bio.singa.simulation.model.modules.concentration.scope

Class SemiDependentUpdate

java.lang.Object

bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

All Implemented Interfaces:

UpdateScope

public class SemiDependentUpdate
extends Object
implements UpdateScope

Independent Updatable ConcentrationBasedModules require the integer state of a subset of updatables. For example MembraneDiffusion might happen between a Vesicle and an AutomatonNode, therefore at least two updatables are changed during calculation. Half step deltas can be calculated independently but, more half deltas need to be stored to evaluate the error of the computation.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
SemiDependentUpdate(ConcentrationBasedModule module) Initializes the update scope for the corresponding module.

Method Summary

Modifier and Type	Method and Description
void	clearPotentialDeltas(Updatable updatable) Clears all concentration deltas that may be assigned to the given updatable.
ConcentrationContainer	getHalfStepConcentration(Updatable updatable) Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.
void	processAllUpdatables(Collection<Updatable> updatables) Processes all given updatables.
void	processUpdatable(Updatable updatable) Calculates the given updatable.

Methods inherited from class java.lang.Object

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

Constructor Detail

SemiDependentUpdate

public SemiDependentUpdate(ConcentrationBasedModule module)

Initializes the update scope for the corresponding module.

Parameters:

module - The module.

Method Detail

processAllUpdatables

public void processAllUpdatables(Collection<Updatable> updatables)

Description copied from interface: UpdateScope

Processes all given updatables. This includes calculating the delta functions of the corresponding module, calculating the current numerical error and pushing potential Deltas to the updatables, ready to be applied.

Specified by:

processAllUpdatables in interface UpdateScope

Parameters:

updatables - The updatables to be processed.

processUpdatable

public void processUpdatable(Updatable updatable)

Description copied from interface: UpdateScope

Calculates the given updatable. If it is required to calculate other updatables to evaluate the state of this updatable this will be done depending on the implementation of the scope.

Specified by:

processUpdatable in interface UpdateScope

Parameters:

updatable - The updatable.

clearPotentialDeltas

public void clearPotentialDeltas(Updatable updatable)

Description copied from interface: UpdateScope

Clears all concentration deltas that may be assigned to the given updatable.

Specified by:

clearPotentialDeltas in interface UpdateScope

Parameters:

updatable - The updatable.

getHalfStepConcentration

public ConcentrationContainer getHalfStepConcentration(Updatable updatable)

Description copied from interface: UpdateScope

Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.

Specified by:

getHalfStepConcentration in interface UpdateScope

Parameters:

updatable - The updatable.

Returns:

A concentration container with the concentrations at the half time step.