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

Class ReactionBuilder.GeneralReactionBuilder

java.lang.Object

bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

All Implemented Interfaces:

ReactionBuilder.ComplexBuildingReactionStep, ReactionBuilder.FinalStep, ReactionBuilder.IrreversibleReactionStep, ReactionBuilder.MichaelisMentenReactionStep, ReactionBuilder.ParameterStep, ReactionBuilder.ReversibleReactionStep, ModuleBuilder

Direct Known Subclasses:

ReactionBuilder.RuleBasedBuilder, ReactionBuilder.StaticBuilder

Enclosing class:

ReactionBuilder

public static class ReactionBuilder.GeneralReactionBuilder
extends Object
implements ModuleBuilder, ReactionBuilder.ReversibleReactionStep, ReactionBuilder.IrreversibleReactionStep, ReactionBuilder.ComplexBuildingReactionStep, ReactionBuilder.MichaelisMentenReactionStep, ReactionBuilder.ParameterStep

Field Summary

Fields

Modifier and Type	Field	Description
protected Reaction	reaction
protected Simulation	simulation

Constructor Summary

Constructors

Constructor	Description
GeneralReactionBuilder(Simulation simulation)

Method Summary

Modifier and Type	Method	Description
ReactionBuilder.ComplexBuildingReactionStep	associationRate(RateConstant rateConstant)
ReactionBuilder.FinalStep	backwardReactionRate(RateConstant rateConstant)
Reaction	build()
ReactionBuilder.FinalStep	condition(ConcentrationCondition condition)
Reaction	createModule(Simulation simulation)
ReactionBuilder.FinalStep	dissociationRate(RateConstant rateConstant)
ReactionBuilder.FinalStep	evidence(bio.singa.features.model.Evidence evidence)
ReactionBuilder.FinalStep	evidence(bio.singa.features.model.Evidence... evidence)
ReactionBuilder.ReversibleReactionStep	forwardReactionRate(RateConstant rateConstant)
Reaction	getModule()
ReactionBuilder.FinalStep	identifier(String identifier)
ReactionBuilder.IrreversibleReactionStep	irreversible()
ReactionBuilder.ParameterStep	kineticLaw(String expression)
ReactionBuilder.MichaelisMentenReactionStep	michaelisConstant(MichaelisConstant michaelisConstant)
ReactionBuilder.MichaelisMentenReactionStep	michaelisMenten()
ReactionBuilder.FinalStep	rate(RateConstant rateConstant)
ReactionBuilder.ParameterStep	referenceParameter(bio.singa.features.model.AbstractScalableQuantitativeFeature<?> scalableFeature)
ReactionBuilder.ParameterStep	referenceParameter(Reactant reactant)
ReactionBuilder.ParameterStep	referenceParameter(Parameter<?> reactant)
ReactionBuilder.ParameterStep	referenceParameter(String parameterIdentifier, double parameter)
ReactionBuilder.ParameterStep	referenceParameter(String parameterIdentifier, double parameter, bio.singa.features.model.Evidence evidence)
ReactionBuilder.ParameterStep	referenceParameter(String parameterIdentifier, bio.singa.features.model.AbstractScalableQuantitativeFeature<?> scalableFeature)
ReactionBuilder.ParameterStep	referenceParameter(String parameterIdentifier, Reactant reactant)
ReactionBuilder.ReversibleReactionStep	reversible()
ReactionBuilder.FinalStep	turnover(TurnoverNumber turnoverNumber)

Methods inherited from class java.lang.Object

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

Field Detail

simulation

protected Simulation simulation

reaction

protected Reaction reaction

Constructor Detail

GeneralReactionBuilder

public GeneralReactionBuilder(Simulation simulation)

Method Detail

getModule

public Reaction getModule()

Specified by:

getModule in interface ModuleBuilder

createModule

public Reaction createModule(Simulation simulation)

Specified by:

createModule in interface ModuleBuilder

reversible

public ReactionBuilder.ReversibleReactionStep reversible()

irreversible

public ReactionBuilder.IrreversibleReactionStep irreversible()

michaelisMenten

public ReactionBuilder.MichaelisMentenReactionStep michaelisMenten()

forwardReactionRate

public ReactionBuilder.ReversibleReactionStep forwardReactionRate(RateConstant rateConstant)

Specified by:

forwardReactionRate in interface ReactionBuilder.ReversibleReactionStep

backwardReactionRate

public ReactionBuilder.FinalStep backwardReactionRate(RateConstant rateConstant)

Specified by:

backwardReactionRate in interface ReactionBuilder.ReversibleReactionStep

rate

public ReactionBuilder.FinalStep rate(RateConstant rateConstant)

Specified by:

rate in interface ReactionBuilder.IrreversibleReactionStep

associationRate

public ReactionBuilder.ComplexBuildingReactionStep associationRate(RateConstant rateConstant)

Specified by:

associationRate in interface ReactionBuilder.ComplexBuildingReactionStep

dissociationRate

public ReactionBuilder.FinalStep dissociationRate(RateConstant rateConstant)

Specified by:

dissociationRate in interface ReactionBuilder.ComplexBuildingReactionStep

michaelisConstant

public ReactionBuilder.MichaelisMentenReactionStep michaelisConstant(MichaelisConstant michaelisConstant)

Specified by:

michaelisConstant in interface ReactionBuilder.MichaelisMentenReactionStep

turnover

public ReactionBuilder.FinalStep turnover(TurnoverNumber turnoverNumber)

Specified by:

turnover in interface ReactionBuilder.MichaelisMentenReactionStep

identifier

public ReactionBuilder.FinalStep identifier(String identifier)

Specified by:

identifier in interface ReactionBuilder.FinalStep

evidence

public ReactionBuilder.FinalStep evidence(bio.singa.features.model.Evidence evidence)

Specified by:

evidence in interface ReactionBuilder.FinalStep

evidence

public ReactionBuilder.FinalStep evidence(bio.singa.features.model.Evidence... evidence)

Specified by:

evidence in interface ReactionBuilder.FinalStep

kineticLaw

public ReactionBuilder.ParameterStep kineticLaw(String expression)

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(bio.singa.features.model.AbstractScalableQuantitativeFeature<?> scalableFeature)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(String parameterIdentifier,
                                                        bio.singa.features.model.AbstractScalableQuantitativeFeature<?> scalableFeature)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(Parameter<?> reactant)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(Reactant reactant)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(String parameterIdentifier,
                                                        Reactant reactant)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(String parameterIdentifier,
                                                        double parameter)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

referenceParameter

public ReactionBuilder.ParameterStep referenceParameter(String parameterIdentifier,
                                                        double parameter,
                                                        bio.singa.features.model.Evidence evidence)

Specified by:

referenceParameter in interface ReactionBuilder.ParameterStep

condition

public ReactionBuilder.FinalStep condition(ConcentrationCondition condition)

Specified by:

condition in interface ReactionBuilder.FinalStep

build

public Reaction build()

Specified by:

build in interface ModuleBuilder

Specified by:

build in interface ReactionBuilder.FinalStep