Hierarchy For All Packages

Package Hierarchies:

org.systemsbiology.chem, org.systemsbiology.chem.app, org.systemsbiology.chem.odetojava, org.systemsbiology.chem.sbml, org.systemsbiology.chem.sbw, org.systemsbiology.data, org.systemsbiology.gui, org.systemsbiology.inference, org.systemsbiology.math, org.systemsbiology.math.probability, org.systemsbiology.util

Class Hierarchy

• class java.lang.Object
  • class org.systemsbiology.chem.app.AboutDialog
  • class org.systemsbiology.data.AbstractComparator
  • class javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • class org.systemsbiology.gui.EmptyTableModel
    • class org.systemsbiology.inference.ObservationsTableModel
  • class org.systemsbiology.util.AppConfig
  • class org.systemsbiology.util.ClassRegistry
  • class org.systemsbiology.util.CommandLineApp
    • class org.systemsbiology.chem.app.SimulationLauncherCommandLine
  • class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • class java.awt.Container
      • class javax.swing.JComponent (implements java.io.Serializable)
        • class javax.swing.JFileChooser (implements javax.accessibility.Accessible)
          • class org.systemsbiology.gui.FileChooser
        • class javax.swing.JMenuBar (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • class org.systemsbiology.chem.app.MainMenu
        • class javax.swing.JOptionPane (implements javax.accessibility.Accessible)
          • class org.systemsbiology.gui.ExceptionNotificationOptionPane
        • class javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • class javax.swing.JTextArea
            • class org.systemsbiology.gui.SimpleTextArea
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Dialog
          • class javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class org.systemsbiology.gui.MatrixStringSelectorDialog
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class org.systemsbiology.gui.DataColumnSelector
            • class org.systemsbiology.chem.app.SimulationResultsPlot
            • class org.systemsbiology.chem.app.SimulationResultsTable
  • class org.systemsbiology.gui.ComponentUtils
  • class org.systemsbiology.chem.Constants
  • class org.systemsbiology.data.DataFileDelimiter (implements java.lang.Comparable)
  • class org.systemsbiology.inference.DataManagerDriver
  • class org.systemsbiology.inference.DataNormalizationMethod
  • class org.systemsbiology.inference.DataNormalizationScale
  • class org.systemsbiology.inference.DataNormalizer
  • class org.systemsbiology.inference.DataNormalizerDriver
  • class org.systemsbiology.inference.DataNormalizerParams
  • class org.systemsbiology.inference.DataNormalizerResults
  • class org.systemsbiology.util.DebugUtils
  • class org.systemsbiology.chem.DelayedReactionSolver
  • class org.systemsbiology.math.probability.DistributionPrinter
  • class org.systemsbiology.math.DoubleVector
  • class org.systemsbiology.chem.app.EditorPane
  • class org.systemsbiology.math.probability.Empirical (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.inference.EvidenceWeightedInferer
  • class org.systemsbiology.inference.EvidenceWeightedInfererDriver
  • class org.systemsbiology.inference.EvidenceWeightedInfererParams
  • class org.systemsbiology.inference.EvidenceWeightedInfererResults
  • class org.systemsbiology.inference.EvidenceWeightType (implements java.lang.Comparable)
  • class org.systemsbiology.util.ExceptionUtils
  • class org.systemsbiology.math.Expression (implements java.lang.Cloneable)
  • class javax.swing.filechooser.FileFilter
    • class org.systemsbiology.chem.app.ChemFileFilter
    • class org.systemsbiology.gui.RegexFileFilter
  • class org.systemsbiology.util.FileUtils
  • class java.text.Format (implements java.lang.Cloneable, java.io.Serializable)
    • class java.text.NumberFormat
      • class java.text.DecimalFormat
        • class org.systemsbiology.math.ScientificNumberFormat
  • class org.systemsbiology.gui.FramePlacer
  • class org.systemsbiology.math.probability.Gamma (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.math.probability.HalfLorentz (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.math.probability.HalfNormal (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.gui.HelpBrowser
  • class org.systemsbiology.gui.IconFactory
  • class org.systemsbiology.util.IncludeHandler
  • class org.systemsbiology.math.probability.Laplace (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.math.probability.Logistic (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.math.probability.Lorentz (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.chem.app.MainApp
  • class org.systemsbiology.chem.app.MainMenu.Menu
  • class org.systemsbiology.chem.app.MainMenu.MenuItem
  • class org.systemsbiology.chem.sbml.MarkupLanguageImporter
  • class org.systemsbiology.math.MathFunctions
  • class org.systemsbiology.data.MatrixString
  • class org.systemsbiology.math.probability.Maxwell (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.chem.Model
  • class org.systemsbiology.chem.ModelBuilderCommandLanguage (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelBuilder)
  • class org.systemsbiology.chem.sbml.ModelBuilderMarkupLanguage (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelBuilder)
  • class org.systemsbiology.chem.app.ModelExporter
  • class org.systemsbiology.chem.ModelExporterCommandLanguage (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelExporter)
  • class org.systemsbiology.chem.ModelExporterHumanReadable (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelExporter)
  • class org.systemsbiology.chem.sbml.ModelExporterMarkupLanguage (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelExporter)
  • class org.systemsbiology.chem.sbml.ModelExporterMarkupLanguage.Specification
  • class org.systemsbiology.chem.ModelExporterOrrellColumnFormat (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelExporter)
  • class org.systemsbiology.chem.app.ModelViewerCytoscape (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelViewer)
  • class org.systemsbiology.chem.app.ModelViewerHumanReadable (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.IModelViewer)
  • class org.systemsbiology.math.MutableBoolean
  • class org.systemsbiology.math.MutableDouble
  • class org.systemsbiology.math.MutableInteger
  • class javax.help.NavigatorView
    • class javax.help.SearchView
      • class org.systemsbiology.gui.ExHelpSearchNavigator
  • class org.systemsbiology.math.probability.Normal (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.inference.ObservationsData (implements java.lang.Cloneable)
  • class org.systemsbiology.chem.app.ParserPicker
  • class org.systemsbiology.inference.PreferencesHandler
  • class org.systemsbiology.data.PriorityQueue.Node
  • class org.systemsbiology.data.Queue
    • class org.systemsbiology.data.ListQueue
    • class org.systemsbiology.data.PriorityQueue
      • class org.systemsbiology.data.IndexedPriorityQueue
  • class org.systemsbiology.math.probability.Rayleigh (implements org.systemsbiology.math.probability.IContinuousDistribution)
  • class org.systemsbiology.chem.ReactionParticipant (implements java.lang.Comparable)
  • class org.systemsbiology.chem.ReactionParticipant.Type
  • class org.systemsbiology.math.ReservedSymbolMapper
    • class org.systemsbiology.chem.ReservedSymbolMapperChemCommandLanguage
  • class org.systemsbiology.inference.SignificanceCalculationMethod (implements java.lang.Comparable)
  • class org.systemsbiology.inference.SignificanceCalculationResults
  • class org.systemsbiology.inference.SignificanceCalculator
  • class org.systemsbiology.inference.SignificanceCalculatorDriver
  • class org.systemsbiology.inference.SignificanceCalculatorParams
  • class org.systemsbiology.inference.SignificancesData
  • class org.systemsbiology.math.SignificantDigitsCalculator
  • class org.systemsbiology.chem.SimulationController
  • class org.systemsbiology.chem.sbw.SimulationDriverModule
  • class org.systemsbiology.chem.sbw.SimulationDriverService (implements org.systemsbiology.chem.sbw.ISimulationDriverService)
  • class org.systemsbiology.chem.app.SimulationLauncher
  • class org.systemsbiology.chem.app.SimulationLauncher.SetModelResult
  • class org.systemsbiology.chem.SimulationProgressReporter
  • class org.systemsbiology.chem.SimulationResults
  • class org.systemsbiology.chem.Simulator
    • class org.systemsbiology.chem.SimulatorDeterministicBase
      • class org.systemsbiology.chem.SimulatorDeterministicRungeKuttaAdaptive (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
      • class org.systemsbiology.chem.SimulatorDeterministicRungeKuttaFixed (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
    • class org.systemsbiology.chem.odetojava.SimulatorOdeToJavaBase (implements odeToJava.modules.ODE, odeToJava.modules.ODERecorder)
      • class org.systemsbiology.chem.odetojava.SimulatorOdeToJavaRungeKuttaAdaptive (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
      • class org.systemsbiology.chem.odetojava.SimulatorOdeToJavaRungeKuttaImplicit (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
    • class org.systemsbiology.chem.SimulatorStochasticBase
      • class org.systemsbiology.chem.SimulatorStochasticGibsonBruck (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
      • class org.systemsbiology.chem.SimulatorStochasticGillespie (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
      • class org.systemsbiology.chem.SimulatorStochasticTauLeapBase
        • class org.systemsbiology.chem.SimulatorStochasticTauLeapComplex (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
        • class org.systemsbiology.chem.SimulatorStochasticTauLeapSimple (implements org.systemsbiology.util.IAliasableClass, org.systemsbiology.chem.ISimulator)
  • class org.systemsbiology.chem.SimulatorParameters
  • class org.systemsbiology.data.SlidingWindowTimeSeriesQueue
  • class org.systemsbiology.gui.SortStatus
  • class org.systemsbiology.chem.SteadyStateAnalyzer
  • class org.systemsbiology.chem.sbml.SubstanceUnit
  • class org.systemsbiology.math.Symbol
  • class org.systemsbiology.math.SymbolEvaluationPostProcessor (implements java.lang.Cloneable)
    • class org.systemsbiology.chem.sbml.SymbolEvaluationPostProcessorChemMarkupLanguage
  • class org.systemsbiology.math.SymbolEvaluator (implements java.lang.Cloneable)
    • class org.systemsbiology.chem.SymbolEvaluatorChem
    • class org.systemsbiology.math.SymbolEvaluatorHashMap
  • class org.systemsbiology.math.SymbolValue (implements java.lang.Comparable)
    • class org.systemsbiology.chem.Compartment
    • class org.systemsbiology.chem.Parameter
    • class org.systemsbiology.chem.Reaction
    • class org.systemsbiology.chem.Species
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class org.systemsbiology.math.AccuracyException
      • class org.systemsbiology.util.DataNotFoundException
      • class org.systemsbiology.util.InvalidInputException
      • class org.systemsbiology.chem.ModelExporterException
      • class org.systemsbiology.chem.ModelViewerException
      • class org.systemsbiology.chem.SimulationFailedException
  • class org.systemsbiology.chem.TimeSeriesOutputFormat
  • class org.systemsbiology.chem.TimeSeriesSymbolValuesReporter
  • class javax.swing.TransferHandler (implements java.io.Serializable)
    • class org.systemsbiology.gui.ImageTransferHandler
  • class org.systemsbiology.math.Value

Interface Hierarchy

• interface org.systemsbiology.math.Expression.IVisitor
• interface org.systemsbiology.math.Expression.SymbolPrinter
• interface org.systemsbiology.util.IAliasableClass
• interface org.systemsbiology.math.probability.IContinuousDistribution
• interface org.systemsbiology.chem.IModelBuilder
• interface org.systemsbiology.chem.IModelExporter
• interface org.systemsbiology.chem.IModelViewer
• interface org.systemsbiology.chem.sbw.ISimulationDriverService
• interface org.systemsbiology.chem.ISimulator
• interface org.systemsbiology.chem.app.SimulationLauncher.Listener