A B C D E F G H I K M N P R S T U V W Z

A

AcChannelDirection - Enum in com.banda.chemistry.domain

AcCollectiveSpeciesReactionAssociationType - Enum in com.banda.chemistry.domain

AcCompartment - Class in com.banda.chemistry.domain

AcCompartment() - Constructor for class com.banda.chemistry.domain.AcCompartment

AcCompartmentAssociation - Class in com.banda.chemistry.domain

AcCompartmentAssociation() - Constructor for class com.banda.chemistry.domain.AcCompartmentAssociation

AcCompartmentChannel - Class in com.banda.chemistry.domain

AcCompartmentChannel() - Constructor for class com.banda.chemistry.domain.AcCompartmentChannel

AcCompartmentChannelGroup - Class in com.banda.chemistry.domain

AcCompartmentChannelGroup() - Constructor for class com.banda.chemistry.domain.AcCompartmentChannelGroup

AcCompartmentDepthComparator - Class in com.banda.chemistry.business

AcCompartmentDepthComparator() - Constructor for class com.banda.chemistry.business.AcCompartmentDepthComparator

AcCompartmentFactory - Class in com.banda.chemistry.business.factory

AcCompartmentFactory(AcReactionSetFactory, AcSpeciesSetFactory) - Constructor for class com.banda.chemistry.business.factory.AcCompartmentFactory

AcCompositeSpecies - Class in com.banda.chemistry.domain

AcCompositeSpecies() - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies

AcCompositeSpecies(Long) - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies

AcCompositeSpecies(String) - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies

AcConcentrationLevel - Class in com.banda.chemistry.domain

AcConcentrationLevel(Double) - Constructor for class com.banda.chemistry.domain.AcConcentrationLevel

AcConcentrationLevel(Double, Double) - Constructor for class com.banda.chemistry.domain.AcConcentrationLevel

AcDNAStrandSpec - Class in com.banda.chemistry.domain

AcDNAStrandSpec() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpec

AcDNAStrandSpecBound - Class in com.banda.chemistry.domain

AcDNAStrandSpecBound() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpecBound

AcDNAStrandSpeciesSet - Class in com.banda.chemistry.domain

AcDNAStrandSpeciesSet() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

AcEvaluatedAction - Class in com.banda.chemistry.domain

AcEvaluatedAction() - Constructor for class com.banda.chemistry.domain.AcEvaluatedAction

AcEvaluatedActionSeries - Class in com.banda.chemistry.domain

AcEvaluatedActionSeries() - Constructor for class com.banda.chemistry.domain.AcEvaluatedActionSeries

AcEvaluatedPerformance - Class in com.banda.chemistry.domain

AcEvaluatedPerformance() - Constructor for class com.banda.chemistry.domain.AcEvaluatedPerformance

AcEvaluatedRun - Class in com.banda.chemistry.domain

AcEvaluatedRun() - Constructor for class com.banda.chemistry.domain.AcEvaluatedRun

AcEvaluatedSpeciesAction - Class in com.banda.chemistry.domain

AcEvaluatedSpeciesAction() - Constructor for class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

AcEvaluation - Class in com.banda.chemistry.domain

AcEvaluation() - Constructor for class com.banda.chemistry.domain.AcEvaluation

AcEvaluationBOFactory - Class in com.banda.chemistry.business

AcEvaluationBOFactory(FunctionEvaluatorFactory) - Constructor for class com.banda.chemistry.business.AcEvaluationBOFactory

AcEvaluationItemState - Enum in com.banda.chemistry.domain

AcEvaluator - Class in com.banda.chemistry.business

AcEvaluator(AcEvaluation, AcTranslatedRun, FunctionEvaluatorFactory) - Constructor for class com.banda.chemistry.business.AcEvaluator

AcInteraction - Class in com.banda.chemistry.domain

AcInteraction() - Constructor for class com.banda.chemistry.domain.AcInteraction

AcInteractionSeries - Class in com.banda.chemistry.domain

AcInteractionSeries() - Constructor for class com.banda.chemistry.domain.AcInteractionSeries

AcInteractionSeries(Long) - Constructor for class com.banda.chemistry.domain.AcInteractionSeries

AcInteractionSeriesFactory - Class in com.banda.chemistry.business.factory

AcInteractionSeriesFactory(FunctionEvaluatorFactory) - Constructor for class com.banda.chemistry.business.factory.AcInteractionSeriesFactory

AcInteractionVariable - Class in com.banda.chemistry.domain

AcInteractionVariable(String) - Constructor for class com.banda.chemistry.domain.AcInteractionVariable

AcInteractionVariable() - Constructor for class com.banda.chemistry.domain.AcInteractionVariable

AcInteractionVariableAssignment - Class in com.banda.chemistry.domain

AcInteractionVariableAssignment() - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment

AcInteractionVariableAssignment(AcInteractionVariable) - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment

AcInteractionVariableAssignment.AcInteractionVariableComparator - Class in com.banda.chemistry.domain

AcInteractionVariableAssignment.AcInteractionVariableComparator() - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment.AcInteractionVariableComparator

AcItemHistoriesHolder<I extends AcItemHistory> - Class in com.banda.chemistry.domain

AcItemHistoriesHolder() - Constructor for class com.banda.chemistry.domain.AcItemHistoriesHolder

AcItemHistoriesHolder(Long) - Constructor for class com.banda.chemistry.domain.AcItemHistoriesHolder

AcItemHistory<H extends AcItemHistoriesHolder> - Class in com.banda.chemistry.domain

AcItemHistory() - Constructor for class com.banda.chemistry.domain.AcItemHistory

AcItemHistory.AcItemHistoryLabelComparator - Class in com.banda.chemistry.domain

AcItemHistory.AcItemHistoryLabelComparator() - Constructor for class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator

AcItemHistory.AcItemHistoryLabelComparator2 - Class in com.banda.chemistry.domain

AcItemHistory.AcItemHistoryLabelComparator2() - Constructor for class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator2

AcKineticsBO - Class in com.banda.chemistry.business

AcKineticsBO(AcReaction, boolean, Collection<AcParameter>) - Constructor for class com.banda.chemistry.business.AcKineticsBO

AcMichaelisMentenToMassActionRSConverter - Class in com.banda.chemistry.business

AcMichaelisMentenToMassActionRSConverter(AcReactionSet, MassActionType) - Constructor for class com.banda.chemistry.business.AcMichaelisMentenToMassActionRSConverter

AcMultiRunAnalysisResult - Class in com.banda.chemistry.domain

AcMultiRunAnalysisResult() - Constructor for class com.banda.chemistry.domain.AcMultiRunAnalysisResult

AcParameter - Class in com.banda.chemistry.domain

AcParameter() - Constructor for class com.banda.chemistry.domain.AcParameter

AcParameterSet - Class in com.banda.chemistry.domain

AcParameterSet() - Constructor for class com.banda.chemistry.domain.AcParameterSet

AcPerturbationPerformance - Class in com.banda.chemistry.domain

AcPerturbationPerformance() - Constructor for class com.banda.chemistry.domain.AcPerturbationPerformance

AcRandomRatePerformance - Class in com.banda.chemistry.domain

AcRandomRatePerformance() - Constructor for class com.banda.chemistry.domain.AcRandomRatePerformance

AcRateConstantType - Enum in com.banda.chemistry.domain

AcRateConstantTypeBound - Class in com.banda.chemistry.domain

AcRateConstantTypeBound() - Constructor for class com.banda.chemistry.domain.AcRateConstantTypeBound

AcRateConstantUtil - Class in com.banda.chemistry.business

AcReaction - Class in com.banda.chemistry.domain

AcReaction() - Constructor for class com.banda.chemistry.domain.AcReaction

AcReaction.ReactionDirection - Enum in com.banda.chemistry.domain

AcReactionContainer - Class in com.banda.chemistry.domain

AcReactionContainer() - Constructor for class com.banda.chemistry.domain.AcReactionContainer

AcReactionConverter - Interface in com.banda.chemistry.business

AcReactionGroup - Class in com.banda.chemistry.domain

AcReactionGroup() - Constructor for class com.banda.chemistry.domain.AcReactionGroup

AcReactionODESolverFactory - Class in com.banda.chemistry.business.reactionode

AcReactionRatePerturbationBO - Class in com.banda.chemistry.business

AcReactionRatePerturbationBO(AcReactionSet, double) - Constructor for class com.banda.chemistry.business.AcReactionRatePerturbationBO

AcReactionRatePerturbationBO(Collection<AcReaction>, double) - Constructor for class com.banda.chemistry.business.AcReactionRatePerturbationBO

AcReactionSet - Class in com.banda.chemistry.domain

AcReactionSet() - Constructor for class com.banda.chemistry.domain.AcReactionSet

AcReactionSetConstraints - Class in com.banda.chemistry.domain

AcReactionSetConstraints(AcReactionToSpeciesConstraints, AcSpeciesToReactionConstraints, Double, AcSpeciesAssociationType) - Constructor for class com.banda.chemistry.domain.AcReactionSetConstraints

AcReactionSetConstraints(AcReactionToSpeciesConstraints, AcSpeciesToReactionConstraints, Double) - Constructor for class com.banda.chemistry.domain.AcReactionSetConstraints

AcReactionSetConstraints() - Constructor for class com.banda.chemistry.domain.AcReactionSetConstraints

AcReactionSetConverter - Class in com.banda.chemistry.business

AcReactionSetConverter(AcReactionSet) - Constructor for class com.banda.chemistry.business.AcReactionSetConverter

AcReactionSetFactory - Class in com.banda.chemistry.business.factory

AcReactionSpeciesForbiddenRedundancy - Enum in com.banda.chemistry.domain

AcReactionToSpeciesConstraints - Class in com.banda.chemistry.domain

AcReactionToSpeciesConstraints() - Constructor for class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

AcReplicator - Class in com.banda.chemistry.business

AcSimulationConfig - Class in com.banda.chemistry.domain

AcSimulationConfig() - Constructor for class com.banda.chemistry.domain.AcSimulationConfig

AcSpecies - Class in com.banda.chemistry.domain

AcSpecies() - Constructor for class com.banda.chemistry.domain.AcSpecies

AcSpecies(Long) - Constructor for class com.banda.chemistry.domain.AcSpecies

AcSpecies(String) - Constructor for class com.banda.chemistry.domain.AcSpecies

AcSpeciesAssociation - Class in com.banda.chemistry.domain

AcSpeciesAssociation(AcSpecies, AcSpeciesAssociationType) - Constructor for class com.banda.chemistry.domain.AcSpeciesAssociation

AcSpeciesAssociationType - Enum in com.banda.chemistry.domain

AcSpeciesGroup - Class in com.banda.chemistry.domain

AcSpeciesGroup(Collection<AcSpecies>) - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup

AcSpeciesGroup() - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup

AcSpeciesGroup(String) - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup

AcSpeciesIndecesToStoreGroup - Class in com.banda.chemistry.business

AcSpeciesIndecesToStoreGroup(int[], int[]) - Constructor for class com.banda.chemistry.business.AcSpeciesIndecesToStoreGroup

AcSpeciesInteraction - Class in com.banda.chemistry.domain

AcSpeciesInteraction() - Constructor for class com.banda.chemistry.domain.AcSpeciesInteraction

AcSpeciesInteraction.AcSpeciesInteractionVariableComparator - Class in com.banda.chemistry.domain

AcSpeciesInteraction.AcSpeciesInteractionVariableComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesInteraction.AcSpeciesInteractionVariableComparator

AcSpeciesReactionAssociation - Class in com.banda.chemistry.domain

AcSpeciesReactionAssociation() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation

AcSpeciesReactionAssociation(AcSpecies, AcSpeciesAssociationType) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation

AcSpeciesReactionAssociation(AcSpecies, Double) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation

AcSpeciesReactionAssociation(AcSpecies, AcSpeciesAssociationType, Double) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator - Class in com.banda.chemistry.domain

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator - Class in com.banda.chemistry.domain

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator - Class in com.banda.chemistry.domain

AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator

AcSpeciesSet - Class in com.banda.chemistry.domain

AcSpeciesSet() - Constructor for class com.banda.chemistry.domain.AcSpeciesSet

AcSpeciesSetFactory - Class in com.banda.chemistry.business.factory

AcSpeciesToReactionConstraints - Class in com.banda.chemistry.domain

AcSpeciesToReactionConstraints() - Constructor for class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

AcSpeciesType - Enum in com.banda.chemistry.domain

AcSymmetricSpec - Class in com.banda.chemistry.domain

AcSymmetricSpec() - Constructor for class com.banda.chemistry.domain.AcSymmetricSpec

AcSymmetricSpecBound - Class in com.banda.chemistry.domain

AcSymmetricSpecBound() - Constructor for class com.banda.chemistry.domain.AcSymmetricSpecBound

AcTranslatedRun - Class in com.banda.chemistry.domain

AcTranslatedRun() - Constructor for class com.banda.chemistry.domain.AcTranslatedRun

AcTranslatedRun(Long) - Constructor for class com.banda.chemistry.domain.AcTranslatedRun

AcTranslatedRunHolder - Interface in com.banda.chemistry.business

AcTranslation - Class in com.banda.chemistry.domain

AcTranslation() - Constructor for class com.banda.chemistry.domain.AcTranslation

AcTranslation.AcTranslationFromTimeComparator - Class in com.banda.chemistry.domain

AcTranslation.AcTranslationFromTimeComparator() - Constructor for class com.banda.chemistry.domain.AcTranslation.AcTranslationFromTimeComparator

AcTranslationItem<T> - Class in com.banda.chemistry.domain

AcTranslationItem() - Constructor for class com.banda.chemistry.domain.AcTranslationItem

AcTranslationItemHistory - Class in com.banda.chemistry.domain

AcTranslationItemHistory() - Constructor for class com.banda.chemistry.domain.AcTranslationItemHistory

AcTranslationItemHistory(AcTranslationVariable) - Constructor for class com.banda.chemistry.domain.AcTranslationItemHistory

AcTranslationSeries - Class in com.banda.chemistry.domain

AcTranslationSeries() - Constructor for class com.banda.chemistry.domain.AcTranslationSeries

AcTranslationSeries(Long) - Constructor for class com.banda.chemistry.domain.AcTranslationSeries

AcTranslationSeriesFactory - Class in com.banda.chemistry.business.factory

AcTranslationSeriesFactory.DefaultTransItemLabel - Enum in com.banda.chemistry.business.factory

AcTranslationVariable - Class in com.banda.chemistry.domain

AcTranslationVariable() - Constructor for class com.banda.chemistry.domain.AcTranslationVariable

acUtil - Variable in class com.banda.chemistry.business.AcReactionSetConverter

AcVariable<M extends AcVariableSetIF> - Class in com.banda.chemistry.domain

AcVariable() - Constructor for class com.banda.chemistry.domain.AcVariable

AcVariable(Long) - Constructor for class com.banda.chemistry.domain.AcVariable

AcVariable(String) - Constructor for class com.banda.chemistry.domain.AcVariable

AcVariable.AcVariableIndexComparator<T extends AcVariable<?>> - Class in com.banda.chemistry.domain

AcVariable.AcVariableIndexComparator() - Constructor for class com.banda.chemistry.domain.AcVariable.AcVariableIndexComparator

AcVariable.AcVariableLabelComparator<T extends AcVariable<?>> - Class in com.banda.chemistry.domain

AcVariable.AcVariableLabelComparator() - Constructor for class com.banda.chemistry.domain.AcVariable.AcVariableLabelComparator

AcVariableGroup<M extends AcVariable<?>> - Class in com.banda.chemistry.domain

AcVariableGroup(Collection<M>) - Constructor for class com.banda.chemistry.domain.AcVariableGroup

AcVariableGroup() - Constructor for class com.banda.chemistry.domain.AcVariableGroup

AcVariableGroupIF<M extends AcVariable<?>> - Interface in com.banda.chemistry.domain

AcVariableSet<M extends AcVariable<? extends AcVariableSet>> - Class in com.banda.chemistry.domain

AcVariableSet() - Constructor for class com.banda.chemistry.domain.AcVariableSet

AcVariableSetIF<M extends AcVariable<? extends AcVariableSetIF>> - Interface in com.banda.chemistry.domain

addAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

addAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addActions(Collection<AcInteraction>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addAssociationForSpecies(AcSpecies, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

addAssociationsForSpecies(Collection<AcSpecies>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

addChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartment

addChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

addComponent(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompositeSpecies

addEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

addEvaluatedActions(Collection<AcEvaluatedAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

addEvaluatedSpeciesAction(AcEvaluatedSpeciesAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

addFullDoubleStrand(AcCompositeSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

addGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReactionSet

addImmutableSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addInteractions(AcInteractionSeries, AcInteractionSeries) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

addItemHistories(Collection<I>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

addItemHistory(I) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

addLowerStrand(AcSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

addMultiRunAnalysisResult(AcMultiRunAnalysisResult) - Method in class com.banda.chemistry.domain.ArtificialChemistry

addPartialDoubleStrand(AcCompositeSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

addRateConstantTypeBound(AcRateConstantTypeBound) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionContainer

addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionGroup

addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionSet

addReactions(Collection<AcReaction>, AcReactionGroup) - Method in class com.banda.chemistry.business.AcReactionSetConverter

addReactions(AcReactionSet, AcReactionSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

addReactions(Collection<AcReaction>) - Method in class com.banda.chemistry.domain.AcReactionSet

addSpecies(Collection<AcReaction>) - Method in class com.banda.chemistry.business.AcReactionSetConverter

addSpeciesActions(Collection<AcSpeciesInteraction>) - Method in class com.banda.chemistry.domain.AcInteraction

addSpeciesAssociation(AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcReaction

addSpeciesAssociation(AcSpeciesReactionAssociation, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

addSpeciesAssociations(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction

addSpeciesAssociations(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

addSpeciesToGroup(AcSpeciesType, AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesSet

addSubActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addSubChannelGroup(AcCompartmentChannelGroup) - Method in class com.banda.chemistry.domain.AcCompartment

addSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment

addToSpeciesActions(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcInteraction

addTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcTranslationSeries

addTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationSeries

addTranslationItem(AcTranslationItem) - Method in class com.banda.chemistry.domain.AcTranslation

addUpperStrand(AcSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

addVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addVariable(String) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addVariable(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesGroup

addVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationSeries

addVariable(M) - Method in class com.banda.chemistry.domain.AcVariableGroup

addVariable(M) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

addVariable(M) - Method in class com.banda.chemistry.domain.AcVariableSet

addVariableAssignment(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteraction

addVariableAssignments(Collection<AcInteractionVariableAssignment>) - Method in class com.banda.chemistry.domain.AcInteraction

addVariables(Collection<AcInteractionVariable>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

addVariables(Collection<AcTranslationVariable>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

addVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableGroup

addVariables(Collection<M>) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

addVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableSet

ArtificialChemistry - Class in com.banda.chemistry.domain

ArtificialChemistry() - Constructor for class com.banda.chemistry.domain.ArtificialChemistry

ArtificialChemistrySpec - Class in com.banda.chemistry.domain

ArtificialChemistrySpec() - Constructor for class com.banda.chemistry.domain.ArtificialChemistrySpec

ArtificialChemistrySpecBound - Class in com.banda.chemistry.domain

ArtificialChemistrySpecBound() - Constructor for class com.banda.chemistry.domain.ArtificialChemistrySpecBound

ArtificialChemistryUtil - Class in com.banda.chemistry.business

B

BndChemistryException - Exception in com.banda.chemistry

BndChemistryException() - Constructor for exception com.banda.chemistry.BndChemistryException

BndChemistryException(String) - Constructor for exception com.banda.chemistry.BndChemistryException

BndChemistryException(String, Throwable) - Constructor for exception com.banda.chemistry.BndChemistryException

BndChemistryValidationException - Exception in com.banda.chemistry.business

BndChemistryValidationException() - Constructor for exception com.banda.chemistry.business.BndChemistryValidationException

BndChemistryValidationException(String) - Constructor for exception com.banda.chemistry.business.BndChemistryValidationException

BndChemistryValidationException(String, Throwable) - Constructor for exception com.banda.chemistry.business.BndChemistryValidationException

C

ChemistryRunSetting - Class in com.banda.chemistry.business

ChemistryRunSetting() - Constructor for class com.banda.chemistry.business.ChemistryRunSetting

clearItemHistories() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

cloneActionSeriesWithActions(AcInteractionSeries) - Method in class com.banda.chemistry.business.AcReplicator

cloneActionSeriesWithActionsRecursively(AcInteractionSeries) - Method in class com.banda.chemistry.business.AcReplicator

cloneActionSeriesWithActionsRecursively(AcInteractionSeries, Map<AcInteractionSeries, AcInteractionSeries>) - Method in class com.banda.chemistry.business.AcReplicator

cloneActionWithSpeciesActions(AcInteraction) - Method in class com.banda.chemistry.business.AcReplicator

cloneActionWithSpeciesActions(AcInteraction, Map<AcInteractionVariable, AcInteractionVariable>) - Method in class com.banda.chemistry.business.AcReplicator

cloneArtificialChemistrySpec(ArtificialChemistrySpec) - Method in class com.banda.chemistry.business.AcReplicator

cloneChannels(AcCompartment, AcCompartment, Map<AcCompartmentChannel, AcCompartmentChannel>) - Method in class com.banda.chemistry.business.AcReplicator

cloneCompartmentWithChannelsRecursively(AcCompartment, Map<AcCompartment, AcCompartment>) - Method in class com.banda.chemistry.business.AcReplicator

cloneCompartmentWithChannelsRecursively(AcCompartment, Map<AcCompartment, AcCompartment>, Map<AcCompartmentChannel, AcCompartmentChannel>) - Method in class com.banda.chemistry.business.AcReplicator

cloneCompartmentWithReactionSet(AcCompartment) - Method in class com.banda.chemistry.business.AcReplicator

cloneEvaluation(AcEvaluation) - Method in class com.banda.chemistry.business.AcReplicator

cloneFunction(Function<IN, OUT>) - Method in class com.banda.chemistry.business.AcReplicator

cloneInteractionVariableAssignment(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.business.AcReplicator

cloneMultiRunAnalysisSpec(MultiRunAnalysisSpec<T>) - Method in class com.banda.chemistry.business.AcReplicator

cloneReaction(AcReaction) - Method in class com.banda.chemistry.business.AcReplicator

cloneReactionGroup(AcReactionGroup) - Method in class com.banda.chemistry.business.AcReplicator

cloneReactionSetWithReactionsAndGroups(AcReactionSet) - Method in class com.banda.chemistry.business.AcReplicator

cloneSingleRunAnalysisSpec(SingleRunAnalysisSpec) - Method in class com.banda.chemistry.business.AcReplicator

cloneSpeciesAction(AcSpeciesInteraction) - Method in class com.banda.chemistry.business.AcReplicator

cloneSpeciesSetWithParameterSet(AcSpeciesSet) - Method in class com.banda.chemistry.business.AcReplicator

cloneSubChannelGroups(AcCompartment, AcCompartment, Map<AcCompartmentChannel, AcCompartmentChannel>) - Method in class com.banda.chemistry.business.AcReplicator

cloneTranslationItem(AcTranslationItem) - Method in class com.banda.chemistry.business.AcReplicator

cloneTranslationSeriesWithTranslations(AcTranslationSeries) - Method in class com.banda.chemistry.business.AcReplicator

cloneTranslationWithItems(AcTranslation) - Method in class com.banda.chemistry.business.AcReplicator

cloneTranslationWithItems(AcTranslation, Map<AcTranslationVariable, AcTranslationVariable>) - Method in class com.banda.chemistry.business.AcReplicator

com.banda.chemistry - package com.banda.chemistry

com.banda.chemistry.business - package com.banda.chemistry.business

com.banda.chemistry.business.factory - package com.banda.chemistry.business.factory

com.banda.chemistry.business.reactionode - package com.banda.chemistry.business.reactionode

com.banda.chemistry.domain - package com.banda.chemistry.domain

compare(AcCompartment, AcCompartment) - Method in class com.banda.chemistry.business.AcCompartmentDepthComparator

compare(AcInteractionVariableAssignment, AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment.AcInteractionVariableComparator

compare(AcItemHistory<?>, AcItemHistory<?>) - Method in class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator

compare(AcItemHistory<?>, AcItemHistory<?>) - Method in class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator2

compare(AcSpeciesInteraction, AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction.AcSpeciesInteractionVariableComparator

compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator

compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator

compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator

compare(AcTranslation, AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslation.AcTranslationFromTimeComparator

compare(T, T) - Method in class com.banda.chemistry.domain.AcVariable.AcVariableIndexComparator

compare(T, T) - Method in class com.banda.chemistry.domain.AcVariable.AcVariableLabelComparator

compareTo(AcCompartmentAssociation) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

compareTo(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

compartmentSpeciesComparator - Static variable in class com.banda.chemistry.business.ArtificialChemistryUtil

containsReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionGroup

containsVariable(M) - Method in class com.banda.chemistry.domain.AcVariableSet

convert(AcReaction) - Method in class com.banda.chemistry.business.AcMichaelisMentenToMassActionRSConverter

convert(AcReaction) - Method in interface com.banda.chemistry.business.AcReactionConverter

convert() - Method in class com.banda.chemistry.business.AcReactionSetConverter

convert(AcReaction) - Method in class com.banda.chemistry.business.AcReactionSetConverter

copyFrom(AcReactionSetConstraints) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

createCollection(Collection<AcSpecies>, AcSpeciesAssociationType) - Static method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

createComplexRS(Collection<AcSpecies>, AcReactionSetConstraints, AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createComplexRS(Collection<AcSpecies>, Collection<AcSpecies>, Collection<AcSpecies>, Collection<AcSpecies>, AcReactionSetConstraints, AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createComplexRS(Map<AcSpeciesAssociationType, Collection<AcSpecies>>, AcReactionSetConstraints, AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createDNAStrandRS(AcDNAStrandSpec, AcDNAStrandSpeciesSet) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createDNAStrandSpeciesSet(AcDNAStrandSpec) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createExpressionParameterIndexMap(Collection<AcParameter>) - Static method in class com.banda.chemistry.business.AcKineticsBO

createFixedOrder(Collection<String>) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createFixedOrder(int) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createFixedOrder(int, int, int, int) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createFoldExpression(Collection<AcSpeciesReactionAssociation>, AcCollectiveSpeciesReactionAssociationType, boolean) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

createFoldOrderedExpression(Collection<AcSpeciesReactionAssociation>, String, boolean) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

createInputOutputTemporalFunSeries(BooleanFunction.BooleanFunctionType, int, int) - Method in class com.banda.chemistry.business.factory.AcInteractionSeriesFactory

createInstance(AcEvaluation, AcTranslatedRun) - Method in class com.banda.chemistry.business.AcEvaluationBOFactory

createInstance(AcReaction, boolean) - Static method in class com.banda.chemistry.business.AcKineticsBO

createInstance(AcReaction, boolean, Collection<AcParameter>) - Static method in class com.banda.chemistry.business.AcKineticsBO

createInstance(ArtificialChemistrySpec, AcSimulationConfig) - Method in class com.banda.chemistry.business.factory.AcCompartmentFactory

createInstance(ODESolverType, double, Double, Collection<AcReaction>, int, Collection<AcParameter>, Map<Integer, Integer>) - Static method in class com.banda.chemistry.business.reactionode.AcReactionODESolverFactory

createOutputFeedbackRS(AcSpeciesSet) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createRandomFunction(RandomDistribution<Double>) - Method in class com.banda.chemistry.business.factory.AcInteractionSeriesFactory

createRandomOrder(Collection<String>) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createRandomOrder(int) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createRandomOrder(int, int, int) - Method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

createRandomReactionSymmetricRS(AcSymmetricSpec, AcSpeciesSet) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createRandomRS(int, int, int, int, int, AcSpeciesSet, AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

createRateFunction() - Method in class com.banda.chemistry.business.AcKineticsBO

createRateFunctionExpression() - Method in class com.banda.chemistry.business.AcKineticsBO

createRateFunctionExpressionWithoutConstants() - Method in class com.banda.chemistry.business.AcKineticsBO

createRateFunctionWithoutConstants() - Method in class com.banda.chemistry.business.AcKineticsBO

createSimplePeriodicFullTS(AggregateFunction, AggregateFunction, AggregateFunction, AcConcentrationLevel, AcConcentrationLevel, AcConcentrationLevel, AggregateFunction, AcInteractionSeries) - Method in class com.banda.chemistry.business.factory.AcTranslationSeriesFactory

createSimplePeriodicInputOutputFeedbackTS(AggregateFunction, AggregateFunction, AggregateFunction, AcConcentrationLevel, AcConcentrationLevel, AcConcentrationLevel, AcInteractionSeries) - Method in class com.banda.chemistry.business.factory.AcTranslationSeriesFactory

createTemporalActionASWithInit(AcSpeciesSet, BooleanFunction.BooleanFunctionType, int, RandomDistribution<Double>, RandomDistribution<Double>, AcConcentrationLevel, AcConcentrationLevel, int, int, int, boolean) - Method in class com.banda.chemistry.business.factory.AcInteractionSeriesFactory

D

DoubleFunctionEvaluatorWrapper<T extends com.banda.function.domain.FunctionHolder<Double,Double>> - Class in com.banda.chemistry.business

DoubleFunctionEvaluatorWrapper(T) - Constructor for class com.banda.chemistry.business.DoubleFunctionEvaluatorWrapper

DoubleFunctionEvaluatorWrapper(T, Map<Integer, Integer>) - Constructor for class com.banda.chemistry.business.DoubleFunctionEvaluatorWrapper

DoubleFunctionEvaluatorWrapper(T, Function<Double, Double>) - Constructor for class com.banda.chemistry.business.DoubleFunctionEvaluatorWrapper

DoubleFunctionEvaluatorWrapper(T, Function<Double, Double>, Map<Integer, Integer>) - Constructor for class com.banda.chemistry.business.DoubleFunctionEvaluatorWrapper

E

equals(Object) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

equals(Object) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

equals(Object) - Method in class com.banda.chemistry.domain.AcSpeciesAssociation

equals(Object) - Method in class com.banda.chemistry.domain.AcVariable

evaluate() - Method in class com.banda.chemistry.business.AcEvaluator

evaluateFull() - Method in class com.banda.chemistry.business.AcEvaluator

evaluateMultiple(int) - Method in class com.banda.chemistry.business.AcEvaluator

F

filterOutSpecies(Collection<AcReaction>, Collection<AcSpecies>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

filterType(Set<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Static method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

fromLabel(String) - Static method in enum com.banda.chemistry.business.factory.AcTranslationSeriesFactory.DefaultTransItemLabel

fromString(String) - Static method in enum com.banda.chemistry.business.MassActionType

FunctionEvaluatorWrapper<T extends com.banda.function.domain.FunctionHolder<IN,OUT>,IN,OUT> - Class in com.banda.chemistry.business

FunctionEvaluatorWrapper(T) - Constructor for class com.banda.chemistry.business.FunctionEvaluatorWrapper

FunctionEvaluatorWrapper(T, Map<Integer, Integer>) - Constructor for class com.banda.chemistry.business.FunctionEvaluatorWrapper

FunctionEvaluatorWrapper(T, Function<IN, OUT>) - Constructor for class com.banda.chemistry.business.FunctionEvaluatorWrapper

FunctionEvaluatorWrapper(T, Function<IN, OUT>, Map<Integer, Integer>) - Constructor for class com.banda.chemistry.business.FunctionEvaluatorWrapper

G

getAc() - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult

Deprecated.

getAcRunTrace() - Method in class com.banda.chemistry.domain.AcTranslatedRun

getAcs() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getAction() - Method in class com.banda.chemistry.domain.AcEvaluatedAction

getAction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

getAction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

getActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getActionSeries() - Method in class com.banda.chemistry.domain.AcInteraction

getAcTranslatedRun() - Method in interface com.banda.chemistry.business.AcTranslatedRunHolder

getAcUtil() - Method in class com.banda.chemistry.business.AcKineticsBO

getAllSetReactions() - Method in class com.banda.chemistry.domain.AcReactionGroup

getApplyTime() - Method in class com.banda.chemistry.domain.AcEvaluatedAction

getAveragedCorrectRates() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getBound() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

getCatalystAssocs() - Method in class com.banda.chemistry.business.AcKineticsBO

getCatalystsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getCatalystsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getCatalystsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getCatalystsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getChannels() - Method in class com.banda.chemistry.domain.AcCompartment

getChannels() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

getCollectiveCatalysisType() - Method in class com.banda.chemistry.domain.AcReaction

getCollectiveInhibitionType() - Method in class com.banda.chemistry.domain.AcReaction

getCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentChannel

getCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

getCompartment() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getCompartment() - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult

getComplementaryStrandsRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

getComplementaryStrandsRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getComplementaryStrandsRatioFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getComplementaryStrandsRatioTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getComponents() - Method in class com.banda.chemistry.domain.AcCompositeSpecies

getConstantSpeciesRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getConstantSpeciesRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getConstantSpeciesRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getConstantSpeciesRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getConvertedSpeciesIndeces() - Method in class com.banda.chemistry.business.AcSpeciesIndecesToStoreGroup

getCreatedBy() - Method in class com.banda.chemistry.domain.AcCompartment

getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluation

getCreatedBy() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

getCreatedBy() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

getCreatedBy() - Method in class com.banda.chemistry.domain.AcReactionContainer

getCreatedBy() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getCreatedBy() - Method in class com.banda.chemistry.domain.AcVariableSet

getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getCreateTime() - Method in class com.banda.chemistry.domain.AcCompartment

getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluation

getCreateTime() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionContainer

getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionGroup

getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionSet

getCreateTime() - Method in class com.banda.chemistry.domain.AcVariableSet

getCreateTime() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getCurrentSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getCurrentSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

Deprecated.

getDefaultRateConstantBoundMap() - Static method in enum com.banda.chemistry.domain.AcRateConstantType

getDefaultVariableValue() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getDirection() - Method in class com.banda.chemistry.domain.AcCompartmentChannel

getDNAStrandSpeciesSetAsString(AcDNAStrandSpeciesSet, String) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getEvalFunction() - Method in class com.banda.chemistry.domain.AcEvaluation

getEvaluatedAction() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

getEvaluatedActions() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

getEvaluatedActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedAction

getEvaluatedRun() - Method in class com.banda.chemistry.business.AcEvaluator

getEvaluatedSpeciesActions() - Method in class com.banda.chemistry.domain.AcEvaluatedAction

getEvaluatedValues() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getEvaluation() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getEvaluation() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getEvaluationFunctionAsString(AcEvaluation) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getEvolFunction() - Method in class com.banda.chemistry.domain.AcParameter

getEvolFunctionAsString(AcParameter) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getFixedAssocsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getFixedCatalystAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getFixedInhibitorAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getFixedPointDetectionPeriodicity() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getFixedPointDetectionPrecision() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getFixedProductAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getFixedReactantAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getForwardRateConstants() - Method in class com.banda.chemistry.domain.AcReaction

getForwardRateConstantsNum() - Method in class com.banda.chemistry.domain.AcReaction

getForwardRateConstantsSafe() - Method in class com.banda.chemistry.domain.AcReaction

getForwardRateFunction() - Method in class com.banda.chemistry.domain.AcReaction

getFrom() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

getFromTime() - Method in class com.banda.chemistry.domain.AcTranslation

getFullDoubleStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

getFunction() - Method in class com.banda.chemistry.domain.AcEvaluation

getFunction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

getFunction() - Method in class com.banda.chemistry.domain.AcParameter

getFunction() - Method in class com.banda.chemistry.domain.AcReaction

getFunction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getFunction() - Method in class com.banda.chemistry.domain.AcTranslationItem

getFunctionAsString(Function<?, ?>, AcReactionSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getFunctionEvaluator() - Method in class com.banda.chemistry.business.FunctionEvaluatorWrapper

getFunctionHolder() - Method in class com.banda.chemistry.business.FunctionEvaluatorWrapper

getGeneratedBySpec() - Method in class com.banda.chemistry.domain.AcCompartment

getGeneratedBySpec() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getGroup() - Method in class com.banda.chemistry.domain.AcReaction

getGroup() - Method in class com.banda.chemistry.domain.AcSpecies

getGroups() - Method in class com.banda.chemistry.domain.AcReactionSet

getGuardVariableIndeces() - Method in class com.banda.chemistry.business.AcKineticsBO

getHighValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

getHolder() - Method in class com.banda.chemistry.domain.AcItemHistory

getId() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

getId() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

getId() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getId() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getId() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getImmutableSpecies() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getIndex() - Method in class com.banda.chemistry.domain.AcReaction

getIndexVariableMap(AcVariableSetIF<M>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getInfluxRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getInfluxRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getInfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getInfluxScale() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getInhibitorAssocs() - Method in class com.banda.chemistry.business.AcKineticsBO

getInhibitorsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getInhibitorsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getInhibitorsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getInhibitorsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getInputReactions() - Method in class com.banda.chemistry.business.AcReactionSetConverter

getInputReactionSet() - Method in class com.banda.chemistry.business.AcReactionSetConverter

getInputSpeciesSet() - Method in class com.banda.chemistry.business.AcReactionSetConverter

getInstance() - Static method in class com.banda.chemistry.business.AcRateConstantUtil

getInstance() - Static method in class com.banda.chemistry.business.AcReplicator

getInstance() - Static method in class com.banda.chemistry.business.ArtificialChemistryUtil

getInstance() - Static method in class com.banda.chemistry.business.factory.AcReactionSetFactory

getInstance() - Static method in class com.banda.chemistry.business.factory.AcSpeciesSetFactory

getInstance() - Static method in class com.banda.chemistry.business.factory.AcTranslationSeriesFactory

getInternalSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getItemHistories() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

getItemLabels() - Method in class com.banda.chemistry.domain.AcTranslation

getItemLabels() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getItemsWithStoichiometry(AcVariableSetIF<M>, Double[]) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getKineticsName() - Method in class com.banda.chemistry.business.AcKineticsBO

getLabel() - Method in class com.banda.chemistry.domain.AcCompartment

getLabel() - Method in class com.banda.chemistry.domain.AcItemHistory

getLabel() - Method in class com.banda.chemistry.domain.AcReaction

getLabel() - Method in class com.banda.chemistry.domain.AcReactionContainer

getLabel() - Method in class com.banda.chemistry.domain.AcReactionGroup

getLabel() - Method in class com.banda.chemistry.domain.AcReactionSet

getLabel() - Method in class com.banda.chemistry.domain.AcTranslationItem

getLabel() - Method in class com.banda.chemistry.domain.AcTranslationItemHistory

getLabel() - Method in class com.banda.chemistry.domain.AcVariable

getLabel() - Method in class com.banda.chemistry.domain.AcVariableGroup

getLabelReactionMap(AcReactionSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getLabelVariableMap(AcVariableSetIF<M>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getLatexTable(AcReactionSet, boolean) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getLength() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getLevel() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getLowerStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

getLowerThreshold() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getLowValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

getMaxCatalystsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMaxInhibitorsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMaxProductsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMaxReactantsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMaxSpeciesAssocsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMiddleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

Works only for low/high concentration levels.

getMinCatalystsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMinInhibitorsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMinProductsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMinReactantsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMinSpeciesAssocsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

getMultiRunAnalysisResults() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getName() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

getName() - Method in class com.banda.chemistry.domain.AcEvaluation

getName() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getName() - Method in class com.banda.chemistry.domain.AcVariableSet

getName() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getName() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getName() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getNewInteractionVariables(AcInteractionSeries, AcInteractionSeries) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getNewSpecies(AcReactionSet, AcReactionSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcParameterSet

getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getNextVarSequenceNum() - Method in interface com.banda.chemistry.domain.AcVariableSetIF

getNonInputFeedbackSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getNonInternalSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getOdeSolverType() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getOperator() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

getOrder() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

getOrder() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getOrderedVariableLabelMap(AcVariableSetIF<?>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getOutfluxNonReactiveRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getOutfluxNonReactiveRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxNonReactiveRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxNonReactiveRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxNonReactiveRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxNonReactiveRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxNonReactiveRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getOutfluxRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getOutfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutfluxRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getOutputSpeciesSet() - Method in class com.banda.chemistry.business.AcReactionSetConverter

getOwnAndInheritedSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet

getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcVariableSet

getOwnAndInheritedVariables() - Method in interface com.banda.chemistry.domain.AcVariableSetIF

getOwnAndInheritedVariablesSorted() - Method in class com.banda.chemistry.domain.AcVariableSet

getParameterIndex(String) - Method in class com.banda.chemistry.business.AcKineticsBO

getParameters() - Method in class com.banda.chemistry.domain.AcCompartment

getParameters() - Method in class com.banda.chemistry.domain.AcReactionSet

getParametersCount() - Method in class com.banda.chemistry.domain.AcCompartment

getParameterSet() - Method in class com.banda.chemistry.domain.AcReaction

getParameterSet() - Method in class com.banda.chemistry.domain.AcReactionSet

getParameterSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getParent() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getParentCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

getParentCompartmentAssociations() - Method in class com.banda.chemistry.domain.AcCompartment

getParentCompartments() - Method in class com.banda.chemistry.domain.AcCompartment

getParentCompartmentSpecies() - Method in class com.banda.chemistry.domain.AcCompartment

getParentSet() - Method in class com.banda.chemistry.domain.AcVariable

getParentSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getPartialDoubleStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

getPeriodicTranslationsNumber() - Method in class com.banda.chemistry.domain.AcEvaluation

getPermeability() - Method in class com.banda.chemistry.domain.AcCompartmentChannel

getPerturbationNum() - Method in class com.banda.chemistry.domain.AcPerturbationPerformance

getPerturbationStrength() - Method in class com.banda.chemistry.domain.AcPerturbationPerformance

getPriority() - Method in class com.banda.chemistry.domain.AcReaction

getProductAssocs() - Method in class com.banda.chemistry.business.AcKineticsBO

getProductsAsString(AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getProductsNum() - Method in class com.banda.chemistry.business.AcKineticsBO

getProductsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getProductsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getProductsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getProductsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getRandomAssocsNumDistribution(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getRandomCatalystAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getRandomInhibitorAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getRandomProductAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getRandomRateGenerationNum() - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

getRandomReactantAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getRateConstant(int) - Method in class com.banda.chemistry.business.AcKineticsBO

getRateConstantBounds(AcCompartment, Map<AcRateConstantType, ValueBound<Double>>, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

getRateConstantBounds(AcReactionSet, Map<AcRateConstantType, ValueBound<Double>>, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

getRateConstantBounds(AcReaction, Map<AcRateConstantType, ValueBound<Double>>, AcReaction.ReactionDirection) - Method in class com.banda.chemistry.business.AcRateConstantUtil

getRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getRateConstants() - Method in class com.banda.chemistry.business.AcKineticsBO

getRateConstants(boolean) - Method in class com.banda.chemistry.domain.AcReaction

getRateConstantsNum() - Method in class com.banda.chemistry.business.AcKineticsBO

getRateConstantsNum(boolean) - Method in class com.banda.chemistry.domain.AcReaction

getRateConstantType() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

getRateConstantTypeBounds() - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

getRateConstantTypes() - Method in class com.banda.chemistry.business.AcKineticsBO

getRateFunction(boolean) - Method in class com.banda.chemistry.domain.AcReaction

getRateFunctionAsString(AcReaction, boolean) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReactantAssocs() - Method in class com.banda.chemistry.business.AcKineticsBO

getReactantMultiplicity() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

getReactantsAsString(AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReactantsNum() - Method in class com.banda.chemistry.business.AcKineticsBO

getReactantsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getReactantsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReactantsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReactantsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReaction() - Method in class com.banda.chemistry.business.AcKineticsBO

getReaction() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getReactionId() - Method in class com.banda.chemistry.business.AcKineticsBO

getReactionNum() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getReactionNum() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReactionNumFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReactionNumTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getReactions() - Method in class com.banda.chemistry.business.AcReactionRatePerturbationBO

getReactions() - Method in class com.banda.chemistry.domain.AcReactionContainer

getReactions() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getReactionSet() - Method in class com.banda.chemistry.domain.AcCompartment

getReactionSet() - Method in class com.banda.chemistry.domain.AcReaction

getReactionSet() - Method in class com.banda.chemistry.domain.AcReactionGroup

getReactionSet() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getReactionsNum() - Method in class com.banda.chemistry.domain.AcReactionContainer

getReactionsNum(int, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

getReactionsPerSpeciesRatio() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

getReactionsPerSpeciesRatioAssocType() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

getReactionToSpeciesConstraints() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

getReferencedSpecies(AcTranslation) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReferencedSpecies(AcTranslationSeries) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReferencedSpecies(AcReactionSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReferencedSpeciesIndeces(AcTranslationSeries) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getReferencedSpeciesIndeces() - Method in class com.banda.chemistry.domain.AcTranslation

getRepeatFromElement() - Method in class com.banda.chemistry.domain.AcInteractionSeries

Overridden for Hibernate mapping only.

getRepeatFromElement() - Method in class com.banda.chemistry.domain.AcTranslationSeries

Overridden for Hibernate mapping only.

getRepetitions() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getRepresentativeReactions(AcReactionSet, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

getRequiredRateConstantsNum() - Method in class com.banda.chemistry.business.AcKineticsBO

getReverseRateConstants() - Method in class com.banda.chemistry.domain.AcReaction

getReverseRateConstantsNum() - Method in class com.banda.chemistry.domain.AcReaction

getReverseRateConstantsSafe() - Method in class com.banda.chemistry.domain.AcReaction

getReverseRateFunction() - Method in class com.banda.chemistry.domain.AcReaction

getSequence() - Method in class com.banda.chemistry.domain.AcItemHistory

getSettingFunction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

getSettingFunction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getSettingFunctionAsString(AcSpeciesInteraction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSettingFunctionAsString(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSimulationConfig() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getSimulationConfig() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getSingleStrandsNum() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

getSingleStrandsNum() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getSingleStrandsNumFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getSingleStrandsNumTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getSingleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

getSkinCompartment() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getSortOrder() - Method in class com.banda.chemistry.domain.AcReaction

getSortOrder() - Method in class com.banda.chemistry.domain.AcVariable

getSourceSpecies() - Method in class com.banda.chemistry.domain.AcCompartmentChannel

getSpecies(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpecies() - Method in class com.banda.chemistry.domain.AcCompartment

getSpecies() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

getSpecies() - Method in class com.banda.chemistry.domain.AcInteraction

getSpecies() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getSpecies() - Method in class com.banda.chemistry.domain.AcReactionSet

getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation

getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet

getSpecies() - Method in class com.banda.chemistry.domain.AcTranslatedRun

getSpecies() - Method in class com.banda.chemistry.domain.AcTranslation

getSpecies() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getSpecies() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getSpeciesAction() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

getSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction

getSpeciesAndInteractionVariablesToRemove(AcInteractionSeries, AcInteractionSeries) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpeciesAssociation() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getSpeciesAssociations(AcSpeciesSet, Double[]) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpeciesAssociations() - Method in class com.banda.chemistry.domain.AcReaction

getSpeciesAssociations(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

getSpeciesAssociationsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

getSpeciesAsString(Collection<? extends AcSpecies>, String) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpeciesCount() - Method in class com.banda.chemistry.domain.AcCompartment

getSpeciesForbiddenRedundancy() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getSpeciesGroup(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet

getSpeciesGroupMap() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getSpeciesId() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getSpeciesId() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getSpeciesIndeces() - Method in class com.banda.chemistry.business.AcSpeciesIndecesToStoreGroup

getSpeciesIndecesNum() - Method in class com.banda.chemistry.business.AcSpeciesIndecesToStoreGroup

getSpeciesIndex() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getSpeciesLabel() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getSpeciesLabels(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpeciesLabelsWithStoichiometry(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getSpeciesNum() - Method in class com.banda.chemistry.domain.AcSymmetricSpec

getSpeciesNum() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getSpeciesNumber(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet

getSpeciesNumFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getSpeciesNumTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcCompartment

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteraction

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcParameterSet

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcReaction

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcReactionSet

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcTranslation

getSpeciesSet() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getSpeciesSet() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getSpeciesToReactionConstraints() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

getSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

Deprecated.

getStoichiometricFactor() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getStructure() - Method in class com.banda.chemistry.domain.AcSpecies

getSubActionSeries() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getSubChannelGroups() - Method in class com.banda.chemistry.domain.AcCompartment

getSubCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

getSubCompartmentAssociations() - Method in class com.banda.chemistry.domain.AcCompartment

getSubCompartments() - Method in class com.banda.chemistry.domain.AcCompartment

getTargetSpecies() - Method in class com.banda.chemistry.domain.AcCompartmentChannel

getTimeCreated() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

getTimeCreated() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getTimeCreated() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getTimeCreated() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

getTimeStep() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getTimeStep() - Method in class com.banda.chemistry.domain.ArtificialChemistry

getTimeSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

getTo() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

getTolerance() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getToTime() - Method in class com.banda.chemistry.domain.AcTranslation

getTranslatedRun() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

getTranslatedRuns() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getTranslation() - Method in class com.banda.chemistry.domain.AcTranslationItem

getTranslationFunction() - Method in class com.banda.chemistry.domain.AcTranslationItem

getTranslationFunctionAsString(AcTranslationItem) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getTranslationFunctionReferencedSpecies(AcTranslationItem) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getTranslationFunctionReferencedVariables(AcTranslationItem) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getTranslationItems() - Method in class com.banda.chemistry.domain.AcTranslation

getTranslations() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getTranslationsCount() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getTranslationSeries() - Method in class com.banda.chemistry.domain.AcEvaluation

getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslatedRun

getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslation

getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslationItem

getTranslationSeriesId() - Method in class com.banda.chemistry.domain.AcTranslatedRun

getType() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation

getType() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

getUpperStrandPartialBindingDistribution() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

getUpperStrandPartialBindingDistributionLocation() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrandPartialBindingDistributionLocationFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrandPartialBindingDistributionLocationTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrandPartialBindingDistributionShape() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrandPartialBindingDistributionShapeFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrandPartialBindingDistributionShapeTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

getUpperThreshold() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getUpperToLowerStrandRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

getUpperToLowerStrandRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperToLowerStrandRatioFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getUpperToLowerStrandRatioTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

getValue() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

getVariable() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

getVariable() - Method in class com.banda.chemistry.domain.AcTranslationItem

getVariable() - Method in class com.banda.chemistry.domain.AcTranslationItemHistory

getVariableAssignments() - Method in class com.banda.chemistry.domain.AcInteraction

getVariableIndeces(AcVariableSetIF<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariableIndeces(Collection<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariableIndex() - Method in class com.banda.chemistry.domain.AcVariable

getVariableLabels(AcVariableSetIF<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariableLabels(Collection<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariableLabelsAsString(Collection<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariableLabelsAsString(Collection<? extends AcVariable<?>>, String) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariablePlaceholder(AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

getVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getVariables() - Method in class com.banda.chemistry.domain.AcVariableGroup

getVariables() - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

getVariables() - Method in class com.banda.chemistry.domain.AcVariableSet

getVariablesNumber() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getVariablesNumber() - Method in class com.banda.chemistry.domain.AcVariableSet

getVariablesSorted() - Method in class com.banda.chemistry.domain.AcVariableSet

getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcInteractionSeries

getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet

getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcTranslationSeries

getVersion() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

getVersion() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

getVersion() - Method in class com.banda.chemistry.domain.AcSimulationConfig

getVersion() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

getVersion() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

H

hasForwardRateConstants() - Method in class com.banda.chemistry.domain.AcReaction

hasGroup() - Method in class com.banda.chemistry.domain.AcReaction

hasGroups() - Method in class com.banda.chemistry.domain.AcReactionSet

hashCode() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation

hashCode() - Method in class com.banda.chemistry.domain.AcVariable

hasItemHistories() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

hasOutfluxNonReactiveRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

hasOutfluxNonReactiveRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

hasOwnVariables() - Method in class com.banda.chemistry.domain.AcVariableSet

hasParentSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet

hasRateConstants(boolean) - Method in class com.banda.chemistry.domain.AcReaction

hasRateConstantsNum() - Method in class com.banda.chemistry.business.AcKineticsBO

hasReactionSet() - Method in class com.banda.chemistry.domain.AcReaction

hasReverseRateConstants() - Method in class com.banda.chemistry.domain.AcReaction

hasReverseRateFunction() - Method in class com.banda.chemistry.domain.AcReaction

hasSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet

hasSpeciesAssociations(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

I

IllegalStateEventHandling - Enum in com.banda.chemistry.domain

initActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries

initGroups() - Method in class com.banda.chemistry.domain.AcReactionSet

initItemHistories() - Method in class com.banda.chemistry.domain.AcTranslatedRun

initReactions() - Method in class com.banda.chemistry.domain.AcReactionContainer

initSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction

initSpeciesAssociations() - Method in class com.banda.chemistry.domain.AcReaction

initVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries

initVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries

initVariables() - Method in class com.banda.chemistry.domain.AcVariableGroup

initVariables() - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

initVariables() - Method in class com.banda.chemistry.domain.AcVariableSet

initVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet

isApplicable(double) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

isConvertible(AcReaction) - Method in class com.banda.chemistry.business.AcMichaelisMentenToMassActionRSConverter

isConvertible(AcReaction) - Method in class com.banda.chemistry.business.AcReactionSetConverter

isEnabled() - Method in class com.banda.chemistry.domain.AcReaction

isFix() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling

isIgnore() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling

isIncludeReverseReactions() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

isMirrorComplementarity() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

isOutfluxAll() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

isReactantOrProduct() - Method in enum com.banda.chemistry.domain.AcSpeciesAssociationType

isSingleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

isStop() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling

isThrowException() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling

isUseGlobalOrder() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

isUseGlobalOrder() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

isVariablesReferenced() - Method in class com.banda.chemistry.domain.AcTranslationSeries

K

KineticsType - Enum in com.banda.chemistry.domain

M

main(String[]) - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

main(String[]) - Static method in class com.banda.chemistry.domain.AcSpeciesSet

MassActionType - Enum in com.banda.chemistry.business

mergeReactionSets(AcReactionSet[]) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

N

notANumberConcentrationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

notANumberConcentrationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

nullIdAndVersion(AcReaction) - Method in class com.banda.chemistry.business.AcReplicator

nullIdAndVersion(AcTranslationSeries) - Method in class com.banda.chemistry.business.AcReplicator

nullIdAndVersionRecursively(AcReactionSet) - Method in class com.banda.chemistry.business.AcReplicator

nullIdAndVersionRecursively(AcInteractionSeries) - Method in class com.banda.chemistry.business.AcReplicator

nullIdAndVersionRecursively(AcCompartment) - Method in class com.banda.chemistry.business.AcReplicator

P

perturbate() - Method in class com.banda.chemistry.business.AcReactionRatePerturbationBO

R

refreshSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

refreshSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

Deprecated.

removeAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

removeAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeAllActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeAllReactions() - Method in class com.banda.chemistry.domain.AcReactionContainer

removeAllSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction

removeAllSubActionSeries() - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeAllVariableAssignments() - Method in class com.banda.chemistry.domain.AcInteraction

removeChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartment

removeChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

removeEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

removeEvaluatedSpeciesAction(AcEvaluatedSpeciesAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

removeFromGroup() - Method in class com.banda.chemistry.domain.AcReaction

removeFromReactionSet() - Method in class com.banda.chemistry.domain.AcReaction

removeFromSpeciesActions(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcInteraction

removeGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReactionSet

removeImmutableSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeItemHistory(I) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

removeMultiRunAnalysisResult(AcMultiRunAnalysisResult) - Method in class com.banda.chemistry.domain.ArtificialChemistry

removeParentCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment

removeReaction(AcReaction) - Method in class com.banda.chemistry.business.AcReactionSetConverter

removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionContainer

removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionGroup

removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionSet

removeSpeciesAssociation(AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcReaction

removeSpeciesAssociations(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction

removeSubActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeSubChannelGroup(AcCompartmentChannelGroup) - Method in class com.banda.chemistry.domain.AcCompartment

removeSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment

removeSubCompartmentAssociation(AcCompartmentAssociation) - Method in class com.banda.chemistry.domain.AcCompartment

removeTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcTranslationSeries

removeTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationSeries

removeTranslationItem(AcTranslationItem) - Method in class com.banda.chemistry.domain.AcTranslation

removeVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionSeries

removeVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationSeries

removeVariable(M) - Method in class com.banda.chemistry.domain.AcVariableGroup

removeVariable(M) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

removeVariable(M) - Method in class com.banda.chemistry.domain.AcVariableSet

removeVariableAssignment(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteraction

replaceIndexPlaceholdersWithVariableLabels(Function<?, ?>, AcVariableSetIF<?>, AcVariableSetIF<?>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceIndexPlaceholdersWithVariableLabels(Function<?, ?>, AcVariableSetIF<?>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceIndexPlaceholdersWithVariableLabels(Function<?, ?>, Collection<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceSpeciesAndParamaterLabelsWithIndexPlaceholders(String, AcSpeciesSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceSpeciesSet(AcReactionSet, AcSpeciesSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceSpeciesSet(AcInteractionSeries, AcSpeciesSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceVariableLabelsWithIndexPlaceholders(String, AcVariableSetIF<?>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replaceVariableLabelsWithIndexPlaceholders(String, Set<Integer>, Collection<? extends AcVariable<?>>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

replicator - Variable in class com.banda.chemistry.business.AcReactionSetConverter

S

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult

Deprecated.

setAcRunTrace(ComponentRunTrace<Double, Pair<AcCompartment, AcSpecies>>) - Method in class com.banda.chemistry.domain.AcTranslatedRun

setAcs(Collection<ArtificialChemistry>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

setActions(Set<AcInteraction>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteraction

setApplyTime(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

setAveragedCorrectRates(Double[]) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setBound(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

setCatalystsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setCatalystsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setCatalystsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setCatalystsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setChannels(Collection<AcCompartmentChannel>) - Method in class com.banda.chemistry.domain.AcCompartment

setChannels(List<AcCompartmentChannel>) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

setCollectiveCatalysisType(AcCollectiveSpeciesReactionAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

setCollectiveInhibitionType(AcCollectiveSpeciesReactionAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentChannel

setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult

setComplementaryStrandsRatio(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setComplementaryStrandsRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setComplementaryStrandsRatioFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setComplementaryStrandsRatioTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setComponents(List<AcSpecies>) - Method in class com.banda.chemistry.domain.AcCompositeSpecies

setConstantSpeciesRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setConstantSpeciesRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setConstantSpeciesRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setConstantSpeciesRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcCompartment

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluation

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcReactionContainer

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcVariableSet

setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcCompartment

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluation

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionContainer

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionGroup

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionSet

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcVariableSet

setCreateTime(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setDefaultVariableValue(Double) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setDirection(AcChannelDirection) - Method in class com.banda.chemistry.domain.AcCompartmentChannel

setEnabled(boolean) - Method in class com.banda.chemistry.domain.AcReaction

setEvalFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcEvaluation

setEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

setEvaluatedActions(Set<AcEvaluatedAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

setEvaluatedActionSeries(AcEvaluatedActionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

setEvaluatedSpeciesActions(Set<AcEvaluatedSpeciesAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

setEvaluatedValues(Double[]) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setEvaluation(AcEvaluation) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setEvaluation(AcEvaluation) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setEvaluationFunctionFromString(String, AcEvaluation) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setEvolFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcParameter

setEvolFunctionFromString(String, AcParameter) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setFixedCatalystAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setFixedInhibitorAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setFixedPointDetectionPeriodicity(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setFixedPointDetectionPrecision(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setFixedProductAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setFixedReactantAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setForwardRateConstant(Double) - Method in class com.banda.chemistry.domain.AcReaction

setForwardRateConstants(Double[]) - Method in class com.banda.chemistry.domain.AcReaction

setForwardRateFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction

setFrom(Double) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

setFromTime(Integer) - Method in class com.banda.chemistry.domain.AcTranslation

setFullDoubleStrands(Collection<AcCompositeSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcEvaluation

setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcParameter

setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction

setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

setFunction(Function<T, Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem

setGeneratedBySpec(ArtificialChemistrySpec) - Method in class com.banda.chemistry.domain.AcCompartment

setGeneratedBySpec(ArtificialChemistrySpec) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReaction

setGroup(AcSpeciesGroup) - Method in class com.banda.chemistry.domain.AcSpecies

setGroups(List<AcReactionGroup>) - Method in class com.banda.chemistry.domain.AcReactionSet

setHighValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel

setHolder(H) - Method in class com.banda.chemistry.domain.AcItemHistory

setId(Long) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

setId(Long) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

setId(Long) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setId(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setId(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setImmutableSpecies(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setIncludeReverseReactions(boolean) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setIndex(Integer) - Method in class com.banda.chemistry.domain.AcReaction

setInfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setInfluxRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setInfluxRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setInfluxScale(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setInhibitorsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setInhibitorsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setInhibitorsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setInhibitorsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setItemHistories(Collection<I>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

setLabel(String) - Method in class com.banda.chemistry.domain.AcCompartment

setLabel(String) - Method in class com.banda.chemistry.domain.AcReaction

setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionContainer

setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionGroup

setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionSet

setLabel(String) - Method in class com.banda.chemistry.domain.AcVariable

setLabel(String) - Method in class com.banda.chemistry.domain.AcVariableGroup

setLength(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setLowerStrands(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

setLowerThreshold(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setLowValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel

setMaxCatalystsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMaxInhibitorsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMaxProductsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMaxReactantsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMinCatalystsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMinInhibitorsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMinProductsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMinReactantsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

setMirrorComplementarity(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setMultiRunAnalysisResults(Collection<AcMultiRunAnalysisResult>) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setName(String) - Method in class com.banda.chemistry.domain.AcEvaluation

setName(String) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setName(String) - Method in class com.banda.chemistry.domain.AcVariableSet

setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOdeSolverType(ODESolverType) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setOrder(Integer) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

setOrder(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setOutfluxAll(boolean) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setOutfluxNonReactiveRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setOutfluxNonReactiveRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxNonReactiveRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxNonReactiveRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxNonReactiveRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxNonReactiveRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxNonReactiveRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setOutfluxRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setOutfluxRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setOutfluxRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setParameterSet(AcParameterSet) - Method in class com.banda.chemistry.domain.AcSpeciesSet

setParent(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setParentCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

setParentCompartmentAssociations(List<AcCompartmentAssociation>) - Method in class com.banda.chemistry.domain.AcCompartment

setParentSet(M) - Method in class com.banda.chemistry.domain.AcVariable

setParentSetUnsafe(AcVariableSetIF<?>) - Method in class com.banda.chemistry.domain.AcVariable

setParentSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcSpeciesSet

setPartialDoubleStrands(Collection<AcCompositeSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

setPeriodicTranslationsNumber(Integer) - Method in class com.banda.chemistry.domain.AcEvaluation

setPermeability(Double) - Method in class com.banda.chemistry.domain.AcCompartmentChannel

setPerturbationNum(Integer) - Method in class com.banda.chemistry.domain.AcPerturbationPerformance

setPerturbationStrength(Double) - Method in class com.banda.chemistry.domain.AcPerturbationPerformance

setPriority(Integer) - Method in class com.banda.chemistry.domain.AcReaction

setProductsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setProductsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setProductsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setProductsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setRandomCatalystAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setRandomInhibitorAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setRandomProductAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setRandomRateConstants(AcReactionSet, Map<AcRateConstantType, ValueBound<Double>>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRandomRateConstants(AcReaction, Map<AcRateConstantType, ValueBound<Double>>, boolean) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRandomRateConstantsIfNotSet(AcReactionSet, Map<AcRateConstantType, ValueBound<Double>>, AcReaction.ReactionDirection) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRandomRateGenerationNum(Integer) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

setRandomReactantAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setRateConstants(AcCompartment, Double[], AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstants(AcReactionSet, Double[], AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstants(Double[], boolean) - Method in class com.banda.chemistry.domain.AcReaction

setRateConstantsFromString(String, AcCompartment, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantsFromString(String, AcReactionSet, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantsFromString(String, AcReaction, AcReaction.ReactionDirection) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantType(AcRateConstantType) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

setRateConstantTypeBounds(Collection<AcRateConstantTypeBound>) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

setRateFunction(Function<Double, Double>, boolean) - Method in class com.banda.chemistry.domain.AcReaction

setRateFunctionFromString(String, AcReaction, boolean) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setReactantMultiplicity(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setReactantsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setReactantsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReactantsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReactantsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setReactionNum(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setReactionNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReactionNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReactionNumTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setReactions(List<AcReaction>) - Method in class com.banda.chemistry.domain.AcReactionContainer

setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcCompartment

setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcReaction

setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcReactionGroup

setReactionsPerSpeciesRatio(Double) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

setReactionsPerSpeciesRatioAssocType(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

setReactionToSpeciesConstraints(AcReactionToSpeciesConstraints) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

setRepeatFromElement(Integer) - Method in class com.banda.chemistry.domain.AcInteractionSeries

Overridden for Hibernate mapping only.

setRepeatFromElement(Integer) - Method in class com.banda.chemistry.domain.AcTranslationSeries

Overridden for Hibernate mapping only.

setRepetitions(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setReverseRateConstant(Double) - Method in class com.banda.chemistry.domain.AcReaction

setReverseRateConstants(Double[]) - Method in class com.banda.chemistry.domain.AcReaction

setReverseRateFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction

setSequence(List<Double>) - Method in class com.banda.chemistry.domain.AcItemHistory

setSettingFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

setSettingFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

setSettingFunctionFromString(String, AcSpeciesInteraction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setSettingFunctionFromString(String, AcInteractionVariableAssignment) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setSimulationConfig(AcSimulationConfig) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setSimulationConfig(AcSimulationConfig) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setSingleStrandsNum(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setSingleStrandsNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setSingleStrandsNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setSingleStrandsNumTo(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setSingleValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel

setSkinCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setSortOrder(Integer) - Method in class com.banda.chemistry.domain.AcReaction

setSortOrder(Integer) - Method in class com.banda.chemistry.domain.AcVariable

setSourceSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompartmentChannel

setSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

setSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setSpeciesAction(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

setSpeciesActions(Set<AcSpeciesInteraction>) - Method in class com.banda.chemistry.domain.AcInteraction

setSpeciesAssociations(Set<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction

setSpeciesAssociations(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction

setSpeciesAssociationsFromString(String, AcSpeciesAssociationType, AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setSpeciesForbiddenRedundancy(AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setSpeciesGroupMap(Map<String, AcSpeciesGroup>) - Method in class com.banda.chemistry.domain.AcSpeciesSet

setSpeciesNum(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec

setSpeciesNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setSpeciesNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setSpeciesNumTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound

setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcParameterSet

setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcReactionSet

setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setSpeciesToReactionConstraints(AcSpeciesToReactionConstraints) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

setSteps(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setSteps(Integer) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

Deprecated.

setStoichiometricFactor(Double) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setStructure(String) - Method in class com.banda.chemistry.domain.AcSpecies

setSubActionSeries(Collection<AcInteractionSeries>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setSubChannelGroups(Collection<AcCompartmentChannelGroup>) - Method in class com.banda.chemistry.domain.AcCompartment

setSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

setSubCompartmentAssociations(List<AcCompartmentAssociation>) - Method in class com.banda.chemistry.domain.AcCompartment

setTargetSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompartmentChannel

setTimeCreated(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance

setTimeCreated(Date) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setTimeCreated(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setTimeCreated(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

setTimeStep(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setTimeSteps(List<Double>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

setTo(Double) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

setTolerance(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setToTime(Integer) - Method in class com.banda.chemistry.domain.AcTranslation

setTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setTranslatedRuns(List<AcTranslatedRun>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationItem

setTranslationFunction(Function<T, Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem

setTranslationFunctionFromString(String, AcTranslationItem) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setTranslationItems(Set<AcTranslationItem>) - Method in class com.banda.chemistry.domain.AcTranslation

setTranslations(Set<AcTranslation>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcEvaluation

setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcTranslatedRun

setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcTranslation

setType(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setType(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Static method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

setUpperStrandPartialBindingDistribution(RandomDistribution<Integer>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setUpperStrandPartialBindingDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrandPartialBindingDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrandPartialBindingDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrandPartialBindingDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrandPartialBindingDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrandPartialBindingDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperStrands(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

setUpperThreshold(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setUpperToLowerStrandRatio(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setUpperToLowerStrandRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperToLowerStrandRatioFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUpperToLowerStrandRatioTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setUseGlobalOrder(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec

setUseGlobalOrder(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound

setValue(Double) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction

setVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment

setVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationItem

setVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationItemHistory

setVariableAssignments(Set<AcInteractionVariableAssignment>) - Method in class com.banda.chemistry.domain.AcInteraction

setVariableIndex(Integer) - Method in class com.banda.chemistry.domain.AcVariable

setVariables(Collection<AcInteractionVariable>) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setVariables(Collection<AcTranslationVariable>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableGroup

setVariables(Collection<M>) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF

setVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableSet

setVariablesReferenced(boolean) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcInteractionSeries

setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesSet

setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setVersion(Long) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation

setVersion(Long) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup

setVersion(Long) - Method in class com.banda.chemistry.domain.AcSimulationConfig

setVersion(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setVersion(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound

storeSpeciesHistorySelectionGroup() - Method in class com.banda.chemistry.business.ChemistryRunSetting

storeSpeciesHistorySelectionGroup(Collection<AcSpecies>) - Method in class com.banda.chemistry.business.ChemistryRunSetting

T

throwMissingAttributeException(String) - Method in class com.banda.chemistry.business.AcKineticsBO

toString() - Method in enum com.banda.chemistry.business.factory.AcTranslationSeriesFactory.DefaultTransItemLabel

toString() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

toString() - Method in class com.banda.chemistry.domain.AcCompartment

toString() - Method in class com.banda.chemistry.domain.AcConcentrationLevel

toString() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries

toString() - Method in class com.banda.chemistry.domain.AcEvaluatedRun

toString() - Method in class com.banda.chemistry.domain.AcEvaluation

toString() - Method in class com.banda.chemistry.domain.AcInteraction

toString() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder

toString() - Method in class com.banda.chemistry.domain.AcItemHistory

toString() - Method in class com.banda.chemistry.domain.AcParameter

toString() - Method in enum com.banda.chemistry.domain.AcRateConstantType

toString() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound

toString() - Method in class com.banda.chemistry.domain.AcReaction

toString() - Method in class com.banda.chemistry.domain.AcReactionContainer

toString() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints

toString() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints

toString() - Method in class com.banda.chemistry.domain.AcSpecies

toString() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction

toString() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation

toString() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

toString() - Method in class com.banda.chemistry.domain.AcTranslatedRun

toString() - Method in class com.banda.chemistry.domain.AcTranslation

toString() - Method in class com.banda.chemistry.domain.AcTranslationItem

toString() - Method in class com.banda.chemistry.domain.AcVariable

toString() - Method in class com.banda.chemistry.domain.AcVariableSet

toString() - Method in class com.banda.chemistry.domain.ArtificialChemistry

U

updateSpeciesAssociations(String, AcSpeciesAssociationType, AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

updateSpeciesAssociations(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType, AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

upperThresholdViolationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

upperThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

V

validate() - Method in class com.banda.chemistry.business.AcKineticsBO

validate(AcReaction) - Method in class com.banda.chemistry.business.AcMichaelisMentenToMassActionRSConverter

validate() - Method in class com.banda.chemistry.business.AcReactionSetConverter

validate(AcReaction) - Method in class com.banda.chemistry.business.AcReactionSetConverter

valueOf(String) - Static method in enum com.banda.chemistry.business.factory.AcTranslationSeriesFactory.DefaultTransItemLabel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.business.MassActionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcChannelDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcEvaluationItemState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcRateConstantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcReaction.ReactionDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcReactionSpeciesForbiddenRedundancy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcSpeciesAssociationType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcSpeciesType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.IllegalStateEventHandling

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.KineticsType

Returns the enum constant of this type with the specified name.

values() - Static method in enum com.banda.chemistry.business.factory.AcTranslationSeriesFactory.DefaultTransItemLabel

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.business.MassActionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcChannelDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcEvaluationItemState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcRateConstantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcReaction.ReactionDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcReactionSpeciesForbiddenRedundancy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcSpeciesAssociationType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.AcSpeciesType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.IllegalStateEventHandling

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.domain.KineticsType

Returns an array containing the constants of this enum type, in the order they are declared.

W

wrapIfNeeded(String, Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

Z

zeroThresholdViolationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

zeroThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

A B C D E F G H I K M N P R S T U V W Z