bio.singa.simulation.model.modules.displacement

Class DisplacementBasedModule

java.lang.Object

bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

All Implemented Interfaces:

UpdateModule

Direct Known Subclasses:

ClathrinMediatedEndocytosis, EndocytosisActinBoost, VesicleAttachment, VesicleDiffusion, VesicleFusion, VesicleTransport

public class DisplacementBasedModule
extends Object
implements UpdateModule

Author:

cl

Field Summary

Fields

Modifier and Type	Field and Description
protected Simulation	simulation The simulation.
protected ModuleState	state
protected UpdateScheduler	updateScheduler

Constructor Summary

Constructors

Constructor and Description
DisplacementBasedModule()

Method Summary

Modifier and Type	Method and Description
void	addDeltaFunction(Function<Vesicle,DisplacementDelta> deltaFunction, Predicate<Vesicle> predicate)
void	calculateUpdates()
void	checkFeatures()
void	determineDeltas(Vesicle vesicle)
protected void	evaluateModuleState()
<FeatureType extends Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<Feature<?>>	getFeatures()
String	getIdentifier()
Set<ChemicalEntity>	getReferencedEntities()
Set<Class<? extends Feature>>	getRequiredFeatures()
protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>	getScaledFeature(ChemicalEntity entity, Class<? extends ScalableFeature<FeatureContentType>> featureClass)
<FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>	getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>> featureClass)
ModuleState	getState()
String	getStringForProtocol()
String	listFeatures(String precedingSpaces)
void	optimizeTimeStep()
void	processAllVesicles(List<Vesicle> vesicles)
void	resetState()
void	scaleScalableFeatures()
<FeatureType extends Feature> void	setFeature(FeatureType feature)
void	setSimulation(Simulation simulation)

Methods inherited from class java.lang.Object

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

Field Detail

simulation

protected Simulation simulation

The simulation.

state

protected ModuleState state

updateScheduler

protected UpdateScheduler updateScheduler

Constructor Detail

DisplacementBasedModule

public DisplacementBasedModule()

Method Detail

addDeltaFunction

public void addDeltaFunction(Function<Vesicle,DisplacementDelta> deltaFunction,
                             Predicate<Vesicle> predicate)

calculateUpdates

public void calculateUpdates()

Specified by:

calculateUpdates in interface UpdateModule

processAllVesicles

public void processAllVesicles(List<Vesicle> vesicles)

determineDeltas

public void determineDeltas(Vesicle vesicle)

setSimulation

public void setSimulation(Simulation simulation)

getState

public ModuleState getState()

Specified by:

getState in interface UpdateModule

resetState

public void resetState()

Specified by:

resetState in interface UpdateModule

scaleScalableFeatures

public void scaleScalableFeatures()

Specified by:

scaleScalableFeatures in interface UpdateModule

getRequiredFeatures

public Set<Class<? extends Feature>> getRequiredFeatures()

Specified by:

getRequiredFeatures in interface UpdateModule

getScaledFeature

public <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType> getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>> featureClass)

Specified by:

getScaledFeature in interface UpdateModule

setFeature

public <FeatureType extends Feature> void setFeature(FeatureType feature)

getFeature

public <FeatureType extends Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

getFeatures

public Collection<Feature<?>> getFeatures()

listFeatures

public String listFeatures(String precedingSpaces)

getScaledFeature

protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType> getScaledFeature(ChemicalEntity entity,
                                                                                                                                              Class<? extends ScalableFeature<FeatureContentType>> featureClass)

optimizeTimeStep

public void optimizeTimeStep()

Specified by:

optimizeTimeStep in interface UpdateModule

evaluateModuleState

protected void evaluateModuleState()

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

getIdentifier

public String getIdentifier()

Specified by:

getIdentifier in interface UpdateModule

getStringForProtocol

public String getStringForProtocol()

Specified by:

getStringForProtocol in interface UpdateModule

getReferencedEntities

public Set<ChemicalEntity> getReferencedEntities()

Specified by:

getReferencedEntities in interface UpdateModule