C API Documentation
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Public Types | |
enum | IntegrationMethod { Deterministic , Stochastic , Hybrid , Other } |
Public Member Functions | |
virtual IntegrationMethod | getIntegrationMethod () const =0 |
virtual void | syncWithModel (ExecutableModel *m) |
Called whenever a new model is loaded to allow integrator to reset internal state. More... | |
virtual void | loadConfigSettings () |
virtual void | loadSBMLSettings (const std::string &filename) |
virtual double | integrate (double t0, double hstep)=0 |
virtual void | restart (double t0)=0 |
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... | |
virtual void | setListener (IntegratorListenerPtr)=0 |
virtual IntegratorListenerPtr | getListener ()=0 |
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) |
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virtual std::string | getName () const =0 |
Get the name of this solver. More... | |
virtual std::string | getDescription () const =0 |
Get the description of this solver. More... | |
virtual std::string | getHint () const =0 |
Get a (user-readable) hint for this solver. More... | |
std::vector< std::string > | getSettings () const |
Get a list of all settings for this solver. More... | |
virtual void | resetSettings () |
Reset all settings to their respective default values. 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... | |
virtual void | setValue (std::string key, const Variant &value) |
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... | |
Additional Inherited Members | |
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typedef std::vector< std::string > | SettingsList |
typedef RR_UNORDERED_MAP< std::string, Variant > | SettingsMap |
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 |
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void | addSetting (std::string name, Variant val, string display_name, std::string hint, std::string description) |
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SettingsList | sorted_settings |
SettingsMap | settings |
DisplayNameMap | display_names_ |
HintMap | hints |
DescriptionMap | descriptions |
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Get tolerance based on concentration of species, will only be used in CVODEIntegrator.
Reimplemented in rr::CVODEIntegrator.
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Set tolerance based on concentration of species, will only be used in CVODEIntegrator.
Reimplemented in rr::CVODEIntegrator.
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Set tolerance for floating species or variables that have a rate rule, will only be used in CVODEIntegrator.
Reimplemented in rr::CVODEIntegrator.
virtual void rr::Solver::setValue |
Pull down the setValue from superclass. We do not need to reimplement this but we make it explicit.
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Called whenever a new model is loaded to allow integrator to reset internal state.
Reimplemented in rr::CVODEIntegrator, rr::RK4Integrator, rr::RK45Integrator, and rr::GillespieIntegrator.
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Return string representation a la Python repr method.
Reimplemented from rr::Solver.
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Return a string representation of the solver.
Reimplemented from rr::Solver.
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virtual |
Fix tolerances for SBML tests.
In order to ensure that the results of the SBML test suite remain valid, this method enforces a lower bound on tolerance values. Sets minimum absolute and relative tolerances to Config::CVODE_MIN_ABSOLUTE and Config::CVODE_MIN_RELATIVE resp.
Reimplemented in rr::CVODEIntegrator.