Search Toolkit Book for CTSE_Handle
#include <objmgr/tse_handle.hpp>
Collaboration diagram for CTSE_Handle:
Public Types | |
| enum | ETopLevelObjectType { eTopLevel_Seq_entry , eTopLevel_Bioseq_set , eTopLevel_Bioseq , eTopLevel_Seq_annot , eTopLevel_Seq_submit } |
| Type of top level object added to scope. More... | |
| typedef CBlobIdKey | TBlobId |
| TSE info getters. More... | |
| typedef CSeq_entry | TObject |
| Unified interface for templates. More... | |
| typedef vector< CSeq_feat_Handle > | TSeq_feat_Handles |
| typedef int | TFeatureIdInt |
| Find features by an integer FeatId. More... | |
| typedef string | TFeatureIdStr |
| Find features by a string FeatId. More... | |
| typedef CObject_id | TFeatureId |
| Find features by CObject_id (string or integer) More... | |
Protected Types | |
| typedef CTSE_ScopeInfo | TScopeInfo |
| typedef vector< CAnnotObject_Info * > | TAnnotObjectList |
Protected Member Functions | |
| CTSE_Handle (TScopeInfo &object) | |
| CSeq_feat_Handle | x_MakeHandle (CAnnotObject_Info *info) const |
| CSeq_feat_Handle | x_MakeHandle (const TAnnotObjectList &info) const |
| TSeq_feat_Handles | x_MakeHandles (const TAnnotObjectList &infos) const |
Private Attributes | |
| CHeapScope | m_Scope |
| CTSE_ScopeUserLock | m_TSE |
Friends | |
| class | CScope_Impl |
| class | CTSE_ScopeInfo |
| class | CScopeInfo_Base |
Detailed Description
Definition at line 75 of file tse_handle.hpp.
Member Typedef Documentation
◆ TAnnotObjectList
|
protected |
Definition at line 293 of file tse_handle.hpp.
◆ TBlobId
| typedef CBlobIdKey CTSE_Handle::TBlobId |
TSE info getters.
Definition at line 100 of file tse_handle.hpp.
◆ TFeatureId
| typedef CObject_id CTSE_Handle::TFeatureId |
Find features by CObject_id (string or integer)
Definition at line 199 of file tse_handle.hpp.
◆ TFeatureIdInt
| typedef int CTSE_Handle::TFeatureIdInt |
Find features by an integer FeatId.
Definition at line 170 of file tse_handle.hpp.
◆ TFeatureIdStr
| typedef string CTSE_Handle::TFeatureIdStr |
Find features by a string FeatId.
Definition at line 184 of file tse_handle.hpp.
◆ TObject
| typedef CSeq_entry CTSE_Handle::TObject |
Unified interface for templates.
Definition at line 119 of file tse_handle.hpp.
◆ TScopeInfo
|
protected |
Definition at line 289 of file tse_handle.hpp.
◆ TSeq_feat_Handles
| typedef vector<CSeq_feat_Handle> CTSE_Handle::TSeq_feat_Handles |
Definition at line 167 of file tse_handle.hpp.
Member Enumeration Documentation
◆ ETopLevelObjectType
Type of top level object added to scope.
| Enumerator | |
|---|---|
| eTopLevel_Seq_entry | |
| eTopLevel_Bioseq_set | |
| eTopLevel_Bioseq | |
| eTopLevel_Seq_annot | |
| eTopLevel_Seq_submit | |
Definition at line 127 of file tse_handle.hpp.
Constructor & Destructor Documentation
◆ CTSE_Handle() [1/4]
|
inline |
Default constructor/destructor and assignment.
Definition at line 319 of file tse_handle.hpp.
◆ CTSE_Handle() [2/4]
| CTSE_Handle::CTSE_Handle | ( | const CTSE_Handle & | tse | ) |
Definition at line 76 of file tse_handle.cpp.
References _CHECK, and _TRACE_TSE_LOCK.
◆ ~CTSE_Handle()
| CTSE_Handle::~CTSE_Handle | ( | void | ) |
Definition at line 85 of file tse_handle.cpp.
References _CHECK, and _TRACE_TSE_LOCK.
◆ CTSE_Handle() [3/4]
|
protected |
Definition at line 58 of file tse_handle.cpp.
References _CHECK, and _TRACE_TSE_LOCK.
◆ CTSE_Handle() [4/4]
| CTSE_Handle::CTSE_Handle | ( | const CTSE_ScopeUserLock & | lock | ) |
Definition at line 67 of file tse_handle.cpp.
References _CHECK, and _TRACE_TSE_LOCK.
Member Function Documentation
◆ AddUsedTSE()
| bool CTSE_Handle::AddUsedTSE | ( | const CTSE_Handle & | tse | ) | const |
Register argument TSE as used by this TSE, so it will be released by scope only after this TSE is released.
- Parameters
-
tse Used TSE handle
- Returns
- True if argument TSE was successfully registered as 'used'. False if argument TSE was not registered as 'used'. Possible reasons: Circular reference in 'used' tree.
Definition at line 223 of file tse_handle.cpp.
References CTSE_ScopeInfo::AddUsedTSE(), m_TSE, and x_GetScopeInfo().
Referenced by CBioseq_Handle::AddUsedBioseq(), CAnnot_Collector::x_SearchLoc(), and CAnnot_Collector::x_SearchMaster().
◆ Blob_IsDead()
| bool CTSE_Handle::Blob_IsDead | ( | void | ) | const |
Definition at line 186 of file tse_handle.cpp.
References CBioseq_Handle::fState_dead, and x_GetTSE_Info().
◆ Blob_IsSuppressed()
| bool CTSE_Handle::Blob_IsSuppressed | ( | void | ) | const |
Definition at line 166 of file tse_handle.cpp.
References Blob_IsSuppressedPerm(), and Blob_IsSuppressedTemp().
◆ Blob_IsSuppressedPerm()
| bool CTSE_Handle::Blob_IsSuppressedPerm | ( | void | ) | const |
Definition at line 179 of file tse_handle.cpp.
References CBioseq_Handle::fState_suppress_perm, and x_GetTSE_Info().
Referenced by Blob_IsSuppressed().
◆ Blob_IsSuppressedTemp()
| bool CTSE_Handle::Blob_IsSuppressedTemp | ( | void | ) | const |
Definition at line 172 of file tse_handle.cpp.
References CBioseq_Handle::fState_suppress_temp, and x_GetTSE_Info().
Referenced by Blob_IsSuppressed().
◆ CanBeEdited()
| bool CTSE_Handle::CanBeEdited | ( | void | ) | const |
Return true if this TSE handle is local to scope and can be edited.
Definition at line 229 of file tse_handle.cpp.
References CTSE_ScopeInfo::CanBeEdited(), and x_GetScopeInfo().
Referenced by CBioseq_EditHandle::CBioseq_EditHandle(), CBioseq_set_EditHandle::CBioseq_set_EditHandle(), CSeq_annot_EditHandle::CSeq_annot_EditHandle(), CSeq_entry_EditHandle::CSeq_entry_EditHandle(), CScope::GetBioseq_setEditHandle(), CScope::GetBioseqEditHandle(), CScope_Impl::GetEditHandle(), CScope::GetSeq_annotEditHandle(), CScope::GetSeq_entryEditHandle(), SetTopLevelSubmit_block(), and CCreateGeneModelTask::x_GetCommand().
◆ DECLARE_OPERATOR_BOOL()
| CTSE_Handle::DECLARE_OPERATOR_BOOL | ( | IsValid() | ) |
◆ GetBioseqHandle() [1/2]
| CBioseq_Handle CTSE_Handle::GetBioseqHandle | ( | const CSeq_id & | id | ) | const |
Get Bioseq handle from this TSE.
Definition at line 217 of file tse_handle.cpp.
References CSeq_id_Handle::GetHandle().
Referenced by CSeq_entry_Handle::GetBioseqHandle(), CCleanup::RepackageProteins(), CValidError_bioseq::ValidateSeqId(), CSeqMap_CI::x_GetBioseq(), CImportFeatTable::x_GetFixedId(), CSeqMap_CI::x_RefTSEMatch(), and CAnnot_Collector::x_SearchRange().
◆ GetBioseqHandle() [2/2]
| CBioseq_Handle CTSE_Handle::GetBioseqHandle | ( | const CSeq_id_Handle & | id | ) | const |
Definition at line 211 of file tse_handle.cpp.
References CScope_Impl::GetBioseqHandleFromTSE(), and x_GetScopeImpl().
◆ GetBlobId()
| CTSE_Handle::TBlobId CTSE_Handle::GetBlobId | ( | void | ) | const |
Definition at line 122 of file tse_handle.cpp.
References CTSE_Info::GetBlobId(), and x_GetTSE_Info().
Referenced by CSampleEditSaver::CommitTransaction(), CDemoApp::Run(), and CSampleEditSaver::UpdateSeq().
◆ GetCompleteObject()
|
inline |
Definition at line 367 of file tse_handle.hpp.
References GetCompleteTSE().
Referenced by CDemoApp::Run().
◆ GetCompleteTSE()
| CConstRef< CSeq_entry > CTSE_Handle::GetCompleteTSE | ( | void | ) | const |
Complete and get const reference to the seq-entry.
Definition at line 193 of file tse_handle.cpp.
References CSeq_entry_Info::GetCompleteSeq_entry(), and x_GetTSE_Info().
Referenced by GetCompleteObject().
◆ GetDataLoader()
| CDataLoader * CTSE_Handle::GetDataLoader | ( | void | ) | const |
Definition at line 128 of file tse_handle.cpp.
References CDataSource::GetDataLoader(), CTSE_Info::GetDataSource(), and x_GetTSE_Info().
Referenced by CSGAlignmentDS::GetDataLoader(), and CDemoApp::Run().
◆ GetFeaturesWithId() [1/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 700 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [2/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 746 of file tse_handle.cpp.
References eFeatId_id, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [3/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 803 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeaturesWithId().
◆ GetFeaturesWithId() [4/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 652 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [5/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::E_Choice | type, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 604 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
Referenced by CFeatureGenePanel::AddReciprocicalXref(), CCdsMatchInfo::AssignXrefMatch(), CCleanup::ExpandGeneToIncludeChildren(), GetFeaturesWithId(), GetGeneForFeature(), CCleanup::RepairXrefs(), CDemoApp::Run(), s_AreLinkedToDifferentFeats(), CValidError_imp::Validate(), CValidError_feat::ValidateSeqFeatXref(), CFeat_CI::x_AddFeaturesWithId(), CValidError_feat::x_HasNonReciprocalXref(), CFeatTree::x_LookupParentByRef(), and CIdentifiersPanel::x_UpdateXrefDescriptions().
◆ GetFeaturesWithId() [6/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 708 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [7/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 756 of file tse_handle.cpp.
References eFeatId_id, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [8/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 811 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeaturesWithId().
◆ GetFeaturesWithId() [9/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 660 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithId() [10/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithId | ( | CSeqFeatData::ESubtype | subtype, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 612 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [1/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 716 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [2/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 766 of file tse_handle.cpp.
References eFeatId_xref, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [3/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 819 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeaturesWithXref().
◆ GetFeaturesWithXref() [4/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 668 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [5/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::E_Choice | type, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 620 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
Referenced by GetFeaturesWithXref(), CDemoApp::Run(), and CFeat_CI::x_AddFeaturesWithId().
◆ GetFeaturesWithXref() [6/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 724 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [7/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 776 of file tse_handle.cpp.
References eFeatId_xref, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [8/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 827 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeaturesWithXref().
◆ GetFeaturesWithXref() [9/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 676 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeaturesWithXref() [10/10]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetFeaturesWithXref | ( | CSeqFeatData::ESubtype | subtype, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 628 of file tse_handle.cpp.
References eFeatId_xref, x_GetTSE_Info(), and x_MakeHandles().
◆ GetFeatureWithId() [1/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 731 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [2/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 785 of file tse_handle.cpp.
References eFeatId_id, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [3/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 835 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeatureWithId().
◆ GetFeatureWithId() [4/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::E_Choice | type, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 683 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [5/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::E_Choice | type, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 635 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
Referenced by CmRNACDSLinker::CompleteHalfFormedXrefPairs(), ExtractSupportModels(), GetFeatureFromTableId(), GetFeatureWithId(), GetmRNAforCDS(), CmRNACDSLinker::GetReferencedmRNA_CDS(), RestoreModelFromPublicMrnaFeature(), CDemoApp::Run(), s_GetCDSformRNA(), s_GetmRNAForCDS(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), and CFeatureGenerator::SImplementation::x_HandleRnaExceptions().
◆ GetFeatureWithId() [6/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id | ||
| ) | const |
Definition at line 738 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [7/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 794 of file tse_handle.cpp.
References eFeatId_id, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [8/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureId & | id, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 843 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetFeatureWithId().
◆ GetFeatureWithId() [9/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::ESubtype | subtype, |
| const TFeatureIdStr & | id | ||
| ) | const |
Definition at line 690 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
◆ GetFeatureWithId() [10/10]
| CSeq_feat_Handle CTSE_Handle::GetFeatureWithId | ( | CSeqFeatData::ESubtype | subtype, |
| TFeatureIdInt | id | ||
| ) | const |
Definition at line 642 of file tse_handle.cpp.
References eFeatId_id, x_GetTSE_Info(), and x_MakeHandle().
◆ GetGeneByRef() [1/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneByRef | ( | const CGene_ref & | ref | ) | const |
Definition at line 887 of file tse_handle.cpp.
References GetGeneWithLocus(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::IsSetLocus(), and CGene_ref_Base::IsSetLocus_tag().
Referenced by GetGeneByRef().
◆ GetGeneByRef() [2/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneByRef | ( | const CGene_ref & | ref, |
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 915 of file tse_handle.cpp.
References GetGeneWithLocus(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::IsSetLocus(), and CGene_ref_Base::IsSetLocus_tag().
◆ GetGeneByRef() [3/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneByRef | ( | const CGene_ref & | ref, |
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 961 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetGeneByRef().
◆ GetGenesByRef() [1/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesByRef | ( | const CGene_ref & | ref | ) | const |
Definition at line 901 of file tse_handle.cpp.
References GetGenesWithLocus(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::IsSetLocus(), and CGene_ref_Base::IsSetLocus_tag().
Referenced by GetGenesByRef(), CGeneFinder::ResolveGeneXref(), and CFeatTree::x_LookupParentByRef().
◆ GetGenesByRef() [2/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesByRef | ( | const CGene_ref & | ref, |
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 930 of file tse_handle.cpp.
References GetGenesWithLocus(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::IsSetLocus(), and CGene_ref_Base::IsSetLocus_tag().
◆ GetGenesByRef() [3/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesByRef | ( | const CGene_ref & | ref, |
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 968 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), and GetGenesByRef().
◆ GetGenesWithLocus() [1/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesWithLocus | ( | const string & | locus, |
| bool | tag | ||
| ) | const |
Definition at line 861 of file tse_handle.cpp.
References tag, x_GetTSE_Info(), and x_MakeHandles().
Referenced by GetGenesByRef(), GetGenesWithLocus(), GetLocalGeneByLocus(), and CGeneFinder::ResolveGeneXref().
◆ GetGenesWithLocus() [2/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesWithLocus | ( | const string & | locus, |
| bool | tag, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 878 of file tse_handle.cpp.
References tag, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandles().
◆ GetGenesWithLocus() [3/3]
| CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesWithLocus | ( | const string & | locus, |
| bool | tag, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 953 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), GetGenesWithLocus(), and tag.
◆ GetGeneWithLocus() [1/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneWithLocus | ( | const string & | locus, |
| bool | tag | ||
| ) | const |
Find genes by locus, locus tag, or Gene-ref.
Definition at line 853 of file tse_handle.cpp.
References tag, x_GetTSE_Info(), and x_MakeHandle().
Referenced by GetGeneByRef(), GetGeneForFeature(), and GetGeneWithLocus().
◆ GetGeneWithLocus() [2/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneWithLocus | ( | const string & | locus, |
| bool | tag, | ||
| const CSeq_annot_Handle & | src_annot | ||
| ) | const |
Definition at line 868 of file tse_handle.cpp.
References tag, CSeq_annot_Handle::x_GetInfo(), x_GetTSE_Info(), and x_MakeHandle().
◆ GetGeneWithLocus() [3/3]
| CSeq_feat_Handle CTSE_Handle::GetGeneWithLocus | ( | const string & | locus, |
| bool | tag, | ||
| const CSeq_feat_Handle & | src | ||
| ) | const |
Definition at line 945 of file tse_handle.cpp.
References CSeq_feat_Handle::GetAnnot(), GetGeneWithLocus(), and tag.
◆ GetObjectCore()
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inline |
Definition at line 374 of file tse_handle.hpp.
References GetTSECore().
◆ GetScope()
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inline |
Returns scope.
Definition at line 325 of file tse_handle.hpp.
References CHeapScope::GetScope(), and m_Scope.
Referenced by GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetCdssForGene(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), GetMrnasForGene(), CBioseq_Handle::GetScope(), CBioseq_set_Handle::GetScope(), CSeq_annot_Handle::GetScope(), CSeq_entry_Handle::GetScope(), and x_MakeHandle().
◆ GetTopLevelEntry()
| CSeq_entry_Handle CTSE_Handle::GetTopLevelEntry | ( | void | ) | const |
Get top level Seq-entry handle.
Definition at line 205 of file tse_handle.cpp.
References x_GetTSE_Info().
Referenced by CValidator::CCacheImpl::GetBioseqHandleFromLocation(), CMacroBioData_FeatIterBase::GetTaxnames(), CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked(), and CCDSTranslationPanel::OnPredictIntervalHyperlinkClicked().
◆ GetTopLevelObjectType()
| CTSE_Handle::ETopLevelObjectType CTSE_Handle::GetTopLevelObjectType | ( | void | ) | const |
Get type of top level object added to scope.
Definition at line 235 of file tse_handle.cpp.
References CTSE_Info::GetTopLevelObjectType(), and x_GetTSE_Info().
Referenced by CDemoApp::Run().
◆ GetTopLevelSeq_submit()
| const CSeq_submit & CTSE_Handle::GetTopLevelSeq_submit | ( | void | ) | const |
Return reference to top-level Seq-submit object Throw an exception if it's not available.
Definition at line 241 of file tse_handle.cpp.
References CTSE_Info::GetTopLevelSeq_submit(), and x_GetTSE_Info().
Referenced by CSeq_entry_Handle::GetTopLevelSeq_submit(), and CDemoApp::Run().
◆ GetTopLevelSubmit_block()
| const CSubmit_block & CTSE_Handle::GetTopLevelSubmit_block | ( | void | ) | const |
More efficient direct access to Seq-submit.sub field.
Definition at line 253 of file tse_handle.cpp.
References CTSE_Info::GetTopLevelSubmit_block(), and x_GetTSE_Info().
Referenced by CSeq_entry_Handle::GetTopLevelSubmit_block().
◆ GetTSECore()
| CConstRef< CSeq_entry > CTSE_Handle::GetTSECore | ( | void | ) | const |
Get const reference to the seq-entry.
Definition at line 199 of file tse_handle.cpp.
References CSeq_entry_Info::GetSeq_entryCore(), and x_GetTSE_Info().
Referenced by GetObjectCore().
◆ GetUsedMemory()
| size_t CTSE_Handle::GetUsedMemory | ( | void | ) | const |
return estimated memory size occupied by this TSE
Definition at line 140 of file tse_handle.cpp.
References CTSE_Info::GetUsedMemory(), and x_GetTSE_Info().
◆ IsTopLevelSeq_submit()
| bool CTSE_Handle::IsTopLevelSeq_submit | ( | void | ) | const |
Definition at line 247 of file tse_handle.cpp.
References CTSE_Info::IsTopLevelSeq_submit(), and x_GetTSE_Info().
Referenced by CSeq_entry_Handle::IsTopLevelSeq_submit().
◆ IsValid()
| bool CTSE_Handle::IsValid | ( | void | ) | const |
State check.
Definition at line 134 of file tse_handle.cpp.
References CTSE_ScopeInfo::IsAttached(), and m_TSE.
◆ operator!=()
|
inline |
Definition at line 346 of file tse_handle.hpp.
References m_TSE.
◆ operator<()
|
inline |
Definition at line 353 of file tse_handle.hpp.
References m_TSE.
◆ operator=()
| CTSE_Handle & CTSE_Handle::operator= | ( | const CTSE_Handle & | tse | ) |
Definition at line 92 of file tse_handle.cpp.
References _CHECK, _TRACE_TSE_LOCK, m_Scope, and m_TSE.
◆ operator==()
|
inline |
Definition at line 339 of file tse_handle.hpp.
References m_TSE.
◆ OrderedBefore()
| bool CTSE_Handle::OrderedBefore | ( | const CTSE_Handle & | tse | ) | const |
Definition at line 146 of file tse_handle.cpp.
References _ASSERT, CTSE_ScopeInfo::GetBlobOrder(), CTSE_ScopeInfo::GetLoadIndex(), and x_GetScopeInfo().
Referenced by CSeq_annot_Handle::OrderedBefore().
◆ Reset()
| void CTSE_Handle::Reset | ( | void | ) |
Reset to null state.
Definition at line 106 of file tse_handle.cpp.
References _CHECK, _TRACE_TSE_LOCK, m_Scope, m_TSE, CRef< C, Locker >::Reset(), and CHeapScope::Reset().
Referenced by SAnnotSelector::SetLimitNone().
◆ SetTopLevelSubmit_block() [1/2]
| CSubmit_block & CTSE_Handle::SetTopLevelSubmit_block | ( | void | ) | const |
Definition at line 259 of file tse_handle.cpp.
References CanBeEdited(), NCBI_THROW, CTSE_Info::SetTopLevelSubmit_block(), and x_GetTSE_Info().
Referenced by CSeq_entry_EditHandle::SetTopLevelSubmit_block().
◆ SetTopLevelSubmit_block() [2/2]
| void CTSE_Handle::SetTopLevelSubmit_block | ( | CSubmit_block & | sub | ) | const |
Definition at line 269 of file tse_handle.cpp.
References CanBeEdited(), NCBI_THROW, CTSE_Info::SetTopLevelSubmit_block(), and x_GetTSE_Info().
◆ Swap()
|
inline |
Definition at line 381 of file tse_handle.hpp.
References m_Scope, m_TSE, CHeapScope::Swap(), and CRef< C, Locker >::Swap().
Referenced by CTSE_ScopeInfo::RemoveFromHistory(), CScopeInfo_Base::x_ResetTSE_Lock(), CScopeInfo_Base::x_SetTSE_Handle(), and CScopeInfo_Base::x_SetTSE_Lock().
◆ x_GetScopeImpl()
|
inline |
Definition at line 332 of file tse_handle.hpp.
References CHeapScope::GetImpl(), and m_Scope.
Referenced by GetBioseqHandle(), CBioseq_Handle::x_GetScopeImpl(), CBioseq_set_Handle::x_GetScopeImpl(), CSeq_annot_Handle::x_GetScopeImpl(), and CSeq_entry_Handle::x_GetScopeImpl().
◆ x_GetScopeInfo()
|
inline |
Definition at line 360 of file tse_handle.hpp.
Referenced by AddUsedTSE(), CanBeEdited(), CScope_Impl::GetEditHandle(), CTSE_ScopeInfo::GetUserLockState(), OrderedBefore(), CScope_Impl::RemoveAnnot(), CScope_Impl::RemoveEntry(), CTSE_ScopeInfo::RemoveFromHistory(), CScope_Impl::RemoveTopLevelSeqEntry(), CScope_Impl::SelectNone(), CScope_Impl::x_AddTSESetWithAnnots(), CScope_Impl::x_AttachAnnot(), CScope_Impl::x_AttachEntry(), CScope_Impl::x_GetBioseqHandle(), CScope_Impl::x_GetBioseqHandleFromTSE(), CScope_Impl::x_SelectSeq(), CScope_Impl::x_SelectSet(), CSeq_annot_Handle::x_Set(), and CScopeInfo_Base::x_SetTSE_Lock().
◆ x_GetTSE_Info()
Definition at line 116 of file tse_handle.cpp.
References m_TSE, and CTSE_ScopeInfo::m_TSE_Lock.
Referenced by Blob_IsDead(), Blob_IsSuppressedPerm(), Blob_IsSuppressedTemp(), CGraphUtils::CalcGraphLevels(), CScope_Impl::GetBioseqHandle(), GetBlobId(), GetCompleteTSE(), GetDataLoader(), GetFeaturesWithId(), GetFeaturesWithXref(), GetFeatureWithId(), GetGenesWithLocus(), GetGeneWithLocus(), CScope_Impl::GetSeq_entryHandle(), CBioseq_Handle::GetState(), GetTopLevelEntry(), GetTopLevelObjectType(), GetTopLevelSeq_submit(), GetTopLevelSubmit_block(), GetTSECore(), GetUsedMemory(), IsTopLevelSeq_submit(), CScope_Impl::RemoveTopLevelAnnot(), CScope_Impl::RemoveTopLevelBioseq(), CScope_Impl::RemoveTopLevelBioseq_set(), SAnnotSelector::SetLimitTSE(), SetTopLevelSubmit_block(), CFeat_CI::x_AddFeaturesWithId(), CAnnot_Collector::x_AddTSE(), CTSE_ScopeInfo::x_CheckAdded(), CTSE_ScopeInfo::x_GetScopeLock(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMaster(), CAnnot_Collector::x_SearchRange(), CAnnot_Collector::x_SearchTSE2(), and CScopeInfo_Base::x_SetTSE_Handle().
◆ x_MakeHandle() [1/2]
|
protected |
Definition at line 576 of file tse_handle.cpp.
References GetScope(), and info.
Referenced by GetFeatureWithId(), GetGeneWithLocus(), x_MakeHandle(), and x_MakeHandles().
◆ x_MakeHandle() [2/2]
|
protected |
Definition at line 583 of file tse_handle.cpp.
References x_MakeHandle().
◆ x_MakeHandles()
|
protected |
Definition at line 590 of file tse_handle.cpp.
References ITERATE, and x_MakeHandle().
Referenced by GetFeaturesWithId(), GetFeaturesWithXref(), and GetGenesWithLocus().
Friends And Related Function Documentation
◆ CScope_Impl
|
friend |
Definition at line 285 of file tse_handle.hpp.
◆ CScopeInfo_Base
|
friend |
Definition at line 287 of file tse_handle.hpp.
◆ CTSE_ScopeInfo
|
friend |
Definition at line 286 of file tse_handle.hpp.
Member Data Documentation
◆ m_Scope
|
private |
Definition at line 300 of file tse_handle.hpp.
Referenced by GetScope(), operator=(), Reset(), Swap(), and x_GetScopeImpl().
◆ m_TSE
|
private |
Definition at line 301 of file tse_handle.hpp.
Referenced by AddUsedTSE(), IsValid(), operator!=(), operator<(), operator=(), operator==(), Reset(), Swap(), x_GetTSE_Info(), and CTSE_ScopeInfo::x_RestoreAdded().
The documentation for this class was generated from the following files:
- include/objmgr/tse_handle.hpp
- src/objmgr/tse_handle.cpp
