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

Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, given an amino acid rate matrix (from a shared_ptr model). More...

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

+ Inheritance diagram for bpp::AbstractCodonAARateSubstitutionModel:
+ Collaboration diagram for bpp::AbstractCodonAARateSubstitutionModel:

Public Member Functions

 AbstractCodonAARateSubstitutionModel (std::shared_ptr< ProteinSubstitutionModelInterface > pmodel, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix, bool paramSynRate=false)
 Build a new AbstractCodonAARateSubstitutionModel object from a pointer to NucleotideSubstitutionModel. More...
 
 AbstractCodonAARateSubstitutionModel (const AbstractCodonAARateSubstitutionModel &model)
 
AbstractCodonAARateSubstitutionModel & operator= (const AbstractCodonAARateSubstitutionModel &model)
 
AbstractCodonAARateSubstitutionModel * clone () const override
 
virtual ~AbstractCodonAARateSubstitutionModel ()
 
void fireParameterChanged (const ParameterList &parameters) override
 
double getCodonsMulRate (size_t i, size_t j) const override
 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...
 
void setNamespace (const std::string &prefix) override
 
void setAAModel (std::shared_ptr< ProteinSubstitutionModelInterface > model)
 
const ProteinSubstitutionModelInterface & aaModel () const
 
const std::shared_ptr< ProteinSubstitutionModelInterface > getAAModel () const
 
const CodonFrequencySetInterface & codonFrequencySet () const override
 
bool hasCodonFrequencySet () const override
 
void setFreq (std::map< int, double > &frequencies) override
 
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 std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
bool hasIndependentParameter (const std::string &name) const
 
const ParameterList & getIndependentParameters () const
 
size_t getNumberOfIndependentParameters () const
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const override
 
const ParameterList & getParameters () const override
 
const Parameter & parameter (const std::string &name) const override
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
size_t getNumberOfParameters () const override
 
std::string getNamespace () const override
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
Parameter & getParameter_ (const std::string &name)
 
Parameter & getParameter_ (size_t index)
 
const Parameter & getParameter_ (size_t index) const
 
Parameter & getParameterWithNamespace_ (const std::string &name)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const
 
ParameterList & getParameters_ () override
 

Private Attributes

std::shared_ptr< ProteinSubstitutionModelInterface > pAAmodel_
 
std::shared_ptr< const GeneticCode > pgencode_
 
double beta_
 
double gamma_
 
std::shared_ptr< const StateMapInterface > stateMap_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, given an amino acid rate matrix (from a shared_ptr model).

Author
Laurent Guéguen

From the generator $g$ between amino-acids, the non-synonymous rate is multiplied with, if the coded amino-acids are $x$ and $y$, $\beta*g(x,y)$ with positive parameter "beta".

If paramSynRate is true, the synonymous substitution rate is multiplied with $\gamma$ (with optional positive parameter "gamma"), else it is multiplied with 1.

Definition at line 36 of file AbstractCodonAARateSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonAARateSubstitutionModel() [1/2]

AbstractCodonAARateSubstitutionModel::AbstractCodonAARateSubstitutionModel ( std::shared_ptr< ProteinSubstitutionModelInterface >  pmodel,
std::shared_ptr< const GeneticCode >  pgencode,
const std::string &  prefix,
bool  paramSynRate = false 
)

Build a new AbstractCodonAARateSubstitutionModel object from a pointer to NucleotideSubstitutionModel.

Parameters
pmodelshared_ptr to an amino_acid generator
pgencodethe genetic code
prefixthe Namespace
paramSynRateis true iff synonymous rate is parameterised (default=false).

Definition at line 15 of file AbstractCodonAARateSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), pAAmodel_, bpp::Parameter::R_PLUS_STAR, and bpp::NumConstants::SMALL().

Referenced by clone().

◆ AbstractCodonAARateSubstitutionModel() [2/2]

bpp::AbstractCodonAARateSubstitutionModel::AbstractCodonAARateSubstitutionModel ( const AbstractCodonAARateSubstitutionModel &  model)
inline

Definition at line 69 of file AbstractCodonAARateSubstitutionModel.h.

◆ ~AbstractCodonAARateSubstitutionModel()

virtual bpp::AbstractCodonAARateSubstitutionModel::~AbstractCodonAARateSubstitutionModel ( )
inlinevirtual

Definition at line 96 of file AbstractCodonAARateSubstitutionModel.h.

Member Function Documentation

◆ aaModel()

const ProteinSubstitutionModelInterface& bpp::AbstractCodonAARateSubstitutionModel::aaModel ( ) const
inline

Definition at line 118 of file AbstractCodonAARateSubstitutionModel.h.

References pAAmodel_.

◆ clone()

AbstractCodonAARateSubstitutionModel* bpp::AbstractCodonAARateSubstitutionModel::clone ( ) const
inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 91 of file AbstractCodonAARateSubstitutionModel.h.

References AbstractCodonAARateSubstitutionModel().

◆ codonFrequencySet()

const CodonFrequencySetInterface& bpp::AbstractCodonAARateSubstitutionModel::codonFrequencySet ( ) const
inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 128 of file AbstractCodonAARateSubstitutionModel.h.

◆ fireParameterChanged()

void AbstractCodonAARateSubstitutionModel::fireParameterChanged ( const ParameterList &  parameters)
overridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 38 of file AbstractCodonAARateSubstitutionModel.cpp.

References beta_, gamma_, bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::hasParameter(), and pAAmodel_.

◆ getAAModel()

const std::shared_ptr<ProteinSubstitutionModelInterface> bpp::AbstractCodonAARateSubstitutionModel::getAAModel ( ) const
inline

Definition at line 123 of file AbstractCodonAARateSubstitutionModel.h.

References pAAmodel_.

◆ getCodonsMulRate()

double AbstractCodonAARateSubstitutionModel::getCodonsMulRate ( size_t  ,
size_t   
) const
overridevirtual

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.

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 48 of file AbstractCodonAARateSubstitutionModel.cpp.

References beta_, gamma_, pAAmodel_, pgencode_, and stateMap_.

◆ hasCodonFrequencySet()

bool bpp::AbstractCodonAARateSubstitutionModel::hasCodonFrequencySet ( ) const
inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 133 of file AbstractCodonAARateSubstitutionModel.h.

◆ operator=()

AbstractCodonAARateSubstitutionModel& bpp::AbstractCodonAARateSubstitutionModel::operator= ( const AbstractCodonAARateSubstitutionModel &  model)
inline

Definition at line 78 of file AbstractCodonAARateSubstitutionModel.h.

References beta_, gamma_, bpp::AbstractParameterAliasable::operator=(), pAAmodel_, pgencode_, and stateMap_.

◆ setAAModel()

void bpp::AbstractCodonAARateSubstitutionModel::setAAModel ( std::shared_ptr< ProteinSubstitutionModelInterface >  model)
inline

Definition at line 113 of file AbstractCodonAARateSubstitutionModel.h.

References pAAmodel_.

◆ setFreq()

void bpp::AbstractCodonAARateSubstitutionModel::setFreq ( std::map< int, double > &  frequencies)
inlineoverridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 138 of file AbstractCodonAARateSubstitutionModel.h.

◆ setNamespace()

void bpp::AbstractCodonAARateSubstitutionModel::setNamespace ( const std::string &  prefix)
inlineoverridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 103 of file AbstractCodonAARateSubstitutionModel.h.

References pAAmodel_, and bpp::AbstractParameterAliasable::setNamespace().

Member Data Documentation

◆ beta_

double bpp::AbstractCodonAARateSubstitutionModel::beta_
private

Definition at line 45 of file AbstractCodonAARateSubstitutionModel.h.

Referenced by fireParameterChanged(), getCodonsMulRate(), and operator=().

◆ gamma_

double bpp::AbstractCodonAARateSubstitutionModel::gamma_
private

Definition at line 47 of file AbstractCodonAARateSubstitutionModel.h.

Referenced by fireParameterChanged(), getCodonsMulRate(), and operator=().

◆ pAAmodel_

std::shared_ptr<ProteinSubstitutionModelInterface> bpp::AbstractCodonAARateSubstitutionModel::pAAmodel_
private

Definition at line 41 of file AbstractCodonAARateSubstitutionModel.h.

Referenced by aaModel(), AbstractCodonAARateSubstitutionModel(), fireParameterChanged(), getAAModel(), getCodonsMulRate(), operator=(), setAAModel(), and setNamespace().

◆ pgencode_

std::shared_ptr<const GeneticCode> bpp::AbstractCodonAARateSubstitutionModel::pgencode_
private

Definition at line 43 of file AbstractCodonAARateSubstitutionModel.h.

Referenced by getCodonsMulRate(), and operator=().

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractCodonAARateSubstitutionModel::stateMap_
private

Definition at line 49 of file AbstractCodonAARateSubstitutionModel.h.

Referenced by getCodonsMulRate(), and operator=().

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