bpp::NonHomogeneousSequenceSimulator Member List

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

alphabet() const override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
alphabet_	bpp::NonHomogeneousSequenceSimulator	mutableprivate
clone() const override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
continuousRates_	bpp::NonHomogeneousSequenceSimulator	private
DetailedSiteSimulatorInterface()	bpp::DetailedSiteSimulatorInterface	inline
dEvolve(size_t initialState, double rate, RASiteSimulationResult &rassr) const	bpp::NonHomogeneousSequenceSimulator	protected
dEvolveInternal(SNode *node, double rate, RASiteSimulationResult &rassr) const	bpp::NonHomogeneousSequenceSimulator	protected
dSimulateSite() const override	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(size_t ancestralStateIndex) const override	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(size_t ancestralStateIndex, double rate) const override	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(double rate) const override	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(size_t ancestralStateIndex, size_t rateClass) const	bpp::NonHomogeneousSequenceSimulator	virtual
enableContinuousRates(bool yn)	bpp::NonHomogeneousSequenceSimulator	inline
evolve(const SNode *node, size_t initialStateIndex, size_t rateClass) const	bpp::NonHomogeneousSequenceSimulator	protected
evolve(const SNode *node, size_t initialStateIndex, double rate) const	bpp::NonHomogeneousSequenceSimulator	protected
evolveInternal(SNode *node, size_t rateClass) const	bpp::NonHomogeneousSequenceSimulator	protected
evolveInternal(SNode *node, double rate) const	bpp::NonHomogeneousSequenceSimulator	protected
getAlphabet() const override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
getRateDistribution() const	bpp::NonHomogeneousSequenceSimulator	inline
getSequenceNames() const override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
getSubstitutionModelSet() const	bpp::NonHomogeneousSequenceSimulator	inline
getTree() const	bpp::NonHomogeneousSequenceSimulator	inline
init()	bpp::NonHomogeneousSequenceSimulator	private
leaves_	bpp::NonHomogeneousSequenceSimulator	private
modelSet_	bpp::NonHomogeneousSequenceSimulator	private
multipleEvolve(const SNode *node, const std::vector< size_t > &initialStateIndices, const std::vector< size_t > &rateClasses, std::vector< size_t > &finalStates) const	bpp::NonHomogeneousSequenceSimulator	protected
multipleEvolve(const std::vector< size_t > &initialStates, const std::vector< size_t > &rateClasses) const	bpp::NonHomogeneousSequenceSimulator	protected
multipleEvolveInternal(SNode *node, const std::vector< size_t > &rateClasses) const	bpp::NonHomogeneousSequenceSimulator	protected
nbClasses_	bpp::NonHomogeneousSequenceSimulator	private
nbNodes_	bpp::NonHomogeneousSequenceSimulator	private
nbStates_	bpp::NonHomogeneousSequenceSimulator	private
NonHomogeneousSequenceSimulator(std::shared_ptr< const SubstitutionModelSet > modelSet, std::shared_ptr< const DiscreteDistributionInterface > rate, std::shared_ptr< const Tree > tree)	bpp::NonHomogeneousSequenceSimulator
NonHomogeneousSequenceSimulator(std::shared_ptr< const TransitionModelInterface > model, std::shared_ptr< const DiscreteDistributionInterface > rate, std::shared_ptr< const Tree > tree)	bpp::NonHomogeneousSequenceSimulator
NonHomogeneousSequenceSimulator(const NonHomogeneousSequenceSimulator &nhss)=default	bpp::NonHomogeneousSequenceSimulator
operator=(const NonHomogeneousSequenceSimulator &nhss)=default	bpp::NonHomogeneousSequenceSimulator
outputInternalSequences(bool yn) override	bpp::NonHomogeneousSequenceSimulator	virtual
outputInternalSequences_	bpp::NonHomogeneousSequenceSimulator	private
outputInternalSites(bool yn) override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
phyloTree_	bpp::NonHomogeneousSequenceSimulator	mutableprivate
rate_	bpp::NonHomogeneousSequenceSimulator	private
rateDistribution() const	bpp::NonHomogeneousSequenceSimulator	inline
seqNames_	bpp::NonHomogeneousSequenceSimulator	private
SequenceSimulatorInterface()	bpp::SequenceSimulatorInterface	inline
simulate(size_t numberOfSites) const override	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite() const override	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex) const override	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex, double rate) const override	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(double rate) const override	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex, size_t rateClass) const	bpp::NonHomogeneousSequenceSimulator	virtual
siteSimulator(size_t pos) const override	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
SiteSimulatorInterface()	bpp::SiteSimulatorInterface	inline
substitutionModelSet() const	bpp::NonHomogeneousSequenceSimulator	inline
supportedStates_	bpp::NonHomogeneousSequenceSimulator	private
templateTree_	bpp::NonHomogeneousSequenceSimulator	private
tree() const	bpp::NonHomogeneousSequenceSimulator	inline
tree_	bpp::NonHomogeneousSequenceSimulator	mutableprivate
~Clonable()=default	bpp::Clonable	virtual
~DetailedSiteSimulatorInterface()	bpp::DetailedSiteSimulatorInterface	inlinevirtual
~NonHomogeneousSequenceSimulator()	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
~SequenceSimulatorInterface()	bpp::SequenceSimulatorInterface	inlinevirtual
~SiteSimulatorInterface()	bpp::SiteSimulatorInterface	inlinevirtual