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

All Implemented Interfaces:

UpdateModule, Runnable

Direct Known Subclasses:

Diffusion, EndocytoticPitAbsorption, LateralMembraneDiffusion, MembraneDiffusion, PorousDiffusion, Reaction, SingleFileChannelMembraneTransport
```
public abstract class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>
extends AbstractUpdateModule
```
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 Description

protected FieldSupplier supplier
Frequently required fields.

Constructor Summary

Constructors
Constructor Description

ConcentrationBasedModule()
Creates a new concentration based module.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`addDeltaFunction(DeltaFunctionType deltaFunction)`	Adds a delta function to the module.
`void`	`calculateUpdates()`
`boolean`	`deltaIsValid(ConcentrationDelta delta)`	Returns true if the delta is valid, i.e.
`NumericalError`	`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.
`CellSubsection`	`getRestrictedSubsection()`
`protected double`	`getScaledFeature(ChemicalEntity entity, Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)`	Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
`double`	`getScaledFeature(Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)`
`UpdateScope`	`getScope()`	Returns the scope of this module.
`UpdateSpecificity`	`getSpecificity()`	Returns the specificity of this module.
`FieldSupplier`	`getSupplier()`	Returns the field supplier.
`void`	`handleDelta(ConcentrationDeltaIdentifier deltaIdentifier, ConcentrationDelta delta)`	Handles a delta based on the current state of the calculation.
`void`	`inBetweenHalfSteps()`
`void`	`initialize()`
`void`	`onCompletion()`
`void`	`onReset()`
`void`	`optimizeTimeStep()`
`void`	`restrictApplication()`
`protected void`	`setApplicationCondition(Predicate<Updatable> applicationCondition)`	Sets the application condition for this module.
`void`	`setRestrictedSubsection(CellSubsection restrictedSubsection)`

Methods inherited from class bio.singa.simulation.model.modules.AbstractUpdateModule
addEvidence, addReferencedEntities, addReferencedEntity, checkFeatures, equals, getEvidence, getFeature, getFeatureManager, getFeatures, getIdentifier, getReferencedChemicalEntities, getRequiredFeatures, getSimulation, getState, hashCode, reset, run, setEvidence, setFeature, setFeatureManager, setIdentifier, setSimulation, setState, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, 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.
  - 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.
  - 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.
  - 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.
  - 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 NumericalError 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 / halfDelta)). 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 class AbstractUpdateModule
  - optimizeTimeStep
```
public void optimizeTimeStep()
```
    Specified by:
    
    optimizeTimeStep in class AbstractUpdateModule
  - inBetweenHalfSteps
```
public void inBetweenHalfSteps()
```
  - getScaledFeature
```
public double getScaledFeature(Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)
```
    Overrides:
    
    getScaledFeature in class AbstractUpdateModule
  - getScaledFeature
```
protected double getScaledFeature(ChemicalEntity entity,
                                  Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)
```
    Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
    
    Parameters:
    
    entity - The chemical entity.
    
    featureClass - The requested feature.
    
    Returns:
    
    The scaled feature.
  - initialize
```
public void initialize()
```
  - restrictApplication
```
public void restrictApplication()
```
  - getRestrictedSubsection
```
public CellSubsection getRestrictedSubsection()
```
  - setRestrictedSubsection
```
public void setRestrictedSubsection(CellSubsection restrictedSubsection)
```
  - onReset
```
public void onReset()
```
  - onCompletion
```
public void onCompletion()
```

Class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class bio.singa.simulation.model.modules.AbstractUpdateModule

Methods inherited from class java.lang.Object

Field Detail

supplier

Constructor Detail

ConcentrationBasedModule

Method Detail

addDeltaFunction

getApplicationCondition

setApplicationCondition

getSupplier

getScope

getSpecificity

handleDelta

deltaIsValid

determineLargestLocalError

calculateUpdates

optimizeTimeStep

inBetweenHalfSteps

getScaledFeature

getScaledFeature

initialize

restrictApplication

getRestrictedSubsection

setRestrictedSubsection

onReset

onCompletion