bpp-phyl3  3.0.0
bpp::RNonHomogeneousMixedTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
AbstractNonHomogeneousTreeLikelihood(const Tree &tree, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool reparametrizeRoot=true)bpp::AbstractNonHomogeneousTreeLikelihood
AbstractNonHomogeneousTreeLikelihood(const AbstractNonHomogeneousTreeLikelihood &lik)bpp::AbstractNonHomogeneousTreeLikelihood
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::AbstractNonHomogeneousTreeLikelihoodvirtual
brLenConstraint_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
brLenParameters_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
clone() constbpp::RNonHomogeneousMixedTreeLikelihoodinlinevirtual
computeAllTransitionProbabilities()bpp::AbstractNonHomogeneousTreeLikelihoodprotectedvirtual
computeDownSubtreeD2Likelihood(const Node *)bpp::RNonHomogeneousMixedTreeLikelihoodprotectedvirtual
computeDownSubtreeDLikelihood(const Node *)bpp::RNonHomogeneousMixedTreeLikelihoodprotectedvirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSubtreeLikelihood(const Node *node)bpp::RNonHomogeneousMixedTreeLikelihoodprotectedvirtual
computeTransitionProbabilitiesForNode(const Node *node)bpp::RNonHomogeneousMixedTreeLikelihoodprotectedvirtual
computeTreeD2Likelihood(const std::string &variable)bpp::RNonHomogeneousMixedTreeLikelihoodvirtual
computeTreeDLikelihood(const std::string &variable)bpp::RNonHomogeneousMixedTreeLikelihoodvirtual
computeTreeLikelihood()bpp::RNonHomogeneousTreeLikelihoodvirtual
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::AbstractNonHomogeneousTreeLikelihoodmutableprotected
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::RNonHomogeneousTreeLikelihoodprotectedvirtual
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
dpxy_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
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)bpp::RNonHomogeneousMixedTreeLikelihoodprotectedvirtual
FirstOrderDerivable()bpp::FirstOrderDerivable
FunctionInterface()bpp::FunctionInterface
bpp::getAlphabet() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getAlphabet() constbpp::AbstractTreeLikelihoodinlinevirtual
getAlphabetStateAsChar(size_t i) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStateAsInt(size_t i) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStates() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getBranchLengthsParameters() const overridebpp::AbstractNonHomogeneousTreeLikelihoodvirtual
getD2LikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getD2LikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getD2LogLikelihood() constbpp::RNonHomogeneousTreeLikelihoodvirtual
getD2LogLikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
bpp::getDerivableParameters() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getDLikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getDLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getDLogLikelihood() constbpp::RNonHomogeneousTreeLikelihoodvirtual
getDLogLikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getFirstOrderDerivative(const std::string &variable) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getHyperNode()bpp::RNonHomogeneousMixedTreeLikelihoodinline
getLikelihood() constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) constbpp::RNonHomogeneousTreeLikelihoodvirtual
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() constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASite(size_t site) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) constbpp::RNonHomogeneousTreeLikelihoodvirtual
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::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getMinimumBranchLength() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getModelForNode(int nodeId) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getModelForNode(int nodeId) overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getModelForSite(int nodeId, size_t siteIndex) const overridebpp::NonHomogeneousTreeLikelihoodinlinevirtual
getModelForSite(int nodeId, size_t siteIndex) overridebpp::NonHomogeneousTreeLikelihoodinlinevirtual
bpp::getNamespace() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::getNamespace() const overridebpp::AbstractParametrizablevirtual
getNewBranchModelIterator(int nodeId) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getNewSiteModelIterator(size_t siteIndex) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
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() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
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
getProbability() constbpp::RNonHomogeneousMixedTreeLikelihood
getRateClassWithMaxPostProbPerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistributionParameters() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getRateWithMaxPostProbPerSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getRootFrequenciesParameters() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSecondOrderDerivative(const std::string &variable) constbpp::RNonHomogeneousTreeLikelihoodvirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
getSiteIndex(size_t site) constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelParameters() const overridebpp::AbstractNonHomogeneousTreeLikelihoodvirtual
getSubstitutionModelSet() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelSet() overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
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) const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getValue() constbpp::RNonHomogeneousTreeLikelihoodvirtual
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
hyperNode_bpp::RNonHomogeneousMixedTreeLikelihoodprivate
idToNode_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
includeParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
init(bool usePatterns)bpp::RNonHomogeneousMixedTreeLikelihoodprivate
init_(bool usePatterns)bpp::RNonHomogeneousTreeLikelihoodprivate
initBranchLengthsParameters(bool verbose=true)bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
initialize()bpp::RNonHomogeneousMixedTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
bpp::isInitialized() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
likelihoodData()bpp::RNonHomogeneousTreeLikelihoodinlinevirtual
likelihoodData() constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
likelihoodData_bpp::RNonHomogeneousTreeLikelihoodmutableprivate
main_bpp::RNonHomogeneousMixedTreeLikelihoodprivate
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
maximumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
minimumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
minusLogLik_bpp::RNonHomogeneousTreeLikelihoodprivate
modelSet_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
mvTreeLikelihoods_bpp::RNonHomogeneousMixedTreeLikelihoodprivate
nbClasses_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbDistinctSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbNodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbStates_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
operator=(const RNonHomogeneousMixedTreeLikelihood &lik)bpp::RNonHomogeneousMixedTreeLikelihood
bpp::RNonHomogeneousTreeLikelihood::operator=(const RNonHomogeneousTreeLikelihood &lik)bpp::RNonHomogeneousTreeLikelihood
bpp::AbstractNonHomogeneousTreeLikelihood::operator=(const AbstractNonHomogeneousTreeLikelihood &lik)bpp::AbstractNonHomogeneousTreeLikelihood
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::AbstractNonHomogeneousTreeLikelihoodmutableprotected
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
reparametrizeRoot_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
resetParameters_()bpp::AbstractParametrizableprotected
RNonHomogeneousMixedTreeLikelihood(const Tree &tree, std::shared_ptr< MixedSubstitutionModelSet > modelSet, const MixedSubstitutionModelSet::HyperNode &hyperNode, int upperNode, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose, bool usePatterns)bpp::RNonHomogeneousMixedTreeLikelihoodprivate
RNonHomogeneousMixedTreeLikelihood(const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< MixedSubstitutionModelSet > modelSet, const MixedSubstitutionModelSet::HyperNode &hyperNode, int upperNode, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose, bool usePatterns)bpp::RNonHomogeneousMixedTreeLikelihoodprivate
RNonHomogeneousMixedTreeLikelihood(const Tree &tree, std::shared_ptr< MixedSubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true)bpp::RNonHomogeneousMixedTreeLikelihood
RNonHomogeneousMixedTreeLikelihood(const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< MixedSubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true)bpp::RNonHomogeneousMixedTreeLikelihood
RNonHomogeneousMixedTreeLikelihood(const RNonHomogeneousMixedTreeLikelihood &lik)bpp::RNonHomogeneousMixedTreeLikelihood
RNonHomogeneousTreeLikelihood(const Tree &tree, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false)bpp::RNonHomogeneousTreeLikelihood
RNonHomogeneousTreeLikelihood(const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false)bpp::RNonHomogeneousTreeLikelihood
RNonHomogeneousTreeLikelihood(const RNonHomogeneousTreeLikelihood &lik)bpp::RNonHomogeneousTreeLikelihood
root1_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
root2_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
rootFreqs_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
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)bpp::RNonHomogeneousMixedTreeLikelihoodvirtual
setMaximumBranchLength(double maximum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
bpp::setNamespace(const std::string &prefix)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::bpp::AbstractParametrizable::setNamespace(const std::string &prefix) overridebpp::AbstractParametrizablevirtual
setParameters(const ParameterList &parameters)bpp::RNonHomogeneousTreeLikelihoodvirtual
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
setProbability(double x)bpp::RNonHomogeneousMixedTreeLikelihood
setSubstitutionModelSet(std::shared_ptr< SubstitutionModelSet > modelSet) overridebpp::AbstractNonHomogeneousTreeLikelihoodvirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParametrizableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
substitutionModelSet() const overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
substitutionModelSet() overridebpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
bpp::tree() const =0bpp::TreeLikelihoodInterfacepure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::tree() constbpp::AbstractTreeLikelihoodinlinevirtual
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinline
upperNode_bpp::RNonHomogeneousMixedTreeLikelihoodprivate
verbose_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractNonHomogeneousTreeLikelihood()bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~DiscreteRatesAcrossSitesTreeLikelihoodInterface()bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterfaceinlinevirtual
~FirstOrderDerivable()bpp::FirstOrderDerivablevirtual
~FunctionInterface()bpp::FunctionInterfacevirtual
~Parametrizable()bpp::Parametrizablevirtual
~RNonHomogeneousMixedTreeLikelihood()bpp::RNonHomogeneousMixedTreeLikelihoodvirtual
~RNonHomogeneousTreeLikelihood()bpp::RNonHomogeneousTreeLikelihoodvirtual
~SecondOrderDerivable()bpp::SecondOrderDerivablevirtual
~TreeLikelihoodInterface()bpp::TreeLikelihoodInterfaceinlinevirtual