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CConservationScoringMethod Class Reference

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CConservationScoringMethod - implementation of IScoringMethod. More...

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

+ Inheritance diagram for CConservationScoringMethod:
+ Collaboration diagram for CConservationScoringMethod:

Public Types

enum  EOptions {
  eOneBit , eTwoBits , eThreeBits , eFourBits ,
  eIdentity
}
 
- 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
 

Public Member Functions

 CConservationScoringMethod ()
 CConservationScoringMethod. More...
 
 CConservationScoringMethod (int colors)
 
 CConservationScoringMethod (const CConservationScoringMethod &orig)
 
virtual ~CConservationScoringMethod ()
 
void SetConservedOption (const string &name)
 
IUITool implementation
virtual IUIToolClone () 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 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)
 
CQualityScoringMethod implementation
virtual TNCBIScore GetSubstitutionScore (int, int) const
 
virtual string GetAllowedSymbols () const
 
IUIToolWithGUI implementation
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 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 bool IsAverageable () const
 return "true" if scores could be averaged More...
 
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...
 
- 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 Member Functions

bool x_IsConserved (const vector< int > &counts, int num_rows, const double *std_prob) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

EOptions m_ConservedOption = eTwoBits
 
CRgbaColor m_NotScored
 
double * m_StdProb = 0
 
- 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
 

Private Member Functions

void x_Init (int colors)
 

Friends

class CConservationScoringPanel
 

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
 

Detailed Description

CConservationScoringMethod - 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 178 of file quality_methods.hpp.

Member Enumeration Documentation

◆ EOptions

Enumerator
eOneBit 
eTwoBits 
eThreeBits 
eFourBits 
eIdentity 

Definition at line 185 of file quality_methods.hpp.

Constructor & Destructor Documentation

◆ CConservationScoringMethod() [1/3]

CConservationScoringMethod::CConservationScoringMethod ( )

CConservationScoringMethod.

Definition at line 515 of file quality_methods.cpp.

References IScoringMethod::sm_DefGradientSize, and x_Init().

Referenced by Clone().

◆ CConservationScoringMethod() [2/3]

CConservationScoringMethod::CConservationScoringMethod ( int  colors)

Definition at line 528 of file quality_methods.cpp.

References colors, and x_Init().

◆ CConservationScoringMethod() [3/3]

CConservationScoringMethod::CConservationScoringMethod ( const CConservationScoringMethod orig)

◆ ~CConservationScoringMethod()

CConservationScoringMethod::~CConservationScoringMethod ( )
virtual

Definition at line 521 of file quality_methods.cpp.

References free(), and m_StdProb.

Member Function Documentation

◆ CalculateScores()

void CConservationScoringMethod::CalculateScores ( char  cons,
const string column,
TScore col_score,
TScoreVector scores 
)
virtual

◆ Clone()

IUITool * CConservationScoringMethod::Clone ( void  ) const
virtual

Implements IUITool.

Definition at line 554 of file quality_methods.cpp.

References CConservationScoringMethod().

◆ CreatePropertiesPanel()

wxWindow * CConservationScoringMethod::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.

Reimplemented from CQualityScoringMethod.

Definition at line 843 of file quality_methods.cpp.

References CConservationScoringPanel.

◆ GetAllowedSymbols()

virtual string CConservationScoringMethod::GetAllowedSymbols ( ) const
inlinevirtual

Implements CQualityScoringMethod.

Definition at line 225 of file quality_methods.hpp.

References NcbiEmptyString.

◆ GetColorForScore()

const CRgbaColor & CConservationScoringMethod::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.

Reimplemented from CQualityScoringMethod.

Definition at line 714 of file quality_methods.cpp.

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

◆ GetDescription()

string CConservationScoringMethod::GetDescription ( ) const
virtual

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

Reimplemented from CQualityScoringMethod.

Definition at line 589 of file quality_methods.cpp.

References CONSERVATION_METOD_DESCR.

◆ GetName()

string CConservationScoringMethod::GetName ( ) const
virtual

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

Implements IUITool.

Definition at line 569 of file quality_methods.cpp.

◆ GetSubstitutionScore()

virtual TNCBIScore CConservationScoringMethod::GetSubstitutionScore ( int  ,
int   
) const
inlinevirtual

Implements CQualityScoringMethod.

Definition at line 221 of file quality_methods.hpp.

◆ GetSupportedColorTypes()

int CConservationScoringMethod::GetSupportedColorTypes ( ) const
virtual

returns a combination of EColorType flags

Reimplemented from CQualityScoringMethod.

Definition at line 708 of file quality_methods.cpp.

References IScoringMethod::fBackground, and IScoringMethod::fForeground.

◆ GetType()

int CConservationScoringMethod::GetType ( ) const
virtual

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

Implements IScoringMethod.

Definition at line 595 of file quality_methods.cpp.

References IAlnExplorer::fProtein.

◆ SetConservedOption()

void CConservationScoringMethod::SetConservedOption ( const string name)

◆ x_Init()

void CConservationScoringMethod::x_Init ( int  colors)
private

◆ x_IsConserved()

bool CConservationScoringMethod::x_IsConserved ( const vector< int > &  counts,
int  num_rows,
const double *  std_prob 
) const
protected

Friends And Related Function Documentation

◆ CConservationScoringPanel

friend class CConservationScoringPanel
friend

Definition at line 183 of file quality_methods.hpp.

Referenced by CreatePropertiesPanel().

Member Data Documentation

◆ m_ConservedOption

EOptions CConservationScoringMethod::m_ConservedOption = eTwoBits
protected

◆ m_NotScored

CRgbaColor CConservationScoringMethod::m_NotScored
protected

Definition at line 248 of file quality_methods.hpp.

Referenced by GetColorForScore(), and x_Init().

◆ m_StdProb

double* CConservationScoringMethod::m_StdProb = 0
protected

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:10:21 2024 by modify_doxy.py rev. 669887