de.bioforscher.singa.simulation.model.graphs

Class AutomatonGraph

java.lang.Object

de.bioforscher.singa.mathematics.graphs.model.AbstractGraph<AutomatonNode,AutomatonEdge,Vector2D,Integer>

de.bioforscher.singa.simulation.model.graphs.AutomatonGraph

All Implemented Interfaces:

Graph<AutomatonNode,AutomatonEdge,Integer>

public class AutomatonGraph
extends AbstractGraph<AutomatonNode,AutomatonEdge,Vector2D,Integer>

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 CellSections that emulate compartments, extracellular space or membranes.

Author:

cl

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	addCellSection(CellSection 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)
void	addNodesToCompartment(EnclosedCompartment enclosedCompartment, Rectangle rectangle) Adds nodes in a rectangular region to the cell section.
CellSection	getCellSection(String identifier) Return the cell section with the given identifier.
Set<CellSection>	getCellSections() Returns all CellSections 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.
Integer	nextNodeIdentifier()

Methods inherited from class de.bioforscher.singa.mathematics.graphs.model.AbstractGraph

addEdgeBetween, addNode, containsEdge, containsNode, getEdge, getEdges, getMaximumDegree, getNode, getNodes, nextEdgeIdentifier, removeNode, removeNode, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.mathematics.graphs.model.Graph

getCopy, getEdgeBetween

Constructor Detail

AutomatonGraph

public AutomatonGraph()

Creates a new empty graph.

AutomatonGraph

public AutomatonGraph(int nodeCapacity,
                      int edgeCapacity)

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

Parameters:

nodeCapacity - The node capacity.

edgeCapacity - The edge capacity.

Method Detail

addEdgeBetween

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

Specified by:

addEdgeBetween in interface Graph<AutomatonNode,AutomatonEdge,Integer>

Specified by:

addEdgeBetween in class AbstractGraph<AutomatonNode,AutomatonEdge,Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(AutomatonNode source,
                          AutomatonNode target)

Specified by:

addEdgeBetween in interface Graph<AutomatonNode,AutomatonEdge,Integer>

Specified by:

addEdgeBetween in class AbstractGraph<AutomatonNode,AutomatonEdge,Vector2D,Integer>

nextNodeIdentifier

public Integer nextNodeIdentifier()

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<CellSection> getCellSections()

Returns all CellSections referenced in this graph.

Returns:

The cell sections.

getCellSection

public CellSection getCellSection(String identifier)

Return the cell section with the given identifier.

Parameters:

identifier - The identifier.

Returns:

The cell section.

addCellSection

public void addCellSection(CellSection cellSection)

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

Parameters:

cellSection - The cell section.

addNodesToCompartment

public void addNodesToCompartment(EnclosedCompartment enclosedCompartment,
                                  Rectangle rectangle)

Adds nodes in a rectangular region to the cell section. Each node in the graph that lies inside of the rectangle is associated to the compartment. Additionally the outermost nodes are assigned as membrane nodes of this compartment.

Parameters:

enclosedCompartment - The enclosed compartment.

rectangle - The rectangle.