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CPagedFile Class Reference

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#include <sra/readers/bam/bgzf.hpp>

+ Inheritance diagram for CPagedFile:
+ Collaboration diagram for CPagedFile:

Public Types

typedef CPagedFilePage::TFilePos TFilePos
 
typedef CBinaryRangeCacheWithLock< TFilePos, CPagedFilePageTPageCache
 
typedef TPageCache::CLock TPage
 
- 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

 CPagedFile (const string &file_name)
 
 ~CPagedFile ()
 
TPage GetPage (TFilePos pos)
 
pair< Uint8, double > GetReadStatistics () const
 
void SetPreviousReadStatistics (const pair< Uint8, double > &stats)
 
size_t GetNextPageSizePow2 () 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
 

Private Member Functions

void x_AddReadStatistics (Uint8 bytes, double seconds)
 
void x_ReadPage (CPagedFilePage &page, TFilePos file_pos, size_t size)
 

Private Attributes

CFastMutex m_Mutex
 
CFileIO m_File
 
AutoPtr< CMemoryFileMapm_MemFile
 
CBamVDBFile m_VDBFile
 
CRef< TPageCachem_PageCache
 
CFastMutex m_StatMutex
 
Uint8 m_TotalReadBytes
 
double m_TotalReadSeconds
 
Uint8 m_PreviousReadBytes
 
double m_PreviousReadSeconds
 

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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 88 of file bgzf.hpp.

Member Typedef Documentation

◆ TFilePos

Definition at line 91 of file bgzf.hpp.

◆ TPage

Definition at line 103 of file bgzf.hpp.

◆ TPageCache

Definition at line 99 of file bgzf.hpp.

Constructor & Destructor Documentation

◆ CPagedFile()

CPagedFile::CPagedFile ( const string file_name)
explicit

◆ ~CPagedFile()

CPagedFile::~CPagedFile ( )

Definition at line 135 of file bgzf.cpp.

References GetReadStatistics(), LOG_POST, and s_GetDebug().

Member Function Documentation

◆ GetNextPageSizePow2()

size_t CPagedFile::GetNextPageSizePow2 ( ) const

Definition at line 188 of file bgzf.cpp.

References GetReadStatistics(), m_PreviousReadBytes, m_PreviousReadSeconds, and stats.

Referenced by GetPage().

◆ GetPage()

CPagedFile::TPage CPagedFile::GetPage ( TFilePos  pos)

◆ GetReadStatistics()

pair< Uint8, double > CPagedFile::GetReadStatistics ( ) const

◆ SetPreviousReadStatistics()

void CPagedFile::SetPreviousReadStatistics ( const pair< Uint8, double > &  stats)

Definition at line 181 of file bgzf.cpp.

References m_PreviousReadBytes, m_PreviousReadSeconds, and stats.

Referenced by CBGZFFile::SetPreviousReadStatistics().

◆ x_AddReadStatistics()

void CPagedFile::x_AddReadStatistics ( Uint8  bytes,
double  seconds 
)
private

Definition at line 212 of file bgzf.cpp.

References m_StatMutex, m_TotalReadBytes, and m_TotalReadSeconds.

Referenced by x_ReadPage().

◆ x_ReadPage()

void CPagedFile::x_ReadPage ( CPagedFilePage page,
TFilePos  file_pos,
size_t  size 
)
private

Member Data Documentation

◆ m_File

CFileIO CPagedFile::m_File
private

Definition at line 121 of file bgzf.hpp.

Referenced by CPagedFile(), and x_ReadPage().

◆ m_MemFile

AutoPtr<CMemoryFileMap> CPagedFile::m_MemFile
private

Definition at line 122 of file bgzf.hpp.

Referenced by CPagedFile(), and x_ReadPage().

◆ m_Mutex

CFastMutex CPagedFile::m_Mutex
private

Definition at line 118 of file bgzf.hpp.

Referenced by x_ReadPage().

◆ m_PageCache

CRef<TPageCache> CPagedFile::m_PageCache
private

Definition at line 126 of file bgzf.hpp.

Referenced by GetPage().

◆ m_PreviousReadBytes

Uint8 CPagedFile::m_PreviousReadBytes
private

Definition at line 131 of file bgzf.hpp.

Referenced by GetNextPageSizePow2(), and SetPreviousReadStatistics().

◆ m_PreviousReadSeconds

double CPagedFile::m_PreviousReadSeconds
private

Definition at line 132 of file bgzf.hpp.

Referenced by GetNextPageSizePow2(), and SetPreviousReadStatistics().

◆ m_StatMutex

CFastMutex CPagedFile::m_StatMutex
mutableprivate

Definition at line 128 of file bgzf.hpp.

Referenced by GetReadStatistics(), and x_AddReadStatistics().

◆ m_TotalReadBytes

Uint8 CPagedFile::m_TotalReadBytes
private

Definition at line 129 of file bgzf.hpp.

Referenced by GetReadStatistics(), and x_AddReadStatistics().

◆ m_TotalReadSeconds

double CPagedFile::m_TotalReadSeconds
private

Definition at line 130 of file bgzf.hpp.

Referenced by GetReadStatistics(), and x_AddReadStatistics().

◆ m_VDBFile

CBamVDBFile CPagedFile::m_VDBFile
private

Definition at line 123 of file bgzf.hpp.

Referenced by CPagedFile(), and x_ReadPage().


The documentation for this class was generated from the following files:
Modified on Sat Jul 20 11:11:03 2024 by modify_doxy.py rev. 669887