bpp-core3  3.0.0
bpp::AbstractHmmLikelihood Member List

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

AbstractHmmLikelihood()bpp::AbstractHmmLikelihood
AbstractHmmLikelihood(const AbstractHmmLikelihood &adhlik)bpp::AbstractHmmLikelihood
clone() const =0bpp::HmmLikelihoodpure virtual
computeD2Likelihood_() const =0bpp::HmmLikelihoodprotectedpure virtual
computeDLikelihood_() const =0bpp::HmmLikelihoodprotectedpure virtual
d2f(const std::string &variable, const ParameterList &parameters)bpp::DerivableSecondOrderinlinevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)bpp::DerivableSecondOrderinlinevirtual
d2LogLik_bpp::AbstractHmmLikelihoodmutableprotected
d2Variable_bpp::AbstractHmmLikelihoodmutableprotected
DerivableFirstOrder()bpp::DerivableFirstOrderinline
DerivableSecondOrder()bpp::DerivableSecondOrderinline
df(const std::string &variable, const ParameterList &parameters)bpp::DerivableFirstOrderinlinevirtual
dLogLik_bpp::AbstractHmmLikelihoodmutableprotected
dVariable_bpp::AbstractHmmLikelihoodmutableprotected
enableFirstOrderDerivatives(bool yn)bpp::AbstractHmmLikelihoodinlinevirtual
enableFirstOrderDerivatives() constbpp::AbstractHmmLikelihoodinlinevirtual
enableSecondOrderDerivatives(bool yn)bpp::AbstractHmmLikelihoodinlinevirtual
enableSecondOrderDerivatives() constbpp::AbstractHmmLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::Functioninlinevirtual
Function()bpp::Functioninline
getBreakPoints() const =0bpp::HmmLikelihoodpure virtual
getD2LogLikelihood() constbpp::AbstractHmmLikelihoodinlinevirtual
getD2LogLikelihoodForASite(size_t site) const =0bpp::HmmLikelihoodpure virtual
getDLogLikelihood() constbpp::AbstractHmmLikelihoodinlinevirtual
getDLogLikelihoodForASite(size_t site) const =0bpp::HmmLikelihoodpure virtual
getFirstOrderDerivative(const std::string &variable) constbpp::AbstractHmmLikelihoodvirtual
getHiddenStatesPosteriorProbabilities(std::vector< std::vector< double > > &probs, bool append) const =0bpp::HmmLikelihoodpure virtual
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const =0bpp::HmmLikelihoodpure virtual
getHmmEmissionProbabilities() const =0bpp::HmmLikelihoodpure virtual
getHmmEmissionProbabilities()=0bpp::HmmLikelihoodpure virtual
getHmmStateAlphabet() const =0bpp::HmmLikelihoodpure virtual
getHmmStateAlphabet()=0bpp::HmmLikelihoodpure virtual
getHmmTransitionMatrix() const =0bpp::HmmLikelihoodpure virtual
getHmmTransitionMatrix()=0bpp::HmmLikelihoodpure virtual
getLikelihoodForASite(size_t site) const =0bpp::HmmLikelihoodpure virtual
getLikelihoodForEachSite() const =0bpp::HmmLikelihoodpure virtual
getLogLikelihood() const =0bpp::HmmLikelihoodpure virtual
getNamespace() const =0bpp::Parametrizablepure virtual
getNumberOfParameters() const =0bpp::Parametrizablepure virtual
getParameter(const std::string &name) const =0bpp::Parametrizablepure virtual
getParameterNameWithoutNamespace(const std::string &name) const =0bpp::Parametrizablepure virtual
getParameters() const =0bpp::Parametrizablepure virtual
getParameters_()=0bpp::Parametrizableprotectedpure virtual
getParameterValue(const std::string &name) const =0bpp::Parametrizablepure virtual
getSecondOrderDerivative(const std::string &variable) constbpp::AbstractHmmLikelihoodvirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) constbpp::AbstractHmmLikelihoodinlinevirtual
getValue() const =0bpp::Functionpure virtual
hasParameter(const std::string &name) const =0bpp::Parametrizablepure virtual
matchParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
operator=(const AbstractHmmLikelihood &adhlik)bpp::AbstractHmmLikelihood
Parametrizable()bpp::Parametrizableinline
setAllParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
setBreakPoints(const std::vector< size_t > &breakPoints)=0bpp::HmmLikelihoodpure virtual
setNamespace(const std::string &prefix)=0bpp::Parametrizablepure virtual
setParameters(const ParameterList &parameters)=0bpp::Functionpure virtual
setParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
setParameterValue(const std::string &name, double value)=0bpp::Parametrizablepure virtual
~Clonable()=defaultbpp::Clonablevirtual
~DerivableFirstOrder()bpp::DerivableFirstOrderinlinevirtual
~DerivableSecondOrder()bpp::DerivableSecondOrderinlinevirtual
~Function()bpp::Functioninlinevirtual
~Parametrizable()bpp::Parametrizableinlinevirtual