bpp::YNGKP_M3 Member List

This is the complete list of members for bpp::YNGKP_M3, including all inherited members.

AbstractBiblioMixedSubstitutionModel(const std::string &prefix)	bpp::AbstractBiblioMixedSubstitutionModel
AbstractBiblioMixedSubstitutionModel(const AbstractBiblioMixedSubstitutionModel &model)	bpp::AbstractBiblioMixedSubstitutionModel
AbstractBiblioSubstitutionModel(const std::string &prefix)	bpp::AbstractBiblioSubstitutionModel
AbstractBiblioSubstitutionModel(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel
bpp::addRateParameter()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::addRateParameter()	bpp::AbstractBiblioSubstitutionModel	virtual
clone() const	bpp::YNGKP_M3	inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModel	pure virtual
bpp::enableEigenDecomposition()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(bool yn)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition()	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::freq(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getAlphabet() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabet() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsChar(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabetStateAsInt(size_t i) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getAlphabetStates() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getColumnRightEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getdPij_dt(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getdPij_dt(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getEigenValues() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getExchangeabilityMatrix() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getFrequencies() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::YNGKP_M3	inlineprivatevirtual
bpp::getGenerator() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getGenerator() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getIEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getIEigenValues() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getInitValue(size_t i, int state) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getInitValue(size_t i, int state) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getMixedModel() const	bpp::YNGKP_M3	inlinevirtual
getMixedModel()	bpp::YNGKP_M3	inlineprivatevirtual
getModel() const	bpp::YNGKP_M3	inlinevirtual
getModel()	bpp::YNGKP_M3	inlineprivatevirtual
bpp::getModelStates(int code) const =0	bpp::SubstitutionModel	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getModelStates(int code) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::AbstractBiblioSubstitutionModel::getModelStates(const std::string &code) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getName() const	bpp::YNGKP_M3	inlinevirtual
getNModel(size_t i) const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
getNModel(size_t i)	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
getNProbability(size_t i) const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
getNRate(size_t i) const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
getNumberOfModels() const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
bpp::getNumberOfStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getNumberOfStates() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getPij_t(double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getProbabilities() const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
bpp::getRate() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getRate() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getRowLeftEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getScale() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getScale() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::getStateMap() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::getStateMap() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
getSubmodelNumbers(std::string &desc) const	bpp::AbstractBiblioMixedSubstitutionModel	virtual
getVRates() const	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
bpp::isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::isDiagonalizable() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::isNonSingular() const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
lParPmodel_	bpp::AbstractBiblioSubstitutionModel	protected
mapParNamesFromPmodel_	bpp::AbstractBiblioSubstitutionModel	protected
MixedSubstitutionModel()	bpp::MixedSubstitutionModel	inline
normalizeVRates()	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
operator=(const YNGKP_M3 &)	bpp::YNGKP_M3
bpp::AbstractBiblioMixedSubstitutionModel::operator=(const AbstractBiblioMixedSubstitutionModel &model)	bpp::AbstractBiblioMixedSubstitutionModel
bpp::AbstractBiblioSubstitutionModel::operator=(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::Pij_t(size_t i, size_t j, double t) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
pmixmodel_	bpp::YNGKP_M3	private
bpp::Qij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::Qij(size_t i, size_t j) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inline
bpp::setFreq(std::map< int, double > &frequencies)	bpp::SubstitutionModel	inlinevirtual
bpp::AbstractBiblioSubstitutionModel::setFreq(std::map< int, double > &frequ)	bpp::AbstractBiblioSubstitutionModel	virtual
bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractBiblioSubstitutionModel	virtual
setNProbability(size_t i, double prob)	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
bpp::setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::setRate(double rate)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
bpp::setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::setScale(double scale)	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
setVRates(const Vdouble &vd)	bpp::AbstractBiblioMixedSubstitutionModel	inlinevirtual
bpp::Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractBiblioSubstitutionModel::Sij(size_t i, size_t j) const	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
SubstitutionModel()	bpp::SubstitutionModel	inline
synfrom_	bpp::YNGKP_M3	private
synto_	bpp::YNGKP_M3	private
updateMatrices()	bpp::YNGKP_M3	protectedvirtual
YNGKP_M3(const GeneticCode *gc, FrequenciesSet *codonFreqs, unsigned int nclass=3)	bpp::YNGKP_M3
YNGKP_M3(const YNGKP_M3 &)	bpp::YNGKP_M3
~AbstractBiblioMixedSubstitutionModel()	bpp::AbstractBiblioMixedSubstitutionModel	virtual
~AbstractBiblioSubstitutionModel()	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
~MixedSubstitutionModel()	bpp::MixedSubstitutionModel	inlinevirtual
~ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual
~YNGKP_M3()	bpp::YNGKP_M3