bpp::AbstractSequencePhyloLikelihood Member List

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

AbstractAlignedPhyloLikelihood(Context &context, size_t nbSites)	bpp::AbstractAlignedPhyloLikelihood	inline
AbstractAlignedPhyloLikelihood(const AbstractAlignedPhyloLikelihood &aasd)	bpp::AbstractAlignedPhyloLikelihood	inlineprotected
AbstractPhyloLikelihood(Context &context)	bpp::AbstractPhyloLikelihood	inline
AbstractPhyloLikelihood(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
AbstractSequencePhyloLikelihood(Context &context, std::shared_ptr< SequenceEvolution > se, size_t nSE=0, size_t nData=0)	bpp::AbstractSequencePhyloLikelihood	inline
AbstractSequencePhyloLikelihood(const AbstractSequencePhyloLikelihood &aspl)	bpp::AbstractSequencePhyloLikelihood	inline
AbstractSingleDataPhyloLikelihood(Context &context, size_t nbSites, size_t nbStates, size_t nData=0)	bpp::AbstractSingleDataPhyloLikelihood	inline
AbstractSingleDataPhyloLikelihood(const AbstractSingleDataPhyloLikelihood &asdpl)	bpp::AbstractSingleDataPhyloLikelihood	inline
accessVariableNode(const Parameter &param)	bpp::AbstractPhyloLikelihood	inlineprotectedstatic
accessVariableNode(const std::string &name) const	bpp::AbstractPhyloLikelihood	inlineprotected
alignedLikelihoodCalculation() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
AlignedPhyloLikelihoodInterface()	bpp::AlignedPhyloLikelihoodInterface	inline
clone() const override=0	bpp::SequencePhyloLikelihoodInterface	protectedpure virtual
bpp::context() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::context()=0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::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
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::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::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::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives(bool yn) override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
f(const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
FirstOrderDerivable()	bpp::FirstOrderDerivable
firstOrderDerivativeNode(const std::string &variable) const	bpp::AbstractPhyloLikelihood	inline
firstOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
FunctionInterface()	bpp::FunctionInterface
getAlignedLikelihoodCalculation() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getAlphabet() const override	bpp::AbstractSequencePhyloLikelihood	inlinevirtual
getBranchLengthParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getData() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
getDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::getFirstOrderDerivative(const std::string &variable) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(const std::string &variable) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getLikelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::getLikelihoodForASite(size_t site) const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(size_t site) const	bpp::AbstractAlignedPhyloLikelihood	inlinevirtual
bpp::getLikelihoodNode() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getLikelihoodNode() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
bpp::getLikelihoodPerSite() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite() const	bpp::AbstractAlignedPhyloLikelihood	inlinevirtual
getLogLikelihood() const	bpp::PhyloLikelihoodInterface	inline
bpp::getLogLikelihoodForASite(size_t site) const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite(size_t site) const	bpp::AbstractAlignedPhyloLikelihood	inlinevirtual
getNamespace() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::getNData() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::getNData() const	bpp::AbstractSingleDataPhyloLikelihood	inlinevirtual
getNonDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getNumberOfParameters() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::getNumberOfSites() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites() const	bpp::AbstractAlignedPhyloLikelihood	inlinevirtual
bpp::getNumberOfStates() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates() const	bpp::AbstractSingleDataPhyloLikelihood	inlinevirtual
getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
getParameters() const=0	bpp::SecondOrderDerivable	pure virtual
getParameters_()=0	bpp::SecondOrderDerivable	protectedpure virtual
getParameterValue(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
getRateDistributionParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getRootFrequenciesParameters() const =0	bpp::PhyloLikelihoodInterface	pure 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::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::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
getSequenceEvolution() const override	bpp::AbstractSequencePhyloLikelihood	inlinevirtual
getSequenceEvolutionNumber() const override	bpp::AbstractSequencePhyloLikelihood	inlinevirtual
getSubstitutionModelParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::getValue() const=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getValue() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
hasParameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
bpp::isInitialized() const =0	bpp::PhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::isInitialized() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
likelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
minusLogLik_	bpp::AbstractPhyloLikelihood	mutableprotected
nbSites_	bpp::AbstractAlignedPhyloLikelihood	protected
nbStates_	bpp::AbstractSingleDataPhyloLikelihood	protected
nData_	bpp::AbstractSingleDataPhyloLikelihood	protected
nSeqEvol_	bpp::AbstractSequencePhyloLikelihood	protected
operator=(const AbstractSequencePhyloLikelihood &aspl)	bpp::AbstractSequencePhyloLikelihood	inline
bpp::AbstractSingleDataPhyloLikelihood::operator=(const AbstractSingleDataPhyloLikelihood &asdpl)	bpp::AbstractSingleDataPhyloLikelihood	inline
bpp::AbstractAlignedPhyloLikelihood::operator=(const AbstractAlignedPhyloLikelihood &aasd)	bpp::AbstractAlignedPhyloLikelihood	inlineprotected
bpp::AbstractPhyloLikelihood::operator=(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
parameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
Parametrizable()	bpp::Parametrizable
PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inline
removeConstraint(const std::string &name)=0	bpp::SecondOrderDerivable	pure virtual
SecondOrderDerivable()	bpp::SecondOrderDerivable
secondOrderDerivativeNode(const std::string &variable1, const std::string &variable2) const	bpp::AbstractPhyloLikelihood	inline
secondOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
seqEvol_	bpp::AbstractSequencePhyloLikelihood	protected
sequenceEvolution() const override	bpp::AbstractSequencePhyloLikelihood	inlinevirtual
setAllParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::SecondOrderDerivable	pure virtual
bpp::setData(std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0)=0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::setData(std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0)	bpp::AbstractSingleDataPhyloLikelihood	inlinevirtual
setNamespace(const std::string &prefix)=0	bpp::SecondOrderDerivable	pure virtual
setNData(size_t nData)	bpp::AbstractSingleDataPhyloLikelihood	inline
setNumberOfSites(size_t nbSites)	bpp::AbstractAlignedPhyloLikelihood	inlineprotected
bpp::setParameters(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::setParameters(const ParameterList &parameters) override	bpp::AbstractPhyloLikelihood	inlinevirtual
setParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::SecondOrderDerivable	pure virtual
shareParameters(const ParameterList &variableNodes)	bpp::AbstractPhyloLikelihood	inline
SingleDataPhyloLikelihoodInterface()	bpp::SingleDataPhyloLikelihoodInterface	inline
~AbstractAlignedPhyloLikelihood()	bpp::AbstractAlignedPhyloLikelihood	inlinevirtual
~AbstractPhyloLikelihood()	bpp::AbstractPhyloLikelihood	inlinevirtual
~AbstractSingleDataPhyloLikelihood()	bpp::AbstractSingleDataPhyloLikelihood	inlinevirtual
~AlignedPhyloLikelihoodInterface()	bpp::AlignedPhyloLikelihoodInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	virtual
~FunctionInterface()	bpp::FunctionInterface	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inlinevirtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	virtual
~SequencePhyloLikelihoodInterface()	bpp::SequencePhyloLikelihoodInterface	inlineprotectedvirtual
~SingleDataPhyloLikelihoodInterface()	bpp::SingleDataPhyloLikelihoodInterface	inlinevirtual