Search Toolkit Book for CAlignCigarScore

#include <gui/widgets/seq_graphic/alignment_cigar_score.hpp>

Inheritance diagram for CAlignCigarScore:

Collaboration diagram for CAlignCigarScore:

Classes
class	CCigarIterator

Public Member Functions
	CAlignCigarScore (const IAlnGraphicDataSource &aln_mgr)

ISGAlnScore interface implementation
virtual void	CalculateScores ()

virtual bool	HasScores () const
	CAlignCigarScore. More...

virtual IAlnScoreIterator *	GetScoreIterator (int row) const

virtual CRgbaColor	GetColorForScore (float score, IScoringMethod::EColorType type) const

virtual int	GetSupportedColorTypes () const

virtual bool	IsAverageable () const

virtual bool	IsCacheable () const

virtual const string &	GetScoringMethod () 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 Member Functions inherited from ISGAlnScore
virtual	~ISGAlnScore ()

Static Public Member Functions
static const string &	GetScoreName ()

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)

Private Attributes
const IAlnGraphicDataSource *	m_AlnMgr

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 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 42 of file alignment_cigar_score.hpp.

Constructor & Destructor Documentation

◆ CAlignCigarScore()

CAlignCigarScore::CAlignCigarScore ( const IAlnGraphicDataSource & aln_mgr )

inline

Definition at line 112 of file alignment_cigar_score.hpp.

Member Function Documentation

◆ CalculateScores()

virtual void CAlignCigarScore::CalculateScores ( )

inlinevirtual

Implements ISGAlnScore.

Definition at line 117 of file alignment_cigar_score.hpp.

◆ GetColorForScore()

CRgbaColor CAlignCigarScore::GetColorForScore	(	float	score,
		IScoringMethod::EColorType	type
	)		const

virtual

Implements ISGAlnScore.

Definition at line 59 of file alignment_cigar_score.cpp.

References IScoringMethod::fBackground.

◆ GetScoreIterator()

IAlnScoreIterator * CAlignCigarScore::GetScoreIterator ( int row ) const

virtual

Implements ISGAlnScore.

Definition at line 47 of file alignment_cigar_score.cpp.

References IScoringAlignment::GetAnchor(), IAlnGraphicDataSource::GetCigar(), IAlnGraphicDataSource::GetSeqStart(), IAlnGraphicDataSource::IsCigarUnambiguous(), m_AlnMgr, and NULL.

◆ GetScoreName()

const string & CAlignCigarScore::GetScoreName ( )

static

Definition at line 99 of file alignment_cigar_score.cpp.

Referenced by GetScoringMethod().

◆ GetScoringMethod()

const string & CAlignCigarScore::GetScoringMethod ( ) const

virtual

Implements ISGAlnScore.

Definition at line 93 of file alignment_cigar_score.cpp.

References GetScoreName().

◆ GetSupportedColorTypes()

int CAlignCigarScore::GetSupportedColorTypes ( ) const

virtual

Implements ISGAlnScore.

Definition at line 81 of file alignment_cigar_score.cpp.

References IScoringMethod::fBackground, and IScoringMethod::fForeground.

◆ HasScores()

bool CAlignCigarScore::HasScores ( ) const

virtual

CAlignCigarScore.

Implements ISGAlnScore.

Definition at line 41 of file alignment_cigar_score.cpp.

References IAlnGraphicDataSource::IsCigarUnambiguous(), and m_AlnMgr.

◆ IsAverageable()

bool CAlignCigarScore::IsAverageable ( ) const

virtual

Implements ISGAlnScore.

Definition at line 75 of file alignment_cigar_score.cpp.

◆ IsCacheable()

bool CAlignCigarScore::IsCacheable ( ) const

virtual

Implements ISGAlnScore.

Definition at line 87 of file alignment_cigar_score.cpp.

Member Data Documentation

◆ m_AlnMgr

const IAlnGraphicDataSource* CAlignCigarScore::m_AlnMgr

private

Definition at line 130 of file alignment_cigar_score.hpp.

Referenced by GetScoreIterator(), and HasScores().

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

include/gui/widgets/seq_graphic/alignment_cigar_score.hpp
src/gui/widgets/seq_graphic/alignment_cigar_score.cpp

Classes

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CAlignCigarScore()

Member Function Documentation

◆ CalculateScores()

◆ GetColorForScore()

◆ GetScoreIterator()

◆ GetScoreName()

◆ GetScoringMethod()

◆ GetSupportedColorTypes()

◆ HasScores()

◆ IsAverageable()

◆ IsCacheable()

Member Data Documentation

◆ m_AlnMgr