bpp::RescaledHmmLikelihood Member List

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

AbstractHmmLikelihood()	bpp::AbstractHmmLikelihood
AbstractHmmLikelihood(const AbstractHmmLikelihood &adhlik)	bpp::AbstractHmmLikelihood
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable	inline
addParameter_(Parameter *parameter)	bpp::AbstractParametrizable	inlineprotectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	inlineprotectedvirtual
backLikelihood_	bpp::RescaledHmmLikelihood	mutableprivate
backLikelihoodUpToDate_	bpp::RescaledHmmLikelihood	mutableprivate
breakPoints_	bpp::RescaledHmmLikelihood	private
clone() const override	bpp::RescaledHmmLikelihood	inlinevirtual
computeBackward_() const	bpp::RescaledHmmLikelihood	protected
computeD2Forward_() const	bpp::RescaledHmmLikelihood	protected
computeD2Likelihood_() const override	bpp::RescaledHmmLikelihood	inlineprotectedvirtual
computeDForward_() const	bpp::RescaledHmmLikelihood	protected
computeDLikelihood_() const override	bpp::RescaledHmmLikelihood	inlineprotectedvirtual
computeForward_()	bpp::RescaledHmmLikelihood	protected
d2f(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	inlinevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)	bpp::SecondOrderDerivable	inlinevirtual
d2Likelihood_	bpp::RescaledHmmLikelihood	mutableprivate
d2LogLik_	bpp::AbstractHmmLikelihood	mutableprotected
d2Scales_	bpp::RescaledHmmLikelihood	mutableprivate
d2Variable_	bpp::AbstractHmmLikelihood	mutableprotected
deleteParameter_(size_t index)	bpp::AbstractParametrizable	inlineprotectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParametrizable	inlineprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParametrizable	inlineprotectedvirtual
df(const std::string &variable, const ParameterList &parameters)	bpp::FirstOrderDerivable	inlinevirtual
dLikelihood_	bpp::RescaledHmmLikelihood	mutableprivate
dLogLik_	bpp::AbstractHmmLikelihood	mutableprotected
dScales_	bpp::RescaledHmmLikelihood	mutableprivate
dVariable_	bpp::AbstractHmmLikelihood	mutableprotected
emissionProbabilities_	bpp::RescaledHmmLikelihood	private
enableFirstOrderDerivatives(bool yn)	bpp::AbstractHmmLikelihood	inlinevirtual
enableFirstOrderDerivatives() const	bpp::AbstractHmmLikelihood	inlinevirtual
enableSecondOrderDerivatives(bool yn)	bpp::AbstractHmmLikelihood	inlinevirtual
enableSecondOrderDerivatives() const	bpp::AbstractHmmLikelihood	inlinevirtual
f(const ParameterList &parameters)	bpp::FunctionInterface	inlinevirtual
fireParameterChanged(const ParameterList &pl) override	bpp::RescaledHmmLikelihood	virtual
FirstOrderDerivable()	bpp::FirstOrderDerivable	inline
FunctionInterface()	bpp::FunctionInterface	inline
getBreakPoints() const override	bpp::RescaledHmmLikelihood	inlinevirtual
getD2LogLikelihood() const	bpp::AbstractHmmLikelihood	inlinevirtual
getD2LogLikelihoodForASite(size_t site) const override	bpp::RescaledHmmLikelihood	virtual
getDLogLikelihood() const	bpp::AbstractHmmLikelihood	inlinevirtual
getDLogLikelihoodForASite(size_t site) const override	bpp::RescaledHmmLikelihood	virtual
getFirstOrderDerivative(const std::string &variable) const	bpp::AbstractHmmLikelihood	virtual
getHiddenStatesPosteriorProbabilities(std::vector< std::vector< double >> &probs, bool append=false) const override	bpp::RescaledHmmLikelihood	virtual
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const override	bpp::RescaledHmmLikelihood	virtual
getHmmEmissionProbabilities() const override	bpp::RescaledHmmLikelihood	inlinevirtual
getHmmEmissionProbabilities() override	bpp::RescaledHmmLikelihood	inlinevirtual
getHmmStateAlphabet() const override	bpp::RescaledHmmLikelihood	inlinevirtual
getHmmStateAlphabet() override	bpp::RescaledHmmLikelihood	inlinevirtual
getHmmTransitionMatrix() const override	bpp::RescaledHmmLikelihood	inlinevirtual
getHmmTransitionMatrix() override	bpp::RescaledHmmLikelihood	inlinevirtual
getLikelihoodForASite(size_t site) const override	bpp::RescaledHmmLikelihood	virtual
getLikelihoodForEachSite() const override	bpp::RescaledHmmLikelihood	virtual
getLogLikelihood() const override	bpp::RescaledHmmLikelihood	inlinevirtual
bpp::getNamespace() const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::getNamespace() const override	bpp::AbstractParametrizable	inlinevirtual
bpp::getNumberOfParameters() const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::getNumberOfParameters() const override	bpp::AbstractParametrizable	inlinevirtual
getParameter(const std::string &name) const	bpp::AbstractParametrizable	inline
getParameter(size_t i) const	bpp::AbstractParametrizable	inlineprotected
getParameter(size_t i)	bpp::AbstractParametrizable	inlineprotected
getParameter_(const std::string &name)	bpp::AbstractParametrizable	inlineprotected
getParameter_(size_t index)	bpp::AbstractParametrizable	inlineprotected
getParameter_(size_t index) const	bpp::AbstractParametrizable	inlineprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParametrizable	virtual
bpp::getParameters() const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::getParameters() const override	bpp::AbstractParametrizable	inlinevirtual
bpp::getParameters_()=0	bpp::Parametrizable	protectedpure virtual
bpp::AbstractParametrizable::getParameters_() override	bpp::AbstractParametrizable	inlineprotectedvirtual
bpp::getParameterValue(const std::string &name) const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const override	bpp::AbstractParametrizable	inlinevirtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParametrizable	inlineprotected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParametrizable	inlineprotected
getSecondOrderDerivative(const std::string &variable) const	bpp::AbstractHmmLikelihood	virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const	bpp::AbstractHmmLikelihood	inlinevirtual
getValue() const override	bpp::RescaledHmmLikelihood	inlinevirtual
bpp::hasParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) const override	bpp::AbstractParametrizable	inlinevirtual
hiddenAlphabet_	bpp::RescaledHmmLikelihood	private
hmmEmissionProbabilities() const override	bpp::RescaledHmmLikelihood	inlinevirtual
hmmEmissionProbabilities() override	bpp::RescaledHmmLikelihood	inlinevirtual
hmmStateAlphabet() const override	bpp::RescaledHmmLikelihood	inlinevirtual
hmmStateAlphabet() override	bpp::RescaledHmmLikelihood	inlinevirtual
hmmTransitionMatrix() const override	bpp::RescaledHmmLikelihood	inlinevirtual
hmmTransitionMatrix() override	bpp::RescaledHmmLikelihood	inlinevirtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	inlineprotectedvirtual
likelihood_	bpp::RescaledHmmLikelihood	private
logLik_	bpp::RescaledHmmLikelihood	private
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	inlinevirtual
nbSites_	bpp::RescaledHmmLikelihood	private
nbStates_	bpp::RescaledHmmLikelihood	private
operator=(const RescaledHmmLikelihood &lik)	bpp::RescaledHmmLikelihood	inline
bpp::AbstractHmmLikelihood::operator=(const AbstractHmmLikelihood &adhlik)	bpp::AbstractHmmLikelihood
bpp::parameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::parameter(const std::string &name) const override	bpp::AbstractParametrizable	inlinevirtual
Parametrizable()	bpp::Parametrizable	inline
bpp::removeConstraint(const std::string &name)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::removeConstraint(const std::string &name) override	bpp::AbstractParametrizable	inlinevirtual
RescaledHmmLikelihood(std::shared_ptr< HmmStateAlphabet > hiddenAlphabet, std::shared_ptr< HmmTransitionMatrix > transitionMatrix, std::shared_ptr< HmmEmissionProbabilities > emissionProbabilities, const std::string &prefix)	bpp::RescaledHmmLikelihood
RescaledHmmLikelihood(const RescaledHmmLikelihood &lik)	bpp::RescaledHmmLikelihood	inline
resetParameters_()	bpp::AbstractParametrizable	inlineprotected
scales_	bpp::RescaledHmmLikelihood	private
SecondOrderDerivable()	bpp::SecondOrderDerivable	inline
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	inlinevirtual
setBreakPoints(const std::vector< size_t > &breakPoints) override	bpp::RescaledHmmLikelihood	inlinevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParametrizable	inlinevirtual
setNamespace(const std::string &nameSpace) override	bpp::RescaledHmmLikelihood	virtual
setParameters(const ParameterList &pl) override	bpp::RescaledHmmLikelihood	inlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	inlinevirtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::Parametrizable	pure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParametrizable	inlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParametrizable	inlineprotectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	inlineprotectedvirtual
transitionMatrix_	bpp::RescaledHmmLikelihood	private
~AbstractParametrizable()	bpp::AbstractParametrizable	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	inlinevirtual
~FunctionInterface()	bpp::FunctionInterface	inlinevirtual
~Parametrizable()	bpp::Parametrizable	inlinevirtual
~RescaledHmmLikelihood()	bpp::RescaledHmmLikelihood	inlinevirtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	inlinevirtual