bpp-phyl3  3.0.0
bpp::LikelihoodCalculationOnABranch Member List

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

AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
AlignedLikelihoodCalculation(Context &context)bpp::AlignedLikelihoodCalculationinline
AlignedLikelihoodCalculation(const AlignedLikelihoodCalculation &lik)bpp::AlignedLikelihoodCalculationinline
catProb_bpp::LikelihoodCalculationOnABranchprivate
cleanAllLikelihoods()bpp::LikelihoodCalculationOnABranchprivatevirtual
clone() constbpp::LikelihoodCalculationOnABranchinlinevirtual
context_bpp::LikelihoodCalculationprivate
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
expandMatrix(ValueRef< MatrixLik > matrix)bpp::LikelihoodCalculationOnABranchinline
expandVector(ValueRef< RowLik > vector)bpp::LikelihoodCalculationOnABranchinline
fireParameterChanged(const ParameterList &parameters)bpp::AbstractParameterAliasablevirtual
getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() constbpp::LikelihoodCalculationOnABranchinline
getContext() constbpp::LikelihoodCalculationinline
getContext_()bpp::LikelihoodCalculationinlineprotected
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getLikelihoodForASite(size_t pos, bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
getLikelihoodNode()bpp::LikelihoodCalculationinline
getLikelihoodNode_()bpp::LikelihoodCalculationinlineprotected
getLikelihoodPerSite()bpp::AlignedLikelihoodCalculationinline
getLogLikelihoodForASite(size_t pos, bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
getModel()bpp::LikelihoodCalculationOnABranchinline
getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfDistinctSites() constbpp::LikelihoodCalculationOnABranchinline
getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfSites() constbpp::LikelihoodCalculationOnABranchinline
getParameter(const std::string &name) constbpp::AbstractParameterAliasable
getParameter(size_t i) constbpp::AbstractParameterAliasableprotected
getParameter(size_t i)bpp::AbstractParameterAliasableprotected
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) constbpp::AbstractParameterAliasableprotected
getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameters() const overridebpp::AbstractParameterAliasablevirtual
getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getRootArrayPosition(size_t currentPosition) constbpp::LikelihoodCalculationOnABranchinline
getRootArrayPositions() constbpp::LikelihoodCalculationOnABranchinline
getRootWeights()bpp::LikelihoodCalculationOnABranchinline
getSiteLikelihoods(bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
getSiteLikelihoods_(size_t nCat)bpp::LikelihoodCalculationOnABranchprivate
getSiteLikelihoodsForAClass(size_t nCat, bool shrunk=false)bpp::LikelihoodCalculationOnABranch
getSiteLikelihoodsForAllClasses(bool shrunk=false)bpp::LikelihoodCalculationOnABranch
getStateMap() constbpp::LikelihoodCalculationOnABranchinline
getWeight(size_t pos) constbpp::LikelihoodCalculationOnABranchinline
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isInitialized() constbpp::LikelihoodCalculationinlinevirtual
likelihood_bpp::LikelihoodCalculationmutableprotected
LikelihoodCalculation(Context &context)bpp::LikelihoodCalculationinline
LikelihoodCalculation(Context &context, ParameterList &paramList)bpp::LikelihoodCalculationinline
LikelihoodCalculation(const LikelihoodCalculation &lik)bpp::LikelihoodCalculationinline
LikelihoodCalculationOnABranch(Context &context, LikelihoodCalculationSingleProcess &likcalsp, uint edgeId)bpp::LikelihoodCalculationOnABranch
LikelihoodCalculationOnABranch(const LikelihoodCalculationOnABranch &lik)bpp::LikelihoodCalculationOnABranch
likelihoodMatrixDim_bpp::LikelihoodCalculationOnABranchprivate
makeLikelihoods()bpp::LikelihoodCalculationOnABranchprivatevirtual
matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model_bpp::LikelihoodCalculationOnABranchprivate
numberOfSites_bpp::LikelihoodCalculationOnABranchprivate
operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
patternedSiteLikelihoods_bpp::AlignedLikelihoodCalculationmutableprotected
prefix_bpp::AbstractParameterAliasableprivate
removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rootPatternLinks_bpp::LikelihoodCalculationOnABranchprivate
rootWeights_bpp::LikelihoodCalculationOnABranchprivate
setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setLikelihoodNode(ValueRef< DataLik > ll)bpp::LikelihoodCalculationinline
setModel(std::shared_ptr< ConfiguredModel > model)bpp::LikelihoodCalculationOnABranchinline
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setSiteLikelihoods(SiteLikelihoodsRef ll, bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
siteLikelihoods_bpp::AlignedLikelihoodCalculationmutableprotected
stateMap() constbpp::LikelihoodCalculationOnABranchinline
unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
vRateCatEdges_bpp::LikelihoodCalculationOnABranchprivate
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual