Uses of Class
bio.singa.simulation.model.graphs.AutomatonGraph

Packages that use AutomatonGraph

Package	Description
bio.singa.simulation.events
bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.surfacelike
bio.singa.simulation.model.graphs
bio.singa.simulation.model.simulation

Uses of AutomatonGraph in bio.singa.simulation.events

Methods in bio.singa.simulation.events that return AutomatonGraph

Modifier and Type	Method and Description
AutomatonGraph	GraphUpdatedEvent.getGraph() Returns the encapsulated graph.

Constructors in bio.singa.simulation.events with parameters of type AutomatonGraph

Constructor and Description
GraphUpdatedEvent(AutomatonGraph graph, javax.measure.Quantity<javax.measure.quantity.Time> elapsedTime) Creates a new GraphUpdatedEvent.

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

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

Modifier and Type	Method and Description
AutomatonGraph	LineLikeAgent.getGraph()

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

Modifier and Type	Method and Description
void	LineLikeAgentTemplate.associateInGraph(AutomatonGraph graph)
void	LineLikeAgent.associateInGraph(AutomatonGraph graph)
void	LineLikeAgent.setGraph(AutomatonGraph graph)

Constructors in bio.singa.simulation.model.agents.linelike with parameters of type AutomatonGraph

Constructor and Description
LineLikeAgent(String type, bio.singa.mathematics.vectors.Vector2D initialPosition, bio.singa.mathematics.vectors.Vector2D initialDirection, AutomatonGraph graph)

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

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

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 List<Membrane>	MembraneTracer.regionsToMembrane(AutomatonGraph graph)

Constructors in bio.singa.simulation.model.agents.surfacelike with parameters of type AutomatonGraph

Constructor and Description
MembraneTracer(AutomatonGraph graph)

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

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

Modifier and Type	Method and Description
static AutomatonGraph	AutomatonGraphs.createRectangularAutomatonGraph(int numberOfColumns, int numberOfRows)
static AutomatonGraph	AutomatonGraphs.singularGraph()
static AutomatonGraph	AutomatonGraphs.singularGraph(CellRegion region)
static AutomatonGraph	AutomatonGraphs.useStructureFrom(bio.singa.mathematics.graphs.grid.GridGraph gridGraph) Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.

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

Modifier and Type	Method and Description
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)
static Map<String,ChemicalEntity>	AutomatonGraphs.generateMapOfEntities(AutomatonGraph graph) Creates and returns a map that contains all chemical entities that are present in the given graph as values and with the name of the entity as key.
static CellRegion	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, CellSubsection innerSection, CellSubsection outerSection, boolean switchSides)

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

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

Modifier and Type	Method and Description
AutomatonGraph	Simulation.getGraph()

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

Modifier and Type	Method and Description
void	Simulation.setGraph(AutomatonGraph graph)