bio.singa.simulation.model.modules.concentration.reactants

Class KineticLaw

java.lang.Object

bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

public class KineticLaw
extends Object

Dynamic kinetic laws allow for the definition of reaction kinetics based on equations.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
KineticLaw(String kineticLawString)

Method Summary

Modifier and Type	Method and Description
double	calculateVelocity(ConcentrationContainer concentrationContainer, boolean isStrutCalculation) Calculates the velocity of the reaction based on the entities in the concentration container.
Map<String,Reactant>	getConcentrationMap()
String	getExpressionString()
Map<String,ScalableQuantityFeature>	getFeatureMap()
Map<String,Parameter>	getParameterMap()
void	referenceConstant(String parameterIdentifier, double constant)
void	referenceConstant(String parameterIdentifier, double constant, Evidence evidence)
void	referenceFeature(ScalableQuantityFeature feature)
void	referenceFeature(String parameterIdentifier, ScalableQuantityFeature feature)
void	referenceParameter(Parameter<?> parameter)
void	referenceReactant(Reactant reactant)
void	referenceReactant(String parameterIdentifier, Reactant reactant)
void	scaleScalableFeatures()
void	setConcentrationMap(Map<String,Reactant> concentrationMap)
void	setFeatureMap(Map<String,ScalableQuantityFeature> featureMap)
void	setParameterMap(Map<String,Parameter> parameterMap)

Methods inherited from class java.lang.Object

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

Constructor Detail

KineticLaw

public KineticLaw(String kineticLawString)

Method Detail

referenceReactant

public void referenceReactant(String parameterIdentifier,
                              Reactant reactant)

referenceReactant

public void referenceReactant(Reactant reactant)

referenceFeature

public void referenceFeature(String parameterIdentifier,
                             ScalableQuantityFeature feature)

referenceFeature

public void referenceFeature(ScalableQuantityFeature feature)

referenceConstant

public void referenceConstant(String parameterIdentifier,
                              double constant)

referenceConstant

public void referenceConstant(String parameterIdentifier,
                              double constant,
                              Evidence evidence)

referenceParameter

public void referenceParameter(Parameter<?> parameter)

getFeatureMap

public Map<String,ScalableQuantityFeature> getFeatureMap()

setFeatureMap

public void setFeatureMap(Map<String,ScalableQuantityFeature> featureMap)

getConcentrationMap

public Map<String,Reactant> getConcentrationMap()

setConcentrationMap

public void setConcentrationMap(Map<String,Reactant> concentrationMap)

getExpressionString

public String getExpressionString()

getParameterMap

public Map<String,Parameter> getParameterMap()

setParameterMap

public void setParameterMap(Map<String,Parameter> parameterMap)

scaleScalableFeatures

public void scaleScalableFeatures()

calculateVelocity

public double calculateVelocity(ConcentrationContainer concentrationContainer,
                                boolean isStrutCalculation)

Calculates the velocity of the reaction based on the entities in the concentration container.

Parameters:

concentrationContainer - The concentration container.

Returns:

The velocity.