bpp::MixedSubstitutionModelSet Member List

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

AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
addEmptyHyperNode()	bpp::MixedSubstitutionModelSet
addHyperNode(const HyperNode &hn)	bpp::MixedSubstitutionModelSet
addModel(std::shared_ptr< TransitionModelInterface > model, const std::vector< int > &nodesId)	bpp::SubstitutionModelSet
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
addToHyperNode(size_t nM, const Vuint &vnS, int nH=-1)	bpp::MixedSubstitutionModelSet
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
alphabet() const	bpp::SubstitutionModelSet	inline
alphabet_	bpp::SubstitutionModelSet	protected
checkOrphanModels(bool throwEx) const	bpp::SubstitutionModelSet	protected
checkOrphanNodes(const Tree &tree, bool throwEx) const	bpp::SubstitutionModelSet	protected
checkUnknownNodes(const Tree &tree, bool throwEx) const	bpp::SubstitutionModelSet	protected
clear()	bpp::MixedSubstitutionModelSet
clone() const	bpp::MixedSubstitutionModelSet	inlinevirtual
complete()	bpp::MixedSubstitutionModelSet
computeHyperNodesProbabilities()	bpp::MixedSubstitutionModelSet
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
fireParameterChanged(const ParameterList &parameters)	bpp::MixedSubstitutionModelSet	virtual
getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getAliases() const	bpp::AbstractParameterAliasable	virtual
getAlphabet() const	bpp::SubstitutionModelSet	inline
getAlphabetStateAsChar(size_t index) const	bpp::SubstitutionModelSet	inline
getAlphabetStateAsInt(size_t index) const	bpp::SubstitutionModelSet	inline
getAlphabetStates() const	bpp::SubstitutionModelSet	inline
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getHyperNode(size_t i)	bpp::MixedSubstitutionModelSet	inline
getHyperNode(size_t i) const	bpp::MixedSubstitutionModelSet	inline
getHyperNodeProbability(const HyperNode &hn) const	bpp::MixedSubstitutionModelSet
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getModel(size_t i) const	bpp::SubstitutionModelSet	inline
getModel(size_t i)	bpp::SubstitutionModelSet	inline
getModelForNode(int nodeId) const	bpp::SubstitutionModelSet	inline
getModelForNode(int nodeId)	bpp::SubstitutionModelSet	inline
getModelIndexForNode(int nodeId) const	bpp::SubstitutionModelSet	inline
getModelParameters(size_t modelIndex) const	bpp::SubstitutionModelSet
getModelStates(int code) const	bpp::SubstitutionModelSet	inline
getModelStates(const std::string &code) const	bpp::SubstitutionModelSet	inline
getNamespace() const override	bpp::AbstractParameterAliasable	virtual
getNodeParameters() const	bpp::SubstitutionModelSet	inline
getNodesWithModel(size_t i) const	bpp::SubstitutionModelSet	inline
getNodesWithParameter(const std::string &name) const	bpp::SubstitutionModelSet
getNumberOfHyperNodes() const	bpp::MixedSubstitutionModelSet	inline
getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getNumberOfModels() const	bpp::SubstitutionModelSet	inline
getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
getNumberOfStates() const	bpp::SubstitutionModelSet	inline
getParameter(const std::string &name) const	bpp::AbstractParameterAliasable
getParameter(size_t i) const	bpp::AbstractParameterAliasable	protected
getParameter(size_t i)	bpp::AbstractParameterAliasable	protected
getParameter_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index) const	bpp::AbstractParameterAliasable	protected
getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameters() const override	bpp::AbstractParameterAliasable	virtual
getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
getParameterValue(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParameterAliasable	protected
getRootFrequencies() const	bpp::SubstitutionModelSet	inline
getRootFrequenciesParameters() const	bpp::SubstitutionModelSet	inline
getRootFrequencySet() const	bpp::SubstitutionModelSet	inline
getStateMap() const	bpp::SubstitutionModelSet	inline
getSubstitutionModel(size_t i) const	bpp::SubstitutionModelSet	inline
getSubstitutionModel(size_t i)	bpp::SubstitutionModelSet	inline
getSubstitutionModelForNode(int nodeId) const	bpp::SubstitutionModelSet	inline
getSubstitutionModelForNode(int nodeId)	bpp::SubstitutionModelSet	inline
hasExclusivePaths() const	bpp::MixedSubstitutionModelSet
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
hasMixedTransitionModel() const	bpp::SubstitutionModelSet
hasOnlySubstitutionModels() const	bpp::SubstitutionModelSet	inline
hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
isFullySetUpFor(const Tree &tree, bool throwEx=true) const	bpp::SubstitutionModelSet	inline
isStationary() const	bpp::SubstitutionModelSet	inline
listModelNames(std::ostream &out=std::cout) const	bpp::SubstitutionModelSet
matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
MixedSubstitutionModelSet(std::shared_ptr< const Alphabet > alpha)	bpp::MixedSubstitutionModelSet	inline
MixedSubstitutionModelSet(const MixedSubstitutionModelSet &set)	bpp::MixedSubstitutionModelSet
MixedSubstitutionModelSet(const SubstitutionModelSet &set)	bpp::MixedSubstitutionModelSet
model(size_t i) const	bpp::SubstitutionModelSet	inline
model(size_t i)	bpp::SubstitutionModelSet	inline
modelParameters_	bpp::SubstitutionModelSet	private
modelSet_	bpp::SubstitutionModelSet	protected
modelToNodes_	bpp::SubstitutionModelSet	mutableprivate
nbStates_	bpp::SubstitutionModelSet	protected
nodeToModel_	bpp::SubstitutionModelSet	mutableprivate
operator=(const MixedSubstitutionModelSet &set)	bpp::MixedSubstitutionModelSet
bpp::SubstitutionModelSet::operator=(const SubstitutionModelSet &set)	bpp::SubstitutionModelSet
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
prefix_	bpp::AbstractParameterAliasable	private
removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
replaceModel(size_t modelIndex, std::shared_ptr< TransitionModelInterface > model)	bpp::SubstitutionModelSet
resetModelToNodeIds()	bpp::SubstitutionModelSet
resetParameters_()	bpp::AbstractParameterAliasable	protected
rootFrequencies_	bpp::SubstitutionModelSet	private
rootFrequencySet() const	bpp::SubstitutionModelSet	inline
setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setNamespace(const std::string &prefix)	bpp::AbstractParameterAliasable	virtual
setNodeToModel(size_t modelIndex, int nodeId)	bpp::SubstitutionModelSet
setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
setRootFrequencies(std::shared_ptr< FrequencySetInterface > rootFreqs)	bpp::SubstitutionModelSet
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
stateMap() const	bpp::SubstitutionModelSet	inline
stationarity_	bpp::SubstitutionModelSet	private
substitutionModel(size_t i) const	bpp::SubstitutionModelSet	inline
SubstitutionModelSet(std::shared_ptr< const Alphabet > alpha)	bpp::SubstitutionModelSet	inline
SubstitutionModelSet(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< FrequencySetInterface > rootFreqs)	bpp::SubstitutionModelSet	inline
SubstitutionModelSet(const SubstitutionModelSet &set)	bpp::SubstitutionModelSet
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateRootFrequencies()	bpp::SubstitutionModelSet	inlineprotected
vpHyperNodes_	bpp::MixedSubstitutionModelSet	private
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~MixedSubstitutionModelSet()	bpp::MixedSubstitutionModelSet
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SubstitutionModelSet()	bpp::SubstitutionModelSet	inlinevirtual