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CWGSDataLoader Class Reference

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#include <sra/data_loaders/wgs/wgsloader.hpp>

+ Inheritance diagram for CWGSDataLoader:
+ Collaboration diagram for CWGSDataLoader:

Classes

struct  SLoaderParams
 

Public Types

typedef SRegisterLoaderInfo< CWGSDataLoaderTRegisterLoaderInfo
 
- 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 TBlobId GetBlobId (const CSeq_id_Handle &idh)
 
virtual TBlobId GetBlobIdFromString (const string &str) const
 
virtual bool CanGetBlobById (void) const
 
virtual TTSE_Lock GetBlobById (const TBlobId &blob_id)
 
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 TTSE_LockSet GetExternalRecords (const CBioseq_Info &bioseq)
 Request from a datasource set of blobs with external annotations. 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 GetOrphanAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
 old Get*AnnotRecords() methods More...
 
virtual void GetChunk (TChunk chunk)
 
virtual void GetChunks (const TChunkSet &chunks)
 
virtual void GetIds (const CSeq_id_Handle &idh, TIds &ids)
 
virtual SAccVerFound GetAccVerFound (const CSeq_id_Handle &idh)
 
virtual SGiFound GetGiFound (const CSeq_id_Handle &idh)
 
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 SHashFound GetSequenceHashFound (const CSeq_id_Handle &idh)
 
virtual STypeFound GetSequenceTypeFound (const CSeq_id_Handle &idh)
 
bool GetAddWGSMasterDescr (void) const
 
void SetAddWGSMasterDescr (bool flag)
 
virtual CObjectManager::TPriority GetDefaultPriority (void) const
 
- 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 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 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 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 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 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 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 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 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...
 
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 SLoaderParams &params, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static TRegisterLoaderInfo RegisterInObjectManager (CObjectManager &om, const string &dir_path, const vector< string > &wgs_files, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)
 
static string GetLoaderNameFromArgs (void)
 
static string GetLoaderNameFromArgs (const SLoaderParams &params)
 
static string GetLoaderNameFromArgs (const string &dir_path, const vector< string > &wgs_files)
 
- 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)
 

Private Types

typedef CParamLoaderMaker< CWGSDataLoader, SLoaderParamsTMaker
 

Private Member Functions

 CWGSDataLoader (void)
 
 CWGSDataLoader (const string &loader_name, const SLoaderParams &params)
 
 ~CWGSDataLoader (void)
 

Private Attributes

CRef< CWGSDataLoader_Implm_Impl
 

Friends

class CParamLoaderMaker< CWGSDataLoader, SLoaderParams >
 

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...
 
- 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...
 
- 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...
 

Detailed Description

Definition at line 49 of file wgsloader.hpp.

Member Typedef Documentation

◆ TMaker

Definition at line 116 of file wgsloader.hpp.

◆ TRegisterLoaderInfo

Definition at line 63 of file wgsloader.hpp.

Constructor & Destructor Documentation

◆ CWGSDataLoader() [1/2]

CWGSDataLoader::CWGSDataLoader ( void  )
private

◆ CWGSDataLoader() [2/2]

CWGSDataLoader::CWGSDataLoader ( const string loader_name,
const SLoaderParams params 
)
private

Definition at line 162 of file wgsloader.cpp.

References m_Impl, and CRef< C, Locker >::Reset().

◆ ~CWGSDataLoader()

CWGSDataLoader::~CWGSDataLoader ( void  )
private

Definition at line 170 of file wgsloader.cpp.

Member Function Documentation

◆ CanGetBlobById()

bool CWGSDataLoader::CanGetBlobById ( void  ) const
virtual

Reimplemented from CDataLoader.

Definition at line 188 of file wgsloader.cpp.

◆ GetAccVerFound()

CDataLoader::SAccVerFound CWGSDataLoader::GetAccVerFound ( const CSeq_id_Handle idh)
virtual

Reimplemented from CDataLoader.

Definition at line 268 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetAccVer(), and m_Impl.

◆ GetAddWGSMasterDescr()

bool CWGSDataLoader::GetAddWGSMasterDescr ( void  ) const

Definition at line 307 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetAddWGSMasterDescr(), and m_Impl.

◆ GetBlobById()

CDataLoader::TTSE_Lock CWGSDataLoader::GetBlobById ( const TBlobId blob_id)
virtual

Reimplemented from CDataLoader.

Definition at line 254 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetBlobById(), CDataLoader::GetDataSource(), and m_Impl.

◆ GetBlobId()

CDataLoader::TBlobId CWGSDataLoader::GetBlobId ( const CSeq_id_Handle idh)
virtual

Reimplemented from CDataLoader.

Definition at line 175 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetBlobId(), and m_Impl.

◆ GetBlobIdFromString()

CDataLoader::TBlobId CWGSDataLoader::GetBlobIdFromString ( const string str) const
virtual

Reimplemented from CDataLoader.

Definition at line 182 of file wgsloader.cpp.

References str().

◆ GetChunk()

void CWGSDataLoader::GetChunk ( TChunk  chunk)
virtual

Reimplemented from CDataLoader.

Definition at line 237 of file wgsloader.cpp.

References CTSE_Chunk_Info::GetBlobId(), CWGSDataLoader_Impl::GetChunk(), and m_Impl.

Referenced by GetChunks().

◆ GetChunks()

void CWGSDataLoader::GetChunks ( const TChunkSet chunks)
virtual

Reimplemented from CDataLoader.

Definition at line 245 of file wgsloader.cpp.

References GetChunk(), and ITERATE.

◆ GetDefaultPriority()

CObjectManager::TPriority CWGSDataLoader::GetDefaultPriority ( void  ) const
virtual

Reimplemented from CDataLoader.

Definition at line 319 of file wgsloader.cpp.

References CObjectManager::kPriority_Replace.

◆ GetExternalAnnotRecords() [1/2]

CDataLoader::TTSE_LockSet CWGSDataLoader::GetExternalAnnotRecords ( const CBioseq_Info bioseq,
const SAnnotSelector sel 
)
virtual

Reimplemented from CDataLoader.

Definition at line 220 of file wgsloader.cpp.

◆ GetExternalAnnotRecords() [2/2]

CDataLoader::TTSE_LockSet CWGSDataLoader::GetExternalAnnotRecords ( const CSeq_id_Handle idh,
const SAnnotSelector sel 
)
virtual

Reimplemented from CDataLoader.

Definition at line 211 of file wgsloader.cpp.

◆ GetExternalRecords()

CDataLoader::TTSE_LockSet CWGSDataLoader::GetExternalRecords ( const CBioseq_Info bioseq)
virtual

Request from a datasource set of blobs with external annotations.

CDataLoader has reasonable default implementation.

Reimplemented from CDataLoader.

Definition at line 203 of file wgsloader.cpp.

◆ GetGiFound()

CDataLoader::SGiFound CWGSDataLoader::GetGiFound ( const CSeq_id_Handle idh)
virtual

Reimplemented from CDataLoader.

Definition at line 275 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetGi(), and m_Impl.

◆ GetIds()

void CWGSDataLoader::GetIds ( const CSeq_id_Handle idh,
TIds ids 
)
virtual

Definition at line 261 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetIds(), and m_Impl.

◆ GetLoaderNameFromArgs() [1/3]

string CWGSDataLoader::GetLoaderNameFromArgs ( const SLoaderParams params)
static

◆ GetLoaderNameFromArgs() [2/3]

string CWGSDataLoader::GetLoaderNameFromArgs ( const string dir_path,
const vector< string > &  wgs_files 
)
static

◆ GetLoaderNameFromArgs() [3/3]

string CWGSDataLoader::GetLoaderNameFromArgs ( void  )
static

◆ GetOrphanAnnotRecords()

CDataLoader::TTSE_LockSet CWGSDataLoader::GetOrphanAnnotRecords ( const CSeq_id_Handle idh,
const SAnnotSelector sel 
)
virtual

old Get*AnnotRecords() methods

Reimplemented from CDataLoader.

Definition at line 229 of file wgsloader.cpp.

◆ GetRecords()

CDataLoader::TTSE_LockSet CWGSDataLoader::GetRecords ( const CSeq_id_Handle idh,
EChoice  choice 
)
virtual

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 195 of file wgsloader.cpp.

References CDataLoader::GetDataSource(), CWGSDataLoader_Impl::GetRecords(), and m_Impl.

◆ GetSequenceHashFound()

CDataLoader::SHashFound CWGSDataLoader::GetSequenceHashFound ( const CSeq_id_Handle idh)
virtual

Reimplemented from CDataLoader.

Definition at line 294 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetSequenceHash(), and m_Impl.

◆ GetSequenceLength()

TSeqPos CWGSDataLoader::GetSequenceLength ( const CSeq_id_Handle idh)
virtual

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 287 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetSequenceLength(), and m_Impl.

◆ GetSequenceTypeFound()

CDataLoader::STypeFound CWGSDataLoader::GetSequenceTypeFound ( const CSeq_id_Handle idh)
virtual

Reimplemented from CDataLoader.

Definition at line 301 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetSequenceType(), and m_Impl.

◆ GetTaxId()

TTaxId CWGSDataLoader::GetTaxId ( const CSeq_id_Handle idh)
virtual

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 281 of file wgsloader.cpp.

References CWGSDataLoader_Impl::GetTaxId(), and m_Impl.

◆ RegisterInObjectManager() [1/3]

◆ RegisterInObjectManager() [2/3]

◆ RegisterInObjectManager() [3/3]

CWGSDataLoader::TRegisterLoaderInfo CWGSDataLoader::RegisterInObjectManager ( CObjectManager om,
const string dir_path,
const vector< string > &  wgs_files,
CObjectManager::EIsDefault  is_default = CObjectManager::eNonDefault,
CObjectManager::TPriority  priority = CObjectManager::kPriority_NotSet 
)
static

◆ SetAddWGSMasterDescr()

void CWGSDataLoader::SetAddWGSMasterDescr ( bool  flag)

Friends And Related Function Documentation

◆ CParamLoaderMaker< CWGSDataLoader, SLoaderParams >

Definition at line 116 of file wgsloader.hpp.

Member Data Documentation

◆ m_Impl

CRef<CWGSDataLoader_Impl> CWGSDataLoader::m_Impl
private

The documentation for this class was generated from the following files:
Modified on Wed Jul 24 17:18:02 2024 by modify_doxy.py rev. 669887