Serialized Form

Package com.banda.chemistry

Class com.banda.chemistry.BndChemistryException extends RuntimeException implements Serializable

Package com.banda.chemistry.domain

Class com.banda.chemistry.domain.AcAction extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

applyTime

Integer applyTime

speciesActions

Set<E> speciesActions

actionSeries

AcActionSeries actionSeries

useAllPreviousActionMagnitudes

boolean useAllPreviousActionMagnitudes

previousActionSpecies

Collection<E> previousActionSpecies

Class com.banda.chemistry.domain.AcActionSeries extends AcSpeciesSetManipulationSeries implements Serializable

Serialized Fields

actions

Set<E> actions

runs

List<E> runs

Class com.banda.chemistry.domain.AcCompartment extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

label

String label

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

parent

AcCompartment parent

subCompartments

Collection<E> subCompartments

channels

Collection<E> channels

outputCompartment

AcCompartment outputCompartment

Deprecated.

reactionSet

AcReactionSet reactionSet

Class com.banda.chemistry.domain.AcCompartmentChannel extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

species

AcSpecies species

direction

AcCompartmentChannelDirection direction

permeability

AcSpecies permeability

Class com.banda.chemistry.domain.AcCompositeSpecies extends AcSpecies implements Serializable

Serialized Fields

components

List<E> components

Class com.banda.chemistry.domain.AcDNAStrandSpeciesSet extends AcSpeciesSet implements Serializable

Serialized Fields

upperStrands

Collection<E> upperStrands

lowerStrands

Collection<E> lowerStrands

fullDoubleStrands

Collection<E> fullDoubleStrands

partialDoubleStrands

Collection<E> partialDoubleStrands

Class com.banda.chemistry.domain.AcEvaluatedAction extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

applyTime

Integer applyTime

action

AcAction action

evaluatedActionSeries

AcEvaluatedActionSeries evaluatedActionSeries

evaluatedSpeciesActions

Set<E> evaluatedSpeciesActions

Class com.banda.chemistry.domain.AcEvaluatedActionSeries extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

actionSeries

AcActionSeries actionSeries

evaluatedActions

Set<E> evaluatedActions

Class com.banda.chemistry.domain.AcEvaluatedPerformance extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

timeCreated

Date timeCreated

createdBy

com.banda.core.domain.um.User createdBy

ac

ArtificialChemistry ac

actionSeries

AcActionSeries actionSeries

evaluation

AcEvaluation evaluation

repetitions

Integer repetitions

averagedCorrectRates

Double[] averagedCorrectRates

Class com.banda.chemistry.domain.AcEvaluatedRun extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

steps

Integer steps

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

evaluationStates

AcEvaluationItemState[] evaluationStates

evaluation

AcEvaluation evaluation

translatedRun

AcTranslatedRun translatedRun

Class com.banda.chemistry.domain.AcEvaluatedSpeciesAction extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

speciesAction

AcSpeciesAction speciesAction

evaluatedAction

AcEvaluatedAction evaluatedAction

value

Double value

Class com.banda.chemistry.domain.AcEvaluation extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

translationSeries

AcTranslationSeries translationSeries

periodicTranslationsNumber

Integer periodicTranslationsNumber

evaluationItems

Set<E> evaluationItems

evaluatedRuns

List<E> evaluatedRuns

Class com.banda.chemistry.domain.AcEvaluationItem extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

state

AcEvaluationItemState state

order

Integer order

evaluationStateApplicableFunction

Function<IN,OUT> evaluationStateApplicableFunction

acEvaluation

AcEvaluation acEvaluation

Class com.banda.chemistry.domain.AcItemHistoriesHolder extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

steps

Integer steps

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

itemHistories

Collection<E> itemHistories

Class com.banda.chemistry.domain.AcItemHistory extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

sequence

Double[] sequence

holder

AcItemHistoriesHolder<I extends AcItemHistory> holder

Class com.banda.chemistry.domain.AcMultiset extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

step

Integer step

Deprecated.

subMultisets

Collection<E> subMultisets

Deprecated.

parent

AcMultiset parent

Deprecated.

stochiometricList

List<E> stochiometricList

Deprecated.

Class com.banda.chemistry.domain.AcParameter extends AcVariable<AcParameterSet> implements Serializable

Serialized Fields

evolFunction

Function<IN,OUT> evolFunction

Class com.banda.chemistry.domain.AcParameterSet extends AcVariableSet<AcParameter> implements Serializable

Serialized Fields

speciesSet

AcSpeciesSet speciesSet

Class com.banda.chemistry.domain.AcPerturbationPerformance extends AcEvaluatedPerformance implements Serializable

Serialized Fields

perturbationNum

Integer perturbationNum

perturbationStrength

Double perturbationStrength

Class com.banda.chemistry.domain.AcRandomRatePerformance extends AcEvaluatedPerformance implements Serializable

Serialized Fields

randomRateGenerationNum

Integer randomRateGenerationNum

rateConstantTypeBounds

Collection<E> rateConstantTypeBounds

Class com.banda.chemistry.domain.AcRangeTranslation extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

fromTime

Integer fromTime

toTime

Integer toTime

translationItems

Set<E> translationItems

translationSeries

AcTranslationSeries translationSeries

Class com.banda.chemistry.domain.AcRateConstantTypeBound extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

rateConstantType

AcReactionRateConstantType rateConstantType

bound

com.banda.core.domain.ValueBound<E> bound

Class com.banda.chemistry.domain.AcReaction extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

label

String label

priority

Integer priority

sortOrder

Integer sortOrder

speciesAssociations

Set<E> speciesAssociations

collectiveCatalysisType

AcCollectiveSpeciesReactionAssociationType collectiveCatalysisType

collectiveInhibitionType

AcCollectiveSpeciesReactionAssociationType collectiveInhibitionType

forwardRateFunction

Function<IN,OUT> forwardRateFunction

reverseRateFunction

Function<IN,OUT> reverseRateFunction

forwardRateConstants

Double[] forwardRateConstants

reverseRateConstants

Double[] reverseRateConstants

enabled

boolean enabled

reactionSet

AcReactionSet reactionSet

group

AcReactionGroup group

index

Integer index

Class com.banda.chemistry.domain.AcReactionContainer extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

label

String label

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

reactions

List<E> reactions

Class com.banda.chemistry.domain.AcReactionGroup extends AcReactionContainer implements Serializable

Serialized Fields

reactionSet

AcReactionSet reactionSet

Class com.banda.chemistry.domain.AcReactionSet extends AcReactionContainer implements Serializable

Serialized Fields

kineticsType

KineticsType kineticsType

speciesSet

AcSpeciesSet speciesSet

parameterSet

AcParameterSet parameterSet

groups

List<E> groups

Class com.banda.chemistry.domain.AcRun extends AcItemHistoriesHolder<AcSpeciesRunHistory> implements Serializable

Serialized Fields

runTime

Double runTime

actionSeries

AcActionSeries actionSeries

ac

ArtificialChemistry ac

evaluatedActionSeries

AcEvaluatedActionSeries evaluatedActionSeries

translatedRuns

List<E> translatedRuns

Class com.banda.chemistry.domain.AcSpecies extends AcVariable<AcSpeciesSet> implements Serializable

Serialized Fields

constantFlag

boolean constantFlag

structure

String structure

group

AcSpeciesGroup group

Class com.banda.chemistry.domain.AcSpeciesAction extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

species

AcSpecies species

action

AcAction action

settingFunction

Function<IN,OUT> settingFunction

Class com.banda.chemistry.domain.AcSpeciesGroup extends AcVariableGroup<AcSpecies> implements Serializable

Class com.banda.chemistry.domain.AcSpeciesReactionAssociation extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

species

AcSpecies species

reaction

AcReaction reaction

stoichiometricFactor

Double stoichiometricFactor

type

AcSpeciesAssociationType type

Class com.banda.chemistry.domain.AcSpeciesRunHistory extends AcItemHistory<AcRun> implements Serializable

Serialized Fields

species

AcSpecies species

Class com.banda.chemistry.domain.AcSpeciesSet extends AcVariableSet<AcSpecies> implements Serializable

Serialized Fields

varSequenceNum

Integer varSequenceNum

parentSpeciesSet

AcSpeciesSet parentSpeciesSet

parameterSet

AcParameterSet parameterSet

speciesGroupMap

Map<K,V> speciesGroupMap

Class com.banda.chemistry.domain.AcSpeciesSetManipulationSeries extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

repetitions

Integer repetitions

periodicity

Integer periodicity

repeatFromElement

Integer repeatFromElement

speciesSet

AcSpeciesSet speciesSet

Class com.banda.chemistry.domain.AcTask extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

steps

Integer steps

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

actionSeries

AcActionSeries actionSeries

translationSeries

AcTranslationSeries translationSeries

taskEvaluation

AcEvaluation taskEvaluation

Class com.banda.chemistry.domain.AcTranslatedRun extends AcItemHistoriesHolder<AcTranslationItemHistory> implements Serializable

Serialized Fields

translationSeries

AcTranslationSeries translationSeries

run

AcRun run

evaluatedRuns

List<E> evaluatedRuns

Class com.banda.chemistry.domain.AcTranslationItem extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

variable

AcTranslationVariable variable

translation

AcRangeTranslation translation

translationFunction

Function<IN,OUT> translationFunction

Class com.banda.chemistry.domain.AcTranslationItemHistory extends AcItemHistory<AcTranslatedRun> implements Serializable

Serialized Fields

variable

AcTranslationVariable variable

Class com.banda.chemistry.domain.AcTranslationSeries extends AcSpeciesSetManipulationSeries implements Serializable

Serialized Fields

varSequenceNum

Integer varSequenceNum

rangeTranslations

Set<E> rangeTranslations

translatedRuns

List<E> translatedRuns

variables

Collection<E> variables

Class com.banda.chemistry.domain.AcTranslationVariable extends AcVariable<AcTranslationSeries> implements Serializable

Class com.banda.chemistry.domain.AcVariable extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

label

String label

sortOrder

Integer sortOrder

variableIndex

Integer variableIndex

parentSet

AcVariableSetIF<M extends AcVariable<? extends AcVariableSetIF>> parentSet

Class com.banda.chemistry.domain.AcVariableGroup extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

label

String label

variables

Collection<E> variables

Class com.banda.chemistry.domain.AcVariableSet extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

variables

Collection<E> variables

Class com.banda.chemistry.domain.ArtificialChemistry extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

createTime

Date createTime

createdBy

com.banda.core.domain.um.User createdBy

skinCompartment

AcCompartment skinCompartment

runs

List<E> runs

generatedBySpec

ArtificialChemistrySpec generatedBySpec

simulationConfig

AcSimulationConfig simulationConfig

multiRunAnalysisResults

Collection<E> multiRunAnalysisResults

Class com.banda.chemistry.domain.EvolutionRule extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

priority

Integer priority

reactants

com.banda.core.MultiSet<E> reactants

products

com.banda.core.MultiSet<E> products

Class com.banda.chemistry.domain.Membrane extends com.banda.core.domain.TechnicalDomainObject implements Serializable

Serialized Fields

name

String name

parent

Membrane<OBJECT_TYPE> parent

subMembranes

List<E> subMembranes

outputMembrane

Membrane<OBJECT_TYPE> outputMembrane

alphabet

String[] alphabet

configuration

com.banda.core.MultiSet<E> configuration

rules

Set<E> rules

Class com.banda.chemistry.domain.MembraneWithAtoms extends Membrane<Integer> implements Serializable

Class com.banda.chemistry.domain.RewritingMembrane extends Membrane<Integer[]> implements Serializable

Package com.banda.chemistry.task

Class com.banda.chemistry.task.AcCoreEvaluateTask extends com.banda.core.domain.task.Task implements Serializable

Serialized Fields

acEvaluation

AcEvaluation acEvaluation

saveEvaluationFlag

boolean saveEvaluationFlag

evaluationSteps

Integer evaluationSteps

evaluateFullFlag

boolean evaluateFullFlag

Class com.banda.chemistry.task.AcCoreRunTask extends com.banda.core.domain.task.Task implements Serializable

Serialized Fields

ac

ArtificialChemistry ac

initialConcentrations

List<E> initialConcentrations

actionSeries

AcActionSeries actionSeries

evaluatedActionSeries

AcEvaluatedActionSeries evaluatedActionSeries

acTask

AcTask acTask

runTime

Integer runTime

repetitions

Integer repetitions

saveRunFlag

boolean saveRunFlag

storeOption

AcCoreRunTask.AcRunStoreOption storeOption

upperThresholdViolationHandling

IllegalStateEventHandling upperThresholdViolationHandling

zeroThresholdViolationHandling

IllegalStateEventHandling zeroThresholdViolationHandling

notANumberConcentrationHandling

IllegalStateEventHandling notANumberConcentrationHandling

storeSpeciesHistorySelectionGroup

Collection<E> storeSpeciesHistorySelectionGroup

Class com.banda.chemistry.task.AcCoreTranslateTask extends com.banda.core.domain.task.Task implements Serializable

Serialized Fields

translationSeries

Collection<E> translationSeries

translationSteps

Integer translationSteps

translateFullRunFlag

boolean translateFullRunFlag

saveTranslationFlag

boolean saveTranslationFlag

storeOption

AcCoreTranslateTask.AcTranslationStoreOption storeOption

Class com.banda.chemistry.task.AcEvaluateTask extends AcCoreEvaluateTask implements Serializable

Serialized Fields

translatedRuns

Collection<E> translatedRuns

ac

ArtificialChemistry ac

translationSeries

AcTranslationSeries translationSeries

acTask

AcTask acTask

Class com.banda.chemistry.task.AcMultiRunAnalysisTask extends com.banda.core.domain.task.Task implements Serializable

Serialized Fields

acs

Collection<E> acs

spec

com.banda.core.domain.dynamics.MultiRunAnalysisSpec<T> spec

Class com.banda.chemistry.task.AcPerformanceEvaluateTask extends com.banda.core.domain.task.Task implements Serializable

Serialized Fields

acEvaluation

AcEvaluation acEvaluation

ac

ArtificialChemistry ac

actionSeries

Collection<E> actionSeries

runTime

Integer runTime

repetitions

Integer repetitions

Class com.banda.chemistry.task.AcPerturbateTask extends AcRunTranslateAndEvaluateTask implements Serializable

Serialized Fields

perturbationStrength

Double perturbationStrength

repetitions

Integer repetitions

Class com.banda.chemistry.task.AcPerturbationPerformanceEvaluateTask extends AcPerformanceEvaluateTask implements Serializable

Serialized Fields

perturbationNum

Integer perturbationNum

perturbationStrengths

Collection<E> perturbationStrengths

Class com.banda.chemistry.task.AcRandomRatePerformanceEvaluateTask extends AcPerformanceEvaluateTask implements Serializable

Serialized Fields

randomRateGenerationNum

Integer randomRateGenerationNum

rateConstantTypeBounds

Collection<E> rateConstantTypeBounds

Class com.banda.chemistry.task.AcRunAndTranslateTask extends AcCoreTranslateTask implements Serializable

Serialized Fields

runTaskDefinition

AcCoreRunTask runTaskDefinition

Class com.banda.chemistry.task.AcRunTask extends AcCoreRunTask implements Serializable

Serialized Fields

eventPublishPeriodicity

Integer eventPublishPeriodicity

runLocal

boolean runLocal

Class com.banda.chemistry.task.AcRunTranslateAndEvaluateTask extends AcCoreEvaluateTask implements Serializable

Serialized Fields

runAndTranslationTaskDefinition

AcRunAndTranslateTask runAndTranslationTaskDefinition

Class com.banda.chemistry.task.AcTranslatedRunEvaluationTask extends AcCoreEvaluateTask implements Serializable

Serialized Fields

translatedRun

AcTranslatedRun translatedRun

Class com.banda.chemistry.task.AcTranslateRunTask extends AcCoreTranslateTask implements Serializable

Serialized Fields

run

AcRun run

Class com.banda.chemistry.task.AcTranslateTask extends AcCoreTranslateTask implements Serializable

Serialized Fields

runs

Collection<E> runs

ac

ArtificialChemistry ac

actionSeries

AcActionSeries actionSeries

acTask

AcTask acTask