Package bio.singa.simulation.model.graphs

Class AutomatonGraphs

java.lang.Object

bio.singa.simulation.model.graphs.AutomatonGraphs

public class AutomatonGraphs
extends Object

Author:

cl

Method Summary

Modifier and Type	Method	Description
static Set<AutomatonNode>	circleRegion(AutomatonGraph graph, CellRegion membraneRegion, bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre, int radius)
static AutomatonGraph	createRectangularAutomatonGraph(int numberOfColumns, int numberOfRows)
static void	fillRegion(AutomatonGraph graph, CellRegion innerRegion, bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre, int radius)
static Map<String,ChemicalEntity>	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 AutomatonGraph	singularGraph()
static AutomatonGraph	singularGraph(CellRegion region)
static CellRegion	splitRectangularGraphWithMembrane(AutomatonGraph graph, CellSubsection innerSection, CellSubsection outerSection, boolean switchSides)
static AutomatonGraph	useStructureFrom(bio.singa.mathematics.graphs.grid.GridGraph gridGraph)	Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

generateMapOfEntities

public static Map<String,ChemicalEntity> 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.

Parameters:

graph - A graph with species

Returns:

All chemical entities in the graph.

createRectangularAutomatonGraph

public static AutomatonGraph createRectangularAutomatonGraph(int numberOfColumns,
                                                             int numberOfRows)

useStructureFrom

public static AutomatonGraph useStructureFrom(bio.singa.mathematics.graphs.grid.GridGraph gridGraph)

Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph. No new data is generated. Indices are persistent. Both Graphs are independently modifiable.

Parameters:

gridGraph - The graph to be cast

Returns:

The generated automaton graph.

singularGraph

public static AutomatonGraph singularGraph()

singularGraph

public static AutomatonGraph singularGraph(CellRegion region)

splitRectangularGraphWithMembrane

public static CellRegion splitRectangularGraphWithMembrane(AutomatonGraph graph,
                                                           CellSubsection innerSection,
                                                           CellSubsection outerSection,
                                                           boolean switchSides)

circleRegion

public static Set<AutomatonNode> circleRegion(AutomatonGraph graph,
                                              CellRegion membraneRegion,
                                              bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre,
                                              int radius)

fillRegion

public static void fillRegion(AutomatonGraph graph,
                              CellRegion innerRegion,
                              bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate centre,
                              int radius)