Hierarchy For All Packages

Package Hierarchies:

• bio.singa.simulation,
• bio.singa.simulation.events,
• bio.singa.simulation.exceptions,
• bio.singa.simulation.features,
• bio.singa.simulation.features.endocytosis,
• bio.singa.simulation.features.permeability,
• bio.singa.simulation.features.scale,
• bio.singa.simulation.model.agents,
• bio.singa.simulation.model.agents.filaments,
• bio.singa.simulation.model.agents.membranes,
• bio.singa.simulation.model.agents.organelles,
• 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,
• bio.singa.simulation.model.modules.concentration.reactants,
• 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.parser.organelles,
• bio.singa.simulation.parser.sbml,
• bio.singa.simulation.parser.sbml.converter,
• bio.singa.simulation.renderer,
• uk.co.cogitolearning.cogpar

Class Hierarchy

• java.lang.Object
  • 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.features.model.AbstractFeature<FeatureContent> (implements bio.singa.features.model.Feature<FeatureContent>)
    • bio.singa.simulation.features.endocytosis.AttachmentDistance
    • bio.singa.simulation.features.endocytosis.MaturationTime
    • bio.singa.simulation.features.endocytosis.TetheringTime
    • bio.singa.simulation.features.endocytosis.VesicleRadius
  • 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.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.core.parser.AbstractParser<ResultType> (implements bio.singa.core.parser.Parser<ResultType>)
    • bio.singa.core.parser.AbstractHTMLParser<ResultType>
      • bio.singa.simulation.parser.sbml.SabioRKParserService
  • javafx.animation.AnimationTimer
    • bio.singa.javafx.renderer.graphs.GraphRenderer<NodeType,EdgeType,IdentifierType,GraphType> (implements bio.singa.javafx.renderer.Renderer)
      • bio.singa.simulation.renderer.AutomatonGraphRenderer (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • javafx.application.Application
    • bio.singa.simulation.model.agents.ClippingPlayground (implements bio.singa.javafx.renderer.Renderer)
    • bio.singa.simulation.model.agents.MacroscopicLayerPlayground (implements bio.singa.javafx.renderer.Renderer)
    • bio.singa.simulation.model.modules.displacement.VesiclePlayground (implements bio.singa.javafx.renderer.Renderer)
  • bio.singa.simulation.model.rules.AppliedExpression
  • bio.singa.simulation.model.rules.AssignmentRule
  • bio.singa.simulation.model.rules.AssignmentRules
  • bio.singa.simulation.model.graphs.AutomatonGraphs
  • bio.singa.simulation.renderer.BioGraphRenderOptions
  • bio.singa.simulation.parser.sbml.BioModelsParserService
  • bio.singa.simulation.model.sections.CellRegion
  • bio.singa.simulation.model.sections.CellRegions
  • bio.singa.simulation.model.sections.CellSubsection (implements java.util.Observer)
  • bio.singa.simulation.model.sections.CellSubsections
  • bio.singa.simulation.parser.sbml.converter.CompartmentHandler
  • bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSectionSelection, bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection, bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSectionSelection, bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection, bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep)
  • bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<DeltaFunctionType> (implements bio.singa.simulation.model.modules.UpdateModule)
    • bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
    • bio.singa.simulation.model.modules.concentration.imlementations.Diffusion
    • bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
    • bio.singa.simulation.model.modules.concentration.imlementations.Reaction
      • bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
      • bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
      • bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
      • bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
    • bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
  • 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.features.DefautFeatureSources
  • bio.singa.simulation.model.modules.concentration.scope.DependentUpdate (implements bio.singa.simulation.model.modules.concentration.scope.UpdateScope)
  • bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep)
  • bio.singa.simulation.model.modules.displacement.DisplacementBasedModule (implements bio.singa.simulation.model.modules.UpdateModule)
    • bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis
    • bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
    • bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion
    • bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
  • bio.singa.simulation.model.modules.displacement.DisplacementDelta
  • bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager
  • bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific (implements bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity<DeltaFunctionType>)
  • bio.singa.simulation.events.EpochUpdateWriter (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • 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.model.modules.concentration.FieldSupplier
  • bio.singa.simulation.model.agents.filaments.FilamentLayer
  • uk.co.cogitolearning.cogpar.FunctionExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • bio.singa.simulation.parser.sbml.FunctionReference
  • java.util.concurrent.FutureTask<V> (implements java.util.concurrent.RunnableFuture<V>)
    • javafx.concurrent.Task<V> (implements javafx.event.EventTarget, javafx.concurrent.Worker<V>)
      • bio.singa.simulation.model.simulation.SimulationManager
  • bio.singa.simulation.events.GraphEventEmitter (implements bio.singa.core.events.UpdateEventEmitter<EventType>)
  • bio.singa.simulation.events.GraphImageWriter (implements bio.singa.core.events.UpdateEventListener<EventType>)
  • bio.singa.simulation.events.GraphUpdatedEvent
  • bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate (implements bio.singa.simulation.model.modules.concentration.scope.UpdateScope)
  • bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
  • bio.singa.simulation.model.modules.concentration.LocalError
  • bio.singa.simulation.model.agents.membranes.Membrane
  • bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.CargoStep)
  • bio.singa.simulation.model.agents.membranes.MembraneLayer
  • bio.singa.simulation.model.agents.membranes.MembraneSegment (implements bio.singa.mathematics.geometry.edges.LineSegment)
  • bio.singa.simulation.model.agents.membranes.MembraneTracer
  • bio.singa.simulation.model.agents.organelles.MicrotubuleOrganizingCentre
  • bio.singa.simulation.model.modules.concentration.ModuleFactory
  • bio.singa.simulation.events.NodeEventEmitter (implements bio.singa.core.events.UpdateEventEmitter<EventType>)
  • bio.singa.simulation.model.agents.organelles.Organelle
  • bio.singa.simulation.parser.organelles.OrganelleImageParser
  • bio.singa.simulation.model.modules.qualitative.QualitativeModule (implements bio.singa.simulation.model.modules.UpdateModule)
    • bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
    • bio.singa.simulation.model.modules.qualitative.implementations.VesicleAttachment
    • bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
  • bio.singa.simulation.model.modules.concentration.reactants.Reactant
    • bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant
    • bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant
  • bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder<TopLevelType,BuilderType>
    • bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.Builder
    • bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.Builder
    • bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder
  • bio.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter
  • bio.singa.simulation.parser.sbml.converter.SBMLExpressionConverter
  • bio.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter
  • bio.singa.simulation.parser.sbml.converter.SBMLParameterConverter
  • bio.singa.simulation.parser.sbml.SBMLParser
  • bio.singa.simulation.parser.sbml.converter.SBMLReactionConverter
  • bio.singa.simulation.parser.sbml.converter.SBMLUnitConverter
  • bio.singa.features.model.ScalableQuantityFeature<QuantityType> (implements bio.singa.features.model.ScalableFeature<FeatureContent>)
    • bio.singa.simulation.features.endocytosis.ActinBoostVelocity
    • bio.singa.simulation.features.scale.AppliedScale
    • bio.singa.simulation.features.endocytosis.BuddingRate
    • bio.singa.simulation.features.permeability.MembraneEntry
    • bio.singa.simulation.features.permeability.MembraneExit
    • bio.singa.simulation.features.permeability.MembraneFlipFlop
    • bio.singa.simulation.features.endocytosis.MotorMovementVelocity
  • 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.model.simulation.Simulation
  • bio.singa.simulation.model.simulation.SimulationExamples
  • bio.singa.simulation.model.parameters.SimulationParameter<QuantityType> (implements bio.singa.chemistry.annotations.Annotatable, bio.singa.features.identifiers.model.Identifiable<IdentifierType>, bio.singa.core.utility.Nameable)
  • bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder (implements bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.BuildStep, bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.CargoStep, bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SolutesStep, bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.TransporterStep)
  • bio.singa.simulation.model.agents.filaments.SkeletalFilament
  • bio.singa.simulation.features.endocytosis.SpawnTimeSampler
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • uk.co.cogitolearning.cogpar.EvaluationException
        • bio.singa.simulation.exceptions.NumericalInstabilityException
        • uk.co.cogitolearning.cogpar.ParserException
  • uk.co.cogitolearning.cogpar.Token
  • uk.co.cogitolearning.cogpar.Tokenizer
  • bio.singa.simulation.model.parameters.UnitScaler
  • 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.model.modules.displacement.Vesicle (implements bio.singa.features.model.Featureable, bio.singa.simulation.model.simulation.Updatable)
  • bio.singa.simulation.model.modules.displacement.VesicleLayer

Interface Hierarchy

• bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSectionSelection
• bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection
• bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSectionSelection
• bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection
• bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep
• bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep
• uk.co.cogitolearning.cogpar.ExpressionNode
• uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
• bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.CargoStep
• javax.measure.Quantity<Q>
  • bio.singa.simulation.features.endocytosis.SpawnRate
• bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.BuildStep
• bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.CargoStep
• bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SolutesStep
• bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.TransporterStep
• bio.singa.simulation.model.simulation.Updatable
• bio.singa.simulation.model.modules.UpdateModule
• 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.renderer.RenderingMode
    • bio.singa.simulation.model.agents.organelles.OrganelleTypes
    • bio.singa.simulation.model.agents.filaments.SkeletalFilament.FilamentBehaviour
    • bio.singa.simulation.model.sections.CellTopology
    • bio.singa.simulation.model.modules.displacement.Vesicle.AttachmentState
    • bio.singa.simulation.model.modules.displacement.Vesicle.TargetDirection
    • bio.singa.simulation.model.modules.concentration.ModuleState
    • bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope
    • bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity
    • bio.singa.simulation.model.modules.concentration.reactants.ReactantRole