Hierarchy For All Packages

Package Hierarchies:

• fern,
• fern.analysis,
• fern.benchmark,
• fern.example,
• fern.network,
• fern.network.creation,
• fern.network.fernml,
• fern.network.modification,
• fern.network.sbml,
• fern.simulation,
• fern.simulation.algorithm,
• fern.simulation.controller,
• fern.simulation.observer,
• fern.tools,
• fern.tools.functions,
• fern.tools.gnuplot,
• 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,
• org.testsuite

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
  • fern.network.AbstractKineticConstantPropensityCalculator (implements fern.network.KineticConstantPropensityCalculator, fern.network.PartialDerivativePropensityCalculator)
    • fern.network.ArrayKineticConstantPropensityCalculator
  • fern.network.AbstractNetworkImpl (implements fern.network.Network)
    • fern.network.creation.AutocatalyticNetwork (implements fern.network.creation.CatalystIterator)
    • fern.network.fernml.FernMLNetwork
    • fern.network.sbml.SBMLNetwork
  • 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
  • fern.simulation.controller.AmountLowerThanController (implements fern.simulation.controller.SimulationController)
  • fern.analysis.AnalysisBase
    • fern.analysis.AutocatalyticNetworkDetection
    • fern.analysis.ShortestPath
  • fern.simulation.controller.AndController (implements fern.simulation.controller.SimulationController)
  • fern.network.AnnotationManagerImpl (implements fern.network.AnnotationManager)
  • 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
  • fern.example.AutocatalyticNetworkExample
  • fern.tools.gnuplot.Axes (implements java.lang.Iterable<T>)
    • fern.tools.gnuplot.ArrayMatrixAxes
      • fern.tools.gnuplot.TransposedArrayMatrixAxes
    • fern.tools.gnuplot.CollectionAxes
  • fern.benchmark.Benchmark
    • fern.benchmark.RandomNumber
    • fern.benchmark.SimulatorPerformance
      • fern.benchmark.SimulatorCorrectness
      • fern.benchmark.SimulatorTime
        • fern.benchmark.SimulatorFireTypes
        • fern.benchmark.SimulatorRandomNumbers
  • org.simulator.examples.BiomodelsExample
  • fern.tools.ColorSpectrum
  • 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
            • fern.tools.gnuplot.GnuPlot
  • fern.example.CompositionRejectionStressTest
  • org.simulator.comp.CompSimulator
  • fern.tools.ConfigReader
  • fern.network.ConstantAmountManager (implements fern.network.AmountManager)
  • org.simulator.examples.ConstraintExample
  • org.simulator.io.CSVImporter
  • fern.example.DecayingDimerizingHistogramDistances
  • fern.example.DecayingDimerizingInteractive
  • fern.example.DecayingDimerizingPlots
  • fern.network.DefaultAmountManager (implements fern.network.AmountManager)
  • fern.simulation.controller.DefaultController (implements fern.simulation.controller.SimulationController)
  • fern.simulation.algorithm.DependencyGraph
  • fern.example.Dsmts
  • org.simulator.sbml.EquationSystem (implements org.simulator.math.odes.DelayedDESystem, org.simulator.math.odes.EventDESystem, org.simulator.math.odes.FastProcessDESystem, java.beans.PropertyChangeListener, org.simulator.math.odes.RichDESystem, org.simulator.sbml.SBMLValueHolder)
    • org.simulator.sbml.SBMLinterpreter
  • org.simulator.math.odes.EventInProgress
    • org.simulator.sbml.SBMLEventInProgress
      • org.simulator.sbml.SBMLEventInProgressWithDelay
  • java.util.EventObject (implements java.io.Serializable)
    • org.simulator.sbml.ConstraintEvent
  • fern.example.ExamplePath
  • org.simulator.examples.FBAExample
  • fern.network.fernml.FernMLAnnotationManager (implements fern.network.AnnotationManager)
  • org.simulator.sedml.FileModelResolver (implements org.jlibsedml.execution.IModelResolver)
  • org.simulator.fba.FluxBalanceAnalysis
  • fern.simulation.algorithm.GroupContainer
  • fern.example.HistogramDistanceTestSet
  • fern.simulation.algorithm.IndexedPriorityQueue
  • fern.example.IrreversibleIsomerization
  • fern.example.LacYComplete
  • fern.example.LacYHistogramDistances
  • fern.example.LacZ
  • fern.example.Mapk
  • fern.example.MapkBenchmark
  • org.simulator.math.Mathematics
  • fern.network.sbml.MathTree
  • org.simulator.math.MatrixOperations
  • org.simulator.math.MeanFunction (implements java.io.Serializable)
    • org.simulator.math.ArithmeticMean
    • org.simulator.math.DistanceSum
  • fern.example.MichaelisMentenKinetic
  • fern.network.modification.ModifierNetwork (implements fern.network.Network)
    • fern.network.modification.CatalysedNetwork
    • fern.network.modification.ExtractSubNetwork
    • fern.network.modification.ReversibleNetwork
  • org.simulator.math.odes.MultiTable.Block.Column (implements java.lang.Iterable<T>)
  • org.simulator.sedml.MultTableSEDMLWrapper (implements org.jlibsedml.execution.IRawSedmlSimulationResults)
  • fern.network.NetworkLoader
  • fern.tools.NetworkTools
  • org.simulator.fba.NewGLPKSolver (implements scpsolver.lpsolver.LinearProgramSolver)
  • fern.analysis.NodeCheckerByAnnotation (implements fern.analysis.NodeChecker)
  • fern.tools.NumberTools
  • fern.simulation.observer.Observer
    • fern.simulation.observer.AmountAtMomentObserver (implements fern.simulation.observer.GnuPlotObserver, fern.simulation.controller.SimulationController)
    • fern.example.CellGrowthObserver
    • fern.simulation.observer.FireTypeObserver (implements fern.simulation.observer.GnuPlotObserver)
    • fern.simulation.observer.InstantOutputObserver
    • fern.simulation.observer.IntervalObserver (implements fern.simulation.observer.GnuPlotObserver)
      • fern.simulation.observer.AmountIntervalObserver
      • fern.simulation.observer.MultiAmountIntervalObserver
      • fern.simulation.observer.ReactionIntervalObserver
    • fern.simulation.observer.LeapObserver (implements fern.simulation.observer.GnuPlotObserver)
    • fern.simulation.observer.RandomNumberGeneratorCallObserver (implements fern.simulation.observer.GnuPlotObserver)
    • fern.simulation.observer.TriggerObserver
      • fern.network.sbml.SBMLEventHandlerObserver
  • org.simulator.omex.OMEXArchive
  • org.simulator.examples.OMEXExample
  • fern.simulation.controller.OrController (implements fern.simulation.controller.SimulationController)
  • cern.colt.PersistentObject (implements java.lang.Cloneable, java.io.Serializable)
    • cern.colt.list.AbstractCollection
      • cern.colt.list.AbstractList
        • cern.colt.list.AbstractIntList (implements cern.colt.buffer.IntBufferConsumer)
          • cern.colt.list.IntArrayList
            • fern.analysis.IntQueue (implements fern.analysis.IntSearchStructure)
            • fern.analysis.IntStack (implements fern.analysis.IntSearchStructure)
  • fern.tools.functions.Probability.Constant (implements fern.tools.functions.Probability)
  • fern.tools.functions.Probability.ReactionProbability (implements fern.tools.functions.Probability)
  • org.simulator.sedml.ProcessSedMLResults
  • org.simulator.math.QualityMeasure (implements java.io.Serializable)
    • org.simulator.math.MaxAbsDistance
    • org.simulator.math.MaxDivergenceTolerance
    • 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.RelativeMaxDistance
  • org.simulator.sbml.astnode.RuleValue
    • org.simulator.sbml.astnode.AssignmentRuleValue
    • org.simulator.sbml.astnode.RateRuleValue
  • fern.example.SBMLMathTreeTest
  • fern.network.sbml.SBMLPropensityCalculator (implements fern.network.ComplexDependenciesPropensityCalculator)
  • org.testsuite.SBMLTestSuiteRunnerWrapper
  • org.simulator.examples.SEDMLExample
  • org.simulator.sedml.SEDMLWriter
  • fern.analysis.ShortestPath.Path
  • org.simulator.sbml.SimpleConstraintListener (implements org.simulator.sbml.ConstraintListener)
  • fern.simulation.Simulator
    • fern.simulation.algorithm.GibsonBruckSimulator
    • fern.simulation.algorithm.GillespieEnhanced
      • fern.simulation.algorithm.AbstractBaseTauLeaping
        • fern.simulation.algorithm.AbstractTauLeapingPropensityBoundSimulator
          • fern.simulation.algorithm.TauLeapingAbsoluteBoundSimulator
          • fern.simulation.algorithm.TauLeapingRelativeBoundSimulator
        • fern.simulation.algorithm.TauLeapingSpeciesPopulationBoundSimulator
      • fern.simulation.algorithm.CompositionRejection
    • fern.simulation.algorithm.GillespieSimple
    • fern.simulation.algorithm.HybridMaximalTimeStep
  • org.simulator.examples.SimulatorExample (implements java.beans.PropertyChangeListener)
  • fern.Start
  • fern.tools.Stochastics
  • org.simulator.sbml.astnode.StoichiometryValue
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • fern.network.FeatureNotSupportedException
      • org.simulator.math.MatrixOperations.MatrixException
      • java.lang.RuntimeException
        • org.simulator.sedml.ExecutionException

Interface Hierarchy

• fern.network.AmountManager
• fern.network.AnnotationManager
• fern.network.creation.CatalystIterator
• 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.DelayedDESystem
  • 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
  • org.simulator.math.odes.EventDESystem
  • org.simulator.math.odes.FastProcessDESystem
  • org.simulator.math.odes.ParameterizedDESystem
  • org.simulator.math.odes.RichDESystem
• fern.simulation.observer.GnuPlotObserver
• fern.analysis.IntSearchStructure
• fern.network.Network
• fern.analysis.NetworkSearchAction
• fern.analysis.NodeChecker
• fern.tools.functions.Probability
• fern.network.PropensityCalculator
  • fern.network.ComplexDependenciesPropensityCalculator
  • fern.network.KineticConstantPropensityCalculator
  • fern.network.PartialDerivativePropensityCalculator
• java.io.Serializable
  • org.simulator.math.odes.DelayedDESystem
  • 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.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)
• fern.simulation.controller.SimulationController

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • fern.analysis.NetworkSearchAction.NeighborType
    • fern.simulation.Simulator.FireType