bpp-phyl3 3.0.0
bpp::AbstractSubstitutionProcess Member List

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

AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractSubstitutionProcess()bpp::AbstractSubstitutionProcessinline
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
bpp::clone() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::AbstractParameterAliasable::clone() const=0bpp::AbstractParameterAliasablepure virtual
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
fireParameterChanged(const ParameterList &parameters)bpp::AbstractParameterAliasablevirtual
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() constbpp::AbstractSubstitutionProcessinline
getBranchLengthParameters(bool independent) const =0bpp::SubstitutionProcessInterfacepure virtual
getClassProbabilities() const =0bpp::SubstitutionProcessInterfacepure virtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getModel(size_t i) const =0bpp::SubstitutionProcessInterfacepure virtual
getModel(unsigned int nodeId, size_t classIndex) const =0bpp::SubstitutionProcessInterfacepure virtual
getModelForNode(unsigned int nodeId) const =0bpp::SubstitutionProcessInterfacepure virtual
getModelNumberForNode(unsigned int nodeId) const =0bpp::SubstitutionProcessInterfacepure virtual
getModelNumbers() const =0bpp::SubstitutionProcessInterfacepure virtual
getModelScenario() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNodesWithModel(size_t i) const =0bpp::SubstitutionProcessInterfacepure virtual
getNonDerivableParameters() constbpp::AbstractSubstitutionProcessvirtual
getNumberOfClasses() constbpp::AbstractSubstitutionProcessinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfModels() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() constbpp::AbstractSubstitutionProcessinlinevirtual
getParameter(const std::string &name) constbpp::AbstractParameterAliasable
getParameter(size_t i) constbpp::AbstractParameterAliasableprotected
getParameter(size_t i)bpp::AbstractParameterAliasableprotected
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) constbpp::AbstractParameterAliasableprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getParametrizablePhyloTree() const =0bpp::SubstitutionProcessInterfacepure virtual
getProbabilityForModel(size_t classIndex) const =0bpp::SubstitutionProcessInterfacepure virtual
getRateDistribution() const =0bpp::SubstitutionProcessInterfacepure virtual
getRateDistribution()=0bpp::SubstitutionProcessInterfacepure virtual
getRateDistributionParameters(bool independent) const =0bpp::SubstitutionProcessInterfacepure virtual
getRateForModel(size_t classIndex) const =0bpp::SubstitutionProcessInterfacepure virtual
getRootFrequencies() const =0bpp::SubstitutionProcessInterfacepure virtual
getRootFrequenciesParameters(bool independent) const =0bpp::SubstitutionProcessInterfacepure virtual
getRootFrequencySet() const =0bpp::SubstitutionProcessInterfacepure virtual
getRootFrequencySet()=0bpp::SubstitutionProcessInterfacepure virtual
getStateMap() const =0bpp::SubstitutionProcessInterfacepure virtual
getSubstitutionModelParameters(bool independent) const =0bpp::SubstitutionProcessInterfacepure virtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
hasRootFrequencySet() const =0bpp::SubstitutionProcessInterfacepure virtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isCompatibleWith(const AlignmentDataInterface &data) constbpp::AbstractSubstitutionProcessinlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model(size_t i) const =0bpp::SubstitutionProcessInterfacepure virtual
model(unsigned int nodeId, size_t classIndex) const =0bpp::SubstitutionProcessInterfacepure virtual
operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
parametrizablePhyloTree() const =0bpp::SubstitutionProcessInterfacepure virtual
prefix_bpp::AbstractParameterAliasableprivate
rateDistribution() const =0bpp::SubstitutionProcessInterfacepure virtual
rateDistribution()=0bpp::SubstitutionProcessInterfacepure virtual
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rootFrequencySet() const =0bpp::SubstitutionProcessInterfacepure virtual
rootFrequencySet()=0bpp::SubstitutionProcessInterfacepure virtual
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
bpp::setNamespace(const std::string &prefix)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
stateMap() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual