Search Toolkit Book for CSimpleScoringMethod

CSimpleScoringMethod - trivial implementation of IScoringMethod. More...

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

Inheritance diagram for CSimpleScoringMethod:

Collaboration diagram for CSimpleScoringMethod:

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

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
	CSimpleScoringMethod ()
	CSimpleScoringMethod. More...

	CSimpleScoringMethod (int colors)

	CSimpleScoringMethod (const CSimpleScoringMethod &orig)

virtual	~CSimpleScoringMethod ()

void	SetOptions (int options)

int	GetOptions ()

void	CreateColorTable (int size)

IUITool implementation
virtual IUITool *	Clone () const

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...

IScoringMethod implementation
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...

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...

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

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

IColumnScoringMethod implementation
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...

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 ()

Public Member Functions inherited from IUITool
virtual	~IUITool ()

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
int	m_Options

CRgbaColor	m_Worst
	combination of EOptions flags More...

CRgbaColor	m_Best

CRgbaGradColorTable	m_ColorTable

vector< int >	m_vCharCounts

char	m_Space
	histogramm of characters More...

char	m_Gap

unique_ptr< CMenuItem >	m_Menu

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	CSimpleScoringPanel

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

CSimpleScoringMethod - trivial implementation of IScoringMethod.

Scores are calculated as frequencies of symbols normalized to fit in range [0, 1]. CreateColorTable() must be called once before any GetColorForScore() calls.

Definition at line 51 of file simple_methods.hpp.

Member Enumeration Documentation

◆ EOptions

enum CSimpleScoringMethod::EOptions

Enumerator
fIgnoreEmptySpace
fIgnoreGaps

Definition at line 60 of file simple_methods.hpp.

Constructor & Destructor Documentation

◆ CSimpleScoringMethod() [1/3]

CSimpleScoringMethod::CSimpleScoringMethod ( )

CSimpleScoringMethod.

Definition at line 132 of file simple_methods.cpp.

References fIgnoreEmptySpace, fIgnoreGaps, m_vCharCounts, SetOptions(), IScoringMethod::sm_DefGradientSize, and x_Init().

Referenced by Clone().

◆ CSimpleScoringMethod() [2/3]

CSimpleScoringMethod::CSimpleScoringMethod ( int colors )

Definition at line 147 of file simple_methods.cpp.

References colors, and x_Init().

◆ CSimpleScoringMethod() [3/3]

CSimpleScoringMethod::CSimpleScoringMethod ( const CSimpleScoringMethod & orig )

Definition at line 166 of file simple_methods.cpp.

References m_ColorTable, m_vCharCounts, orig, and SetOptions().

◆ ~CSimpleScoringMethod()

CSimpleScoringMethod::~CSimpleScoringMethod ( )

virtual

Definition at line 142 of file simple_methods.cpp.

Member Function Documentation

◆ CalculateScores()

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

virtual

Implements IColumnScoringMethod.

Reimplemented in CSNPScoringMethod.

Definition at line 235 of file simple_methods.cpp.

References _ASSERT, column, i, ITERATE, IColumnScoringMethod::kAmbiguousResidueScore, IColumnScoringMethod::m_AmbiguousResidue, m_Gap, m_Space, and m_vCharCounts.

◆ CanCalculateScores()

bool CSimpleScoringMethod::CanCalculateScores ( const IScoringAlignment & aln )

virtual

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

Implements IColumnScoringMethod.

Reimplemented in CSNPScoringMethod.

Definition at line 271 of file simple_methods.cpp.

◆ Clone()

IUITool * CSimpleScoringMethod::Clone ( void ) const

virtual

Implements IUITool.

Reimplemented in CSNPScoringMethod.

Definition at line 179 of file simple_methods.cpp.

References CSimpleScoringMethod().

◆ CreateColorTable()

void CSimpleScoringMethod::CreateColorTable ( int size )

Definition at line 199 of file simple_methods.cpp.

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

Referenced by CSimpleScoringPanel::OnApply(), and x_Init().

◆ CreatePropertiesPanel()

wxWindow * CSimpleScoringMethod::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 CSNPScoringMethod.

Definition at line 413 of file simple_methods.cpp.

References CSimpleScoringPanel.

◆ GetColorForNoScore()

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

virtual

Call for display colors when CanCalculateScores returns false.

Implements IScoringMethod.

Reimplemented in CSNPScoringMethod.

Definition at line 277 of file simple_methods.cpp.

References _ASSERT.

◆ GetColorForScore()

const CRgbaColor & CSimpleScoringMethod::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 CSNPScoringMethod.

Definition at line 297 of file simple_methods.cpp.

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

Referenced by CSNPScoringMethod::GetColorForScore().

◆ GetDescription()

string CSimpleScoringMethod::GetDescription ( ) const

virtual

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

Implements IUITool.

Reimplemented in CSNPScoringMethod.

Definition at line 218 of file simple_methods.cpp.

References SIMPLE_DESCR.

◆ GetMenu()

const CMenuItem * CSimpleScoringMethod::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.

Reimplemented in CSNPScoringMethod.

Definition at line 321 of file simple_methods.cpp.

References m_Menu.

◆ GetName()

string CSimpleScoringMethod::GetName ( ) const

virtual

returns unique name of the method that is used in UI to identify it

Implements IUITool.

Reimplemented in CSNPScoringMethod.

Definition at line 208 of file simple_methods.cpp.

◆ GetOptions()

int CSimpleScoringMethod::GetOptions ( void )

Definition at line 193 of file simple_methods.cpp.

References m_Options.

Referenced by CSimpleScoringPanel::Init(), and CSNPScoringPanel::Init().

◆ GetSupportedColorTypes()

int CSimpleScoringMethod::GetSupportedColorTypes ( ) const

virtual

returns a combination of EColorType flags

Implements IScoringMethod.

Reimplemented in CSNPScoringMethod.

Definition at line 291 of file simple_methods.cpp.

References IScoringMethod::fBackground.

◆ GetType()

int CSimpleScoringMethod::GetType ( ) const

virtual

returns combination of EAlignType flags defining types of alignments that can be colored with this method

Implements IScoringMethod.

Definition at line 224 of file simple_methods.cpp.

References IAlnExplorer::fDNA, and IAlnExplorer::fProtein.

◆ HasPropertiesPanel()

bool CSimpleScoringMethod::HasPropertiesPanel ( ) const

virtual

returns true if the method supports properties dialog

Implements IUIToolWithGUI.

Reimplemented in CSNPScoringMethod.

Definition at line 331 of file simple_methods.cpp.

◆ IsAverageable()

bool CSimpleScoringMethod::IsAverageable ( ) const

virtual

return "true" if scores could be averaged

Implements IScoringMethod.

Definition at line 230 of file simple_methods.cpp.

◆ SetColorForNoScore()

void CSimpleScoringMethod::SetColorForNoScore	(	EColorType	type,
		const CRgbaColor &	color
	)

virtual

Implements IScoringMethod.

Reimplemented in CSNPScoringMethod.

Definition at line 285 of file simple_methods.cpp.

◆ SetOptions()

void CSimpleScoringMethod::SetOptions ( int options )

Definition at line 185 of file simple_methods.cpp.

References fIgnoreEmptySpace, fIgnoreGaps, m_Gap, m_Options, and m_Space.

Referenced by CSimpleScoringMethod(), CSimpleScoringPanel::OnApply(), CSNPScoringPanel::OnApply(), and x_Init().

◆ x_Init()

void CSimpleScoringMethod::x_Init ( int colors )

private

Definition at line 154 of file simple_methods.cpp.

References colors, CreateColorTable(), fIgnoreEmptySpace, m_Best, m_vCharCounts, m_Worst, CRgbaColor::Set(), and SetOptions().

Referenced by CSimpleScoringMethod().

Friends And Related Function Documentation

◆ CSimpleScoringPanel

friend class CSimpleScoringPanel

friend

Definition at line 58 of file simple_methods.hpp.

Referenced by CreatePropertiesPanel().

Member Data Documentation

◆ m_Best

CRgbaColor CSimpleScoringMethod::m_Best

protected

Definition at line 113 of file simple_methods.hpp.

Referenced by CreateColorTable(), CSimpleScoringPanel::CreateControls(), CSNPScoringPanel::CreateControls(), CSimpleScoringPanel::OnApply(), and x_Init().

◆ m_ColorTable

CRgbaGradColorTable CSimpleScoringMethod::m_ColorTable

protected

Definition at line 114 of file simple_methods.hpp.

Referenced by CreateColorTable(), CSimpleScoringPanel::CreateControls(), CSimpleScoringMethod(), and GetColorForScore().

◆ m_Gap

char CSimpleScoringMethod::m_Gap

protected

Definition at line 118 of file simple_methods.hpp.

Referenced by CalculateScores(), CSNPScoringMethod::CalculateScores(), and SetOptions().

◆ m_Menu

unique_ptr<CMenuItem> CSimpleScoringMethod::m_Menu

protected

Definition at line 120 of file simple_methods.hpp.

Referenced by GetMenu(), and CSNPScoringMethod::GetMenu().

◆ m_Options

int CSimpleScoringMethod::m_Options

protected

Definition at line 111 of file simple_methods.hpp.

Referenced by GetOptions(), and SetOptions().

◆ m_Space

char CSimpleScoringMethod::m_Space

protected

histogramm of characters

Definition at line 117 of file simple_methods.hpp.

Referenced by CalculateScores(), CSNPScoringMethod::CalculateScores(), and SetOptions().

◆ m_vCharCounts

vector<int> CSimpleScoringMethod::m_vCharCounts

protected

Definition at line 116 of file simple_methods.hpp.

Referenced by CalculateScores(), CSimpleScoringMethod(), and x_Init().

◆ m_Worst

CRgbaColor CSimpleScoringMethod::m_Worst

protected

combination of EOptions flags

Definition at line 112 of file simple_methods.hpp.

Referenced by CreateColorTable(), CSimpleScoringPanel::CreateControls(), CSNPScoringPanel::CreateControls(), CSimpleScoringPanel::OnApply(), and x_Init().

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

include/gui/widgets/aln_score/simple_methods.hpp
src/gui/widgets/aln_score/simple_methods.cpp

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EOptions

Constructor & Destructor Documentation

◆ CSimpleScoringMethod() [1/3]

◆ CSimpleScoringMethod() [2/3]

◆ CSimpleScoringMethod() [3/3]

◆ ~CSimpleScoringMethod()

Member Function Documentation

◆ CalculateScores()

◆ CanCalculateScores()

◆ Clone()

◆ CreateColorTable()

◆ CreatePropertiesPanel()

◆ GetColorForNoScore()

◆ GetColorForScore()

◆ GetDescription()

◆ GetMenu()

◆ GetName()

◆ GetOptions()

◆ GetSupportedColorTypes()

◆ GetType()

◆ HasPropertiesPanel()

◆ IsAverageable()

◆ SetColorForNoScore()

◆ SetOptions()

◆ x_Init()

Friends And Related Function Documentation

◆ CSimpleScoringPanel

Member Data Documentation

◆ m_Best

◆ m_ColorTable

◆ m_Gap

◆ m_Menu

◆ m_Options

◆ m_Space

◆ m_vCharCounts

◆ m_Worst