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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, TBlobVersionTBlobOrder
 
typedef CTSE_Handle::ETopLevelObjectType ETopLevelObjectType
 
typedef map< TIntId, CBioseq_set_Info * > TBioseq_sets
 
typedef CBioseq_InfoTBioseqInfo
 
typedef map< CSeq_id_Handle, TBioseqInfoTBioseqs
 
typedef SIdAnnotObjs::TRange TRange
 
typedef SIdAnnotObjs::TRangeMap TRangeMap
 
typedef SIdAnnotObjs::TAnnotSet TAnnotSet
 
typedef SIdAnnotObjs::TSNPSet TSNPSet
 
typedef map< CSeq_id_Handle, SIdAnnotObjsTAnnotObjs
 
typedef map< CAnnotName, TAnnotObjsTNamedAnnotObjs
 
typedef set< CAnnotNameTNames
 
typedef map< CSeq_id_Handle, SIdAnnotInfoTIdAnnotInfoMap
 
typedef int TFeatIdInt
 
typedef string TFeatIdStr
 
typedef CObject_id TFeatId
 
typedef map< CSeqFeatData::ESubtype, SFeatIdIndexTFeatIdIndex
 
typedef pair< string, boolTLocusKey
 
typedef multimap< TLocusKey, CAnnotObject_Info * > TLocusIndex
 
typedef vector< CSeq_id_HandleTSeqIds
 
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_LockTSeq_annot_Lock
 
typedef pair< TSeq_annot_Lock, intTSeq_feat_Lock
 
- 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< TChunkIdTChunkIds
 
- 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< Uint8TCounter
 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
 
CDataSourceGetDataSource (void) const
 
bool IsLocked (void) const
 
CConstRef< CSeq_entryGetCompleteTSE (void) const
 
CConstRef< CSeq_entryGetTSECore (void) const
 
const CTSE_InfoGetTSE_Info (void) const
 
CTSE_InfoGetTSE_Info (void)
 
CTSE_InfoAssign (const CTSE_Lock &tse)
 
CTSE_InfoAssign (const CTSE_Lock &tse, CRef< CSeq_entry > entry)
 
const TBlobIdGetBlobId (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 CSerialObjectGetTopLevelObjectPtr () const
 
void SetTopLevelObject (ETopLevelObjectType type, CSerialObject *ptr)
 
void SetTopLevelObjectType (ETopLevelObjectType type)
 
bool IsTopLevelSeq_submit () const
 
const CSeq_submitGetTopLevelSeq_submit () const
 
const CSubmit_blockGetTopLevelSubmit_block () const
 
CSubmit_blockSetTopLevelSubmit_block () const
 
void SetTopLevelSubmit_block (CSubmit_block &sub) const
 
const CAnnotNameGetName (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_InfoFindBioseq (const CSeq_id_Handle &id) const
 
CSeq_id_Handle ContainsMatchingBioseq (const CSeq_id_Handle &id) const
 
CConstRef< CBioseq_InfoFindMatchingBioseq (const CSeq_id_Handle &id) const
 
SSeqMatch_TSE GetSeqMatch (const CSeq_id_Handle &id) const
 
CConstRef< CBioseq_InfoGetSegSetMaster (void) const
 
CConstRef< CMasterSeqSegmentsGetMasterSeqSegments (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_InfoGetSplitInfo (void)
 
const CTSE_Split_InfoGetSplitInfo (void) const
 
bool HasSplitInfo (void) const
 
bool x_NeedsDelayedMainChunk (void) const
 
void x_LoadDelayedMainChunk (void) const
 
const CSeq_id_HandleGetRequestedId (void) const
 
void SetRequestedId (const CSeq_id_Handle &requested_id) const
 
TAnnotLockGetAnnotLock (void) const
 
CRef< IEditSaverGetEditSaver () const
 
CBioseq_set_Infox_GetBioseq_set (int id)
 
CBioseq_Infox_GetBioseq (const CSeq_id_Handle &id)
 
CTSE_Info_Objectx_FindBioObject (const CBioObjectId &uniq_id) const
 
SFeatIdIndex::TIndexIntx_GetFeatIdIndexInt (CSeqFeatData::ESubtype type)
 
SFeatIdIndex::TIndexStrx_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_submitx_GetTopLevelSeq_submit () 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
 
CDataSourceGetDataSource (void) const
 
bool HasTSE_Info (void) const
 
bool BelongsToTSE_Info (const CTSE_Info &tse) const
 
const CTSE_InfoGetTSE_Info (void) const
 
CTSE_InfoGetTSE_Info (void)
 
bool HasParent_Info (void) const
 
const CTSE_Info_ObjectGetBaseParent_Info (void) const
 
CTSE_Info_ObjectGetBaseParent_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...
 
CObjectoperator= (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)
 
TAnnotObjsx_SetAnnotObjs (const CAnnotName &name)
 
const TAnnotObjsx_GetAnnotObjs (const CAnnotName &name) const
 
const TAnnotObjsx_GetUnnamedAnnotObjs (void) const
 
void x_RemoveAnnotObjs (const CAnnotName &name)
 
const SIdAnnotObjsx_GetIdObjects (const TAnnotObjs &objs, const CSeq_id_Handle &idh) const
 
const SIdAnnotObjsx_GetIdObjects (const CAnnotName &name, const CSeq_id_Handle &id) const
 
const SIdAnnotObjsx_GetUnnamedIdObjects (const CSeq_id_Handle &id) const
 
bool x_HasIdObjects (const CSeq_id_Handle &id) const
 
pair< SIdAnnotObjs *, boolx_SetIdObjects (TAnnotObjs &objs, const CAnnotName &name, const CSeq_id_Handle &id)
 
pair< SIdAnnotObjs *, boolx_SetIdObjects (const CAnnotName &name, const CSeq_id_Handle &idh)
 
CRef< CSeq_annot_SNP_Infox_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_Infooperator= (const CTSE_Info &)
 

Private Attributes

CDataSourcem_DataSource
 
TBlobId m_BlobId
 
TBlobVersion m_BlobVersion
 
TBlobState m_BlobState
 
ETopLevelObjectType m_TopLevelObjectType
 
CRef< CSerialObjectm_TopLevelObjectPtr
 
CAnnotName m_Name
 
size_t m_UsedMemory
 
atomic< ELoadStatem_LoadState
 
ECacheState m_CacheState
 
TTSE_Cache::iterator m_CachePosition
 
CAtomicCounter_WithAutoInit m_LockCounter
 
CRef< CLoadMutexm_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_Infom_Split
 
CRef< CTSE_SetObjectInfom_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< SBaseTSEm_BaseTSE
 
CRef< IEditSaverm_EditSaver
 
int m_InternalBioObjNumber
 
TBioObjects m_BioObjects
 
bool m_MasterSeqSegmentsLoaded
 
CConstRef< CMasterSeqSegmentsm_MasterSeqSegments
 
CRef< CBioseqUpdaterm_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 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...
 

Detailed Description

Definition at line 182 of file tse_info.hpp.

Member Typedef Documentation

◆ 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

Definition at line 409 of file tse_info.hpp.

◆ TAnnotLockReadGuard

Definition at line 410 of file tse_info.hpp.

◆ TAnnotLockWriteGuard

Definition at line 411 of file tse_info.hpp.

◆ TAnnotObjects

Definition at line 426 of file tse_info.hpp.

◆ TAnnotObjs

Definition at line 305 of file tse_info.hpp.

◆ TAnnotSet

Definition at line 302 of file tse_info.hpp.

◆ TBioObjects

Definition at line 775 of file tse_info.hpp.

◆ TBioseq_sets

Definition at line 296 of file tse_info.hpp.

◆ TBioseqInfo

Definition at line 297 of file tse_info.hpp.

◆ TBioseqs

Definition at line 298 of file tse_info.hpp.

◆ TBioseqsIds

Definition at line 352 of file tse_info.hpp.

◆ TBlobId

Definition at line 210 of file tse_info.hpp.

◆ TBlobOrder

Definition at line 213 of file tse_info.hpp.

◆ TBlobState

Definition at line 211 of file tse_info.hpp.

◆ TBlobVersion

Definition at line 212 of file tse_info.hpp.

◆ TFeatId

Definition at line 337 of file tse_info.hpp.

◆ TFeatIdIndex

Definition at line 347 of file tse_info.hpp.

◆ TFeatIdInt

Definition at line 335 of file tse_info.hpp.

◆ TFeatIdStr

Definition at line 336 of file tse_info.hpp.

◆ TIdAnnotInfoMap

Definition at line 313 of file tse_info.hpp.

◆ TLocusIndex

Definition at line 349 of file tse_info.hpp.

◆ TLocusKey

Definition at line 348 of file tse_info.hpp.

◆ TNamedAnnotObjs

Definition at line 306 of file tse_info.hpp.

◆ TNames

Definition at line 307 of file tse_info.hpp.

◆ TParent

Definition at line 184 of file tse_info.hpp.

◆ TRange

Definition at line 300 of file tse_info.hpp.

◆ TRangeMap

Definition at line 301 of file tse_info.hpp.

◆ TSeq_annot_Lock

Definition at line 483 of file tse_info.hpp.

◆ TSeq_feat_Lock

Definition at line 484 of file tse_info.hpp.

◆ TSeqIds

Definition at line 351 of file tse_info.hpp.

◆ 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

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

◆ CTSE_Info() [4/6]

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

◆ CTSE_Info() [5/6]

CTSE_Info::CTSE_Info ( const CTSE_Lock tse)
explicit

◆ ~CTSE_Info()

CTSE_Info::~CTSE_Info ( void  )
virtual

◆ CTSE_Info() [6/6]

CTSE_Info::CTSE_Info ( const CTSE_Info )
private

Member Function Documentation

◆ AddUsedMemory()

void CTSE_Info::AddUsedMemory ( size_t  size)

◆ Assign() [1/2]

CTSE_Info & CTSE_Info::Assign ( const CTSE_Lock tse)

◆ Assign() [2/2]

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

◆ ContainsBioseq()

bool CTSE_Info::ContainsBioseq ( const CSeq_id_Handle id) const

◆ ContainsMatchingBioseq()

CSeq_id_Handle CTSE_Info::ContainsMatchingBioseq ( const CSeq_id_Handle id) const

◆ FindBioseq()

CConstRef< CBioseq_Info > CTSE_Info::FindBioseq ( const CSeq_id_Handle id) const

◆ FindMatchingBioseq()

CConstRef< CBioseq_Info > CTSE_Info::FindMatchingBioseq ( const CSeq_id_Handle id) const

◆ 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

◆ GetBioseqsIds()

void CTSE_Info::GetBioseqsIds ( TSeqIds ids) const
virtual

◆ GetBlobId()

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

◆ 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

◆ 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

◆ 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

◆ GetDescription()

string CTSE_Info::GetDescription ( void  ) const
virtual

◆ 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

◆ GetName()

const CAnnotName & CTSE_Info::GetName ( void  ) const
inline

◆ 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

◆ GetSeqMatch()

SSeqMatch_TSE CTSE_Info::GetSeqMatch ( const CSeq_id_Handle id) const

◆ GetSplitInfo() [1/2]

CTSE_Split_Info & CTSE_Info::GetSplitInfo ( void  )

◆ 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

◆ GetTopLevelSubmit_block()

const CSubmit_block & CTSE_Info::GetTopLevelSubmit_block ( ) const

◆ 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

◆ HasDataSource()

bool CTSE_Info::HasDataSource ( void  ) const
inline

◆ HasMatchingAnnotIds()

bool CTSE_Info::HasMatchingAnnotIds ( void  ) const
inline

◆ 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

◆ 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

◆ IsLocked()

bool CTSE_Info::IsLocked ( void  ) const
inline

◆ IsTopLevelSeq_submit()

bool CTSE_Info::IsTopLevelSeq_submit ( ) const

◆ 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

◆ 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)

◆ SetBlobState()

void CTSE_Info::SetBlobState ( TBlobState  state)
inline

◆ SetBlobVersion()

void CTSE_Info::SetBlobVersion ( TBlobVersion  version)

◆ SetName()

void CTSE_Info::SetName ( const CAnnotName name)

◆ 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(), CPSGDataLoader_Impl::GetCDDAnnotsOnce(), CSNPSeqInfo::LoadAnnotBlob(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CWGSFileInfo::LoadBlob(), CBamRefSeqInfo::LoadMainEntry(), CBamRefSeqInfo::LoadMainSplit(), CCSRAFileInfo::LoadReadsBlob(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CTSE_Default_Assigner::LoadSeq_entry(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CLoadLockSetter::SetSeq_entry(), x_CreateEmptyLocalCDDEntry(), CBuffer_DataLoader::x_LoadData(), CBlastDbDataLoader::x_LoadData(), CLDS2_DataLoader::x_LoadTSE(), CPSGDataLoader_Impl::x_ReadBlobData(), 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)

◆ SetTopLevelSubmit_block() [1/2]

CSubmit_block & CTSE_Info::SetTopLevelSubmit_block ( ) const

◆ 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

◆ 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)

◆ 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

◆ UpdateFeatIdIndex() [1/2]

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

◆ UpdateFeatIdIndex() [2/2]

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

◆ 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

◆ 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

◆ 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

◆ 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

◆ x_DoUpdate()

void CTSE_Info::x_DoUpdate ( TNeedUpdateFlags  flags)
privatevirtual

◆ x_DSAttachContents()

void CTSE_Info::x_DSAttachContents ( CDataSource ds)
virtual

◆ x_DSDetachContents()

void CTSE_Info::x_DSDetachContents ( CDataSource ds)
virtual

◆ 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

◆ 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

◆ x_GetAnnotObjs()

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

◆ x_GetBioseq()

CBioseq_Info & CTSE_Info::x_GetBioseq ( const CSeq_id_Handle id)

◆ x_GetBioseq_set()

CBioseq_set_Info & CTSE_Info::x_GetBioseq_set ( int  id)

◆ x_GetFeatIdIndexInt()

CTSE_Info::SFeatIdIndex::TIndexInt & CTSE_Info::x_GetFeatIdIndexInt ( CSeqFeatData::ESubtype  type)

◆ x_GetFeatIdIndexStr()

CTSE_Info::SFeatIdIndex::TIndexStr & CTSE_Info::x_GetFeatIdIndexStr ( CSeqFeatData::ESubtype  type)

◆ 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

◆ 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

◆ 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

◆ 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

◆ x_GetFeaturesByLocus()

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

◆ 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

◆ x_GetRecords()

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

◆ x_GetSNP_Info()

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

◆ x_GetTopLevelSeq_submit()

CSeq_submit & CTSE_Info::x_GetTopLevelSeq_submit ( ) const

◆ x_GetUnnamedAnnotObjs()

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

◆ x_GetUnnamedIdObjects()

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

◆ x_HasFeaturesWithId()

bool CTSE_Info::x_HasFeaturesWithId ( CSeqFeatData::ESubtype  subtype) const

◆ 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

◆ x_IndexBioseq()

CBioObjectId CTSE_Info::x_IndexBioseq ( CBioseq_Info info)
private

◆ x_IndexBioseq_set()

CBioObjectId CTSE_Info::x_IndexBioseq_set ( CBioseq_set_Info info)
private

◆ 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

◆ x_LoadChunk()

void CTSE_Info::x_LoadChunk ( TChunkId  chunk_id) const

◆ 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

◆ x_MapAnnotObject() [2/4]

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

◆ x_MapAnnotObject() [3/4]

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

◆ x_MapAnnotObject() [4/4]

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

◆ 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

◆ x_MapChunkByFeatId() [6/9]

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

◆ 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

◆ x_MapChunkByFeatId() [9/9]

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

◆ 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

◆ 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

◆ x_MapFeatById() [3/3]

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

◆ x_MapFeatByLocus()

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

◆ 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

◆ x_NeedsDelayedMainChunk()

bool CTSE_Info::x_NeedsDelayedMainChunk ( void  ) const

◆ x_RegisterBioObject()

CBioObjectId CTSE_Info::x_RegisterBioObject ( CTSE_Info_Object info)
private

◆ x_RemoveAnnotObjs()

void CTSE_Info::x_RemoveAnnotObjs ( const CAnnotName name)
private

◆ x_Reset()

void CTSE_Info::x_Reset ( void  )
private

◆ x_ResetBioseq_setId()

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

◆ x_ResetBioseqId()

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

◆ 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

◆ x_SetBioseq_setId()

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

◆ x_SetBioseqId()

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

◆ x_SetBioseqIds()

void CTSE_Info::x_SetBioseqIds ( CBioseq_Info info)
private

◆ 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

◆ x_UnindexAnnotTSE()

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

◆ 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

◆ x_UnmapAnnotObject() [2/4]

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

◆ x_UnmapAnnotObject() [3/4]

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

◆ x_UnmapAnnotObject() [4/4]

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

◆ x_UnmapAnnotObjects()

void CTSE_Info::x_UnmapAnnotObjects ( const SAnnotObjectsIndex infos)
private

◆ 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

◆ x_UnmapFeatById() [3/3]

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

◆ x_UnmapFeatByLocus()

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

◆ 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

◆ x_UnregisterBioObject()

void CTSE_Info::x_UnregisterBioObject ( CTSE_Info_Object info)
private

◆ x_UpdateAnnotIndexContents()

void CTSE_Info::x_UpdateAnnotIndexContents ( CTSE_Info tse)
virtual

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

◆ 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

◆ 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

◆ m_Bioseqs

TBioseqs CTSE_Info::m_Bioseqs
private

◆ m_BioseqsMutex

CFastMutex CTSE_Info::m_BioseqsMutex
mutableprivate

◆ 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

◆ 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

◆ 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

◆ m_IdAnnotInfoMap

TIdAnnotInfoMap CTSE_Info::m_IdAnnotInfoMap
private

◆ 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

◆ m_LoadState

atomic<ELoadState> CTSE_Info::m_LoadState
private

◆ m_LockCounter

CAtomicCounter_WithAutoInit CTSE_Info::m_LockCounter
mutableprivate

◆ 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

◆ 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

◆ 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

◆ m_UsedMemory

size_t CTSE_Info::m_UsedMemory
private

The documentation for this class was generated from the following files:
Modified on Thu Apr 11 15:05:28 2024 by modify_doxy.py rev. 669887