bpp::PhyloLikelihoodFormula Member List

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

AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
AbstractPhyloLikelihood(Context &context)	bpp::AbstractPhyloLikelihood	inline
AbstractPhyloLikelihood(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
AbstractPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, bool inCollection=true, const std::string &prefix="")	bpp::AbstractPhyloLikelihoodSet
AbstractPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true, const std::string &prefix="")	bpp::AbstractPhyloLikelihoodSet
AbstractPhyloLikelihoodSet(const AbstractPhyloLikelihoodSet &sd)	bpp::AbstractPhyloLikelihoodSet	inlineprotected
accessVariableNode(const Parameter &param)	bpp::AbstractPhyloLikelihood	inlineprotectedstatic
accessVariableNode(const std::string &name) const	bpp::AbstractPhyloLikelihood	inlineprotected
addParameter_(Parameter *parameter)	bpp::AbstractParametrizable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
addPhyloLikelihood(size_t nPhyl, const std::string &suff="") override	bpp::AbstractPhyloLikelihoodSet	virtual
clone() const	bpp::PhyloLikelihoodFormula	inlineprotectedvirtual
compTree_	bpp::PhyloLikelihoodFormula	private
bpp::context() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::context()=0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::AbstractPhyloLikelihood::context() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::AbstractPhyloLikelihood::context() override	bpp::AbstractPhyloLikelihood	inlinevirtual
context_	bpp::AbstractPhyloLikelihood	protected
d2f(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
deleteParameter_(size_t index)	bpp::AbstractParametrizable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParametrizable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParametrizable	protectedvirtual
df(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
bpp::enableFirstOrderDerivatives(bool yn)=0	bpp::SecondOrderDerivable	pure virtual
bpp::enableFirstOrderDerivatives() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives(bool yn) override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::enableSecondOrderDerivatives(bool yn)=0	bpp::SecondOrderDerivable	pure virtual
bpp::enableSecondOrderDerivatives() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives(bool yn) override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
f(const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
fireParameterChanged(const ParameterList &params) override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
FirstOrderDerivable()	bpp::FirstOrderDerivable
firstOrderDerivativeNode(const std::string &variable) const	bpp::AbstractPhyloLikelihood	inline
firstOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
FunctionInterface()	bpp::FunctionInterface
getBranchLengthParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
getDerivableParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
bpp::getFirstOrderDerivative(const std::string &variable) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(const std::string &variable) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getLikelihoodCalculation() const	bpp::PhyloLikelihoodFormula	inlinevirtual
bpp::getLikelihoodNode() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::AbstractPhyloLikelihood::getLikelihoodNode() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getLogLikelihood() const	bpp::PhyloLikelihoodInterface	inline
bpp::getNamespace() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::getNamespace() const override	bpp::AbstractParametrizable	virtual
getNonDerivableParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
bpp::getNumberOfParameters() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::getNumberOfParameters() const override	bpp::AbstractParametrizable	virtual
getNumbersOfPhyloLikelihoods() const override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
getParameter(const std::string &name) const	bpp::AbstractParametrizable
getParameter(size_t i) const	bpp::AbstractParametrizable	protected
getParameter(size_t i)	bpp::AbstractParametrizable	protected
getParameter_(const std::string &name)	bpp::AbstractParametrizable	protected
getParameter_(size_t index)	bpp::AbstractParametrizable	protected
getParameter_(size_t index) const	bpp::AbstractParametrizable	protected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParametrizable	virtual
bpp::getParameters() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::getParameters() const override	bpp::AbstractParametrizable	virtual
bpp::getParameters_()=0	bpp::SecondOrderDerivable	protectedpure virtual
bpp::AbstractParametrizable::getParameters_() override	bpp::AbstractParametrizable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const override	bpp::AbstractParametrizable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParametrizable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParametrizable	protected
getPhyloContainer() override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
getPhyloContainer() const override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
getPhyloLikelihood(size_t nPhyl) const override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
getPhyloLikelihood(size_t nPhyl) override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
getRateDistributionParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
getRootFrequenciesParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
bpp::getSecondOrderDerivative(const std::string &variable) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getSubstitutionModelParameters() const override	bpp::AbstractPhyloLikelihoodSet	virtual
bpp::getValue() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::getValue() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::hasParameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) const override	bpp::AbstractParametrizable	virtual
hasPhyloLikelihood(size_t nPhyl) override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
isInitialized() const override	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
likCal_	bpp::PhyloLikelihoodFormula	private
likelihoodCalculation() const	bpp::PhyloLikelihoodFormula	inlinevirtual
makeLikelihoods()	bpp::PhyloLikelihoodFormula	inlineprivate
makeLikelihoodsFromOperator(std::shared_ptr< Operator > op)	bpp::PhyloLikelihoodFormula	private
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
minusLogLik_	bpp::AbstractPhyloLikelihood	mutableprotected
nPhylo_	bpp::AbstractPhyloLikelihoodSet	protected
operator=(const PhyloLikelihoodFormula &sd)	bpp::PhyloLikelihoodFormula	inlineprotected
bpp::AbstractPhyloLikelihoodSet::operator=(const AbstractPhyloLikelihoodSet &sd)	bpp::AbstractPhyloLikelihoodSet	inlineprotected
bpp::AbstractPhyloLikelihood::operator=(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
output() const	bpp::PhyloLikelihoodFormula
bpp::parameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::parameter(const std::string &name) const override	bpp::AbstractParametrizable	virtual
parameters_	bpp::AbstractParametrizable	private
Parametrizable()	bpp::Parametrizable
PhyloLikelihoodFormula(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::string &formula, bool inCollection=true)	bpp::PhyloLikelihoodFormula
PhyloLikelihoodFormula(const PhyloLikelihoodFormula &sd)	bpp::PhyloLikelihoodFormula	inlineprotected
PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inline
pPhyloCont_	bpp::AbstractPhyloLikelihoodSet	protected
prefix_	bpp::AbstractParametrizable	private
readFormula(const std::string &formula, bool inCollection=true)	bpp::PhyloLikelihoodFormula
bpp::removeConstraint(const std::string &name)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::removeConstraint(const std::string &name) override	bpp::AbstractParametrizable	virtual
resetParameters_()	bpp::AbstractParametrizable	protected
SecondOrderDerivable()	bpp::SecondOrderDerivable
secondOrderDerivativeNode(const std::string &variable1, const std::string &variable2) const	bpp::AbstractPhyloLikelihood	inline
secondOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParametrizable	virtual
bpp::setNamespace(const std::string &prefix)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::setNamespace(const std::string &prefix) override	bpp::AbstractParametrizable	virtual
bpp::setParameters(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractPhyloLikelihood::setParameters(const ParameterList &parameters) override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParametrizable	virtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParametrizable	protectedvirtual
shareParameters(const ParameterList &variableNodes)	bpp::AbstractPhyloLikelihood	inline
shareParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
vLikCal_	bpp::AbstractPhyloLikelihoodSet	mutableprotected
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractPhyloLikelihood()	bpp::AbstractPhyloLikelihood	inlinevirtual
~AbstractPhyloLikelihoodSet()	bpp::AbstractPhyloLikelihoodSet	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	virtual
~FunctionInterface()	bpp::FunctionInterface	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~PhyloLikelihoodFormula()	bpp::PhyloLikelihoodFormula	inlinevirtual
~PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inlinevirtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	virtual