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

Packages that use CellSubsection

Package	Description
bio.singa.simulation.features
bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.concentrations
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.imlementations.transport
bio.singa.simulation.model.modules.concentration.specifity
bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.sections
bio.singa.simulation.model.simulation
bio.singa.simulation.trajectories.nested

Uses of CellSubsection in bio.singa.simulation.features

Methods in bio.singa.simulation.features with parameters of type CellSubsection

Modifier and Type	Method	Description
protected AffectedSection	AffectedSection.Builder.createObject(CellSubsection quantity)
static AffectedSection.Builder	AffectedSection.of(CellSubsection quantity)

Constructors in bio.singa.simulation.features with parameters of type CellSubsection

Constructor	Description
AffectedSection(CellSubsection subsection)
Builder(CellSubsection quantity)

Uses of CellSubsection in bio.singa.simulation.model.agents.pointlike

Methods in bio.singa.simulation.model.agents.pointlike that return types with arguments of type CellSubsection

Modifier and Type	Method	Description
Set<CellSubsection>	Vesicle.getAllReferencedSections()

Uses of CellSubsection in bio.singa.simulation.model.concentrations

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

Modifier and Type	Method	Description
CellSubsection	InitialConcentration.getSubsection()
CellSubsection	SectionCondition.getSubsection()

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

Modifier and Type	Method	Description
static SectionCondition	SectionCondition.forSection(CellSubsection section)
void	InitialConcentration.setSubsection(CellSubsection subsection)
ConcentrationBuilder.ConcentrationStep	ConcentrationBuilder.ConcentrationBuilderImpl.subsection(CellSubsection subsection)
ConcentrationBuilder.ConcentrationStep	ConcentrationBuilder.PoolStep.subsection(CellSubsection subsection)

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

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

Modifier and Type	Method	Description
CellSubsection	AutomatonNode.AreaMapping.getSubsection()

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

Modifier and Type	Method	Description
Set<CellSubsection>	AutomatonNode.getAllReferencedSections()	Returns all referenced sections in this node.
Map<CellSubsection,List<AutomatonNode.AreaMapping>>	AutomatonNode.getSubsectionAdjacency()
Map<CellSubsection,bio.singa.mathematics.geometry.model.Polygon>	AutomatonNode.getSubsectionRepresentations()

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

Modifier and Type	Method	Description
void	AutomatonNode.addAreaMapping(CellSubsection subsection, AutomatonNode.AreaMapping mapping)
void	AutomatonNode.addSubsectionRepresentation(CellSubsection subsection, bio.singa.mathematics.geometry.model.Polygon representation)
static CellRegion	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, CellSubsection innerSection, CellSubsection outerSection, boolean switchSides)

Constructors in bio.singa.simulation.model.graphs with parameters of type CellSubsection

Constructor	Description
AreaMapping(AutomatonNode source, AutomatonNode target, CellSubsection subsection, double relativeArea)

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

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

Modifier and Type	Method	Description
CellSubsection	ConcentrationDelta.getCellSubsection()	Returns the subsection.
CellSubsection	FieldSupplier.getCurrentSubsection()	Returns the current subsection.
CellSubsection	ConcentrationBasedModule.getRestrictedSubsection()
CellSubsection	ConcentrationDeltaIdentifier.getSubsection()	Returns the cell section the delta is assigned to.

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

Modifier and Type	Method	Description
void	FieldSupplier.setCurrentSubsection(CellSubsection subsection)	Sets the current subsection.
void	ConcentrationBasedModule.setRestrictedSubsection(CellSubsection restrictedSubsection)

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

Constructor	Description
ConcentrationDelta(UpdateModule module, CellSubsection cellSubsection, ChemicalEntity chemicalEntity, double value)	Creates a new concentration delta.
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, ChemicalEntity entity)	Creates a new DeltaIdentifier.
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, String reference, ChemicalEntity entity)

Uses of CellSubsection in bio.singa.simulation.model.modules.concentration.imlementations.transport

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

Modifier and Type	Method	Description
Diffusion.BuildStep	Diffusion.DiffusionBuilder.forSection(CellSubsection subsection)
Diffusion.BuildStep	Diffusion.SectionLimitationStep.forSection(CellSubsection subsection)

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

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

Modifier and Type	Method	Description
void	EntitySpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	SectionSpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	UpdatableSpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	UpdateSpecificity.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)

Uses of CellSubsection in bio.singa.simulation.model.modules.qualitative.implementations

Methods in bio.singa.simulation.model.modules.qualitative.implementations that return types with arguments of type CellSubsection

Modifier and Type	Method	Description
Set<CellSubsection>	EndocytoticPit.getAllReferencedSections()

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

Fields in bio.singa.simulation.model.sections declared as CellSubsection

Modifier and Type	Field	Description
static CellSubsection	CellSubsections.CELL_OUTER_MEMBRANE
static CellSubsection	CellSubsections.CYTOPLASM
static CellSubsection	CellSubsections.EARLY_ENDOSOME_LUMEN
static CellSubsection	CellSubsections.EARLY_ENDOSOME_MEMBRANE
static CellSubsection	CellSubsections.EXTRACELLULAR_REGION
static CellSubsection	CellSubsections.NUCLEAR_MEMBRANE
static CellSubsection	CellSubsections.NUCLEOPLASM
static CellSubsection	CellSubsections.PIT_MEMBRANE
static CellSubsection	CellSubsections.VESICLE_LUMEN
static CellSubsection	CellSubsections.VESICLE_MEMBRANE

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

Modifier and Type	Method	Description
CellSubsection	CellRegion.getInnerSubsection()
CellSubsection	ConcentrationContainer.getInnerSubsection()	Returns the inner subsection.
CellSubsection	CellRegion.getMembraneSubsection()
CellSubsection	ConcentrationContainer.getMembraneSubsection()	Returns the membrane subsection.
CellSubsection	CellRegion.getOuterSubsection()
CellSubsection	ConcentrationContainer.getOuterSubsection()	Returns the outer subsection.
CellSubsection	ConcentrationContainer.getSubsection(CellTopology topology)	Returns the subsection corresponding to the topology.

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

Modifier and Type	Method	Description
Map.Entry<CellSubsection,ConcentrationPool>	ConcentrationContainer.getPool(CellTopology topology)	Returns the subsection and concentration pool for the topology.
Set<CellSubsection>	ConcentrationContainer.getReferencedSubsections()	Returns all subsections, referenced in this container.
Collection<CellSubsection>	CellRegion.getSubsections()

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

Modifier and Type	Method	Description
void	CellRegion.addSubsection(CellTopology topology, CellSubsection subsection)
boolean	ConcentrationContainer.containsEntity(CellSubsection subsection, ChemicalEntity entity)
double	ConcentrationContainer.get(CellSubsection subsection, ChemicalEntity entity)	Returns the concentration of the entity in the corresponding subsection.
Map.Entry<CellTopology,ConcentrationPool>	ConcentrationContainer.getPool(CellSubsection subsection)	Returns the topology and concentration pool for the subsection.
void	ConcentrationContainer.initialize(CellSubsection subsection, 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(CellSubsection subsection)	Removes a subsection, the corresponding topology and concentration pool from the container.
void	ConcentrationContainer.set(CellSubsection subsection, ChemicalEntity entity, double concentration)	Sets the concentration of the given entity in the given subsection.

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

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

Modifier and Type	Method	Description
Set<CellSubsection>	Updatable.getAllReferencedSections()

Uses of CellSubsection in bio.singa.simulation.trajectories.nested

Methods in bio.singa.simulation.trajectories.nested that return types with arguments of type CellSubsection

Modifier and Type	Method	Description
Map<CellSubsection,TrajectoryDataPoint.SubsectionDataPoint>	TrajectoryDataPoint.getSubsectionData()

Methods in bio.singa.simulation.trajectories.nested with parameters of type CellSubsection

Modifier and Type	Method	Description
void	TrajectoryDataPoint.put(CellSubsection cellSection, TrajectoryDataPoint.SubsectionDataPoint dataPoint)