bpp-phyl  2.4.0
bpp::DiscreteRatesAcrossSitesTreeLikelihood Member List

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

clone() const =0bpp::TreeLikelihoodpure virtual
d2f(const std::string &variable, const ParameterList &parameters)bpp::DerivableSecondOrdervirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)bpp::DerivableSecondOrdervirtual
DerivableFirstOrder()bpp::DerivableFirstOrder
DerivableSecondOrder()bpp::DerivableSecondOrder
df(const std::string &variable, const ParameterList &parameters)bpp::DerivableSecondOrdervirtual
DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinline
enableDerivatives(bool yn)=0bpp::TreeLikelihoodpure virtual
enableFirstOrderDerivatives(bool yn)=0bpp::DerivableSecondOrderpure virtual
enableFirstOrderDerivatives() const =0bpp::DerivableSecondOrderpure virtual
enableSecondOrderDerivatives(bool yn)=0bpp::DerivableSecondOrderpure virtual
enableSecondOrderDerivatives() const =0bpp::DerivableSecondOrderpure virtual
f(const ParameterList &parameters)bpp::DerivableSecondOrdervirtual
Function()bpp::Function
getAlphabet() const =0bpp::TreeLikelihoodpure virtual
getAlphabetStateAsChar(size_t i) const =0bpp::TreeLikelihoodpure virtual
getAlphabetStateAsInt(size_t i) const =0bpp::TreeLikelihoodpure virtual
getAlphabetStates() const =0bpp::TreeLikelihoodpure virtual
getBranchLengthsParameters() const =0bpp::TreeLikelihoodpure virtual
getData() const =0bpp::TreeLikelihoodpure virtual
getDerivableParameters() const =0bpp::TreeLikelihoodpure virtual
getFirstOrderDerivative(const std::string &variable) const =0bpp::DerivableSecondOrderpure virtual
getLikelihood() const =0bpp::TreeLikelihoodpure virtual
getLikelihoodData()=0bpp::TreeLikelihoodpure virtual
getLikelihoodData() const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLikelihoodForASiteForAState(size_t site, int state) const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForEachSite() const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForEachSiteForEachRateClass() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLikelihoodForEachSiteForEachRateClassForEachState() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLikelihoodForEachSiteForEachState() const =0bpp::TreeLikelihoodpure virtual
getLogLikelihood() const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForEachSite() const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForEachSiteForEachRateClass() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLogLikelihoodForEachSiteForEachState() const =0bpp::TreeLikelihoodpure virtual
getModelForSite(int nodeId, size_t siteIndex) const =0bpp::TreeLikelihoodpure virtual
getModelForSite(int nodeId, size_t siteIndex)=0bpp::TreeLikelihoodpure virtual
getNamespace() const =0bpp::DerivableSecondOrderpure virtual
getNewBranchModelIterator(int nodeId) const =0bpp::TreeLikelihoodpure virtual
getNewSiteModelIterator(size_t siteIndex) const =0bpp::TreeLikelihoodpure virtual
getNonDerivableParameters() const =0bpp::TreeLikelihoodpure virtual
getNumberOfClasses() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getNumberOfParameters() const =0bpp::DerivableSecondOrderpure virtual
getNumberOfSites() const =0bpp::TreeLikelihoodpure virtual
getNumberOfStates() const =0bpp::TreeLikelihoodpure virtual
getParameter(const std::string &name) const =0bpp::DerivableSecondOrderpure virtual
getParameterNameWithoutNamespace(const std::string &name) const =0bpp::DerivableSecondOrderpure virtual
getParameters() const =0bpp::DerivableSecondOrderpure virtual
getParameterValue(const std::string &name) const =0bpp::DerivableSecondOrderpure virtual
getPosteriorProbabilitiesOfEachRate() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getPosteriorRateOfEachSite() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRateClassWithMaxPostProbOfEachSite() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRateDistribution() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRateDistribution()=0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRateDistributionParameters() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRateWithMaxPostProbOfEachSite() const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getRootFrequencies(size_t siteIndex) const =0bpp::TreeLikelihoodpure virtual
getSecondOrderDerivative(const std::string &variable) const =0bpp::DerivableSecondOrderpure virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const =0bpp::DerivableSecondOrderpure virtual
getSiteIndex(size_t site) const =0bpp::TreeLikelihoodpure virtual
getSubstitutionModelParameters() const =0bpp::TreeLikelihoodpure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const =0bpp::TreeLikelihoodpure virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getTree() const =0bpp::TreeLikelihoodpure virtual
getValue() const =0bpp::DerivableSecondOrderpure virtual
hasParameter(const std::string &name) const =0bpp::DerivableSecondOrderpure virtual
initialize()=0bpp::TreeLikelihoodpure virtual
isInitialized() const =0bpp::TreeLikelihoodpure virtual
matchParametersValues(const ParameterList &parameters)=0bpp::DerivableSecondOrderpure virtual
Parametrizable()bpp::Parametrizable
setAllParametersValues(const ParameterList &parameters)=0bpp::DerivableSecondOrderpure virtual
setData(const SiteContainer &sites)=0bpp::TreeLikelihoodpure virtual
setNamespace(const std::string &prefix)=0bpp::DerivableSecondOrderpure virtual
setParameters(const ParameterList &parameters)=0bpp::DerivableSecondOrderpure virtual
setParametersValues(const ParameterList &parameters)=0bpp::DerivableSecondOrderpure virtual
setParameterValue(const std::string &name, double value)=0bpp::DerivableSecondOrderpure virtual
TreeLikelihood()bpp::TreeLikelihoodinline
~Clonable()=defaultbpp::Clonablevirtual
~DerivableFirstOrder()bpp::DerivableFirstOrdervirtual
~DerivableSecondOrder()bpp::DerivableSecondOrdervirtual
~DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~Function()bpp::Functionvirtual
~Parametrizable()bpp::Parametrizablevirtual
~TreeLikelihood()bpp::TreeLikelihoodinlinevirtual