bpp::DRTreeLikelihood Member List

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

clone() const =0	bpp::DRTreeLikelihood	pure virtual
computeLikelihoodAtNode(int nodeId, VVVdouble &likelihoodArray) const =0	bpp::DRTreeLikelihood	pure virtual
DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inline
DRTreeLikelihood()	bpp::DRTreeLikelihood	inline
enableDerivatives(bool yn)=0	bpp::TreeLikelihood	pure virtual
getAlphabet() const =0	bpp::TreeLikelihood	pure virtual
getAlphabetStateAsChar(size_t i) const =0	bpp::TreeLikelihood	pure virtual
getAlphabetStateAsInt(size_t i) const =0	bpp::TreeLikelihood	pure virtual
getAlphabetStates() const =0	bpp::TreeLikelihood	pure virtual
getBranchLengthsParameters() const =0	bpp::TreeLikelihood	pure virtual
getData() const =0	bpp::TreeLikelihood	pure virtual
getDerivableParameters() const =0	bpp::TreeLikelihood	pure virtual
getLikelihood() const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodData()=0	bpp::DRTreeLikelihood	pure virtual
getLikelihoodData() const =0	bpp::DRTreeLikelihood	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForEachSite() const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForEachSiteForEachRateClass() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForEachSiteForEachRateClassForEachState() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForEachSiteForEachState() const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihood() const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForEachSite() const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForEachSiteForEachRateClass() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForEachSiteForEachState() const =0	bpp::TreeLikelihood	pure virtual
getNewBranchModelIterator(int nodeId) const =0	bpp::TreeLikelihood	pure virtual
getNewSiteModelIterator(size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getNonDerivableParameters() const =0	bpp::TreeLikelihood	pure virtual
getNumberOfClasses() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getNumberOfSites() const =0	bpp::TreeLikelihood	pure virtual
getNumberOfStates() const =0	bpp::TreeLikelihood	pure virtual
getPosteriorProbabilitiesOfEachRate() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getPosteriorRateOfEachSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRateClassWithMaxPostProbOfEachSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRateDistribution() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRateDistribution()=0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRateDistributionParameters() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRateWithMaxPostProbOfEachSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getRootFrequencies(size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getSiteIndex(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getSubstitutionModel(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getSubstitutionModel(int nodeId, size_t siteIndex)=0	bpp::TreeLikelihood	pure virtual
getSubstitutionModelParameters() const =0	bpp::TreeLikelihood	pure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getTree() const =0	bpp::TreeLikelihood	pure virtual
initialize()=0	bpp::TreeLikelihood	pure virtual
isInitialized() const =0	bpp::TreeLikelihood	pure virtual
setData(const SiteContainer &sites)=0	bpp::TreeLikelihood	pure virtual
TreeLikelihood()	bpp::TreeLikelihood	inline
~DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~DRTreeLikelihood()	bpp::DRTreeLikelihood	inlinevirtual
~TreeLikelihood()	bpp::TreeLikelihood	inlinevirtual