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CDataSource_ScopeInfo Class Reference

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#include <objmgr/impl/scope_info.hpp>

+ Inheritance diagram for CDataSource_ScopeInfo:
+ Collaboration diagram for CDataSource_ScopeInfo:

Public Types

typedef CRef< CDataSource > TDataSourceLock
 
typedef CRef< CTSE_ScopeInfo > TTSE_ScopeInfo
 
typedef CBlobIdKey TBlobId
 
typedef map< TBlobId, TTSE_ScopeInfo > TTSE_InfoMap
 
typedef CTSE_LockSet TTSE_LockSet
 
typedef multimap< CSeq_id_Handle, TTSE_ScopeInfo > TTSE_BySeqId
 
typedef CDeleteQueue< const CTSE_ScopeInfo *, CTSE_ScopeInternalLock > TTSE_UnlockQueue
 
typedef CMutex TTSE_InfoMapMutex
 
typedef CMutex TTSE_LockSetMutex
 
typedef CTSE_ScopeUserLock TTSE_Lock
 
typedef pair< CConstRef< CSeq_entry_Info >, TTSE_Lock > TSeq_entry_Lock
 
typedef pair< CConstRef< CSeq_annot_Info >, TTSE_Lock > TSeq_annot_Lock
 
typedef pair< CConstRef< CBioseq_set_Info >, TTSE_Lock > TBioseq_set_Lock
 
typedef CScopeInfo_Ref< CBioseq_ScopeInfo > TBioseq_Lock
 
typedef pair< TSeq_annot_Lock, int > TSeq_feat_Lock
 
typedef map< CSeq_id_Handle, SSeqMatch_Scope > TSeqMatchMap
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8 > TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CDataSource_ScopeInfo (CScope_Impl &scope, CDataSource &ds)
 
 ~CDataSource_ScopeInfo (void)
 
CScope_Impl & GetScopeImpl (void) const
 
void DetachScope (void)
 
void ResetDS (void)
 
void ResetHistory (int action_if_locked)
 
const TTSE_InfoMap & GetTSE_InfoMap (void) const
 
TTSE_InfoMapMutex & GetTSE_InfoMapMutex (void) const
 
const TTSE_LockSet & GetTSE_LockSet (void) const
 
TTSE_LockSetMutex & GetTSE_LockSetMutex (void) const
 
void ReleaseTSEUserLock (CTSE_ScopeInfo &tse)
 
void AcquireTSEUserLock (CTSE_ScopeInfo &tse)
 
void ForgetTSELock (CTSE_ScopeInfo &tse)
 
void RemoveFromHistory (CTSE_ScopeInfo &tse, bool drop_from_ds=false)
 
bool TSEIsInQueue (const CTSE_ScopeInfo &tse) const
 
void RemoveTSE_Lock (const CTSE_Lock &lock)
 
void AddTSE_Lock (const CTSE_Lock &lock)
 
void UnlockedTSEsSave (void)
 
void UnlockedTSEsRelease (void)
 
CDataSource & GetDataSource (void)
 
const CDataSource & GetDataSource (void) const
 
CDataLoader * GetDataLoader (void)
 
bool CanBeEdited (void) const
 
bool IsConst (void) const
 
void SetConst (void)
 
void SetCanRemoveOnResetHistory (void)
 
bool CanRemoveOnResetHistory (void) const
 
TTSE_Lock GetTSE_Lock (const CTSE_Lock &tse)
 
TTSE_Lock FindTSE_Lock (const CSeq_entry &tse)
 
TSeq_entry_Lock GetSeq_entry_Lock (const CBlobIdKey &blob_id)
 
TSeq_entry_Lock FindSeq_entry_Lock (const CSeq_entry &entry)
 
TSeq_annot_Lock FindSeq_annot_Lock (const CSeq_annot &annot)
 
TBioseq_set_Lock FindBioseq_set_Lock (const CBioseq_set &seqset)
 
TBioseq_Lock FindBioseq_Lock (const CBioseq &bioseq)
 
TSeq_feat_Lock FindSeq_feat_Lock (const CSeq_id_Handle &loc_id, TSeqPos loc_pos, const CSeq_feat &feat)
 
SSeqMatch_Scope BestResolve (const CSeq_id_Handle &idh, int get_flag)
 
SSeqMatch_Scope Resolve (const CSeq_id_Handle &idh, CTSE_ScopeInfo &tse)
 
void AttachTSE (CTSE_ScopeInfo &tse, const CTSE_Lock &lock)
 
void GetBlobs (TSeqMatchMap &match_map)
 
bool TSEIsReplaced (const TBlobId &blob_id) const
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObject & operator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Protected Member Functions

SSeqMatch_Scope x_GetSeqMatch (const CSeq_id_Handle &idh)
 
SSeqMatch_Scope x_FindBestTSE (const CSeq_id_Handle &idh)
 
void x_SetMatch (SSeqMatch_Scope &match, CTSE_ScopeInfo &tse, const CSeq_id_Handle &idh) const
 
void x_SetMatch (SSeqMatch_Scope &match, const SSeqMatch_DS &ds_match)
 
void x_IndexTSE (CTSE_ScopeInfo &tse)
 
void x_UnindexTSE (const CTSE_ScopeInfo &tse)
 
TTSE_ScopeInfo x_FindBestTSEInIndex (const CSeq_id_Handle &idh) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Static Protected Member Functions

static bool x_IsBetter (const CSeq_id_Handle &idh, const CTSE_ScopeInfo &tse1, const CTSE_ScopeInfo &tse2)
 

Private Member Functions

 CDataSource_ScopeInfo (const CDataSource_ScopeInfo &)
 
const CDataSource_ScopeInfo & operator= (const CDataSource_ScopeInfo &)
 

Private Attributes

CScope_Impl * m_Scope
 
TDataSourceLock m_DataSource
 
bool m_CanBeUnloaded
 
bool m_CanBeEdited
 
bool m_CanRemoveOnResetHistory
 
int m_NextTSEIndex
 
TTSE_InfoMap m_TSE_InfoMap
 
TTSE_InfoMapMutex m_TSE_InfoMapMutex
 
TTSE_BySeqId m_TSE_BySeqId
 
TTSE_LockSet m_TSE_LockSet
 
TTSE_LockSetMutex m_TSE_LockSetMutex
 
TTSE_UnlockQueue m_TSE_UnlockQueue
 
TTSE_LockSetMutex m_TSE_UnlockQueueMutex
 
CRef< CDataSource_ScopeInfo > m_EditDS
 
set< TBlobId > m_ReplacedTSEs
 

Friends

class CScope_Impl
 
class CTSE_ScopeInfo
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Detailed Description

Definition at line 207 of file scope_info.hpp.

Member Typedef Documentation

◆ TBioseq_Lock

typedef CScopeInfo_Ref<CBioseq_ScopeInfo> CDataSource_ScopeInfo::TBioseq_Lock

Definition at line 264 of file scope_info.hpp.

◆ TBioseq_set_Lock

typedef pair<CConstRef<CBioseq_set_Info>, TTSE_Lock> CDataSource_ScopeInfo::TBioseq_set_Lock

Definition at line 263 of file scope_info.hpp.

◆ TBlobId

typedef CBlobIdKey CDataSource_ScopeInfo::TBlobId

Definition at line 212 of file scope_info.hpp.

◆ TDataSourceLock

typedef CRef<CDataSource> CDataSource_ScopeInfo::TDataSourceLock

Definition at line 210 of file scope_info.hpp.

◆ TSeq_annot_Lock

typedef pair<CConstRef<CSeq_annot_Info>, TTSE_Lock> CDataSource_ScopeInfo::TSeq_annot_Lock

Definition at line 262 of file scope_info.hpp.

◆ TSeq_entry_Lock

typedef pair<CConstRef<CSeq_entry_Info>, TTSE_Lock> CDataSource_ScopeInfo::TSeq_entry_Lock

Definition at line 261 of file scope_info.hpp.

◆ TSeq_feat_Lock

typedef pair<TSeq_annot_Lock, int> CDataSource_ScopeInfo::TSeq_feat_Lock

Definition at line 265 of file scope_info.hpp.

◆ TSeqMatchMap

typedef map<CSeq_id_Handle, SSeqMatch_Scope> CDataSource_ScopeInfo::TSeqMatchMap

Definition at line 283 of file scope_info.hpp.

◆ TTSE_BySeqId

typedef multimap<CSeq_id_Handle, TTSE_ScopeInfo> CDataSource_ScopeInfo::TTSE_BySeqId

Definition at line 215 of file scope_info.hpp.

◆ TTSE_InfoMap

typedef map<TBlobId, TTSE_ScopeInfo> CDataSource_ScopeInfo::TTSE_InfoMap

Definition at line 213 of file scope_info.hpp.

◆ TTSE_InfoMapMutex

typedef CMutex CDataSource_ScopeInfo::TTSE_InfoMapMutex

Definition at line 228 of file scope_info.hpp.

◆ TTSE_Lock

typedef CTSE_ScopeUserLock CDataSource_ScopeInfo::TTSE_Lock

Definition at line 260 of file scope_info.hpp.

◆ TTSE_LockSet

typedef CTSE_LockSet CDataSource_ScopeInfo::TTSE_LockSet

Definition at line 214 of file scope_info.hpp.

◆ TTSE_LockSetMutex

typedef CMutex CDataSource_ScopeInfo::TTSE_LockSetMutex

Definition at line 232 of file scope_info.hpp.

◆ TTSE_ScopeInfo

typedef CRef<CTSE_ScopeInfo> CDataSource_ScopeInfo::TTSE_ScopeInfo

Definition at line 211 of file scope_info.hpp.

◆ TTSE_UnlockQueue

typedef CDeleteQueue<const CTSE_ScopeInfo*, CTSE_ScopeInternalLock> CDataSource_ScopeInfo::TTSE_UnlockQueue

Definition at line 217 of file scope_info.hpp.

Constructor & Destructor Documentation

◆ CDataSource_ScopeInfo() [1/2]

CDataSource_ScopeInfo::CDataSource_ScopeInfo ( CScope_Impl &  scope,
CDataSource &  ds 
)

Definition at line 106 of file scope_info.cpp.

◆ ~CDataSource_ScopeInfo()

CDataSource_ScopeInfo::~CDataSource_ScopeInfo ( void  )

Definition at line 121 of file scope_info.cpp.

References _ASSERT, m_DataSource, and m_Scope.

◆ CDataSource_ScopeInfo() [2/2]

CDataSource_ScopeInfo::CDataSource_ScopeInfo ( const CDataSource_ScopeInfo &  )
private

Member Function Documentation

◆ AcquireTSEUserLock()

void CDataSource_ScopeInfo::AcquireTSEUserLock ( CTSE_ScopeInfo &  tse)

Definition at line 579 of file scope_info.cpp.

References _ASSERT, CDeleteQueue< Key, Value >::Erase(), CTSE_ScopeInfo::GetTSE_Lock(), CTSE_ScopeInfo::m_DS_Info, CTSE_ScopeInfo::m_TSE_Lock, CTSE_ScopeInfo::m_TSE_LockAssigned, m_TSE_UnlockQueue, m_TSE_UnlockQueueMutex, CTSE_ScopeInfo::m_UnloadedInfo, CTSE_ScopeInfo::m_UserLockCounter, NCBI_THROW, and CTSE_ScopeInfo::SetTSE_Lock().

Referenced by CTSE_ScopeInfo::x_UserLockTSE().

◆ AddTSE_Lock()

void CDataSource_ScopeInfo::AddTSE_Lock ( const CTSE_Lock &  lock)

Definition at line 266 of file scope_info.cpp.

References _VERIFY, CTSE_LockSet::AddLock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

Referenced by CTSE_ScopeInfo::x_SetTSE_Lock().

◆ AttachTSE()

void CDataSource_ScopeInfo::AttachTSE ( CTSE_ScopeInfo &  tse,
const CTSE_Lock &  lock 
)

Definition at line 492 of file scope_info.cpp.

References _ASSERT, _VERIFY, CTSE_Info::GetBlobId(), GetDataSource(), CTSE_Info::GetDataSource(), info, map_checker< Container >::insert(), m_CanBeUnloaded, m_TSE_InfoMap, m_TSE_InfoMapMutex, Ref(), and x_IndexTSE().

Referenced by CTSE_ScopeInfo::SetEditTSE().

◆ BestResolve()

SSeqMatch_Scope CDataSource_ScopeInfo::BestResolve ( const CSeq_id_Handle &  idh,
int  get_flag 
)

Definition at line 832 of file scope_info.cpp.

References _ASSERT, CDataSource::BestResolve(), CScope::eGetBioseq_All, CTSE_Info::FindBioseq(), GetDataSource(), SSeqMatch_TSE::m_Bioseq, SSeqMatch_TSE::m_Seq_id, SSeqMatch_Scope::m_TSE_Lock, CTSE_ScopeInfo::m_TSE_Lock, CTSE_ScopeInfo::m_TSE_LockAssigned, x_GetSeqMatch(), and x_SetMatch().

Referenced by CScope_Impl::x_FindBioseqInfo().

◆ CanBeEdited()

bool CDataSource_ScopeInfo::CanBeEdited ( void  ) const
inline

Definition at line 694 of file scope_info.hpp.

References m_CanBeEdited.

Referenced by CTSE_ScopeInfo::CanBeEdited(), CPriorityNode::CPriorityNode(), CScope_Impl::GetConstDS(), CScope_Impl::GetEditDataSource(), CScope_Impl::GetEditDS(), CScope_Impl::GetEditHandle(), IsConst(), RemoveFromHistory(), CScope_Impl::RemoveTopLevelSeqEntry(), CScope_Impl::ResetDataAndHistory(), SetCanRemoveOnResetHistory(), SetConst(), and CTSE_ScopeInfo::SetEditTSE().

◆ CanRemoveOnResetHistory()

bool CDataSource_ScopeInfo::CanRemoveOnResetHistory ( void  ) const
inline

Definition at line 701 of file scope_info.hpp.

References m_CanRemoveOnResetHistory.

Referenced by RemoveFromHistory(), and SetCanRemoveOnResetHistory().

◆ DetachScope()

void CDataSource_ScopeInfo::DetachScope ( void  )

Definition at line 168 of file scope_info.cpp.

References _ASSERT, GetScopeImpl(), m_DataSource, CScope_Impl::m_ObjMgr, m_Scope, CObjectManager::ReleaseDataSource(), and ResetDS().

Referenced by CScope_Impl::GetEditHandle(), CScope_Impl::RemoveDataLoader(), CScope_Impl::RemoveTopLevelSeqEntry(), and CScope_Impl::ResetScope().

◆ FindBioseq_Lock()

CDataSource_ScopeInfo::TBioseq_Lock CDataSource_ScopeInfo::FindBioseq_Lock ( const CBioseq &  bioseq)

Definition at line 798 of file scope_info.cpp.

References CDataSource::FindBioseq_Lock(), CTSE_ScopeInfo::GetBioseqLock(), GetDataSource(), GetTSE_Lock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

◆ FindBioseq_set_Lock()

CDataSource_ScopeInfo::TBioseq_set_Lock CDataSource_ScopeInfo::FindBioseq_set_Lock ( const CBioseq_set &  seqset)

Definition at line 783 of file scope_info.cpp.

References CDataSource::FindBioseq_set_Lock(), GetDataSource(), GetTSE_Lock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

◆ FindSeq_annot_Lock()

CDataSource_ScopeInfo::TSeq_annot_Lock CDataSource_ScopeInfo::FindSeq_annot_Lock ( const CSeq_annot &  annot)

Definition at line 768 of file scope_info.cpp.

References CDataSource::FindSeq_annot_Lock(), GetDataSource(), GetTSE_Lock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

◆ FindSeq_entry_Lock()

CDataSource_ScopeInfo::TSeq_entry_Lock CDataSource_ScopeInfo::FindSeq_entry_Lock ( const CSeq_entry &  entry)

Definition at line 753 of file scope_info.cpp.

References CDataSource::FindSeq_entry_Lock(), GetDataSource(), GetTSE_Lock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

◆ FindSeq_feat_Lock()

CDataSource_ScopeInfo::TSeq_feat_Lock CDataSource_ScopeInfo::FindSeq_feat_Lock ( const CSeq_id_Handle &  loc_id,
TSeqPos  loc_pos,
const CSeq_feat &  feat 
)

Definition at line 813 of file scope_info.cpp.

References CDataSource::FindSeq_feat_Lock(), GetDataSource(), GetTSE_Lock(), and m_TSE_LockSetMutex.

◆ FindTSE_Lock()

CDataSource_ScopeInfo::TTSE_Lock CDataSource_ScopeInfo::FindTSE_Lock ( const CSeq_entry &  tse)

Definition at line 723 of file scope_info.cpp.

References CDataSource::FindTSE_Lock(), GetDataSource(), GetTSE_Lock(), m_TSE_LockSet, and m_TSE_LockSetMutex.

◆ ForgetTSELock()

void CDataSource_ScopeInfo::ForgetTSELock ( CTSE_ScopeInfo &  tse)

Definition at line 607 of file scope_info.cpp.

References CTSE_ScopeInfo::ForgetTSE_Lock(), CTSE_ScopeInfo::m_TSE_LockAssigned, and CTSE_ScopeInfo::m_TSE_LockCounter.

Referenced by CTSE_ScopeInfo::x_InternalUnlockTSE().

◆ GetBlobs()

void CDataSource_ScopeInfo::GetBlobs ( TSeqMatchMap &  match_map)

Definition at line 974 of file scope_info.cpp.

References map_checker< Container >::empty(), map_checker< Container >::erase(), CDataSource::GetBlobs(), GetDataSource(), map_checker< Container >::insert(), ITERATE, x_GetSeqMatch(), and x_SetMatch().

◆ GetDataLoader()

CDataLoader * CDataSource_ScopeInfo::GetDataLoader ( void  )

Definition at line 138 of file scope_info.cpp.

References CDataSource::GetDataLoader(), and GetDataSource().

Referenced by CScope_Impl::GetEditDataSource(), and CScope_Impl::RemoveTopLevelSeqEntry().

◆ GetDataSource() [1/2]

CDataSource & CDataSource_ScopeInfo::GetDataSource ( void  )
inline

Definition at line 665 of file scope_info.hpp.

References m_DataSource.

Referenced by CScope_Impl::AddBioseq(), CScope_Impl::AddSeq_annot(), CScope_Impl::AddSeq_entry(), CScope_Impl::AddSeq_submit(), CScope_Impl::AddSharedBioseq(), CScope_Impl::AddSharedSeq_annot(), CScope_Impl::AddSharedSeq_entry(), AttachTSE(), BestResolve(), CPriorityNode::CPriorityNode(), FindBioseq_Lock(), FindBioseq_set_Lock(), FindSeq_annot_Lock(), FindSeq_entry_Lock(), FindSeq_feat_Lock(), FindTSE_Lock(), GetBlobs(), GetDataLoader(), CScope_Impl::GetEditHandle(), GetSeq_entry_Lock(), IsConst(), RemoveFromHistory(), CScope_Impl::RemoveTopLevelSeqEntry(), CScope_Impl::ResetDataAndHistory(), SetCanRemoveOnResetHistory(), SetConst(), CTSE_ScopeInfo::SetEditTSE(), x_FindBestTSE(), and CScope_Impl::x_GetTSESetWithBioseqAnnots().

◆ GetDataSource() [2/2]

const CDataSource & CDataSource_ScopeInfo::GetDataSource ( void  ) const
inline

Definition at line 672 of file scope_info.hpp.

References m_DataSource.

◆ GetScopeImpl()

CScope_Impl & CDataSource_ScopeInfo::GetScopeImpl ( void  ) const

Definition at line 128 of file scope_info.cpp.

References m_Scope, and NCBI_THROW.

Referenced by DetachScope(), CTSE_ScopeInfo::GetScopeImpl(), CScope_Impl::RemoveTopLevelSeqEntry(), CScope_Impl::x_FindBioseqInfo(), and CScope_Impl::x_GetTSE_Lock().

◆ GetSeq_entry_Lock()

CDataSource_ScopeInfo::TSeq_entry_Lock CDataSource_ScopeInfo::GetSeq_entry_Lock ( const CBlobIdKey &  blob_id)

Definition at line 738 of file scope_info.cpp.

References GetDataSource(), CDataSource::GetSeq_entry_Lock(), GetTSE_Lock(), and m_TSE_LockSetMutex.

Referenced by CScope_Impl::GetSeq_entryHandle().

◆ GetTSE_InfoMap()

const CDataSource_ScopeInfo::TTSE_InfoMap & CDataSource_ScopeInfo::GetTSE_InfoMap ( void  ) const

Definition at line 181 of file scope_info.cpp.

References m_TSE_InfoMap.

Referenced by CScope_Impl::RemoveDataLoader().

◆ GetTSE_InfoMapMutex()

CDataSource_ScopeInfo::TTSE_InfoMapMutex & CDataSource_ScopeInfo::GetTSE_InfoMapMutex ( void  ) const
inline

Definition at line 680 of file scope_info.hpp.

References m_TSE_InfoMapMutex.

Referenced by CScope_Impl::RemoveDataLoader(), and x_FindBestTSE().

◆ GetTSE_Lock()

CTSE_ScopeUserLock CDataSource_ScopeInfo::GetTSE_Lock ( const CTSE_Lock &  tse)

Definition at line 444 of file scope_info.cpp.

References _ASSERT, _VERIFY, CTSE_ScopeInfo, CDeleteQueue< Key, Value >::Erase(), CTSE_Info::GetBlobId(), info, m_CanBeUnloaded, m_EditDS, m_NextTSEIndex, m_TSE_InfoMap, m_TSE_InfoMapMutex, m_TSE_UnlockQueue, m_TSE_UnlockQueueMutex, CRef< C, Locker >::Reset(), TSEIsReplaced(), and x_IndexTSE().

Referenced by CScope_Impl::AddBioseq(), CScope_Impl::AddSeq_annot(), CScope_Impl::AddSeq_entry(), CScope_Impl::AddSeq_submit(), CScope_Impl::AddSharedBioseq(), CScope_Impl::AddSharedSeq_annot(), CScope_Impl::AddSharedSeq_entry(), FindBioseq_Lock(), FindBioseq_set_Lock(), FindSeq_annot_Lock(), FindSeq_entry_Lock(), FindSeq_feat_Lock(), FindTSE_Lock(), GetSeq_entry_Lock(), CScope_Impl::x_GetTSE_Lock(), and x_SetMatch().

◆ GetTSE_LockSet()

const CDataSource_ScopeInfo::TTSE_LockSet & CDataSource_ScopeInfo::GetTSE_LockSet ( void  ) const

Definition at line 188 of file scope_info.cpp.

References m_TSE_LockSet.

◆ GetTSE_LockSetMutex()

CDataSource_ScopeInfo::TTSE_LockSetMutex & CDataSource_ScopeInfo::GetTSE_LockSetMutex ( void  ) const
inline

Definition at line 687 of file scope_info.hpp.

References m_TSE_LockSetMutex.

◆ IsConst()

bool CDataSource_ScopeInfo::IsConst ( void  ) const

Definition at line 144 of file scope_info.cpp.

References CDataSource::CanBeEdited(), CanBeEdited(), and GetDataSource().

Referenced by CPriorityNode::CPriorityNode(), CScope_Impl::GetConstDS(), CScope_Impl::GetEditHandle(), CScope_Impl::ResetDataAndHistory(), and SetConst().

◆ operator=()

const CDataSource_ScopeInfo& CDataSource_ScopeInfo::operator= ( const CDataSource_ScopeInfo &  )
private

◆ ReleaseTSEUserLock()

void CDataSource_ScopeInfo::ReleaseTSEUserLock ( CTSE_ScopeInfo &  tse)

Definition at line 555 of file scope_info.cpp.

References CDeleteQueue< Key, Value >::Erase(), CTSE_ScopeInfo::GetTSE_Lock(), m_TSE_UnlockQueue, m_TSE_UnlockQueueMutex, CTSE_ScopeInfo::m_UserLockCounter, CDeleteQueue< Key, Value >::Put(), and CUnlockedTSEsGuard::SaveInternal().

Referenced by CTSE_ScopeInfo::x_UserUnlockTSE().

◆ RemoveFromHistory()

void CDataSource_ScopeInfo::RemoveFromHistory ( CTSE_ScopeInfo &  tse,
bool  drop_from_ds = false 
)

Definition at line 686 of file scope_info.cpp.

References _ASSERT, _VERIFY, CanBeEdited(), CTSE_ScopeInfo::CanBeUnloaded(), CanRemoveOnResetHistory(), CDataSource::DropStaticTSE(), CDeleteQueue< Key, Value >::Erase(), map_checker< Container >::erase(), CTSE_ScopeInfo::GetBlobId(), GetDataSource(), CTSE_ScopeInfo::GetTSE_Lock(), CTSE_ScopeInfo::m_DS_Info, m_TSE_InfoMap, m_TSE_InfoMapMutex, m_TSE_UnlockQueue, m_TSE_UnlockQueueMutex, CTSE_ScopeInfo::m_UserLockCounter, CTSE_ScopeInfo::ReleaseUsedTSEs(), CTSE_ScopeInfo::ResetTSE_Lock(), CTSE_ScopeInfo::RestoreReplacedTSE(), CTSE_ScopeInfo::x_DetachDS(), and x_UnindexTSE().

Referenced by CTSE_ScopeInfo::RemoveFromHistory(), ResetHistory(), and CTSE_ScopeInfo::SetEditTSE().

◆ RemoveTSE_Lock()

void CDataSource_ScopeInfo::RemoveTSE_Lock ( const CTSE_Lock &  lock)

Definition at line 258 of file scope_info.cpp.

References _VERIFY, m_TSE_LockSet, m_TSE_LockSetMutex, CTSE_LockSet::RemoveLock(), and CUnlockedTSEsGuard::SaveLock().

Referenced by CTSE_ScopeInfo::x_ResetTSE_Lock().

◆ ResetDS()

void CDataSource_ScopeInfo::ResetDS ( void  )

Definition at line 622 of file scope_info.cpp.

References map_checker< Container >::clear(), multimap_checker< Container >::clear(), CDeleteQueue< Key, Value >::Clear(), CTSE_LockSet::clear(), m_NextTSEIndex, m_ReplacedTSEs, m_TSE_BySeqId, m_TSE_InfoMap, m_TSE_InfoMapMutex, m_TSE_LockSet, m_TSE_LockSetMutex, m_TSE_UnlockQueue, m_TSE_UnlockQueueMutex, NON_CONST_ITERATE, and CUnlockedTSEsGuard::SaveInternal().

Referenced by DetachScope(), CScope_Impl::ResetDataAndHistory(), and ResetHistory().

◆ ResetHistory()

void CDataSource_ScopeInfo::ResetHistory ( int  action_if_locked)

Definition at line 651 of file scope_info.cpp.

References CScope::eKeepIfLocked, CScope::eRemoveIfLocked, CScope::eThrowIfLocked, ITERATE, m_TSE_InfoMap, m_TSE_InfoMapMutex, NCBI_THROW, RemoveFromHistory(), ResetDS(), and map_checker< Container >::size().

Referenced by CScope_Impl::RemoveDataLoader().

◆ Resolve()

SSeqMatch_Scope CDataSource_ScopeInfo::Resolve ( const CSeq_id_Handle &  idh,
CTSE_ScopeInfo &  tse 
)

Definition at line 856 of file scope_info.cpp.

References x_SetMatch().

Referenced by CTSE_ScopeInfo::Resolve().

◆ SetCanRemoveOnResetHistory()

void CDataSource_ScopeInfo::SetCanRemoveOnResetHistory ( void  )

Definition at line 159 of file scope_info.cpp.

References _ASSERT, CanBeEdited(), CanRemoveOnResetHistory(), GetDataSource(), and m_CanRemoveOnResetHistory.

Referenced by CScope_Impl::GetEditDataSource().

◆ SetConst()

void CDataSource_ScopeInfo::SetConst ( void  )

Definition at line 150 of file scope_info.cpp.

References _ASSERT, CanBeEdited(), GetDataSource(), IsConst(), and m_CanBeEdited.

Referenced by CScope_Impl::GetConstDS().

◆ TSEIsInQueue()

bool CDataSource_ScopeInfo::TSEIsInQueue ( const CTSE_ScopeInfo &  tse) const

Definition at line 1002 of file scope_info.cpp.

References CDeleteQueue< Key, Value >::Contains(), m_TSE_UnlockQueue, and m_TSE_UnlockQueueMutex.

◆ TSEIsReplaced()

bool CDataSource_ScopeInfo::TSEIsReplaced ( const TBlobId &  blob_id) const

Definition at line 1009 of file scope_info.cpp.

References m_EditDS, m_ReplacedTSEs, and TSEIsReplaced().

Referenced by GetTSE_Lock(), and TSEIsReplaced().

◆ UnlockedTSEsRelease()

void CDataSource_ScopeInfo::UnlockedTSEsRelease ( void  )

◆ UnlockedTSEsSave()

void CDataSource_ScopeInfo::UnlockedTSEsSave ( void  )

◆ x_FindBestTSE()

SSeqMatch_Scope CDataSource_ScopeInfo::x_FindBestTSE ( const CSeq_id_Handle &  idh)
protected

Definition at line 885 of file scope_info.cpp.

References GetDataSource(), CDataSource::GetMatches(), GetTSE_InfoMapMutex(), ITERATE, m_CanBeUnloaded, SSeqMatch_Scope::m_TSE_Lock, m_TSE_LockSet, m_TSE_LockSetMutex, x_FindBestTSEInIndex(), x_IsBetter(), and x_SetMatch().

Referenced by x_GetSeqMatch().

◆ x_FindBestTSEInIndex()

CDataSource_ScopeInfo::TTSE_ScopeInfo CDataSource_ScopeInfo::x_FindBestTSEInIndex ( const CSeq_id_Handle &  idh) const
protected

Definition at line 541 of file scope_info.cpp.

References multimap_checker< Container >::end(), multimap_checker< Container >::lower_bound(), m_TSE_BySeqId, and x_IsBetter().

Referenced by x_FindBestTSE().

◆ x_GetSeqMatch()

SSeqMatch_Scope CDataSource_ScopeInfo::x_GetSeqMatch ( const CSeq_id_Handle &  idh)
protected

Definition at line 865 of file scope_info.cpp.

References eAllowWeakMatch, CSeq_id_Handle::GetMatchingHandles(), CSeq_id_Handle::HaveMatchingHandles(), CSeq_id_Handle::IsBetter(), ITERATE, SSeqMatch_TSE::m_Seq_id, match(), and x_FindBestTSE().

Referenced by BestResolve(), and GetBlobs().

◆ x_IndexTSE()

void CDataSource_ScopeInfo::x_IndexTSE ( CTSE_ScopeInfo &  tse)
protected

Definition at line 516 of file scope_info.cpp.

References CTSE_ScopeInfo::GetBioseqsIds(), multimap_checker< Container >::insert(), ITERATE, m_TSE_BySeqId, and Ref().

Referenced by AttachTSE(), and GetTSE_Lock().

◆ x_IsBetter()

bool CDataSource_ScopeInfo::x_IsBetter ( const CSeq_id_Handle &  idh,
const CTSE_ScopeInfo &  tse1,
const CTSE_ScopeInfo &  tse2 
)
staticprotected

Definition at line 920 of file scope_info.cpp.

References CTSE_ScopeInfo::GetBlobOrder(), CTSE_ScopeInfo::GetLoadIndex(), and CTSE_ScopeInfo::HasResolvedBioseq().

Referenced by x_FindBestTSE(), and x_FindBestTSEInIndex().

◆ x_SetMatch() [1/2]

void CDataSource_ScopeInfo::x_SetMatch ( SSeqMatch_Scope &  match,
const SSeqMatch_DS &  ds_match 
)
protected

Definition at line 956 of file scope_info.cpp.

References _ASSERT, GetTSE_Lock(), SSeqMatch_TSE::m_Bioseq, SSeqMatch_TSE::m_Seq_id, SSeqMatch_DS::m_TSE_Lock, and match().

◆ x_SetMatch() [2/2]

void CDataSource_ScopeInfo::x_SetMatch ( SSeqMatch_Scope &  match,
CTSE_ScopeInfo &  tse,
const CSeq_id_Handle &  idh 
) const
protected

Definition at line 942 of file scope_info.cpp.

References _ASSERT, and match().

Referenced by BestResolve(), GetBlobs(), Resolve(), and x_FindBestTSE().

◆ x_UnindexTSE()

void CDataSource_ScopeInfo::x_UnindexTSE ( const CTSE_ScopeInfo &  tse)
protected

Definition at line 524 of file scope_info.cpp.

References multimap_checker< Container >::end(), multimap_checker< Container >::erase(), CTSE_ScopeInfo::GetBioseqsIds(), ITERATE, multimap_checker< Container >::lower_bound(), and m_TSE_BySeqId.

Referenced by RemoveFromHistory().

Friends And Related Function Documentation

◆ CScope_Impl

friend class CScope_Impl
friend

Definition at line 289 of file scope_info.hpp.

◆ CTSE_ScopeInfo

friend class CTSE_ScopeInfo
friend

Definition at line 290 of file scope_info.hpp.

Referenced by GetTSE_Lock().

Member Data Documentation

◆ m_CanBeEdited

bool CDataSource_ScopeInfo::m_CanBeEdited
private

Definition at line 311 of file scope_info.hpp.

Referenced by CanBeEdited(), and SetConst().

◆ m_CanBeUnloaded

bool CDataSource_ScopeInfo::m_CanBeUnloaded
private

Definition at line 310 of file scope_info.hpp.

Referenced by AttachTSE(), GetTSE_Lock(), and x_FindBestTSE().

◆ m_CanRemoveOnResetHistory

bool CDataSource_ScopeInfo::m_CanRemoveOnResetHistory
private

Definition at line 312 of file scope_info.hpp.

Referenced by CanRemoveOnResetHistory(), and SetCanRemoveOnResetHistory().

◆ m_DataSource

TDataSourceLock CDataSource_ScopeInfo::m_DataSource
private

Definition at line 309 of file scope_info.hpp.

Referenced by DetachScope(), GetDataSource(), and ~CDataSource_ScopeInfo().

◆ m_EditDS

CRef<CDataSource_ScopeInfo> CDataSource_ScopeInfo::m_EditDS
private

Definition at line 321 of file scope_info.hpp.

Referenced by CScope_Impl::GetEditDataSource(), GetTSE_Lock(), TSEIsReplaced(), and CScope_Impl::x_GetTSESetWithOrphanAnnots().

◆ m_NextTSEIndex

int CDataSource_ScopeInfo::m_NextTSEIndex
private

Definition at line 313 of file scope_info.hpp.

Referenced by GetTSE_Lock(), and ResetDS().

◆ m_ReplacedTSEs

set<TBlobId> CDataSource_ScopeInfo::m_ReplacedTSEs
private

Definition at line 322 of file scope_info.hpp.

Referenced by CTSE_ScopeInfo::ReplaceTSE(), ResetDS(), CTSE_ScopeInfo::RestoreReplacedTSE(), and TSEIsReplaced().

◆ m_Scope

CScope_Impl* CDataSource_ScopeInfo::m_Scope
private

Definition at line 308 of file scope_info.hpp.

Referenced by DetachScope(), GetScopeImpl(), and ~CDataSource_ScopeInfo().

◆ m_TSE_BySeqId

TTSE_BySeqId CDataSource_ScopeInfo::m_TSE_BySeqId
private

Definition at line 316 of file scope_info.hpp.

Referenced by ResetDS(), x_FindBestTSEInIndex(), x_IndexTSE(), and x_UnindexTSE().

◆ m_TSE_InfoMap

TTSE_InfoMap CDataSource_ScopeInfo::m_TSE_InfoMap
private

Definition at line 314 of file scope_info.hpp.

Referenced by AttachTSE(), GetTSE_InfoMap(), GetTSE_Lock(), RemoveFromHistory(), ResetDS(), and ResetHistory().

◆ m_TSE_InfoMapMutex

TTSE_InfoMapMutex CDataSource_ScopeInfo::m_TSE_InfoMapMutex
mutableprivate

Definition at line 315 of file scope_info.hpp.

Referenced by AttachTSE(), GetTSE_InfoMapMutex(), GetTSE_Lock(), RemoveFromHistory(), ResetDS(), and ResetHistory().

◆ m_TSE_LockSet

TTSE_LockSet CDataSource_ScopeInfo::m_TSE_LockSet
private

Definition at line 317 of file scope_info.hpp.

Referenced by AddTSE_Lock(), FindBioseq_Lock(), FindBioseq_set_Lock(), FindSeq_annot_Lock(), FindSeq_entry_Lock(), FindTSE_Lock(), GetTSE_LockSet(), RemoveTSE_Lock(), ResetDS(), and x_FindBestTSE().

◆ m_TSE_LockSetMutex

TTSE_LockSetMutex CDataSource_ScopeInfo::m_TSE_LockSetMutex
mutableprivate

Definition at line 318 of file scope_info.hpp.

Referenced by AddTSE_Lock(), FindBioseq_Lock(), FindBioseq_set_Lock(), FindSeq_annot_Lock(), FindSeq_entry_Lock(), FindSeq_feat_Lock(), FindTSE_Lock(), GetSeq_entry_Lock(), GetTSE_LockSetMutex(), RemoveTSE_Lock(), ResetDS(), and x_FindBestTSE().

◆ m_TSE_UnlockQueue

TTSE_UnlockQueue CDataSource_ScopeInfo::m_TSE_UnlockQueue
private

Definition at line 319 of file scope_info.hpp.

Referenced by AcquireTSEUserLock(), GetTSE_Lock(), ReleaseTSEUserLock(), RemoveFromHistory(), ResetDS(), and TSEIsInQueue().

◆ m_TSE_UnlockQueueMutex

TTSE_LockSetMutex CDataSource_ScopeInfo::m_TSE_UnlockQueueMutex
mutableprivate

Definition at line 320 of file scope_info.hpp.

Referenced by AcquireTSEUserLock(), GetTSE_Lock(), ReleaseTSEUserLock(), RemoveFromHistory(), ResetDS(), and TSEIsInQueue().

The documentation for this class was generated from the following files:
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Modified on Wed Nov 29 02:16:19 2023 by modify_doxy.py rev. 669887