bpp-phyl3 3.0.0
bpp::RegisterRatesSubstitutionModel Member List

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

AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinline
AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractSubstitutionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
AbstractTransitionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)bpp::AbstractTransitionModel
AbstractTransitionModel(const AbstractTransitionModel &model)=defaultbpp::AbstractTransitionModel
AbstractWrappedModel(const std::string &prefix)bpp::AbstractWrappedModelinline
AbstractWrappedSubstitutionModel(const std::string &prefix)bpp::AbstractWrappedSubstitutionModelinline
AbstractWrappedTransitionModel(const std::string &prefix)bpp::AbstractWrappedTransitionModelinline
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
addRateParameter() overridebpp::RegisterRatesSubstitutionModelinlinevirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
alphabet() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
alphabet_bpp::AbstractTransitionModelprotected
BranchModelInterface()bpp::BranchModelInterfaceinline
clone() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
computeFreq_bpp::AbstractSubstitutionModelprotected
bpp::computeFrequencies() const =0bpp::TransitionModelInterfacepure virtual
bpp::computeFrequencies(bool yn)=0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::computeFrequencies() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::AbstractSubstitutionModel::computeFrequencies(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractLkTransitionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
d2pijt_bpp::AbstractTransitionModelmutableprotected
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
bpp::dLik_dt(const Eigen::VectorXd &values, double t) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractLkTransitionModel::dLik_dt(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::dPij_dt(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
dpijt_bpp::AbstractTransitionModelmutableprotected
eigenDecompose_bpp::AbstractSubstitutionModelprotected
eigenValues_bpp::AbstractSubstitutionModelprotected
bpp::enableEigenDecomposition(bool yn)=0bpp::SubstitutionModelInterfacepure virtual
bpp::enableEigenDecomposition()=0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition()bpp::AbstractSubstitutionModelinlinevirtual
exchangeability_bpp::AbstractSubstitutionModelprotected
bpp::exchangeabilityMatrix() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::exchangeabilityMatrix() constbpp::AbstractSubstitutionModelinlinevirtual
fireParameterChanged(const ParameterList &parameters) overridebpp::RegisterRatesSubstitutionModelinlinevirtual
bpp::freq(size_t i) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::freq(size_t i) const overridebpp::AbstractTransitionModelinlinevirtual
freq_bpp::AbstractTransitionModelprotected
frequencySet() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
bpp::generator() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::generator() constbpp::AbstractSubstitutionModelinlinevirtual
generator_bpp::AbstractSubstitutionModelprotected
getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getAlphabetStateAsChar(size_t s) const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getAlphabetStateAsInt(size_t i) const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getAlphabetStates() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
bpp::getColumnRightEigenVectors() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getColumnRightEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getd2Pij_dt2(double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getd2Pij_dt2(double t) constbpp::AbstractSubstitutionModelvirtual
bpp::getdPij_dt(double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getdPij_dt(double t) constbpp::AbstractSubstitutionModelvirtual
bpp::getEigenValues() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getFrequencies() const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getFrequencies() const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getFrequencies_()=0bpp::TransitionModelInterfaceprotectedpure virtual
bpp::AbstractSubstitutionModel::getFrequencies_() overridebpp::AbstractTransitionModelinlineprotectedvirtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getIEigenValues() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getIEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getInitValue(size_t i, int state) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getInitValue(size_t i, int state) const overridebpp::AbstractTransitionModelvirtual
getModelStates(int i) const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getModelStates(const std::string &s) const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getName() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
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
getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameters() const overridebpp::AbstractParameterAliasablevirtual
getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
bpp::getPij_t(double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getPij_t(double t) constbpp::AbstractSubstitutionModelvirtual
getRate() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
getRegisterName() constbpp::RegisterRatesSubstitutionModelinline
bpp::getRowLeftEigenVectors() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getRowLeftEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getScale() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::getScale() constbpp::AbstractSubstitutionModelvirtual
getStateMap() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
iEigenValues_bpp::AbstractSubstitutionModelprotected
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
bpp::isDiagonalizable() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::isDiagonalizable() constbpp::AbstractSubstitutionModelinlinevirtual
isDiagonalizable_bpp::AbstractSubstitutionModelprotected
bpp::isNonSingular() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::isNonSingular() constbpp::AbstractSubstitutionModelinlinevirtual
isNonSingular_bpp::AbstractSubstitutionModelprotected
bpp::isScalable() const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::isScalable() constbpp::AbstractSubstitutionModelinlinevirtual
isScalable_bpp::AbstractSubstitutionModelprotected
leftEigenVectors_bpp::AbstractSubstitutionModelprotected
lik_bpp::AbstractLkTransitionModelmutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractLkTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model() const overridebpp::AbstractWrappedTransitionModelinlinevirtual
model_()bpp::AbstractWrappedTransitionModelinlineprotected
nbTypes_bpp::RegisterRatesSubstitutionModelprivate
bpp::normalize()=0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::normalize()bpp::AbstractSubstitutionModelvirtual
operator=(const RegisterRatesSubstitutionModel &fmsm)bpp::RegisterRatesSubstitutionModelinline
bpp::AbstractWrappedSubstitutionModel::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
bpp::AbstractTransitionModel::operator=(const AbstractTransitionModel &model)=defaultbpp::AbstractTransitionModel
originalModel_bpp::RegisterRatesSubstitutionModelprivate
parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
bpp::Pij_t(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::Pij_t(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
pijt_bpp::AbstractTransitionModelmutableprotected
prefix_bpp::AbstractParameterAliasableprivate
bpp::Qij(size_t i, size_t j) const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::Qij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
rate_bpp::AbstractTransitionModelprotected
registerName_bpp::RegisterRatesSubstitutionModelprivate
RegisterRatesSubstitutionModel(std::unique_ptr< SubstitutionModelInterface > originalModel, const SubstitutionRegisterInterface &reg, bool isNormalized=false)bpp::RegisterRatesSubstitutionModel
RegisterRatesSubstitutionModel(const RegisterRatesSubstitutionModel &fmsm)bpp::RegisterRatesSubstitutionModelinline
removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rightEigenVectors_bpp::AbstractSubstitutionModelprotected
setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
bpp::setDiagonal()=0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::setDiagonal()bpp::AbstractSubstitutionModelvirtual
bpp::setFreq(std::map< int, double > &frequencies)=0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::setFreq(std::map< int, double > &freqs) overridebpp::AbstractTransitionModelvirtual
bpp::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)=0bpp::TransitionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) overridebpp::AbstractTransitionModelvirtual
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setRate(double rate) overridebpp::RegisterRatesSubstitutionModelinlinevirtual
setRegStates_()bpp::RegisterRatesSubstitutionModelprivate
bpp::setScalable(bool scalable)=0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::setScalable(bool scalable)bpp::AbstractSubstitutionModelinlinevirtual
bpp::setScale(double scale)=0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::setScale(double scale)bpp::AbstractSubstitutionModelvirtual
setVerboseLevel(short level)bpp::AbstractTransitionModelinline
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
bpp::Sij(size_t i, size_t j) const =0bpp::SubstitutionModelInterfacepure virtual
bpp::AbstractSubstitutionModel::Sij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
size_bpp::AbstractTransitionModelprotected
stateMap() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
stateMap_bpp::AbstractTransitionModelprotected
substitutionModel() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
substitutionModel_() overridebpp::RegisterRatesSubstitutionModelinlineprotectedvirtual
SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinline
tmpMat_bpp::AbstractSubstitutionModelmutableprotected
transitionModel() const overridebpp::RegisterRatesSubstitutionModelinlinevirtual
transitionModel_() overridebpp::RegisterRatesSubstitutionModelinlineprotectedvirtual
TransitionModelInterface()bpp::TransitionModelInterfaceinline
unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
updateMatrices_() overridebpp::RegisterRatesSubstitutionModelprotectedvirtual
verboseLevel() constbpp::AbstractTransitionModelinline
verboseLevel_bpp::AbstractTransitionModelprotected
vPowGen_bpp::AbstractSubstitutionModelprotected
vRates_bpp::RegisterRatesSubstitutionModelprivate
vRegStates_bpp::RegisterRatesSubstitutionModelprivate
WrappedModelInterface()bpp::WrappedModelInterfaceinline
WrappedSubstitutionModelInterface()bpp::WrappedSubstitutionModelInterfaceinline
WrappedTransitionModelInterface()bpp::WrappedTransitionModelInterfaceinline
~AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractSubstitutionModel()bpp::AbstractSubstitutionModelinlinevirtual
~AbstractTransitionModel()bpp::AbstractTransitionModelinlinevirtual
~AbstractWrappedModel()bpp::AbstractWrappedModelinlinevirtual
~AbstractWrappedSubstitutionModel()bpp::AbstractWrappedSubstitutionModelinlinevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~RegisterRatesSubstitutionModel()bpp::RegisterRatesSubstitutionModelinlinevirtual
~SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinlinevirtual
~TransitionModelInterface()bpp::TransitionModelInterfaceinlinevirtual
~WrappedModelInterface()bpp::WrappedModelInterfaceinlinevirtual
~WrappedSubstitutionModelInterface()bpp::WrappedSubstitutionModelInterfaceinlinevirtual
~WrappedTransitionModelInterface()bpp::WrappedTransitionModelInterfaceinlinevirtual