bpp::CodonDistanceFrequenciesSubstitutionModel Member List

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

AbstractCodonDistanceSubstitutionModel(const AlphabetIndex2 *pdist, const std::string &prefix, bool paramSynRate=false)	bpp::AbstractCodonDistanceSubstitutionModel
AbstractCodonDistanceSubstitutionModel(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
AbstractCodonFrequenciesSubstitutionModel(FrequenciesSet *pfreq, const std::string &prefix)	bpp::AbstractCodonFrequenciesSubstitutionModel
AbstractCodonFrequenciesSubstitutionModel(const AbstractCodonFrequenciesSubstitutionModel &model)	bpp::AbstractCodonFrequenciesSubstitutionModel	inline
AbstractCodonSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, const std::string &st, bool paramRates=false)	bpp::AbstractCodonSubstitutionModel
AbstractCodonSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod1, NucleotideSubstitutionModel *pmod2, NucleotideSubstitutionModel *pmod3, const std::string &st, bool paramRates=false)	bpp::AbstractCodonSubstitutionModel
AbstractCodonSubstitutionModel(const AbstractCodonSubstitutionModel &model)	bpp::AbstractCodonSubstitutionModel	inline
AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
AbstractWordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(SubstitutionModel *pmodel, unsigned int num, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const Alphabet *alph, StateMap *stateMap, const std::string &prefix)	bpp::AbstractWordSubstitutionModel	protected
bpp::addRateParameter()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::addRateParameter()	bpp::AbstractSubstitutionModel	virtual
alphabet_	bpp::AbstractSubstitutionModel	protected
clone() const	bpp::CodonDistanceFrequenciesSubstitutionModel	inlinevirtual
CodonDistanceFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)	bpp::CodonDistanceFrequenciesSubstitutionModel
CodonDistanceFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod1, NucleotideSubstitutionModel *pmod2, NucleotideSubstitutionModel *pmod3, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)	bpp::CodonDistanceFrequenciesSubstitutionModel
CodonSubstitutionModel()	bpp::CodonSubstitutionModel	inline
completeMatrices()	bpp::AbstractCodonSubstitutionModel	protectedvirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
d2pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
dpijt_	bpp::AbstractSubstitutionModel	mutableprotected
eigenDecompose_	bpp::AbstractSubstitutionModel	protected
eigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModel	pure virtual
bpp::enableEigenDecomposition()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::enableEigenDecomposition(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractWordSubstitutionModel::enableEigenDecomposition()	bpp::AbstractSubstitutionModel	inlinevirtual
exchangeability_	bpp::AbstractSubstitutionModel	protected
extractAlph(const std::vector< SubstitutionModel *> &modelVector)	bpp::AbstractWordSubstitutionModel	protectedstatic
fireParameterChanged(const ParameterList &parameterlist)	bpp::CodonDistanceFrequenciesSubstitutionModel	virtual
bpp::freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::freq(size_t i) const	bpp::AbstractSubstitutionModel	inlinevirtual
freq_	bpp::AbstractSubstitutionModel	protected
generator_	bpp::AbstractSubstitutionModel	protected
bpp::getAlphabet() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getAlphabet() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getAlphabetStateAsChar(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getAlphabetStateAsInt(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getAlphabetStates() const	bpp::AbstractSubstitutionModel	inlinevirtual
getCodonsMulRate(size_t i, size_t j) const	bpp::CodonDistanceFrequenciesSubstitutionModel	virtual
bpp::getColumnRightEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getColumnRightEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getd2Pij_dt2(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getdPij_dt(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getdPij_dt(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getExchangeabilityMatrix() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getExchangeabilityMatrix() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getFrequencies() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getFrequenciesSet() const	bpp::SubstitutionModel	inlinevirtual
bpp::AbstractCodonFrequenciesSubstitutionModel::getFrequenciesSet() const	bpp::AbstractCodonFrequenciesSubstitutionModel	inlinevirtual
bpp::getGenerator() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getGenerator() const	bpp::AbstractSubstitutionModel	inlinevirtual
getGeneticCode() const	bpp::AbstractCodonSubstitutionModel	inlinevirtual
bpp::getIEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getIEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getInitValue(size_t i, int state) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getInitValue(size_t i, int state) const	bpp::AbstractSubstitutionModel	virtual
bpp::getModelStates(int code) const =0	bpp::SubstitutionModel	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getModelStates(int code) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractWordSubstitutionModel::getModelStates(const std::string &code) const	bpp::AbstractSubstitutionModel	inlinevirtual
getName() const	bpp::CodonDistanceFrequenciesSubstitutionModel	virtual
getNModel(size_t i) const	bpp::AbstractWordSubstitutionModel	inline
getNumberOfModels() const	bpp::AbstractWordSubstitutionModel	inline
bpp::getNumberOfStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getNumberOfStates() const	bpp::AbstractWordSubstitutionModel	virtual
bpp::getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getPij_t(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getRate() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getRate() const	bpp::AbstractSubstitutionModel	virtual
bpp::getRowLeftEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getRowLeftEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getScale() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getScale() const	bpp::AbstractSubstitutionModel	virtual
bpp::getStateMap() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::getStateMap() const	bpp::AbstractSubstitutionModel	inlinevirtual
iEigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::isDiagonalizable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isDiagonalizable_	bpp::AbstractSubstitutionModel	protected
bpp::isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::isNonSingular() const	bpp::AbstractSubstitutionModel	inlinevirtual
isNonSingular_	bpp::AbstractSubstitutionModel	protected
leftEigenVectors_	bpp::AbstractSubstitutionModel	protected
bpp::operator=(const AbstractCodonSubstitutionModel &model)	bpp::AbstractCodonSubstitutionModel	inline
bpp::AbstractWordSubstitutionModel::operator=(const AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
bpp::AbstractCodonDistanceSubstitutionModel::operator=(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
bpp::AbstractCodonFrequenciesSubstitutionModel::operator=(const AbstractCodonFrequenciesSubstitutionModel &model)	bpp::AbstractCodonFrequenciesSubstitutionModel	inline
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::Pij_t(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::Qij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::Qij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
rate_	bpp::AbstractSubstitutionModel	protected
rightEigenVectors_	bpp::AbstractSubstitutionModel	protected
setFreq(std::map< int, double > &frequencies)	bpp::CodonDistanceFrequenciesSubstitutionModel	virtual
bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractSubstitutionModel	virtual
setNamespace(const std::string &)	bpp::CodonDistanceFrequenciesSubstitutionModel
bpp::setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::setRate(double rate)	bpp::AbstractSubstitutionModel	virtual
bpp::setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::setScale(double scale)	bpp::AbstractSubstitutionModel	virtual
bpp::Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractWordSubstitutionModel::Sij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
size_	bpp::AbstractSubstitutionModel	protected
stateMap_	bpp::AbstractSubstitutionModel	protected
SubstitutionModel()	bpp::SubstitutionModel	inline
tmpMat_	bpp::AbstractSubstitutionModel	mutableprotected
updateMatrices()	bpp::AbstractCodonSubstitutionModel	virtual
VnestedPrefix_	bpp::AbstractWordSubstitutionModel	protected
vPowGen_	bpp::AbstractSubstitutionModel	protected
Vrate_	bpp::AbstractWordSubstitutionModel	protected
VSubMod_	bpp::AbstractWordSubstitutionModel	protected
~AbstractCodonDistanceSubstitutionModel()	bpp::AbstractCodonDistanceSubstitutionModel	inlinevirtual
~AbstractCodonFrequenciesSubstitutionModel()	bpp::AbstractCodonFrequenciesSubstitutionModel	virtual
~AbstractCodonSubstitutionModel()	bpp::AbstractCodonSubstitutionModel	inlinevirtual
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~AbstractWordSubstitutionModel()	bpp::AbstractWordSubstitutionModel	virtual
~CodonDistanceFrequenciesSubstitutionModel()	bpp::CodonDistanceFrequenciesSubstitutionModel	inlinevirtual
~CodonSubstitutionModel()	bpp::CodonSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual