1 #ifndef GUI_WIDGETS_ALN_SCORE___QUALITY_SCORING_METHODS__HPP
2 #define GUI_WIDGETS_ALN_SCORE___QUALITY_SCORING_METHODS__HPP
58 fIgnoreEmptySpace = 0x01,
60 fScoreWholeColumn = 0x04
70 void CreateColorTable(
int size);
74 bool IsScoreWholeColumn()
const;
75 void SetOptions(
int options);
76 int GetOptions()
const;
134 virtual string GetName()
const;
138 virtual string GetAllowedSymbols()
const;
139 virtual TNCBIScore GetSubstitutionScore(
int aa1,
int aa2)
const;
156 virtual string GetName()
const;
160 virtual TNCBIScore GetSubstitutionScore(
int aa1,
int aa2)
const;
161 virtual string GetAllowedSymbols()
const;
202 virtual string GetName()
const;
216 TScore& col_score, TScoreVector& scores);
236 void SetConservedOption(
const string& name);
242 bool x_IsConserved(
const vector<int>& counts,
244 const double* std_prob)
const;
249 double* m_StdProb = 0;
CConservationScoringMethod - implementation of IScoringMethod.
virtual string GetAllowedSymbols() const
virtual TNCBIScore GetSubstitutionScore(int, int) const
CConservationScoringPanel.
CQualityScoringMethodAA - Quality scoring method for Amino Acids (Protein alignments).
const SNCBIPackedScoreMatrix * m_SubstMatrix
SNCBIFullScoreMatrix m_FullSubstMatrix
CQualityScoringMethodNA - Quality scoring method for Nucleic Acids (DNA alignments).
CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment ...
CRgbaGradColorTable m_ColorTable
virtual TNCBIScore GetSubstitutionScore(int aa1, int aa2) const =0
virtual string GetAllowedSymbols() const =0
class CRgbaColor provides a simple abstraction for managing colors.
CRgbaGradColorTable Provides a storage for colors (to eliminate color creation overhead) and Function...
IColumnScoringMethod - column-based method.
virtual void CalculateScores(char cons, const string &column, IScoringMethod::TScore &col_score, IScoringMethod::TScoreVector &scores)=0
virtual bool CanCalculateScores(const IScoringAlignment &aln)=0
Do we have what it takes to calculate scores? e.g. a master row selected?
IScoringMethod represents an abstract algorithm for calculating alignment scores and assigning colors...
virtual void SetColorForNoScore(IScoringMethod::EColorType type, const CRgbaColor &color)=0
virtual int GetSupportedColorTypes() const =0
returns a combination of EColorType flags
virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const =0
returns a color corresponding to a given score value.
virtual bool IsAverageable() const =0
return "true" if scores could be averaged
vector< TScore > TScoreVector
virtual const CRgbaColor & GetColorForNoScore(IScoringMethod::EColorType type) const =0
Call for display colors when CanCalculateScores returns false.
virtual int GetType() const =0
returns combination of EAlignType flags defining types of alignments that can be colored with this me...
static const Colors colors
Include a standard set of the NCBI C++ Toolkit most basic headers.
static const char * column
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define NCBI_GUIWIDGETS_ALNSCORE_EXPORT
where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig
const struct ncbi::grid::netcache::search::fields::SIZE size