bpp-phyl  2.2.0
bpp::RNonHomogeneousTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(DiscreteDistribution *rDist, bool verbose=true)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
AbstractNonHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=true)bpp::AbstractNonHomogeneousTreeLikelihood
AbstractNonHomogeneousTreeLikelihood(const AbstractNonHomogeneousTreeLikelihood &lik)bpp::AbstractNonHomogeneousTreeLikelihood
AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinline
AbstractTreeLikelihood(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
applyParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
brLenConstraint_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
brLenParameters_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
clone() constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
computeAllTransitionProbabilities()bpp::AbstractNonHomogeneousTreeLikelihoodprotectedvirtual
computeDownSubtreeD2Likelihood(const Node *)bpp::RNonHomogeneousTreeLikelihoodprotectedvirtual
computeDownSubtreeDLikelihood(const Node *)bpp::RNonHomogeneousTreeLikelihoodprotectedvirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSubtreeLikelihood(const Node *node)bpp::RNonHomogeneousTreeLikelihoodprotectedvirtual
computeTransitionProbabilitiesForNode(const Node *node)bpp::AbstractNonHomogeneousTreeLikelihoodprotectedvirtual
computeTreeD2Likelihood(const std::string &variable)bpp::RNonHomogeneousTreeLikelihoodvirtual
computeTreeDLikelihood(const std::string &variable)bpp::RNonHomogeneousTreeLikelihoodvirtual
computeTreeLikelihood()bpp::RNonHomogeneousTreeLikelihoodvirtual
d2pxy_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
data_bpp::AbstractTreeLikelihoodprotected
DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinline
displayLikelihood(const Node *node)bpp::RNonHomogeneousTreeLikelihoodprotectedvirtual
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
dpxy_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
bpp::enableDerivatives(bool yn)=0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::enableDerivatives(bool yn)bpp::AbstractTreeLikelihoodinlinevirtual
enableFirstOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinline
enableFirstOrderDerivatives() constbpp::AbstractTreeLikelihoodinline
enableSecondOrderDerivatives(bool yn)bpp::AbstractTreeLikelihoodinline
enableSecondOrderDerivatives() constbpp::AbstractTreeLikelihoodinline
fireParameterChanged(const ParameterList &params)bpp::RNonHomogeneousTreeLikelihoodprotected
bpp::getAlphabet() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getAlphabet() constbpp::AbstractTreeLikelihoodinlinevirtual
getAlphabetStateAsChar(size_t i) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStateAsInt(size_t i) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStates() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getBranchLengthsParameters() constbpp::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::getData() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getData() constbpp::AbstractTreeLikelihoodinlinevirtual
bpp::getDerivableParameters() const =0bpp::TreeLikelihoodpure 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::RNonHomogeneousTreeLikelihood
getLikelihood() constbpp::RNonHomogeneousTreeLikelihoodvirtual
getLikelihoodData()bpp::RNonHomogeneousTreeLikelihoodinlinevirtual
getLikelihoodData() constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
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::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLikelihoodForEachSite() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSite() constbpp::AbstractTreeLikelihoodvirtual
getLikelihoodForEachSiteForEachRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihoodForEachSiteForEachRateClassForEachState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLikelihoodForEachSiteForEachState() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachState() 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::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(size_t site, int state) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLogLikelihoodForEachSite() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSite() constbpp::AbstractTreeLikelihoodvirtual
getLogLikelihoodForEachSiteForEachRateClass() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
bpp::getLogLikelihoodForEachSiteForEachState() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachState() constbpp::AbstractTreeLikelihoodvirtual
getMaximumBranchLength() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getMinimumBranchLength() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getNewBranchModelIterator(int nodeId) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getNewSiteModelIterator(size_t siteIndex) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
bpp::getNonDerivableParameters() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getNumberOfClasses() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
bpp::getNumberOfSites() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfSites() constbpp::AbstractTreeLikelihoodinlinevirtual
getNumberOfStates() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getPosteriorProbabilitiesOfEachRate() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getPosteriorRateOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateClassWithMaxPostProbOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistributionParameters() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getRateWithMaxPostProbOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getRootFrequenciesParameters() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSecondOrderDerivative(const std::string &variable) constbpp::RNonHomogeneousTreeLikelihood
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) constbpp::RNonHomogeneousTreeLikelihoodinline
getSiteIndex(size_t site) constbpp::RNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) constbpp::NonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex)bpp::NonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelForNode(int nodeId) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelForNode(int nodeId)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelParameters() constbpp::AbstractNonHomogeneousTreeLikelihoodvirtual
getSubstitutionModelSet() constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelSet()bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
bpp::getTransitionProbabilities(int nodeId, size_t siteIndex) const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(int nodeId, size_t siteIndex) constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) constbpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
bpp::getTree() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTree() constbpp::AbstractTreeLikelihoodinlinevirtual
getValue() constbpp::RNonHomogeneousTreeLikelihood
idToNode_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
init_(bool usePatterns)bpp::RNonHomogeneousTreeLikelihoodprivate
initBranchLengthsParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
initialize()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
bpp::isInitialized() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
likelihoodData_bpp::RNonHomogeneousTreeLikelihoodmutableprivate
maximumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
minimumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
minusLogLik_bpp::RNonHomogeneousTreeLikelihoodprivate
modelSet_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbClasses_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbDistinctSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbNodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbStates_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
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
pxy_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
rateDistribution_bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodprotected
reparametrizeRoot_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
RNonHomogeneousMixedTreeLikelihood classbpp::RNonHomogeneousTreeLikelihoodfriend
RNonHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false)bpp::RNonHomogeneousTreeLikelihood
RNonHomogeneousTreeLikelihood(const Tree &tree, const SiteContainer &data, SubstitutionModelSet *modelSet, DiscreteDistribution *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
setData(const SiteContainer &sites)bpp::RNonHomogeneousTreeLikelihoodvirtual
setMaximumBranchLength(double maximum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
setParameters(const ParameterList &parameters)bpp::RNonHomogeneousTreeLikelihood
setSubstitutionModelSet(SubstitutionModelSet *modelSet)bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihood()bpp::TreeLikelihoodinline
verbose_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractNonHomogeneousTreeLikelihood()bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~RNonHomogeneousTreeLikelihood()bpp::RNonHomogeneousTreeLikelihoodvirtual
~TreeLikelihood()bpp::TreeLikelihoodinlinevirtual