bpp-phyl  2.2.0
bpp::AbstractNonHomogeneousTreeLikelihood Member List

This is the complete list of members for bpp::AbstractNonHomogeneousTreeLikelihood, 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() const =0bpp::NonHomogeneousTreeLikelihoodpure virtual
computeAllTransitionProbabilities()bpp::AbstractNonHomogeneousTreeLikelihoodprotectedvirtual
computeFirstOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeSecondOrderDerivatives_bpp::AbstractTreeLikelihoodprotected
computeTransitionProbabilitiesForNode(const Node *node)bpp::AbstractNonHomogeneousTreeLikelihoodprotectedvirtual
d2pxy_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
data_bpp::AbstractTreeLikelihoodprotected
DiscreteRatesAcrossSitesTreeLikelihood()bpp::DiscreteRatesAcrossSitesTreeLikelihoodinline
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
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
bpp::getData() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getData() constbpp::AbstractTreeLikelihoodinlinevirtual
bpp::getDerivableParameters() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters() constbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihoodvirtual
getLikelihood() const =0bpp::TreeLikelihoodpure virtual
getLikelihoodData()=0bpp::TreeLikelihoodpure virtual
getLikelihoodData() const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodpure virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
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() const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForASite(size_t site) const =0bpp::TreeLikelihoodpure virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0bpp::DiscreteRatesAcrossSitesTreeLikelihoodpure virtual
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
getSiteIndex(size_t site) const =0bpp::TreeLikelihoodpure virtual
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
idToNode_bpp::AbstractNonHomogeneousTreeLikelihoodmutableprotected
init_(const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose)bpp::AbstractNonHomogeneousTreeLikelihoodprivate
initBranchLengthsParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
initialize()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
initialized_bpp::AbstractTreeLikelihoodprotected
initParameters()bpp::AbstractNonHomogeneousTreeLikelihoodvirtual
bpp::isInitialized() const =0bpp::TreeLikelihoodpure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() constbpp::AbstractTreeLikelihoodinlinevirtual
maximumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
minimumBrLen_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
modelSet_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbClasses_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbDistinctSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbNodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbSites_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nbStates_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
nodes_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
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
root1_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
root2_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
rootFreqs_bpp::AbstractNonHomogeneousTreeLikelihoodprotected
setData(const SiteContainer &sites)=0bpp::TreeLikelihoodpure virtual
setMaximumBranchLength(double maximum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
setMinimumBranchLength(double minimum)bpp::AbstractNonHomogeneousTreeLikelihoodinlinevirtual
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
~TreeLikelihood()bpp::TreeLikelihoodinlinevirtual