Hierarchy For All Packages

Package Hierarchies:

• de.bioforscher.singa.simulation.events,
• de.bioforscher.singa.simulation.features.permeability,
• de.bioforscher.singa.simulation.model.compartments,
• de.bioforscher.singa.simulation.model.graphs,
• de.bioforscher.singa.simulation.model.parameters,
• de.bioforscher.singa.simulation.model.rules,
• de.bioforscher.singa.simulation.modules.diffusion,
• de.bioforscher.singa.simulation.modules.membranetransport,
• de.bioforscher.singa.simulation.modules.model,
• de.bioforscher.singa.simulation.modules.model.updates,
• de.bioforscher.singa.simulation.modules.reactions.implementations,
• de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations,
• de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model,
• de.bioforscher.singa.simulation.modules.reactions.model,
• de.bioforscher.singa.simulation.parser.graphs,
• de.bioforscher.singa.simulation.parser.sbml,
• de.bioforscher.singa.simulation.parser.sbml.converter,
• de.bioforscher.singa.simulation.research,
• uk.co.cogitolearning.cogpar

Class Hierarchy

• java.lang.Object
  • de.bioforscher.singa.mathematics.graphs.model.AbstractEdge<NodeType> (implements de.bioforscher.singa.mathematics.graphs.model.Edge<NodeType>)
    • de.bioforscher.singa.simulation.model.graphs.BioEdge
  • de.bioforscher.singa.features.model.AbstractFeature<FeatureContent> (implements de.bioforscher.singa.features.model.Feature<FeatureContent>)
    • de.bioforscher.singa.simulation.features.permeability.MembraneEntry
    • de.bioforscher.singa.simulation.features.permeability.MembraneExit
    • de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
  • de.bioforscher.singa.mathematics.graphs.model.AbstractGraph<NodeType,EdgeType,VectorType,IdentifierType> (implements de.bioforscher.singa.mathematics.graphs.model.Graph<NodeType,EdgeType,IdentifierType>)
    • de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
  • de.bioforscher.singa.mathematics.algorithms.optimization.AbstractGridSearch
    • de.bioforscher.singa.simulation.research.DiffusionGridSearch
  • de.bioforscher.singa.mathematics.graphs.model.AbstractNode<NodeType,VectorType,IdentifierType> (implements de.bioforscher.singa.mathematics.graphs.model.Node<NodeType,VectorType,IdentifierType>)
    • de.bioforscher.singa.simulation.model.graphs.BioNode
  • de.bioforscher.singa.core.parser.AbstractParser<ResultType> (implements de.bioforscher.singa.core.parser.Parser<ResultType>)
    • de.bioforscher.singa.core.parser.AbstractHTMLParser<ResultType>
      • de.bioforscher.singa.core.parser.AbstractXMLParser<ResultType>
        • de.bioforscher.singa.simulation.parser.graphs.GraphMLParserService
      • de.bioforscher.singa.simulation.parser.sbml.SabioRKParserService
  • de.bioforscher.singa.simulation.modules.membranetransport.ActiveMembraneTransport (implements de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior, de.bioforscher.singa.simulation.modules.model.Module)
  • de.bioforscher.singa.simulation.model.rules.AppliedExpression
  • de.bioforscher.singa.simulation.model.rules.AssignmentRule
  • de.bioforscher.singa.simulation.model.rules.AssignmentRules
  • de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs
  • de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService
  • de.bioforscher.singa.simulation.model.compartments.CellSection (implements de.bioforscher.singa.core.utility.Nameable)
    • de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment
    • de.bioforscher.singa.simulation.model.compartments.Membrane
  • de.bioforscher.singa.chemistry.descriptive.entities.ChemicalEntity<IdentifierType> (implements de.bioforscher.singa.chemistry.descriptive.annotations.Annotatable, de.bioforscher.singa.features.model.Featureable, de.bioforscher.singa.core.identifier.model.Identifiable<IdentifierType>, de.bioforscher.singa.core.utility.Nameable)
    • de.bioforscher.singa.chemistry.descriptive.entities.Protein
      • de.bioforscher.singa.simulation.model.compartments.MembraneProtein
  • de.bioforscher.singa.simulation.parser.sbml.converter.CompartmentHandler
  • uk.co.cogitolearning.cogpar.ConstantExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • de.bioforscher.singa.simulation.research.DiffusionResearch
  • de.bioforscher.singa.simulation.modules.diffusion.DiffusionUtilities
  • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw (implements de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw)
  • de.bioforscher.singa.simulation.events.EpochUpdateWriter (implements de.bioforscher.singa.core.events.UpdateEventListener<EventType>)
  • uk.co.cogitolearning.cogpar.ExponentiationExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion (implements de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior, de.bioforscher.singa.simulation.modules.model.Module)
  • uk.co.cogitolearning.cogpar.FunctionExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)
  • de.bioforscher.singa.simulation.parser.sbml.FunctionReference
  • de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler (implements org.xml.sax.ContentHandler)
  • de.bioforscher.singa.simulation.parser.graphs.GraphMLExportService
  • de.bioforscher.singa.simulation.events.GraphUpdatedEvent
  • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameter<ParameterType>
    • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.EntityDependentKineticParameter<ParameterType>
  • de.bioforscher.singa.simulation.model.graphs.MembraneContainer (implements de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer)
  • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat (implements de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw)
  • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM (implements de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw)
  • de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer (implements de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer)
  • de.bioforscher.singa.simulation.events.NodeUpdatedEvent
  • uk.co.cogitolearning.cogpar.Parser
  • de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport (implements de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior, de.bioforscher.singa.simulation.modules.model.Module)
  • de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
  • de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdates
  • de.bioforscher.singa.simulation.modules.reactions.model.Reactant
    • de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant
    • de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
  • de.bioforscher.singa.simulation.modules.reactions.model.Reaction
    • de.bioforscher.singa.simulation.modules.reactions.implementations.BiochemicalReaction
    • de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
    • de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
    • de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
  • de.bioforscher.singa.simulation.modules.reactions.model.Reactions (implements de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior, de.bioforscher.singa.simulation.modules.model.Module)
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLExpressionConverter
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLParameterConverter
  • de.bioforscher.singa.simulation.parser.sbml.SBMLParser
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLReactionConverter
  • de.bioforscher.singa.simulation.parser.sbml.converter.SBMLUnitConverter
  • 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)
  • de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer (implements de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer)
  • de.bioforscher.singa.simulation.modules.model.Simulation (implements de.bioforscher.singa.core.events.UpdateEventEmitter<EventType>)
  • de.bioforscher.singa.simulation.modules.model.SimulationExamples
  • de.bioforscher.singa.simulation.model.parameters.SimulationParameter<QuantityType> (implements de.bioforscher.singa.chemistry.descriptive.annotations.Annotatable, de.bioforscher.singa.core.identifier.model.Identifiable<IdentifierType>, de.bioforscher.singa.core.utility.Nameable)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • uk.co.cogitolearning.cogpar.EvaluationException
        • uk.co.cogitolearning.cogpar.ParserException
  • uk.co.cogitolearning.cogpar.Token
  • uk.co.cogitolearning.cogpar.Tokenizer
  • de.bioforscher.singa.simulation.model.parameters.UnitScaler
  • uk.co.cogitolearning.cogpar.VariableExpressionNode (implements uk.co.cogitolearning.cogpar.ExpressionNode)

Interface Hierarchy

• de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer
• uk.co.cogitolearning.cogpar.ExpressionNode
• uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
• de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw
• de.bioforscher.singa.simulation.modules.model.Module
• de.bioforscher.singa.simulation.modules.model.updates.UpdateBehavior
  • de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • de.bioforscher.singa.simulation.model.compartments.NodeState
    • de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameterType
    • de.bioforscher.singa.simulation.modules.reactions.model.ReactantRole