bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

Class DynamicKineticLaw

java.lang.Object

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

All Implemented Interfaces:

KineticLaw

public class DynamicKineticLaw
extends Object
implements KineticLaw

Author:

cl

Constructor Summary

Constructors

Constructor and Description
DynamicKineticLaw(Reaction reaction, String kineticLawString)

Method Summary

Modifier and Type	Method and Description
double	determineVelocity(ReactionEvent reactionEvent)
Map<String,Reactant>	getConcentrationMap()
String	getExpressionString()
Map<String,bio.singa.features.model.ScalableQuantitativeFeature>	getFeatureMap()
Map<String,Parameter>	getParameterMap()
void	referenceConstant(String parameterIdentifier, double constant)
void	referenceConstant(String parameterIdentifier, double constant, bio.singa.features.model.Evidence evidence)
void	referenceFeature(bio.singa.features.model.ScalableQuantitativeFeature feature)
void	referenceFeature(String parameterIdentifier, bio.singa.features.model.ScalableQuantitativeFeature feature)
void	referenceParameter(Parameter<?> parameter)
void	referenceReactant(Reactant reactant)
void	referenceReactant(String parameterIdentifier, Reactant reactant)
void	setConcentrationMap(Map<String,Reactant> concentrationMap)
void	setFeatureMap(Map<String,bio.singa.features.model.ScalableQuantitativeFeature> 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

DynamicKineticLaw

public DynamicKineticLaw(Reaction reaction,
                         String kineticLawString)

Method Detail

referenceReactant

public void referenceReactant(String parameterIdentifier,
                              Reactant reactant)

referenceReactant

public void referenceReactant(Reactant reactant)

referenceFeature

public void referenceFeature(String parameterIdentifier,
                             bio.singa.features.model.ScalableQuantitativeFeature feature)

referenceFeature

public void referenceFeature(bio.singa.features.model.ScalableQuantitativeFeature feature)

referenceConstant

public void referenceConstant(String parameterIdentifier,
                              double constant)

referenceConstant

public void referenceConstant(String parameterIdentifier,
                              double constant,
                              bio.singa.features.model.Evidence evidence)

referenceParameter

public void referenceParameter(Parameter<?> parameter)

getFeatureMap

public Map<String,bio.singa.features.model.ScalableQuantitativeFeature> getFeatureMap()

setFeatureMap

public void setFeatureMap(Map<String,bio.singa.features.model.ScalableQuantitativeFeature> 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)

determineVelocity

public double determineVelocity(ReactionEvent reactionEvent)

Specified by:

determineVelocity in interface KineticLaw