Hierarchy For All Packages

Package Hierarchies:

• bio.singa.simulation.entities,
• bio.singa.simulation.events,
• bio.singa.simulation.exceptions,
• bio.singa.simulation.export,
• bio.singa.simulation.export.features,
• bio.singa.simulation.export.format,
• bio.singa.simulation.export.modules,
• bio.singa.simulation.export.reactiongraph,
• bio.singa.simulation.features,
• bio.singa.simulation.features.model,
• bio.singa.simulation.model.agents.linelike,
• bio.singa.simulation.model.agents.organelles,
• bio.singa.simulation.model.agents.pointlike,
• bio.singa.simulation.model.agents.surfacelike,
• bio.singa.simulation.model.agents.volumelike,
• bio.singa.simulation.model.concentrations,
• bio.singa.simulation.model.graphs,
• bio.singa.simulation.model.modules,
• bio.singa.simulation.model.modules.concentration,
• bio.singa.simulation.model.modules.concentration.functions,
• bio.singa.simulation.model.modules.concentration.imlementations.reactions,
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas,
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws,
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants,
• bio.singa.simulation.model.modules.concentration.imlementations.transport,
• bio.singa.simulation.model.modules.concentration.scope,
• bio.singa.simulation.model.modules.concentration.specifity,
• bio.singa.simulation.model.modules.displacement,
• bio.singa.simulation.model.modules.displacement.implementations,
• bio.singa.simulation.model.modules.qualitative,
• bio.singa.simulation.model.modules.qualitative.implementations,
• bio.singa.simulation.model.parameters,
• bio.singa.simulation.model.rules,
• bio.singa.simulation.model.sections,
• bio.singa.simulation.model.simulation,
• bio.singa.simulation.model.simulation.error,
• bio.singa.simulation.reactions,
• bio.singa.simulation.reactions.conditions,
• bio.singa.simulation.reactions.modifications,
• bio.singa.simulation.reactions.reactors,
• bio.singa.simulation.trajectories,
• bio.singa.simulation.trajectories.errors,
• bio.singa.simulation.trajectories.flat,
• bio.singa.simulation.trajectories.nested,
• uk.co.cogitolearning.cogpar

Class Hierarchy

• java.lang.Object
  • bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification (implements bio.singa.simulation.reactions.modifications.ComplexEntityModification)
    • bio.singa.simulation.reactions.modifications.AddModification
    • bio.singa.simulation.reactions.modifications.BindModification
    • bio.singa.simulation.reactions.modifications.ReleaseModification
    • bio.singa.simulation.reactions.modifications.RemoveModification
  • bio.singa.simulation.model.concentrations.AbstractConcentrationCondition (implements bio.singa.simulation.model.concentrations.ConcentrationCondition)
    • bio.singa.simulation.model.concentrations.AreaCondition
    • bio.singa.simulation.model.concentrations.NodeIdentifierCondition
    • bio.singa.simulation.model.concentrations.NodeTypeCondition
    • bio.singa.simulation.model.concentrations.RegionCondition
    • bio.singa.simulation.model.concentrations.SectionCondition
    • bio.singa.simulation.model.concentrations.TimedCondition
    • bio.singa.simulation.model.concentrations.TopologyCondition
  • bio.singa.simulation.model.modules.concentration.functions.AbstractDeltaFunction<FunctionReturnType>
    • bio.singa.simulation.model.modules.concentration.functions.EntityDeltaFunction
    • bio.singa.simulation.model.modules.concentration.functions.SectionDeltaFunction
    • bio.singa.simulation.model.modules.concentration.functions.UpdatableDeltaFunction
  • bio.singa.mathematics.graphs.model.AbstractEdge<NodeType> (implements bio.singa.mathematics.graphs.model.Edge<NodeType>)
    • bio.singa.simulation.model.graphs.AutomatonEdge
    • bio.singa.mathematics.graphs.model.DirectedWeightedEdge<NodeType> (implements bio.singa.mathematics.graphs.model.Weighted<WeightType>)
      • bio.singa.simulation.export.reactiongraph.ReactionGraphEdge
    • bio.singa.simulation.entities.GraphComplexEdge
  • bio.singa.features.model.AbstractFeature<FeatureContent> (implements bio.singa.features.model.Feature<FeatureContent>)
    • bio.singa.features.model.AbstractQuantitativeFeature<FeatureContent> (implements bio.singa.features.model.QuantitativeFeature<FeatureContent>)
      • bio.singa.simulation.features.EndocytosisCheckpointConcentration
      • bio.singa.simulation.features.EndocytosisCheckpointTime
      • bio.singa.simulation.features.FusionTime
      • bio.singa.simulation.model.concentrations.InitialConcentration
      • bio.singa.simulation.features.MaturationTime
      • bio.singa.simulation.features.MembraneTickness
      • bio.singa.simulation.features.Ratio
      • bio.singa.simulation.features.SNAREFusionPairs
    • bio.singa.features.model.AbstractScalableQuantitativeFeature<FeatureContent> (implements bio.singa.features.model.QuantitativeFeature<FeatureContent>)
      • bio.singa.simulation.features.ActinBoostVelocity
      • bio.singa.simulation.features.AttachmentDistance
      • bio.singa.simulation.features.MotorMovementVelocity
      • bio.singa.simulation.features.PitFormationRate
      • bio.singa.chemistry.features.reactions.RateConstant<ReactionRateType>
        • bio.singa.chemistry.features.reactions.FirstOrderRateConstant
          • bio.singa.simulation.features.CargoAdditionRate (implements bio.singa.chemistry.features.reactions.ForwardsRateConstant<ReactionRateType>)
      • bio.singa.simulation.features.VesicleRadius
    • bio.singa.features.model.QualitativeFeature<FeatureContent>
      • bio.singa.simulation.features.AffectedSection
      • bio.singa.simulation.features.model.EntityFeature
        • bio.singa.simulation.features.AttachedMotor
        • bio.singa.simulation.features.BoostMediatingEntity
        • bio.singa.simulation.features.Cargo
        • bio.singa.simulation.features.Transporter
      • bio.singa.simulation.features.InitialConcentrations
      • bio.singa.simulation.features.model.MultiEntityFeature
        • bio.singa.simulation.features.Cargoes
        • bio.singa.simulation.features.MatchingQSnares
        • bio.singa.simulation.features.MatchingRSnares
        • bio.singa.simulation.features.PrimaryCargoes
        • bio.singa.simulation.features.ScalingEntities
        • bio.singa.simulation.features.Solutes
      • bio.singa.simulation.features.model.MultiStringFeature
        • bio.singa.simulation.features.BlackListVesicleStates
        • bio.singa.simulation.features.WhiteListVesicleStates
      • bio.singa.simulation.features.model.RegionFeature
        • bio.singa.simulation.features.AffectedRegion
        • bio.singa.simulation.features.ContainmentRegion
      • bio.singa.features.model.StringFeature
        • bio.singa.simulation.features.AppliedVesicleState
        • bio.singa.simulation.features.AttachedFilament
        • bio.singa.simulation.features.MotorPullDirection
        • bio.singa.simulation.features.RequiredVesicleState
  • bio.singa.features.model.AbstractFeature.Builder<FeatureContent,TopLevelType,BuilderType>
    • bio.singa.simulation.features.ActinBoostVelocity.Builder
    • bio.singa.simulation.features.AffectedRegion.Builder
    • bio.singa.simulation.features.AffectedSection.Builder
    • bio.singa.simulation.features.AppliedVesicleState.Builder
    • bio.singa.simulation.features.AttachedFilament.Builder
    • bio.singa.simulation.features.AttachedMotor.Builder
    • bio.singa.simulation.features.AttachmentDistance.Builder
    • bio.singa.simulation.features.BlackListVesicleStates.Builder
    • bio.singa.simulation.features.BoostMediatingEntity.Builder
    • bio.singa.simulation.features.Cargo.Builder
    • bio.singa.simulation.features.CargoAdditionRate.Builder
    • bio.singa.simulation.features.Cargoes.Builder
    • bio.singa.simulation.features.ContainmentRegion.Builder
    • bio.singa.simulation.features.EndocytosisCheckpointConcentration.Builder
    • bio.singa.simulation.features.EndocytosisCheckpointTime.Builder
    • bio.singa.simulation.features.FusionTime.Builder
    • bio.singa.simulation.features.InitialConcentrations.Builder
    • bio.singa.simulation.features.MatchingQSnares.Builder
    • bio.singa.simulation.features.MatchingRSnares.Builder
    • bio.singa.simulation.features.MaturationTime.Builder
    • bio.singa.simulation.features.MembraneTickness.Builder
    • bio.singa.simulation.features.MotorMovementVelocity.Builder
    • bio.singa.simulation.features.MotorPullDirection.Builder
    • bio.singa.simulation.features.PitFormationRate.Builder
    • bio.singa.simulation.features.PrimaryCargoes.Builder
    • bio.singa.simulation.features.Ratio.Builder
    • bio.singa.simulation.features.RequiredVesicleState.Builder
    • bio.singa.simulation.features.ScalingEntities.Builder
    • bio.singa.simulation.features.SNAREFusionPairs.Builder
    • bio.singa.simulation.features.Solutes.Builder
    • bio.singa.simulation.features.Transporter.Builder
    • bio.singa.simulation.features.VesicleRadius.Builder
    • bio.singa.simulation.features.WhiteListVesicleStates.Builder
  • bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor (implements bio.singa.simulation.reactions.reactors.ComplexReactor)
    • bio.singa.simulation.reactions.reactors.OneToOneReactor
    • bio.singa.simulation.reactions.reactors.OneToTwoReactor
    • bio.singa.simulation.reactions.reactors.TwoToOneReactor
  • bio.singa.mathematics.graphs.grid.AbstractGridGraph<NodeType,EdgeType,VectorType> (implements bio.singa.mathematics.graphs.model.Graph<NodeType,EdgeType,IdentifierType>)
    • bio.singa.simulation.model.graphs.AutomatonGraph
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.KineticLaw)
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.IrreversibleKineticLaw
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.MichaelisMentenKineticLaw
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.ReversibleKineticLaw
  • bio.singa.mathematics.graphs.model.AbstractMapGraph<NodeType,EdgeType,VectorType,IdentifierType> (implements bio.singa.mathematics.graphs.model.Graph<NodeType,EdgeType,IdentifierType>)
    • bio.singa.simulation.entities.ComplexEntity (implements bio.singa.simulation.entities.ChemicalEntity)
    • bio.singa.mathematics.graphs.model.DirectedWeightedGraph<NodeType,EdgeType>
      • bio.singa.simulation.export.reactiongraph.ReactionGraph
  • bio.singa.mathematics.graphs.model.AbstractNode<NodeType,VectorType,IdentifierType> (implements bio.singa.mathematics.graphs.model.Node<NodeType,VectorType,IdentifierType>)
    • bio.singa.simulation.model.graphs.AutomatonNode (implements bio.singa.simulation.model.simulation.Updatable)
    • bio.singa.simulation.entities.GraphComplexNode
    • bio.singa.simulation.export.reactiongraph.ReactionGraphNode
  • bio.singa.simulation.model.modules.AbstractUpdateModule (implements bio.singa.simulation.model.modules.UpdateModule)
    • bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<DeltaFunctionType>
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion
      • bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction
      • bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport
    • bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
      • bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
      • bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion
      • bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion
      • bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
    • bio.singa.simulation.model.modules.qualitative.QualitativeModule
      • bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
      • bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationApplier
      • bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange
      • bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling
      • bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
      • bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
      • bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment
  • bio.singa.simulation.model.rules.AssignmentRule
  • bio.singa.simulation.model.rules.AssignmentRules
  • bio.singa.simulation.model.graphs.AutomatonGraphs
  • bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping
  • bio.singa.simulation.entities.BindingSite
  • bio.singa.simulation.reactions.conditions.CandidateConditionBuilder
  • bio.singa.simulation.model.sections.CellRegion
  • bio.singa.simulation.model.sections.CellRegions
  • bio.singa.simulation.model.sections.CellSubsection
  • bio.singa.simulation.model.sections.CellSubsections
  • bio.singa.simulation.entities.ChemicalEntities
  • bio.singa.simulation.entities.ComplexEntityBuilder
  • bio.singa.simulation.entities.ComplexEntityBuilder.ComplexEntityCombiner (implements bio.singa.simulation.entities.ComplexEntityBuilder.CombineStep)
  • bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder
  • bio.singa.simulation.model.concentrations.ConcentrationBuilder
  • bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl (implements bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep, bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationStep, bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep, bio.singa.simulation.model.concentrations.ConcentrationBuilder.EntityStep, bio.singa.simulation.model.concentrations.ConcentrationBuilder.PoolStep, bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep)
  • bio.singa.simulation.model.sections.ConcentrationContainer
  • bio.singa.simulation.model.modules.concentration.ConcentrationDelta
  • bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier
  • bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager
  • bio.singa.simulation.model.sections.ConcentrationPool
  • uk.co.cogitolearning.cogpar.ConstantExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • bio.singa.simulation.trajectories.errors.DebugRecorder (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.model.modules.concentration.scope.DependentUpdate (implements bio.singa.simulation.model.modules.concentration.scope.UpdateScope)
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.EntityLimitationStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SectionLimitationStep, bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>)
  • bio.singa.simulation.model.modules.displacement.DisplacementDelta
  • bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager
  • bio.singa.simulation.model.simulation.error.DisplacementDeviation
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.KineticLaw)
  • bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit (implements bio.singa.simulation.model.simulation.Updatable)
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.AccelerationStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.InhibitionStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.RateStep, bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>)
  • bio.singa.simulation.entities.EntityRegistry
  • bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific (implements bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity<DeltaFunctionType>)
  • bio.singa.simulation.model.simulation.error.ErrorManager
  • uk.co.cogitolearning.cogpar.ExponentiationExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • uk.co.cogitolearning.cogpar.ExpressionParser
  • bio.singa.simulation.model.parameters.FeatureManager (implements bio.singa.features.model.Featureable)
  • bio.singa.simulation.features.FeatureRandomizer
  • bio.singa.simulation.export.features.FeatureTable
  • bio.singa.simulation.export.features.FeatureTableRow
  • bio.singa.simulation.model.modules.concentration.FieldSupplier
  • bio.singa.simulation.trajectories.flat.FlatUpdateRecorder (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder (implements bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.BuildStep, bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.ConcentrationUnitStep, bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.DirectoryStep, bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.SimulationStep, bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep, bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.WorkspaceStep)
  • bio.singa.simulation.export.format.FormatFeature
  • bio.singa.simulation.export.format.FormatModule
  • bio.singa.simulation.export.format.FormatReactionEquation
  • bio.singa.simulation.export.format.FormatReactionKinetics
  • uk.co.cogitolearning.cogpar.FunctionExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • bio.singa.simulation.export.modules.GeneralModuleRow (implements bio.singa.simulation.export.modules.ModuleTableRow)
  • bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.events.GraphEventEmitter (implements bio.singa.core.events.UpdateEventEmitter<EventType>)
  • bio.singa.simulation.events.GraphUpdatedEvent
  • bio.singa.simulation.model.agents.surfacelike.GridImageReader
  • bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder
  • bio.singa.simulation.reactions.conditions.HasAnyNumberOfEntities (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.reactions.conditions.HasNoMoreThanNumberOfPartners (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.reactions.conditions.HasNumberOfEntities (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.reactions.conditions.HasOccupiedBindingSite (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.reactions.conditions.HasUnoccupiedBindingSite (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate (implements bio.singa.simulation.model.modules.concentration.scope.UpdateScope)
  • bio.singa.simulation.reactions.conditions.IsOnlyBoundAt (implements bio.singa.simulation.reactions.conditions.CandidateCondition)
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.SectionLimitationStep, bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>)
  • bio.singa.simulation.model.agents.linelike.LineLikeAgent
  • bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
  • bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
  • bio.singa.simulation.model.agents.surfacelike.Membrane
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.CargoStep, bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>)
  • bio.singa.simulation.model.agents.surfacelike.MembraneLayer
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.MembraneRestrictedBehavior (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior)
  • bio.singa.simulation.model.agents.surfacelike.MembraneSegment (implements bio.singa.mathematics.geometry.edges.LineSegment)
  • bio.singa.simulation.model.agents.surfacelike.MembraneTracer
  • bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre
  • bio.singa.simulation.model.modules.concentration.ModuleFactory
  • bio.singa.simulation.export.features.ModuleSummaryTable
  • bio.singa.simulation.export.modules.ModuleTable
  • bio.singa.simulation.export.modules.ModuleTableConverter
  • bio.singa.simulation.model.graphs.NeighborhoodMappingManager
  • bio.singa.simulation.trajectories.nested.NestedUpdateRecorder (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior)
  • bio.singa.simulation.events.NodeEventEmitter (implements bio.singa.core.events.UpdateEventEmitter<EventType>)
  • bio.singa.simulation.model.simulation.error.NumericalError
  • bio.singa.simulation.model.agents.organelles.OrganelleImageParser
  • bio.singa.simulation.model.agents.organelles.OrganelleTemplate
  • bio.singa.simulation.model.parameters.Parameter<QuantityType>
  • bio.singa.simulation.model.parameters.ParameterStorage
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>, bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep)
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantConcentration
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantDelta
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder (implements bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ComplexBuildingReactionStep, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.IrreversibleReactionStep, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ReversibleReactionStep)
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep, bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedStep)
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep)
  • bio.singa.simulation.reactions.reactors.ReactionChain
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder (implements bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep)
    • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactionChainBuilder (implements bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorPrimaryConditionStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorSecondarySubstrateStep)
    • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder (implements bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorPrimaryConditionStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondaryConditionStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondarySubstrateStep)
    • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactionChainBuilder (implements bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorPrimaryConditionStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep)
    • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactionChainBuilder (implements bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorPrimaryConditionStep, bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorSecondarySubstrateStep)
  • bio.singa.simulation.reactions.reactors.ReactionElement
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent
  • bio.singa.simulation.export.reactiongraph.ReactionGraphConverter
  • bio.singa.simulation.reactions.ReactionNetworkGenerator
  • bio.singa.simulation.export.modules.ReactionTableRow (implements bio.singa.simulation.export.modules.ModuleTableRow)
  • bio.singa.simulation.reactions.reactors.ReactionTrack
  • bio.singa.simulation.trajectories.Recorders
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.RuleBasedReactantBehavior (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior)
  • bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific (implements bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity<DeltaFunctionType>)
  • bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate (implements bio.singa.simulation.model.modules.concentration.scope.UpdateScope)
  • uk.co.cogitolearning.cogpar.SequenceExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
    • uk.co.cogitolearning.cogpar.AdditionExpressionNode
    • uk.co.cogitolearning.cogpar.MultiplicationExpressionNode
  • uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term
  • uk.co.cogitolearning.cogpar.SetVariable (implements uk.co.cogitolearning.cogpar.ExpressionNodeVisitor)
  • bio.singa.simulation.entities.SimpleEntity (implements bio.singa.simulation.entities.ChemicalEntity)
  • bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder
  • bio.singa.simulation.model.simulation.Simulation
  • bio.singa.simulation.model.simulation.SimulationManager (implements java.lang.Runnable)
  • bio.singa.simulation.model.simulation.SimulationStatus (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder (implements bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>, bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.CargoStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SolutesStep, bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.TransporterStep)
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior (implements bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior)
  • bio.singa.simulation.export.TeXFormat
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • uk.co.cogitolearning.cogpar.EvaluationException
        • bio.singa.simulation.exceptions.ModuleCalculationException
        • bio.singa.simulation.exceptions.NumericalInstabilityException
        • uk.co.cogitolearning.cogpar.ParserException
  • bio.singa.simulation.model.simulation.error.TimeStepManager (implements bio.singa.core.events.UpdateEventEmitter<EventType>)
  • uk.co.cogitolearning.cogpar.Token
  • uk.co.cogitolearning.cogpar.Tokenizer
  • bio.singa.simulation.trajectories.nested.Trajectories
  • bio.singa.simulation.trajectories.nested.TrajectoryData
  • bio.singa.simulation.trajectories.nested.TrajectoryDataPoint
  • bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint
  • bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific (implements bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity<DeltaFunctionType>)
  • bio.singa.simulation.events.UpdatableUpdatedEvent
  • bio.singa.simulation.model.simulation.UpdateScheduler
  • uk.co.cogitolearning.cogpar.VariableExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • bio.singa.simulation.export.features.VariationTable
  • bio.singa.simulation.model.agents.pointlike.Vesicle (implements bio.singa.features.model.Featureable, bio.singa.simulation.model.simulation.Updatable)
  • bio.singa.simulation.model.agents.pointlike.VesicleLayer
  • bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
  • bio.singa.simulation.model.agents.volumelike.VolumeLayer
  • bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent
  • bio.singa.simulation.model.agents.volumelike.VolumeLikeAgentFactory

Interface Hierarchy

• bio.singa.simulation.reactions.conditions.CandidateCondition
• bio.singa.simulation.entities.ComplexEntityBuilder.CombineStep
• bio.singa.simulation.reactions.modifications.ComplexEntityModification
• bio.singa.simulation.reactions.reactors.ComplexReactor
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.BuildStep
  • bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationStep
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.EntityStep
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.PoolStep
• bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep
• bio.singa.simulation.model.concentrations.ConcentrationCondition
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior
• bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.EntityLimitationStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SectionLimitationStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.AccelerationStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.InhibitionStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.RateStep
• uk.co.cogitolearning.cogpar.ExpressionNode
• uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
• bio.singa.features.model.Featureable
  • bio.singa.simulation.entities.ChemicalEntity
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.BuildStep
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.ConcentrationUnitStep
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.DirectoryStep
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.SimulationStep
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep
• bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.WorkspaceStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.KineticLaw
• bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.SectionLimitationStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.CargoStep
• bio.singa.simulation.model.modules.concentration.ModuleBuilder<ModuleType>
• bio.singa.simulation.export.modules.ModuleTableRow
• bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep
• javax.measure.Quantity<Q>
  • bio.singa.simulation.features.SpawnRate
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ComplexBuildingReactionStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.FinalStep
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.IrreversibleReactionStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep
  • bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ReversibleReactionStep
• bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorSecondarySubstrateStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondarySubstrateStep
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorPrimaryConditionStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorPrimaryConditionStep
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondaryConditionStep
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorPrimaryConditionStep
  • bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorPrimaryConditionStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep
• bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorSecondarySubstrateStep
• java.lang.Runnable
  • bio.singa.simulation.model.modules.UpdateModule
• bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.CargoStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SolutesStep
• bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.TransporterStep
• bio.singa.simulation.model.simulation.Updatable
• bio.singa.simulation.model.modules.concentration.scope.UpdateScope
• bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity<DeltaFunctionType>

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • bio.singa.simulation.model.sections.CellTopology
    • bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage
    • bio.singa.simulation.model.simulation.error.ErrorManager.Reason
    • bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour
    • bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope
    • bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity
    • bio.singa.simulation.model.modules.concentration.ModuleState
    • bio.singa.simulation.model.agents.organelles.OrganelleTypes
    • bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantRole
    • bio.singa.simulation.model.concentrations.TimedCondition.Relation