bio.singa.simulation.model.modules.concentration

Class ConcentrationDeltaManager

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

public class ConcentrationDeltaManager
extends Object

The ConcentrationDeltaManager handles current concentrations of an updatable and the updates to those concentrations that should be applied during simulation.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
ConcentrationDeltaManager(ConcentrationContainer initialConcentrations) Creates a new Concentration Delta Manager.

Method Summary

Modifier and Type	Method and Description
void	addPotentialDelta(ConcentrationDelta potentialDelta) Adds a potential delta to this updatable.
void	applyDeltas() Applies all final deltas and clears the delta list.
void	backupConcentrations()
void	clearPotentialDeltas() Clears the list of potential deltas.
void	clearPotentialDeltasBut(UpdateModule module) Clears the list of potential deltas retaining updates from a specific module.
void	determineComparisionConcentrations()
double	determineGlobalNumericalError()
ConcentrationContainer	getConcentrationContainer() Returns the current concentration container.
List<ConcentrationDelta>	getFinalDeltas() Returns all deltas that are going to be applied to this node.
ConcentrationContainer	getOriginalConcentrations()
List<ConcentrationDelta>	getPotentialDeltas() Returns all potential deltas that should be applied.
boolean	hasDeltas()
boolean	isConcentrationFixed() Returns true if the concentration is fixed - no deltas are applied.
boolean	isObserved() Returns true if the concentrations are observed.
void	revertToOriginalConcentrations()
void	setConcentrationContainer(ConcentrationContainer concentrations) Sets the current concentration container.
void	setConcentrationFixed(boolean concentrationFixed) Sets the concentration to be fixed - no deltas will be applied.
void	setInterimAndUpdateCurrentConcentrations()
void	setObserved(boolean observed) Sets the concentrations to be observed, this additional requires seting up a UpdateEventListener.
void	shiftDeltas() Shifts the deltas from the potential delta list to the final delta list.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConcentrationDeltaManager

public ConcentrationDeltaManager(ConcentrationContainer initialConcentrations)

Creates a new Concentration Delta Manager.

Parameters:

initialConcentrations - The initial concentrations.

Method Detail

getConcentrationContainer

public ConcentrationContainer getConcentrationContainer()

Returns the current concentration container.

Returns:

The current concentration container.

setConcentrationContainer

public void setConcentrationContainer(ConcentrationContainer concentrations)

Sets the current concentration container.

Parameters:

concentrations - The current concentration container.

getOriginalConcentrations

public ConcentrationContainer getOriginalConcentrations()

isObserved

public boolean isObserved()

Returns true if the concentrations are observed.

Returns:

True if the concentrations are observed.

setObserved

public void setObserved(boolean observed)

Sets the concentrations to be observed, this additional requires seting up a UpdateEventListener.

Parameters:

observed - True if th concentrations should be observed.

isConcentrationFixed

public boolean isConcentrationFixed()

Returns true if the concentration is fixed - no deltas are applied.

Returns:

true if the concentration is fixed - no deltas are applied.

setConcentrationFixed

public void setConcentrationFixed(boolean concentrationFixed)

Sets the concentration to be fixed - no deltas will be applied.

Parameters:

concentrationFixed - True if the concentration should be fixed.

hasDeltas

public boolean hasDeltas()

setInterimAndUpdateCurrentConcentrations

public void setInterimAndUpdateCurrentConcentrations()

determineComparisionConcentrations

public void determineComparisionConcentrations()

determineGlobalNumericalError

public double determineGlobalNumericalError()

getFinalDeltas

public List<ConcentrationDelta> getFinalDeltas()

Returns all deltas that are going to be applied to this node.

Returns:

All deltas that are going to be applied to this node.

getPotentialDeltas

public List<ConcentrationDelta> getPotentialDeltas()

Returns all potential deltas that should be applied.

Returns:

All potential deltas that should be applied.

addPotentialDelta

public void addPotentialDelta(ConcentrationDelta potentialDelta)

Adds a potential delta to this updatable.

Parameters:

potentialDelta - The potential delta.

backupConcentrations

public void backupConcentrations()

revertToOriginalConcentrations

public void revertToOriginalConcentrations()

clearPotentialDeltas

public void clearPotentialDeltas()

Clears the list of potential deltas. Usually done after shiftDeltas() or after rejecting a time step.

clearPotentialDeltasBut

public void clearPotentialDeltasBut(UpdateModule module)

Clears the list of potential deltas retaining updates from a specific module. Usually done after shiftDeltas() or after rejecting a time step.

Parameters:

module - The module.

shiftDeltas

public void shiftDeltas()

Shifts the deltas from the potential delta list to the final delta list.

applyDeltas

public void applyDeltas()

Applies all final deltas and clears the delta list.