Uses of Class
de.bioforscher.singa.simulation.model.graphs.AutomatonGraph

Packages that use AutomatonGraph

Package	Description
de.bioforscher.singa.simulation.events
de.bioforscher.singa.simulation.model.compartments
de.bioforscher.singa.simulation.model.graphs
de.bioforscher.singa.simulation.modules.diffusion
de.bioforscher.singa.simulation.modules.membranetransport
de.bioforscher.singa.simulation.modules.model
de.bioforscher.singa.simulation.modules.model.updates
de.bioforscher.singa.simulation.modules.reactions.model
de.bioforscher.singa.simulation.parser.graphs

Uses of AutomatonGraph in de.bioforscher.singa.simulation.events

Methods in de.bioforscher.singa.simulation.events that return AutomatonGraph

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

Constructors in de.bioforscher.singa.simulation.events with parameters of type AutomatonGraph

Constructor and Description
GraphUpdatedEvent(AutomatonGraph graph)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.model.compartments

Methods in de.bioforscher.singa.simulation.model.compartments with parameters of type AutomatonGraph

Modifier and Type	Method and Description
void	Membrane.initializeNodes(AutomatonGraph automatonGraph)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.model.graphs

Methods in de.bioforscher.singa.simulation.model.graphs that return AutomatonGraph

Modifier and Type	Method and Description
static AutomatonGraph	AutomatonGraphs.copyStructureToBioGraph(UndirectedGraph undirectedGraph) Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.
static AutomatonGraph	AutomatonGraphs.createRectangularAutomatonGraph(int numberOfColumns, int numberOfRows)

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

Modifier and Type	Method and Description
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 void	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, GridCoordinateConverter converter, EnclosedCompartment innerSection, CellSection outerSection)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.modules.diffusion

Methods in de.bioforscher.singa.simulation.modules.diffusion with parameters of type AutomatonGraph

Modifier and Type	Method and Description
void	FreeDiffusion.applyTo(AutomatonGraph graph)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.modules.membranetransport

Methods in de.bioforscher.singa.simulation.modules.membranetransport with parameters of type AutomatonGraph

Modifier and Type	Method and Description
void	PassiveMembraneTransport.applyTo(AutomatonGraph graph)
void	ActiveMembraneTransport.applyTo(AutomatonGraph graph)
void	PassiveMembraneTransport.updateGraph(AutomatonGraph graph)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.modules.model

Methods in de.bioforscher.singa.simulation.modules.model that return AutomatonGraph

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

Methods in de.bioforscher.singa.simulation.modules.model with parameters of type AutomatonGraph

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

Uses of AutomatonGraph in de.bioforscher.singa.simulation.modules.model.updates

Methods in de.bioforscher.singa.simulation.modules.model.updates with parameters of type AutomatonGraph

Modifier and Type	Method and Description
void	UpdateBehavior.updateGraph(AutomatonGraph graph)
default void	CumulativeUpdateBehavior.updateGraph(AutomatonGraph graph) Calculates all updates and applies them afterwards.

Uses of AutomatonGraph in de.bioforscher.singa.simulation.modules.reactions.model

Methods in de.bioforscher.singa.simulation.modules.reactions.model with parameters of type AutomatonGraph

Modifier and Type	Method and Description
void	Reactions.applyTo(AutomatonGraph graph)

Uses of AutomatonGraph in de.bioforscher.singa.simulation.parser.graphs

Methods in de.bioforscher.singa.simulation.parser.graphs that return AutomatonGraph

Modifier and Type	Method and Description
AutomatonGraph	GraphMLContentHandler.getGraph()
AutomatonGraph	GraphMLParserService.parse()

Methods in de.bioforscher.singa.simulation.parser.graphs with parameters of type AutomatonGraph

Modifier and Type	Method and Description
static void	GraphMLExportService.exportGraph(AutomatonGraph graph, File file) Exports a Graph to a GraphML file.