bpp-core3
3.0.0
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A simple funciton with two parameters, mostly for testing and debugging :) More...
#include <Bpp/Numeric/Function/Functions.h>
Public Member Functions | |
TestFunction (double x=0, double y=0) | |
Clonable * | clone () const |
Create a copy of this object and send a pointer to it. More... | |
void | setParameters (const ParameterList ¶meters) |
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 ¶meters) |
Notify the class when one or several parameters have changed. More... | |
virtual double | f (const ParameterList ¶meters) |
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 ¶meters)=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 ¶meters)=0 |
Update the parameters from parameters. More... | |
virtual bool | matchParametersValues (const ParameterList ¶meters)=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... | |
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... | |
const std::shared_ptr< Parameter > & | getSharedParameter (const std::string &name) const |
double | getParameterValue (const std::string &name) const |
Get the value for parameter of name 'name'. More... | |
void | setAllParametersValues (const ParameterList ¶meters) |
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 ¶meters) |
Update the parameters from parameters. More... | |
bool | matchParametersValues (const ParameterList ¶meters) |
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... | |
Protected Member Functions | |
virtual ParameterList & | getParameters_ ()=0 |
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 ¶meters) |
virtual void | shareParameter_ (const std::shared_ptr< Parameter > ¶meter) |
virtual void | shareParameters_ (const ParameterList ¶meters) |
virtual void | includeParameters_ (const ParameterList ¶meters) |
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 |
ParameterList & | getParameters_ () |
Get all parameters available. More... | |
Private Attributes | |
ParameterList | parameters_ |
std::string | prefix_ |
A simple funciton with two parameters, mostly for testing and debugging :)
Definition at line 600 of file Functions.h.
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inline |
Definition at line 605 of file Functions.h.
References bpp::AbstractParametrizable::addParameter_().
Referenced by clone().
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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 TestFunction().
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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().
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inlinevirtual |
Create a copy of this object and send a pointer to it.
Implements bpp::Clonable.
Definition at line 612 of file Functions.h.
References TestFunction().
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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_().
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inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 170 of file AbstractParametrizable.h.
References bpp::ParameterList::deleteParameter(), and bpp::AbstractParametrizable::parameters_.
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inlineprotectedvirtualinherited |
Reimplemented in bpp::AbstractParameterAliasable.
Definition at line 175 of file AbstractParametrizable.h.
References bpp::ParameterList::deleteParameters(), and bpp::AbstractParametrizable::parameters_.
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inlinevirtualinherited |
Get the value of the function according to a given set of parameters.
parameters | The parameter set to pass to the function. |
Exception | If 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().
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inlinevirtual |
Notify the class when one or several parameters have changed.
parameters | A ParameterList object with parameters that changed. |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 626 of file Functions.h.
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inlinevirtualinherited |
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().
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pure virtualinherited |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getNamespace().
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inlinevirtualinherited |
Get 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().
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pure virtualinherited |
Get the number of parameters.
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
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inlinevirtualinherited |
Get the parameter with specified name.
name | The name of the parameter to look for. |
ParameterNotFoundException | if 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(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and getValue().
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pure virtualinherited |
Get the parameter with specified name.
name | The name of the parameter to look for. |
ParameterNotFoundException | if no parameter with this name is found. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameter().
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inlineprotectedinherited |
name | The name of the parameter. |
ParameterNotFoundException | If 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().
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inlineprotectedinherited |
Definition at line 216 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
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inlineprotectedinherited |
Definition at line 223 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::size().
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virtualinherited |
Resolves a parameter name according to the current namespace.
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_().
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pure virtualinherited |
Resolves a parameter name according to the current namespace.
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().
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inlinevirtualinherited |
Get 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().
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pure virtualinherited |
Get 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().
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inlineprotectedvirtualinherited |
Get 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=().
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protectedpure virtualinherited |
Get all parameters available.
Implemented in bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameters_().
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inlinevirtualinherited |
Get the value for parameter of name 'name'.
name | The name of the parameter. |
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().
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pure virtualinherited |
Get the value for parameter of name 'name'.
name | The name of the parameter. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::getParameterValue().
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inlineprotectedinherited |
name | The name of the parameter, including its namespace. |
ParameterNotFoundException | If no parameter with that name is found in the list. |
Definition at line 202 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::getParameter_().
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inlineprotectedinherited |
name | The name of the parameter, including its namespace. |
ParameterNotFoundException | If no parameter with that name is found in the list. |
Definition at line 211 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::getParameter().
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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().
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inlineprotectedinherited |
Definition at line 242 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
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inlineprotectedinherited |
Definition at line 237 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
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inlinevirtual |
Get the value of the function at the current point.
Exception | If no point is specified or if an error occured. |
Implements bpp::Function.
Definition at line 619 of file Functions.h.
References bpp::AbstractParametrizable::getParameter(), and bpp::Parameter::getValue().
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inlinevirtualinherited |
Tell if there is a parameter with specified name.
name | The name of the parameter to look for. |
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().
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pure virtualinherited |
Tell if there is a parameter with specified name.
name | The name of the parameter to look for. |
Implemented in bpp::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.
Referenced by bpp::FunctionWrapper::hasParameter().
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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_().
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inlinevirtualinherited |
Update the parameters from parameters.
Only common parameters with parameters will be updated.
parameters | A list of parameters. |
ConstraintException | If 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(), setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().
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pure virtualinherited |
Update the parameters from parameters.
Only common parameters with parameters will be updated.
parameters | A list of parameters. |
ConstraintException | If 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().
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inlineprotectedinherited |
Definition at line 180 of file AbstractParametrizable.h.
References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().
Referenced by bpp::AbstractParameterAliasable::resetParameters_().
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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 | A list with all parameters. |
ParameterNotFoundException | If a some parameter in the list is not in params. |
ConstraintException | If 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().
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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 | A list with all parameters. |
ParameterNotFoundException | If a some parameter in the list is not in params. |
ConstraintException | If 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().
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virtualinherited |
Set the namespace for the parameter names.
prefix | The '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().
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pure virtualinherited |
Set the namespace for the parameter names.
prefix | The '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().
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inlinevirtual |
Set the point where the function must be computed.
parameters | The parameter set to pass to the function. |
Implements bpp::Function.
Definition at line 614 of file Functions.h.
References bpp::AbstractParametrizable::matchParametersValues().
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inlinevirtualinherited |
Update the parameters from parameters.
parameters must be a subset of all parameters available.
parameters | A list containing all parameters to update. |
ParameterNotFoundException | If a some parameter in params is not in the list. |
ConstraintException | If 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().
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pure virtualinherited |
Update the parameters from parameters.
parameters must be a subset of all parameters available.
parameters | A list containing all parameters to update. |
ParameterNotFoundException | If a some parameter in params is not in the list. |
ConstraintException | If 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().
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inlinevirtualinherited |
Set the value of parameter with name name to be equal to value.
name | the name of the parameter to set. |
value | The value of the parameter. |
ParameterNotFoundException | If no parameter in the list has the name name. |
ConstraintException | If 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().
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pure virtualinherited |
Set the value of parameter with name name to be equal to value.
name | the name of the parameter to set. |
value | The value of the parameter. |
ParameterNotFoundException | If no parameter in the list has the name name. |
ConstraintException | If 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().
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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_().
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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_().
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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_().
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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().