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CMatrixScoringMethod Class Reference

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CMatrixScoringMethod. More...

#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 IScoringMethodClone () const
 
virtual bool Load (CNcbiRegistry &reg)
 
virtual int GetSupportedColorTypes () const
 returns a combination of EColorType flags More...
 
virtual const CRgbaColorGetColorForScore (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 CRgbaColorGetColorForNoScore (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 CMenuItemGetMenu ()
 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...
 
CObjectoperator= (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< TScorem_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< Uint8TCounter
 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< TScoreTScoreVector
 
typedef CAttrRangeCollection< TScore, TSeqPosTScoreColl
 
- 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

Enumerator
eNone 
eConsensus 
eNonConsesus 
eBoth 

Definition at line 241 of file template_methods.hpp.

Constructor & Destructor Documentation

◆ CMatrixScoringMethod()

CMatrixScoringMethod::CMatrixScoringMethod ( )

◆ ~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

◆ 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.

◆ GetSupportedColorTypes()

int CMatrixScoringMethod::GetSupportedColorTypes ( ) const
virtual

returns a combination of EColorType flags

Reimplemented from CTemplateScoringMethod.

Definition at line 1226 of file template_methods.cpp.

References IScoringMethod::fBackground.

◆ GetWindowSize()

size_t CMatrixScoringMethod::GetWindowSize ( ) const
virtual

Implements IWindowScoringMethod.

Definition at line 1273 of file template_methods.cpp.

References m_WindowSize.

◆ HasPropertiesPanel()

bool CMatrixScoringMethod::HasPropertiesPanel ( ) const
virtual

returns true if the method supports properties dialog

Implements IUIToolWithGUI.

Definition at line 1284 of file template_methods.cpp.

◆ Load()

bool CMatrixScoringMethod::Load ( CNcbiRegistry reg)
virtual

◆ SetColorForNoScore()

void CMatrixScoringMethod::SetColorForNoScore ( EColorType  type,
const CRgbaColor color 
)
virtual

Implements IScoringMethod.

Definition at line 1245 of file template_methods.cpp.

References _VERIFY, color, IScoringMethod::fBackground, and m_UndefColor.

◆ x_BaseToIndex()

int CMatrixScoringMethod::x_BaseToIndex ( char  c)
staticprotected

Definition at line 1002 of file template_methods.cpp.

References i, and kMatrixSize.

Referenced by CalculateScores(), and Load().

◆ x_CalculateConsensusRange()

void CMatrixScoringMethod::x_CalculateConsensusRange ( )
protected

◆ x_CalculateNonConsensusRange()

void CMatrixScoringMethod::x_CalculateNonConsensusRange ( )
protected

◆ x_CreateScoreTable()

void CMatrixScoringMethod::x_CreateScoreTable ( CNcbiRegistry reg)
protected

Friends And Related Function Documentation

◆ CMatrixScoringPanel

friend class CMatrixScoringPanel
friend

Definition at line 194 of file template_methods.hpp.

Referenced by CreatePropertiesPanel().

Member Data Documentation

◆ m_CalculateRange

unsigned char CMatrixScoringMethod::m_CalculateRange
protected

◆ m_ColorTable

CRgbaGradColorTable CMatrixScoringMethod::m_ColorTable
protected

◆ m_ConsensusMaxScore

TScore CMatrixScoringMethod::m_ConsensusMaxScore
protected

Definition at line 255 of file template_methods.hpp.

Referenced by CreateColorTable(), Load(), and x_CalculateConsensusRange().

◆ m_ConsensusMinScore

TScore CMatrixScoringMethod::m_ConsensusMinScore
protected

Definition at line 254 of file template_methods.hpp.

Referenced by CreateColorTable(), Load(), and x_CalculateConsensusRange().

◆ m_MaxColor

CRgbaColor CMatrixScoringMethod::m_MaxColor
protected

◆ m_MaxScore

TScore CMatrixScoringMethod::m_MaxScore
protected

◆ m_MidColor

CRgbaColor CMatrixScoringMethod::m_MidColor
protected

◆ m_MinColor

CRgbaColor CMatrixScoringMethod::m_MinColor
protected

◆ m_MinScore

TScore CMatrixScoringMethod::m_MinScore
protected

◆ m_NonConsensusMaxScore

TScore CMatrixScoringMethod::m_NonConsensusMaxScore
protected

Definition at line 257 of file template_methods.hpp.

Referenced by CreateColorTable(), Load(), and x_CalculateNonConsensusRange().

◆ m_NonConsensusMinScore

TScore CMatrixScoringMethod::m_NonConsensusMinScore
protected

Definition at line 256 of file template_methods.hpp.

Referenced by CreateColorTable(), Load(), and x_CalculateNonConsensusRange().

◆ m_UndefColor

CRgbaColor CMatrixScoringMethod::m_UndefColor
protected

◆ m_UseConsensus

bool CMatrixScoringMethod::m_UseConsensus
protected

◆ m_vScore

CNcbiMatrix<TScore> CMatrixScoringMethod::m_vScore
protected

◆ m_WindowSize

size_t CMatrixScoringMethod::m_WindowSize
protected

The documentation for this class was generated from the following files:
Modified on Sat Jul 13 13:35:51 2024 by modify_doxy.py rev. 669887