Search Toolkit Book for CMatrixScoringMethod

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

Inheritance diagram for CMatrixScoringMethod:

Collaboration diagram for CMatrixScoringMethod:

Public Member Functions
	CMatrixScoringMethod ()

virtual	~CMatrixScoringMethod ()

virtual void	CreateColorTable (int size)

IScoringMethod implementation
virtual IScoringMethod *	Clone () const

virtual bool	Load (CNcbiRegistry &reg)

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

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

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

void	SetColorForNoScore (EColorType type, const CRgbaColor &color)

IWindowScoringMethod implementation
size_t	GetWindowSize () const

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 CTemplateScoringMethod
	CTemplateScoringMethod ()
	CTemplateScoringMethod. More...

virtual	~CTemplateScoringMethod ()

virtual bool	LoadInfo (CNcbiRegistry &reg)
	loads only descriptive information More...

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

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

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

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

void	SetName (const string &s)

void	SetDescription (const string &s)

virtual bool	SaveInfo (CNcbiRegistry &reg)
	saves only descriptive information More...

virtual bool	Save (CNcbiRegistry &reg)

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 ()

Public Member Functions inherited from IUITool
virtual	~IUITool ()

Public Member Functions inherited from ITemplateUITool
virtual	~ITemplateUITool ()
	ITemplateUITool. 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 ()

Public Member Functions inherited from IWindowScoringMethod
virtual	~IWindowScoringMethod ()

Protected Types
enum	TRangeType { eNone = 0 , eConsensus = 1 , eNonConsesus = 2 , eBoth = 3 }

Protected Member Functions
void	x_CreateScoreTable (CNcbiRegistry &reg)

void	x_CalculateConsensusRange ()

void	x_CalculateNonConsensusRange ()

Protected Member Functions inherited from CTemplateScoringMethod
CRgbaColor	x_GetColor (CNcbiRegistry &reg, const string &key, const string def_value)

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

Static Protected Member Functions
static int	x_BaseToIndex (char c)

Protected Attributes
unsigned char	m_CalculateRange

CNcbiMatrix< TScore >	m_vScore

TScore	m_MinScore

TScore	m_MaxScore

TScore	m_ConsensusMinScore

TScore	m_ConsensusMaxScore

TScore	m_NonConsensusMinScore

TScore	m_NonConsensusMaxScore

CRgbaColor	m_MinColor

CRgbaColor	m_MidColor

CRgbaColor	m_MaxColor

CRgbaColor	m_UndefColor

bool	m_UseConsensus

CRgbaGradColorTable	m_ColorTable

size_t	m_WindowSize

Protected Attributes inherited from CTemplateScoringMethod
string	m_Name

string	m_Descr

int	m_Type

bool	m_Averageable

EColorGradType	m_ColorGradType

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

Friends
class	CMatrixScoringPanel

Additional Inherited Members
Public Types inherited from CTemplateScoringMethod
enum	EColorGradType { eTwoColorGradient , eThreeColorGradient }

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

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

Detailed Description

CMatrixScoringMethod.

Definition at line 188 of file template_methods.hpp.

Member Enumeration Documentation

◆ TRangeType

enum CMatrixScoringMethod::TRangeType

protected

Enumerator
eNone
eConsensus
eNonConsesus
eBoth

Definition at line 241 of file template_methods.hpp.

Constructor & Destructor Documentation

◆ CMatrixScoringMethod()

CMatrixScoringMethod::CMatrixScoringMethod ( )

Definition at line 980 of file template_methods.cpp.

References CreateColorTable(), kMatrixSize, CTemplateScoringMethod::m_Averageable, m_MaxScore, m_vScore, CNcbiMatrix< T >::Resize(), and IScoringMethod::sm_DefGradientSize.

Referenced by Clone().

◆ ~CMatrixScoringMethod()

CMatrixScoringMethod::~CMatrixScoringMethod ( )

virtual

Definition at line 998 of file template_methods.cpp.

Member Function Documentation

◆ CalculateScores()

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

virtual

Implements IColumnScoringMethod.

Definition at line 1154 of file template_methods.cpp.

References _ASSERT, column, CNcbiMatrix< T >::GetCols(), CNcbiMatrix< T >::GetRows(), i, int, m_MaxScore, m_UseConsensus, m_vScore, and x_BaseToIndex().

◆ CanCalculateScores()

bool CMatrixScoringMethod::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 1232 of file template_methods.cpp.

◆ Clone()

IScoringMethod * CMatrixScoringMethod::Clone ( void ) const

virtual

Implements IUITool.

Definition at line 1042 of file template_methods.cpp.

References CMatrixScoringMethod().

◆ CreateColorTable()

void CMatrixScoringMethod::CreateColorTable ( int size )

virtual

◆ CreatePropertiesPanel()

wxWindow * CMatrixScoringMethod::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.

Definition at line 1419 of file template_methods.cpp.

References CMatrixScoringPanel.

◆ GetColorForNoScore()

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

virtual

Call for display colors when CanCalculateScores returns false.

Implements IScoringMethod.

Definition at line 1238 of file template_methods.cpp.

References _VERIFY, IScoringMethod::fBackground, and m_UndefColor.

◆ GetColorForScore()

const CRgbaColor & CMatrixScoringMethod::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.

Definition at line 1253 of file template_methods.cpp.

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

◆ GetMenu()

const CMenuItem * CMatrixScoringMethod::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 1278 of file template_methods.cpp.

References NULL.