bpp::MvaFrequencySet Member List

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

AbstractFrequencySet(std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix, const std::string &name)	bpp::AbstractFrequencySet	inline
AbstractFrequencySet(const AbstractFrequencySet &af)	bpp::AbstractFrequencySet	inline
AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
bpp::alphabet() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::alphabet() const override	bpp::AbstractFrequencySet	inlinevirtual
alphabet_	bpp::AbstractFrequencySet	private
clone() const override	bpp::MvaFrequencySet	inlinevirtual
columnWeights_	bpp::MvaFrequencySet	protected
computeCoordsFirstSpaceCOA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)	bpp::MvaFrequencySet
computeCoordsFirstSpacePCA(std::vector< double > &tmpFreqs, std::vector< double > &freqs)	bpp::MvaFrequencySet
computeReverseCOA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)	bpp::MvaFrequencySet
computeReversePCA(const std::vector< double > &positions, std::vector< double > &tmpFreqs)	bpp::MvaFrequencySet
defineParameters()	bpp::MvaFrequencySet
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
fireParameterChanged(const ParameterList &parameters) override	bpp::MvaFrequencySet	virtual
freq_	bpp::AbstractFrequencySet	private
FREQUENCE_CONSTRAINT_CENTI	bpp::FrequencySetInterface	static
FREQUENCE_CONSTRAINT_MILLI	bpp::FrequencySetInterface	static
FREQUENCE_CONSTRAINT_SMALL	bpp::FrequencySetInterface	static
bpp::getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getAliases() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getAliases() const	bpp::AbstractParameterAliasable	virtual
bpp::getAlphabet() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getAlphabet() const override	bpp::AbstractFrequencySet	inlinevirtual
bpp::getAlphabetStatesFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getAlphabetStatesFrequencies() const override	bpp::AbstractFrequencySet	virtual
getFreq_(size_t i)	bpp::AbstractFrequencySet	inlineprotected
getFreq_(size_t i) const	bpp::AbstractFrequencySet	inlineprotected
bpp::getFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getFrequencies() const override	bpp::AbstractFrequencySet	inlinevirtual
getFrequencies_()	bpp::AbstractFrequencySet	inlineprotected
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getName() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getName() const override	bpp::AbstractFrequencySet	inlinevirtual
bpp::getNamespace() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNamespace() const override	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getNumberOfFrequencies() const override	bpp::AbstractFrequencySet	inlinevirtual
bpp::getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
getParameter(const std::string &name) const	bpp::AbstractParameterAliasable
getParameter(size_t i) const	bpp::AbstractParameterAliasable	protected
getParameter(size_t i)	bpp::AbstractParameterAliasable	protected
getParameter_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index) const	bpp::AbstractParameterAliasable	protected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParameterAliasable	protected
getProteicAlphabet() const override	bpp::MvaFrequencySet	inlinevirtual
bpp::getStateMap() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::getStateMap() const override	bpp::AbstractFrequencySet	inlinevirtual
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
initSet(const CoalaCore &coala)	bpp::MvaFrequencySet
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
model_	bpp::MvaFrequencySet	protected
MvaFrequencySet(std::shared_ptr< const ProteicAlphabet > alpha)	bpp::MvaFrequencySet
name_	bpp::AbstractFrequencySet	private
nbrOfAxes_	bpp::MvaFrequencySet	protected
normalize()	bpp::AbstractFrequencySet	inline
operator=(const AbstractFrequencySet &af)	bpp::AbstractFrequencySet	inline
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
paramValues_	bpp::MvaFrequencySet	protected
prefix_	bpp::AbstractParameterAliasable	private
bpp::removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
rowCoords_	bpp::MvaFrequencySet	protected
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setFrequencies(const std::vector< double > &frequencies) override	bpp::MvaFrequencySet	virtual
setFrequencies_(const std::vector< double > &frequencies)	bpp::AbstractFrequencySet	inlineprotected
bpp::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies) override	bpp::AbstractFrequencySet	virtual
setMatrixOfRowCoords(const RowMatrix< double > &matrix)	bpp::MvaFrequencySet	inline
setModelName(const std::string &modelName)	bpp::MvaFrequencySet	inline
bpp::setNamespace(const std::string &prefix)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix)	bpp::AbstractParameterAliasable	virtual
setNbrOfAxes(const size_t &nAxes)	bpp::MvaFrequencySet	inline
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
setParamValues(std::map< std::string, std::string > &valuesSettings)	bpp::MvaFrequencySet	inline
setTransposeMatrixOfPpalAxes(const RowMatrix< double > &matrix)	bpp::MvaFrequencySet	inline
setVectorOfColumnWeights(const std::vector< double > &cw)	bpp::MvaFrequencySet	inline
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::stateMap() const =0	bpp::FrequencySetInterface	pure virtual
bpp::AbstractFrequencySet::stateMap() const override	bpp::AbstractFrequencySet	inlinevirtual
stateMap_	bpp::AbstractFrequencySet	private
tPpalAxes_	bpp::MvaFrequencySet	protected
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractFrequencySet::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateFrequencies()	bpp::MvaFrequencySet
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual