bpp-phyl3  3.0.0
bpp::DRHomogeneousTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
AbstractHomogeneousTreeLikelihood(const Tree &tree, std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rDist, bool checkRooted=true, bool verbose=true)bpp::AbstractHomogeneousTreeLikelihood
AbstractHomogeneousTreeLikelihood(const AbstractHomogeneousTreeLikelihood &lik)bpp::AbstractHomogeneousTreeLikelihood
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
applyParameters()bpp::AbstractHomogeneousTreeLikelihoodvirtual
brLenConstraint_bpp::AbstractHomogeneousTreeLikelihoodprotected
brLenParameters_bpp::AbstractHomogeneousTreeLikelihoodprotected
clone() const overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
computeAllTransitionProbabilities()bpp::AbstractHomogeneousTreeLikelihoodprotectedvirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeLikelihoodAtNode(int nodeId, VVVdouble &likelihoodArray) const overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
computeLikelihoodAtNode_(const Node *node, VVVdouble &likelihoodArray, const Node *sonNode=0) constbpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeLikelihoodFromArrays(const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)bpp::DRHomogeneousTreeLikelihoodprotectedstatic
computeLikelihoodFromArrays(const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, const VVVdouble *iLikR, const VVVdouble *tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)bpp::DRHomogeneousTreeLikelihoodprotectedstatic
computeRootLikelihood()bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSubtreeLikelihoodPostfix(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeSubtreeLikelihoodPrefix(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeTransitionProbabilitiesForNode(const Node *node)bpp::AbstractHomogeneousTreeLikelihoodprotectedvirtual
computeTreeD2LikelihoodAtNode(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeTreeD2Likelihoods()bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeTreeDLikelihoodAtNode(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeTreeDLikelihoods()bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
computeTreeLikelihood()bpp::DRHomogeneousTreeLikelihood
d2f(const std::string &variable, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
d2pxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
bpp::data() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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
displayLikelihood(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
dpxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
DRHomogeneousMixedTreeLikelihood classbpp::DRHomogeneousTreeLikelihoodfriend
DRHomogeneousTreeLikelihood(const Tree &tree, std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rDist, bool checkRooted=true, bool verbose=true)bpp::DRHomogeneousTreeLikelihood
DRHomogeneousTreeLikelihood(const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rDist, bool checkRooted=true, bool verbose=true)bpp::DRHomogeneousTreeLikelihood
DRHomogeneousTreeLikelihood(const DRHomogeneousTreeLikelihood &lik)bpp::DRHomogeneousTreeLikelihood
DRTreeLikelihoodInterface()bpp::DRTreeLikelihoodInterfaceinline
bpp::enableDerivatives(bool yn)=0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
bpp::enableFirstOrderDerivatives(bool yn)=0bpp::SecondOrderDerivablepure virtual
bpp::enableFirstOrderDerivatives() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableFirstOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableFirstOrderDerivatives() constbpp::AbstractTreeLikelihoodinlinevirtual
bpp::enableSecondOrderDerivatives(bool yn)=0bpp::SecondOrderDerivablepure virtual
bpp::enableSecondOrderDerivatives() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableSecondOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableSecondOrderDerivatives() constbpp::AbstractTreeLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
fireParameterChanged(const ParameterList &params) overridebpp::DRHomogeneousTreeLikelihoodprotectedvirtual
FirstOrderDerivable()bpp::FirstOrderDerivable
FunctionInterface()bpp::FunctionInterface
bpp::getAlphabet() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getAlphabet() constbpp::AbstractTreeLikelihoodinlinevirtual
getAlphabetStateAsChar(size_t i) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStateAsInt(size_t i) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStates() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getBranchLengthsParameters() constbpp::AbstractHomogeneousTreeLikelihoodvirtual
bpp::getDerivableParameters() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getFirstOrderDerivative(const std::string &variable) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLikelihood() const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLikelihoodForASite(size_t site) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
bpp::getLikelihoodForASiteForAState(size_t site, int state) const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLikelihoodPerSite() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSite() constbpp::AbstractTreeLikelihoodvirtual
getLikelihoodPerSitePerRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodPerSitePerRateClassPerState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLikelihoodPerSitePerState() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerState() constbpp::AbstractTreeLikelihoodvirtual
getLogLikelihood() const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASite(size_t site) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
bpp::getLogLikelihoodForASiteForAState(size_t site, int state) const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLogLikelihoodPerSite() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSite() constbpp::AbstractTreeLikelihoodvirtual
getLogLikelihoodPerSitePerRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodPerSitePerRateClassPerState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLogLikelihoodPerSitePerState() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerState() constbpp::AbstractTreeLikelihoodvirtual
getMaximumBranchLength() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getMinimumBranchLength() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getModel() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getModel(int nodeId, size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinline
getModel()bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getModel(int nodeId, size_t siteIndex)bpp::AbstractHomogeneousTreeLikelihoodinline
getModelForSite(int nodeId, size_t siteIndex) constbpp::HomogeneousTreeLikelihoodinlinevirtual
getModelForSite(int nodeId, size_t siteIndex)bpp::HomogeneousTreeLikelihoodinlinevirtual
bpp::getNamespace() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getNamespace() const overridebpp::AbstractParametrizablevirtual
getNewBranchModelIterator(int nodeId) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getNewSiteModelIterator(size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
bpp::getNonDerivableParameters() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getNumberOfClasses() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
bpp::getNumberOfParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getNumberOfParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getNumberOfSites() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfSites() constbpp::AbstractTreeLikelihoodinlinevirtual
getNumberOfStates() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
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::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParametrizablevirtual
bpp::getParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getParameters_()=0bpp::SecondOrderDerivableprotectedpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getParameters_() overridebpp::AbstractParametrizableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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::AbstractHomogeneousTreeLikelihoodinlinevirtual
getRateWithMaxPostProbPerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSecondOrderDerivative(const std::string &variable) const overridebpp::DRHomogeneousTreeLikelihoodvirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
getSiteIndex(size_t site) const overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelParameters() constbpp::AbstractHomogeneousTreeLikelihoodvirtual
bpp::getTransitionProbabilities(int nodeId, size_t siteIndex) const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(int nodeId, size_t siteIndex) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getValue() const overridebpp::DRHomogeneousTreeLikelihoodvirtual
bpp::hasLikelihoodData() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::hasLikelihoodData() constbpp::AbstractTreeLikelihoodinlinevirtual
bpp::hasParameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::hasParameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
init_()bpp::DRHomogeneousTreeLikelihoodprivate
initBranchLengthsParameters(bool verbose=true)bpp::AbstractHomogeneousTreeLikelihoodvirtual
initialize()bpp::AbstractHomogeneousTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::AbstractHomogeneousTreeLikelihoodvirtual
bpp::isInitialized() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
likelihoodData() overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
likelihoodData() const overridebpp::DRHomogeneousTreeLikelihoodinlinevirtual
likelihoodData_bpp::DRHomogeneousTreeLikelihoodmutableprivate
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
maximumBrLen_bpp::AbstractHomogeneousTreeLikelihoodprotected
minimumBrLen_bpp::AbstractHomogeneousTreeLikelihoodprotected
minusLogLik_bpp::DRHomogeneousTreeLikelihoodprotected
model_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbClasses_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbDistinctSites_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbNodes_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbSites_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbStates_bpp::AbstractHomogeneousTreeLikelihoodprotected
nodes_bpp::AbstractHomogeneousTreeLikelihoodprotected
operator=(const DRHomogeneousTreeLikelihood &lik)bpp::DRHomogeneousTreeLikelihood
bpp::AbstractHomogeneousTreeLikelihood::operator=(const AbstractHomogeneousTreeLikelihood &lik)bpp::AbstractHomogeneousTreeLikelihood
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::parameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
parameters_bpp::AbstractParametrizableprivate
Parametrizable()bpp::Parametrizable
prefix_bpp::AbstractParametrizableprivate
pxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
rateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
rateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
rateDistribution_bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodprotected
bpp::removeConstraint(const std::string &name)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::removeConstraint(const std::string &name) overridebpp::AbstractParametrizablevirtual
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
resetLikelihoodArrays(const Node *node)bpp::DRHomogeneousTreeLikelihoodprotectedvirtual
resetParameters_()bpp::AbstractParametrizableprotected
rootFreqs_bpp::AbstractHomogeneousTreeLikelihoodprotected
SecondOrderDerivable()bpp::SecondOrderDerivable
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParametrizablevirtual
setData(const AlignmentDataInterface &sites) overridebpp::DRHomogeneousTreeLikelihoodvirtual
setMaximumBranchLength(double maximum)bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
setModel(std::shared_ptr< TransitionModelInterface > model)bpp::AbstractHomogeneousTreeLikelihoodvirtual
bpp::setNamespace(const std::string &prefix)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::setNamespace(const std::string &prefix) overridebpp::AbstractParametrizablevirtual
setParameters(const ParameterList &parameters) overridebpp::DRHomogeneousTreeLikelihoodvirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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
bpp::tree() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::tree() constbpp::AbstractTreeLikelihoodinlinevirtual
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinline
verbose_bpp::AbstractHomogeneousTreeLikelihoodprotected
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractHomogeneousTreeLikelihood()bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~DiscreteRatesAcrossSitesTreeLikelihoodInterface()bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfaceinlinevirtual
~DRHomogeneousTreeLikelihood()bpp::DRHomogeneousTreeLikelihoodinlinevirtual
~DRTreeLikelihoodInterface()bpp::DRTreeLikelihoodInterfaceinlinevirtual
~FirstOrderDerivable()bpp::FirstOrderDerivablevirtual
~FunctionInterface()bpp::FunctionInterfacevirtual
~Parametrizable()bpp::Parametrizablevirtual
~SecondOrderDerivable()bpp::SecondOrderDerivablevirtual
~TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinlinevirtual