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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCPSGDataLoader.html below:

NCBI C++ ToolKit: CPSGDataLoader Class Reference

Search Toolkit Book for CPSGDataLoader

#include <objtools/data_loaders/genbank/psg_loader.hpp>

TBlobId GetBlobIdFromSatSatKey (int sat, int sat_key, int sub_sat) const override TBlobId GetBlobId (const CSeq_id_Handle &idh) override TBlobId GetBlobIdFromString (const string &str) const override bool CanGetBlobById (void) const override TTSE_Lock GetBlobById (const TBlobId &blob_id) override TTSE_LockSet GetRecords (const CSeq_id_Handle &idh, EChoice choice) override 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 GetOrphanAnnotRecordsNA (const TSeq_idSet &seq_ids, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override TTSE_LockSet GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override void GetChunk (TChunk chunk) override void GetChunks (const TChunkSet &chunks) override void GetBlobs (TTSE_LockSets &tse_sets) override void GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret) override void GetIds (const CSeq_id_Handle &idh, TIds &ids) override SAccVerFound GetAccVerFound (const CSeq_id_Handle &idh) override SGiFound GetGiFound (const CSeq_id_Handle &idh) override TTaxId GetTaxId (const CSeq_id_Handle &idh) override Request for a taxonomy id of a sequence. More...
TSeqPos GetSequenceLength (const CSeq_id_Handle &idh) override Request for a length of a sequence. More...
SHashFound GetSequenceHashFound (const CSeq_id_Handle &idh) override STypeFound GetSequenceTypeFound (const CSeq_id_Handle &idh) override int GetSequenceState (const CSeq_id_Handle &idh) override Request for a state of a sequence. More...
void DropTSE (CRef< CTSE_Info > tse_info) override TNamedAnnotNames GetNamedAnnotAccessions (const CSeq_id_Handle &idh) override TNamedAnnotNames GetNamedAnnotAccessions (const CSeq_id_Handle &idh, const string &named_acc) override bool HaveCache (TCacheType) override void PurgeCache (TCacheType, time_t=0) override void CloseCache (void) override void GetBulkIds (const TIds &ids, TLoaded &loaded, TBulkIds &ret) override void GetAccVers (const TIds &ids, TLoaded &loaded, TIds &ret) override void GetGis (const TIds &ids, TLoaded &loaded, TGis &ret) override void GetLabels (const TIds &ids, TLoaded &loaded, TLabels &ret) override void GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret) override void GetSequenceStates (const TIds &ids, TLoaded &loaded, TSequenceStates &ret) override void GetSequenceHashes (const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known) override void GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret) override void GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret) override virtual ~CGBDataLoader (void) CConstRef< CSeqref > GetSatSatkey (const CSeq_id_Handle &idh) CConstRef< CSeqref > GetSatSatkey (const CSeq_id &id) TRealBlobId GetRealBlobId (const TBlobId &blob_id) const TRealBlobId GetRealBlobId (const CTSE_Info &tse_info) const TExpirationTimeout GetIdExpirationTimeout (void) const void SetIdExpirationTimeout (TExpirationTimeout timeout) bool GetAlwaysLoadExternal (void) const void SetAlwaysLoadExternal (bool flag) bool GetAlwaysLoadNamedAcc (void) const void SetAlwaysLoadNamedAcc (bool flag) bool GetAddWGSMasterDescr (void) const void SetAddWGSMasterDescr (bool flag) bool HasHUPIncluded (void) const EGBErrorAction GetPTISErrorAction (void) const void SetPTISErrorAction (EGBErrorAction action) virtual CObjectManager::TPriority GetDefaultPriority (void) const override virtual bool GetTrackSplitSeq () const override 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 GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, 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 TGi GetGi (const CSeq_id_Handle &idh) Request for a gi of a sequence. More...
virtual string GetLabel (const CSeq_id_Handle &idh) Request for a label string 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 int GetSequenceHash (const CSeq_id_Handle &idh) Request for a sequence hash. More...
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 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 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 Uint4 EstimateLoadBytes (const CTSE_Chunk_Info &chunk) const virtual double EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const virtual unsigned GetDefaultBlobCacheSizeLimit () 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 static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const CGBLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static CSeq_id::ESNPScaleLimit GetSNP_Scale_Limit (void) static void SetSNP_Scale_Limit (CSeq_id::ESNPScaleLimit value) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (CReader *reader=0) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &reader_name, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (const string &reader_name) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, EIncludeHUP include_hup, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (EIncludeHUP include_hup) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, EIncludeHUP include_hup, const string &web_cookie, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (EIncludeHUP include_hup, const string &web_cookie) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &reader_name, EIncludeHUP include_hup, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (const string &reader_name, EIncludeHUP include_hup) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &reader_name, EIncludeHUP include_hup, const string &web_cookie, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (const string &reader_name, EIncludeHUP include_hup, const string &web_cookie) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const TParamTree &params, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (const TParamTree &params) static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const CGBLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet) static string GetLoaderNameFromArgs (const CGBLoaderParams &params) static TParamTree * GetParamsSubnode (TParamTree *params, const string &subnode_name) static TParamTree * GetLoaderParams (TParamTree *params) static TParamTree * GetReaderParams (TParamTree *params, const string &reader_name) static void SetParam (TParamTree *params, const string &param_name, const string &param_value) static const TParamTree * GetParamsSubnode (const TParamTree *params, const string &subnode_name) static const TParamTree * GetLoaderParams (const TParamTree *params) static const TParamTree * GetReaderParams (const TParamTree *params, const string &reader_name) static string GetParam (const TParamTree *params, const string &param_name) static bool IsUsingPSGLoader (void) 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 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 void EnableDebugDump (bool on) enum EIncludeHUP { eIncludeHUP } enum ECacheType { fCache_Id = CReaderCacheManager::fCache_Id , fCache_Blob = CReaderCacheManager::fCache_Blob , fCache_Any = CReaderCacheManager::fCache_Any } typedef unsigned TConn typedef CBlob_id TRealBlobId typedef set< string > TNamedAnnotNames typedef SRegisterLoaderInfo< CGBDataLoader > TRegisterLoaderInfo typedef TPluginManagerParamTree TParamTree typedef CReaderCacheManager::TCacheType TCacheType typedef Uint4 TExpirationTimeout 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...
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...
CGBDataLoader (const string &loader_name, const CGBLoaderParams &params) CDataLoader (void) CDataLoader (const string &loader_name) void SetName (const string &loader_name) CDataSource * GetDataSource (void) const virtual void DeleteThis (void) Virtual method "deleting" this object. More...
static string x_GetLoaderMethod (const TParamTree *params) 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...
TExpirationTimeout m_IdExpirationTimeout bool m_AlwaysLoadExternal bool m_AlwaysLoadNamedAcc bool m_AddWGSMasterDescr bool m_HasHUPIncluded EGBErrorAction m_PTISErrorAction string m_WebCookie

Definition at line 123 of file psg_loader.hpp.

◆ CPSGDataLoader() [1/2] CPSGDataLoader::CPSGDataLoader ( void ) private ◆ CPSGDataLoader() [2/2] ◆ ~CPSGDataLoader() CPSGDataLoader::~CPSGDataLoader ( void ) private

Definition at line 208 of file psg_loader.cpp.

◆ CanGetBlobById() bool CPSGDataLoader::CanGetBlobById ( void ) const overridevirtual ◆ CloseCache() void CPSGDataLoader::CloseCache ( void ) inlineoverridevirtual ◆ DropTSE() ◆ GetAccVerFound() ◆ GetAccVers() ◆ GetBlobById() ◆ GetBlobId() ◆ GetBlobIdFromSatSatKey() ◆ GetBlobIdFromString() ◆ GetBlobs() ◆ GetBulkIds() ◆ GetCDDAnnots() ◆ GetChunk() void CPSGDataLoader::GetChunk ( TChunk chunk ) overridevirtual ◆ GetChunks() ◆ GetExternalAnnotRecordsNA() ◆ GetGiFound() ◆ GetGis() ◆ GetIds() ◆ GetLabels() ◆ GetNamedAnnotAccessions() [1/2] ◆ GetNamedAnnotAccessions() [2/2] ◆ GetOrphanAnnotRecordsNA() ◆ GetRecords() ◆ GetSequenceHashes() ◆ GetSequenceHashFound() ◆ GetSequenceLength() ◆ GetSequenceLengths() ◆ GetSequenceState() ◆ GetSequenceStates() ◆ GetSequenceTypeFound() ◆ GetSequenceTypes() ◆ GetSNP_Scale_Limit() ◆ GetTaxId() ◆ GetTaxIds() ◆ HaveCache() ◆ PurgeCache() void CPSGDataLoader::PurgeCache ( TCacheType , time_t = 0 ) inlineoverridevirtual ◆ RegisterInObjectManager() [1/2] ◆ RegisterInObjectManager() [2/2] ◆ SetSNP_Scale_Limit() ◆ x_GetRealBlobId() ◆ CGBLoaderMaker< CPSGDataLoader > ◆ m_Impl

Definition at line 208 of file psg_loader.hpp.

Referenced by CPSGDataLoader(), DropTSE(), GetAccVerFound(), GetAccVers(), GetBlobById(), GetBlobId(), GetBlobs(), GetBulkIds(), GetCDDAnnots(), GetChunk(), GetChunks(), GetExternalAnnotRecordsNA(), GetGiFound(), GetGis(), GetIds(), GetLabels(), GetOrphanAnnotRecordsNA(), GetRecords(), GetSequenceHashes(), GetSequenceHashFound(), GetSequenceLength(), GetSequenceLengths(), GetSequenceState(), GetSequenceStates(), GetSequenceTypeFound(), GetSequenceTypes(), GetTaxId(), and GetTaxIds().

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

include/objtools/data_loaders/genbank/psg_loader.hpp
src/objtools/data_loaders/genbank/psg_loader.cpp

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