A B C E F G H I K M R S T U V

A

AcAction - Class in com.banda.chemistry.domain

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

AcActionSeries - Class in com.banda.chemistry.domain

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

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

AcCollectiveSpeciesReactionAssociationType - Enum in com.banda.chemistry.domain

AcCompartment - Class in com.banda.chemistry.domain

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

AcCompartmentChannel - Class in com.banda.chemistry.domain

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

AcCompartmentChannelDirection - Enum in com.banda.chemistry.domain

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

AcCoreEvaluateTask - Class in com.banda.chemistry.task

AcCoreEvaluateTask() - Constructor for class com.banda.chemistry.task.AcCoreEvaluateTask

AcCoreRunTask - Class in com.banda.chemistry.task

AcCoreRunTask() - Constructor for class com.banda.chemistry.task.AcCoreRunTask

AcCoreRunTask.AcRunStoreOption - Enum in com.banda.chemistry.task

AcCoreTranslateTask - Class in com.banda.chemistry.task

AcCoreTranslateTask() - Constructor for class com.banda.chemistry.task.AcCoreTranslateTask

AcCoreTranslateTask.AcTranslationStoreOption - Enum in com.banda.chemistry.task

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

AcEvaluateTask - Class in com.banda.chemistry.task

AcEvaluateTask() - Constructor for class com.banda.chemistry.task.AcEvaluateTask

AcEvaluation - Class in com.banda.chemistry.domain

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

AcEvaluationItem - Class in com.banda.chemistry.domain

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

AcEvaluationItem.AcEvaluationItemOrderComparator - Class in com.banda.chemistry.domain

AcEvaluationItem.AcEvaluationItemOrderComparator() - Constructor for class com.banda.chemistry.domain.AcEvaluationItem.AcEvaluationItemOrderComparator

AcEvaluationItemState - Enum in com.banda.chemistry.domain

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(int) - 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

AcMultiRunAnalysisResult - Class in com.banda.chemistry.domain

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

AcMultiRunAnalysisTask - Class in com.banda.chemistry.task

AcMultiRunAnalysisTask() - Constructor for class com.banda.chemistry.task.AcMultiRunAnalysisTask

AcMultiset - Class in com.banda.chemistry.domain

Deprecated.

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

Deprecated.

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

AcPerformanceEvaluateTask - Class in com.banda.chemistry.task

AcPerformanceEvaluateTask() - Constructor for class com.banda.chemistry.task.AcPerformanceEvaluateTask

AcPerturbateTask - Class in com.banda.chemistry.task

AcPerturbateTask() - Constructor for class com.banda.chemistry.task.AcPerturbateTask

AcPerturbationPerformance - Class in com.banda.chemistry.domain

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

AcPerturbationPerformanceEvaluateTask - Class in com.banda.chemistry.task

AcPerturbationPerformanceEvaluateTask() - Constructor for class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

AcRandomRatePerformance - Class in com.banda.chemistry.domain

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

AcRandomRatePerformanceEvaluateTask - Class in com.banda.chemistry.task

AcRandomRatePerformanceEvaluateTask() - Constructor for class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

AcRangeTranslation - Class in com.banda.chemistry.domain

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

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

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

AcRateConstantTypeBound - Class in com.banda.chemistry.domain

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

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

AcReactionGroup - Class in com.banda.chemistry.domain

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

AcReactionRateConstantType - Enum in com.banda.chemistry.domain

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

AcReactionSetSpec - Class in com.banda.chemistry.domain

Deprecated.

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

Deprecated.

AcReactionSpeciesForbiddenRedundancy - Enum in com.banda.chemistry.domain

AcReactionToSpeciesConstraints - Class in com.banda.chemistry.domain

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

AcRun - Class in com.banda.chemistry.domain

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

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

AcRunAndTranslateTask - Class in com.banda.chemistry.task

AcRunAndTranslateTask() - Constructor for class com.banda.chemistry.task.AcRunAndTranslateTask

AcRunEventData - Class in com.banda.chemistry.task

AcRunEventData(Collection<Collection<Double>>, Collection<AcEvaluatedAction>) - Constructor for class com.banda.chemistry.task.AcRunEventData

AcRunTask - Class in com.banda.chemistry.task

AcRunTask() - Constructor for class com.banda.chemistry.task.AcRunTask

AcRunTranslateAndEvaluateTask - Class in com.banda.chemistry.task

AcRunTranslateAndEvaluateTask() - Constructor for class com.banda.chemistry.task.AcRunTranslateAndEvaluateTask

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

AcSpeciesAction - Class in com.banda.chemistry.domain

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

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

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

AcSpeciesRunHistory - Class in com.banda.chemistry.domain

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

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

AcSpeciesRunHistory.AcSpeciesHistoryVarIndexComparator - Class in com.banda.chemistry.domain

AcSpeciesRunHistory.AcSpeciesHistoryVarIndexComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesRunHistory.AcSpeciesHistoryVarIndexComparator

AcSpeciesSet - Class in com.banda.chemistry.domain

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

AcSpeciesSetManipulationSeries - Class in com.banda.chemistry.domain

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

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

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

AcTask - Class in com.banda.chemistry.domain

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

AcTaskParts - Interface in com.banda.chemistry.task

AcTaskParts.AcActionSeriesHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcEvaluatedActionSeriesHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcEvaluationHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcMultipleActionSeriesHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcMultipleRateConstantTypeBoundHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcMultipleTranslationSeriesHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcRunsHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcTaskHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcTranslatedRunsHolder - Interface in com.banda.chemistry.task

AcTaskParts.AcTranslationSeriesHolder - Interface in com.banda.chemistry.task

AcTaskParts.MultipleAcHolder - Interface in com.banda.chemistry.task

AcTaskParts.MultiRunAnalysisSpecHolder<T> - Interface in com.banda.chemistry.task

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

AcTranslatedRunEvaluationTask - Class in com.banda.chemistry.task

AcTranslatedRunEvaluationTask() - Constructor for class com.banda.chemistry.task.AcTranslatedRunEvaluationTask

AcTranslateRunTask - Class in com.banda.chemistry.task

AcTranslateRunTask() - Constructor for class com.banda.chemistry.task.AcTranslateRunTask

AcTranslateTask - Class in com.banda.chemistry.task

AcTranslateTask() - Constructor for class com.banda.chemistry.task.AcTranslateTask

AcTranslationItem - 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

AcTranslationItemHistory(AcTranslationVariable, int) - 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

AcTranslationVariable - Class in com.banda.chemistry.domain

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

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 - Class in com.banda.chemistry.domain

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

AcVariable.AcVariableLabelComparator - 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(AcAction) - Method in class com.banda.chemistry.domain.AcActionSeries

addActions(Collection<AcAction>) - Method in class com.banda.chemistry.domain.AcActionSeries

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

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

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

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

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

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

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

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

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

addObject(OBJECT_TYPE) - Method in class com.banda.chemistry.domain.Membrane

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

addPerturbationStrength(Double) - Method in class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

addProduct(TYPE) - Method in class com.banda.chemistry.domain.EvolutionRule

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

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

addRateConstantTypeBound(AcRateConstantTypeBound) - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

addReactant(TYPE) - Method in class com.banda.chemistry.domain.EvolutionRule

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>) - Method in class com.banda.chemistry.domain.AcReactionSet

addRule(EvolutionRule<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

addRun(AcRun) - Method in class com.banda.chemistry.domain.AcActionSeries

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

addSpeciesActions(Collection<AcSpeciesAction>) - Method in class com.banda.chemistry.domain.AcAction

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

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

addSubMembrane(Membrane<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

addSubMultiset(AcMultiset) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

addToSpeciesActions(AcSpeciesAction) - Method in class com.banda.chemistry.domain.AcAction

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

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

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

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

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

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

areAcsComplete() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

areAcsComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.MultipleAcHolder

areAcsDefined() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

areAcsDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.MultipleAcHolder

areActionSeriesComplete() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

areActionSeriesComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleActionSeriesHolder

areActionSeriesDefined() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

areActionSeriesDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleActionSeriesHolder

areRateConstantTypeBoundComplete() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

areRateConstantTypeBoundComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleRateConstantTypeBoundHolder

areRateConstantTypeBoundDefined() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

areRateConstantTypeBoundDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleRateConstantTypeBoundHolder

areRunsComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcRunsHolder

areRunsComplete() - Method in class com.banda.chemistry.task.AcTranslateTask

areRunsDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcRunsHolder

areRunsDefined() - Method in class com.banda.chemistry.task.AcTranslateTask

areTranslatedRunsComplete() - Method in class com.banda.chemistry.task.AcEvaluateTask

areTranslatedRunsComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslatedRunsHolder

areTranslatedRunsDefined() - Method in class com.banda.chemistry.task.AcEvaluateTask

areTranslatedRunsDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslatedRunsHolder

areTranslationSeriesComplete() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

areTranslationSeriesComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleTranslationSeriesHolder

areTranslationSeriesDefined() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

areTranslationSeriesDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleTranslationSeriesHolder

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

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

C

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

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

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

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

compare(AcEvaluationItem, AcEvaluationItem) - Method in class com.banda.chemistry.domain.AcEvaluationItem.AcEvaluationItemOrderComparator

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

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

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

compare(AcSpeciesRunHistory, AcSpeciesRunHistory) - Method in class com.banda.chemistry.domain.AcSpeciesRunHistory.AcSpeciesHistoryVarIndexComparator

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

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

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

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

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

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

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

copyFrom(AcCoreEvaluateTask) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

copyFrom(AcCoreRunTask) - Method in class com.banda.chemistry.task.AcCoreRunTask

copyFrom(AcCoreTranslateTask) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

copyFrom(AcRunAndTranslateTask) - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

countStates(AcEvaluationItemState, Integer, Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

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

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

createInstances(AcEvaluateTask) - Static method in class com.banda.chemistry.task.AcTranslatedRunEvaluationTask

createInstances(AcTranslateTask) - Static method in class com.banda.chemistry.task.AcTranslateRunTask

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.AcSpeciesRunHistory

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

EvolutionRule<TYPE> - Class in com.banda.chemistry.domain

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

F

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

fromString(String) - Static method in enum com.banda.chemistry.task.AcCoreRunTask.AcRunStoreOption

G

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

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

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

getAc() - Method in class com.banda.chemistry.task.AcCoreRunTask

getAc() - Method in class com.banda.chemistry.task.AcEvaluateTask

getAc() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getAc() - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

getAc() - Method in interface com.banda.chemistry.task.AcTaskParts.AcHolder

getAc() - Method in class com.banda.chemistry.task.AcTranslateTask

getAcEvaluation() - Method in class com.banda.chemistry.domain.AcEvaluationItem

getAcEvaluation() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

getAcEvaluation() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getAcEvaluation() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluationHolder

getAcEvaluationId() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

getAcEvaluationId() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getAcId() - Method in class com.banda.chemistry.task.AcCoreRunTask

getAcId() - Method in class com.banda.chemistry.task.AcEvaluateTask

getAcId() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getAcId() - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

getAcId() - Method in class com.banda.chemistry.task.AcTranslateTask

getAcIds() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

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

getAcs() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

getAcs() - Method in interface com.banda.chemistry.task.AcTaskParts.MultipleAcHolder

getAcTask() - Method in class com.banda.chemistry.task.AcCoreRunTask

getAcTask() - Method in class com.banda.chemistry.task.AcEvaluateTask

getAcTask() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTaskHolder

getAcTask() - Method in class com.banda.chemistry.task.AcTranslateTask

getAcTaskId() - Method in class com.banda.chemistry.task.AcCoreRunTask

getAcTaskId() - Method in class com.banda.chemistry.task.AcEvaluateTask

getAcTaskId() - Method in class com.banda.chemistry.task.AcTranslateTask

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

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

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

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

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.AcRun

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

getActionSeries() - Method in class com.banda.chemistry.task.AcCoreRunTask

getActionSeries() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getActionSeries() - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

getActionSeries() - Method in interface com.banda.chemistry.task.AcTaskParts.AcActionSeriesHolder

getActionSeries() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleActionSeriesHolder

getActionSeries() - Method in class com.banda.chemistry.task.AcTranslateTask

getActionSeriesId() - Method in class com.banda.chemistry.task.AcCoreRunTask

getActionSeriesId() - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

getActionSeriesId() - Method in class com.banda.chemistry.task.AcTranslateTask

getActionSeriesIds() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getActionSeriesIds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleActionSeriesHolder

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

getAlphabet() - Method in class com.banda.chemistry.domain.Membrane

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

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

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

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

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

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

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

getConfiguration() - Method in class com.banda.chemistry.domain.Membrane

getConstantSpeciesNum() - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

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.AcReactionContainer

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

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

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

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

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.AcSpeciesSetManipulationSeries

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

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

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

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

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

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

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

getEvaluatedActions() - Method in class com.banda.chemistry.task.AcRunEventData

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

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

getEvaluatedActionSeries() - Method in class com.banda.chemistry.task.AcCoreRunTask

getEvaluatedActionSeries() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluatedActionSeriesHolder

getEvaluatedActionSeriesId() - Method in class com.banda.chemistry.task.AcCoreRunTask

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

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

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

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

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

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

getEvaluationStateApplicableFunction() - Method in class com.banda.chemistry.domain.AcEvaluationItem

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

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

getEvaluationSteps() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

getEventPublishPeriodicity() - Method in class com.banda.chemistry.task.AcRunTask

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

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

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.AcRangeTranslation

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

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

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.AcSpeciesAction

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

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

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.AcReactionSetSpec

Deprecated.

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

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

getInfluxNum() - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

Deprecated.

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

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

getInitialConcentrations() - Method in class com.banda.chemistry.task.AcCoreRunTask

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

getIntRunTime() - Method in class com.banda.chemistry.domain.AcRun

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

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

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

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

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.AcSpeciesRunHistory

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

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

getMultiRunAnalysisSpec() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

getMultiRunAnalysisSpec() - Method in interface com.banda.chemistry.task.AcTaskParts.MultiRunAnalysisSpecHolder

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.AcReactionSetSpec

Deprecated.

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

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

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

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

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

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

getNotANumberConcentrationHandling() - Method in class com.banda.chemistry.task.AcCoreRunTask

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

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

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

getOutfluxNum() - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

Deprecated.

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

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

Deprecated.

getOutputMembrane() - Method in class com.banda.chemistry.domain.Membrane

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

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

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.AcCompartment

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

Deprecated.

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

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

getPeriodicity() - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

getPerturbationNum() - Method in class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

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

getPerturbationStrength() - Method in class com.banda.chemistry.task.AcPerturbateTask

getPerturbationStrengths() - Method in class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

getPreviousActionSpecies() - Method in class com.banda.chemistry.domain.AcAction

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

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

getProducts() - Method in class com.banda.chemistry.domain.EvolutionRule

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

getRandomRateGenerationNum() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

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

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

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

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

Deprecated.

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

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

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

getRateConstantTypeBoundIds() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

getRateConstantTypeBoundIds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleRateConstantTypeBoundHolder

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

getRateConstantTypeBounds() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

getRateConstantTypeBounds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleRateConstantTypeBoundHolder

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

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

getReactants() - Method in class com.banda.chemistry.domain.EvolutionRule

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.domain.AcSpeciesReactionAssociation

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

getReactionRateConstantTypeBoundMap() - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

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

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

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

Overridden for Hibernate mapping only.

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

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

Overridden for Hibernate mapping only.

getRepeatFromElementSafe() - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

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

getRepetitions() - Method in class com.banda.chemistry.task.AcCoreRunTask

getRepetitions() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

getRepetitions() - Method in class com.banda.chemistry.task.AcPerturbateTask

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

getRules() - Method in class com.banda.chemistry.domain.Membrane

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

getRun() - Method in class com.banda.chemistry.task.AcTranslateRunTask

getRunAndTranslationTaskDefinition() - Method in class com.banda.chemistry.task.AcRunTranslateAndEvaluateTask

getRunIds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcRunsHolder

getRunIds() - Method in class com.banda.chemistry.task.AcTranslateTask

getRuns() - Method in class com.banda.chemistry.domain.AcActionSeries

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

getRuns() - Method in interface com.banda.chemistry.task.AcTaskParts.AcRunsHolder

getRuns() - Method in class com.banda.chemistry.task.AcTranslateTask

getRunTaskDefinition() - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

getRunTime() - Method in class com.banda.chemistry.domain.AcRun

getRunTime() - Method in class com.banda.chemistry.task.AcCoreRunTask

getRunTime() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.AcAction

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

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

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

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

Deprecated.

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.AcSpeciesAction

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

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

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

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

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

getSpeciesRunHistorySequences() - Method in class com.banda.chemistry.task.AcRunEventData

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

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

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

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

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.AcRun

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

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

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

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

getState() - Method in class com.banda.chemistry.domain.AcEvaluationItem

getStep() - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

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

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

getStochiometricList() - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

getStochiometricVector() - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

getStoreOption() - Method in class com.banda.chemistry.task.AcCoreRunTask

getStoreOption() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

getStoreSpeciesHistorySelectionGroup() - Method in class com.banda.chemistry.task.AcCoreRunTask

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

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

getSubMembranes() - Method in class com.banda.chemistry.domain.Membrane

getSubMultisets() - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

getTaskEvaluation() - Method in class com.banda.chemistry.domain.AcTask

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

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

Deprecated.

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.AcRun

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

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

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

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

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

getTranslatedRun() - Method in class com.banda.chemistry.task.AcTranslatedRunEvaluationTask

getTranslatedRunIds() - Method in class com.banda.chemistry.task.AcEvaluateTask

getTranslatedRunIds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslatedRunsHolder

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

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

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

getTranslatedRuns() - Method in class com.banda.chemistry.task.AcEvaluateTask

getTranslatedRuns() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslatedRunsHolder

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

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

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

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

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

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

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

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

getTranslationSeries() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

getTranslationSeries() - Method in class com.banda.chemistry.task.AcEvaluateTask

getTranslationSeries() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleTranslationSeriesHolder

getTranslationSeries() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslationSeriesHolder

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

getTranslationSeriesId() - Method in class com.banda.chemistry.task.AcEvaluateTask

getTranslationSeriesIds() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

getTranslationSeriesIds() - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleTranslationSeriesHolder

getTranslationSteps() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

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

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

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

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

getUpperThresholdViolationHandling() - Method in class com.banda.chemistry.task.AcCoreRunTask

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.AcTranslationItem

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

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

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.AcSpeciesSet

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

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

Deprecated.

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

getZeroThresholdViolationHandling() - Method in class com.banda.chemistry.task.AcCoreRunTask

H

hasEvaluatedActionSeries() - Method in class com.banda.chemistry.domain.AcRun

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

hasInitialConcentrations() - Method in class com.banda.chemistry.task.AcCoreRunTask

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

hasPreviousActionSpecies() - Method in class com.banda.chemistry.domain.AcAction

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

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

hasUpperThresholdViolationHandling() - Method in class com.banda.chemistry.task.AcCoreRunTask

I

IllegalStateEventHandling - Enum in com.banda.chemistry.task

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

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

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

initItemHistories(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcRun

initItemHistories(Integer) - 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.AcAction

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

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

isAcComplete() - Method in class com.banda.chemistry.task.AcCoreRunTask

isAcComplete() - Method in class com.banda.chemistry.task.AcEvaluateTask

isAcComplete() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

isAcComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcHolder

isAcComplete() - Method in class com.banda.chemistry.task.AcTranslateTask

isAcDefined() - Method in class com.banda.chemistry.task.AcCoreRunTask

isAcDefined() - Method in class com.banda.chemistry.task.AcEvaluateTask

isAcDefined() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

isAcDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcHolder

isAcDefined() - Method in class com.banda.chemistry.task.AcTranslateTask

isAcEvaluationComplete() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

isAcEvaluationComplete() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

isAcEvaluationComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluationHolder

isAcEvaluationDefined() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

isAcEvaluationDefined() - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

isAcEvaluationDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluationHolder

isAcTaskComplete() - Method in class com.banda.chemistry.task.AcCoreRunTask

isAcTaskComplete() - Method in class com.banda.chemistry.task.AcEvaluateTask

isAcTaskComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTaskHolder

isAcTaskComplete() - Method in class com.banda.chemistry.task.AcTranslateTask

isAcTaskDefined() - Method in class com.banda.chemistry.task.AcCoreRunTask

isAcTaskDefined() - Method in class com.banda.chemistry.task.AcEvaluateTask

isAcTaskDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTaskHolder

isAcTaskDefined() - Method in class com.banda.chemistry.task.AcTranslateTask

isActionSeriesComplete() - Method in class com.banda.chemistry.task.AcCoreRunTask

isActionSeriesComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcActionSeriesHolder

isActionSeriesComplete() - Method in class com.banda.chemistry.task.AcTranslateTask

isActionSeriesDefined() - Method in class com.banda.chemistry.task.AcCoreRunTask

isActionSeriesDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcActionSeriesHolder

isActionSeriesDefined() - Method in class com.banda.chemistry.task.AcTranslateTask

isApplicable(double, int) - Method in class com.banda.chemistry.domain.AcAction

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

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

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

isEvaluatedActionSeriesComplete() - Method in class com.banda.chemistry.task.AcCoreRunTask

isEvaluatedActionSeriesComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluatedActionSeriesHolder

isEvaluatedActionSeriesDefined() - Method in class com.banda.chemistry.task.AcCoreRunTask

isEvaluatedActionSeriesDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluatedActionSeriesHolder

isEvaluateFullFlag() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

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

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

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

Deprecated.

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

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

isMultiRunAnalysisSpecComplete() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

isMultiRunAnalysisSpecComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.MultiRunAnalysisSpecHolder

isMultiRunAnalysisSpecDefined() - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

isMultiRunAnalysisSpecDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.MultiRunAnalysisSpecHolder

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

isPeriodic() - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

isReactantOrProduct() - Method in enum com.banda.chemistry.domain.AcSpeciesAssociationType

isRunLocal() - Method in class com.banda.chemistry.task.AcRunTask

isSaveEvaluationFlag() - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

isSaveRunFlag() - Method in class com.banda.chemistry.task.AcCoreRunTask

isSaveTranslationFlag() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

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

isStop() - Method in enum com.banda.chemistry.task.IllegalStateEventHandling

isThrowException() - Method in enum com.banda.chemistry.task.IllegalStateEventHandling

isTranslateFullRunFlag() - Method in class com.banda.chemistry.task.AcCoreTranslateTask

isTranslationSeriesComplete() - Method in class com.banda.chemistry.task.AcEvaluateTask

isTranslationSeriesComplete() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslationSeriesHolder

isTranslationSeriesDefined() - Method in class com.banda.chemistry.task.AcEvaluateTask

isTranslationSeriesDefined() - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslationSeriesHolder

isUseAllPreviousActionMagnitudes() - Method in class com.banda.chemistry.domain.AcAction

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

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

isWithinRepetition(int) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

Membrane<OBJECT_TYPE> - Class in com.banda.chemistry.domain

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

MembraneWithAtoms - Class in com.banda.chemistry.domain

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

R

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

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

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

removeAction(AcAction) - Method in class com.banda.chemistry.domain.AcActionSeries

removeAllActions() - Method in class com.banda.chemistry.domain.AcActionSeries

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

removeAllSpeciesActions() - Method in class com.banda.chemistry.domain.AcAction

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

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

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

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

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

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

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

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

removeFromSpeciesActions(AcSpeciesAction) - Method in class com.banda.chemistry.domain.AcAction

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

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

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

removeObject(OBJECT_TYPE) - Method in class com.banda.chemistry.domain.Membrane

removeProduct(TYPE) - Method in class com.banda.chemistry.domain.EvolutionRule

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

removeReactant(TYPE) - Method in class com.banda.chemistry.domain.EvolutionRule

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

removeRule(Membrane<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

removeRule(EvolutionRule<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

removeRun(AcRun) - Method in class com.banda.chemistry.domain.AcActionSeries

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

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

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

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

removeSubMultiset(AcMultiset) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

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

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

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

RewritingMembrane - Class in com.banda.chemistry.domain

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

S

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

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

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

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.task.AcCoreRunTask

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.task.AcEvaluateTask

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

setAc(ArtificialChemistry) - Method in interface com.banda.chemistry.task.AcTaskParts.AcHolder

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.task.AcTranslateTask

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

setAcEvaluation(AcEvaluation) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

setAcEvaluation(AcEvaluation) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setAcEvaluation(AcEvaluation) - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluationHolder

setAcEvaluationId(Long) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

setAcEvaluationId(Long) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setAcId(Long) - Method in class com.banda.chemistry.task.AcCoreRunTask

setAcId(Long) - Method in class com.banda.chemistry.task.AcEvaluateTask

setAcId(Long) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setAcId(Long) - Method in class com.banda.chemistry.task.AcTranslateTask

setAcIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

setAcs(Collection<ArtificialChemistry>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec

setAcs(Collection<ArtificialChemistry>) - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

setAcs(Collection<ArtificialChemistry>) - Method in interface com.banda.chemistry.task.AcTaskParts.MultipleAcHolder

setAcTask(AcTask) - Method in class com.banda.chemistry.task.AcCoreRunTask

setAcTask(AcTask) - Method in class com.banda.chemistry.task.AcEvaluateTask

setAcTask(AcTask) - Method in interface com.banda.chemistry.task.AcTaskParts.AcTaskHolder

setAcTask(AcTask) - Method in class com.banda.chemistry.task.AcTranslateTask

setAcTaskId(Long) - Method in class com.banda.chemistry.task.AcCoreRunTask

setAcTaskId(Long) - Method in class com.banda.chemistry.task.AcEvaluateTask

setAcTaskId(Long) - Method in class com.banda.chemistry.task.AcTranslateTask

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

setAction(AcAction) - Method in class com.banda.chemistry.domain.AcSpeciesAction

setActions(Set<AcAction>) - Method in class com.banda.chemistry.domain.AcActionSeries

setActionSeries(AcActionSeries) - Method in class com.banda.chemistry.domain.AcAction

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

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

setActionSeries(AcActionSeries) - Method in class com.banda.chemistry.domain.AcRun

setActionSeries(AcActionSeries) - Method in class com.banda.chemistry.domain.AcTask

setActionSeries(AcActionSeries) - Method in class com.banda.chemistry.task.AcCoreRunTask

setActionSeries(Collection<AcActionSeries>) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setActionSeries(AcActionSeries) - Method in interface com.banda.chemistry.task.AcTaskParts.AcActionSeriesHolder

setActionSeries(Collection<AcActionSeries>) - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleActionSeriesHolder

setActionSeries(AcActionSeries) - Method in class com.banda.chemistry.task.AcTranslateTask

setActionSeriesId(Long) - Method in class com.banda.chemistry.task.AcCoreRunTask

setActionSeriesId(Long) - Method in class com.banda.chemistry.task.AcTranslateTask

setActionSeriesIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setAlphabet(String[]) - Method in class com.banda.chemistry.domain.Membrane

setApplyTime(Integer) - Method in class com.banda.chemistry.domain.AcAction

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

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

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

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

setConfiguration(MultiSet<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

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

setConstantSpeciesNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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.AcReactionContainer

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcTask

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

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

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.AcSpeciesSetManipulationSeries

setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcTask

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

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

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

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

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

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

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

setEvaluatedActionSeries(AcEvaluatedActionSeries) - Method in class com.banda.chemistry.task.AcCoreRunTask

setEvaluatedActionSeries(AcEvaluatedActionSeries) - Method in interface com.banda.chemistry.task.AcTaskParts.AcEvaluatedActionSeriesHolder

setEvaluatedActionSeriesId(Long) - Method in class com.banda.chemistry.task.AcCoreRunTask

setEvaluatedRuns(List<AcEvaluatedRun>) - Method in class com.banda.chemistry.domain.AcEvaluation

setEvaluatedRuns(List<AcEvaluatedRun>) - Method in class com.banda.chemistry.domain.AcTranslatedRun

setEvaluatedSpeciesActions(Set<AcEvaluatedSpeciesAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedAction

setEvaluateFullFlag(boolean) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

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

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

setEvaluationItems(Set<AcEvaluationItem>) - Method in class com.banda.chemistry.domain.AcEvaluation

setEvaluationStateApplicableFunction(Function<Double, Boolean>) - Method in class com.banda.chemistry.domain.AcEvaluationItem

setEvaluationStates(AcEvaluationItemState[]) - Method in class com.banda.chemistry.domain.AcEvaluatedRun

setEvaluationSteps(Integer) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

setEventPublishPeriodicity(Integer) - Method in class com.banda.chemistry.task.AcRunTask

setEvolFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcParameter

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

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

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.AcRangeTranslation

setFullDoubleStrands(Collection<AcCompositeSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet

setFunction(Function<Double, Boolean>) - Method in class com.banda.chemistry.domain.AcEvaluationItem

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.AcSpeciesAction

setFunction(Function<Double[], Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem

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.AcReactionSetSpec

Deprecated.

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

setIncludeReverseReactions(boolean) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

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

setInfluxNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

setInfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

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

setInitialConcentrations(List<Double>) - Method in class com.banda.chemistry.task.AcCoreRunTask

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

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

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

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

setMultiRunAnalysisSpec(MultiRunAnalysisSpec<Double>) - Method in class com.banda.chemistry.task.AcMultiRunAnalysisTask

setMultiRunAnalysisSpec(MultiRunAnalysisSpec<T>) - Method in interface com.banda.chemistry.task.AcTaskParts.MultiRunAnalysisSpecHolder

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

setName(String) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

setName(String) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

setName(String) - Method in class com.banda.chemistry.domain.AcTask

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

setName(String) - Method in class com.banda.chemistry.domain.Membrane

setNotANumberConcentrationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.task.AcCoreRunTask

setOrder(Integer) - Method in class com.banda.chemistry.domain.AcEvaluationItem

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

setOutfluxNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

setOutfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

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

Deprecated.

setOutputMembrane(Membrane<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

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

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

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

setParent(AcMultiset) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

setParent(Membrane<OBJECT_TYPE>) - Method in class com.banda.chemistry.domain.Membrane

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

setPeriodicity(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

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

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

setPerturbationNum(Integer) - Method in class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

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

setPerturbationStrength(Double) - Method in class com.banda.chemistry.task.AcPerturbateTask

setPerturbationStrengths(Collection<Double>) - Method in class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask

setPreviousActionSpecies(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcAction

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

setPriority(Integer) - Method in class com.banda.chemistry.domain.EvolutionRule

setProducts(MultiSet<TYPE>) - Method in class com.banda.chemistry.domain.EvolutionRule

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

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

setRandomRateGenerationNum(Integer) - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

setRandomReactantAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints

setRangeTranslations(Set<AcRangeTranslation>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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(Double[], boolean) - Method in class com.banda.chemistry.domain.AcReaction

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

setRateConstantTypeBoundIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

setRateConstantTypeBounds(Collection<AcRateConstantTypeBound>) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance

setRateConstantTypeBounds(Collection<AcRateConstantTypeBound>) - Method in class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask

setRateConstantTypeBounds(Collection<AcRateConstantTypeBound>) - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleRateConstantTypeBoundHolder

setRateFunction(Function<Double, Double>, boolean) - Method in class com.banda.chemistry.domain.AcReaction

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

setReactants(MultiSet<TYPE>) - Method in class com.banda.chemistry.domain.EvolutionRule

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.AcActionSeries

Overridden for Hibernate mapping only.

setRepeatFromElement(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

setRepetitions(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

setRepetitions(Integer) - Method in class com.banda.chemistry.task.AcCoreRunTask

setRepetitions(Integer) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setRepetitions(Integer) - Method in class com.banda.chemistry.task.AcPerturbateTask

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

setRules(Set<EvolutionRule<OBJECT_TYPE>>) - Method in class com.banda.chemistry.domain.Membrane

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

setRun(AcRun) - Method in class com.banda.chemistry.task.AcTranslateRunTask

setRun(AcRun) - Method in class com.banda.chemistry.task.AcTranslateTask

setRunAndTranslationTaskDefinition(AcRunAndTranslateTask) - Method in class com.banda.chemistry.task.AcRunTranslateAndEvaluateTask

setRunId(Long) - Method in class com.banda.chemistry.task.AcTranslateTask

setRunIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcTranslateTask

setRunIdsAsStrings(Collection<String>) - Method in class com.banda.chemistry.task.AcTranslateTask

setRunLocal(boolean) - Method in class com.banda.chemistry.task.AcRunTask

setRuns(List<AcRun>) - Method in class com.banda.chemistry.domain.AcActionSeries

setRuns(List<AcRun>) - Method in class com.banda.chemistry.domain.ArtificialChemistry

setRuns(Collection<AcRun>) - Method in interface com.banda.chemistry.task.AcTaskParts.AcRunsHolder

setRuns(Collection<AcRun>) - Method in class com.banda.chemistry.task.AcTranslateTask

setRunTaskDefinition(AcCoreRunTask) - Method in class com.banda.chemistry.task.AcRunAndTranslateTask

setRunTime(Double) - Method in class com.banda.chemistry.domain.AcRun

setRunTime(Integer) - Method in class com.banda.chemistry.task.AcCoreRunTask

setRunTime(Integer) - Method in class com.banda.chemistry.task.AcPerformanceEvaluateTask

setSaveEvaluationFlag(boolean) - Method in class com.banda.chemistry.task.AcCoreEvaluateTask

setSaveRunFlag(boolean) - Method in class com.banda.chemistry.task.AcCoreRunTask

setSaveTranslationFlag(boolean) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setSequence(Double[]) - Method in class com.banda.chemistry.domain.AcItemHistory

setSequenceElementAt(int, Double) - Method in class com.banda.chemistry.domain.AcItemHistory

setSettingFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcSpeciesAction

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

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

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

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

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

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

setSpeciesActions(Set<AcSpeciesAction>) - Method in class com.banda.chemistry.domain.AcAction

setSpeciesAssociations(Set<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction

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

setSpeciesForbiddenRedundancy(AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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.AcParameterSet

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

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

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

setState(AcEvaluationItemState) - Method in class com.banda.chemistry.domain.AcEvaluationItem

setStep(Integer) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

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

setSteps(Integer) - Method in class com.banda.chemistry.domain.AcTask

setStochiometricList(List<Double>) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

setStochiometricVector(double[]) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

setStoreOption(AcCoreRunTask.AcRunStoreOption) - Method in class com.banda.chemistry.task.AcCoreRunTask

setStoreOption(AcCoreTranslateTask.AcTranslationStoreOption) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setStoreSpeciesHistorySelectionGroup(Collection<AcSpecies>) - Method in class com.banda.chemistry.task.AcCoreRunTask

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

setSubCompartments(Collection<AcCompartment>) - Method in class com.banda.chemistry.domain.AcCompartment

setSubMembranes(List<Membrane<OBJECT_TYPE>>) - Method in class com.banda.chemistry.domain.Membrane

setSubMultisets(Collection<AcMultiset>) - Method in class com.banda.chemistry.domain.AcMultiset

Deprecated.

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

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

setTimeCreated(Date) - Method in class com.banda.chemistry.domain.AcReactionSetSpec

Deprecated.

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

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

setToTime(Integer) - Method in class com.banda.chemistry.domain.AcRangeTranslation

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

setTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.task.AcTranslatedRunEvaluationTask

setTranslatedRunId(Long) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslatedRunIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslatedRunIdsAsStrings(Collection<String>) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslatedRuns(List<AcTranslatedRun>) - Method in class com.banda.chemistry.domain.AcRun

setTranslatedRuns(List<AcTranslatedRun>) - Method in class com.banda.chemistry.domain.AcTranslationSeries

setTranslatedRuns(Collection<AcTranslatedRun>) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslatedRuns(Collection<AcTranslatedRun>) - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslatedRunsHolder

setTranslateFullRunFlag(boolean) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

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

setTranslationFunction(Function<Double[], Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem

setTranslationItems(Set<AcTranslationItem>) - Method in class com.banda.chemistry.domain.AcRangeTranslation

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

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

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

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

setTranslationSeries(Collection<AcTranslationSeries>) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslationSeries(Collection<AcTranslationSeries>) - Method in interface com.banda.chemistry.task.AcTaskParts.AcMultipleTranslationSeriesHolder

setTranslationSeries(AcTranslationSeries) - Method in interface com.banda.chemistry.task.AcTaskParts.AcTranslationSeriesHolder

setTranslationSeriesId(Long) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setTranslationSeriesId(Long) - Method in class com.banda.chemistry.task.AcEvaluateTask

setTranslationSeriesIds(Collection<Long>) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setTranslationSeriesIdsAsStrings(Collection<String>) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

setTranslationSteps(Integer) - Method in class com.banda.chemistry.task.AcCoreTranslateTask

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

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

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

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

setUpperThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.task.AcCoreRunTask

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

setUseAllPreviousActionMagnitudes(boolean) - Method in class com.banda.chemistry.domain.AcAction

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

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

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

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

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.AcReactionSetSpec

Deprecated.

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

setZeroThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.task.AcCoreRunTask

shouldStoreEvaluatedActions() - Method in enum com.banda.chemistry.task.AcCoreRunTask.AcRunStoreOption

shouldStoreSpeciesHistories() - Method in enum com.banda.chemistry.task.AcCoreRunTask.AcRunStoreOption

T

toString() - Method in class com.banda.chemistry.domain.AcAction

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.AcEvaluationItem

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.AcMultiset

Deprecated.

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

toString() - Method in class com.banda.chemistry.domain.AcRangeTranslation

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 enum com.banda.chemistry.domain.AcReactionRateConstantType

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.AcSpeciesAction

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

toString() - Method in class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries

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

toString() - Method in class com.banda.chemistry.domain.AcTask

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

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

UpdateAlgorithmType - Enum in com.banda.chemistry.domain

V

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.AcCompartmentChannelDirection

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.AcReaction.ReactionDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcReactionRateConstantType

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.KineticsType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.domain.UpdateAlgorithmType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.task.AcCoreRunTask.AcRunStoreOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.task.AcCoreTranslateTask.AcTranslationStoreOption

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum com.banda.chemistry.task.IllegalStateEventHandling

Returns the enum constant of this type with the specified name.

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.AcCompartmentChannelDirection

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.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.AcReactionRateConstantType

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.KineticsType

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.UpdateAlgorithmType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.task.AcCoreRunTask.AcRunStoreOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.task.AcCoreTranslateTask.AcTranslationStoreOption

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum com.banda.chemistry.task.IllegalStateEventHandling

Returns an array containing the constants of this enum type, in the order they are declared.

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