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

Packages that use CellRegion

Package	Description
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.graphs
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.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(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<Vector2D,CellRegion>	OrganelleTemplate.getInverseRegionMap()
Map<CellRegion,Set<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)

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<Vector2D>> regionMap, 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<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<Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, AutomatonGraph graph, Map<Vector2D,CellRegion> regions)
static Membrane	MembraneFactory.createLinearMembrane(Collection<Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, NeumannRectangularDirection innerDirection, AutomatonGraph graph, Map<Vector2D,CellRegion> regions, 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<Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, AutomatonGraph graph, Map<Vector2D,CellRegion> regions)
static Membrane	MembraneFactory.createLinearMembrane(Collection<Vector2D> vectors, CellRegion innerRegion, CellRegion membraneRegion, NeumannRectangularDirection innerDirection, AutomatonGraph graph, Map<Vector2D,CellRegion> regions, Rectangle globalClipper)
static CellRegion	MembraneTracer.getRegion(Map<CellRegion,Set<Vector2D>> regionMap, Vector2D vector)
void	Membrane.setRegionMap(Map<CellRegion,Set<Vector2D>> regionMap)

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

Constructor and Description
MembraneFactory(Collection<Vector2D> membraneVectors, AutomatonGraph graph, Map<Vector2D,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 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, RectangularCoordinate centre, int radius)
static void	AutomatonGraphs.fillRegion(AutomatonGraph graph, CellRegion innerRegion, RectangularCoordinate centre, int radius)
void	AutomatonNode.setCellRegion(CellRegion cellRegion)

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_OUTER_MEMBRANE_REGION
static CellRegion	CellRegion.CYTOSOL_A
static CellRegion	CellRegion.CYTOSOL_B
static CellRegion	CellRegions.EARLY_ENDOSOME_VESICLE_REGION
static CellRegion	CellRegions.EXTRACELLULAR_REGION
static CellRegion	CellRegion.MEMBRANE

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

Modifier and Type	Method and Description
static CellRegion	CellRegion.forVesicle(String identifier)

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

Modifier and Type	Method and Description
static javafx.scene.paint.Color	CellSubsections.getColor(CellRegion cellRegion)

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<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, Evidence evidence)
SectionConcentration(CellRegion region, CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<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()