bio.singa.simulation.model.graphs

Class AutomatonGraph

java.lang.Object

bio.singa.mathematics.graphs.grid.AbstractGridGraph<AutomatonNode,AutomatonEdge,Vector2D>

bio.singa.simulation.model.graphs.AutomatonGraph

All Implemented Interfaces:

Graph<AutomatonNode,AutomatonEdge,RectangularCoordinate>

public class AutomatonGraph
extends AbstractGridGraph<AutomatonNode,AutomatonEdge,Vector2D>

The Automaton graph class is the underlying graph of cellular graph automaton Simulations. Each AutomatonNode is placed in a two dimensional simulation space, neighbourhoods are defined by AutomatonEdges. Nodes can be assigned to groups using CellRegions that emulate compartments, extracellular space or membranes.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
AutomatonGraph(int columns, int rows) Creates a new empty graph, initialized with node and edge capacity.

Method Summary

Modifier and Type	Method and Description
void	addCellRegion(CellRegion cellSection) Adds a cell section to this graph but does not associate any node to it.
int	addEdgeBetween(AutomatonNode source, AutomatonNode target)
int	addEdgeBetween(int identifier, AutomatonNode source, AutomatonNode target)
CellRegion	getCellRegion(String identifier) Return the cell section with the given identifier.
Set<CellRegion>	getCellSections() Returns all CellSubsections referenced in this graph.
void	initializeSpeciesWithConcentration(ChemicalEntity entity, double concentration) Initializes the concentration of the given chemical entity of every node in this graph to to the given concentration in mol/l.
void	initializeSpeciesWithConcentration(ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration) Initializes the concentration of the given chemical entity of every node in this graph.

Methods inherited from class bio.singa.mathematics.graphs.grid.AbstractGridGraph

addEdgeBetween, addNode, containsEdge, containsNode, getEdge, getEdges, getNode, getNode, getNodes, getNodesOfColumn, getNodesOfRow, getNumberOfColumns, getNumberOfRows, nextNodeIdentifier, removeNode, removeNode

Methods inherited from class java.lang.Object

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

Methods inherited from interface bio.singa.mathematics.graphs.model.Graph

getCopy, getEdgeBetween, nextEdgeIdentifier

Constructor Detail

AutomatonGraph

public AutomatonGraph(int columns,
                      int rows)

Creates a new empty graph, initialized with node and edge capacity.

Parameters:

columns - The node capacity.

rows - The edge capacity.

Method Detail

addEdgeBetween

public int addEdgeBetween(int identifier,
                          AutomatonNode source,
                          AutomatonNode target)

addEdgeBetween

public int addEdgeBetween(AutomatonNode source,
                          AutomatonNode target)

initializeSpeciesWithConcentration

public void initializeSpeciesWithConcentration(ChemicalEntity entity,
                                               double concentration)

Initializes the concentration of the given chemical entity of every node in this graph to to the given concentration in mol/l.

Parameters:

entity - The chemical entity.

concentration - The concentration in mol/l.

initializeSpeciesWithConcentration

public void initializeSpeciesWithConcentration(ChemicalEntity entity,
                                               javax.measure.Quantity<MolarConcentration> concentration)

Initializes the concentration of the given chemical entity of every node in this graph.

Parameters:

entity - The chemical entity.

concentration - The concentration.

getCellSections

public Set<CellRegion> getCellSections()

Returns all CellSubsections referenced in this graph.

Returns:

The cell sections.

getCellRegion

public CellRegion getCellRegion(String identifier)

Return the cell section with the given identifier.

Parameters:

identifier - The identifier.

Returns:

The cell section.

addCellRegion

public void addCellRegion(CellRegion cellSection)

Adds a cell section to this graph but does not associate any node to it.

Parameters:

cellSection - The cell section.