Hierarchy For All Packages

Package Hierarchies:

affectors, genegui, initialconditions, integrators, iterators, main, parameterrules, parameters, stat, stoppers

Class Hierarchy

• class java.lang.Object
  • class javax.swing.text.AbstractDocument (implements javax.swing.text.Document, java.io.Serializable)
    • class javax.swing.text.DefaultStyledDocument (implements javax.swing.text.StyledDocument)
      • class main.NetworkFile
  • class affectors.Affector (implements java.lang.Cloneable)
    • class affectors.Affector_Template
    • class affectors.Cleavage2A_ICAff
    • class affectors.Cleavage2B_ICAff
    • class affectors.CleavageA_ECAff
    • class affectors.CleavageA_ICAff
    • class affectors.CleavageA_ICDipAff
    • class affectors.CleavageB_ECAff
    • class affectors.CleavageB_ICAff
    • class affectors.CleavageB_ICDipAff
    • class affectors.CleaveA_Aff
    • class affectors.CleaveB_Aff
    • class affectors.CompAct2Aff
    • class affectors.ConstantInputAff
    • class affectors.ConstantLevelAff
    • class affectors.ConversionEAff
    • class affectors.ConversionIAff
    • class affectors.DecayAff
    • class affectors.DecayRegDownAff
    • class affectors.DecayRegUpAff
    • class affectors.DefinedValuesAff
    • class affectors.DefinedValuesIndicatorAff
    • class affectors.Dephosphor1StepA_ICAff
    • class affectors.Dephosphor1StepB_ICAff
    • class affectors.DephosphorylateA_Aff
    • class affectors.DephosphorylateB_Aff
    • class affectors.DephosphorylationA_ICAff
    • class affectors.DephosphorylationB_ICAff
    • class affectors.Dimerize_AAff
      • class affectors.HeterodimerizeA_EC2Aff
      • class affectors.HeterodimerizeA_ICAff
    • class affectors.Dimerize_BAff
      • class affectors.HeterodimerizeB_EC2Aff
      • class affectors.HeterodimerizeB_ICAff
    • class affectors.DimerizeAllMembrane_AAff
      • class affectors.HeterodimerizeA_EC_XAff
    • class affectors.DimerizeAllMembrane_BAff
      • class affectors.HeterodimerizeB_EC_XAff
    • class affectors.DimerizeCrossMembrane_AAff
      • class affectors.HeterodimerizeA_ECAff
    • class affectors.DimerizeCrossMembrane_BAff
      • class affectors.HeterodimerizeB_ECAff
    • class affectors.DimerizeCytoMem_AAff
    • class affectors.DimerizeCytoMem_BAff
    • class affectors.DimerizeCytoMem_CAff
    • class affectors.DimerizeMemCyto_AAff
      • class affectors.HeterodimerizeA_ECICAff
    • class affectors.DimerizeMemCyto_BAff
      • class affectors.HeterodimerizeB_ECICAff
    • class affectors.DimerizeMemCyto_CAff
      • class affectors.HeterodimerizeC_ECICAff
    • class affectors.DissociationA_Aff
    • class affectors.DissociationB_Aff
    • class affectors.DissociationC_Aff
    • class affectors.DissociationCytoMemA_Aff
    • class affectors.DissociationCytoMemB_Aff
    • class affectors.DissociationCytoMemC_Aff
    • class affectors.DissociationEC_Com_Aff
    • class affectors.DissociationEC_Lig_Aff
    • class affectors.DissociationEC_Rec_Aff
    • class affectors.EndoEAff
    • class affectors.EndoIAff
    • class affectors.EnhancerRegionAff
      • class affectors.MultiEnhancerAff (implements java.lang.Cloneable)
      • class affectors.Product (implements java.lang.Cloneable)
      • class affectors.ProductAff (implements java.lang.Cloneable)
      • class affectors.SaturationEnhancerAff
      • class affectors.SumAff (implements java.lang.Cloneable)
    • class affectors.EnzymeConversionEC_Pro_Aff
    • class affectors.EnzymeConversionEC_Sub_Aff
    • class affectors.ExoEAff
    • class affectors.ExoIAff
    • class affectors.Formula1Aff
    • class affectors.HeatShockAff
    • class affectors.LMxferEAff
    • class affectors.LMxferIAff
    • class affectors.MxferInAff
    • class affectors.MxferOutAff
    • class affectors.NoChangeAff
    • class affectors.Phosphor1StepA_ICAff
    • class affectors.Phosphor1StepB_ICAff
    • class affectors.PhosphorylateA_Aff
    • class affectors.PhosphorylateB_Aff
    • class affectors.PhosphorylationA_ICAff
    • class affectors.PhosphorylationB_ICAff
    • class affectors.PlaceHolderAff
    • class affectors.PsiAff
    • class affectors.PsiECAff
    • class affectors.RecycleAAff
    • class affectors.RecycleBAff
    • class affectors.TlnAff
    • class affectors.TlnRegUpAff
    • class affectors.Txn1Aff
    • class affectors.Txn1ECAff
    • class affectors.Txn2aAff
    • class affectors.Txn2aDipAff
    • class affectors.Txn2bAff
    • class affectors.Txn2bDipAff
    • class affectors.Txn3aAff
    • class affectors.Txn3bAff
    • class affectors.Txn4Aff
    • class affectors.Txn4DipAff
    • class affectors.Txn5Aff
    • class affectors.Txn6aAff
    • class affectors.Txn6bAff
    • class affectors.TxnLeakyCyceAff
    • class affectors.TxnSiteActInhibit2Aff
    • class affectors.TxnSiteActInhibit3Aff
    • class affectors.TxnSiteActInhibitAff
    • class affectors.TxnSiteActivatorAff
      • class affectors.TxnSiteActivator1Aff
    • class affectors.TxnSiteAddInhibitorAff
    • class affectors.TxnSiteInhibitorAff
    • class affectors.VonForresterA_Aff
    • class affectors.VonForresterA_ECAff
    • class affectors.VonForresterA_ICAff
    • class affectors.VonForresterB_Aff
    • class affectors.VonForresterB_ECAff
    • class affectors.VonForresterB_ICAff
    • class affectors.WhiteNoiseAff
    • class affectors.XferInAff
    • class affectors.XferOutAff
  • class main.AffectorTemplate
  • class main.BetterTokenizer
  • class main.Cell
  • class genegui.CellState
  • 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.JInternalFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
          • class genegui.CellSurfaceViewer (implements genegui.GuiInterface, genegui.ModelStateChangeListener)
          • class genegui.FileEditor
          • class genegui.HTMLViewer
          • class genegui.IteratorViewer (implements java.io.Serializable)
          • class genegui.ModelStateEditor (implements genegui.GuiInterface)
          • class genegui.ModelStateNodePalette (implements genegui.GuiInterface)
          • class genegui.NetworkViewer2 (implements genegui.GuiInterface, genegui.ModelStateChangeListener)
          • class genegui.NodeStateViewer (implements genegui.GuiInterface, genegui.ModelStateChangeListener)
          • class genegui.ParameterViewer (implements genegui.GuiInterface)
          • class genegui.PhasePortraitDlog (implements java.awt.event.ActionListener)
          • class genegui.TimeGraph (implements genegui.GuiInterface, genegui.ModelStateChangeListener, genegui.OptionsPanelInterface)
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class genegui.AffectorViewPanel (implements genegui.GuiInterface)
          • class genegui.ModelStateToolBox
          • class genegui.ModelStateView (implements genegui.GuiInterface, genegui.NodeStateChangeListener)
          • class genegui.NetworkPaintPanel
          • class genegui.NetworkPaintPanel.AffectorDisplay
          • class genegui.NetworkPaintPanel.NodeDisplay
          • class genegui.NodeViewPanel (implements genegui.GuiInterface)
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class genegui.MainGui (implements genegui.GuiInterface, genegui.ModelStateChangeListener)
            • class genegui.SingleCellSelector
          • class genegui.ParInspector (implements java.awt.event.ActionListener, java.awt.event.ItemListener, java.lang.Runnable)
  • class genegui.Configuration (implements java.io.Serializable)
  • class genegui.ErrorPopUp
  • class main.Experiment
  • class iterators.Function
    • class iterators.CooptimizerFunction
    • class iterators.ICSamplingFunction
    • class iterators.ICVaryingFunction
    • class iterators.UberIteratorFunction
  • class main.GeneNet (implements genegui.GuiInterface, java.lang.Runnable)
  • class genegui.GeneNetInterface
  • class main.GeneralInput
  • class main.GlobalIO
  • class main.Globals
  • class initialconditions.InitialCondition
    • class initialconditions.CellIC
    • class initialconditions.CenterIC
    • class initialconditions.ColumnIC
    • class initialconditions.IncrementingACSC1
    • class initialconditions.IncrementingIC
    • class initialconditions.NeuroNoiseIC
    • class initialconditions.RowIC
    • class initialconditions.SequenceACSC1
  • class initialconditions.InitialConditionSet
  • class initialconditions.InitialConditionStorage
  • class genegui.InspectorList (implements java.awt.event.ActionListener)
  • class integrators.Integrator
    • class integrators.AdamsIntegrator
    • class integrators.BackwardEulerIntegrator
    • class integrators.CashKarpIntegrator
    • class integrators.HuenIntegrator
    • class integrators.MidpointIntegrator
    • class integrators.SemiExplicitAPCIntegrator
  • class integrators.Integrator.NVmatrix
  • class integrators.Integrator.NVvector
  • class integrators.IntegratorList
  • class main.Model (implements genegui.ModelStateChangeListener)
  • class iterators.ModelIterator (implements java.lang.Runnable)
    • class iterators.ACSC_SwitchIterator (implements java.lang.Runnable)
    • class iterators.ACSCIterator (implements java.lang.Runnable)
    • class iterators.EllipIterator
    • class iterators.FilterCamIterator (implements java.lang.Runnable)
    • class iterators.FindVolumeIterator
    • class iterators.MatingIterator
    • class iterators.PhasePortraitIterator (implements java.lang.Runnable)
    • class iterators.PopEvolveExpanderIterator
    • class iterators.PowellIterator (implements java.lang.Runnable)
    • class iterators.RandInitRunIterator (implements java.lang.Runnable)
    • class iterators.SteepestDescentIterator (implements java.lang.Runnable)
    • class iterators.SurfaceIterator
    • class iterators.TransectIterator (implements java.lang.Runnable)
    • class iterators.UberIterator (implements java.lang.Runnable)
    • class iterators.VulvaClassifyIterator (implements java.lang.Runnable)
  • class main.ModelRunner (implements java.lang.Runnable)
  • class genegui.ModelState
  • class main.MoreMath
  • class main.MoreMath.PartialDerivRec
  • class iterators.MultiFloatReturn
  • class main.NetInput
  • class main.Network
  • class main.Node (implements java.lang.Cloneable)
    • class main.CalculatorNode (implements java.lang.Cloneable)
  • class main.NodeSpecifier
  • class main.NodeTemplate
  • class integrators.NodeValues
  • class main.NoiseGenerator
  • class java.io.OutputStream
    • class java.io.FilterOutputStream
      • class java.io.PrintStream
        • class genegui.Console
  • class parameters.Parameter
  • class parameterrules.ParameterRule (implements java.lang.Cloneable)
    • class parameterrules.BoundaryRule
    • class parameterrules.DimerHalfMaxRule
    • class parameterrules.LessThanRule
    • class parameterrules.MultiplyParameterRule
    • class parameterrules.ProductBetweenRule
    • class parameterrules.RatioBetweenRule
  • class parameterrules.ParameterRuleSet
  • class parameters.ParameterSet
  • class parameters.ParameterSetArray
  • class genegui.Pointer
  • class java.awt.Polygon (implements java.io.Serializable, java.awt.Shape)
    • class main.Cell.Hexagon
    • class main.Cell.Square
  • class java.beans.SimpleBeanInfo (implements java.beans.BeanInfo)
    • class genegui.ModelStateBeanInfo
    • class genegui.SuccessListBeanInfo
  • class stoppers.SimpleStop
    • class stoppers.CellSurround2Stop
    • class stoppers.CellSurroundStop
    • class stoppers.CellThresholdStop
    • class stoppers.FindMaxRatioStop
    • class stoppers.FPStripeStop
    • class stoppers.MetaFPStripeStop
    • class stoppers.MetaStop
    • class stoppers.MetaStopTwo
    • class stoppers.MetaStripeStop
    • class stoppers.MultiNodeThresholdStop
    • class stoppers.NeuroNoiseStop
    • class stoppers.NeuroTest2Stop
    • class stoppers.NeuroTest3Stop
    • class stoppers.NoChangeStop
    • class stoppers.OscillatingStripeStop
    • class stoppers.OscillatorStop
    • class stoppers.OscillatorStopSpecial
    • class stoppers.PulseStop
    • class stoppers.StripeStop
    • class stoppers.ThresholdStop
    • class stoppers.TwoCellDifferenceStop
  • class stat.Stat (implements java.lang.Runnable)
    • class stat.CenterCenterDistanceStat (implements java.lang.Runnable)
    • class stat.CrossCorrStat (implements java.lang.Runnable)
    • class stat.DumpStat
    • class stat.DumpSuccessArrayStat
    • class stat.DumpValueFieldsStat
    • class stat.FilterParamsStat (implements java.lang.Runnable)
    • class stat.ParamTendenciesStat (implements main.MoreMath.Comparer, java.lang.Runnable)
    • class stat.SummaryStat (implements java.lang.Runnable)
    • class stat.ValueFieldHistogramStat (implements java.lang.Runnable)
  • class genegui.SuccessList
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class main.ModelLoadingException

Interface Hierarchy

• interface genegui.GuiInterface
• interface genegui.ModelStateChangeListener
• interface main.MoreMath.Comparer
• interface genegui.NodeStateChangeListener
• interface genegui.OptionsPanelInterface