bpp::AbstractCodonDistanceSubstitutionModel Member List

This is the complete list of members for bpp::AbstractCodonDistanceSubstitutionModel, including all inherited members.

AbstractCodonDistanceSubstitutionModel(const AlphabetIndex2 *pdist, const std::string &prefix, bool paramSynRate=false)	bpp::AbstractCodonDistanceSubstitutionModel
AbstractCodonDistanceSubstitutionModel(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
addRateParameter()=0	bpp::SubstitutionModel	pure virtual
alpha_	bpp::AbstractCodonDistanceSubstitutionModel	private
beta_	bpp::AbstractCodonDistanceSubstitutionModel	private
clone() const =0	bpp::CodonSubstitutionModel	pure virtual
CodonSubstitutionModel()	bpp::CodonSubstitutionModel	inline
d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
dPij_dt(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModel	pure virtual
enableEigenDecomposition()=0	bpp::SubstitutionModel	pure virtual
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractCodonDistanceSubstitutionModel
freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
gamma_	bpp::AbstractCodonDistanceSubstitutionModel	private
getAlphabet() const =0	bpp::SubstitutionModel	pure virtual
getAlphabetStateAsChar(size_t index) const =0	bpp::SubstitutionModel	pure virtual
getAlphabetStateAsInt(size_t index) const =0	bpp::SubstitutionModel	pure virtual
getAlphabetStates() const =0	bpp::SubstitutionModel	pure virtual
getCodonsMulRate(size_t i, size_t j) const	bpp::AbstractCodonDistanceSubstitutionModel	virtual
getColumnRightEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
getd2Pij_dt2(double t) const =0	bpp::SubstitutionModel	pure virtual
getdPij_dt(double t) const =0	bpp::SubstitutionModel	pure virtual
getEigenValues() const =0	bpp::SubstitutionModel	pure virtual
getExchangeabilityMatrix() const =0	bpp::SubstitutionModel	pure virtual
getFrequencies() const =0	bpp::SubstitutionModel	pure virtual
getFrequenciesSet() const	bpp::SubstitutionModel	inlinevirtual
getGenerator() const =0	bpp::SubstitutionModel	pure virtual
getGeneticCode() const =0	bpp::CodonSubstitutionModel	pure virtual
getIEigenValues() const =0	bpp::SubstitutionModel	pure virtual
getInitValue(size_t i, int state) const =0	bpp::SubstitutionModel	pure virtual
getModelStates(int code) const =0	bpp::SubstitutionModel	pure virtual
getModelStates(const std::string &code) const =0	bpp::SubstitutionModel	pure virtual
getName() const =0	bpp::SubstitutionModel	pure virtual
getNumberOfStates() const =0	bpp::SubstitutionModel	pure virtual
getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
getRate() const =0	bpp::SubstitutionModel	pure virtual
getRowLeftEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
getScale() const =0	bpp::SubstitutionModel	pure virtual
getStateMap() const =0	bpp::SubstitutionModel	pure virtual
isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
operator=(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
pdistance_	bpp::AbstractCodonDistanceSubstitutionModel	private
Pij_t(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
Qij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
setFreq(std::map< int, double > &frequencies)	bpp::SubstitutionModel	inlinevirtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0	bpp::SubstitutionModel	pure virtual
setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
SubstitutionModel()	bpp::SubstitutionModel	inline
~AbstractCodonDistanceSubstitutionModel()	bpp::AbstractCodonDistanceSubstitutionModel	inlinevirtual
~CodonSubstitutionModel()	bpp::CodonSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual