bpp::SubstitutionModelSet Member List

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

addModel(SubstitutionModel *model, const std::vector< int > &nodesId)	bpp::SubstitutionModelSet
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::SubstitutionModelSet
clone() const	bpp::SubstitutionModelSet	inline
fireParameterChanged(const ParameterList &parameters)	bpp::SubstitutionModelSet	virtual
getAlphabet() const	bpp::SubstitutionModelSet	inline
getAlphabetStateAsChar(size_t index) const	bpp::SubstitutionModelSet	inlinevirtual
getAlphabetStateAsInt(size_t index) const	bpp::SubstitutionModelSet	inlinevirtual
getAlphabetStates() const	bpp::SubstitutionModelSet	inlinevirtual
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	inlinevirtual
getModelStates(const std::string &code) const	bpp::SubstitutionModelSet	inlinevirtual
getNodeParameters() const	bpp::SubstitutionModelSet	inline
getNodesWithModel(size_t i) const	bpp::SubstitutionModelSet	inline
getNodesWithParameter(const std::string &name) const	bpp::SubstitutionModelSet
getNumberOfModels() const	bpp::SubstitutionModelSet	inline
getNumberOfStates() const	bpp::SubstitutionModelSet	inline
getRootFrequencies() const	bpp::SubstitutionModelSet	inline
getRootFrequenciesParameters() const	bpp::SubstitutionModelSet	inline
getRootFrequenciesSet() const	bpp::SubstitutionModelSet	inline
getStateMap() const	bpp::SubstitutionModelSet	inlinevirtual
hasMixedSubstitutionModel() const	bpp::SubstitutionModelSet
isFullySetUpFor(const Tree &tree, bool throwEx=true) const	bpp::SubstitutionModelSet	inline
listModelNames(std::ostream &out=std::cout) const	bpp::SubstitutionModelSet
modelParameters_	bpp::SubstitutionModelSet	private
modelSet_	bpp::SubstitutionModelSet	protected
modelToNodes_	bpp::SubstitutionModelSet	mutableprivate
nbStates_	bpp::SubstitutionModelSet	protected
nodeToModel_	bpp::SubstitutionModelSet	mutableprivate
operator=(const SubstitutionModelSet &set)	bpp::SubstitutionModelSet
replaceModel(size_t modelIndex, SubstitutionModel *model)	bpp::SubstitutionModelSet
rootFrequencies_	bpp::SubstitutionModelSet	private
setRootFrequencies(FrequenciesSet *rootFreqs)	bpp::SubstitutionModelSet
stationarity_	bpp::SubstitutionModelSet	private
SubstitutionModelSet(const Alphabet *alpha)	bpp::SubstitutionModelSet	inline
SubstitutionModelSet(const Alphabet *alpha, FrequenciesSet *rootFreqs)	bpp::SubstitutionModelSet	inline
SubstitutionModelSet(const SubstitutionModelSet &set)	bpp::SubstitutionModelSet
updateRootFrequencies()	bpp::SubstitutionModelSet	inlineprotected
~SubstitutionModelSet()	bpp::SubstitutionModelSet	inlinevirtual