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

Packages that use CellRegion

Package	Description
bio.singa.simulation.features
bio.singa.simulation.features.variation
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.graphs
bio.singa.simulation.model.modules.displacement.implementations
bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.sections
bio.singa.simulation.model.sections.concentration
bio.singa.simulation.model.simulation

Uses of CellRegion in bio.singa.simulation.features

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

Constructor and Description
AffectedRegion(CellRegion region)
AffectedRegion(CellRegion region, bio.singa.features.model.Evidence evidence)
AffectedRegion(CellRegion region, List<bio.singa.features.model.Evidence> evidence)
ContainmentRegion(CellRegion region)
ContainmentRegion(CellRegion region, bio.singa.features.model.Evidence evidence)
ContainmentRegion(CellRegion region, List<bio.singa.features.model.Evidence> evidence)
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.features.variation

Methods in bio.singa.simulation.features.variation that return CellRegion

Modifier and Type	Method and Description
CellRegion	ConcentrationVariation.getCellRegion()

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

Constructor and Description
ConcentrationVariation(CellRegion cellRegion, CellSubsection subsection, ChemicalEntity entity)

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 and 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 and 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 and Description
void	OrganelleTemplate.initializeGroup(CellRegion region)
void	OrganelleTemplate.initializeGroup(int groupIdentifier, 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 and Description
CellRegion	Vesicle.getCellRegion()
CellRegion	Vesicle.getRegion()

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

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

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

Constructor and 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 and 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)

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

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

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

Modifier and Type	Method and Description
static Membrane	MembraneFactory.createClosedMembrane(Collection<bio.singa.mathematics.vectors.Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, AutomatonGraph graph, Map<bio.singa.mathematics.vectors.Vector2D,CellRegion> regions)
static Membrane	MembraneFactory.createLinearMembrane(Collection<bio.singa.mathematics.vectors.Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, bio.singa.mathematics.topology.grids.rectangular.NeumannRectangularDirection innerDirection, AutomatonGraph graph, Map<bio.singa.mathematics.vectors.Vector2D,CellRegion> regions, bio.singa.mathematics.geometry.faces.Rectangle globalClipper)
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 and Description
static Membrane	MembraneFactory.createClosedMembrane(Collection<bio.singa.mathematics.vectors.Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, AutomatonGraph graph, Map<bio.singa.mathematics.vectors.Vector2D,CellRegion> regions)
static Membrane	MembraneFactory.createLinearMembrane(Collection<bio.singa.mathematics.vectors.Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, bio.singa.mathematics.topology.grids.rectangular.NeumannRectangularDirection innerDirection, AutomatonGraph graph, Map<bio.singa.mathematics.vectors.Vector2D,CellRegion> regions, bio.singa.mathematics.geometry.faces.Rectangle globalClipper)
static CellRegion	MembraneTracer.getRegion(Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>> regionMap, bio.singa.mathematics.vectors.Vector2D vector)
void	Membrane.setRegionMap(Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>> regionMap)

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 and Description
CellRegion	VolumeLikeAgent.getCellRegion()

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

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

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

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

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

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

Modifier and Type	Method and Description
CellRegion	AutomatonNode.getCellRegion()
CellRegion	AutomatonGraph.getCellRegion(String identifier) Return the cell section with the given identifier.
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 and 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 and 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.displacement.implementations

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

Modifier and Type	Method and Description
CellRegion	VesicleConfinedDiffusion.getConfinedVolume()

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

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

Modifier and Type	Method and Description
void	ClathrinMediatedEndocytosis.setMembraneRegion(CellRegion region)

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

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

Modifier and Type	Field and Description
static CellRegion	CellRegions.CELL_CORTEX
static CellRegion	CellRegions.CELL_OUTER_MEMBRANE_REGION
static CellRegion	CellRegions.CYTOPLASM_REGION
static CellRegion	CellRegion.CYTOSOL_A
static CellRegion	CellRegion.CYTOSOL_B
static CellRegion	CellRegions.EXTRACELLULAR_REGION
static CellRegion	CellRegion.MEMBRANE
static CellRegion	CellRegions.PERINUCLEAR_REGION
static CellRegion	CellRegions.VESICLE_REGION

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

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

Modifier and Type	Method and Description
CellRegion	SectionConcentration.getRegion()
CellRegion	MembraneConcentration.getRegion()

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

Modifier and Type	Method and Description
void	ConcentrationInitializer.addInitialConcentration(CellRegion region, CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)
void	SectionConcentration.setRegion(CellRegion region)
void	MembraneConcentration.setRegion(CellRegion region)

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

Constructor and Description
MembraneConcentration(CellRegion region, ChemicalEntity entity, javax.measure.Quantity<javax.measure.quantity.Area> area, double numberOfMolecules, bio.singa.features.model.Evidence evidence)
SectionConcentration(CellRegion region, CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)

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

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

Modifier and Type	Method and Description
CellRegion	Updatable.getCellRegion()