bpp::AbstractBiblioSubstitutionModel Member List

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

AbstractBiblioSubstitutionModel(const std::string &prefix)	bpp::AbstractBiblioSubstitutionModel
AbstractBiblioSubstitutionModel(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel
addRateParameter()	bpp::AbstractBiblioSubstitutionModel	virtual
clone() const =0	bpp::AbstractBiblioSubstitutionModel	pure virtual
d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
dPij_dt(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
enableEigenDecomposition(bool yn)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
enableEigenDecomposition()	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
freq(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getAlphabet() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getAlphabetStateAsChar(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getAlphabetStateAsInt(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getAlphabetStates() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getColumnRightEigenVectors() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getd2Pij_dt2(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getdPij_dt(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getEigenValues() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getExchangeabilityMatrix() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getFrequencies() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getGenerator() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getIEigenValues() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getInitValue(size_t i, int state) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getModel() const =0	bpp::AbstractBiblioSubstitutionModel	pure virtual
getModel()=0	bpp::AbstractBiblioSubstitutionModel	protectedpure virtual
getModelStates(int code) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getModelStates(const std::string &code) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getName() const =0	bpp::SubstitutionModel	pure virtual
getNumberOfStates() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getPij_t(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getRate() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getRowLeftEigenVectors() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getScale() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getStateMap() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
isDiagonalizable() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
isNonSingular() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
lParPmodel_	bpp::AbstractBiblioSubstitutionModel	protected
mapParNamesFromPmodel_	bpp::AbstractBiblioSubstitutionModel	protected
operator=(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel
Pij_t(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
Qij(size_t i, size_t j) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
setFreq(std::map< int, double > &frequ)	bpp::AbstractBiblioSubstitutionModel	virtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractBiblioSubstitutionModel	virtual
setRate(double rate)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
setScale(double scale)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
Sij(size_t i, size_t j) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
SubstitutionModel()	bpp::SubstitutionModel	inline
updateMatrices()	bpp::AbstractBiblioSubstitutionModel	protectedvirtual
~AbstractBiblioSubstitutionModel()	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual