bpp-core3
3.0.0
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Plain collection of parametrizable objects. More...
#include <Bpp/Numeric/ParametrizableCollection.h>
Public Member Functions | |
ParametrizableCollection () | |
Create an empty object set. More... | |
ParametrizableCollection (const ParametrizableCollection< N > &set) | |
ParametrizableCollection< N > & | operator= (const ParametrizableCollection< N > &set) |
void | clear () |
Resets all the information contained in this object. More... | |
~ParametrizableCollection () | |
ParametrizableCollection< N > * | clone () const |
Create a copy of this object and send a pointer to it. More... | |
void | fireParameterChanged (const ParameterList ¶meters) |
std::vector< size_t > | hasChanged () const |
void | clearChanged () |
size_t | getNumberOfObjects () const |
bool | hasObject (size_t objectIndex) const |
Says if there is a object with a given index. More... | |
bool | hasObject (std::shared_ptr< N > object) const |
Says if there is an object in the map. More... | |
size_t | getFirstKey (std::shared_ptr< N > object) const |
Return the first key mapping an object in the map. More... | |
const std::vector< size_t > | keys () const |
Returns the keys of the set. More... | |
std::shared_ptr< const N > | operator[] (size_t objectIndex) const |
Get one object from the set knowing its index. More... | |
std::shared_ptr< N > | operator[] (size_t objectIndex) |
ParameterList | getParametersForObject (size_t objectIndex) const |
Get the paramters of the Collection corresponding to an object from the set knowing its index. More... | |
void | addObject (std::shared_ptr< N > object, size_t objectIndex) |
Add a new object to the set with a given number. More... | |
std::shared_ptr< N > | removeObject (size_t objectIndex) |
Remove a object from the set, and all corresponding parameters. More... | |
std::shared_ptr< N > | replaceObject (std::shared_ptr< N > object, size_t objectIndex) |
Replace a object in the set, and returns the replaced one. More... | |
void | setNamespace (const std::string &prefix) |
Set the namespace for the parameter names. More... | |
bool | hasIndependentParameter (const std::string &name) const |
const ParameterList & | getIndependentParameters () const |
Get the minimal list of parameters to set the model. More... | |
size_t | getNumberOfIndependentParameters () const |
Get the number of independent parameters. More... | |
void | aliasParameters (const std::string &p1, const std::string &p2) |
alias the parameters. More... | |
void | aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose) |
alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More... | |
void | unaliasParameters (const std::string &p1, const std::string &p2) |
Detach two parameters previously set as 'aliased'. More... | |
ParameterList | getAliasedParameters (const ParameterList &pl) const |
Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More... | |
ParameterList | getFromParameters (const ParameterList &pl) const |
Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not). More... | |
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 |
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... | |
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 | |
void | addParameter_ (Parameter *parameter) |
void | addParameters_ (const ParameterList ¶meters) |
void | shareParameter_ (const std::shared_ptr< Parameter > ¶meter) |
void | shareParameters_ (const ParameterList ¶meters) |
void | includeParameters_ (const ParameterList ¶meters) |
void | deleteParameter_ (size_t index) |
void | deleteParameter_ (std::string &name) |
void | deleteParameters_ (const std::vector< std::string > &names) |
void | resetParameters_ () |
const std::shared_ptr< Parameter > & | getSharedParameter (size_t i) const |
std::shared_ptr< Parameter > & | getSharedParameter (size_t i) |
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... | |
Protected Attributes | |
std::map< size_t, std::shared_ptr< N > > | objectsSet_ |
Contains all objects used. More... | |
std::vector< size_t > | vChanged_ |
A vector of the numbers of objects that have changed during the last fireParameterChanged. More... | |
Private Attributes | |
ParameterList | independentParameters_ |
std::map< std::string, AliasParameterListener * > | aliasListenersRegister_ |
ParameterList | parameters_ |
std::string | prefix_ |
Plain collection of parametrizable objects.
The collection is a map from unsigned integers to Parametrizables.
The access to the parameters of the objects will be done through this collection.
Definition at line 65 of file ParametrizableCollection.h.
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Create an empty object set.
Definition at line 89 of file ParametrizableCollection.h.
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Definition at line 95 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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Definition at line 137 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::clear().
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Add a new object to the set with a given number.
Exception | if the number is already used. See replace function instead. |
object | A pointer toward an object, that will added to the set. |
WARNING! The set will now be the owner of the pointer, and will destroy it if needed! Copy the object first if you don't want it to be lost!
objectIndex | The number of the object in the Collection |
Definition at line 320 of file ParametrizableCollection.h.
References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::Parameter::setName(), and bpp::TextTools::toString().
Referenced by bpp::ParametrizableCollection< N >::replaceObject().
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 244 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::shareParameter().
Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ConstantDistribution::ConstantDistribution(), bpp::DirichletDiscreteDistribution::DirichletDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::Simplex::Simplex(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 250 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().
Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), and bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions().
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virtualinherited |
alias the parameters.
p1 | name of the parameter to which the other parameter is aliased |
p2 | name of the aliased parameter, which will be deleted from independent parameters list |
Implements bpp::ParameterAliasable.
Definition at line 119 of file AbstractParameterAliasable.cpp.
References bpp::Parameter::addParameterListener(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::ParameterList::deleteParameter(), bpp::ApplicationTools::displayWarning(), bpp::Parameter::getConstraint(), bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::Parameter::hasConstraint(), bpp::AbstractParametrizable::hasParameter(), bpp::ParameterList::hasParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::Parameter::setConstraint(), bpp::ParameterList::shareParameters(), and bpp::ParameterList::size().
Referenced by bpp::ParametrizableCollection< N >::addObject(), and bpp::AbstractParameterAliasable::aliasParameters().
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virtualinherited |
alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden.
unparsedParams | the map of the links : <A,B> matches for A->B aliasing. |
verbose | verbosity |
Implements bpp::ParameterAliasable.
Definition at line 173 of file AbstractParameterAliasable.cpp.
References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::Parameter::clone(), bpp::Clonable::clone(), bpp::ApplicationTools::displayResult(), bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::matchParametersValues(), bpp::ParameterList::size(), and bpp::TextTools::toString().
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Resets all the information contained in this object.
Definition at line 129 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_, bpp::AbstractParameterAliasable::resetParameters_(), and bpp::ParametrizableCollection< N >::vChanged_.
Referenced by bpp::ParametrizableCollection< N >::operator=(), and bpp::ParametrizableCollection< N >::~ParametrizableCollection().
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Definition at line 183 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::vChanged_.
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Create a copy of this object and send a pointer to it.
Implements bpp::Clonable.
Definition at line 142 of file ParametrizableCollection.h.
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 285 of file AbstractParameterAliasable.h.
References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameter_(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.
Referenced by bpp::AbstractParameterAliasable::deleteParameters_(), and bpp::ParametrizableCollection< N >::removeObject().
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 293 of file AbstractParameterAliasable.h.
References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 300 of file AbstractParameterAliasable.h.
References bpp::AbstractParameterAliasable::deleteParameter_().
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To be called when a parameter has changed. Depending on parameters, this will actualize the corresponding objects in the set.
parameters | The modified parameters. |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 150 of file ParametrizableCollection.h.
References bpp::ParameterList::addParameter(), bpp::ParametrizableCollection< N >::hasObject(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::ParameterList::size(), and bpp::ParametrizableCollection< N >::vChanged_.
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name | The name of the parameter to look for. |
Implements bpp::ParameterAliasable.
Definition at line 260 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::VectorTools::append().
Referenced by bpp::AbstractParameterAliasable::getAliases(), and bpp::ParametrizableCollection< N >::removeObject().
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Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list.
Definition at line 304 of file AbstractParameterAliasable.cpp.
References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getParameter(), and bpp::ParameterList::hasParameter().
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Implements bpp::ParameterAliasable.
Definition at line 283 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::AbstractParameterAliasable::getAlias().
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Return the first key mapping an object in the map.
object | Object in the set. |
Throw Exception if object not found.
Definition at line 228 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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inherited |
name | The name of the parameter to look for. |
Definition at line 344 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_.
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inherited |
Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not).
Definition at line 363 of file AbstractParameterAliasable.cpp.
References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getParameter(), and bpp::ParameterList::hasParameter().
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inlinevirtualinherited |
Get the minimal list of parameters to set the model.
If no parameters are aliased, this is the same a getParameters().
Implements bpp::ParameterAliasable.
Definition at line 171 of file AbstractParameterAliasable.h.
References bpp::AbstractParameterAliasable::independentParameters_.
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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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Get the number of independent parameters.
Implements bpp::ParameterAliasable.
Definition at line 173 of file AbstractParameterAliasable.h.
References bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::size().
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Definition at line 191 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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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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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 bpp::TestFunction::getValue().
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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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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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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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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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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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Get the paramters of the Collection corresponding to an object from the set knowing its index.
objectIndex | Index of the object in the set. |
Definition at line 287 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_, bpp::ParameterList::size(), and bpp::TextTools::toString().
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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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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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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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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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Definition at line 242 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
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Definition at line 237 of file AbstractParametrizable.h.
References bpp::ParameterList::getSharedParameter(), and bpp::AbstractParametrizable::parameters_.
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Definition at line 178 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::vChanged_.
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Definition at line 169 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::getNamespace(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.
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Says if there is a object with a given index.
objectIndex | Index of the object in the set. |
Definition at line 199 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
Referenced by bpp::ParametrizableCollection< N >::fireParameterChanged().
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Says if there is an object in the map.
object | Object in the set. |
Definition at line 210 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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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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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 275 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().
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Returns the keys of the set.
Definition at line 244 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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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(), bpp::TestFunction::setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().
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Definition at line 108 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::AbstractParameterAliasable::operator=(), and bpp::ParametrizableCollection< N >::vChanged_.
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Definition at line 271 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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Get one object from the set knowing its index.
objectIndex | Index of the object in the set. |
Definition at line 262 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::objectsSet_.
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Remove a object from the set, and all corresponding parameters.
objectIndex | The index of the object in the set. |
Definition at line 360 of file ParametrizableCollection.h.
References bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParameterAliasable::getAlias(), bpp::AbstractParametrizable::getParameters(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::ParameterList::size(), and bpp::AbstractParameterAliasable::unaliasParameters().
Referenced by bpp::ParametrizableCollection< N >::replaceObject().
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Replace a object in the set, and returns the replaced one.
objectIndex | The index of the object to be replaced in the set. |
object | the replacing N |
Definition at line 406 of file ParametrizableCollection.h.
References bpp::ParametrizableCollection< N >::addObject(), and bpp::ParametrizableCollection< N >::removeObject().
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inlineprotectedinherited |
Definition at line 310 of file AbstractParameterAliasable.h.
References bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::reset(), and bpp::AbstractParametrizable::resetParameters_().
Referenced by bpp::ParametrizableCollection< N >::clear().
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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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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, and bpp::InvariantMixedDiscreteDistribution.
Definition at line 240 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::setNamespace(), and bpp::TextTools::startsWith().
Referenced by bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::MixtureOfDiscreteDistributions::setNamespace().
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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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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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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 260 of file AbstractParameterAliasable.h.
References bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), and bpp::AbstractParametrizable::shareParameter_().
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inlineprotectedvirtualinherited |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 266 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), bpp::AbstractParametrizable::shareParameters_(), and bpp::ParameterList::size().
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virtualinherited |
Detach two parameters previously set as 'aliased'.
The values of the two parameters will now be independent.
p1 | Original parameter. |
p2 | Aliased parameter. |
ParameterNotFoundException | if p1 or p2 do not correspond to existing parameters. |
Exception | when trying to perform non-valid dissociation. |
Implements bpp::ParameterAliasable.
Definition at line 221 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::Parameter::removeParameterListener(), and bpp::ParameterList::shareParameter().
Referenced by bpp::ParametrizableCollection< N >::removeObject().
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privateinherited |
Contains all parameter listeners for maintening alias relationships. The registry will be updated appropriately upon cloning and deleting.
Definition at line 151 of file AbstractParameterAliasable.h.
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::getAlias(), bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::AbstractParameterAliasable::getAliases(), bpp::AbstractParameterAliasable::getFrom(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::setNamespace(), bpp::AbstractParameterAliasable::unaliasParameters(), and bpp::AbstractParameterAliasable::~AbstractParameterAliasable().
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mutableprivateinherited |
Definition at line 145 of file AbstractParameterAliasable.h.
Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParameterAliasable::getIndependentParameters(), bpp::AbstractParameterAliasable::getNumberOfIndependentParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::resetParameters_(), bpp::AbstractParameterAliasable::shareParameter_(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().
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protected |
Contains all objects used.
Definition at line 73 of file ParametrizableCollection.h.
Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::fireParameterChanged(), bpp::ParametrizableCollection< N >::getFirstKey(), bpp::ParametrizableCollection< N >::getNumberOfObjects(), bpp::ParametrizableCollection< N >::getParametersForObject(), bpp::ParametrizableCollection< N >::hasObject(), bpp::ParametrizableCollection< N >::keys(), bpp::ParametrizableCollection< N >::operator=(), bpp::ParametrizableCollection< N >::operator[](), bpp::ParametrizableCollection< N >::ParametrizableCollection(), and bpp::ParametrizableCollection< N >::removeObject().
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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().
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protected |
A vector of the numbers of objects that have changed during the last fireParameterChanged.
Definition at line 81 of file ParametrizableCollection.h.
Referenced by bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::clearChanged(), bpp::ParametrizableCollection< N >::fireParameterChanged(), bpp::ParametrizableCollection< N >::hasChanged(), and bpp::ParametrizableCollection< N >::operator=().