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bpp::TwoTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(DiscreteDistribution *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::AbstractParametrizableprotected
addParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotected
applyParameters()bpp::TwoTreeLikelihoodprotectedvirtual
brLen_bpp::TwoTreeLikelihoodprivate
brLenConstraint_bpp::TwoTreeLikelihoodprivate
brLenParameters_bpp::TwoTreeLikelihoodprivate
Clonable()bpp::Clonable
clone() const bpp::TwoTreeLikelihoodinlinevirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeTreeD2Likelihood()bpp::TwoTreeLikelihoodprotectedvirtual
computeTreeDLikelihood()bpp::TwoTreeLikelihoodprotectedvirtual
computeTreeLikelihood()bpp::TwoTreeLikelihoodprotectedvirtual
d2Likelihoods_bpp::TwoTreeLikelihoodmutableprivate
d2pxy_bpp::TwoTreeLikelihoodmutableprivate
data_bpp::AbstractTreeLikelihoodprotected
deleteParameter_(size_t index)bpp::AbstractParametrizableprotected
DerivableFirstOrder()bpp::DerivableFirstOrder
DerivableSecondOrder()bpp::DerivableSecondOrder
DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinline
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
dLikelihoods_bpp::TwoTreeLikelihoodmutableprivate
dpxy_bpp::TwoTreeLikelihoodmutableprivate
enableDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableFirstOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableFirstOrderDerivatives() const bpp::AbstractTreeLikelihoodinlinevirtual
enableSecondOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableSecondOrderDerivatives() const bpp::AbstractTreeLikelihoodinlinevirtual
fireParameterChanged(const ParameterList &params)bpp::TwoTreeLikelihoodprotectedvirtual
Function()bpp::Function
getAlphabet() const bpp::AbstractTreeLikelihoodinlinevirtual
getBranchLengthsParameters() const bpp::TwoTreeLikelihoodvirtual
getData() const bpp::AbstractTreeLikelihoodinlinevirtual
getDerivableParameters() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getFirstOrderDerivative(const std::string &variable) const bpp::TwoTreeLikelihoodvirtual
getLikelihood() const bpp::TwoTreeLikelihoodvirtual
getLikelihoodData()bpp::TwoTreeLikelihoodinlinevirtual
getLikelihoodData() const bpp::TwoTreeLikelihoodinlinevirtual
getLikelihoodForASite(size_t site) const bpp::TwoTreeLikelihoodvirtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const bpp::TwoTreeLikelihoodvirtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const bpp::TwoTreeLikelihoodvirtual
getLikelihoodForASiteForAState(size_t site, int state) const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodForEachSite() const bpp::AbstractTreeLikelihoodvirtual
getLikelihoodForEachSiteForEachRateClass() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodForEachSiteForEachRateClassForEachState() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodForEachSiteForEachState() const bpp::AbstractTreeLikelihoodvirtual
getLogLikelihood() const bpp::TwoTreeLikelihoodvirtual
getLogLikelihoodForASite(size_t site) const bpp::TwoTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const bpp::TwoTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const bpp::TwoTreeLikelihoodvirtual
getLogLikelihoodForASiteForAState(size_t site, int state) const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodForEachSite() const bpp::AbstractTreeLikelihoodvirtual
getLogLikelihoodForEachSiteForEachRateClass() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodForEachSiteForEachState() const bpp::AbstractTreeLikelihoodvirtual
getMinimumBranchLength() const bpp::TwoTreeLikelihoodinlinevirtual
getNewBranchModelIterator(int nodeId) const bpp::TwoTreeLikelihoodinlinevirtual
getNewSiteModelIterator(size_t siteIndex) const bpp::TwoTreeLikelihoodinlinevirtual
getNonDerivableParameters() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getNumberOfClasses() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getNumberOfSites() const bpp::AbstractTreeLikelihoodinlinevirtual
getNumberOfStates() const bpp::AbstractTreeLikelihoodinlinevirtual
getPosteriorProbabilitiesOfEachRate() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getPosteriorRateOfEachSite() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateClassWithMaxPostProbOfEachSite() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateDistribution() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistributionParameters() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateWithMaxPostProbOfEachSite() const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) const bpp::TwoTreeLikelihoodinlinevirtual
getSecondOrderDerivative(const std::string &variable) const bpp::TwoTreeLikelihoodvirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const bpp::TwoTreeLikelihoodinlinevirtual
getSiteIndex(size_t site) const bpp::TwoTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex)bpp::TwoTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) const bpp::TwoTreeLikelihoodinlinevirtual
getSubstitutionModel() const bpp::TwoTreeLikelihoodinline
getSubstitutionModel()bpp::TwoTreeLikelihoodinline
getSubstitutionModelParameters() const bpp::TwoTreeLikelihoodvirtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const bpp::TwoTreeLikelihoodinlinevirtual
getTree() const bpp::AbstractTreeLikelihoodinlinevirtual
getValue() const bpp::TwoTreeLikelihood
initBranchLengthsParameters()bpp::TwoTreeLikelihoodvirtual
initialize()bpp::TwoTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::TwoTreeLikelihoodprotectedvirtual
initTreeLikelihoods(const SequenceContainer &sequences)bpp::TwoTreeLikelihoodprotectedvirtual
isInitialized() const bpp::AbstractTreeLikelihoodinlinevirtual
leafLikelihoods1_bpp::TwoTreeLikelihoodmutableprivate
leafLikelihoods2_bpp::TwoTreeLikelihoodmutableprivate
minimumBrLen_bpp::TwoTreeLikelihoodprivate
model_bpp::TwoTreeLikelihoodprivate
nbClasses_bpp::TwoTreeLikelihoodprivate
nbDistinctSites_bpp::TwoTreeLikelihoodprivate
nbSites_bpp::TwoTreeLikelihoodprivate
nbStates_bpp::TwoTreeLikelihoodprivate
operator=(const TwoTreeLikelihood &lik)bpp::TwoTreeLikelihood
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
Parametrizable()bpp::Parametrizable
pxy_bpp::TwoTreeLikelihoodmutableprivate
rateDistribution_bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodprotected
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
resetParameters_()bpp::AbstractParametrizableprotected
rootLikelihoods_bpp::TwoTreeLikelihoodmutableprivate
rootLikelihoodsS_bpp::TwoTreeLikelihoodmutableprivate
rootLikelihoodsSR_bpp::TwoTreeLikelihoodmutableprivate
rootPatternLinks_bpp::TwoTreeLikelihoodprivate
rootWeights_bpp::TwoTreeLikelihoodprivate
seqnames_bpp::TwoTreeLikelihoodprivate
setData(const SiteContainer &sites)bpp::TwoTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::TwoTreeLikelihoodinlinevirtual
setNamespace(const std::string &prefix)bpp::AbstractParametrizable
setParameters(const ParameterList &parameters)bpp::TwoTreeLikelihoodvirtual
shrunkData_bpp::TwoTreeLikelihoodprivate
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihood()bpp::TreeLikelihoodinline
TwoTreeLikelihood(const std::string &seq1, const std::string &seq2, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool verbose)bpp::TwoTreeLikelihood
TwoTreeLikelihood(const TwoTreeLikelihood &lik)bpp::TwoTreeLikelihood
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~Clonable()bpp::Clonablevirtual
~DerivableFirstOrder()bpp::DerivableFirstOrdervirtual
~DerivableSecondOrder()bpp::DerivableSecondOrdervirtual
~DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~Function()bpp::Functionvirtual
~Parametrizable()bpp::Parametrizablevirtual
~TreeLikelihood()bpp::TreeLikelihoodinlinevirtual
~TwoTreeLikelihood()bpp::TwoTreeLikelihoodvirtual