Hierarchy For All Packages

Package Hierarchies:

• org.simulator,
• org.simulator.comp,
• org.simulator.examples,
• org.simulator.fba,
• org.simulator.io,
• org.simulator.math,
• org.simulator.math.odes,
• org.simulator.omex,
• org.simulator.plot,
• org.simulator.sbml,
• org.simulator.sbml.astnode,
• org.simulator.sedml

Class Hierarchy

• java.lang.Object
  • org.simulator.About
  • org.simulator.math.odes.AbstractDESSolver (implements org.simulator.math.odes.DelayValueHolder, org.simulator.math.odes.DESSolver, org.apache.commons.math.ode.events.EventHandler)
    • org.simulator.math.odes.AdaptiveStepsizeIntegrator
      • org.simulator.math.odes.FirstOrderSolver
        • org.simulator.math.odes.AdamsBashforthSolver
        • org.simulator.math.odes.AdamsMoultonSolver
        • org.simulator.math.odes.DormandPrince54Solver
        • org.simulator.math.odes.DormandPrince853Solver
        • org.simulator.math.odes.GraggBulirschStoerSolver
        • org.simulator.math.odes.HighamHall54Solver
      • org.simulator.math.odes.RosenbrockSolver
    • org.simulator.math.odes.EulerMethod
    • org.simulator.math.odes.RungeKutta_EventSolver
  • org.jlibsedml.execution.AbstractSedmlExecutor
    • org.simulator.sedml.SedMLSBMLSimulatorExecutor
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • org.simulator.math.odes.MultiTable (implements java.lang.Iterable<T>)
    • org.simulator.math.odes.MultiTable.Block
  • org.simulator.sbml.AddMetaInfo
  • org.simulator.sbml.AlgebraicRuleConverter
  • org.simulator.sbml.astnode.ASTNodeInterpreter
  • org.simulator.sbml.astnode.ASTNodeValue
    • org.simulator.sbml.astnode.CompartmentOrParameterValue
    • org.simulator.sbml.astnode.DivideValue
    • org.simulator.sbml.astnode.FunctionValue
    • org.simulator.sbml.astnode.IntegerValue
    • org.simulator.sbml.astnode.LocalParameterValue
    • org.simulator.sbml.astnode.MinusValue
    • org.simulator.sbml.astnode.NamedValue
    • org.simulator.sbml.astnode.PlusValue
    • org.simulator.sbml.astnode.PowerValue
    • org.simulator.sbml.astnode.ReactionValue
    • org.simulator.sbml.astnode.RootFunctionValue
    • org.simulator.sbml.astnode.SpeciesReferenceValue
    • org.simulator.sbml.astnode.SpeciesValue
    • org.simulator.sbml.astnode.TimesValue
  • org.simulator.examples.BiomodelsExample
  • org.simulator.fba.COBRAsolver
  • org.simulator.examples.COBRAsolverExample
  • org.simulator.examples.CompExample
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.jfree.ui.ApplicationFrame (implements java.awt.event.WindowListener)
              • org.simulator.plot.PlotMultiTable
              • org.simulator.plot.PlotProcessedSedmlResults
  • org.simulator.comp.CompSimulator
  • org.simulator.examples.ConstraintExample
  • org.simulator.io.CSVImporter
  • org.simulator.math.odes.EventInProgress
    • org.simulator.sbml.SBMLEventInProgress
      • org.simulator.sbml.SBMLEventInProgressWithDelay
  • java.util.EventObject (implements java.io.Serializable)
    • org.simulator.sbml.ConstraintEvent
  • org.simulator.sedml.FileModelResolver (implements org.jlibsedml.execution.IModelResolver)
  • org.simulator.math.Mathematics
  • org.simulator.math.MatrixOperations
  • org.simulator.math.MeanFunction (implements java.io.Serializable)
    • org.simulator.math.ArithmeticMean
    • org.simulator.math.DistanceSum
  • org.simulator.math.odes.MultiTable.Block.Column (implements java.lang.Iterable<T>)
  • org.simulator.sedml.MultTableSEDMLWrapper (implements org.jlibsedml.execution.IRawSedmlSimulationResults)
  • org.simulator.omex.OMEXArchive
  • org.simulator.examples.OMEXExample
  • org.simulator.sedml.ProcessSedMLResults
  • org.simulator.math.QualityMeasure (implements java.io.Serializable)
    • org.simulator.math.N_Metric
      • org.simulator.math.EuclideanDistance
      • org.simulator.math.ManhattanDistance
      • org.simulator.math.RelativeSquaredError
    • org.simulator.math.PearsonCorrelation
    • org.simulator.math.Relative_N_Metric
      • org.simulator.math.RelativeEuclideanDistance
      • org.simulator.math.RelativeManhattanDistance
  • org.simulator.math.RNG
  • org.simulator.sbml.astnode.RuleValue
    • org.simulator.sbml.astnode.AssignmentRuleValue
    • org.simulator.sbml.astnode.RateRuleValue
  • org.simulator.sbml.SBMLinterpreter (implements org.simulator.math.odes.DelayedDESystem, org.simulator.math.odes.EventDESystem, org.simulator.math.odes.FastProcessDESystem, org.simulator.math.odes.RichDESystem, org.simulator.sbml.SBMLValueHolder)
  • org.simulator.examples.SEDMLExample
  • org.simulator.sedml.SEDMLWriter
  • org.simulator.sbml.SimpleConstraintListener (implements org.simulator.sbml.ConstraintListener)
  • org.simulator.examples.SimulatorExample
  • org.simulator.sbml.astnode.StoichiometryValue
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.simulator.math.MatrixOperations.MatrixException
      • java.lang.RuntimeException
        • org.simulator.sedml.ExecutionException

Interface Hierarchy

• java.lang.Cloneable
  • org.simulator.math.odes.DESSolver (also extends java.io.Serializable)
• java.util.EventListener
  • org.simulator.sbml.ConstraintListener
• org.apache.commons.math.ode.FirstOrderDifferentialEquations
  • org.simulator.math.odes.DESystem (also extends java.io.Serializable)
    • org.simulator.math.odes.DelayedDESystem
    • org.simulator.math.odes.EventDESystem
    • org.simulator.math.odes.FastProcessDESystem
    • org.simulator.math.odes.ParameterizedDESystem
    • org.simulator.math.odes.RichDESystem
• java.io.Serializable
  • org.simulator.math.odes.DelayValueHolder
    • org.simulator.sbml.SBMLValueHolder (also extends java.io.Serializable)
  • org.simulator.math.odes.DESSolver (also extends java.lang.Cloneable)
  • org.simulator.math.odes.DESystem (also extends org.apache.commons.math.ode.FirstOrderDifferentialEquations)
    • org.simulator.math.odes.DelayedDESystem
    • org.simulator.math.odes.EventDESystem
    • org.simulator.math.odes.FastProcessDESystem
    • org.simulator.math.odes.ParameterizedDESystem
    • org.simulator.math.odes.RichDESystem
  • org.simulator.sbml.SBMLValueHolder (also extends org.simulator.math.odes.DelayValueHolder)