CodonSiteTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_CODONSITETOOLS_H
#define BPP_SEQ_CODONSITETOOLS_H
 
#include <Bpp/Exceptions.h>
 
#include "Alphabet/CodonAlphabet.h"
#include "GeneticCode/GeneticCode.h"
#include "Site.h"
#include "SymbolListTools.h"
 
// From the STL:
#include <map>
 
namespace bpp
{
class CodonSiteTools :
  public SymbolListTools
{
public:
  CodonSiteTools() {}
  virtual ~CodonSiteTools() {}
 
public:
  static bool hasGapOrStop(const Site& site, const GeneticCode& gCode);
 
  static bool hasStop(const Site& site, const GeneticCode& gCode);
 
  static bool isMonoSitePolymorphic(const Site& site);
 
  static bool isSynonymousPolymorphic(const Site& site, const GeneticCode& gCode);
 
  static std::unique_ptr<Site> generateCodonSiteWithoutRareVariant(const Site& site, const GeneticCode& gCode, double freqmin);
 
  static size_t numberOfDifferences(int i, int j, const CodonAlphabet& ca);
 
  static double numberOfSynonymousDifferences(int i, int j, const GeneticCode& gCode, bool minchange = false);
 
  static double piSynonymous(const Site& site, const GeneticCode& gCode, bool minchange = false);
 
  static double piNonSynonymous(const Site& site, const GeneticCode& gCode, bool minchange = false);
 
  static double numberOfSynonymousPositions(int i, const GeneticCode& gCode,  double ratio = 1.0);
 
  static double meanNumberOfSynonymousPositions(const Site& site, const GeneticCode& gCode, double ratio = 1);
 
  static size_t numberOfSubstitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.);
 
  static size_t numberOfNonSynonymousSubstitutions(const Site& site, const GeneticCode& gCode, double freqmin = 0.);
 
  static std::vector<size_t> fixedDifferences(const Site& siteIn, const Site& siteOut, int i, int j, const GeneticCode& gCode);
 
  static bool isFourFoldDegenerated(const Site& site, const GeneticCode& gCode);
};
} // end of namespace bpp.
#endif // BPP_SEQ_CODONSITETOOLS_H