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

Packages that use CellTopology

Package	Description
bio.singa.simulation.model.modules.concentration.imlementations.reactions
bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants
bio.singa.simulation.model.sections

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

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

Modifier and Type	Method and Description
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicReactantStep.targetProductToTopology(ChemicalEntity affectedEntity, CellTopology targetTopology)
ReactionBuilder.DynamicReactantStep	ReactionBuilder.DynamicBuilder.targetProductToTopology(ChemicalEntity affectedEntity, CellTopology targetTopology)

Uses of CellTopology in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants that return CellTopology

Modifier and Type	Method and Description
CellTopology	Reactant.getPreferredTopology()

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants that return types with arguments of type CellTopology

Modifier and Type	Method and Description
List<CellTopology>	DynamicChemicalEntity.getPossibleTopologies()
Map<ChemicalEntity,CellTopology>	DynamicReactantBehavior.getTargetTopologies()

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with parameters of type CellTopology

Modifier and Type	Method and Description
void	DynamicChemicalEntity.addPossibleTopology(CellTopology possibleTopology)
DynamicChemicalEntity.Builder	DynamicChemicalEntity.Builder.addPossibleTopology(CellTopology topology)
void	DynamicReactantBehavior.addTargetTopology(ChemicalEntity splitTargetEntity, CellTopology targetTopology)
List<ChemicalEntity>	DynamicChemicalEntity.getMatchingEntities(Updatable updatable, CellTopology topology)
void	Reactant.setPreferredTopology(CellTopology preferredTopology)

Method parameters in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with type arguments of type CellTopology

Modifier and Type	Method and Description
void	DynamicChemicalEntity.setPossibleTopologies(List<CellTopology> possibleTopologies)

Constructors in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with parameters of type CellTopology

Constructor and Description
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology)
Reactant(ChemicalEntity chemicalEntity, ReactantRole role, CellTopology topology, double stoichiometricNumber)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, double stoichiometricNumber, double reactionOrder)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

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

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

Modifier and Type	Method and Description
static CellTopology	CellTopology.valueOf(String name) Returns the enum constant of this type with the specified name.
static CellTopology[]	CellTopology.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method and Description
Map.Entry<CellTopology,ConcentrationPool>	ConcentrationContainer.getPool(CellSubsection subsection) Returns the topology and concentration pool for the subsection.

Methods in bio.singa.simulation.model.sections with parameters of type CellTopology

Modifier and Type	Method and Description
void	CellRegion.addSubsection(CellTopology topology, CellSubsection subsection)
boolean	ConcentrationContainer.containsEntity(CellTopology topology, ChemicalEntity entity)
Optional<ChemicalEntity>	ConcentrationContainer.containsHiddenEntity(CellTopology topology, ChemicalEntity entity)
double	ConcentrationContainer.get(CellTopology topology, ChemicalEntity entity) Returns the concentration of the entity in the corresponding topology.
Map.Entry<CellSubsection,ConcentrationPool>	ConcentrationContainer.getPool(CellTopology topology) Returns the subsection and concentration pool for the topology.
CellSubsection	ConcentrationContainer.getSubsection(CellTopology topology) Returns the subsection corresponding to the topology.
void	ConcentrationContainer.initialize(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)
void	ConcentrationContainer.initializeSubsection(CellSubsection subsection, CellTopology topology) Initializes a new concentration pool for the corresponding subsection and topology.
void	ConcentrationContainer.putSubsectionPool(CellSubsection subsection, CellTopology topology, ConcentrationPool concentrationPool) Adds a concentration pool, referenced to the subsection and topology.
void	ConcentrationContainer.removeSubsection(CellTopology topology) Removes a subsection, the given topology and concentration pool from the container.
void	ConcentrationContainer.set(CellTopology topology, ChemicalEntity entity, double concentration) Sets the concentration of the given entity in the given topology.