C API Documentation
Public Member Functions | Static 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

Public Member Functions

 GillespieIntegrator (ExecutableModel *model)
 
virtual void syncWithModel (ExecutableModel *m)
 Called whenever a new model is loaded to allow integrator to reset internal state. More...
 
std::string getName () const
 Get the name for this integrator. More...
 
std::string getDescription () const
 Get the description for this integrator. More...
 
std::string getHint () const
 Get the hint for this integrator. More...
 
IntegrationMethod getIntegrationMethod () const
 Always stochastic for Gillespie. More...
 
void setValue (std::string setting, const Variant &value)
 Sets the value of an integrator setting (e.g. absolute_tolerance) More...
 
void resetSettings ()
 Reset all integrator settings to their respective default values. More...
 
double integrate (double t0, double tf)
 Main integration routine. More...
 
void restart (double timeStart)
 Reset time to zero and reinitialize model. More...
 
IntegratorListenerPtr getListener ()
 Gets the integrator listener. More...
 
void setListener (IntegratorListenerPtr)
 Sets the integrator listener. More...
 
- Public Member Functions inherited from rr::Integrator
virtual void loadConfigSettings ()
 
virtual void loadSBMLSettings (const std::string &filename)
 
virtual void tweakTolerances ()
 Fix tolerances for SBML tests. More...
 
virtual void setIndividualTolerance (string sid, double value)
 Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator. More...
 
virtual void setConcentrationTolerance (const Variant &value)
 Set tolerance based on concentration of species, will only be used in CVODEIntegrator. More...
 
virtual std::vector< double > getConcentrationTolerance ()
 Get tolerance based on concentration of species, will only be used in CVODEIntegrator. More...
 
std::string toString () const
 Return a string representation of the solver. More...
 
virtual std::string toRepr () const
 Return string representation a la Python repr method. More...
 
virtual void setValue (std::string key, const Variant &value)
 
- Public Member Functions inherited from rr::Solver
std::vector< std::string > getSettings () const
 Get a list of all settings for this solver. More...
 
virtual Variant getValue (std::string key) const
 Get the value of an integrator setting. More...
 
virtual Variant hasValue (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 int getValueAsInt (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual unsigned int getValueAsUInt (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual long getValueAsLong (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual unsigned long getValueAsULong (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual float getValueAsFloat (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual double getValueAsDouble (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual std::vector< double > getValueAsDoubleVector (std::string key)
 Wrapper for getValue which converts output to a specific type.
 
virtual char getValueAsChar (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual unsigned char getValueAsUChar (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual std::string getValueAsString (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual bool getValueAsBool (std::string key)
 Wrapper for getValue which converts output to a specific type. More...
 
const std::string & getDisplayName (std::string key) const
 Gets the hint associated with a given key. More...
 
const std::string & getHint (std::string key) const
 Gets the hint associated with a given key. More...
 
const std::string & getDescription (std::string key) const
 Gets the description associated with a given key. More...
 
const Variant::TypeId getType (std::string key)
 Gets the type associated with a given key. More...
 
std::string getSettingsRepr () const
 Get the solver settings as a string. More...
 
std::string settingsPyDictRepr () const
 Python dictionary-style string representation of settings. More...
 

Static Public Member Functions

static std::string getGillespieName ()
 Get the name for this integrator. More...
 
static std::string getGillespieDescription ()
 Get the description for this integrator. More...
 
static std::string getGillespieHint ()
 Get the hint for this integrator. More...
 

Additional Inherited Members

- Public Types inherited from rr::Integrator
enum  IntegrationMethod { Deterministic , Stochastic , Hybrid , Other }
 
- Protected Types inherited from rr::Solver
typedef std::vector< std::string > SettingsList
 
typedef RR_UNORDERED_MAP< std::string, VariantSettingsMap
 
typedef RR_UNORDERED_MAP< std::string, std::string > DisplayNameMap
 
typedef RR_UNORDERED_MAP< std::string, std::string > HintMap
 
typedef RR_UNORDERED_MAP< std::string, std::string > DescriptionMap
 
- Protected Member Functions inherited from rr::Solver
void addSetting (std::string name, Variant val, string display_name, std::string hint, std::string description)
 
- Protected Attributes inherited from rr::Solver
SettingsList sorted_settings
 
SettingsMap settings
 
DisplayNameMap display_names_
 
HintMap hints
 
DescriptionMap descriptions
 

Detailed Description

RoadRunner's implementation of the Gillespie SSA.

Author
WBC, ETS

Member Function Documentation

◆ getDescription()

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

Get the description for this integrator.

Author
WBC
Note
Delegates to getDescription

Implements rr::Solver.

◆ getGillespieDescription()

static std::string rr::GillespieIntegrator::getGillespieDescription ( )
static

Get the description for this integrator.

Author
JKM

◆ getGillespieHint()

static std::string rr::GillespieIntegrator::getGillespieHint ( )
static

Get the hint for this integrator.

Author
JKM

◆ getGillespieName()

static std::string rr::GillespieIntegrator::getGillespieName ( )
static

Get the name for this integrator.

Author
JKM

◆ getHint()

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

Get the hint for this integrator.

Author
WBC
Note
Delegates to getHint

Implements rr::Solver.

◆ getIntegrationMethod()

IntegrationMethod rr::GillespieIntegrator::getIntegrationMethod ( ) const
virtual

Always stochastic for Gillespie.

Author
WBC, ETS

Implements rr::Integrator.

◆ getListener()

IntegratorListenerPtr rr::GillespieIntegrator::getListener ( )
virtual

Gets the integrator listener.

Author
WBC, ETS

Implements rr::Integrator.

◆ getName()

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

Get the name for this integrator.

Author
WBC
Note
Delegates to getName

Implements rr::Solver.

◆ integrate()

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

Main integration routine.

Author
WBC, ETS

Implements rr::Integrator.

◆ resetSettings()

void rr::GillespieIntegrator::resetSettings ( )
virtual

Reset all integrator settings to their respective default values.

Author
JKM

Reimplemented from rr::Solver.

◆ restart()

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

Reset time to zero and reinitialize model.

Author
WBC, ETS

Implements rr::Integrator.

◆ setListener()

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

Sets the integrator listener.

Author
WBC, ETS

Implements rr::Integrator.

◆ setValue()

void rr::GillespieIntegrator::setValue ( std::string  setting,
const Variant value 
)
virtual

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

Author
WBC, ETS

Reimplemented from rr::Solver.

◆ syncWithModel()

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

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 file: