bpp-phyl3  3.0.0
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinline
AbstractTreeLikelihood(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
addParameter_(Parameter *parameter)bpp::AbstractParametrizableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
bpp::clone() const override=0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractParametrizable::clone() const=0bpp::AbstractParametrizablepure virtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
d2f(const std::string &variable, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
data() constbpp::AbstractTreeLikelihoodinlinevirtual
data_bpp::AbstractTreeLikelihoodprotected
deleteParameter_(size_t index)bpp::AbstractParametrizableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParametrizableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParametrizableprotectedvirtual
df(const std::string &variable, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
DiscreteRatesAcrossSitesTreeLikelihoodInterface()bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfaceinline
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
enableDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableFirstOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableFirstOrderDerivatives() constbpp::AbstractTreeLikelihoodinlinevirtual
enableSecondOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableSecondOrderDerivatives() constbpp::AbstractTreeLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
fireParameterChanged(const ParameterList &parameters)bpp::AbstractParametrizablevirtual
FirstOrderDerivable()bpp::FirstOrderDerivable
FunctionInterface()bpp::FunctionInterface
getAlphabet() constbpp::AbstractTreeLikelihoodinlinevirtual
getAlphabetStateAsChar(size_t i) const =0bpp::TreeLikelihoodInterfacepure virtual
getAlphabetStateAsInt(size_t i) const =0bpp::TreeLikelihoodInterfacepure virtual
getAlphabetStates() const =0bpp::TreeLikelihoodInterfacepure virtual
getBranchLengthsParameters() const =0bpp::TreeLikelihoodInterfacepure virtual
getDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getFirstOrderDerivative(const std::string &variable) const=0bpp::SecondOrderDerivablepure virtual
getLikelihood() const =0bpp::TreeLikelihoodInterfacepure virtual
getLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodInterfacepure virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfacepure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfacepure virtual
getLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodPerSite() constbpp::AbstractTreeLikelihoodvirtual
getLikelihoodPerSitePerRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodPerSitePerRateClassPerState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodPerSitePerState() constbpp::AbstractTreeLikelihoodvirtual
getLogLikelihood() const =0bpp::TreeLikelihoodInterfacepure virtual
getLogLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodInterfacepure virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfacepure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfacepure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodPerSite() constbpp::AbstractTreeLikelihoodvirtual
getLogLikelihoodPerSitePerRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodPerSitePerRateClassPerState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodPerSitePerState() constbpp::AbstractTreeLikelihoodvirtual
getModelForSite(int nodeId, size_t siteIndex) const =0bpp::TreeLikelihoodInterfacepure virtual
getModelForSite(int nodeId, size_t siteIndex)=0bpp::TreeLikelihoodInterfacepure virtual
bpp::getNamespace() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getNamespace() const overridebpp::AbstractParametrizablevirtual
getNewBranchModelIterator(int nodeId) const =0bpp::TreeLikelihoodInterfacepure virtual
getNewSiteModelIterator(size_t siteIndex) const =0bpp::TreeLikelihoodInterfacepure virtual
getNonDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getNumberOfClasses() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
bpp::getNumberOfParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getNumberOfParameters() const overridebpp::AbstractParametrizablevirtual
getNumberOfSites() constbpp::AbstractTreeLikelihoodinlinevirtual
getNumberOfStates() const =0bpp::TreeLikelihoodInterfacepure virtual
getParameter(const std::string &name) constbpp::AbstractParametrizable
getParameter(size_t i) constbpp::AbstractParametrizableprotected
getParameter(size_t i)bpp::AbstractParametrizableprotected
getParameter_(const std::string &name)bpp::AbstractParametrizableprotected
getParameter_(size_t index)bpp::AbstractParametrizableprotected
getParameter_(size_t index) constbpp::AbstractParametrizableprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParametrizablevirtual
bpp::getParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getParameters_()=0bpp::SecondOrderDerivableprotectedpure virtual
bpp::AbstractParametrizable::getParameters_() overridebpp::AbstractParametrizableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const overridebpp::AbstractParametrizablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParametrizableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParametrizableprotected
getPosteriorProbabilitiesPerRate() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getPosteriorRatePerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateClassWithMaxPostProbPerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistributionParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateWithMaxPostProbPerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) const =0bpp::TreeLikelihoodInterfacepure virtual
getSecondOrderDerivative(const std::string &variable) const=0bpp::SecondOrderDerivablepure virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const=0bpp::SecondOrderDerivablepure virtual
getSiteIndex(size_t site) const =0bpp::TreeLikelihoodInterfacepure virtual
getSubstitutionModelParameters() const =0bpp::TreeLikelihoodInterfacepure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfacepure virtual
getValue() const=0bpp::SecondOrderDerivablepure virtual
hasLikelihoodData() constbpp::AbstractTreeLikelihoodinlinevirtual
bpp::hasParameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
initialize()bpp::AbstractTreeLikelihoodinlinevirtual
initialized_bpp::AbstractTreeLikelihoodprotected
isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
likelihoodData()=0bpp::TreeLikelihoodInterfacepure virtual
likelihoodData() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
bpp::parameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::parameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
parameters_bpp::AbstractParametrizableprivate
Parametrizable()bpp::Parametrizable
prefix_bpp::AbstractParametrizableprivate
rateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
rateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
rateDistribution_bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodprotected
bpp::removeConstraint(const std::string &name)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::removeConstraint(const std::string &name) overridebpp::AbstractParametrizablevirtual
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
resetParameters_()bpp::AbstractParametrizableprotected
SecondOrderDerivable()bpp::SecondOrderDerivable
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParametrizablevirtual
setData(const AlignmentDataInterface &sites)=0bpp::TreeLikelihoodInterfacepure virtual
bpp::setNamespace(const std::string &prefix)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setNamespace(const std::string &prefix) overridebpp::AbstractParametrizablevirtual
setParameters(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParametrizablevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParametrizableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
tree() constbpp::AbstractTreeLikelihoodinlinevirtual
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinline
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~DiscreteRatesAcrossSitesTreeLikelihoodInterface()bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfaceinlinevirtual
~FirstOrderDerivable()bpp::FirstOrderDerivablevirtual
~FunctionInterface()bpp::FunctionInterfacevirtual
~Parametrizable()bpp::Parametrizablevirtual
~SecondOrderDerivable()bpp::SecondOrderDerivablevirtual
~TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinlinevirtual