ConcentrationBasedModule (singa-simulation 0.4.2 API)

java.lang.Object
- bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<DeltaFunctionType>

All Implemented Interfaces:

UpdateModule

Direct Known Subclasses:

ComplexBuildingReaction, Diffusion, MembraneDiffusion, Reaction, SingleFileChannelMembraneTransport
```
public abstract class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>
extends Object
implements UpdateModule
```
Concentration based modules handle updates that are applied to the concentrations in Updatables during a simulation. Each module has a UpdateScope that regulates the dependence of this module to other parts of the simulation. Further, the UpdateSpecificity defines how fine-grained the updates are calculated. New modules should be created with the ModuleFactory.

Author:

cl

Field Summary

Fields
Modifier and Type Field and Description

protected FieldSupplier supplier
Frequently required fields.

Fields
Modifier and Type	Field and Description
`protected FieldSupplier`	`supplier` Frequently required fields.

Constructor Summary

Constructors
Constructor and Description

ConcentrationBasedModule()
Creates a new concentration based module.

Constructors
Constructor and Description
`ConcentrationBasedModule()` Creates a new concentration based module.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`addDeltaFunction(DeltaFunctionType deltaFunction)` Adds a delta function to the module.
`protected void`	`addModuleToSimulation()` References the module and referenced entities to the referenced simulation.
`protected void`	`addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities)` Adds multiple referenced chemical entities.
`protected void`	`addReferencedEntity(ChemicalEntity chemicalEntity)` Adds a referenced chemical entity.
`void`	`calculateUpdates()`
`void`	`checkFeatures()`
`boolean`	`deltaIsValid(ConcentrationDelta delta)` Returns true if the delta is valid, i.e.
`LocalError`	`determineLargestLocalError()` The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned.
`Predicate<Updatable>`	`getApplicationCondition()` Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.
`double`	`getDeltaCutoff()` Returns the cutoff where deltas are validated to be effectively zero.
`double`	`getErrorCutoff()` Returns the cutoff where numerical errors to be considered irretrievably unstable.
`<FeatureType extends Feature> FeatureType`	`getFeature(Class<FeatureType> featureTypeClass)` Returns the requested feature.
`Collection<Feature<?>>`	`getFeatures()` Returns all features of this module (not its entities).
`String`	`getIdentifier()` Returns the identifier of this module.
`Set<ChemicalEntity>`	`getReferencedEntities()` Returns all chemical entities that might be accessed by this module.
`Set<Class<? extends Feature>>`	`getRequiredFeatures()`
`protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>`	`getScaledFeature(ChemicalEntity entity, Class<? extends ScalableFeature<FeatureContentType>> featureClass)` Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
`<FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>`	`getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>> featureClass)`
`UpdateScope`	`getScope()` Returns the scope of this module.
`Simulation`	`getSimulation()` Returns the referenced simulation.
`UpdateSpecificity`	`getSpecificity()` Returns the specificity of this module.
`ModuleState`	`getState()`
`String`	`getStringForProtocol()`
`FieldSupplier`	`getSupplier()` Returns the field supplier.
`void`	`handleDelta(ConcentrationDeltaIdentifier deltaIdentifier, ConcentrationDelta delta)` Handles a delta based on the current state of the calculation.
`protected String`	`listFeatures(String precedingSpaces)` Returns a formatted string of the features of this module.
`void`	`onCompletion()`
`void`	`onReset()`
`void`	`optimizeTimeStep()`
`void`	`resetState()`
`void`	`scaleScalableFeatures()`
`protected void`	`setApplicationCondition(Predicate<Updatable> applicationCondition)` Sets the application condition for this module.
`void`	`setDeltaCutoff(double deltaCutoff)` Sets the cutoff where deltas are validated to be effectively zero.
`void`	`setErrorCutoff(double errorCutoff)` Sets the cutoff where numerical errors to be considered irretrievably unstable.
`<FeatureType extends Feature> void`	`setFeature(FeatureType feature)` Sets a feature.
`void`	`setIdentifier(String identifier)` Sets the identifier of this module.
`void`	`setSimulation(Simulation simulation)` References the simulation to this module.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - supplier
```
protected FieldSupplier supplier
```
    Frequently required fields.
- Constructor Detail
  - ConcentrationBasedModule
```
public ConcentrationBasedModule()
```
    Creates a new concentration based module.
- Method Detail
  - addDeltaFunction
```
protected void addDeltaFunction(DeltaFunctionType deltaFunction)
```
    Adds a delta function to the module. Delta functions are applied according to UpdateScope and UpdateSpecificity.
    
    Parameters:
    
    deltaFunction - The delta function.
  - setApplicationCondition
```
protected void setApplicationCondition(Predicate<Updatable> applicationCondition)
```
    Sets the application condition for this module. The module is only evaluated if the updatable fulfills the given predicate.
    
    Parameters:
    
    applicationCondition - The application condition.
  - getApplicationCondition
```
public Predicate<Updatable> getApplicationCondition()
```
    Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.
    
    Returns:
    
    The application condition.
  - getReferencedEntities
```
public Set<ChemicalEntity> getReferencedEntities()
```
    Returns all chemical entities that might be accessed by this module.
    
    Specified by:
    
    getReferencedEntities 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.
  - getStringForProtocol
```
public String getStringForProtocol()
```
    Specified by:
    
    getStringForProtocol in interface UpdateModule
  - getDeltaCutoff
```
public double getDeltaCutoff()
```
    Returns the cutoff where deltas are validated to be effectively zero.
    
    Returns:
    
    The delta cutoff.
  - setDeltaCutoff
```
public void setDeltaCutoff(double deltaCutoff)
```
    Sets the cutoff where deltas are validated to be effectively zero.
    
    Parameters:
    
    deltaCutoff - The delta cutoff.
  - getErrorCutoff
```
public double getErrorCutoff()
```
    Returns the cutoff where numerical errors to be considered irretrievably unstable.
    
    Returns:
    
    The error cutoff.
  - setErrorCutoff
```
public void setErrorCutoff(double errorCutoff)
```
    Sets the cutoff where numerical errors to be considered irretrievably unstable.
    
    Parameters:
    
    errorCutoff - The error cutoff.
  - getSimulation
```
public Simulation getSimulation()
```
    Returns the referenced simulation.
    
    Returns:
    
    The referenced simulation.
  - setSimulation
```
public void setSimulation(Simulation simulation)
```
    References the simulation to this module.
    
    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.
  - getSupplier
```
public FieldSupplier getSupplier()
```
    Returns the field supplier.
    
    Returns:
    
    The field supplier.
  - getScope
```
public UpdateScope getScope()
```
    Returns the scope of this module.
    
    Returns:
    
    The scope of this module.
  - getSpecificity
```
public UpdateSpecificity getSpecificity()
```
    Returns the specificity of this module.
    
    Returns:
    
    The specificity of this module.
  - getState
```
public ModuleState getState()
```
    Specified by:
    
    getState in interface UpdateModule
  - handleDelta
```
public void handleDelta(ConcentrationDeltaIdentifier deltaIdentifier,
                        ConcentrationDelta delta)
```
    Handles a delta based on the current state of the calculation.
    
    Parameters:
    
    deltaIdentifier - The unique identifier of the delta.
    
    delta - The delta itself.
  - deltaIsValid
```
public boolean deltaIsValid(ConcentrationDelta delta)
```
    Returns true if the delta is valid, i.e. it is not zero and nor below the numerical threshold.
    
    Parameters:
    
    delta - The delta to be evaluated.
    
    Returns:
    
    true if the delta is valid, i.e. it is not zero and nor below the numerical threshold.
  - determineLargestLocalError
```
public LocalError determineLargestLocalError()
```
    The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned. The local error is calculated according to the midpoint method E = abs(1 - (fullDelta / 2.0 * halfDelta)). Intuitively, applying the the delta for the current time step once results in the same result as if the delta for half the time step would be applied twice. This method calculates the difference between the full delta and twice the half delta. If the difference is large the error is large and vice versa.
    
    Returns:
    
    The calculated local error.
    
    Throws:
    
    NumericalInstabilityException - if any of the encountered errors is the result of an numerical instability.
  - calculateUpdates
```
public void calculateUpdates()
```
    Specified by:
    
    calculateUpdates in interface UpdateModule
  - optimizeTimeStep
```
public void optimizeTimeStep()
```
    Specified by:
    
    optimizeTimeStep in interface UpdateModule
  - resetState
```
public void resetState()
```
    Specified by:
    
    resetState in interface UpdateModule
  - addModuleToSimulation
```
protected void addModuleToSimulation()
```
    References the module and referenced entities to the referenced simulation.
  - 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
  - getScaledFeature
```
protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType> getScaledFeature(ChemicalEntity entity,
                                                                                                                                              Class<? extends ScalableFeature<FeatureContentType>> featureClass)
```
    Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
    
    Type Parameters:
    
    FeatureContentType - The resulting content type.
    
    Parameters:
    
    entity - The chemical entity.
    
    featureClass - The requested feature.
    
    Returns:
    
    The scaled feature.
  - getFeature
```
public <FeatureType extends Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)
```
    Returns the requested feature.
    
    Type Parameters:
    
    FeatureType - The resulting content type.
    
    Parameters:
    
    featureTypeClass - The requested feature.
    
    Returns:
    
    The requested feature.
  - setFeature
```
public <FeatureType extends Feature> void setFeature(FeatureType feature)
```
    Sets a feature.
    
    Type Parameters:
    
    FeatureType - The class of the feature.
    
    Parameters:
    
    feature - The feature.
  - getFeatures
```
public Collection<Feature<?>> getFeatures()
```
    Returns all features of this module (not its entities).
    
    Returns:
    
    all features of this module.
  - listFeatures
```
protected String listFeatures(String precedingSpaces)
```
    Returns a formatted string of the features of this module.
    
    Parameters:
    
    precedingSpaces - The number of preceding spaces.
    
    Returns:
    
    A formatted string of the features of this module.
  - onReset
```
public void onReset()
```
    Specified by:
    
    onReset in interface UpdateModule
  - onCompletion
```
public void onCompletion()
```
    Specified by:
    
    onCompletion in interface UpdateModule
  - checkFeatures
```
public void checkFeatures()
```
    Specified by:
    
    checkFeatures in interface UpdateModule
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

supplier

Constructor Detail

ConcentrationBasedModule

Method Detail

addDeltaFunction

setApplicationCondition

getApplicationCondition

getReferencedEntities

addReferencedEntity

addReferencedEntities

getStringForProtocol

getDeltaCutoff

setDeltaCutoff

getErrorCutoff

setErrorCutoff

getSimulation

setSimulation

getIdentifier

setIdentifier

getSupplier

getScope

getSpecificity

getState

handleDelta

deltaIsValid

determineLargestLocalError

calculateUpdates

optimizeTimeStep

resetState

addModuleToSimulation

scaleScalableFeatures

getRequiredFeatures

getScaledFeature

getScaledFeature

getFeature

setFeature

getFeatures

listFeatures

onReset

onCompletion

checkFeatures

toString