsRemoved ( void ) const inline ◆ IsRemoved() [3/7] bool CSeq_align_Handle::IsRemoved ( void ) const ◆ IsRemoved() [4/7] bool CSeq_annot_Handle::IsRemoved ( void ) const inline ◆ IsRemoved() [5/7] bool CSeq_entry_Handle::IsRemoved ( void ) const inline ◆ IsRemoved() [6/7] bool CSeq_feat_Handle::IsRemoved ( void ) const ◆ IsRemoved() [7/7] bool CSeq_graph_Handle::IsRemoved ( void ) const ◆ IsSeq() bool CSeq_entry_Handle::IsSeq ( void ) const inline

Definition at line 674 of file seq_entry_handle.hpp.

References CSeq_entry_Base::e_Seq, and CSeq_entry_Handle::Which().

Referenced by DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Add(), DescDBFunc< CSeq_entry_EditHandle >::Add(), AddOrgToDefline(), AddSeqEntryToSeqEntry(), CApplyRNAITSDlg::Apply_RNAITS_ToBioseqSet(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CSeq_entry_EditHandle::ConvertSeqToSet(), CSeq_entry_EditHandle::ConvertSetToSeq(), CEditObjectSeq_desc::CreateWindow(), CSeq_descr_CI::CSeq_descr_CI(), CSeq_entry_SelectNone_EditCommand::Do(), CCmdDelBioseqInst::Execute(), CEditingActionFeatGeneLocus::FindRelated(), GetAccessionFromObjects(), CValidError_base::GetAppropriateXrefParent(), GetBioseqForSeqFeat(), CValidator::CCacheImpl::GetBioseqHandleFromLocation(), CModifySeqId::GetCommand(), CEditObjectSeq_desc::GetEditCommand(), CEditSequence::GetSequence(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), handler_eErr_SEQ_INST_HistoryGiCollision(), handler_eErr_SEQ_INST_InternalNsInSeqRaw(), IsSeqOrNP(), LaunchBioseqEditor(), CEditObjectSeq_desc::LocationChange(), CEditingActionDescLocalId::Modify(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CSequesterSets::OnSequester(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), DescDBFunc< CSeq_entry_EditHandle >::Remove(), CRemoveGeneXrefs::RemoveOrphanLocus(), CRemoveGeneXrefs::RemoveOrphanLocus_tag(), RemoveSequence(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Reset(), s_AddBioseqToNucProtSet(), s_DoSmartProcessing(), s_GetAccession(), s_GetAccessionForSeqdesc(), s_MatchProteinById(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Set(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CSplitCacheApp::TestSplitBioseq(), UpdateAllDefinitionLine(), CValidError_imp::Validate(), CValidError_annot::ValidateSeqAnnotContext(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CBioseqContext::x_IsPart(), CBioseq_CI::x_PushEntry(), CBioseq_CI::x_Settle(), and CGff2Writer::x_WriteSeqEntryHandle().

◆ IsSeq_table() bool CSeq_annot_Handle::IsSeq_table ( void ) const ◆ IsSet() bool CSeq_entry_Handle::IsSet ( void ) const inline

Definition at line 681 of file seq_entry_handle.hpp.

References CSeq_entry_Base::e_Set, and CSeq_entry_Handle::Which().

Referenced by DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Add(), DescDBFunc< CSeq_entry_EditHandle >::Add(), AddDescToSeqEntry(), CCleanup::AddGenBankWrapper(), AddOrgToDefline(), CCleanup::AddProtein(), AddSeqEntryToSeqEntry(), CPackageFeaturesOnParts::apply(), CApplyObject::ApplyChange(), CheckDeflineMatches(), CSeq_entry_EditHandle::CollapseSet(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CSequenceEditingEventHandler::ConvertSetType(), CTopLevelSeqEntryContext::CTopLevelSeqEntryContext(), DemoteCDSToNucSeq(), CSeq_entry_SelectNone_EditCommand::Do(), CMRnaForCDS::DoesMrnaExist(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdAddSeqEntry::Execute(), CCmdPromoteCDS::Execute(), CFlatFileGenerator::Generate(), GetAccessionFromObjects(), CValidError_base::GetAppropriateXrefParent(), CValidator::CCacheImpl::GetBioseqHandleFromLocation(), CBioseq_Handle::GetComplexityLevel(), CBioseq_set_Handle::GetComplexityLevel(), IEditingActionFeat::GetCurrentSeqEntryHandleFromFeatHandle(), CEditObjectSeq_desc::GetEditCommand(), CBioseq_Handle::GetExactComplexityLevel(), CAutoDef::GetMasterLocation(), GetNucBioseq(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), GetSetParent(), CSeq_entry_Handle::GetSingleSubEntry(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CSGSequenceDS::IsPopSet(), CAutoDef::IsSegment(), IsSeqOrNP(), CCdsToMatPeptide::MergeConvert(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CSequesterSets::OnSequester(), PromoteCDSToNucProtSet(), PropagateDescriptor(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), DescDBFunc< CSeq_entry_EditHandle >::Remove(), CRemoveSet::remove_sets_from_set(), CCleanup::RenormalizeNucProtSets(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Reset(), s_ActualizeUpdateDate(), s_AddBioseqToBioseq(), s_DescriptorPropagateDown(), s_HasTopSetSiblings(), s_MakeGroupsForUniqueValues(), s_MatchProteinById(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_StandaloneProt(), SegregateSetsByBioseqList(), DBFunc< CSeq_entry_EditHandle, CSeq_descr >::Set(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), IEditingAction::SetTopSeqEntry(), CCmdAddCDS::Unexecute(), CCmdCreateCDS::Unexecute(), CCmdPromoteCDS::Unexecute(), UpdateAllDefinitionLine(), CValidError_imp::Validate(), CValidError_annot::ValidateSeqAnnotContext(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CGather_Iter::x_AddSeqEntryToStack(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CBioseqContext::x_IsPart(), CSeq_entry_CI::x_Next(), CSeq_annot_CI::x_Push(), CMRNAValidator::x_ValidateCommonMRNAProduct(), CGff2Writer::x_WriteSeqEntryHandle(), and CEditObjectFeaturePropagate::xInit().

◆ IsSetA() bool CSeq_graph_Handle::IsSetA ( void ) const inline ◆ IsSetB() bool CSeq_graph_Handle::IsSetB ( void ) const inline ◆ IsSetBounds() bool CSeq_align_Handle::IsSetBounds ( void ) const inline ◆ IsSetCit() bool CSeq_feat_Handle::IsSetCit ( void ) const inline ◆ IsSetClass() bool CBioseq_set_Handle::IsSetClass ( void ) const

Definition at line 193 of file bioseq_set_handle.cpp.

References CBioseq_set_Info::IsSetClass(), and CBioseq_set_Handle::x_GetInfo().

Referenced by AddDescToSeqEntry(), CCleanup::AddGenBankWrapper(), AddOrgToDefline(), CCleanup::AddProtein(), CReportTrim::AdjustAndTranslate(), CPackageFeaturesOnParts::apply(), CRemAllProtTitles::apply(), CRemProtTitles::apply(), CApplyObject::ApplyChange(), COrgGeneralPanel::ApplyCommand(), ApplySrcTableToSeqEntry(), BOOST_AUTO_TEST_CASE(), CApplyObject::CApplyObject(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CCleanup::ConvertSrcFeatsToSrcDescs(), CountDefLineConflicts(), CNewCleanup_imp::CreateMissingMolInfo(), CSeqsetIndex::CSeqsetIndex(), DeleteProteinAndRenormalizeNucProtSet(), DemoteCDSToNucSeq(), CCmdAddSeqEntry::Execute(), CCmdCreateFeat::Execute(), CCmdPromoteCDS::Execute(), CValidError_base::GetAppropriateXrefParent(), CFarPointerSeq::GetCommand(), GetDeleteSequenceCommand(), CEditObjectSeq_desc::GetEditCommand(), CBioseq_Handle::GetExactComplexityLevel(), CBioseq_set_Handle::GetExactComplexityLevel(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CMiscSeqTableColumn::GetRelatedApplyObjects(), GetSetParent(), GetTextObjectDescription(), IsInGenProdSet(), CSGSequenceDS::IsPopSet(), CmRNACDSLinker::LinkByProduct(), CInfluenzaSet::MakeSet(), CCleanup::MoveOneFeatToPubdesc(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CSequesterSets::OnSequester(), PromoteCDSToNucProtSet(), CSequesterSets::RecursiveCollectSets(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), CNewCleanup_imp::RemoveBadProteinTitle(), CCleanup::RenormalizeNucProtSets(), s_DescriptorPropagateDown(), s_GetNPParent(), s_GetSeq_featAcc(), s_MakeGroupsForUniqueValues(), CMacroFunction_RemoveSingleItemSet::s_RemoveSingleItemSet(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), s_StandaloneProt(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), IEditingAction::SetTopSeqEntry(), CMacroFunction_ApplyPublication::TheFunction(), CCmdPromoteCDS::Unexecute(), UpdateAllDefinitionLine(), CBiosampleChkApp::UpdateBioSource(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CGather_Iter::x_AddSeqEntryToStack(), CSubmissionWizard::x_ApplySourceDescriptorToRecord(), CSubmissionWizard::x_ApplyUserDescriptorToRecord(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CFlatFileGenerator::x_DeduceTarget(), CAsn2FlatApp::x_DeduceTarget(), CAdjustFeaturesForGaps::x_DoOne(), CSequenceUpdater::x_GetOldBseq_EntryHandle(), CBioseqContext::x_IsPart(), CMRNAValidator::x_ValidateCommonMRNAProduct(), and CGff2Writer::x_WriteSeqEntryHandle().

◆ IsSetColl() bool CBioseq_set_Handle::IsSetColl ( void ) const ◆ IsSetComment() [1/2] bool CSeq_feat_Handle::IsSetComment ( void ) const inline

Definition at line 411 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Handle::IsSetSNPComment(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CExplodeRNAFeats::apply(), CDemoApp::Run(), s_AreFeatureLabelsSame(), s_CheckQuals_conflict(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualProtNote(), CSourceFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualSeqfeatNote(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualsSite(), CFeatureItem::x_AddRegulatoryClassQual(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CFeatureItem::x_CleanQuals(), CAutoDef::x_Is5SList(), CAutoDef::x_IsSingleMiscFeat(), CFeatureSearchJob::x_SearchFeatures(), CGff3Writer::xAssignFeatureAttributeNote(), and CGtfWriter::xAssignFeatureAttributeNote().

◆ IsSetComment() [2/2] bool CSeq_graph_Handle::IsSetComment ( void ) const inline ◆ IsSetComp() bool CSeq_graph_Handle::IsSetComp ( void ) const inline ◆ IsSetData() bool CSeq_feat_Handle::IsSetData ( void ) const

Definition at line 258 of file seq_feat_handle.cpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetData(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

Referenced by CReportTrim::AdjustAndTranslate(), CRemoveGenomeProjectsDB::apply_to_seq_and_feat(), CRemoveStructuredComment::apply_to_seq_and_feat(), CModifyStructuredComment::apply_to_seq_and_feat(), CApplyObject::ApplyChange(), CDiscrepancyVisitorImpl< _Name >::Autofix(), DeleteProteinAndRenormalizeNucProtSet(), CAsn2FastaApp::HandleSeqEntry(), IsLocationInFrame(), CDesktopViewContext::OnCutSelection(), s_IsPreprotein(), sGetClosestGeneRef(), CFastaOstreamEx::x_AddProteinNameAttribute(), CBioseqIndex::x_InitFeats(), CVectorTrimPanel::x_TrimSelected(), CGff2Writer::xAssignFeatureAttributeCodeBreak(), CGff2Writer::xAssignFeatureAttributeDbxref(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), CGff3Writer::xAssignFeatureAttributeNote(), CGff2Writer::xAssignFeatureAttributeProduct(), and CGff2Writer::xAssignFeatureAttributeTranslationTable().

◆ IsSetDate() bool CBioseq_set_Handle::IsSetDate ( void ) const ◆ IsSetDbxref() bool CSeq_feat_Handle::IsSetDbxref ( void ) const inline

Definition at line 525 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetDbxref(), and CSeq_feat_Handle::IsTableSNP().

Referenced by variation::GetFocusLocusIDs(), GetMrnasForGene(), HasGeneIdXref(), IsDuplicate(), CDemoApp::Run(), variation::CVariationUtil::CVariantPropertiesIndex::s_GetGeneID(), CFeatureItem::x_AddQualDbXref(), CSourceFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualsGene(), CSeq_id_Resolver__LRG::x_Create(), CFeatureGenerator::SImplementation::x_CreateGeneFeature(), CVcfWriter::x_WriteFeatureInfo(), and CGff2Writer::xAssignFeatureAttributeDbxref().

◆ IsSetDescr() [1/3] bool CBioseq_Handle::IsSetDescr ( void ) const ◆ IsSetDescr() [2/3] bool CBioseq_set_Handle::IsSetDescr ( void ) const ◆ IsSetDescr() [3/3] bool CSeq_entry_Handle::IsSetDescr ( void ) const ◆ IsSetDim() bool CSeq_align_Handle::IsSetDim ( void ) const inline ◆ IsSetExcept() bool CSeq_feat_Handle::IsSetExcept ( void ) const inline

Definition at line 396 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetExcept(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CDemoApp::Run(), s_CdsFlags(), s_CheckQuals_cdregion(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualExceptions(), CSingleFeatValidator::x_ValidateGeneXRef(), CGff2Writer::xAssignFeatureAttributeException(), CGtfWriter::xAssignFeaturesTranscript(), and CGff2Writer::xGenerateMissingTranscript().

◆ IsSetExcept_text() bool CSeq_feat_Handle::IsSetExcept_text ( void ) const inline

Definition at line 555 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetExcept_text(), and CSeq_feat_Handle::IsTableSNP().

◆ IsSetExp_ev() bool CSeq_feat_Handle::IsSetExp_ev ( void ) const inline ◆ IsSetExt() bool CSeq_feat_Handle::IsSetExt ( void ) const inline

Definition at line 465 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetExt(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CGvfWriteRecord::AssignSource(), CGvfWriteRecord::AssignType(), CWriteUtil::GetModelEvidence(), CDemoApp::Run(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualExt(), CFeatureItem::x_AddQualsRegion(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeParent(), CGvfWriteRecord::x_AssignAttributesCustom(), CGvfWriteRecord::x_AssignAttributeVarType(), CFeatureItem::x_HasMethodtRNAscanSE(), CVcfWriter::x_WriteFeatureFilter(), CVcfWriter::x_WriteFeatureInfo(), CVcfWriter::x_WriteFeatureQual(), CGff2Writer::xAssignFeatureAttributesGoMarkup(), and CGtfWriter::xAssignFeatureMethod().

◆ IsSetExts() bool CSeq_feat_Handle::IsSetExts ( void ) const inline ◆ IsSetId() [1/3] bool CBioseq_Handle::IsSetId ( void ) const

Definition at line 159 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetId(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddProteinTitle(), CRemProtTitles::apply(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CAutogeneratedCleanup::BasicCleanupBioseqHandle(), CNewCleanup_imp::BasicCleanupSeqIds(), CEditSequenceEnds::CollectLabels(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CResetIds_EditCommand::Do(), CReorderSequencesDlg::GetIdLabel(), CFileSubpanel::OnSelectButton(), CNewCleanup_imp::ProtSeqBC(), s_IsSwissProt(), CFileSubpanel::SetClusters(), CBulkEditFeatDlg::x_IsRefSeq(), and CGenericPropsPanel::x_IsRefSeq().

◆ IsSetId() [2/3] bool CBioseq_set_Handle::IsSetId ( void ) const ◆ IsSetId() [3/3] bool CSeq_feat_Handle::IsSetId ( void ) const inline

Definition at line 374 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetId(), and CSeq_feat_Handle::IsTableSNP().

◆ IsSetIds() bool CSeq_feat_Handle::IsSetIds ( void ) const inline ◆ IsSetInst() bool CBioseq_Handle::IsSetInst ( void ) const

Definition at line 195 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetInst(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddProteinTitle(), CConvertGapsBySize::apply(), CExpandGaps::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CCombineAdjacentGaps::apply_impl(), CAutogeneratedCleanup::BasicCleanupBioseqHandle(), CBioseqIndex::CBioseqIndex(), CNewCleanup_imp::FixUnsetMolFromBiomol(), CMolInfoField::GetApplyObjects(), CAddLinkageToGaps::GetCommand(), GetDeltaSeqSummary(), MemetoFunctions< CBioseq_EditHandle, CSeq_inst >::IsSet(), CNewCleanup_imp::ProtSeqBC(), CNewCleanup_imp::RemoveSingleStrand(), s_CheckDataStatus(), s_IsSegmented(), s_NsAreGaps(), CCleanup::SetMolinfoTech(), CValidError_imp::ValidateBioSourceForSeq(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_imp::ValidateSeqLoc(), CCleanup::WGSCleanup(), x_FindLatestSequence(), CDeflineGenerator::x_GetLongestProtein(), CBioseqContext::x_Init(), CValidError_bioseq::x_IsRangeGap(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), CDeflineGenerator::x_SetFlags(), CValidError_bioseq::x_ValidateAbuttingRNA(), and CCdregionValidator::x_ValidateParentPartialness().

◆ IsSetInst_Ext() bool CBioseq_Handle::IsSetInst_Ext ( void ) const

Definition at line 351 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetInst_Ext(), and CBioseq_Handle::x_GetInfo().

Referenced by CBioseqIndex::CBioseqIndex(), GetDeltaSeqSummary(), CLocusItem::GetDivision(), s_IsConOrScaffold(), s_NsAreGaps(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst(), CSeqdesc_CI::x_CheckRef(), CBioseqContext::x_IsDeltaLitOnly(), CDeflineGenerator::x_SetFlags(), and xf_IsDeltaLitOnly().

◆ IsSetInst_Fuzz() bool CBioseq_Handle::IsSetInst_Fuzz ( void ) const ◆ IsSetInst_Hist() bool CBioseq_Handle::IsSetInst_Hist ( void ) const ◆ IsSetInst_Length() bool CBioseq_Handle::IsSetInst_Length ( void ) const ◆ IsSetInst_Mol() bool CBioseq_Handle::IsSetInst_Mol ( void ) const

Definition at line 231 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetInst_Mol(), and CBioseq_Handle::x_GetInfo().

Referenced by CCleanup::AddPartialToProteinTitle(), CNewCleanup_imp::FixUnsetMolFromBiomol(), CMolInfoSubpanel::OnSelectButton(), CNewCleanup_imp::ProtSeqBC(), s_ReplaceAllMolinfo(), CMolInfoSubpanel::SetClusters(), CValidError_bioseq::ValidateRawConst(), CEditSeqId::x_CollectChangedIds(), CLocusItem::x_SetStrand(), and CValidError_bioseq::x_ValidateMolInfoForBioSource().

◆ IsSetInst_Repr() bool CBioseq_Handle::IsSetInst_Repr ( void ) const

Definition at line 213 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetInst_Repr(), and CBioseq_Handle::x_GetInfo().

Referenced by CBioseqIndex::CBioseqIndex(), GetDeltaSeqForPosition(), GetDeltaSeqSummary(), CLocusItem::GetDivision(), CMasterContext::GetPartNumber(), IsDeltaOrFarSeg(), CSGUtils::IsSegSet(), s_IsConOrScaffold(), s_IsSegmented(), CAssemblyGapValidator::Validate(), CValidError_imp::ValidateSeqLoc(), CAutogeneratedCleanup::x_BasicCleanupBioseq_inst(), CSingleFeatValidator::x_CalculateLocationGaps(), CSeqdesc_CI::x_CheckRef(), CFlatGatherer::x_DoMultipleSections(), CSingleFeatValidator::x_FindStartOfGap(), CBioseqContext::x_GetRepr(), CSingleFeatValidator::x_IsMostlyNs(), CSeqUpdateWorker::x_LaunchSingleUpdateSequence(), CDeflineGenerator::x_SetFlags(), CMasterContext::x_SetNumParts(), CValidError_bioseq::x_SetupCommonFlags(), CUpdateSeqPanel::x_SetUpdateTypes(), and CValidError_bioseq::x_ValidateAbuttingRNA().

◆ IsSetInst_Seq_data() bool CBioseq_Handle::IsSetInst_Seq_data ( void ) const ◆ IsSetInst_Strand() bool CBioseq_Handle::IsSetInst_Strand ( void ) const ◆ IsSetInst_Topology() bool CBioseq_Handle::IsSetInst_Topology ( void ) const

Definition at line 296 of file bioseq_handle.cpp.

References CBioseq_Info::IsSetInst_Topology(), and CBioseq_Handle::x_GetInfo().

Referenced by CBioseqIndex::CBioseqIndex(), GetOverlappingFeatures(), CWriteUtil::IsSequenceCircular(), CMolInfoSubpanel::OnSelectButton(), CNewCleanup_imp::ProtSeqBC(), s_GetTopology(), s_ReplaceAllMolinfo(), CMolInfoSubpanel::SetClusters(), ShouldCheckForNsAndGap(), CValidError_bioseq::ValidateNsAndGaps(), CEditObjectSeq_feat::x_IsCircular(), and CValidError_imp::x_ReportInvalidFuzz().

◆ IsSetLevel() bool CBioseq_set_Handle::IsSetLevel ( void ) const ◆ IsSetLoc() bool CSeq_graph_Handle::IsSetLoc ( void ) const inline ◆ IsSetPartial() bool CSeq_feat_Handle::IsSetPartial ( void ) const virtual ◆ IsSetProduct() bool CSeq_feat_Handle::IsSetProduct ( void ) const inline

Definition at line 427 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetProduct(), and CSeq_feat_Handle::x_HasAnnotObjectInfo().

◆ IsSetPseudo() bool CSeq_feat_Handle::IsSetPseudo ( void ) const inline ◆ IsSetQual() bool CSeq_feat_Handle::IsSetQual ( void ) const inline

Definition at line 435 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetQual(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CDemoApp::Run(), s_AreDifferentVariations(), s_AreGBQualsIdentical(), CFeatureItem::x_AddQualsGb(), CFeatureItem::x_ImportQuals(), CGff2Writer::xAssignFeatureAttributeExonNumber(), CGff2Writer::xAssignFeatureAttributeOldLocusTag(), CGff2Writer::xAssignFeatureAttributeProduct(), CGtfWriter::xAssignFeatureMethod(), CGff2Writer::xAssignFeatureScore(), and CGtfWriter::xAssignFeatureType().

◆ IsSetRelease() bool CBioseq_set_Handle::IsSetRelease ( void ) const ◆ IsSetScore() bool CSeq_align_Handle::IsSetScore ( void ) const inline ◆ IsSetSNPComment() bool CSeq_feat_Handle::IsSetSNPComment ( void ) const inline ◆ IsSetSNPExtra() bool CSeq_feat_Handle::IsSetSNPExtra ( void ) const inline ◆ IsSetSNPQualityCode() bool CSeq_feat_Handle::IsSetSNPQualityCode ( void ) const inline ◆ IsSetTitle() [1/2] bool CSeq_feat_Handle::IsSetTitle ( void ) const inline ◆ IsSetTitle() [2/2] bool CSeq_graph_Handle::IsSetTitle ( void ) const inline ◆ IsSetTitle_x() bool CSeq_graph_Handle::IsSetTitle_x ( void ) const inline ◆ IsSetTitle_y() bool CSeq_graph_Handle::IsSetTitle_y ( void ) const inline ◆ IsSetXref() bool CSeq_feat_Handle::IsSetXref ( void ) const inline

Definition at line 510 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::GetSeq_feat(), CSeq_feat_Base::IsSetXref(), and CSeq_feat_Handle::IsTableSNP().

Referenced by CmRNACDSLinker::CompleteHalfFormedXrefPairs(), CCleanup::FixGeneXrefSkew(), CGeneFinder::GetSuppressionCheckGeneRef(), CCleanup::RepairXrefs(), CGeneFinder::ResolveGeneObjectId(), CDemoApp::Run(), CDesktopFeatItem::s_GetProteinName(), sGetClosestGeneRef(), and CFeatureItem::x_AddQualsIdx().

◆ IsSNPMinusStrand() bool CSeq_feat_Handle::IsSNPMinusStrand ( void ) const inline ◆ IsSortedTableFeat() bool CSeq_feat_Handle::IsSortedTableFeat ( void ) const ◆ IsSynonym() [1/2]

Check if this id can be used to obtain this bioseq handle.

Definition at line 526 of file bioseq_handle.cpp.

References CSeq_id_Handle::GetHandle().

Referenced by CEditSeqEndsWithAlign::FindRow(), CSequenceUpdater::FindRowInAlignment(), CGeneFinder::GeneSearchNormalizeLoc(), GetBestCdsForMrna(), GetBestMrnaForCds(), CGeneFinder::IsMixedStrand(), CSeqUtils::MixLocToLoc(), CAnnotObjectType_Less::CNearnessTester::operator()(), CRevCompSequencesDlg::RevCompBioSeq(), s_MatchProteinById(), s_PrintLocAsJavascriptArray(), s_SeqLocEndsOnBioseq(), sFindAnchorRow(), UpdateDensegAlignment(), and CAnnotObject_Less::x_GetExtremes().

◆ IsSynonym() [2/2] ◆ IsTableFeat() bool CSeq_feat_Handle::IsTableFeat ( void ) const ◆ IsTableSNP() bool CSeq_feat_Handle::IsTableSNP ( void ) const

Check if this is SNP table feature.

Definition at line 110 of file seq_feat_handle.cpp.

References CSeq_feat_Handle::x_GetSeq_annot_Info(), CSeq_feat_Handle::x_HasAnnotObjectInfo(), and CSeq_annot_Info::x_HasSNP_annot_Info().

◆ IsTopLevelEntry() bool CSeq_entry_Handle::IsTopLevelEntry ( void ) const ◆ IsTopLevelSeq_submit() bool CSeq_entry_Handle::IsTopLevelSeq_submit ( void ) const ◆ MapLocation() ◆ MoveTo() [1/2]

Move current bioseq into seqset.

Parameters: entry Current bioseq will be inserted into seqset pointed by this handle. index Start index is 0 and -1 means end

Returns: Edit handle to inserted bioseq

Definition at line 728 of file bioseq_handle.cpp.

References CBioseq_set_EditHandle::TakeBioseq().

◆ MoveTo() [2/2] ◆ MoveToSeq()

Move current bioseq into seq-entry and set seq-entry as bioseq.

Parameters: entry seq-entry pointed by entry handle will be set to bioseq

Returns: Edit handle to inserted bioseq

Definition at line 736 of file bioseq_handle.cpp.

References CSeq_entry_EditHandle::TakeSeq().

◆ operator!=() [1/5] ◆ operator!=() [2/5] ◆ operator!=() [3/5] ◆ operator!=() [4/5] ◆ operator!=() [5/5] ◆ operator*() [1/2] ◆ operator*() [2/2] ◆ operator++() [1/2] ◆ operator++() [2/2] ◆ operator->() [1/2] ◆ operator->() [2/2] ◆ operator<() [1/5] ◆ operator<() [2/5] ◆ operator<() [3/5] ◆ operator<() [4/5] ◆ operator<() [5/5] ◆ operator==() [1/5] ◆ operator==() [2/5] ◆ operator==() [3/5] ◆ operator==() [4/5] ◆ operator==() [5/5] ◆ OrderedBefore() ◆ Remove() [1/8]

Definition at line 741 of file bioseq_handle.cpp.

References IScopeTransaction_Impl::Commit(), CBioseq_EditHandle::eKeepSeq_entry, CBioseq_EditHandle::GetParentEntry(), CSeq_entry_EditHandle::Remove(), CBioseq_EditHandle::x_Detach(), and CBioseq_Handle::x_GetScopeImpl().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), DeleteProteinAndRenormalizeNucProtSet(), CRemoveBioseqChecker::Do(), CCmdDelBioseqInst::Execute(), CCmdDelBioseq::Execute(), CFlatFileGenerator::Generate(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), ProcessForTrimAndSplitUpdates(), CCleanup::RemovePseudoProduct(), CDemoApp::Run(), CSeq_entry_EditHandle::TakeSeq(), CCleanupApp::x_RemoveDuplicateFeatures(), and CBioseqContext::~CBioseqContext().

◆ Remove() [2/8] ◆ Remove() [3/8] void CSeq_align_Handle::Remove ( void ) const ◆ Remove() [4/8] void CSeq_annot_EditHandle::Remove ( void ) const

Remove current annot.

Definition at line 298 of file seq_annot_handle.cpp.

References CCommandProcessor::run(), and CSeq_annot_Handle::x_GetScopeImpl().

Referenced by CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), CCleanup::ConvertSrcFeatsToSrcDescs(), DemoteCDSToNucSeq(), CCmdChangeBioseqSet::Execute(), CCmdDelSeq_annot::Execute(), CPromote::PromoteCdregion(), PromoteCDSToNucProtSet(), CPromote::PromoteFeatures(), CPromote::PromotePub(), CPromote::PromoteRna(), CScope::RemoveAnnot(), CScope::ReplaceAnnot(), CCleanup::RescueSiteRefPubs(), s_DetachAnnotFromScope(), CSeq_entry_EditHandle::TakeAnnot(), CCmdPromoteCDS::Unexecute(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), and CNewCleanup_imp::x_RemoveEmptyFeatureTables().

◆ Remove() [5/8] void CSeq_entry_EditHandle::Remove ( void ) const

Remove this Seq-entry from parent, or scope if it's top level Seq-entry.

Definition at line 520 of file seq_entry_handle.cpp.

References CSeq_entry_EditHandle::GetParentEntry(), CCommandProcessor::run(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by CCmdChangeBioseqSet::Execute(), CInfluenzaSet::MakeSet(), CBioseq_EditHandle::Remove(), CBioseq_set_EditHandle::Remove(), CScope::RemoveEntry(), CBioseq_set_EditHandle::TakeEntry(), CCmdAddSeqEntry::Unexecute(), CCmdInsertBioseqSet::Unexecute(), CNewCleanup_imp::x_CollapseSet(), and CSequenceUpdater::x_FormNewAlignment().

◆ Remove() [6/8] void CSeq_feat_Handle::Remove ( void ) const ◆ Remove() [7/8] void CSeq_feat_EditHandle::Remove ( void ) const

Remove the feature from Seq-annot.

Definition at line 499 of file seq_feat_handle.cpp.

References CSeq_feat_EditHandle::GetAnnot(), and CCommandProcessor::run().

Referenced by AddExceptionsToShortIntron(), CApplyObject::ApplyChange(), CDiscrepancyVisitorImpl< _Name >::Autofix(), ConvertRawToDeltaByNs(), CCleanup::ConvertSrcFeatsToSrcDescs(), DeleteProteinAndRenormalizeNucProtSet(), CRemoveFeatChecker::Do(), CCmdDelSeq_feat::Execute(), GetDeleteAllFeaturesCommand_Ex(), CCleanup::MoveOneFeatToPubdesc(), ProcessForTrimAndSplitUpdates(), CSeq_feat_Handle::Remove(), CCleanup::RescueSiteRefPubs(), s_MoveProteinSpecificFeats(), CSeq_annot_EditHandle::TakeFeat(), CCleanupApp::x_RemoveDuplicateFeatures(), CNewCleanup_imp::x_RemoveEmptyFeatures(), and CNewCleanup_imp::x_RemoveOldFeatures().

◆ Remove() [8/8] void CSeq_graph_Handle::Remove ( void ) const ◆ RemoveExceptText() void CSeq_feat_EditHandle::RemoveExceptText ( const string & exception_text ) ◆ RemoveFeatId() [1/3] ◆ RemoveFeatId() [2/3] void CSeq_feat_EditHandle::RemoveFeatId ( const string & id ) ◆ RemoveFeatId() [3/3] void CSeq_feat_EditHandle::RemoveFeatId ( int id ) ◆ RemoveFeatXref() [1/3] ◆ RemoveFeatXref() [2/3] void CSeq_feat_EditHandle::RemoveFeatXref ( const string & id ) ◆ RemoveFeatXref() [3/3] void CSeq_feat_EditHandle::RemoveFeatXref ( int id ) ◆ RemoveId() ◆ RemoveQualifier() void CSeq_feat_EditHandle::RemoveQualifier ( const string & qual_name ) ◆ RemoveSeqdesc() [1/3] ◆ RemoveSeqdesc() [2/3] ◆ RemoveSeqdesc() [3/3] ◆ ReorderFtable() [1/2] void CSeq_annot_EditHandle::ReorderFtable ( CFeat_CI & feat_ci ) const ◆ ReorderFtable() [2/2] ◆ Replace() [1/4] ◆ Replace() [2/4] ◆ Replace() [3/4] void CSeq_feat_EditHandle::Replace ( const CSeq_feat & new_feat ) const

Replace the feature with new Seq-feat object.

All indexes are updated correspondingly.

Definition at line 507 of file seq_feat_handle.cpp.

References CSeq_feat_EditHandle::GetAnnot(), and CCommandProcessor::run().

Referenced by AddCodeBreak(), AddException(), AdjustForCDSPartials(), CApplyObject::ApplyChange(), ApplyPolicyToFeature(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CAutogeneratedCleanup::BasicCleanupSeqFeat(), CNewCleanup_imp::BasicCleanupSeqFeatHandle(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CCleanup::CleanupCollectionDates(), CCleanup::ClearInternalPartials(), ConvertProteinToImp(), ConvertRawToDeltaByNs(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqFeat(), ExtendPartialFeatureEnds(), ExtendToGapsOrEnds(), CCleanup::FixECNumbers(), CCleanup::FixGeneXrefSkew(), g_InstantiateMissingProteins(), CFeatTableEdit::GenerateLocusTags(), CFeatTableEdit::InferPartials(), CNewCleanup_imp::MoveCitationQuals(), CCleanup::MoveFeatToProtein(), CCleanup::NormalizeGeneQuals(), CFeatTableEdit::ProcessCodonRecognized(), ProcessForTrimAndSplitUpdates(), CHugeFileDemoApp::ProcessHugeSeqEntry(), CNewCleanup_imp::ProtSeqBC(), CCleanup::RemoveUnnecessaryGeneXrefs(), CCleanup::RepairXrefs(), CSeq_feat_Handle::Replace(), CDiscrepancyContext::ReplaceSeq_feat(), RetranslateCdregion(), RetranslateCDS(), s_RemoveTaxnameFromProtRef(), CInvertProcess::SeqEntryProcess(), CCleanup::SetGeneticCodes(), CCleanup::SetProteinName(), CFeatTableEdit::SubmitFixProducts(), CCleanup::TaxonomyLookup(), TrimSequenceAndAnnotation(), CCleanup::WGSCleanup(), CCleanup::x_AddLowQualityException(), CSequenceUpdater::x_ChangeIDInFeature(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CCleanupApp::x_FixCDS(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CSeq_feat_EditHandle::x_RealReplace(), CNewCleanup_imp::x_RemoveEmptyFeatures(), CCmdChangeSeq_feat::x_Switch(), CVcfWriter::x_WriteData(), CFeatTableEdit::xAdjustExistingParentGene(), CFeatTableEdit::xFeatureSetProduct(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

◆ Replace() [4/4] ◆ ReplaceSeqdesc() [1/3] ◆ ReplaceSeqdesc() [2/3] ◆ ReplaceSeqdesc() [3/3] ◆ Reset() [1/7] void CBioseq_Handle::Reset ( void )

Reset handle and make it not to point to any bioseq.

Definition at line 88 of file bioseq_handle.cpp.

References CBioseq_Handle::m_Handle_Seq_id, CBioseq_Handle::m_Info, CSeq_id_Handle::Reset(), and CScopeInfo_Ref< Info >::Reset().

Referenced by CLocationPanel::CreateControls(), GetBioseqFromSeqLoc(), CSelectFeatureDlg::OnButtonLoadFile(), CDemoApp::Run(), CValidError_bioseq::ValidateBioseq(), CHugeFileDemoApp::x_AddUserObjects(), CSeqdesc_CI::x_CheckRef(), variation::CVariationUtil::CCdregionIndex::x_Index(), CBioseq_CI::x_Settle(), and CSeq_descr_CI::x_Step().

◆ Reset() [2/7] void CBioseq_set_Handle::Reset ( void ) ◆ Reset() [3/7] void CSeq_align_Handle::Reset ( void ) ◆ Reset() [4/7] void CSeq_annot_Handle::Reset ( void ) ◆ Reset() [5/7] void CSeq_entry_Handle::Reset ( void )

Reset handle and make it not to point to any seq-entry.

Definition at line 77 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::m_Info, and CScopeInfo_Ref< Info >::Reset().

Referenced by CApplyObject::CApplyObject(), CSequenceEditingEventHandler::CSequenceEditingEventHandler(), CBioseq_Handle::GetExactComplexityLevel(), CBioseq_set_Handle::GetExactComplexityLevel(), CSelectFeatures::GetMainObject(), CSequenceEditingEventHandler::PrepareSeqSubmit(), CFlatFileContext::Reset(), CCitSubUpdater::sx_GetCitSubForSequence(), CBioseq_CI::x_NextEntry(), CBioseq_CI::x_PopEntry(), CBioseq_CI::x_PushEntry(), CSeq_entry_CI::x_SetCurrentEntry(), CSeq_annot_CI::x_Settle(), and CSequenceEditingEventHandler::x_SetUpTSEandUnDoManager().

◆ Reset() [6/7] void CSeq_feat_Handle::Reset ( void )

Definition at line 95 of file seq_feat_handle.cpp.

References CSeq_feat_Handle::m_CreatedFeat, CSeq_feat_Handle::m_CreatedOriginalFeat, CSeq_feat_Handle::m_FeatIndex, CSeq_feat_Handle::m_Seq_annot, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), and CSeq_annot_Handle::Reset().

Referenced by CEditingActionFeatGeneLocusCdsGeneProt::Find(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CMappedFeat::Reset(), IEditingActionFeat::SetFeatForAnotherFeat(), CSeq_annot_ftable_CI::x_Reset(), and CSeq_annot_ftable_I::x_Reset().

◆ Reset() [7/7] void CSeq_graph_Handle::Reset ( void ) ◆ ResetClass() void CBioseq_set_EditHandle::ResetClass ( void ) const ◆ ResetColl() void CBioseq_set_EditHandle::ResetColl ( void ) const ◆ ResetDate() void CBioseq_set_EditHandle::ResetDate ( void ) const ◆ ResetDescr() [1/3] void CBioseq_EditHandle::ResetDescr ( void ) const ◆ ResetDescr() [2/3] void CBioseq_set_EditHandle::ResetDescr ( void ) const ◆ ResetDescr() [3/3] void CSeq_entry_EditHandle::ResetDescr ( void ) const ◆ ResetId() [1/2] void CBioseq_EditHandle::ResetId ( void ) const ◆ ResetId() [2/2] void CBioseq_set_EditHandle::ResetId ( void ) const ◆ ResetLevel() void CBioseq_set_EditHandle::ResetLevel ( void ) const ◆ ResetRelease() void CBioseq_set_EditHandle::ResetRelease ( void ) const ◆ SelectNone() void CSeq_entry_EditHandle::SelectNone ( void ) const ◆ SelectSeq() [1/3]

Make the empty Seq-entry be in seq state with specified Bioseq object.

Returns new Bioseq handle.

Definition at line 604 of file seq_entry_handle.cpp.

References Ref().

Referenced by CBioseq_set_EditHandle::AttachBioseq(), CSeq_entry_EditHandle::CollapseSet(), CSeq_entry_EditHandle::ConvertSeqToSet(), CSeq_entry_EditHandle::ConvertSetToSeq(), CSeq_entry_EditHandle::CopySeq(), CFlatFileGenerator::Generate(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CSequesterSets::OnAccept(), CSequesterSets::RestoreTextView(), CDemoApp::Run(), CSeq_entry_EditHandle::TakeSeq(), and CSourceModParserWrapper::x_ApplyAllMods().

◆ SelectSeq() [2/3]

Make the empty Seq-entry be in seq state with Bioseq object from the argument seqset.

The seq argument must point to removed Bioseq. Returns Bioseq handle which could be different from the argument is the argument is from another scope.

◆ SelectSeq() [3/3] ◆ SelectSet() [1/4] ◆ SelectSet() [2/4] TSet CSeq_entry_EditHandle::SelectSet ( const TSet & seqset ) const

Make the empty Seq-entry be in set state with Bioseq-set object from the argument seqset.

The seqset argument must point to removed Bioseq-set. Returns new Bioseq-set handle which could be different from the argument is the argument is from another scope.

◆ SelectSet() [3/4] ◆ SelectSet() [4/4]

Convert the empty Seq-entry to Bioseq-set.

Returns new Bioseq-set handle.

Definition at line 535 of file seq_entry_handle.cpp.

References IScopeTransaction_Impl::Commit(), CBioseq_set_Base::eClass_not_set, CBioseq_set_EditHandle::SetClass(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by CSeq_entry_EditHandle::CollapseSet(), CSeq_entry_EditHandle::ConvertSeqToSet(), CSeq_entry_EditHandle::CopySet(), CFlatFileGenerator::Generate(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CSequesterSets::OnAccept(), CSequesterSets::OnSequester(), CSequesterSets::RestoreTextView(), CSeq_entry_EditHandle::SelectSet(), CSeq_entry_EditHandle::TakeSet(), and CCmdDelBioseqSet::Unexecute().

◆ Seq_annot_CanGetDb() bool CSeq_annot_Handle::Seq_annot_CanGetDb ( void ) const ◆ Seq_annot_CanGetDesc() bool CSeq_annot_Handle::Seq_annot_CanGetDesc ( void ) const ◆ Seq_annot_CanGetId() bool CSeq_annot_Handle::Seq_annot_CanGetId ( void ) const ◆ Seq_annot_CanGetName() bool CSeq_annot_Handle::Seq_annot_CanGetName ( void ) const ◆ Seq_annot_GetDb() ◆ Seq_annot_GetDesc() ◆ Seq_annot_GetId() ◆ Seq_annot_GetName() ◆ Seq_annot_IsSetDb() bool CSeq_annot_Handle::Seq_annot_IsSetDb ( void ) const ◆ Seq_annot_IsSetDesc() bool CSeq_annot_Handle::Seq_annot_IsSetDesc ( void ) const ◆ Seq_annot_IsSetId() bool CSeq_annot_Handle::Seq_annot_IsSetId ( void ) const ◆ Seq_annot_IsSetName() bool CSeq_annot_Handle::Seq_annot_IsSetName ( void ) const ◆ SetClass() void CBioseq_set_EditHandle::SetClass ( TClass v ) const ◆ SetColl() void CBioseq_set_EditHandle::SetColl ( TColl & v ) const ◆ SetDate() void CBioseq_set_EditHandle::SetDate ( TDate & v ) const ◆ SetDescr() [1/6] void CBioseq_EditHandle::SetDescr ( TDescr & v ) const

Definition at line 798 of file bioseq_handle.cpp.

References CCommandProcessor::run(), and CBioseq_Handle::x_GetScopeImpl().

Referenced by CCleanup::AddProteinTitle(), AdjustForCDSPartials(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BioseqSetDescriptorPropagateUp(), CSequesterSets::BioseqSetDescriptorPropagateUp(), CCleanup::ConvertSrcFeatsToSrcDescs(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCleanup::MoveOneFeatToPubdesc(), CAutoDef::RegenerateSequenceDefLines(), RetranslateCdregion(), SetTargetedLocusName(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CPromote::x_PromoteRna(), CNewCleanup_imp::x_RemoveOldFeatures(), and CBlastFormat::x_ReverseQuery().

◆ SetDescr() [2/6] void CBioseq_set_EditHandle::SetDescr ( TDescr & v ) const ◆ SetDescr() [3/6] void CSeq_entry_EditHandle::SetDescr ( TDescr & v ) const ◆ SetDescr() [4/6] ◆ SetDescr() [5/6] ◆ SetDescr() [6/6] ◆ SetFeatId() [1/3] ◆ SetFeatId() [2/3] void CSeq_feat_EditHandle::SetFeatId ( const string & id ) ◆ SetFeatId() [3/3] void CSeq_feat_EditHandle::SetFeatId ( int id ) ◆ SetGeneXref() [1/2] void CSeq_feat_EditHandle::SetGeneXref ( CGene_ref & value ) ◆ SetGeneXref() [2/2] CGene_ref & CSeq_feat_EditHandle::SetGeneXref ( void ) ◆ SetId() void CBioseq_set_EditHandle::SetId ( TId & id ) const ◆ SetInst() void CBioseq_EditHandle::SetInst ( TInst & v ) const

Definition at line 849 of file bioseq_handle.cpp.

References CCommandProcessor::run(), and CBioseq_Handle::x_GetScopeImpl().

Referenced by CTrimN::apply(), CApplyObject::ApplyChange(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CCleanup::ConvertDeltaSeqToRaw(), ConvertRawToDeltaByNs(), CCmdChangeBioseqInst::Execute(), RetranslateCdregion(), RetranslateCDS(), CMacroFunction_TrimTerminalNs::TheFunction(), TrimSequenceAndAnnotation(), CCleanup::WGSCleanup(), CUpdateSeq_Input::x_ReadAccession(), CSequenceAmbigTrimmer::x_SliceBioseq(), CVectorTrimPanel::x_TrimSelected(), and CSequenceAmbigTrimmer::x_TrimToNothing().

◆ SetInst_Ext() void CBioseq_EditHandle::SetInst_Ext ( TInst_Ext & v ) const ◆ SetInst_Fuzz() void CBioseq_EditHandle::SetInst_Fuzz ( TInst_Fuzz & v ) const ◆ SetInst_Hist() void CBioseq_EditHandle::SetInst_Hist ( TInst_Hist & v ) const ◆ SetInst_Length() void CBioseq_EditHandle::SetInst_Length ( TInst_Length v ) const ◆ SetInst_Mol() void CBioseq_EditHandle::SetInst_Mol ( TInst_Mol v ) const ◆ SetInst_Repr() void CBioseq_EditHandle::SetInst_Repr ( TInst_Repr v ) const ◆ SetInst_Seq_data() void CBioseq_EditHandle::SetInst_Seq_data ( TInst_Seq_data & v ) const ◆ SetInst_Strand() void CBioseq_EditHandle::SetInst_Strand ( TInst_Strand v ) const ◆ SetInst_Topology() ◆ SetLevel() void CBioseq_set_EditHandle::SetLevel ( TLevel v ) const ◆ SetProtXref() [1/2] void CSeq_feat_EditHandle::SetProtXref ( CProt_ref & value ) ◆ SetProtXref() [2/2] CProt_ref & CSeq_feat_EditHandle::SetProtXref ( void ) ◆ SetRelease() void CBioseq_set_EditHandle::SetRelease ( TRelease & v ) const ◆ SetSeq()

Definition at line 327 of file seq_entry_handle.cpp.

References CScope_Impl::GetBioseqHandle(), CBioseq_Handle::GetEditHandle(), CSeq_entry_Handle::GetTSE_Handle(), CSeq_entry_EditHandle::x_GetInfo(), and CSeq_entry_Handle::x_GetScopeImpl().

Referenced by BOOST_AUTO_TEST_CASE(), CSeq_entry_EditHandle::CollapseSet(), CSeq_entry_EditHandle::ConvertSeqToSet(), CSeq_entry_EditHandle::ConvertSetToSeq(), CSeq_entry_SelectNone_EditCommand::Do(), CFlatFileGenerator::Generate(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), and CCleanup::RenormalizeNucProtSets().

◆ SetSeqMap() CSeqMap & CBioseq_EditHandle::SetSeqMap ( void ) const ◆ SetSet()

Definition at line 319 of file seq_entry_handle.cpp.

References CSeq_entry_EditHandle::CBioseq_set_EditHandle, CSeq_entry_Handle::GetTSE_Handle(), and CSeq_entry_EditHandle::x_GetInfo().

Referenced by CCleanup::AddProtein(), CSeq_entry_EditHandle::AttachBioseq(), CSeq_entry_EditHandle::AttachEntry(), CScope::AttachEntry(), CSeq_entry_EditHandle::CollapseSet(), CSeq_entry_EditHandle::CopyBioseq(), CSeq_entry_EditHandle::CopyEntry(), CSeq_entry_SelectNone_EditCommand::Do(), CCmdAddCDS::Execute(), CCmdCreateCDS::Execute(), CCmdAddSeqEntry::Execute(), CFlatFileGenerator::Generate(), CAsn2FastaApp::HandleSeqEntry(), CAsn2FlatApp::HandleSeqEntryHandle(), CSeq_entry_EditHandle::TakeBioseq(), CSeq_entry_EditHandle::TakeEntry(), CCmdDelBioseqInst::Unexecute(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), and CFeatureTableReader::xMoveCdRegions().

◆ SetTopLevelSubmit_block() [1/2] void CSeq_entry_EditHandle::SetTopLevelSubmit_block ( CSubmit_block & sub ) const ◆ SetTopLevelSubmit_block() [2/2] CSubmit_block & CSeq_entry_EditHandle::SetTopLevelSubmit_block ( void ) const ◆ State_Confidential() bool CBioseq_Handle::State_Confidential ( void ) const inline ◆ State_Conflict() bool CBioseq_Handle::State_Conflict ( void ) const inline ◆ State_Dead() bool CBioseq_Handle::State_Dead ( void ) const inline ◆ State_NoData() bool CBioseq_Handle::State_NoData ( void ) const inline ◆ State_NotFound() bool CBioseq_Handle::State_NotFound ( void ) const inline ◆ State_Suppressed() bool CBioseq_Handle::State_Suppressed ( void ) const inline ◆ State_SuppressedPerm() bool CBioseq_Handle::State_SuppressedPerm ( void ) const inline ◆ State_SuppressedTemp() bool CBioseq_Handle::State_SuppressedTemp ( void ) const inline ◆ State_Withdrawn() bool CBioseq_Handle::State_Withdrawn ( void ) const inline ◆ Swap() [1/2] ◆ Swap() [2/2] ◆ sx_GetComplexityTable() ◆ TakeAlign() ◆ TakeAllAnnots() [1/2] ◆ TakeAllAnnots() [2/2] ◆ TakeAllDescr() ◆ TakeAnnot() [1/3] ◆ TakeAnnot() [2/3] ◆ TakeAnnot() [3/3] ◆ TakeBioseq() [1/2] ◆ TakeBioseq() [2/2] ◆ TakeEntry() [1/2] ◆ TakeEntry() [2/2] ◆ TakeFeat()

Definition at line 336 of file seq_annot_handle.cpp.

References CSeq_annot_EditHandle::AddFeat(), CScopeTransaction::Commit(), CSeq_feat_Handle::GetScope(), CSeq_feat_Handle::GetSeq_feat(), CScope::GetTransaction(), and CSeq_feat_EditHandle::Remove().

Referenced by CApplyObject::ApplyChange(), DemoteCDSToNucSeq(), CCmdPromoteCDS::Execute(), CCleanup::MoveFeatToProtein(), PromoteCDSToNucProtSet(), CSeq_annot_EditHandle::TakeAllAnnots(), and CNewCleanup_imp::x_MergeAdjacentFeatureTables().

◆ TakeGraph() ◆ TakeSeq() ◆ TakeSet() ◆ Update() [1/4] void CSeq_align_Handle::Update ( void ) const ◆ Update() [2/4] void CSeq_annot_EditHandle::Update ( void ) const ◆ Update() [3/4] void CSeq_feat_EditHandle::Update ( void ) const ◆ Update() [4/4] void CSeq_graph_Handle::Update ( void ) const ◆ UpdateAnnotations() void CSeq_entry_EditHandle::UpdateAnnotations ( void ) const ◆ Which() [1/2] ◆ Which() [2/2] ◆ x_Detach() [1/2] void CBioseq_EditHandle::x_Detach ( void ) const protected ◆ x_Detach() [2/2] void CBioseq_set_EditHandle::x_Detach ( void ) const protected ◆ x_GetAnnotObject_Info() ◆ x_GetAnnotObject_InfoAny() ◆ x_GetFeatIndex()

Definition at line 299 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::kFeatIndexMask, and CSeq_feat_Handle::m_FeatIndex.

◆ x_GetInfo() [1/8]

Definition at line 117 of file bioseq_handle.cpp.

References CBioseq_ScopeInfo::GetObjectInfo(), and CBioseq_Handle::m_Info.

◆ x_GetInfo() [2/8]

Definition at line 834 of file bioseq_handle.hpp.

References CBioseq_Handle::x_GetInfo().

◆ x_GetInfo() [3/8]

Definition at line 72 of file bioseq_set_handle.cpp.

References CBioseq_set_ScopeInfo::GetObjectInfo(), and CBioseq_set_Handle::m_Info.

◆ x_GetInfo() [4/8]

Definition at line 387 of file bioseq_set_handle.cpp.

References CBioseq_set_Handle::x_GetInfo().

◆ x_GetInfo() [5/8]

Definition at line 71 of file seq_annot_handle.cpp.

References CSeq_annot_ScopeInfo::GetObjectInfo(), and CSeq_annot_Handle::m_Info.

Referenced by CSeq_entry_EditHandle::CopyAnnot(), CSeq_annot_ftable_CI::CSeq_annot_ftable_CI(), CSeq_annot_Handle::GetCompleteSeq_annot(), CTSE_Handle::GetFeaturesWithId(), CTSE_Handle::GetFeaturesWithXref(), CTSE_Handle::GetFeatureWithId(), CTSE_Handle::GetGenesWithLocus(), CTSE_Handle::GetGeneWithLocus(), CSeq_annot_Handle::GetName(), CSeq_table_CI::GetOriginalLocation(), CSeq_annot_Handle::GetParentEntry(), CAnnotObject_Ref::GetSeq_annot_Info(), CSeq_annot_Handle::IsNamed(), CSeq_align_Handle::IsRemoved(), CSeq_graph_Handle::IsRemoved(), CSeq_annot_Handle::OrderedBefore(), CScope_Impl::RemoveTopLevelAnnot(), SAnnotSelector::SetLimitSeqAnnot(), CTableFieldHandle_Base::x_FindColumn(), CTableFieldHandle_Base::x_GetColumn(), CSeq_annot_EditHandle::x_GetInfo(), CSeq_align_Handle::x_GetSeq_align(), CSeq_feat_Handle::x_GetSeq_annot_Info(), CSeq_annot_Handle::x_GetSeq_annotCore(), CSeq_graph_Handle::x_GetSeq_graph(), CAnnot_Collector::x_SearchObjects(), CAnnot_Collector::x_SearchRange(), and CSeq_annot_ftable_CI::x_Settle().

◆ x_GetInfo() [6/8]

Definition at line 285 of file seq_annot_handle.cpp.

References CSeq_annot_Handle::x_GetInfo().

◆ x_GetInfo() [7/8]

Definition at line 87 of file seq_entry_handle.cpp.

References CSeq_entry_ScopeInfo::GetObjectInfo(), and CSeq_entry_Handle::m_Info.

◆ x_GetInfo() [8/8]

Definition at line 313 of file seq_entry_handle.cpp.

References CSeq_entry_Handle::x_GetInfo().

◆ x_GetPlainSeq_feat() ◆ x_GetScopeImpl() [1/4] CScope_Impl & CBioseq_Handle::x_GetScopeImpl ( void ) const inlineprotected

Definition at line 798 of file bioseq_handle.hpp.

References CBioseq_Handle::GetTSE_Handle(), and CTSE_Handle::x_GetScopeImpl().

◆ x_GetScopeImpl() [2/4] CScope_Impl & CBioseq_set_Handle::x_GetScopeImpl ( void ) const inlineprotected

Definition at line 548 of file bioseq_set_handle.hpp.

References CBioseq_set_Handle::GetTSE_Handle(), and CTSE_Handle::x_GetScopeImpl().

◆ x_GetScopeImpl() [3/4] CScope_Impl & CSeq_annot_Handle::x_GetScopeImpl ( void ) const inline

Definition at line 311 of file seq_annot_handle.hpp.

References CSeq_annot_Handle::GetTSE_Handle(), and CTSE_Handle::x_GetScopeImpl().

Referenced by CSeq_annot_EditHandle::AddAlign(), CSeq_annot_EditHandle::AddFeat(), CSeq_annot_EditHandle::AddGraph(), CSeq_annot_Handle::GetEditHandle(), CSeq_annot_EditHandle::Remove(), CSeq_annot_EditHandle::Update(), CSeq_annot_EditHandle::x_RealAdd(), CSeq_align_Handle::x_RealReplace(), CSeq_feat_EditHandle::x_RealReplace(), and CSeq_graph_Handle::x_RealReplace().

◆ x_GetScopeImpl() [4/4] CScope_Impl & CSeq_entry_Handle::x_GetScopeImpl ( void ) const inlineprotected

Definition at line 618 of file seq_entry_handle.hpp.

References CSeq_entry_Handle::GetTSE_Handle(), and CTSE_Handle::x_GetScopeImpl().

◆ x_GetScopeInfo() [1/8] ◆ x_GetScopeInfo() [2/8] ◆ x_GetScopeInfo() [3/8] ◆ x_GetScopeInfo() [4/8] ◆ x_GetScopeInfo() [5/8] ◆ x_GetScopeInfo() [6/8] ◆ x_GetScopeInfo() [7/8] ◆ x_GetScopeInfo() [8/8] ◆ x_GetSeq_align()

Definition at line 63 of file seq_align_handle.cpp.

References _ASSERT, CSeq_annot_Info::GetInfo(), info, CSeq_align_Handle::m_Annot, CSeq_align_Handle::m_AnnotIndex, NCBI_THROW, and CSeq_annot_Handle::x_GetInfo().

Referenced by CSeq_align_Handle::GetBounds(), CSeq_align_Handle::GetDim(), CSeq_align_Handle::GetScore(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CSeq_align_Handle::GetType(), CSeq_align_Handle::IsSetBounds(), CSeq_align_Handle::IsSetDim(), and CSeq_align_Handle::IsSetScore().

◆ x_GetSeq_annot_Info() ◆ x_GetSeq_annotCore()

Definition at line 142 of file seq_annot_handle.cpp.

References CSeq_annot_Info::GetSeq_annotCore(), and CSeq_annot_Handle::x_GetInfo().

◆ x_GetSeq_graph()

Definition at line 63 of file seq_graph_handle.cpp.

References _ASSERT, CSeq_annot_Info::GetInfo(), info, CSeq_graph_Handle::m_Annot, CSeq_graph_Handle::m_AnnotIndex, NCBI_THROW, and CSeq_annot_Handle::x_GetInfo().

◆ x_GetSNP_annot_Info() ◆ x_GetSNP_Info()

Definition at line 174 of file seq_feat_handle.cpp.

References info, NCBI_THROW, and CSeq_feat_Handle::x_GetSNP_InfoAny().

◆ x_GetSNP_InfoAny() ◆ x_HasAnnotObjectInfo() bool CSeq_feat_Handle::x_HasAnnotObjectInfo ( void ) const inlineprotected

Definition at line 292 of file seq_feat_handle.hpp.

References CSeq_feat_Handle::kNoAnnotObjectInfo, and CSeq_feat_Handle::m_FeatIndex.

Referenced by CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Handle::GetFeatType(), CSeq_feat_Handle::GetLocationId(), CSeq_feat_Handle::GetPartial(), CSeq_feat_Handle::GetRange(), CSeq_feat_Handle::IsPlainFeat(), CSeq_feat_Handle::IsRemoved(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Handle::IsSetPartial(), CSeq_feat_Handle::IsSetProduct(), CSeq_feat_Handle::IsSortedTableFeat(), CSeq_feat_Handle::IsTableFeat(), CSeq_feat_Handle::IsTableSNP(), and CSeq_feat_Handle::x_GetAnnotObject_InfoAny().

◆ x_IsExcluded() [1/2] bool CSeq_annot_ftable_CI::x_IsExcluded ( void ) const protected ◆ x_IsExcluded() [2/2] bool CSeq_annot_ftable_I::x_IsExcluded ( void ) const protected ◆ x_RealAdd() [1/3] ◆ x_RealAdd() [2/3] ◆ x_RealAdd() [3/3] ◆ x_RealAddId() ◆ x_RealAddSeq_descr() [1/3] void CBioseq_EditHandle::x_RealAddSeq_descr ( TDescr & v ) const ◆ x_RealAddSeq_descr() [2/3] void CBioseq_set_EditHandle::x_RealAddSeq_descr ( TDescr & v ) const ◆ x_RealAddSeq_descr() [3/3] void CSeq_entry_EditHandle::x_RealAddSeq_descr ( TDescr & v ) const ◆ x_RealAddSeqdesc() [1/3] bool CBioseq_EditHandle::x_RealAddSeqdesc ( CSeqdesc & d ) const ◆ x_RealAddSeqdesc() [2/3] bool CBioseq_set_EditHandle::x_RealAddSeqdesc ( CSeqdesc & d ) const ◆ x_RealAddSeqdesc() [3/3] bool CSeq_entry_EditHandle::x_RealAddSeqdesc ( CSeqdesc & v ) const ◆ x_RealRemove() [1/3] void CSeq_align_Handle::x_RealRemove ( void ) const private ◆ x_RealRemove() [2/3] void CSeq_feat_EditHandle::x_RealRemove ( void ) const protected ◆ x_RealRemove() [3/3] void CSeq_graph_Handle::x_RealRemove ( void ) const private ◆ x_RealRemoveId() ◆ x_RealRemoveSeqdesc() [1/3] ◆ x_RealRemoveSeqdesc() [2/3] ◆ x_RealRemoveSeqdesc() [3/3] ◆ x_RealReplace() [1/3] ◆ x_RealReplace() [2/3] void CSeq_feat_EditHandle::x_RealReplace ( const CSeq_feat & new_feat ) const protected ◆ x_RealReplace() [3/3] ◆ x_RealReplaceSeqdesc() [1/3] ◆ x_RealReplaceSeqdesc() [2/3] ◆ x_RealReplaceSeqdesc() [3/3] ◆ x_RealResetClass() void CBioseq_set_EditHandle::x_RealResetClass ( void ) const ◆ x_RealResetColl() void CBioseq_set_EditHandle::x_RealResetColl ( void ) const ◆ x_RealResetDate() void CBioseq_set_EditHandle::x_RealResetDate ( void ) const ◆ x_RealResetDescr() [1/3] void CBioseq_EditHandle::x_RealResetDescr ( void ) const ◆ x_RealResetDescr() [2/3] void CBioseq_set_EditHandle::x_RealResetDescr ( void ) const ◆ x_RealResetDescr() [3/3] void CSeq_entry_EditHandle::x_RealResetDescr ( void ) const ◆ x_RealResetId() [1/2] void CBioseq_EditHandle::x_RealResetId ( void ) const ◆ x_RealResetId() [2/2] void CBioseq_set_EditHandle::x_RealResetId ( void ) const ◆ x_RealResetInst() void CBioseq_EditHandle::x_RealResetInst ( ) const ◆ x_RealResetInst_Ext() void CBioseq_EditHandle::x_RealResetInst_Ext ( ) const ◆ x_RealResetInst_Fuzz() void CBioseq_EditHandle::x_RealResetInst_Fuzz ( ) const ◆ x_RealResetInst_Hist() void CBioseq_EditHandle::x_RealResetInst_Hist ( ) const ◆ x_RealResetInst_Length() void CBioseq_EditHandle::x_RealResetInst_Length ( ) const ◆ x_RealResetInst_Mol() void CBioseq_EditHandle::x_RealResetInst_Mol ( ) const ◆ x_RealResetInst_Repr() void CBioseq_EditHandle::x_RealResetInst_Repr ( ) const ◆ x_RealResetInst_Seq_data() void CBioseq_EditHandle::x_RealResetInst_Seq_data ( ) const ◆ x_RealResetInst_Strand() void CBioseq_EditHandle::x_RealResetInst_Strand ( ) const ◆ x_RealResetInst_Topology() void CBioseq_EditHandle::x_RealResetInst_Topology ( ) const ◆ x_RealResetLevel() void CBioseq_set_EditHandle::x_RealResetLevel ( void ) const ◆ x_RealResetRelease() void CBioseq_set_EditHandle::x_RealResetRelease ( void ) const ◆ x_RealSetClass() void CBioseq_set_EditHandle::x_RealSetClass ( TClass v ) const ◆ x_RealSetColl() void CBioseq_set_EditHandle::x_RealSetColl ( TColl & v ) const ◆ x_RealSetDate() void CBioseq_set_EditHandle::x_RealSetDate ( TDate & v ) const ◆ x_RealSetDescr() [1/3] void CBioseq_EditHandle::x_RealSetDescr ( TDescr & v ) const ◆ x_RealSetDescr() [2/3] void CBioseq_set_EditHandle::x_RealSetDescr ( TDescr & v ) const ◆ x_RealSetDescr() [3/3] void CSeq_entry_EditHandle::x_RealSetDescr ( TDescr & v ) const ◆ x_RealSetId() void CBioseq_set_EditHandle::x_RealSetId ( TId & id ) const ◆ x_RealSetInst() void CBioseq_EditHandle::x_RealSetInst ( TInst & v ) const ◆ x_RealSetInst_Ext() void CBioseq_EditHandle::x_RealSetInst_Ext ( TInst_Ext & v ) const ◆ x_RealSetInst_Fuzz() void CBioseq_EditHandle::x_RealSetInst_Fuzz ( TInst_Fuzz & v ) const ◆ x_RealSetInst_Hist() void CBioseq_EditHandle::x_RealSetInst_Hist ( TInst_Hist & v ) const ◆ x_RealSetInst_Length() void CBioseq_EditHandle::x_RealSetInst_Length ( TInst_Length v ) const ◆ x_RealSetInst_Mol() void CBioseq_EditHandle::x_RealSetInst_Mol ( TInst_Mol v ) const ◆ x_RealSetInst_Repr() void CBioseq_EditHandle::x_RealSetInst_Repr ( TInst_Repr v ) const ◆ x_RealSetInst_Seq_data() void CBioseq_EditHandle::x_RealSetInst_Seq_data ( TInst_Seq_data & v ) const ◆ x_RealSetInst_Strand() void CBioseq_EditHandle::x_RealSetInst_Strand ( TInst_Strand v ) const ◆ x_RealSetInst_Topology() void CBioseq_EditHandle::x_RealSetInst_Topology ( TInst_Topology v ) const ◆ x_RealSetLevel() void CBioseq_set_EditHandle::x_RealSetLevel ( TLevel v ) const ◆ x_RealSetRelease() void CBioseq_set_EditHandle::x_RealSetRelease ( TRelease & v ) const ◆ x_Reset() [1/2] void CSeq_annot_ftable_CI::x_Reset ( void ) protected ◆ x_Reset() [2/2] void CSeq_annot_ftable_I::x_Reset ( void ) protected ◆ x_Set() ◆ x_Settle() [1/2] void CSeq_annot_ftable_CI::x_Settle ( void ) protected

Definition at line 801 of file seq_feat_handle.cpp.

References CSeq_annot_ftable_CI::fOnlyTable, CSeq_annot_ftable_CI::GetAnnot(), CSeq_feat_Handle::IsRemoved(), CSeq_feat_Handle::IsTableSNP(), CSeq_feat_Handle::kNoAnnotObjectInfo, CSeq_annot_ftable_CI::m_Feat, CSeq_feat_Handle::m_FeatIndex, CSeq_annot_ftable_CI::m_Flags, CSeq_annot_Info::x_GetAnnotCount(), CSeq_annot_Handle::x_GetInfo(), CSeq_annot_Info::x_GetSNPFeatCount(), and CSeq_annot_ftable_CI::x_Reset().

Referenced by CSeq_annot_ftable_CI::CSeq_annot_ftable_CI(), and CSeq_annot_ftable_CI::x_Step().

◆ x_Settle() [2/2] void CSeq_annot_ftable_I::x_Settle ( void ) protected

Definition at line 863 of file seq_feat_handle.cpp.

References CSeq_annot_ftable_I::fOnlyTable, CSeq_annot_ftable_I::GetAnnot(), CSeq_feat_Handle::IsRemoved(), CSeq_feat_Handle::IsTableSNP(), CSeq_feat_Handle::kNoAnnotObjectInfo, CSeq_annot_ftable_I::m_Feat, CSeq_feat_Handle::m_FeatIndex, CSeq_annot_ftable_I::m_Flags, CSeq_annot_Info::x_GetAnnotCount(), CSeq_annot_EditHandle::x_GetInfo(), CSeq_annot_Info::x_GetSNPFeatCount(), and CSeq_annot_ftable_I::x_Reset().

Referenced by CSeq_annot_ftable_I::CSeq_annot_ftable_I(), and CSeq_annot_ftable_I::x_Step().

◆ x_Step() [1/2] void CSeq_annot_ftable_CI::x_Step ( void ) protected ◆ x_Step() [2/2] void CSeq_annot_ftable_I::x_Step ( void ) protected ◆ ~CSeq_feat_Handle() ◆ m_Annot [1/3] ◆ m_Annot [2/3] ◆ m_Annot [3/3] ◆ m_AnnotIndex [1/2] TIndex CSeq_align_Handle::m_AnnotIndex private ◆ m_AnnotIndex [2/2] TIndex CSeq_graph_Handle::m_AnnotIndex private ◆ m_CreatedFeat ◆ m_CreatedOriginalFeat ◆ m_Feat [1/2] ◆ m_Feat [2/2] ◆ m_FeatIndex ◆ m_Flags [1/2] TFlags CSeq_annot_ftable_CI::m_Flags private ◆ m_Flags [2/2] TFlags CSeq_annot_ftable_I::m_Flags private ◆ m_Handle_Seq_id ◆ m_Info [1/4] TLock CBioseq_Handle::m_Info protected

Definition at line 482 of file bioseq_handle.hpp.

Referenced by CScope_Impl::GetBioseqHandle(), CBioseq_Handle::GetState(), CBioseq_Handle::GetTSE_Handle(), CBioseq_Handle::IsRemoved(), CBioseq_Handle::operator!=(), CBioseq_Handle::operator<(), CBioseq_Handle::operator==(), CBioseq_Handle::Reset(), CScope_Impl::x_GetBioseqHandle(), CBioseq_Handle::x_GetInfo(), CBioseq_Handle::x_GetScopeInfo(), and CScope_Impl::x_SelectSeq().

◆ m_Info [2/4] TLock CBioseq_set_Handle::m_Info protected ◆ m_Info [3/4]

Definition at line 203 of file seq_annot_handle.hpp.

Referenced by CSeq_annot_Handle::GetTSE_Handle(), CSeq_annot_Handle::IsRemoved(), CSeq_annot_Handle::operator!=(), CSeq_annot_Handle::operator<(), CSeq_annot_Handle::operator==(), CSeq_annot_Handle::Reset(), CSeq_annot_Handle::Swap(), CSeq_annot_Handle::x_GetInfo(), CSeq_annot_Handle::x_GetScopeInfo(), CSeq_annot_EditHandle::x_GetScopeInfo(), and CSeq_annot_Handle::x_Set().

◆ m_Info [4/4] TLock CSeq_entry_Handle::m_Info protected ◆ m_Seq_annot ◆ sm_ComplexityTable Initial value:

= {

}

Definition at line 249 of file bioseq_set_handle.hpp.

Referenced by CBioseq_set_Handle::sx_GetComplexityTable().

◆ CAlign_CI ◆ CAnnot_Collector ◆ CAnnotObject_Ref ◆ CAnnotTypes_CI ◆ CBioseq_EditHandle [1/3] ◆ CBioseq_EditHandle [2/3] ◆ CBioseq_EditHandle [3/3] ◆ CBioseq_Handle [1/2] ◆ CBioseq_Handle [2/2] ◆ CBioseq_set_EditHandle [1/2] ◆ CBioseq_set_EditHandle [2/2] ◆ CBioseq_set_Handle ◆ CCreatedFeat_Ref ◆ CFeat_CI ◆ CMappedFeat [1/2] ◆ CMappedFeat [2/2] ◆ CMappedGraph ◆ CScope_Impl [1/9] ◆ CScope_Impl [2/9] ◆ CScope_Impl [3/9] ◆ CScope_Impl [4/9] ◆ CScope_Impl [5/9] ◆ CScope_Impl [6/9] ◆ CScope_Impl [7/9] ◆ CScope_Impl [8/9] ◆ CScope_Impl [9/9] ◆ CSeq_annot_Add_EditCommand< CSeq_align_Handle > [1/2] ◆ CSeq_annot_Add_EditCommand< CSeq_align_Handle > [2/2] ◆ CSeq_annot_Add_EditCommand< CSeq_feat_EditHandle > [1/2] ◆ CSeq_annot_Add_EditCommand< CSeq_feat_EditHandle > [2/2] ◆ CSeq_annot_Add_EditCommand< CSeq_graph_Handle > [1/2] ◆ CSeq_annot_Add_EditCommand< CSeq_graph_Handle > [2/2] ◆ CSeq_annot_CI [1/2] ◆ CSeq_annot_CI [2/2] ◆ CSeq_annot_EditHandle [1/4] ◆ CSeq_annot_EditHandle [2/4] ◆ CSeq_annot_EditHandle [3/4] ◆ CSeq_annot_EditHandle [4/4] ◆ CSeq_annot_ftable_CI ◆ CSeq_annot_ftable_I [1/2] ◆ CSeq_annot_ftable_I [2/2] ◆ CSeq_annot_Handle [1/2] ◆ CSeq_annot_Handle [2/2] ◆ CSeq_annot_Info ◆ CSeq_annot_Remove_EditCommand< CSeq_align_Handle > ◆ CSeq_annot_Remove_EditCommand< CSeq_feat_EditHandle > ◆ CSeq_annot_Remove_EditCommand< CSeq_graph_Handle > ◆ CSeq_annot_Replace_EditCommand< CSeq_align_Handle > ◆ CSeq_annot_Replace_EditCommand< CSeq_feat_EditHandle > ◆ CSeq_annot_Replace_EditCommand< CSeq_graph_Handle > ◆ CSeq_entry_CI [1/2] ◆ CSeq_entry_CI [2/2] ◆ CSeq_entry_EditHandle [1/4] ◆ CSeq_entry_EditHandle [2/4] ◆ CSeq_entry_EditHandle [3/4] ◆ CSeq_entry_EditHandle [4/4] ◆ CSeq_entry_Handle ◆ CSeq_entry_I ◆ CSeqMap_CI [1/2] ◆ CSeqMap_CI [2/2] ◆ CSynonymsSet ◆ CTSE_Handle [1/2] ◆ CTSE_Handle [2/2]

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