de.bioforscher.singa.simulation.model.graphs

Class AutomatonGraph

java.lang.Object

de.bioforscher.singa.mathematics.graphs.model.AbstractGraph<BioNode,BioEdge,Vector2D,Integer>

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

All Implemented Interfaces:

Graph<BioNode,BioEdge,Integer>

public class AutomatonGraph
extends AbstractGraph<BioNode,BioEdge,Vector2D,Integer>

Constructor Summary

Constructors

Constructor and Description
AutomatonGraph()
AutomatonGraph(int nodeCapacity, int edgeCapacity)

Method Summary

Modifier and Type	Method and Description
int	addEdgeBetween(BioNode source, BioNode target)
int	addEdgeBetween(int identifier, BioNode source, BioNode target)
void	addNodesToCompartment(EnclosedCompartment enclosedCompartment, Rectangle rectangle)
void	addSection(CellSection cellSection)
CellSection	getSection(String identifier)
Set<CellSection>	getSections()
javax.measure.Quantity<MolarConcentration>	getSteepestDifference(ChemicalEntity entity)
void	initializeSpeciesWithConcentration(ChemicalEntity entity, double concentration)
void	initializeSpeciesWithConcentration(ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration)
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()

AutomatonGraph

public AutomatonGraph(int nodeCapacity,
                      int edgeCapacity)

Method Detail

addEdgeBetween

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

Specified by:

addEdgeBetween in interface Graph<BioNode,BioEdge,Integer>

Specified by:

addEdgeBetween in class AbstractGraph<BioNode,BioEdge,Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(BioNode source,
                          BioNode target)

Specified by:

addEdgeBetween in interface Graph<BioNode,BioEdge,Integer>

Specified by:

addEdgeBetween in class AbstractGraph<BioNode,BioEdge,Vector2D,Integer>

nextNodeIdentifier

public Integer nextNodeIdentifier()

initializeSpeciesWithConcentration

public void initializeSpeciesWithConcentration(ChemicalEntity entity,
                                               double concentration)

initializeSpeciesWithConcentration

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

getSteepestDifference

public javax.measure.Quantity<MolarConcentration> getSteepestDifference(ChemicalEntity entity)

getSections

public Set<CellSection> getSections()

getSection

public CellSection getSection(String identifier)

addSection

public void addSection(CellSection cellSection)

addNodesToCompartment

public void addNodesToCompartment(EnclosedCompartment enclosedCompartment,
                                  Rectangle rectangle)