bio.singa.simulation.model.modules.concentration.imlementations

Class DynamicReaction

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<UpdatableDeltaFunction>

bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction

All Implemented Interfaces:

UpdateModule

public class DynamicReaction
extends ConcentrationBasedModule<UpdatableDeltaFunction>

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	DynamicReaction.BuildStep
static class	DynamicReaction.DynamicReactionBuilder
static interface	DynamicReaction.KineticLawStep
static interface	DynamicReaction.ParameterStep

Field Summary

Fields inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

supplier

Constructor Summary

Constructors

Constructor and Description
DynamicReaction()

Method Summary

Modifier and Type	Method and Description
void	addReactant(Reactant reactant)
static ModuleBuilder	getBuilder(Simulation simulation)
List<Reactant>	getCatalysts()
KineticLaw	getKineticLaw() Returns the kinetic law.
List<Reactant>	getProducts()
Set<Class<? extends Feature>>	getRequiredFeatures()
List<Reactant>	getSubstrates()
void	initialize()
static DynamicReaction.KineticLawStep	inSimulation(Simulation simulation)
void	scaleScalableFeatures()
void	setKineticLaw(KineticLaw kineticLaw) Sets the kinetic law.

Methods inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

addDeltaFunction, addModuleToSimulation, addReferencedEntities, addReferencedEntity, calculateUpdates, checkFeatures, deltaIsValid, determineLargestLocalError, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, onCompletion, onReset, optimizeTimeStep, resetState, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

DynamicReaction

public DynamicReaction()

Method Detail

inSimulation

public static DynamicReaction.KineticLawStep inSimulation(Simulation simulation)

initialize

public void initialize()

addReactant

public void addReactant(Reactant reactant)

getSubstrates

public List<Reactant> getSubstrates()

getProducts

public List<Reactant> getProducts()

getCatalysts

public List<Reactant> getCatalysts()

getKineticLaw

public KineticLaw getKineticLaw()

Returns the kinetic law.

Returns:

The kinetic law.

setKineticLaw

public void setKineticLaw(KineticLaw kineticLaw)

Sets the kinetic law.

Parameters:

kineticLaw - The kinetic law.

getRequiredFeatures

public Set<Class<? extends Feature>> getRequiredFeatures()

Specified by:

getRequiredFeatures in interface UpdateModule

Overrides:

getRequiredFeatures in class ConcentrationBasedModule<UpdatableDeltaFunction>

scaleScalableFeatures

public void scaleScalableFeatures()

Specified by:

scaleScalableFeatures in interface UpdateModule

Overrides:

scaleScalableFeatures in class ConcentrationBasedModule<UpdatableDeltaFunction>

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)