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

Abstract class for modelling of CpG -> CpA or TpG (symmetric) hypermutability substitution rate inside codons. Note that the neihbouring effects between codons are not considered. More...

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

+ Inheritance diagram for bpp::AbstractCodonCpGSubstitutionModel:
+ Collaboration diagram for bpp::AbstractCodonCpGSubstitutionModel:

Public Member Functions

 AbstractCodonCpGSubstitutionModel (std::shared_ptr< const CodonAlphabet > alphabet, const std::string &prefix)
 Build a new AbstractCodonCpGSubstitutionModel object from a pointer to NucleotideSubstitutionModel. More...
 
 AbstractCodonCpGSubstitutionModel (const AbstractCodonCpGSubstitutionModel &model)
 
AbstractCodonCpGSubstitutionModel & operator= (const AbstractCodonCpGSubstitutionModel &model)
 
AbstractCodonCpGSubstitutionModel * clone () const override
 
virtual ~AbstractCodonCpGSubstitutionModel ()
 
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...
 
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 void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
void setNamespace (const std::string &prefix)
 
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

double rho_
 
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 CpG -> CpA or TpG (symmetric) hypermutability substitution rate inside codons. Note that the neihbouring effects between codons are not considered.

Author
Laurent Guéguen

Substitution rate from C to T (resp. from G to A) is multiplied by a factor $\rho$ if C is followed by a G (resp. if G is following a C).

Hypermutability parameter is named "rho".

Definition at line 27 of file AbstractCodonCpGSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractCodonCpGSubstitutionModel() [1/2]

AbstractCodonCpGSubstitutionModel::AbstractCodonCpGSubstitutionModel ( std::shared_ptr< const CodonAlphabet >  alphabet,
const std::string &  prefix 
)

Build a new AbstractCodonCpGSubstitutionModel object from a pointer to NucleotideSubstitutionModel.

Parameters
alphabetthe codon alphabet
prefixthe Namespace

Definition at line 15 of file AbstractCodonCpGSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), and bpp::NumConstants::SMALL().

Referenced by clone().

◆ AbstractCodonCpGSubstitutionModel() [2/2]

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

Definition at line 48 of file AbstractCodonCpGSubstitutionModel.h.

◆ ~AbstractCodonCpGSubstitutionModel()

virtual bpp::AbstractCodonCpGSubstitutionModel::~AbstractCodonCpGSubstitutionModel ( )
inlinevirtual

Definition at line 68 of file AbstractCodonCpGSubstitutionModel.h.

Member Function Documentation

◆ clone()

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

Implements bpp::AbstractParameterAliasable.

Definition at line 63 of file AbstractCodonCpGSubstitutionModel.h.

References AbstractCodonCpGSubstitutionModel().

◆ codonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 75 of file AbstractCodonCpGSubstitutionModel.h.

◆ fireParameterChanged()

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

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 25 of file AbstractCodonCpGSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::getParameterValue(), and rho_.

◆ getCodonsMulRate()

double AbstractCodonCpGSubstitutionModel::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 30 of file AbstractCodonCpGSubstitutionModel.cpp.

References rho_, and stateMap_.

◆ hasCodonFrequencySet()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 80 of file AbstractCodonCpGSubstitutionModel.h.

◆ operator=()

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

Definition at line 54 of file AbstractCodonCpGSubstitutionModel.h.

References bpp::AbstractParameterAliasable::operator=(), rho_, and stateMap_.

◆ setFreq()

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

Implements bpp::CoreCodonSubstitutionModelInterface.

Definition at line 85 of file AbstractCodonCpGSubstitutionModel.h.

Member Data Documentation

◆ rho_

double bpp::AbstractCodonCpGSubstitutionModel::rho_
private

Definition at line 32 of file AbstractCodonCpGSubstitutionModel.h.

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

◆ stateMap_

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

Definition at line 34 of file AbstractCodonCpGSubstitutionModel.h.

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

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