Uses of Class
de.bioforscher.singa.simulation.model.compartments.CellSection

Packages that use CellSection

Package	Description
de.bioforscher.singa.simulation.model.compartments
de.bioforscher.singa.simulation.model.concentrations
de.bioforscher.singa.simulation.model.graphs
de.bioforscher.singa.simulation.modules.model
de.bioforscher.singa.simulation.modules.reactions.implementations

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

Subclasses of CellSection in de.bioforscher.singa.simulation.model.compartments

Modifier and Type	Class and Description
class	EnclosedCompartment An EnclosedCompartment is a CellSection that is bordered or enclosed by a Membrane.
class	Membrane

Methods in de.bioforscher.singa.simulation.model.compartments that return CellSection

Modifier and Type	Method and Description
CellSection	Membrane.getInnerLayer()
CellSection	Membrane.getOuterLayer()

Uses of CellSection in de.bioforscher.singa.simulation.model.concentrations

Methods in de.bioforscher.singa.simulation.model.concentrations that return CellSection

Modifier and Type	Method and Description
CellSection	Delta.getCellSection() Returns the cell section.
CellSection	MembraneContainer.getInnerLayerSection()
CellSection	MembraneContainer.getInnerPhaseSection()
CellSection	MembraneContainer.getOuterLayerSection()
CellSection	MembraneContainer.getOuterPhaseSection()

Methods in de.bioforscher.singa.simulation.model.concentrations that return types with arguments of type CellSection

Modifier and Type	Method and Description
Set<CellSection>	MultiConcentrationContainer.getAllReferencedSections()
Set<CellSection>	MembraneContainer.getAllReferencedSections()
Set<CellSection>	ConcentrationContainer.getAllReferencedSections() Returns all Compartments that are referenced in this container.
Set<CellSection>	SimpleConcentrationContainer.getAllReferencedSections()

Methods in de.bioforscher.singa.simulation.model.concentrations with parameters of type CellSection

Modifier and Type	Method and Description
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	MultiConcentrationContainer.getAllConcentrationsForSection(CellSection cellSection)
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	MembraneContainer.getAllConcentrationsForSection(CellSection cellSection)
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	ConcentrationContainer.getAllConcentrationsForSection(CellSection cellSection) Returns all concentrations for a particular CellSection.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	SimpleConcentrationContainer.getAllConcentrationsForSection(CellSection cellSection)
javax.measure.Quantity<MolarConcentration>	MultiConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	MembraneContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	ConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity) Returns the concentration of the specified ChemicalEntity available in the CellSection.
javax.measure.Quantity<MolarConcentration>	SimpleConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
void	MultiConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)
void	MembraneContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)
void	ConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the available concentration based on the given compartment.
void	SimpleConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)

Constructors in de.bioforscher.singa.simulation.model.concentrations with parameters of type CellSection

Constructor and Description
Delta(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> quantity) Creates a new delta for a specific ChemicalEntity in a specific CellSection.
MembraneContainer(CellSection outerPhaseSection, CellSection innerPhaseSection, Membrane membrane)
SimpleConcentrationContainer(CellSection cellSection)

Constructor parameters in de.bioforscher.singa.simulation.model.concentrations with type arguments of type CellSection

Constructor and Description
MultiConcentrationContainer(Set<CellSection> cellSections)

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

Methods in de.bioforscher.singa.simulation.model.graphs that return CellSection

Modifier and Type	Method and Description
CellSection	AutomatonNode.getCellSection() Returns the primary cell section of this node (Membrane nodes may belong to multiple sections).
CellSection	AutomatonGraph.getCellSection(String identifier) Return the cell section with the given identifier.

Methods in de.bioforscher.singa.simulation.model.graphs that return types with arguments of type CellSection

Modifier and Type	Method and Description
Set<CellSection>	AutomatonNode.getAllReferencedSections() Returns all referenced sections in this node.
Set<CellSection>	AutomatonGraph.getCellSections() Returns all CellSections referenced in this graph.

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

Modifier and Type	Method and Description
void	AutomatonGraph.addCellSection(CellSection cellSection) Adds a cell section to this graph but does not associate any node to it.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	AutomatonNode.getAllConcentrationsForSection(CellSection cellSection) Returns all concentrations of all chemical entities in the given cell section.
javax.measure.Quantity<MolarConcentration>	AutomatonNode.getAvailableConcentration(ChemicalEntity entity, CellSection cellSection) Returns the concentration of the given chemical entity in the given compartment.
void	AutomatonNode.setAvailableConcentration(ChemicalEntity entity, CellSection cellSection, javax.measure.Quantity<MolarConcentration> quantity) Gets the concentration of the given chemical entity in the given compartment.
void	AutomatonNode.setCellSection(CellSection cellSection) Sets the cell section of this node and references the node in the corresponding section.
static Membrane	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, GridCoordinateConverter converter, EnclosedCompartment innerSection, CellSection outerSection)

Uses of CellSection in de.bioforscher.singa.simulation.modules.model

Methods in de.bioforscher.singa.simulation.modules.model that return CellSection

Modifier and Type	Method and Description
CellSection	AbstractSectionSpecificModule.getCurrentCellSection()
CellSection	AbstractNeighbourIndependentModule.getCurrentCellSection()
CellSection	AbstractNeighbourDependentModule.getCurrentCellSection()

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

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations that return CellSection

Modifier and Type	Method and Description
CellSection	DynamicKineticLaw.getCurrentCellSection()

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

Modifier and Type	Method and Description
void	DynamicKineticLaw.setCurrentCellSection(CellSection currentCellSection)