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

Packages that use AcSpecies

Package	Description
com.banda.chemistry.domain

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	AcSpeciesReactionAssociation.getSpecies()
AcSpecies	AcSpeciesAssociation.getSpecies()
AcSpecies	AcCompartmentChannel.getTargetSpecies()

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

Modifier and Type	Method and Description
com.banda.core.domain.ComponentRunTrace<Double,com.banda.core.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>	AcReactionSet.getSpecies()
Collection<AcSpecies>	AcCompartment.getSpecies()
Collection<AcSpecies>	AcInteractionSeries.getSpecies()
Collection<AcSpecies>	AcTranslatedRun.getSpecies()
Collection<AcSpecies>	AcInteraction.getSpecies()
Collection<AcSpecies>	AcTranslation.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(com.banda.core.domain.ComponentRunTrace<Double,com.banda.core.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)