CBlastDbDataLoader Member List

This is the complete list of members for CBlastDbDataLoader, including all inherited members.

AddReference(void) const	CObject	inline
CanBeDeleted(void) const THROWS_NONE	CObject	inline
CanGetBlobById() const	CBlastDbDataLoader	virtual
CBlastDbDataLoader()	CBlastDbDataLoader	inlineprotected
CBlastDbDataLoader(const string &loader_name, const SBlastDbParam &param)	CBlastDbDataLoader	protected
CBlastDbDataLoader(const CBlastDbDataLoader &)	CBlastDbDataLoader	protected
CDataLoader(void)	CDataLoader	protected
CDataLoader(const string &loader_name)	CDataLoader	protected
CDataLoader(const CDataLoader &)	CDataLoader	private
CDebugDumpable(void)	CDebugDumpable	inline
CheckReferenceOverflow(TCount count) const	CObject	private
ChoiceToDetails(EChoice choice) const	CDataLoader	virtual
CObject(void)	CObject
CObject(const CObject &src)	CObject
CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam > class	CBlastDbDataLoader	friend
DebugDump(CDebugDumpContext ddc, unsigned int depth) const	CBlastDbDataLoader	virtual
DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const	CDebugDumpable
DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const	CDebugDumpable
DeleteThis(void)	CObject	protectedvirtual
DetailsToChoice(const SRequestDetails::TAnnotSet &annots) const	CDataLoader	virtual
DetailsToChoice(const SRequestDetails &details) const	CDataLoader	virtual
DoDeleteThisObject(void)	CObject	virtual
DoNotDeleteThisObject(void)	CObject	virtual
DropTSE(CRef< CTSE_Info > tse_info)	CDataLoader	virtual
DumpToConsole(void) const	CDebugDumpable
eAlign enum value	CDataLoader
eAll enum value	CDataLoader
EAllocFillMode enum name	CObject
eAllocFillNone enum value	CObject
eAllocFillPattern enum value	CObject
eAllocFillZero enum value	CObject
eAnnot enum value	CDataLoader
eBioseq enum value	CDataLoader
eBioseqCore enum value	CDataLoader
eBlob enum value	CDataLoader
EChoice enum name	CDataLoader
eCore enum value	CDataLoader
eCounterBitsCanBeDeleted	CObject	static
eCounterBitsInPlainHeap	CObject	static
eCounterBitsPlaceMask	CObject	static
eCounterStateMask	CObject	static
eCounterStep	CObject	static
eCounterValid	CObject	static
EDbType enum name	CBlastDbDataLoader
eExtAlign enum value	CDataLoader
eExtAnnot enum value	CDataLoader
eExtFeatures enum value	CDataLoader
eExtGraph enum value	CDataLoader
eFeatures enum value	CDataLoader
eGraph enum value	CDataLoader
EnableDebugDump(bool on)	CDebugDumpable	static
eNucleotide enum value	CBlastDbDataLoader
eOrphanAnnot enum value	CDataLoader
eProtein enum value	CBlastDbDataLoader
eSequence enum value	CDataLoader
EstimateLoadBytes(const CTSE_Chunk_Info &chunk) const	CDataLoader	virtual
EstimateLoadSeconds(const CTSE_Chunk_Info &chunk, Uint4 bytes) const	CDataLoader	virtual
eUnknown enum value	CBlastDbDataLoader
GC(void)	CDataLoader	virtual
GetAccVer(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetAccVerFound(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetAccVers(const TIds &ids, TLoaded &loaded, TIds &ret)	CDataLoader	virtual
GetAllocFillMode(void)	CObject	static
GetBlobById(const TBlobId &blob_id)	CBlastDbDataLoader	virtual
GetBlobId(const CSeq_id_Handle &idh)	CBlastDbDataLoader	virtual
GetBlobIdFromString(const string &str) const	CDataLoader	virtual
GetBlobs(TTSE_LockSets &tse_sets)	CDataLoader	virtual
GetBlobVersion(const TBlobId &id)	CDataLoader	virtual
GetBulkIds(const TIds &ids, TLoaded &loaded, TBulkIds &ret)	CDataLoader	virtual
GetCDDAnnots(const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)	CDataLoader	virtual
GetChunk(TChunk chunk)	CBlastDbDataLoader	virtual
GetChunks(const TChunkSet &chunks)	CDataLoader	virtual
GetDataSource(void) const	CDataLoader	protected
GetDefaultBlobCacheSizeLimit() const	CDataLoader	virtual
GetDefaultPriority(void) const	CDataLoader	virtual
GetDetailedRecords(const CSeq_id_Handle &idh, const SRequestDetails &details)	CDataLoader	virtual
GetEditSaver() const	CDataLoader	virtual
GetExternalAnnotRecords(const CSeq_id_Handle &idh, const SAnnotSelector *sel)	CDataLoader	virtual
GetExternalAnnotRecords(const CBioseq_Info &bioseq, const SAnnotSelector *sel)	CDataLoader	virtual
GetExternalAnnotRecordsNA(const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)	CDataLoader	virtual
GetExternalAnnotRecordsNA(const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas)	CDataLoader	virtual
GetExternalRecords(const CBioseq_Info &bioseq)	CDataLoader	virtual
GetGi(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetGiFound(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetGis(const TIds &ids, TLoaded &loaded, TGis &ret)	CDataLoader	virtual
GetIds(const CSeq_id_Handle &idh, TIds &ids)	CDataLoader	virtual
GetLabel(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetLabels(const TIds &ids, TLoaded &loaded, TLabels &ret)	CDataLoader	virtual
GetLoaderNameFromArgs(CConstRef< CSeqDB > db_handle)	CBlastDbDataLoader	static
GetLoaderNameFromArgs(const SBlastDbParam &param)	CBlastDbDataLoader	static
GetLoaderNameFromArgs(const string &dbname="nr", const EDbType dbtype=eUnknown)	CBlastDbDataLoader	inlinestatic
GetName(void) const	CDataLoader
GetOrphanAnnotRecords(const CSeq_id_Handle &idh, const SAnnotSelector *sel)	CDataLoader	virtual
GetOrphanAnnotRecordsNA(const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)	CDataLoader	virtual
GetOrphanAnnotRecordsNA(const TSeq_idSet &ids, const SAnnotSelector *sel, TProcessedNAs *processed_nas)	CDataLoader	virtual
GetRecords(const CSeq_id_Handle &idh, EChoice choice)	CBlastDbDataLoader	virtual
GetRecordsNoBlobState(const CSeq_id_Handle &idh, EChoice choice)	CDataLoader
GetSequenceHash(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetSequenceHashes(const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)	CDataLoader	virtual
GetSequenceHashFound(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetSequenceLength(const CSeq_id_Handle &idh)	CBlastDbDataLoader	virtual
GetSequenceLengths(const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)	CBlastDbDataLoader	virtual
CDataLoader::GetSequenceLengths(const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)	CDataLoader	virtual
GetSequenceState(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetSequenceStates(const TIds &ids, TLoaded &loaded, TSequenceStates &ret)	CDataLoader	virtual
GetSequenceType(const CSeq_id_Handle &idh)	CBlastDbDataLoader	virtual
GetSequenceTypeFound(const CSeq_id_Handle &idh)	CDataLoader	virtual
GetSequenceTypes(const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)	CBlastDbDataLoader	virtual
CDataLoader::GetSequenceTypes(const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)	CDataLoader	virtual
GetTaxId(const CSeq_id_Handle &idh)	CBlastDbDataLoader	virtual
GetTaxIds(const TIds &ids, TLoaded &loaded, TTaxIds &ret)	CBlastDbDataLoader	virtual
CDataLoader::GetTaxIds(const TIds &ids, TLoaded &loaded, TTaxIds &ret)	CDataLoader	virtual
GetTrackSplitSeq() const	CDataLoader	virtual
InitCounter(void)	CObject	inlineprivate
InvalidObject(void) const	CObject	private
IsAllocatedInPool(void) const THROWS_NONE	CObject	inline
IsProcessedNA(const string &na, const TProcessedNAs *processed_nas)	CDataLoader	static
IsRequestedAnyNA(const SAnnotSelector *sel)	CDataLoader	static
IsRequestedNA(const string &na, const SAnnotSelector *sel)	CDataLoader	static
m_BlastDb	CBlastDbDataLoader	protected
m_Counter	CObject	mutableprivate
m_DataSource	CDataLoader	private
m_DBName	CBlastDbDataLoader	protected
m_DBType	CBlastDbDataLoader	protected
m_Ids	CBlastDbDataLoader	protected
m_Name	CDataLoader	private
m_UseFixedSizeSlices	CBlastDbDataLoader	protected
ObjectStateCanBeDeleted(TCount count)	CObject	inlineprivatestatic
ObjectStateIsAllocatedInPool(TCount count)	CObject	inlineprivatestatic
ObjectStateReferenced(TCount count)	CObject	inlineprivatestatic
ObjectStateReferencedOnlyOnce(TCount count)	CObject	inlineprivatestatic
ObjectStateUnreferenced(TCount count)	CObject	inlineprivatestatic
ObjectStateValid(TCount count)	CObject	inlineprivatestatic
operator delete(void *ptr)	CObject
operator delete(void *ptr, void *place)	CObject
operator delete(void *ptr, CObjectMemoryPool *place)	CObject
operator delete[](void *ptr)	CObject
operator new(size_t size)	CObject
operator new(size_t size, void *place)	CObject
operator new(size_t size, CObjectMemoryPool *place)	CObject
operator new[](size_t size)	CObject
operator=(const CBlastDbDataLoader &)	CBlastDbDataLoader	protected
CObject::operator=(const CObject &src) THROWS_NONE	CObject	inline
Referenced(void) const THROWS_NONE	CObject	inline
ReferencedOnlyOnce(void) const THROWS_NONE	CObject	inline
RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)	CBlastDbDataLoader	static
RegisterInObjectManager(CObjectManager &om, CRef< CSeqDB > db_handle, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)	CBlastDbDataLoader	static
RegisterInObjectManager(CObjectManager &om, const string &dbname, const EDbType dbtype, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)	CBlastDbDataLoader	static
RegisterInObjectManager(CObjectManager &om, CRef< CSeqDB > db_handle, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)	CBlastDbDataLoader	static
CDataLoader::RegisterInObjectManager(CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)	CDataLoader	protectedstatic
ReleaseReference(void) const	CObject
RemoveLastReference(TCount count) const	CObject	private
RemoveReference(void) const	CObject	inline
ResolveConflict(const CSeq_id_Handle &id, const TTSE_LockSet &tse_set)	CDataLoader	virtual
SequenceExists(const CSeq_id_Handle &idh)	CDataLoader
SetAllocFillMode(EAllocFillMode mode)	CObject	static
SetAllocFillMode(const string &value)	CObject	static
SetName(const string &loader_name)	CDataLoader	protected
SetProcessedNA(const string &na, TProcessedNAs *processed_nas)	CDataLoader	static
SetTargetDataSource(CDataSource &data_source)	CDataLoader
sm_DumpEnabled	CDebugDumpable	privatestatic
TBioseq_setId typedef	CBlastDbDataLoader	protected
TBioseqId typedef	CBlastDbDataLoader	protected
TBlobId typedef	CDataLoader
TBlobVersion typedef	CDataLoader
TBulkIds typedef	CDataLoader
TCDD_Locks typedef	CDataLoader
TChunk typedef	CDataLoader
TChunkSet typedef	CDataLoader
TCount typedef	CObject
TCounter typedef	CObject
TEditSaver typedef	CDataLoader
TGis typedef	CDataLoader
THashKnown typedef	CDataLoader
ThrowNullPointerException(void)	CObject	static
ThrowNullPointerException(const type_info &type)	CObject	static
TIdMap typedef	CBlastDbDataLoader
TIds typedef	CDataLoader
TLabels typedef	CDataLoader
TLoaded typedef	CDataLoader
TLockerType typedef	CObject
TMaker typedef	CBlastDbDataLoader	protected
TPlace typedef	CBlastDbDataLoader	protected
TProcessedNAs typedef	CDataLoader
TRegisterLoaderInfo typedef	CBlastDbDataLoader
TSeq_idSet typedef	CDataLoader
TSeqIdSets typedef	CDataLoader
TSequenceHashes typedef	CDataLoader
TSequenceLengths typedef	CDataLoader
TSequenceStates typedef	CDataLoader
TSequenceTypes typedef	CDataLoader
TTaxIds typedef	CDataLoader
TTSE_Lock typedef	CDataLoader
TTSE_LockSet typedef	CDataLoader
TTSE_LockSets typedef	CDataLoader
x_GetOid(const CSeq_id_Handle &idh)	CBlastDbDataLoader	protected
x_GetOid(const TBlobId &blob_id) const	CBlastDbDataLoader	protected
x_LoadData(const CSeq_id_Handle &idh, int oid, CTSE_LoadLock &lock, int slice_size)	CBlastDbDataLoader	protected
~CBlastDbDataLoader()	CBlastDbDataLoader	virtual
~CDataLoader(void)	CDataLoader	virtual
~CDebugDumpable(void)	CDebugDumpable	virtual
~CObject(void)	CObject	virtual