Uses of Class
de.bioforscher.singa.simulation.model.graphs.BioNode

Packages that use BioNode

Package	Description
de.bioforscher.singa.simulation.events
de.bioforscher.singa.simulation.model.compartments
de.bioforscher.singa.simulation.model.graphs
de.bioforscher.singa.simulation.model.rules
de.bioforscher.singa.simulation.modules.diffusion
de.bioforscher.singa.simulation.modules.membranetransport
de.bioforscher.singa.simulation.modules.model.updates
de.bioforscher.singa.simulation.modules.reactions.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
de.bioforscher.singa.simulation.modules.reactions.model

Uses of BioNode in de.bioforscher.singa.simulation.events

Methods in de.bioforscher.singa.simulation.events that return BioNode

Modifier and Type	Method and Description
BioNode	NodeUpdatedEvent.getNode()

Methods in de.bioforscher.singa.simulation.events with parameters of type BioNode

Modifier and Type	Method and Description
void	EpochUpdateWriter.addNodeToObserve(BioNode node)

Constructors in de.bioforscher.singa.simulation.events with parameters of type BioNode

Constructor and Description
NodeUpdatedEvent(int epoch, BioNode node)

Uses of BioNode in de.bioforscher.singa.simulation.model.compartments

Methods in de.bioforscher.singa.simulation.model.compartments that return types with arguments of type BioNode

Modifier and Type	Method and Description
Set<BioNode>	CellSection.getContent() Returns the nodes belonging to this cell section.

Methods in de.bioforscher.singa.simulation.model.compartments with parameters of type BioNode

Modifier and Type	Method and Description
void	CellSection.addNode(BioNode node) Adds a node to the section, without altering the state of the node.

Method parameters in de.bioforscher.singa.simulation.model.compartments with type arguments of type BioNode

Modifier and Type	Method and Description
void	CellSection.setContent(Set<BioNode> content) Sets the content of this cell section.

Uses of BioNode in de.bioforscher.singa.simulation.model.graphs

Methods in de.bioforscher.singa.simulation.model.graphs with parameters of type BioNode

Modifier and Type	Method and Description
int	AutomatonGraph.addEdgeBetween(BioNode source, BioNode target)
int	AutomatonGraph.addEdgeBetween(int identifier, BioNode source, BioNode target)

Uses of BioNode in de.bioforscher.singa.simulation.model.rules

Methods in de.bioforscher.singa.simulation.model.rules with parameters of type BioNode

Modifier and Type	Method and Description
void	AssignmentRule.applyRule(BioNode node)

Uses of BioNode in de.bioforscher.singa.simulation.modules.diffusion

Methods in de.bioforscher.singa.simulation.modules.diffusion with parameters of type BioNode

Modifier and Type	Method and Description
List<PotentialUpdate>	FreeDiffusion.calculateUpdates(BioNode node)

Uses of BioNode in de.bioforscher.singa.simulation.modules.membranetransport

Methods in de.bioforscher.singa.simulation.modules.membranetransport with parameters of type BioNode

Modifier and Type	Method and Description
List<PotentialUpdate>	PassiveMembraneTransport.calculateUpdates(BioNode node)
List<PotentialUpdate>	ActiveMembraneTransport.calculateUpdates(BioNode node)

Uses of BioNode in de.bioforscher.singa.simulation.modules.model.updates

Methods in de.bioforscher.singa.simulation.modules.model.updates that return BioNode

Modifier and Type	Method and Description
BioNode	PotentialUpdate.getNode()

Methods in de.bioforscher.singa.simulation.modules.model.updates with parameters of type BioNode

Modifier and Type	Method and Description
List<PotentialUpdate>	UpdateBehavior.calculateUpdates(BioNode node)
static List<PotentialUpdate>	PotentialUpdates.collectChanges(BioNode node)

Constructors in de.bioforscher.singa.simulation.modules.model.updates with parameters of type BioNode

Constructor and Description
PotentialUpdate(BioNode node, CellSection cellSection, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> quantity)

Uses of BioNode in de.bioforscher.singa.simulation.modules.reactions.implementations

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations with parameters of type BioNode

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	NthOrderReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	EquilibriumReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	DynamicReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	BiochemicalReaction.calculateAcceleration(BioNode node, CellSection section)

Uses of BioNode in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations with parameters of type BioNode

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	MichaelsMentenWithKM.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	MichaelisMentenWithKCat.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	DynamicKineticLaw.calculateAcceleration(BioNode node, CellSection section)

Uses of BioNode in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model with parameters of type BioNode

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	KineticLaw.calculateAcceleration(BioNode node, CellSection section)

Uses of BioNode in de.bioforscher.singa.simulation.modules.reactions.model

Methods in de.bioforscher.singa.simulation.modules.reactions.model with parameters of type BioNode

Modifier and Type	Method and Description
abstract javax.measure.Quantity<ReactionRate>	Reaction.calculateAcceleration(BioNode node, CellSection section) Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.
PotentialUpdate	Reactions.calculateUpdate(BioNode node, CellSection section, ChemicalEntity entity)
List<PotentialUpdate>	Reactions.calculateUpdates(BioNode node)
protected javax.measure.Quantity<MolarConcentration>	Reaction.determineConcentration(BioNode node, CellSection section, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.