Hierarchy For All Packages

Package Hierarchies:

fern, fern.analysis, fern.benchmark, fern.cellDesigner, fern.cellDesigner.ui, fern.cytoscape, fern.cytoscape.ui, 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

Class Hierarchy

• java.lang.Object
  • 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.cellDesigner.CellDesignerNetworkWrapper
    • fern.cytoscape.CytoscapeNetworkWrapper
    • fern.network.fernml.FernMLNetwork
    • fern.network.sbml.SBMLNetwork
  • 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)
  • 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
  • CellDesignerPlugin
    • fern.cellDesigner.FernCellDesignerPlugin
  • fern.cytoscape.ColorCalculator (implements java.lang.Cloneable)
  • fern.tools.ColorSpectrum
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • fern.cellDesigner.ui.ExtendedPane
          • fern.cytoscape.ui.ExtendedPane
          • fern.cellDesigner.ui.OverviewPane
          • fern.cytoscape.ui.OverviewPane
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • fern.cytoscape.ui.ColorPicker
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • fern.tools.gnuplot.GnuPlot
            • fern.cellDesigner.ui.MainFrame
            • fern.cytoscape.ui.MainFrame
  • fern.example.CompositionRejectionStressTest
  • fern.tools.ConfigReader
  • fern.network.ConstantAmountManager (implements fern.network.AmountManager)
  • CytoscapeAction
    • fern.cytoscape.CytoscapeVisualizer.ShowMainFrameAction
  • CytoscapeAction
    • fern.cytoscape.CytoscapeVisualizer.SimulationAction
  • fern.cytoscape.CytoscapeAnnotationManager (implements fern.network.AnnotationManager)
  • CytoscapePlugin
    • fern.cytoscape.CytoscapeVisualizer
  • 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
  • fern.example.ExamplePath
  • fern.network.fernml.FernMLAnnotationManager (implements fern.network.AnnotationManager)
  • 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
  • fern.network.sbml.MathTree
  • fern.network.sbml.MathTree.Node
    • fern.network.sbml.MathTree.ConstLeaf
    • fern.network.sbml.MathTree.GlobalLeaf
    • fern.network.sbml.MathTree.InnerNode
    • fern.network.sbml.MathTree.VarLeaf
  • fern.example.MichaelisMentenKinetic
  • fern.network.modification.ModifierNetwork (implements fern.network.Network)
    • fern.network.modification.CatalysedNetwork
    • fern.network.modification.ExtractSubNetwork
    • fern.network.modification.MultiplierNetwork
    • fern.network.modification.ReversibleNetwork
  • fern.cytoscape.NetworkChecker
  • fern.cytoscape.NetworkChecker.EdgeClassifierByDirection (implements fern.cytoscape.NetworkChecker.EdgeClassifier)
  • fern.cytoscape.NetworkChecker.EdgeClassifierByIdentifier (implements fern.cytoscape.NetworkChecker.EdgeClassifier)
  • fern.cytoscape.NetworkChecker.NodeClassifierByAnnotation<T> (implements fern.cytoscape.NetworkChecker.NodeClassifier)
  • fern.cytoscape.NetworkChecker.NodeParameter
  • fern.network.NetworkLoader
  • fern.tools.NetworkTools
  • 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.cytoscape.CytoscapeColorChangeObserver
    • 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
  • 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)
  • fern.example.SBMLMathTreeTest
  • fern.network.sbml.SBMLPropensityCalculator (implements fern.network.ComplexDependenciesPropensityCalculator)
    • fern.cellDesigner.CellDesignerPropensityCalculator
  • fern.analysis.ShortestPath.Path
  • 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
  • fern.Start
  • fern.tools.Stochastics
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • fern.network.FeatureNotSupportedException
  • VisualStyle
    • fern.cytoscape.FernVisualStyle

Interface Hierarchy

• fern.network.AmountManager
• fern.network.AnnotationManager
• fern.network.creation.CatalystIterator
• fern.simulation.observer.GnuPlotObserver
• fern.analysis.IntSearchStructure
• fern.network.Network
• fern.cytoscape.NetworkChecker.EdgeClassifier
• fern.cytoscape.NetworkChecker.NodeClassifier
• fern.analysis.NetworkSearchAction
• fern.analysis.NodeChecker
• fern.tools.functions.Probability
• fern.network.PropensityCalculator
  • fern.network.ComplexDependenciesPropensityCalculator
  • fern.network.KineticConstantPropensityCalculator
  • fern.network.PartialDerivativePropensityCalculator
• 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.cytoscape.ColorCalculator.Scale
    • fern.simulation.Simulator.FireType