#include <sra/readers/sra/csraread.hpp>

Inheritance diagram for CCSraDb_Impl:

Collaboration diagram for CCSraDb_Impl:

Classes
struct	SAlnTableCursor

struct	SRefInfo

struct	SRefTableCursor

struct	SSeqTableCursor

Public Types
typedef list< SRefInfo >	TRefInfoList

typedef map< string, TRefInfoList::iterator, PNocase >	TRefInfoMapByName

typedef map< CSeq_id_Handle, TRefInfoList::iterator >	TRefInfoMapBySeq_id

typedef vector< string >	TSpotGroups

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 Types inherited from SCSraDb_Defs
enum	ERefIdType { eRefId_SEQ_ID , eRefId_gnl_NAME }

enum	EPathInIdType { ePathInId_config , ePathInId_yes , ePathInId_no }

enum	EAlignType { fPrimaryAlign = 1<<0 , fSecondaryAlign = 1<<1 , fAnyAlign = fPrimaryAlign \| fSecondaryAlign }

typedef EAlignType	TAlignType

Public Member Functions
	CCSraDb_Impl (CVDBMgr &mgr, const string &csra_path, IIdMapper *ref_id_mapper, ERefIdType ref_id_type, const string &sra_id_part)

virtual	~CCSraDb_Impl (void)

const TRefInfoList &	GetRefInfoList (void) const

const TRefInfoMapByName &	GetRefInfoMapByName (void) const

const TRefInfoMapBySeq_id &	GetRefInfoMapBySeq_id (void) const

TSeqPos	GetRowSize (void) const

void	GetSpotGroups (TSpotGroups &spot_groups)

const string &	GetCSraPath (void) const

const string &	GetSraIdPart (void) const

void	SetSraIdPart (const string &s)

CRef< CSeq_id >	MakeShortReadId (TVDBRowId id1, INSDC_coord_one id2) const

void	SetShortReadId (string &str, TVDBRowId id1, INSDC_coord_one id2) const

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 Member Functions
void	x_CalcSeqLength (const SRefInfo &info)

CRef< SRefTableCursor >	Ref (void)

CRef< SAlnTableCursor >	Aln (bool is_secondary)

CRef< SSeqTableCursor >	Seq (void)

void	Put (CRef< SRefTableCursor > &curs)

void	Put (CRef< SAlnTableCursor > &curs)

void	Put (CRef< SSeqTableCursor > &curs)

void	OpenRefTable (void)

void	OpenAlnTable (bool is_secondary)

void	OpenSeqTable (void)

const CVDBTable &	RefTable (void)

const CVDBTable &	AlnTable (bool is_secondary)

const CVDBTable &	SeqTable (void)

void	x_MakeRefSeq_ids (SRefInfo &info, IIdMapper *ref_id_mapper, int ref_id_type)

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

Friends
class	CCSraRefSeqIterator

class	CCSraAlignIterator

class	CCSraShortReadIterator

struct	SSeqTableCursor

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 87 of file csraread.hpp.

Member Typedef Documentation

◆ TRefInfoList

typedef list<SRefInfo> CCSraDb_Impl::TRefInfoList

Definition at line 115 of file csraread.hpp.

◆ TRefInfoMapByName

typedef map<string, TRefInfoList::iterator, PNocase> CCSraDb_Impl::TRefInfoMapByName

Definition at line 116 of file csraread.hpp.

◆ TRefInfoMapBySeq_id

typedef map<CSeq_id_Handle, TRefInfoList::iterator> CCSraDb_Impl::TRefInfoMapBySeq_id

Definition at line 117 of file csraread.hpp.

◆ TSpotGroups

typedef vector<string> CCSraDb_Impl::TSpotGroups

Definition at line 133 of file csraread.hpp.

Constructor & Destructor Documentation

◆ CCSraDb_Impl()

CCSraDb_Impl::CCSraDb_Impl	(	CVDBMgr &	mgr,
		const string &	csra_path,
		IIdMapper *	ref_id_mapper,
		ERefIdType	ref_id_type,
		const string &	sra_id_part
	)

◆ ~CCSraDb_Impl()

CCSraDb_Impl::~CCSraDb_Impl ( void )

virtual

Definition at line 374 of file csraread.cpp.

Member Function Documentation

◆ Aln()

CRef< CCSraDb_Impl::SAlnTableCursor > CCSraDb_Impl::Aln ( bool is_secondary )

protected

Definition at line 548 of file csraread.cpp.

References AlnTable(), and m_Aln.

Referenced by CCSraAlignIterator::CCSraAlignIterator(), CCSraShortReadIterator::GetRefSeqIter(), and CCSraAlignIterator::x_Settle().

◆ AlnTable()

const CVDBTable& CCSraDb_Impl::AlnTable ( bool is_secondary )

inlineprotected

Definition at line 186 of file csraread.hpp.

References m_AlnTable, OpenAlnTable(), and table.

Referenced by Aln().

◆ GetCSraPath()

const string& CCSraDb_Impl::GetCSraPath ( void ) const

inline

Definition at line 136 of file csraread.hpp.

References m_CSraPath.

Referenced by OpenSeqTable().

◆ GetRefInfoList()

const TRefInfoList& CCSraDb_Impl::GetRefInfoList ( void ) const

inline

Definition at line 119 of file csraread.hpp.

References m_RefList.

◆ GetRefInfoMapByName()

const TRefInfoMapByName& CCSraDb_Impl::GetRefInfoMapByName ( void ) const

inline

Definition at line 122 of file csraread.hpp.

References m_RefMapByName.

◆ GetRefInfoMapBySeq_id()

const TRefInfoMapBySeq_id& CCSraDb_Impl::GetRefInfoMapBySeq_id ( void ) const

inline

Definition at line 125 of file csraread.hpp.

References m_RefMapBySeq_id.

◆ GetRowSize()

TSeqPos CCSraDb_Impl::GetRowSize ( void ) const

inline

Definition at line 129 of file csraread.hpp.

References m_RowSize.

Referenced by CCSraRefSeqIterator::GetAlignCountAtPos(), CCSraRefSeqIterator::GetAlnOverStarts(), CCSraRefSeqIterator::GetAlnOverToOpen(), CCSraRefSeqIterator::GetRefLiterals(), CCSraDb::GetRowSize(), CCSraAlignIterator::Select(), and x_CalcSeqLength().

◆ GetSpotGroups()

void CCSraDb_Impl::GetSpotGroups ( TSpotGroups & spot_groups )

Definition at line 424 of file csraread.cpp.

References i, m_Db, and names.

Referenced by CCSraDb::GetSpotGroups().

◆ GetSraIdPart()

const string& CCSraDb_Impl::GetSraIdPart ( void ) const

inline

Definition at line 140 of file csraread.hpp.

References m_SraIdPart.

◆ MakeShortReadId()

CRef< CSeq_id > CCSraDb_Impl::MakeShortReadId	(	TVDBRowId	id1,
		INSDC_coord_one	id2
	)		const

Definition at line 1319 of file csraread.cpp.

References CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), SetShortReadId(), and CDbtag_Base::SetTag().

Referenced by CCSraAlignIterator::GetMateShortSeq_id(), CCSraAlignIterator::GetShortSeq_id(), and CCSraShortReadIterator::GetShortSeq_id().

◆ OpenAlnTable()

void CCSraDb_Impl::OpenAlnTable ( bool is_secondary )

protected

Definition at line 512 of file csraread.cpp.

References m_AlnTable, m_Db, and m_TableMutex.

Referenced by AlnTable().

◆ OpenRefTable()

void CCSraDb_Impl::OpenRefTable ( void )

protected

Definition at line 503 of file csraread.cpp.

References m_Db, m_RefTable, and m_TableMutex.

Referenced by RefTable().

◆ OpenSeqTable()

void CCSraDb_Impl::OpenSeqTable ( void )

protected

Definition at line 523 of file csraread.cpp.

References GetCSraPath(), m_Db, m_Mgr, m_SeqTable, and m_TableMutex.

Referenced by SeqTable().

◆ Put() [1/3]

void CCSraDb_Impl::Put ( CRef< SAlnTableCursor > & curs )

protected

Definition at line 576 of file csraread.cpp.

References m_Aln.

◆ Put() [2/3]

void CCSraDb_Impl::Put ( CRef< SRefTableCursor > & curs )

protected

Definition at line 570 of file csraread.cpp.

References m_Ref.

Referenced by CCSraDb_Impl(), CCSraRefSeqIterator::GetAlignCountAtPos(), CCSraRefSeqIterator::GetAlnOverStarts(), CCSraRefSeqIterator::GetCoverageGraph(), CCSraRefSeqIterator::GetEstimatedNumberOfAlignments(), CCSraRefSeqIterator::GetRefLiterals(), CCSraShortReadIterator::GetRefSeqIter(), CCSraAlignIterator::Reset(), CCSraShortReadIterator::Reset(), x_CalcSeqLength(), and CCSraAlignIterator::x_Settle().

◆ Put() [3/3]

void CCSraDb_Impl::Put ( CRef< SSeqTableCursor > & curs )

protected

Definition at line 584 of file csraread.cpp.

References m_Seq.

◆ Ref()

CRef< CCSraDb_Impl::SRefTableCursor > CCSraDb_Impl::Ref ( void )

protected

Definition at line 537 of file csraread.cpp.

References m_Ref, and RefTable().

Referenced by CCSraDb_Impl(), and x_CalcSeqLength().

◆ RefTable()

const CVDBTable& CCSraDb_Impl::RefTable ( void )

inlineprotected

Definition at line 179 of file csraread.hpp.

References m_RefTable, OpenRefTable(), and table.

Referenced by Ref().

◆ Seq()

CRef< CCSraDb_Impl::SSeqTableCursor > CCSraDb_Impl::Seq ( void )

protected

Definition at line 559 of file csraread.cpp.

References m_Seq, SeqTable(), and SSeqTableCursor.

Referenced by CCSraShortReadIterator::x_Init().

◆ SeqTable()

const CVDBTable& CCSraDb_Impl::SeqTable ( void )

inlineprotected

Definition at line 193 of file csraread.hpp.

References m_SeqTable, OpenSeqTable(), and table.

Referenced by CCSraDb_Impl(), and Seq().

◆ SetShortReadId()

void CCSraDb_Impl::SetShortReadId	(	string &	str,
		TVDBRowId	id1,
		INSDC_coord_one	id2
	)		const

Definition at line 1330 of file csraread.cpp.

References m_SraIdPart, and str().

Referenced by CCSraAlignIterator::GetMatchAlign(), and MakeShortReadId().

◆ SetSraIdPart()

void CCSraDb_Impl::SetSraIdPart ( const string & s )

inline

Definition at line 143 of file csraread.hpp.

References m_SraIdPart.

◆ x_CalcSeqLength()

void CCSraDb_Impl::x_CalcSeqLength ( const SRefInfo & info )

protected

Definition at line 590 of file csraread.cpp.

References GetRowSize(), info, Put(), and Ref().

Referenced by CCSraRefSeqIterator::GetSeqLength().

◆ x_MakeRefSeq_ids()

void CCSraDb_Impl::x_MakeRefSeq_ids	(	SRefInfo &	info,
		IIdMapper *	ref_id_mapper,
		int	ref_id_type
	)

protected

Definition at line 437 of file csraread.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Local, CSerialObject::Equals(), SCSraDb_Defs::eRefId_SEQ_ID, info, CSeq_id_Base::IsLocal(), m_SraIdPart, IIdMapper::MapObject(), NON_CONST_ITERATE, NPOS, and CSeq_id::ParseIDs().

Referenced by CCSraDb_Impl().

Friends And Related Function Documentation

◆ CCSraAlignIterator

friend class CCSraAlignIterator

friend

Definition at line 152 of file csraread.hpp.

◆ CCSraRefSeqIterator

friend class CCSraRefSeqIterator

friend

Definition at line 151 of file csraread.hpp.

◆ CCSraShortReadIterator

friend class CCSraShortReadIterator

friend

Definition at line 153 of file csraread.hpp.

◆ SSeqTableCursor

friend struct SSeqTableCursor

friend

Definition at line 163 of file csraread.hpp.

Referenced by Seq().

Member Data Documentation

◆ m_Aln

CVDBObjectCache<SAlnTableCursor> CCSraDb_Impl::m_Aln[2]

private

Definition at line 218 of file csraread.hpp.

Referenced by Aln(), and Put().

◆ m_AlnTable

CVDBTable CCSraDb_Impl::m_AlnTable[2]

private

Definition at line 214 of file csraread.hpp.

Referenced by AlnTable(), and OpenAlnTable().

◆ m_CSraPath

string CCSraDb_Impl::m_CSraPath

private

Definition at line 208 of file csraread.hpp.

Referenced by GetCSraPath().

◆ m_Db

CVDB CCSraDb_Impl::m_Db

private

Definition at line 207 of file csraread.hpp.

Referenced by CCSraDb_Impl(), GetSpotGroups(), OpenAlnTable(), OpenRefTable(), and OpenSeqTable().

◆ m_Mgr

CVDBMgr CCSraDb_Impl::m_Mgr

private

Definition at line 206 of file csraread.hpp.

Referenced by OpenSeqTable().

◆ m_OverlapMutex

CFastMutex CCSraDb_Impl::m_OverlapMutex

private

Definition at line 212 of file csraread.hpp.

◆ m_Ref

CVDBObjectCache<SRefTableCursor> CCSraDb_Impl::m_Ref

private

Definition at line 217 of file csraread.hpp.

Referenced by Put(), and Ref().

◆ m_RefList

TRefInfoList CCSraDb_Impl::m_RefList

private

Definition at line 222 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoList().

◆ m_RefMapByName

TRefInfoMapByName CCSraDb_Impl::m_RefMapByName

private

Definition at line 223 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoMapByName().

◆ m_RefMapBySeq_id

TRefInfoMapBySeq_id CCSraDb_Impl::m_RefMapBySeq_id

private

Definition at line 224 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoMapBySeq_id().

◆ m_RefTable

CVDBTable CCSraDb_Impl::m_RefTable

private

Definition at line 213 of file csraread.hpp.

Referenced by OpenRefTable(), and RefTable().

◆ m_RowSize

TSeqPos CCSraDb_Impl::m_RowSize

private

Definition at line 221 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRowSize().

◆ m_Seq

CVDBObjectCache<SSeqTableCursor> CCSraDb_Impl::m_Seq

private

Definition at line 219 of file csraread.hpp.

Referenced by Put(), and Seq().

◆ m_SeqTable

CVDBTable CCSraDb_Impl::m_SeqTable

private

Definition at line 215 of file csraread.hpp.

Referenced by OpenSeqTable(), and SeqTable().

◆ m_SraIdPart

string CCSraDb_Impl::m_SraIdPart

private

Definition at line 209 of file csraread.hpp.

Referenced by CCSraDb_Impl(), GetSraIdPart(), SetShortReadId(), SetSraIdPart(), and x_MakeRefSeq_ids().

◆ m_TableMutex

CFastMutex CCSraDb_Impl::m_TableMutex

private

Definition at line 211 of file csraread.hpp.

Referenced by OpenAlnTable(), OpenRefTable(), and OpenSeqTable().

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

include/sra/readers/sra/csraread.hpp
src/sra/readers/sra/csraread.cpp

Private Attributes
CVDBMgr	m_Mgr

CVDB	m_Db

string	m_CSraPath

string	m_SraIdPart

CFastMutex	m_TableMutex

CFastMutex	m_OverlapMutex

CVDBTable	m_RefTable

CVDBTable	m_AlnTable [2]

CVDBTable	m_SeqTable

CVDBObjectCache< SRefTableCursor >	m_Ref

CVDBObjectCache< SAlnTableCursor >	m_Aln [2]

CVDBObjectCache< SSeqTableCursor >	m_Seq

TSeqPos	m_RowSize

TRefInfoList	m_RefList

TRefInfoMapByName	m_RefMapByName

TRefInfoMapBySeq_id	m_RefMapBySeq_id

Classes

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TRefInfoList

◆ TRefInfoMapByName

◆ TRefInfoMapBySeq_id

◆ TSpotGroups

Constructor & Destructor Documentation

◆ CCSraDb_Impl()

◆ ~CCSraDb_Impl()

Member Function Documentation

◆ Aln()

◆ AlnTable()

◆ GetCSraPath()

◆ GetRefInfoList()

◆ GetRefInfoMapByName()

◆ GetRefInfoMapBySeq_id()

◆ GetRowSize()

◆ GetSpotGroups()

◆ GetSraIdPart()

◆ MakeShortReadId()

◆ OpenAlnTable()

◆ OpenRefTable()

◆ OpenSeqTable()

◆ Put() [1/3]

◆ Put() [2/3]

◆ Put() [3/3]

◆ Ref()

◆ RefTable()

◆ Seq()

◆ SeqTable()

◆ SetShortReadId()

◆ SetSraIdPart()

◆ x_CalcSeqLength()

◆ x_MakeRefSeq_ids()

Friends And Related Function Documentation

◆ CCSraAlignIterator

◆ CCSraRefSeqIterator

◆ CCSraShortReadIterator

◆ SSeqTableCursor

Member Data Documentation

◆ m_Aln

◆ m_AlnTable

◆ m_CSraPath

◆ m_Db

◆ m_Mgr

◆ m_OverlapMutex

◆ m_Ref

◆ m_RefList

◆ m_RefMapByName

◆ m_RefMapBySeq_id

◆ m_RefTable

◆ m_RowSize

◆ m_Seq

◆ m_SeqTable

◆ m_SraIdPart

◆ m_TableMutex