bpp-phyl3  3.0.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::LegacyOptimizationTools::ScaleFunction Class Referenceabstract
+ Inheritance diagram for bpp::LegacyOptimizationTools::ScaleFunction:
+ Collaboration diagram for bpp::LegacyOptimizationTools::ScaleFunction:

Public Member Functions

 ScaleFunction (std::shared_ptr< TreeLikelihoodInterface > tl)
 
 ScaleFunction (const ScaleFunction &sf)
 
ScaleFunction & operator= (const ScaleFunction &sf)
 
virtual ~ScaleFunction ()
 
ScaleFunction * clone () const
 
void setParameters (const ParameterList &lambda)
 
double getValue () const
 
const ParameterList & getParameters () const
 
const Parameter & parameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 
size_t getNumberOfParameters () const
 
size_t getNumberOfIndependentParameters () const
 
virtual double f (const ParameterList &parameters)
 
virtual bool hasParameter (const std::string &name) const=0
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 
virtual void setParameterValue (const std::string &name, double value)=0
 
virtual void setParametersValues (const ParameterList &parameters)=0
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 
virtual void removeConstraint (const std::string &name)=0
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 
virtual void setNamespace (const std::string &prefix)=0
 
virtual std::string getNamespace () const=0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const=0
 
bool hasParameter (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
void setNamespace (const std::string &prefix) override
 
std::string getNamespace () const override
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 

Protected Member Functions

ParameterList & getParameters_ ()
 

Protected Attributes

ParameterList parameters_
 
Parameter parameter_
 

Private Attributes

std::shared_ptr< TreeLikelihoodInterface > tl_
 
ParameterList brLen_
 
ParameterList lambda_
 

Detailed Description

Definition at line 337 of file OptimizationTools.h.

Constructor & Destructor Documentation

◆ ScaleFunction() [1/2]

LegacyOptimizationTools::ScaleFunction::ScaleFunction ( std::shared_ptr< TreeLikelihoodInterface >  tl)

Definition at line 35 of file OptimizationTools.cpp.

References bpp::ParameterList::addParameter(), brLen_, bpp::ParameterList::deleteParameter(), bpp::ParameterList::hasParameter(), and lambda_.

Referenced by clone().

◆ ScaleFunction() [2/2]

bpp::LegacyOptimizationTools::ScaleFunction::ScaleFunction ( const ScaleFunction &  sf)
inline

Definition at line 348 of file OptimizationTools.h.

◆ ~ScaleFunction()

LegacyOptimizationTools::ScaleFunction::~ScaleFunction ( )
virtual

Definition at line 48 of file OptimizationTools.cpp.

Member Function Documentation

◆ clone()

ScaleFunction* bpp::LegacyOptimizationTools::ScaleFunction::clone ( ) const
inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 364 of file OptimizationTools.h.

References ScaleFunction().

◆ getNumberOfIndependentParameters()

size_t bpp::LegacyOptimizationTools::ScaleFunction::getNumberOfIndependentParameters ( ) const
inline

Definition at line 380 of file OptimizationTools.h.

◆ getNumberOfParameters()

size_t bpp::LegacyOptimizationTools::ScaleFunction::getNumberOfParameters ( ) const
inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 379 of file OptimizationTools.h.

◆ getParameters()

const ParameterList& bpp::LegacyOptimizationTools::ScaleFunction::getParameters ( ) const
inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 369 of file OptimizationTools.h.

References lambda_.

◆ getParameters_()

ParameterList& bpp::LegacyOptimizationTools::ScaleFunction::getParameters_ ( )
inlineprotectedvirtual

Implements bpp::FunctionInterface.

Definition at line 383 of file OptimizationTools.h.

References lambda_.

◆ getParameterValue()

double bpp::LegacyOptimizationTools::ScaleFunction::getParameterValue ( const std::string &  name) const
inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 375 of file OptimizationTools.h.

References bpp::Parameter::getValue(), lambda_, and bpp::ParameterList::parameter().

◆ getValue()

double LegacyOptimizationTools::ScaleFunction::getValue ( ) const
virtual

Implements bpp::FunctionInterface.

Definition at line 57 of file OptimizationTools.cpp.

References bpp::exp(), and bpp::ParameterList::size().

◆ operator=()

ScaleFunction& bpp::LegacyOptimizationTools::ScaleFunction::operator= ( const ScaleFunction &  sf)
inline

Definition at line 354 of file OptimizationTools.h.

References brLen_, lambda_, and tl_.

◆ parameter()

const Parameter& bpp::LegacyOptimizationTools::ScaleFunction::parameter ( const std::string &  name) const
inlinevirtual

Implements bpp::FunctionInterface.

Definition at line 370 of file OptimizationTools.h.

References lambda_.

◆ setParameters()

void LegacyOptimizationTools::ScaleFunction::setParameters ( const ParameterList &  lambda)
virtual

Implements bpp::FunctionInterface.

Definition at line 50 of file OptimizationTools.cpp.

References bpp::ParameterList::size().

Member Data Documentation

◆ brLen_

ParameterList bpp::LegacyOptimizationTools::ScaleFunction::brLen_
mutableprivate

Definition at line 343 of file OptimizationTools.h.

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

◆ lambda_

ParameterList bpp::LegacyOptimizationTools::ScaleFunction::lambda_
private

Definition at line 343 of file OptimizationTools.h.

Referenced by getParameters(), getParameters_(), getParameterValue(), operator=(), parameter(), and ScaleFunction().

◆ tl_

std::shared_ptr<TreeLikelihoodInterface> bpp::LegacyOptimizationTools::ScaleFunction::tl_
private

Definition at line 342 of file OptimizationTools.h.

Referenced by operator=().

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