NCBI C++ ToolKit
Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
IColumnScoringMethod Class Referenceabstract

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IColumnScoringMethod - column-based method. More...

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

+ Inheritance diagram for IColumnScoringMethod:

Public Member Functions

virtual ~IColumnScoringMethod ()
virtual bool CanCalculateScores (const IScoringAlignment &aln)=0
 Do we have what it takes to calculate scores? e.g. a master row selected? More...
virtual void CalculateScores (char cons, const string &column, IScoringMethod::TScore &col_score, IScoringMethod::TScoreVector &scores)=0
virtual bool NeedsTranslation () const
virtual void UpdateSettings (const IScoringAlignment &aln)
 Set alignment specifi settings. More...

Static Public Attributes

static const int kAmbiguousResidueScore = 1000

Protected Attributes

char m_AmbiguousResidue = ' '
 Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins. More...
std::function< bool(char c, char b)> mf_CompareResidue

Detailed Description

IColumnScoringMethod - column-based method.

Definition at line 157 of file scoring_method.hpp.

Constructor & Destructor Documentation

◆ ~IColumnScoringMethod()

virtual IColumnScoringMethod::~IColumnScoringMethod ( )

Definition at line 162 of file scoring_method.hpp.

Member Function Documentation

◆ CalculateScores()

virtual void IColumnScoringMethod::CalculateScores ( char  cons,
const string column,
IScoringMethod::TScore col_score,
IScoringMethod::TScoreVector scores 
pure virtual

◆ CanCalculateScores()

virtual bool IColumnScoringMethod::CanCalculateScores ( const IScoringAlignment aln)
pure virtual

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

Implemented in CNonSynonymousScoringMethod, CMatrixScoringMethod, CColumnScoringMethod, CSNPScoringMethod, CSimpleScoringMethod, and CQualityScoringMethod.

Referenced by CScoringJob::Calculate().

◆ NeedsTranslation()

virtual bool IColumnScoringMethod::NeedsTranslation ( ) const

Reimplemented in CNonSynonymousScoringMethod.

Definition at line 171 of file scoring_method.hpp.

Referenced by CScoringJob::x_CalculateAlignmentScores().

◆ UpdateSettings()

void IColumnScoringMethod::UpdateSettings ( const IScoringAlignment aln)

Set alignment specifi settings.

Definition at line 105 of file simple_methods.cpp.

References b, fProtein, IScoringAlignment::GetAlignType(), m_AmbiguousResidue, mf_CompareResidue, s_CompareBases(), and s_CompareResidues().

Referenced by CScoringJob::Calculate().

Member Data Documentation

◆ kAmbiguousResidueScore

const int IColumnScoringMethod::kAmbiguousResidueScore = 1000

◆ m_AmbiguousResidue

char IColumnScoringMethod::m_AmbiguousResidue = ' '

Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins.

Definition at line 180 of file scoring_method.hpp.

Referenced by CQualityScoringMethod::CalculateScores(), CSimpleScoringMethod::CalculateScores(), CSNPScoringMethod::CalculateScores(), and UpdateSettings().

◆ mf_CompareResidue

std::function<bool(char c, char b)> IColumnScoringMethod::mf_CompareResidue

Definition at line 181 of file scoring_method.hpp.

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

The documentation for this class was generated from the following files:
Modified on Wed Jun 12 11:13:14 2024 by rev. 669887