bpp::MixedSubstitutionModel Member List

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

addRateParameter()=0	bpp::SubstitutionModel	pure virtual
clone() const =0	bpp::MixedSubstitutionModel	pure virtual
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
freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
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
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
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
getNModel(size_t i) const =0	bpp::MixedSubstitutionModel	pure virtual
getNModel(size_t i)=0	bpp::MixedSubstitutionModel	pure virtual
getNProbability(size_t i) const =0	bpp::MixedSubstitutionModel	pure virtual
getNRate(size_t i) const =0	bpp::MixedSubstitutionModel	pure virtual
getNumberOfModels() const =0	bpp::MixedSubstitutionModel	pure virtual
getNumberOfStates() const =0	bpp::SubstitutionModel	pure virtual
getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
getProbabilities() const =0	bpp::MixedSubstitutionModel	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
getSubmodelNumbers(std::string &desc) const =0	bpp::MixedSubstitutionModel	pure virtual
getVRates() const =0	bpp::MixedSubstitutionModel	pure virtual
isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
MixedSubstitutionModel()	bpp::MixedSubstitutionModel	inline
normalizeVRates()=0	bpp::MixedSubstitutionModel	pure virtual
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
setNProbability(size_t i, double prob)=0	bpp::MixedSubstitutionModel	pure virtual
setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
setVRates(const Vdouble &vd)=0	bpp::MixedSubstitutionModel	pure virtual
Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
SubstitutionModel()	bpp::SubstitutionModel	inline
~MixedSubstitutionModel()	bpp::MixedSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual