bio.singa.simulation.model.modules.displacement

Class DisplacementBasedModule

java.lang.Object

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

All Implemented Interfaces:

UpdateModule, Runnable

Direct Known Subclasses:

EndocytosisActinBoost, VesicleConfinedDiffusion, VesicleCytoplasmDiffusion, 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 bio.singa.features.model.Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<bio.singa.features.model.Feature<?>>	getFeatures()
String	getIdentifier()
Set<ChemicalEntity>	getReferencedEntities()
Set<Class<? extends bio.singa.features.model.Feature>>	getRequiredFeatures()
protected double	getScaledFeature(ChemicalEntity entity, Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)
double	getScaledFeature(Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)
Simulation	getSimulation()
ModuleState	getState()
void	initialize()
void	onCompletion()
void	onReset()
void	optimizeTimeStep()
void	processAllVesicles(List<Vesicle> vesicles)
void	resetState()
void	run()
void	setFeature(bio.singa.features.model.Feature<?> feature) Sets a feature.
void	setIdentifier(String identifier)
void	setSimulation(Simulation simulation)
String	toString()

Methods inherited from class java.lang.Object

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

run

public void run()

Specified by:

run in interface Runnable

setIdentifier

public void setIdentifier(String identifier)

addDeltaFunction

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

initialize

public void initialize()

Specified by:

initialize in interface UpdateModule

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)

Specified by:

setSimulation in interface UpdateModule

getSimulation

public Simulation getSimulation()

getState

public ModuleState getState()

Specified by:

getState in interface UpdateModule

resetState

public void resetState()

Specified by:

resetState in interface UpdateModule

getRequiredFeatures

public Set<Class<? extends bio.singa.features.model.Feature>> getRequiredFeatures()

Specified by:

getRequiredFeatures in interface UpdateModule

getScaledFeature

public double getScaledFeature(Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)

Specified by:

getScaledFeature in interface UpdateModule

setFeature

public void setFeature(bio.singa.features.model.Feature<?> feature)

Sets a feature.

Specified by:

setFeature in interface UpdateModule

Parameters:

feature - The feature.

getFeature

public <FeatureType extends bio.singa.features.model.Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

getFeatures

public Collection<bio.singa.features.model.Feature<?>> getFeatures()

Specified by:

getFeatures in interface UpdateModule

getScaledFeature

protected double getScaledFeature(ChemicalEntity entity,
                                  Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> 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

onReset

public void onReset()

Specified by:

onReset in interface UpdateModule

onCompletion

public void onCompletion()

Specified by:

onCompletion in interface UpdateModule

getIdentifier

public String getIdentifier()

Specified by:

getIdentifier in interface UpdateModule

getReferencedEntities

public Set<ChemicalEntity> getReferencedEntities()

Specified by:

getReferencedEntities in interface UpdateModule

toString

public String toString()

Overrides:

toString in class Object