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

Packages that use AcSpecies

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

Uses of AcSpecies in com.banda.chemistry.business

Fields in com.banda.chemistry.business with type parameters of type AcSpecies

Modifier and Type	Field and Description
static PairComparator<AcCompartment,AcSpecies>	ArtificialChemistryUtil.compartmentSpeciesComparator

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

Modifier and Type	Method and Description
Set<AcSpecies>	ArtificialChemistryUtil.filterOutSpecies(Collection<AcReaction> reactions, Collection<AcSpecies> species, AcSpeciesAssociationType type)
Collection<AcSpecies>	ArtificialChemistryUtil.getNewSpecies(AcReactionSet reactionSet, AcReactionSet additionalReactionSet)
Set<AcSpecies>	ArtificialChemistryUtil.getReferencedSpecies(AcReactionSet reactionSet)
Set<AcSpecies>	ArtificialChemistryUtil.getReferencedSpecies(AcTranslation rangeTranslation)
Set<AcSpecies>	ArtificialChemistryUtil.getReferencedSpecies(AcTranslationSeries translationSeries)
Collection<AcSpecies>	ArtificialChemistryUtil.getSpecies(Collection<AcSpeciesReactionAssociation> assocs)
Collection<AcSpecies>	ArtificialChemistryUtil.getTranslationFunctionReferencedSpecies(AcTranslationItem translationItem)
Collection<AcSpecies>	ChemistryRunSetting.storeSpeciesHistorySelectionGroup()

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

Modifier and Type	Method and Description
Set<AcSpecies>	ArtificialChemistryUtil.filterOutSpecies(Collection<AcReaction> reactions, Collection<AcSpecies> species, AcSpeciesAssociationType type)
String	ArtificialChemistryUtil.getSpeciesAsString(Collection<? extends AcSpecies> species, String separator)
void	ChemistryRunSetting.storeSpeciesHistorySelectionGroup(Collection<AcSpecies> storeSpeciesHistorySelectionGroup)

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

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

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(Collection<AcSpecies> allowedReactantSpecies, Collection<AcSpecies> allowedProductSpecies, Collection<AcSpecies> allowedCatalystSpecies, Collection<AcSpecies> allowedInhibitorSpecies, 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(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)

Uses of AcSpecies in com.banda.chemistry.domain

Subclasses of AcSpecies in com.banda.chemistry.domain

Modifier and Type	Class and Description
class	AcCompositeSpecies

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

Modifier and Type	Method and Description
AcSpecies	AcCompartmentChannel.getSourceSpecies()
AcSpecies	AcEvaluatedSpeciesAction.getSpecies()
AcSpecies	AcSpeciesInteraction.getSpecies()
AcSpecies	AcSpeciesAssociation.getSpecies()
AcSpecies	AcSpeciesReactionAssociation.getSpecies()
AcSpecies	AcCompartmentChannel.getTargetSpecies()

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

Modifier and Type	Method and Description
ComponentRunTrace<Double,Pair<AcCompartment,AcSpecies>>	AcTranslatedRun.getAcRunTrace()
List<AcSpecies>	AcCompositeSpecies.getComponents()
Collection<AcSpecies>	AcInteractionSeries.getImmutableSpecies()
Collection<AcSpecies>	AcSpeciesSet.getInternalSpecies()
Collection<AcSpecies>	AcDNAStrandSpeciesSet.getLowerStrands()
Collection<AcSpecies>	AcSpeciesSet.getNonInputFeedbackSpecies()
Collection<AcSpecies>	AcSpeciesSet.getNonInternalSpecies()
Collection<AcSpecies>	AcSpeciesSet.getOwnAndInheritedSpecies(AcSpeciesType type)
Collection<AcSpecies>	AcSpeciesSet.getOwnAndInheritedVariables()
Collection<AcSpecies>	AcCompartment.getParentCompartmentSpecies()
Collection<AcSpecies>	AcTranslationSeries.getSpecies()
Collection<AcSpecies>	AcInteraction.getSpecies()
Collection<AcSpecies>	AcReactionSet.getSpecies()
Collection<AcSpecies>	AcTranslation.getSpecies()
Collection<AcSpecies>	AcCompartment.getSpecies()
Collection<AcSpecies>	AcInteractionSeries.getSpecies()
Collection<AcSpecies>	AcTranslatedRun.getSpecies()
Collection<AcSpecies>	ArtificialChemistry.getSpecies()
Collection<AcSpecies>	AcSpeciesSet.getSpecies(AcSpeciesType type)
Collection<AcSpecies>	AcDNAStrandSpeciesSet.getUpperStrands()

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

Modifier and Type	Method and Description
void	AcReaction.addAssociationForSpecies(AcSpecies species, AcSpeciesAssociationType type)
void	AcCompositeSpecies.addComponent(AcSpecies component)
void	AcInteractionSeries.addImmutableSpecies(AcSpecies species)
void	AcDNAStrandSpeciesSet.addLowerStrand(AcSpecies lowerStrand)
void	AcSpeciesSet.addSpeciesToGroup(AcSpeciesType type, AcSpecies species)
void	AcDNAStrandSpeciesSet.addUpperStrand(AcSpecies upperStrand)
void	AcSpeciesGroup.addVariable(AcSpecies variable)
void	AcInteractionSeries.removeImmutableSpecies(AcSpecies species)
void	AcCompartmentChannel.setSourceSpecies(AcSpecies sourceSpecies)
void	AcSpeciesInteraction.setSpecies(AcSpecies species)
void	AcSpeciesReactionAssociation.setSpecies(AcSpecies species)
void	AcCompartmentChannel.setTargetSpecies(AcSpecies targetSpecies)

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

Modifier and Type	Method and Description
void	AcReaction.addAssociationsForSpecies(Collection<AcSpecies> species, AcSpeciesAssociationType type)
static Collection<AcSpeciesReactionAssociation>	AcSpeciesReactionAssociation.createCollection(Collection<AcSpecies> species, AcSpeciesAssociationType assocType)
void	AcTranslatedRun.setAcRunTrace(ComponentRunTrace<Double,Pair<AcCompartment,AcSpecies>> acRunTrace)
void	AcCompositeSpecies.setComponents(List<AcSpecies> components)
void	AcInteractionSeries.setImmutableSpecies(Collection<AcSpecies> immutableSpecies)
void	AcDNAStrandSpeciesSet.setLowerStrands(Collection<AcSpecies> lowerStrands)
void	AcDNAStrandSpeciesSet.setUpperStrands(Collection<AcSpecies> upperStrands)

Constructors in com.banda.chemistry.domain with parameters of type AcSpecies

Constructor and Description
AcSpeciesAssociation(AcSpecies species, AcSpeciesAssociationType type)
AcSpeciesReactionAssociation(AcSpecies species, AcSpeciesAssociationType type)
AcSpeciesReactionAssociation(AcSpecies species, AcSpeciesAssociationType type, Double stoichiometricFactor)
AcSpeciesReactionAssociation(AcSpecies species, Double stoichiometricFactor)

Constructor parameters in com.banda.chemistry.domain with type arguments of type AcSpecies

Constructor and Description
AcSpeciesGroup(Collection<AcSpecies> species)