bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | List of all members
bpp::CoreCodonSubstitutionModelInterface Class Referenceabstract

Interface for codon models. More...

#include <Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h>

+ Inheritance diagram for bpp::CoreCodonSubstitutionModelInterface:
+ Collaboration diagram for bpp::CoreCodonSubstitutionModelInterface:

Public Member Functions

 CoreCodonSubstitutionModelInterface ()
 
virtual ~CoreCodonSubstitutionModelInterface ()
 
virtual CoreCodonSubstitutionModelInterface * clone () const override=0
 
virtual double getCodonsMulRate (size_t, size_t) const =0
 Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. More...
 
virtual const CodonFrequencySetInterface & codonFrequencySet () const =0
 
virtual bool hasCodonFrequencySet () const =0
 
virtual void setFreq (std::map< int, double > &frequencies)=0
 
virtual size_t getNumberOfIndependentParameters () const=0
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 
virtual const ParameterList & getIndependentParameters () const=0
 
virtual std::vector< std::string > getAlias (const std::string &name) const=0
 
virtual std::map< std::string, std::string > getAliases () const=0
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual const ParameterList & getParameters () const=0
 
virtual const Parameter & parameter (const std::string &name) const=0
 
virtual double getParameterValue (const std::string &name) const=0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
virtual size_t getNumberOfParameters () const=0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 

Detailed Description

Interface for codon models.

Author
Laurent Guéguen

This class aims at defining methods needed for inheriting codon.

Definition at line 22 of file CodonSubstitutionModel.h.

Constructor & Destructor Documentation

◆ CoreCodonSubstitutionModelInterface()

bpp::CoreCodonSubstitutionModelInterface::CoreCodonSubstitutionModelInterface ( )
inline

Definition at line 26 of file CodonSubstitutionModel.h.

◆ ~CoreCodonSubstitutionModelInterface()

virtual bpp::CoreCodonSubstitutionModelInterface::~CoreCodonSubstitutionModelInterface ( )
inlinevirtual

Definition at line 27 of file CodonSubstitutionModel.h.

Member Function Documentation

◆ clone()

virtual CoreCodonSubstitutionModelInterface* bpp::CoreCodonSubstitutionModelInterface::clone ( ) const
overridepure virtual

Implements bpp::ParameterAliasable.

Implemented in bpp::CodonReversibleSubstitutionModelInterface, bpp::CodonSubstitutionModelInterface, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.

◆ codonFrequencySet()

virtual const CodonFrequencySetInterface& bpp::CoreCodonSubstitutionModelInterface::codonFrequencySet ( ) const
pure virtual

Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.

Referenced by bpp::CodonSameAARateSubstitutionModel::CodonSameAARateSubstitutionModel().

◆ getCodonsMulRate()

virtual double bpp::CoreCodonSubstitutionModelInterface::getCodonsMulRate ( size_t  ,
size_t   
) const
pure virtual

Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.

Implemented in bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, and bpp::CodonDistanceSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), and bpp::RE08Codon::getCodonsMulRate().

◆ hasCodonFrequencySet()

virtual bool bpp::CoreCodonSubstitutionModelInterface::hasCodonFrequencySet ( ) const
pure virtual

Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.

◆ setFreq()

virtual void bpp::CoreCodonSubstitutionModelInterface::setFreq ( std::map< int, double > &  frequencies)
pure virtual

Implemented in bpp::RE08Codon, bpp::YN98, bpp::SENCA, bpp::MG94, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, and bpp::AbstractCodonAAFitnessSubstitutionModel.

Referenced by bpp::CodonSameAARateSubstitutionModel::setFreq().

The documentation for this class was generated from the following file: