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