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

Packages that use UpdateModule

Package	Description
bio.singa.simulation.export.format
bio.singa.simulation.export.modules
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.displacement.implementations
bio.singa.simulation.model.modules.qualitative
bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.simulation
bio.singa.simulation.model.simulation.error

Uses of UpdateModule in bio.singa.simulation.export.format

Methods in bio.singa.simulation.export.format with parameters of type UpdateModule

Modifier and Type	Method	Description
static Map<String,List<String>>	FormatFeature.formatFeatures(UpdateModule module)

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

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

Modifier and Type	Method	Description
static ModuleTableRow	GeneralModuleRow.from(UpdateModule module)

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

Constructor	Description
GeneralModuleRow(UpdateModule module)

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

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

Modifier and Type	Class	Description
class	AbstractUpdateModule

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	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	Description
UpdateModule	ConcentrationDelta.getModule()	Returns the module, that calculated this delta.

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

Constructor	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	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	Description
class	Diffusion	Diffusion is the fundamental force governing the random movement of molecules in cells.
class	EndocytoticPitAbsorption
class	LateralMembraneDiffusion
class	MembraneDiffusion	The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.
class	PorousDiffusion	Calculates diffusion through large pores (pore significantly larger than the cargo) in the membrane.
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	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	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	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	Description
class	ClathrinMediatedEndocytosis
class	ConcentrationApplier
class	ConcentrationStateChange
class	DiffusivityScaling
class	LineLikeAgentAttachment
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	Description
UpdateModule	SimulationStatus.getLocalErrorModule()

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

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

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

Modifier and Type	Method	Description
void	Simulation.addModule(UpdateModule module)
void	UpdateScheduler.addModule(UpdateModule module)

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

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

Modifier and Type	Method	Description
UpdateModule	ErrorManager.getLocalDisplacementDeviationModule()
UpdateModule	ErrorManager.getLocalNumericalErrorModule()

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

Modifier and Type	Method	Description
void	ErrorManager.setLargestLocalDisplacementDeviation(DisplacementDeviation localDeviation, UpdateModule associatedModule)
void	ErrorManager.setLargestLocalNumericalError(NumericalError localError, UpdateModule associatedModule, double associatedConcentration)
void	ErrorManager.setLocalErrorModule(UpdateModule localErrorModule)