CScope_Impl Class Reference

Search Toolkit Book for CScope_Impl

#include <objmgr/impl/scope_impl.hpp>

Inheritance diagram for CScope_Impl:

Collaboration diagram for CScope_Impl:

Public Types
enum	EGetBioseqFlag2 { fUserFlagMask = 0xff , fNoLockFlag = 0x100 }
typedef CTSE_ScopeUserLock	TTSE_Lock
typedef map< CSeq_id_Handle, SSeq_id_ScopeInfo >	TSeq_idMap
typedef TSeq_idMap::value_type	TSeq_idMapValue
typedef set< CSeq_id_Handle >	TSeq_idSet
typedef vector< pair< CTSE_Handle, CSeq_id_Handle > >	TTSE_LockMatchSet
typedef int	TPriority
typedef map< CConstRef< CObject >, CRef< CObject > >	TEditInfoMap
typedef map< CRef< CDataSource >, CRef< CDataSource_ScopeInfo > >	TDSMap
typedef vector< CSeq_id_Handle >	TIds
typedef vector< TIds >	TBulkIds
typedef vector< CSeq_entry_Handle >	TTSE_Handles
typedef int	TMissing
typedef int	TExist
typedef int	TGetFlags
typedef vector< CBioseq_Handle >	TBioseqHandles
	Bulk retrieval methods. More...
typedef vector< CTSE_Handle >	TCDD_Entries
typedef vector< TGi >	TGIs
typedef vector< string >	TLabels
typedef vector< TTaxId >	TTaxIds
typedef vector< TSeqPos >	TSequenceLengths
typedef vector< CSeq_inst::TMol >	TSequenceTypes
typedef vector< int >	TSequenceStates
typedef vector< int >	TSequenceHashes
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 CDataSource_ScopeInfo::TBioseq_Lock	TBioseq_Lock
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
CObjectManager &	GetObjectManager (void)
void	AddDefaults (TPriority priority)
void	AddDataLoader (const string &loader_name, TPriority priority)
void	AddScope (CScope_Impl &scope, TPriority priority)
CSeq_entry_Handle	AddSeq_entry (CSeq_entry &entry, TPriority pri, TExist action)
CSeq_entry_Handle	AddSharedSeq_entry (const CSeq_entry &entry, TPriority pri, TExist action)
CBioseq_Handle	AddBioseq (CBioseq &bioseq, TPriority pri, TExist action)
CBioseq_Handle	AddSharedBioseq (const CBioseq &bioseq, TPriority pri, TExist action)
CSeq_annot_Handle	AddSeq_annot (CSeq_annot &annot, TPriority pri, TExist action)
CSeq_annot_Handle	AddSharedSeq_annot (const CSeq_annot &annot, TPriority pri, TExist action)
CSeq_entry_Handle	AddSeq_submit (CSeq_submit &submit, TPriority pri)
CTSE_Handle	GetEditHandle (const CTSE_Handle &src_tse)
CBioseq_EditHandle	GetEditHandle (const CBioseq_Handle &seq)
CSeq_entry_EditHandle	GetEditHandle (const CSeq_entry_Handle &entry)
CSeq_annot_EditHandle	GetEditHandle (const CSeq_annot_Handle &annot)
CBioseq_set_EditHandle	GetEditHandle (const CBioseq_set_Handle &seqset)
CSeq_entry_EditHandle	AttachEntry (const CBioseq_set_EditHandle &seqset, CSeq_entry &entry, int index=-1)
CSeq_entry_EditHandle	AttachEntry (const CBioseq_set_EditHandle &seqset, CRef< CSeq_entry_Info > entry, int index=-1)
CSeq_entry_EditHandle	AttachEntry (const CBioseq_set_EditHandle &seqset, const CSeq_entry_EditHandle &entry, int index=-1)
CSeq_annot_EditHandle	AttachAnnot (const CSeq_entry_EditHandle &entry, CSeq_annot &annot)
CSeq_annot_EditHandle	AttachAnnot (const CSeq_entry_EditHandle &entry, CRef< CSeq_annot_Info > annot)
CSeq_annot_EditHandle	AttachAnnot (const CSeq_entry_EditHandle &entry, const CSeq_annot_EditHandle &annot)
void	RemoveEntry (const CSeq_entry_EditHandle &entry)
void	RemoveBioseq (const CBioseq_EditHandle &seq)
void	RemoveBioseq_set (const CBioseq_set_EditHandle &seqset)
void	RemoveAnnot (const CSeq_annot_EditHandle &annot)
void	RemoveTopLevelBioseq (const CBioseq_Handle &seq)
void	RemoveTopLevelBioseq_set (const CBioseq_set_Handle &seqset)
void	RemoveTopLevelAnnot (const CSeq_annot_Handle &annot)
void	SelectNone (const CSeq_entry_EditHandle &entry)
CBioseq_EditHandle	SelectSeq (const CSeq_entry_EditHandle &entry, CBioseq &seq)
CBioseq_EditHandle	SelectSeq (const CSeq_entry_EditHandle &entry, CRef< CBioseq_Info > seq)
CBioseq_EditHandle	SelectSeq (const CSeq_entry_EditHandle &entry, const CBioseq_EditHandle &seq)
CBioseq_set_EditHandle	SelectSet (const CSeq_entry_EditHandle &entry, CBioseq_set &seqset)
CBioseq_set_EditHandle	SelectSet (const CSeq_entry_EditHandle &entry, CRef< CBioseq_set_Info > seqset)
CBioseq_set_EditHandle	SelectSet (const CSeq_entry_EditHandle &entry, const CBioseq_set_EditHandle &seqset)
CBioseq_Handle	GetBioseqHandle (const CSeq_id_Handle &id, int get_flag)
bool	IsSameBioseq (const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, int get_flag)
CBioseq_Handle	GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CTSE_Handle &tse)
CBioseq_Handle	GetBioseqHandle (const CSeq_loc &loc, int get_flag)
void	ResetScope (void)
void	ResetHistory (int action)
void	ResetDataAndHistory (void)
void	RemoveFromHistory (const CTSE_Handle &tse, int action)
void	RemoveFromHistory (const CSeq_id_Handle &seq_id)
void	RemoveDataLoader (const string &loader_name, int action)
void	RemoveTopLevelSeqEntry (const CTSE_Handle &entry)
CSeq_entry_Handle	GetSeq_entryHandle (CDataLoader *loader, const CBlobIdKey &blob_id, TMissing action)
CBioseq_Handle	GetBioseqHandle (const CBioseq &bioseq, TMissing action)
CBioseq_set_Handle	GetBioseq_setHandle (const CBioseq_set &seqset, TMissing action)
CSeq_entry_Handle	GetSeq_entryHandle (const CSeq_entry &entry, TMissing action)
CSeq_annot_Handle	GetSeq_annotHandle (const CSeq_annot &annot, TMissing action)
CSeq_entry_Handle	GetSeq_entryHandle (const CTSE_Handle &tse)
CSeq_feat_Handle	GetSeq_featHandle (const CSeq_feat &feat, TMissing action)
CScope &	GetScope (void)
bool	Exists (const CSeq_id_Handle &id)
TIds	GetIds (const CSeq_id_Handle &idh, TGetFlags flags=0)
CSeq_id_Handle	GetAccVer (const CSeq_id_Handle &idh, TGetFlags flags)
TGi	GetGi (const CSeq_id_Handle &idh, TGetFlags flags)
string	GetLabel (const CSeq_id_Handle &idh, TGetFlags flags)
TTaxId	GetTaxId (const CSeq_id_Handle &idh, TGetFlags flags)
TBioseqHandles	GetBioseqHandles (const TIds &ids)
TCDD_Entries	GetCDDAnnots (const TIds &idhs)
TCDD_Entries	GetCDDAnnots (const TBioseqHandles &bhs)
void	GetBulkIds (TBulkIds &ret, const TIds &idhs, TGetFlags flags)
void	GetAccVers (TIds &ret, const TIds &idhs, TGetFlags flags)
void	GetGis (TGIs &ret, const TIds &idhs, TGetFlags flags)
void	GetLabels (TLabels &ret, const TIds &idhs, TGetFlags flags)
void	GetTaxIds (TTaxIds &ret, const TIds &idhs, TGetFlags flags)
CConstRef< CSynonymsSet >	GetSynonyms (const CSeq_id_Handle &id, int get_flag)
CConstRef< CSynonymsSet >	GetSynonyms (const CBioseq_Handle &bh)
void	GetAllTSEs (TTSE_Handles &tses, int kind)
IScopeTransaction_Impl *	CreateTransaction ()
void	SetActiveTransaction (IScopeTransaction_Impl *)
IScopeTransaction_Impl &	GetTransaction ()
bool	IsTransactionActive () const
TSeqPos	GetSequenceLength (const CSeq_id_Handle &id, TGetFlags flags)
CSeq_inst::TMol	GetSequenceType (const CSeq_id_Handle &id, TGetFlags flags)
int	GetSequenceState (const CSeq_id_Handle &id, TGetFlags flags)
int	GetSequenceHash (const CSeq_id_Handle &id, TGetFlags flags)
void	GetSequenceLengths (TSequenceLengths &ret, const TIds &idhs, TGetFlags flags)
void	GetSequenceTypes (TSequenceTypes &ret, const TIds &idhs, TGetFlags flags)
void	GetSequenceStates (TSequenceStates &ret, const TIds &idhs, TGetFlags flags)
void	GetSequenceHashes (TSequenceHashes &ret, const TIds &idhs, TGetFlags flags)
void	x_ClearCacheOnRemoveData (const CTSE_Info *old_tse=0)
void	x_ClearAnnotCache (void)
void	x_ClearCacheOnNewAnnot (const CTSE_Info &new_tse)
TTSE_Lock	x_GetTSE_Lock (const CSeq_entry &tse, int action)
TSeq_entry_Lock	x_GetSeq_entry_Lock (const CSeq_entry &entry, int action)
TSeq_annot_Lock	x_GetSeq_annot_Lock (const CSeq_annot &annot, int action)
TBioseq_set_Lock	x_GetBioseq_set_Lock (const CBioseq_set &seqset, int action)
TBioseq_Lock	x_GetBioseq_Lock (const CBioseq &bioseq, int action)
TTSE_Lock	x_GetTSE_Lock (const CTSE_Lock &lock, CDataSource_ScopeInfo &ds)
TTSE_Lock	x_GetTSE_Lock (const CTSE_ScopeInfo &tse)
CRef< CDataSource_ScopeInfo >	x_GetDSInfo (CDataSource &ds)
CRef< CDataSource_ScopeInfo >	AddDS (CRef< CDataSource > ds, TPriority priority)
CRef< CDataSource_ScopeInfo >	GetEditDS (TPriority priority)
CRef< CDataSource_ScopeInfo >	GetConstDS (TPriority priority)
CRef< CDataSource_ScopeInfo >	AddDSBefore (CRef< CDataSource > ds, CRef< CDataSource_ScopeInfo > ds2, const CTSE_ScopeInfo *replaced_tse=0)
bool	GetKeepExternalAnnotsForEdit () const
void	SetKeepExternalAnnotsForEdit (bool keep=true)
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

Private Types
typedef vector< CBioseq_Handle >	TBioseq_HandleSet
typedef int	TBioseqLevelFlag
typedef CBioseq_ScopeInfo::TTSE_MatchSet	TTSE_MatchSet
typedef CDataSource::TTSE_LockMatchSet	TTSE_LockMatchSet_DS
typedef CRWLock	TConfLock
typedef TConfLock::TReadLockGuard	TConfReadLockGuard
typedef TConfLock::TWriteLockGuard	TConfWriteLockGuard
typedef CFastMutex	TSeq_idMapLock

Private Member Functions
	CScope_Impl (CObjectManager &objmgr)
virtual	~CScope_Impl (void)
	CScope_Impl (const CScope_Impl &)
CScope_Impl &	operator= (const CScope_Impl &)
CDataSource *	GetFirstLoaderSource (void)
void	GetTSESetWithAnnots (const CSeq_id_Handle &idh, TTSE_LockMatchSet &tse_set)
void	GetTSESetWithAnnots (const CBioseq_Handle &bh, TTSE_LockMatchSet &tse_set)
void	GetTSESetWithAnnots (const CSeq_id_Handle &idh, TTSE_LockMatchSet &tse_set, const SAnnotSelector &sel)
void	GetTSESetWithAnnots (const CBioseq_Handle &bh, TTSE_LockMatchSet &tse_set, const SAnnotSelector &sel)
void	x_AttachToOM (CObjectManager &objmgr)
void	x_DetachFromOM (void)
void	x_ReportNewDataConflict (const CSeq_id_Handle *conflict_id=0)
void	x_ClearCacheOnNewDS (void)
void	x_ClearCacheOnEdit (const CTSE_ScopeInfo &replaced_tse)
void	x_ClearCacheOnNewData (const TIds &seq_ids, const TIds &annot_ids)
void	x_ClearCacheOnNewData (const CTSE_Info &new_tse)
void	x_ClearCacheOnNewData (const CTSE_Info &new_tse, const CSeq_id_Handle &new_id)
void	x_ClearCacheOnNewData (const CTSE_Info &new_tse, const CSeq_entry_Info &new_entry)
void	x_ClearCacheOnRemoveSeqId (const CSeq_id_Handle &id, CBioseq_ScopeInfo &seq)
void	x_ClearCacheOnRemoveAnnot (const CTSE_Info &old_tse)
CRef< CDataSource_ScopeInfo >	GetEditDataSource (CDataSource_ScopeInfo &ds, const CTSE_ScopeInfo *replaced_tse=0)
CSeq_entry_EditHandle	x_AttachEntry (const CBioseq_set_EditHandle &seqset, CRef< CSeq_entry_Info > entry, int index)
void	x_AttachEntry (const CBioseq_set_EditHandle &seqset, const CSeq_entry_EditHandle &entry, int index)
CSeq_annot_EditHandle	x_AttachAnnot (const CSeq_entry_EditHandle &entry, CRef< CSeq_annot_Info > annot)
void	x_AttachAnnot (const CSeq_entry_EditHandle &entry, const CSeq_annot_EditHandle &annot)
CBioseq_EditHandle	x_SelectSeq (const CSeq_entry_EditHandle &entry, CRef< CBioseq_Info > bioseq)
CBioseq_set_EditHandle	x_SelectSet (const CSeq_entry_EditHandle &entry, CRef< CBioseq_set_Info > seqset)
void	x_SelectSeq (const CSeq_entry_EditHandle &entry, const CBioseq_EditHandle &bioseq)
void	x_SelectSet (const CSeq_entry_EditHandle &entry, const CBioseq_set_EditHandle &seqset)
void	x_ResolveSeq_id (TSeq_idMapValue &id, int get_flag, SSeqMatch_Scope &match)
SSeqMatch_Scope	x_FindBioseqInfo (const CPriorityTree &tree, const CSeq_id_Handle &idh, int get_flag)
SSeqMatch_Scope	x_FindBioseqInfo (const CPriorityNode &node, const CSeq_id_Handle &idh, int get_flag)
SSeqMatch_Scope	x_FindBioseqInfo (CDataSource_ScopeInfo &ds_info, const CSeq_id_Handle &idh, int get_flag)
CBioseq_Handle	x_GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CTSE_Handle &tse)
void	x_UpdateHandleSeq_id (CBioseq_Handle &bh)
CBioseq_Handle	GetBioseqHandle (const CBioseq_Info &seq, const CTSE_Handle &tse)
CBioseq_Handle	x_GetBioseqHandle (const CBioseq_Info &seq, const CTSE_Handle &tse)
CRef< CSeq_entry >	x_MakeDummyTSE (CBioseq &seq) const
CRef< CSeq_entry >	x_MakeDummyTSE (CBioseq_set &seqset) const
CRef< CSeq_entry >	x_MakeDummyTSE (CSeq_annot &annot) const
CRef< CSeq_entry >	x_MakeDummyTSE (CSeq_submit &submit) const
bool	x_IsDummyTSE (const CTSE_Info &tse, const CBioseq_Info &seq) const
bool	x_IsDummyTSE (const CTSE_Info &tse, const CBioseq_set_Info &seqset) const
bool	x_IsDummyTSE (const CTSE_Info &tse, const CSeq_annot_Info &annot) const
void	x_GetBioseqHandlesSorted (const TIds &ids, size_t from, size_t count, TBioseqHandles &ret)
	Bulk retrieval methods. More...
void	x_PopulateBioseq_HandleSet (const CSeq_entry_Handle &tse, TBioseq_HandleSet &handles, CSeq_inst::EMol filter, TBioseqLevelFlag level)
CConstRef< CSynonymsSet >	x_GetSynonyms (CBioseq_ScopeInfo &info)
void	x_AddSynonym (const CSeq_id_Handle &idh, CSynonymsSet &syn_set, CBioseq_ScopeInfo &info)
TSeq_idMapValue &	x_GetSeq_id_Info (const CSeq_id_Handle &id)
TSeq_idMapValue &	x_GetSeq_id_Info (const CBioseq_Handle &bh)
TSeq_idMapValue *	x_FindSeq_id_Info (const CSeq_id_Handle &id)
CRef< CBioseq_ScopeInfo >	x_InitBioseq_Info (TSeq_idMapValue &info, int get_flag, SSeqMatch_Scope &match)
bool	x_InitBioseq_Info (TSeq_idMapValue &info, CBioseq_ScopeInfo &bioseq_info)
CRef< CBioseq_ScopeInfo >	x_GetBioseq_Info (const CSeq_id_Handle &id, int get_flag, SSeqMatch_Scope &match)
CRef< CBioseq_ScopeInfo >	x_FindBioseq_Info (const CSeq_id_Handle &id, int get_flag, SSeqMatch_Scope &match)
CBioseq_ScopeInfo::TAnnotRefInfo &	x_GetAnnotRef_Info (const SAnnotSelector *sel, CBioseq_ScopeInfo::TAnnotRefInfo &main_info, CBioseq_ScopeInfo::TNAAnnotRefInfo &na_info)
void	x_GetTSESetWithAnnots (TTSE_LockMatchSet &lock, CBioseq_ScopeInfo &binfo, const SAnnotSelector *sel=0)
void	x_GetTSESetWithAnnots (TTSE_LockMatchSet &lock, TTSE_MatchSet *save_match, CBioseq_ScopeInfo &binfo, const SAnnotSelector *sel=0)
void	x_GetTSESetWithAnnots (TTSE_LockMatchSet &lock, TSeq_idMapValue &info, const SAnnotSelector *sel=0)
void	x_GetTSESetWithAnnots (TTSE_LockMatchSet &lock, TTSE_MatchSet *save_match, TSeq_idMapValue &info, const SAnnotSelector *sel=0)
void	x_AddTSESetWithAnnots (TTSE_LockMatchSet &lock, TTSE_MatchSet *save_match, const TTSE_LockMatchSet_DS &add, CDataSource_ScopeInfo &ds_info, CDataLoader::TProcessedNAs *filter_nas=0)
void	x_GetTSESetWithOrphanAnnots (TTSE_LockMatchSet &lock, TTSE_MatchSet *save_match, const TSeq_idSet &ids, CBioseq_ScopeInfo *binfo, const SAnnotSelector *sel)
void	x_GetTSESetWithBioseqAnnots (TTSE_LockMatchSet &lock, TTSE_MatchSet *save_match, CBioseq_ScopeInfo &binfo, const SAnnotSelector *sel)
void	x_GetTSESetWithBioseqAnnots (TTSE_LockMatchSet &lock, CBioseq_ScopeInfo &binfo, const SAnnotSelector *sel)
void	x_UpdateProcessedNAs (const SAnnotSelector *&sel, unique_ptr< SAnnotSelector > &sel_copy, CDataLoader::TProcessedNAs &filter_nas, CDataLoader::TProcessedNAs &processed_nas)
void	x_LockMatchSet (TTSE_LockMatchSet &lock, const TTSE_MatchSet &match)

Private Attributes
CScope *	m_HeapScope
CRef< CObjectManager >	m_ObjMgr
CPriorityTree	m_setDataSrc
TDSMap	m_DSMap
CInitMutexPool	m_MutexPool
TConfLock	m_ConfLock
TSeq_idMap	m_Seq_idMap
TSeq_idMapLock	m_Seq_idMapLock
IScopeTransaction_Impl *	m_Transaction
atomic< int >	m_BioseqChangeCounter
atomic< int >	m_AnnotChangeCounter
bool	m_KeepExternalAnnotsForEdit

Friends
class	CScope
class	CHeapScope
class	CObjectManager
class	CSeqVector
class	CDataSource
class	CBioseq_CI
class	CAnnot_Collector
class	CBioseq_Handle
class	CBioseq_set_Handle
class	CSeq_entry_Handle
class	CBioseq_EditHandle
class	CBioseq_set_EditHandle
class	CSeq_entry_EditHandle
class	CSeq_annot_EditHandle
class	CTSE_CI
class	CSeq_annot_CI
class	CSeqMap_CI
class	CPrefetchTokenOld_Impl
class	CDataSource_ScopeInfo
class	CTSE_ScopeInfo
class	CScopeTransaction_Impl
class	CBioseq_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...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 130 of file scope_impl.hpp.

Member Typedef Documentation

TBioseq_HandleSet

typedef vector<CBioseq_Handle> CScope_Impl::TBioseq_HandleSet

private

Definition at line 558 of file scope_impl.hpp.

TBioseq_Lock

typedef CDataSource_ScopeInfo::TBioseq_Lock CScope_Impl::TBioseq_Lock

Definition at line 524 of file scope_impl.hpp.

TBioseq_set_Lock

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

Definition at line 523 of file scope_impl.hpp.

TBioseqHandles

typedef vector<CBioseq_Handle> CScope_Impl::TBioseqHandles

Bulk retrieval methods.

Definition at line 347 of file scope_impl.hpp.

TBioseqLevelFlag

typedef int CScope_Impl::TBioseqLevelFlag

private

Definition at line 559 of file scope_impl.hpp.

TBulkIds

typedef vector<TIds> CScope_Impl::TBulkIds

Definition at line 144 of file scope_impl.hpp.

TCDD_Entries

typedef vector<CTSE_Handle> CScope_Impl::TCDD_Entries

Definition at line 350 of file scope_impl.hpp.

TConfLock

typedef CRWLock CScope_Impl::TConfLock

private

Definition at line 644 of file scope_impl.hpp.

TConfReadLockGuard

typedef TConfLock::TReadLockGuard CScope_Impl::TConfReadLockGuard

private

Definition at line 645 of file scope_impl.hpp.

TConfWriteLockGuard

typedef TConfLock::TWriteLockGuard CScope_Impl::TConfWriteLockGuard

private

Definition at line 646 of file scope_impl.hpp.

TDSMap

typedef map<CRef<CDataSource>, CRef<CDataSource_ScopeInfo> > CScope_Impl::TDSMap

Definition at line 142 of file scope_impl.hpp.

TEditInfoMap

typedef map<CConstRef<CObject>, CRef<CObject> > CScope_Impl::TEditInfoMap

Definition at line 141 of file scope_impl.hpp.

TExist

typedef int CScope_Impl::TExist

Definition at line 152 of file scope_impl.hpp.

TGetFlags

typedef int CScope_Impl::TGetFlags

Definition at line 334 of file scope_impl.hpp.

TGIs

typedef vector<TGi> CScope_Impl::TGIs

Definition at line 361 of file scope_impl.hpp.

TIds

typedef vector<CSeq_id_Handle> CScope_Impl::TIds

Definition at line 143 of file scope_impl.hpp.

TLabels

typedef vector<string> CScope_Impl::TLabels

Definition at line 365 of file scope_impl.hpp.

TMissing

typedef int CScope_Impl::TMissing

Definition at line 151 of file scope_impl.hpp.

TPriority

typedef int CScope_Impl::TPriority

Definition at line 140 of file scope_impl.hpp.

TSeq_annot_Lock

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

Definition at line 522 of file scope_impl.hpp.

TSeq_entry_Lock

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

Definition at line 521 of file scope_impl.hpp.

TSeq_idMap

typedef map<CSeq_id_Handle, SSeq_id_ScopeInfo> CScope_Impl::TSeq_idMap

Definition at line 136 of file scope_impl.hpp.

TSeq_idMapLock

typedef CFastMutex CScope_Impl::TSeq_idMapLock

private

Definition at line 647 of file scope_impl.hpp.

TSeq_idMapValue

typedef TSeq_idMap::value_type CScope_Impl::TSeq_idMapValue

Definition at line 137 of file scope_impl.hpp.

TSeq_idSet

typedef set<CSeq_id_Handle> CScope_Impl::TSeq_idSet

Definition at line 138 of file scope_impl.hpp.

TSequenceHashes

typedef vector<int> CScope_Impl::TSequenceHashes

Definition at line 403 of file scope_impl.hpp.

TSequenceLengths

typedef vector<TSeqPos> CScope_Impl::TSequenceLengths

Definition at line 391 of file scope_impl.hpp.

TSequenceStates

typedef vector<int> CScope_Impl::TSequenceStates

Definition at line 399 of file scope_impl.hpp.

TSequenceTypes

typedef vector<CSeq_inst::TMol> CScope_Impl::TSequenceTypes

Definition at line 395 of file scope_impl.hpp.

TTaxIds

typedef vector<TTaxId> CScope_Impl::TTaxIds

Definition at line 369 of file scope_impl.hpp.

TTSE_Handles

typedef vector<CSeq_entry_Handle> CScope_Impl::TTSE_Handles

Definition at line 145 of file scope_impl.hpp.

TTSE_Lock

typedef CTSE_ScopeUserLock CScope_Impl::TTSE_Lock

Definition at line 133 of file scope_impl.hpp.

TTSE_LockMatchSet

typedef vector< pair<CTSE_Handle, CSeq_id_Handle> > CScope_Impl::TTSE_LockMatchSet

Definition at line 139 of file scope_impl.hpp.

TTSE_LockMatchSet_DS

typedef CDataSource::TTSE_LockMatchSet CScope_Impl::TTSE_LockMatchSet_DS

private

Definition at line 586 of file scope_impl.hpp.

TTSE_MatchSet

typedef CBioseq_ScopeInfo::TTSE_MatchSet CScope_Impl::TTSE_MatchSet

private

Definition at line 585 of file scope_impl.hpp.

Member Enumeration Documentation

EGetBioseqFlag2

enum CScope_Impl::EGetBioseqFlag2

Enumerator
fUserFlagMask
fNoLockFlag

Definition at line 284 of file scope_impl.hpp.

Constructor & Destructor Documentation

CScope_Impl() [1/2]

CScope_Impl::CScope_Impl ( CObjectManager &  objmgr )

private

Definition at line 102 of file scope_impl.cpp.

~CScope_Impl()

CScope_Impl::~CScope_Impl ( void  )

privatevirtual

Definition at line 115 of file scope_impl.cpp.

References m_ConfLock, and x_DetachFromOM().

CScope_Impl() [2/2]

CScope_Impl::CScope_Impl ( const CScope_Impl &  )

private

Member Function Documentation

AddBioseq()

CBioseq_Handle CScope_Impl::AddBioseq	(	CBioseq &	bioseq,
		TPriority	pri,
		TExist	action
	)

Definition at line 274 of file scope_impl.cpp.

References CDataSource::AddStaticTSE(), CBioseq_Handle, CScope::eExist_Throw, CScope::eMissing_Null, CTSE_Handle::eTopLevel_Bioseq, CDataSource_ScopeInfo::GetDataSource(), GetEditDS(), CSeq_entry_Info::GetSeq(), CDataSource_ScopeInfo::GetTSE_Lock(), m_ConfLock, NCBI_THROW, CTSE_Info::SetTopLevelObjectType(), x_ClearCacheOnNewData(), x_GetBioseq_Lock(), x_GetBioseqHandle(), and x_MakeDummyTSE().

Referenced by CScope::AddBioseq().

AddDataLoader()

void CScope_Impl::AddDataLoader	(	const string &	loader_name,
		TPriority	priority
	)

Definition at line 194 of file scope_impl.cpp.

References CObjectManager::AcquireDataLoader(), CDataSource::GetDefaultPriority(), CPriorityTree::Insert(), CScope::kPriority_Default, m_ConfLock, m_ObjMgr, m_setDataSrc, x_ClearCacheOnNewDS(), and x_GetDSInfo().

Referenced by CScope::AddDataLoader().

AddDefaults()

void CScope_Impl::AddDefaults

(

TPriority

priority

)

Definition at line 179 of file scope_impl.cpp.

References CObjectManager::AcquireDefaultDataSources(), CPriorityTree::Insert(), CScope::kPriority_Default, m_ConfLock, m_ObjMgr, m_setDataSrc, NON_CONST_ITERATE, x_ClearCacheOnNewDS(), and x_GetDSInfo().

Referenced by CScope::AddDefaults().

AddDS()

CRef< CDataSource_ScopeInfo > CScope_Impl::AddDS	(	CRef< CDataSource >	ds,
		TPriority	priority
	)

Definition at line 1312 of file scope_impl.cpp.

References CDataSource::GetDefaultPriority(), CDataSource::GetSharedTSE(), CPriorityTree::Insert(), CScope::kPriority_Default, m_ConfLock, m_setDataSrc, x_ClearCacheOnNewData(), x_ClearCacheOnNewDS(), and x_GetDSInfo().

Referenced by AddSharedBioseq(), AddSharedSeq_annot(), and AddSharedSeq_entry().

AddDSBefore()

CRef< CDataSource_ScopeInfo > CScope_Impl::AddDSBefore	(	CRef< CDataSource >	ds,
		CRef< CDataSource_ScopeInfo >	ds2,
		const CTSE_ScopeInfo *	replaced_tse = 0
	)

Definition at line 1379 of file scope_impl.cpp.

References m_ConfLock, m_setDataSrc, NCBI_THROW, x_ClearCacheOnEdit(), and x_GetDSInfo().

Referenced by GetEditDataSource().

AddScope()

void CScope_Impl::AddScope	(	CScope_Impl &	scope,
		TPriority	priority
	)

Definition at line 206 of file scope_impl.cpp.

References CPriorityTree::Insert(), CScope::kPriority_Default, m_ConfLock, m_setDataSrc, CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), and x_ClearCacheOnNewDS().

Referenced by CScope::AddScope().

AddSeq_annot()

CSeq_annot_Handle CScope_Impl::AddSeq_annot	(	CSeq_annot &	annot,
		TPriority	pri,
		TExist	action
	)

Definition at line 335 of file scope_impl.cpp.

References CDataSource::AddStaticTSE(), CScope::eExist_Throw, CScope::eMissing_Null, CTSE_Handle::eTopLevel_Seq_annot, CBioseq_Base_Info::GetAnnot(), CDataSource_ScopeInfo::GetDataSource(), GetEditDS(), CSeq_entry_Info::GetSet(), CDataSource_ScopeInfo::GetTSE_Lock(), m_ConfLock, NCBI_THROW, CTSE_Info::SetTopLevelObjectType(), x_ClearCacheOnNewAnnot(), x_GetSeq_annot_Lock(), and x_MakeDummyTSE().

Referenced by CScope::AddSeq_annot().

AddSeq_entry()

CSeq_entry_Handle CScope_Impl::AddSeq_entry	(	CSeq_entry &	entry,
		TPriority	pri,
		TExist	action
	)

Definition at line 219 of file scope_impl.cpp.

References CDataSource::AddStaticTSE(), CSeq_entry_Handle, CScope::eExist_Throw, CScope::eMissing_Null, CDataSource_ScopeInfo::GetDataSource(), GetEditDS(), CDataSource_ScopeInfo::GetTSE_Lock(), m_ConfLock, NCBI_THROW, x_ClearCacheOnNewData(), and x_GetSeq_entry_Lock().

Referenced by CScope::AddTopLevelSeqEntry().

AddSeq_submit()

CSeq_entry_Handle CScope_Impl::AddSeq_submit	(	CSeq_submit &	submit,
		TPriority	pri
	)

Definition at line 398 of file scope_impl.cpp.

References CDataSource::AddStaticTSE(), CSeq_entry_Handle, CTSE_Handle::eTopLevel_Seq_submit, CDataSource_ScopeInfo::GetDataSource(), GetEditDS(), CDataSource_ScopeInfo::GetTSE_Lock(), m_ConfLock, CTSE_Info::SetTopLevelObject(), x_ClearCacheOnNewAnnot(), and x_MakeDummyTSE().

Referenced by CScope::AddSeq_submit().

AddSharedBioseq()

CBioseq_Handle CScope_Impl::AddSharedBioseq	(	const CBioseq &	bioseq,
		TPriority	pri,
		TExist	action
	)

Definition at line 301 of file scope_impl.cpp.

References _ASSERT, CObjectManager::AcquireSharedBioseq(), AddDS(), CDataSource::AddStaticTSE(), CBioseq_Handle, CScope::eExist_Throw, CScope::eMissing_Null, CTSE_Handle::eTopLevel_Bioseq, CBioseq_Info::GetBioseqCore(), GetConstDS(), CDataSource_ScopeInfo::GetDataSource(), CSeq_entry_Info::GetSeq(), CDataSource::GetSharedTSE(), CDataSource_ScopeInfo::GetTSE_Lock(), CSeq_entry_Info::IsSeq(), m_ConfLock, m_ObjMgr, NCBI_THROW, CTSE_Info::SetTopLevelObjectType(), x_GetBioseq_Lock(), x_GetBioseqHandle(), and x_MakeDummyTSE().

Referenced by CScope::AddBioseq().

AddSharedSeq_annot()

CSeq_annot_Handle CScope_Impl::AddSharedSeq_annot	(	const CSeq_annot &	annot,
		TPriority	pri,
		TExist	action
	)

Definition at line 362 of file scope_impl.cpp.

References _ASSERT, CObjectManager::AcquireSharedSeq_annot(), AddDS(), CDataSource::AddStaticTSE(), CScope::eExist_Throw, CScope::eMissing_Null, CTSE_Handle::eTopLevel_Seq_annot, CBioseq_Base_Info::GetAnnot(), GetConstDS(), CDataSource_ScopeInfo::GetDataSource(), CSeq_entry_Info::GetSet(), CDataSource::GetSharedTSE(), CDataSource_ScopeInfo::GetTSE_Lock(), CSeq_entry_Info::IsSet(), CBioseq_Base_Info::IsSetAnnot(), m_ConfLock, m_ObjMgr, NCBI_THROW, CTSE_Info::SetTopLevelObjectType(), x_GetSeq_annot_Lock(), and x_MakeDummyTSE().

Referenced by CScope::AddSeq_annot().

AddSharedSeq_entry()

CSeq_entry_Handle CScope_Impl::AddSharedSeq_entry	(	const CSeq_entry &	entry,
		TPriority	pri,
		TExist	action
	)

Definition at line 243 of file scope_impl.cpp.

References _ASSERT, CObjectManager::AcquireSharedSeq_entry(), AddDS(), CDataSource::AddStaticTSE(), CSeq_entry_Handle, CScope::eExist_Throw, CScope::eMissing_Null, GetConstDS(), CDataSource_ScopeInfo::GetDataSource(), CDataSource::GetSharedTSE(), CDataSource_ScopeInfo::GetTSE_Lock(), CTSE_Info::GetTSECore(), m_ConfLock, m_ObjMgr, NCBI_THROW, x_ClearCacheOnNewData(), and x_GetSeq_entry_Lock().

Referenced by CScope::AddTopLevelSeqEntry().

AttachAnnot() [1/3]

CSeq_annot_EditHandle CScope_Impl::AttachAnnot	(	const CSeq_entry_EditHandle &	entry,
		const CSeq_annot_EditHandle &	annot
	)

Definition at line 925 of file scope_impl.cpp.

References _ASSERT, AttachAnnot(), CHECK_HANDLE, CHECK_REMOVED_HANDLE, CSeq_annot_Handle::IsRemoved(), and x_AttachAnnot().

AttachAnnot() [2/3]

CSeq_annot_EditHandle CScope_Impl::AttachAnnot	(	const CSeq_entry_EditHandle &	entry,
		CRef< CSeq_annot_Info >	annot
	)

Definition at line 889 of file scope_impl.cpp.

References _ASSERT, AttachAnnot(), CHECK_HANDLE, and x_AttachAnnot().

AttachAnnot() [3/3]

CSeq_annot_EditHandle CScope_Impl::AttachAnnot	(	const CSeq_entry_EditHandle &	entry,
		CSeq_annot &	annot
	)

Definition at line 878 of file scope_impl.cpp.

References Ref().

Referenced by AttachAnnot(), CAttachAnnot_EditCommand< Annot >::Do(), and RemoveAction< CSeq_annot_EditHandle >::Undo().

AttachEntry() [1/3]

CSeq_entry_EditHandle CScope_Impl::AttachEntry	(	const CBioseq_set_EditHandle &	seqset,
		const CSeq_entry_EditHandle &	entry,
		int	index = -1
	)

Definition at line 744 of file scope_impl.cpp.

References _ASSERT, AttachEntry(), CHECK_HANDLE, CHECK_REMOVED_HANDLE, CSeq_entry_Handle::IsRemoved(), and x_AttachEntry().

AttachEntry() [2/3]

CSeq_entry_EditHandle CScope_Impl::AttachEntry	(	const CBioseq_set_EditHandle &	seqset,
		CRef< CSeq_entry_Info >	entry,
		int	index = -1
	)

Definition at line 704 of file scope_impl.cpp.

References _ASSERT, AttachEntry(), CHECK_HANDLE, and x_AttachEntry().

AttachEntry() [3/3]

CSeq_entry_EditHandle CScope_Impl::AttachEntry	(	const CBioseq_set_EditHandle &	seqset,
		CSeq_entry &	entry,
		int	index = -1
	)

Definition at line 696 of file scope_impl.cpp.

References Ref().

Referenced by AttachEntry(), CAttachEntry_EditCommand< Entry >::Do(), and CSeq_entry_Remove_EditCommand::Undo().

CreateTransaction()

IScopeTransaction_Impl * CScope_Impl::CreateTransaction

(

)

Definition at line 3239 of file scope_impl.cpp.

References CScopeTransaction_Impl, and m_Transaction.

Referenced by GetTransaction().

Exists()

bool CScope_Impl::Exists

(

const CSeq_id_Handle &

id

)

Definition at line 2692 of file scope_impl.cpp.

References CSeq_inst_Base::eMol_not_set, and GetSequenceType().

Referenced by CScope::Exists().

GetAccVer()

CSeq_id_Handle CScope_Impl::GetAccVer	(	const CSeq_id_Handle &	idh,
		TGetFlags	flags
	)

Definition at line 2736 of file scope_impl.cpp.

References data, CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, info, CSeq_id_Handle::IsAccVer(), CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, x_FindBioseq_Info(), and CScope::x_GetAccVer().

Referenced by CScope::GetAccVer().

GetAccVers()

void CScope_Impl::GetAccVers	(	TIds &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3460 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), x_FindBioseq_Info(), and CScope::x_GetAccVer().

GetAllTSEs()

void CScope_Impl::GetAllTSEs	(	TTSE_Handles &	tses,
		int	kind
	)

Definition at line 3202 of file scope_impl.cpp.

References CScope::eManualTSEs, ITERATE, m_ConfLock, m_setDataSrc, and x_GetTSE_Lock().

Referenced by CScope::GetAllTSEs().

GetBioseq_setHandle()

CBioseq_set_Handle CScope_Impl::GetBioseq_setHandle	(	const CBioseq_set &	seqset,
		TMissing	action
	)

Definition at line 1215 of file scope_impl.cpp.

References CBioseq_set_Handle, m_ConfLock, and x_GetBioseq_set_Lock().

Referenced by CScope::GetBioseq_setEditHandle(), and CScope::GetBioseq_setHandle().

GetBioseqHandle() [1/4]

CBioseq_Handle CScope_Impl::GetBioseqHandle	(	const CBioseq &	bioseq,
		TMissing	action
	)

Definition at line 1254 of file scope_impl.cpp.

References m_ConfLock, CBioseq_Handle::m_Info, x_GetBioseq_Lock(), and x_UpdateHandleSeq_id().

GetBioseqHandle() [2/4]

CBioseq_Handle CScope_Impl::GetBioseqHandle ( const CBioseq_Info &  seq, const CTSE_Handle &  tse  )

private

Definition at line 2081 of file scope_impl.cpp.

References m_ConfLock, and x_GetBioseqHandle().

GetBioseqHandle() [3/4]

CBioseq_Handle CScope_Impl::GetBioseqHandle	(	const CSeq_id_Handle &	id,
		int	get_flag
	)

Definition at line 1858 of file scope_impl.cpp.

References fNoLockFlag, fUserFlagMask, info, m_ConfLock, CBioseq_Handle::m_Handle_Seq_id, CBioseq_Handle::m_Info, match(), CScopeInfo_Ref< Info >::Reset(), and x_GetBioseq_Info().

Referenced by CSeq_loc_Conversion::Convert(), CSeq_loc_Conversion_Set::Convert(), CSeq_loc_Conversion::ConvertSimpleLoc(), CScope::GetBioseqEditHandle(), CScope::GetBioseqHandle(), GetBioseqHandle(), CSeq_entry_Handle::GetSeq(), GetSequenceHash(), GetSequenceHashes(), IsSameBioseq(), CSeq_entry_EditHandle::SetSeq(), CAnnot_Collector::x_GetBioseqHandle(), and x_GetBioseqHandlesSorted().

GetBioseqHandle() [4/4]

CBioseq_Handle CScope_Impl::GetBioseqHandle	(	const CSeq_loc &	loc,
		int	get_flag
	)

Definition at line 2012 of file scope_impl.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::empty(), CMasterSeqSegments::FindSeg(), GetBioseqHandle(), CTSE_Info::GetMasterSeqSegments(), CTSE_Info::GetSegSetMaster(), CBioseq_Handle::GetTSE_Handle(), set< Key, Compare >::insert(), ITERATE, NCBI_THROW, CConstRef< C, Locker >::Reset(), set< Key, Compare >::size(), and CTSE_Handle::x_GetTSE_Info().

GetBioseqHandleFromTSE()

CBioseq_Handle CScope_Impl::GetBioseqHandleFromTSE	(	const CSeq_id_Handle &	id,
		const CTSE_Handle &	tse
	)

Definition at line 2001 of file scope_impl.cpp.

References x_GetBioseqHandleFromTSE().

Referenced by CAnnot_Collector::CanResolveId(), CTSE_Handle::GetBioseqHandle(), and CScope::GetBioseqHandleFromTSE().

GetBioseqHandles()

CScope_Impl::TBioseqHandles CScope_Impl::GetBioseqHandles

(

const TIds &

ids

)

Definition at line 3329 of file scope_impl.cpp.

References cnt, CSortedSeq_ids::GetSortedIds(), CSortedSeq_ids::RestoreOrder(), and x_GetBioseqHandlesSorted().

Referenced by CScope::GetBioseqHandles(), and GetCDDAnnots().

GetBulkIds()

void CScope_Impl::GetBulkIds	(	TBulkIds &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3402 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingSequence, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), and x_FindBioseq_Info().

GetCDDAnnots() [1/2]

CScope_Impl::TCDD_Entries CScope_Impl::GetCDDAnnots

(

const TBioseqHandles &

bhs

)

Definition at line 3362 of file scope_impl.cpp.

References CSortedBioseqs::GetSortedBioseqs(), i, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, CSortedBioseqs::RestoreOrder(), sx_CountFalse(), x_GetDSInfo(), and x_GetTSE_Lock().

GetCDDAnnots() [2/2]

CScope_Impl::TCDD_Entries CScope_Impl::GetCDDAnnots

(

const TIds &

idhs

)

Definition at line 3355 of file scope_impl.cpp.

References GetBioseqHandles().

Referenced by CScope::GetCDDAnnots().

GetConstDS()

CRef< CDataSource_ScopeInfo > CScope_Impl::GetConstDS

(

TPriority

priority

)

Definition at line 1354 of file scope_impl.cpp.

References _ASSERT, CDataSource::CanBeEdited(), CDataSource_ScopeInfo::CanBeEdited(), CPriorityTree::GetTree(), CDataSource_ScopeInfo::IsConst(), multimap_checker< Container >::lower_bound(), m_ConfLock, m_setDataSrc, Ref(), CDataSource_ScopeInfo::SetConst(), and x_GetDSInfo().

Referenced by AddSharedBioseq(), AddSharedSeq_annot(), and AddSharedSeq_entry().

GetEditDataSource()

CRef< CDataSource_ScopeInfo > CScope_Impl::GetEditDataSource ( CDataSource_ScopeInfo &  ds, const CTSE_ScopeInfo *  replaced_tse = 0  )

private

Definition at line 1898 of file scope_impl.cpp.

References _ASSERT, AddDSBefore(), CDataSource::CanBeEdited(), CDataSource_ScopeInfo::CanBeEdited(), CDataSource_ScopeInfo::GetDataLoader(), m_ConfLock, CDataSource_ScopeInfo::m_EditDS, Ref(), and CDataSource_ScopeInfo::SetCanRemoveOnResetHistory().

Referenced by GetEditHandle().

GetEditDS()

CRef< CDataSource_ScopeInfo > CScope_Impl::GetEditDS

(

TPriority

priority

)

Definition at line 1332 of file scope_impl.cpp.

References _ASSERT, CDataSource::CanBeEdited(), CDataSource_ScopeInfo::CanBeEdited(), CPriorityTree::GetTree(), multimap_checker< Container >::lower_bound(), m_ConfLock, m_setDataSrc, Ref(), and x_GetDSInfo().

Referenced by AddBioseq(), AddSeq_annot(), AddSeq_entry(), and AddSeq_submit().

GetEditHandle() [1/5]

CBioseq_EditHandle CScope_Impl::GetEditHandle

(

const CBioseq_Handle &

seq

)

Definition at line 1964 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CTSE_Handle::CanBeEdited(), CBioseq_EditHandle, CHECK_HANDLE, GetEditHandle(), and CBioseq_Handle::GetTSE_Handle().

GetEditHandle() [2/5]

CBioseq_set_EditHandle CScope_Impl::GetEditHandle

(

const CBioseq_set_Handle &

seqset

)

Definition at line 1991 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CTSE_Handle::CanBeEdited(), CBioseq_set_EditHandle, CHECK_HANDLE, GetEditHandle(), and CBioseq_set_Handle::GetTSE_Handle().

GetEditHandle() [3/5]

CSeq_annot_EditHandle CScope_Impl::GetEditHandle

(

const CSeq_annot_Handle &

annot

)

Definition at line 1982 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CTSE_Handle::CanBeEdited(), CHECK_HANDLE, CSeq_annot_EditHandle, GetEditHandle(), and CSeq_annot_Handle::GetTSE_Handle().

GetEditHandle() [4/5]

CSeq_entry_EditHandle CScope_Impl::GetEditHandle

(

const CSeq_entry_Handle &

entry

)

Definition at line 1973 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CTSE_Handle::CanBeEdited(), CHECK_HANDLE, CSeq_entry_EditHandle, GetEditHandle(), and CSeq_entry_Handle::GetTSE_Handle().

GetEditHandle() [5/5]

CTSE_Handle CScope_Impl::GetEditHandle

(

const CTSE_Handle &

src_tse

)

Definition at line 1918 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CDataSource::AddStaticTSE(), CDataSource_ScopeInfo::CanBeEdited(), CTSE_Handle::CanBeEdited(), CDataSource_ScopeInfo::DetachScope(), CDataSource::DropStaticTSE(), CPriorityTree::Erase(), map_checker< Container >::erase(), CDataSource::GetDataLoader(), CDataSource_ScopeInfo::GetDataSource(), CTSE_ScopeInfo::GetDSInfo(), GetEditDataSource(), CDataSource::GetSharedObject(), CDataSource_ScopeInfo::IsConst(), CTSE_Info::m_BaseTSE, m_ConfLock, m_DSMap, m_setDataSrc, CTSE_ScopeInfo::m_TSE_Lock, CTSE_ScopeInfo::ReplaceTSE(), CRef< C, Locker >::Reset(), CTSE_ScopeInfo::SetEditTSE(), and CTSE_Handle::x_GetScopeInfo().

Referenced by CScope::GetBioseq_setEditHandle(), CScope::GetBioseqEditHandle(), GetEditHandle(), CScope::GetEditHandle(), CBioseq_Handle::GetEditHandle(), CSeq_annot_Handle::GetEditHandle(), CScope::GetSeq_annotEditHandle(), and CScope::GetSeq_entryEditHandle().

GetFirstLoaderSource()

CDataSource * CScope_Impl::GetFirstLoaderSource ( void  )

private

Definition at line 3219 of file scope_impl.cpp.

References m_ConfLock, and m_setDataSrc.

Referenced by CPrefetchTokenOld_Impl::x_InitPrefetch().

GetGi()

TGi CScope_Impl::GetGi	(	const CSeq_id_Handle &	idh,
		TGetFlags	flags
	)

Definition at line 2791 of file scope_impl.cpp.

References data, CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, x_FindBioseq_Info(), CScope::x_GetGi(), and ZERO_GI.

Referenced by CScope::GetGi().

GetGis()

void CScope_Impl::GetGis	(	TGIs &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3531 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), x_FindBioseq_Info(), CScope::x_GetGi(), and ZERO_GI.

GetIds()

CScope_Impl::TIds CScope_Impl::GetIds	(	const CSeq_id_Handle &	idh,
		TGetFlags	flags = 0
	)

Definition at line 2697 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingSequence, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, and x_FindBioseq_Info().

Referenced by CScope::GetIds(), and CAnnot_Collector::x_SearchLoc().

GetKeepExternalAnnotsForEdit()

bool CScope_Impl::GetKeepExternalAnnotsForEdit ( ) const

inline

Definition at line 550 of file scope_impl.hpp.

References m_KeepExternalAnnotsForEdit.

Referenced by CScope::GetKeepExternalAnnotsForEdit(), x_GetTSESetWithBioseqAnnots(), and x_GetTSESetWithOrphanAnnots().

GetLabel()

string CScope_Impl::GetLabel	(	const CSeq_id_Handle &	idh,
		TGetFlags	flags
	)

Definition at line 2839 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingSequence, GetDirectLabel(), GetLabel(), info, m_ConfLock, m_setDataSrc, match(), NCBI_THROW, string, and x_FindBioseq_Info().

Referenced by CScope::GetLabel().

GetLabels()

void CScope_Impl::GetLabels	(	TLabels &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3602 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, ctll::empty(), CScope::fForceLoad, flags, CScope::fThrowOnMissing, GetDirectLabel(), GetLabel(), CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), and x_FindBioseq_Info().

GetObjectManager()

CObjectManager & CScope_Impl::GetObjectManager ( void  )

inline

Definition at line 687 of file scope_impl.hpp.

References m_ObjMgr.

Referenced by CScope::GetObjectManager(), and CScopeSource::GetScope().

GetScope()

CScope & CScope_Impl::GetScope

(

void

)

Definition at line 122 of file scope_impl.cpp.

References _ASSERT, and m_HeapScope.

GetSeq_annotHandle()

CSeq_annot_Handle CScope_Impl::GetSeq_annotHandle	(	const CSeq_annot &	annot,
		TMissing	action
	)

Definition at line 1241 of file scope_impl.cpp.

References m_ConfLock, and x_GetSeq_annot_Lock().

Referenced by CScope::GetSeq_annotEditHandle(), and CScope::GetSeq_annotHandle().

GetSeq_entryHandle() [1/3]

CSeq_entry_Handle CScope_Impl::GetSeq_entryHandle	(	CDataLoader *	loader,
		const CBlobIdKey &	blob_id,
		TMissing	action
	)

Definition at line 1191 of file scope_impl.cpp.

References CSeq_entry_Handle, CScope::eMissing_Null, CDataLoader::GetDataSource(), CDataSource_ScopeInfo::GetSeq_entry_Lock(), m_ConfLock, NCBI_THROW, and x_GetDSInfo().

Referenced by CScope::GetSeq_entryEditHandle(), and CScope::GetSeq_entryHandle().

GetSeq_entryHandle() [2/3]

CSeq_entry_Handle CScope_Impl::GetSeq_entryHandle	(	const CSeq_entry &	entry,
		TMissing	action
	)

Definition at line 1228 of file scope_impl.cpp.

References CSeq_entry_Handle, m_ConfLock, and x_GetSeq_entry_Lock().

GetSeq_entryHandle() [3/3]

CSeq_entry_Handle CScope_Impl::GetSeq_entryHandle

(

const CTSE_Handle &

tse

)

Definition at line 1267 of file scope_impl.cpp.

References CSeq_entry_Handle, and CTSE_Handle::x_GetTSE_Info().

GetSeq_featHandle()

CSeq_feat_Handle CScope_Impl::GetSeq_featHandle	(	const CSeq_feat &	feat,
		TMissing	action
	)

Definition at line 1273 of file scope_impl.cpp.

References CScope::eMissing_Null, CSeq_feat_Base::GetLocation(), kInvalidSeqPos, m_ConfLock, m_setDataSrc, and NCBI_THROW.

Referenced by CScope::GetSeq_featHandle().

GetSequenceHash()

int CScope_Impl::GetSequenceHash	(	const CSeq_id_Handle &	id,
		TGetFlags	flags
	)

Definition at line 3060 of file scope_impl.cpp.

References data, CScope::eGetBioseq_All, CScope::fDoNotRecalculate, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, GetBioseqHandle(), CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, NCBI_THROW, NCBI_THROW_FMT, and sx_CalcHash().

Referenced by CScope::GetSequenceHash().

GetSequenceHashes()

void CScope_Impl::GetSequenceHashes	(	TSequenceHashes &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3894 of file scope_impl.cpp.

References CScope::eGetBioseq_All, CScope::fDoNotRecalculate, flags, CScope::fThrowOnMissing, CScope::fThrowOnMissingData, GetBioseqHandle(), CSortedSeq_ids::GetSortedIds(), i, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, NCBI_THROW, NCBI_THROW_FMT, CSortedSeq_ids::RestoreOrder(), sx_CalcHash(), and sx_CountFalse().

GetSequenceLength()

TSeqPos CScope_Impl::GetSequenceLength	(	const CSeq_id_Handle &	id,
		TGetFlags	flags
	)

Definition at line 2936 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingSequence, info, CPrefetchManager::IsActive(), kInvalidSeqPos, m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, and x_FindBioseq_Info().

Referenced by CScope::GetSequenceLength().

GetSequenceLengths()

void CScope_Impl::GetSequenceLengths	(	TSequenceLengths &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3732 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissing, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), kInvalidSeqPos, m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), and x_FindBioseq_Info().

GetSequenceState()

int CScope_Impl::GetSequenceState	(	const CSeq_id_Handle &	id,
		TGetFlags	flags
	)

Definition at line 3010 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_not_found, CScope::fThrowOnMissingSequence, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, and x_FindBioseq_Info().

Referenced by CScope::GetSequenceState().

GetSequenceStates()

void CScope_Impl::GetSequenceStates	(	TSequenceStates &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3838 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_not_found, CScope::fThrowOnMissing, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), and x_FindBioseq_Info().

GetSequenceType()

CSeq_inst::TMol CScope_Impl::GetSequenceType	(	const CSeq_id_Handle &	id,
		TGetFlags	flags
	)

Definition at line 2973 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CSeq_inst_Base::eMol_not_set, CScope::fForceLoad, flags, CScope::fThrowOnMissingSequence, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, CDataLoader::STypeFound::sequence_found, CDataLoader::STypeFound::type, and x_FindBioseq_Info().

Referenced by Exists(), and CScope::GetSequenceType().

GetSequenceTypes()

void CScope_Impl::GetSequenceTypes	(	TSequenceTypes &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3785 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CSeq_inst_Base::eMol_not_set, CScope::fForceLoad, flags, CScope::fThrowOnMissing, CSortedSeq_ids::GetSortedIds(), i, info, CPrefetchManager::IsActive(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), and x_FindBioseq_Info().

GetSynonyms() [1/2]

CConstRef< CSynonymsSet > CScope_Impl::GetSynonyms

(

const CBioseq_Handle &

bh

)

Definition at line 3127 of file scope_impl.cpp.

References m_ConfLock, CBioseq_Handle::x_GetScopeInfo(), and x_GetSynonyms().

GetSynonyms() [2/2]

CConstRef< CSynonymsSet > CScope_Impl::GetSynonyms	(	const CSeq_id_Handle &	id,
		int	get_flag
	)

Definition at line 3113 of file scope_impl.cpp.

References _ASSERT, info, m_ConfLock, match(), x_GetBioseq_Info(), and x_GetSynonyms().

Referenced by CScope::GetSynonyms(), CAnnot_Collector::x_SearchLoc(), and CAnnot_Collector::x_SearchMaster().

GetTaxId()

TTaxId CScope_Impl::GetTaxId	(	const CSeq_id_Handle &	idh,
		TGetFlags	flags
	)

Definition at line 2880 of file scope_impl.cpp.

References CSeq_id_Base::e_General, CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissingData, CScope::fThrowOnMissingSequence, CDbtag_Base::GetDb(), CObject_id_Base::GetId(), CSeq_id_Handle::GetSeqId(), CDbtag_Base::GetTag(), info, INVALID_TAX_ID, CObject_id_Base::IsId(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, NCBI_THROW_FMT, TAX_ID_FROM, CSeq_id_Handle::Which(), x_FindBioseq_Info(), and ZERO_TAX_ID.

Referenced by CScope::GetTaxId().

GetTaxIds()

void CScope_Impl::GetTaxIds	(	TTaxIds &	ret,
		const TIds &	idhs,
		TGetFlags	flags
	)

Definition at line 3664 of file scope_impl.cpp.

References CSeq_id_Base::e_General, CScope::eGetBioseq_Resolved, CScope::fForceLoad, flags, CScope::fThrowOnMissing, CDbtag_Base::GetDb(), CObject_id_Base::GetId(), CSortedSeq_ids::GetSortedIds(), CDbtag_Base::GetTag(), i, info, INVALID_TAX_ID, CPrefetchManager::IsActive(), CObject_id_Base::IsId(), m_ConfLock, m_setDataSrc, match(), NCBI_THROW, CSortedSeq_ids::RestoreOrder(), sx_CountFalse(), TAX_ID_FROM, and x_FindBioseq_Info().

GetTransaction()

IScopeTransaction_Impl & CScope_Impl::GetTransaction

(

)

Definition at line 3231 of file scope_impl.cpp.

References CreateTransaction(), and m_Transaction.

Referenced by CCommandProcessor::run(), and CScopeTransaction_Impl::x_CanCommitRollBack().

GetTSESetWithAnnots() [1/4]

void CScope_Impl::GetTSESetWithAnnots ( const CBioseq_Handle &  bh, TTSE_LockMatchSet &  tse_set  )

private

Definition at line 2251 of file scope_impl.cpp.

References _ASSERT, CBioseq_ScopeInfo::HasBioseq(), m_ConfLock, CBioseq_Handle::x_GetScopeInfo(), and x_GetTSESetWithAnnots().

GetTSESetWithAnnots() [2/4]

void CScope_Impl::GetTSESetWithAnnots ( const CBioseq_Handle &  bh, TTSE_LockMatchSet &  tse_set, const SAnnotSelector &  sel  )

private

Definition at line 2283 of file scope_impl.cpp.

References _ASSERT, CBioseq_ScopeInfo::HasBioseq(), m_ConfLock, CBioseq_Handle::x_GetScopeInfo(), and x_GetTSESetWithAnnots().

GetTSESetWithAnnots() [3/4]

void CScope_Impl::GetTSESetWithAnnots ( const CSeq_id_Handle &  idh, TTSE_LockMatchSet &  tse_set  )

private

Definition at line 2232 of file scope_impl.cpp.

References CScope::eGetBioseq_All, CBioseq_ScopeInfo::HasBioseq(), info, m_ConfLock, x_GetSeq_id_Info(), x_GetTSESetWithAnnots(), and x_InitBioseq_Info().

Referenced by CAnnot_Collector::x_SearchLoc(), and CAnnot_Collector::x_SearchMaster().

GetTSESetWithAnnots() [4/4]

void CScope_Impl::GetTSESetWithAnnots ( const CSeq_id_Handle &  idh, TTSE_LockMatchSet &  tse_set, const SAnnotSelector &  sel  )

private

Definition at line 2265 of file scope_impl.cpp.

References CScope::eGetBioseq_All, CBioseq_ScopeInfo::HasBioseq(), info, m_ConfLock, x_GetSeq_id_Info(), x_GetTSESetWithAnnots(), and x_InitBioseq_Info().

IsSameBioseq()

bool CScope_Impl::IsSameBioseq	(	const CSeq_id_Handle &	id1,
		const CSeq_id_Handle &	id2,
		int	get_flag
	)

Definition at line 1881 of file scope_impl.cpp.

References fNoLockFlag, and GetBioseqHandle().

Referenced by CScope::IsSameBioseq().

IsTransactionActive()

bool CScope_Impl::IsTransactionActive

(

)

const

Definition at line 3261 of file scope_impl.cpp.

References m_Transaction.

operator=()

CScope_Impl& CScope_Impl::operator= ( const CScope_Impl &  )

private

RemoveAnnot()

void CScope_Impl::RemoveAnnot

(

const CSeq_annot_EditHandle &

annot

)

Definition at line 1634 of file scope_impl.cpp.

References CSeq_annot_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), m_ConfLock, CTSE_ScopeInfo::RemoveAnnot(), x_ClearAnnotCache(), x_ClearCacheOnRemoveAnnot(), CSeq_annot_EditHandle::x_GetInfo(), CSeq_annot_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

Referenced by RemoveAction< CSeq_annot_EditHandle >::Do(), and CAttachAnnot_EditCommand< Annot >::Undo().

RemoveBioseq()

void CScope_Impl::RemoveBioseq

(

const CBioseq_EditHandle &

seq

)

Definition at line 1661 of file scope_impl.cpp.

References CBioseq_EditHandle::GetParentEntry(), and SelectNone().

RemoveBioseq_set()

void CScope_Impl::RemoveBioseq_set

(

const CBioseq_set_EditHandle &

seqset

)

Definition at line 1667 of file scope_impl.cpp.

References CBioseq_set_EditHandle::GetParentEntry(), and SelectNone().

RemoveDataLoader()

void CScope_Impl::RemoveDataLoader	(	const string &	loader_name,
		int	action
	)

Definition at line 442 of file scope_impl.cpp.

References _VERIFY, CObjectManager::AcquireDataLoader(), CDataSource_ScopeInfo::DetachScope(), map_checker< Container >::end(), CPriorityTree::Erase(), map_checker< Container >::erase(), CScope::eRemoveIfLocked, CScope::eThrowIfLocked, map_checker< Container >::find(), CDataSource_ScopeInfo::GetTSE_InfoMap(), CDataSource_ScopeInfo::GetTSE_InfoMapMutex(), ITERATE, m_ConfLock, m_DSMap, m_ObjMgr, m_setDataSrc, NCBI_THROW, CRef< C, Locker >::Reset(), CDataSource_ScopeInfo::ResetHistory(), and x_ClearCacheOnRemoveData().

Referenced by CScope::RemoveDataLoader().

RemoveEntry()

void CScope_Impl::RemoveEntry

(

const CSeq_entry_EditHandle &

entry

)

Definition at line 1509 of file scope_impl.cpp.

References CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_EditHandle::GetParentEntry(), CSeq_entry_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), m_ConfLock, CTSE_ScopeInfo::RemoveEntry(), RemoveTopLevelSeqEntry(), x_ClearCacheOnRemoveData(), CSeq_entry_EditHandle::x_GetInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

Referenced by CSeq_entry_Remove_EditCommand::Do(), and CAttachEntry_EditCommand< Entry >::Undo().

RemoveFromHistory() [1/2]

void CScope_Impl::RemoveFromHistory

(

const CSeq_id_Handle &

seq_id

)

Definition at line 2606 of file scope_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CScopeInfo_Base::IsDetached(), m_ConfLock, m_Seq_idMap, CBioseq_ScopeInfo::m_SynCache, CInitMutex< C >::Reset(), and CBioseq_ScopeInfo::x_ResetAnnotRef_Info().

RemoveFromHistory() [2/2]

void CScope_Impl::RemoveFromHistory	(	const CTSE_Handle &	tse,
		int	action
	)

Definition at line 2586 of file scope_impl.cpp.

References _ASSERT, CScope::eKeepIfLocked, m_ConfLock, CTSE_ScopeInfo::RemoveFromHistory(), and x_ClearCacheOnRemoveData().

Referenced by CScope::RemoveFromHistory().

RemoveTopLevelAnnot()

void CScope_Impl::RemoveTopLevelAnnot

(

const CSeq_annot_Handle &

annot

)

Definition at line 1695 of file scope_impl.cpp.

References CSeq_annot_Handle::GetTSE_Handle(), NCBI_THROW, RemoveTopLevelSeqEntry(), CSeq_annot_Handle::x_GetInfo(), CTSE_Handle::x_GetTSE_Info(), and x_IsDummyTSE().

Referenced by CScope::RemoveSeq_annot().

RemoveTopLevelBioseq()

void CScope_Impl::RemoveTopLevelBioseq

(

const CBioseq_Handle &

seq

)

Definition at line 1673 of file scope_impl.cpp.

References CBioseq_Handle::GetTSE_Handle(), NCBI_THROW, RemoveTopLevelSeqEntry(), CBioseq_Handle::x_GetInfo(), CTSE_Handle::x_GetTSE_Info(), and x_IsDummyTSE().

Referenced by CScope::RemoveBioseq().

RemoveTopLevelBioseq_set()

void CScope_Impl::RemoveTopLevelBioseq_set

(

const CBioseq_set_Handle &

seqset

)

Definition at line 1684 of file scope_impl.cpp.

References CBioseq_set_Handle::GetTSE_Handle(), NCBI_THROW, RemoveTopLevelSeqEntry(), CBioseq_set_Handle::x_GetInfo(), CTSE_Handle::x_GetTSE_Info(), and x_IsDummyTSE().

RemoveTopLevelSeqEntry()

void CScope_Impl::RemoveTopLevelSeqEntry

(

const CTSE_Handle &

entry

)

Definition at line 483 of file scope_impl.cpp.

References _ASSERT, _VERIFY, CDataSource_ScopeInfo::CanBeEdited(), CDataSource_ScopeInfo::DetachScope(), CPriorityTree::Erase(), map_checker< Container >::erase(), CScope::eRemoveIfLocked, CDataSource_ScopeInfo::GetDataLoader(), CDataSource_ScopeInfo::GetDataSource(), CDataSource_ScopeInfo::GetScopeImpl(), m_ConfLock, m_DSMap, m_setDataSrc, NCBI_THROW, CTSE_ScopeInfo::RemoveFromHistory(), CRef< C, Locker >::Reset(), CTSE_Lock::Reset(), x_ClearCacheOnRemoveData(), and CTSE_Handle::x_GetScopeInfo().

Referenced by CRemoveTSE_EditCommand::Do(), RemoveEntry(), RemoveTopLevelAnnot(), RemoveTopLevelBioseq(), RemoveTopLevelBioseq_set(), and CScope::RemoveTopLevelSeqEntry().

ResetDataAndHistory()

void CScope_Impl::ResetDataAndHistory

(

void

)

Definition at line 2639 of file scope_impl.cpp.

References CDataSource_ScopeInfo::CanBeEdited(), map_checker< Container >::clear(), CDataSource::DropAllTSEs(), CScope::eRemoveIfLocked, CDataSource_ScopeInfo::GetDataSource(), CDataSource_ScopeInfo::IsConst(), m_ConfLock, m_DSMap, m_Seq_idMap, NON_CONST_ITERATE, CDataSource_ScopeInfo::ResetDS(), and x_ClearCacheOnRemoveData().

Referenced by CScope::ResetDataAndHistory().

ResetHistory()

void CScope_Impl::ResetHistory

(

int

action

)

Definition at line 2628 of file scope_impl.cpp.

References m_ConfLock, m_DSMap, NON_CONST_ITERATE, and x_ClearCacheOnRemoveData().

Referenced by CScope::ResetHistory().

ResetScope()

void CScope_Impl::ResetScope

(

void

)

Definition at line 2657 of file scope_impl.cpp.

References map_checker< Container >::begin(), map_checker< Container >::clear(), CPriorityTree::Clear(), CDataSource_ScopeInfo::DetachScope(), map_checker< Container >::empty(), map_checker< Container >::erase(), m_ConfLock, m_DSMap, m_Seq_idMap, and m_setDataSrc.

Referenced by CScope::ResetDataAndHistory(), and x_DetachFromOM().

SelectNone()

void CScope_Impl::SelectNone

(

const CSeq_entry_EditHandle &

entry

)

Definition at line 1646 of file scope_impl.cpp.

References _ASSERT, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), m_ConfLock, CTSE_ScopeInfo::ResetEntry(), x_ClearCacheOnRemoveData(), CSeq_entry_EditHandle::x_GetInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

Referenced by RemoveAction< CBioseq_EditHandle >::Do(), RemoveAction< CBioseq_set_EditHandle >::Do(), CSeq_entry_SelectNone_EditCommand::Do(), RemoveBioseq(), RemoveBioseq_set(), and CSeq_entry_Select_EditCommand< Handle, Data >::Undo().

SelectSeq() [1/3]

CBioseq_EditHandle CScope_Impl::SelectSeq	(	const CSeq_entry_EditHandle &	entry,
		CBioseq &	seq
	)

Definition at line 760 of file scope_impl.cpp.

References Ref().

Referenced by SeqEntrySelectAction< CBioseq_EditHandle, Data >::Do(), SelectSeq(), CSeq_entry_SelectNone_EditCommand::Undo(), and RemoveAction< CBioseq_EditHandle >::Undo().

SelectSeq() [2/3]

CBioseq_EditHandle CScope_Impl::SelectSeq	(	const CSeq_entry_EditHandle &	entry,
		const CBioseq_EditHandle &	seq
	)

Definition at line 802 of file scope_impl.cpp.

References _ASSERT, CHECK_HANDLE, CHECK_REMOVED_HANDLE, CBioseq_Handle::IsRemoved(), SelectSeq(), and x_SelectSeq().

SelectSeq() [3/3]

CBioseq_EditHandle CScope_Impl::SelectSeq	(	const CSeq_entry_EditHandle &	entry,
		CRef< CBioseq_Info >	seq
	)

Definition at line 769 of file scope_impl.cpp.

References _ASSERT, CHECK_HANDLE, SelectSeq(), and x_SelectSeq().

SelectSet() [1/3]

CBioseq_set_EditHandle CScope_Impl::SelectSet	(	const CSeq_entry_EditHandle &	entry,
		CBioseq_set &	seqset
	)

Definition at line 817 of file scope_impl.cpp.

References Ref().

Referenced by SeqEntrySelectAction< CBioseq_set_EditHandle, Data >::Do(), SelectSet(), CSeq_entry_SelectNone_EditCommand::Undo(), and RemoveAction< CBioseq_set_EditHandle >::Undo().

SelectSet() [2/3]

CBioseq_set_EditHandle CScope_Impl::SelectSet	(	const CSeq_entry_EditHandle &	entry,
		const CBioseq_set_EditHandle &	seqset
	)

Definition at line 863 of file scope_impl.cpp.

References _ASSERT, CHECK_HANDLE, CHECK_REMOVED_HANDLE, CBioseq_set_Handle::IsRemoved(), SelectSet(), and x_SelectSet().

SelectSet() [3/3]

CBioseq_set_EditHandle CScope_Impl::SelectSet	(	const CSeq_entry_EditHandle &	entry,
		CRef< CBioseq_set_Info >	seqset
	)

Definition at line 827 of file scope_impl.cpp.

References _ASSERT, CHECK_HANDLE, SelectSet(), and x_SelectSet().

SetActiveTransaction()

void CScope_Impl::SetActiveTransaction

(

IScopeTransaction_Impl *

transaction

)

Definition at line 3250 of file scope_impl.cpp.

References IScopeTransaction_Impl::AddScope(), IScopeTransaction_Impl::HasScope(), m_Transaction, and NCBI_THROW.

Referenced by CScopeTransaction_Impl::x_DoFinish().

SetKeepExternalAnnotsForEdit()

void CScope_Impl::SetKeepExternalAnnotsForEdit

(

bool

keep = true

)

Definition at line 171 of file scope_impl.cpp.

References m_ConfLock, m_KeepExternalAnnotsForEdit, and x_ClearAnnotCache().

Referenced by CScope::SetKeepExternalAnnotsForEdit().

x_AddSynonym()

void CScope_Impl::x_AddSynonym ( const CSeq_id_Handle &  idh, CSynonymsSet &  syn_set, CBioseq_ScopeInfo &  info  )

private

Definition at line 3137 of file scope_impl.cpp.

References _ASSERT, CSynonymsSet::AddSynonym(), CSeq_id_Handle::AsString(), CSynonymsSet::ContainsSynonym(), ERR_POST_X, CBioseq_ScopeInfo::IdString(), info, Warning(), x_GetSeq_id_Info(), and x_InitBioseq_Info().

Referenced by x_GetSynonyms().

x_AddTSESetWithAnnots()

void CScope_Impl::x_AddTSESetWithAnnots ( TTSE_LockMatchSet &  lock, TTSE_MatchSet *  save_match, const TTSE_LockMatchSet_DS &  add, CDataSource_ScopeInfo &  ds_info, CDataLoader::TProcessedNAs *  filter_nas = 0  )

private

Definition at line 2401 of file scope_impl.cpp.

References ITERATE, Ref(), CTSE_Handle::x_GetScopeInfo(), and x_GetTSE_Lock().

Referenced by x_GetTSESetWithBioseqAnnots(), and x_GetTSESetWithOrphanAnnots().

x_AttachAnnot() [1/2]

void CScope_Impl::x_AttachAnnot ( const CSeq_entry_EditHandle &  entry, const CSeq_annot_EditHandle &  annot  )

private

Definition at line 663 of file scope_impl.cpp.

References _ASSERT, CTSE_ScopeInfo::AddAnnot(), CSeq_entry_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), CSeq_annot_Handle::IsRemoved(), m_ConfLock, x_ClearCacheOnNewAnnot(), CSeq_annot_EditHandle::x_GetInfo(), CSeq_annot_EditHandle::x_GetScopeInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

x_AttachAnnot() [2/2]

CSeq_annot_EditHandle CScope_Impl::x_AttachAnnot ( const CSeq_entry_EditHandle &  entry, CRef< CSeq_annot_Info >  annot  )

private

Definition at line 647 of file scope_impl.cpp.

References _ASSERT, CSeq_entry_Info::AddAnnot(), CSeq_annot_EditHandle, CSeq_entry_Handle::GetTSE_Handle(), m_ConfLock, x_ClearCacheOnNewAnnot(), and CSeq_entry_EditHandle::x_GetInfo().

Referenced by AttachAnnot().

x_AttachEntry() [1/2]

void CScope_Impl::x_AttachEntry ( const CBioseq_set_EditHandle &  seqset, const CSeq_entry_EditHandle &  entry, int  index  )

private

Definition at line 546 of file scope_impl.cpp.

References _ASSERT, CTSE_ScopeInfo::AddEntry(), CBioseq_set_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), CSeq_entry_Handle::IsRemoved(), m_ConfLock, x_ClearCacheOnNewData(), CBioseq_set_EditHandle::x_GetInfo(), CSeq_entry_EditHandle::x_GetInfo(), CBioseq_set_EditHandle::x_GetScopeInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

x_AttachEntry() [2/2]

CSeq_entry_EditHandle CScope_Impl::x_AttachEntry ( const CBioseq_set_EditHandle &  seqset, CRef< CSeq_entry_Info >  entry, int  index  )

private

Definition at line 529 of file scope_impl.cpp.

References _ASSERT, CBioseq_set_Info::AddEntry(), CSeq_entry_EditHandle, CBioseq_set_Handle::GetTSE_Handle(), m_ConfLock, x_ClearCacheOnNewData(), and CBioseq_set_EditHandle::x_GetInfo().

Referenced by AttachEntry().

x_AttachToOM()

void CScope_Impl::x_AttachToOM ( CObjectManager &  objmgr )

private

Definition at line 129 of file scope_impl.cpp.

References _ASSERT, m_ObjMgr, CObjectManager::RegisterScope(), and CRef< C, Locker >::Reset().

x_ClearAnnotCache()

void CScope_Impl::x_ClearAnnotCache

(

void

)

Definition at line 1092 of file scope_impl.cpp.

References m_AnnotChangeCounter, m_Seq_idMap, NON_CONST_ITERATE, and CBioseq_ScopeInfo::x_ResetAnnotRef_Info().

Referenced by RemoveAnnot(), SetKeepExternalAnnotsForEdit(), CSeq_annot_EditHandle::Update(), CScope::UpdateAnnotIndex(), x_ClearCacheOnNewAnnot(), x_ClearCacheOnNewData(), x_ClearCacheOnRemoveAnnot(), CSeq_annot_EditHandle::x_RealAdd(), CSeq_align_Handle::x_RealReplace(), CSeq_feat_EditHandle::x_RealReplace(), and CSeq_graph_Handle::x_RealReplace().

x_ClearCacheOnEdit()

void CScope_Impl::x_ClearCacheOnEdit ( const CTSE_ScopeInfo &  replaced_tse )

private

Definition at line 1065 of file scope_impl.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::erase(), CBioseq_ScopeInfo::HasBioseq(), m_BioseqChangeCounter, m_Seq_idMap, CBioseq_ScopeInfo::m_SynCache, CBioseq_ScopeInfo::m_UnresolvedTimestamp, CInitMutex< C >::Reset(), CScopeInfo_Base::x_GetTSE_ScopeInfo(), and CBioseq_ScopeInfo::x_ResetAnnotRef_Info().

Referenced by AddDSBefore().

x_ClearCacheOnNewAnnot()

void CScope_Impl::x_ClearCacheOnNewAnnot

(

const CTSE_Info &

new_tse

)

Definition at line 1108 of file scope_impl.cpp.

References x_ClearAnnotCache().

Referenced by AddSeq_annot(), AddSeq_submit(), and x_AttachAnnot().

x_ClearCacheOnNewData() [1/4]

void CScope_Impl::x_ClearCacheOnNewData ( const CTSE_Info &  new_tse )

private

Definition at line 956 of file scope_impl.cpp.

References CSeq_entry_Info::GetSeqAndAnnotIds(), and x_ClearCacheOnNewData().

x_ClearCacheOnNewData() [2/4]

void CScope_Impl::x_ClearCacheOnNewData ( const CTSE_Info &  new_tse, const CSeq_entry_Info &  new_entry  )

private

Definition at line 975 of file scope_impl.cpp.

References CSeq_entry_Info::GetSeqAndAnnotIds(), and x_ClearCacheOnNewData().

x_ClearCacheOnNewData() [3/4]

void CScope_Impl::x_ClearCacheOnNewData ( const CTSE_Info &  new_tse, const CSeq_id_Handle &  new_id  )

private

Definition at line 967 of file scope_impl.cpp.

References x_ClearCacheOnNewData().

x_ClearCacheOnNewData() [4/4]

void CScope_Impl::x_ClearCacheOnNewData ( const TIds &  seq_ids, const TIds &  annot_ids  )

private

Definition at line 984 of file scope_impl.cpp.

References map_checker< Container >::begin(), map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::find(), first(), CBioseq_ScopeInfo::HasBioseq(), ITERATE, log, m_BioseqChangeCounter, m_Seq_idMap, CBioseq_ScopeInfo::m_UnresolvedTimestamp, max(), min(), NON_CONST_ITERATE, map_checker< Container >::size(), x_ClearAnnotCache(), and x_ReportNewDataConflict().

Referenced by AddBioseq(), AddDS(), CBioseq_ScopeInfo::AddId(), AddSeq_entry(), AddSharedSeq_entry(), x_AttachEntry(), x_ClearCacheOnNewData(), x_SelectSeq(), and x_SelectSet().

x_ClearCacheOnNewDS()

void CScope_Impl::x_ClearCacheOnNewDS ( void  )

private

Definition at line 1115 of file scope_impl.cpp.

References map_checker< Container >::empty(), m_AnnotChangeCounter, m_BioseqChangeCounter, m_Seq_idMap, and x_ReportNewDataConflict().

Referenced by AddDataLoader(), AddDefaults(), AddDS(), and AddScope().

x_ClearCacheOnRemoveAnnot()

void CScope_Impl::x_ClearCacheOnRemoveAnnot ( const CTSE_Info &  old_tse )

private

Definition at line 1184 of file scope_impl.cpp.

References x_ClearAnnotCache().

Referenced by RemoveAnnot().

x_ClearCacheOnRemoveData()

void CScope_Impl::x_ClearCacheOnRemoveData

(

const CTSE_Info *

old_tse = 0

)

Definition at line 1129 of file scope_impl.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::erase(), CScopeInfo_Base::IsDetached(), m_Seq_idMap, CBioseq_ScopeInfo::m_SynCache, CInitMutex< C >::Reset(), and CBioseq_ScopeInfo::x_ResetAnnotRef_Info().

Referenced by RemoveDataLoader(), RemoveEntry(), RemoveFromHistory(), RemoveTopLevelSeqEntry(), ResetDataAndHistory(), ResetHistory(), and SelectNone().

x_ClearCacheOnRemoveSeqId()

void CScope_Impl::x_ClearCacheOnRemoveSeqId ( const CSeq_id_Handle &  id, CBioseq_ScopeInfo &  seq  )

private

Definition at line 1149 of file scope_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CBioseq_ScopeInfo::GetIds(), ITERATE, m_Seq_idMap, CBioseq_ScopeInfo::m_SynCache, and CInitMutex< C >::Reset().

Referenced by CBioseq_ScopeInfo::RemoveId(), and CBioseq_ScopeInfo::ResetId().

x_DetachFromOM()

void CScope_Impl::x_DetachFromOM ( void  )

private

Definition at line 137 of file scope_impl.cpp.

References _ASSERT, m_ObjMgr, CRef< C, Locker >::Reset(), ResetScope(), and CObjectManager::RevokeScope().

Referenced by ~CScope_Impl().

x_FindBioseq_Info()

CRef< CBioseq_ScopeInfo > CScope_Impl::x_FindBioseq_Info ( const CSeq_id_Handle &  id, int  get_flag, SSeqMatch_Scope &  match  )

private

Definition at line 1814 of file scope_impl.cpp.

References _ASSERT, CBioseq_ScopeInfo::HasBioseq(), info, match(), x_FindSeq_id_Info(), CScopeInfo_Base::x_GetScopeImpl(), and x_InitBioseq_Info().

Referenced by GetAccVer(), GetAccVers(), GetBulkIds(), GetGi(), GetGis(), GetIds(), GetLabel(), GetLabels(), GetSequenceLength(), GetSequenceLengths(), GetSequenceState(), GetSequenceStates(), GetSequenceType(), GetSequenceTypes(), GetTaxId(), GetTaxIds(), and x_GetBioseqHandleFromTSE().

x_FindBioseqInfo() [1/3]

SSeqMatch_Scope CScope_Impl::x_FindBioseqInfo ( CDataSource_ScopeInfo &  ds_info, const CSeq_id_Handle &  idh, int  get_flag  )

private

Definition at line 2161 of file scope_impl.cpp.

References _ASSERT, CDataSource_ScopeInfo::BestResolve(), CBlobStateException::GetBlobState(), CDataSource_ScopeInfo::GetScopeImpl(), CPrefetchManager::IsActive(), and SSeqMatch_Scope::m_BlobState.

x_FindBioseqInfo() [2/3]

SSeqMatch_Scope CScope_Impl::x_FindBioseqInfo ( const CPriorityNode &  node, const CSeq_id_Handle &  idh, int  get_flag  )

private

Definition at line 2178 of file scope_impl.cpp.

References CPriorityNode::GetLeaf(), CPriorityNode::GetTree(), CPriorityNode::IsLeaf(), CPriorityNode::IsTree(), and x_FindBioseqInfo().

x_FindBioseqInfo() [3/3]

SSeqMatch_Scope CScope_Impl::x_FindBioseqInfo ( const CPriorityTree &  tree, const CSeq_id_Handle &  idh, int  get_flag  )

private

Definition at line 2118 of file scope_impl.cpp.

References _ASSERT, CTSE_ScopeInfo::CanBeEdited(), CBioseq_Handle::fState_conflict, CTSE_ScopeInfo::GetScopeImpl(), ITERATE, SSeqMatch_TSE::m_Bioseq, SSeqMatch_Scope::m_BlobState, SSeqMatch_Scope::m_TSE_Lock, and CConstRef< C, Locker >::Reset().

Referenced by x_FindBioseqInfo(), and x_ResolveSeq_id().

x_FindSeq_id_Info()

CScope_Impl::TSeq_idMapValue * CScope_Impl::x_FindSeq_id_Info ( const CSeq_id_Handle &  id )

private

Definition at line 1758 of file scope_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::lower_bound(), m_Seq_idMap, and m_Seq_idMapLock.

Referenced by x_FindBioseq_Info().

x_GetAnnotRef_Info()

CBioseq_ScopeInfo::TAnnotRefInfo & CScope_Impl::x_GetAnnotRef_Info ( const SAnnotSelector *  sel, CBioseq_ScopeInfo::TAnnotRefInfo &  main_info, CBioseq_ScopeInfo::TNAAnnotRefInfo &  na_info  )

private

Definition at line 2299 of file scope_impl.cpp.

References CSeq_id::eSNPScaleLimit_Default, SAnnotSelector::GetNamedAnnotAccessions(), SAnnotSelector::GetSNPScaleLimit(), SAnnotSelector::IsIncludedAnyNamedAnnotAccession(), and m_Seq_idMapLock.

Referenced by x_GetTSESetWithAnnots().

x_GetBioseq_Info()

CRef< CBioseq_ScopeInfo > CScope_Impl::x_GetBioseq_Info ( const CSeq_id_Handle &  id, int  get_flag, SSeqMatch_Scope &  match  )

private

Definition at line 1805 of file scope_impl.cpp.

References match(), x_GetSeq_id_Info(), and x_InitBioseq_Info().

Referenced by GetBioseqHandle(), and GetSynonyms().

x_GetBioseq_Lock()

CScope_Impl::TBioseq_Lock CScope_Impl::x_GetBioseq_Lock	(	const CBioseq &	bioseq,
		int	action
	)

Definition at line 1477 of file scope_impl.cpp.

References CScope::eMissing_Null, m_setDataSrc, and NCBI_THROW.

Referenced by AddBioseq(), AddSharedBioseq(), and GetBioseqHandle().

x_GetBioseq_set_Lock()

CScope_Impl::TBioseq_set_Lock CScope_Impl::x_GetBioseq_set_Lock	(	const CBioseq_set &	seqset,
		int	action
	)

Definition at line 1459 of file scope_impl.cpp.

References CScope::eMissing_Null, m_setDataSrc, and NCBI_THROW.

Referenced by GetBioseq_setHandle().

x_GetBioseqHandle()

CBioseq_Handle CScope_Impl::x_GetBioseqHandle ( const CBioseq_Info &  seq, const CTSE_Handle &  tse  )

private

Definition at line 2093 of file scope_impl.cpp.

References ConstRef(), CTSE_ScopeInfo::GetBioseqLock(), CBioseq_Handle::m_Info, CTSE_Handle::x_GetScopeInfo(), and x_UpdateHandleSeq_id().

Referenced by AddBioseq(), AddSharedBioseq(), GetBioseqHandle(), and x_PopulateBioseq_HandleSet().

x_GetBioseqHandleFromTSE()

CBioseq_Handle CScope_Impl::x_GetBioseqHandleFromTSE ( const CSeq_id_Handle &  id, const CTSE_Handle &  tse  )

private

Definition at line 1830 of file scope_impl.cpp.

References _ASSERT, CBioseq_Handle, CTSE_ScopeInfo::ContainsMatchingBioseq(), CScope::eGetBioseq_Loaded, CTSE_ScopeInfo::GetBioseqInfo(), info, m_ConfLock, match(), CTSE_ScopeInfo::Resolve(), x_FindBioseq_Info(), and CTSE_Handle::x_GetScopeInfo().

Referenced by GetBioseqHandleFromTSE(), and x_UpdateHandleSeq_id().

x_GetBioseqHandlesSorted()

void CScope_Impl::x_GetBioseqHandlesSorted ( const TIds &  ids, size_t  from, size_t  count, TBioseqHandles &  ret  )

private

Bulk retrieval methods.

Definition at line 3281 of file scope_impl.cpp.

References CBioseq_ScopeInfo, CScope::eGetBioseq_Loaded, CScope::eGetBioseq_Resolved, CInitGuard::force, CBioseq_Handle::fState_not_found, GetBioseqHandle(), i, info, init(), m_BioseqChangeCounter, m_ConfLock, m_MutexPool, m_setDataSrc, match(), and x_GetSeq_id_Info().

Referenced by GetBioseqHandles().

x_GetDSInfo()

CRef< CDataSource_ScopeInfo > CScope_Impl::x_GetDSInfo

(

CDataSource &

ds

)

Definition at line 1397 of file scope_impl.cpp.

References CDataSource_ScopeInfo, m_DSMap, and Ref().

Referenced by AddDataLoader(), AddDefaults(), AddDS(), AddDSBefore(), CPriorityNode::CPriorityNode(), GetCDDAnnots(), GetConstDS(), GetEditDS(), and GetSeq_entryHandle().

x_GetSeq_annot_Lock()

CScope_Impl::TSeq_annot_Lock CScope_Impl::x_GetSeq_annot_Lock	(	const CSeq_annot &	annot,
		int	action
	)

Definition at line 1442 of file scope_impl.cpp.

References CScope::eMissing_Null, m_setDataSrc, and NCBI_THROW.

Referenced by AddSeq_annot(), AddSharedSeq_annot(), and GetSeq_annotHandle().

x_GetSeq_entry_Lock()

CScope_Impl::TSeq_entry_Lock CScope_Impl::x_GetSeq_entry_Lock	(	const CSeq_entry &	entry,
		int	action
	)

Definition at line 1425 of file scope_impl.cpp.

References CScope::eMissing_Null, m_setDataSrc, and NCBI_THROW.

Referenced by AddSeq_entry(), AddSharedSeq_entry(), and GetSeq_entryHandle().

x_GetSeq_id_Info() [1/2]

TSeq_idMapValue& CScope_Impl::x_GetSeq_id_Info ( const CBioseq_Handle &  bh )

private

x_GetSeq_id_Info() [2/2]

CScope_Impl::TSeq_idMapValue & CScope_Impl::x_GetSeq_id_Info ( const CSeq_id_Handle &  id )

private

Definition at line 1707 of file scope_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::insert(), map_checker< Container >::lower_bound(), m_Seq_idMap, and m_Seq_idMapLock.

Referenced by GetTSESetWithAnnots(), x_AddSynonym(), x_GetBioseq_Info(), and x_GetBioseqHandlesSorted().

x_GetSynonyms()

CConstRef< CSynonymsSet > CScope_Impl::x_GetSynonyms ( CBioseq_ScopeInfo &  info )

private

Definition at line 3161 of file scope_impl.cpp.

References CSeq_id_Handle::GetHandle(), CSeq_id::GetTextseq_Id(), info, init(), ITERATE, m_MutexPool, CTextseq_id_Base::ResetName(), SerialClone(), and x_AddSynonym().

Referenced by GetSynonyms(), and x_GetTSESetWithBioseqAnnots().

x_GetTSE_Lock() [1/3]

CScope_Impl::TTSE_Lock CScope_Impl::x_GetTSE_Lock	(	const CSeq_entry &	tse,
		int	action
	)

Definition at line 1407 of file scope_impl.cpp.

References CScope::eMissing_Null, m_setDataSrc, and NCBI_THROW.

Referenced by GetAllTSEs(), GetCDDAnnots(), x_AddTSESetWithAnnots(), and x_LockMatchSet().

x_GetTSE_Lock() [2/3]

CScope_Impl::TTSE_Lock CScope_Impl::x_GetTSE_Lock	(	const CTSE_Lock &	lock,
		CDataSource_ScopeInfo &	ds
	)

Definition at line 1494 of file scope_impl.cpp.

References _ASSERT, CDataSource_ScopeInfo::GetScopeImpl(), and CDataSource_ScopeInfo::GetTSE_Lock().

x_GetTSE_Lock() [3/3]

CScope_Impl::TTSE_Lock CScope_Impl::x_GetTSE_Lock

(

const CTSE_ScopeInfo &

tse

)

Definition at line 1502 of file scope_impl.cpp.

References _ASSERT, and CTSE_ScopeInfo::GetScopeImpl().

x_GetTSESetWithAnnots() [1/4]

void CScope_Impl::x_GetTSESetWithAnnots ( TTSE_LockMatchSet &  lock, CBioseq_ScopeInfo &  binfo, const SAnnotSelector *  sel = 0  )

private

Definition at line 2318 of file scope_impl.cpp.

References CTSE_ScopeInfo::CanBeEdited(), CInitGuard::force, CBioseq_ScopeInfo::GetObjectInfo(), init(), m_AnnotChangeCounter, CBioseq_ScopeInfo::m_BioseqAnnotRef_Info, CBioseq_Info::m_IdChangeCounter, m_MutexPool, CBioseq_ScopeInfo::m_NABioseqAnnotRef_Info, x_GetAnnotRef_Info(), CScopeInfo_Base::x_GetTSE_ScopeInfo(), x_GetTSESetWithBioseqAnnots(), and x_LockMatchSet().

Referenced by GetTSESetWithAnnots(), and x_GetTSESetWithAnnots().

x_GetTSESetWithAnnots() [2/4]

void CScope_Impl::x_GetTSESetWithAnnots ( TTSE_LockMatchSet &  lock, TSeq_idMapValue &  info, const SAnnotSelector *  sel = 0  )

private

Definition at line 2354 of file scope_impl.cpp.

References CInitGuard::force, info, init(), m_AnnotChangeCounter, m_MutexPool, x_GetAnnotRef_Info(), x_GetTSESetWithAnnots(), and x_LockMatchSet().

x_GetTSESetWithAnnots() [3/4]

void CScope_Impl::x_GetTSESetWithAnnots ( TTSE_LockMatchSet &  lock, TTSE_MatchSet *  save_match, CBioseq_ScopeInfo &  binfo, const SAnnotSelector *  sel = 0  )

private

Definition at line 2381 of file scope_impl.cpp.

References x_GetTSESetWithBioseqAnnots().

x_GetTSESetWithAnnots() [4/4]

void CScope_Impl::x_GetTSESetWithAnnots ( TTSE_LockMatchSet &  lock, TTSE_MatchSet *  save_match, TSeq_idMapValue &  info, const SAnnotSelector *  sel = 0  )

private

Definition at line 2390 of file scope_impl.cpp.

References info, and x_GetTSESetWithOrphanAnnots().

x_GetTSESetWithBioseqAnnots() [1/2]

void CScope_Impl::x_GetTSESetWithBioseqAnnots ( TTSE_LockMatchSet &  lock, CBioseq_ScopeInfo &  binfo, const SAnnotSelector *  sel  )

private

Definition at line 2566 of file scope_impl.cpp.

References CDataSource_ScopeInfo::GetDataSource(), CTSE_ScopeInfo::GetDSInfo(), CBioseq_ScopeInfo::GetLock(), CDataSource::GetTSESetWithBioseqAnnots(), ct::sort(), x_AddTSESetWithAnnots(), and CScopeInfo_Base::x_GetTSE_ScopeInfo().

x_GetTSESetWithBioseqAnnots() [2/2]

void CScope_Impl::x_GetTSESetWithBioseqAnnots ( TTSE_LockMatchSet &  lock, TTSE_MatchSet *  save_match, CBioseq_ScopeInfo &  binfo, const SAnnotSelector *  sel  )

private

Definition at line 2506 of file scope_impl.cpp.

References CDataSource_ScopeInfo::GetDataSource(), CTSE_ScopeInfo::GetDSInfo(), GetKeepExternalAnnotsForEdit(), CBioseq_ScopeInfo::GetLock(), CDataSource::GetTSESetWithBioseqAnnots(), CDataSource::GetTSESetWithExternalAnnots(), CDataSource::GetTSESetWithOrphanAnnots(), CPriorityTree::HasSeveralNodes(), set< Key, Compare >::insert(), CPrefetchManager::IsActive(), ITERATE, m_setDataSrc, CTSE_ScopeInfo::m_TSE_Lock, ct::sort(), x_AddTSESetWithAnnots(), x_GetSynonyms(), CScopeInfo_Base::x_GetTSE_ScopeInfo(), and x_UpdateProcessedNAs().

Referenced by x_GetTSESetWithAnnots().

x_GetTSESetWithOrphanAnnots()

void CScope_Impl::x_GetTSESetWithOrphanAnnots ( TTSE_LockMatchSet &  lock, TTSE_MatchSet *  save_match, const TSeq_idSet &  ids, CBioseq_ScopeInfo *  binfo, const SAnnotSelector *  sel  )

private

Definition at line 2466 of file scope_impl.cpp.

References CTSE_ScopeInfo::GetDSInfo(), GetKeepExternalAnnotsForEdit(), CBioseq_ScopeInfo::GetLock(), CDataSource::GetTSESetWithExternalAnnots(), CDataSource::GetTSESetWithOrphanAnnots(), CPrefetchManager::IsActive(), CDataSource_ScopeInfo::m_EditDS, m_setDataSrc, CTSE_ScopeInfo::m_TSE_Lock, x_AddTSESetWithAnnots(), CScopeInfo_Base::x_GetTSE_ScopeInfo(), and x_UpdateProcessedNAs().

Referenced by x_GetTSESetWithAnnots().

x_InitBioseq_Info() [1/2]

bool CScope_Impl::x_InitBioseq_Info ( TSeq_idMapValue &  info, CBioseq_ScopeInfo &  bioseq_info  )

private

Definition at line 1789 of file scope_impl.cpp.

References _ASSERT, CInitGuard::force, info, init(), m_BioseqChangeCounter, m_MutexPool, and CScopeInfo_Base::x_GetScopeImpl().

x_InitBioseq_Info() [2/2]

CRef< CBioseq_ScopeInfo > CScope_Impl::x_InitBioseq_Info ( TSeq_idMapValue &  info, int  get_flag, SSeqMatch_Scope &  match  )

private

Definition at line 1769 of file scope_impl.cpp.

References CScope::eGetBioseq_Resolved, CInitGuard::force, info, init(), m_BioseqChangeCounter, m_MutexPool, match(), and x_ResolveSeq_id().

Referenced by GetTSESetWithAnnots(), x_AddSynonym(), x_FindBioseq_Info(), and x_GetBioseq_Info().

x_IsDummyTSE() [1/3]

bool CScope_Impl::x_IsDummyTSE ( const CTSE_Info &  tse, const CBioseq_Info &  seq  ) const

private

Definition at line 1571 of file scope_impl.cpp.

References CBioseq_Base_Info::GetParentSeq_entry_Info().

Referenced by RemoveTopLevelAnnot(), RemoveTopLevelBioseq(), and RemoveTopLevelBioseq_set().

x_IsDummyTSE() [2/3]

bool CScope_Impl::x_IsDummyTSE ( const CTSE_Info &  tse, const CBioseq_set_Info &  seqset  ) const

private

Definition at line 1581 of file scope_impl.cpp.

References CBioseq_Base_Info::GetParentSeq_entry_Info().

x_IsDummyTSE() [3/3]

bool CScope_Impl::x_IsDummyTSE ( const CTSE_Info &  tse, const CSeq_annot_Info &  annot  ) const

private

Definition at line 1591 of file scope_impl.cpp.

References CBioseq_Base_Info::GetAnnot(), CSeq_annot_Info::GetParentSeq_entry_Info(), CSeq_entry_Info::GetSet(), CBioseq_set_Info::IsEmptySeq_set(), CSeq_entry_Info::IsSet(), CBioseq_Base_Info::IsSetAnnot(), CBioseq_set_Info::IsSetClass(), CBioseq_set_Info::IsSetColl(), CBioseq_set_Info::IsSetDate(), CBioseq_Base_Info::IsSetDescr(), CBioseq_set_Info::IsSetId(), CBioseq_set_Info::IsSetLevel(), CBioseq_set_Info::IsSetRelease(), and CBioseq_set_Info::IsSetSeq_set().

x_LockMatchSet()

void CScope_Impl::x_LockMatchSet ( TTSE_LockMatchSet &  lock, const TTSE_MatchSet &  match  )

private

Definition at line 2433 of file scope_impl.cpp.

References first(), i, match(), ncbi::grid::netcache::search::fields::size, and x_GetTSE_Lock().

Referenced by x_GetTSESetWithAnnots().

x_MakeDummyTSE() [1/4]

CRef< CSeq_entry > CScope_Impl::x_MakeDummyTSE ( CBioseq &  seq ) const

private

Definition at line 1528 of file scope_impl.cpp.

References CSeq_entry_Base::SetSeq().

Referenced by AddBioseq(), AddSeq_annot(), AddSeq_submit(), AddSharedBioseq(), and AddSharedSeq_annot().

x_MakeDummyTSE() [2/4]

CRef< CSeq_entry > CScope_Impl::x_MakeDummyTSE ( CBioseq_set &  seqset ) const

private

Definition at line 1536 of file scope_impl.cpp.

References CSeq_entry_Base::SetSet().

x_MakeDummyTSE() [3/4]

CRef< CSeq_entry > CScope_Impl::x_MakeDummyTSE ( CSeq_annot &  annot ) const

private

Definition at line 1544 of file scope_impl.cpp.

References Ref(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

x_MakeDummyTSE() [4/4]

CRef< CSeq_entry > CScope_Impl::x_MakeDummyTSE ( CSeq_submit &  submit ) const

private

Definition at line 1553 of file scope_impl.cpp.

References CSeq_submit_Base::C_Data::e_Annots, CSeq_submit_Base::C_Data::e_Entrys, CSeq_submit_Base::C_Data::GetAnnots(), CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeq_submit_Base::C_Data::Which().

x_PopulateBioseq_HandleSet()

void CScope_Impl::x_PopulateBioseq_HandleSet ( const CSeq_entry_Handle &  tse, TBioseq_HandleSet &  handles, CSeq_inst::EMol  filter, TBioseqLevelFlag  level  )

private

Definition at line 2672 of file scope_impl.cpp.

References CSeq_entry_Handle::GetTSE_Handle(), info, ITERATE, m_ConfLock, x_GetBioseqHandle(), and CSeq_entry_Handle::x_GetInfo().

x_ReportNewDataConflict()

void CScope_Impl::x_ReportNewDataConflict ( const CSeq_id_Handle *  conflict_id = 0 )

private

Definition at line 939 of file scope_impl.cpp.

References CSeq_id_Handle::AsString(), Info(), and LOG_POST_X.

Referenced by x_ClearCacheOnNewData(), and x_ClearCacheOnNewDS().

x_ResolveSeq_id()

void CScope_Impl::x_ResolveSeq_id ( TSeq_idMapValue &  id, int  get_flag, SSeqMatch_Scope &  match  )

private

Definition at line 2196 of file scope_impl.cpp.

References _ASSERT, CBioseq_ScopeInfo, CScope::eGetBioseq_All, CTSE_ScopeInfo::GetBioseqInfo(), CTSE_ScopeInfo::GetScopeImpl(), CBioseq_ScopeInfo::HasBioseq(), m_BioseqChangeCounter, m_setDataSrc, match(), CBioseq_ScopeInfo::SetUnresolved(), x_FindBioseqInfo(), and CScopeInfo_Base::x_GetScopeImpl().

Referenced by x_InitBioseq_Info().

x_SelectSeq() [1/2]

void CScope_Impl::x_SelectSeq ( const CSeq_entry_EditHandle &  entry, const CBioseq_EditHandle &  bioseq  )

private

Definition at line 608 of file scope_impl.cpp.

References _ASSERT, CSeq_entry_Base::e_not_set, CSeq_entry_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), CBioseq_Handle::IsRemoved(), m_ConfLock, CTSE_ScopeInfo::SelectSeq(), CSeq_entry_Handle::Which(), x_ClearCacheOnNewData(), CSeq_entry_EditHandle::x_GetInfo(), CBioseq_EditHandle::x_GetScopeInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

x_SelectSeq() [2/2]

CBioseq_EditHandle CScope_Impl::x_SelectSeq ( const CSeq_entry_EditHandle &  entry, CRef< CBioseq_Info >  bioseq  )

private

Definition at line 566 of file scope_impl.cpp.

References _ASSERT, CSeq_entry_Base::e_not_set, CTSE_ScopeInfo::GetBioseqLock(), m_ConfLock, CBioseq_Handle::m_Info, CSeq_entry_Info::SelectSeq(), CSeq_entry_Handle::Which(), x_ClearCacheOnNewData(), CSeq_entry_EditHandle::x_GetInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), CScopeInfo_Base::x_GetTSE_ScopeInfo(), and x_UpdateHandleSeq_id().

Referenced by SelectSeq().

x_SelectSet() [1/2]

void CScope_Impl::x_SelectSet ( const CSeq_entry_EditHandle &  entry, const CBioseq_set_EditHandle &  seqset  )

private

Definition at line 627 of file scope_impl.cpp.

References _ASSERT, CSeq_entry_Base::e_not_set, CSeq_entry_Handle::GetTSE_Handle(), CTSE_Info_Object::GetTSE_Info(), CBioseq_set_Handle::IsRemoved(), m_ConfLock, CTSE_ScopeInfo::SelectSet(), CSeq_entry_Handle::Which(), x_ClearCacheOnNewData(), CSeq_entry_EditHandle::x_GetInfo(), CBioseq_set_EditHandle::x_GetScopeInfo(), CSeq_entry_EditHandle::x_GetScopeInfo(), and CTSE_Handle::x_GetScopeInfo().

x_SelectSet() [2/2]

CBioseq_set_EditHandle CScope_Impl::x_SelectSet ( const CSeq_entry_EditHandle &  entry, CRef< CBioseq_set_Info >  seqset  )

private

Definition at line 590 of file scope_impl.cpp.

References _ASSERT, CBioseq_set_EditHandle, CSeq_entry_Base::e_not_set, CSeq_entry_Handle::GetTSE_Handle(), m_ConfLock, CSeq_entry_Info::SelectSet(), CSeq_entry_Handle::Which(), x_ClearCacheOnNewData(), and CSeq_entry_EditHandle::x_GetInfo().

Referenced by SelectSet().

x_UpdateHandleSeq_id()

void CScope_Impl::x_UpdateHandleSeq_id ( CBioseq_Handle &  bh )

private

Definition at line 2103 of file scope_impl.cpp.

References CBioseq_Handle::GetId(), CBioseq_Handle::GetTSE_Handle(), ITERATE, CBioseq_Handle::m_Handle_Seq_id, x_GetBioseqHandleFromTSE(), and CBioseq_Handle::x_GetInfo().

Referenced by GetBioseqHandle(), x_GetBioseqHandle(), and x_SelectSeq().

x_UpdateProcessedNAs()

void CScope_Impl::x_UpdateProcessedNAs ( const SAnnotSelector *&  sel, unique_ptr< SAnnotSelector > &  sel_copy, CDataLoader::TProcessedNAs &  filter_nas, CDataLoader::TProcessedNAs &  processed_nas  )

private

Definition at line 2445 of file scope_impl.cpp.

References set< Key, Compare >::empty(), SAnnotSelector::ExcludeNamedAnnotAccession(), and set< Key, Compare >::insert().

Referenced by x_GetTSESetWithBioseqAnnots(), and x_GetTSESetWithOrphanAnnots().

Friends And Related Function Documentation

CAnnot_Collector

friend class CAnnot_Collector

friend

Definition at line 666 of file scope_impl.hpp.

CBioseq_CI

friend class CBioseq_CI

friend

Definition at line 665 of file scope_impl.hpp.

CBioseq_EditHandle

friend class CBioseq_EditHandle

friend

Definition at line 670 of file scope_impl.hpp.

Referenced by GetEditHandle().

CBioseq_Handle

friend class CBioseq_Handle

friend

Definition at line 667 of file scope_impl.hpp.

Referenced by AddBioseq(), AddSharedBioseq(), and x_GetBioseqHandleFromTSE().

CBioseq_ScopeInfo

friend class CBioseq_ScopeInfo

friend

Definition at line 682 of file scope_impl.hpp.

Referenced by x_GetBioseqHandlesSorted(), and x_ResolveSeq_id().

CBioseq_set_EditHandle

friend class CBioseq_set_EditHandle

friend

Definition at line 671 of file scope_impl.hpp.

Referenced by GetEditHandle(), and x_SelectSet().

CBioseq_set_Handle

friend class CBioseq_set_Handle

friend

Definition at line 668 of file scope_impl.hpp.

Referenced by GetBioseq_setHandle().

CDataSource

friend class CDataSource

friend

Definition at line 664 of file scope_impl.hpp.

CDataSource_ScopeInfo

friend class CDataSource_ScopeInfo

friend

Definition at line 678 of file scope_impl.hpp.

Referenced by x_GetDSInfo().

CHeapScope

friend class CHeapScope

friend

Definition at line 661 of file scope_impl.hpp.

CObjectManager

friend class CObjectManager

friend

Definition at line 662 of file scope_impl.hpp.

CPrefetchTokenOld_Impl

friend class CPrefetchTokenOld_Impl

friend

Definition at line 677 of file scope_impl.hpp.

CScope

friend class CScope

friend

Definition at line 660 of file scope_impl.hpp.

CScopeTransaction_Impl

friend class CScopeTransaction_Impl

friend

Definition at line 680 of file scope_impl.hpp.

Referenced by CreateTransaction().

CSeq_annot_CI

friend class CSeq_annot_CI

friend

Definition at line 675 of file scope_impl.hpp.

CSeq_annot_EditHandle

friend class CSeq_annot_EditHandle

friend

Definition at line 673 of file scope_impl.hpp.

Referenced by GetEditHandle(), and x_AttachAnnot().

CSeq_entry_EditHandle

friend class CSeq_entry_EditHandle

friend

Definition at line 672 of file scope_impl.hpp.

Referenced by GetEditHandle(), and x_AttachEntry().

CSeq_entry_Handle

friend class CSeq_entry_Handle

friend

Definition at line 669 of file scope_impl.hpp.

Referenced by AddSeq_entry(), AddSeq_submit(), AddSharedSeq_entry(), and GetSeq_entryHandle().

CSeqMap_CI

friend class CSeqMap_CI

friend

Definition at line 676 of file scope_impl.hpp.

CSeqVector

friend class CSeqVector

friend

Definition at line 663 of file scope_impl.hpp.

CTSE_CI

friend class CTSE_CI

friend

Definition at line 674 of file scope_impl.hpp.

CTSE_ScopeInfo

friend class CTSE_ScopeInfo

friend

Definition at line 679 of file scope_impl.hpp.

Member Data Documentation

m_AnnotChangeCounter

atomic<int> CScope_Impl::m_AnnotChangeCounter

private

Definition at line 657 of file scope_impl.hpp.

Referenced by x_ClearAnnotCache(), x_ClearCacheOnNewDS(), and x_GetTSESetWithAnnots().

m_BioseqChangeCounter

atomic<int> CScope_Impl::m_BioseqChangeCounter

private

Definition at line 656 of file scope_impl.hpp.

Referenced by x_ClearCacheOnEdit(), x_ClearCacheOnNewData(), x_ClearCacheOnNewDS(), x_GetBioseqHandlesSorted(), x_InitBioseq_Info(), and x_ResolveSeq_id().

m_ConfLock

TConfLock CScope_Impl::m_ConfLock

mutableprivate

Definition at line 649 of file scope_impl.hpp.

Referenced by AddBioseq(), AddDataLoader(), AddDefaults(), AddDS(), AddDSBefore(), AddScope(), AddSeq_annot(), AddSeq_entry(), AddSeq_submit(), AddSharedBioseq(), AddSharedSeq_annot(), AddSharedSeq_entry(), GetAccVer(), GetAccVers(), GetAllTSEs(), GetBioseq_setHandle(), GetBioseqHandle(), GetBulkIds(), GetCDDAnnots(), GetConstDS(), GetEditDataSource(), GetEditDS(), GetEditHandle(), GetFirstLoaderSource(), GetGi(), GetGis(), GetIds(), GetLabel(), GetLabels(), GetSeq_annotHandle(), GetSeq_entryHandle(), GetSeq_featHandle(), GetSequenceHash(), GetSequenceHashes(), GetSequenceLength(), GetSequenceLengths(), GetSequenceState(), GetSequenceStates(), GetSequenceType(), GetSequenceTypes(), GetSynonyms(), GetTaxId(), GetTaxIds(), GetTSESetWithAnnots(), RemoveAnnot(), RemoveDataLoader(), RemoveEntry(), RemoveFromHistory(), RemoveTopLevelSeqEntry(), ResetDataAndHistory(), ResetHistory(), ResetScope(), SelectNone(), SetKeepExternalAnnotsForEdit(), x_AttachAnnot(), x_AttachEntry(), x_GetBioseqHandleFromTSE(), x_GetBioseqHandlesSorted(), CAnnot_Collector::x_Initialize(), x_PopulateBioseq_HandleSet(), x_SelectSeq(), x_SelectSet(), and ~CScope_Impl().

m_DSMap

TDSMap CScope_Impl::m_DSMap

private

Definition at line 640 of file scope_impl.hpp.

Referenced by GetEditHandle(), RemoveDataLoader(), RemoveTopLevelSeqEntry(), ResetDataAndHistory(), ResetHistory(), ResetScope(), and x_GetDSInfo().

m_HeapScope

CScope* CScope_Impl::m_HeapScope

private

Definition at line 635 of file scope_impl.hpp.

Referenced by GetScope(), and CScope::~CScope().

m_KeepExternalAnnotsForEdit

bool CScope_Impl::m_KeepExternalAnnotsForEdit

private

Definition at line 658 of file scope_impl.hpp.

Referenced by GetKeepExternalAnnotsForEdit(), and SetKeepExternalAnnotsForEdit().

m_MutexPool

CInitMutexPool CScope_Impl::m_MutexPool

private

Definition at line 642 of file scope_impl.hpp.

Referenced by x_GetBioseqHandlesSorted(), x_GetSynonyms(), x_GetTSESetWithAnnots(), and x_InitBioseq_Info().

m_ObjMgr

CRef<CObjectManager> CScope_Impl::m_ObjMgr

private

Definition at line 637 of file scope_impl.hpp.

Referenced by AddDataLoader(), AddDefaults(), AddSharedBioseq(), AddSharedSeq_annot(), AddSharedSeq_entry(), CDataSource_ScopeInfo::DetachScope(), GetObjectManager(), RemoveDataLoader(), x_AttachToOM(), and x_DetachFromOM().

m_Seq_idMap

TSeq_idMap CScope_Impl::m_Seq_idMap

private

Definition at line 651 of file scope_impl.hpp.

Referenced by RemoveFromHistory(), ResetDataAndHistory(), ResetScope(), x_ClearAnnotCache(), x_ClearCacheOnEdit(), x_ClearCacheOnNewData(), x_ClearCacheOnNewDS(), x_ClearCacheOnRemoveData(), x_ClearCacheOnRemoveSeqId(), x_FindSeq_id_Info(), and x_GetSeq_id_Info().

m_Seq_idMapLock

TSeq_idMapLock CScope_Impl::m_Seq_idMapLock

mutableprivate

Definition at line 652 of file scope_impl.hpp.

Referenced by x_FindSeq_id_Info(), x_GetAnnotRef_Info(), and x_GetSeq_id_Info().

m_setDataSrc

CPriorityTree CScope_Impl::m_setDataSrc

private

Definition at line 638 of file scope_impl.hpp.

Referenced by AddDataLoader(), AddDefaults(), AddDS(), AddDSBefore(), AddScope(), GetAccVer(), GetAccVers(), GetAllTSEs(), GetBulkIds(), GetCDDAnnots(), GetConstDS(), GetEditDS(), GetEditHandle(), GetFirstLoaderSource(), GetGi(), GetGis(), GetIds(), GetLabel(), GetLabels(), GetSeq_featHandle(), GetSequenceHash(), GetSequenceHashes(), GetSequenceLength(), GetSequenceLengths(), GetSequenceState(), GetSequenceStates(), GetSequenceType(), GetSequenceTypes(), GetTaxId(), GetTaxIds(), RemoveDataLoader(), RemoveTopLevelSeqEntry(), ResetScope(), x_GetBioseq_Lock(), x_GetBioseq_set_Lock(), x_GetBioseqHandlesSorted(), x_GetSeq_annot_Lock(), x_GetSeq_entry_Lock(), x_GetTSE_Lock(), x_GetTSESetWithBioseqAnnots(), x_GetTSESetWithOrphanAnnots(), and x_ResolveSeq_id().

m_Transaction

IScopeTransaction_Impl* CScope_Impl::m_Transaction

private

Definition at line 654 of file scope_impl.hpp.

Referenced by CreateTransaction(), GetTransaction(), IsTransactionActive(), and SetActiveTransaction().

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The documentation for this class was generated from the following files:

• include/objmgr/impl/scope_impl.hpp
• src/objmgr/scope_impl.cpp