Uses of Class
bio.singa.simulation.model.simulation.Simulation

Packages that use Simulation

Package	Description
bio.singa.simulation.events
bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.imlementations
bio.singa.simulation.model.modules.displacement
bio.singa.simulation.model.modules.qualitative
bio.singa.simulation.model.sections.concentration
bio.singa.simulation.model.simulation

Uses of Simulation in bio.singa.simulation.events

Methods in bio.singa.simulation.events with parameters of type Simulation

Modifier and Type	Method and Description
EpochUpdateWriter.EntitiesStep	EpochUpdateWriter.SimulationStep.simulation(Simulation simulation)
EpochUpdateWriter.EntitiesStep	EpochUpdateWriter.EpochUpdateWriterBuilder.simulation(Simulation simulation)

Uses of Simulation in bio.singa.simulation.model.agents.linelike

Constructors in bio.singa.simulation.model.agents.linelike with parameters of type Simulation

Constructor and Description
LineLikeAgentLayer(Simulation simulation, MembraneLayer membraneLayer)
MicrotubuleOrganizingCentre(Simulation simulation, MembraneLayer membraneLayer, Circle circleRepresentation, int initialFilaments)

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

Methods in bio.singa.simulation.model.agents.pointlike that return Simulation

Modifier and Type	Method and Description
Simulation	VesicleLayer.getSimulation()

Methods in bio.singa.simulation.model.agents.pointlike with parameters of type Simulation

Modifier and Type	Method and Description
void	VesicleLayer.setSimulation(Simulation simulation)

Constructors in bio.singa.simulation.model.agents.pointlike with parameters of type Simulation

Constructor and Description
VesicleLayer(Simulation simulation)

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

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

Modifier and Type	Method and Description
Simulation	ConcentrationBasedModule.getSimulation() Returns the referenced simulation.

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

Modifier and Type	Method and Description
ModuleType	ModuleBuilder.createModule(Simulation simulation)
void	ConcentrationBasedModule.setSimulation(Simulation simulation) References the simulation to this module.

Uses of Simulation in bio.singa.simulation.model.modules.concentration.imlementations

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

Modifier and Type	Method and Description
MembraneDiffusion	MembraneDiffusion.MembraneDiffusionBuilder.createModule(Simulation simulation)
DynamicReaction	DynamicReaction.DynamicReactionBuilder.createModule(Simulation simulation)
SingleFileChannelMembraneTransport	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.createModule(Simulation simulation)
Diffusion	Diffusion.DiffusionBuilder.createModule(Simulation simulation)
ComplexBuildingReaction	ComplexBuildingReaction.ComplexBuildingReactionBuilder.createModule(Simulation simulation)
TopLevelType	Reaction.Builder.createModule(Simulation simulation)
protected MichaelisMentenReaction	MichaelisMentenReaction.MichaelisMentenReactionBuilder.createObject(Simulation simulation)
protected ReversibleReaction	ReversibleReaction.ReversibleReactionBuilder.createObject(Simulation simulation)
protected NthOrderReaction	NthOrderReaction.NthOrderReactionBuilder.createObject(Simulation simulation)
protected abstract TopLevelType	Reaction.Builder.createObject(Simulation primaryIdentifer)
static ModuleBuilder	MembraneDiffusion.getBuilder(Simulation simulation)
static ModuleBuilder	MichaelisMentenReaction.getBuilder(Simulation simulation)
static ModuleBuilder	DynamicReaction.getBuilder(Simulation simulation)
static ModuleBuilder	SingleFileChannelMembraneTransport.getBuilder(Simulation simulation)
static ModuleBuilder	Diffusion.getBuilder(Simulation simulation)
static ModuleBuilder	ReversibleReaction.getBuilder(Simulation simulation)
static ModuleBuilder	NthOrderReaction.getBuilder(Simulation simulation)
static ModuleBuilder	ComplexBuildingReaction.getBuilder(Simulation simulation)
static MembraneDiffusion.CargoStep	MembraneDiffusion.inSimulation(Simulation simulation)
static MichaelisMentenReaction.MichaelisMentenReactionBuilder	MichaelisMentenReaction.inSimulation(Simulation simulation)
static DynamicReaction.KineticLawStep	DynamicReaction.inSimulation(Simulation simulation)
static SingleFileChannelMembraneTransport.TransporterStep	SingleFileChannelMembraneTransport.inSimulation(Simulation simulation)
static Diffusion.SelectionStep	Diffusion.inSimulation(Simulation simulation)
static ReversibleReaction.ReversibleReactionBuilder	ReversibleReaction.inSimulation(Simulation simulation)
static NthOrderReaction.NthOrderReactionBuilder	NthOrderReaction.inSimulation(Simulation simulation)
static ComplexBuildingReaction.BindeeSelection	ComplexBuildingReaction.inSimulation(Simulation simulation)

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

Constructor and Description
Builder(Simulation simulation)
ComplexBuildingReactionBuilder(Simulation simulation)
DiffusionBuilder(Simulation simulation)
DynamicReactionBuilder(Simulation simulation)
MembraneDiffusionBuilder(Simulation simulation)
MichaelisMentenReactionBuilder(Simulation simulation)
NthOrderReactionBuilder(Simulation simulation)
ReversibleReactionBuilder(Simulation identifier)
SingleFileChannelMembraneTransportBuilder(Simulation simulation)

Uses of Simulation in bio.singa.simulation.model.modules.displacement

Fields in bio.singa.simulation.model.modules.displacement declared as Simulation

Modifier and Type	Field and Description
protected Simulation	DisplacementBasedModule.simulation The simulation.

Methods in bio.singa.simulation.model.modules.displacement with parameters of type Simulation

Modifier and Type	Method and Description
void	DisplacementBasedModule.setSimulation(Simulation simulation)

Uses of Simulation in bio.singa.simulation.model.modules.qualitative

Fields in bio.singa.simulation.model.modules.qualitative declared as Simulation

Modifier and Type	Field and Description
protected Simulation	QualitativeModule.simulation The simulation.

Methods in bio.singa.simulation.model.modules.qualitative with parameters of type Simulation

Modifier and Type	Method and Description
void	QualitativeModule.setSimulation(Simulation simulation)

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

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

Modifier and Type	Method and Description
void	ConcentrationInitializer.initialize(Simulation simulation)
void	SectionConcentration.initialize(Simulation simulation)
void	MembraneConcentration.initialize(Simulation simulation)
void	InitialConcentration.initialize(Simulation simulation)

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

Methods in bio.singa.simulation.model.simulation that return Simulation

Modifier and Type	Method and Description
protected Simulation	SimulationManager.call()
static Simulation	SimulationExamples.createCompartmentTestEnvironment()
static Simulation	SimulationExamples.createDecompositionReactionExample() This simulation simulates the thermal decomposition of dinitrogen pentaoxide.
static Simulation	SimulationExamples.createDiffusionModuleExample(int numberOfNodes, javax.measure.Quantity<javax.measure.quantity.Time> timeStep) This simulation simulates a diffusion of small molecules in a rectangular gird graph.
static Simulation	SimulationExamples.createEquilibriumReactionExample() This simulation simulates a equilibrium reaction.
static Simulation	SimulationExamples.createIodineMultiReactionExample() This simulation simulates a multiple reactions involving iodine.
static Simulation	SimulationExamples.createMichaelisMentenReactionExample() This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.
static Simulation	SimulationExamples.createSynthesisReactionExample() This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).
Simulation	SimulationManager.getSimulation() Returns the simulation.

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

Modifier and Type	Method and Description
void	SimulationManager.emitGraphEvent(Simulation simulation)
void	SimulationManager.emitNodeEvent(Simulation simulation, Updatable updatable)

Method parameters in bio.singa.simulation.model.simulation with type arguments of type Simulation

Modifier and Type	Method and Description
void	SimulationManager.setTerminationCondition(Predicate<Simulation> terminationCondition) Sets a condition determining when the simulation should be terminated.
void	SimulationManager.setUpdateEmissionCondition(Predicate<Simulation> emitCondition) Sets a condition determining when events should be emitted.

Constructors in bio.singa.simulation.model.simulation with parameters of type Simulation

Constructor and Description
SimulationManager(Simulation simulation) Creates a new simulation manager for the given simulation.
UpdateScheduler(Simulation simulation)