bpp-phyl3  3.0.0
bpp::AlignedPhyloLikelihoodAutoCorrelation Member List

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

AbstractAlignedPhyloLikelihood(Context &context, size_t nbSites)bpp::AbstractAlignedPhyloLikelihoodinline
AbstractAlignedPhyloLikelihood(const AbstractAlignedPhyloLikelihood &aasd)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
AbstractAlignedPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, bool inCollection=true, const std::string &prefix="")bpp::AbstractAlignedPhyloLikelihoodSet
AbstractAlignedPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true, const std::string &prefix="")bpp::AbstractAlignedPhyloLikelihoodSet
AbstractAlignedPhyloLikelihoodSet(const AbstractAlignedPhyloLikelihoodSet &soap)bpp::AbstractAlignedPhyloLikelihoodSetinlineprotected
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractPhyloLikelihood(Context &context)bpp::AbstractPhyloLikelihoodinline
AbstractPhyloLikelihood(const AbstractPhyloLikelihood &apl)bpp::AbstractPhyloLikelihoodinline
AbstractPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, bool inCollection=true, const std::string &prefix="")bpp::AbstractPhyloLikelihoodSet
AbstractPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true, const std::string &prefix="")bpp::AbstractPhyloLikelihoodSet
AbstractPhyloLikelihoodSet(const AbstractPhyloLikelihoodSet &sd)bpp::AbstractPhyloLikelihoodSetinlineprotected
accessVariableNode(const Parameter &param)bpp::AbstractPhyloLikelihoodinlineprotectedstatic
accessVariableNode(const std::string &name) constbpp::AbstractPhyloLikelihoodinlineprotected
addParameter_(Parameter *parameter)bpp::AbstractParametrizableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
addPhyloLikelihood(size_t nPhyl, const std::string &suff) overridebpp::AbstractAlignedPhyloLikelihoodSetvirtual
alignedLikelihoodCalculation() constbpp::AlignedPhyloLikelihoodAutoCorrelationinlinevirtual
alignedPhyloLikelihood(size_t nPhyl) const overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
alignedPhyloLikelihood(size_t nPhyl) overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
AlignedPhyloLikelihoodAutoCorrelation(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true)bpp::AlignedPhyloLikelihoodAutoCorrelation
AlignedPhyloLikelihoodAutoCorrelation(const AlignedPhyloLikelihoodAutoCorrelation &mlc)bpp::AlignedPhyloLikelihoodAutoCorrelationinlineprotected
AlignedPhyloLikelihoodInterface()bpp::AlignedPhyloLikelihoodInterfaceinline
clone() constbpp::AlignedPhyloLikelihoodAutoCorrelationinlineprotectedvirtual
bpp::context() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::context()=0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::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::AbstractPhyloLikelihoodSet::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::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives(bool yn) overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
f(const ParameterList &parameters)bpp::SecondOrderDerivablevirtual
fireParameterChanged(const ParameterList &parameters)bpp::AlignedPhyloLikelihoodAutoCorrelationvirtual
FirstOrderDerivable()bpp::FirstOrderDerivable
firstOrderDerivativeNode(const std::string &variable) constbpp::AbstractPhyloLikelihoodinline
firstOrderDerivativeNodes_bpp::AbstractPhyloLikelihoodmutableprotected
FunctionInterface()bpp::FunctionInterface
getAlignedLikelihoodCalculation() constbpp::AlignedPhyloLikelihoodAutoCorrelationinlinevirtual
getAlignedPhyloLikelihood(size_t nPhyl) const overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
getAlignedPhyloLikelihood(size_t nPhyl) overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
bpp::getBranchLengthParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getBranchLengthParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
bpp::getDerivableParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getDerivableParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
bpp::getFirstOrderDerivative(const std::string &variable) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(const std::string &variable) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
getHmmTransitionMatrix() constbpp::AlignedPhyloLikelihoodAutoCorrelationinline
getLikelihoodCalculation() constbpp::AlignedPhyloLikelihoodAutoCorrelationinlinevirtual
bpp::getLikelihoodForASite(size_t site) const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(size_t site) constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
getLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
bpp::getLikelihoodNode() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::getLikelihoodNode() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::getLikelihoodPerSite() const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite() constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
getLogLikelihood() constbpp::PhyloLikelihoodInterfaceinline
bpp::getLogLikelihoodForASite(size_t site) const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite(size_t site) constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
getLogLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const overridebpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
bpp::getNamespace() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getNamespace() const overridebpp::AbstractParametrizablevirtual
bpp::getNonDerivableParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getNonDerivableParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
bpp::getNumberOfParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getNumberOfParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getNumberOfSites() const =0bpp::AlignedPhyloLikelihoodInterfacepure virtual
bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites() constbpp::AbstractAlignedPhyloLikelihoodinlinevirtual
bpp::getNumbersOfPhyloLikelihoods() const =0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getNumbersOfPhyloLikelihoods() const overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
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::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParametrizablevirtual
bpp::getParameters() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getParameters() const overridebpp::AbstractParametrizablevirtual
bpp::getParameters_()=0bpp::SecondOrderDerivableprotectedpure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getParameters_() overridebpp::AbstractParametrizableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::getParameterValue(const std::string &name) const overridebpp::AbstractParametrizablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParametrizableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParametrizableprotected
bpp::getPhyloContainer()=0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::getPhyloContainer() const =0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getPhyloContainer() overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
bpp::AbstractPhyloLikelihoodSet::getPhyloContainer() const overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
bpp::getPhyloLikelihood(size_t nPhyl) const =0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::getPhyloLikelihood(size_t nPhyl)=0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(size_t nPhyl) const overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(size_t nPhyl) overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
getPosteriorProbabilitiesForASitePerAligned(size_t site) constbpp::AlignedPhyloLikelihoodAutoCorrelationinline
getPosteriorProbabilitiesPerSitePerAligned() constbpp::AlignedPhyloLikelihoodAutoCorrelationinline
bpp::getRateDistributionParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getRateDistributionParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
bpp::getRootFrequenciesParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getRootFrequenciesParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
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::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::getSubstitutionModelParameters() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::getSubstitutionModelParameters() const overridebpp::AbstractPhyloLikelihoodSetvirtual
bpp::getValue() const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::getValue() const overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::hasParameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::hasParameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
bpp::hasPhyloLikelihood(size_t nPhyl)=0bpp::PhyloLikelihoodSetInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::hasPhyloLikelihood(size_t nPhyl) overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
hma_bpp::AlignedPhyloLikelihoodAutoCorrelationprivate
hmm_bpp::AlignedPhyloLikelihoodAutoCorrelationmutableprivate
hpep_bpp::AlignedPhyloLikelihoodAutoCorrelationprivate
htm_bpp::AlignedPhyloLikelihoodAutoCorrelationprivate
includeParameters_(const ParameterList &parameters)bpp::AbstractParametrizableprotectedvirtual
bpp::isInitialized() const =0bpp::PhyloLikelihoodInterfacepure virtual
bpp::AbstractPhyloLikelihoodSet::isInitialized() const overridebpp::AbstractPhyloLikelihoodSetinlinevirtual
likelihoodCalculation() constbpp::AlignedPhyloLikelihoodAutoCorrelationinlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
minusLogLik_bpp::AbstractPhyloLikelihoodmutableprotected
nbSites_bpp::AbstractAlignedPhyloLikelihoodprotected
nPhylo_bpp::AbstractPhyloLikelihoodSetprotected
operator=(const AlignedPhyloLikelihoodAutoCorrelation &mlc)bpp::AlignedPhyloLikelihoodAutoCorrelationinlineprotected
bpp::AbstractAlignedPhyloLikelihoodSet::operator=(const AbstractAlignedPhyloLikelihoodSet &soap)bpp::AbstractAlignedPhyloLikelihoodSetinlineprotected
bpp::AbstractPhyloLikelihoodSet::operator=(const AbstractPhyloLikelihoodSet &sd)bpp::AbstractPhyloLikelihoodSetinlineprotected
bpp::AbstractPhyloLikelihood::operator=(const AbstractPhyloLikelihood &apl)bpp::AbstractPhyloLikelihoodinline
bpp::AbstractAlignedPhyloLikelihood::operator=(const AbstractAlignedPhyloLikelihood &aasd)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
bpp::parameter(const std::string &name) const=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::parameter(const std::string &name) const overridebpp::AbstractParametrizablevirtual
parameters_bpp::AbstractParametrizableprivate
Parametrizable()bpp::Parametrizable
PhyloLikelihoodInterface()bpp::PhyloLikelihoodInterfaceinline
pPhyloCont_bpp::AbstractPhyloLikelihoodSetprotected
prefix_bpp::AbstractParametrizableprivate
bpp::removeConstraint(const std::string &name)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::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
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParametrizablevirtual
setNamespace(const std::string &nameSpace)bpp::AlignedPhyloLikelihoodAutoCorrelationvirtual
setNumberOfSites(size_t nbSites)bpp::AbstractAlignedPhyloLikelihoodinlineprotected
bpp::setParameters(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractPhyloLikelihood::setParameters(const ParameterList &parameters) overridebpp::AbstractPhyloLikelihoodinlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParametrizablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::SecondOrderDerivablepure virtual
bpp::AbstractPhyloLikelihoodSet::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
vLikCal_bpp::AbstractPhyloLikelihoodSetmutableprotected
~AbstractAlignedPhyloLikelihood()bpp::AbstractAlignedPhyloLikelihoodinlinevirtual
~AbstractAlignedPhyloLikelihoodSet()bpp::AbstractAlignedPhyloLikelihoodSetinlinevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractPhyloLikelihood()bpp::AbstractPhyloLikelihoodinlinevirtual
~AbstractPhyloLikelihoodSet()bpp::AbstractPhyloLikelihoodSetinlinevirtual
~AlignedPhyloLikelihoodAutoCorrelation()bpp::AlignedPhyloLikelihoodAutoCorrelationinlinevirtual
~AlignedPhyloLikelihoodInterface()bpp::AlignedPhyloLikelihoodInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~FirstOrderDerivable()bpp::FirstOrderDerivablevirtual
~FunctionInterface()bpp::FunctionInterfacevirtual
~Parametrizable()bpp::Parametrizablevirtual
~PhyloLikelihoodInterface()bpp::PhyloLikelihoodInterfaceinlinevirtual
~SecondOrderDerivable()bpp::SecondOrderDerivablevirtual