bpp-phyl3 3.0.0
bpp::LikelihoodCalculationSingleProcess Member List

This is the complete list of members for bpp::LikelihoodCalculationSingleProcess, 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::LikelihoodCalculationSingleProcessprivate
cleanAllLikelihoods()bpp::LikelihoodCalculationSingleProcessvirtual
clone() constbpp::LikelihoodCalculationSingleProcessinlinevirtual
condLikelihoodTree_bpp::LikelihoodCalculationSingleProcessprivate
context_bpp::LikelihoodCalculationprivate
data() constbpp::LikelihoodCalculationSingleProcessinline
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::LikelihoodCalculationSingleProcessinline
expandVector(ValueRef< RowLik > vector)bpp::LikelihoodCalculationSingleProcessinline
fireParameterChanged(const ParameterList &parameters)bpp::AbstractParameterAliasablevirtual
getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getAliases() constbpp::AbstractParameterAliasablevirtual
getBackwardLikelihoodsAtEdgeForClass(uint edgeId, size_t nCat)bpp::LikelihoodCalculationSingleProcess
getBackwardLikelihoodsAtNodeForClass(uint nodeId, size_t nCat)bpp::LikelihoodCalculationSingleProcess
getBackwardLikelihoodTree(size_t nCat)bpp::LikelihoodCalculationSingleProcess
getConditionalLikelihoodsAtNodeForClass(uint nodeId, size_t nCat)bpp::LikelihoodCalculationSingleProcess
getContext() constbpp::LikelihoodCalculationinline
getContext_()bpp::LikelihoodCalculationinlineprotected
getData() constbpp::LikelihoodCalculationSingleProcessinline
getEdgesIds(uint speciesId, size_t nCat) constbpp::LikelihoodCalculationSingleProcess
getForwardLikelihoodsAtNodeForClass(uint nodeId, size_t nCat)bpp::LikelihoodCalculationSingleProcess
getForwardLikelihoodTree(size_t nCat)bpp::LikelihoodCalculationSingleProcess
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
getLikelihoodsAtNode(uint nodeId, bool shrunk=false)bpp::LikelihoodCalculationSingleProcessinline
getLikelihoodsAtNodeForClass(uint nodeId, size_t nCat)bpp::LikelihoodCalculationSingleProcess
getLogLikelihoodForASite(size_t pos, bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNodesIds(uint speciesId) constbpp::LikelihoodCalculationSingleProcess
getNumberOfClasses() constbpp::LikelihoodCalculationSingleProcessinline
getNumberOfDistinctSites() constbpp::LikelihoodCalculationSingleProcessinline
getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfSites() constbpp::LikelihoodCalculationSingleProcessinline
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::LikelihoodCalculationSingleProcessinline
getRootArrayPositions() constbpp::LikelihoodCalculationSingleProcessinline
getRootFreqs()bpp::LikelihoodCalculationSingleProcessinline
getRootPatternLinks() constbpp::LikelihoodCalculationSingleProcessinline
getRootWeights()bpp::LikelihoodCalculationSingleProcessinline
getShrunkData() constbpp::LikelihoodCalculationSingleProcessinline
getSiteLikelihoods(bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
getSiteLikelihoodsForAClass(size_t nCat, bool shrunk=false)bpp::LikelihoodCalculationSingleProcess
getSiteLikelihoodsForAllClasses(bool shrunk=false)bpp::LikelihoodCalculationSingleProcess
getSiteLikelihoodsTree_(size_t nCat)bpp::LikelihoodCalculationSingleProcessprivate
getStateMap() constbpp::LikelihoodCalculationSingleProcessinline
getSubstitutionProcess() constbpp::LikelihoodCalculationSingleProcessinline
getTreeNode(size_t nCat)bpp::LikelihoodCalculationSingleProcessinline
getWeight(size_t pos) constbpp::LikelihoodCalculationSingleProcessinline
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
LikelihoodCalculationOnABranchbpp::LikelihoodCalculationSingleProcessfriend
LikelihoodCalculationSingleProcess(Context &context, std::shared_ptr< const AlignmentDataInterface > sites, std::shared_ptr< const SubstitutionProcessInterface > process)bpp::LikelihoodCalculationSingleProcess
LikelihoodCalculationSingleProcess(Context &context, std::shared_ptr< const SubstitutionProcessInterface > process)bpp::LikelihoodCalculationSingleProcess
LikelihoodCalculationSingleProcess(std::shared_ptr< CollectionNodes > collection, std::shared_ptr< const AlignmentDataInterface > sites, size_t nProcess)bpp::LikelihoodCalculationSingleProcess
LikelihoodCalculationSingleProcess(std::shared_ptr< CollectionNodes > collection, size_t nProcess)bpp::LikelihoodCalculationSingleProcess
LikelihoodCalculationSingleProcess(const LikelihoodCalculationSingleProcess &lik)bpp::LikelihoodCalculationSingleProcess
makeForwardLikelihoodTree_()bpp::LikelihoodCalculationSingleProcessprivate
makeLikelihoods()bpp::LikelihoodCalculationSingleProcessinlinevirtual
makeLikelihoodsAtDAGNode_(uint nodeId)bpp::LikelihoodCalculationSingleProcessprivate
makeLikelihoodsAtNode_(uint nodeId)bpp::LikelihoodCalculationSingleProcessprivate
makeLikelihoodsAtRoot_()bpp::LikelihoodCalculationSingleProcessprivate
makeLikelihoodsTree()bpp::LikelihoodCalculationSingleProcessinline
makeProcessNodes_()bpp::LikelihoodCalculationSingleProcessprivate
makeProcessNodes_(CollectionNodes &pl, size_t nProc)bpp::LikelihoodCalculationSingleProcessprivate
makeRootFreqs_()bpp::LikelihoodCalculationSingleProcessprivate
matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
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
process_bpp::LikelihoodCalculationSingleProcessprivate
processNodes_bpp::LikelihoodCalculationSingleProcessprivate
psites_bpp::LikelihoodCalculationSingleProcessprivate
removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
rFreqs_bpp::LikelihoodCalculationSingleProcessprivate
rootPatternLinks_bpp::LikelihoodCalculationSingleProcessprivate
rootWeights_bpp::LikelihoodCalculationSingleProcessprivate
setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setClockLike(double rate=1)bpp::LikelihoodCalculationSingleProcess
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setData(std::shared_ptr< const AlignmentDataInterface > sites)bpp::LikelihoodCalculationSingleProcessinline
setLikelihoodNode(ValueRef< DataLik > ll)bpp::LikelihoodCalculationinline
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setNumericalDerivateConfiguration(double delta, const NumericalDerivativeType &config)bpp::LikelihoodCalculationSingleProcess
setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setPatterns_()bpp::LikelihoodCalculationSingleProcessprivate
setSiteLikelihoods(SiteLikelihoodsRef ll, bool shrunk=false)bpp::AlignedLikelihoodCalculationinline
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
shrunkData() constbpp::LikelihoodCalculationSingleProcessinline
shrunkData_bpp::LikelihoodCalculationSingleProcessprivate
siteLikelihoods_bpp::AlignedLikelihoodCalculationmutableprotected
stateMap() constbpp::LikelihoodCalculationSingleProcessinline
substitutionProcess() constbpp::LikelihoodCalculationSingleProcessinline
unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
vRateCatTrees_bpp::LikelihoodCalculationSingleProcessprivate
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual