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CWGSFileInfo Class Reference

Search Toolkit Book for CWGSFileInfo

#include <sra/data_loaders/wgs/impl/wgsloader_impl.hpp>

+ Inheritance diagram for CWGSFileInfo:
+ Collaboration diagram for CWGSFileInfo:

Classes

struct  SAccFileInfo
 

Public Member Functions

 CWGSFileInfo (CWGSDataLoader_Impl &impl, CTempString prefix)
 
CTempString GetWGSPrefix (void) const
 
bool FindGi (SAccFileInfo &info, TGi gi) const
 
bool FindProtAcc (SAccFileInfo &info, const string &acc) const
 
const CWGSDbGetDb (void) const
 
 operator const CWGSDb & (void) const
 
void LoadBlob (const CWGSBlobId &blob_id, CTSE_LoadLock &load_lock) const
 
void LoadChunk (const CWGSBlobId &blob_id, CTSE_Chunk_Info &chunk) const
 
CWGSSeqIterator GetContigIterator (const CWGSBlobId &blob_id) const
 
CWGSScaffoldIterator GetScaffoldIterator (const CWGSBlobId &blob_id) const
 
CWGSProteinIterator GetProteinIterator (const CWGSBlobId &blob_id) 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
 

Protected Member Functions

void x_Initialize (CWGSDataLoader_Impl &impl, CTempString prefix)
 
void x_InitMasterDescr (void)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

string m_WGSPrefix
 
CWGSDb m_WGSDb
 

Friends

class CWGSDataLoader_Impl
 

Additional Inherited Members

- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 53 of file wgsloader_impl.hpp.

Constructor & Destructor Documentation

CWGSFileInfo::CWGSFileInfo ( CWGSDataLoader_Impl impl,
CTempString  prefix 
)

Member Function Documentation

bool CWGSFileInfo::FindGi ( SAccFileInfo info,
TGi  gi 
) const
bool CWGSFileInfo::FindProtAcc ( SAccFileInfo info,
const string acc 
) const
CWGSSeqIterator CWGSFileInfo::GetContigIterator ( const CWGSBlobId blob_id) const
const CWGSDb& CWGSFileInfo::GetDb ( void  ) const
inline
CWGSProteinIterator CWGSFileInfo::GetProteinIterator ( const CWGSBlobId blob_id) const
CWGSScaffoldIterator CWGSFileInfo::GetScaffoldIterator ( const CWGSBlobId blob_id) const
CTempString CWGSFileInfo::GetWGSPrefix ( void  ) const
inline
void CWGSFileInfo::LoadBlob ( const CWGSBlobId blob_id,
CTSE_LoadLock load_lock 
) const
void CWGSFileInfo::LoadChunk ( const CWGSBlobId blob_id,
CTSE_Chunk_Info chunk 
) const
CWGSFileInfo::operator const CWGSDb & ( void  ) const
inline

Definition at line 106 of file wgsloader_impl.hpp.

void CWGSFileInfo::x_Initialize ( CWGSDataLoader_Impl impl,
CTempString  prefix 
)
protected
void CWGSFileInfo::x_InitMasterDescr ( void  )
protected

Friends And Related Function Documentation

friend class CWGSDataLoader_Impl
friend

Definition at line 121 of file wgsloader_impl.hpp.

Member Data Documentation

CWGSDb CWGSFileInfo::m_WGSDb
protected

Definition at line 128 of file wgsloader_impl.hpp.

Referenced by FindGi(), FindProtAcc(), x_Initialize(), and x_InitMasterDescr().

string CWGSFileInfo::m_WGSPrefix
protected

Definition at line 127 of file wgsloader_impl.hpp.

Referenced by x_Initialize().


The documentation for this class was generated from the following files:
Modified on Thu Feb 22 13:23:25 2018 by modify_doxy.py rev. 546573