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

Inheritance diagram for CBamFileInfo:

Collaboration diagram for CBamFileInfo:

Public Member Functions
	CBamFileInfo (const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam, const string &refseq_label=kEmptyStr, const CSeq_id_Handle &seq_id=CSeq_id_Handle())

const string &	GetBamName (void) const

const string &	GetAnnotName (void) const

void	GetShortSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

void	GetRefSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const

CBamRefSeqInfo *	GetRefSeqInfo (const CSeq_id_Handle &seq_id) const

TSeqPos	GetRefSeqLength (const string &id) const

CMutex &	GetMutex (void) const

CBamDb &	GetBamDb (void)

	operator CBamDb & (void)

void	AddRefSeq (const string &refseq_label, const CSeq_id_Handle &refseq_id)

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

Protected Types
typedef map< CSeq_id_Handle, CRef< CBamRefSeqInfo > >	TRefSeqs

Protected Member Functions
void	x_Initialize (const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam)

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

Protected Attributes
string	m_BamName

string	m_AnnotName

CMutex	m_BamMutex

CBamDb	m_BamDb

TRefSeqs	m_RefSeqs

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

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

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 208 of file bamloader_impl.hpp.

Member Typedef Documentation

◆ TRefSeqs

typedef map<CSeq_id_Handle, CRef<CBamRefSeqInfo> > CBamFileInfo::TRefSeqs

protected

Definition at line 255 of file bamloader_impl.hpp.

Constructor & Destructor Documentation

◆ CBamFileInfo()

CBamFileInfo::CBamFileInfo	(	const CBAMDataLoader_Impl &	impl,
		const CBAMDataLoader::SBamFileName &	bam,
		const string &	refseq_label = `kEmptyStr`,
		const CSeq_id_Handle &	seq_id = `CSeq_id_Handle()`
	)

Definition at line 724 of file bamloader_impl.cpp.

References AddRefSeq(), CStopWatch::Elapsed(), GetDebugLevel(), CSeq_id_Handle::GetHandle(), Info(), LOG_POST_X, m_BamDb, CBAMDataLoader::SBamFileName::m_BamName, CStopWatch::Start(), sw, and x_Initialize().

Member Function Documentation

◆ AddRefSeq()

void CBamFileInfo::AddRefSeq	(	const string &	refseq_label,
		const CSeq_id_Handle &	refseq_id
	)

Definition at line 775 of file bamloader_impl.cpp.

References ERR_POST_X, GetBamName(), GetDebugLevel(), Info(), LOG_POST_X, m_BamName, and m_RefSeqs.

Referenced by CBamFileInfo(), and CBAMDataLoader_Impl::OpenBAMFilesOnce().

◆ GetAnnotName()

const string& CBamFileInfo::GetAnnotName ( void ) const

inline

Definition at line 220 of file bamloader_impl.hpp.

References m_AnnotName.

Referenced by CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::LoadAlignChunk(), CBamRefSeqInfo::LoadMainSplit(), CBamRefSeqInfo::LoadPileupChunk(), and CBamRefSeqInfo::x_LoadRangesEstimated().

◆ GetBamDb()

CBamDb& CBamFileInfo::GetBamDb ( void )

inline

Definition at line 242 of file bamloader_impl.hpp.

References m_BamDb.

Referenced by CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::EstimateAlignLoadSeconds(), CBamRefSeqInfo::EstimatePileupLoadSeconds(), CBamRefSeqInfo::EstimateSeqLoadSeconds(), CBamRefSeqInfo::LoadMainSplit(), operator CBamDb &(), CBamRefSeqInfo::x_AddSeqChunk(), CBamRefSeqInfo::x_LoadRangesCov(), and CBamRefSeqInfo::x_LoadRangesEstimated().

◆ GetBamName()

const string& CBamFileInfo::GetBamName ( void ) const

inline

Definition at line 216 of file bamloader_impl.hpp.

References m_BamName.

Referenced by AddRefSeq(), CBamRefSeqInfo::SetBlobId(), and CBamRefSeqInfo::x_LoadRangesEstimated().

◆ GetMutex()

CMutex& CBamFileInfo::GetMutex ( void ) const

inline

Definition at line 237 of file bamloader_impl.hpp.

References m_BamMutex.

◆ GetRefSeqBlobId()

void CBamFileInfo::GetRefSeqBlobId	(	CRef< CBAMBlobId > &	ret,
		const CSeq_id_Handle &	idh
	)		const

Definition at line 802 of file bamloader_impl.cpp.

References GetRefSeqInfo(), and info.

◆ GetRefSeqInfo()

CBamRefSeqInfo * CBamFileInfo::GetRefSeqInfo ( const CSeq_id_Handle & seq_id ) const

Definition at line 812 of file bamloader_impl.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_RefSeqs.

Referenced by GetRefSeqBlobId(), and CBAMDataLoader_Impl::OpenBAMFilesOnce().

◆ GetRefSeqLength()

TSeqPos CBamFileInfo::GetRefSeqLength ( const string & id ) const

inline

Definition at line 232 of file bamloader_impl.hpp.

References CBamDb::GetRefSeqLength(), and m_BamDb.

Referenced by CBamRefSeqInfo::LoadPileupChunk(), CBamRefSeqInfo::x_InitAlignIterator(), CBamRefSeqInfo::x_LoadRangesScan(), and CBamRefSeqInfo::x_LoadRangesStat().

◆ GetShortSeqBlobId()

void CBamFileInfo::GetShortSeqBlobId	(	CRef< CBAMBlobId > &	ret,
		const CSeq_id_Handle &	idh
	)		const

Definition at line 793 of file bamloader_impl.cpp.

References ITERATE, and m_RefSeqs.

◆ operator CBamDb &()

CBamFileInfo::operator CBamDb & ( void )

inline

Definition at line 246 of file bamloader_impl.hpp.

References GetBamDb().

◆ x_Initialize()

void CBamFileInfo::x_Initialize	(	const CBAMDataLoader_Impl &	impl,
		const CBAMDataLoader::SBamFileName &	bam
	)

protected

Definition at line 751 of file bamloader_impl.cpp.

References eNoOwnership, CDirEntry::GetBase(), GetIncludeAlignTagsParam(), CBamDb::IncludeAlignTag(), m_AnnotName, m_BamDb, CBAMDataLoader::SBamFileName::m_BamName, m_BamName, CBAMDataLoader::SBamFileName::m_IndexName, CBamDb::SetIdMapper(), NStr::Split(), and tag.

Referenced by CBamFileInfo().

Member Data Documentation

◆ m_AnnotName

string CBamFileInfo::m_AnnotName

protected

Definition at line 261 of file bamloader_impl.hpp.

Referenced by GetAnnotName(), and x_Initialize().

◆ m_BamDb

CBamDb CBamFileInfo::m_BamDb

protected

Definition at line 263 of file bamloader_impl.hpp.

Referenced by CBamFileInfo(), GetBamDb(), GetRefSeqLength(), and x_Initialize().

◆ m_BamMutex

CMutex CBamFileInfo::m_BamMutex

mutableprotected

Definition at line 262 of file bamloader_impl.hpp.

Referenced by GetMutex().

◆ m_BamName

string CBamFileInfo::m_BamName

protected

Definition at line 260 of file bamloader_impl.hpp.

Referenced by AddRefSeq(), GetBamName(), and x_Initialize().

◆ m_RefSeqs

TRefSeqs CBamFileInfo::m_RefSeqs

protected

Definition at line 264 of file bamloader_impl.hpp.

Referenced by AddRefSeq(), GetRefSeqInfo(), and GetShortSeqBlobId().

The documentation for this class was generated from the following files:

include/sra/data_loaders/bam/impl/bamloader_impl.hpp
src/sra/data_loaders/bam/bamloader_impl.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TRefSeqs

Constructor & Destructor Documentation

◆ CBamFileInfo()

Member Function Documentation

◆ AddRefSeq()

◆ GetAnnotName()

◆ GetBamDb()

◆ GetBamName()

◆ GetMutex()

◆ GetRefSeqBlobId()

◆ GetRefSeqInfo()

◆ GetRefSeqLength()

◆ GetShortSeqBlobId()

◆ operator CBamDb &()

◆ x_Initialize()

Member Data Documentation

◆ m_AnnotName

◆ m_BamDb

◆ m_BamMutex

◆ m_BamName

◆ m_RefSeqs