bpp-phyl  2.2.0
bpp::RHomogeneousTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(DiscreteDistribution *rDist, bool verbose=true)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
AbstractHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true)bpp::AbstractHomogeneousTreeLikelihood
AbstractHomogeneousTreeLikelihood(const AbstractHomogeneousTreeLikelihood &lik)bpp::AbstractHomogeneousTreeLikelihood
AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinline
AbstractTreeLikelihood(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
applyParameters()bpp::AbstractHomogeneousTreeLikelihoodvirtual
brLenConstraint_bpp::AbstractHomogeneousTreeLikelihoodprotected
brLenParameters_bpp::AbstractHomogeneousTreeLikelihoodprotected
clone() constbpp::RHomogeneousTreeLikelihoodinlinevirtual
computeAllTransitionProbabilities()bpp::AbstractHomogeneousTreeLikelihoodprotectedvirtual
computeDownSubtreeD2Likelihood(const Node *)bpp::RHomogeneousTreeLikelihoodprotectedvirtual
computeDownSubtreeDLikelihood(const Node *)bpp::RHomogeneousTreeLikelihoodprotectedvirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSubtreeLikelihood(const Node *node)bpp::RHomogeneousTreeLikelihoodprotectedvirtual
computeTransitionProbabilitiesForNode(const Node *node)bpp::AbstractHomogeneousTreeLikelihoodprotectedvirtual
computeTreeD2Likelihood(const std::string &variable)bpp::RHomogeneousTreeLikelihoodvirtual
computeTreeDLikelihood(const std::string &variable)bpp::RHomogeneousTreeLikelihoodvirtual
computeTreeLikelihood()bpp::RHomogeneousTreeLikelihood
d2pxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
data_bpp::AbstractTreeLikelihoodprotected
DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinline
displayLikelihood(const Node *node)bpp::RHomogeneousTreeLikelihoodprotectedvirtual
displayLikelihoodArray(const VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
dpxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
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::RHomogeneousTreeLikelihoodprotected
bpp::getAlphabet() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getAlphabet() constbpp::AbstractTreeLikelihoodinlinevirtual
getAlphabetStateAsChar(size_t i) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStateAsInt(size_t i) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getAlphabetStates() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getBranchLengthsParameters() constbpp::AbstractHomogeneousTreeLikelihoodvirtual
getD2LikelihoodForASite(size_t site) constbpp::RHomogeneousTreeLikelihoodvirtual
getD2LikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RHomogeneousTreeLikelihoodvirtual
getD2LogLikelihood() constbpp::RHomogeneousTreeLikelihoodvirtual
getD2LogLikelihoodForASite(size_t site) constbpp::RHomogeneousTreeLikelihoodvirtual
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::RHomogeneousTreeLikelihoodvirtual
getDLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RHomogeneousTreeLikelihoodvirtual
getDLogLikelihood() constbpp::RHomogeneousTreeLikelihoodvirtual
getDLogLikelihoodForASite(size_t site) constbpp::RHomogeneousTreeLikelihoodvirtual
getFirstOrderDerivative(const std::string &variable) constbpp::RHomogeneousTreeLikelihood
getLikelihood() constbpp::RHomogeneousTreeLikelihoodvirtual
getLikelihoodData()bpp::RHomogeneousTreeLikelihoodinlinevirtual
getLikelihoodData() constbpp::RHomogeneousTreeLikelihoodinlinevirtual
getLikelihoodForASite(size_t site) constbpp::RHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RHomogeneousTreeLikelihoodvirtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) constbpp::RHomogeneousTreeLikelihoodvirtual
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::RHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASite(size_t site) constbpp::RHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) constbpp::RHomogeneousTreeLikelihoodvirtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) constbpp::RHomogeneousTreeLikelihoodvirtual
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::AbstractHomogeneousTreeLikelihoodinlinevirtual
getMinimumBranchLength() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getNewBranchModelIterator(int nodeId) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getNewSiteModelIterator(size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
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::AbstractHomogeneousTreeLikelihoodinlinevirtual
getPosteriorProbabilitiesOfEachRate() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getPosteriorRateOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateClassWithMaxPostProbOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRateDistribution() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistribution()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
getRateDistributionParameters() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getRateWithMaxPostProbOfEachSite() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getRootFrequencies(size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSecondOrderDerivative(const std::string &variable) constbpp::RHomogeneousTreeLikelihood
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) constbpp::RHomogeneousTreeLikelihoodinline
getSiteIndex(size_t site) constbpp::RHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel() constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) constbpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel()bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex)bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
getSubstitutionModelParameters() constbpp::AbstractHomogeneousTreeLikelihoodvirtual
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::AbstractHomogeneousTreeLikelihoodinlinevirtual
bpp::getTree() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTree() constbpp::AbstractTreeLikelihoodinlinevirtual
getValue() constbpp::RHomogeneousTreeLikelihood
init_(bool usePatterns)bpp::RHomogeneousTreeLikelihoodprivate
initBranchLengthsParameters()bpp::AbstractHomogeneousTreeLikelihoodvirtual
initialize()bpp::AbstractHomogeneousTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::AbstractHomogeneousTreeLikelihoodvirtual
bpp::isInitialized() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
likelihoodData_bpp::RHomogeneousTreeLikelihoodmutableprivate
maximumBrLen_bpp::AbstractHomogeneousTreeLikelihoodprotected
minimumBrLen_bpp::AbstractHomogeneousTreeLikelihoodprotected
minusLogLik_bpp::RHomogeneousTreeLikelihoodprotected
model_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbClasses_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbDistinctSites_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbNodes_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbSites_bpp::AbstractHomogeneousTreeLikelihoodprotected
nbStates_bpp::AbstractHomogeneousTreeLikelihoodprotected
nodes_bpp::AbstractHomogeneousTreeLikelihoodprotected
operator=(const RHomogeneousTreeLikelihood &lik)bpp::RHomogeneousTreeLikelihood
bpp::AbstractHomogeneousTreeLikelihood::operator=(const AbstractHomogeneousTreeLikelihood &lik)bpp::AbstractHomogeneousTreeLikelihood
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)bpp::AbstractTreeLikelihoodinline
pxy_bpp::AbstractHomogeneousTreeLikelihoodmutableprotected
rateDistribution_bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodprotected
resetLikelihoodArray(VVVdouble &likelihoodArray)bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodstatic
RHomogeneousMixedTreeLikelihood classbpp::RHomogeneousTreeLikelihoodfriend
RHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true, bool usePatterns=true)bpp::RHomogeneousTreeLikelihood
RHomogeneousTreeLikelihood(const Tree &tree, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool checkRooted=true, bool verbose=true, bool usePatterns=true)bpp::RHomogeneousTreeLikelihood
RHomogeneousTreeLikelihood(const RHomogeneousTreeLikelihood &lik)bpp::RHomogeneousTreeLikelihood
rootFreqs_bpp::AbstractHomogeneousTreeLikelihoodprotected
setData(const SiteContainer &sites)bpp::RHomogeneousTreeLikelihoodvirtual
setMaximumBranchLength(double maximum)bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
setParameters(const ParameterList &parameters)bpp::RHomogeneousTreeLikelihood
setSubstitutionModel(SubstitutionModel *model)bpp::AbstractHomogeneousTreeLikelihoodvirtual
tree_bpp::AbstractTreeLikelihoodmutableprotected
TreeLikelihood()bpp::TreeLikelihoodinline
verbose_bpp::AbstractHomogeneousTreeLikelihoodprotected
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~AbstractHomogeneousTreeLikelihood()bpp::AbstractHomogeneousTreeLikelihoodinlinevirtual
~AbstractTreeLikelihood()bpp::AbstractTreeLikelihoodinlinevirtual
~DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinlinevirtual
~RHomogeneousTreeLikelihood()bpp::RHomogeneousTreeLikelihoodvirtual
~TreeLikelihood()bpp::TreeLikelihoodinlinevirtual