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

Packages that use CellTopology

Package	Description
bio.singa.simulation.model.concentrations
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.concentrations

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

Modifier and Type	Method	Description
CellTopology	InitialConcentration.getTopology()
CellTopology	TopologyCondition.getTopology()

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

Modifier and Type	Method	Description
static TopologyCondition	TopologyCondition.isTopology(CellTopology topology)
void	InitialConcentration.setTopology(CellTopology topology)
ConcentrationBuilder.ConcentrationStep	ConcentrationBuilder.ConcentrationBuilderImpl.topology(CellTopology topology)
ConcentrationBuilder.ConcentrationStep	ConcentrationBuilder.PoolStep.topology(CellTopology topology)

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	Description
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)

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	Description
CellTopology	Reactant.getPreferredTopology()

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

Modifier and Type	Method	Description
void	Reactant.setPreferredTopology(CellTopology preferredTopology)

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

Constructor	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	Description
static CellTopology	CellTopology.getTopology(int index)
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	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	Description
void	CellRegion.addSubsection(CellTopology topology, CellSubsection subsection)
boolean	ConcentrationContainer.containsEntity(CellTopology topology, ChemicalEntity entity)
Optional<ChemicalEntity>	ConcentrationContainer.containsHiddenEntity(CellTopology topology, ChemicalEntity query)
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.
boolean	CellRegion.has(CellTopology 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.