bpp-core3  3.0.0
bpp::AbstractHmmTransitionMatrix Member List

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

AbstractHmmTransitionMatrix(std::shared_ptr< const HmmStateAlphabet > alph, const std::string &prefix="")bpp::AbstractHmmTransitionMatrix
AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix &hptm)bpp::AbstractHmmTransitionMatrix
alph_bpp::AbstractHmmTransitionMatrixprivate
clone() const override=0bpp::HmmTransitionMatrixpure virtual
eqFreq_bpp::AbstractHmmTransitionMatrixmutableprotected
getEquilibriumFrequencies() const =0bpp::HmmTransitionMatrixpure virtual
getHmmStateAlphabet() constbpp::AbstractHmmTransitionMatrixinlinevirtual
getNamespace() const =0bpp::Parametrizablepure virtual
getNumberOfParameters() const =0bpp::Parametrizablepure virtual
getNumberOfStates() constbpp::AbstractHmmTransitionMatrixinlinevirtual
getParameterNameWithoutNamespace(const std::string &name) const =0bpp::Parametrizablepure virtual
getParameters() const =0bpp::Parametrizablepure virtual
getParameters_()=0bpp::Parametrizableprotectedpure virtual
getParameterValue(const std::string &name) const =0bpp::Parametrizablepure virtual
getPij() const =0bpp::HmmTransitionMatrixpure virtual
hasParameter(const std::string &name) const =0bpp::Parametrizablepure virtual
hmmStateAlphabet() constbpp::AbstractHmmTransitionMatrixinlinevirtual
matchParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
operator=(const AbstractHmmTransitionMatrix &hptm)bpp::AbstractHmmTransitionMatrix
parameter(const std::string &name) const =0bpp::Parametrizablepure virtual
Parametrizable()bpp::Parametrizableinline
Pij(size_t i, size_t j) const =0bpp::HmmTransitionMatrixpure virtual
pij_bpp::AbstractHmmTransitionMatrixmutableprotected
removeConstraint(const std::string &name)=0bpp::Parametrizablepure virtual
sample(size_t size) constbpp::AbstractHmmTransitionMatrix
setAllParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::Parametrizablepure virtual
setHmmStateAlphabet(std::shared_ptr< const HmmStateAlphabet > stateAlphabet)bpp::AbstractHmmTransitionMatrixvirtual
setNamespace(const std::string &prefix)=0bpp::Parametrizablepure virtual
setParametersValues(const ParameterList &parameters)=0bpp::Parametrizablepure virtual
setParameterValue(const std::string &name, double value)=0bpp::Parametrizablepure virtual
tmpmat_bpp::AbstractHmmTransitionMatrixmutableprotected
upToDate_bpp::AbstractHmmTransitionMatrixmutableprotected
~Clonable()=defaultbpp::Clonablevirtual
~Parametrizable()bpp::Parametrizableinlinevirtual