bpp::HmmLikelihood Member List

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

Clonable()	bpp::Clonable	inline
clone() const =0	bpp::HmmLikelihood	pure virtual
computeD2Likelihood_() const =0	bpp::HmmLikelihood	protectedpure virtual
computeDLikelihood_() const =0	bpp::HmmLikelihood	protectedpure virtual
d2f(const std::string &variable, const ParameterList &parameters)	bpp::DerivableSecondOrder	inlinevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)	bpp::DerivableSecondOrder	inlinevirtual
DerivableFirstOrder()	bpp::DerivableFirstOrder	inline
DerivableSecondOrder()	bpp::DerivableSecondOrder	inline
df(const std::string &variable, const ParameterList &parameters)	bpp::DerivableFirstOrder	inlinevirtual
enableFirstOrderDerivatives(bool yn)=0	bpp::DerivableFirstOrder	pure virtual
enableFirstOrderDerivatives() const =0	bpp::DerivableFirstOrder	pure virtual
enableSecondOrderDerivatives(bool yn)=0	bpp::DerivableSecondOrder	pure virtual
enableSecondOrderDerivatives() const =0	bpp::DerivableSecondOrder	pure virtual
f(const ParameterList &parameters)	bpp::Function	inlinevirtual
Function()	bpp::Function	inline
getBreakPoints() const =0	bpp::HmmLikelihood	pure virtual
getD2LogLikelihood() const =0	bpp::HmmLikelihood	pure virtual
getDLogLikelihood() const =0	bpp::HmmLikelihood	pure virtual
getFirstOrderDerivative(const std::string &variable) const =0	bpp::DerivableFirstOrder	pure virtual
getHiddenStatesPosteriorProbabilities(std::vector< std::vector< double > > &probs, bool append) const =0	bpp::HmmLikelihood	pure virtual
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getHmmEmissionProbabilities() const =0	bpp::HmmLikelihood	pure virtual
getHmmEmissionProbabilities()=0	bpp::HmmLikelihood	pure virtual
getHmmStateAlphabet() const =0	bpp::HmmLikelihood	pure virtual
getHmmStateAlphabet()=0	bpp::HmmLikelihood	pure virtual
getHmmTransitionMatrix() const =0	bpp::HmmLikelihood	pure virtual
getHmmTransitionMatrix()=0	bpp::HmmLikelihood	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getLikelihoodForEachSite() const =0	bpp::HmmLikelihood	pure virtual
getLogLikelihood() const =0	bpp::HmmLikelihood	pure virtual
getNamespace() const =0	bpp::Parametrizable	pure virtual
getNumberOfParameters() const =0	bpp::Parametrizable	pure virtual
getParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameters() const =0	bpp::Parametrizable	pure virtual
getParameterValue(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getSecondOrderDerivative(const std::string &variable) const =0	bpp::DerivableSecondOrder	pure virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const =0	bpp::DerivableSecondOrder	pure virtual
getValue() const =0	bpp::Function	pure virtual
hasParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
Parametrizable()	bpp::Parametrizable	inline
setAllParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setBreakPoints(const std::vector< size_t > &breakPoints)=0	bpp::HmmLikelihood	pure virtual
setNamespace(const std::string &prefix)=0	bpp::Parametrizable	pure virtual
setParameters(const ParameterList &parameters)=0	bpp::Function	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::Parametrizable	pure virtual
~Clonable()	bpp::Clonable	inlinevirtual
~DerivableFirstOrder()	bpp::DerivableFirstOrder	inlinevirtual
~DerivableSecondOrder()	bpp::DerivableSecondOrder	inlinevirtual
~Function()	bpp::Function	inlinevirtual
~Parametrizable()	bpp::Parametrizable	inlinevirtual