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CTSE_Handle Class Reference

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#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_HandleTSeq_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...
 

Public Member Functions

 CTSE_Handle (void)
 Default constructor/destructor and assignment. More...
 
 CTSE_Handle (const CTSE_Handle &tse)
 
CTSE_Handleoperator= (const CTSE_Handle &tse)
 
 ~CTSE_Handle (void)
 
CScopeGetScope (void) const
 Returns scope. More...
 
bool IsValid (void) const
 State check. More...
 
 DECLARE_OPERATOR_BOOL (IsValid())
 
bool operator== (const CTSE_Handle &tse) const
 
bool operator!= (const CTSE_Handle &tse) const
 
bool operator< (const CTSE_Handle &tse) const
 
bool OrderedBefore (const CTSE_Handle &tse) const
 
void Reset (void)
 Reset to null state. More...
 
TBlobId GetBlobId (void) const
 
CDataLoaderGetDataLoader (void) const
 
size_t GetUsedMemory (void) const
 return estimated memory size occupied by this TSE More...
 
bool Blob_IsSuppressed (void) const
 
bool Blob_IsSuppressedTemp (void) const
 
bool Blob_IsSuppressedPerm (void) const
 
bool Blob_IsDead (void) const
 
CConstRef< CSeq_entryGetCompleteTSE (void) const
 Complete and get const reference to the seq-entry. More...
 
CConstRef< CSeq_entryGetTSECore (void) const
 Get const reference to the seq-entry. More...
 
CConstRef< TObjectGetCompleteObject (void) const
 
CConstRef< TObjectGetObjectCore (void) const
 
CSeq_entry_Handle GetTopLevelEntry (void) const
 Get top level Seq-entry handle. More...
 
ETopLevelObjectType GetTopLevelObjectType () const
 Get type of top level object added to scope. More...
 
bool IsTopLevelSeq_submit () const
 
const CSeq_submitGetTopLevelSeq_submit () const
 Return reference to top-level Seq-submit object Throw an exception if it's not available. More...
 
const CSubmit_blockGetTopLevelSubmit_block () const
 More efficient direct access to Seq-submit.sub field. More...
 
CSubmit_blockSetTopLevelSubmit_block () const
 
void SetTopLevelSubmit_block (CSubmit_block &sub) const
 
CBioseq_Handle GetBioseqHandle (const CSeq_id &id) const
 Get Bioseq handle from this TSE. More...
 
CBioseq_Handle GetBioseqHandle (const CSeq_id_Handle &id) const
 
bool 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. More...
 
bool CanBeEdited (void) const
 Return true if this TSE handle is local to scope and can be edited. More...
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::E_Choice type, TFeatureIdInt id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::ESubtype subtype, TFeatureIdInt id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::E_Choice type, TFeatureIdInt id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::ESubtype subtype, TFeatureIdInt id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::E_Choice type, TFeatureIdInt id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::ESubtype subtype, TFeatureIdInt id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::E_Choice type, const TFeatureIdStr &id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::ESubtype subtype, const TFeatureIdStr &id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::E_Choice type, const TFeatureIdStr &id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::ESubtype subtype, const TFeatureIdStr &id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::E_Choice type, const TFeatureIdStr &id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::ESubtype subtype, const TFeatureIdStr &id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::E_Choice type, const TFeatureId &id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::E_Choice type, const TFeatureId &id) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::ESubtype subtype, const TFeatureId &id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::E_Choice type, const TFeatureId &id) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
TSeq_feat_Handles GetFeaturesWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
TSeq_feat_Handles GetFeaturesWithXref (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::E_Choice type, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
CSeq_feat_Handle GetFeatureWithId (CSeqFeatData::ESubtype subtype, const TFeatureId &id, const CSeq_feat_Handle &src) const
 
CSeq_feat_Handle GetGeneWithLocus (const string &locus, bool tag) const
 Find genes by locus, locus tag, or Gene-ref. More...
 
TSeq_feat_Handles GetGenesWithLocus (const string &locus, bool tag) const
 
CSeq_feat_Handle GetGeneByRef (const CGene_ref &ref) const
 
TSeq_feat_Handles GetGenesByRef (const CGene_ref &ref) const
 
CSeq_feat_Handle GetGeneWithLocus (const string &locus, bool tag, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetGenesWithLocus (const string &locus, bool tag, const CSeq_annot_Handle &src_annot) const
 
CSeq_feat_Handle GetGeneByRef (const CGene_ref &ref, const CSeq_annot_Handle &src_annot) const
 
TSeq_feat_Handles GetGenesByRef (const CGene_ref &ref, const CSeq_annot_Handle &src_annot) const
 
CSeq_feat_Handle GetGeneWithLocus (const string &locus, bool tag, const CSeq_feat_Handle &src) const
 
TSeq_feat_Handles GetGenesWithLocus (const string &locus, bool tag, const CSeq_feat_Handle &src) const
 
CSeq_feat_Handle GetGeneByRef (const CGene_ref &ref, const CSeq_feat_Handle &src) const
 
TSeq_feat_Handles GetGenesByRef (const CGene_ref &ref, const CSeq_feat_Handle &src) const
 
void Swap (CTSE_Handle &tse)
 
 CTSE_Handle (const CTSE_ScopeUserLock &lock)
 
TScopeInfox_GetScopeInfo (void) const
 
const CTSE_Infox_GetTSE_Info (void) const
 
CScope_Implx_GetScopeImpl (void) const
 

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

Definition at line 293 of file tse_handle.hpp.

◆ TBlobId

TSE info getters.

Definition at line 100 of file tse_handle.hpp.

◆ TFeatureId

Find features by CObject_id (string or integer)

Definition at line 199 of file tse_handle.hpp.

◆ TFeatureIdInt

Find features by an integer FeatId.

Definition at line 170 of file tse_handle.hpp.

◆ TFeatureIdStr

Find features by a string FeatId.

Definition at line 184 of file tse_handle.hpp.

◆ TObject

Unified interface for templates.

Definition at line 119 of file tse_handle.hpp.

◆ TScopeInfo

Definition at line 289 of file tse_handle.hpp.

◆ 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]

CTSE_Handle::CTSE_Handle ( void  )
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]

CTSE_Handle::CTSE_Handle ( TScopeInfo object)
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
tseUsed 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

◆ DECLARE_OPERATOR_BOOL()

CTSE_Handle::DECLARE_OPERATOR_BOOL ( IsValid()  )

◆ GetBioseqHandle() [1/2]

CBioseq_Handle CTSE_Handle::GetBioseqHandle ( const CSeq_id id) const

◆ 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

◆ GetCompleteObject()

CConstRef< CSeq_entry > CTSE_Handle::GetCompleteObject ( void  ) const
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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ GetGeneByRef() [2/3]

CSeq_feat_Handle CTSE_Handle::GetGeneByRef ( const CGene_ref ref,
const CSeq_annot_Handle src_annot 
) const

◆ 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

◆ GetGenesByRef() [2/3]

CTSE_Handle::TSeq_feat_Handles CTSE_Handle::GetGenesByRef ( const CGene_ref ref,
const CSeq_annot_Handle src_annot 
) const

◆ 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

◆ 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()

CConstRef< CSeq_entry > CTSE_Handle::GetObjectCore ( void  ) const
inline

Definition at line 374 of file tse_handle.hpp.

References GetTSECore().

◆ GetScope()

CScope & CTSE_Handle::GetScope ( void  ) const
inline

◆ GetTopLevelEntry()

CSeq_entry_Handle CTSE_Handle::GetTopLevelEntry ( void  ) const

◆ 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

◆ 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!=()

bool CTSE_Handle::operator!= ( const CTSE_Handle tse) const
inline

Definition at line 346 of file tse_handle.hpp.

References m_TSE.

◆ operator<()

bool CTSE_Handle::operator< ( const CTSE_Handle tse) const
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==()

bool CTSE_Handle::operator== ( const CTSE_Handle tse) const
inline

Definition at line 339 of file tse_handle.hpp.

References m_TSE.

◆ OrderedBefore()

bool CTSE_Handle::OrderedBefore ( const CTSE_Handle tse) const

◆ 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

◆ SetTopLevelSubmit_block() [2/2]

void CTSE_Handle::SetTopLevelSubmit_block ( CSubmit_block sub) const

◆ Swap()

void CTSE_Handle::Swap ( CTSE_Handle tse)
inline

◆ x_GetScopeImpl()

CScope_Impl & CTSE_Handle::x_GetScopeImpl ( void  ) const
inline

◆ x_GetScopeInfo()

CTSE_Handle::TScopeInfo & CTSE_Handle::x_GetScopeInfo ( void  ) const
inline

◆ x_GetTSE_Info()

const CTSE_Info & CTSE_Handle::x_GetTSE_Info ( void  ) const

◆ x_MakeHandle() [1/2]

CSeq_feat_Handle CTSE_Handle::x_MakeHandle ( CAnnotObject_Info info) const
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]

CSeq_feat_Handle CTSE_Handle::x_MakeHandle ( const TAnnotObjectList info) const
protected

Definition at line 583 of file tse_handle.cpp.

References x_MakeHandle().

◆ x_MakeHandles()

CTSE_Handle::TSeq_feat_Handles CTSE_Handle::x_MakeHandles ( const TAnnotObjectList infos) const
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 class CScope_Impl
friend

Definition at line 285 of file tse_handle.hpp.

◆ CScopeInfo_Base

friend class CScopeInfo_Base
friend

Definition at line 287 of file tse_handle.hpp.

◆ CTSE_ScopeInfo

friend class CTSE_ScopeInfo
friend

Definition at line 286 of file tse_handle.hpp.

Member Data Documentation

◆ m_Scope

CHeapScope CTSE_Handle::m_Scope
private

Definition at line 300 of file tse_handle.hpp.

Referenced by GetScope(), operator=(), Reset(), Swap(), and x_GetScopeImpl().

◆ m_TSE

CTSE_ScopeUserLock CTSE_Handle::m_TSE
private

The documentation for this class was generated from the following files:
Modified on Tue Apr 16 20:10:18 2024 by modify_doxy.py rev. 669887