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

Packages that use CellSubsection

Package	Description
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.reactants
bio.singa.simulation.model.modules.displacement
bio.singa.simulation.model.sections
bio.singa.simulation.model.simulation
bio.singa.simulation.parser.sbml

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

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

Modifier and Type	Method and Description
Set<CellSubsection>	AutomatonNode.getAllReferencedSections() Returns all referenced sections in this node.
Map<CellSubsection,Polygon>	AutomatonNode.getSubsectionRepresentations()

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

Modifier and Type	Method and Description
void	AutomatonNode.addSubsectionRepresentation(CellSubsection subsection, Polygon representation)
javax.measure.Quantity<MolarConcentration>	AutomatonNode.getConcentration(CellSubsection section, ChemicalEntity entity) Returns the concentration of the given chemical entity in the given compartment.
static CellRegion	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, CellSubsection innerSection, CellSubsection outerSection, boolean switchSides)

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 and Description
CellSubsection	ConcentrationDelta.getCellSubsection() Returns the subsection.
CellSubsection	FieldSupplier.getCurrentSubsection() Returns the current subsection.
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 and Description
void	FieldSupplier.setCurrentSubsection(CellSubsection subsection) Sets the current subsection.

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

Constructor and Description
ConcentrationDelta(UpdateModule module, CellSubsection cellSubsection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> quantity) Creates a new concentration delta.
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, ChemicalEntity entity) Creates a new DeltaIdentifier.

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

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

Modifier and Type	Method and Description
CellSubsection	KineticLaw.getCurrentCellSection() Returns the current cell section the kinetic law is applied to.

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

Modifier and Type	Method and Description
void	KineticLaw.setCurrentCellSection(CellSubsection currentCellSection) Sets the current cell section the kinetic law is applied to.

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

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

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

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

Modifier and Type	Method and Description
javax.measure.Quantity<MolarConcentration>	Vesicle.getConcentration(CellSubsection cellSection, ChemicalEntity chemicalEntity)

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

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

Modifier and Type	Field and 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	CellSubsection.MEMBRANE A general membrane subsection.
static CellSubsection	CellSubsections.NUCLEAR_MEMBRANE
static CellSubsection	CellSubsections.NUCLEOPLASM
static CellSubsection	CellSubsection.SECTION_A A cellular subsection "A".
static CellSubsection	CellSubsection.SECTION_B A cellular subsection "B".

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

Modifier and Type	Method and Description
CellSubsection	ConcentrationContainer.getInnerSubsection() Returns the inner subsection.
CellSubsection	CellRegion.getInnerSubsection()
CellSubsection	ConcentrationContainer.getMembraneSubsection() Returns the membrane subsection.
CellSubsection	CellRegion.getMembraneSubsection()
CellSubsection	ConcentrationContainer.getOuterSubsection() Returns the outer subsection.
CellSubsection	CellRegion.getOuterSubsection()
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 and 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 and Description
void	CellRegion.addSubSection(CellTopology topology, CellSubsection subsection)
javax.measure.Quantity<MolarConcentration>	ConcentrationContainer.get(CellSubsection subsection, ChemicalEntity entity) Returns the concentration of the entity in the corresponding subsection.
static javafx.scene.paint.Color	CellSubsections.getColor(CellSubsection 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<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.
void	ConcentrationContainer.set(CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> 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 and Description
Set<CellSubsection>	Updatable.getAllReferencedSections()

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

Modifier and Type	Method and Description
javax.measure.Quantity<MolarConcentration>	Updatable.getConcentration(CellSubsection cellSection, ChemicalEntity chemicalEntity)

Uses of CellSubsection in bio.singa.simulation.parser.sbml

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

Modifier and Type	Method and Description
Map<CellSubsection,Double>	SBMLParser.getCompartments()