Package bio.singa.simulation.model.modules

Class AbstractUpdateModule

java.lang.Object

bio.singa.simulation.model.modules.AbstractUpdateModule

All Implemented Interfaces:

UpdateModule, Runnable

Direct Known Subclasses:

ConcentrationBasedModule, DisplacementBasedModule, QualitativeModule

public abstract class AbstractUpdateModule
extends Object
implements UpdateModule

Author:

cl

Constructor Summary

Constructors

Constructor	Description
AbstractUpdateModule()

Method Summary

Modifier and Type	Method	Description
void	addEvidence(bio.singa.features.model.Evidence evidence)
protected void	addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities)	Adds multiple referenced chemical entities.
protected void	addReferencedEntity(ChemicalEntity chemicalEntity)	Adds a referenced chemical entity.
protected abstract void	calculateUpdates()
void	checkFeatures()
boolean	equals(Object o)
List<bio.singa.features.model.Evidence>	getEvidence()
<FeatureType extends bio.singa.features.model.Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
FeatureManager	getFeatureManager()
Collection<bio.singa.features.model.Feature<?>>	getFeatures()
String	getIdentifier()	Returns the identifier of this module.
Set<ChemicalEntity>	getReferencedChemicalEntities()	Returns all chemical entities that might be accessed by this module.
Set<Class<? extends bio.singa.features.model.Feature>>	getRequiredFeatures()
double	getScaledFeature(Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)
Simulation	getSimulation()	Returns the referenced simulation.
ModuleState	getState()
int	hashCode()
protected abstract void	optimizeTimeStep()
void	reset()
void	run()
void	setEvidence(List<bio.singa.features.model.Evidence> evidence)
void	setFeature(bio.singa.features.model.Feature<?> feature)	Sets a feature.
void	setFeatureManager(FeatureManager featureManager)
void	setIdentifier(String identifier)	Sets the identifier of this module.
void	setSimulation(Simulation simulation)	References the simulation to this module.
void	setState(ModuleState state)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

initialize, onCompletion, onReset

Constructor Detail

AbstractUpdateModule

public AbstractUpdateModule()

Method Detail

run

public void run()

Specified by:

run in interface Runnable

calculateUpdates

protected abstract void calculateUpdates()

optimizeTimeStep

protected abstract void optimizeTimeStep()

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)

getScaledFeature

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

getFeatures

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

Specified by:

getFeatures in interface UpdateModule

getRequiredFeatures

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

Specified by:

getRequiredFeatures in interface UpdateModule

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

reset

public void reset()

Specified by:

reset in interface UpdateModule

getSimulation

public Simulation getSimulation()

Returns the referenced simulation.

Returns:

The referenced simulation.

setSimulation

public void setSimulation(Simulation simulation)

References the simulation to this module.

Specified by:

setSimulation in interface UpdateModule

Parameters:

simulation - The simulation.

getIdentifier

public String getIdentifier()

Returns the identifier of this module.

Specified by:

getIdentifier in interface UpdateModule

Returns:

The identifier.

setIdentifier

public void setIdentifier(String identifier)

Sets the identifier of this module.

Parameters:

identifier - The identifier.

getState

public ModuleState getState()

Specified by:

getState in interface UpdateModule

setState

public void setState(ModuleState state)

getFeatureManager

public FeatureManager getFeatureManager()

setFeatureManager

public void setFeatureManager(FeatureManager featureManager)

getReferencedChemicalEntities

public Set<ChemicalEntity> getReferencedChemicalEntities()

Returns all chemical entities that might be accessed by this module.

Specified by:

getReferencedChemicalEntities in interface UpdateModule

Returns:

All chemical entities that might be accessed by this module.

addReferencedEntity

protected void addReferencedEntity(ChemicalEntity chemicalEntity)

Adds a referenced chemical entity.

Parameters:

chemicalEntity - The chemical entity.

addReferencedEntities

protected void addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities)

Adds multiple referenced chemical entities.

Parameters:

chemicalEntities - The chemical entities.

getEvidence

public List<bio.singa.features.model.Evidence> getEvidence()

Specified by:

getEvidence in interface UpdateModule

addEvidence

public void addEvidence(bio.singa.features.model.Evidence evidence)

setEvidence

public void setEvidence(List<bio.singa.features.model.Evidence> evidence)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object