CAlnMap::CAlnChunk Class Reference

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#include <objtools/alnmgr/alnmap.hpp>

Inheritance diagram for CAlnMap::CAlnChunk:

Collaboration diagram for CAlnMap::CAlnChunk:

Public Member Functions
TSegTypeFlags	GetType (void) const
CAlnChunk &	SetType (TSegTypeFlags type_flags)
const TSignedRange &	GetRange (void) const
const TSignedRange &	GetAlnRange (void) const
bool	IsGap (void) 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

Private Member Functions
	CAlnChunk (void)
TSignedRange &	SetRange (void)
TSignedRange &	SetAlnRange (void)

Private Attributes
TSegTypeFlags	m_TypeFlags
TSignedRange	m_SeqRange
TSignedRange	m_AlnRange

Friends
CConstRef< CAlnChunk >	CAlnChunkVec::operator[] (TNumchunk i) const

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

Definition at line 293 of file alnmap.hpp.

Constructor & Destructor Documentation

CAlnChunk()

CAlnMap::CAlnChunk::CAlnChunk ( void  )

inlineprivate

Definition at line 310 of file alnmap.hpp.

Member Function Documentation

GetAlnRange()

const TSignedRange& CAlnMap::CAlnChunk::GetAlnRange ( void  ) const

inline

Definition at line 302 of file alnmap.hpp.

References m_AlnRange.

GetRange()

const TSignedRange& CAlnMap::CAlnChunk::GetRange ( void  ) const

inline

Definition at line 300 of file alnmap.hpp.

References m_SeqRange.

GetType()

TSegTypeFlags CAlnMap::CAlnChunk::GetType ( void  ) const

inline

Definition at line 296 of file alnmap.hpp.

References m_TypeFlags.

IsGap()

bool CAlnMap::CAlnChunk::IsGap ( void  ) const

inline

Definition at line 304 of file alnmap.hpp.

References CRange_Base::GetFrom(), and m_SeqRange.

SetAlnRange()

TSignedRange& CAlnMap::CAlnChunk::SetAlnRange ( void  )

inlineprivate

Definition at line 312 of file alnmap.hpp.

References m_AlnRange.

SetRange()

TSignedRange& CAlnMap::CAlnChunk::SetRange ( void  )

inlineprivate

Definition at line 311 of file alnmap.hpp.

References m_SeqRange.

SetType()

CAlnChunk& CAlnMap::CAlnChunk::SetType ( TSegTypeFlags  type_flags )

inline

Definition at line 297 of file alnmap.hpp.

References m_TypeFlags.

Friends And Related Function Documentation

CAlnChunkVec::operator[]

CConstRef<CAlnChunk> CAlnChunkVec::operator[] ( TNumchunk  i ) const

friend

Member Data Documentation

m_AlnRange

TSignedRange CAlnMap::CAlnChunk::m_AlnRange

private

Definition at line 316 of file alnmap.hpp.

Referenced by GetAlnRange(), and SetAlnRange().

m_SeqRange

TSignedRange CAlnMap::CAlnChunk::m_SeqRange

private

Definition at line 315 of file alnmap.hpp.

Referenced by GetRange(), IsGap(), and SetRange().

m_TypeFlags

TSegTypeFlags CAlnMap::CAlnChunk::m_TypeFlags

private

Definition at line 314 of file alnmap.hpp.

Referenced by GetType(), and SetType().

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

• include/objtools/alnmgr/alnmap.hpp