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

Packages that use AutomatonGraph

Package	Description
bio.singa.simulation.events
bio.singa.simulation.model.agents.membranes
bio.singa.simulation.model.graphs
bio.singa.simulation.model.simulation
bio.singa.simulation.renderer

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.membranes

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

Modifier and Type	Method and Description
static Membrane	MembraneTracer.membraneToRegion(Organelle organelle, AutomatonGraph graph)
static List<Membrane>	MembraneTracer.regionsToMembrane(AutomatonGraph graph)

Constructors in bio.singa.simulation.model.agents.membranes 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.useStructureFrom(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, RectangularCoordinate centre, int radius)
static void	AutomatonGraphs.fillRegion(AutomatonGraph graph, CellRegion innerRegion, 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)

Uses of AutomatonGraph in bio.singa.simulation.renderer

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

Modifier and Type	Method and Description
void	AutomatonGraphRenderer.render(AutomatonGraph graph)
void	AutomatonGraphRenderer.rescaleColors(AutomatonGraph graph)

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

Constructor and Description
AutomatonGraphRenderer(AutomatonGraph graph)