bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
bpp::AbstractCodonAAFitnessSubstitutionModel 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/AbstractCodonAAFitnessSubstitutionModel.h>

+ Inheritance diagram for bpp::AbstractCodonAAFitnessSubstitutionModel:
+ Collaboration diagram for bpp::AbstractCodonAAFitnessSubstitutionModel:

Public Member Functions

 AbstractCodonAAFitnessSubstitutionModel (std::shared_ptr< FrequencySetInterface > pfitset, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix)
 
 AbstractCodonAAFitnessSubstitutionModel (const AbstractCodonAAFitnessSubstitutionModel &model)
 
AbstractCodonAAFitnessSubstitutionModel & operator= (const AbstractCodonAAFitnessSubstitutionModel &model)
 
AbstractCodonAAFitnessSubstitutionModel * clone () const override
 
virtual ~AbstractCodonAAFitnessSubstitutionModel ()
 
void fireParameterChanged (const ParameterList &parameters) override
 
void setFreq (std::map< int, double > &frequencies) override
 
const CodonFrequencySetInterface & codonFrequencySet () const override
 
bool hasCodonFrequencySet () const 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 & aaFitness () const
 
std::shared_ptr< const FrequencySetInterface > getAAFitness () const
 
void addNsParameter ()
 
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< FrequencySetInterface > pfitset_
 
std::shared_ptr< const GeneticCode > pgencode_
 
std::string fitName_
 
std::shared_ptr< const StateMapInterface > stateMap_
 
std::shared_ptr< const StateMapInterface > protStateMap_
 
double Ns_
 The Ns of the model (default: 1), The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...
 
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
Laurent Guéguen

The fitness of an amino acid is a value between 0 and 1 defining the relative advantage of an amino acid, compared to others. If an amino acid $i$ 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

\[-\frac{\log\left((\frac{\phi_i}{\phi_j})^{s}\right)}{1-\left(\frac{\phi_i}{\phi_j}\right)^{s}}\]

where $s$ is a positive Ns coefficient (default value: 1).

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

Definition at line 38 of file AbstractCodonAAFitnessSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonAAFitnessSubstitutionModel() [1/2]

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

Definition at line 14 of file AbstractCodonAAFitnessSubstitutionModel.cpp.

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

Referenced by clone().

◆ AbstractCodonAAFitnessSubstitutionModel() [2/2]

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

Definition at line 66 of file AbstractCodonAAFitnessSubstitutionModel.h.

◆ ~AbstractCodonAAFitnessSubstitutionModel()

AbstractCodonAAFitnessSubstitutionModel::~AbstractCodonAAFitnessSubstitutionModel ( )
virtual

Definition at line 30 of file AbstractCodonAAFitnessSubstitutionModel.cpp.

Member Function Documentation

◆ aaFitness()

const FrequencySetInterface& bpp::AbstractCodonAAFitnessSubstitutionModel::aaFitness ( ) const
inline

Definition at line 119 of file AbstractCodonAAFitnessSubstitutionModel.h.

References pfitset_.

◆ addNsParameter()

void bpp::AbstractCodonAAFitnessSubstitutionModel::addNsParameter ( )
inline

Definition at line 123 of file AbstractCodonAAFitnessSubstitutionModel.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::getNamespace(), and bpp::NumConstants::MILLI().

◆ clone()

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

Implements bpp::AbstractParameterAliasable.

Definition at line 89 of file AbstractCodonAAFitnessSubstitutionModel.h.

References AbstractCodonAAFitnessSubstitutionModel().

◆ codonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 101 of file AbstractCodonAAFitnessSubstitutionModel.h.

◆ fireParameterChanged()

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

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 33 of file AbstractCodonAAFitnessSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractParameterAliasable::hasParameter(), Ns_, and pfitset_.

◆ getAAFitness()

std::shared_ptr<const FrequencySetInterface> bpp::AbstractCodonAAFitnessSubstitutionModel::getAAFitness ( ) const
inline

Definition at line 121 of file AbstractCodonAAFitnessSubstitutionModel.h.

References pfitset_.

◆ getCodonsMulRate()

double AbstractCodonAAFitnessSubstitutionModel::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 AbstractCodonAAFitnessSubstitutionModel.cpp.

References bpp::log(), Ns_, pfitset_, pgencode_, bpp::pow(), protStateMap_, and stateMap_.

◆ hasCodonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 106 of file AbstractCodonAAFitnessSubstitutionModel.h.

◆ operator=()

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

Definition at line 76 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

◆ setFreq()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 42 of file AbstractCodonAAFitnessSubstitutionModel.cpp.

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

◆ setNamespace()

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

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 111 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

Member Data Documentation

◆ fitName_

std::string bpp::AbstractCodonAAFitnessSubstitutionModel::fitName_
private

Definition at line 47 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

◆ Ns_

double bpp::AbstractCodonAAFitnessSubstitutionModel::Ns_
private

The Ns of the model (default: 1), The generator (and all its vectorial components) is independent of the rate, since it should be normalized.

Definition at line 58 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

◆ pfitset_

std::shared_ptr<FrequencySetInterface> bpp::AbstractCodonAAFitnessSubstitutionModel::pfitset_
private

Definition at line 43 of file AbstractCodonAAFitnessSubstitutionModel.h.

Referenced by aaFitness(), AbstractCodonAAFitnessSubstitutionModel(), fireParameterChanged(), getAAFitness(), getCodonsMulRate(), operator=(), setFreq(), and setNamespace().

◆ pgencode_

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

Definition at line 45 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

◆ protStateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractCodonAAFitnessSubstitutionModel::protStateMap_
private

Definition at line 51 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

◆ stateMap_

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

Definition at line 49 of file AbstractCodonAAFitnessSubstitutionModel.h.

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

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