Search Toolkit Book for CScore_Overlap

Inheritance diagram for CScore_Overlap:

Collaboration diagram for CScore_Overlap:

Public Member Functions
	CScore_Overlap (int row, bool include_gaps)

virtual void	PrintHelp (CNcbiOstream &ostr) const

virtual EComplexity	GetComplexity () const

virtual bool	IsInteger () const

virtual double	Get (const CSeq_align &align, CScope *) const

virtual void	UpdateState (const objects::CSeq_align &align)
	For any IScore subclasses that have an internal state, this function will be called to update it for any alignment that matches the filter. More...

Public Member Functions inherited from CScoreLookup::IScore
virtual	~IScore ()

virtual double	Get (const objects::CSeq_align &align, objects::CScope *scope) const =0

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 Attributes
int	m_Row

bool	m_IncludeGaps

CSeq_id	m_CurrentSeq

CRangeCollection< TSeqPos >	m_CoveredRanges

Additional Inherited Members
Public Types inherited from CScoreLookup::IScore
enum	EComplexity { eEasy , eHard }

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 1343 of file score_lookup.cpp.

Constructor & Destructor Documentation

◆ CScore_Overlap()

CScore_Overlap::CScore_Overlap	(	int	row,
		bool	include_gaps
	)

inline

Definition at line 1346 of file score_lookup.cpp.

Member Function Documentation

◆ Get()

virtual double CScore_Overlap::Get	(	const CSeq_align &	align,
		CScope *
	)		const

inlinevirtual

Definition at line 1368 of file score_lookup.cpp.

References CSeq_align::GetAlignedBases(), CRangeCollection< Position >::GetCoveredLength(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), m_CoveredRanges, m_CurrentSeq, m_IncludeGaps, m_Row, and CSeq_id::Match().

◆ GetComplexity()

virtual EComplexity CScore_Overlap::GetComplexity ( ) const

inlinevirtual

Reimplemented from CScoreLookup::IScore.

Definition at line 1364 of file score_lookup.cpp.

References CScoreLookup::IScore::eEasy.

◆ IsInteger()

virtual bool CScore_Overlap::IsInteger ( void ) const

inlinevirtual

Reimplemented from CScoreLookup::IScore.

Definition at line 1366 of file score_lookup.cpp.

◆ PrintHelp()

virtual void CScore_Overlap::PrintHelp ( CNcbiOstream & ostr ) const

inlinevirtual

Implements CScoreLookup::IScore.

Definition at line 1352 of file score_lookup.cpp.

References m_IncludeGaps, and m_Row.

◆ UpdateState()

virtual void CScore_Overlap::UpdateState ( const objects::CSeq_align & )

inlinevirtual

For any IScore subclasses that have an internal state, this function will be called to update it for any alignment that matches the filter.

Reimplemented from CScoreLookup::IScore.

Definition at line 1382 of file score_lookup.cpp.

References CSeq_id::Assign(), CRangeCollection< Position >::clear(), m_CoveredRanges, m_CurrentSeq, m_IncludeGaps, m_Row, and CSeq_id::Match().

Member Data Documentation

◆ m_CoveredRanges

CRangeCollection<TSeqPos> CScore_Overlap::m_CoveredRanges

private

Definition at line 1400 of file score_lookup.cpp.

Referenced by Get(), and UpdateState().

◆ m_CurrentSeq

CSeq_id CScore_Overlap::m_CurrentSeq

private

Definition at line 1399 of file score_lookup.cpp.

Referenced by Get(), and UpdateState().

◆ m_IncludeGaps

bool CScore_Overlap::m_IncludeGaps

private

Definition at line 1398 of file score_lookup.cpp.

Referenced by Get(), PrintHelp(), and UpdateState().

◆ m_Row

int CScore_Overlap::m_Row

private

Definition at line 1397 of file score_lookup.cpp.

Referenced by Get(), PrintHelp(), and UpdateState().

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

src/algo/align/util/score_lookup.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CScore_Overlap()

Member Function Documentation

◆ Get()

◆ GetComplexity()

◆ IsInteger()

◆ PrintHelp()

◆ UpdateState()

Member Data Documentation

◆ m_CoveredRanges

◆ m_CurrentSeq

◆ m_IncludeGaps

◆ m_Row