CDataLoader Class Reference

Search Toolkit Book for CDataLoader

#include <objmgr/data_loader.hpp>

Inheritance diagram for CDataLoader:

Collaboration diagram for CDataLoader:

Classes
struct	SAccVerFound
	Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left for compatibility. More...
struct	SGiFound
	Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for compatibility. More...
struct	SHashFound
	Better replacement of GetSequenceHash(), this method should be defined in data loaders, GetSequenceHash() is left for compatibility. More...
struct	STypeFound
	Better replacement of GetSequenceType(), this method should be defined in data loaders, GetSequenceType() is left for compatibility. More...

Public Types
enum	EChoice {   eBlob , eBioseq , eCore , eBioseqCore ,   eSequence , eFeatures , eGraph , eAlign ,   eAnnot , eExtFeatures , eExtGraph , eExtAlign ,   eExtAnnot , eOrphanAnnot , eAll }
	main blob is blob with sequence all other blobs are external and contain external annotations More...
typedef CTSE_Lock	TTSE_Lock
typedef set< TTSE_Lock >	TTSE_LockSet
typedef CRef< CTSE_Chunk_Info >	TChunk
typedef vector< TChunk >	TChunkSet
typedef set< string >	TProcessedNAs
typedef set< CSeq_id_Handle >	TSeq_idSet
typedef vector< CSeq_id_Handle >	TIds
typedef vector< bool >	TLoaded
	Bulk loading interface for a small pieces of information per id. More...
typedef vector< TIds >	TBulkIds
typedef vector< TGi >	TGis
typedef vector< string >	TLabels
typedef vector< TTaxId >	TTaxIds
typedef vector< TSeqPos >	TSequenceLengths
typedef vector< CSeq_inst::TMol >	TSequenceTypes
typedef vector< int >	TSequenceStates
typedef vector< int >	TSequenceHashes
typedef vector< bool >	THashKnown
typedef map< CSeq_id_Handle, TTSE_LockSet >	TTSE_LockSets
typedef vector< vector< CSeq_id_Handle > >	TSeqIdSets
typedef vector< CTSE_Lock >	TCDD_Locks
typedef CBlobIdKey	TBlobId
typedef int	TBlobVersion
typedef CRef< IEditSaver >	TEditSaver
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
virtual	~CDataLoader (void)
virtual TTSE_LockSet	GetRecords (const CSeq_id_Handle &idh, EChoice choice)
	Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...
TTSE_LockSet	GetRecordsNoBlobState (const CSeq_id_Handle &idh, EChoice choice)
	The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateException. More...
virtual TTSE_LockSet	GetDetailedRecords (const CSeq_id_Handle &idh, const SRequestDetails &details)
	Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...
virtual TTSE_LockSet	GetExternalRecords (const CBioseq_Info &bioseq)
	Request from a datasource set of blobs with external annotations. More...
virtual TTSE_LockSet	GetOrphanAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
	old Get*AnnotRecords() methods More...
virtual TTSE_LockSet	GetExternalAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
virtual TTSE_LockSet	GetExternalAnnotRecords (const CBioseq_Info &bioseq, const SAnnotSelector *sel)
virtual TTSE_LockSet	GetOrphanAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
	new Get*AnnotRecords() methods More...
virtual TTSE_LockSet	GetOrphanAnnotRecordsNA (const TSeq_idSet &ids, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
virtual TTSE_LockSet	GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
virtual TTSE_LockSet	GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
virtual void	GetIds (const CSeq_id_Handle &idh, TIds &ids)
	Request for a list of all Seq-ids of a sequence. More...
bool	SequenceExists (const CSeq_id_Handle &idh)
	helper function to check if sequence exists, uses GetIds() More...
virtual CSeq_id_Handle	GetAccVer (const CSeq_id_Handle &idh)
	Request for a accession.version Seq-id of a sequence. More...
virtual SAccVerFound	GetAccVerFound (const CSeq_id_Handle &idh)
virtual TGi	GetGi (const CSeq_id_Handle &idh)
	Request for a gi of a sequence. More...
virtual SGiFound	GetGiFound (const CSeq_id_Handle &idh)
virtual string	GetLabel (const CSeq_id_Handle &idh)
	Request for a label string of a sequence. More...
virtual TTaxId	GetTaxId (const CSeq_id_Handle &idh)
	Request for a taxonomy id of a sequence. More...
virtual TSeqPos	GetSequenceLength (const CSeq_id_Handle &idh)
	Request for a length of a sequence. More...
virtual CSeq_inst::TMol	GetSequenceType (const CSeq_id_Handle &idh)
	Request for a type of a sequence Returns CSeq_inst::eMol_not_set if sequence is not known. More...
virtual STypeFound	GetSequenceTypeFound (const CSeq_id_Handle &idh)
virtual int	GetSequenceState (const CSeq_id_Handle &idh)
	Request for a state of a sequence. More...
virtual int	GetSequenceHash (const CSeq_id_Handle &idh)
	Request for a sequence hash. More...
virtual SHashFound	GetSequenceHashFound (const CSeq_id_Handle &idh)
virtual void	GetBulkIds (const TIds &ids, TLoaded &loaded, TBulkIds &ret)
	Bulk request for all Seq-ids of a set of sequences. More...
virtual void	GetAccVers (const TIds &ids, TLoaded &loaded, TIds &ret)
	Bulk request for accession.version Seq-ids of a set of sequences. More...
virtual void	GetGis (const TIds &ids, TLoaded &loaded, TGis &ret)
	Bulk request for gis of a set of sequences. More...
virtual void	GetLabels (const TIds &ids, TLoaded &loaded, TLabels &ret)
	Bulk request for label strings of a set of sequences. More...
virtual void	GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)
	Bulk request for taxonomy ids of a set of sequences. More...
virtual void	GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)
	Bulk request for lengths of a set of sequences. More...
virtual void	GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)
	Bulk request for types of a set of sequences. More...
virtual void	GetSequenceStates (const TIds &ids, TLoaded &loaded, TSequenceStates &ret)
	Bulk request for states of a set of sequences. More...
virtual void	GetSequenceHashes (const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)
	Bulk request for hashes of a set of sequences. More...
virtual void	GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)
virtual void	GetBlobs (TTSE_LockSets &tse_sets)
virtual TBlobId	GetBlobId (const CSeq_id_Handle &idh)
virtual TBlobId	GetBlobIdFromString (const string &str) const
virtual TBlobVersion	GetBlobVersion (const TBlobId &id)
virtual bool	CanGetBlobById (void) const
virtual TTSE_Lock	GetBlobById (const TBlobId &blob_id)
virtual SRequestDetails	ChoiceToDetails (EChoice choice) const
virtual EChoice	DetailsToChoice (const SRequestDetails::TAnnotSet &annots) const
virtual EChoice	DetailsToChoice (const SRequestDetails &details) const
virtual void	GetChunk (TChunk chunk_info)
virtual void	GetChunks (const TChunkSet &chunks)
virtual void	DropTSE (CRef< CTSE_Info > tse_info)
void	SetTargetDataSource (CDataSource &data_source)
	Specify datasource to send loaded data to. More...
string	GetName (void) const
virtual TTSE_Lock	ResolveConflict (const CSeq_id_Handle &id, const TTSE_LockSet &tse_set)
	Resolve TSE conflict *select the best TSE from the set of dead TSEs. More...
virtual void	GC (void)
virtual TEditSaver	GetEditSaver () const
virtual CObjectManager::TPriority	GetDefaultPriority (void) const
virtual Uint4	EstimateLoadBytes (const CTSE_Chunk_Info &chunk) const
virtual double	EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
virtual unsigned	GetDefaultBlobCacheSizeLimit () const
virtual bool	GetTrackSplitSeq () 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

Static Public Member Functions
static bool	IsRequestedAnyNA (const SAnnotSelector *sel)
static bool	IsRequestedNA (const string &na, const SAnnotSelector *sel)
static bool	IsProcessedNA (const string &na, const TProcessedNAs *processed_nas)
static void	SetProcessedNA (const string &na, TProcessedNAs *processed_nas)
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)

Protected Member Functions
	CDataLoader (void)
	CDataLoader (const string &loader_name)
void	SetName (const string &loader_name)
CDataSource *	GetDataSource (void) const
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Static Protected Member Functions
static void	RegisterInObjectManager (CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)
	Register the loader only if the name is not yet registered in the object manager. More...

Private Member Functions
	CDataLoader (const CDataLoader &)
CDataLoader &	operator= (const CDataLoader &)

Private Attributes
string	m_Name
CDataSource *	m_DataSource

Friends
class	CGBReaderRequestResult
class	CScope_Impl
class	CObjectManager

Additional Inherited Members
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...
static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...
static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...
static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...
static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Detailed Description

Definition at line 198 of file data_loader.hpp.

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

• include/objmgr/data_loader.hpp
• src/objmgr/data_loader.cpp