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

Packages that use Simulation

Package	Description
bio.singa.simulation.export.reactiongraph
bio.singa.simulation.export.reactiontable
bio.singa.simulation.features.variation
bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.pointlike
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.modules.displacement
bio.singa.simulation.model.modules.qualitative
bio.singa.simulation.model.sections.concentration
bio.singa.simulation.model.simulation
bio.singa.simulation.trajectories.flat
bio.singa.simulation.trajectories.nested

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 and Description
static ReactionGraph	ReactionGraphConverter.convert(Simulation simulation)

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

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

Modifier and Type	Method and Description
static ReactionTable	ReactionTableConverter.convert(Simulation simulation)

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

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

Modifier and Type	Method and Description
static void	VariationSet.applyParameters(Simulation simulation, List<?> parameterVariations)

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)

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

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

Modifier and Type	Method and Description
void	UpdateModule.setSimulation(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.reactions

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

Modifier and Type	Field and 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 and Description
Reaction	ReactionBuilder.GeneralReactionBuilder.createModule(Simulation simulation)
static ReactionBuilder.DynamicReactantStep	ReactionBuilder.dynamicReactants(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 and Description
DynamicBuilder(Simulation simulation)
GeneralReactionBuilder(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 and Description
MembraneDiffusion	MembraneDiffusion.MembraneDiffusionBuilder.createModule(Simulation simulation)
SingleFileChannelMembraneTransport	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.createModule(Simulation simulation)
Diffusion	Diffusion.DiffusionBuilder.createModule(Simulation simulation)
static ModuleBuilder	MembraneDiffusion.getBuilder(Simulation simulation)
static ModuleBuilder	SingleFileChannelMembraneTransport.getBuilder(Simulation simulation)
static ModuleBuilder	Diffusion.getBuilder(Simulation simulation)
static MembraneDiffusion.CargoStep	MembraneDiffusion.inSimulation(Simulation simulation)
static SingleFileChannelMembraneTransport.TransporterStep	SingleFileChannelMembraneTransport.inSimulation(Simulation simulation)
static Diffusion.SelectionStep	Diffusion.inSimulation(Simulation simulation)

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

Constructor and Description
DiffusionBuilder(Simulation simulation)
MembraneDiffusionBuilder(Simulation simulation)
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 that return Simulation

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

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 that return Simulation

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

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)
default 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
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 Michaelis-Menten reaction, where D-Fructose 1-phosphate is converted to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.
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.
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 and Description
FlatUpdateRecorder.ConcentrationUnitStep	FlatUpdateRecorder.SimulationStep.simulation(Simulation simulation)
FlatUpdateRecorder.ConcentrationUnitStep	FlatUpdateRecorder.EpochUpdateWriterBuilder.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 and Description
NestedUpdateRecorder(Simulation simulation)
NestedUpdateRecorder(Simulation simulation, javax.measure.Unit<javax.measure.quantity.Time> timeUnit, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> concentrationUnit)