bpp::CodonFrequencySetInterface Member List

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

aliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0	bpp::ParameterAliasable	pure virtual
alphabet() const =0	bpp::FrequencySetInterface	pure virtual
clone() const override=0	bpp::CodonFrequencySetInterface	pure virtual
F0	bpp::CodonFrequencySetInterface	static
F1X4	bpp::CodonFrequencySetInterface	static
F3X4	bpp::CodonFrequencySetInterface	static
F61	bpp::CodonFrequencySetInterface	static
FREQUENCE_CONSTRAINT_CENTI	bpp::FrequencySetInterface	static
FREQUENCE_CONSTRAINT_MILLI	bpp::FrequencySetInterface	static
FREQUENCE_CONSTRAINT_SMALL	bpp::FrequencySetInterface	static
getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getAliases() const=0	bpp::ParameterAliasable	pure virtual
getAlphabet() const =0	bpp::FrequencySetInterface	pure virtual
getAlphabetStatesFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
getCodonAlphabet() const =0	bpp::CodonFrequencySetInterface	pure virtual
getFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
getFrequencySetForCodons(short option, std::shared_ptr< const GeneticCode > gCode, const std::string &mgmtStopCodon="quadratic", unsigned short method=1)	bpp::CodonFrequencySetInterface	static
getGeneticCode() const =0	bpp::CodonFrequencySetInterface	pure virtual
getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getName() const =0	bpp::FrequencySetInterface	pure virtual
getNamespace() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfFrequencies() const =0	bpp::FrequencySetInterface	pure virtual
getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getParameters() const=0	bpp::ParameterAliasable	pure virtual
getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getStateMap() const =0	bpp::FrequencySetInterface	pure virtual
hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
ParameterAliasable()	bpp::ParameterAliasable
Parametrizable()	bpp::Parametrizable
removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
setFrequencies(const std::vector< double > &frequencies)=0	bpp::FrequencySetInterface	pure virtual
setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0	bpp::FrequencySetInterface	pure virtual
setNamespace(const std::string &prefix)=0	bpp::ParameterAliasable	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
stateMap() const =0	bpp::FrequencySetInterface	pure virtual
unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
~Clonable()=default	bpp::Clonable	virtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual