#include <objtools/alnmgr/alnmatch.hpp>

Inheritance diagram for CAlnMixMatch:

Collaboration diagram for CAlnMixMatch:

Public Member Functions
	CAlnMixMatch (void)

	CAlnMixMatch (const CAlnMixMatch &match)

CAlnMixMatch &	operator= (const CAlnMixMatch &match)

bool	IsGood (const CAlnMixSeq::TMatchList &list, CAlnMixSeq::TMatchList::const_iterator iter) const

bool	IsGood (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

Public Attributes
int	m_Score

int	m_ChainScore

CAlnMixSeq *	m_AlnSeq1

CAlnMixSeq *	m_AlnSeq2

TSeqPos	m_Start1

TSeqPos	m_Start2

TSeqPos	m_Len

bool	m_StrandsDiffer

int	m_DsIdx

CAlnMixSeq::TMatchList::iterator	m_MatchIter1

CAlnMixSeq::TMatchList::iterator	m_MatchIter2

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 122 of file alnmatch.hpp.

Constructor & Destructor Documentation

◆ CAlnMixMatch() [1/2]

CAlnMixMatch::CAlnMixMatch ( void )

inline

Definition at line 125 of file alnmatch.hpp.

◆ CAlnMixMatch() [2/2]

CAlnMixMatch::CAlnMixMatch ( const CAlnMixMatch & match )

inline

Definition at line 131 of file alnmatch.hpp.

References match().

Member Function Documentation

◆ IsGood() [1/2]

bool CAlnMixMatch::IsGood	(	const CAlnMixSeq::TMatchList &	list,
		CAlnMixSeq::TMatchList::const_iterator	iter
	)		const

inline

Definition at line 159 of file alnmatch.hpp.

References ITERATE.

◆ IsGood() [2/2]

bool CAlnMixMatch::IsGood ( void ) const

inline

Definition at line 168 of file alnmatch.hpp.

References m_AlnSeq1, m_AlnSeq2, m_MatchIter1, m_MatchIter2, and CAlnMixSeq::m_MatchList.

◆ operator=()

CAlnMixMatch& CAlnMixMatch::operator= ( const CAlnMixMatch & match )

inline

Definition at line 139 of file alnmatch.hpp.

References m_AlnSeq1, m_AlnSeq2, m_ChainScore, m_DsIdx, m_Len, m_MatchIter1, m_MatchIter2, m_Score, m_Start1, m_Start2, m_StrandsDiffer, and match().

Member Data Documentation

◆ m_AlnSeq1

CAlnMixSeq* CAlnMixMatch::m_AlnSeq1

Definition at line 178 of file alnmatch.hpp.

Referenced by IsGood(), and operator=().

◆ m_AlnSeq2

CAlnMixSeq * CAlnMixMatch::m_AlnSeq2

Definition at line 178 of file alnmatch.hpp.

Referenced by IsGood(), and operator=().

◆ m_ChainScore

int CAlnMixMatch::m_ChainScore

Definition at line 177 of file alnmatch.hpp.

Referenced by operator=().

◆ m_DsIdx

int CAlnMixMatch::m_DsIdx

Definition at line 181 of file alnmatch.hpp.

Referenced by operator=().

◆ m_Len

TSeqPos CAlnMixMatch::m_Len

Definition at line 179 of file alnmatch.hpp.

Referenced by operator=().

◆ m_MatchIter1

CAlnMixSeq::TMatchList::iterator CAlnMixMatch::m_MatchIter1

Definition at line 182 of file alnmatch.hpp.

Referenced by IsGood(), and operator=().

◆ m_MatchIter2

CAlnMixSeq::TMatchList::iterator CAlnMixMatch::m_MatchIter2

Definition at line 182 of file alnmatch.hpp.

Referenced by IsGood(), and operator=().

◆ m_Score

int CAlnMixMatch::m_Score

Definition at line 177 of file alnmatch.hpp.

Referenced by operator=().

◆ m_Start1

TSeqPos CAlnMixMatch::m_Start1

Definition at line 179 of file alnmatch.hpp.

Referenced by operator=().

◆ m_Start2

TSeqPos CAlnMixMatch::m_Start2

Definition at line 179 of file alnmatch.hpp.

Referenced by operator=().

◆ m_StrandsDiffer

bool CAlnMixMatch::m_StrandsDiffer

Definition at line 180 of file alnmatch.hpp.

Referenced by operator=().

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

include/objtools/alnmgr/alnmatch.hpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CAlnMixMatch() [1/2]

◆ CAlnMixMatch() [2/2]

Member Function Documentation

◆ IsGood() [1/2]

◆ IsGood() [2/2]

◆ operator=()

Member Data Documentation

◆ m_AlnSeq1

◆ m_AlnSeq2

◆ m_ChainScore

◆ m_DsIdx

◆ m_Len

◆ m_MatchIter1

◆ m_MatchIter2

◆ m_Score

◆ m_Start1

◆ m_Start2

◆ m_StrandsDiffer