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

Abstract Class for substitution models on codons parametrized by a frequency. More...

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

+ Inheritance diagram for bpp::AbstractCodonPhaseFrequenciesSubstitutionModel:
+ Collaboration diagram for bpp::AbstractCodonPhaseFrequenciesSubstitutionModel:

Public Member Functions

 AbstractCodonPhaseFrequenciesSubstitutionModel (std::unique_ptr< CodonFrequencySetInterface > pfreq, const std::string &prefix)
 Build a AbstractCodonPhaseFrequenciesSubstitutionModel instance. More...
 
 AbstractCodonPhaseFrequenciesSubstitutionModel (const AbstractCodonPhaseFrequenciesSubstitutionModel &model)
 
AbstractCodonPhaseFrequenciesSubstitutionModel & operator= (const AbstractCodonPhaseFrequenciesSubstitutionModel &model)
 
AbstractCodonPhaseFrequenciesSubstitutionModel * clone () const override
 
virtual ~AbstractCodonPhaseFrequenciesSubstitutionModel ()
 
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, size_t) 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 CodonFrequencySetInterface & codonFrequencySet () const override
 
const FrequencySetInterface & frequencySet () const
 
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< CodonFrequencySetInterface > posFreqSet_
 Position dependent version of Codon Frequencies Set. More...
 
std::string freqName_
 
ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Abstract Class for substitution models on codons parametrized by a frequency.

Author
Laurent Guéguen

This class should be used with models which equilibrium distribution is fixed, and does not depend on the parameters. Otherwise there may be problems of identifiability of the parameters.

If we denote $F$ the given frequencies for codons, $F_{j_k}$ is the frequency of letter $j$ in phase $k$.

For codons $i=i_1i_2i_3$ and $j=j_1j_2j_3$, the generator term defined from inherited and inheriting classes, $Q_{ij})$, is multiplied by the product of the $F_{j_k}$ for each $k \in 1, 2, 3$ such that $i_k \neq j_k$.

Definition at line 34 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonPhaseFrequenciesSubstitutionModel() [1/2]

AbstractCodonPhaseFrequenciesSubstitutionModel::AbstractCodonPhaseFrequenciesSubstitutionModel ( std::unique_ptr< CodonFrequencySetInterface >  pfreq,
const std::string &  prefix 
)

Build a AbstractCodonPhaseFrequenciesSubstitutionModel instance.

Parameters
pfreqpointer to the AbstractFrequencySet equilibrium frequencies. It is owned by the instance.
prefixthe Namespace

Definition at line 15 of file AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), fireParameterChanged(), freqName_, and posFreqSet_.

Referenced by clone().

◆ AbstractCodonPhaseFrequenciesSubstitutionModel() [2/2]

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

Definition at line 57 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

◆ ~AbstractCodonPhaseFrequenciesSubstitutionModel()

AbstractCodonPhaseFrequenciesSubstitutionModel::~AbstractCodonPhaseFrequenciesSubstitutionModel ( )
virtual

Definition at line 57 of file AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractParameterAliasable.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 72 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References AbstractCodonPhaseFrequenciesSubstitutionModel().

◆ codonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 91 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References posFreqSet_.

Referenced by bpp::CodonDistancePhaseFrequenciesSubstitutionModel::codonFrequencySet(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), and bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq().

◆ fireParameterChanged()

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

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 61 of file AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.

References posFreqSet_.

Referenced by AbstractCodonPhaseFrequenciesSubstitutionModel(), and bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::frequencySet ( ) const
inline

Definition at line 96 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References posFreqSet_.

◆ getCodonsMulRate()

double AbstractCodonPhaseFrequenciesSubstitutionModel::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::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 76 of file AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.

References bpp::WordFrequencySetInterface::frequencySetForLetter(), and bpp::FrequencySetInterface::getFrequencies().

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

◆ hasCodonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 101 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References posFreqSet_.

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

◆ operator=()

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

Definition at line 63 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References freqName_, bpp::AbstractParameterAliasable::operator=(), and posFreqSet_.

◆ setFreq()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 68 of file AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.

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

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

◆ setNamespace()

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

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel.

Definition at line 83 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

References freqName_, posFreqSet_, and bpp::AbstractParameterAliasable::setNamespace().

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

Member Data Documentation

◆ freqName_

std::string bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::freqName_
private

Definition at line 43 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

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

◆ posFreqSet_

std::unique_ptr<CodonFrequencySetInterface> bpp::AbstractCodonPhaseFrequenciesSubstitutionModel::posFreqSet_
private

Position dependent version of Codon Frequencies Set.

Definition at line 42 of file AbstractCodonPhaseFrequenciesSubstitutionModel.h.

Referenced by AbstractCodonPhaseFrequenciesSubstitutionModel(), codonFrequencySet(), fireParameterChanged(), frequencySet(), hasCodonFrequencySet(), operator=(), setFreq(), and setNamespace().

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