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CGBDataLoader_Native Class Reference

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

+ Inheritance diagram for CGBDataLoader_Native:
+ Collaboration diagram for CGBDataLoader_Native:

Public Types

enum  ECacheType { fCache_Id = CGBReaderCacheManager::fCache_Id , fCache_Blob = CGBReaderCacheManager::fCache_Blob , fCache_Any = CGBReaderCacheManager::fCache_Any }
 
typedef unsigned TConn
 
typedef CBlob_id TRealBlobId
 
typedef set< stringTNamedAnnotNames
 
typedef CGBReaderCacheManager::TCacheType TCacheType
 
- Public Types inherited from CGBDataLoader
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< stringTNamedAnnotNames
 
typedef SRegisterLoaderInfo< CGBDataLoaderTRegisterLoaderInfo
 
typedef TPluginManagerParamTree TParamTree
 
typedef CReaderCacheManager::TCacheType TCacheType
 
typedef Uint4 TExpirationTimeout
 
- Public Types inherited from CDataLoader
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_LockTTSE_LockSet
 
typedef CRef< CTSE_Chunk_InfoTChunk
 
typedef vector< TChunkTChunkSet
 
typedef set< stringTProcessedNAs
 
typedef set< CSeq_id_HandleTSeq_idSet
 
typedef vector< CSeq_id_HandleTIds
 
typedef vector< boolTLoaded
 Bulk loading interface for a small pieces of information per id. More...
 
typedef vector< TIdsTBulkIds
 
typedef vector< TGiTGis
 
typedef vector< stringTLabels
 
typedef vector< TTaxIdTTaxIds
 
typedef vector< TSeqPosTSequenceLengths
 
typedef vector< CSeq_inst::TMolTSequenceTypes
 
typedef vector< intTSequenceStates
 
typedef vector< intTSequenceHashes
 
typedef vector< boolTHashKnown
 
typedef map< CSeq_id_Handle, TTSE_LockSetTTSE_LockSets
 
typedef vector< vector< CSeq_id_Handle > > TSeqIdSets
 
typedef vector< CTSE_LockTCDD_Locks
 
typedef CBlobIdKey TBlobId
 
typedef int TBlobVersion
 
typedef CRef< IEditSaverTEditSaver
 
- 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

virtual ~CGBDataLoader_Native (void)
 
virtual void DropTSE (CRef< CTSE_Info > tse_info) override
 
virtual void GetIds (const CSeq_id_Handle &idh, TIds &ids) override
 
virtual SAccVerFound GetAccVerFound (const CSeq_id_Handle &idh) override
 
virtual SGiFound GetGiFound (const CSeq_id_Handle &idh) override
 
virtual string GetLabel (const CSeq_id_Handle &idh) override
 Request for a label string of a sequence. More...
 
virtual TTaxId GetTaxId (const CSeq_id_Handle &idh) override
 Request for a taxonomy id of a sequence. More...
 
virtual int GetSequenceState (const CSeq_id_Handle &idh) override
 Request for a state of a sequence. More...
 
virtual SHashFound GetSequenceHashFound (const CSeq_id_Handle &idh) override
 
virtual TSeqPos GetSequenceLength (const CSeq_id_Handle &sih) override
 Request for a length of a sequence. More...
 
virtual STypeFound GetSequenceTypeFound (const CSeq_id_Handle &sih) override
 
virtual void GetBulkIds (const TIds &ids, TLoaded &loader, TBulkIds &ret) override
 
virtual void GetAccVers (const TIds &ids, TLoaded &loader, TIds &ret) override
 
virtual void GetGis (const TIds &ids, TLoaded &loader, TGis &ret) override
 
virtual void GetLabels (const TIds &ids, TLoaded &loader, TLabels &ret) override
 
virtual void GetTaxIds (const TIds &ids, TLoaded &loader, TTaxIds &ret) override
 
virtual void GetSequenceStates (const TIds &ids, TLoaded &loader, TSequenceStates &ret) override
 
virtual void GetSequenceHashes (const TIds &ids, TLoaded &loader, TSequenceHashes &ret, THashKnown &known) override
 
virtual void GetSequenceLengths (const TIds &ids, TLoaded &loader, TSequenceLengths &ret) override
 
virtual void GetSequenceTypes (const TIds &ids, TLoaded &loader, TSequenceTypes &ret) override
 
virtual 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...
 
virtual TTSE_LockSet GetDetailedRecords (const CSeq_id_Handle &idh, const SRequestDetails &details) 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...
 
virtual TTSE_LockSet GetExternalRecords (const CBioseq_Info &bioseq) override
 Request from a datasource set of blobs with external annotations. More...
 
virtual TTSE_LockSet GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override
 
virtual TTSE_LockSet GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override
 
virtual TTSE_LockSet GetOrphanAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas) override
 new Get*AnnotRecords() methods More...
 
virtual void GetChunk (TChunk chunk) override
 
virtual void GetChunks (const TChunkSet &chunks) override
 
virtual void GetBlobs (TTSE_LockSets &tse_sets) override
 
virtual void GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret) override
 
virtual TBlobId GetBlobId (const CSeq_id_Handle &idh) override
 
virtual TBlobId GetBlobIdFromString (const string &str) const override
 
virtual TBlobVersion GetBlobVersion (const TBlobId &id) override
 
virtual bool CanGetBlobById (void) const override
 
virtual TTSE_Lock GetBlobById (const TBlobId &id) override
 
virtual TTSE_Lock ResolveConflict (const CSeq_id_Handle &handle, const TTSE_LockSet &tse_set) override
 Resolve TSE conflict *select the best TSE from the set of dead TSEs. More...
 
virtual void GC (void) override
 
virtual TNamedAnnotNames GetNamedAnnotAccessions (const CSeq_id_Handle &idh) override
 
virtual TNamedAnnotNames GetNamedAnnotAccessions (const CSeq_id_Handle &idh, const string &named_acc) override
 
CReadDispatcherGetDispatcher (void)
 
CGBInfoManagerGetInfoManager (void)
 
bool HaveCache (TCacheType cache_type=fCache_Any) override
 
void PurgeCache (TCacheType cache_type, time_t access_timeout=0) override
 
void CloseCache (void) override
 
- Public Member Functions inherited from CGBDataLoader
virtual ~CGBDataLoader (void)
 
TBlobId GetBlobIdFromSatSatKey (int sat, int sat_key, int sub_sat=0) const
 
CConstRef< CSeqrefGetSatSatkey (const CSeq_id_Handle &idh)
 
CConstRef< CSeqrefGetSatSatkey (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
 
- Public Member Functions inherited from CDataLoader
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 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 TSeq_idSet &ids, 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 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 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 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
 
- 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
 

Static Public Member Functions

static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const CGBLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
- Static Public Member Functions inherited from CGBDataLoader
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 TParamTreeGetParamsSubnode (TParamTree *params, const string &subnode_name)
 
static TParamTreeGetLoaderParams (TParamTree *params)
 
static TParamTreeGetReaderParams (TParamTree *params, const string &reader_name)
 
static void SetParam (TParamTree *params, const string &param_name, const string &param_value)
 
static const TParamTreeGetParamsSubnode (const TParamTree *params, const string &subnode_name)
 
static const TParamTreeGetLoaderParams (const TParamTree *params)
 
static const TParamTreeGetReaderParams (const TParamTree *params, const string &reader_name)
 
static string GetParam (const TParamTree *params, const string &param_name)
 
static bool IsUsingPSGLoader (void)
 
- Static Public Member Functions inherited from CDataLoader
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

TBlobContentsMask x_MakeContentMask (EChoice choice) const
 
TBlobContentsMask x_MakeContentMask (const SRequestDetails &details) const
 
TTSE_LockSet x_GetRecords (const CSeq_id_Handle &idh, TBlobContentsMask sr_mask, const SAnnotSelector *sel, TProcessedNAs *processed_nas=0)
 
- Protected Member Functions inherited from CGBDataLoader
 CGBDataLoader (const string &loader_name, const CGBLoaderParams &params)
 
- Protected Member Functions inherited from CDataLoader
 CDataLoader (void)
 
 CDataLoader (const string &loader_name)
 
void SetName (const string &loader_name)
 
CDataSourceGetDataSource (void) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Types

typedef CPluginManager< CReaderTReaderManager
 
typedef CPluginManager< CWriterTWriterManager
 

Private Member Functions

TRealBlobId x_GetRealBlobId (const TBlobId &blob_id) const override
 
 CGBDataLoader_Native (const string &loader_name, const CGBLoaderParams &params)
 
void x_CreateDriver (const CGBLoaderParams &params)
 
pair< string, stringGetReaderWriterName (const TParamTree *params, const CGBLoaderParams &loader_params) const
 
bool x_CreateReaders (const string &str, const TParamTree *params, const CGBLoaderParams &gb_params, CGBLoaderParams::EPreopenConnection preopen)
 
void x_CreateWriters (const string &str, const TParamTree *params)
 
CReaderx_CreateReader (const string &names, const CGBLoaderParams &gb_params, const TParamTree *params=0)
 
CWriterx_CreateWriter (const string &names, const TParamTree *params=0)
 
 CGBDataLoader_Native (const CGBDataLoader_Native &)
 
CGBDataLoader_Nativeoperator= (const CGBDataLoader_Native &)
 

Static Private Member Functions

static CRef< TReaderManagerx_GetReaderManager (void)
 
static CRef< TWriterManagerx_GetWriterManager (void)
 

Private Attributes

CInitMutexPool m_MutexPool
 
CRef< CReadDispatcherm_Dispatcher
 
CRef< CGBInfoManagerm_InfoManager
 
CGBReaderCacheManager m_CacheManager
 

Friends

class CGBReaderRequestResult
 
class CGBDataLoader
 
class CGBLoaderMaker< CGBDataLoader_Native >
 

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...
 
- Static Protected Member Functions inherited from CGBDataLoader
static string x_GetLoaderMethod (const TParamTree *params)
 
- Static Protected Member Functions inherited from CDataLoader
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...
 
- Protected Attributes inherited from CGBDataLoader
TExpirationTimeout m_IdExpirationTimeout
 
bool m_AlwaysLoadExternal
 
bool m_AlwaysLoadNamedAcc
 
bool m_AddWGSMasterDescr
 
bool m_HasHUPIncluded
 
EGBErrorAction m_PTISErrorAction
 
string m_WebCookie
 

Detailed Description

Definition at line 112 of file gbnative.hpp.

Member Typedef Documentation

◆ TCacheType

Definition at line 211 of file gbnative.hpp.

◆ TConn

typedef unsigned CGBDataLoader_Native::TConn

Definition at line 116 of file gbnative.hpp.

◆ TNamedAnnotNames

Definition at line 118 of file gbnative.hpp.

◆ TReaderManager

Definition at line 261 of file gbnative.hpp.

◆ TRealBlobId

Definition at line 117 of file gbnative.hpp.

◆ TWriterManager

Definition at line 262 of file gbnative.hpp.

Member Enumeration Documentation

◆ ECacheType

Enumerator
fCache_Id 
fCache_Blob 
fCache_Any 

Definition at line 206 of file gbnative.hpp.

Constructor & Destructor Documentation

◆ ~CGBDataLoader_Native()

CGBDataLoader_Native::~CGBDataLoader_Native ( void  )
virtual

Definition at line 168 of file gbnative.cpp.

References CloseCache(), and GBLOG_POST_X.

◆ CGBDataLoader_Native() [1/2]

CGBDataLoader_Native::CGBDataLoader_Native ( const string loader_name,
const CGBLoaderParams params 
)
private

Definition at line 159 of file gbnative.cpp.

References GBLOG_POST_X, and x_CreateDriver().

◆ CGBDataLoader_Native() [2/2]

CGBDataLoader_Native::CGBDataLoader_Native ( const CGBDataLoader_Native )
private

Member Function Documentation

◆ CanGetBlobById()

bool CGBDataLoader_Native::CanGetBlobById ( void  ) const
overridevirtual

Reimplemented from CDataLoader.

Definition at line 1115 of file gbnative.cpp.

◆ CloseCache()

void CGBDataLoader_Native::CloseCache ( void  )
overridevirtual

◆ DropTSE()

void CGBDataLoader_Native::DropTSE ( CRef< CTSE_Info tse_info)
overridevirtual

Reimplemented from CDataLoader.

Definition at line 1669 of file gbnative.cpp.

◆ GC()

void CGBDataLoader_Native::GC ( void  )
overridevirtual

Reimplemented from CDataLoader.

Definition at line 1006 of file gbnative.cpp.

◆ GetAccVerFound()

CDataLoader::SAccVerFound CGBDataLoader_Native::GetAccVerFound ( const CSeq_id_Handle idh)
overridevirtual

◆ GetAccVers()

void CGBDataLoader_Native::GetAccVers ( const TIds ids,
TLoaded loader,
TIds ret 
)
overridevirtual

◆ GetBlobById()

CDataLoader::TTSE_Lock CGBDataLoader_Native::GetBlobById ( const TBlobId id)
overridevirtual

◆ GetBlobId()

CDataLoader::TBlobId CGBDataLoader_Native::GetBlobId ( const CSeq_id_Handle idh)
overridevirtual

◆ GetBlobIdFromString()

CDataLoader::TBlobId CGBDataLoader_Native::GetBlobIdFromString ( const string str) const
overridevirtual

Reimplemented from CDataLoader.

Definition at line 552 of file gbnative.cpp.

References CBlob_id::CreateFromString(), and str().

◆ GetBlobs()

void CGBDataLoader_Native::GetBlobs ( TTSE_LockSets tse_sets)
overridevirtual

◆ GetBlobVersion()

CDataLoader::TBlobVersion CGBDataLoader_Native::GetBlobVersion ( const TBlobId id)
overridevirtual

◆ GetBulkIds()

void CGBDataLoader_Native::GetBulkIds ( const TIds ids,
TLoaded loader,
TBulkIds ret 
)
overridevirtual

◆ GetCDDAnnots()

void CGBDataLoader_Native::GetCDDAnnots ( const TSeqIdSets id_sets,
TLoaded loaded,
TCDD_Locks ret 
)
overridevirtual

◆ GetChunk()

void CGBDataLoader_Native::GetChunk ( TChunk  chunk)
overridevirtual

◆ GetChunks()

void CGBDataLoader_Native::GetChunks ( const TChunkSet chunks)
overridevirtual

◆ GetDetailedRecords()

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetDetailedRecords ( const CSeq_id_Handle idh,
const SRequestDetails details 
)
overridevirtual

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.

Default implementation will call GetRecords().

Reimplemented from CDataLoader.

Definition at line 1108 of file gbnative.cpp.

References x_GetRecords(), and x_MakeContentMask().

◆ GetDispatcher()

CReadDispatcher& CGBDataLoader_Native::GetDispatcher ( void  )
inline

Definition at line 197 of file gbnative.hpp.

References m_Dispatcher.

Referenced by x_GetDispatcher().

◆ GetExternalAnnotRecordsNA() [1/2]

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetExternalAnnotRecordsNA ( const CBioseq_Info bioseq,
const SAnnotSelector sel,
TProcessedNAs processed_nas 
)
overridevirtual

◆ GetExternalAnnotRecordsNA() [2/2]

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetExternalAnnotRecordsNA ( const CSeq_id_Handle idh,
const SAnnotSelector sel,
TProcessedNAs processed_nas 
)
overridevirtual

Reimplemented from CDataLoader.

Definition at line 1209 of file gbnative.cpp.

References fBlobHasExtAnnot, fBlobHasNamedAnnot, and x_GetRecords().

Referenced by GetExternalAnnotRecordsNA().

◆ GetExternalRecords()

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetExternalRecords ( const CBioseq_Info bioseq)
overridevirtual

Request from a datasource set of blobs with external annotations.

CDataLoader has reasonable default implementation.

Reimplemented from CDataLoader.

Definition at line 1187 of file gbnative.cpp.

References CSeq_id_Base::e_Gi, CDataLoader::eExtAnnot, GetBlobId(), CBioseq_Info::GetId(), GetRecords(), ITERATE, ct::sort(), and set< Key, Compare >::swap().

◆ GetGiFound()

CDataLoader::SGiFound CGBDataLoader_Native::GetGiFound ( const CSeq_id_Handle idh)
overridevirtual

◆ GetGis()

void CGBDataLoader_Native::GetGis ( const TIds ids,
TLoaded loader,
TGis ret 
)
overridevirtual

◆ GetIds()

void CGBDataLoader_Native::GetIds ( const CSeq_id_Handle idh,
TIds ids 
)
overridevirtual

◆ GetInfoManager()

CGBInfoManager& CGBDataLoader_Native::GetInfoManager ( void  )
inline

Definition at line 201 of file gbnative.hpp.

References m_InfoManager.

◆ GetLabel()

string CGBDataLoader_Native::GetLabel ( const CSeq_id_Handle idh)
overridevirtual

Request for a label string of a sequence.

Returns empty string if sequence with requested id is not known. The result must be non-empty for existing sequences

Reimplemented from CDataLoader.

Definition at line 611 of file gbnative.cpp.

References CReadDispatcher::CannotProcess(), CLoadLockLabel::GetLabel(), CLoadLockLabel::IsLoadedLabel(), CReadDispatcher::LoadSeq_idLabel(), m_Dispatcher, result, and string.

◆ GetLabels()

void CGBDataLoader_Native::GetLabels ( const TIds ids,
TLoaded loader,
TLabels ret 
)
overridevirtual

◆ GetNamedAnnotAccessions() [1/2]

CGBDataLoader::TNamedAnnotNames CGBDataLoader_Native::GetNamedAnnotAccessions ( const CSeq_id_Handle idh)
overridevirtual

◆ GetNamedAnnotAccessions() [2/2]

CGBDataLoader::TNamedAnnotNames CGBDataLoader_Native::GetNamedAnnotAccessions ( const CSeq_id_Handle idh,
const string named_acc 
)
overridevirtual

◆ GetOrphanAnnotRecordsNA()

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetOrphanAnnotRecordsNA ( const CSeq_id_Handle idh,
const SAnnotSelector sel,
TProcessedNAs processed_nas 
)
overridevirtual

◆ GetReaderWriterName()

pair< string, string > CGBDataLoader_Native::GetReaderWriterName ( const TParamTree params,
const CGBLoaderParams loader_params 
) const
private

◆ GetRecords()

CDataLoader::TTSE_LockSet CGBDataLoader_Native::GetRecords ( const CSeq_id_Handle idh,
EChoice  choice 
)
overridevirtual

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.

The GetRecords() may throw CBlobStateException if the sequence is not available (not known or disabled), and blob state is different from minimal fState_no_data. The actual blob state can be read from the exception in this case.

Reimplemented from CDataLoader.

Definition at line 1101 of file gbnative.cpp.

References x_GetRecords(), and x_MakeContentMask().

Referenced by GetExternalRecords().

◆ GetSequenceHashes()

void CGBDataLoader_Native::GetSequenceHashes ( const TIds ids,
TLoaded loader,
TSequenceHashes ret,
THashKnown known 
)
overridevirtual

◆ GetSequenceHashFound()

CDataLoader::SHashFound CGBDataLoader_Native::GetSequenceHashFound ( const CSeq_id_Handle idh)
overridevirtual

◆ GetSequenceLength()

TSeqPos CGBDataLoader_Native::GetSequenceLength ( const CSeq_id_Handle idh)
overridevirtual

Request for a length of a sequence.

Returns kInvalidSeqPos if sequence with requested id is not known. The result must not be kInvalidSeqPos for existing sequences

Reimplemented from CDataLoader.

Definition at line 742 of file gbnative.cpp.

References CReadDispatcher::CannotProcess(), CLoadLockLength::GetLength(), CLoadLockLength::IsLoadedLength(), kInvalidSeqPos, CReadDispatcher::LoadSequenceLength(), m_Dispatcher, and result.

◆ GetSequenceLengths()

void CGBDataLoader_Native::GetSequenceLengths ( const TIds ids,
TLoaded loader,
TSequenceLengths ret 
)
overridevirtual

◆ GetSequenceState()

int CGBDataLoader_Native::GetSequenceState ( const CSeq_id_Handle idh)
overridevirtual

Request for a state of a sequence.

Returns CBioseq_Handle::fState_not_found|fState_no_data if sequence with requested id is not known. Result mustn't be fState_not_found|fState_no_data if sequence exists

Reimplemented from CDataLoader.

Definition at line 643 of file gbnative.cpp.

References CReadDispatcher::CannotProcess(), CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_not_found, and GetSequenceStates().

◆ GetSequenceStates()

void CGBDataLoader_Native::GetSequenceStates ( const TIds ids,
TLoaded loader,
TSequenceStates ret 
)
overridevirtual

◆ GetSequenceTypeFound()

CDataLoader::STypeFound CGBDataLoader_Native::GetSequenceTypeFound ( const CSeq_id_Handle sih)
overridevirtual

◆ GetSequenceTypes()

void CGBDataLoader_Native::GetSequenceTypes ( const TIds ids,
TLoaded loader,
TSequenceTypes ret 
)
overridevirtual

◆ GetTaxId()

TTaxId CGBDataLoader_Native::GetTaxId ( const CSeq_id_Handle idh)
overridevirtual

Request for a taxonomy id of a sequence.

Returns -1 if sequence with requested id is not known. Returns 0 if existing sequence doesn't have TaxID

Reimplemented from CDataLoader.

Definition at line 625 of file gbnative.cpp.

References CReadDispatcher::CannotProcess(), CDataLoader::GetTaxId(), CLoadLockTaxId::GetTaxId(), INVALID_TAX_ID, CLoadLockTaxId::IsLoadedTaxId(), CReadDispatcher::LoadSeq_idTaxId(), m_Dispatcher, and result.

◆ GetTaxIds()

void CGBDataLoader_Native::GetTaxIds ( const TIds ids,
TLoaded loader,
TTaxIds ret 
)
overridevirtual

◆ HaveCache()

bool CGBDataLoader_Native::HaveCache ( TCacheType  cache_type = fCache_Any)
overridevirtual

Implements CGBDataLoader.

Definition at line 973 of file gbnative.cpp.

References CGBReaderCacheManager::GetCaches(), ITERATE, and m_CacheManager.

◆ operator=()

CGBDataLoader_Native& CGBDataLoader_Native::operator= ( const CGBDataLoader_Native )
private

◆ PurgeCache()

void CGBDataLoader_Native::PurgeCache ( TCacheType  cache_type,
time_t  access_timeout = 0 
)
overridevirtual

Implements CGBDataLoader.

Definition at line 984 of file gbnative.cpp.

References CGBReaderCacheManager::GetCaches(), ITERATE, and m_CacheManager.

◆ RegisterInObjectManager()

CGBDataLoader::TRegisterLoaderInfo CGBDataLoader_Native::RegisterInObjectManager ( CObjectManager om,
const CGBLoaderParams params,
CObjectManager::EIsDefault  is_default = CObjectManager::eDefault,
CObjectManager::TPriority  priority = CObjectManager::kPriority_NotSet 
)
static

◆ ResolveConflict()

CDataLoader::TTSE_Lock CGBDataLoader_Native::ResolveConflict ( const CSeq_id_Handle id,
const TTSE_LockSet tse_set 
)
overridevirtual

Resolve TSE conflict *select the best TSE from the set of dead TSEs.

*select the live TSE from the list of live TSEs and mark the others one as dead.

Reimplemented from CDataLoader.

Definition at line 893 of file gbnative.cpp.

References _ASSERT, _TRACE, CSeq_id_Handle::AsString(), CGBDataLoader::GetRealBlobId(), CTSE_Info::IsDead(), ITERATE, and result.

◆ x_CreateDriver()

void CGBDataLoader_Native::x_CreateDriver ( const CGBLoaderParams params)
private

Definition at line 182 of file gbnative.cpp.

References CConfig::ConvertRegToTree(), DEFAULT_ID_EXPIRATION_TIMEOUT, DEFAULT_ID_GC_SIZE, eGBErrorAction_ignore, eGBErrorAction_report, eGBErrorAction_throw, CGBLoaderParams::ePreopenAlways, CGBLoaderParams::ePreopenByConfig, CGBLoaderParams::ePreopenNever, NStr::EqualNocase(), CNcbiApplicationAPI::GetConfig(), CGBDataLoader::GetLoaderParams(), CGBDataLoader::GetParam(), CGBLoaderParams::GetParamTree(), CGBLoaderParams::GetPreopenConnection(), CGBLoaderParams::GetReaderName(), CGBLoaderParams::GetReaderPtr(), GetReaderWriterName(), CGBLoaderParams::GetWebCookie(), CReadDispatcher::InsertReader(), CNcbiApplicationAPI::InstanceGuard(), CGBDataLoader::m_AddWGSMasterDescr, CGBDataLoader::m_AlwaysLoadExternal, CGBDataLoader::m_AlwaysLoadNamedAcc, m_Dispatcher, CGBDataLoader::m_IdExpirationTimeout, m_InfoManager, CGBDataLoader::m_PTISErrorAction, CGBDataLoader::m_WebCookie, NCBI_GBLOADER_PARAM_ADD_WGS_MASTER, NCBI_GBLOADER_PARAM_ALWAYS_LOAD_EXTERNAL, NCBI_GBLOADER_PARAM_ALWAYS_LOAD_NAMED_ACC, NCBI_GBLOADER_PARAM_ID_EXPIRATION_TIMEOUT, NCBI_GBLOADER_PARAM_ID_GC_SIZE, NCBI_GBLOADER_PARAM_PREOPEN, NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION, NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_IGNORE, NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_REPORT, NCBI_GBLOADER_PARAM_PTIS_ERROR_ACTION_THROW, NCBI_RETHROW_FMT, NCBI_THROW_FMT, CReader::OpenInitialConnection(), NStr::StartsWith(), NStr::StringToBool(), NStr::StringToUInt(), NStr::ToLower(), x_CreateReaders(), and x_CreateWriters().

Referenced by CGBDataLoader_Native().

◆ x_CreateReader()

CReader * CGBDataLoader_Native::x_CreateReader ( const string names,
const CGBLoaderParams gb_params,
const TParamTree params = 0 
)
private

◆ x_CreateReaders()

bool CGBDataLoader_Native::x_CreateReaders ( const string str,
const TParamTree params,
const CGBLoaderParams gb_params,
CGBLoaderParams::EPreopenConnection  preopen 
)
private

◆ x_CreateWriter()

CWriter * CGBDataLoader_Native::x_CreateWriter ( const string names,
const TParamTree params = 0 
)
private

◆ x_CreateWriters()

void CGBDataLoader_Native::x_CreateWriters ( const string str,
const TParamTree params 
)
private

◆ x_GetReaderManager()

CRef< CPluginManager< CReader > > CGBDataLoader_Native::x_GetReaderManager ( void  )
staticprivate

◆ x_GetRealBlobId()

CGBDataLoader::TRealBlobId CGBDataLoader_Native::x_GetRealBlobId ( const TBlobId blob_id) const
overrideprivatevirtual

Implements CGBDataLoader.

Definition at line 176 of file gbnative.cpp.

◆ x_GetRecords()

CDataLoader::TTSE_LockSet CGBDataLoader_Native::x_GetRecords ( const CSeq_id_Handle idh,
TBlobContentsMask  sr_mask,
const SAnnotSelector sel,
TProcessedNAs processed_nas = 0 
)
protected

◆ x_GetWriterManager()

CRef< CPluginManager< CWriter > > CGBDataLoader_Native::x_GetWriterManager ( void  )
staticprivate

Definition at line 470 of file gbnative.cpp.

References _ASSERT, GenBankWriters_Register_Cache(), and NCBI_PARAM_TYPE().

Referenced by x_CreateWriter().

◆ x_MakeContentMask() [1/2]

TBlobContentsMask CGBDataLoader_Native::x_MakeContentMask ( const SRequestDetails details) const
protected

◆ x_MakeContentMask() [2/2]

TBlobContentsMask CGBDataLoader_Native::x_MakeContentMask ( EChoice  choice) const
protected

Friends And Related Function Documentation

◆ CGBDataLoader

friend class CGBDataLoader
friend

Definition at line 230 of file gbnative.hpp.

◆ CGBLoaderMaker< CGBDataLoader_Native >

friend class CGBLoaderMaker< CGBDataLoader_Native >
friend

Definition at line 230 of file gbnative.hpp.

◆ CGBReaderRequestResult

friend class CGBReaderRequestResult
friend

Definition at line 219 of file gbnative.hpp.

Member Data Documentation

◆ m_CacheManager

CGBReaderCacheManager CGBDataLoader_Native::m_CacheManager
private

Definition at line 244 of file gbnative.hpp.

Referenced by CloseCache(), HaveCache(), PurgeCache(), x_CreateReader(), and x_CreateWriter().

◆ m_Dispatcher

CRef<CReadDispatcher> CGBDataLoader_Native::m_Dispatcher
private

◆ m_InfoManager

CRef<CGBInfoManager> CGBDataLoader_Native::m_InfoManager
private

Definition at line 241 of file gbnative.hpp.

Referenced by GetInfoManager(), and x_CreateDriver().

◆ m_MutexPool

CInitMutexPool CGBDataLoader_Native::m_MutexPool
private

Definition at line 238 of file gbnative.hpp.

Referenced by CGBReaderRequestResult::GetMutexPool().


The documentation for this class was generated from the following files:
Modified on Mon Jul 15 05:31:07 2024 by modify_doxy.py rev. 669887