Package bio.singa.simulation.model.simulation

Class Simulation

java.lang.Object

bio.singa.simulation.model.simulation.Simulation

public class Simulation
extends Object

Author:

cl

Constructor Summary

Constructors

Constructor	Description
Simulation()	Creates a new plain simulation.

Method Summary

Modifier and Type	Method	Description
void	addConcentration(InitialConcentration initialConcentration)
void	addModule(UpdateModule module)
void	addReferencedEntity(ChemicalEntity chemicalEntity)
void	applyAssignmentRules()	Apply all referenced assignment rules.
void	clearPreviouslyObservedDeltas()
void	collectUpdatables()
Collection<ChemicalEntity>	getChemicalEntities()	Returns the chemical entities.
ChemicalEntity	getChemicalEntity(String primaryIdentifier)
List<InitialConcentration>	getConcentrations()
DebugRecorder	getDebugRecorder()
long	getEpoch()
long	getEpochWithRescaledTimeStep()
AutomatonGraph	getGraph()
LineLikeAgentLayer	getLineLayer()
MembraneLayer	getMembraneLayer()
List<UpdateModule>	getModules()
Set<Updatable>	getObservedUpdatables()
List<ConcentrationDelta>	getPreviousObservedDeltas(Updatable updatable)
UpdateScheduler	getScheduler()
bio.singa.mathematics.geometry.faces.Rectangle	getSimulationRegion()
List<Updatable>	getUpdatables()
VesicleLayer	getVesicleLayer()
VolumeLayer	getVolumeLayer()
void	initializeSpatialRepresentations()
boolean	isDebug()
void	nextEpoch()	Calculates the next epoch.
void	setAssignmentRules(List<AssignmentRule> assignmentRules)	Adds a list of assignment rules, sorting them by their dependencies.
void	setConcentrations(List<InitialConcentration> concentrations)
void	setDebug(boolean debug)
void	setDebugRecorder(DebugRecorder debugRecorder)
void	setEpochWithRescaledTimeStep(long epochWithRescaledTimeStep)
void	setGraph(AutomatonGraph graph)
void	setLineLayer(LineLikeAgentLayer lineLayer)
void	setMaximalTimeStep(javax.measure.Quantity<javax.measure.quantity.Time> maximalTimeStep)
void	setMembraneLayer(MembraneLayer membraneLayer)
void	setScheduler(UpdateScheduler scheduler)
void	setSimulationRegion(bio.singa.mathematics.geometry.faces.Rectangle simulationRegion)
void	setVesicleLayer(VesicleLayer vesicleLayer)
void	setVolumeLayer(VolumeLayer volumeLayer)

Methods inherited from class java.lang.Object

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

Constructor Detail

Simulation

public Simulation()

Creates a new plain simulation.

Method Detail

nextEpoch

public void nextEpoch()

Calculates the next epoch.

addConcentration

public void addConcentration(InitialConcentration initialConcentration)

getConcentrations

public List<InitialConcentration> getConcentrations()

setConcentrations

public void setConcentrations(List<InitialConcentration> concentrations)

initializeSpatialRepresentations

public void initializeSpatialRepresentations()

getVesicleLayer

public VesicleLayer getVesicleLayer()

setVesicleLayer

public void setVesicleLayer(VesicleLayer vesicleLayer)

getMembraneLayer

public MembraneLayer getMembraneLayer()

setMembraneLayer

public void setMembraneLayer(MembraneLayer membraneLayer)

getVolumeLayer

public VolumeLayer getVolumeLayer()

setVolumeLayer

public void setVolumeLayer(VolumeLayer volumeLayer)

getLineLayer

public LineLikeAgentLayer getLineLayer()

setLineLayer

public void setLineLayer(LineLikeAgentLayer lineLayer)

getSimulationRegion

public bio.singa.mathematics.geometry.faces.Rectangle getSimulationRegion()

setSimulationRegion

public void setSimulationRegion(bio.singa.mathematics.geometry.faces.Rectangle simulationRegion)

collectUpdatables

public void collectUpdatables()

applyAssignmentRules

public void applyAssignmentRules()

Apply all referenced assignment rules.

setAssignmentRules

public void setAssignmentRules(List<AssignmentRule> assignmentRules)

Adds a list of assignment rules, sorting them by their dependencies.

Parameters:

assignmentRules - The assignment rules.

See Also:

AssignmentRules.sortAssignmentRulesByPriority(List)

getUpdatables

public List<Updatable> getUpdatables()

getModules

public List<UpdateModule> getModules()

addModule

public void addModule(UpdateModule module)

getScheduler

public UpdateScheduler getScheduler()

setScheduler

public void setScheduler(UpdateScheduler scheduler)

setMaximalTimeStep

public void setMaximalTimeStep(javax.measure.Quantity<javax.measure.quantity.Time> maximalTimeStep)

getGraph

public AutomatonGraph getGraph()

setGraph

public void setGraph(AutomatonGraph graph)

getEpoch

public long getEpoch()

getChemicalEntities

public Collection<ChemicalEntity> getChemicalEntities()

Returns the chemical entities.

Returns:

The chemical entities.

getChemicalEntity

public ChemicalEntity getChemicalEntity(String primaryIdentifier)

addReferencedEntity

public void addReferencedEntity(ChemicalEntity chemicalEntity)

getObservedUpdatables

public Set<Updatable> getObservedUpdatables()

getPreviousObservedDeltas

public List<ConcentrationDelta> getPreviousObservedDeltas(Updatable updatable)

clearPreviouslyObservedDeltas

public void clearPreviouslyObservedDeltas()

isDebug

public boolean isDebug()

setDebug

public void setDebug(boolean debug)

getDebugRecorder

public DebugRecorder getDebugRecorder()

setDebugRecorder

public void setDebugRecorder(DebugRecorder debugRecorder)

getEpochWithRescaledTimeStep

public long getEpochWithRescaledTimeStep()

setEpochWithRescaledTimeStep

public void setEpochWithRescaledTimeStep(long epochWithRescaledTimeStep)