bpp-phyl3  3.0.0
bpp::RE08Nucleotide Member List

This is the complete list of members for bpp::RE08Nucleotide, 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
AbstractReversibleSubstitutionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)bpp::AbstractReversibleSubstitutionModelinline
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
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
addRateParameter() overridebpp::AbstractTransitionModelvirtual
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
alphabet() const overridebpp::AbstractTransitionModelinlinevirtual
alphabet_bpp::AbstractTransitionModelprotected
BranchModelInterface()bpp::BranchModelInterfaceinline
clone() const overridebpp::RE08Nucleotideinlinevirtual
computeFreq_bpp::AbstractSubstitutionModelprotected
computeFrequencies() constbpp::AbstractSubstitutionModelinlinevirtual
computeFrequencies(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
d2Lik_dt2(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
d2Pij_dt2(size_t i, size_t j, double d) const overridebpp::RE08virtual
d2pijt_bpp::AbstractTransitionModelmutableprotected
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
dLik_dt(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
dPij_dt(size_t i, size_t j, double d) const overridebpp::RE08virtual
dpijt_bpp::AbstractTransitionModelmutableprotected
eigenDecompose_bpp::AbstractSubstitutionModelprotected
eigenValues_bpp::AbstractSubstitutionModelprotected
enableEigenDecomposition(bool yn)bpp::AbstractSubstitutionModelinlinevirtual
enableEigenDecomposition()bpp::AbstractSubstitutionModelinlinevirtual
exchangeability_bpp::AbstractSubstitutionModelprotected
exchangeabilityMatrix() constbpp::AbstractSubstitutionModelinlinevirtual
exp_bpp::RE08mutableprivate
fireParameterChanged(const ParameterList &parameters) overridebpp::RE08inlinevirtual
freq(size_t i) const overridebpp::AbstractTransitionModelinlinevirtual
freq_bpp::AbstractTransitionModelprotected
frequencySet() const overridebpp::AbstractTransitionModelinlinevirtual
generator() constbpp::AbstractSubstitutionModelinlinevirtual
generator_bpp::AbstractSubstitutionModelprotected
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() const overridebpp::AbstractTransitionModelinlinevirtual
getAlphabetStateAsChar(size_t index) const overridebpp::AbstractTransitionModelinlinevirtual
getAlphabetStateAsInt(size_t index) const overridebpp::AbstractTransitionModelinlinevirtual
getAlphabetStates() const overridebpp::AbstractTransitionModelinlinevirtual
getColumnRightEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
getd2Pij_dt2(double d) const overridebpp::RE08virtual
getdPij_dt(double d) const overridebpp::RE08virtual
getEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
getFrequencies() const overridebpp::AbstractTransitionModelinlinevirtual
getFrequencies_() overridebpp::AbstractTransitionModelinlineprotectedvirtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getIEigenValues() constbpp::AbstractSubstitutionModelinlinevirtual
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getInitValue(size_t i, int state) const overridebpp::RE08virtual
getModelStates(int code) const overridebpp::AbstractTransitionModelinlinevirtual
getModelStates(const std::string &code) const overridebpp::AbstractTransitionModelinlinevirtual
getName() const overridebpp::RE08inlinevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNucleicAlphabet() const overridebpp::RE08Nucleotideinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() const overridebpp::RE08Nucleotideinlinevirtual
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
getPij_t(double d) const overridebpp::RE08virtual
getRate() const overridebpp::AbstractTransitionModelvirtual
getRowLeftEigenVectors() constbpp::AbstractSubstitutionModelinlinevirtual
getScale() constbpp::AbstractSubstitutionModelvirtual
getStateMap() const overridebpp::AbstractTransitionModelinlinevirtual
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
iEigenValues_bpp::AbstractSubstitutionModelprotected
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isDiagonalizable() constbpp::AbstractSubstitutionModelinlinevirtual
isDiagonalizable_bpp::AbstractSubstitutionModelprotected
isNonSingular() constbpp::AbstractSubstitutionModelinlinevirtual
isNonSingular_bpp::AbstractSubstitutionModelprotected
isScalable() constbpp::AbstractSubstitutionModelinlinevirtual
isScalable_bpp::AbstractSubstitutionModelprotected
lambda_bpp::RE08private
leftEigenVectors_bpp::AbstractSubstitutionModelprotected
lik_bpp::AbstractLkTransitionModelmutableprivate
Lik_t(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
mu_bpp::RE08private
nestedModel() constbpp::RE08Nucleotideinline
nestedModel_()bpp::RE08inlineprotected
nestedPrefix_bpp::RE08private
normalize()bpp::AbstractSubstitutionModelvirtual
operator=(const RE08 &model)bpp::RE08inline
bpp::AbstractReversibleSubstitutionModel::operator=(const AbstractSubstitutionModel &model)bpp::AbstractSubstitutionModelinline
bpp::AbstractTransitionModel::operator=(const AbstractTransitionModel &model)=defaultbpp::AbstractTransitionModel
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
p_bpp::RE08mutableprivate
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
Pij_t(size_t i, size_t j, double d) const overridebpp::RE08virtual
pijt_bpp::AbstractTransitionModelmutableprotected
prefix_bpp::AbstractParameterAliasableprivate
Qij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
rate_bpp::AbstractTransitionModelprotected
RE08(std::unique_ptr< ReversibleSubstitutionModelInterface > simpleModel, double lambda=0.1, double mu=0.1)bpp::RE08
RE08(const RE08 &model)bpp::RE08inline
RE08Nucleotide(std::unique_ptr< NucleotideReversibleSubstitutionModelInterface > nucleotideModel, double lambda=0.1, double mu=0.1)bpp::RE08Nucleotideinline
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
ReversibleSubstitutionModelInterface()bpp::ReversibleSubstitutionModelInterfaceinline
rightEigenVectors_bpp::AbstractSubstitutionModelprotected
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
setDiagonal()bpp::AbstractSubstitutionModelvirtual
setFreq(std::map< int, double > &frequencies) overridebpp::RE08inlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) overridebpp::RE08inlinevirtual
setNamespace(const std::string &prefix) overridebpp::RE08virtual
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
setRate(double rate) overridebpp::AbstractTransitionModelvirtual
setScalable(bool scalable)bpp::AbstractSubstitutionModelinlinevirtual
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
Sij(size_t i, size_t j) constbpp::AbstractSubstitutionModelinlinevirtual
simpleExchangeabilities_bpp::RE08private
simpleGenerator_bpp::RE08private
simpleModel_bpp::RE08private
size_bpp::AbstractTransitionModelprotected
stateMap() const overridebpp::AbstractTransitionModelinlinevirtual
stateMap_bpp::AbstractTransitionModelprotected
SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinline
tmpMat_bpp::AbstractSubstitutionModelmutableprotected
TransitionModelInterface()bpp::TransitionModelInterfaceinline
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
updateMatrices_() overridebpp::RE08protectedvirtual
verboseLevel() constbpp::AbstractTransitionModelinline
verboseLevel_bpp::AbstractTransitionModelprotected
vPowGen_bpp::AbstractSubstitutionModelprotected
~AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractReversibleSubstitutionModel()bpp::AbstractReversibleSubstitutionModelinlinevirtual
~AbstractSubstitutionModel()bpp::AbstractSubstitutionModelinlinevirtual
~AbstractTransitionModel()bpp::AbstractTransitionModelinlinevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~NucleotideSubstitutionModelInterface()bpp::NucleotideSubstitutionModelInterfaceinlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~RE08()bpp::RE08inlinevirtual
~RE08Nucleotide()bpp::RE08Nucleotideinlinevirtual
~ReversibleSubstitutionModelInterface()bpp::ReversibleSubstitutionModelInterfaceinlinevirtual
~SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinlinevirtual
~TransitionModelInterface()bpp::TransitionModelInterfaceinlinevirtual