bpp::ProteinSubstitutionModel Member List

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

addRateParameter()=0	bpp::SubstitutionModel	pure virtual
clone() const =0	bpp::ProteinSubstitutionModel	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
getNumberOfStates() const	bpp::ProteinSubstitutionModel	inlinevirtual
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
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
~ProteinSubstitutionModel()	bpp::ProteinSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual