bpp-core3  3.0.0
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
bpp::ReparametrizationDerivableFirstOrderWrapper Class Referenceabstract

Function wrapper that remove simple constraints on parameters. Also transform first order derivatives. More...

#include <Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h>

+ Inheritance diagram for bpp::ReparametrizationDerivableFirstOrderWrapper:
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Public Member Functions

 ReparametrizationDerivableFirstOrderWrapper (DerivableFirstOrder *function, bool verbose=true)
 Build a new reparametrization wrapper for the given function, using all available parameters. More...
 
 ReparametrizationDerivableFirstOrderWrapper (DerivableFirstOrder *function, const ParameterList &parameters, bool verbose=true)
 Build a new reparametrization wrapper for the given function, using only the specified parameters. More...
 
virtual ~ReparametrizationDerivableFirstOrderWrapper ()
 
ReparametrizationDerivableFirstOrderWrapper * clone () const
 Create a copy of this object and send a pointer to it. More...
 
void enableFirstOrderDerivatives (bool yn)
 Tell if derivatives must be computed. More...
 
bool enableFirstOrderDerivatives () const
 Tell if derivatives must be computed. More...
 
double getFirstOrderDerivative (const std::string &variable) const
 Get the derivative of the function at the current point. More...
 
virtual double df (const std::string &variable, const ParameterList &parameters)
 Get the value of the first derivative of the function according to a given set of parameters. More...
 
virtual void setParameters (const ParameterList &parameters)=0
 Set the point where the function must be computed. More...
 
virtual double getValue () const =0
 Get the value of the function at the current point. More...
 
virtual double f (const ParameterList &parameters)
 Get the value of the function according to a given set of parameters. More...
 
virtual bool hasParameter (const std::string &name) const =0
 Tell if there is a parameter with specified name. More...
 
virtual const ParameterList & getParameters () const =0
 Get all parameters available. More...
 
virtual const Parameter & getParameter (const std::string &name) const =0
 Get the parameter with specified name. More...
 
virtual double getParameterValue (const std::string &name) const =0
 Get the value for parameter of name 'name'. More...
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 Set the parameters values to be equals to those of parameters. More...
 
virtual void setParameterValue (const std::string &name, double value)=0
 Set the value of parameter with name name to be equal to value. More...
 
virtual void setParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters. More...
 
virtual void setNamespace (const std::string &prefix)=0
 Set the namespace for the parameter names. More...
 
virtual std::string getNamespace () const =0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 Resolves a parameter name according to the current namespace. More...
 
virtual const Function & getFunction () const
 
virtual Function & getFunction ()
 
void setParameters (const ParameterList &parameters)
 Set the point where the function must be computed. More...
 
double getValue () const
 Get the value of the function at the current point. More...
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 
bool hasParameter (const std::string &name) const
 Tell if there is a parameter with specified name. More...
 
const ParameterList & getParameters () const
 Get all parameters available. More...
 
const Parameter & getParameter (const std::string &name) const
 Get the parameter with specified name. More...
 
double getParameterValue (const std::string &name) const
 Get the value for parameter of name 'name'. More...
 
void setAllParametersValues (const ParameterList &parameters)
 Set the parameters values to be equals to those of parameters. More...
 
void setParameterValue (const std::string &name, double value)
 Set the value of parameter with name name to be equal to value. More...
 
void setParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
bool matchParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
size_t getNumberOfParameters () const
 Get the number of parameters. More...
 
void setNamespace (const std::string &prefix)
 Set the namespace for the parameter names. More...
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 Resolves a parameter name according to the current namespace. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 

Protected Member Functions

virtual ParameterList & getParameters_ ()=0
 Get all parameters available. More...
 
ParameterList & getParameters_ ()
 Get all parameters available. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (size_t i) const
 
std::shared_ptr< Parameter > & getSharedParameter (size_t i)
 
virtual void addParameter_ (Parameter *parameter)
 
virtual void addParameters_ (const ParameterList &parameters)
 
virtual void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
virtual void shareParameters_ (const ParameterList &parameters)
 
virtual void includeParameters_ (const ParameterList &parameters)
 
virtual void deleteParameter_ (size_t index)
 
virtual void deleteParameter_ (std::string &name)
 
virtual 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
 

Private Member Functions

void init_ (bool verbose)
 

Private Attributes

Function * function_
 
ParameterList functionParameters_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

Function wrapper that remove simple constraints on parameters. Also transform first order derivatives.

This function takes as input another function and reparametrize it when possible. currently, only constraint of the type ]a, b[ where a and b can be +/- inf.

Definition at line 145 of file ReparametrizationFunctionWrapper.h.

Constructor & Destructor Documentation

◆ ReparametrizationDerivableFirstOrderWrapper() [1/2]

bpp::ReparametrizationDerivableFirstOrderWrapper::ReparametrizationDerivableFirstOrderWrapper ( DerivableFirstOrder *  function,
bool  verbose = true 
)
inline

Build a new reparametrization wrapper for the given function, using all available parameters.

Parameters
functionThe function to reparametrize.
verbosePrint some information.

Definition at line 156 of file ReparametrizationFunctionWrapper.h.

Referenced by clone().

◆ ReparametrizationDerivableFirstOrderWrapper() [2/2]

bpp::ReparametrizationDerivableFirstOrderWrapper::ReparametrizationDerivableFirstOrderWrapper ( DerivableFirstOrder *  function,
const ParameterList &  parameters,
bool  verbose = true 
)
inline

Build a new reparametrization wrapper for the given function, using only the specified parameters.

Parameters
functionThe function to reparametrize.
parametersThe list of parameters that will be reparametrized. The intersection with the list of function parameters will be used in the reparametrized function. Any other parameters (in the given list or in the original function) will be ignored.
verbosePrint some information.

Definition at line 169 of file ReparametrizationFunctionWrapper.h.

◆ ~ReparametrizationDerivableFirstOrderWrapper()

virtual bpp::ReparametrizationDerivableFirstOrderWrapper::~ReparametrizationDerivableFirstOrderWrapper ( )
inlinevirtual

Definition at line 173 of file ReparametrizationFunctionWrapper.h.

Member Function Documentation

◆ addParameter_()

virtual void bpp::AbstractParametrizable::addParameter_ ( Parameter *  parameter)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::addParameter_(), bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), and bpp::TestFunction::TestFunction().

◆ addParameters_()

virtual void bpp::AbstractParametrizable::addParameters_ ( const ParameterList &  parameters)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 143 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::addParameters_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().

◆ clone()

ReparametrizationDerivableFirstOrderWrapper* bpp::ReparametrizationDerivableFirstOrderWrapper::clone ( ) const
inlinevirtual

Create a copy of this object and send a pointer to it.

Returns
A pointer toward the copy object.

Implements bpp::DerivableFirstOrder.

Reimplemented in bpp::ReparametrizationDerivableSecondOrderWrapper.

Definition at line 175 of file ReparametrizationFunctionWrapper.h.

References ReparametrizationDerivableFirstOrderWrapper().

◆ deleteParameter_() [1/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( size_t  index)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 163 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::deleteParameter_().

◆ deleteParameter_() [2/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( std::string &  name)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 170 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), and bpp::AbstractParametrizable::parameters_.

◆ deleteParameters_()

virtual void bpp::AbstractParametrizable::deleteParameters_ ( const std::vector< std::string > &  names)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 175 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters(), and bpp::AbstractParametrizable::parameters_.

◆ df()

virtual double bpp::DerivableFirstOrder::df ( const std::string &  variable,
const ParameterList &  parameters 
)
inlinevirtualinherited

Get the value of the first derivative of the function according to a given set of parameters.

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 173 of file Functions.h.

References bpp::DerivableFirstOrder::getFirstOrderDerivative(), and bpp::Function::setParameters().

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives ( ) const
inlinevirtual

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 183 of file ReparametrizationFunctionWrapper.h.

References enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by enableFirstOrderDerivatives().

◆ enableFirstOrderDerivatives() [2/2]

void bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives ( bool  yn)
inlinevirtual

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableFirstOrder.

Definition at line 181 of file ReparametrizationFunctionWrapper.h.

References enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by enableFirstOrderDerivatives().

◆ f()

virtual double bpp::Function::f ( const ParameterList &  parameters)
inlinevirtualinherited

Get the value of the function according to a given set of parameters.

Parameters
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, and bpp::AbstractNumericalDerivative.

Definition at line 117 of file Functions.h.

References bpp::Function::getValue(), and bpp::Function::setParameters().

Referenced by bpp::BrentOneDimension::doInit(), bpp::DownhillSimplexMethod::doInit(), bpp::GoldenSectionSearch::doInit(), bpp::NewtonBacktrackOneDimension::doInit(), bpp::NewtonOneDimension::doInit(), bpp::PowellMultiDimensions::doInit(), bpp::BfgsMultiDimensions::doStep(), bpp::BrentOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::FunctionWrapper::f(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::PowellMultiDimensions::optimize(), bpp::AbstractOptimizer::step(), bpp::DownhillSimplexMethod::tryExtrapolation(), and bpp::NumTools::uniRoot().

◆ fireParameterChanged()

void ReparametrizationFunctionWrapper::fireParameterChanged ( const ParameterList &  parameters)
virtualinherited

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 177 of file ReparametrizationFunctionWrapper.cpp.

References bpp::ApplicationTools::error, and bpp::Parameter::setValue().

◆ getFirstOrderDerivative()

double bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative ( const std::string &  variable) const
inlinevirtual

Get the derivative of the function at the current point.

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::DerivableFirstOrder.

Definition at line 185 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::getFunction(), and bpp::AbstractParametrizable::getParameter().

Referenced by bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative().

◆ getFunction() [1/2]

virtual Function& bpp::ReparametrizationFunctionWrapper::getFunction ( )
inlinevirtualinherited

Definition at line 120 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ getFunction() [2/2]

virtual const Function& bpp::ReparametrizationFunctionWrapper::getFunction ( ) const
inlinevirtualinherited

Definition at line 118 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

Referenced by enableFirstOrderDerivatives(), bpp::ReparametrizationDerivableSecondOrderWrapper::enableSecondOrderDerivatives(), getFirstOrderDerivative(), and bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative().

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const
inlinevirtualinherited
Returns
The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNamespace() [2/2]

virtual std::string bpp::Parametrizable::getNamespace ( ) const
pure virtualinherited
Returns
The current namespace used. This is an empty string if no namespace is currently defined.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getNamespace().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const
inlinevirtualinherited

Get the number of parameters.

See also
getNumberOfIndependentParameters If some parameters are aliased.
Returns
The number of parameters.

Implements bpp::Parametrizable.

Definition at line 121 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ getNumberOfParameters() [2/2]

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const
pure virtualinherited

Get the number of parameters.

See also
getNumberOfIndependentParameters If some parameters are aliased.
Returns
The number of parameters.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getParameter() [1/2]

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string &  name) const
inlinevirtualinherited

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 79 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::getAliasedParameters(), getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().

◆ getParameter() [2/2]

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string &  name) const
pure virtualinherited

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
inlineprotectedinherited
Parameters
nameThe name of the parameter.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index)
inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

◆ getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index) const
inlineprotectedinherited

Definition at line 223 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

std::string AbstractParametrizable::getParameterNameWithoutNamespace ( const std::string &  name) const
virtualinherited

Resolves a parameter name according to the current namespace.

Returns
The parameter name without the namespace prefix, if any.

Implements bpp::Parametrizable.

Definition at line 65 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::shareParameters_().

◆ getParameterNameWithoutNamespace() [2/2]

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string &  name) const
pure virtualinherited

Resolves a parameter name according to the current namespace.

Returns
The parameter name without the namespace prefix, if any.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().

◆ getParameters() [1/2]

const ParameterList& bpp::AbstractParametrizable::getParameters ( ) const
inlinevirtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 77 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().

◆ getParameters() [2/2]

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const
pure virtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::NewtonOneDimension::doStep(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::FunctionWrapper::getParameters(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

◆ getParameters_() [1/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )
inlineprotectedvirtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 231 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), and bpp::AbstractParameterAliasable::operator=().

◆ getParameters_() [2/2]

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )
protectedpure virtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameters_().

◆ getParameterValue() [1/2]

double bpp::AbstractParametrizable::getParameterValue ( const std::string &  name) const
inlinevirtualinherited

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 89 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter(), and bpp::Parameter::getValue().

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ConstantDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ getParameterValue() [2/2]

virtual double bpp::Parametrizable::getParameterValue ( const std::string &  name) const
pure virtualinherited

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterValue().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 202 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name) const
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 211 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getSharedParameter() [1/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( const std::string &  name) const
inlineinherited

Definition at line 84 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getSharedParameter() [2/3]

std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( size_t  i)
inlineprotectedinherited

Definition at line 242 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.

◆ getSharedParameter() [3/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( size_t  i) const
inlineprotectedinherited
Returns
The shared_ptr parameter at a given position.
Warning
No check is performed on the validity of the index given as input!

Definition at line 237 of file AbstractParametrizable.h.

References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.

◆ getValue() [1/2]

double bpp::ReparametrizationFunctionWrapper::getValue ( ) const
inlinevirtualinherited

Get the value of the function at the current point.

Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 131 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_, and bpp::Function::getValue().

◆ getValue() [2/2]

virtual double bpp::Function::getValue ( ) const
pure virtualinherited

Get the value of the function at the current point.

Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implemented in bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::TwoPointsNumericalDerivative, bpp::ThreePointsNumericalDerivative, bpp::ReparametrizationFunctionWrapper, bpp::TestFunction, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::FivePointsNumericalDerivative, and bpp::DirectionFunction.

Referenced by bpp::MetaOptimizer::doInit(), bpp::MetaOptimizer::doStep(), bpp::SimpleMultiDimensions::doStep(), bpp::SimpleNewtonMultiDimensions::doStep(), bpp::Function::f(), bpp::FunctionWrapper::getValue(), bpp::InfinityFunctionWrapper::getValue(), bpp::ReparametrizationFunctionWrapper::getValue(), and bpp::AbstractOptimizer::init().

◆ hasParameter() [1/2]

bool bpp::AbstractParametrizable::hasParameter ( const std::string &  name) const
inlinevirtualinherited

Tell if there is a parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
y/n.

Implements bpp::Parametrizable.

Definition at line 75 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ hasParameter() [2/2]

virtual bool bpp::Parametrizable::hasParameter ( const std::string &  name) const
pure virtualinherited

Tell if there is a parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
y/n.

Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::hasParameter().

◆ includeParameters_()

virtual void bpp::AbstractParametrizable::includeParameters_ ( const ParameterList &  parameters)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 158 of file AbstractParametrizable.h.

References bpp::ParameterList::includeParameters(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::includeParameters_().

◆ init_()

void bpp::ReparametrizationDerivableFirstOrderWrapper::init_ ( bool  verbose)
private

◆ matchParametersValues() [1/2]

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList &  parameters)
inlinevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 112 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareSubList().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::TestFunction::setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ matchParametersValues() [2/2]

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList &  parameters)
pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )
inlineprotectedinherited

Definition at line 180 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().

Referenced by bpp::AbstractParameterAliasable::resetParameters_().

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters)
inlinevirtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 94 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setAllParametersValues().

◆ setAllParametersValues() [2/2]

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList &  parameters)
pure virtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

◆ setNamespace() [1/2]

void AbstractParametrizable::setNamespace ( const std::string &  prefix)
virtualinherited

Set the namespace for the parameter names.

Parameters
prefixThe 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implements bpp::Parametrizable.

Reimplemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

Definition at line 47 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::LogsumHmmLikelihood::setNamespace(), bpp::LowMemoryRescaledHmmLikelihood::setNamespace(), bpp::RescaledHmmLikelihood::setNamespace(), and bpp::AbstractParameterAliasable::setNamespace().

◆ setNamespace() [2/2]

virtual void bpp::Parametrizable::setNamespace ( const std::string &  prefix)
pure virtualinherited

Set the namespace for the parameter names.

Parameters
prefixThe 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::AbstractParametrizable, bpp::AbstractParameterAliasable, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::LogsumHmmLikelihood::setNamespace(), bpp::FunctionWrapper::setNamespace(), and bpp::InvariantMixedDiscreteDistribution::setNamespace().

◆ setParameters() [1/2]

void bpp::ReparametrizationFunctionWrapper::setParameters ( const ParameterList &  parameters)
inlinevirtualinherited

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implements bpp::Function.

Definition at line 122 of file ReparametrizationFunctionWrapper.h.

References bpp::ParameterList::createSubList(), bpp::ReparametrizationFunctionWrapper::function_, bpp::ReparametrizationFunctionWrapper::functionParameters_, bpp::ParameterList::getParameterNames(), bpp::AbstractParametrizable::matchParametersValues(), and bpp::Function::setParameters().

◆ setParameters() [2/2]

virtual void bpp::Function::setParameters ( const ParameterList &  parameters)
pure virtualinherited

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implemented in bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::ReparametrizationFunctionWrapper, bpp::TestFunction, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractNumericalDerivative.

Referenced by bpp::DerivableSecondOrder::d2f(), bpp::DerivableFirstOrder::df(), bpp::MetaOptimizer::doInit(), bpp::BfgsMultiDimensions::doInit(), bpp::ConjugateGradientMultiDimensions::doInit(), bpp::SimpleMultiDimensions::doInit(), bpp::SimpleNewtonMultiDimensions::doInit(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::Function::f(), bpp::AbstractNumericalDerivative::setParameters(), bpp::FunctionWrapper::setParameters(), bpp::InfinityFunctionWrapper::setParameters(), and bpp::ReparametrizationFunctionWrapper::setParameters().

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters)
inlinevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 106 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setParametersValues().

Referenced by bpp::LogsumHmmLikelihood::setParameters(), bpp::LowMemoryRescaledHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().

◆ setParametersValues() [2/2]

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList &  parameters)
pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

void bpp::AbstractParametrizable::setParameterValue ( const std::string &  name,
double  value 
)
inlinevirtualinherited

Set the value of parameter with name name to be equal to value.

Parameters
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 100 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, and bpp::ParameterList::setParameterValue().

◆ setParameterValue() [2/2]

virtual void bpp::Parametrizable::setParameterValue ( const std::string &  name,
double  value 
)
pure virtualinherited

Set the value of parameter with name name to be equal to value.

Parameters
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().

◆ shareParameter_()

virtual void bpp::AbstractParametrizable::shareParameter_ ( const std::shared_ptr< Parameter > &  parameter)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 148 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareParameter().

Referenced by bpp::AbstractParameterAliasable::shareParameter_().

◆ shareParameters_()

virtual void bpp::AbstractParametrizable::shareParameters_ ( const ParameterList &  parameters)
inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 153 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractParameterAliasable::shareParameters_().

Member Data Documentation

◆ function_

Function* bpp::ReparametrizationFunctionWrapper::function_
privateinherited

Definition at line 62 of file ReparametrizationFunctionWrapper.h.

Referenced by bpp::ReparametrizationFunctionWrapper::getFunction(), bpp::ReparametrizationFunctionWrapper::getValue(), bpp::ReparametrizationFunctionWrapper::operator=(), and bpp::ReparametrizationFunctionWrapper::setParameters().

◆ functionParameters_

ParameterList bpp::ReparametrizationFunctionWrapper::functionParameters_
privateinherited

Definition at line 63 of file ReparametrizationFunctionWrapper.h.

Referenced by bpp::ReparametrizationFunctionWrapper::operator=(), and bpp::ReparametrizationFunctionWrapper::setParameters().

◆ parameters_

ParameterList bpp::AbstractParametrizable::parameters_
privateinherited

Definition at line 66 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::addParameter_(), bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::deleteParameter_(), bpp::AbstractParametrizable::deleteParameters_(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParametrizable::matchParametersValues(), bpp::AbstractParametrizable::resetParameters_(), bpp::AbstractParametrizable::setAllParametersValues(), bpp::AbstractParametrizable::setParametersValues(), bpp::AbstractParametrizable::setParameterValue(), bpp::AbstractParametrizable::shareParameter_(), and bpp::AbstractParametrizable::shareParameters_().

◆ prefix_

std::string bpp::AbstractParametrizable::prefix_
privateinherited

Definition at line 67 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), and bpp::AbstractParametrizable::setParameterValue().

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