Uses of Interface
bio.singa.simulation.model.modules.UpdateModule

Packages that use UpdateModule

Package	Description
bio.singa.simulation.features.variation
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.displacement.implementations
bio.singa.simulation.model.modules.qualitative
bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.simulation

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

Methods in bio.singa.simulation.features.variation that return UpdateModule

Modifier and Type	Method and Description
UpdateModule	ModuleFeatureVariationEntry.getModule()
UpdateModule	ModuleFeatureVariation.getModule()

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

Modifier and Type	Method and Description
void	ModuleFeatureVariationEntry.setModule(UpdateModule module)

Constructors in bio.singa.simulation.features.variation with parameters of type UpdateModule

Constructor and Description
ModuleFeatureVariation(UpdateModule module, Class<? extends bio.singa.features.model.Feature<FeatureType>> featureClass)
ModuleFeatureVariationEntry(UpdateModule module, bio.singa.features.model.Feature<?> feature)

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

Classes in bio.singa.simulation.model.modules.concentration that implement UpdateModule

Modifier and Type	Class and Description
class	ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction> Concentration based modules handle updates that are applied to the concentrations in Updatables during a simulation.

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

Modifier and Type	Method and Description
UpdateModule	ConcentrationDelta.getModule() Returns the module, that calculated this delta.

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

Modifier and Type	Method and Description
void	ConcentrationDeltaManager.clearPotentialDeltasBut(UpdateModule module) Clears the list of potential deltas retaining updates from a specific module.

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

Constructor and Description
ConcentrationDelta(UpdateModule module, CellSubsection cellSubsection, ChemicalEntity chemicalEntity, double value) Creates a new concentration delta.

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

Classes in bio.singa.simulation.model.modules.concentration.imlementations.reactions that implement UpdateModule

Modifier and Type	Class and Description
class	Reaction

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

Classes in bio.singa.simulation.model.modules.concentration.imlementations.transport that implement UpdateModule

Modifier and Type	Class and Description
class	Diffusion Diffusion is the fundamental force governing the random movement of molecules in cells.
class	MembraneDiffusion The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.
class	SingleFileChannelMembraneTransport The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels.

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

Classes in bio.singa.simulation.model.modules.displacement that implement UpdateModule

Modifier and Type	Class and Description
class	DisplacementBasedModule

Uses of UpdateModule in bio.singa.simulation.model.modules.displacement.implementations

Classes in bio.singa.simulation.model.modules.displacement.implementations that implement UpdateModule

Modifier and Type	Class and Description
class	EndocytosisActinBoost
class	VesicleConfinedDiffusion
class	VesicleCytoplasmDiffusion
class	VesicleTransport

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

Classes in bio.singa.simulation.model.modules.qualitative that implement UpdateModule

Modifier and Type	Class and Description
class	QualitativeModule

Uses of UpdateModule in bio.singa.simulation.model.modules.qualitative.implementations

Classes in bio.singa.simulation.model.modules.qualitative.implementations that implement UpdateModule

Modifier and Type	Class and Description
class	ActinCortexDiffusivityScaling
class	ClathrinMediatedEndocytosis
class	ConcentrationStateChange
class	DiffusivityScaling
class	LineLikeAgentAttachment
class	LineLikeAgentDetachment
class	VesicleFusion
class	VolumeLikeAgentContainment For vesicles state changes upon entering certain regions represented by volume like agents

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

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

Modifier and Type	Method and Description
UpdateModule	UpdateScheduler.getLocalErrorModule()

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

Modifier and Type	Method and Description
List<UpdateModule>	Simulation.getModules()

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

Modifier and Type	Method and Description
void	Simulation.addModule(UpdateModule module)
void	UpdateScheduler.addModule(UpdateModule module)
boolean	UpdateScheduler.interruptAllBut(Thread callingThread, UpdateModule callingModule) Returns true if the calling module was the first to call the method, therefore being allowed to optimize the time step.
void	UpdateScheduler.setLargestLocalError(LocalError localError, UpdateModule associatedModule, double associatedConcentration)