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CQualityScoringMethod Class Referenceabstract

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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< 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
 

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 CRgbaColorGetColorForScore (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 CRgbaColorGetColorForNoScore (EColorType type) const
 Call for display colors when CanCalculateScores returns false. More...
 
virtual void SetColorForNoScore (EColorType type, const CRgbaColor &color)
 
IUIToolWithGUI implementation
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 ()
 
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 IUIToolClone () 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

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() [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

◆ 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)

◆ 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

◆ 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.

◆ GetOptions()

int CQualityScoringMethod::GetOptions ( void  ) const

Definition at line 100 of file quality_methods.cpp.

References m_Options.

Referenced by CQualityScoringPanel::Init().

◆ GetSubstitutionScore()

virtual TNCBIScore CQualityScoringMethod::GetSubstitutionScore ( int  aa1,
int  aa2 
) const
pure virtual

◆ GetSupportedColorTypes()

int CQualityScoringMethod::GetSupportedColorTypes ( ) const
virtual

returns a combination of EColorType flags

Implements IScoringMethod.

Reimplemented in CConservationScoringMethod.

Definition at line 223 of file quality_methods.cpp.

References IScoringMethod::fBackground.

◆ HasPropertiesPanel()

bool CQualityScoringMethod::HasPropertiesPanel ( ) const
virtual

returns true if the method supports properties dialog

Implements IUIToolWithGUI.

Definition at line 255 of file quality_methods.cpp.

◆ IsAverageable()

bool CQualityScoringMethod::IsAverageable ( ) const
virtual

return "true" if scores could be averaged

Implements IScoringMethod.

Definition at line 131 of file quality_methods.cpp.

◆ IsScoreWholeColumn()

bool CQualityScoringMethod::IsScoreWholeColumn ( ) const

Definition at line 106 of file quality_methods.cpp.

References fScoreWholeColumn, m_Options, and true.

Referenced by CalculateScores().

◆ SetColorForNoScore()

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

Implements IScoringMethod.

Definition at line 217 of file quality_methods.cpp.

◆ SetOptions()

void CQualityScoringMethod::SetOptions ( int  options)

Definition at line 91 of file quality_methods.cpp.

References fIgnoreGaps, m_Gap, m_Options, and m_Space.

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

◆ x_Init()

void CQualityScoringMethod::x_Init ( int  colors)
private

Friends And Related Function Documentation

◆ CQualityScoringPanel

friend class CQualityScoringPanel
friend

Definition at line 63 of file quality_methods.hpp.

Referenced by CreatePropertiesPanel().

Member Data Documentation

◆ m_Best

CRgbaColor CQualityScoringMethod::m_Best
protected

◆ m_ColorTable

CRgbaGradColorTable CQualityScoringMethod::m_ColorTable
protected

◆ m_Gap

char CQualityScoringMethod::m_Gap
protected

Definition at line 119 of file quality_methods.hpp.

Referenced by CalculateScores(), and SetOptions().

◆ m_Options

int CQualityScoringMethod::m_Options
protected

Definition at line 117 of file quality_methods.hpp.

Referenced by GetOptions(), IsScoreWholeColumn(), and SetOptions().

◆ m_Space

char CQualityScoringMethod::m_Space
protected

Definition at line 118 of file quality_methods.hpp.

Referenced by CalculateScores(), and SetOptions().

◆ m_Worst

CRgbaColor CQualityScoringMethod::m_Worst
protected

The documentation for this class was generated from the following files:
Modified on Wed Apr 24 14:16:28 2024 by modify_doxy.py rev. 669887