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

Packages that use Simulation

Package	Description
bio.singa.simulation.export.features
bio.singa.simulation.export.modules
bio.singa.simulation.export.reactiongraph
bio.singa.simulation.features
bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.concentrations
bio.singa.simulation.model.modules
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.imlementations.reactions
bio.singa.simulation.model.modules.concentration.imlementations.transport
bio.singa.simulation.model.simulation
bio.singa.simulation.trajectories.flat
bio.singa.simulation.trajectories.nested

Uses of Simulation in bio.singa.simulation.export.features

Methods in bio.singa.simulation.export.features with parameters of type Simulation

Modifier and Type	Method	Description
static ModuleSummaryTable	ModuleSummaryTable.from(Simulation simulation)
static FeatureTable	FeatureTable.fromSimulation(Simulation simulation)
void	FeatureTable.generate(Simulation simulation)

Uses of Simulation in bio.singa.simulation.export.modules

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

Modifier and Type	Method	Description
static ModuleTable	ModuleTableConverter.convert(Simulation simulation)

Uses of Simulation in bio.singa.simulation.export.reactiongraph

Methods in bio.singa.simulation.export.reactiongraph with parameters of type Simulation

Modifier and Type	Method	Description
static ReactionGraph	ReactionGraphConverter.convert(Simulation simulation)

Uses of Simulation in bio.singa.simulation.features

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

Modifier and Type	Method	Description
VolumeLikeAgent	ContainmentRegion.retrieveAreaAgent(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	Description
LineLikeAgentLayer(Simulation simulation, MembraneLayer membraneLayer)

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	Description
Simulation	VesicleLayer.getSimulation()

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

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

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

Constructor	Description
VesicleLayer(Simulation simulation)

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

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

Modifier and Type	Method	Description
void	InitialConcentration.apply(Simulation simulation)
static ConcentrationBuilder.EntityStep	ConcentrationBuilder.create(Simulation simulation)

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

Constructor	Description
ConcentrationBuilderImpl(Simulation simulation)

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

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

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

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

Modifier and Type	Method	Description
void	AbstractUpdateModule.setSimulation(Simulation simulation)	References the simulation to this module.
void	UpdateModule.setSimulation(Simulation simulation)

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

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

Modifier and Type	Method	Description
ModuleType	ModuleBuilder.createModule(Simulation simulation)

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

Fields in bio.singa.simulation.model.modules.concentration.imlementations.reactions declared as Simulation

Modifier and Type	Field	Description
protected Simulation	ReactionBuilder.GeneralReactionBuilder.simulation

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

Modifier and Type	Method	Description
Reaction	ReactionBuilder.GeneralReactionBuilder.createModule(Simulation simulation)
static ReactionBuilder.RuleBasedStep	ReactionBuilder.ruleBased(Simulation simulation)
static ReactionBuilder.StaticReactantStep	ReactionBuilder.staticReactants(Simulation simulation)

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

Constructor	Description
GeneralReactionBuilder(Simulation simulation)
RuleBasedBuilder(Simulation simulation)
StaticBuilder(Simulation simulation)

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

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

Modifier and Type	Method	Description
Diffusion	Diffusion.DiffusionBuilder.createModule(Simulation simulation)
EndocytoticPitAbsorption	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.createModule(Simulation simulation)
LateralMembraneDiffusion	LateralMembraneDiffusion.LateralMembraneDiffusionBuilder.createModule(Simulation simulation)
MembraneDiffusion	MembraneDiffusion.MembraneDiffusionBuilder.createModule(Simulation simulation)
PorousDiffusion	PorousDiffusion.PorousDiffusionBuilder.createModule(Simulation simulation)
SingleFileChannelMembraneTransport	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.createModule(Simulation simulation)
static ModuleBuilder	Diffusion.getBuilder(Simulation simulation)
static ModuleBuilder	EndocytoticPitAbsorption.getBuilder(Simulation simulation)
static ModuleBuilder	LateralMembraneDiffusion.getBuilder(Simulation simulation)
static ModuleBuilder	MembraneDiffusion.getBuilder(Simulation simulation)
static ModuleBuilder	PorousDiffusion.getBuilder(Simulation simulation)
static ModuleBuilder	SingleFileChannelMembraneTransport.getBuilder(Simulation simulation)
static Diffusion.EntityLimitationStep	Diffusion.inSimulation(Simulation simulation)
static EndocytoticPitAbsorption.EntityStep	EndocytoticPitAbsorption.inSimulation(Simulation simulation)
static LateralMembraneDiffusion.EntityLimitationStep	LateralMembraneDiffusion.inSimulation(Simulation simulation)
static MembraneDiffusion.CargoStep	MembraneDiffusion.inSimulation(Simulation simulation)
static PorousDiffusion.FeatureStep	PorousDiffusion.inSimulation(Simulation simulation)
static SingleFileChannelMembraneTransport.TransporterStep	SingleFileChannelMembraneTransport.inSimulation(Simulation simulation)

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

Constructor	Description
DiffusionBuilder(Simulation simulation)
EndocytoticPitAbsorptionBuilder(Simulation simulation)
LateralMembraneDiffusionBuilder(Simulation simulation)
MembraneDiffusionBuilder(Simulation simulation)
PorousDiffusionBuilder(Simulation simulation)
SingleFileChannelMembraneTransportBuilder(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	Description
Simulation	SimulationManager.getSimulation()	Returns the simulation.
Simulation	UpdateScheduler.getSimulation()

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

Modifier and Type	Method	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	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	Description
SimulationManager(Simulation simulation)	Creates a new simulation manager for the given simulation.
SimulationStatus(Simulation simulation)
UpdateScheduler(Simulation simulation)

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

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

Modifier and Type	Method	Description
FlatUpdateRecorder.ConcentrationUnitStep	FlatUpdateRecorder.EpochUpdateWriterBuilder.simulation(Simulation simulation)
FlatUpdateRecorder.ConcentrationUnitStep	FlatUpdateRecorder.SimulationStep.simulation(Simulation simulation)

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

Constructors in bio.singa.simulation.trajectories.nested with parameters of type Simulation

Constructor	Description
NestedUpdateRecorder(Simulation simulation)
NestedUpdateRecorder(Simulation simulation, javax.measure.Unit<javax.measure.quantity.Time> timeUnit, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)