bpp-phyl3  3.0.0
bpp::SimpleSubstitutionProcess Member List

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

AbstractAutonomousSubstitutionProcess(std::shared_ptr< const PhyloTree > tree=0, std::shared_ptr< FrequencySetInterface > rootFrequencies=0, const std::string &prefix="")bpp::AbstractAutonomousSubstitutionProcessprotected
AbstractAutonomousSubstitutionProcess(std::shared_ptr< ParametrizablePhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFrequencies=0, const std::string &prefix="")bpp::AbstractAutonomousSubstitutionProcessprotected
AbstractAutonomousSubstitutionProcess(const AbstractAutonomousSubstitutionProcess &asp)bpp::AbstractAutonomousSubstitutionProcessprotected
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::AbstractSubstitutionProcess::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
clone() const overridebpp::SimpleSubstitutionProcessinlinevirtual
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
fireParameterChanged(const ParameterList &pl) overridebpp::SimpleSubstitutionProcessprotectedvirtual
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() constbpp::AbstractSubstitutionProcessinline
getBranchLengthParameters(bool independent) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getClassProbabilities() const overridebpp::SimpleSubstitutionProcessinlinevirtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getModel(unsigned int nodeId, size_t classIndex) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getModel(size_t n) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getModelForNode(unsigned int nodeId) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getModelNumberForNode(unsigned int nodeId) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getModelNumbers() const overridebpp::SimpleSubstitutionProcessinlinevirtual
getModelScenario() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNodesWithModel(size_t i) const overridebpp::SimpleSubstitutionProcessinlinevirtual
bpp::getNonDerivableParameters() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::AbstractSubstitutionProcess::getNonDerivableParameters() constbpp::AbstractSubstitutionProcessvirtual
bpp::getNumberOfClasses() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::AbstractSubstitutionProcess::getNumberOfClasses() constbpp::AbstractSubstitutionProcessinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfModels() const overridebpp::SimpleSubstitutionProcessinlinevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getNumberOfStates() const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::AbstractSubstitutionProcess::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::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::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() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
getProbabilityForModel(size_t classIndex) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getRateDistribution() const overridebpp::SimpleSubstitutionProcessinlinevirtual
getRateDistribution() overridebpp::SimpleSubstitutionProcessinlinevirtual
getRateDistributionParameters(bool independent) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getRateForModel(size_t classIndex) const overridebpp::SimpleSubstitutionProcessinlinevirtual
getRootFrequencies() const overridebpp::SimpleSubstitutionProcessinlinevirtual
getRootFrequenciesParameters(bool independent) constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
getRootFrequencySet() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
getRootFrequencySet()bpp::AbstractAutonomousSubstitutionProcessinlinevirtual
getStateMap() const overridebpp::SimpleSubstitutionProcessinlinevirtual
getSubstitutionModelParameters(bool independent) const overridebpp::SimpleSubstitutionProcessinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
hasRootFrequencySet() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
bpp::isCompatibleWith(const AlignmentDataInterface &data) const =0bpp::SubstitutionProcessInterfacepure virtual
bpp::AbstractSubstitutionProcess::isCompatibleWith(const AlignmentDataInterface &data) constbpp::AbstractSubstitutionProcessinlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model(unsigned int nodeId, size_t classIndex) const overridebpp::SimpleSubstitutionProcessinlinevirtual
model(size_t n) const overridebpp::SimpleSubstitutionProcessinlinevirtual
model_bpp::SimpleSubstitutionProcessprotected
modelScenario_bpp::AbstractAutonomousSubstitutionProcessprotected
operator=(const SimpleSubstitutionProcess &ssp)bpp::SimpleSubstitutionProcess
bpp::AbstractAutonomousSubstitutionProcess::operator=(const AbstractAutonomousSubstitutionProcess &asp)bpp::AbstractAutonomousSubstitutionProcessprotected
bpp::AbstractSubstitutionProcess::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
parametrizablePhyloTree() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
prefix_bpp::AbstractParameterAliasableprivate
pTree_bpp::AbstractAutonomousSubstitutionProcessprotected
rateDistribution() const overridebpp::SimpleSubstitutionProcessinlinevirtual
rateDistribution() overridebpp::SimpleSubstitutionProcessinlinevirtual
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rootFrequencies_bpp::AbstractAutonomousSubstitutionProcessprotected
rootFrequencySet() constbpp::AbstractAutonomousSubstitutionProcessinlinevirtual
rootFrequencySet()bpp::AbstractAutonomousSubstitutionProcessinlinevirtual
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setModelScenario(std::shared_ptr< ModelScenario > modelpath) overridebpp::SimpleSubstitutionProcessvirtual
bpp::setNamespace(const std::string &prefix)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setPhyloTree(const PhyloTree &phyloTree)bpp::AbstractAutonomousSubstitutionProcessvirtual
setRootFrequencySet(std::shared_ptr< FrequencySetInterface > rootfrequency)bpp::AbstractAutonomousSubstitutionProcessinlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
SimpleSubstitutionProcess(std::shared_ptr< BranchModelInterface > model, std::shared_ptr< const PhyloTree > tree=nullptr, std::shared_ptr< FrequencySetInterface > rootFrequencies=nullptr)bpp::SimpleSubstitutionProcess
SimpleSubstitutionProcess(std::shared_ptr< BranchModelInterface > model, std::shared_ptr< ParametrizablePhyloTree > tree, std::shared_ptr< FrequencySetInterface > rootFrequencies=nullptr)bpp::SimpleSubstitutionProcess
SimpleSubstitutionProcess(const SimpleSubstitutionProcess &ssp)bpp::SimpleSubstitutionProcess
stateMap() const overridebpp::SimpleSubstitutionProcessinlinevirtual
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractSubstitutionProcess::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