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

Packages that use CellRegion

Package	Description
bio.singa.simulation.features
bio.singa.simulation.features.model
bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.organelles
bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.agents.surfacelike
bio.singa.simulation.model.agents.volumelike
bio.singa.simulation.model.concentrations
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules.concentration.imlementations.transport
bio.singa.simulation.model.modules.displacement.implementations
bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.sections
bio.singa.simulation.model.simulation

Uses of CellRegion in bio.singa.simulation.features

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

Modifier and Type	Method	Description
protected AffectedRegion	AffectedRegion.Builder.createObject(CellRegion quantity)
protected ContainmentRegion	ContainmentRegion.Builder.createObject(CellRegion quantity)
static AffectedRegion.Builder	AffectedRegion.of(CellRegion quantity)
static ContainmentRegion.Builder	ContainmentRegion.of(CellRegion quantity)

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

Constructor	Description
AffectedRegion(CellRegion region)
Builder(CellRegion quantity)
Builder(CellRegion quantity)
ContainmentRegion(CellRegion region)

Uses of CellRegion in bio.singa.simulation.features.model

Constructors in bio.singa.simulation.features.model with parameters of type CellRegion

Constructor	Description
RegionFeature(CellRegion region)
RegionFeature(CellRegion region, bio.singa.features.model.Evidence evidence)
RegionFeature(CellRegion region, List<bio.singa.features.model.Evidence> evidence)

Uses of CellRegion in bio.singa.simulation.model.agents.linelike

Methods in bio.singa.simulation.model.agents.linelike that return CellRegion

Modifier and Type	Method	Description
CellRegion	LineLikeAgentLayer.getTargetMembrane()

Methods in bio.singa.simulation.model.agents.linelike with parameters of type CellRegion

Modifier and Type	Method	Description
void	MicrotubuleOrganizingCentre.initializeActin(LineLikeAgentLayer layer, CellRegion targetedMembrane, int numberOfFilaments)
void	MicrotubuleOrganizingCentre.initializeMicrotubules(LineLikeAgentLayer layer, CellRegion targetedMembrane, int numberOfFilaments)
void	LineLikeAgentLayer.setTargetMembrane(CellRegion targetMembrane)

Uses of CellRegion in bio.singa.simulation.model.agents.organelles

Methods in bio.singa.simulation.model.agents.organelles that return CellRegion

Modifier and Type	Method	Description
CellRegion	OrganelleTemplate.getInnerRegion()
CellRegion	OrganelleTypes.getInnerRegion()
CellRegion	OrganelleTemplate.getMembraneRegion()
CellRegion	OrganelleTypes.getMembraneRegion()
CellRegion	OrganelleTemplate.getRegion(bio.singa.mathematics.vectors.Vector2D vector)
CellRegion	OrganelleTemplate.initializeGroup(int groupIdentifier, String identifier, String goTerm)

Methods in bio.singa.simulation.model.agents.organelles that return types with arguments of type CellRegion

Modifier and Type	Method	Description
Map<bio.singa.mathematics.vectors.Vector2D,CellRegion>	OrganelleTemplate.getInverseRegionMap()
Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>>	OrganelleTemplate.getRegionMap()
Collection<CellRegion>	OrganelleTemplate.getRegions()

Methods in bio.singa.simulation.model.agents.organelles with parameters of type CellRegion

Modifier and Type	Method	Description
void	OrganelleTemplate.initializeGroup(int groupIdentifier, CellRegion region)
void	OrganelleTemplate.initializeGroup(CellRegion region)
void	OrganelleTemplate.setInnerRegion(CellRegion innerRegion)
void	OrganelleTemplate.setMembraneRegion(CellRegion membraneRegion)

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

Methods in bio.singa.simulation.model.agents.pointlike that return CellRegion

Modifier and Type	Method	Description
CellRegion	Vesicle.getCellRegion()
CellRegion	Vesicle.getRegion()

Methods in bio.singa.simulation.model.agents.pointlike with parameters of type CellRegion

Modifier and Type	Method	Description
void	Vesicle.setRegion(CellRegion region)

Constructors in bio.singa.simulation.model.agents.pointlike with parameters of type CellRegion

Constructor	Description
Vesicle(CellRegion region, bio.singa.mathematics.vectors.Vector2D position, javax.measure.Quantity<javax.measure.quantity.Length> radius)

Uses of CellRegion in bio.singa.simulation.model.agents.surfacelike

Methods in bio.singa.simulation.model.agents.surfacelike that return CellRegion

Modifier and Type	Method	Description
CellRegion	Membrane.getInnerRegion()
CellRegion	Membrane.getMembraneRegion()
static CellRegion	MembraneTracer.getRegion(Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>> regionMap, bio.singa.mathematics.vectors.Vector2D vector)	Deprecated.

Methods in bio.singa.simulation.model.agents.surfacelike that return types with arguments of type CellRegion

Modifier and Type	Method	Description
Map<bio.singa.core.utility.Pair<Integer>,CellRegion>	GridMembraneBuilder.getMembraneMapping()
Map<CellRegion,Membrane>	GridMembraneBuilder.getMembranes()
Map<Integer,CellRegion>	GridMembraneBuilder.getRegionMapping()

Methods in bio.singa.simulation.model.agents.surfacelike with parameters of type CellRegion

Modifier and Type	Method	Description
void	Membrane.setInnerRegion(CellRegion innerRegion)
void	Membrane.setMembraneRegion(CellRegion membraneRegion)

Method parameters in bio.singa.simulation.model.agents.surfacelike with type arguments of type CellRegion

Modifier and Type	Method	Description
static CellRegion	MembraneTracer.getRegion(Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>> regionMap, bio.singa.mathematics.vectors.Vector2D vector)	Deprecated.
void	GridMembraneBuilder.setMembraneMapping(Map<bio.singa.core.utility.Pair<Integer>,CellRegion> membraneMapping)
void	GridMembraneBuilder.setMembranes(Map<CellRegion,Membrane> membranes)
void	GridMembraneBuilder.setRegionMapping(Map<Integer,CellRegion> regionMapping)

Uses of CellRegion in bio.singa.simulation.model.agents.volumelike

Methods in bio.singa.simulation.model.agents.volumelike that return CellRegion

Modifier and Type	Method	Description
CellRegion	VolumeLikeAgent.getCellRegion()

Methods in bio.singa.simulation.model.agents.volumelike with parameters of type CellRegion

Modifier and Type	Method	Description
void	VolumeLikeAgent.setCellRegion(CellRegion cellRegion)

Constructors in bio.singa.simulation.model.agents.volumelike with parameters of type CellRegion

Constructor	Description
VolumeLikeAgent(bio.singa.mathematics.geometry.model.Polygon area, CellRegion cellRegion)

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

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

Modifier and Type	Method	Description
List<CellRegion>	RegionCondition.getRegions()

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

Modifier and Type	Method	Description
static AreaCondition	AreaCondition.forRegion(CellRegion region)
static RegionCondition	RegionCondition.forRegion(CellRegion identifier)
static RegionCondition	RegionCondition.forRegions(CellRegion... identifiers)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.AdditionalConditionsStep.inRegionArea(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.ConcentrationBuilderImpl.inRegionArea(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.AdditionalConditionsStep.region(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.ConcentrationBuilderImpl.region(CellRegion region)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.AdditionalConditionsStep.regions(CellRegion... regions)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.ConcentrationBuilderImpl.regions(CellRegion... regions)

Method parameters in bio.singa.simulation.model.concentrations with type arguments of type CellRegion

Modifier and Type	Method	Description
static RegionCondition	RegionCondition.forRegions(List<CellRegion> identifiers)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.AdditionalConditionsStep.regions(List<CellRegion> regions)
ConcentrationBuilder.AdditionalConditionsStep	ConcentrationBuilder.ConcentrationBuilderImpl.regions(List<CellRegion> regions)

Constructor parameters in bio.singa.simulation.model.concentrations with type arguments of type CellRegion

Constructor	Description
RegionCondition(List<CellRegion> regions)

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

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

Modifier and Type	Method	Description
CellRegion	AutomatonGraph.getCellRegion(String identifier)	Return the cell section with the given identifier.
CellRegion	AutomatonNode.getCellRegion()
static CellRegion	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, CellSubsection innerSection, CellSubsection outerSection, boolean switchSides)

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

Modifier and Type	Method	Description
Set<CellRegion>	AutomatonGraph.getCellSections()	Returns all CellSubsections referenced in this graph.

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

Modifier and Type	Method	Description
void	AutomatonGraph.addCellRegion(CellRegion cellSection)	Adds a cell section to this graph but does not associate any node to it.
static Set<AutomatonNode>	AutomatonGraphs.circleRegion(AutomatonGraph graph, CellRegion membraneRegion, bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre, int radius)
static void	AutomatonGraphs.fillRegion(AutomatonGraph graph, CellRegion innerRegion, bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre, int radius)
void	AutomatonNode.setCellRegion(CellRegion cellRegion)
static AutomatonGraph	AutomatonGraphs.singularGraph(CellRegion region)

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

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

Modifier and Type	Method	Description
LateralMembraneDiffusion.BuildStep	LateralMembraneDiffusion.LateralMembraneDiffusionBuilder.forMembrane(CellRegion region)
LateralMembraneDiffusion.BuildStep	LateralMembraneDiffusion.SectionLimitationStep.forMembrane(CellRegion subsection)

Uses of CellRegion in bio.singa.simulation.model.modules.displacement.implementations

Methods in bio.singa.simulation.model.modules.displacement.implementations that return CellRegion

Modifier and Type	Method	Description
CellRegion	VesicleConfinedDiffusion.getConfinedVolume()

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

Methods in bio.singa.simulation.model.modules.qualitative.implementations that return CellRegion

Modifier and Type	Method	Description
CellRegion	EndocytoticPit.getCellRegion()

Methods in bio.singa.simulation.model.modules.qualitative.implementations with parameters of type CellRegion

Modifier and Type	Method	Description
void	EndocytoticPit.setCellRegion(CellRegion cellRegion)

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

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

Modifier and Type	Field	Description
static CellRegion	CellRegions.CELL_CORTEX
static CellRegion	CellRegions.CELL_INNER_MEMBRANE_REGION
static CellRegion	CellRegions.CELL_OUTER_MEMBRANE_REGION
static CellRegion	CellRegions.CYTOPLASM_REGION
static CellRegion	CellRegions.EXTRACELLULAR_REGION
static CellRegion	CellRegions.PERINUCLEAR_REGION
static CellRegion	CellRegions.VESICLE_REGION

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

Methods in bio.singa.simulation.model.simulation that return CellRegion

Modifier and Type	Method	Description
CellRegion	Updatable.getCellRegion()