bpp::NonHomogeneousSequenceSimulator Member List

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

alphabet_	bpp::NonHomogeneousSequenceSimulator	private
clone() const	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
continuousRates_	bpp::NonHomogeneousSequenceSimulator	private
DetailedSiteSimulator()	bpp::DetailedSiteSimulator	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	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(size_t ancestralStateIndex) const	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(size_t ancestralStateIndex, double rate) const	bpp::NonHomogeneousSequenceSimulator	virtual
dSimulateSite(double rate) const	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	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
getRateDistribution() const	bpp::NonHomogeneousSequenceSimulator	inline
getSequencesNames() const	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(const SubstitutionModelSet *modelSet, const DiscreteDistribution *rate, const Tree *tree)	bpp::NonHomogeneousSequenceSimulator
NonHomogeneousSequenceSimulator(const SubstitutionModel *model, const DiscreteDistribution *rate, const Tree *tree)	bpp::NonHomogeneousSequenceSimulator
NonHomogeneousSequenceSimulator(const NonHomogeneousSequenceSimulator &nhss)	bpp::NonHomogeneousSequenceSimulator	inline
operator=(const NonHomogeneousSequenceSimulator &nhss)	bpp::NonHomogeneousSequenceSimulator	inline
ownModelSet_	bpp::NonHomogeneousSequenceSimulator	private
rate_	bpp::NonHomogeneousSequenceSimulator	private
seqNames_	bpp::NonHomogeneousSequenceSimulator	private
SequenceSimulator()	bpp::SequenceSimulator	inline
simulate(size_t numberOfSites) const	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite() const	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex) const	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex, double rate) const	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(double rate) const	bpp::NonHomogeneousSequenceSimulator	virtual
simulateSite(size_t ancestralStateIndex, size_t rateClass) const	bpp::NonHomogeneousSequenceSimulator	virtual
SiteSimulator()	bpp::SiteSimulator	inline
supportedStates_	bpp::NonHomogeneousSequenceSimulator	private
templateTree_	bpp::NonHomogeneousSequenceSimulator	private
tree_	bpp::NonHomogeneousSequenceSimulator	mutableprivate
~DetailedSiteSimulator()	bpp::DetailedSiteSimulator	inlinevirtual
~NonHomogeneousSequenceSimulator()	bpp::NonHomogeneousSequenceSimulator	inlinevirtual
~SequenceSimulator()	bpp::SequenceSimulator	inlinevirtual
~SiteSimulator()	bpp::SiteSimulator	inlinevirtual