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NCBI C++ ToolKit: include/gui/widgets/aln_score/scoring_method.hpp Source File

sm_DefGradientSize = 32;

try_reverse_dir =

)

= 0;

kAmbiguousResidueScore = 1000;

m_AmbiguousResidue =

;

()

;

GetType()

;

IsAverageable()

;

GetSupportedColorTypes()

;

SetName(

& s);

SetDescription(

& s);

&

,

def_value);

class CRgbaColor provides a simple abstraction for managing colors.

CTemplateMethod - describes a class of similar methods.

EColorGradType m_ColorGradType

ESearchDirection

Position search options.

Alignment segment iterator interface.

IColumnScoringMethod - column-based method.

virtual ~IColumnScoringMethod()

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

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?

virtual bool NeedsTranslation() const

IRowScoringMethod - row-based method.

virtual void CalculateScores(IAlnExplorer::TNumrow row, const IScoringAlignment &aln, IScoringMethod::TScoreColl &scores)=0

virtual ~IRowScoringMethod()

virtual TSeqPos GetAlnStart() const =0

virtual bool IsMixedAlign() const

New interfaces to handle alignemnt with mixed type (protein-to-genomic) To make them backward compati...

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual int GetGenCode(IAlnExplorer::TNumrow row) const =0

virtual TSeqPos GetAlnStop() const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(IAlnExplorer::TNumrow, const IAlnExplorer::TSignedRange &, IAlnSegmentIterator::EFlags) const =0

unique_ptr< vector< int > > m_GenCodeCache

virtual TSignedSeqPos GetSeqPosFromAlnPos(IAlnExplorer::TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual ~IScoringAlignment()

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 ~IScoringMethod()

virtual const CRgbaColor & GetColorForScore(TScore score, EColorType type) const =0

returns a color corresponding to a given score value.

CAttrRangeCollection< TScore, TSeqPos > TScoreColl

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...

IWindowScoringMethod - Method that can be windowed, i.e.

virtual size_t GetWindowSize() const =0

virtual ~IWindowScoringMethod()

static const char * column

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_ALNSCORE_EXPORT

const struct ncbi::grid::netcache::search::fields::KEY key

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

#define row(bind, expected)

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