bpp-core3
3.0.0
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Discretized Uniform distribution. All categories are equidistributed all along a given interval. More...
#include <Bpp/Numeric/Prob/UniformDiscreteDistribution.h>
Public Member Functions | |
UniformDiscreteDistribution (unsigned int n, double min=0., double max=1.) | |
Build a new discretized uniform distribution. More... | |
UniformDiscreteDistribution (const UniformDiscreteDistribution &) | |
UniformDiscreteDistribution & | operator= (const UniformDiscreteDistribution &) |
virtual | ~UniformDiscreteDistribution () |
UniformDiscreteDistribution * | clone () const |
Create a copy of this object and send a pointer to it. More... | |
std::string | getName () const |
Get the name of the distribution. More... | |
void | fireParameterChanged (const ParameterList ¶meters) |
Notify the class when one or several parameters have changed. More... | |
double | randC () const |
Draw a random number from the continuous version of this distribution, if it exists. More... | |
double | qProb (double x) const |
Return the quantile of the continuous version of the distribution, ie y such that . More... | |
double | pProb (double x) const |
Return the cumulative quantile of the continuous version of the distribution, ie . More... | |
double | Expectation (double a) const |
Return a primitive function used for the expectation of the continuous version of the distribution, ie . More... | |
virtual void | restrictToConstraint (const Constraint &c) |
Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints. More... | |
virtual size_t | getNumberOfIndependentParameters () const =0 |
Get the number of independent parameters. More... | |
size_t | getNumberOfIndependentParameters () const |
Get the number of independent parameters. More... | |
virtual void | aliasParameters (const std::string &p1, const std::string &p2)=0 |
Set two parameters as 'aliased'. More... | |
virtual void | aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0 |
alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. 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... | |
virtual void | unaliasParameters (const std::string &p1, const std::string &p2)=0 |
Detach two parameters previously set as 'aliased'. More... | |
void | unaliasParameters (const std::string &p1, const std::string &p2) |
Detach two parameters previously set as 'aliased'. More... | |
virtual const ParameterList & | getIndependentParameters () const =0 |
Get the minimal list of parameters to set the model. More... | |
const ParameterList & | getIndependentParameters () const |
Get the minimal list of parameters to set the model. More... | |
virtual std::vector< std::string > | getAlias (const std::string &name) const =0 |
virtual std::vector< std::string > | getAlias (const std::string &name) const |
virtual std::map< std::string, std::string > | getAliases () const =0 |
virtual std::map< std::string, std::string > | getAliases () const |
virtual bool | hasParameter (const std::string &name) const =0 |
Tell if there is a parameter with specified name. More... | |
bool | hasParameter (const std::string &name) const |
Tell if there is a parameter with specified name. More... | |
virtual const ParameterList & | getParameters () const =0 |
Get all parameters available. More... | |
const ParameterList & | getParameters () const |
Get all parameters available. More... | |
virtual const Parameter & | getParameter (const std::string &name) const =0 |
Get the parameter with specified name. More... | |
const Parameter & | getParameter (const std::string &name) const |
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... | |
double | getParameterValue (const std::string &name) const |
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... | |
void | setAllParametersValues (const ParameterList ¶meters) |
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... | |
void | setParameterValue (const std::string &name, double value) |
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... | |
void | setParametersValues (const ParameterList ¶meters) |
Update the parameters from parameters. More... | |
virtual bool | matchParametersValues (const ParameterList ¶meters)=0 |
Update the parameters from parameters. More... | |
bool | matchParametersValues (const ParameterList ¶meters) |
Update the parameters from parameters. More... | |
virtual size_t | getNumberOfParameters () const =0 |
Get the number of parameters. More... | |
size_t | getNumberOfParameters () const |
Get the number of parameters. More... | |
virtual void | setNamespace (const std::string &prefix)=0 |
Set the namespace for the parameter names. More... | |
void | setNamespace (const std::string &prefix) |
Set the namespace for the parameter names. More... | |
virtual std::string | getNamespace () const =0 |
std::string | getNamespace () const |
virtual std::string | getParameterNameWithoutNamespace (const std::string &name) const =0 |
Resolves a parameter name according to the current namespace. More... | |
std::string | getParameterNameWithoutNamespace (const std::string &name) const |
Resolves a parameter name according to the current namespace. More... | |
bool | hasIndependentParameter (const std::string &name) const |
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... | |
std::string | getFrom (const std::string &name) const |
const std::shared_ptr< Parameter > & | getSharedParameter (const std::string &name) const |
The DiscreteDistribution interface. | |
size_t | getNumberOfCategories () const |
void | setNumberOfCategories (size_t nbClasses) |
sets the number of categories and discretizes if there is a change in this number. More... | |
double | getCategory (size_t categoryIndex) const |
double | getProbability (size_t categoryIndex) const |
double | getProbability (double category) const |
Vdouble | getCategories () const |
Vdouble | getProbabilities () const |
double | getValueCategory (double value) const |
size_t | getCategoryIndex (double value) const |
void | set (double category, double probability) |
Set the probability associated to a class. More... | |
void | add (double category, double probability) |
Modify the probability associated to a class. More... | |
double | getInfCumulativeProbability (double category) const |
double | getIInfCumulativeProbability (double category) const |
double | getSupCumulativeProbability (double category) const |
double | getSSupCumulativeProbability (double category) const |
double | rand () const |
Draw a random number from this distribution. More... | |
double | getBound (size_t i) const |
double | getLowerBound () const |
methods about the range of the definition More... | |
double | getUpperBound () const |
bool | strictLowerBound () const |
bool | strictUpperBound () const |
Vdouble | getBounds () const |
void | print (OutputStream &out) const |
Print the distribution (categories and corresponding probabilities) to a stream. More... | |
double | precision () const |
void | setMedian (bool median) |
Sets the median value to true to say that the value in a class is proportional to the median value of the class, the proportionality factor being such that the sum of the values equals the expectation of the distribution. If it is set to false, the value is the mean value in the class. More... | |
virtual void | discretize () |
Discretizes the distribution in equiprobable classes. More... | |
Protected Member Functions | |
virtual ParameterList & | getParameters_ ()=0 |
Get all parameters available. More... | |
ParameterList & | getParameters_ () |
Get all parameters available. More... | |
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 |
Protected Attributes | |
size_t | numberOfCategories_ |
std::map< double, double, Order > | distribution_ |
std::vector< double > | bounds_ |
std::shared_ptr< IntervalConstraint > | intMinMax_ |
the interval where the distribution is defined/restricted. More... | |
bool | median_ |
Private Attributes | |
double | min_ |
double | max_ |
ParameterList | independentParameters_ |
std::map< std::string, AliasParameterListener * > | aliasListenersRegister_ |
ParameterList | parameters_ |
std::string | prefix_ |
Discretized Uniform distribution. All categories are equidistributed all along a given interval.
Definition at line 57 of file UniformDiscreteDistribution.h.
UniformDiscreteDistribution::UniformDiscreteDistribution | ( | unsigned int | n, |
double | min = 0. , |
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double | max = 1. |
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Build a new discretized uniform distribution.
n | the number of categories to use. |
min | The minimun value (default 0) |
max | The maximum value (default 1) |
Constructor:
Definition at line 55 of file UniformDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::intMinMax_, max_, and min_.
Referenced by clone().
UniformDiscreteDistribution::UniformDiscreteDistribution | ( | const UniformDiscreteDistribution & | udd | ) |
Definition at line 66 of file UniformDiscreteDistribution.cpp.
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virtual |
Definition at line 81 of file UniformDiscreteDistribution.cpp.
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virtualinherited |
Modify the probability associated to a class.
If the category does not exist, a new category is created with the corresponding probability. if the category exists, add 'probability' to the existing probability. The sum of all probabilities is not checked.
category | The class value. |
probability | The class probability. |
Implements bpp::DiscreteDistribution.
Definition at line 181 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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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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pure virtualinherited |
Set two parameters as 'aliased'.
The values of the two parameters will be synchronized, so that setting the value of one parameter will automatically set the value of the other one accordingly.
p1 | Original parameter. |
p2 | Aliased parameter. |
ParameterNotFoundException | if p1 or p2 do not correspond to existing parameters. |
Exception | when trying to perform non-valid association. |
Implemented in bpp::AbstractParameterAliasable.
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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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pure 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 |
Implemented in bpp::AbstractParameterAliasable.
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inlinevirtual |
Create a copy of this object and send a pointer to it.
Implements bpp::DiscreteDistribution.
Definition at line 79 of file UniformDiscreteDistribution.h.
References UniformDiscreteDistribution().
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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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virtualinherited |
Discretizes the distribution in equiprobable classes.
Implements bpp::DiscreteDistribution.
Reimplemented in bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, and bpp::ConstantDistribution.
Definition at line 325 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::bounds_, bpp::AbstractDiscreteDistribution::distribution_, bpp::DiscreteDistribution::Expectation(), bpp::AbstractDiscreteDistribution::intMinMax_, bpp::AbstractDiscreteDistribution::median_, bpp::AbstractDiscreteDistribution::numberOfCategories_, bpp::DiscreteDistribution::pProb(), bpp::AbstractDiscreteDistribution::precision(), bpp::DiscreteDistribution::qProb(), and bpp::NumConstants::TINY().
Referenced by bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::AbstractDiscreteDistribution::restrictToConstraint(), bpp::AbstractDiscreteDistribution::setMedian(), bpp::AbstractDiscreteDistribution::setNumberOfCategories(), bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(), and UniformDiscreteDistribution().
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inlinevirtual |
Return a primitive function used for the expectation of the continuous version of the distribution, ie .
Implements bpp::DiscreteDistribution.
Definition at line 104 of file UniformDiscreteDistribution.h.
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virtual |
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 85 of file UniformDiscreteDistribution.cpp.
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virtualinherited |
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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pure virtualinherited |
name | The name of the parameter to look for. |
Implemented in bpp::AbstractParameterAliasable.
Referenced by bpp::BppOParametrizableFormat::write().
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inherited |
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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virtualinherited |
Implements bpp::ParameterAliasable.
Definition at line 283 of file AbstractParameterAliasable.cpp.
References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::AbstractParameterAliasable::getAlias().
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pure virtualinherited |
Implemented in bpp::AbstractParameterAliasable.
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inlinevirtualinherited |
Implements bpp::DiscreteDistribution.
Definition at line 173 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::bounds_, and bpp::AbstractDiscreteDistribution::numberOfCategories_.
Referenced by bpp::AbstractDiscreteDistribution::getBounds().
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virtualinherited |
Implements bpp::DiscreteDistribution.
Definition at line 472 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::getBound(), bpp::AbstractDiscreteDistribution::getLowerBound(), bpp::AbstractDiscreteDistribution::getUpperBound(), and bpp::AbstractDiscreteDistribution::numberOfCategories_.
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virtualinherited |
Implements bpp::DiscreteDistribution.
Definition at line 142 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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virtualinherited |
categoryIndex | Class index. |
Implements bpp::DiscreteDistribution.
Definition at line 111 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
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virtualinherited |
value |
Implements bpp::DiscreteDistribution.
Definition at line 308 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::bounds_, bpp::AbstractDiscreteDistribution::intMinMax_, and bpp::TextTools::toString().
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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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virtualinherited |
category | The class value. |
Implements bpp::DiscreteDistribution.
Definition at line 230 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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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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pure virtualinherited |
Get the minimal list of parameters to set the model.
If no parameters are aliased, this is the same a getParameters().
Implemented in bpp::AbstractParameterAliasable.
Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
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virtualinherited |
category | The class value. |
Implements bpp::DiscreteDistribution.
Definition at line 215 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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inlinevirtualinherited |
methods about the range of the definition
Reimplemented from bpp::DiscreteDistribution.
Reimplemented in bpp::SimpleDiscreteDistribution, and bpp::ConstantDistribution.
Definition at line 185 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::intMinMax_.
Referenced by bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::AbstractDiscreteDistribution::getBounds(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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inlinevirtual |
Get the name of the distribution.
Implements bpp::DiscreteDistribution.
Definition at line 82 of file UniformDiscreteDistribution.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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virtualinherited |
Implements bpp::DiscreteDistribution.
Definition at line 91 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::numberOfCategories_.
Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
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inlinevirtualinherited |
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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pure virtualinherited |
Get the number of independent parameters.
Implemented in bpp::AbstractParameterAliasable.
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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 bpp::TestFunction::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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virtualinherited |
Implements bpp::DiscreteDistribution.
Definition at line 158 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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virtualinherited |
category | The value associated to the class. |
Implements bpp::DiscreteDistribution.
Definition at line 135 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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virtualinherited |
categoryIndex | Class index. |
Implements bpp::DiscreteDistribution.
Definition at line 123 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().
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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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virtualinherited |
category | The class value. |
Implements bpp::DiscreteDistribution.
Definition at line 264 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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virtualinherited |
category | The class value. |
Implements bpp::DiscreteDistribution.
Definition at line 247 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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inlinevirtualinherited |
Reimplemented from bpp::DiscreteDistribution.
Reimplemented in bpp::SimpleDiscreteDistribution, and bpp::ConstantDistribution.
Definition at line 190 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::intMinMax_.
Referenced by bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::AbstractDiscreteDistribution::getBounds(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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virtualinherited |
value |
Implements bpp::DiscreteDistribution.
Definition at line 289 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::bounds_, bpp::AbstractDiscreteDistribution::distribution_, bpp::AbstractDiscreteDistribution::intMinMax_, and bpp::TextTools::toString().
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inlineinherited |
Definition at line 169 of file AbstractParameterAliasable.h.
References bpp::AbstractParametrizable::getNamespace(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.
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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 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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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(), bpp::TestFunction::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().
UniformDiscreteDistribution & UniformDiscreteDistribution::operator= | ( | const UniformDiscreteDistribution & | udd | ) |
Definition at line 72 of file UniformDiscreteDistribution.cpp.
References max_, min_, and bpp::AbstractDiscreteDistribution::operator=().
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inlinevirtual |
Return the cumulative quantile of the continuous version of the distribution, ie .
Implements bpp::DiscreteDistribution.
Definition at line 99 of file UniformDiscreteDistribution.h.
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inlineinherited |
Definition at line 209 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::distribution_.
Referenced by bpp::AbstractDiscreteDistribution::discretize(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution().
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virtualinherited |
Print the distribution (categories and corresponding probabilities) to a stream.
out | The outstream where to print the distribution. |
Implements bpp::DiscreteDistribution.
Definition at line 279 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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inlinevirtual |
Return the quantile of the continuous version of the distribution, ie y such that .
Implements bpp::DiscreteDistribution.
Definition at line 94 of file UniformDiscreteDistribution.h.
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virtualinherited |
Draw a random number from this distribution.
This number will be one of the class values, drawn according to the class probabilities.
Implements bpp::DiscreteDistribution.
Definition at line 197 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_, and bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry().
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inlinevirtual |
Draw a random number from the continuous version of this distribution, if it exists.
Uses the continuous version of this distribution to draw a random number.
Exception | If there is no continuous version of this distribution. |
Reimplemented from bpp::AbstractDiscreteDistribution.
Definition at line 86 of file UniformDiscreteDistribution.h.
References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), bpp::AbstractDiscreteDistribution::intMinMax_, max_, and min_.
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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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virtualinherited |
Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints.
c | The Constraint to respect. |
Implements bpp::DiscreteDistribution.
Reimplemented in bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, and bpp::ConstantDistribution.
Definition at line 484 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::intMinMax_.
Referenced by bpp::ConstantDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint().
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virtualinherited |
Set the probability associated to a class.
If the category does not exist, a new category is created with the corresponding probability. If the category already exist, its probability is set to 'probability'. The sum of all probabilities is not checked.
category | The class value. |
probability | The class probability. |
Implements bpp::DiscreteDistribution.
Definition at line 174 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::distribution_.
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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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inlinevirtualinherited |
Sets the median value to true to say that the value in a class is proportional to the median value of the class, the proportionality factor being such that the sum of the values equals the expectation of the distribution. If it is set to false, the value is the mean value in the class.
If the median value is modified, the discretization process is launched.
median | tells how the value associated to each class is computed. |
Implements bpp::DiscreteDistribution.
Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.
Definition at line 211 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::median_.
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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, 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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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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virtualinherited |
sets the number of categories and discretizes if there is a change in this number.
Implements bpp::DiscreteDistribution.
Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.
Definition at line 96 of file AbstractDiscreteDistribution.cpp.
References bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::numberOfCategories_.
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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 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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inlinevirtualinherited |
Reimplemented from bpp::DiscreteDistribution.
Definition at line 195 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::intMinMax_.
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inlinevirtualinherited |
Reimplemented from bpp::DiscreteDistribution.
Definition at line 200 of file AbstractDiscreteDistribution.h.
References bpp::AbstractDiscreteDistribution::intMinMax_.
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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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pure 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. |
Implemented in bpp::AbstractParameterAliasable.
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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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protectedinherited |
Definition at line 114 of file AbstractDiscreteDistribution.h.
Referenced by bpp::AbstractDiscreteDistribution::discretize(), bpp::SimpleDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::getBound(), bpp::AbstractDiscreteDistribution::getCategoryIndex(), bpp::AbstractDiscreteDistribution::getValueCategory(), bpp::AbstractDiscreteDistribution::operator=(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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protectedinherited |
These fields must be initialized in the constructor of the derived classes.
Definition at line 112 of file AbstractDiscreteDistribution.h.
Referenced by bpp::AbstractDiscreteDistribution::add(), bpp::ConstantDistribution::ConstantDistribution(), bpp::AbstractDiscreteDistribution::discretize(), bpp::SimpleDiscreteDistribution::discretize(), bpp::SimpleDiscreteDistribution::Expectation(), bpp::ConstantDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractDiscreteDistribution::getCategories(), bpp::AbstractDiscreteDistribution::getCategory(), bpp::AbstractDiscreteDistribution::getIInfCumulativeProbability(), bpp::AbstractDiscreteDistribution::getInfCumulativeProbability(), bpp::SimpleDiscreteDistribution::getLowerBound(), bpp::AbstractDiscreteDistribution::getProbabilities(), bpp::AbstractDiscreteDistribution::getProbability(), bpp::AbstractDiscreteDistribution::getSSupCumulativeProbability(), bpp::AbstractDiscreteDistribution::getSupCumulativeProbability(), bpp::SimpleDiscreteDistribution::getUpperBound(), bpp::AbstractDiscreteDistribution::getValueCategory(), bpp::AbstractDiscreteDistribution::operator=(), bpp::SimpleDiscreteDistribution::pProb(), bpp::AbstractDiscreteDistribution::precision(), bpp::AbstractDiscreteDistribution::print(), bpp::SimpleDiscreteDistribution::qProb(), bpp::AbstractDiscreteDistribution::rand(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::AbstractDiscreteDistribution::set(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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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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protectedinherited |
the interval where the distribution is defined/restricted.
Definition at line 121 of file AbstractDiscreteDistribution.h.
Referenced by bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::AbstractDiscreteDistribution::discretize(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::AbstractDiscreteDistribution::getCategoryIndex(), bpp::AbstractDiscreteDistribution::getLowerBound(), bpp::AbstractDiscreteDistribution::getUpperBound(), bpp::AbstractDiscreteDistribution::getValueCategory(), bpp::AbstractDiscreteDistribution::operator=(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), randC(), bpp::AbstractDiscreteDistribution::restrictToConstraint(), bpp::ConstantDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::AbstractDiscreteDistribution::strictLowerBound(), bpp::AbstractDiscreteDistribution::strictUpperBound(), bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(), UniformDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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private |
Definition at line 62 of file UniformDiscreteDistribution.h.
Referenced by Expectation(), operator=(), pProb(), qProb(), randC(), and UniformDiscreteDistribution().
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protectedinherited |
Tells if the values in the classes is associated to the median or not (default: false)
Definition at line 128 of file AbstractDiscreteDistribution.h.
Referenced by bpp::AbstractDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::operator=(), bpp::AbstractDiscreteDistribution::setMedian(), bpp::InvariantMixedDiscreteDistribution::setMedian(), and bpp::MixtureOfDiscreteDistributions::setMedian().
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private |
Definition at line 61 of file UniformDiscreteDistribution.h.
Referenced by Expectation(), operator=(), pProb(), qProb(), randC(), and UniformDiscreteDistribution().
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protectedinherited |
Definition at line 108 of file AbstractDiscreteDistribution.h.
Referenced by bpp::AbstractDiscreteDistribution::discretize(), bpp::SimpleDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::getBound(), bpp::AbstractDiscreteDistribution::getBounds(), bpp::AbstractDiscreteDistribution::getNumberOfCategories(), bpp::AbstractDiscreteDistribution::operator=(), bpp::AbstractDiscreteDistribution::setNumberOfCategories(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().
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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().