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

#include <GillespieIntegrator.h>

Inheritance diagram for rr::GillespieIntegrator:

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...

Solver *	construct (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 ExecutableModel *	getModel () 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
ExecutableModel *	mModel = 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:

GillespieIntegrator.h
GillespieIntegrator.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ construct()

◆ getDescription()

◆ getHint()

◆ getIntegrationMethod()

◆ getListener()

◆ getName()

◆ integrate()

◆ resetSettings()

◆ restart()

◆ setListener()

◆ setValue()

◆ syncWithModel()