bpp-core  2.2.0
bpp::LowMemoryRescaledHmmLikelihood Member List

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

AbstractHmmLikelihood()bpp::AbstractHmmLikelihood
AbstractHmmLikelihood(const AbstractHmmLikelihood &adhlik)bpp::AbstractHmmLikelihood
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizableinline
addParameter_(Parameter *parameter)bpp::AbstractParametrizableinlineprotected
addParameters_(const ParameterList &parameters)bpp::AbstractParametrizableinlineprotected
breakPoints_bpp::LowMemoryRescaledHmmLikelihoodprivate
Clonable()bpp::Clonableinline
clone() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
computeD2Likelihood_() constbpp::LowMemoryRescaledHmmLikelihoodinlineprotectedvirtual
computeDLikelihood_() constbpp::LowMemoryRescaledHmmLikelihoodinlineprotectedvirtual
computeForward_()bpp::LowMemoryRescaledHmmLikelihoodprotected
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
deleteParameter_(size_t index)bpp::AbstractParametrizableinlineprotected
deleteParameter_(std::string &name)bpp::AbstractParametrizableinlineprotected
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParametrizableinlineprotected
DerivableFirstOrder()bpp::DerivableFirstOrderinline
DerivableSecondOrder()bpp::DerivableSecondOrderinline
df(const std::string &variable, const ParameterList &parameters)bpp::DerivableFirstOrderinlinevirtual
dLogLik_bpp::AbstractHmmLikelihoodmutableprotected
dVariable_bpp::AbstractHmmLikelihoodmutableprotected
emissionProbabilities_bpp::LowMemoryRescaledHmmLikelihoodprivate
enableFirstOrderDerivatives(bool yn)bpp::AbstractHmmLikelihoodinlinevirtual
enableFirstOrderDerivatives() constbpp::AbstractHmmLikelihoodinlinevirtual
enableSecondOrderDerivatives(bool yn)bpp::AbstractHmmLikelihoodinlinevirtual
enableSecondOrderDerivatives() constbpp::AbstractHmmLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::Functioninlinevirtual
fireParameterChanged(const ParameterList &pl)bpp::LowMemoryRescaledHmmLikelihoodvirtual
Function()bpp::Functioninline
getBreakPoints() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getD2LogLikelihood() constbpp::AbstractHmmLikelihoodinlinevirtual
getDLogLikelihood() constbpp::AbstractHmmLikelihoodinlinevirtual
getFirstOrderDerivative(const std::string &variable) constbpp::AbstractHmmLikelihoodvirtual
getHiddenStatesPosteriorProbabilities(std::vector< std::vector< double > > &probs, bool append=false) constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmEmissionProbabilities() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmEmissionProbabilities()bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmStateAlphabet() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmStateAlphabet()bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmTransitionMatrix() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getHmmTransitionMatrix()bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getLikelihoodForASite(size_t site) constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getLikelihoodForEachSite() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
getLogLikelihood() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
bpp::getNamespace() const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getNamespace() constbpp::AbstractParametrizableinlinevirtual
bpp::getNumberOfParameters() const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getNumberOfParameters() constbpp::AbstractParametrizableinlinevirtual
bpp::getParameter(const std::string &name) const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getParameter(const std::string &name) constbpp::AbstractParametrizableinlinevirtual
getParameter_(const std::string &name)bpp::AbstractParametrizableinlineprotected
getParameter_(size_t index)bpp::AbstractParametrizableinlineprotected
getParameter_(size_t index) constbpp::AbstractParametrizableinlineprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) constbpp::AbstractParametrizablevirtual
bpp::getParameters() const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getParameters() constbpp::AbstractParametrizableinlinevirtual
getParameters_()bpp::AbstractParametrizableinlineprotected
bpp::getParameterValue(const std::string &name) const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) constbpp::AbstractParametrizableinlinevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParametrizableinlineprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParametrizableinlineprotected
getSecondOrderDerivative(const std::string &variable) constbpp::AbstractHmmLikelihoodvirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) constbpp::AbstractHmmLikelihoodinlinevirtual
getValue() constbpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
bpp::hasParameter(const std::string &name) const =0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) constbpp::AbstractParametrizableinlinevirtual
hiddenAlphabet_bpp::LowMemoryRescaledHmmLikelihoodprivate
likelihood1_bpp::LowMemoryRescaledHmmLikelihoodprivate
likelihood2_bpp::LowMemoryRescaledHmmLikelihoodprivate
logLik_bpp::LowMemoryRescaledHmmLikelihoodprivate
LowMemoryRescaledHmmLikelihood(HmmStateAlphabet *hiddenAlphabet, HmmTransitionMatrix *transitionMatrix, HmmEmissionProbabilities *emissionProbabilities, const std::string &prefix, size_t maxSize=1000000)bpp::LowMemoryRescaledHmmLikelihood
LowMemoryRescaledHmmLikelihood(const LowMemoryRescaledHmmLikelihood &lik)bpp::LowMemoryRescaledHmmLikelihoodinline
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters)bpp::AbstractParametrizableinlinevirtual
maxSize_bpp::LowMemoryRescaledHmmLikelihoodprivate
nbSites_bpp::LowMemoryRescaledHmmLikelihoodprivate
nbStates_bpp::LowMemoryRescaledHmmLikelihoodprivate
operator=(const LowMemoryRescaledHmmLikelihood &lik)bpp::LowMemoryRescaledHmmLikelihoodinline
bpp::AbstractHmmLikelihood::operator=(const AbstractHmmLikelihood &adhlik)bpp::AbstractHmmLikelihood
Parametrizable()bpp::Parametrizableinline
resetParameters_()bpp::AbstractParametrizableinlineprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters)bpp::AbstractParametrizableinlinevirtual
setBreakPoints(const std::vector< size_t > &breakPoints)bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
bpp::setNamespace(const std::string &prefix)=0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::setNamespace(const std::string &prefix)bpp::AbstractParametrizablevirtual
setParameters(const ParameterList &pl)bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters)bpp::AbstractParametrizableinlinevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::Parametrizablepure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value)bpp::AbstractParametrizableinlinevirtual
transitionMatrix_bpp::LowMemoryRescaledHmmLikelihoodprivate
~AbstractParametrizable()bpp::AbstractParametrizableinlinevirtual
~Clonable()bpp::Clonableinlinevirtual
~DerivableFirstOrder()bpp::DerivableFirstOrderinlinevirtual
~DerivableSecondOrder()bpp::DerivableSecondOrderinlinevirtual
~Function()bpp::Functioninlinevirtual
~LowMemoryRescaledHmmLikelihood()bpp::LowMemoryRescaledHmmLikelihoodinlinevirtual
~Parametrizable()bpp::Parametrizableinlinevirtual