A B C E F G H I K M R S T V 

A

AcChannelDirection - Enum in com.banda.chemistry.domain
 
AcCollectiveSpeciesReactionAssociationType - Enum in com.banda.chemistry.domain
 
AcCompartment - Class in com.banda.chemistry.domain
 
AcCompartment() - Constructor for class com.banda.chemistry.domain.AcCompartment
 
AcCompartmentAssociation - Class in com.banda.chemistry.domain
 
AcCompartmentAssociation() - Constructor for class com.banda.chemistry.domain.AcCompartmentAssociation
 
AcCompartmentChannel - Class in com.banda.chemistry.domain
 
AcCompartmentChannel() - Constructor for class com.banda.chemistry.domain.AcCompartmentChannel
 
AcCompartmentChannelGroup - Class in com.banda.chemistry.domain
 
AcCompartmentChannelGroup() - Constructor for class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
AcCompositeSpecies - Class in com.banda.chemistry.domain
 
AcCompositeSpecies() - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies
 
AcCompositeSpecies(Long) - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies
 
AcCompositeSpecies(String) - Constructor for class com.banda.chemistry.domain.AcCompositeSpecies
 
AcConcentrationLevel - Class in com.banda.chemistry.domain
 
AcConcentrationLevel(Double) - Constructor for class com.banda.chemistry.domain.AcConcentrationLevel
 
AcConcentrationLevel(Double, Double) - Constructor for class com.banda.chemistry.domain.AcConcentrationLevel
 
AcDNAStrandSpec - Class in com.banda.chemistry.domain
 
AcDNAStrandSpec() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpec
 
AcDNAStrandSpecBound - Class in com.banda.chemistry.domain
 
AcDNAStrandSpecBound() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
AcDNAStrandSpeciesSet - Class in com.banda.chemistry.domain
 
AcDNAStrandSpeciesSet() - Constructor for class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
AcEvaluatedAction - Class in com.banda.chemistry.domain
 
AcEvaluatedAction() - Constructor for class com.banda.chemistry.domain.AcEvaluatedAction
 
AcEvaluatedActionSeries - Class in com.banda.chemistry.domain
 
AcEvaluatedActionSeries() - Constructor for class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
AcEvaluatedPerformance - Class in com.banda.chemistry.domain
 
AcEvaluatedPerformance() - Constructor for class com.banda.chemistry.domain.AcEvaluatedPerformance
 
AcEvaluatedRun - Class in com.banda.chemistry.domain
 
AcEvaluatedRun() - Constructor for class com.banda.chemistry.domain.AcEvaluatedRun
 
AcEvaluatedSpeciesAction - Class in com.banda.chemistry.domain
 
AcEvaluatedSpeciesAction() - Constructor for class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
AcEvaluation - Class in com.banda.chemistry.domain
 
AcEvaluation() - Constructor for class com.banda.chemistry.domain.AcEvaluation
 
AcEvaluationItemState - Enum in com.banda.chemistry.domain
 
AcInteraction - Class in com.banda.chemistry.domain
 
AcInteraction() - Constructor for class com.banda.chemistry.domain.AcInteraction
 
AcInteractionSeries - Class in com.banda.chemistry.domain
 
AcInteractionSeries() - Constructor for class com.banda.chemistry.domain.AcInteractionSeries
 
AcInteractionSeries(Long) - Constructor for class com.banda.chemistry.domain.AcInteractionSeries
 
AcInteractionVariable - Class in com.banda.chemistry.domain
 
AcInteractionVariable(String) - Constructor for class com.banda.chemistry.domain.AcInteractionVariable
 
AcInteractionVariable() - Constructor for class com.banda.chemistry.domain.AcInteractionVariable
 
AcInteractionVariableAssignment - Class in com.banda.chemistry.domain
 
AcInteractionVariableAssignment() - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
AcInteractionVariableAssignment(AcInteractionVariable) - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
AcInteractionVariableAssignment.AcInteractionVariableComparator - Class in com.banda.chemistry.domain
 
AcInteractionVariableAssignment.AcInteractionVariableComparator() - Constructor for class com.banda.chemistry.domain.AcInteractionVariableAssignment.AcInteractionVariableComparator
 
AcItemHistoriesHolder<I extends AcItemHistory> - Class in com.banda.chemistry.domain
 
AcItemHistoriesHolder() - Constructor for class com.banda.chemistry.domain.AcItemHistoriesHolder
 
AcItemHistoriesHolder(Long) - Constructor for class com.banda.chemistry.domain.AcItemHistoriesHolder
 
AcItemHistory<H extends AcItemHistoriesHolder> - Class in com.banda.chemistry.domain
 
AcItemHistory() - Constructor for class com.banda.chemistry.domain.AcItemHistory
 
AcItemHistory.AcItemHistoryLabelComparator - Class in com.banda.chemistry.domain
 
AcItemHistory.AcItemHistoryLabelComparator() - Constructor for class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator
 
AcItemHistory.AcItemHistoryLabelComparator2 - Class in com.banda.chemistry.domain
 
AcItemHistory.AcItemHistoryLabelComparator2() - Constructor for class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator2
 
AcMultiRunAnalysisResult - Class in com.banda.chemistry.domain
 
AcMultiRunAnalysisResult() - Constructor for class com.banda.chemistry.domain.AcMultiRunAnalysisResult
 
AcParameter - Class in com.banda.chemistry.domain
 
AcParameter() - Constructor for class com.banda.chemistry.domain.AcParameter
 
AcParameterSet - Class in com.banda.chemistry.domain
 
AcParameterSet() - Constructor for class com.banda.chemistry.domain.AcParameterSet
 
AcPerturbationPerformance - Class in com.banda.chemistry.domain
 
AcPerturbationPerformance() - Constructor for class com.banda.chemistry.domain.AcPerturbationPerformance
 
AcRandomRatePerformance - Class in com.banda.chemistry.domain
 
AcRandomRatePerformance() - Constructor for class com.banda.chemistry.domain.AcRandomRatePerformance
 
AcRateConstantType - Enum in com.banda.chemistry.domain
 
AcRateConstantTypeBound - Class in com.banda.chemistry.domain
 
AcRateConstantTypeBound() - Constructor for class com.banda.chemistry.domain.AcRateConstantTypeBound
 
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
 
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
 
AcReactionSpeciesForbiddenRedundancy - Enum in com.banda.chemistry.domain
 
AcReactionToSpeciesConstraints - Class in com.banda.chemistry.domain
 
AcReactionToSpeciesConstraints() - Constructor for class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
AcSimulationConfig - Class in com.banda.chemistry.domain
 
AcSimulationConfig() - Constructor for class com.banda.chemistry.domain.AcSimulationConfig
 
AcSpecies - Class in com.banda.chemistry.domain
 
AcSpecies() - Constructor for class com.banda.chemistry.domain.AcSpecies
 
AcSpecies(Long) - Constructor for class com.banda.chemistry.domain.AcSpecies
 
AcSpecies(String) - Constructor for class com.banda.chemistry.domain.AcSpecies
 
AcSpeciesAssociation - Class in com.banda.chemistry.domain
 
AcSpeciesAssociation(AcSpecies, AcSpeciesAssociationType) - Constructor for class com.banda.chemistry.domain.AcSpeciesAssociation
 
AcSpeciesAssociationType - Enum in com.banda.chemistry.domain
 
AcSpeciesGroup - Class in com.banda.chemistry.domain
 
AcSpeciesGroup(Collection<AcSpecies>) - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup
 
AcSpeciesGroup() - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup
 
AcSpeciesGroup(String) - Constructor for class com.banda.chemistry.domain.AcSpeciesGroup
 
AcSpeciesInteraction - Class in com.banda.chemistry.domain
 
AcSpeciesInteraction() - Constructor for class com.banda.chemistry.domain.AcSpeciesInteraction
 
AcSpeciesInteraction.AcSpeciesInteractionVariableComparator - Class in com.banda.chemistry.domain
 
AcSpeciesInteraction.AcSpeciesInteractionVariableComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesInteraction.AcSpeciesInteractionVariableComparator
 
AcSpeciesReactionAssociation - Class in com.banda.chemistry.domain
 
AcSpeciesReactionAssociation() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
AcSpeciesReactionAssociation(AcSpecies, AcSpeciesAssociationType) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
AcSpeciesReactionAssociation(AcSpecies, Double) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
AcSpeciesReactionAssociation(AcSpecies, AcSpeciesAssociationType, Double) - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator - Class in com.banda.chemistry.domain
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator - Class in com.banda.chemistry.domain
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator - Class in com.banda.chemistry.domain
 
AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator() - Constructor for class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator
 
AcSpeciesSet - Class in com.banda.chemistry.domain
 
AcSpeciesSet() - Constructor for class com.banda.chemistry.domain.AcSpeciesSet
 
AcSpeciesToReactionConstraints - Class in com.banda.chemistry.domain
 
AcSpeciesToReactionConstraints() - Constructor for class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
AcSpeciesType - Enum in com.banda.chemistry.domain
 
AcSymmetricSpec - Class in com.banda.chemistry.domain
 
AcSymmetricSpec() - Constructor for class com.banda.chemistry.domain.AcSymmetricSpec
 
AcSymmetricSpecBound - Class in com.banda.chemistry.domain
 
AcSymmetricSpecBound() - Constructor for class com.banda.chemistry.domain.AcSymmetricSpecBound
 
AcTranslatedRun - Class in com.banda.chemistry.domain
 
AcTranslatedRun() - Constructor for class com.banda.chemistry.domain.AcTranslatedRun
 
AcTranslatedRun(Long) - Constructor for class com.banda.chemistry.domain.AcTranslatedRun
 
AcTranslation - Class in com.banda.chemistry.domain
 
AcTranslation() - Constructor for class com.banda.chemistry.domain.AcTranslation
 
AcTranslation.AcTranslationFromTimeComparator - Class in com.banda.chemistry.domain
 
AcTranslation.AcTranslationFromTimeComparator() - Constructor for class com.banda.chemistry.domain.AcTranslation.AcTranslationFromTimeComparator
 
AcTranslationItem<T> - Class in com.banda.chemistry.domain
 
AcTranslationItem() - Constructor for class com.banda.chemistry.domain.AcTranslationItem
 
AcTranslationItemHistory - Class in com.banda.chemistry.domain
 
AcTranslationItemHistory() - Constructor for class com.banda.chemistry.domain.AcTranslationItemHistory
 
AcTranslationItemHistory(AcTranslationVariable) - Constructor for class com.banda.chemistry.domain.AcTranslationItemHistory
 
AcTranslationSeries - Class in com.banda.chemistry.domain
 
AcTranslationSeries() - Constructor for class com.banda.chemistry.domain.AcTranslationSeries
 
AcTranslationSeries(Long) - Constructor for class com.banda.chemistry.domain.AcTranslationSeries
 
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<T extends AcVariable<?>> - Class in com.banda.chemistry.domain
 
AcVariable.AcVariableIndexComparator() - Constructor for class com.banda.chemistry.domain.AcVariable.AcVariableIndexComparator
 
AcVariable.AcVariableLabelComparator<T extends AcVariable<?>> - Class in com.banda.chemistry.domain
 
AcVariable.AcVariableLabelComparator() - Constructor for class com.banda.chemistry.domain.AcVariable.AcVariableLabelComparator
 
AcVariableGroup<M extends AcVariable<?>> - Class in com.banda.chemistry.domain
 
AcVariableGroup(Collection<M>) - Constructor for class com.banda.chemistry.domain.AcVariableGroup
 
AcVariableGroup() - Constructor for class com.banda.chemistry.domain.AcVariableGroup
 
AcVariableGroupIF<M extends AcVariable<?>> - Interface in com.banda.chemistry.domain
 
AcVariableSet<M extends AcVariable<? extends AcVariableSet>> - Class in com.banda.chemistry.domain
 
AcVariableSet() - Constructor for class com.banda.chemistry.domain.AcVariableSet
 
AcVariableSetIF<M extends AcVariable<? extends AcVariableSetIF>> - Interface in com.banda.chemistry.domain
 
addAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
addAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addActions(Collection<AcInteraction>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addAssociationForSpecies(AcSpecies, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
addAssociationsForSpecies(Collection<AcSpecies>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
addChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartment
 
addChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
addComponent(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompositeSpecies
 
addEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
addEvaluatedActions(Collection<AcEvaluatedAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
addEvaluatedSpeciesAction(AcEvaluatedSpeciesAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
addFullDoubleStrand(AcCompositeSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
addGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReactionSet
 
addImmutableSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addItemHistories(Collection<I>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
addItemHistory(I) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
addLowerStrand(AcSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
addMultiRunAnalysisResult(AcMultiRunAnalysisResult) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
addPartialDoubleStrand(AcCompositeSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
addRateConstantTypeBound(AcRateConstantTypeBound) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance
 
addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionGroup
 
addReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionSet
 
addReactions(Collection<AcReaction>) - Method in class com.banda.chemistry.domain.AcReactionSet
 
addSpeciesActions(Collection<AcSpeciesInteraction>) - Method in class com.banda.chemistry.domain.AcInteraction
 
addSpeciesAssociation(AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcReaction
 
addSpeciesAssociation(AcSpeciesReactionAssociation, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
addSpeciesAssociations(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction
 
addSpeciesAssociations(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
addSpeciesToGroup(AcSpeciesType, AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
addSubActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addSubChannelGroup(AcCompartmentChannelGroup) - Method in class com.banda.chemistry.domain.AcCompartment
 
addSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment
 
addToSpeciesActions(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcInteraction
 
addTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
addTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
addTranslationItem(AcTranslationItem) - Method in class com.banda.chemistry.domain.AcTranslation
 
addUpperStrand(AcSpecies) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
addVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addVariable(String) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addVariable(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesGroup
 
addVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
addVariable(M) - Method in class com.banda.chemistry.domain.AcVariableGroup
 
addVariable(M) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
addVariable(M) - Method in class com.banda.chemistry.domain.AcVariableSet
 
addVariableAssignment(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteraction
 
addVariableAssignments(Collection<AcInteractionVariableAssignment>) - Method in class com.banda.chemistry.domain.AcInteraction
 
addVariables(Collection<AcInteractionVariable>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
addVariables(Collection<AcTranslationVariable>) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
addVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableGroup
 
addVariables(Collection<M>) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
addVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableSet
 
ArtificialChemistry - Class in com.banda.chemistry.domain
 
ArtificialChemistry() - Constructor for class com.banda.chemistry.domain.ArtificialChemistry
 
ArtificialChemistrySpec - Class in com.banda.chemistry.domain
 
ArtificialChemistrySpec() - Constructor for class com.banda.chemistry.domain.ArtificialChemistrySpec
 
ArtificialChemistrySpecBound - Class in com.banda.chemistry.domain
 
ArtificialChemistrySpecBound() - Constructor for class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 

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
 
compare(AcInteractionVariableAssignment, AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment.AcInteractionVariableComparator
 
compare(AcItemHistory<?>, AcItemHistory<?>) - Method in class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator
 
compare(AcItemHistory<?>, AcItemHistory<?>) - Method in class com.banda.chemistry.domain.AcItemHistory.AcItemHistoryLabelComparator2
 
compare(AcSpeciesInteraction, AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction.AcSpeciesInteractionVariableComparator
 
compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationIndexComparator
 
compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationLabelComparator
 
compare(AcSpeciesReactionAssociation, AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation.AcSpeciesReactionAssociationOrderComparator
 
compare(AcTranslation, AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslation.AcTranslationFromTimeComparator
 
compare(T, T) - Method in class com.banda.chemistry.domain.AcVariable.AcVariableIndexComparator
 
compare(T, T) - Method in class com.banda.chemistry.domain.AcVariable.AcVariableLabelComparator
 
compareTo(AcCompartmentAssociation) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
compareTo(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
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
 
createCollection(Collection<AcSpecies>, AcSpeciesAssociationType) - Static method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 

E

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

F

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

G

getAc() - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult
Deprecated.
getAcRunTrace() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
getAcs() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getAction() - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
getAction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
getAction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
getActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getActionSeries() - Method in class com.banda.chemistry.domain.AcInteraction
 
getAllSetReactions() - Method in class com.banda.chemistry.domain.AcReactionGroup
 
getApplyTime() - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
getAveragedCorrectRates() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getBound() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
getCatalystsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
getCatalystsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getCatalystsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getCatalystsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getChannels() - Method in class com.banda.chemistry.domain.AcCompartment
 
getChannels() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
getCollectiveCatalysisType() - Method in class com.banda.chemistry.domain.AcReaction
 
getCollectiveInhibitionType() - Method in class com.banda.chemistry.domain.AcReaction
 
getCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
getCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
getCompartment() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getCompartment() - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult
 
getComplementaryStrandsRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
getComplementaryStrandsRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getComplementaryStrandsRatioFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getComplementaryStrandsRatioTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getComponents() - Method in class com.banda.chemistry.domain.AcCompositeSpecies
 
getConstantSpeciesRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getConstantSpeciesRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getConstantSpeciesRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getConstantSpeciesRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcCompartment
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getCreatedBy() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getCreatedBy() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcCompartment
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionGroup
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getCreateTime() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getCreateTime() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getCurrentSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getCurrentSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
Deprecated.
getDefaultRateConstantBoundMap() - Static method in enum com.banda.chemistry.domain.AcRateConstantType
 
getDefaultVariableValue() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getDirection() - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
getEvalFunction() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getEvaluatedAction() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
getEvaluatedActions() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
getEvaluatedActionSeries() - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
getEvaluatedSpeciesActions() - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
getEvaluatedValues() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getEvaluation() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getEvaluation() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
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
 
getFixedPointDetectionPeriodicity() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getFixedPointDetectionPrecision() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getFixedProductAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getFixedReactantAssocsNum() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getForwardRateConstants() - Method in class com.banda.chemistry.domain.AcReaction
 
getForwardRateConstantsNum() - Method in class com.banda.chemistry.domain.AcReaction
 
getForwardRateConstantsSafe() - Method in class com.banda.chemistry.domain.AcReaction
 
getForwardRateFunction() - Method in class com.banda.chemistry.domain.AcReaction
 
getFrom() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
getFromTime() - Method in class com.banda.chemistry.domain.AcTranslation
 
getFullDoubleStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
getFunction() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getFunction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
getFunction() - Method in class com.banda.chemistry.domain.AcParameter
 
getFunction() - Method in class com.banda.chemistry.domain.AcReaction
 
getFunction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getFunction() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getGeneratedBySpec() - Method in class com.banda.chemistry.domain.AcCompartment
 
getGeneratedBySpec() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getGroup() - Method in class com.banda.chemistry.domain.AcReaction
 
getGroup() - Method in class com.banda.chemistry.domain.AcSpecies
 
getGroups() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getHighValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
getHolder() - Method in class com.banda.chemistry.domain.AcItemHistory
 
getId() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
getId() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
getId() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getId() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getId() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getImmutableSpecies() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getIndex() - Method in class com.banda.chemistry.domain.AcReaction
 
getInfluxRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getInfluxRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getInfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getInfluxScale() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
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
 
getInternalSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getItemHistories() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
getItemLabels() - Method in class com.banda.chemistry.domain.AcTranslation
 
getItemLabels() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getLabel() - Method in class com.banda.chemistry.domain.AcCompartment
 
getLabel() - Method in class com.banda.chemistry.domain.AcItemHistory
 
getLabel() - Method in class com.banda.chemistry.domain.AcReaction
 
getLabel() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
getLabel() - Method in class com.banda.chemistry.domain.AcReactionGroup
 
getLabel() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getLabel() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getLabel() - Method in class com.banda.chemistry.domain.AcTranslationItemHistory
 
getLabel() - Method in class com.banda.chemistry.domain.AcVariable
 
getLabel() - Method in class com.banda.chemistry.domain.AcVariableGroup
 
getLength() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getLevel() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getLowerStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
getLowerThreshold() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getLowValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
getMaxCatalystsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMaxInhibitorsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMaxProductsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMaxReactantsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMaxSpeciesAssocsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMiddleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
Works only for low/high concentration levels.
getMinCatalystsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMinInhibitorsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMinProductsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMinReactantsNum() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMinSpeciesAssocsNum(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
getMultiRunAnalysisResults() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getName() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
 
getName() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getName() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getName() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getName() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getName() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getName() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcParameterSet
 
getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getNextVarSequenceNum() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getNextVarSequenceNum() - Method in interface com.banda.chemistry.domain.AcVariableSetIF
 
getNonInputFeedbackSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getNonInternalSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getOdeSolverType() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getOperator() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
 
getOrder() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
getOrder() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
getOutfluxNonReactiveRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getOutfluxNonReactiveRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxNonReactiveRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxNonReactiveRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxNonReactiveRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxNonReactiveRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxNonReactiveRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getOutfluxRateConstantDistributionLocation() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistributionLocationFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistributionLocationTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistributionShapeFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRateConstantDistributionShapeTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getOutfluxRatio() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRatioFrom() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOutfluxRatioTo() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getOwnAndInheritedSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getOwnAndInheritedVariables() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getOwnAndInheritedVariables() - Method in interface com.banda.chemistry.domain.AcVariableSetIF
 
getOwnAndInheritedVariablesSorted() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getParameters() - Method in class com.banda.chemistry.domain.AcCompartment
 
getParameters() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getParametersCount() - Method in class com.banda.chemistry.domain.AcCompartment
 
getParameterSet() - Method in class com.banda.chemistry.domain.AcReaction
 
getParameterSet() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getParameterSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getParent() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getParentCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
getParentCompartmentAssociations() - Method in class com.banda.chemistry.domain.AcCompartment
 
getParentCompartments() - Method in class com.banda.chemistry.domain.AcCompartment
 
getParentCompartmentSpecies() - Method in class com.banda.chemistry.domain.AcCompartment
 
getParentSet() - Method in class com.banda.chemistry.domain.AcVariable
 
getParentSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getPartialDoubleStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
getPeriodicTranslationsNumber() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getPermeability() - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
getPerturbationNum() - Method in class com.banda.chemistry.domain.AcPerturbationPerformance
 
getPerturbationStrength() - Method in class com.banda.chemistry.domain.AcPerturbationPerformance
 
getPriority() - Method in class com.banda.chemistry.domain.AcReaction
 
getProductsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
getProductsPerReactionNumber() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getProductsPerReactionNumberFrom() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getProductsPerReactionNumberTo() - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
getRandomAssocsNumDistribution(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getRandomCatalystAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getRandomInhibitorAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getRandomProductAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
getRandomRateGenerationNum() - Method in class com.banda.chemistry.domain.AcRandomRatePerformance
 
getRandomReactantAssocsNumDistribution() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
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
 
getRateConstantTypeBounds() - Method in class com.banda.chemistry.domain.AcRandomRatePerformance
 
getRateFunction(boolean) - Method in class com.banda.chemistry.domain.AcReaction
 
getReactantMultiplicity() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
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
 
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.AcTranslation
 
getRepeatFromElement() - Method in class com.banda.chemistry.domain.AcInteractionSeries
Overridden for Hibernate mapping only.
getRepeatFromElement() - Method in class com.banda.chemistry.domain.AcTranslationSeries
Overridden for Hibernate mapping only.
getRepetitions() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getReverseRateConstants() - Method in class com.banda.chemistry.domain.AcReaction
 
getReverseRateConstantsNum() - Method in class com.banda.chemistry.domain.AcReaction
 
getReverseRateConstantsSafe() - Method in class com.banda.chemistry.domain.AcReaction
 
getReverseRateFunction() - Method in class com.banda.chemistry.domain.AcReaction
 
getSequence() - Method in class com.banda.chemistry.domain.AcItemHistory
 
getSettingFunction() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
getSettingFunction() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getSimulationConfig() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getSimulationConfig() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getSingleStrandsNum() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
getSingleStrandsNum() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getSingleStrandsNumFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getSingleStrandsNumTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getSingleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
getSkinCompartment() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getSortOrder() - Method in class com.banda.chemistry.domain.AcReaction
 
getSortOrder() - Method in class com.banda.chemistry.domain.AcVariable
 
getSourceSpecies() - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
getSpecies() - Method in class com.banda.chemistry.domain.AcCompartment
 
getSpecies() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
getSpecies() - Method in class com.banda.chemistry.domain.AcInteraction
 
getSpecies() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getSpecies() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation
 
getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getSpecies() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
getSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getSpecies() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
getSpecies() - Method in class com.banda.chemistry.domain.AcTranslation
 
getSpecies() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getSpecies() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getSpeciesAction() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
getSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction
 
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.ArtificialChemistrySpec
 
getSpeciesGroup(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getSpeciesGroupMap() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getSpeciesId() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getSpeciesId() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
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
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcCompartment
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteraction
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcParameterSet
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcReaction
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcReactionSet
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcTranslation
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getSpeciesSet() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getSpeciesToReactionConstraints() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
getSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
Deprecated.
getStoichiometricFactor() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
getStructure() - Method in class com.banda.chemistry.domain.AcSpecies
 
getSubActionSeries() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getSubChannelGroups() - Method in class com.banda.chemistry.domain.AcCompartment
 
getSubCompartment() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
getSubCompartmentAssociations() - Method in class com.banda.chemistry.domain.AcCompartment
 
getSubCompartments() - Method in class com.banda.chemistry.domain.AcCompartment
 
getTargetSpecies() - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
getTimeCreated() - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
getTimeCreated() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getTimeCreated() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getTimeCreated() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
getTimeStep() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getTimeStep() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
getTimeSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
getTo() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
getTolerance() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getToTime() - Method in class com.banda.chemistry.domain.AcTranslation
 
getTranslatedRun() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
getTranslatedRuns() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getTranslation() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getTranslationFunction() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getTranslationItems() - Method in class com.banda.chemistry.domain.AcTranslation
 
getTranslations() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getTranslationsCount() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getTranslationSeries() - Method in class com.banda.chemistry.domain.AcEvaluation
 
getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslation
 
getTranslationSeries() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getTranslationSeriesId() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
getType() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation
 
getType() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
getUpperStrandPartialBindingDistribution() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
getUpperStrandPartialBindingDistributionLocation() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrandPartialBindingDistributionLocationFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrandPartialBindingDistributionLocationTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrandPartialBindingDistributionShape() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrandPartialBindingDistributionShapeFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrandPartialBindingDistributionShapeTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperStrands() - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
getUpperThreshold() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getUpperToLowerStrandRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
getUpperToLowerStrandRatio() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperToLowerStrandRatioFrom() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getUpperToLowerStrandRatioTo() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
getValue() - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
getVariable() - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
getVariable() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
getVariable() - Method in class com.banda.chemistry.domain.AcTranslationItemHistory
 
getVariableAssignments() - Method in class com.banda.chemistry.domain.AcInteraction
 
getVariableIndex() - Method in class com.banda.chemistry.domain.AcVariable
 
getVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getVariables() - Method in class com.banda.chemistry.domain.AcVariableGroup
 
getVariables() - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
getVariables() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getVariablesNumber() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getVariablesNumber() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getVariablesSorted() - Method in class com.banda.chemistry.domain.AcVariableSet
 
getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
getVarSequenceNum() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
getVersion() - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
getVersion() - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
getVersion() - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
getVersion() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
getVersion() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 

H

hasForwardRateConstants() - Method in class com.banda.chemistry.domain.AcReaction
 
hasGroup() - Method in class com.banda.chemistry.domain.AcReaction
 
hasGroups() - Method in class com.banda.chemistry.domain.AcReactionSet
 
hashCode() - Method in class com.banda.chemistry.domain.AcSpeciesAssociation
 
hashCode() - Method in class com.banda.chemistry.domain.AcVariable
 
hasItemHistories() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
hasOutfluxNonReactiveRateConstantDistribution() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
hasOutfluxNonReactiveRateConstantDistributionShape() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
hasOwnVariables() - Method in class com.banda.chemistry.domain.AcVariableSet
 
hasParentSpeciesSet() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
hasRateConstants(boolean) - Method in class com.banda.chemistry.domain.AcReaction
 
hasReactionSet() - Method in class com.banda.chemistry.domain.AcReaction
 
hasReverseRateConstants() - Method in class com.banda.chemistry.domain.AcReaction
 
hasReverseRateFunction() - Method in class com.banda.chemistry.domain.AcReaction
 
hasSpecies(AcSpeciesType) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
hasSpeciesAssociations(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 

I

IllegalStateEventHandling - Enum in com.banda.chemistry.domain
 
initActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
initGroups() - Method in class com.banda.chemistry.domain.AcReactionSet
 
initItemHistories() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
initReactions() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
initSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction
 
initSpeciesAssociations() - Method in class com.banda.chemistry.domain.AcReaction
 
initVariables() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
initVariables() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
initVariables() - Method in class com.banda.chemistry.domain.AcVariableGroup
 
initVariables() - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
initVariables() - Method in class com.banda.chemistry.domain.AcVariableSet
 
initVarSequenceNum() - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
isApplicable(double) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
isEnabled() - Method in class com.banda.chemistry.domain.AcReaction
 
isFix() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling
 
isIgnore() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling
 
isIncludeReverseReactions() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
isMirrorComplementarity() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
isOutfluxAll() - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
isReactantOrProduct() - Method in enum com.banda.chemistry.domain.AcSpeciesAssociationType
 
isSingleValue() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
isStop() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling
 
isThrowException() - Method in enum com.banda.chemistry.domain.IllegalStateEventHandling
 
isUseGlobalOrder() - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
isUseGlobalOrder() - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
isVariablesReferenced() - Method in class com.banda.chemistry.domain.AcTranslationSeries
 

K

KineticsType - Enum in com.banda.chemistry.domain
 

M

main(String[]) - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
 
main(String[]) - Static method in class com.banda.chemistry.domain.AcSpeciesSet
 

R

refreshSteps() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
refreshSteps() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
Deprecated.
removeAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
removeAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeAllActions() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeAllReactions() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
removeAllSpeciesActions() - Method in class com.banda.chemistry.domain.AcInteraction
 
removeAllSubActionSeries() - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeAllVariableAssignments() - Method in class com.banda.chemistry.domain.AcInteraction
 
removeChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartment
 
removeChannel(AcCompartmentChannel) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
removeEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
removeEvaluatedSpeciesAction(AcEvaluatedSpeciesAction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
removeFromGroup() - Method in class com.banda.chemistry.domain.AcReaction
 
removeFromReactionSet() - Method in class com.banda.chemistry.domain.AcReaction
 
removeFromSpeciesActions(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcInteraction
 
removeGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReactionSet
 
removeImmutableSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeItemHistory(I) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
removeMultiRunAnalysisResult(AcMultiRunAnalysisResult) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
removeParentCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment
 
removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionGroup
 
removeReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcReactionSet
 
removeSpeciesAssociation(AcSpeciesReactionAssociation) - Method in class com.banda.chemistry.domain.AcReaction
 
removeSpeciesAssociations(Collection<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction
 
removeSubActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeSubChannelGroup(AcCompartmentChannelGroup) - Method in class com.banda.chemistry.domain.AcCompartment
 
removeSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartment
 
removeSubCompartmentAssociation(AcCompartmentAssociation) - Method in class com.banda.chemistry.domain.AcCompartment
 
removeTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
removeTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
removeTranslationItem(AcTranslationItem) - Method in class com.banda.chemistry.domain.AcTranslation
 
removeVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
removeVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
removeVariable(M) - Method in class com.banda.chemistry.domain.AcVariableGroup
 
removeVariable(M) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
removeVariable(M) - Method in class com.banda.chemistry.domain.AcVariableSet
 
removeVariableAssignment(AcInteractionVariableAssignment) - Method in class com.banda.chemistry.domain.AcInteraction
 

S

setAc(ArtificialChemistry) - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult
Deprecated.
setAcRunTrace(ComponentRunTrace<Double, Pair<AcCompartment, AcSpecies>>) - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
setAcs(Collection<ArtificialChemistry>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
setAction(AcInteraction) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
setActions(Set<AcInteraction>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setActionSeries(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteraction
 
setApplyTime(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
setAveragedCorrectRates(Double[]) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setBound(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
setCatalystsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setCatalystsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setCatalystsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setCatalystsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setChannels(Collection<AcCompartmentChannel>) - Method in class com.banda.chemistry.domain.AcCompartment
 
setChannels(List<AcCompartmentChannel>) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
setCollectiveCatalysisType(AcCollectiveSpeciesReactionAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
setCollectiveInhibitionType(AcCollectiveSpeciesReactionAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcMultiRunAnalysisResult
 
setComplementaryStrandsRatio(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setComplementaryStrandsRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setComplementaryStrandsRatioFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setComplementaryStrandsRatioTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setComponents(List<AcSpecies>) - Method in class com.banda.chemistry.domain.AcCompositeSpecies
 
setConstantSpeciesRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setConstantSpeciesRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setConstantSpeciesRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setConstantSpeciesRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcCompartment
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.AcVariableSet
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setCreatedBy(User) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcCompartment
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionGroup
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcReactionSet
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.AcVariableSet
 
setCreateTime(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setDefaultVariableValue(Double) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setDirection(AcChannelDirection) - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
setEnabled(boolean) - Method in class com.banda.chemistry.domain.AcReaction
 
setEvalFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setEvaluatedAction(AcEvaluatedAction) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
setEvaluatedActions(Set<AcEvaluatedAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
setEvaluatedActionSeries(AcEvaluatedActionSeries) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
setEvaluatedSpeciesActions(Set<AcEvaluatedSpeciesAction>) - Method in class com.banda.chemistry.domain.AcEvaluatedAction
 
setEvaluatedValues(Double[]) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
setEvaluation(AcEvaluation) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setEvaluation(AcEvaluation) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
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
 
setFixedPointDetectionPeriodicity(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setFixedPointDetectionPrecision(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setFixedProductAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setFixedReactantAssocsNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setForwardRateConstant(Double) - Method in class com.banda.chemistry.domain.AcReaction
 
setForwardRateConstants(Double[]) - Method in class com.banda.chemistry.domain.AcReaction
 
setForwardRateFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction
 
setFrom(Double) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
setFromTime(Integer) - Method in class com.banda.chemistry.domain.AcTranslation
 
setFullDoubleStrands(Collection<AcCompositeSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcParameter
 
setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction
 
setFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
setFunction(Function<T, Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem
 
setGeneratedBySpec(ArtificialChemistrySpec) - Method in class com.banda.chemistry.domain.AcCompartment
 
setGeneratedBySpec(ArtificialChemistrySpec) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setGroup(AcReactionGroup) - Method in class com.banda.chemistry.domain.AcReaction
 
setGroup(AcSpeciesGroup) - Method in class com.banda.chemistry.domain.AcSpecies
 
setGroups(List<AcReactionGroup>) - Method in class com.banda.chemistry.domain.AcReactionSet
 
setHighValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
setHolder(H) - Method in class com.banda.chemistry.domain.AcItemHistory
 
setId(Long) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
setId(Long) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
setId(Long) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setId(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setId(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setImmutableSpecies(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setIncludeReverseReactions(boolean) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setIndex(Integer) - Method in class com.banda.chemistry.domain.AcReaction
 
setInfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setInfluxRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setInfluxRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setInfluxScale(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setInhibitorsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setInhibitorsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setInhibitorsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setInhibitorsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setItemHistories(Collection<I>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcCompartment
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcReaction
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionGroup
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcReactionSet
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcVariable
 
setLabel(String) - Method in class com.banda.chemistry.domain.AcVariableGroup
 
setLength(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setLowerStrands(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
setLowerThreshold(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setLowValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
setMaxCatalystsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMaxInhibitorsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMaxProductsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMaxReactantsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMinCatalystsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMinInhibitorsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMinProductsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMinReactantsNum(Integer) - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
setMirrorComplementarity(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setMultiRunAnalysisResults(Collection<AcMultiRunAnalysisResult>) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setName(String) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setName(String) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setName(String) - Method in class com.banda.chemistry.domain.AcVariableSet
 
setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setName(String) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOdeSolverType(ODESolverType) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setOrder(Integer) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
setOrder(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setOutfluxAll(boolean) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setOutfluxNonReactiveRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setOutfluxNonReactiveRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxNonReactiveRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxNonReactiveRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxNonReactiveRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxNonReactiveRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxNonReactiveRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setOutfluxRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRatio(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setOutfluxRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRatioFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setOutfluxRatioTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setParameterSet(AcParameterSet) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
setParent(AcInteractionSeries) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setParentCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
setParentCompartmentAssociations(List<AcCompartmentAssociation>) - Method in class com.banda.chemistry.domain.AcCompartment
 
setParentSet(M) - Method in class com.banda.chemistry.domain.AcVariable
 
setParentSetUnsafe(AcVariableSetIF<?>) - Method in class com.banda.chemistry.domain.AcVariable
 
setParentSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
setPartialDoubleStrands(Collection<AcCompositeSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
setPeriodicTranslationsNumber(Integer) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setPermeability(Double) - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
setPerturbationNum(Integer) - Method in class com.banda.chemistry.domain.AcPerturbationPerformance
 
setPerturbationStrength(Double) - Method in class com.banda.chemistry.domain.AcPerturbationPerformance
 
setPriority(Integer) - Method in class com.banda.chemistry.domain.AcReaction
 
setProductsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setProductsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setProductsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setProductsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setRandomCatalystAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setRandomInhibitorAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setRandomProductAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setRandomRateGenerationNum(Integer) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance
 
setRandomReactantAssocsNumDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setRateConstantDistribution(RandomDistribution<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setRateConstantDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstantDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstantDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstantDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstantDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstantDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setRateConstants(Double[], boolean) - Method in class com.banda.chemistry.domain.AcReaction
 
setRateConstantType(AcRateConstantType) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
setRateConstantTypeBounds(Collection<AcRateConstantTypeBound>) - Method in class com.banda.chemistry.domain.AcRandomRatePerformance
 
setRateFunction(Function<Double, Double>, boolean) - Method in class com.banda.chemistry.domain.AcReaction
 
setReactantMultiplicity(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
setReactantsPerReactionNumber(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setReactantsPerReactionNumber(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReactantsPerReactionNumberFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReactantsPerReactionNumberTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReaction(AcReaction) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setReactionNum(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setReactionNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReactionNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReactionNumTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setReactions(List<AcReaction>) - Method in class com.banda.chemistry.domain.AcReactionContainer
 
setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcCompartment
 
setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcReaction
 
setReactionSet(AcReactionSet) - Method in class com.banda.chemistry.domain.AcReactionGroup
 
setReactionsPerSpeciesRatio(Double) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
setReactionsPerSpeciesRatioAssocType(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
setReactionToSpeciesConstraints(AcReactionToSpeciesConstraints) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
setRepeatFromElement(Integer) - Method in class com.banda.chemistry.domain.AcInteractionSeries
Overridden for Hibernate mapping only.
setRepeatFromElement(Integer) - Method in class com.banda.chemistry.domain.AcTranslationSeries
Overridden for Hibernate mapping only.
setRepetitions(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setReverseRateConstant(Double) - Method in class com.banda.chemistry.domain.AcReaction
 
setReverseRateConstants(Double[]) - Method in class com.banda.chemistry.domain.AcReaction
 
setReverseRateFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcReaction
 
setSequence(List<Double>) - Method in class com.banda.chemistry.domain.AcItemHistory
 
setSettingFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
setSettingFunction(Function<Double, Double>) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
setSimulationConfig(AcSimulationConfig) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setSimulationConfig(AcSimulationConfig) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setSingleStrandsNum(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setSingleStrandsNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setSingleStrandsNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setSingleStrandsNumTo(Integer) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setSingleValue(Double) - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
setSkinCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.ArtificialChemistry
 
setSortOrder(Integer) - Method in class com.banda.chemistry.domain.AcReaction
 
setSortOrder(Integer) - Method in class com.banda.chemistry.domain.AcVariable
 
setSourceSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
setSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
setSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setSpeciesAction(AcSpeciesInteraction) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
setSpeciesActions(Set<AcSpeciesInteraction>) - Method in class com.banda.chemistry.domain.AcInteraction
 
setSpeciesAssociations(Set<AcSpeciesReactionAssociation>) - Method in class com.banda.chemistry.domain.AcReaction
 
setSpeciesAssociations(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcReaction
 
setSpeciesForbiddenRedundancy(AcReactionSpeciesForbiddenRedundancy) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setSpeciesGroupMap(Map<String, AcSpeciesGroup>) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
setSpeciesNum(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpec
 
setSpeciesNum(ValueBound<Integer>) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setSpeciesNumFrom(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setSpeciesNumTo(Integer) - Method in class com.banda.chemistry.domain.AcSymmetricSpecBound
 
setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcParameterSet
 
setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcReactionSet
 
setSpeciesSet(AcSpeciesSet) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setSpeciesToReactionConstraints(AcSpeciesToReactionConstraints) - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
setSteps(Integer) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
setSteps(Integer) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
Deprecated.
setStoichiometricFactor(Double) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setStructure(String) - Method in class com.banda.chemistry.domain.AcSpecies
 
setSubActionSeries(Collection<AcInteractionSeries>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setSubChannelGroups(Collection<AcCompartmentChannelGroup>) - Method in class com.banda.chemistry.domain.AcCompartment
 
setSubCompartment(AcCompartment) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
setSubCompartmentAssociations(List<AcCompartmentAssociation>) - Method in class com.banda.chemistry.domain.AcCompartment
 
setTargetSpecies(AcSpecies) - Method in class com.banda.chemistry.domain.AcCompartmentChannel
 
setTimeCreated(Date) - Method in class com.banda.chemistry.domain.AcEvaluatedPerformance
 
setTimeCreated(Date) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setTimeCreated(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setTimeCreated(Date) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 
setTimeStep(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setTimeSteps(List<Double>) - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
setTo(Double) - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
setTolerance(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setToTime(Integer) - Method in class com.banda.chemistry.domain.AcTranslation
 
setTranslatedRun(AcTranslatedRun) - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
setTranslatedRuns(List<AcTranslatedRun>) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setTranslation(AcTranslation) - Method in class com.banda.chemistry.domain.AcTranslationItem
 
setTranslationFunction(Function<T, Double>) - Method in class com.banda.chemistry.domain.AcTranslationItem
 
setTranslationItems(Set<AcTranslationItem>) - Method in class com.banda.chemistry.domain.AcTranslation
 
setTranslations(Set<AcTranslation>) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcEvaluation
 
setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
setTranslationSeries(AcTranslationSeries) - Method in class com.banda.chemistry.domain.AcTranslation
 
setType(AcSpeciesAssociationType) - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setType(Collection<AcSpeciesReactionAssociation>, AcSpeciesAssociationType) - Static method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
setUpperStrandPartialBindingDistribution(RandomDistribution<Integer>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setUpperStrandPartialBindingDistributionLocation(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrandPartialBindingDistributionLocationFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrandPartialBindingDistributionLocationTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrandPartialBindingDistributionShape(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrandPartialBindingDistributionShapeFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrandPartialBindingDistributionShapeTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperStrands(Collection<AcSpecies>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpeciesSet
 
setUpperThreshold(Double) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setUpperToLowerStrandRatio(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setUpperToLowerStrandRatio(ValueBound<Double>) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperToLowerStrandRatioFrom(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUpperToLowerStrandRatioTo(Double) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setUseGlobalOrder(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpec
 
setUseGlobalOrder(boolean) - Method in class com.banda.chemistry.domain.AcDNAStrandSpecBound
 
setValue(Double) - Method in class com.banda.chemistry.domain.AcEvaluatedSpeciesAction
 
setVariable(AcInteractionVariable) - Method in class com.banda.chemistry.domain.AcInteractionVariableAssignment
 
setVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationItem
 
setVariable(AcTranslationVariable) - Method in class com.banda.chemistry.domain.AcTranslationItemHistory
 
setVariableAssignments(Set<AcInteractionVariableAssignment>) - Method in class com.banda.chemistry.domain.AcInteraction
 
setVariableIndex(Integer) - Method in class com.banda.chemistry.domain.AcVariable
 
setVariables(Collection<AcInteractionVariable>) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setVariables(Collection<AcTranslationVariable>) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableGroup
 
setVariables(Collection<M>) - Method in interface com.banda.chemistry.domain.AcVariableGroupIF
 
setVariables(Collection<M>) - Method in class com.banda.chemistry.domain.AcVariableSet
 
setVariablesReferenced(boolean) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcInteractionSeries
 
setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcSpeciesSet
 
setVarSequenceNum(Integer) - Method in class com.banda.chemistry.domain.AcTranslationSeries
 
setVersion(Long) - Method in class com.banda.chemistry.domain.AcCompartmentAssociation
 
setVersion(Long) - Method in class com.banda.chemistry.domain.AcCompartmentChannelGroup
 
setVersion(Long) - Method in class com.banda.chemistry.domain.AcSimulationConfig
 
setVersion(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpec
 
setVersion(Long) - Method in class com.banda.chemistry.domain.ArtificialChemistrySpecBound
 

T

toString() - Method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
 
toString() - Method in class com.banda.chemistry.domain.AcCompartment
 
toString() - Method in class com.banda.chemistry.domain.AcConcentrationLevel
 
toString() - Method in class com.banda.chemistry.domain.AcEvaluatedActionSeries
 
toString() - Method in class com.banda.chemistry.domain.AcEvaluatedRun
 
toString() - Method in class com.banda.chemistry.domain.AcEvaluation
 
toString() - Method in class com.banda.chemistry.domain.AcInteraction
 
toString() - Method in class com.banda.chemistry.domain.AcItemHistoriesHolder
 
toString() - Method in class com.banda.chemistry.domain.AcItemHistory
 
toString() - Method in class com.banda.chemistry.domain.AcParameter
 
toString() - Method in enum com.banda.chemistry.domain.AcRateConstantType
 
toString() - Method in class com.banda.chemistry.domain.AcRateConstantTypeBound
 
toString() - Method in class com.banda.chemistry.domain.AcReaction
 
toString() - Method in class com.banda.chemistry.domain.AcReactionContainer
 
toString() - Method in class com.banda.chemistry.domain.AcReactionSetConstraints
 
toString() - Method in class com.banda.chemistry.domain.AcReactionToSpeciesConstraints
 
toString() - Method in class com.banda.chemistry.domain.AcSpecies
 
toString() - Method in class com.banda.chemistry.domain.AcSpeciesInteraction
 
toString() - Method in class com.banda.chemistry.domain.AcSpeciesReactionAssociation
 
toString() - Method in class com.banda.chemistry.domain.AcSpeciesToReactionConstraints
 
toString() - Method in class com.banda.chemistry.domain.AcTranslatedRun
 
toString() - Method in class com.banda.chemistry.domain.AcTranslation
 
toString() - Method in class com.banda.chemistry.domain.AcTranslationItem
 
toString() - Method in class com.banda.chemistry.domain.AcVariable
 
toString() - Method in class com.banda.chemistry.domain.AcVariableSet
 
toString() - Method in class com.banda.chemistry.domain.ArtificialChemistry
 

V

valueOf(String) - Static method in enum com.banda.chemistry.domain.AcChannelDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcEvaluationItemState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcRateConstantType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcReaction.ReactionDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcReactionSpeciesForbiddenRedundancy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcSpeciesAssociationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.AcSpeciesType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.IllegalStateEventHandling
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.banda.chemistry.domain.KineticsType
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.banda.chemistry.domain.AcChannelDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcCollectiveSpeciesReactionAssociationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcEvaluationItemState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcRateConstantType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcReaction.ReactionDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcReactionSpeciesForbiddenRedundancy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcSpeciesAssociationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.AcSpeciesType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.IllegalStateEventHandling
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.banda.chemistry.domain.KineticsType
Returns an array containing the constants of this enum type, in the order they are declared.
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