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

Packages that use AcReactionSet

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

Uses of AcReactionSet in com.banda.chemistry.business

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

Modifier and Type	Method and Description
AcReactionSet	AcReplicator.cloneReactionSetWithReactionsAndGroups(AcReactionSet reactionSet)
AcReactionSet	AcReactionSetConverter.convert()
protected AcReactionSet	AcReactionSetConverter.getInputReactionSet()

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

Modifier and Type	Method and Description
void	ArtificialChemistryUtil.addReactions(AcReactionSet reactionSet, AcReactionSet additionalReactionSet)
AcReactionSet	AcReplicator.cloneReactionSetWithReactionsAndGroups(AcReactionSet reactionSet)
String	ArtificialChemistryUtil.getFunctionAsString(com.banda.function.domain.Function<?,?> function, AcReactionSet reactionSet)
Map<String,AcReaction>	ArtificialChemistryUtil.getLabelReactionMap(AcReactionSet reactionSet)
String	ArtificialChemistryUtil.getLatexTable(AcReactionSet reactionSet, boolean includeRates)
Collection<AcSpecies>	ArtificialChemistryUtil.getNewSpecies(AcReactionSet reactionSet, AcReactionSet additionalReactionSet)
Collection<ValueBound<Double>>	AcRateConstantUtil.getRateConstantBounds(AcReactionSet reactionSet, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
Set<AcSpecies>	ArtificialChemistryUtil.getReferencedSpecies(AcReactionSet reactionSet)
Collection<AcReaction>	AcRateConstantUtil.getRepresentativeReactions(AcReactionSet reactionSet, Collection<AcReactionGroup> reactionGroupsToOmit)
void	AcReplicator.nullIdAndVersionRecursively(AcReactionSet reactionSet)
void	ArtificialChemistryUtil.replaceSpeciesSet(AcReactionSet reactionSet, AcSpeciesSet newSpeciesSet)
void	AcRateConstantUtil.setRandomRateConstants(AcReactionSet reactionSet, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap)
void	AcRateConstantUtil.setRandomRateConstantsIfNotSet(AcReactionSet reactionSet, Map<AcRateConstantType,ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection)
void	AcRateConstantUtil.setRateConstants(AcReactionSet reactionSet, Double[] rateConstants, AcReaction.ReactionDirection direction, 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 AcReactionSet

Constructor and Description
AcMichaelisMentenToMassActionRSConverter(AcReactionSet inputReactionSet, MassActionType massActionType)
AcReactionRatePerturbationBO(AcReactionSet reactionSet, double pertrubationStrength)
AcReactionSetConverter(AcReactionSet inputReactionSet)

Uses of AcReactionSet in com.banda.chemistry.business.factory

Methods in com.banda.chemistry.business.factory that return AcReactionSet

Modifier and Type	Method and Description
AcReactionSet	AcReactionSetFactory.createComplexRS(Collection<AcSpecies> species, AcReactionSetConstraints reactionSetConstraints, AcReactionSpeciesForbiddenRedundancy speciesForbiddenRedundancy)
AcReactionSet	AcReactionSetFactory.createComplexRS(Collection<AcSpecies> allowedReactantSpecies, Collection<AcSpecies> allowedProductSpecies, Collection<AcSpecies> allowedCatalystSpecies, Collection<AcSpecies> allowedInhibitorSpecies, AcReactionSetConstraints reactionSetConstraints, AcReactionSpeciesForbiddenRedundancy speciesForbiddenRedundancy)
AcReactionSet	AcReactionSetFactory.createComplexRS(Map<AcSpeciesAssociationType,Collection<AcSpecies>> assocTypeAllowedSpeciesMap, AcReactionSetConstraints reactionSetConstraints, AcReactionSpeciesForbiddenRedundancy speciesForbiddenRedundancy)
AcReactionSet	AcReactionSetFactory.createDNAStrandRS(AcDNAStrandSpec spec, AcDNAStrandSpeciesSet speciesSet)
AcReactionSet	AcReactionSetFactory.createOutputFeedbackRS(AcSpeciesSet speciesSet)
AcReactionSet	AcReactionSetFactory.createRandomReactionSymmetricRS(AcSymmetricSpec spec, AcSpeciesSet speciesSet)
AcReactionSet	AcReactionSetFactory.createRandomRS(int reactionsNumber, int reactantsNumber, int productsNumber, int catalystsNumber, int inhibitorsNumber, AcSpeciesSet speciesSet, AcReactionSpeciesForbiddenRedundancy speciesForbiddenRedundancy)
AcReactionSet	AcReactionSetFactory.mergeReactionSets(AcReactionSet[] reactionSets)

Methods in com.banda.chemistry.business.factory with parameters of type AcReactionSet

Modifier and Type	Method and Description
AcReactionSet	AcReactionSetFactory.mergeReactionSets(AcReactionSet[] reactionSets)

Uses of AcReactionSet in com.banda.chemistry.domain

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

Modifier and Type	Method and Description
AcReactionSet	AcReactionGroup.getReactionSet()
AcReactionSet	AcCompartment.getReactionSet()
AcReactionSet	AcReaction.getReactionSet()
AcReactionSet	ArtificialChemistry.getReactionSet()

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

Modifier and Type	Method and Description
protected void	AcReactionGroup.setReactionSet(AcReactionSet reactionSet)
void	AcCompartment.setReactionSet(AcReactionSet reactionSet)
protected void	AcReaction.setReactionSet(AcReactionSet reactionSet)