bio.singa.simulation.model.modules.qualitative

Class QualitativeModule

java.lang.Object

bio.singa.simulation.model.modules.qualitative.QualitativeModule

All Implemented Interfaces:

UpdateModule, Runnable

Direct Known Subclasses:

ActinCortexDiffusivityScaling, ClathrinMediatedEndocytosis, ConcentrationStateChange, DiffusivityScaling, LineLikeAgentAttachment, LineLikeAgentDetachment, VesicleFusion, VolumeLikeAgentContainment

public abstract class QualitativeModule
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
QualitativeModule()

Method Summary

Modifier and Type	Method and Description
void	checkFeatures()
<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()
double	getScaledFeature(Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)
Simulation	getSimulation()
ModuleState	getState()
void	initialize()
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

Methods inherited from interface bio.singa.simulation.model.modules.UpdateModule

calculateUpdates, onCompletion, onReset, optimizeTimeStep

Field Detail

simulation

protected Simulation simulation

The simulation.

updateScheduler

protected UpdateScheduler updateScheduler

state

protected ModuleState state

Constructor Detail

QualitativeModule

public QualitativeModule()

Method Detail

run

public void run()

Specified by:

run in interface Runnable

initialize

public void initialize()

Specified by:

initialize in interface UpdateModule

setIdentifier

public void setIdentifier(String identifier)

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)

getReferencedEntities

public Set<ChemicalEntity> getReferencedEntities()

Specified by:

getReferencedEntities in interface UpdateModule

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

getFeatures

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

Specified by:

getFeatures in interface UpdateModule

getIdentifier

public String getIdentifier()

Specified by:

getIdentifier in interface UpdateModule

toString

public String toString()

Overrides:

toString in class Object