Search Toolkit Book for CQualityScoringMethod

CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment column and residue, based on how different each residue is from the columns consensus. More...

#include <gui/widgets/aln_score/quality_methods.hpp>

Inheritance diagram for CQualityScoringMethod:

Collaboration diagram for CQualityScoringMethod:

Public Types
enum	EOptions { fIgnoreEmptySpace = 0x01 , fIgnoreGaps = 0x02 , fScoreWholeColumn = 0x04 }

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...

Public Types inherited from IScoringMethod
enum	EColorType { fBackground = 0x1 , fForeground = 0x2 }

typedef float	TScore

typedef vector< TScore >	TScoreVector

typedef CAttrRangeCollection< TScore, TSeqPos >	TScoreColl

Public Member Functions
	CQualityScoringMethod ()
	CQualityScoringMethod. More...

	CQualityScoringMethod (int colors)

	CQualityScoringMethod (const CQualityScoringMethod &orig)

virtual	~CQualityScoringMethod ()

void	CreateColorTable (int size)

virtual TNCBIScore	GetSubstitutionScore (int aa1, int aa2) const =0

virtual string	GetAllowedSymbols () const =0

bool	IsScoreWholeColumn () const

void	SetOptions (int options)

int	GetOptions () const

IScoringMethod implementation
virtual string	GetDescription () const
	returns a detailed description of the method that is used in UI More...

virtual bool	IsAverageable () const
	return "true" if scores could be averaged More...

virtual int	GetSupportedColorTypes () const
	returns a combination of EColorType flags More...

virtual const CRgbaColor &	GetColorForScore (TScore score, EColorType type) const
	returns a color corresponding to a given score value. More...

IColumnScoringMethod implementaion
virtual void	CalculateScores (char cons, const string &column, TScore &col_score, TScoreVector &scores)

virtual bool	CanCalculateScores (const IScoringAlignment &aln)
	Do we have what it takes to calculate scores? e.g. a master row selected? More...

virtual const CRgbaColor &	GetColorForNoScore (EColorType type) const
	Call for display colors when CanCalculateScores returns false. More...

virtual void	SetColorForNoScore (EColorType type, const CRgbaColor &color)

IUIToolWithGUI implementation
virtual const CMenuItem *	GetMenu ()
	Returns a pointer to the submenu. More...

virtual bool	HasPropertiesPanel () const
	returns true if the method supports properties dialog More...

virtual wxWindow *	CreatePropertiesPanel (wxWindow *parent)
	This a factory method that shall produce a CPropertiesPanel representing properties of the method; the panel Apply() must take care of appying changes to the method. 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

Public Member Functions inherited from IScoringMethod
virtual	~IScoringMethod ()

virtual int	GetType () const =0
	returns combination of EAlignType flags defining types of alignments that can be colored with this method More...

Public Member Functions inherited from IUITool
virtual	~IUITool ()

virtual IUITool *	Clone () const =0

virtual string	GetName () const =0
	returns unique name of the method that is used in UI to identify it More...

Public Member Functions inherited from IColumnScoringMethod
virtual	~IColumnScoringMethod ()

virtual bool	NeedsTranslation () const

virtual void	UpdateSettings (const IScoringAlignment &aln)
	Set alignment specifi settings. More...

Public Member Functions inherited from IUIToolWithGUI
virtual	~IUIToolWithGUI ()

virtual	~IUIToolWithGUI ()

Protected Attributes
CRgbaColor	m_Worst

CRgbaColor	m_Best

CRgbaGradColorTable	m_ColorTable

int	m_Options

char	m_Space

char	m_Gap

Protected Attributes inherited from IColumnScoringMethod
char	m_AmbiguousResidue = ' '
	Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins. More...

std::function< bool(char c, char b)>	mf_CompareResidue

Private Member Functions
void	x_Init (int colors)

Friends
class	CQualityScoringPanel

Additional Inherited Members
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 Member Functions inherited from IScoringMethod
static const char *	GetAlignmentTagByType (IAlnExplorer::EAlignType type)
	returns symbolic label for the given alignment type, should be More...

static IAlnExplorer::EAlignType	GetAlignmentTypeByTag (const string &tag)

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...

Static Public Attributes inherited from IScoringMethod
static const int	sm_DefGradientSize = 32
	default number of colors in gradient More...

Static Public Attributes inherited from IColumnScoringMethod
static const int	kAmbiguousResidueScore = 1000

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

Detailed Description

CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment column and residue, based on how different each residue is from the columns consensus.

Definition at line 50 of file quality_methods.hpp.

Member Enumeration Documentation

◆ EOptions

enum CQualityScoringMethod::EOptions

Enumerator
fIgnoreEmptySpace	Do not count unaligned regions in score.
fIgnoreGaps	Do not count gaps in the alignment in the score.
fScoreWholeColumn	The column's total score is also the score for each residue.

Definition at line 57 of file quality_methods.hpp.

Constructor & Destructor Documentation

◆ CQualityScoringMethod() [1/3]

CQualityScoringMethod::CQualityScoringMethod ( )

CQualityScoringMethod.

Definition at line 51 of file quality_methods.cpp.

References IScoringMethod::sm_DefGradientSize, and x_Init().

◆ CQualityScoringMethod() [2/3]

CQualityScoringMethod::CQualityScoringMethod ( int colors )

Definition at line 63 of file quality_methods.cpp.

References colors, and x_Init().

◆ CQualityScoringMethod() [3/3]

CQualityScoringMethod::CQualityScoringMethod ( const CQualityScoringMethod & orig )

Definition at line 80 of file quality_methods.cpp.

References m_ColorTable, and orig.

◆ ~CQualityScoringMethod()

CQualityScoringMethod::~CQualityScoringMethod ( )

virtual

Definition at line 58 of file quality_methods.cpp.

Member Function Documentation

◆ CalculateScores()

void CQualityScoringMethod::CalculateScores	(	char	cons,
		const string &	column,
		TScore &	col_score,
		TScoreVector &	scores
	)

virtual

Implements IColumnScoringMethod.

Reimplemented in CConservationScoringMethod.

Definition at line 137 of file quality_methods.cpp.

References _ASSERT, column, GetAllowedSymbols(), GetSubstitutionScore(), i, IsScoreWholeColumn(), ITERATE, IColumnScoringMethod::kAmbiguousResidueScore, IColumnScoringMethod::m_AmbiguousResidue, m_Gap, m_Space, NCBI_FSM_DIM, and r().

◆ CanCalculateScores()

bool CQualityScoringMethod::CanCalculateScores ( const IScoringAlignment & aln )

virtual

Do we have what it takes to calculate scores? e.g. a master row selected?

Implements IColumnScoringMethod.

Definition at line 203 of file quality_methods.cpp.

◆ CreateColorTable()

void CQualityScoringMethod::CreateColorTable ( int size )

Definition at line 112 of file quality_methods.cpp.

References _ASSERT, CRgbaGradColorTable::FillGradient(), m_Best, m_ColorTable, m_Worst, CRgbaGradColorTable::SetSize(), and ncbi::grid::netcache::search::fields::size.

Referenced by CQualityScoringPanel::OnApply(), CConservationScoringPanel::OnApply(), x_Init(), and CConservationScoringMethod::x_Init().

◆ CreatePropertiesPanel()

wxWindow * CQualityScoringMethod::CreatePropertiesPanel ( wxWindow * parent )

virtual

This a factory method that shall produce a CPropertiesPanel representing properties of the method; the panel Apply() must take care of appying changes to the method.

Implements IUIToolWithGUI.

Reimplemented in CConservationScoringMethod.

Definition at line 377 of file quality_methods.cpp.

References CQualityScoringPanel.

◆ GetAllowedSymbols()

virtual string CQualityScoringMethod::GetAllowedSymbols ( ) const

pure virtual

Implemented in CConservationScoringMethod, CQualityScoringMethodAA, and CQualityScoringMethodNA.

Referenced by CalculateScores().

◆ GetColorForNoScore()

const CRgbaColor & CQualityScoringMethod::GetColorForNoScore ( EColorType type ) const

virtual

Call for display colors when CanCalculateScores returns false.

Implements IScoringMethod.

Definition at line 209 of file quality_methods.cpp.

References _ASSERT.

◆ GetColorForScore()

const CRgbaColor & CQualityScoringMethod::GetColorForScore	(	TScore	score,
		EColorType	type
	)		const

virtual

returns a color corresponding to a given score value.

It is recommended that this method be implemented using color table, on-the-fly creation of colors is expensive.

Implements IScoringMethod.

Reimplemented in CConservationScoringMethod.

Definition at line 229 of file quality_methods.cpp.

References _ASSERT, IScoringMethod::fBackground, CRgbaGradColorTable::GetSize(), int, kMaxScore, m_ColorTable, min(), and ncbi::grid::netcache::search::fields::size.

◆ GetDescription()

string CQualityScoringMethod::GetDescription ( ) const

virtual

returns a detailed description of the method that is used in UI

Implements IUITool.

Reimplemented in CConservationScoringMethod.

Definition at line 125 of file quality_methods.cpp.

References QUALITY_DESCR.

◆ GetMenu()

const CMenuItem * CQualityScoringMethod::GetMenu ( )

virtual

Returns a pointer to the submenu.

If the pointer is not NULL, then this submenu is integrated into the application's menu. If method is derived from CCommandTarget it will recieve command events.

Implements IUIToolWithGUI.

Definition at line 249 of file quality_methods.cpp.