# Hierarchy For All Packages

Package Hierarchies:

- ur_rna,
- ur_rna.GUITester,
- ur_rna.GUITester.GuiTools,
- ur_rna.GUITester.GuiTools.Matchers,
- ur_rna.GUITester.ScriptParser,
- ur_rna.RNAstructure,
- ur_rna.RNAstructure.backend,
- ur_rna.RNAstructureUI,
- ur_rna.RNAstructureUI.drawing,
- ur_rna.RNAstructureUI.drawing.dialogs,
- ur_rna.RNAstructureUI.drawing.menus,
- ur_rna.RNAstructureUI.drawing.proxy,
- ur_rna.RNAstructureUI.drawing.runners,
- ur_rna.RNAstructureUI.menus,
- ur_rna.RNAstructureUI.ui,
- ur_rna.RNAstructureUI.utilities,
- ur_rna.RNAstructureUI.windows,
- ur_rna.StructureEditor,
- ur_rna.StructureEditor.menus,
- ur_rna.StructureEditor.models,
- ur_rna.StructureEditor.services,
- ur_rna.StructureEditor.services.drawing,
- ur_rna.StructureEditor.services.drawing.export,
- ur_rna.StructureEditor.services.fileIO,
- ur_rna.StructureEditor.ui,
- ur_rna.StructureEditor.windows,
- ur_rna.Utilities,
- ur_rna.Utilities.annotation,
- ur_rna.Utilities.geom,
- ur_rna.Utilities.prefs,
- ur_rna.Utilities.swing,
- ur_rna.Utilities.testing

## Class Hierarchy

- java.lang.Object
  - javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    - ur_rna.Utilities.swing.UiAction
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractList<E> (implements java.util.List<E>)
      - java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        - ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
        - ur_rna.RNAstructureUI.menus.MenuList (implements ur_rna.Utilities.swing.IMenuItem)
        - ur_rna.StructureEditor.models.RnaSceneGroup
        - ur_rna.Utilities.SimpleDataSerializer.SSONList
      - ur_rna.StructureEditor.models.Strand (implements ur_rna.StructureEditor.models.INucGroup)
      - ur_rna.StructureEditor.models.StrandList
  - java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    - java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      - ur_rna.RNAstructureUI.utilities.CalcParams
      - java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
        - ur_rna.Utilities.SimpleDataSerializer.SSONMap
  - javax.swing.undo.AbstractUndoableEdit (implements java.io.Serializable, javax.swing.undo.UndoableEdit)
    - javax.swing.undo.CompoundEdit
      - javax.swing.undo.UndoManager (implements javax.swing.event.UndoableEditListener)
        - ur_rna.StructureEditor.windows.NewFileWindow.IgnoreStylesUndoManager
  - ur_rna.Utilities.swing.AcceleratorKey
  - ur_rna.Utilities.ActionHandlers
  - ur_rna.Utilities.swing.ActionHelper
  - ur_rna.StructureEditor.AppActions
  - ur_rna.Utilities.AppInfo
  - ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider (implements ur_rna.Utilities.AppInfo.AppInfoProvider)
  - ur_rna.Utilities.AppLog
  - ur_rna.RNAstructureUI.utilities.BackgroundWorker.ErrorInfo
  - abbot.finder.BasicFinder (implements abbot.finder.ComponentFinder)
    - ur_rna.GUITester.GuiTools.GuiFinder
  - ur_rna.StructureEditor.models.Bond (implements java.lang.Cloneable, java.lang.Comparable<T>)
  - ur_rna.StructureEditor.models.Bond.BondInfo
  - ur_rna.RNAstructureUI.ui.BorderBuilder (implements java.io.Serializable)
  - javax.swing.ButtonGroup (implements java.io.Serializable)
    - ur_rna.Utilities.swing.ButtonGroupList
  - ur_rna.RNAstructure.backend.CDblVector
  - ur_rna.Utilities.CharConstants
  - ur_rna.Utilities.CharType
  - ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
  - ur_rna.RNAstructure.backend.CIntVector
  - ur_rna.Utilities.ClassLoaderInfo
  - ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl (implements ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl)
    - ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
    - ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
  - ur_rna.Utilities.Colors
  - ur_rna.Utilities.CommandLineParser
  - ur_rna.Utilities.CommandLineParser.Argument
    - ur_rna.Utilities.CommandLineParser.FlagArg
    - ur_rna.Utilities.CommandLineParser.UnnamedArg
  - ur_rna.Utilities.CommandLineParser.FlagDef
  - ur_rna.Utilities.CommandLineParser.ParseResults
  - ur_rna.Utilities.CommandLineSplitter
  - 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.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          - javax.swing.JButton (implements javax.accessibility.Accessible)
            - ur_rna.Utilities.swing.JFlatButton
            - ur_rna.Utilities.swing.MergeButton (implements ur_rna.Utilities.swing.IMergeItem)
            - ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
            - ur_rna.RNAstructureUI.ui.RecentFileButton
          - javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            - javax.swing.JCheckBoxMenuItem (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
              - ur_rna.Utilities.swing.CheckMergeItem (implements ur_rna.Utilities.swing.IMergeItem)
            - javax.swing.JMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
              - ur_rna.Utilities.swing.MergeMenu (implements ur_rna.Utilities.swing.IMenuItem, ur_rna.Utilities.swing.IMergeItem)
                - ur_rna.StructureEditor.menus.DrawingEditMenu
                - ur_rna.StructureEditor.menus.DrawingFileMenu
                - ur_rna.StructureEditor.menus.DrawingFormatMenu
                - ur_rna.StructureEditor.menus.DrawingViewMenu
                - ur_rna.RNAstructureUI.menus.MainMenu (implements java.awt.event.ActionListener)
                  - ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
                  - ur_rna.RNAstructureUI.menus.ConstraintsMenu
                  - ur_rna.RNAstructureUI.drawing.menus.DotsMenu
                  - ur_rna.RNAstructureUI.menus.FileMenu
                  - ur_rna.RNAstructureUI.menus.HelpMenu
                  - ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu
                  - ur_rna.RNAstructureUI.menus.NucleicAcidMenu
                  - ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoWalkResultsMenu
                  - ur_rna.RNAstructureUI.drawing.menus.PlotMenu
                  - ur_rna.RNAstructureUI.menus.PredictMenu
                  - ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
                  - ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
                  - ur_rna.RNAstructureUI.drawing.menus.StructureMenu
                - ur_rna.StructureEditor.menus.MainMenu
                  - ur_rna.StructureEditor.menus.FileMenu
                  - ur_rna.StructureEditor.menus.SettingsMenu
                  - ur_rna.StructureEditor.menus.WindowsMenu
            - ur_rna.Utilities.swing.MergeItem (implements ur_rna.Utilities.swing.IMergeItem)
              - ur_rna.StructureEditor.menus.WindowsMenu.WindowItem
          - javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            - javax.swing.JCheckBox (implements javax.accessibility.Accessible)
              - ur_rna.RNAstructureUI.ui.HTMLCheckBox
            - ur_rna.Utilities.swing.MergeToggleButton (implements ur_rna.Utilities.swing.IMergeItem)
        - javax.swing.JComboBox<E> (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          - ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
        - javax.swing.JFileChooser (implements javax.accessibility.Accessible)
          - ur_rna.Utilities.swing.FileDialog
          - ur_rna.RNAstructureUI.ui.StandardFileChooser
        - javax.swing.JInternalFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
          - ur_rna.RNAstructureUI.windows.AboutWindow (implements java.awt.event.ActionListener)
          - ur_rna.RNAstructureUI.windows.ChildWindow (implements java.awt.event.FocusListener)
          - ur_rna.StructureEditor.windows.DashboardFrame
          - ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog (implements java.awt.print.Printable)
            - ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
            - ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
          - ur_rna.RNAstructureUI.windows.InternalWindow (implements java.awt.event.ActionListener)
            - ur_rna.RNAstructureUI.windows.DrawingWindow
            - ur_rna.RNAstructureUI.windows.ModuleWindow
              - ur_rna.RNAstructureUI.windows.AccessFoldWindow
              - ur_rna.RNAstructureUI.windows.DesignWindow
              - ur_rna.RNAstructureUI.windows.DuplexFoldWindow
              - ur_rna.RNAstructureUI.windows.DynalignFoldWindow
              - ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
              - ur_rna.RNAstructureUI.windows.Efn2Window
              - ur_rna.RNAstructureUI.windows.FoldDoubleWindow
              - ur_rna.RNAstructureUI.windows.FoldSingleWindow
              - ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
              - ur_rna.RNAstructureUI.windows.MaxExpectWindow
              - ur_rna.RNAstructureUI.windows.MultiWindow
                - ur_rna.RNAstructureUI.windows.MultilignWindow
                - ur_rna.RNAstructureUI.windows.TurboFoldWindow
              - ur_rna.RNAstructureUI.windows.OligoScreenWindow
              - ur_rna.RNAstructureUI.windows.OligoWalkWindow
              - ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
              - ur_rna.RNAstructureUI.windows.PartitionSingleWindow
              - ur_rna.RNAstructureUI.windows.ProbKnotWindow
              - ur_rna.RNAstructureUI.windows.PseudoknotWindow
              - ur_rna.RNAstructureUI.windows.RefoldWindow
              - ur_rna.RNAstructureUI.windows.StochasticWindow
            - ur_rna.RNAstructureUI.windows.PredictionResultsWindow
            - ur_rna.RNAstructureUI.windows.PredictWindowBase
              - ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
              - ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
              - ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
              - ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
            - ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
          - ur_rna.Utilities.swing.MdiChildFrame
            - ur_rna.StructureEditor.windows.ChildFrame
              - ur_rna.StructureEditor.windows.AboutWindow (implements java.awt.event.ActionListener)
              - ur_rna.StructureEditor.windows.DrawWindow
              - ur_rna.StructureEditor.windows.NewFileWindow
          - ur_rna.StructureEditor.ui.ToolWindow
            - ur_rna.StructureEditor.ui.SliderToolWindow
        - javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - ur_rna.Utilities.swing.JActionLabel
        - javax.swing.JPanel (implements javax.accessibility.Accessible)
          - ur_rna.RNAstructureUI.ui.BorderedButtonPanel
          - ur_rna.StructureEditor.ui.DrawPanel (implements ur_rna.StructureEditor.services.drawing.ICanvas)
          - ur_rna.RNAstructureUI.ui.FieldPanel
            - ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
          - ur_rna.StructureEditor.windows.InsertBasesDialog
          - ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
          - ur_rna.RNAstructureUI.ui.ProgressPanel
          - ur_rna.RNAstructureUI.ui.RadioButtonPanel
        - javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          - ur_rna.RNAstructureUI.ui.ScrollerPane
        - javax.swing.JSeparator (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - javax.swing.JPopupMenu.Separator
            - ur_rna.Utilities.swing.MergeItem.Separator (implements ur_rna.Utilities.swing.IMergeItem)
          - javax.swing.JToolBar.Separator
            - ur_rna.Utilities.swing.MergeButton.Separator (implements ur_rna.Utilities.swing.IMergeItem)
        - javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          - javax.swing.JEditorPane
            - javax.swing.JTextPane
              - ur_rna.StructureEditor.windows.NewFileWindow.JWrapTextPane
          - javax.swing.JTextField (implements javax.swing.SwingConstants)
            - ur_rna.RNAstructureUI.ui.FileField
            - ur_rna.RNAstructureUI.ui.NumberField
              - ur_rna.RNAstructureUI.ui.NumberField.DoubleField
              - ur_rna.RNAstructureUI.ui.NumberField.FloatField
              - ur_rna.RNAstructureUI.ui.NumberField.IntegerField
      - java.awt.Window (implements javax.accessibility.Accessible)
        - java.awt.Dialog
          - javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - ur_rna.StructureEditor.windows.ColorizeDialog (implements java.awt.event.ActionListener)
            - ur_rna.RNAstructureUI.ui.ValueSelectionDialog
              - ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
              - ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
              - ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
              - ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.ZoomDialog
              - ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
              - ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
            - ur_rna.Utilities.swing.WaitDialog
        - java.awt.Frame (implements java.awt.MenuContainer)
          - javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - ur_rna.RNAstructureUI.AppMainFrame
            - ur_rna.Utilities.swing.MdiParentFrame (implements javax.swing.event.InternalFrameListener)
              - ur_rna.StructureEditor.MainFrame
  - ur_rna.Utilities.swing.Components
  - ur_rna.GUITester.GuiTools.Matchers.ComposableBase (implements ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher)
    - ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
      - ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
      - ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
    - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
      - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.And
      - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Or
      - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Xor
    - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
    - ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
    - ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
    - ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
  - ur_rna.Utilities.ConsoleTools
  - ur_rna.Utilities.Constants
  - ur_rna.Utilities.Convert
  - ur_rna.Utilities.ConverterFilter<T,C>
    - ur_rna.Utilities.ConverterFilter.SimpleCast
  - ur_rna.Utilities.ConverterFilter.FilterIterator (implements java.util.Iterator<E>)
  - ur_rna.StructureEditor.windows.DashboardFrame.ListItem
  - ur_rna.RNAstructure.backend.datatable
  - ur_rna.Utilities.DateHelper
  - ur_rna.RNAstructureUI.ui.Dialogs (implements java.io.Serializable)
  - ur_rna.Utilities.swing.Dialogs
  - java.awt.geom.Dimension2D (implements java.lang.Cloneable)
    - ur_rna.StructureEditor.services.drawing.export.PageSize
  - ur_rna.RNAstructure.backend.DotBracketFormat.SwigNext
  - ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
  - ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
  - ur_rna.StructureEditor.services.drawing.DrawHandle
    - ur_rna.StructureEditor.services.drawing.BranchSlider
    - ur_rna.StructureEditor.services.drawing.LoopResizer
    - ur_rna.StructureEditor.services.drawing.SelectionRotater
    - ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
  - ur_rna.StructureEditor.services.drawing.DrawHint
    - ur_rna.StructureEditor.services.drawing.DrawHint.DrawShape
    - ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
  - ur_rna.StructureEditor.services.fileIO.DrawingFileIO
  - ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
  - ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
    - ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTEWriter
  - ur_rna.StructureEditor.models.DrawSettings (implements java.lang.Cloneable)
  - ur_rna.StructureEditor.windows.DrawWindow.SceneInfo
  - ur_rna.Utilities.geom.Ellipses
  - ur_rna.Utilities.EventArgs
    - ur_rna.RNAstructureUI.utilities.BackgroundWorker.StateChangeEventArgs
    - ur_rna.Utilities.EventArgs.ActionEventArgs
    - ur_rna.Utilities.EventArgs.BoolEventArgs
    - ur_rna.Utilities.EventArgs.EventObjectArgs
    - ur_rna.Utilities.EventArgs.InfoBagEventArgs
    - ur_rna.Utilities.EventArgs.IntEventArgs
    - ur_rna.Utilities.EventArgs.ObjEventArgs<T>
    - ur_rna.Utilities.EventArgs.StringEventArgs
  - java.util.EventObject (implements java.io.Serializable)
    - java.awt.AWTEvent
      - java.awt.event.ActionEvent
        - ur_rna.RNAstructureUI.utilities.FileSelectedEvent
  - ur_rna.Utilities.EventSource<TSubscriber>
    - ur_rna.Utilities.EventSource.NoArg
    - ur_rna.Utilities.EventSource.OneArg<TArg>
    - ur_rna.Utilities.EventSource.TwoArgs<TArg1,TArg2>
  - ur_rna.Utilities.EventSource.Manager
  - ur_rna.Utilities.EventSource.Manager.Subscriber
  - ur_rna.Utilities.ExceptionHelper
  - ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel.ButtonListener (implements java.awt.event.ActionListener)
  - ur_rna.RNAstructureUI.utilities.FileFilters
  - ur_rna.Utilities.prefs.FilePreferences.Factory (implements java.util.prefs.PreferencesFactory)
  - ur_rna.Utilities.Filter<T>
  - ur_rna.Utilities.Filter.FilterIterator (implements java.util.Iterator<E>)
  - ur_rna.Utilities.swing.FontUtil
  - ur_rna.Utilities.swing.FontUtil.FontExpressivenessComparator (implements java.util.Comparator<T>)
  - java.awt.Graphics
    - java.awt.Graphics2D
      - ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder (implements java.lang.Cloneable)
  - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ActionOp (implements ur_rna.StructureEditor.services.drawing.export.GraphicsOp)
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
  - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ControlOp (implements ur_rna.StructureEditor.services.drawing.export.GraphicsOp)
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.EndOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.GroupEndOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.GroupStartOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.InitOp
  - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StateOp (implements ur_rna.StructureEditor.services.drawing.export.GraphicsOp)
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearHintsOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
    - ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp
  - ur_rna.StructureEditor.services.drawing.export.GraphicsStyle (implements java.lang.Cloneable)
  - ur_rna.Utilities.geom.GraphicsUtil
  - ur_rna.GUITester.GuiTools.GuiAppManager
  - ur_rna.GUITester.GuiTools.GuiItemRef
  - ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher (implements abbot.finder.Matcher)
  - ur_rna.GUITester.GUITesterStartup
  - ur_rna.GUITester.GUITesterStartup.AppOptions
  - ur_rna.GUITester.ScriptParser.GuiTestScriptParser (implements ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants, ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants)
  - ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
  - ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager (implements ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants)
  - ur_rna.StructureEditor.services.History<T>
  - ur_rna.StructureEditor.models.HistoryState
  - ur_rna.StructureEditor.models.HistoryUpdateEvent
  - ur_rna.RNAstructureUI.utilities.ImageGrabber (implements java.io.Serializable)
  - ur_rna.Utilities.swing.ImageUtil
  - ur_rna.Utilities.swing.IMergeItem.Proxy (implements ur_rna.Utilities.swing.IMergeItem)
  - ur_rna.Utilities.swing.InputAdapter
  - ur_rna.Utilities.swing.InputAdapter.Keyboard (implements java.awt.event.KeyListener)
  - ur_rna.Utilities.swing.InputAdapter.Mouse (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
    - ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
  - ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
  - ur_rna.GUITester.ScriptParser.JavaCharStream
  - ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
  - ur_rna.Utilities.JniLoader
  - ur_rna.Utilities.swing.KeyMnemonic
  - ur_rna.Utilities.MathUtil
  - ur_rna.Utilities.geom.Matrix3D (implements java.lang.Cloneable, java.io.Serializable)
  - ur_rna.RNAstructureUI.menus.MenuRolloverAdapter (implements java.awt.event.MouseListener, java.io.Serializable)
  - ur_rna.Utilities.swing.Menus
  - ur_rna.Utilities.swing.MergeManager
  - ur_rna.StructureEditor.models.Motif
  - ur_rna.StructureEditor.models.Motif.Branch (implements ur_rna.StructureEditor.models.IMotif)
  - ur_rna.StructureEditor.models.Motif.Helix (implements ur_rna.StructureEditor.models.IMotif)
  - ur_rna.StructureEditor.models.Motif.IntervalStack
  - ur_rna.StructureEditor.models.Motif.MultiLoop (implements ur_rna.StructureEditor.models.IMotif)
  - ur_rna.StructureEditor.models.Motif.Segment (implements ur_rna.StructureEditor.models.INucGroup)
    - ur_rna.StructureEditor.models.Motif.Domain (implements ur_rna.StructureEditor.models.IMotif)
    - ur_rna.StructureEditor.models.Motif.Loop (implements ur_rna.StructureEditor.models.IMotif)
  - ur_rna.RNAstructureUI.utilities.MRUFileStorage
  - ur_rna.Utilities.NamedArg
  - ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  - ur_rna.StructureEditor.models.Nuc (implements java.lang.Cloneable, java.lang.Comparable<T>, ur_rna.StructureEditor.models.INucGroup)
  - ur_rna.StructureEditor.services.drawing.NucLayout
  - ur_rna.RNAstructure.Nucleobase
  - ur_rna.StructureEditor.models.NucStyle (implements java.lang.Cloneable)
  - ur_rna.Utilities.ObjTools
  - ur_rna.Utilities.ObjTools.RefBool
  - ur_rna.Utilities.ObjTools.RefInt
  - ur_rna.Utilities.ObjTools.RefStr
  - ur_rna.Utilities.OSInfo (implements java.io.Serializable)
  - java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    - java.io.ByteArrayOutputStream
      - ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream
    - ur_rna.Utilities.ConsoleTools.FixedStream
    - java.io.FilterOutputStream
      - java.io.PrintStream (implements java.lang.Appendable, java.io.Closeable)
        - ur_rna.Utilities.NullPrintStream
  - ur_rna.Utilities.Pair<K,V> (implements java.util.Map.Entry<K,V>)
  - ur_rna.Utilities.PathTools
  - ur_rna.Utilities.PathTools.FileName
  - java.awt.geom.Point2D (implements java.lang.Cloneable)
    - java.awt.geom.Point2D.Double (implements java.io.Serializable)
      - ur_rna.Utilities.geom.Vec2D (implements java.lang.Cloneable)
  - ur_rna.Utilities.geom.PointMath
  - ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
  - ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
  - ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
  - ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
  - ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase (implements ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask)
    - ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
    - ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
    - ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
    - ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
  - java.util.prefs.Preferences
    - java.util.prefs.AbstractPreferences
      - ur_rna.Utilities.prefs.FilePreferences
        - ur_rna.Utilities.prefs.FilePreferences.RootNode
  - ur_rna.StructureEditor.Program (implements ur_rna.Utilities.AppInfo.AppInfoProvider)
  - ur_rna.StructureEditor.Program.StartupArgs
  - ur_rna.RNAstructure.backend.ProgressHandler
    - ur_rna.RNAstructure.backend.PartialProgress
    - ur_rna.RNAstructure.backend.SimpleProgressHandler
    - ur_rna.RNAstructure.backend.TProgressDialog
  - java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    - java.io.BufferedReader
      - ur_rna.Utilities.ExtendedBufferedReader
  - ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter (implements java.io.FileFilter)
  - ur_rna.StructureEditor.services.RecentFileList (implements java.lang.Iterable<T>)
  - ur_rna.StructureEditor.services.RecentFileList.RecentFile
  - ur_rna.StructureEditor.services.RecentFileMenuManager
  - ur_rna.Utilities.geom.Rectangles
  - java.awt.geom.RectangularShape (implements java.lang.Cloneable, java.awt.Shape)
    - java.awt.geom.Ellipse2D
      - java.awt.geom.Ellipse2D.Float (implements java.io.Serializable)
        - ur_rna.Utilities.geom.Ellipses.Circle
  - ur_rna.RNAstructureUI.utilities.RequestFocusListener (implements javax.swing.event.AncestorListener)
  - ur_rna.Utilities.ResourceLoader
  - ur_rna.RNAstructureUI.utilities.Resources
  - ur_rna.RNAstructure.backend.RestraintType.SwigNext
  - ur_rna.RNAstructure.backend.RNABackend (implements ur_rna.RNAstructure.backend.RNABackendConstants)
  - ur_rna.RNAstructure.backend.RNABackendJNI
  - ur_rna.StructureEditor.services.RnaDrawController (implements ur_rna.StructureEditor.services.SceneController, ur_rna.StructureEditor.services.SceneRenderer)
  - ur_rna.StructureEditor.services.RnaDrawController.Colors
  - ur_rna.StructureEditor.services.RnaDrawController.NucGroup (implements ur_rna.StructureEditor.models.INucGroup)
  - ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc (implements ur_rna.StructureEditor.models.IScreenObject)
  - ur_rna.StructureEditor.services.fileIO.RnaFileIO
  - ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork<TResult> (implements ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask<TResult>)
    - ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc<TResult>
  - ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
    - ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
    - ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.MultiStrand
  - ur_rna.StructureEditor.models.RnaScene (implements java.lang.Cloneable)
  - ur_rna.StructureEditor.models.RnaSceneState
  - ur_rna.StructureEditor.models.RnaSceneState.NucState
  - ur_rna.RNAstructureUI.RNAstructure (implements java.io.Serializable)
  - ur_rna.RNAstructureUI.RNAstructureBackendCalculator
  - ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
  - abbot.tester.Robot (implements abbot.tester.AWTConstants)
    - ur_rna.GUITester.GuiTools.GuiRobot
  - ur_rna.RNAstructureUI.menus.RolloverListener (implements java.awt.event.MouseListener, java.io.Serializable)
  - ur_rna.RNAstructureUI.utilities.RunFunc (implements java.lang.Runnable)
  - ur_rna.RNAstructureUI.drawing.runners.RunnerTemplate
    - ur_rna.RNAstructureUI.drawing.runners.PlotRunner (implements java.io.Serializable)
    - ur_rna.RNAstructureUI.drawing.runners.StructureRunner (implements java.io.Serializable)
  - ur_rna.Utilities.RunOnce (implements ur_rna.Utilities.RunnableOnce)
  - ur_rna.GUITester.RuntimeTools
  - ur_rna.StructureEditor.services.SceneColorizer
  - ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
  - ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
  - ur_rna.StructureEditor.services.SceneController.DragOpts
  - ur_rna.StructureEditor.services.SceneUpdateEvent
  - ur_rna.StructureEditor.models.SceneUpdateInfo
  - ur_rna.GUITester.GuiTools.ScreenCapture
  - ur_rna.StructureEditor.services.drawing.ScreenShape (implements ur_rna.StructureEditor.models.IScreenObject)
  - ur_rna.GUITester.Script
  - ur_rna.GUITester.ScriptActions
  - ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
  - ur_rna.GUITester.ScriptRunner (implements java.lang.Runnable)
  - ur_rna.GUITester.ScriptRuntime
  - ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
  - ur_rna.StructureEditor.Settings
  - ur_rna.StructureEditor.windows.SettingsWindow
  - ur_rna.Utilities.geom.ShapeUtil
  - ur_rna.Utilities.SimpleDataSerializer
  - ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings (implements java.lang.Cloneable)
  - ur_rna.Utilities.SimpleDataSerializer.ParseContext
  - ur_rna.Utilities.SimpleDataSerializer.Token
  - ur_rna.GUITester.ScriptParser.SimpleNode (implements ur_rna.GUITester.ScriptParser.Node)
    - ur_rna.GUITester.ScriptParser.ScriptNode (implements ur_rna.GUITester.ScriptParser.ScriptNodePropConstants)
      - ur_rna.GUITester.ScriptParser.ASTAction
      - ur_rna.GUITester.ScriptParser.ASTAssignment
      - ur_rna.GUITester.ScriptParser.ASTGuiReference
      - ur_rna.GUITester.ScriptParser.ASTGuiSearchCriteria
      - ur_rna.GUITester.ScriptParser.ASTLiteral
      - ur_rna.GUITester.ScriptParser.ASTNamedArgument
      - ur_rna.GUITester.ScriptParser.ASTRoot
      - ur_rna.GUITester.ScriptParser.ASTVarRef
  - ur_rna.RNAstructure.backend.singlestructure
  - ur_rna.Utilities.StopWatch
  - ur_rna.Utilities.StringBuilderEx (implements java.lang.Appendable, java.lang.CharSequence, java.io.Serializable)
  - ur_rna.Utilities.Strings
  - ur_rna.RNAstructure.backend.structure
  - ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
  - ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
  - ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  - ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
  - javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    - ur_rna.RNAstructureUI.utilities.BackgroundWorker (implements java.beans.PropertyChangeListener)
  - ur_rna.Utilities.testing.TestUtils
  - ur_rna.Utilities.swing.TextDocListener (implements javax.swing.event.DocumentListener)
  - ur_rna.RNAstructure.backend.Thermodynamics
    - ur_rna.RNAstructure.backend.RNA
      - ur_rna.RNAstructure.backend.HybridRNA
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Error
      - ur_rna.GUITester.ScriptParser.GuiTestScriptParser.LookaheadSuccess
      - ur_rna.GUITester.ScriptParser.TokenMgrError
    - java.lang.Exception
      - ur_rna.Utilities.ExtensibleException
        - ur_rna.GUITester.GuiTools.GuiItemNotFoundException
        - ur_rna.GUITester.ScriptRuntimeException
          - ur_rna.GUITester.RuntimeTools.ActionException
            - ur_rna.GUITester.RuntimeTools.ActionArgumentException
            - ur_rna.GUITester.RuntimeTools.UnsupportedActionException
      - ur_rna.Utilities.FormatterException
      - ur_rna.Utilities.swing.FormValidationException
      - ur_rna.Utilities.JniLoader.NativeLibLoadError
      - ur_rna.GUITester.ScriptParser.ParseException
        - ur_rna.GUITester.ScriptParser.ParseFormatException
      - ur_rna.RNAstructure.RnaBackendException
      - java.lang.RuntimeException
        - ur_rna.Utilities.KeyAlreadyExistsException
      - ur_rna.Utilities.SyntaxErrorException
  - ur_rna.GUITester.ScriptParser.Token (implements java.io.Serializable)
  - ur_rna.Utilities.TreeNode<T>
  - ur_rna.Utilities.Tuple
  - ur_rna.Utilities.Tuple.Pair<T1,T2> (implements java.lang.Cloneable)
  - ur_rna.Utilities.Tuple.Quad<T1,T2,T3,T4>
  - ur_rna.Utilities.Tuple.Singlet<T1>
  - ur_rna.Utilities.Tuple.Triplet<T1,T2,T3> (implements java.lang.Cloneable)
  - ur_rna.RNAstructure.backend.TwoRNA
    - ur_rna.RNAstructure.backend.Dynalign_object
  - ur_rna.RNAstructureUI.utilities.UserOptions
  - ur_rna.StructureEditor.services.UserPrefs
  - ur_rna.Utilities.Version (implements java.lang.Comparable<T>)
  - ur_rna.StructureEditor.services.drawing.View2D

## Interface Hierarchy

- ur_rna.Utilities.ActionHandler<T>
- ur_rna.Utilities.AppInfo.AppInfoProvider
- java.lang.Cloneable
  - ur_rna.Utilities.swing.IMergeItem
- ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
- ur_rna.Utilities.Displayable
- ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
- ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
- java.util.EventListener
  - javax.swing.event.DocumentListener
    - ur_rna.Utilities.swing.SimpleDocumentListener
- ur_rna.StructureEditor.services.drawing.export.GraphicsOp
- ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
- ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
- ur_rna.StructureEditor.services.drawing.ICanvas
- ur_rna.Utilities.swing.IContainer
- ur_rna.Utilities.swing.IMenuItem
- ur_rna.StructureEditor.models.IScreenObject
- java.lang.Iterable<T>
  - ur_rna.StructureEditor.models.INucGroup
    - ur_rna.StructureEditor.models.IMotif
- ur_rna.Utilities.Listener<T>
- abbot.finder.Matcher
  - ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
- ur_rna.GUITester.ScriptParser.Node
- ur_rna.RNAstructure.backend.RNABackendConstants
- ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask<TResult>
- ur_rna.RNAstructure.RNAstructureVersion
- java.lang.Runnable
  - ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
  - ur_rna.Utilities.RunnableOnce
- ur_rna.StructureEditor.services.SceneColorizer.ColorMode
- ur_rna.StructureEditor.services.SceneColorizer.DoubleComparer
- ur_rna.StructureEditor.services.SceneController
- ur_rna.StructureEditor.services.SceneRenderer
- ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
- ur_rna.Utilities.testing.TestUtils.TestMethod

## Annotation Type Hierarchy

- ur_rna.Utilities.annotation.ToFriendlyString (implements java.lang.annotation.Annotation)
- ur_rna.Utilities.annotation.Nullable (implements java.lang.annotation.Annotation)
- ur_rna.Utilities.annotation.NotNull (implements java.lang.annotation.Annotation)
- ur_rna.Utilities.annotation.MagicConstant (implements java.lang.annotation.Annotation)
- ur_rna.Utilities.annotation.ApplicationInfo (implements java.lang.annotation.Annotation)

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - ur_rna.GUITester.GUITesterStartup.ScriptSource
    - ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
    - ur_rna.GUITester.GuiTools.GuiRelative
    - ur_rna.RNAstructure.backend.RestraintType
    - ur_rna.RNAstructure.backend.DotBracketFormat
    - ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog.DrawOptions
    - ur_rna.RNAstructureUI.utilities.FileType
    - ur_rna.StructureEditor.FileType
    - ur_rna.StructureEditor.models.Motif.Loop.LoopType
    - ur_rna.StructureEditor.models.BondType
    - ur_rna.StructureEditor.models.Bond.MultiLoopRole
    - ur_rna.StructureEditor.services.SceneUpdateCategory
    - ur_rna.StructureEditor.services.SceneDrawMode
    - ur_rna.StructureEditor.services.SceneColorizer.Comparison
    - ur_rna.StructureEditor.services.RnaDrawController.BehaviorMode
    - ur_rna.StructureEditor.services.RnaDrawController.SelectionType
    - ur_rna.StructureEditor.services.drawing.SelectionRotater.RotationCenter
    - ur_rna.Utilities.Verbosity
    - ur_rna.Utilities.SimpleDataSerializer.TokenPattern
    - ur_rna.Utilities.OSInfo.OSType
    - ur_rna.Utilities.CommandLineParser.ParamAffinity
    - ur_rna.Utilities.swing.InputAdapter.InputType
    - ur_rna.Utilities.swing.ActionHelper.KeyBindFocus