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NCBI C++ ToolKit: CSplitDataLoader Class Reference
Search Toolkit Book for CSplitDataLoader
#include "split_loader.hpp"
(Private to src/app/objmgr/split_demo.)
typedef SRegisterLoaderInfo< CSplitDataLoader > TRegisterLoaderInfo 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 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...
virtual ~CSplitDataLoader (void) virtual void DropTSE (CRef< CTSE_Info > tse_info) 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...
virtual void GetChunk (TChunk chunk) virtual TBlobId GetBlobId (const CSeq_id_Handle &idh) virtual bool CanGetBlobById (void) const virtual TTSE_Lock GetBlobById (const TBlobId &blob_id) virtual ~CDataLoader (void) 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 GetBlobIdFromString (const string &str) const virtual TBlobVersion GetBlobVersion (const TBlobId &id) virtual SRequestDetails ChoiceToDetails (EChoice choice) const virtual EChoice DetailsToChoice (const SRequestDetails::TAnnotSet &annots) const virtual EChoice DetailsToChoice (const SRequestDetails &details) const virtual void GetChunks (const TChunkSet &chunks) 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 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...
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 CSplitDataLoader (const string &loader_name, const string &data_file) CSplitDataLoader (const CSplitDataLoader &) CSplitDataLoader & operator= (const CSplitDataLoader &) void x_LoadData (CTSE_LoadLock &load_lock) void x_SplitSeq (TChunks &chunks, CBioseq &bioseq) void x_SplitSet (TChunks &chunks, CBioseq_set &seqset) void x_SplitSeqData (TChunks &chunks, CSeq_id_Handle idh, CBioseq &bioseq) void x_SplitDescr (TChunks &chunks, TPlace place, CSeq_descr &descr) void x_SplitAnnot (TChunks &chunks, TPlace place, CBioseq::TAnnot &annots) void x_SplitFeats (CTSE_Chunk_Info &chunk, const CSeq_annot &annot) void x_SplitAligns (CTSE_Chunk_Info &chunk, const CSeq_annot &annot) void x_SplitGraphs (CTSE_Chunk_Info &chunk, const CSeq_annot &annot)
Definition at line 54 of file split_loader.hpp.
◆ TAnnotChunks ◆ TAnnots ◆ TChunks ◆ TDescrChunks ◆ TIds ◆ TPlace ◆ TRegisterLoaderInfo ◆ TSequenceChunks ◆ TSplitLoaderMaker ◆ ~CSplitDataLoader() CSplitDataLoader::~CSplitDataLoader ( void ) virtual
Definition at line 79 of file split_loader.cpp.
◆ CSplitDataLoader() [1/2] ◆ CSplitDataLoader() [2/2] ◆ CanGetBlobById() bool CSplitDataLoader::CanGetBlobById ( void ) const virtual ◆ DropTSE() ◆ GetBlobById() ◆ GetBlobId() ◆ GetChunk() void CSplitDataLoader::GetChunk ( TChunk chunk ) virtual
Reimplemented from CDataLoader.
Definition at line 112 of file split_loader.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), CTSE_Chunk_Info::GetChunkId(), CTSE_Chunk_Info::IsLoaded(), ITERATE, m_AnnotChunks, m_DescrChunks, m_SeqChunks, CTSE_Chunk_Info::SetLoaded(), CTSE_Chunk_Info::x_LoadAnnot(), CTSE_Chunk_Info::x_LoadDescr(), and CTSE_Chunk_Info::x_LoadSequence().
◆ GetLoaderNameFromArgs() ◆ GetRecords() ◆ operator=() ◆ RegisterInObjectManager() ◆ x_LoadData()
Definition at line 178 of file split_loader.cpp.
References _ASSERT, eSerial_AsnText, info, CSeq_entry_Base::IsSeq(), m_DataFile, m_NextChunkId, m_NextSeqsetId, m_TSE, NON_CONST_ITERATE, CObjectIStream::Open(), CRef< C, Locker >::Reset(), CTSE_LoadLock::SetLoaded(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), x_SplitSeq(), and x_SplitSet().
Referenced by GetBlobById().
◆ x_SplitAligns()
Definition at line 371 of file split_loader.cpp.
References _ASSERT, CSeq_align::CheckNumRows(), CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::GetAlign(), CSeq_annot_Base::GetData(), CSeq_id_Handle::GetHandle(), CSeq_align::GetSeq_id(), set< Key, Compare >::insert(), CSeq_annot_Base::C_Data::IsAlign(), ITERATE, row, and CTSE_Chunk_Info::x_AddAnnotType().
Referenced by x_SplitAnnot().
◆ x_SplitAnnot()
Definition at line 311 of file split_loader.cpp.
References data, CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::GetData(), m_AnnotChunks, m_NextChunkId, NON_CONST_ITERATE, CSeq_annot_Base::C_Data::Which(), CTSE_Chunk_Info::x_AddAnnotPlace(), x_SplitAligns(), x_SplitFeats(), and x_SplitGraphs().
Referenced by x_SplitSeq(), and x_SplitSet().
◆ x_SplitDescr() ◆ x_SplitFeats()
Definition at line 346 of file split_loader.cpp.
References _ASSERT, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), set< Key, Compare >::insert(), CSeq_annot_Base::C_Data::IsFtable(), CSeq_feat_Base::IsSetProduct(), ITERATE, CSeqFeatData_Base::Which(), and CTSE_Chunk_Info::x_AddAnnotType().
Referenced by x_SplitAnnot().
◆ x_SplitGraphs() ◆ x_SplitSeq() void CSplitDataLoader::x_SplitSeq ( TChunks & chunks, CBioseq & bioseq ) private
Definition at line 210 of file split_loader.cpp.
References CBioseq::GetFirstId(), CSeq_id_Handle::GetHandle(), CBioseq_Base::IsSetAnnot(), CBioseq_Base::IsSetDescr(), CBioseq_Base::ResetDescr(), CBioseq_Base::SetAnnot(), CBioseq_Base::SetDescr(), x_SplitAnnot(), x_SplitDescr(), and x_SplitSeqData().
Referenced by x_LoadData(), and x_SplitSet().
◆ x_SplitSeqData() ◆ x_SplitSet()
Definition at line 228 of file split_loader.cpp.
References CObject_id_Base::GetId(), CBioseq_set_Base::GetId(), CBioseq_set_Base::IsSetAnnot(), CBioseq_set_Base::IsSetDescr(), m_NextSeqsetId, NON_CONST_ITERATE, CBioseq_set_Base::ResetDescr(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetDescr(), CBioseq_set_Base::SetId(), CBioseq_set_Base::SetSeq_set(), x_SplitAnnot(), x_SplitDescr(), and x_SplitSeq().
Referenced by x_LoadData().
◆ CParamLoaderMaker< CSplitDataLoader, const string & > ◆ m_AnnotChunks ◆ m_DataFile string CSplitDataLoader::m_DataFile private ◆ m_DescrChunks ◆ m_Ids ◆ m_NextChunkId int CSplitDataLoader::m_NextChunkId private ◆ m_NextSeqsetId int CSplitDataLoader::m_NextSeqsetId private ◆ m_SeqChunks ◆ m_TSE
The documentation for this class was generated from the following files:
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