Search Toolkit Book for CBAMDataLoader_Impl

#include <sra/data_loaders/bam/impl/bamloader_impl.hpp>

Inheritance diagram for CBAMDataLoader_Impl:

Collaboration diagram for CBAMDataLoader_Impl:

Classes
struct	SDirSeqInfo

Public Types
typedef pair< CBamFileInfo , const CBamRefSeqInfo >	TRefSeqInfo

typedef vector< CSeq_id_Handle >	TIds

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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CBAMDataLoader_Impl (const CBAMDataLoader::SLoaderParams &params)

	~CBAMDataLoader_Impl (void)

void	AddSrzDef (void)

void	AddBamFile (const CBAMDataLoader::SBamFileName &bam)

void	OpenBAMFiles ()

void	OpenBAMFilesOnce ()

bool	BAMFilesOpened () const

CRef< CBAMBlobId >	GetShortSeqBlobId (const CSeq_id_Handle &idh)

CRef< CBAMBlobId >	GetRefSeqBlobId (const CSeq_id_Handle &idh)

CBamRefSeqInfo *	GetRefSeqInfo (const CBAMBlobId &blob_id)

void	LoadBAMEntry (const CBAMBlobId &blob_id, CTSE_LoadLock &load_lock)

void	LoadChunk (const CBAMBlobId &blob_id, CTSE_Chunk_Info &chunk)

double	EstimateLoadSeconds (const CBAMBlobId &blob_id, const CTSE_Chunk_Info &chunk, Uint4 bytes)

CBAMDataLoader::TAnnotNames	GetPossibleAnnotNames (void) const

bool	IsShortSeq (const CSeq_id_Handle &idh)

void	GetIds (const CSeq_id_Handle &idh, TIds &ids)

CDataSource::SAccVerFound	GetAccVer (const CSeq_id_Handle &idh)

CDataSource::SGiFound	GetGi (const CSeq_id_Handle &idh)

string	GetLabel (const CSeq_id_Handle &idh)

TTaxId	GetTaxId (const CSeq_id_Handle &idh)

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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 Types
typedef map< string, CRef< CBamFileInfo > >	TBamFiles

typedef vector< SDirSeqInfo >	TSeqInfos

Private Attributes
CMutex	m_Mutex

CBamMgr	m_Mgr

string	m_DirPath

TSeqInfos	m_SeqInfos

TBamFiles	m_BamFiles

AutoPtr< IIdMapper >	m_IdMapper

Friends
class	CBamFileInfo

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...