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CQualityScoringMethodAA Class Reference

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CQualityScoringMethodAA - Quality scoring method for Amino Acids (Protein alignments). More...

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

+ Inheritance diagram for CQualityScoringMethodAA:
+ Collaboration diagram for CQualityScoringMethodAA:

Public Member Functions

 CQualityScoringMethodAA ()
 CQualityScoringMethodAA. More...
 
 CQualityScoringMethodAA (int colors)
 
 CQualityScoringMethodAA (const CQualityScoringMethodAA &orig)
 
virtual ~CQualityScoringMethodAA ()
 
virtual string GetName () const
 returns unique name of the method that is used in UI to identify it More...
 
virtual IUIToolClone () const
 
virtual int GetType () const
 returns combination of EAlignType flags defining types of alignments that can be colored with this method More...
 
virtual TNCBIScore GetSubstitutionScore (int aa1, int aa2) const
 
virtual string GetAllowedSymbols () const
 
void SetSubstitutionMatrix (const SNCBIPackedScoreMatrix *m)
 
const SNCBIPackedScoreMatrixGetSubstitutionMatrix ()
 
- Public Member Functions inherited from CQualityScoringMethod
 CQualityScoringMethod ()
 CQualityScoringMethod. More...
 
 CQualityScoringMethod (int colors)
 
 CQualityScoringMethod (const CQualityScoringMethod &orig)
 
virtual ~CQualityScoringMethod ()
 
void CreateColorTable (int size)
 
bool IsScoreWholeColumn () const
 
void SetOptions (int options)
 
int GetOptions () const
 
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 CRgbaColorGetColorForScore (TScore score, EColorType type) const
 returns a color corresponding to a given score value. More...
 
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 CRgbaColorGetColorForNoScore (EColorType type) const
 Call for display colors when CanCalculateScores returns false. More...
 
virtual void SetColorForNoScore (EColorType type, const CRgbaColor &color)
 
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 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 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

const SNCBIPackedScoreMatrixm_SubstMatrix
 
SNCBIFullScoreMatrix m_FullSubstMatrix
 
- Protected Attributes inherited from CQualityScoringMethod
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
 

Additional Inherited Members

- Public Types inherited from CQualityScoringMethod
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< 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
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

CQualityScoringMethodAA - Quality scoring method for Amino Acids (Protein alignments).

Use a user specified substition table.

Definition at line 148 of file quality_methods.hpp.

Constructor & Destructor Documentation

◆ CQualityScoringMethodAA() [1/3]

CQualityScoringMethodAA::CQualityScoringMethodAA ( )

CQualityScoringMethodAA.

Definition at line 441 of file quality_methods.cpp.

References NCBISM_Blosum62, and SetSubstitutionMatrix().

Referenced by Clone().

◆ CQualityScoringMethodAA() [2/3]

CQualityScoringMethodAA::CQualityScoringMethodAA ( int  colors)

Definition at line 449 of file quality_methods.cpp.

References NCBISM_Blosum62, and SetSubstitutionMatrix().

◆ CQualityScoringMethodAA() [3/3]

CQualityScoringMethodAA::CQualityScoringMethodAA ( const CQualityScoringMethodAA orig)

Definition at line 457 of file quality_methods.cpp.

References orig, and SetSubstitutionMatrix().

◆ ~CQualityScoringMethodAA()

CQualityScoringMethodAA::~CQualityScoringMethodAA ( )
virtual

Definition at line 464 of file quality_methods.cpp.

Member Function Documentation

◆ Clone()

IUITool * CQualityScoringMethodAA::Clone ( void  ) const
virtual

Implements IUITool.

Definition at line 475 of file quality_methods.cpp.

References CQualityScoringMethodAA().

◆ GetAllowedSymbols()

string CQualityScoringMethodAA::GetAllowedSymbols ( ) const
virtual

Implements CQualityScoringMethod.

Definition at line 493 of file quality_methods.cpp.

References m_SubstMatrix, and SNCBIPackedScoreMatrix::symbols.

◆ GetName()

string CQualityScoringMethodAA::GetName ( ) const
virtual

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

Implements IUITool.

Definition at line 469 of file quality_methods.cpp.

◆ GetSubstitutionMatrix()

const SNCBIPackedScoreMatrix * CQualityScoringMethodAA::GetSubstitutionMatrix ( )

Definition at line 506 of file quality_methods.cpp.

References m_SubstMatrix.

Referenced by CQualityScoringPanel::CreateControls().

◆ GetSubstitutionScore()

TNCBIScore CQualityScoringMethodAA::GetSubstitutionScore ( int  aa1,
int  aa2 
) const
virtual

Implements CQualityScoringMethod.

Definition at line 487 of file quality_methods.cpp.

References m_FullSubstMatrix, and SNCBIFullScoreMatrix::s.

◆ GetType()

int CQualityScoringMethodAA::GetType ( ) const
virtual

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

Implements IScoringMethod.

Definition at line 481 of file quality_methods.cpp.

References IAlnExplorer::fProtein.

◆ SetSubstitutionMatrix()

void CQualityScoringMethodAA::SetSubstitutionMatrix ( const SNCBIPackedScoreMatrix m)

Member Data Documentation

◆ m_FullSubstMatrix

SNCBIFullScoreMatrix CQualityScoringMethodAA::m_FullSubstMatrix
protected

Definition at line 168 of file quality_methods.hpp.

Referenced by GetSubstitutionScore(), and SetSubstitutionMatrix().

◆ m_SubstMatrix

const SNCBIPackedScoreMatrix* CQualityScoringMethodAA::m_SubstMatrix
protected

The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:39:46 2024 by modify_doxy.py rev. 669887