Search Toolkit Book for CSeqDBIdSet_Vector

Helper class to allow copy-on-write semantics for CSeqDBIdSet. More...

#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>

Inheritance diagram for CSeqDBIdSet_Vector:

Collaboration diagram for CSeqDBIdSet_Vector:

Public Member Functions
	CSeqDBIdSet_Vector ()
	Default constructor. More...

	CSeqDBIdSet_Vector (const vector< Int4 > &ids)
	Construct from an 'int' set. More...

	CSeqDBIdSet_Vector (const vector< Int8 > &ids)
	Construct from an 'Int8' set. More...

	CSeqDBIdSet_Vector (const vector< Uint8 > &ids)
	Construct from an 'Uint8' set. More...

	CSeqDBIdSet_Vector (const vector< string > &ids)

	CSeqDBIdSet_Vector (const vector< TGi > &ids)
	Construct from a 'TGi' set when NCBI_STRICT_GI is in force. More...

vector< Int8 > &	Set ()
	Access the Int8 set. More...

const vector< Int8 > &	Get () const
	Access the Int8 set. More...

vector< string > &	SetSeqIDs ()
	Access the string set. More...

const vector< string > &	GetSeqIDs () const
	Access the string set. More...

size_t	Size () const
	Get the number of elements stored here. More...

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 Member Functions
	CSeqDBIdSet_Vector (CSeqDBIdSet_Vector &)
	Prevent copy construction. More...

CSeqDBIdSet_Vector &	operator= (CSeqDBIdSet_Vector &)
	Prevent copy assignment. More...

Private Attributes
vector< Int8 >	m_Ids
	The actual list elements. More...

vector< string >	m_SeqIds

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...

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

Detailed Description

Helper class to allow copy-on-write semantics for CSeqDBIdSet.

This class owns the actual vector of IDs for the CSeqDBIdSet list.

Definition at line 1465 of file seqdbcommon.hpp.

Constructor & Destructor Documentation

◆ CSeqDBIdSet_Vector() [1/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( )

inline

Default constructor.

Definition at line 1468 of file seqdbcommon.hpp.

◆ CSeqDBIdSet_Vector() [2/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( const vector< Int4 > & ids )

inline

Construct from an 'int' set.

Definition at line 1473 of file seqdbcommon.hpp.

References ITERATE, and m_Ids.

◆ CSeqDBIdSet_Vector() [3/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( const vector< Int8 > & ids )

inline

Construct from an 'Int8' set.

Definition at line 1481 of file seqdbcommon.hpp.

References m_Ids.

◆ CSeqDBIdSet_Vector() [4/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( const vector< Uint8 > & ids )

inline

Construct from an 'Uint8' set.

Definition at line 1487 of file seqdbcommon.hpp.

References ITERATE, and m_Ids.

◆ CSeqDBIdSet_Vector() [5/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( const vector< string > & ids )

inline

Definition at line 1494 of file seqdbcommon.hpp.

References ITERATE, and m_SeqIds.

◆ CSeqDBIdSet_Vector() [6/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( const vector< TGi > & ids )

inline

Construct from a 'TGi' set when NCBI_STRICT_GI is in force.

Definition at line 1504 of file seqdbcommon.hpp.

References GI_TO, ITERATE, and m_Ids.

◆ CSeqDBIdSet_Vector() [7/7]

CSeqDBIdSet_Vector::CSeqDBIdSet_Vector ( CSeqDBIdSet_Vector & )

private

Prevent copy construction.

Member Function Documentation

◆ Get()

const vector<Int8>& CSeqDBIdSet_Vector::Get ( void ) const

inline

Access the Int8 set.

Definition at line 1519 of file seqdbcommon.hpp.

References m_Ids.

Referenced by CSeqDBIdSet::Compute().

◆ GetSeqIDs()

const vector<string>& CSeqDBIdSet_Vector::GetSeqIDs ( ) const

inline

Access the string set.

Definition at line 1531 of file seqdbcommon.hpp.

References m_SeqIds.

◆ operator=()

CSeqDBIdSet_Vector& CSeqDBIdSet_Vector::operator= ( CSeqDBIdSet_Vector & )

private

Prevent copy assignment.

◆ Set()

vector<Int8>& CSeqDBIdSet_Vector::Set ( void )

inline

Access the Int8 set.

Definition at line 1513 of file seqdbcommon.hpp.

References m_Ids.

Referenced by CSeqDBIdSet::Compute(), CSeqDBIdSet::CSeqDBIdSet(), CSeqDBIdSet::GetNegativeList(), and CSeqDBIdSet::GetPositiveList().

◆ SetSeqIDs()

vector<string>& CSeqDBIdSet_Vector::SetSeqIDs ( )

inline

Access the string set.

Definition at line 1525 of file seqdbcommon.hpp.

References m_SeqIds.

Referenced by CSeqDBIdSet::CSeqDBIdSet(), and CSeqDBIdSet::GetNegativeList().

◆ Size()

size_t CSeqDBIdSet_Vector::Size ( void ) const

inline

Get the number of elements stored here.

Definition at line 1537 of file seqdbcommon.hpp.

References m_Ids, m_SeqIds, and n.

Referenced by CSeqDBIdSet::Blank(), CSeqDBIdSet::GetNegativeList(), and CSeqDBIdSet::GetPositiveList().

Member Data Documentation

◆ m_Ids

vector<Int8> CSeqDBIdSet_Vector::m_Ids

private

The actual list elements.

Definition at line 1548 of file seqdbcommon.hpp.

Referenced by CSeqDBIdSet_Vector(), Get(), Set(), and Size().

◆ m_SeqIds

vector<string> CSeqDBIdSet_Vector::m_SeqIds

private

Definition at line 1550 of file seqdbcommon.hpp.

Referenced by CSeqDBIdSet_Vector(), GetSeqIDs(), SetSeqIDs(), and Size().

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

include/objtools/blast/seqdb_reader/seqdbcommon.hpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSeqDBIdSet_Vector() [1/7]

◆ CSeqDBIdSet_Vector() [2/7]

◆ CSeqDBIdSet_Vector() [3/7]

◆ CSeqDBIdSet_Vector() [4/7]

◆ CSeqDBIdSet_Vector() [5/7]

◆ CSeqDBIdSet_Vector() [6/7]

◆ CSeqDBIdSet_Vector() [7/7]

Member Function Documentation

◆ Get()

◆ GetSeqIDs()

◆ operator=()

◆ Set()

◆ SetSeqIDs()

◆ Size()

Member Data Documentation

◆ m_Ids

◆ m_SeqIds