All Classes
AboutWindow
AboutWindow
AcceleratorKey
AccessFoldWindow
ActionHandler
ActionHandlers
ActionHelper
ActionHelper.KeyBindFocus
AnnotationMenu
AppActions
AppInfo
AppInfo.AnnotationAppInfoProvider
AppInfo.AppInfoProvider
ApplicationInfo
AppLog
AppMainFrame
ASTAction
ASTAssignment
ASTGuiReference
ASTGuiSearchCriteria
ASTLiteral
ASTNamedArgument
ASTRoot
ASTVarRef
BackgroundWorker
BackgroundWorker.ErrorInfo
BackgroundWorker.StateChangeEventArgs
Bond
Bond.BondInfo
Bond.MultiLoopRole
BondType
BorderBuilder
BorderedButtonPanel
BranchSlider
ButtonGroupList
CalcParams
CDblVector
CharConstants
CharType
CheckMergeItem
ChildFrame
ChildWindow
ChildWindow.CommandInfo
CIntVector
ClassLoaderInfo
ClassMatcher
ClassMatcher.MultiClassMatcher
ClassMatcher.SingleClassMatcher
ColorizeDialog
ColorizeDialog.ColorEditControl
ColorizeDialog.SimpleColorControl
ColorizeDialog.SymbolColorRule
ColorizeDialog.ValueColorRule
Colors
CommandLineParser
CommandLineParser.Argument
CommandLineParser.FlagArg
CommandLineParser.FlagDef
CommandLineParser.ParamAffinity
CommandLineParser.ParseResults
CommandLineParser.UnnamedArg
CommandLineSplitter
Components
ComposableBase
ComposableBase.BinaryMatcher
ComposableBase.BinaryMatcher.And
ComposableBase.BinaryMatcher.Or
ComposableBase.BinaryMatcher.Xor
ComposableBase.Identity
ComposableBase.Inverse
ComposableMatcher
ConsoleTools
ConsoleTools.FixedStream
Constants
ConstraintsMenu
Convert
ConverterFilter
DashboardFrame
DashboardFrame.ListItem
datatable
DateHelper
DescriptionMatcher
DesignWindow
Dialogs
Dialogs
Displayable
DotBracketFormat
DotBracketFormat.SwigNext
DotPlotBackend
DotPlotBackendProxyJNI
DotsMenu
DrawHandle
DrawHint
DrawHint.DrawShape
DrawHint.DrawText
DrawingEditMenu
DrawingFileIO
DrawingFileIO.CTE
DrawingFileIO.CTEWriter
DrawingFileIO.NSD
DrawingFileIO.SimpleScanner
DrawingFileIO.TextWriter
DrawingFileMenu
DrawingFormatMenu
DrawingViewMenu
DrawingWindow
DrawPanel
DrawSettings
DrawWindow
DrawWindow.SceneInfo
DrawWindow.ToolButtonList
DuplexFoldWindow
Dynalign_object
DynalignFoldWindow
DynalignRefoldWindow
Efn2Window
Ellipses
Ellipses.Circle
EventArgs
EventArgs.ActionEventArgs
EventArgs.BoolEventArgs
EventArgs.EventObjectArgs
EventArgs.InfoBagEventArgs
EventArgs.IntEventArgs
EventArgs.ObjEventArgs
EventArgs.StringEventArgs
EventSource
EventSource.Manager
EventSource.Manager.Subscriber
EventSource.NoArg
EventSource.OneArg
EventSource.TwoArgs
ExceptionHelper
ExtendedBufferedReader
ExtensibleException
FieldPanel
FieldPanel.FilePanel
FileDialog
FileField
FileFilters
FileMenu
FileMenu
FilePreferences
FilePreferences.Factory
FilePreferences.RootNode
FileSelectedEvent
FileType
FileType
Filter
FoldDoubleWindow
FoldSingleWindow
FoldSuboptimalWindow
FontUtil
FontUtil.FontExpressivenessComparator
FormatterException
FormValidationException
Graphics2DRecorder
GraphicsOp
GraphicsOp.ActionOp
GraphicsOp.BackgroundOp
GraphicsOp.ClearHintsOp
GraphicsOp.ClearOp
GraphicsOp.ClipOp
GraphicsOp.ColorOp
GraphicsOp.CompositeOp
GraphicsOp.ControlOp
GraphicsOp.DrawImageOp
GraphicsOp.DrawShapeOp
GraphicsOp.DrawStringOp
GraphicsOp.EndOp
GraphicsOp.FontOp
GraphicsOp.GroupEndOp
GraphicsOp.GroupStartOp
GraphicsOp.HintOp
GraphicsOp.InitOp
GraphicsOp.PaintOp
GraphicsOp.StateOp
GraphicsOp.StrokeOp
GraphicsOp.TransformOp
GraphicsOp.XorModeOp
GraphicsStyle
GraphicsUtil
GuiAppManager
GuiFinder
GuiItemNotFoundException
GuiItemRef
GuiItemRef.ComponentMatcher
GuiRelative
GuiRobot
GuiRobot.ModifierKey
GUITesterStartup
GUITesterStartup.AppOptions
GUITesterStartup.ScriptSource
GuiTestScriptParser
GuiTestScriptParser.JJCalls
GuiTestScriptParser.LookaheadSuccess
GuiTestScriptParserConstants
GuiTestScriptParserTokenManager
GuiTestScriptParserTreeConstants
HelpMenu
History
HistoryState
HistoryUpdateEvent
HTMLCheckBox
HybridRNA
ICanvas
IContainer
ImageDialog
ImageGrabber
ImageUtil
IMenuItem
IMergeItem
IMergeItem.Proxy
IMotif
InputAdapter
InputAdapter.InputType
InputAdapter.Keyboard
InputAdapter.Mouse
InsertBasesDialog
InternalWindow
InternalWindow.CommandInfo
INucGroup
IScreenObject
JActionLabel
JavaCharStream
JFlatButton
JJTGuiTestScriptParserState
JniLoader
JniLoader.NativeLibLoadError
KeyAlreadyExistsException
KeyMnemonic
Listener
LoopResizer
MagicConstant
MainFrame
MainMenu
MainMenu
MathUtil
Matrix3D
MaxExpectWindow
MdiChildFrame
MdiParentFrame
MenuList
MenuRolloverAdapter
Menus
MergeButton
MergeButton.Separator
MergeItem
MergeItem.Separator
MergeManager
MergeMenu
MergeToggleButton
ModuleWindow
Motif
Motif.Branch
Motif.Domain
Motif.Helix
Motif.IntervalStack
Motif.Loop
Motif.Loop.LoopType
Motif.MultiLoop
Motif.Segment
MRUFileStorage
MultilignWindow
MultiWindow
NamedArg
NewFileWindow
NewFileWindow.IgnoreStylesUndoManager
NewFileWindow.JWrapTextPane
NewFileWindow.StructItem
Node
NotNull
Nuc
NucLayout
NucleicAcidMenu
Nucleobase
NucStyle
Nullable
NullPrintStream
NullPrintStream.NullByteArrayOutputStream
NumberField
NumberField.DoubleField
NumberField.FloatField
NumberField.IntegerField
ObjTools
ObjTools.RefBool
ObjTools.RefInt
ObjTools.RefStr
OligoScreenWindow
OligoWalkWindow
OSInfo
OSInfo.OSType
PageSize
Pair
ParseException
ParseFormatException
PartialProgress
PartitionDoubleWindow
PartitionSingleWindow
PathTools
PathTools.FileName
PlotDialog
PlotMenu
PlotRunner
PointMath
PredictBimolStructureWindow
PredictionResultsWindow
PredictionResultsWindow.PlotResult
PredictMenu
PredictMultiStructureWindow
PredictSingleStructureWindow
PredictTwoStructureWindow
PredictWindowBase
PredictWindowBase.BackgroundTask
PredictWindowBase.PredictTaskBase
ProbKnotWindow
Program
Program.StartupArgs
ProgressHandler
ProgressPanel
PseudoknotWindow
RadioButtonPanel
RecentFileButton
RecentFileButton.ExtensionFileFilter
RecentFileList
RecentFileList.RecentFile
RecentFileMenuManager
Rectangles
RefoldWindow
RequestFocusListener
ResourceLoader
Resources
RestraintType
RestraintType.SwigNext
RNA
RNABackend
RNABackendConstants
RnaBackendException
RNABackendJNI
RnaDrawController
RnaDrawController.BehaviorMode
RnaDrawController.Colors
RnaDrawController.NucGroup
RnaDrawController.ScreenNuc
RnaDrawController.SelectionType
RnaFileIO
RnaFileIO.AsyncTask
RnaFileIO.BackendCalc
RnaFileIO.BackgroundWork
RnaFileIO.NucIndexConverter
RnaFileIO.NucIndexConverter.DoubleStrand
RnaFileIO.NucIndexConverter.MultiStrand
RnaScene
RnaSceneGroup
RnaSceneState
RnaSceneState.NucState
RNAstructure
RNAstructureBackendCalculator
RNAstructureBackendCalculatorProxyJNI
RNAstructureVersion
RolloverListener
RunFunc
RunnableOnce
RunnerTemplate
RunOnce
RuntimeTools
RuntimeTools.ActionArgumentException
RuntimeTools.ActionException
RuntimeTools.UnsupportedActionException
SceneColorizer
SceneColorizer.ColorMode
SceneColorizer.Comparison
SceneColorizer.DoubleComparer
SceneColorizer.NumberRangeList
SceneColorizer.PairProbabilityData
SceneController
SceneController.DragOpts
SceneDrawMode
SceneRenderer
SceneUpdateCategory
SceneUpdateEvent
SceneUpdateInfo
ScreenCapture
ScreenShape
Script
ScriptActions
ScriptNode
ScriptNodePropConstants
ScriptRunner
ScriptRuntime
ScriptRuntimeException
ScrollerPane
SelectionRotater
SelectionRotater.CenterPoint
SelectionRotater.RotationCenter
SequenceDisplayWindow
Settings
SettingsMenu
SettingsWindow
ShapeUtil
SimpleDataSerializer
SimpleDataSerializer.OutputFormatSettings
SimpleDataSerializer.SSONList
SimpleDataSerializer.SSONMap
SimpleDataSerializer.Token
SimpleDataSerializer.TokenPattern
SimpleDocumentListener
SimpleNode
SimpleProgressHandler
singlestructure
SliderToolWindow
StandardFileChooser
StochasticWindow
StopWatch
Strand
StrandList
StringBuilderEx
Strings
structure
StructureBackend
StructureBackendProxyJNI
StructureDialog
StructureDialog.DrawOptions
StructureMenu
StructureRunner
SvgGraphicsExporter
SwingClassMatchers
SyntaxErrorException
TestUtils
TestUtils.TestMethod
TextDocListener
Thermodynamics
ToFriendlyString
Token
TokenMgrError
ToolWindow
TProgressDialog
TreeNode
Tuple
Tuple.Pair
Tuple.Quad
Tuple.Singlet
Tuple.Triplet
TurboFoldWindow
TwoRNA
UiAction
UserOptions
UserPrefs
ValueSelectionDialog
Vec2D
Verbosity
Version
View2D
VisibilityMatcher
WaitDialog
WindowsMenu
WindowsMenu.WindowItem