CTSE_Info Class Reference

Search Toolkit Book for CTSE_Info

#include <objmgr/impl/tse_info.hpp>

Inheritance diagram for CTSE_Info:

Collaboration diagram for CTSE_Info:

Classes
class	CLoadMutex
struct	SBaseTSE
struct	SFeatIdIndex
struct	SFeatIdInfo
struct	SIdAnnotInfo

Public Types
typedef CBlobIdKey	TBlobId
typedef CBioseq_Handle::TBioseqStateFlags	TBlobState
typedef int	TBlobVersion
typedef pair< TBlobState, TBlobVersion >	TBlobOrder
typedef CTSE_Handle::ETopLevelObjectType	ETopLevelObjectType
typedef map< TIntId, CBioseq_set_Info * >	TBioseq_sets
typedef CBioseq_Info *	TBioseqInfo
typedef map< CSeq_id_Handle, TBioseqInfo >	TBioseqs
typedef SIdAnnotObjs::TRange	TRange
typedef SIdAnnotObjs::TRangeMap	TRangeMap
typedef SIdAnnotObjs::TAnnotSet	TAnnotSet
typedef SIdAnnotObjs::TSNPSet	TSNPSet
typedef map< CSeq_id_Handle, SIdAnnotObjs >	TAnnotObjs
typedef map< CAnnotName, TAnnotObjs >	TNamedAnnotObjs
typedef set< CAnnotName >	TNames
typedef map< CSeq_id_Handle, SIdAnnotInfo >	TIdAnnotInfoMap
typedef int	TFeatIdInt
typedef string	TFeatIdStr
typedef CObject_id	TFeatId
typedef map< CSeqFeatData::ESubtype, SFeatIdIndex >	TFeatIdIndex
typedef pair< string, bool >	TLocusKey
typedef multimap< TLocusKey, CAnnotObject_Info * >	TLocusIndex
typedef vector< CSeq_id_Handle >	TSeqIds
typedef TSeqIds	TBioseqsIds
typedef CMutex	TAnnotLock
typedef TAnnotLock::TReadLockGuard	TAnnotLockReadGuard
typedef TAnnotLock::TWriteLockGuard	TAnnotLockWriteGuard
typedef vector< CAnnotObject_Info * >	TAnnotObjects
typedef pair< CConstRef< CSeq_annot_Info >, CTSE_Lock >	TSeq_annot_Lock
typedef pair< TSeq_annot_Lock, int >	TSeq_feat_Lock
Public Types inherited from CSeq_entry_Info
typedef CSeq_entry	TObject
typedef TObject::E_Choice	E_Choice
typedef CBioseq_set_Info	TSet
typedef CBioseq_Info	TSeq
typedef CSeq_descr	TDescr
typedef CSeq_descr::Tdata::const_iterator	TDesc_CI
typedef unsigned	TDescTypeMask
typedef vector< CRef< CSeq_annot_Info > >	TAnnot
typedef vector< CSeq_id_Handle >	TSeqIds
Public Types inherited from CTSE_Info_Object
enum	ENeedUpdateAux { kNeedUpdate_bits = 8 }
enum	ENeedUpdate {   fNeedUpdate_this = (1<<kNeedUpdate_bits)-1 , fNeedUpdate_children = fNeedUpdate_this<<kNeedUpdate_bits , fNeedUpdate_descr = 1<<0 , fNeedUpdate_annot = 1<<1 ,   fNeedUpdate_seq_data = 1<<2 , fNeedUpdate_core = 1<<3 , fNeedUpdate_assembly = 1<<4 , fNeedUpdate_bioseq = 1<<5 ,   fNeedUpdate_children_descr = fNeedUpdate_descr <<kNeedUpdate_bits , fNeedUpdate_children_annot = fNeedUpdate_annot <<kNeedUpdate_bits , fNeedUpdate_children_seq_data = fNeedUpdate_seq_data<<kNeedUpdate_bits , fNeedUpdate_children_core = fNeedUpdate_core <<kNeedUpdate_bits ,   fNeedUpdate_children_assembly = fNeedUpdate_assembly<<kNeedUpdate_bits , fNeedUpdate_children_bioseq = fNeedUpdate_bioseq <<kNeedUpdate_bits }
typedef map< CConstRef< CObject >, CRef< CObject > >	TObjectCopyMap
typedef int	TNeedUpdateFlags
typedef int	TChunkId
typedef vector< TChunkId >	TChunkIds
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
	CTSE_Info (void)
	CTSE_Info (const TBlobId &blob_id, TBlobVersion blob_version=-1)
	CTSE_Info (CSeq_entry &tse, TBlobState state=CBioseq_Handle::fState_none)
	CTSE_Info (CSeq_entry &tse, TBlobState blob_state, const TBlobId &blob_id, TBlobVersion blob_version=-1)
	CTSE_Info (const CTSE_Lock &tse)
virtual	~CTSE_Info (void)
bool	HasDataSource (void) const
CDataSource &	GetDataSource (void) const
bool	IsLocked (void) const
CConstRef< CSeq_entry >	GetCompleteTSE (void) const
CConstRef< CSeq_entry >	GetTSECore (void) const
const CTSE_Info &	GetTSE_Info (void) const
CTSE_Info &	GetTSE_Info (void)
CTSE_Info &	Assign (const CTSE_Lock &tse)
CTSE_Info &	Assign (const CTSE_Lock &tse, CRef< CSeq_entry > entry)
const TBlobId &	GetBlobId (void) const
TBlobVersion	GetBlobVersion (void) const
void	SetBlobVersion (TBlobVersion version)
TBlobState	GetBlobState (void) const
void	ResetBlobState (TBlobState state=CBioseq_Handle::fState_none)
void	SetBlobState (TBlobState state)
bool	IsDead (void) const
bool	IsUnavailable (void) const
TBlobState	GetBlobStateOrder (void) const
TBlobOrder	GetBlobOrder (void) const
ETopLevelObjectType	GetTopLevelObjectType () const
const CSerialObject *	GetTopLevelObjectPtr () const
void	SetTopLevelObject (ETopLevelObjectType type, CSerialObject *ptr)
void	SetTopLevelObjectType (ETopLevelObjectType type)
bool	IsTopLevelSeq_submit () const
const CSeq_submit &	GetTopLevelSeq_submit () const
const CSubmit_block &	GetTopLevelSubmit_block () const
CSubmit_block &	SetTopLevelSubmit_block () const
void	SetTopLevelSubmit_block (CSubmit_block &sub) const
const CAnnotName &	GetName (void) const
void	SetName (const CAnnotName &name)
void	SetSeq_entry (CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)
size_t	GetUsedMemory (void) const
void	SetUsedMemory (size_t size)
void	AddUsedMemory (size_t size)
bool	HasAnnot (const CAnnotName &name) const
bool	HasUnnamedAnnot (void) const
bool	HasNamedAnnot (const string &name) const
bool	HasMatchingAnnotIds (void) const
bool	OnlyGiAnnotIds (void) const
bool	ContainsBioseq (const CSeq_id_Handle &id) const
CConstRef< CBioseq_Info >	FindBioseq (const CSeq_id_Handle &id) const
CSeq_id_Handle	ContainsMatchingBioseq (const CSeq_id_Handle &id) const
CConstRef< CBioseq_Info >	FindMatchingBioseq (const CSeq_id_Handle &id) const
SSeqMatch_TSE	GetSeqMatch (const CSeq_id_Handle &id) const
CConstRef< CBioseq_Info >	GetSegSetMaster (void) const
CConstRef< CMasterSeqSegments >	GetMasterSeqSegments (void) const
virtual void	GetBioseqsIds (TSeqIds &ids) const
virtual void	GetAnnotIds (TSeqIds &ids) const
void	SetBioseqUpdater (CRef< CBioseqUpdater > updater)
void	UpdateAnnotIndex (const CSeq_id_Handle &id) const
void	UpdateAnnotIndex (void) const
void	UpdateAnnotIndex (const CTSE_Info_Object &object) const
void	UpdateAnnotIndex (void)
void	UpdateAnnotIndex (CTSE_Info_Object &object)
void	UpdateFeatIdIndex (CSeqFeatData::E_Choice type, EFeatIdType id_type) const
void	UpdateFeatIdIndex (CSeqFeatData::ESubtype subtype, EFeatIdType id_type) const
void	x_UpdateAnnotIndexContents (CTSE_Info &tse)
void	x_DSAttachContents (CDataSource &ds)
void	x_DSDetachContents (CDataSource &ds)
virtual void	x_SetDirtyAnnotIndexNoParent (void)
virtual void	x_ResetDirtyAnnotIndexNoParent (void)
void	x_GetRecords (const CSeq_id_Handle &id, bool bioseq) const
void	x_LoadChunk (TChunkId chunk_id) const
void	x_LoadChunks (const TChunkIds &chunk_ids) const
CTSE_Split_Info &	GetSplitInfo (void)
const CTSE_Split_Info &	GetSplitInfo (void) const
bool	HasSplitInfo (void) const
bool	x_NeedsDelayedMainChunk (void) const
void	x_LoadDelayedMainChunk (void) const
const CSeq_id_Handle &	GetRequestedId (void) const
void	SetRequestedId (const CSeq_id_Handle &requested_id) const
TAnnotLock &	GetAnnotLock (void) const
CRef< IEditSaver >	GetEditSaver () const
CBioseq_set_Info &	x_GetBioseq_set (int id)
CBioseq_Info &	x_GetBioseq (const CSeq_id_Handle &id)
CTSE_Info_Object *	x_FindBioObject (const CBioObjectId &uniq_id) const
SFeatIdIndex::TIndexInt &	x_GetFeatIdIndexInt (CSeqFeatData::ESubtype type)
SFeatIdIndex::TIndexStr &	x_GetFeatIdIndexStr (CSeqFeatData::ESubtype type)
bool	x_HasFeaturesWithId (CSeqFeatData::ESubtype subtype) const
void	x_AddFeaturesById (TAnnotObjects &objects, const SFeatIdIndex &index, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
void	x_AddFeaturesById (TAnnotObjects &objects, CSeqFeatData::ESubtype subtype, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
void	x_AddAllFeaturesById (TAnnotObjects &objects, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::E_Choice type, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::ESubtype subtype, TFeatIdInt id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
void	x_AddFeaturesById (TAnnotObjects &objects, const SFeatIdIndex &index, const TFeatIdStr &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
void	x_AddFeaturesById (TAnnotObjects &objects, CSeqFeatData::ESubtype subtype, const TFeatIdStr &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
void	x_AddAllFeaturesById (TAnnotObjects &objects, const TFeatIdStr &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::E_Choice type, const TFeatIdStr &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::ESubtype subtype, const TFeatIdStr &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::E_Choice type, const TFeatId &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesById (CSeqFeatData::ESubtype subtype, const TFeatId &id, EFeatIdType id_type, const CSeq_annot_Info *src_annot=0) const
TAnnotObjects	x_GetFeaturesByLocus (const string &locus, bool tag, const CSeq_annot_Info *src_annot=0) const
TSeq_feat_Lock	x_FindSeq_feat (const CSeq_id_Handle &loc_id, TSeqPos loc_pos, const CSeq_feat &feat) const
virtual string	GetDescription (void) const
CSeq_submit &	x_GetTopLevelSeq_submit () const
Public Member Functions inherited from CSeq_entry_Info
	CSeq_entry_Info (void)
	CSeq_entry_Info (const CSeq_entry_Info &info, TObjectCopyMap *copy_map)
	CSeq_entry_Info (CSeq_entry &entry)
virtual	~CSeq_entry_Info (void)
const CBioseq_set_Info &	GetParentBioseq_set_Info (void) const
CBioseq_set_Info &	GetParentBioseq_set_Info (void)
const CSeq_entry_Info &	GetParentSeq_entry_Info (void) const
CSeq_entry_Info &	GetParentSeq_entry_Info (void)
const CSeq_entry_Info &	GetXrefTSE () const
virtual const CBioObjectId &	GetBioObjectId (void) const
bool	HasNoSeq_entry (void) const
CConstRef< TObject >	GetCompleteSeq_entry (void) const
CConstRef< TObject >	GetSeq_entryCore (void) const
CConstRef< TObject >	GetSeq_entrySkeleton (void) const
E_Choice	Which (void) const
void	x_CheckWhich (E_Choice which) const
void	Reset (void)
bool	IsSet (void) const
const TSet &	GetSet (void) const
TSet &	SetSet (void)
TSet &	SelectSet (void)
TSet &	SelectSet (TSet &seqset)
TSet &	SelectSet (CBioseq_set &seqset)
bool	IsSeq (void) const
const TSeq &	GetSeq (void) const
TSeq &	SetSeq (void)
TSeq &	SelectSeq (TSeq &seq)
TSeq &	SelectSeq (CBioseq &seq)
bool	IsSetDescr (void) const
const TDescr &	GetDescr (void) const
void	ResetDescr (void)
void	SetDescr (TDescr &v)
TDescr &	SetDescr (void)
bool	AddSeqdesc (CSeqdesc &d)
CRef< CSeqdesc >	RemoveSeqdesc (const CSeqdesc &d)
CRef< CSeqdesc >	ReplaceSeqdesc (const CSeqdesc &old_desc, CSeqdesc &new_desc)
void	AddSeq_descr (const TDescr &v)
const CBioseq_Base_Info &	x_GetBaseInfo (void) const
bool	x_IsEndDesc (TDesc_CI iter) const
TDesc_CI	x_GetFirstDesc (TDescTypeMask types) const
TDesc_CI	x_GetNextDesc (TDesc_CI iter, TDescTypeMask types) const
CRef< CSeq_annot_Info >	AddAnnot (CSeq_annot &annot)
void	AddAnnot (CRef< CSeq_annot_Info > annot)
void	RemoveAnnot (CRef< CSeq_annot_Info > annot)
const TAnnot &	GetLoadedAnnot (void) const
CRef< CSeq_entry_Info >	AddEntry (CSeq_entry &entry, int index=-1)
void	AddEntry (CRef< CSeq_entry_Info > entry, int index=-1)
void	RemoveEntry (CRef< CSeq_entry_Info > entry)
void	x_ParentAttach (CBioseq_set_Info &parent)
void	x_ParentDetach (CBioseq_set_Info &parent)
virtual void	x_TSEAttachContents (CTSE_Info &tse_info)
virtual void	x_TSEDetachContents (CTSE_Info &tse_info)
void	UpdateAnnotIndex (void) const
void	x_SetBioseqChunkId (TChunkId chunk_id)
void	x_GetBioseqsIds (TSeqIds &ids) const
void	x_GetAnnotIds (TSeqIds &ids) const
virtual void	GetSeqAndAnnotIds (TSeqIds &seq_ids, TSeqIds &annot_ids) const
Public Member Functions inherited from CTSE_Info_Object
	CTSE_Info_Object (void)
	CTSE_Info_Object (const CTSE_Info_Object &src, TObjectCopyMap *copy_map)
virtual	~CTSE_Info_Object (void)
virtual void	SetBioObjectId (const CBioObjectId &id)
bool	HasDataSource (void) const
CDataSource &	GetDataSource (void) const
bool	HasTSE_Info (void) const
bool	BelongsToTSE_Info (const CTSE_Info &tse) const
const CTSE_Info &	GetTSE_Info (void) const
CTSE_Info &	GetTSE_Info (void)
bool	HasParent_Info (void) const
const CTSE_Info_Object &	GetBaseParent_Info (void) const
CTSE_Info_Object &	GetBaseParent_Info (void)
void	x_DSAttach (CDataSource &ds)
void	x_DSDetach (CDataSource &ds)
void	x_TSEAttach (CTSE_Info &tse)
void	x_TSEDetach (CTSE_Info &tse)
bool	x_DirtyAnnotIndex (void) const
void	x_SetDirtyAnnotIndex (void)
void	x_SetParentDirtyAnnotIndex (void)
void	x_ResetDirtyAnnotIndex (void)
void	x_UpdateAnnotIndex (CTSE_Info &tse)
bool	x_NeedUpdate (ENeedUpdate flag) const
void	x_SetNeedUpdate (TNeedUpdateFlags flags)
virtual void	x_SetNeedUpdateParent (TNeedUpdateFlags flags)
void	x_Update (TNeedUpdateFlags flags) const
void	x_UpdateComplete (void) const
void	x_UpdateCore (void) const
void	x_LoadChunk (TChunkId chunk_id) const
void	x_LoadChunks (const TChunkIds &chunk_ids) const
Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...
	CObject (const CObject &src)
	Copy constructor. More...
virtual	~CObject (void)
	Destructor. More...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

Private Types
enum	ELoadState { eNotLoaded , eLoaded , eDropped }
enum	ECacheState { eNotInCache , eInCache }
enum	EAnnotIdsFlags { fAnnotIds_NonGi = 1 << 0 , fAnnotIds_Matching = 1 << 1 }
typedef CSeq_entry_Info	TParent
typedef list< CRef< CTSE_Info > >	TTSE_Cache
typedef int	TAnnotIdsFlags
typedef map< CBioObjectId, CTSE_Info_Object * >	TBioObjects

Private Member Functions
void	x_Initialize (void)
void	x_Reset (void)
void	x_DSMapObject (CConstRef< TObject > obj, CDataSource &ds)
void	x_DSUnmapObject (CConstRef< TObject > obj, CDataSource &ds)
void	x_SetBioseqId (const CSeq_id_Handle &id, CBioseq_Info *info)
void	x_SetBioseqIds (CBioseq_Info *info)
void	x_ResetBioseqId (const CSeq_id_Handle &id, CBioseq_Info *info)
void	x_SetBioseq_setId (int key, CBioseq_set_Info *info)
void	x_ResetBioseq_setId (int key, CBioseq_set_Info *info)
TAnnotObjs &	x_SetAnnotObjs (const CAnnotName &name)
const TAnnotObjs *	x_GetAnnotObjs (const CAnnotName &name) const
const TAnnotObjs *	x_GetUnnamedAnnotObjs (void) const
void	x_RemoveAnnotObjs (const CAnnotName &name)
const SIdAnnotObjs *	x_GetIdObjects (const TAnnotObjs &objs, const CSeq_id_Handle &idh) const
const SIdAnnotObjs *	x_GetIdObjects (const CAnnotName &name, const CSeq_id_Handle &id) const
const SIdAnnotObjs *	x_GetUnnamedIdObjects (const CSeq_id_Handle &id) const
bool	x_HasIdObjects (const CSeq_id_Handle &id) const
pair< SIdAnnotObjs *, bool >	x_SetIdObjects (TAnnotObjs &objs, const CAnnotName &name, const CSeq_id_Handle &id)
pair< SIdAnnotObjs *, bool >	x_SetIdObjects (const CAnnotName &name, const CSeq_id_Handle &idh)
CRef< CSeq_annot_SNP_Info >	x_GetSNP_Info (const CConstRef< CSeq_annot > &annot)
bool	x_MapSNP_Table (const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)
void	x_UnmapSNP_Table (const CAnnotName &name, const CSeq_id_Handle &key, const CSeq_annot_SNP_Info &snp_info)
void	x_MapAnnotObject (TRangeMap &rangeMap, const SAnnotObject_Key &key, const SAnnotObject_Index &index)
bool	x_UnmapAnnotObject (TRangeMap &rangeMap, const CAnnotObject_Info &info, const SAnnotObject_Key &key)
void	x_MapAnnotObject (SIdAnnotObjs &objs, const SAnnotObject_Key &key, const SAnnotObject_Index &index)
bool	x_UnmapAnnotObject (SIdAnnotObjs &objs, const CAnnotObject_Info &info, const SAnnotObject_Key &key)
bool	x_MapAnnotObject (TAnnotObjs &objs, const CAnnotName &name, const SAnnotObject_Key &key, const SAnnotObject_Index &index)
bool	x_MapAnnotObject (const CAnnotName &name, const SAnnotObject_Key &key, const SAnnotObject_Index &index)
bool	x_UnmapAnnotObject (TAnnotObjs &objs, const CAnnotName &name, const CAnnotObject_Info &info, const SAnnotObject_Key &key)
void	x_UnmapAnnotObject (const CAnnotName &name, const CAnnotObject_Info &info, const SAnnotObject_Key &key)
void	x_UnmapAnnotObjects (const SAnnotObjectsIndex &infos)
void	x_MapFeatById (TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)
void	x_UnmapFeatById (TFeatIdInt id, CAnnotObject_Info &info, EFeatIdType type)
void	x_MapFeatById (const TFeatIdStr &id, CAnnotObject_Info &info, EFeatIdType type)
void	x_UnmapFeatById (const TFeatIdStr &id, CAnnotObject_Info &info, EFeatIdType type)
void	x_MapFeatById (const TFeatId &id, CAnnotObject_Info &info, EFeatIdType type)
void	x_UnmapFeatById (const TFeatId &id, CAnnotObject_Info &info, EFeatIdType type)
void	x_MapFeatByLocus (const string &locus, bool tag, CAnnotObject_Info &info)
void	x_UnmapFeatByLocus (const string &locus, bool tag, CAnnotObject_Info &info)
void	x_MapChunkByFeatType (CSeqFeatData::ESubtype subtype, TChunkId chunk_id)
void	x_MapChunkByFeatType (CSeqFeatData::E_Choice type, TChunkId chunk_id)
void	x_MapChunkByFeatType (const SAnnotTypeSelector &type, TChunkId chunk_id)
void	x_MapChunkByFeatId (TFeatIdInt id, CSeqFeatData::ESubtype subtype, TChunkId chunk_id, EFeatIdType type)
void	x_MapChunkByFeatId (TFeatIdInt id, CSeqFeatData::E_Choice type, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (TFeatIdInt id, const SAnnotTypeSelector &type, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatIdStr &id, CSeqFeatData::ESubtype subtype, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatIdStr &id, CSeqFeatData::E_Choice type, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatIdStr &id, const SAnnotTypeSelector &type, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatId &id, CSeqFeatData::ESubtype subtype, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatId &id, CSeqFeatData::E_Choice type, TChunkId chunk_id, EFeatIdType id_type)
void	x_MapChunkByFeatId (const TFeatId &id, const SAnnotTypeSelector &type, TChunkId chunk_id, EFeatIdType id_type)
void	x_IndexSeqTSE (const CSeq_id_Handle &id)
void	x_UnindexSeqTSE (const CSeq_id_Handle &id)
bool	x_IndexAnnotTSE (const CAnnotName &name, const CSeq_id_Handle &id)
void	x_UnindexAnnotTSE (const CAnnotName &name, const CSeq_id_Handle &id)
void	x_DoUpdate (TNeedUpdateFlags flags)
CBioObjectId	x_IndexBioseq (CBioseq_Info *)
CBioObjectId	x_IndexBioseq_set (CBioseq_set_Info *)
CBioObjectId	x_RegisterBioObject (CTSE_Info_Object &info)
void	x_UnregisterBioObject (CTSE_Info_Object &info)
	CTSE_Info (const CTSE_Info &)
CTSE_Info &	operator= (const CTSE_Info &)

Private Attributes
CDataSource *	m_DataSource
TBlobId	m_BlobId
TBlobVersion	m_BlobVersion
TBlobState	m_BlobState
ETopLevelObjectType	m_TopLevelObjectType
CRef< CSerialObject >	m_TopLevelObjectPtr
CAnnotName	m_Name
size_t	m_UsedMemory
atomic< ELoadState >	m_LoadState
ECacheState	m_CacheState
TTSE_Cache::iterator	m_CachePosition
CAtomicCounter_WithAutoInit	m_LockCounter
CRef< CLoadMutex >	m_LoadMutex
TBioseq_sets	m_Bioseq_sets
TBioseqs	m_Bioseqs
TBioseq_sets	m_Removed_Bioseq_sets
TBioseqs	m_Removed_Bioseqs
CFastMutex	m_BioseqsMutex
CRef< CTSE_Split_Info >	m_Split
CRef< CTSE_SetObjectInfo >	m_SetObjectInfo
TNamedAnnotObjs	m_NamedAnnotObjs
TIdAnnotInfoMap	m_IdAnnotInfoMap
TFeatIdIndex	m_FeatIdIndex
TLocusIndex	m_LocusIndex
TAnnotLock	m_AnnotLock
CSeq_id_Handle	m_RequestedId
TAnnotIdsFlags	m_AnnotIdsFlags
unique_ptr< SBaseTSE >	m_BaseTSE
CRef< IEditSaver >	m_EditSaver
int	m_InternalBioObjNumber
TBioObjects	m_BioObjects
bool	m_MasterSeqSegmentsLoaded
CConstRef< CMasterSeqSegments >	m_MasterSeqSegments
CRef< CBioseqUpdater >	m_BioseqUpdater

Friends
class	CTSE_Guard
class	CDataSource
class	CScope_Impl
class	CTSE_ScopeInfo
class	CDataLoader
class	CAnnot_Collector
class	CSeq_entry_Info
class	CSeq_annot_Info
class	CBioseq_Info
class	CBioseq_set_Info
class	CTSE_Info_Object
class	CTSE_Chunk_Info
class	CTSE_Split_Info
class	CSeq_annot_SNP_Info
class	ITSE_Assigner
class	CTSE_Default_Assigner
class	CSeq_annot_Finder
class	CTSEAnnotObjectMapper
class	CTSE_Lock
class	CTSE_LoadLock
class	CTSE_LoadLockGuard

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 CSeq_entry_Info
void	x_AttachContents (void)
void	x_DetachContents (void)
TObject &	x_GetObject (void)
const TObject &	x_GetObject (void) const
void	x_SetObject (TObject &obj)
void	x_SetObject (const CSeq_entry_Info &info, TObjectCopyMap *copy_map)
void	x_Select (CSeq_entry::E_Choice which, CBioseq_Base_Info *contents)
void	x_Select (CSeq_entry::E_Choice which, CRef< CBioseq_Base_Info > contents)
void	x_DSMapObject (CConstRef< TObject > obj, CDataSource &ds)
void	x_DSUnmapObject (CConstRef< TObject > obj, CDataSource &ds)
void	x_UpdateSkeleton () const
void	x_Update (TNeedUpdateFlags flags) const
void	x_SetNeedUpdateContents (TNeedUpdateFlags flags)
CSeq_entry_Info &	operator= (const CSeq_entry_Info &)
Protected Member Functions inherited from CTSE_Info_Object
void	x_BaseParentAttach (CTSE_Info_Object &parent)
void	x_BaseParentDetach (CTSE_Info_Object &parent)
void	x_AttachObject (CTSE_Info_Object &object)
void	x_DetachObject (CTSE_Info_Object &object)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...
Static Protected Member Functions inherited from CSeq_entry_Info
static CRef< TObject >	sx_ShallowCopy (TObject &obj)
Protected Attributes inherited from CSeq_entry_Info
CRef< TObject >	m_Object
E_Choice	m_Which
CRef< CBioseq_Base_Info >	m_Contents

Detailed Description

Definition at line 182 of file tse_info.hpp.

Member Typedef Documentation

ETopLevelObjectType

typedef CTSE_Handle::ETopLevelObjectType CTSE_Info::ETopLevelObjectType

Definition at line 214 of file tse_info.hpp.

TAnnotIdsFlags

typedef int CTSE_Info::TAnnotIdsFlags

private

Definition at line 755 of file tse_info.hpp.

TAnnotLock

typedef CMutex CTSE_Info::TAnnotLock

Definition at line 409 of file tse_info.hpp.

TAnnotLockReadGuard

typedef TAnnotLock::TReadLockGuard CTSE_Info::TAnnotLockReadGuard

Definition at line 410 of file tse_info.hpp.

TAnnotLockWriteGuard

typedef TAnnotLock::TWriteLockGuard CTSE_Info::TAnnotLockWriteGuard

Definition at line 411 of file tse_info.hpp.

TAnnotObjects

typedef vector<CAnnotObject_Info*> CTSE_Info::TAnnotObjects

Definition at line 426 of file tse_info.hpp.

TAnnotObjs

typedef map<CSeq_id_Handle, SIdAnnotObjs> CTSE_Info::TAnnotObjs

Definition at line 305 of file tse_info.hpp.

TAnnotSet

typedef SIdAnnotObjs::TAnnotSet CTSE_Info::TAnnotSet

Definition at line 302 of file tse_info.hpp.

TBioObjects

typedef map<CBioObjectId, CTSE_Info_Object*> CTSE_Info::TBioObjects

private

Definition at line 775 of file tse_info.hpp.

TBioseq_sets

typedef map<TIntId, CBioseq_set_Info*> CTSE_Info::TBioseq_sets

Definition at line 296 of file tse_info.hpp.

TBioseqInfo

typedef CBioseq_Info* CTSE_Info::TBioseqInfo

Definition at line 297 of file tse_info.hpp.

TBioseqs

typedef map<CSeq_id_Handle, TBioseqInfo> CTSE_Info::TBioseqs

Definition at line 298 of file tse_info.hpp.

TBioseqsIds

typedef TSeqIds CTSE_Info::TBioseqsIds

Definition at line 352 of file tse_info.hpp.

TBlobId

typedef CBlobIdKey CTSE_Info::TBlobId

Definition at line 210 of file tse_info.hpp.

TBlobOrder

typedef pair<TBlobState, TBlobVersion> CTSE_Info::TBlobOrder

Definition at line 213 of file tse_info.hpp.

TBlobState

typedef CBioseq_Handle::TBioseqStateFlags CTSE_Info::TBlobState

Definition at line 211 of file tse_info.hpp.

TBlobVersion

typedef int CTSE_Info::TBlobVersion

Definition at line 212 of file tse_info.hpp.

TFeatId

typedef CObject_id CTSE_Info::TFeatId

Definition at line 337 of file tse_info.hpp.

TFeatIdIndex

typedef map<CSeqFeatData::ESubtype, SFeatIdIndex> CTSE_Info::TFeatIdIndex

Definition at line 347 of file tse_info.hpp.

TFeatIdInt

typedef int CTSE_Info::TFeatIdInt

Definition at line 335 of file tse_info.hpp.

TFeatIdStr

typedef string CTSE_Info::TFeatIdStr

Definition at line 336 of file tse_info.hpp.

TIdAnnotInfoMap

typedef map<CSeq_id_Handle, SIdAnnotInfo> CTSE_Info::TIdAnnotInfoMap

Definition at line 313 of file tse_info.hpp.

TLocusIndex

typedef multimap<TLocusKey, CAnnotObject_Info*> CTSE_Info::TLocusIndex

Definition at line 349 of file tse_info.hpp.

TLocusKey

typedef pair<string, bool> CTSE_Info::TLocusKey

Definition at line 348 of file tse_info.hpp.

TNamedAnnotObjs

typedef map<CAnnotName, TAnnotObjs> CTSE_Info::TNamedAnnotObjs

Definition at line 306 of file tse_info.hpp.

TNames

typedef set<CAnnotName> CTSE_Info::TNames

Definition at line 307 of file tse_info.hpp.

TParent

typedef CSeq_entry_Info CTSE_Info::TParent

private

Definition at line 184 of file tse_info.hpp.

TRange

typedef SIdAnnotObjs::TRange CTSE_Info::TRange

Definition at line 300 of file tse_info.hpp.

TRangeMap

typedef SIdAnnotObjs::TRangeMap CTSE_Info::TRangeMap

Definition at line 301 of file tse_info.hpp.

TSeq_annot_Lock

typedef pair<CConstRef<CSeq_annot_Info>, CTSE_Lock> CTSE_Info::TSeq_annot_Lock

Definition at line 483 of file tse_info.hpp.

TSeq_feat_Lock

typedef pair<TSeq_annot_Lock, int> CTSE_Info::TSeq_feat_Lock

Definition at line 484 of file tse_info.hpp.

TSeqIds

typedef vector<CSeq_id_Handle> CTSE_Info::TSeqIds

Definition at line 351 of file tse_info.hpp.

TSNPSet

typedef SIdAnnotObjs::TSNPSet CTSE_Info::TSNPSet

Definition at line 303 of file tse_info.hpp.

TTSE_Cache

typedef list< CRef<CTSE_Info> > CTSE_Info::TTSE_Cache

private

Definition at line 715 of file tse_info.hpp.

Member Enumeration Documentation

EAnnotIdsFlags

enum CTSE_Info::EAnnotIdsFlags

private

Enumerator
fAnnotIds_NonGi
fAnnotIds_Matching

Definition at line 751 of file tse_info.hpp.

ECacheState

enum CTSE_Info::ECacheState

private

Enumerator
eNotInCache
eInCache

Definition at line 708 of file tse_info.hpp.

ELoadState

enum CTSE_Info::ELoadState

private

Enumerator
eNotLoaded
eLoaded
eDropped

Definition at line 703 of file tse_info.hpp.

Constructor & Destructor Documentation

CTSE_Info() [1/6]

CTSE_Info::CTSE_Info ( void  )

explicit

Definition at line 126 of file tse_info.cpp.

References x_Initialize(), and CTSE_Info_Object::x_TSEAttach().

CTSE_Info() [2/6]

CTSE_Info::CTSE_Info ( const TBlobId &  blob_id, TBlobVersion  blob_version = -1  )

explicit

Definition at line 136 of file tse_info.cpp.

References m_BlobId, m_BlobVersion, x_Initialize(), and CTSE_Info_Object::x_TSEAttach().

CTSE_Info() [3/6]

CTSE_Info::CTSE_Info ( CSeq_entry &  tse, TBlobState  state = CBioseq_Handle::fState_none  )

explicit

Definition at line 170 of file tse_info.cpp.

References eLoaded, m_BlobState, m_LoadState, SetSeq_entry(), x_Initialize(), and CTSE_Info_Object::x_TSEAttach().

CTSE_Info() [4/6]

CTSE_Info::CTSE_Info ( CSeq_entry &  tse, TBlobState  blob_state, const TBlobId &  blob_id, TBlobVersion  blob_version = -1  )

explicit

Definition at line 150 of file tse_info.cpp.

References eLoaded, m_BlobId, m_BlobState, m_BlobVersion, m_LoadState, SetSeq_entry(), x_Initialize(), and CTSE_Info_Object::x_TSEAttach().

CTSE_Info() [5/6]

CTSE_Info::CTSE_Info ( const CTSE_Lock &  tse )

explicit

Definition at line 186 of file tse_info.cpp.

References eLoaded, CTSE_Info_Object::fNeedUpdate_children_bioseq, CTSE_Info_Object::fNeedUpdate_children_seq_data, CTSE_Split_Info::GetAssigner(), CDataSource::GetDataLoader(), GetDataSource(), CDataLoader::GetEditSaver(), HasDataSource(), m_BaseTSE, m_BioseqUpdater, m_BlobId, m_BlobState, m_EditSaver, m_LoadState, m_Name, m_Split, m_TopLevelObjectType, m_UsedMemory, CRef< C, Locker >::Reset(), x_Initialize(), CSeq_entry_Info::x_SetObject(), CTSE_Info_Object::x_TSEAttach(), CTSE_Split_Info::x_TSEAttach(), and CSeq_entry_Info::x_Update().

~CTSE_Info()

CTSE_Info::~CTSE_Info ( void  )

virtual

Definition at line 223 of file tse_info.cpp.

References _ASSERT, CAtomicCounter::Get(), m_DataSource, m_LockCounter, m_Split, and CTSE_Split_Info::x_TSEDetach().

CTSE_Info() [6/6]

CTSE_Info::CTSE_Info ( const CTSE_Info &  )

private

Member Function Documentation

AddUsedMemory()

void CTSE_Info::AddUsedMemory

(

size_t

size

)

Definition at line 345 of file tse_info.cpp.

References m_UsedMemory, and ncbi::grid::netcache::search::fields::size.

Referenced by CTSE_Split_Info::x_AddUsedMemory().

Assign() [1/2]

CTSE_Info & CTSE_Info::Assign

(

const CTSE_Lock &

tse

)

Definition at line 232 of file tse_info.cpp.

References CTSE_Split_Info::GetAssigner(), m_BlobState, CSeq_entry_Info::m_Contents, m_Name, m_Split, m_TopLevelObjectType, m_UsedMemory, NULL, CRef< C, Locker >::Reset(), CSeq_entry_Info::x_SetObject(), and CTSE_Split_Info::x_TSEAttach().

Referenced by CDataLoaderPatcher::x_PatchLock().

Assign() [2/2]

CTSE_Info & CTSE_Info::Assign	(	const CTSE_Lock &	tse,
		CRef< CSeq_entry >	entry
	)

Definition at line 255 of file tse_info.cpp.

References CTSE_Split_Info::GetAssigner(), m_BlobState, m_Name, m_Split, m_TopLevelObjectType, m_UsedMemory, CRef< C, Locker >::Reset(), SetSeq_entry(), and CTSE_Split_Info::x_TSEAttach().

ContainsBioseq()

bool CTSE_Info::ContainsBioseq

(

const CSeq_id_Handle &

id

)

const

Definition at line 724 of file tse_info.cpp.

References CTSE_Split_Info::ContainsBioseq(), map_checker< Container >::end(), map_checker< Container >::find(), m_Bioseqs, m_BioseqsMutex, and m_Split.

Referenced by CTSE_ScopeInfo::ContainsBioseq(), and ContainsMatchingBioseq().

ContainsMatchingBioseq()

CSeq_id_Handle CTSE_Info::ContainsMatchingBioseq

(

const CSeq_id_Handle &

id

)

const

Definition at line 740 of file tse_info.cpp.

References ContainsBioseq(), eAllowWeakMatch, and ITERATE.

Referenced by CTSE_ScopeInfo::ContainsMatchingBioseq(), CDataSource::x_AddTSEOrphanAnnots(), x_IndexAnnotTSE(), and CAnnot_Collector::x_SearchTSE2().

FindBioseq()

CConstRef< CBioseq_Info > CTSE_Info::FindBioseq

(

const CSeq_id_Handle &

id

)

const

Definition at line 760 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_Bioseqs, m_BioseqsMutex, and x_GetRecords().

Referenced by CDataSource_ScopeInfo::BestResolve(), CTSE_ScopeInfo::GetBioseqLock(), GetSeqMatch(), CSeqMap::x_GetBioseqInfo(), and CDataSource::x_GetSeqMatch().

FindMatchingBioseq()

CConstRef< CBioseq_Info > CTSE_Info::FindMatchingBioseq

(

const CSeq_id_Handle &

id

)

const

Definition at line 776 of file tse_info.cpp.

References GetSeqMatch(), and SSeqMatch_TSE::m_Bioseq.

Referenced by CMasterSeqSegments::CMasterSeqSegments(), CReader::LoadSeq_idTaxId(), CReader::LoadSequenceLength(), CReader::LoadSequenceType(), CBioseq_Info::x_CalcBioseqLength(), and CSeqMap::x_ResolveSegmentLength().

GetAnnotIds()

void CTSE_Info::GetAnnotIds ( TSeqIds &  ids ) const

virtual

Reimplemented from CSeq_entry_Info.

Definition at line 709 of file tse_info.cpp.

References GetAnnotLock(), ITERATE, m_NamedAnnotObjs, and UpdateAnnotIndex().

GetAnnotLock()

CTSE_Info::TAnnotLock & CTSE_Info::GetAnnotLock ( void  ) const

inline

Definition at line 914 of file tse_info.hpp.

References m_AnnotLock.

Referenced by GetAnnotIds(), HasAnnot(), CTSE_Default_Assigner::UpdateAnnotIndex(), UpdateAnnotIndex(), CDataSource::x_AddTSEBioseqAnnots(), CDataSource::x_AddTSEOrphanAnnots(), CSeq_annot_Finder::x_Find(), CSeq_annot_Info::x_MapAnnotObject(), CAnnot_Collector::x_SearchRange(), CAnnot_Collector::x_SearchTSE2(), CSeq_annot_Info::x_UnmapAnnotObject(), and CTSE_Chunk_Info::x_UpdateAnnotIndex().

GetBioseqsIds()

void CTSE_Info::GetBioseqsIds ( TSeqIds &  ids ) const

virtual

Reimplemented from CSeq_entry_Info.

Definition at line 691 of file tse_info.cpp.

References CTSE_Split_Info::GetBioseqsIds(), ITERATE, m_Bioseqs, m_BioseqsMutex, and m_Split.

Referenced by CWGSMasterSupport::AddWGSMaster(), and CTSE_ScopeInfo::SUnloadedInfo::SUnloadedInfo().

GetBlobId()

const CTSE_Info::TBlobId & CTSE_Info::GetBlobId ( void  ) const

inline

Definition at line 907 of file tse_info.hpp.

References m_BlobId.

Referenced by CDataSource_ScopeInfo::AttachTSE(), CTSE_ScopeInfo::CTSE_ScopeInfo(), CPSGDataLoader::DropTSE(), CTSE_ScopeInfo::GetBlobId(), CSeq_entry_Handle::GetBlobId(), CTSE_Handle::GetBlobId(), GetDescription(), CGBDataLoader::GetRealBlobId(), GetSplitInfo(), CDataSource_ScopeInfo::GetTSE_Lock(), CPSGL_Blob_Processor::HasChunksToAssign(), CTSE_ScopeInfo::ReplaceTSE(), CLDS2_DataLoader::ResolveConflict(), CLoadLockSetter::SetLoaded(), SPsgBlobInfo::SPsgBlobInfo(), CPSGL_Blob_Processor::TSE_ToOM(), UpdateOMBlobId(), CDataLoaderPatcher::x_ApplyPatches(), x_CreateEmptyLocalCDDEntry(), CDataLoaderPatcher::x_IsPatchNeeded(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

GetBlobOrder()

CTSE_Info::TBlobOrder CTSE_Info::GetBlobOrder ( void  ) const

inline

Definition at line 884 of file tse_info.hpp.

References GetBlobStateOrder(), and GetBlobVersion().

Referenced by CTSE_ScopeInfo::GetBlobOrder(), and CTSE_LockSet::IsBetter().

GetBlobState()

CTSE_Info::TBlobState CTSE_Info::GetBlobState ( void  ) const

inline

Definition at line 834 of file tse_info.hpp.

References m_BlobState.

Referenced by CLoadLockSetter::GetBlobState(), CWGSDataLoader_Impl::GetRecordsOnce(), CBioseq_Handle::GetState(), CBioseq_ScopeInfo::x_AttachTSE(), and CGBDataLoader_Native::x_GetRecords().

GetBlobStateOrder()

CTSE_Info::TBlobState CTSE_Info::GetBlobStateOrder ( void  ) const

inline

Definition at line 869 of file tse_info.hpp.

References CBioseq_Handle::fState_dead, CBioseq_Handle::fState_no_data, and m_BlobState.

Referenced by GetBlobOrder().

GetBlobVersion()

CTSE_Info::TBlobVersion CTSE_Info::GetBlobVersion ( void  ) const

inline

Definition at line 877 of file tse_info.hpp.

References m_BlobVersion.

Referenced by GetBlobOrder(), CSeq_entry_Handle::GetBlobVersion(), CLoadLockBlob::GetKnownBlobVersion(), and GetSplitInfo().

GetCompleteTSE()

CConstRef< CSeq_entry > CTSE_Info::GetCompleteTSE

(

void

)

const

Definition at line 551 of file tse_info.cpp.

References CSeq_entry_Info::GetCompleteSeq_entry().

Referenced by CSplitCacheApp::ProcessBlob().

GetDataSource()

CDataSource & CTSE_Info::GetDataSource ( void  ) const

inline

Definition at line 805 of file tse_info.hpp.

References _ASSERT, and m_DataSource.

Referenced by CDataSource_ScopeInfo::AttachTSE(), CGraphUtils::CalcGraphLevels(), CTSE_Info(), CTSE_Handle::GetDataLoader(), CTSE_Info_Object::GetDataSource(), CGBDataLoader::GetRealBlobId(), CTSE_Default_Assigner::LoadAnnot(), CTSE_Default_Assigner::LoadBioseq(), CTSE_Default_Assigner::LoadChunkBioseqs(), CTSE_ScopeInfo::SetEditTSE(), SetSeq_entry(), CTSE_Default_Assigner::UpdateAnnotIndex(), UpdateAnnotIndex(), x_IndexAnnotTSE(), x_IndexSeqTSE(), CDataSource::x_ReleaseLastTSELock(), x_ResetDirtyAnnotIndexNoParent(), x_SetBioseqIds(), x_SetDirtyAnnotIndexNoParent(), x_UnindexAnnotTSE(), x_UnindexSeqTSE(), and CTSE_Chunk_Info::x_UpdateAnnotIndex().

GetDescription()

string CTSE_Info::GetDescription ( void  ) const

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 2049 of file tse_info.cpp.

References GetBlobId(), CAnnotName::GetName(), GetName(), m_BlobId, NStr::PtrToString(), and CBlobIdKey::ToString().

Referenced by CSeq_annot_Info::GetDescription(), and CTSE_ScopeInfo::ReplaceTSE().

GetEditSaver()

CRef< IEditSaver > CTSE_Info::GetEditSaver ( ) const

inline

Definition at line 949 of file tse_info.hpp.

References m_EditSaver.

Referenced by GetEditSaver().

GetMasterSeqSegments()

CConstRef< CMasterSeqSegments > CTSE_Info::GetMasterSeqSegments

(

void

)

const

Definition at line 803 of file tse_info.cpp.

References ERR_POST, GetSegSetMaster(), m_AnnotLock, m_MasterSeqSegments, and m_MasterSeqSegmentsLoaded.

Referenced by CScope_Impl::GetBioseqHandle(), CSeq_annot_Info::x_InitAlignKeys(), CSeq_annot_Info::x_InitFeatKeys(), CSeq_annot_Info::x_InitFeatTableKeys(), CSeq_annot_Info::x_InitGraphKeys(), CSeq_annot_Info::x_InitLocsKeys(), CSeq_annot_Info::x_MapAnnotObject(), and CBioseq_Base_Info::x_UpdateAnnotIndexContents().

GetName()

const CAnnotName & CTSE_Info::GetName ( void  ) const

inline

Definition at line 893 of file tse_info.hpp.

References m_Name.

Referenced by GetDescription(), CLoadLockSetter::SetLoaded(), CTSE_Chunk_Info::x_UpdateAnnotIndexContents(), and CSeq_annot_Info::x_UpdateName().

GetRequestedId()

const CSeq_id_Handle & CTSE_Info::GetRequestedId ( void  ) const

inline

Definition at line 921 of file tse_info.hpp.

References m_RequestedId.

GetSegSetMaster()

CConstRef< CBioseq_Info > CTSE_Info::GetSegSetMaster

(

void

)

const

Definition at line 783 of file tse_info.cpp.

References ConstRef(), CBioseq_set_Base::eClass_segset, first(), CBioseq_set_Info::GetClass(), and CBioseq_set_Info::GetFirstEntry().

Referenced by CScope_Impl::GetBioseqHandle(), and GetMasterSeqSegments().

GetSeqMatch()

SSeqMatch_TSE CTSE_Info::GetSeqMatch

(

const CSeq_id_Handle &

id

)

const

Definition at line 824 of file tse_info.cpp.

References eAllowWeakMatch, FindBioseq(), ITERATE, SSeqMatch_TSE::m_Bioseq, and SSeqMatch_TSE::m_Seq_id.

Referenced by FindMatchingBioseq().

GetSplitInfo() [1/2]

CTSE_Split_Info & CTSE_Info::GetSplitInfo

(

void

)

Definition at line 1395 of file tse_info.cpp.

References _ASSERT, CTSE_Split_Info, eNotLoaded, GetBlobId(), GetBlobVersion(), m_LoadState, m_Split, and CTSE_Split_Info::x_TSEAttach().

Referenced by CWGSMasterSupport::AddWGSMaster(), CPSGL_Blob_Processor::AssignChunks(), CPSGL_Blob_Processor::Chunk_ToOM(), CLoadLockSetter::GetSplitInfo(), CLoadLockBlob::GetSplitInfo(), CSNPSeqInfo::LoadAnnotBlob(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CWGSFileInfo::LoadBlob(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CProcessor_ID2::ProcessData(), CPSGL_NA_Processor::ProcessItemSlow(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), SetSeq_entry(), CPSGL_Blob_Processor::TSE_ToOM(), CPSGDataLoader_Impl::x_CheckAnnotCache(), x_CreateLocalCDDEntry(), CDataSource::x_IndexSeqTSELocked(), CBlastDbDataLoader::x_LoadData(), and CLDS2_DataLoader::x_LoadTSE().

GetSplitInfo() [2/2]

const CTSE_Split_Info & CTSE_Info::GetSplitInfo

(

void

)

const

Definition at line 1388 of file tse_info.cpp.

References _ASSERT, HasSplitInfo(), and m_Split.

GetTopLevelObjectPtr()

const CSerialObject * CTSE_Info::GetTopLevelObjectPtr

(

void

)

const

Definition at line 2072 of file tse_info.cpp.

References CRef< C, Locker >::GetPointerOrNull(), and m_TopLevelObjectPtr.

GetTopLevelObjectType()

CTSE_Info::ETopLevelObjectType CTSE_Info::GetTopLevelObjectType

(

void

)

const

Definition at line 2066 of file tse_info.cpp.

References m_TopLevelObjectType.

Referenced by CTSE_Handle::GetTopLevelObjectType(), and IsTopLevelSeq_submit().

GetTopLevelSeq_submit()

const CSeq_submit & CTSE_Info::GetTopLevelSeq_submit

(

)

const

Definition at line 2108 of file tse_info.cpp.

References CSeq_submit_Base::C_Data::e_Annots, CSeq_submit_Base::C_Data::e_Entrys, set< Key, Compare >::empty(), CSeq_submit_Base::GetData(), CSeq_entry_Info::GetSet(), CSeq_entry_Info::IsSet(), CSeq_submit_Base::SetData(), CSeq_submit_Base::C_Data::Which(), and x_GetTopLevelSeq_submit().

Referenced by CTSE_Handle::GetTopLevelSeq_submit().

GetTopLevelSubmit_block()

const CSubmit_block & CTSE_Info::GetTopLevelSubmit_block

(

)

const

Definition at line 2137 of file tse_info.cpp.

References CSeq_submit_Base::GetSub(), and x_GetTopLevelSeq_submit().

Referenced by CTSE_Handle::GetTopLevelSubmit_block().

GetTSE_Info() [1/2]

CTSE_Info & CTSE_Info::GetTSE_Info ( void  )

inline

Definition at line 827 of file tse_info.hpp.

GetTSE_Info() [2/2]

const CTSE_Info & CTSE_Info::GetTSE_Info ( void  ) const

inline

Definition at line 820 of file tse_info.hpp.

Referenced by UpdateAnnotIndex().

GetTSECore()

CConstRef< CSeq_entry > CTSE_Info::GetTSECore

(

void

)

const

Definition at line 557 of file tse_info.cpp.

References CSeq_entry_Info::GetSeq_entryCore().

Referenced by CScope_Impl::AddSharedSeq_entry(), and x_IsEmptyCDD().

GetUsedMemory()

size_t CTSE_Info::GetUsedMemory ( void  ) const

inline

Definition at line 900 of file tse_info.hpp.

References m_UsedMemory.

Referenced by CTSE_Handle::GetUsedMemory().

HasAnnot()

bool CTSE_Info::HasAnnot

(

const CAnnotName &

name

)

const

Definition at line 532 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), GetAnnotLock(), and m_NamedAnnotObjs.

Referenced by HasNamedAnnot(), and HasUnnamedAnnot().

HasDataSource()

bool CTSE_Info::HasDataSource ( void  ) const

inline

Definition at line 798 of file tse_info.hpp.

References m_DataSource.

Referenced by CTSE_Info(), CTSE_Info_Object::HasDataSource(), CTSE_Default_Assigner::LoadAnnot(), CTSE_Default_Assigner::LoadBioseq(), CTSE_Default_Assigner::LoadChunkBioseqs(), CDataSource::SetLoaded(), SetSeq_entry(), CTSE_Default_Assigner::UpdateAnnotIndex(), UpdateAnnotIndex(), x_IndexAnnotTSE(), x_IndexSeqTSE(), CDataSource::x_ReleaseLastTSELock(), x_ResetDirtyAnnotIndexNoParent(), x_SetBioseqIds(), x_SetDirtyAnnotIndexNoParent(), x_UnindexAnnotTSE(), x_UnindexSeqTSE(), and CTSE_Chunk_Info::x_UpdateAnnotIndex().

HasMatchingAnnotIds()

bool CTSE_Info::HasMatchingAnnotIds ( void  ) const

inline

Definition at line 935 of file tse_info.hpp.

References fAnnotIds_Matching, and m_AnnotIdsFlags.

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

HasNamedAnnot()

bool CTSE_Info::HasNamedAnnot

(

const string &

name

)

const

Definition at line 539 of file tse_info.cpp.

References HasAnnot().

HasSplitInfo()

bool CTSE_Info::HasSplitInfo

(

void

)

const

Definition at line 1382 of file tse_info.cpp.

References m_Split.

Referenced by CPSGL_Blob_Processor::AssignChunks(), CPSGL_Blob_Processor::Chunk_ToOM(), GetSplitInfo(), CPSGL_Blob_Processor::HasChunksToAssign(), SetSeq_entry(), and CDataSource::x_IndexSeqTSELocked().

HasUnnamedAnnot()

bool CTSE_Info::HasUnnamedAnnot

(

void

)

const

Definition at line 545 of file tse_info.cpp.

References HasAnnot().

IsDead()

bool CTSE_Info::IsDead ( void  ) const

inline

Definition at line 855 of file tse_info.hpp.

References CBioseq_Handle::fState_dead, and m_BlobState.

Referenced by CDataSource::IsLive(), and CGBDataLoader_Native::ResolveConflict().

IsLocked()

bool CTSE_Info::IsLocked ( void  ) const

inline

Definition at line 813 of file tse_info.hpp.

References CAtomicCounter::Get(), and m_LockCounter.

Referenced by CDataSource::x_ReleaseLastTSELock(), and CDataSource::x_SetLoadLock().

IsTopLevelSeq_submit()

bool CTSE_Info::IsTopLevelSeq_submit

(

)

const

Definition at line 2085 of file tse_info.cpp.

References CTSE_Handle::eTopLevel_Seq_submit, and GetTopLevelObjectType().

Referenced by CTSE_Handle::IsTopLevelSeq_submit(), and x_GetTopLevelSeq_submit().

IsUnavailable()

bool CTSE_Info::IsUnavailable ( void  ) const

inline

Definition at line 862 of file tse_info.hpp.

References CBioseq_Handle::fState_no_data, and m_BlobState.

OnlyGiAnnotIds()

bool CTSE_Info::OnlyGiAnnotIds ( void  ) const

inline

Definition at line 942 of file tse_info.hpp.

References fAnnotIds_NonGi, and m_AnnotIdsFlags.

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

operator=()

CTSE_Info& CTSE_Info::operator= ( const CTSE_Info &  )

private

ResetBlobState()

void CTSE_Info::ResetBlobState ( TBlobState  state = CBioseq_Handle::fState_none )

inline

Definition at line 841 of file tse_info.hpp.

References m_BlobState.

SetBioseqUpdater()

void CTSE_Info::SetBioseqUpdater

(

CRef< CBioseqUpdater >

updater

)

Definition at line 2036 of file tse_info.cpp.

References set< Key, Compare >::insert(), m_Bioseqs, m_BioseqsMutex, m_BioseqUpdater, NON_CONST_ITERATE, and CBioseqUpdater::Update().

Referenced by CWGSMasterSupport::AddWGSMaster(), and CTSE_Split_Info::x_SetBioseqUpdater().

SetBlobState()

void CTSE_Info::SetBlobState ( TBlobState  state )

inline

Definition at line 848 of file tse_info.hpp.

References m_BlobState.

Referenced by CWGSFileInfo::LoadBlob(), CReaderRequestResult::SetLoadedBlobState(), CPSGL_Blob_Processor::TSE_ToOM(), UpdateOMBlobId(), and CLoadLockSetter::x_ObtainTSE_LoadLock().

SetBlobVersion()

void CTSE_Info::SetBlobVersion

(

TBlobVersion

version

)

Definition at line 324 of file tse_info.cpp.

References _ASSERT, eNotLoaded, m_BlobVersion, m_LoadState, CSeq_entry_Info::m_Object, and dtl::version.

Referenced by CReaderRequestResult::SetLoadedBlobVersion(), CPSGL_Blob_Processor::TSE_ToOM(), and CLoadLockSetter::x_ObtainTSE_LoadLock().

SetName()

void CTSE_Info::SetName

(

const CAnnotName &

name

)

Definition at line 333 of file tse_info.cpp.

References m_Name.

Referenced by CCDDDataLoader_Impl::GetBlobBySeq_ids(), CProcessor_AnnotInfo::LoadBlob(), CReader::LoadBlobs(), CProcessor_ExtAnnot::Process(), CLoadLockSetter::SetLoaded(), UpdateOMBlobId(), and CPSGDataLoader_Impl::x_CheckAnnotCache().

SetRequestedId()

void CTSE_Info::SetRequestedId ( const CSeq_id_Handle &  requested_id ) const

inline

Definition at line 928 of file tse_info.hpp.

References m_RequestedId.

SetSeq_entry()

void CTSE_Info::SetSeq_entry	(	CSeq_entry &	entry,
		CTSE_SetObjectInfo *	set_info = 0
	)

Definition at line 351 of file tse_info.cpp.

References map_checker< Container >::clear(), CSeq_entry_Base::e_not_set, map_checker< Container >::empty(), eNotLoaded, GetDataSource(), GetSplitInfo(), HasDataSource(), HasSplitInfo(), CTSE_Chunk_Info::kDelayedMain_ChunkId, m_AnnotIdsFlags, CSeq_entry_Info::m_Contents, m_LoadState, CSeq_entry_Info::m_Object, m_Removed_Bioseq_sets, m_Removed_Bioseqs, m_RequestedId, CTSE_SetObjectInfo::m_Seq_annot_InfoMap, m_SetObjectInfo, m_Split, CSeq_entry_Info::m_Which, NCBI_THROW, CSeq_entry::Parentize(), CRef< C, Locker >::Reset(), CSeq_id_Handle::Reset(), CSeq_entry_Info::Reset(), UpdateAnnotIndex(), CSeq_entry_Info::x_DetachContents(), and CSeq_entry_Info::x_SetObject().

Referenced by Assign(), CTSE_Info(), CAsnCache_DataLoader::GetBlobById(), CSRADataLoader::GetBlobById(), CHugeAsnDataLoader::GetBlobById(), CVDBGraphDataLoader_Impl::GetBlobByIdOnce(), CCDDDataLoader_Impl::GetBlobBySeq_ids(), CSNPSeqInfo::LoadAnnotBlob(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CWGSFileInfo::LoadBlob(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CCSRAFileInfo::LoadReadsBlob(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CTSE_Default_Assigner::LoadSeq_entry(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), CLoadLockSetter::SetSeq_entry(), CPSGL_Blob_Processor::TSE_ToOM(), x_CreateEmptyLocalCDDEntry(), CBuffer_DataLoader::x_LoadData(), CBlastDbDataLoader::x_LoadData(), CLDS2_DataLoader::x_LoadTSE(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

SetTopLevelObject()

void CTSE_Info::SetTopLevelObject	(	ETopLevelObjectType	type,
		CSerialObject *	ptr
	)

Definition at line 2078 of file tse_info.cpp.

References m_TopLevelObjectPtr, m_TopLevelObjectType, and type.

Referenced by CScope_Impl::AddSeq_submit(), and SetTopLevelObjectType().

SetTopLevelObjectType()

void CTSE_Info::SetTopLevelObjectType

(

ETopLevelObjectType

type

)

Definition at line 2155 of file tse_info.cpp.

References SetTopLevelObject().

Referenced by CScope_Impl::AddBioseq(), CScope_Impl::AddSeq_annot(), CScope_Impl::AddSharedBioseq(), and CScope_Impl::AddSharedSeq_annot().

SetTopLevelSubmit_block() [1/2]

CSubmit_block & CTSE_Info::SetTopLevelSubmit_block

(

)

const

Definition at line 2143 of file tse_info.cpp.

References CSeq_submit_Base::SetSub(), and x_GetTopLevelSeq_submit().

Referenced by CTSE_Handle::SetTopLevelSubmit_block().

SetTopLevelSubmit_block() [2/2]

void CTSE_Info::SetTopLevelSubmit_block

(

CSubmit_block &

sub

)

const

Definition at line 2149 of file tse_info.cpp.

References CSeq_submit_Base::SetSub(), and x_GetTopLevelSeq_submit().

SetUsedMemory()

void CTSE_Info::SetUsedMemory

(

size_t

size

)

Definition at line 339 of file tse_info.cpp.

References m_UsedMemory, and ncbi::grid::netcache::search::fields::size.

UpdateAnnotIndex() [1/5]

void CTSE_Info::UpdateAnnotIndex

(

const CSeq_id_Handle &

id

)

const

Definition at line 1009 of file tse_info.cpp.

References UpdateAnnotIndex(), and x_GetRecords().

Referenced by CSeq_entry_Info::GetAnnotIds(), CDataSource::UpdateAnnotIndex(), CBioseq_set_Info::UpdateAnnotIndex(), CSeq_annot_Info::UpdateAnnotIndex(), CSeq_entry_Info::UpdateAnnotIndex(), CSeq_annot_Finder::x_Find(), CAnnot_Collector::x_SearchLoc(), CAnnot_Collector::x_SearchMaster(), CAnnot_Collector::x_SearchRange(), and CAnnot_Collector::x_SearchTSE2().

UpdateAnnotIndex() [2/5]

void CTSE_Info::UpdateAnnotIndex

(

const CTSE_Info_Object &

object

)

const

Definition at line 1022 of file tse_info.cpp.

References UpdateAnnotIndex().

UpdateAnnotIndex() [3/5]

void CTSE_Info::UpdateAnnotIndex

(

CTSE_Info_Object &

object

)

Definition at line 1035 of file tse_info.cpp.

References _ASSERT, eEmptyGuard, GetAnnotLock(), GetDataSource(), GetTSE_Info(), CDSAnnotLockWriteGuard::Guard(), HasDataSource(), and CTSE_Info_Object::x_DirtyAnnotIndex().

UpdateAnnotIndex() [4/5]

void CTSE_Info::UpdateAnnotIndex

(

void

)

Definition at line 1029 of file tse_info.cpp.

References UpdateAnnotIndex().

UpdateAnnotIndex() [5/5]

void CTSE_Info::UpdateAnnotIndex

(

void

)

const

Definition at line 1016 of file tse_info.cpp.

Referenced by GetAnnotIds(), SetSeq_entry(), UpdateAnnotIndex(), UpdateFeatIdIndex(), x_AddFeaturesById(), and x_GetFeaturesByLocus().

UpdateFeatIdIndex() [1/2]

void CTSE_Info::UpdateFeatIdIndex	(	CSeqFeatData::E_Choice	type,
		EFeatIdType	id_type
	)		const

Definition at line 989 of file tse_info.cpp.

References CRef< C, Locker >::GetNCObject(), m_Split, UpdateAnnotIndex(), and CTSE_Split_Info::x_UpdateFeatIdIndex().

Referenced by x_GetFeaturesById().

UpdateFeatIdIndex() [2/2]

void CTSE_Info::UpdateFeatIdIndex	(	CSeqFeatData::ESubtype	subtype,
		EFeatIdType	id_type
	)		const

Definition at line 999 of file tse_info.cpp.

References CRef< C, Locker >::GetNCObject(), m_Split, UpdateAnnotIndex(), and CTSE_Split_Info::x_UpdateFeatIdIndex().

x_AddAllFeaturesById() [1/2]

void CTSE_Info::x_AddAllFeaturesById	(	TAnnotObjects &	objects,
		const TFeatIdStr &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1548 of file tse_info.cpp.

References ITERATE, m_FeatIdIndex, and x_AddFeaturesById().

x_AddAllFeaturesById() [2/2]

void CTSE_Info::x_AddAllFeaturesById	(	TAnnotObjects &	objects,
		TFeatIdInt	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1482 of file tse_info.cpp.

References ITERATE, m_FeatIdIndex, and x_AddFeaturesById().

Referenced by x_GetFeaturesById().

x_AddFeaturesById() [1/4]

void CTSE_Info::x_AddFeaturesById	(	TAnnotObjects &	objects,
		const SFeatIdIndex &	index,
		const TFeatIdStr &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1494 of file tse_info.cpp.

References multimap_checker< Container >::end(), multimap_checker< Container >::find(), CSeq_annot_Info::GetXrefTSE(), info, CTSE_Info::SFeatIdIndex::m_Chunks, CTSE_Info::SFeatIdIndex::m_IndexStr, UpdateAnnotIndex(), x_LoadChunk(), and x_LoadChunks().

x_AddFeaturesById() [2/4]

void CTSE_Info::x_AddFeaturesById	(	TAnnotObjects &	objects,
		const SFeatIdIndex &	index,
		TFeatIdInt	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1421 of file tse_info.cpp.

References multimap_checker< Container >::end(), multimap_checker< Container >::find(), CSeq_annot_Info::GetXrefTSE(), info, CTSE_Info::SFeatIdIndex::m_Chunks, CTSE_Info::SFeatIdIndex::m_IndexInt, UpdateAnnotIndex(), x_LoadChunk(), and x_LoadChunks().

Referenced by x_AddAllFeaturesById(), x_AddFeaturesById(), and x_GetFeaturesById().

x_AddFeaturesById() [3/4]

void CTSE_Info::x_AddFeaturesById	(	TAnnotObjects &	objects,
		CSeqFeatData::ESubtype	subtype,
		const TFeatIdStr &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1534 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_FeatIdIndex, and x_AddFeaturesById().

x_AddFeaturesById() [4/4]

void CTSE_Info::x_AddFeaturesById	(	TAnnotObjects &	objects,
		CSeqFeatData::ESubtype	subtype,
		TFeatIdInt	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1468 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_FeatIdIndex, and x_AddFeaturesById().

x_DoUpdate()

void CTSE_Info::x_DoUpdate ( TNeedUpdateFlags  flags )

privatevirtual

Reimplemented from CSeq_entry_Info.

Definition at line 671 of file tse_info.cpp.

References flags, CTSE_Info_Object::fNeedUpdate_children_core, CTSE_Info_Object::fNeedUpdate_core, m_Split, CSeq_entry_Info::x_DoUpdate(), and CTSE_Split_Info::x_UpdateCore().

x_DSAttachContents()

void CTSE_Info::x_DSAttachContents ( CDataSource &  ds )

virtual

Reimplemented from CSeq_entry_Info.

Definition at line 563 of file tse_info.cpp.

References _ASSERT, ITERATE, m_Bioseqs, m_DataSource, m_Split, CTSE_Split_Info::x_DSAttach(), CSeq_entry_Info::x_DSAttachContents(), CDataSource::x_IndexAnnotTSEs(), and CDataSource::x_IndexSeqTSE().

x_DSDetachContents()

void CTSE_Info::x_DSDetachContents ( CDataSource &  ds )

virtual

Reimplemented from CSeq_entry_Info.

Definition at line 579 of file tse_info.cpp.

References _ASSERT, ITERATE, m_Bioseqs, m_DataSource, m_Split, CTSE_Split_Info::x_DSDetach(), CSeq_entry_Info::x_DSDetachContents(), CDataSource::x_UnindexAnnotTSEs(), and CDataSource::x_UnindexSeqTSE().

x_DSMapObject()

void CTSE_Info::x_DSMapObject ( CConstRef< TObject >  obj, CDataSource &  ds  )

private

Definition at line 595 of file tse_info.cpp.

References CSeq_entry_Info::x_DSMapObject(), and CDataSource::x_Map().

x_DSUnmapObject()

void CTSE_Info::x_DSUnmapObject ( CConstRef< TObject >  obj, CDataSource &  ds  )

private

Definition at line 602 of file tse_info.cpp.

References CSeq_entry_Info::x_DSUnmapObject(), and CDataSource::x_Unmap().

x_FindBioObject()

CTSE_Info_Object * CTSE_Info::x_FindBioObject

(

const CBioObjectId &

uniq_id

)

const

Definition at line 463 of file tse_info.cpp.

References _ASSERT, map_checker< Container >::end(), CBioObjectId::eSeqId, CBioObjectId::eSetId, CBioObjectId::eUniqNumber, map_checker< Container >::find(), CBioObjectId::GetSeqId(), CBioObjectId::GetSetId(), CBioObjectId::GetType(), i, m_BioObjects, m_Bioseq_sets, m_Bioseqs, m_BioseqsMutex, NULL, and x_GetRecords().

Referenced by GetBase(), GetBioseq(), GetBioseq_set(), and GetSeq_entry().

x_FindSeq_feat()

CTSE_Info::TSeq_feat_Lock CTSE_Info::x_FindSeq_feat	(	const CSeq_id_Handle &	loc_id,
		TSeqPos	loc_pos,
		const CSeq_feat &	feat
	)		const

Definition at line 1995 of file tse_info.cpp.

References CRangeMapBase< Traits >::begin(), CAnnotObject_Info::GetAnnotIndex(), CSeq_feat_Base::GetData(), CAnnotObject_Info::GetFeatFast(), CAnnotObject_Info::GetSeq_annot_Info(), CSeqFeatData::GetSubtype(), CAnnotType_Index::GetSubtypeIndex(), CAnnotObject_Info::IsRegular(), ITERATE, m_NamedAnnotObjs, compile_time_bits::range(), x_GetIdObjects(), SIdAnnotObjs::x_GetRangeMap(), and SIdAnnotObjs::x_RangeMapIsEmpty().

x_GetAnnotObjs()

const CTSE_Info::TAnnotObjs * CTSE_Info::x_GetAnnotObjs ( const CAnnotName &  name ) const

private

Definition at line 1087 of file tse_info.cpp.

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

Referenced by x_GetIdObjects().

x_GetBioseq()

CBioseq_Info & CTSE_Info::x_GetBioseq

(

const CSeq_id_Handle &

id

)

Definition at line 1363 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_Bioseqs, m_BioseqsMutex, m_Removed_Bioseqs, m_Split, and NCBI_THROW.

x_GetBioseq_set()

CBioseq_set_Info & CTSE_Info::x_GetBioseq_set

(

int

id

)

Definition at line 1345 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_Bioseq_sets, m_Removed_Bioseq_sets, m_Split, and NCBI_THROW.

Referenced by ITSE_Assigner::x_GetBioseq_set().

x_GetFeatIdIndexInt()

CTSE_Info::SFeatIdIndex::TIndexInt & CTSE_Info::x_GetFeatIdIndexInt

(

CSeqFeatData::ESubtype

type

)

Definition at line 1561 of file tse_info.cpp.

References m_FeatIdIndex, CTSE_Info::SFeatIdIndex::m_IndexInt, and type.

Referenced by x_MapChunkByFeatId(), x_MapFeatById(), and x_UnmapFeatById().

x_GetFeatIdIndexStr()

CTSE_Info::SFeatIdIndex::TIndexStr & CTSE_Info::x_GetFeatIdIndexStr

(

CSeqFeatData::ESubtype

type

)

Definition at line 1573 of file tse_info.cpp.

References m_FeatIdIndex, CTSE_Info::SFeatIdIndex::m_IndexStr, and type.

Referenced by x_MapChunkByFeatId(), x_MapFeatById(), and x_UnmapFeatById().

x_GetFeaturesById() [1/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::E_Choice	type,
		const TFeatId &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1950 of file tse_info.cpp.

References GetId(), and x_GetFeaturesById().

x_GetFeaturesById() [2/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::E_Choice	type,
		const TFeatIdStr &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1909 of file tse_info.cpp.

References CSeqFeatData_Base::e_not_set, CAnnotType_Index::GetFeatTypeRange(), CAnnotType_Index::GetSubtypeForIndex(), compile_time_bits::range(), UpdateFeatIdIndex(), x_AddAllFeaturesById(), and x_AddFeaturesById().

x_GetFeaturesById() [3/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::E_Choice	type,
		TFeatIdInt	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1867 of file tse_info.cpp.

References CSeqFeatData_Base::e_not_set, CAnnotType_Index::GetFeatTypeRange(), CAnnotType_Index::GetSubtypeForIndex(), compile_time_bits::range(), UpdateFeatIdIndex(), x_AddAllFeaturesById(), and x_AddFeaturesById().

Referenced by x_GetFeaturesById().

x_GetFeaturesById() [4/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::ESubtype	subtype,
		const TFeatId &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1933 of file tse_info.cpp.

References GetId(), and x_GetFeaturesById().

x_GetFeaturesById() [5/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::ESubtype	subtype,
		const TFeatIdStr &	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1891 of file tse_info.cpp.

References CSeqFeatData::eSubtype_any, UpdateFeatIdIndex(), x_AddAllFeaturesById(), and x_AddFeaturesById().

x_GetFeaturesById() [6/6]

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesById	(	CSeqFeatData::ESubtype	subtype,
		TFeatIdInt	id,
		EFeatIdType	id_type,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1849 of file tse_info.cpp.

References CSeqFeatData::eSubtype_any, UpdateFeatIdIndex(), x_AddAllFeaturesById(), and x_AddFeaturesById().

x_GetFeaturesByLocus()

CTSE_Info::TAnnotObjects CTSE_Info::x_GetFeaturesByLocus	(	const string &	locus,
		bool	tag,
		const CSeq_annot_Info *	src_annot = 0
	)		const

Definition at line 1966 of file tse_info.cpp.

References multimap_checker< Container >::end(), CSeq_entry_Info::GetXrefTSE(), CSeq_annot_Info::GetXrefTSE(), multimap_checker< Container >::lower_bound(), m_LocusIndex, tag, and UpdateAnnotIndex().

x_GetIdObjects() [1/2]

const SIdAnnotObjs * CTSE_Info::x_GetIdObjects ( const CAnnotName &  name, const CSeq_id_Handle &  id  ) const

private

Definition at line 1145 of file tse_info.cpp.

References x_GetAnnotObjs(), and x_GetIdObjects().

x_GetIdObjects() [2/2]

const SIdAnnotObjs * CTSE_Info::x_GetIdObjects ( const TAnnotObjs &  objs, const CSeq_id_Handle &  idh  ) const

private

Definition at line 1134 of file tse_info.cpp.

References map_checker< Container >::end(), and map_checker< Container >::find().

Referenced by CSeq_annot_Finder::x_Find(), x_FindSeq_feat(), x_GetIdObjects(), x_GetUnnamedIdObjects(), x_HasIdObjects(), CAnnot_Collector::x_SearchRange(), and CAnnot_Collector::x_SearchTSE2().

x_GetRecords()

void CTSE_Info::x_GetRecords	(	const CSeq_id_Handle &	id,
		bool	bioseq
	)		const

Definition at line 848 of file tse_info.cpp.

References m_Split, and CTSE_Split_Info::x_GetRecords().

Referenced by FindBioseq(), UpdateAnnotIndex(), CDataSource::x_AddTSEBioseqAnnots(), CDataSource::x_AddTSEOrphanAnnots(), and x_FindBioObject().

x_GetSNP_Info()

CRef< CSeq_annot_SNP_Info > CTSE_Info::x_GetSNP_Info ( const CConstRef< CSeq_annot > &  annot )

private

Definition at line 517 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CTSE_SetObjectInfo::m_Seq_annot_InfoMap, and m_SetObjectInfo.

Referenced by CSeq_annot_Info::x_TSEAttachContents().

x_GetTopLevelSeq_submit()

CSeq_submit & CTSE_Info::x_GetTopLevelSeq_submit

(

)

const

Definition at line 2091 of file tse_info.cpp.

References CRef< C, Locker >::GetNCPointerOrNull(), IsTopLevelSeq_submit(), m_TopLevelObjectPtr, and NCBI_THROW.

Referenced by GetTopLevelSeq_submit(), GetTopLevelSubmit_block(), and SetTopLevelSubmit_block().

x_GetUnnamedAnnotObjs()

const CTSE_Info::TAnnotObjs * CTSE_Info::x_GetUnnamedAnnotObjs ( void  ) const

private

Definition at line 1098 of file tse_info.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), and m_NamedAnnotObjs.

Referenced by x_GetUnnamedIdObjects().

x_GetUnnamedIdObjects()

const SIdAnnotObjs * CTSE_Info::x_GetUnnamedIdObjects ( const CSeq_id_Handle &  id ) const

private

Definition at line 1157 of file tse_info.cpp.

References x_GetIdObjects(), and x_GetUnnamedAnnotObjs().

Referenced by CSeq_annot_Finder::x_Find(), and CAnnot_Collector::x_SearchTSE2().

x_HasFeaturesWithId()

bool CTSE_Info::x_HasFeaturesWithId

(

CSeqFeatData::ESubtype

subtype

)

const

Definition at line 1461 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_FeatIdIndex.

Referenced by CFeat_CI::x_AddFeaturesWithId().

x_HasIdObjects()

bool CTSE_Info::x_HasIdObjects ( const CSeq_id_Handle &  id ) const

private

Definition at line 1167 of file tse_info.cpp.

References ITERATE, m_NamedAnnotObjs, and x_GetIdObjects().

Referenced by CDataSource::x_AddTSEAnnots().

x_IndexAnnotTSE()

bool CTSE_Info::x_IndexAnnotTSE ( const CAnnotName &  name, const CSeq_id_Handle &  id  )

private

Definition at line 627 of file tse_info.cpp.

References _VERIFY, ContainsMatchingBioseq(), map_checker< Container >::end(), fAnnotIds_Matching, fAnnotIds_NonGi, GetDataSource(), HasDataSource(), map_checker< Container >::insert(), map_checker< Container >::lower_bound(), m_AnnotIdsFlags, m_IdAnnotInfoMap, and CDataSource::x_IndexAnnotTSE().

Referenced by x_SetIdObjects().

x_IndexBioseq()

CBioObjectId CTSE_Info::x_IndexBioseq ( CBioseq_Info *  info )

private

Definition at line 404 of file tse_info.cpp.

References _ASSERT, CBioObjectId::eUnSet, CBioObjectId::GetType(), info, ITERATE, x_RegisterBioObject(), and x_SetBioseqIds().

Referenced by CBioseq_Info::x_TSEAttachContents().

x_IndexBioseq_set()

CBioObjectId CTSE_Info::x_IndexBioseq_set ( CBioseq_set_Info *  info )

private

Definition at line 426 of file tse_info.cpp.

References _ASSERT, CBioObjectId::eSetId, CBioObjectId::eUnSet, info, and x_RegisterBioObject().

Referenced by CBioseq_set_Info::x_TSEAttachContents().

x_IndexSeqTSE()

void CTSE_Info::x_IndexSeqTSE ( const CSeq_id_Handle &  id )

inlineprivate

Definition at line 610 of file tse_info.cpp.

References GetDataSource(), HasDataSource(), and CDataSource::x_IndexSeqTSE().

Referenced by x_SetBioseqId().

x_Initialize()

void CTSE_Info::x_Initialize ( void  )

private

Definition at line 289 of file tse_info.cpp.

References eNotInCache, eNotLoaded, CTSE_Handle::eTopLevel_Seq_entry, CBioseq_Handle::fState_none, m_AnnotIdsFlags, m_BlobState, m_BlobVersion, m_CacheState, m_DataSource, m_LoadState, m_TopLevelObjectType, and m_UsedMemory.

Referenced by CTSE_Info().

x_LoadChunk()

void CTSE_Info::x_LoadChunk

(

TChunkId

chunk_id

)

const

Definition at line 856 of file tse_info.cpp.

References m_Split, and CTSE_Split_Info::x_LoadChunk().

Referenced by CCSRADataLoader_Impl::GetRecordsOnce(), x_AddFeaturesById(), and CTSE_Info_Object::x_LoadChunk().

x_LoadChunks()

void CTSE_Info::x_LoadChunks

(

const TChunkIds &

chunk_ids

)

const

Definition at line 862 of file tse_info.cpp.

References m_Split, and CTSE_Split_Info::x_LoadChunks().

Referenced by x_AddFeaturesById(), and CTSE_Info_Object::x_LoadChunks().

x_LoadDelayedMainChunk()

void CTSE_Info::x_LoadDelayedMainChunk

(

void

)

const

Definition at line 1413 of file tse_info.cpp.

References m_Split, and CTSE_Split_Info::x_LoadDelayedMainChunk().

Referenced by CSeq_entry_Info::x_UpdateSkeleton().

x_MapAnnotObject() [1/4]

bool CTSE_Info::x_MapAnnotObject ( const CAnnotName &  name, const SAnnotObject_Key &  key, const SAnnotObject_Index &  index  )

private

Definition at line 1298 of file tse_info.cpp.

References ncbi::grid::netcache::search::fields::key, x_MapAnnotObject(), and x_SetAnnotObjs().

x_MapAnnotObject() [2/4]

void CTSE_Info::x_MapAnnotObject ( SIdAnnotObjs &  objs, const SAnnotObject_Key &  key, const SAnnotObject_Index &  index  )

private

Definition at line 1206 of file tse_info.cpp.

References CAnnotObject_Info::GetLocsTypes(), CAnnotType_Index::GetTypeIndex(), CAnnotObject_Info::IsLocs(), ITERATE, ncbi::grid::netcache::search::fields::key, SAnnotObject_Index::m_AnnotObject_Info, SIdAnnotObjs::x_GetRangeMap(), and x_MapAnnotObject().

x_MapAnnotObject() [3/4]

bool CTSE_Info::x_MapAnnotObject ( TAnnotObjs &  objs, const CAnnotName &  name, const SAnnotObject_Key &  key, const SAnnotObject_Index &  index  )

private

Definition at line 1248 of file tse_info.cpp.

References ncbi::grid::netcache::search::fields::key, x_MapAnnotObject(), and x_SetIdObjects().

x_MapAnnotObject() [4/4]

void CTSE_Info::x_MapAnnotObject ( TRangeMap &  rangeMap, const SAnnotObject_Key &  key, const SAnnotObject_Index &  index  )

inlineprivate

Definition at line 1180 of file tse_info.cpp.

References CRangeMultimap< Mapped, Position >::insert(), and ncbi::grid::netcache::search::fields::key.

Referenced by CTSEAnnotObjectMapper::Map(), and x_MapAnnotObject().

x_MapChunkByFeatId() [1/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatId &  id, const SAnnotTypeSelector &  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1802 of file tse_info.cpp.

References GetId(), and x_MapChunkByFeatId().

x_MapChunkByFeatId() [2/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatId &  id, CSeqFeatData::E_Choice  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1788 of file tse_info.cpp.

References GetId(), and x_MapChunkByFeatId().

x_MapChunkByFeatId() [3/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatId &  id, CSeqFeatData::ESubtype  subtype, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1774 of file tse_info.cpp.

References GetId(), and x_MapChunkByFeatId().

x_MapChunkByFeatId() [4/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatIdStr &  id, const SAnnotTypeSelector &  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1760 of file tse_info.cpp.

References CSeqFeatData::eSubtype_any, and x_MapChunkByFeatId().

x_MapChunkByFeatId() [5/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatIdStr &  id, CSeqFeatData::E_Choice  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1745 of file tse_info.cpp.

References CAnnotType_Index::GetFeatTypeRange(), CAnnotType_Index::GetSubtypeForIndex(), compile_time_bits::range(), and x_MapChunkByFeatId().

x_MapChunkByFeatId() [6/9]

void CTSE_Info::x_MapChunkByFeatId ( const TFeatIdStr &  id, CSeqFeatData::ESubtype  subtype, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1734 of file tse_info.cpp.

References multimap_checker< Container >::insert(), rapidjson::value, and x_GetFeatIdIndexStr().

x_MapChunkByFeatId() [7/9]

void CTSE_Info::x_MapChunkByFeatId ( TFeatIdInt  id, const SAnnotTypeSelector &  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1720 of file tse_info.cpp.

References CSeqFeatData::eSubtype_any, and x_MapChunkByFeatId().

x_MapChunkByFeatId() [8/9]

void CTSE_Info::x_MapChunkByFeatId ( TFeatIdInt  id, CSeqFeatData::E_Choice  type, TChunkId  chunk_id, EFeatIdType  id_type  )

private

Definition at line 1705 of file tse_info.cpp.

References CAnnotType_Index::GetFeatTypeRange(), CAnnotType_Index::GetSubtypeForIndex(), compile_time_bits::range(), and x_MapChunkByFeatId().

x_MapChunkByFeatId() [9/9]

void CTSE_Info::x_MapChunkByFeatId ( TFeatIdInt  id, CSeqFeatData::ESubtype  subtype, TChunkId  chunk_id, EFeatIdType  type  )

private

Definition at line 1694 of file tse_info.cpp.

References multimap_checker< Container >::insert(), rapidjson::value, and x_GetFeatIdIndexInt().

Referenced by x_MapChunkByFeatId(), and CTSE_Chunk_Info::x_UpdateAnnotIndexContents().

x_MapChunkByFeatType() [1/3]

void CTSE_Info::x_MapChunkByFeatType ( const SAnnotTypeSelector &  type, TChunkId  chunk_id  )

private

Definition at line 1836 of file tse_info.cpp.

References CSeqFeatData::eSubtype_any, and x_MapChunkByFeatType().

x_MapChunkByFeatType() [2/3]

void CTSE_Info::x_MapChunkByFeatType ( CSeqFeatData::E_Choice  type, TChunkId  chunk_id  )

private

Definition at line 1823 of file tse_info.cpp.

References CAnnotType_Index::GetFeatTypeRange(), CAnnotType_Index::GetSubtypeForIndex(), compile_time_bits::range(), and x_MapChunkByFeatType().

x_MapChunkByFeatType() [3/3]

void CTSE_Info::x_MapChunkByFeatType ( CSeqFeatData::ESubtype  subtype, TChunkId  chunk_id  )

private

Definition at line 1816 of file tse_info.cpp.

References m_FeatIdIndex.

Referenced by x_MapChunkByFeatType(), and CTSE_Chunk_Info::x_UpdateAnnotIndexContents().

x_MapFeatById() [1/3]

void CTSE_Info::x_MapFeatById ( const TFeatId &  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1644 of file tse_info.cpp.

References GetId(), info, and x_MapFeatById().

x_MapFeatById() [2/3]

void CTSE_Info::x_MapFeatById ( const TFeatIdStr &  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1614 of file tse_info.cpp.

References info, multimap_checker< Container >::insert(), rapidjson::value, and x_GetFeatIdIndexStr().

x_MapFeatById() [3/3]

void CTSE_Info::x_MapFeatById ( TFeatIdInt  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1584 of file tse_info.cpp.

References info, multimap_checker< Container >::insert(), rapidjson::value, and x_GetFeatIdIndexInt().

Referenced by CSeq_annot_Info::AddFeatId(), CSeq_annot_Info::x_MapFeatById(), and x_MapFeatById().

x_MapFeatByLocus()

void CTSE_Info::x_MapFeatByLocus ( const string &  locus, bool  tag, CAnnotObject_Info &  info  )

private

Definition at line 1670 of file tse_info.cpp.

References info, multimap_checker< Container >::insert(), m_LocusIndex, and tag.

Referenced by CSeq_annot_Info::x_MapFeatByGene().

x_MapSNP_Table()

bool CTSE_Info::x_MapSNP_Table ( const CAnnotName &  name, const CSeq_id_Handle &  key, const CSeq_annot_SNP_Info &  snp_info  )

private

Definition at line 1274 of file tse_info.cpp.

References ConstRef(), ncbi::grid::netcache::search::fields::key, and x_SetIdObjects().

Referenced by CSeq_annot_SNP_Info::x_UpdateAnnotIndexContents().

x_NeedsDelayedMainChunk()

bool CTSE_Info::x_NeedsDelayedMainChunk

(

void

)

const

Definition at line 1407 of file tse_info.cpp.

References m_Split, and CTSE_Split_Info::x_NeedsDelayedMainChunk().

Referenced by CGBDataLoader_Native::GetCDDAnnots(), CPSGDataLoader_Impl::GetCDDAnnotsOnce(), CProcessor_AnnotInfo::LoadBlob(), CLoadLockBlob::NeedsDelayedMainChunk(), CProcessor_ExtAnnot::Process(), CPSGL_NA_Processor::ProcessItemSlow(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), CPSGL_Blob_Processor::TSE_ToOM(), CPSGDataLoader_Impl::x_CheckAnnotCache(), x_CreateLocalCDDEntry(), x_IsEmptyCDD(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

x_RegisterBioObject()

CBioObjectId CTSE_Info::x_RegisterBioObject ( CTSE_Info_Object &  info )

private

Definition at line 437 of file tse_info.cpp.

References map_checker< Container >::end(), CBioObjectId::eUniqNumber, map_checker< Container >::find(), CBioObjectId::GetType(), info, m_BioObjects, and m_InternalBioObjNumber.

Referenced by x_IndexBioseq(), x_IndexBioseq_set(), and CSeq_annot_Info::x_TSEAttachContents().

x_RemoveAnnotObjs()

void CTSE_Info::x_RemoveAnnotObjs ( const CAnnotName &  name )

private

Definition at line 1080 of file tse_info.cpp.

References map_checker< Container >::erase(), and m_NamedAnnotObjs.

Referenced by CTSEAnnotObjectMapper::Unmap(), x_UnmapAnnotObject(), and x_UnmapAnnotObjects().

x_Reset()

void CTSE_Info::x_Reset ( void  )

private

Definition at line 302 of file tse_info.cpp.

References map_checker< Container >::clear(), CSeq_entry_Base::e_not_set, m_BaseTSE, m_BioObjects, m_Bioseq_sets, m_Bioseqs, CSeq_entry_Info::m_Contents, m_EditSaver, m_FeatIdIndex, m_IdAnnotInfoMap, m_InternalBioObjNumber, m_NamedAnnotObjs, CSeq_entry_Info::m_Object, m_Removed_Bioseq_sets, m_Removed_Bioseqs, m_SetObjectInfo, m_Split, CSeq_entry_Info::m_Which, and CRef< C, Locker >::Reset().

Referenced by CTSE_LoadLock::ReleaseLoadLock().

x_ResetBioseq_setId()

void CTSE_Info::x_ResetBioseq_setId ( int  key, CBioseq_set_Info *  info  )

private

Definition at line 957 of file tse_info.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), info, map_checker< Container >::insert(), ncbi::grid::netcache::search::fields::key, map_checker< Container >::lower_bound(), m_Bioseq_sets, m_Removed_Bioseq_sets, and m_Split.

Referenced by CBioseq_set_Info::x_TSEDetachContents().

x_ResetBioseqId()

void CTSE_Info::x_ResetBioseqId ( const CSeq_id_Handle &  id, CBioseq_Info *  info  )

private

Definition at line 918 of file tse_info.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), info, map_checker< Container >::insert(), map_checker< Container >::lower_bound(), m_Bioseqs, m_BioseqsMutex, m_Removed_Bioseqs, m_Split, and x_UnindexSeqTSE().

Referenced by CBioseq_Info::RemoveId(), CBioseq_Info::ResetId(), and CBioseq_Info::x_TSEDetachContents().

x_ResetDirtyAnnotIndexNoParent()

void CTSE_Info::x_ResetDirtyAnnotIndexNoParent ( void  )

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 981 of file tse_info.cpp.

References GetDataSource(), HasDataSource(), and CDataSource::x_ResetDirtyAnnotIndex().

x_SetAnnotObjs()

CTSE_Info::TAnnotObjs & CTSE_Info::x_SetAnnotObjs ( const CAnnotName &  name )

private

Definition at line 1069 of file tse_info.cpp.

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

Referenced by x_MapAnnotObject(), x_SetIdObjects(), x_UnmapAnnotObject(), and x_UnmapAnnotObjects().

x_SetBioseq_setId()

void CTSE_Info::x_SetBioseq_setId ( int  key, CBioseq_set_Info *  info  )

private

Definition at line 941 of file tse_info.cpp.

References info, map_checker< Container >::insert(), NStr::IntToString(), ncbi::grid::netcache::search::fields::key, m_Bioseq_sets, and NCBI_THROW.

Referenced by CBioseq_set_Info::x_TSEAttachContents().

x_SetBioseqId()

void CTSE_Info::x_SetBioseqId ( const CSeq_id_Handle &  id, CBioseq_Info *  info  )

private

Definition at line 870 of file tse_info.cpp.

References _ASSERT, info, map_checker< Container >::insert(), m_Bioseqs, m_BioseqsMutex, NCBI_THROW_FMT, and x_IndexSeqTSE().

Referenced by CBioseq_Info::AddId().

x_SetBioseqIds()

void CTSE_Info::x_SetBioseqIds ( CBioseq_Info *  info )

private

Definition at line 891 of file tse_info.cpp.

References _ASSERT, GetDataSource(), HasDataSource(), info, map_checker< Container >::insert(), ITERATE, m_Bioseqs, m_BioseqsMutex, m_BioseqUpdater, NCBI_THROW, CBioseqUpdater::Update(), and CDataSource::x_IndexSeqTSE().

Referenced by x_IndexBioseq().

x_SetDirtyAnnotIndexNoParent()

void CTSE_Info::x_SetDirtyAnnotIndexNoParent ( void  )

virtual

Reimplemented from CTSE_Info_Object.

Definition at line 973 of file tse_info.cpp.

References GetDataSource(), HasDataSource(), and CDataSource::x_SetDirtyAnnotIndex().

x_SetIdObjects() [1/2]

pair< SIdAnnotObjs *, bool > CTSE_Info::x_SetIdObjects ( const CAnnotName &  name, const CSeq_id_Handle &  idh  )

private

Definition at line 1127 of file tse_info.cpp.

References x_SetAnnotObjs(), and x_SetIdObjects().

x_SetIdObjects() [2/2]

pair< SIdAnnotObjs *, bool > CTSE_Info::x_SetIdObjects ( TAnnotObjs &  objs, const CAnnotName &  name, const CSeq_id_Handle &  id  )

private

Definition at line 1109 of file tse_info.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), map_checker< Container >::insert(), and x_IndexAnnotTSE().

Referenced by x_MapAnnotObject(), x_MapSNP_Table(), x_SetIdObjects(), and x_UnmapSNP_Table().

x_UnindexAnnotTSE()

void CTSE_Info::x_UnindexAnnotTSE ( const CAnnotName &  name, const CSeq_id_Handle &  id  )

private

Definition at line 653 of file tse_info.cpp.

References _VERIFY, map_checker< Container >::end(), map_checker< Container >::erase(), GetDataSource(), HasDataSource(), map_checker< Container >::lower_bound(), m_IdAnnotInfoMap, and CDataSource::x_UnindexAnnotTSE().

Referenced by x_UnmapAnnotObject().

x_UnindexSeqTSE()

void CTSE_Info::x_UnindexSeqTSE ( const CSeq_id_Handle &  id )

inlineprivate

Definition at line 619 of file tse_info.cpp.

References GetDataSource(), HasDataSource(), and CDataSource::x_UnindexSeqTSE().

Referenced by x_ResetBioseqId().

x_UnmapAnnotObject() [1/4]

void CTSE_Info::x_UnmapAnnotObject ( const CAnnotName &  name, const CAnnotObject_Info &  info, const SAnnotObject_Key &  key  )

private

Definition at line 1306 of file tse_info.cpp.

References map_checker< Container >::empty(), info, ncbi::grid::netcache::search::fields::key, x_RemoveAnnotObjs(), x_SetAnnotObjs(), and x_UnmapAnnotObject().

x_UnmapAnnotObject() [2/4]

bool CTSE_Info::x_UnmapAnnotObject ( SIdAnnotObjs &  objs, const CAnnotObject_Info &  info, const SAnnotObject_Key &  key  )

private

Definition at line 1230 of file tse_info.cpp.

References _ASSERT, CAnnotType_Index::GetTypeIndex(), info, ncbi::grid::netcache::search::fields::key, SIdAnnotObjs::m_SNPSet, SIdAnnotObjs::x_CleanRangeMaps(), SIdAnnotObjs::x_GetRangeMap(), SIdAnnotObjs::x_GetRangeMapCount(), and x_UnmapAnnotObject().

x_UnmapAnnotObject() [3/4]

bool CTSE_Info::x_UnmapAnnotObject ( TAnnotObjs &  objs, const CAnnotName &  name, const CAnnotObject_Info &  info, const SAnnotObject_Key &  key  )

private

Definition at line 1259 of file tse_info.cpp.

References map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), info, ncbi::grid::netcache::search::fields::key, x_UnindexAnnotTSE(), and x_UnmapAnnotObject().

x_UnmapAnnotObject() [4/4]

bool CTSE_Info::x_UnmapAnnotObject ( TRangeMap &  rangeMap, const CAnnotObject_Info &  info, const SAnnotObject_Key &  key  )

inlineprivate

Definition at line 1190 of file tse_info.cpp.

References _ASSERT, CRangeMapBase< Traits >::empty(), CRangeMapBase< Traits >::erase(), CRangeMapBase< Traits >::find(), info, and ncbi::grid::netcache::search::fields::key.

Referenced by CTSEAnnotObjectMapper::Unmap(), x_UnmapAnnotObject(), and x_UnmapAnnotObjects().

x_UnmapAnnotObjects()

void CTSE_Info::x_UnmapAnnotObjects ( const SAnnotObjectsIndex &  infos )

private

Definition at line 1320 of file tse_info.cpp.

References map_checker< Container >::empty(), SAnnotObjectsIndex::GetInfos(), SAnnotObjectsIndex::GetKey(), SAnnotObjectsIndex::GetName(), i, SAnnotObjectsIndex::IsIndexed(), ITERATE, x_RemoveAnnotObjs(), x_SetAnnotObjs(), and x_UnmapAnnotObject().

Referenced by CSeq_annot_Info::x_UnmapAnnotObjects().

x_UnmapFeatById() [1/3]

void CTSE_Info::x_UnmapFeatById ( const TFeatId &  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1657 of file tse_info.cpp.

References GetId(), info, and x_UnmapFeatById().

x_UnmapFeatById() [2/3]

void CTSE_Info::x_UnmapFeatById ( const TFeatIdStr &  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1626 of file tse_info.cpp.

References _ASSERT, multimap_checker< Container >::end(), multimap_checker< Container >::erase(), info, multimap_checker< Container >::lower_bound(), and x_GetFeatIdIndexStr().

x_UnmapFeatById() [3/3]

void CTSE_Info::x_UnmapFeatById ( TFeatIdInt  id, CAnnotObject_Info &  info, EFeatIdType  type  )

private

Definition at line 1596 of file tse_info.cpp.

References _ASSERT, multimap_checker< Container >::end(), multimap_checker< Container >::erase(), info, multimap_checker< Container >::lower_bound(), and x_GetFeatIdIndexInt().

Referenced by CSeq_annot_Info::ClearFeatIds(), CSeq_annot_Info::RemoveFeatId(), CSeq_annot_Info::x_UnmapFeatById(), and x_UnmapFeatById().

x_UnmapFeatByLocus()

void CTSE_Info::x_UnmapFeatByLocus ( const string &  locus, bool  tag, CAnnotObject_Info &  info  )

private

Definition at line 1677 of file tse_info.cpp.

References multimap_checker< Container >::end(), multimap_checker< Container >::erase(), info, multimap_checker< Container >::lower_bound(), m_LocusIndex, and tag.

Referenced by CSeq_annot_Info::x_UnmapFeatByGene().

x_UnmapSNP_Table()

void CTSE_Info::x_UnmapSNP_Table ( const CAnnotName &  name, const CSeq_id_Handle &  key, const CSeq_annot_SNP_Info &  snp_info  )

private

Definition at line 1284 of file tse_info.cpp.

References ConstRef(), ncbi::grid::netcache::search::fields::key, SIdAnnotObjs::m_SNPSet, and x_SetIdObjects().

Referenced by CSeq_annot_SNP_Info::x_UnmapAnnotObjects().

x_UnregisterBioObject()

void CTSE_Info::x_UnregisterBioObject ( CTSE_Info_Object &  info )

private

Definition at line 451 of file tse_info.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), CBioObjectId::eUniqNumber, map_checker< Container >::find(), CBioObjectId::GetType(), i, info, and m_BioObjects.

Referenced by CSeq_annot_Info::x_TSEDetachContents(), and CTSE_Info_Object::x_TSEDetachContents().

x_UpdateAnnotIndexContents()

void CTSE_Info::x_UpdateAnnotIndexContents ( CTSE_Info &  tse )

virtual

Reimplemented from CSeq_entry_Info.

Definition at line 1059 of file tse_info.cpp.

References _ASSERT, m_Split, CTSE_Split_Info::x_UpdateAnnotIndex(), and CSeq_entry_Info::x_UpdateAnnotIndexContents().

Friends And Related Function Documentation

CAnnot_Collector

friend class CAnnot_Collector

friend

Definition at line 499 of file tse_info.hpp.

CBioseq_Info

friend class CBioseq_Info

friend

Definition at line 502 of file tse_info.hpp.

CBioseq_set_Info

friend class CBioseq_set_Info

friend

Definition at line 503 of file tse_info.hpp.

CDataLoader

friend class CDataLoader

friend

Definition at line 498 of file tse_info.hpp.

CDataSource

friend class CDataSource

friend

Definition at line 495 of file tse_info.hpp.

CScope_Impl

friend class CScope_Impl

friend

Definition at line 496 of file tse_info.hpp.

CSeq_annot_Finder

friend class CSeq_annot_Finder

friend

Definition at line 511 of file tse_info.hpp.

CSeq_annot_Info

friend class CSeq_annot_Info

friend

Definition at line 501 of file tse_info.hpp.

CSeq_annot_SNP_Info

friend class CSeq_annot_SNP_Info

friend

Definition at line 507 of file tse_info.hpp.

CSeq_entry_Info

friend class CSeq_entry_Info ( void  )

friend

Definition at line 500 of file tse_info.hpp.

CTSE_Chunk_Info

friend class CTSE_Chunk_Info

friend

Definition at line 505 of file tse_info.hpp.

CTSE_Default_Assigner

friend class CTSE_Default_Assigner

friend

Definition at line 510 of file tse_info.hpp.

CTSE_Guard

friend class CTSE_Guard

friend

Definition at line 494 of file tse_info.hpp.

CTSE_Info_Object

friend class CTSE_Info_Object ( void  )

friend

Definition at line 504 of file tse_info.hpp.

CTSE_LoadLock

friend class CTSE_LoadLock

friend

Definition at line 674 of file tse_info.hpp.

CTSE_LoadLockGuard

friend class CTSE_LoadLockGuard

friend

Definition at line 675 of file tse_info.hpp.

CTSE_Lock

friend class CTSE_Lock

friend

Definition at line 673 of file tse_info.hpp.

CTSE_ScopeInfo

friend class CTSE_ScopeInfo

friend

Definition at line 497 of file tse_info.hpp.

CTSE_Split_Info

friend class CTSE_Split_Info

friend

Definition at line 506 of file tse_info.hpp.

Referenced by GetSplitInfo().

CTSEAnnotObjectMapper

friend class CTSEAnnotObjectMapper

friend

Definition at line 656 of file tse_info.hpp.

ITSE_Assigner

friend class ITSE_Assigner

friend

Definition at line 509 of file tse_info.hpp.

Member Data Documentation

m_AnnotIdsFlags

TAnnotIdsFlags CTSE_Info::m_AnnotIdsFlags

private

Definition at line 758 of file tse_info.hpp.

Referenced by HasMatchingAnnotIds(), OnlyGiAnnotIds(), SetSeq_entry(), x_IndexAnnotTSE(), and x_Initialize().

m_AnnotLock

TAnnotLock CTSE_Info::m_AnnotLock

mutableprivate

Definition at line 748 of file tse_info.hpp.

Referenced by GetAnnotLock(), and GetMasterSeqSegments().

m_BaseTSE

unique_ptr<SBaseTSE> CTSE_Info::m_BaseTSE

private

Definition at line 771 of file tse_info.hpp.

Referenced by CTSE_Info(), CScope_Impl::GetEditHandle(), CTSE_ScopeInfo::SetEditTSE(), and x_Reset().

m_BioObjects

TBioObjects CTSE_Info::m_BioObjects

private

Definition at line 776 of file tse_info.hpp.

Referenced by x_FindBioObject(), x_RegisterBioObject(), x_Reset(), and x_UnregisterBioObject().

m_Bioseq_sets

TBioseq_sets CTSE_Info::m_Bioseq_sets

private

Definition at line 730 of file tse_info.hpp.

Referenced by x_FindBioObject(), x_GetBioseq_set(), x_Reset(), x_ResetBioseq_setId(), and x_SetBioseq_setId().

m_Bioseqs

TBioseqs CTSE_Info::m_Bioseqs

private

Definition at line 731 of file tse_info.hpp.

Referenced by ContainsBioseq(), FindBioseq(), GetBioseqsIds(), SetBioseqUpdater(), x_DSAttachContents(), x_DSDetachContents(), x_FindBioObject(), x_GetBioseq(), x_Reset(), x_ResetBioseqId(), x_SetBioseqId(), and x_SetBioseqIds().

m_BioseqsMutex

CFastMutex CTSE_Info::m_BioseqsMutex

mutableprivate

Definition at line 734 of file tse_info.hpp.

Referenced by ContainsBioseq(), FindBioseq(), GetBioseqsIds(), SetBioseqUpdater(), x_FindBioObject(), x_GetBioseq(), x_ResetBioseqId(), x_SetBioseqId(), and x_SetBioseqIds().

m_BioseqUpdater

CRef<CBioseqUpdater> CTSE_Info::m_BioseqUpdater

private

Definition at line 781 of file tse_info.hpp.

Referenced by CTSE_Info(), SetBioseqUpdater(), and x_SetBioseqIds().

m_BlobId

TBlobId CTSE_Info::m_BlobId

private

Definition at line 684 of file tse_info.hpp.

Referenced by CTSE_Info(), GetBlobId(), and GetDescription().

m_BlobState

TBlobState CTSE_Info::m_BlobState

private

Definition at line 688 of file tse_info.hpp.

Referenced by Assign(), CTSE_Info(), GetBlobState(), GetBlobStateOrder(), IsDead(), IsUnavailable(), ResetBlobState(), SetBlobState(), and x_Initialize().

m_BlobVersion

TBlobVersion CTSE_Info::m_BlobVersion

private

Definition at line 685 of file tse_info.hpp.

Referenced by CTSE_Info(), GetBlobVersion(), SetBlobVersion(), and x_Initialize().

m_CachePosition

TTSE_Cache::iterator CTSE_Info::m_CachePosition

mutableprivate

Definition at line 716 of file tse_info.hpp.

Referenced by CDataSource::x_ReleaseLastTSELock().

m_CacheState

ECacheState CTSE_Info::m_CacheState

mutableprivate

Definition at line 713 of file tse_info.hpp.

Referenced by x_Initialize(), and CDataSource::x_ReleaseLastTSELock().

m_DataSource

CDataSource* CTSE_Info::m_DataSource

private

Definition at line 678 of file tse_info.hpp.

Referenced by GetDataSource(), HasDataSource(), x_DSAttachContents(), x_DSDetachContents(), x_Initialize(), and ~CTSE_Info().

m_EditSaver

CRef<IEditSaver> CTSE_Info::m_EditSaver

private

Definition at line 773 of file tse_info.hpp.

Referenced by CTSE_Info(), GetEditSaver(), and x_Reset().

m_FeatIdIndex

TFeatIdIndex CTSE_Info::m_FeatIdIndex

private

Definition at line 745 of file tse_info.hpp.

Referenced by x_AddAllFeaturesById(), x_AddFeaturesById(), x_GetFeatIdIndexInt(), x_GetFeatIdIndexStr(), x_HasFeaturesWithId(), x_MapChunkByFeatType(), and x_Reset().

m_IdAnnotInfoMap

TIdAnnotInfoMap CTSE_Info::m_IdAnnotInfoMap

private

Definition at line 744 of file tse_info.hpp.

Referenced by x_IndexAnnotTSE(), CDataSource::x_IndexAnnotTSEs(), x_Reset(), x_UnindexAnnotTSE(), and CDataSource::x_UnindexAnnotTSEs().

m_InternalBioObjNumber

int CTSE_Info::m_InternalBioObjNumber

private

Definition at line 774 of file tse_info.hpp.

Referenced by x_RegisterBioObject(), and x_Reset().

m_LoadMutex

CRef<CLoadMutex> CTSE_Info::m_LoadMutex

private

Definition at line 727 of file tse_info.hpp.

Referenced by CDataSource::GetTSE_LoadLock(), CDataSource::SetLoaded(), CTSE_LoadLock::SetLoaded(), and CDataSource::x_SetLoadLock().

m_LoadState

atomic<ELoadState> CTSE_Info::m_LoadState

private

Definition at line 712 of file tse_info.hpp.

Referenced by CTSE_Info(), GetSplitInfo(), CDataSource::IsLoaded(), SetBlobVersion(), CDataSource::SetLoaded(), SetSeq_entry(), and x_Initialize().

m_LockCounter

CAtomicCounter_WithAutoInit CTSE_Info::m_LockCounter

mutableprivate

Definition at line 719 of file tse_info.hpp.

Referenced by CDataSource::GetTSE_LoadLockIfLoaded(), IsLocked(), CTSE_LoadLock::operator=(), CTSE_LoadLock::Reset(), CDataSource::x_SetLoadLock(), and ~CTSE_Info().

m_LocusIndex

TLocusIndex CTSE_Info::m_LocusIndex

private

Definition at line 746 of file tse_info.hpp.

Referenced by x_GetFeaturesByLocus(), x_MapFeatByLocus(), and x_UnmapFeatByLocus().

m_MasterSeqSegments

CConstRef<CMasterSeqSegments> CTSE_Info::m_MasterSeqSegments

mutableprivate

Definition at line 779 of file tse_info.hpp.

Referenced by GetMasterSeqSegments().

m_MasterSeqSegmentsLoaded

bool CTSE_Info::m_MasterSeqSegmentsLoaded

mutableprivate

Definition at line 778 of file tse_info.hpp.

Referenced by GetMasterSeqSegments().

m_Name

CAnnotName CTSE_Info::m_Name

private

Definition at line 695 of file tse_info.hpp.

Referenced by Assign(), CTSE_Info(), GetName(), and SetName().

m_NamedAnnotObjs

TNamedAnnotObjs CTSE_Info::m_NamedAnnotObjs

private

Definition at line 743 of file tse_info.hpp.

Referenced by GetAnnotIds(), HasAnnot(), x_FindSeq_feat(), x_GetAnnotObjs(), x_GetUnnamedAnnotObjs(), x_HasIdObjects(), x_RemoveAnnotObjs(), x_Reset(), CAnnot_Collector::x_SearchTSE2(), and x_SetAnnotObjs().

m_Removed_Bioseq_sets

TBioseq_sets CTSE_Info::m_Removed_Bioseq_sets

private

Definition at line 732 of file tse_info.hpp.

Referenced by SetSeq_entry(), x_GetBioseq_set(), x_Reset(), and x_ResetBioseq_setId().

m_Removed_Bioseqs

TBioseqs CTSE_Info::m_Removed_Bioseqs

private

Definition at line 733 of file tse_info.hpp.

Referenced by SetSeq_entry(), x_GetBioseq(), x_Reset(), and x_ResetBioseqId().

m_RequestedId

CSeq_id_Handle CTSE_Info::m_RequestedId

mutableprivate

Definition at line 749 of file tse_info.hpp.

Referenced by GetRequestedId(), SetRequestedId(), and SetSeq_entry().

m_SetObjectInfo

CRef<CTSE_SetObjectInfo> CTSE_Info::m_SetObjectInfo

private

Definition at line 740 of file tse_info.hpp.

Referenced by SetSeq_entry(), x_GetSNP_Info(), and x_Reset().

m_Split

CRef<CTSE_Split_Info> CTSE_Info::m_Split

private

Definition at line 737 of file tse_info.hpp.

Referenced by Assign(), ContainsBioseq(), CTSE_Info(), GetBioseqsIds(), GetSplitInfo(), HasSplitInfo(), SetSeq_entry(), UpdateFeatIdIndex(), x_DoUpdate(), x_DSAttachContents(), x_DSDetachContents(), x_GetBioseq(), x_GetBioseq_set(), x_GetRecords(), x_LoadChunk(), x_LoadChunks(), x_LoadDelayedMainChunk(), x_NeedsDelayedMainChunk(), x_Reset(), x_ResetBioseq_setId(), x_ResetBioseqId(), x_UpdateAnnotIndexContents(), and ~CTSE_Info().

m_TopLevelObjectPtr

CRef<CSerialObject> CTSE_Info::m_TopLevelObjectPtr

private

Definition at line 692 of file tse_info.hpp.

Referenced by GetTopLevelObjectPtr(), SetTopLevelObject(), and x_GetTopLevelSeq_submit().

m_TopLevelObjectType

ETopLevelObjectType CTSE_Info::m_TopLevelObjectType

private

Definition at line 691 of file tse_info.hpp.

Referenced by Assign(), CTSE_Info(), GetTopLevelObjectType(), SetTopLevelObject(), and x_Initialize().

m_UsedMemory

size_t CTSE_Info::m_UsedMemory

private

Definition at line 698 of file tse_info.hpp.

Referenced by AddUsedMemory(), Assign(), CTSE_Info(), GetUsedMemory(), SetUsedMemory(), and x_Initialize().

---

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

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