| 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 ¶meters)=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 ¶meters)=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 ¶meters)=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 |
1.9.1 
