Uses of Class
bio.singa.simulation.model.sections.ConcentrationContainer

Packages that use ConcentrationContainer

Package	Description
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.functions
bio.singa.simulation.model.modules.concentration.imlementations
bio.singa.simulation.model.modules.concentration.reactants
bio.singa.simulation.model.modules.concentration.scope
bio.singa.simulation.model.modules.concentration.specifity
bio.singa.simulation.model.modules.displacement
bio.singa.simulation.model.sections
bio.singa.simulation.model.simulation

Uses of ConcentrationContainer in bio.singa.simulation.model.graphs

Methods in bio.singa.simulation.model.graphs that return ConcentrationContainer

Modifier and Type	Method and Description
ConcentrationContainer	AutomatonNode.getConcentrationContainer() Returns the ConcentrationContainer used by this node.

Methods in bio.singa.simulation.model.graphs with parameters of type ConcentrationContainer

Modifier and Type	Method and Description
void	AutomatonNode.setConcentrationContainer(ConcentrationContainer concentrationContainer) Sets the ConcentrationContainer for this node.

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

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

Modifier and Type	Method and Description
ConcentrationContainer	ConcentrationDeltaManager.getConcentrationContainer() Returns the current concentration container.

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

Modifier and Type	Method and Description
void	ConcentrationDeltaManager.setConcentrationContainer(ConcentrationContainer concentrations) Sets the current concentration container.

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

Constructor and Description
ConcentrationDeltaManager(ConcentrationContainer initialConcentrations) Creates a new Concentration Delta Manager.

Uses of ConcentrationContainer in bio.singa.simulation.model.modules.concentration.functions

Methods in bio.singa.simulation.model.modules.concentration.functions that return types with arguments of type ConcentrationContainer

Modifier and Type	Method and Description
Predicate<ConcentrationContainer>	AbstractDeltaFunction.getCondition() Returns the application condition.
Function<ConcentrationContainer,List<ConcentrationDelta>>	SectionDeltaFunction.getFunction() Returns the function.
Function<ConcentrationContainer,ConcentrationDelta>	EntityDeltaFunction.getFunction() Returns the function.
Function<ConcentrationContainer,Map<ConcentrationDeltaIdentifier,ConcentrationDelta>>	UpdatableDeltaFunction.getFunction() Returns the function.

Constructor parameters in bio.singa.simulation.model.modules.concentration.functions with type arguments of type ConcentrationContainer

Constructor and Description
EntityDeltaFunction(Function<ConcentrationContainer,ConcentrationDelta> function, Predicate<ConcentrationContainer> condition) Creates a new entity delta function with the specified condition and function.
EntityDeltaFunction(Function<ConcentrationContainer,ConcentrationDelta> function, Predicate<ConcentrationContainer> condition) Creates a new entity delta function with the specified condition and function.
SectionDeltaFunction(Function<ConcentrationContainer,List<ConcentrationDelta>> function, Predicate<ConcentrationContainer> condition) Creates a new section delta function with the specified condition and function.
SectionDeltaFunction(Function<ConcentrationContainer,List<ConcentrationDelta>> function, Predicate<ConcentrationContainer> condition) Creates a new section delta function with the specified condition and function.
UpdatableDeltaFunction(Function<ConcentrationContainer,Map<ConcentrationDeltaIdentifier,ConcentrationDelta>> function, Predicate<ConcentrationContainer> condition) Creates a new updatable delta function with the specified condition and function.
UpdatableDeltaFunction(Function<ConcentrationContainer,Map<ConcentrationDeltaIdentifier,ConcentrationDelta>> function, Predicate<ConcentrationContainer> condition) Creates a new updatable delta function with the specified condition and function.

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

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

Modifier and Type	Method and Description
protected List<ConcentrationDelta>	Reaction.calculateDeltas(ConcentrationContainer concentrationContainer) Calculates all deltas for all reactants for the reaction.
double	MichaelisMentenReaction.calculateVelocity(ConcentrationContainer concentrationContainer)
double	NthOrderReaction.calculateVelocity(ConcentrationContainer concentrationContainer)
double	DynamicReaction.calculateVelocity(ConcentrationContainer concentrationContainer)
abstract double	Reaction.calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the reaction velocity, depending on the kinetic law.
double	ReversibleReaction.calculateVelocity(ConcentrationContainer concentrationContainer)
protected double	Reaction.determineEffectiveConcentration(ConcentrationContainer concentrationContainer, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.

Uses of ConcentrationContainer in bio.singa.simulation.model.modules.concentration.reactants

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

Modifier and Type	Method and Description
double	KineticLaw.calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the velocity of the reaction based on the entities in the concentration container.

Uses of ConcentrationContainer in bio.singa.simulation.model.modules.concentration.scope

Methods in bio.singa.simulation.model.modules.concentration.scope that return ConcentrationContainer

Modifier and Type	Method and Description
ConcentrationContainer	DependentUpdate.getHalfStepConcentration(Updatable updatable)
ConcentrationContainer	UpdateScope.getHalfStepConcentration(Updatable updatable) Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.
ConcentrationContainer	SemiDependentUpdate.getHalfStepConcentration(Updatable updatable)
ConcentrationContainer	IndependentUpdate.getHalfStepConcentration(Updatable updatable)

Uses of ConcentrationContainer in bio.singa.simulation.model.modules.concentration.specifity

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

Modifier and Type	Method and Description
void	UpdateSpecificity.determineDeltas(ConcentrationContainer container) Determines all deltas for a Concentration container.
void	SectionSpecific.determineDeltas(ConcentrationContainer container)
void	EntitySpecific.determineDeltas(ConcentrationContainer container)
void	UpdatableSpecific.determineDeltas(ConcentrationContainer container)
void	UpdateSpecificity.processContainer(ConcentrationContainer container) Processes a concentration container.
void	SectionSpecific.processContainer(ConcentrationContainer container)
void	EntitySpecific.processContainer(ConcentrationContainer container)
void	UpdatableSpecific.processContainer(ConcentrationContainer container)

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

Methods in bio.singa.simulation.model.modules.displacement that return ConcentrationContainer

Modifier and Type	Method and Description
ConcentrationContainer	Vesicle.getConcentrationContainer()

Uses of ConcentrationContainer in bio.singa.simulation.model.sections

Methods in bio.singa.simulation.model.sections that return ConcentrationContainer

Modifier and Type	Method and Description
ConcentrationContainer	ConcentrationContainer.emptyCopy() Returns a empty copy of this container, keeping subsections and cell topologies associated.
ConcentrationContainer	ConcentrationContainer.fullCopy() Returns a full copy of this container, keeping concentrations.
ConcentrationContainer	CellRegion.setUpConcentrationContainer()

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

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

Modifier and Type	Method and Description
ConcentrationContainer	Updatable.getConcentrationContainer()