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

Packages that use AcSpeciesSet

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

Uses of AcSpeciesSet in com.banda.chemistry.business

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

Modifier and Type	Method and Description
AcSpeciesSet	AcReplicator.cloneSpeciesSetWithParameterSet(AcSpeciesSet speciesSet)
protected AcSpeciesSet	AcReactionSetConverter.getInputSpeciesSet()
protected AcSpeciesSet	AcReactionSetConverter.getOutputSpeciesSet()

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

Modifier and Type	Method and Description
AcSpeciesSet	AcReplicator.cloneSpeciesSetWithParameterSet(AcSpeciesSet speciesSet)
Set<AcSpeciesReactionAssociation>	ArtificialChemistryUtil.getSpeciesAssociations(AcSpeciesSet speciesSet, Double[] stoichiometricVector)
String	ArtificialChemistryUtil.replaceSpeciesAndParamaterLabelsWithIndexPlaceholders(String formula, AcSpeciesSet speciesSet)
void	ArtificialChemistryUtil.replaceSpeciesSet(AcInteractionSeries interactionSeries, AcSpeciesSet newSpeciesSet)
void	ArtificialChemistryUtil.replaceSpeciesSet(AcReactionSet reactionSet, AcSpeciesSet newSpeciesSet)

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

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

Modifier and Type	Method and Description
AcSpeciesSet	AcSpeciesSetFactory.createFixedOrder(Collection<String> speciesLabels)
AcSpeciesSet	AcSpeciesSetFactory.createFixedOrder(int speciesNumber)
AcSpeciesSet	AcSpeciesSetFactory.createFixedOrder(int internalSpeciesNum, int inputSpeciesNumber, int outputSpeciesNum, int functionalSpeciesNum)
AcSpeciesSet	AcSpeciesSetFactory.createRandomOrder(Collection<String> speciesLabels)
AcSpeciesSet	AcSpeciesSetFactory.createRandomOrder(int speciesNumber)
AcSpeciesSet	AcSpeciesSetFactory.createRandomOrder(int speciesNumber, int startingSequenceNum, int startingLabel)

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

Modifier and Type	Method and Description
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)
AcInteractionSeries	AcInteractionSeriesFactory.createTemporalActionASWithInit(AcSpeciesSet speciesSet, com.banda.function.domain.BooleanFunction.BooleanFunctionType functionType, int timeWindowLength, com.banda.math.domain.rand.RandomDistribution<Double> initInternalConcDistribution, com.banda.math.domain.rand.RandomDistribution<Double> initWeightConcDistribution, AcConcentrationLevel inputConcentrationLevel, AcConcentrationLevel feedbackConcentrationLevel, int actionsNum, int afterInitStartingTimeStep, int actionInterval, boolean nullOutputSpecies)

Uses of AcSpeciesSet in com.banda.chemistry.domain

Subclasses of AcSpeciesSet in com.banda.chemistry.domain

Modifier and Type	Class and Description
class	AcDNAStrandSpeciesSet

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

Modifier and Type	Method and Description
AcSpeciesSet	AcSpeciesSet.getParentSpeciesSet()
AcSpeciesSet	AcTranslationSeries.getSpeciesSet()
AcSpeciesSet	AcParameterSet.getSpeciesSet()
AcSpeciesSet	AcInteraction.getSpeciesSet()
AcSpeciesSet	AcInteractionVariableAssignment.getSpeciesSet()
AcSpeciesSet	AcSpeciesInteraction.getSpeciesSet()
AcSpeciesSet	AcReactionSet.getSpeciesSet()
AcSpeciesSet	AcTranslation.getSpeciesSet()
AcSpeciesSet	AcCompartment.getSpeciesSet()
AcSpeciesSet	AcInteractionSeries.getSpeciesSet()
AcSpeciesSet	AcReaction.getSpeciesSet()
AcSpeciesSet	ArtificialChemistry.getSpeciesSet()

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

Modifier and Type	Method and Description
void	AcSpeciesSet.setParentSpeciesSet(AcSpeciesSet parentSpeciesSet)
void	AcTranslationSeries.setSpeciesSet(AcSpeciesSet speciesSet)
void	AcParameterSet.setSpeciesSet(AcSpeciesSet speciesSet)
void	AcReactionSet.setSpeciesSet(AcSpeciesSet speciesSet)
void	AcInteractionSeries.setSpeciesSet(AcSpeciesSet speciesSet)