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

Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...

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

+ Inheritance diagram for bpp::AbstractCodonFitnessSubstitutionModel:
+ Collaboration diagram for bpp::AbstractCodonFitnessSubstitutionModel:

Public Member Functions

 AbstractCodonFitnessSubstitutionModel (std::unique_ptr< FrequencySetInterface > pfitset, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix)
 
 AbstractCodonFitnessSubstitutionModel (const AbstractCodonFitnessSubstitutionModel &model)
 
AbstractCodonFitnessSubstitutionModel & operator= (const AbstractCodonFitnessSubstitutionModel &model)
 
AbstractCodonFitnessSubstitutionModel * clone () const override
 
virtual ~AbstractCodonFitnessSubstitutionModel ()
 
void fireParameterChanged (const ParameterList &parameters) override
 
void setFreq (std::map< int, double > &frequencies) override
 
void setNamespace (const std::string &prefix) 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...
 
const FrequencySetInterface & fitness () const
 
const CodonFrequencySetInterface & codonFrequencySet () const override
 
bool hasCodonFrequencySet () const 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::unique_ptr< FrequencySetInterface > pfitset_
 
std::shared_ptr< const GeneticCode > pgencode_
 
std::string fitName_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not.

Author
Fanny Pouyet, Laurent Guéguen

The fitness of a codon is a value between 0 and 1 defining the relative advantage of a codon, compared to others. If a codon $i$ has a fitness $\phi_i$ and another one ( $j$) has a fitness $\phi_j$, the substitution rate from codon $i$ to codon $j$ is multiplied by

\[-\frac{\log(\frac{\phi_i}{\phi_j})}{1-\frac{\phi_i}{\phi_j}}\]

The set of fitnesses is implemented through a Codon FrequencySet object. The parameters are named "fit_NameOfTheParameterInTheFrequencySet".

Definition at line 33 of file AbstractCodonFitnessSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonFitnessSubstitutionModel() [1/2]

AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel ( std::unique_ptr< FrequencySetInterface >  pfitset,
std::shared_ptr< const GeneticCode >  pgencode,
const std::string &  prefix 
)

Definition at line 11 of file AbstractCodonFitnessSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), fitName_, and pfitset_.

Referenced by clone().

◆ AbstractCodonFitnessSubstitutionModel() [2/2]

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

Definition at line 50 of file AbstractCodonFitnessSubstitutionModel.h.

◆ ~AbstractCodonFitnessSubstitutionModel()

AbstractCodonFitnessSubstitutionModel::~AbstractCodonFitnessSubstitutionModel ( )
virtual

Definition at line 28 of file AbstractCodonFitnessSubstitutionModel.cpp.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::SENCA.

Definition at line 66 of file AbstractCodonFitnessSubstitutionModel.h.

References AbstractCodonFitnessSubstitutionModel().

◆ codonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::SENCA.

Definition at line 93 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by bpp::SENCA::codonFrequencySet().

◆ fireParameterChanged()

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

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::SENCA.

Definition at line 32 of file AbstractCodonFitnessSubstitutionModel.cpp.

References pfitset_.

Referenced by bpp::SENCA::fireParameterChanged().

◆ fitness()

const FrequencySetInterface& bpp::AbstractCodonFitnessSubstitutionModel::fitness ( ) const
inline

Definition at line 88 of file AbstractCodonFitnessSubstitutionModel.h.

References pfitset_.

◆ getCodonsMulRate()

double AbstractCodonFitnessSubstitutionModel::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.

Reimplemented in bpp::SENCA.

Definition at line 47 of file AbstractCodonFitnessSubstitutionModel.cpp.

References bpp::log(), and pfitset_.

Referenced by bpp::SENCA::getCodonsMulRate().

◆ hasCodonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::SENCA.

Definition at line 98 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by bpp::SENCA::hasCodonFrequencySet().

◆ operator=()

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

Definition at line 57 of file AbstractCodonFitnessSubstitutionModel.h.

References fitName_, bpp::AbstractParameterAliasable::operator=(), pfitset_, and pgencode_.

◆ setFreq()

void AbstractCodonFitnessSubstitutionModel::setFreq ( std::map< int, double > &  frequencies)
overridevirtual

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::SENCA.

Definition at line 39 of file AbstractCodonFitnessSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::matchParametersValues(), and pfitset_.

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

◆ setNamespace()

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

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::SENCA.

Definition at line 80 of file AbstractCodonFitnessSubstitutionModel.h.

References fitName_, pfitset_, and bpp::AbstractParameterAliasable::setNamespace().

Referenced by bpp::SENCA::setNamespace().

Member Data Documentation

◆ fitName_

std::string bpp::AbstractCodonFitnessSubstitutionModel::fitName_
private

Definition at line 42 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by AbstractCodonFitnessSubstitutionModel(), operator=(), and setNamespace().

◆ pfitset_

std::unique_ptr<FrequencySetInterface> bpp::AbstractCodonFitnessSubstitutionModel::pfitset_
private

Definition at line 38 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by AbstractCodonFitnessSubstitutionModel(), fireParameterChanged(), fitness(), getCodonsMulRate(), operator=(), setFreq(), and setNamespace().

◆ pgencode_

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

Definition at line 40 of file AbstractCodonFitnessSubstitutionModel.h.

Referenced by operator=().

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