Uses of Interface
bio.singa.simulation.model.simulation.Updatable

Packages that use Updatable

Package	Description
bio.singa.simulation.events
bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.imlementations.reactions
bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants
bio.singa.simulation.model.modules.concentration.scope
bio.singa.simulation.model.sections.concentration
bio.singa.simulation.model.simulation
bio.singa.simulation.trajectories.flat
bio.singa.simulation.trajectories.nested

Uses of Updatable in bio.singa.simulation.events

Methods in bio.singa.simulation.events that return Updatable

Modifier and Type	Method and Description
Updatable	UpdatableUpdatedEvent.getUpdatable() Returns the updatable

Constructors in bio.singa.simulation.events with parameters of type Updatable

Constructor and Description
UpdatableUpdatedEvent(javax.measure.Quantity<javax.measure.quantity.Time> time, Updatable updatable) Creates a new NodeUpdatedEvent.

Uses of Updatable in bio.singa.simulation.model.agents.pointlike

Classes in bio.singa.simulation.model.agents.pointlike that implement Updatable

Modifier and Type	Class and Description
class	Vesicle

Uses of Updatable in bio.singa.simulation.model.graphs

Classes in bio.singa.simulation.model.graphs that implement Updatable

Modifier and Type	Class and Description
class	AutomatonNode A node of the AutomatonGraph.

Uses of Updatable in bio.singa.simulation.model.modules.concentration

Methods in bio.singa.simulation.model.modules.concentration that return Updatable

Modifier and Type	Method and Description
Updatable	FieldSupplier.getCurrentUpdatable() Returns the current updatable.
Updatable	ConcentrationDeltaIdentifier.getUpdatable() Returns the object the delta is assigned to.
Updatable	LocalError.getUpdatable() Returns the node where the error occurred.

Methods in bio.singa.simulation.model.modules.concentration that return types with arguments of type Updatable

Modifier and Type	Method and Description
Predicate<Updatable>	ConcentrationBasedModule.getApplicationCondition() Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.

Methods in bio.singa.simulation.model.modules.concentration with parameters of type Updatable

Modifier and Type	Method and Description
void	FieldSupplier.setCurrentUpdatable(Updatable updatable) Sets the current updatable.

Method parameters in bio.singa.simulation.model.modules.concentration with type arguments of type Updatable

Modifier and Type	Method and Description
protected void	ConcentrationBasedModule.setApplicationCondition(Predicate<Updatable> applicationCondition) Sets the application condition for this module.

Constructors in bio.singa.simulation.model.modules.concentration with parameters of type Updatable

Constructor and Description
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, ChemicalEntity entity) Creates a new DeltaIdentifier.
LocalError(Updatable updatable, ChemicalEntity entity, double value) Creates a new LocalError.

Uses of Updatable in bio.singa.simulation.model.modules.concentration.imlementations.reactions

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions with parameters of type Updatable

Modifier and Type	Method and Description
List<ReactantDelta>	ReactionEvent.collectDeltas(Updatable updatable)

Uses of Updatable in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with parameters of type Updatable

Modifier and Type	Method and Description
List<ReactantSet>	DynamicReactantBehavior.generateReactantSets(Updatable updatable)
List<ReactantSet>	ReactantBehavior.generateReactantSets(Updatable updatable)
List<ReactantSet>	StaticReactantBehavior.generateReactantSets(Updatable updatable)
List<ChemicalEntity>	DynamicChemicalEntity.getMatchingEntities(Updatable updatable, CellTopology topology)

Uses of Updatable in bio.singa.simulation.model.modules.concentration.scope

Methods in bio.singa.simulation.model.modules.concentration.scope with parameters of type Updatable

Modifier and Type	Method and Description
ConcentrationContainer	IndependentUpdate.getHalfStepConcentration(Updatable updatable)
ConcentrationContainer	SemiDependentUpdate.getHalfStepConcentration(Updatable updatable)
ConcentrationContainer	UpdateScope.getHalfStepConcentration(Updatable updatable) Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.
ConcentrationContainer	DependentUpdate.getHalfStepConcentration(Updatable updatable)
void	IndependentUpdate.processUpdatable(Updatable updatable)
void	SemiDependentUpdate.processUpdatable(Updatable updatable)
void	UpdateScope.processUpdatable(Updatable updatable) Calculates the given updatable.
void	DependentUpdate.processUpdatable(Updatable updatable)

Method parameters in bio.singa.simulation.model.modules.concentration.scope with type arguments of type Updatable

Modifier and Type	Method and Description
void	IndependentUpdate.processAllUpdatables(Collection<Updatable> updatables)
void	SemiDependentUpdate.processAllUpdatables(Collection<Updatable> updatables)
void	UpdateScope.processAllUpdatables(Collection<Updatable> updatables) Processes all given updatables.
void	DependentUpdate.processAllUpdatables(Collection<Updatable> updatables)

Uses of Updatable in bio.singa.simulation.model.sections.concentration

Methods in bio.singa.simulation.model.sections.concentration with parameters of type Updatable

Modifier and Type	Method and Description
void	SectionConcentration.initialize(Updatable updatable)
void	MembraneConcentration.initialize(Updatable updatable)
void	InitialConcentration.initialize(Updatable updatable)

Uses of Updatable in bio.singa.simulation.model.simulation

Methods in bio.singa.simulation.model.simulation that return types with arguments of type Updatable

Modifier and Type	Method and Description
Set<Updatable>	Simulation.getObservedUpdatables()
ArrayList<Updatable>	Simulation.getUpdatables()

Methods in bio.singa.simulation.model.simulation with parameters of type Updatable

Modifier and Type	Method and Description
void	SimulationManager.emitNodeEvent(Simulation simulation, Updatable updatable)
List<ConcentrationDelta>	Simulation.getPreviousObservedDeltas(Updatable updatable)
void	Simulation.observe(Updatable updatable)

Uses of Updatable in bio.singa.simulation.trajectories.flat

Methods in bio.singa.simulation.trajectories.flat with parameters of type Updatable

Modifier and Type	Method and Description
void	FlatUpdateRecorder.addUpdatableToObserve(Updatable updatable) Initializes a updatable that will be observed during simulation.

Uses of Updatable in bio.singa.simulation.trajectories.nested

Methods in bio.singa.simulation.trajectories.nested that return types with arguments of type Updatable

Modifier and Type	Method and Description
Map<Updatable,TrajactoryDataPoint>	TrajectoryData.getConcentrationData()

Methods in bio.singa.simulation.trajectories.nested with parameters of type Updatable

Modifier and Type	Method and Description
static TrajactoryDataPoint	TrajactoryDataPoint.of(Updatable updatable, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)

Method parameters in bio.singa.simulation.trajectories.nested with type arguments of type Updatable

Modifier and Type	Method and Description
static TrajectoryData	TrajectoryData.of(Collection<Updatable> updatables, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)