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CVDBGraphDataLoader_Impl Class Reference

Search Toolkit Book for CVDBGraphDataLoader_Impl

#include <sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp>

+ Inheritance diagram for CVDBGraphDataLoader_Impl:
+ Collaboration diagram for CVDBGraphDataLoader_Impl:

Classes

struct  SVDBFileInfo
 

Public Types

typedef vector< stringTVDBFiles
 
typedef CDataLoader::TBlobId TBlobId
 
typedef CDataLoader::TTSE_Lock TTSE_Lock
 
typedef CDataLoader::TTSE_LockSet TTSE_LockSet
 
typedef vector< CAnnotNameTAnnotNames
 
- 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

 CVDBGraphDataLoader_Impl (const TVDBFiles &vdb_files)
 
 ~CVDBGraphDataLoader_Impl (void)
 
CObjectManager::TPriority GetDefaultPriority (void) const
 
TAnnotNames GetPossibleAnnotNames (void) const
 
template<class Call >
std::invoke_result< Call >::type CallWithRetry (Call &&call, const char *name, unsigned retry_count=0)
 
TBlobId GetBlobId (const CSeq_id_Handle &idh)
 
TBlobId GetBlobIdFromString (const string &str) const
 
TTSE_Lock GetBlobById (CDataSource *ds, const TBlobId &blob_id)
 
TTSE_Lock GetBlobByIdOnce (CDataSource *ds, const TBlobId &blob_id)
 
TTSE_LockSet GetRecords (CDataSource *ds, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)
 
TTSE_LockSet GetOrphanAnnotRecords (CDataSource *ds, const CSeq_id_Handle &idh, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)
 
TTSE_LockSet GetOrphanAnnotRecordsOnce (CDataSource *ds, const CSeq_id_Handle &idh, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)
 
void GetChunk (CTSE_Chunk_Info &chunk)
 
void GetChunkOnce (CTSE_Chunk_Info &chunk)
 
CRef< CSeq_entryLoadFullEntry (const CVDBGraphBlobId &blob_id)
 
void LoadSplitEntry (CTSE_Info &tse, const CVDBGraphBlobId &blob_id)
 
CRef< SVDBFileInfoOpenVDBGraphFile (const string &name)
 
CRef< SVDBFileInfoOpenVDBGraphFileOnce (const string &name)
 
- 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
 

Protected Types

typedef map< string, CRef< SVDBFileInfo > > TFixedFileMap
 
typedef limited_size_map< string, CRef< SVDBFileInfo > > TAutoFileMap
 
typedef limited_size_map< string, boolTMissingFileSet
 

Protected Member Functions

CRef< SVDBFileInfox_GetFileInfo (const string &name)
 
CRef< SVDBFileInfox_GetNAFileInfo (const string &na_acc)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CMutex m_Mutex
 
CVDBMgr m_Mgr
 
unsigned m_RetryCount
 
TFixedFileMap m_FixedFileMap
 
TAutoFileMap m_AutoFileMap
 
TMissingFileSet m_MissingFileSet
 

Additional Inherited Members

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

Detailed Description

Definition at line 49 of file vdbgraphloader_impl.hpp.

Member Typedef Documentation

◆ TAnnotNames

Definition at line 62 of file vdbgraphloader_impl.hpp.

◆ TAutoFileMap

Definition at line 107 of file vdbgraphloader_impl.hpp.

◆ TBlobId

Definition at line 53 of file vdbgraphloader_impl.hpp.

◆ TFixedFileMap

Definition at line 106 of file vdbgraphloader_impl.hpp.

◆ TMissingFileSet

Definition at line 108 of file vdbgraphloader_impl.hpp.

◆ TTSE_Lock

Definition at line 54 of file vdbgraphloader_impl.hpp.

◆ TTSE_LockSet

Definition at line 55 of file vdbgraphloader_impl.hpp.

◆ TVDBFiles

Definition at line 52 of file vdbgraphloader_impl.hpp.

Constructor & Destructor Documentation

◆ CVDBGraphDataLoader_Impl()

CVDBGraphDataLoader_Impl::CVDBGraphDataLoader_Impl ( const TVDBFiles vdb_files)
explicit

◆ ~CVDBGraphDataLoader_Impl()

CVDBGraphDataLoader_Impl::~CVDBGraphDataLoader_Impl ( void  )

Definition at line 254 of file vdbgraphloader_impl.cpp.

Member Function Documentation

◆ CallWithRetry()

template<class Call >
std::invoke_result< Call >::type CVDBGraphDataLoader_Impl::CallWithRetry ( Call &&  call,
const char *  name,
unsigned  retry_count = 0 
)

◆ GetBlobById()

CDataLoader::TTSE_Lock CVDBGraphDataLoader_Impl::GetBlobById ( CDataSource ds,
const TBlobId blob_id 
)

◆ GetBlobByIdOnce()

CDataLoader::TTSE_Lock CVDBGraphDataLoader_Impl::GetBlobByIdOnce ( CDataSource ds,
const TBlobId blob_id 
)

◆ GetBlobId()

CDataLoader::TBlobId CVDBGraphDataLoader_Impl::GetBlobId ( const CSeq_id_Handle idh)

Definition at line 368 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader::GetBlobId().

◆ GetBlobIdFromString()

CDataLoader::TBlobId CVDBGraphDataLoader_Impl::GetBlobIdFromString ( const string str) const

Definition at line 376 of file vdbgraphloader_impl.cpp.

References str().

Referenced by CVDBGraphDataLoader::GetBlobIdFromString().

◆ GetChunk()

void CVDBGraphDataLoader_Impl::GetChunk ( CTSE_Chunk_Info chunk)

Definition at line 598 of file vdbgraphloader_impl.cpp.

References CallWithRetry(), and GetChunkOnce().

Referenced by CVDBGraphDataLoader::GetChunk().

◆ GetChunkOnce()

void CVDBGraphDataLoader_Impl::GetChunkOnce ( CTSE_Chunk_Info chunk)

◆ GetDefaultPriority()

CObjectManager::TPriority CVDBGraphDataLoader_Impl::GetDefaultPriority ( void  ) const

◆ GetOrphanAnnotRecords()

CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::GetOrphanAnnotRecords ( CDataSource ds,
const CSeq_id_Handle idh,
const SAnnotSelector sel,
CDataLoader::TProcessedNAs processed_nas 
)

◆ GetOrphanAnnotRecordsOnce()

CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce ( CDataSource ds,
const CSeq_id_Handle idh,
const SAnnotSelector sel,
CDataLoader::TProcessedNAs processed_nas 
)

◆ GetPossibleAnnotNames()

CVDBGraphDataLoader_Impl::TAnnotNames CVDBGraphDataLoader_Impl::GetPossibleAnnotNames ( void  ) const

◆ GetRecords()

CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::GetRecords ( CDataSource ds,
const CSeq_id_Handle idh,
CDataLoader::EChoice  choice 
)

◆ LoadFullEntry()

CRef< CSeq_entry > CVDBGraphDataLoader_Impl::LoadFullEntry ( const CVDBGraphBlobId blob_id)

◆ LoadSplitEntry()

void CVDBGraphDataLoader_Impl::LoadSplitEntry ( CTSE_Info tse,
const CVDBGraphBlobId blob_id 
)

◆ OpenVDBGraphFile()

CRef< CVDBGraphDataLoader_Impl::SVDBFileInfo > CVDBGraphDataLoader_Impl::OpenVDBGraphFile ( const string name)

Definition at line 303 of file vdbgraphloader_impl.cpp.

References CallWithRetry(), and OpenVDBGraphFileOnce().

Referenced by CVDBGraphDataLoader_Impl().

◆ OpenVDBGraphFileOnce()

CRef< CVDBGraphDataLoader_Impl::SVDBFileInfo > CVDBGraphDataLoader_Impl::OpenVDBGraphFileOnce ( const string name)

Definition at line 312 of file vdbgraphloader_impl.cpp.

References GetLookupType(), CDirEntry::GetName(), info, and m_Mgr.

Referenced by OpenVDBGraphFile().

◆ x_GetFileInfo()

CRef< CVDBGraphDataLoader_Impl::SVDBFileInfo > CVDBGraphDataLoader_Impl::x_GetFileInfo ( const string name)
protected

◆ x_GetNAFileInfo()

CRef< CVDBGraphDataLoader_Impl::SVDBFileInfo > CVDBGraphDataLoader_Impl::x_GetNAFileInfo ( const string na_acc)
protected

Member Data Documentation

◆ m_AutoFileMap

TAutoFileMap CVDBGraphDataLoader_Impl::m_AutoFileMap
protected

Definition at line 118 of file vdbgraphloader_impl.hpp.

Referenced by GetOrphanAnnotRecordsOnce(), and x_GetNAFileInfo().

◆ m_FixedFileMap

TFixedFileMap CVDBGraphDataLoader_Impl::m_FixedFileMap
protected

◆ m_Mgr

CVDBMgr CVDBGraphDataLoader_Impl::m_Mgr
protected

Definition at line 115 of file vdbgraphloader_impl.hpp.

Referenced by OpenVDBGraphFileOnce(), and x_GetNAFileInfo().

◆ m_MissingFileSet

TMissingFileSet CVDBGraphDataLoader_Impl::m_MissingFileSet
protected

Definition at line 119 of file vdbgraphloader_impl.hpp.

Referenced by GetOrphanAnnotRecordsOnce(), and x_GetNAFileInfo().

◆ m_Mutex

CMutex CVDBGraphDataLoader_Impl::m_Mutex
protected

Definition at line 114 of file vdbgraphloader_impl.hpp.

Referenced by x_GetNAFileInfo().

◆ m_RetryCount

unsigned CVDBGraphDataLoader_Impl::m_RetryCount
protected

Definition at line 116 of file vdbgraphloader_impl.hpp.

Referenced by CallWithRetry().


The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:42:35 2024 by modify_doxy.py rev. 669887