Uses of Class
com.banda.chemistry.domain.AcReaction

Packages that use AcReaction

Package	Description
com.banda.chemistry.business
com.banda.chemistry.business.reactionode
com.banda.chemistry.domain

Uses of AcReaction in com.banda.chemistry.business

Methods in com.banda.chemistry.business that return AcReaction

Modifier and Type	Method and Description
AcReaction	AcReplicator.cloneReaction(AcReaction reaction)
AcReaction	AcReactionConverter.convert(AcReaction inputReaction)
protected AcReaction	AcKineticsBO.getReaction()

Methods in com.banda.chemistry.business that return types with arguments of type AcReaction

Modifier and Type	Method and Description
protected Collection<AcReaction>	AcMichaelisMentenToMassActionRSConverter.convert(AcReaction inputReaction)
protected abstract Collection<AcReaction>	AcReactionSetConverter.convert(AcReaction inputReaction)
protected Collection<AcReaction>	AcReactionSetConverter.getInputReactions()
Map<String,AcReaction>	ArtificialChemistryUtil.getLabelReactionMap(AcReactionSet reactionSet)
Collection<AcReaction>	AcReactionRatePerturbationBO.getReactions()
Collection<AcReaction>	AcRateConstantUtil.getRepresentativeReactions(AcReactionSet reactionSet, Collection<AcReactionGroup> reactionGroupsToOmit)

Methods in com.banda.chemistry.business with parameters of type AcReaction

Modifier and Type	Method and Description
AcReaction	AcReplicator.cloneReaction(AcReaction reaction)
protected Collection<AcReaction>	AcMichaelisMentenToMassActionRSConverter.convert(AcReaction inputReaction)
AcReaction	AcReactionConverter.convert(AcReaction inputReaction)
protected abstract Collection<AcReaction>	AcReactionSetConverter.convert(AcReaction inputReaction)
static AcKineticsBO	AcKineticsBO.createInstance(AcReaction reaction, boolean forwardReactionFlag)
static AcKineticsBO	AcKineticsBO.createInstance(AcReaction reaction, boolean forwardReactionFlag, Collection<AcParameter> substitutionParameters)
Collection<String>	ArtificialChemistryUtil.getProductsAsString(AcReaction reaction)
Collection<ValueBound<Double>>	AcRateConstantUtil.getRateConstantBounds(AcReaction reaction, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection)
String	ArtificialChemistryUtil.getRateFunctionAsString(AcReaction reaction, boolean forwardFlag)
Collection<String>	ArtificialChemistryUtil.getReactantsAsString(AcReaction reaction)
protected boolean	AcMichaelisMentenToMassActionRSConverter.isConvertible(AcReaction inputReaction)
protected abstract boolean	AcReactionSetConverter.isConvertible(AcReaction inputReaction)
void	AcReplicator.nullIdAndVersion(AcReaction reaction)
protected void	AcReactionSetConverter.removeReaction(AcReaction reaction)
void	AcRateConstantUtil.setRandomRateConstants(AcReaction reaction, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, boolean forwardFlag)
void	AcRateConstantUtil.setRateConstantsFromString(String rateConstantsString, AcReaction reaction, AcReaction.ReactionDirection reactionDirection)
void	ArtificialChemistryUtil.setRateFunctionFromString(String formula, AcReaction reaction, boolean forwardFlag)
void	ArtificialChemistryUtil.setSpeciesAssociationsFromString(String speciesAssociationsString, AcSpeciesAssociationType assocType, AcReaction reaction)
void	ArtificialChemistryUtil.updateSpeciesAssociations(Collection<AcSpeciesReactionAssociation> newSpeciesAssociations, AcSpeciesAssociationType assocType, AcReaction reaction)
void	ArtificialChemistryUtil.updateSpeciesAssociations(String speciesAssociationsString, AcSpeciesAssociationType assocType, AcReaction reaction)
protected void	AcMichaelisMentenToMassActionRSConverter.validate(AcReaction inputReaction)
protected abstract void	AcReactionSetConverter.validate(AcReaction reaction)

Method parameters in com.banda.chemistry.business with type arguments of type AcReaction

Modifier and Type	Method and Description
protected void	AcReactionSetConverter.addReactions(Collection<AcReaction> newReactions, AcReactionGroup originalReactionGroup)
protected void	AcReactionSetConverter.addSpecies(Collection<AcReaction> newReactions)
Set<AcSpecies>	ArtificialChemistryUtil.filterOutSpecies(Collection<AcReaction> reactions, Collection<AcSpecies> species, AcSpeciesAssociationType type)
Collection<ValueBound<Double>>	AcRateConstantUtil.getRateConstantBounds(AcCompartment compartment, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
Collection<ValueBound<Double>>	AcRateConstantUtil.getRateConstantBounds(AcReactionSet reactionSet, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	AcRateConstantUtil.setRateConstants(AcCompartment compartment, Double[] rateAndPermeabilityConstants, AcReaction.ReactionDirection direction, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	AcRateConstantUtil.setRateConstants(AcReactionSet reactionSet, Double[] rateConstants, AcReaction.ReactionDirection direction, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	AcRateConstantUtil.setRateConstantsFromString(String rateConstantsString, AcCompartment compartment, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	AcRateConstantUtil.setRateConstantsFromString(String rateConstantsString, AcReactionSet reactionSet, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)

Constructors in com.banda.chemistry.business with parameters of type AcReaction

Constructor and Description
AcKineticsBO(AcReaction reaction, boolean forwardReactionFlag, Collection<AcParameter> substitutionParameters)

Constructor parameters in com.banda.chemistry.business with type arguments of type AcReaction

Constructor and Description
AcReactionRatePerturbationBO(Collection<AcReaction> reactions, double pertrubationStrength)

Uses of AcReaction in com.banda.chemistry.business.reactionode

Method parameters in com.banda.chemistry.business.reactionode with type arguments of type AcReaction

Modifier and Type	Method and Description
static ODESolver	AcReactionODESolverFactory.createInstance(com.banda.function.domain.ODESolverType solverType, double timeStep, Double tolerance, Collection<AcReaction> reactions, int speciesCount, Collection<AcParameter> params, Map<Integer,Integer> magnitudeIndexConversionMap)

Uses of AcReaction in com.banda.chemistry.domain

Methods in com.banda.chemistry.domain that return AcReaction

Modifier and Type	Method and Description
AcReaction	AcSpeciesReactionAssociation.getReaction()

Methods in com.banda.chemistry.domain that return types with arguments of type AcReaction

Modifier and Type	Method and Description
List<AcReaction>	AcReactionGroup.getAllSetReactions()
List<AcReaction>	AcReactionContainer.getReactions()
Collection<AcReaction>	ArtificialChemistry.getReactions()

Methods in com.banda.chemistry.domain with parameters of type AcReaction

Modifier and Type	Method and Description
void	AcReactionContainer.addReaction(AcReaction reaction)
void	AcReactionGroup.addReaction(AcReaction reaction)
void	AcReactionSet.addReaction(AcReaction reaction)
boolean	AcReactionGroup.containsReaction(AcReaction reaction)
void	AcReactionContainer.removeReaction(AcReaction reaction)
void	AcReactionGroup.removeReaction(AcReaction reaction)
void	AcReactionSet.removeReaction(AcReaction reaction)
protected void	AcSpeciesReactionAssociation.setReaction(AcReaction reaction)

Method parameters in com.banda.chemistry.domain with type arguments of type AcReaction

Modifier and Type	Method and Description
void	AcReactionSet.addReactions(Collection<AcReaction> reactions)
void	AcReactionContainer.setReactions(List<AcReaction> reactions)