AbstractHmmTransitionMatrix(std::shared_ptr< const HmmStateAlphabet > alph, const std::string &prefix="") | bpp::AbstractHmmTransitionMatrix | |
AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix &hptm) | bpp::AbstractHmmTransitionMatrix | |
AbstractParametrizable(const std::string &prefix) | bpp::AbstractParametrizable | inline |
addParameter_(Parameter *parameter) | bpp::AbstractParametrizable | inlineprotectedvirtual |
addParameters_(const ParameterList ¶meters) | bpp::AbstractParametrizable | inlineprotectedvirtual |
AutoCorrelationTransitionMatrix(std::shared_ptr< const HmmStateAlphabet > alph, const std::string &prefix="") | bpp::AutoCorrelationTransitionMatrix | |
AutoCorrelationTransitionMatrix(const AutoCorrelationTransitionMatrix &hptm) | bpp::AutoCorrelationTransitionMatrix | |
clone() const override | bpp::AutoCorrelationTransitionMatrix | inlinevirtual |
deleteParameter_(size_t index) | bpp::AbstractParametrizable | inlineprotectedvirtual |
deleteParameter_(std::string &name) | bpp::AbstractParametrizable | inlineprotectedvirtual |
deleteParameters_(const std::vector< std::string > &names) | bpp::AbstractParametrizable | inlineprotectedvirtual |
eqFreq_ | bpp::AbstractHmmTransitionMatrix | mutableprotected |
fireParameterChanged(const ParameterList ¶meters) override | bpp::AutoCorrelationTransitionMatrix | virtual |
getEquilibriumFrequencies() const override | bpp::AutoCorrelationTransitionMatrix | virtual |
getHmmStateAlphabet() const | bpp::AbstractHmmTransitionMatrix | inlinevirtual |
bpp::getNamespace() const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::getNamespace() const override | bpp::AbstractParametrizable | inlinevirtual |
bpp::getNumberOfParameters() const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::getNumberOfParameters() const override | bpp::AbstractParametrizable | inlinevirtual |
getNumberOfStates() const | bpp::AbstractHmmTransitionMatrix | inlinevirtual |
getParameter(const std::string &name) const | bpp::AbstractParametrizable | inline |
getParameter(size_t i) const | bpp::AbstractParametrizable | inlineprotected |
getParameter(size_t i) | bpp::AbstractParametrizable | inlineprotected |
getParameter_(const std::string &name) | bpp::AbstractParametrizable | inlineprotected |
getParameter_(size_t index) | bpp::AbstractParametrizable | inlineprotected |
getParameter_(size_t index) const | bpp::AbstractParametrizable | inlineprotected |
bpp::getParameterNameWithoutNamespace(const std::string &name) const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const override | bpp::AbstractParametrizable | virtual |
bpp::getParameters() const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::getParameters() const override | bpp::AbstractParametrizable | inlinevirtual |
bpp::getParameters_()=0 | bpp::Parametrizable | protectedpure virtual |
bpp::AbstractParametrizable::getParameters_() override | bpp::AbstractParametrizable | inlineprotectedvirtual |
bpp::getParameterValue(const std::string &name) const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const override | bpp::AbstractParametrizable | inlinevirtual |
getParameterWithNamespace_(const std::string &name) | bpp::AbstractParametrizable | inlineprotected |
getParameterWithNamespace_(const std::string &name) const | bpp::AbstractParametrizable | inlineprotected |
getPij() const override | bpp::AutoCorrelationTransitionMatrix | virtual |
bpp::hasParameter(const std::string &name) const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::hasParameter(const std::string &name) const override | bpp::AbstractParametrizable | inlinevirtual |
hmmStateAlphabet() const | bpp::AbstractHmmTransitionMatrix | inlinevirtual |
includeParameters_(const ParameterList ¶meters) | bpp::AbstractParametrizable | inlineprotectedvirtual |
bpp::matchParametersValues(const ParameterList ¶meters)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::matchParametersValues(const ParameterList ¶meters) override | bpp::AbstractParametrizable | inlinevirtual |
operator=(const AutoCorrelationTransitionMatrix &hptm) | bpp::AutoCorrelationTransitionMatrix | |
bpp::AbstractHmmTransitionMatrix::operator=(const AbstractHmmTransitionMatrix &hptm) | bpp::AbstractHmmTransitionMatrix | |
bpp::parameter(const std::string &name) const =0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::parameter(const std::string &name) const override | bpp::AbstractParametrizable | inlinevirtual |
Parametrizable() | bpp::Parametrizable | inline |
Pij(size_t i, size_t j) const override | bpp::AutoCorrelationTransitionMatrix | inlinevirtual |
pij_ | bpp::AbstractHmmTransitionMatrix | mutableprotected |
bpp::removeConstraint(const std::string &name)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::removeConstraint(const std::string &name) override | bpp::AbstractParametrizable | inlinevirtual |
resetParameters_() | bpp::AbstractParametrizable | inlineprotected |
sample(size_t size) const | bpp::AbstractHmmTransitionMatrix | |
bpp::setAllParametersValues(const ParameterList ¶meters)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList ¶meters) override | bpp::AbstractParametrizable | inlinevirtual |
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override | bpp::AbstractParametrizable | inlinevirtual |
setHmmStateAlphabet(std::shared_ptr< const HmmStateAlphabet > stateAlphabet) | bpp::AbstractHmmTransitionMatrix | virtual |
bpp::setNamespace(const std::string &prefix)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::setNamespace(const std::string &prefix) override | bpp::AbstractParametrizable | virtual |
bpp::setParametersValues(const ParameterList ¶meters)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::setParametersValues(const ParameterList ¶meters) override | bpp::AbstractParametrizable | inlinevirtual |
bpp::setParameterValue(const std::string &name, double value)=0 | bpp::Parametrizable | pure virtual |
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) override | bpp::AbstractParametrizable | inlinevirtual |
shareParameter_(const std::shared_ptr< Parameter > ¶meter) | bpp::AbstractParametrizable | inlineprotectedvirtual |
shareParameters_(const ParameterList ¶meters) | bpp::AbstractParametrizable | inlineprotectedvirtual |
tmpmat_ | bpp::AbstractHmmTransitionMatrix | mutableprotected |
upToDate_ | bpp::AbstractHmmTransitionMatrix | mutableprotected |
vAutocorrel_ | bpp::AutoCorrelationTransitionMatrix | private |
~AbstractParametrizable() | bpp::AbstractParametrizable | inlinevirtual |
~Clonable()=default | bpp::Clonable | virtual |
~Parametrizable() | bpp::Parametrizable | inlinevirtual |