roadrunner  2.6.0
Fast simulator for SBML models
Public Member Functions | List of all members
rr::GillespieIntegrator Class Reference

RoadRunner's implementation of the Gillespie SSA. More...

#include <GillespieIntegrator.h>

Inheritance diagram for rr::GillespieIntegrator:
rr::Integrator rr::Solver rr::Registrable

Public Member Functions

 GillespieIntegrator (ExecutableModel *model)
 
void syncWithModel (ExecutableModel *m) override
 Called whenever a new model is loaded to allow integrator to reset internal state. More...
 
std::string getName () const override
 Get the name for this integrator. More...
 
std::string getDescription () const override
 Get the description for this integrator. More...
 
std::string getHint () const override
 Get the hint for this integrator. More...
 
Solverconstruct (ExecutableModel *executableModel) const override
 Constructs a new Solver of a given type. More...
 
IntegrationMethod getIntegrationMethod () const override
 Always stochastic for Gillespie. More...
 
void setValue (const std::string &setting, Setting value) override
 Sets the value of an integrator setting (e.g. absolute_tolerance) More...
 
void resetSettings () override
 Reset all integrator settings to their respective default values. More...
 
double integrate (double t0, double tf) override
 Main integration routine. More...
 
void restart (double timeStart) override
 Reset time to zero and reinitialize model. More...
 
IntegratorListenerPtr getListener () override
 Gets the integrator listener. More...
 
void setListener (IntegratorListenerPtr) override
 Sets the integrator listener. More...
 
 Integrator (ExecutableModel *model)
 
 Integrator ()
 
- Public Member Functions inherited from rr::Integrator
 Integrator (ExecutableModel *model)
 
virtual void loadConfigSettings ()
 
virtual void loadSBMLSettings (const std::string &filename)
 
virtual void tweakTolerances ()
 Fix tolerances for SBML tests. More...
 
virtual void setIndividualTolerance (std::string sid, double value)
 Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator. More...
 
virtual std::vector< double > getAbsoluteToleranceVector ()
 Get the absolute tolerance vector for the solver. More...
 
std::string toString () const
 Return a std::string representation of the solver. More...
 
virtual std::string toRepr () const
 Return std::string representation a la Python repr method. More...
 
void setIntegrationStartTime (double time)
 
 Solver ()=default
 
 Solver (ExecutableModel *model)
 
virtual void setValue (const std::string &key, Setting value)
 Pull down the setValue from superclass. More...
 
- Public Member Functions inherited from rr::Solver
 Solver (ExecutableModel *model)
 
void updateSettings (Dictionary *inputSettings)
 Update settings values. More...
 
std::vector< std::string > getSettings () const
 Get a list of all settings for this solver. More...
 
std::unordered_map< std::string, Setting > & getSettingsMap ()
 get settings for this solver More...
 
virtual Setting getValue (const std::string &key) const
 Get the value of an integrator setting. More...
 
virtual Setting hasValue (const std::string &key) const
 Return true if this setting is supported by the integrator. More...
 
virtual size_t getNumParams () const
 Get the number of parameters. More...
 
virtual std::string getParamName (size_t n) const
 Get the name of the parameter at index n. More...
 
virtual std::string getParamDisplayName (int n) const
 Get the display name of the parameter at index n. More...
 
virtual std::string getParamHint (int n) const
 Get the hint of the parameter at index n. More...
 
virtual std::string getParamDesc (int n) const
 Get the description of the parameter at index n. More...
 
virtual std::string getValueAsString (const std::string &key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual std::string getSettingsRepr () const
 Get the solver settings as a std::string. More...
 
virtual std::string settingsPyDictRepr () const
 Python dictionary-style std::string representation of settings. More...
 
const std::string & getDisplayName (const std::string &key) const
 Gets the hint associated with a given key. More...
 
const std::string & getHint (const std::string &key) const
 Gets the hint associated with a given key. More...
 
const std::string & getDescription (const std::string &key) const
 Gets the description associated with a given key. More...
 
Setting::TypeId getType (const std::string &key) const
 Gets the type associated with a given key. More...
 
virtual ExecutableModelgetModel () const
 returns the pointer to the ExecutableModel
 
virtual std::string getName () const=0
 Gets the name associated with this Solver type. More...
 
virtual std::string getHint () const=0
 Gets the hint associated with this Solver type. More...
 
virtual std::string getDescription () const=0
 Gets the description associated with this Solver type. More...
 

Additional Inherited Members

- Public Types inherited from rr::Integrator
enum  IntegrationMethod { Deterministic , Stochastic , Hybrid , Other }
 
- Public Types inherited from rr::Solver
using SettingsList = std::vector< std::string >
 
using SettingsMap = std::unordered_map< std::string, Setting >
 
using DisplayNameMap = std::unordered_map< std::string, std::string >
 
using HintMap = std::unordered_map< std::string, std::string >
 
using DescriptionMap = std::unordered_map< std::string, std::string >
 
- Public Attributes inherited from rr::Solver
SettingsList sorted_settings
 
SettingsMap settings
 
DisplayNameMap display_names_
 
HintMap hints
 
DescriptionMap descriptions
 
- Protected Member Functions inherited from rr::Solver
void addSetting (const std::string &name, const Setting &val, const std::string &display_name, const std::string &hint, const std::string &description)
 
- Protected Attributes inherited from rr::Integrator
double mIntegrationStartTime
 
- Protected Attributes inherited from rr::Solver
ExecutableModelmModel = nullptr
 non-owning pointer to model
 

Detailed Description

RoadRunner's implementation of the Gillespie SSA.

Author
WBC, ETS

Member Function Documentation

◆ construct()

Solver * rr::GillespieIntegrator::construct ( ExecutableModel model) const
overridevirtual

Constructs a new Solver of a given type.

Author
JKM, WBC

the caller is responsible for deleting memory associated with the returned Solver*.

Implements rr::Registrable.

◆ getDescription()

std::string rr::GillespieIntegrator::getDescription ( ) const
overridevirtual

Get the description for this integrator.

Author
WBC
Note
Delegates to getDescription

Implements rr::Registrable.

◆ getHint()

std::string rr::GillespieIntegrator::getHint ( ) const
overridevirtual

Get the hint for this integrator.

Author
WBC
Note
Delegates to getHint

Implements rr::Registrable.

◆ getIntegrationMethod()

Integrator::IntegrationMethod rr::GillespieIntegrator::getIntegrationMethod ( ) const
overridevirtual

Always stochastic for Gillespie.

Author
WBC, ETS

Implements rr::Integrator.

◆ getListener()

IntegratorListenerPtr rr::GillespieIntegrator::getListener ( )
overridevirtual

Gets the integrator listener.

Author
WBC, ETS

Implements rr::Integrator.

◆ getName()

std::string rr::GillespieIntegrator::getName ( ) const
overridevirtual

Get the name for this integrator.

Author
WBC
Note
Delegates to getName

Implements rr::Registrable.

◆ integrate()

double rr::GillespieIntegrator::integrate ( double  t0,
double  tf 
)
overridevirtual

Main integration routine.

Author
WBC, ETS

Implements rr::Integrator.

◆ resetSettings()

void rr::GillespieIntegrator::resetSettings ( )
overridevirtual

Reset all integrator settings to their respective default values.

Author
JKM

Reimplemented from rr::Solver.

◆ restart()

void rr::GillespieIntegrator::restart ( double  timeStart)
overridevirtual

Reset time to zero and reinitialize model.

Author
WBC, ETS

Implements rr::Integrator.

◆ setListener()

void rr::GillespieIntegrator::setListener ( IntegratorListenerPtr  )
overridevirtual

Sets the integrator listener.

Author
WBC, ETS

Implements rr::Integrator.

◆ setValue()

void rr::GillespieIntegrator::setValue ( const std::string &  setting,
Setting  value 
)
overridevirtual

Sets the value of an integrator setting (e.g. absolute_tolerance)

Author
WBC, ETS

Reimplemented from rr::Solver.

◆ syncWithModel()

void rr::GillespieIntegrator::syncWithModel ( ExecutableModel m)
overridevirtual

Called whenever a new model is loaded to allow integrator to reset internal state.

Author
JKM

Reimplemented from rr::Integrator.


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