bpp::AutonomousSubstitutionProcessInterface Member List

This is the complete list of members for bpp::AutonomousSubstitutionProcessInterface, 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
clone() const =0	bpp::SubstitutionProcessInterface	pure virtual
getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getAliases() const=0	bpp::ParameterAliasable	pure virtual
getBranchLengthParameters(bool independent) const =0	bpp::SubstitutionProcessInterface	pure virtual
getClassProbabilities() const =0	bpp::SubstitutionProcessInterface	pure virtual
getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getModel(size_t i) const =0	bpp::SubstitutionProcessInterface	pure virtual
getModel(unsigned int nodeId, size_t classIndex) const =0	bpp::SubstitutionProcessInterface	pure virtual
getModelForNode(unsigned int nodeId) const =0	bpp::SubstitutionProcessInterface	pure virtual
getModelNumberForNode(unsigned int nodeId) const =0	bpp::SubstitutionProcessInterface	pure virtual
getModelNumbers() const =0	bpp::SubstitutionProcessInterface	pure virtual
getModelScenario() const =0	bpp::SubstitutionProcessInterface	pure virtual
getNamespace() const=0	bpp::ParameterAliasable	pure virtual
getNodesWithModel(size_t i) const =0	bpp::SubstitutionProcessInterface	pure virtual
getNonDerivableParameters() const =0	bpp::SubstitutionProcessInterface	pure virtual
getNumberOfClasses() const =0	bpp::SubstitutionProcessInterface	pure virtual
getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfModels() const =0	bpp::SubstitutionProcessInterface	pure virtual
getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfStates() const =0	bpp::SubstitutionProcessInterface	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
getParametrizablePhyloTree() const =0	bpp::SubstitutionProcessInterface	pure virtual
getProbabilityForModel(size_t classIndex) const =0	bpp::SubstitutionProcessInterface	pure virtual
getRateDistribution() const =0	bpp::SubstitutionProcessInterface	pure virtual
getRateDistribution()=0	bpp::SubstitutionProcessInterface	pure virtual
getRateDistributionParameters(bool independent) const =0	bpp::SubstitutionProcessInterface	pure virtual
getRateForModel(size_t classIndex) const =0	bpp::SubstitutionProcessInterface	pure virtual
getRootFrequencies() const =0	bpp::SubstitutionProcessInterface	pure virtual
getRootFrequenciesParameters(bool independent) const =0	bpp::SubstitutionProcessInterface	pure virtual
getRootFrequencySet() const =0	bpp::SubstitutionProcessInterface	pure virtual
getRootFrequencySet()=0	bpp::SubstitutionProcessInterface	pure virtual
getStateMap() const =0	bpp::SubstitutionProcessInterface	pure virtual
getSubstitutionModelParameters(bool independent) const =0	bpp::SubstitutionProcessInterface	pure virtual
hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
hasRootFrequencySet() const =0	bpp::SubstitutionProcessInterface	pure virtual
isCompatibleWith(const AlignmentDataInterface &data) const =0	bpp::SubstitutionProcessInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
model(size_t i) const =0	bpp::SubstitutionProcessInterface	pure virtual
model(unsigned int nodeId, size_t classIndex) const =0	bpp::SubstitutionProcessInterface	pure virtual
parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
ParameterAliasable()	bpp::ParameterAliasable
Parametrizable()	bpp::Parametrizable
parametrizablePhyloTree() const =0	bpp::SubstitutionProcessInterface	pure virtual
rateDistribution() const =0	bpp::SubstitutionProcessInterface	pure virtual
rateDistribution()=0	bpp::SubstitutionProcessInterface	pure virtual
removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
rootFrequencySet() const =0	bpp::SubstitutionProcessInterface	pure virtual
rootFrequencySet()=0	bpp::SubstitutionProcessInterface	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
setModelScenario(std::shared_ptr< ModelScenario > modelScenario)=0	bpp::AutonomousSubstitutionProcessInterface	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
setPhyloTree(const PhyloTree &phyloTree)=0	bpp::AutonomousSubstitutionProcessInterface	pure virtual
setRootFrequencySet(std::shared_ptr< FrequencySetInterface > rootfrequency)=0	bpp::AutonomousSubstitutionProcessInterface	pure virtual
stateMap() const =0	bpp::SubstitutionProcessInterface	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