bpp-phyl3  3.0.0
bpp::OneProcessSequencePhyloLikelihood Member List

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

AbstractAlignedPhyloLikelihood(Context &context, size_t nbSites)bpp::AbstractAlignedPhyloLikelihoodinline
AbstractAlignedPhyloLikelihood(const AbstractAlignedPhyloLikelihood &aasd)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractParametrizableSequencePhyloLikelihood(Context &context, std::shared_ptr< SequenceEvolution > se, size_t nSE=0, size_t nData=0)bpp::AbstractParametrizableSequencePhyloLikelihoodinline
AbstractParametrizableSequencePhyloLikelihood(const AbstractParametrizableSequencePhyloLikelihood &apspl)bpp::AbstractParametrizableSequencePhyloLikelihoodinline
AbstractPhyloLikelihood(Context &context)bpp::AbstractPhyloLikelihoodinline
AbstractPhyloLikelihood(const AbstractPhyloLikelihood &apl)bpp::AbstractPhyloLikelihoodinline
AbstractSequencePhyloLikelihood(Context &context, std::shared_ptr< SequenceEvolution > se, size_t nSE=0, size_t nData=0)bpp::AbstractSequencePhyloLikelihoodinline
AbstractSequencePhyloLikelihood(const AbstractSequencePhyloLikelihood &aspl)bpp::AbstractSequencePhyloLikelihoodinline
AbstractSingleDataPhyloLikelihood(Context &context, size_t nbSites, size_t nbStates, size_t nData=0)bpp::AbstractSingleDataPhyloLikelihoodinline
AbstractSingleDataPhyloLikelihood(const AbstractSingleDataPhyloLikelihood &asdpl)bpp::AbstractSingleDataPhyloLikelihoodinline
accessVariableNode(const Parameter &param)bpp::AbstractPhyloLikelihoodinlineprotectedstatic
accessVariableNode(const std::string &name) constbpp::AbstractPhyloLikelihoodinlineprotected
addParameter_(Parameter *parameter)bpp::AbstractParametrizableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
alignedLikelihoodCalculation() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
AlignedPhyloLikelihoodInterface()bpp::AlignedPhyloLikelihoodInterfaceinline
clone() const overridebpp::OneProcessSequencePhyloLikelihoodinlineprotectedvirtual
bpp::context() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::context()=0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::context() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::context() overridebpp::AbstractPhyloLikelihoodinlinevirtual
context_bpp::AbstractPhyloLikelihoodprotected
d2f(const std::string &variable, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
deleteParameter_(size_t index)bpp::AbstractParametrizableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParametrizableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParametrizableprotectedvirtual
df(const std::string &variable, const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
bpp::enableFirstOrderDerivatives(bool yn)=0bpp::SecondOrderDerivablepure virtual
bpp::enableFirstOrderDerivatives() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives(bool yn) overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::enableSecondOrderDerivatives(bool yn)=0bpp::SecondOrderDerivablepure virtual
bpp::enableSecondOrderDerivatives() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives(bool yn) overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
fireParameterChanged(const ParameterList &parameters) overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlineprotectedvirtual
FirstOrderDerivable()bpp::FirstOrderDerivable
firstOrderDerivativeNode(const std::string &variable) constbpp::AbstractPhyloLikelihoodinline
firstOrderDerivativeNodes_bpp::AbstractPhyloLikelihoodmutableprotected
firstOrderDerivativeVector(const std::string &variable) constbpp::OneProcessSequencePhyloLikelihoodinline
firstOrderDerivativeVectors_bpp::OneProcessSequencePhyloLikelihoodmutableprivate
FunctionInterface()bpp::FunctionInterface
getAlignedLikelihoodCalculation() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
getAlphabet() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
getBranchLengthParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
getClassWithMaxPostProbPerSite() constbpp::OneProcessSequencePhyloLikelihood
getData() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
getDerivableParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
bpp::getFirstOrderDerivative(const std::string &variable) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(const std::string &variable) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
getFirstOrderDerivativeVector(const std::string &variable) constbpp::OneProcessSequencePhyloLikelihoodinline
getLikelihoodCalculation() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
getLikelihoodCalculationSingleProcess() constbpp::OneProcessSequencePhyloLikelihoodinline
bpp::getLikelihoodForASite(size_t site) const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(size_t site) constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
bpp::getLikelihoodNode() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getLikelihoodNode() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::getLikelihoodPerSite() const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite() constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
getLikelihoodPerSitePerClass() constbpp::OneProcessSequencePhyloLikelihood
getLogLikelihood() constbpp::PhyloLikelihoodInterfaceinline
bpp::getLogLikelihoodForASite(size_t site) const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite(size_t site) constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
bpp::getNamespace() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getNamespace() const overridebpp::AbstractParametrizablevirtual
bpp::getNData() const =0bpp::SingleDataPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::getNData() constbpp::AbstractSingleDataPhyloLikelihoodinlinevirtual
getNonDerivableParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
getNumberOfClasses() constbpp::OneProcessSequencePhyloLikelihoodinline
bpp::getNumberOfParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getNumberOfParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getNumberOfSites() const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites() constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
bpp::getNumberOfStates() const =0bpp::SingleDataPhyloLikelihoodInterfacepure virtual
bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates() constbpp::AbstractSingleDataPhyloLikelihoodinlinevirtual
getParameter(const std::string &name) constbpp::AbstractParametrizable
getParameter(size_t i) constbpp::AbstractParametrizableprotected
getParameter(size_t i)bpp::AbstractParametrizableprotected
getParameter_(const std::string &name)bpp::AbstractParametrizableprotected
getParameter_(size_t index)bpp::AbstractParametrizableprotected
getParameter_(size_t index) constbpp::AbstractParametrizableprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParametrizablevirtual
bpp::getParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getParameters_()=0bpp::SecondOrderDerivableprotectedpure virtual
bpp::AbstractParametrizable::getParameters_() overridebpp::AbstractParametrizableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const overridebpp::AbstractParametrizablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParametrizableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParametrizableprotected
getPosteriorProbabilitiesForSitePerClass(size_t pos) constbpp::OneProcessSequencePhyloLikelihood
getPosteriorProbabilitiesPerSitePerClass() constbpp::OneProcessSequencePhyloLikelihood
getPosteriorRatePerSite() constbpp::OneProcessSequencePhyloLikelihood
getPosteriorStateFrequencies(uint nodeId)bpp::OneProcessSequencePhyloLikelihood
getRateDistributionParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
getRootFrequenciesParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
bpp::getSecondOrderDerivative(const std::string &variable) const=0bpp::SecondOrderDerivablepure virtual
bpp::getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
getSecondOrderDerivativeVector(const std::string &variable) constbpp::OneProcessSequencePhyloLikelihoodinline
getSecondOrderDerivativeVector(const std::string &variable1, const std::string &variable2) constbpp::OneProcessSequencePhyloLikelihoodinline
getSequenceEvolution() const overridebpp::AbstractSequencePhyloLikelihoodinlinevirtual
getSequenceEvolutionNumber() const overridebpp::AbstractSequencePhyloLikelihoodinlinevirtual
getSubstitutionModelParameters() const overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
getSubstitutionProcess() constbpp::OneProcessSequencePhyloLikelihoodinline
getSubstitutionProcessParameters() constbpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
bpp::getValue() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::getValue() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::hasParameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
isInitialized() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
likCal_bpp::OneProcessSequencePhyloLikelihoodmutableprotected
likelihoodCalculation() const overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
likelihoodCalculationSingleProcess() constbpp::OneProcessSequencePhyloLikelihoodinline
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
minusLogLik_bpp::AbstractPhyloLikelihoodmutableprotected
mSeqEvol_bpp::OneProcessSequencePhyloLikelihoodprivate
nbSites_bpp::AbstractAlignedPhyloLikelihoodprotected
nbStates_bpp::AbstractSingleDataPhyloLikelihoodprotected
nData_bpp::AbstractSingleDataPhyloLikelihoodprotected
nSeqEvol_bpp::AbstractSequencePhyloLikelihoodprotected
OneProcessSequencePhyloLikelihood(Context &context, std::shared_ptr< OneProcessSequenceEvolution > evol, size_t nSeqEvol=0)bpp::OneProcessSequencePhyloLikelihood
OneProcessSequencePhyloLikelihood(Context &context, std::shared_ptr< const AlignmentDataInterface > data, std::shared_ptr< OneProcessSequenceEvolution > evol, size_t nSeqEvol=0, size_t nData=0)bpp::OneProcessSequencePhyloLikelihood
OneProcessSequencePhyloLikelihood(std::shared_ptr< const AlignmentDataInterface > data, std::shared_ptr< OneProcessSequenceEvolution > evol, std::shared_ptr< CollectionNodes > collNodes, size_t nSeqEvol=0, size_t nData=0)bpp::OneProcessSequencePhyloLikelihood
OneProcessSequencePhyloLikelihood(const OneProcessSequencePhyloLikelihood &lik)bpp::OneProcessSequencePhyloLikelihoodinlineprotected
operator=(const OneProcessSequencePhyloLikelihood &lik)bpp::OneProcessSequencePhyloLikelihoodinlineprotected
bpp::AbstractParametrizableSequencePhyloLikelihood::operator=(const AbstractParametrizableSequencePhyloLikelihood &apspl)bpp::AbstractParametrizableSequencePhyloLikelihoodinline
bpp::AbstractSequencePhyloLikelihood::operator=(const AbstractSequencePhyloLikelihood &aspl)bpp::AbstractSequencePhyloLikelihoodinline
bpp::AbstractSingleDataPhyloLikelihood::operator=(const AbstractSingleDataPhyloLikelihood &asdpl)bpp::AbstractSingleDataPhyloLikelihoodinline
bpp::AbstractAlignedPhyloLikelihood::operator=(const AbstractAlignedPhyloLikelihood &aasd)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
bpp::AbstractPhyloLikelihood::operator=(const AbstractPhyloLikelihood &apl)bpp::AbstractPhyloLikelihoodinline
bpp::parameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::parameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
parameters_bpp::AbstractParametrizableprivate
Parametrizable()bpp::Parametrizable
PhyloLikelihoodInterface()bpp::PhyloLikelihoodInterfaceinline
prefix_bpp::AbstractParametrizableprivate
bpp::removeConstraint(const std::string &name)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::removeConstraint(const std::string &name) overridebpp::AbstractParametrizablevirtual
resetParameters_()bpp::AbstractParametrizableprotected
SecondOrderDerivable()bpp::SecondOrderDerivable
secondOrderDerivativeNode(const std::string &variable1, const std::string &variable2) constbpp::AbstractPhyloLikelihoodinline
secondOrderDerivativeNodes_bpp::AbstractPhyloLikelihoodmutableprotected
secondOrderDerivativeVector(const std::string &variable1, const std::string &variable2) constbpp::OneProcessSequencePhyloLikelihoodinline
secondOrderDerivativeVectors_bpp::OneProcessSequencePhyloLikelihoodmutableprivate
seqEvol_bpp::AbstractSequencePhyloLikelihoodprotected
sequenceEvolution() const overridebpp::AbstractSequencePhyloLikelihoodinlinevirtual
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParametrizablevirtual
setData(std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0) overridebpp::OneProcessSequencePhyloLikelihoodinlinevirtual
setNamespace(const std::string &nameSpace) overridebpp::AbstractParametrizableSequencePhyloLikelihoodinlinevirtual
setNData(size_t nData)bpp::AbstractSingleDataPhyloLikelihoodinline
setNumberOfSites(size_t nbSites)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
bpp::setParameters(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractSingleDataPhyloLikelihood::bpp::AbstractAlignedPhyloLikelihood::bpp::AbstractPhyloLikelihood::setParameters(const ParameterList &parameters) overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParametrizablevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParametrizableprotectedvirtual
shareParameters(const ParameterList &variableNodes)bpp::AbstractPhyloLikelihoodinline
shareParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
SingleDataPhyloLikelihoodInterface()bpp::SingleDataPhyloLikelihoodInterfaceinline
substitutionProcess() constbpp::OneProcessSequencePhyloLikelihoodinline
tree() constbpp::OneProcessSequencePhyloLikelihoodinline
~AbstractAlignedPhyloLikelihood()bpp::AbstractAlignedPhyloLikelihoodinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractPhyloLikelihood()bpp::AbstractPhyloLikelihoodinlinevirtual
~AbstractSingleDataPhyloLikelihood()bpp::AbstractSingleDataPhyloLikelihoodinlinevirtual
~AlignedPhyloLikelihoodInterface()bpp::AlignedPhyloLikelihoodInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~FirstOrderDerivable()bpp::FirstOrderDerivablevirtual
~FunctionInterface()bpp::FunctionInterfacevirtual
~OneProcessSequencePhyloLikelihood()bpp::OneProcessSequencePhyloLikelihoodinlinevirtual
~Parametrizable()bpp::Parametrizablevirtual
~PhyloLikelihoodInterface()bpp::PhyloLikelihoodInterfaceinlinevirtual
~SecondOrderDerivable()bpp::SecondOrderDerivablevirtual
~SequencePhyloLikelihoodInterface()bpp::SequencePhyloLikelihoodInterfaceinlineprotectedvirtual
~SingleDataPhyloLikelihoodInterface()bpp::SingleDataPhyloLikelihoodInterfaceinlinevirtual