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

A

AcCompartmentDepthComparator - Class in com.banda.chemistry.business

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

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

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

AcEvaluationBOFactory - Class in com.banda.chemistry.business

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

AcEvaluator - Class in com.banda.chemistry.business

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

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

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

AcKineticsBO - Class in com.banda.chemistry.business

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

AcMichaelisMentenToMassActionRSConverter - Class in com.banda.chemistry.business

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

AcRateConstantUtil - Class in com.banda.chemistry.business

AcReactionConverter - Interface in com.banda.chemistry.business

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

AcReactionRatePerturbationBO - Class in com.banda.chemistry.business

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

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

AcReactionSetConverter - Class in com.banda.chemistry.business

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

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

AcReplicator - Class in com.banda.chemistry.business

AcSpeciesIndecesToStoreGroup - Class in com.banda.chemistry.business

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

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

AcTranslatedRunHolder - Interface in com.banda.chemistry.business

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

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

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

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

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

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

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

ArtificialChemistryUtil - Class in com.banda.chemistry.business

B

BndChemistryValidationException - Exception in com.banda.chemistry.business

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

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

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

C

ChemistryRunSetting - Class in com.banda.chemistry.business

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

clone(T) - Method in class com.banda.chemistry.business.AcReplicator

clone(T, Class<T>) - Method in class com.banda.chemistry.business.AcReplicator

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

E

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

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

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

F

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

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

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

G

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

H

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

I

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

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

M

MassActionType - Enum in com.banda.chemistry.business

mergeReactionSets(AcReactionSet[]) - Method in class com.banda.chemistry.business.factory.AcReactionSetFactory

N

notANumberConcentrationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

notANumberConcentrationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

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

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

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

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

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

P

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

R

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

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

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

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

replaceSpeciesAndParamaterLabelsWithIndexPlaceholders(String, AcSpeciesSet) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

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

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

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

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

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

S

setEvaluationFunctionFromString(String, AcEvaluation) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setEvolFunctionFromString(String, AcParameter) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setRandomRateConstants(AcReactionSet, Map<AcRateConstantType, ValueBound<Double>>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

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

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

setRateConstants(AcCompartment, Double[], AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstants(AcReactionSet, Double[], AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantsFromString(String, AcCompartment, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantsFromString(String, AcReactionSet, AcReaction.ReactionDirection, Collection<AcReaction>, Collection<AcReactionGroup>) - Method in class com.banda.chemistry.business.AcRateConstantUtil

setRateConstantsFromString(String, AcReaction, AcReaction.ReactionDirection) - Method in class com.banda.chemistry.business.AcRateConstantUtil

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

setSettingFunctionFromString(String, AcSpeciesInteraction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setSettingFunctionFromString(String, AcInteractionVariableAssignment) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setSpeciesAssociationsFromString(String, AcSpeciesAssociationType, AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

setTranslationFunctionFromString(String, AcTranslationItem) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

storeSpeciesHistorySelectionGroup() - Method in class com.banda.chemistry.business.ChemistryRunSetting

storeSpeciesHistorySelectionGroup(Collection<AcSpecies>) - Method in class com.banda.chemistry.business.ChemistryRunSetting

T

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

toString() - Method in enum com.banda.chemistry.business.factory.AcTranslationSeriesFactory.DefaultTransItemLabel

U

updateSpeciesAssociations(String, AcSpeciesAssociationType, AcReaction) - Method in class com.banda.chemistry.business.ArtificialChemistryUtil

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

upperThresholdViolationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

upperThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

V

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

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

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

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

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

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

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

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

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

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

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

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

W

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

Z

zeroThresholdViolationHandling() - Method in class com.banda.chemistry.business.ChemistryRunSetting

zeroThresholdViolationHandling(IllegalStateEventHandling) - Method in class com.banda.chemistry.business.ChemistryRunSetting

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