de.bioforscher.singa.simulation.modules.reactions.model

Class Reactions

java.lang.Object

de.bioforscher.singa.simulation.modules.reactions.model.Reactions

All Implemented Interfaces:

Module, CumulativeUpdateBehavior, UpdateBehavior

public class Reactions
extends Object
implements Module, CumulativeUpdateBehavior

The Reactions module defines the entirety of chemical conversions that take place in the Simulation. All Reactions are calculated according to their specified KineticLawss and new concentrations are set using the applyTo(AutomatonGraph) method.

Constructor Summary

Constructors

Constructor and Description
Reactions()

Method Summary

Modifier and Type	Method and Description
void	applyTo(AutomatonGraph graph)
PotentialUpdate	calculateUpdate(BioNode node, CellSection section, ChemicalEntity entity)
List<PotentialUpdate>	calculateUpdates(BioNode node)
Set<ChemicalEntity<?>>	collectAllReferencedEntities()
List<Reaction>	getReactions()
void	setReactions(List<Reaction> reactions)

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior

updateGraph

Constructor Detail

Reactions

public Reactions()

Method Detail

getReactions

public List<Reaction> getReactions()

setReactions

public void setReactions(List<Reaction> reactions)

applyTo

public void applyTo(AutomatonGraph graph)

Specified by:

applyTo in interface Module

collectAllReferencedEntities

public Set<ChemicalEntity<?>> collectAllReferencedEntities()

Specified by:

collectAllReferencedEntities in interface Module

calculateUpdates

public List<PotentialUpdate> calculateUpdates(BioNode node)

Specified by:

calculateUpdates in interface UpdateBehavior

calculateUpdate

public PotentialUpdate calculateUpdate(BioNode node,
                                       CellSection section,
                                       ChemicalEntity entity)