$ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

## $

$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
$$$getRootComponent$$$() - Method in class ur_rna.StructureEditor.windows.AboutWindow
$$$getRootComponent$$$() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
$$$getRootComponent$$$() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
$$$getRootComponent$$$() - Method in class ur_rna.StructureEditor.windows.InsertBasesDialog
$$$getRootComponent$$$() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.ui.SliderToolWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.AboutWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.InsertBasesDialog
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!
$$$setupUI$$$() - Method in class ur_rna.StructureEditor.windows.SettingsWindow
  Method generated by IntelliJ IDEA GUI Designer DO NOT edit this method OR call it in your code!

## A

A - Static variable in class ur_rna.RNAstructure.Nucleobase
A0 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A1 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A2 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A3 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A4 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A5 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
A6 - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
abbrev - Variable in enum ur_rna.StructureEditor.models.BondType
AboutWindow - Class in ur_rna.RNAstructureUI.windows
AboutWindow() - Constructor for class ur_rna.RNAstructureUI.windows.AboutWindow
AboutWindow - Class in ur_rna.StructureEditor.windows
AboutWindow() - Constructor for class ur_rna.StructureEditor.windows.AboutWindow
AcceleratorKey - Class in ur_rna.Utilities.swing
  Utility for getting KeyStrokes from Strings or chars
AcceleratorKey() - Constructor for class ur_rna.Utilities.swing.AcceleratorKey
accept(File) - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
  Tests whether or not the specified pathname should be included in a pathname list.
accept() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
acceptAll - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
AcceptAll(boolean) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
acceptAll() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
AccessFold(double, float, int, int, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFold(double, float, int, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFold(double, float, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFold(double, float) - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFold(double) - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFold() - Method in class ur_rna.RNAstructure.backend.HybridRNA
AccessFoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the AccessFold module, which folds two strands of nucleic acids into their likely hybrid structure.
AccessFoldWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.AccessFoldWindow
  Constructor.
acidName - Variable in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
Action() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
action - Variable in class ur_rna.Utilities.swing.JActionLabel
ActionArgumentException() - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionArgumentException
ActionArgumentException(String) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionArgumentException
ActionArgumentException(Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionArgumentException
ActionArgumentException(String, Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionArgumentException
actionBreakBonds - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionChooseStructure - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionClose - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionColorHelices - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionCommand - Variable in class ur_rna.Utilities.swing.JActionLabel
actionEditNucs - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionEditRedo - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionEditUndo - Variable in class ur_rna.StructureEditor.windows.DrawWindow
ActionEventArgs(ActionEvent) - Constructor for class ur_rna.Utilities.EventArgs.ActionEventArgs
ActionException() - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionException
ActionException(String) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionException
ActionException(Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionException
ActionException(String, Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.ActionException
actionExport - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionFlipScene - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionFold - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionFormatColor - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionFormatRemoveAllColor - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionFormatRemoveColor - Variable in class ur_rna.StructureEditor.windows.DrawWindow
ActionHandler<T extends EventArgs> - Interface in ur_rna.Utilities
ActionHandlers - Class in ur_rna.Utilities
ActionHandlers() - Constructor for class ur_rna.Utilities.ActionHandlers
ActionHelper - Class in ur_rna.Utilities.swing
  Helps add actions to a Frame/Window etc.
ActionHelper() - Constructor for class ur_rna.Utilities.swing.ActionHelper
ActionHelper.KeyBindFocus - Enum in ur_rna.Utilities.swing
actionIdentifyPseudoKnots - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionInsertNucs - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionJoinStrands - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionLocalRedraw - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionNextStructure - Variable in class ur_rna.StructureEditor.windows.DrawWindow
ActionOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ActionOp
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel.ButtonListener
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
  Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
actionPerformed(ActionEvent) - Method in class ur_rna.StructureEditor.windows.AboutWindow
actionPerformed(ActionEvent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
actionPerformed(ActionEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
actionPerformed(ActionEvent) - Method in class ur_rna.Utilities.swing.UiAction
actionPrevStructure - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionRedraw - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionRedrawCirc - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionRedrawLinear - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionRemoveNucs - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSave - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSaveAs - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSelectAll - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSelectBranch - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSelectExpand - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSelectHelix - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSelectNuc - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSetBondTypeBanned - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSetBondTypeForced - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSetBondTypeNormal - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSetBondTypePseduo - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSetBondTypeSpecial - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionShowEnergy - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionSplitStrand - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionWhenSet - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
actionZoomAuto - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionZoomIn - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionZoomOut - Variable in class ur_rna.StructureEditor.windows.DrawWindow
actionZoomReset - Variable in class ur_rna.StructureEditor.windows.DrawWindow
activate() - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
activate() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Activate data input for this window.
activate() - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
activateChild(MdiChildFrame) - Method in class ur_rna.Utilities.swing.MdiParentFrame
activateMultilign() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
activateTurboFold() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
activeRoot - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
add(Node) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
add(double) - Method in class ur_rna.RNAstructure.backend.CDblVector
add(int) - Method in class ur_rna.RNAstructure.backend.CIntVector
add(MergeMenu, int) - Method in class ur_rna.RNAstructureUI.menus.MenuList
add(MergeMenu...) - Method in class ur_rna.RNAstructureUI.menus.MenuList
add(MergeMenu) - Method in class ur_rna.RNAstructureUI.menus.MenuList
add(int, MergeMenu) - Method in class ur_rna.RNAstructureUI.menus.MenuList
add(JMenuItem, String) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
add(String) - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
add(String) - Method in class ur_rna.StructureEditor.models.Strand
add() - Method in class ur_rna.StructureEditor.models.Strand
add(int, Nuc) - Method in class ur_rna.StructureEditor.models.Strand
add() - Method in class ur_rna.StructureEditor.models.StrandList
add(int) - Method in class ur_rna.StructureEditor.models.StrandList
add(GraphicsOp) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Add the operation and apply it to the current graphics context.
add(String) - Method in class ur_rna.StructureEditor.services.RecentFileList
add(String, FileType) - Method in class ur_rna.StructureEditor.services.RecentFileList
add(T) - Method in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
add(Action) - Method in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
add(TSubscriber) - Method in class ur_rna.Utilities.EventSource
add(EventSource<T>, T) - Method in class ur_rna.Utilities.EventSource.Manager
add(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Adds a scalar to each component of this matrix.
add(double, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Adds a scalar to each component of the matrix m1 and places the result into this.
add(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the matrix sum of matrices m1 and m2.
add(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the sum of itself and matrix m1.
add(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
add(double, double) - Method in class ur_rna.Utilities.geom.Vec2D
add(Action) - Method in class ur_rna.Utilities.swing.MergeMenu
  Creates a new menu item attached to the specified `Action` object and appends it to the end of this menu.
add(Action, int) - Method in class ur_rna.Utilities.swing.MergeMenu
add(MergeItem, int) - Method in class ur_rna.Utilities.swing.MergeMenu
add(JMenuItem) - Method in class ur_rna.Utilities.swing.MergeMenu
add(Object) - Method in class ur_rna.Utilities.swing.TextDocListener
add(T) - Method in class ur_rna.Utilities.TreeNode
addAcidMenuItem(String, String, String) - Method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
addAction(JComponent, String, Consumer<ActionEvent>) - Static method in class ur_rna.Utilities.swing.ActionHelper
addAction(String, Consumer<ActionEvent>) - Method in class ur_rna.Utilities.swing.MdiChildFrame
addAction(String, Consumer<ActionEvent>) - Method in class ur_rna.Utilities.swing.MdiParentFrame
addActionListener(ActionListener) - Method in class ur_rna.Utilities.swing.JActionLabel
addActionListeners(AbstractButton...) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
addAll(CharSequence) - Method in class ur_rna.StructureEditor.models.Strand
addAll(int, CharSequence) - Method in class ur_rna.StructureEditor.models.Strand
addAll(Collection<? extends Nuc>) - Method in class ur_rna.StructureEditor.models.Strand
addAll(int, Collection<? extends Nuc>) - Method in class ur_rna.StructureEditor.models.Strand
addAll(Container, Component[]) - Static method in class ur_rna.Utilities.swing.Components
addAll(Container, Iterable<? extends Component>) - Static method in class ur_rna.Utilities.swing.Components
addAll(Component...) - Method in class ur_rna.Utilities.swing.MergeMenu
addAnnotationProbability(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
addAnnotationSHAPE(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
addBackendTuple(String, String) - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
addBackendTuple(String, String) - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Add a tuple to the calculation back end.
addBackendTuple(String, String) - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
addBond(Bond.BondInfo) - Method in class ur_rna.StructureEditor.models.RnaScene
addBond(Nuc, Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
addBond(Nuc, Nuc, BondType) - Method in class ur_rna.StructureEditor.models.RnaScene
addBond(int, int, BondType) - Method in class ur_rna.StructureEditor.models.RnaScene
addBond(Bond) - Method in class ur_rna.StructureEditor.models.RnaScene
addBond(Nuc, Nuc) - Method in class ur_rna.StructureEditor.services.RnaDrawController
AddBonds - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
addBoxClickHandler(ColorizeDialog) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
addCancelListener(ActionListener) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
addChangeHandler(Runnable) - Method in class ur_rna.StructureEditor.Settings
addCheck(String, String, String) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
addCheck(Action) - Method in class ur_rna.Utilities.swing.MergeMenu
addCheckItem(String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a check box menu item with tooltip text.
addCheckItem(String, String, boolean) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
addChild(JInternalFrame) - Method in class ur_rna.RNAstructureUI.AppMainFrame
addChild(MdiChildFrame) - Method in class ur_rna.StructureEditor.MainFrame
addChild(MdiChildFrame) - Method in class ur_rna.Utilities.swing.MdiParentFrame
addClickHandler(JComponent, Consumer<MouseEvent>) - Static method in class ur_rna.StructureEditor.windows.ColorizeDialog
addClickListener() - Method in class ur_rna.Utilities.swing.JActionLabel
addClosingListener(JDialog) - Method in class ur_rna.RNAstructureUI.drawing.runners.RunnerTemplate
  Add a listener to the dialog spawned by this template that exits the application when the dialog is closed.
addClosingListener(JInternalFrame) - Method in class ur_rna.RNAstructureUI.drawing.runners.RunnerTemplate
AddComment(String, int) - Method in class ur_rna.RNAstructure.backend.RNA
AddComment(String) - Method in class ur_rna.RNAstructure.backend.RNA
addComponentInfo(Component, StringBuilder) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
AddDouble(int) - Method in class ur_rna.RNAstructure.backend.structure
addExtensions(StringBuilder) - Method in enum ur_rna.StructureEditor.FileType
addField(JTextField) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
addField(JTextField, String) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
addField(JTextField, String, String) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
addField(JTextField, String, String, ActionListener) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
addField(JComponent, String, String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
addFieldCore(JTextField, String, String, ActionListener, GridBagConstraints) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
addFieldCore(JTextField, String, String, ActionListener, GridBagConstraints) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
addFile(String, String) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
addFileField(String, JTextComponent, String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
addFileField(String, JTextComponent, String, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
addFileField(String, JTextComponent, String, boolean, String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
addFilters(String) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Adds a set of filter-specs to the list of file filters for the FileChooser.
addFilters(String) - Method in class ur_rna.Utilities.swing.FileDialog
  Adds a set of filter-specs to the list of file filters for the FileChooser.
addFilterString(StringBuilder) - Method in enum ur_rna.StructureEditor.FileType
addFlag(String, boolean) - Method in class ur_rna.Utilities.CommandLineParser
  Add a flag and specify whether or not it requires a following parameter.
addFlag(String...) - Method in class ur_rna.Utilities.CommandLineParser
addFlag(String, CommandLineParser.ParamAffinity, boolean, String...) - Method in class ur_rna.Utilities.CommandLineParser
addFlag(CommandLineParser.FlagDef) - Method in class ur_rna.Utilities.CommandLineParser
addFlagAlias(String, String) - Method in class ur_rna.Utilities.CommandLineParser
addFlagAlias(CommandLineParser.FlagDef, String) - Method in class ur_rna.Utilities.CommandLineParser
addFlagPrefix(String) - Method in class ur_rna.Utilities.CommandLineParser
addFlags(String...) - Method in class ur_rna.Utilities.CommandLineParser
  Define flags that do NOT have parameters.
addFlagsWithParams(String...) - Method in class ur_rna.Utilities.CommandLineParser
  Define flags that have (and require) parameters.
AddForbiddenPair(int, int) - Method in class ur_rna.RNAstructure.backend.structure
addFromToolTips(JComponent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
  Convert tooltips to rollover text.
addGeneralSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Add a menu section of general constraints commands.
addGuiInfo(Component) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
AddGUPair(int) - Method in class ur_rna.RNAstructure.backend.structure
addHint(Shape) - Method in class ur_rna.StructureEditor.services.RnaDrawController
addHint(String, double, double) - Method in class ur_rna.StructureEditor.services.RnaDrawController
addHint(Shape) - Method in interface ur_rna.StructureEditor.services.SceneController
addHint(String, double, double) - Method in interface ur_rna.StructureEditor.services.SceneController
addHistoryListener(Consumer<HistoryUpdateEvent>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
addHistoryListener(Consumer<HistoryUpdateEvent>) - Method in interface ur_rna.StructureEditor.services.SceneController
addItem(String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a plain text menu item with tooltip text.
addItem(String, String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a plain text menu item with tooltip text.
addItem(String, String, char) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a menu item with tooltip text and a key stroke which can activate it.
addItem(String, String, KeyStroke) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a plain text menu item with tooltip text and a key stroke which can activate it.
addItem(String, String, String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a plain text menu item with tooltip text.
addItem(String, String, char, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a plain text menu item with tooltip text.
addItem(String, String, KeyStroke, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Add a menu item with tooltip text.
addItem(Action) - Method in class ur_rna.StructureEditor.menus.MainMenu
addItem(Action, int) - Method in class ur_rna.StructureEditor.menus.MainMenu
addKeyAction(JComponent, KeyStroke, String, Consumer<ActionEvent>) - Static method in class ur_rna.Utilities.swing.ActionHelper
  Combine addKeyBinding with addAction
addKeyAction(JComponent, KeyStroke, String, Consumer<ActionEvent>, ActionHelper.KeyBindFocus) - Static method in class ur_rna.Utilities.swing.ActionHelper
  Combine addKeyBinding with addAction
addKeyBinding(JComponent, char, String) - Static method in class ur_rna.Utilities.swing.ActionHelper
addKeyBinding(JComponent, int, int, String) - Static method in class ur_rna.Utilities.swing.ActionHelper
addKeyBinding(JComponent, KeyStroke, String) - Static method in class ur_rna.Utilities.swing.ActionHelper
addKeyBinding(JComponent, KeyStroke, String, ActionHelper.KeyBindFocus) - Static method in class ur_rna.Utilities.swing.ActionHelper
addKeyBinding(char, String) - Method in class ur_rna.Utilities.swing.MdiChildFrame
addKeyBinding(int, int, String) - Method in class ur_rna.Utilities.swing.MdiChildFrame
addKeyBinding(char, String) - Method in class ur_rna.Utilities.swing.MdiParentFrame
addKeyBinding(int, int, String) - Method in class ur_rna.Utilities.swing.MdiParentFrame
addLibName(String) - Method in class ur_rna.Utilities.JniLoader
addList() - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONList
addListener(Consumer<DocumentEvent>) - Method in class ur_rna.Utilities.swing.TextDocListener
  Add a method that will receive DocumentEvents generated by the Documents this class is listening to.
addListener(Runnable) - Method in class ur_rna.Utilities.swing.TextDocListener
  Add a method that will be called whenever the the Documents this class is listening to generate DocumentEvents.
addListener(ActionListener) - Method in class ur_rna.Utilities.swing.UiAction
  Add an ActionListener to be notified when this Action is invoked.
addMainActions() - Method in class ur_rna.StructureEditor.MainFrame
addMainMenu(MergeMenu, int) - Method in class ur_rna.RNAstructureUI.AppMainFrame
addMainMenu(MergeMenu, int) - Method in class ur_rna.StructureEditor.MainFrame
addMap() - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONList
addMaxPairingDistanceSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Add a menu section that handles maximum pairing distance.
AddModified(int) - Method in class ur_rna.RNAstructure.backend.structure
addMultilignTuple(String, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
addNode(String) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
addNode(String, int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
addOptionControls(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
addOptionControls(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
AddPair(int, int) - Method in class ur_rna.RNAstructure.backend.structure
addPlaceholders(int, int) - Method in class ur_rna.StructureEditor.models.Strand
addPlaceholders(int) - Method in class ur_rna.StructureEditor.models.Strand
addPlot(String, String, Supplier<InternalWindow>) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
addPlotHeader(String, int) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
addPlotSeparator() - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
addProbColorRule(String, Color) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
addRecentFile(String, FileType) - Method in class ur_rna.StructureEditor.MainFrame
addRelative(GuiItemRef) - Method in exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
addRenderingHints(Map<?, ?>) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
addSaveRestoreSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Add a menu section that handles saving and restoring constraints.
addScaled(Point2D, double) - Method in class ur_rna.Utilities.geom.Vec2D
addSceneUpdateListener(Consumer<SceneUpdateEvent>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
addSceneUpdateListener(Consumer<SceneUpdateEvent>) - Method in interface ur_rna.StructureEditor.services.SceneController
addSearchDir(String) - Method in class ur_rna.Utilities.ResourceLoader
  Add a sub-directory (relative to the resource base directory) that will be searched to find requested resources.
addSearchDirs(String...) - Method in class ur_rna.Utilities.ResourceLoader
  Add a list of sub-directories (relative to the resource base directory) that will be searched to find requested resources.
addSeparator() - Method in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
addSeparator() - Method in class ur_rna.Utilities.swing.MergeMenu
  Add a menu separator
addSeparator(int) - Method in class ur_rna.Utilities.swing.MergeMenu
  Add a menu separator with the specified mergePos
addSequence(String, String, String) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
addSequenceFile(String, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
addSHAPESection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Add a menu section that handles SHAPE constraints.
addShowResetSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Add a menu section that handles showing and resetting constraints.
AddSingle(int) - Method in class ur_rna.RNAstructure.backend.structure
addSlash(String) - Static method in class ur_rna.Utilities.PathTools
addStrand() - Method in class ur_rna.StructureEditor.models.RnaScene
AddStructure() - Method in class ur_rna.RNAstructure.backend.structure
addSymbolColorRule(String, Color) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
addToBottom(String, FileType) - Method in class ur_rna.StructureEditor.services.RecentFileList
addToggle(Action) - Method in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
addToGroup(Element) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
addToolButton(Action, int) - Method in class ur_rna.StructureEditor.MainFrame
addToPanel(JComponent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
addToPanel(JComponent, int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
addToPanel(JComponent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
addToPanel(JComponent, int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
addTurboFoldTuple(String, String, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
addTurboFoldTuple(String, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
addUndo(SceneUpdateInfo) - Method in class ur_rna.StructureEditor.services.RnaDrawController
addUndo(SceneUpdateInfo) - Method in interface ur_rna.StructureEditor.services.SceneController
addUpdateListener(ActionListener) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
addValueColorRule(String, Color) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
adjustBeginLineColumn(int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Method to adjust line and column numbers for the start of a token.
AdjustBuffSize() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
advanceToNextStep(int) - Method in class ur_rna.RNAstructure.backend.PartialProgress
ALERT - Static variable in class ur_rna.Utilities.CharConstants
aliases - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
AliceBlue - Static variable in class ur_rna.Utilities.Colors
Alignment - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
ALL - Static variable in class ur_rna.Utilities.CharType
  All character types.
all(Iterable<T>, Predicate<T>) - Static method in class ur_rna.Utilities.ObjTools
  Returns true if the test function returns true for all of the items in the iterable.
allNucs() - Method in class ur_rna.StructureEditor.models.RnaScene
  Returns a read-only list of all nucleotides.
allNucs() - Method in class ur_rna.StructureEditor.models.StrandList
  Returns a read-only list of all nucleotides.
allNucs - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
allNucsFitCircle(Nuc, Nuc, Ellipses.Circle) - Method in class ur_rna.StructureEditor.services.RnaDrawController
allocateconstant() - Method in class ur_rna.RNAstructure.backend.structure
AllocateSHAPE() - Method in class ur_rna.RNAstructure.backend.structure
allocatetem() - Method in class ur_rna.RNAstructure.backend.structure
allowBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
allowBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
allowCancel() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
allowedChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
allowedNames - Variable in class ur_rna.Utilities.JniLoader
allowedSymbols - Static variable in class ur_rna.RNAstructure.Nucleobase
allowHidden - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
allowRepeats - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
allowUndefinedFlags - Variable in class ur_rna.Utilities.CommandLineParser
  Whether or not to allow undefined flags when parsing the command line.
allSearchDirs - Variable in class ur_rna.Utilities.ResourceLoader
allTypes - Static variable in enum ur_rna.StructureEditor.FileType
almostEqual(double, double) - Static method in class ur_rna.Utilities.geom.Matrix3D
alnWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
ALPHA - Static variable in class ur_rna.Utilities.CharType
ALPHA_NUM - Static variable in class ur_rna.Utilities.CharType
alphabet - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
ALPHABET_RNA - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
ALWAYS - Static variable in class ur_rna.RNAstructureUI.ui.ScrollerPane
  A generic constant symbolizing that a scroll bar must always be used.
ANCESTOR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
ancestorAdded(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
ancestorMoved(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
ancestorRemoved(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
ancestorResizeListener - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
and(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
and(Matcher, Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
And(Matcher, Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.And
and(Matcher) - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
ANDASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
angleBetween(Vec2D) - Method in class ur_rna.Utilities.geom.Vec2D
  Gets the smallest angle between two vectors.
angleTo(Vec2D) - Method in class ur_rna.Utilities.geom.Vec2D
  Gets the full angle from this vector to v2, sweeping counter-clockwise.
AnnotationAppInfoProvider(ApplicationInfo) - Constructor for class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
AnnotationMenu - Class in ur_rna.RNAstructureUI.drawing.menus
  A class that handles a menu which can annotate a drawn structure.
AnnotationMenu(StructureDialog) - Constructor for class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
  Constructor.
AntiqueWhite - Static variable in class ur_rna.Utilities.Colors
ANY - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
any(Iterable<T>, Predicate<T>) - Static method in class ur_rna.Utilities.ObjTools
  Returns true if the test function returns true for any of the items in the iterable.
anyFilesMatch(String, String) - Static method in class ur_rna.Utilities.PathTools
  Returns the true if any files in the given directory match the specified filter, which should be a a glob expression such as "*.{java,class,jar}" Glob expressions are fairly uniform across platforms.
app() - Static method in class ur_rna.StructureEditor.AppActions
app() - Method in class ur_rna.StructureEditor.services.UserPrefs
  Store application-wide settings that are not user-specific here.
AppActions - Class in ur_rna.StructureEditor
AppActions() - Constructor for class ur_rna.StructureEditor.AppActions
append - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
append - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
append(float) - Method in class ur_rna.Utilities.StringBuilderEx
append(Object) - Method in class ur_rna.Utilities.StringBuilderEx
append(String) - Method in class ur_rna.Utilities.StringBuilderEx
append(StringBuffer) - Method in class ur_rna.Utilities.StringBuilderEx
  Appends the specified `StringBuffer` to this sequence.
append(CharSequence) - Method in class ur_rna.Utilities.StringBuilderEx
append(CharSequence, int, int) - Method in class ur_rna.Utilities.StringBuilderEx
append(char[]) - Method in class ur_rna.Utilities.StringBuilderEx
append(char[], int, int) - Method in class ur_rna.Utilities.StringBuilderEx
append(boolean) - Method in class ur_rna.Utilities.StringBuilderEx
append(char) - Method in class ur_rna.Utilities.StringBuilderEx
append(int) - Method in class ur_rna.Utilities.StringBuilderEx
append(long) - Method in class ur_rna.Utilities.StringBuilderEx
append(double) - Method in class ur_rna.Utilities.StringBuilderEx
appendCodePoint(int) - Method in class ur_rna.Utilities.StringBuilderEx
appendGuiSearchParam(ComposableMatcher, String, Object) - Method in class ur_rna.GUITester.ScriptRuntime
appendGuiTree(String, Component, HashMap<Component, Integer>, StringBuilder) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
appendIfEmpty(String) - Method in class ur_rna.Utilities.StringBuilderEx
appendIfNotEmpty(String) - Method in class ur_rna.Utilities.StringBuilderEx
appendInfo(StringBuilder, String, String) - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
appendSeparator(String) - Method in class ur_rna.Utilities.StringBuilderEx
  Appends the given separator, but only if there is existing text and it does not already end with the separator.
appendStyle(StringBuilder, String, Object) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
appendText(StringBuilder, String, String) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
AppInfo - Class in ur_rna.Utilities
  Provides information on the current running application.
AppInfo() - Constructor for class ur_rna.Utilities.AppInfo
AppInfo.AnnotationAppInfoProvider - Class in ur_rna.Utilities
AppInfo.AppInfoProvider - Interface in ur_rna.Utilities
ApplicationInfo - Annotation Type in ur_rna.Utilities.annotation
  Indicates the Application name, title, and version when placed on the startup class (which contains main())
AppLog - Class in ur_rna.Utilities
  A utility class to streamline and standardize logging across applications.
AppLog() - Constructor for class ur_rna.Utilities.AppLog
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ActionOp
apply(GraphicsStyle) - Method in interface ur_rna.StructureEditor.services.drawing.export.GraphicsOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearHintsOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ControlOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
apply(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp
applyColors(int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
applyHistoryState(HistoryState) - Method in class ur_rna.StructureEditor.services.RnaDrawController
applyNativeLookAndFeel() - Static method in class ur_rna.Utilities.OSInfo
  Check the OS to see if it's a Mac, and if it is, set a few system properties to make things more "Mac-like."
applyOperation(GraphicsOp) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
applyStyleToStructure(NewFileWindow.StructItem, Style) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
AppMainFrame - Class in ur_rna.RNAstructureUI
  A class that creates the application frame of the RNAstructure GUI.
AppMainFrame() - Constructor for class ur_rna.RNAstructureUI.AppMainFrame
  Constructor.
APPNAME - Static variable in class ur_rna.StructureEditor.Program
appName - Static variable in class ur_rna.Utilities.AppInfo
appNode - Variable in class ur_rna.StructureEditor.services.UserPrefs
AppOptions() - Constructor for class ur_rna.GUITester.GUITesterStartup.AppOptions
approveSelection() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
approveSelection() - Method in class ur_rna.Utilities.swing.FileDialog
appTitle - Static variable in class ur_rna.Utilities.AppInfo
appVersion - Static variable in class ur_rna.Utilities.AppInfo
Aqua - Static variable in class ur_rna.Utilities.Colors
Aquamarine - Static variable in class ur_rna.Utilities.Colors
arc(Point2D, double, double, double, int) - Static method in class ur_rna.Utilities.geom.Ellipses
arc(Point2D, double, double, double, boolean, int) - Static method in class ur_rna.Utilities.geom.Ellipses
  The normal Arc2D constructor expects the angles in degrees.
arc(double, double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
arcAngleTo(Vec2D, boolean) - Method in class ur_rna.Utilities.geom.Vec2D
  This calculates the angle from one vector to another, similar to `Vec2D.angleTo(Vec2D)` except that the output is intended for applications in which the direction of travel is indicated by the sign of the result and the extent of travel is indicated by its absolute value.
arg - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
Argument(String, int) - Constructor for class ur_rna.Utilities.CommandLineParser.Argument
ArgumentList() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
arguments - Variable in class ur_rna.Utilities.CommandLineParser.ParseResults
arrJoin(Object[], String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
ARROW - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
asBool(Object) - Static method in class ur_rna.Utilities.ObjTools
  If obj is a boolean, its value is returned.
asBool(String, boolean) - Static method in class ur_rna.Utilities.Strings
  Attempts to convert a string representing a conceptual "true/false" into a boolean.
asBool(String) - Static method in class ur_rna.Utilities.Strings
asMergeItem(Component) - Static method in interface ur_rna.Utilities.swing.IMergeItem
asMergeItems(Collection<? extends Component>) - Static method in interface ur_rna.Utilities.swing.IMergeItem
assertError(TestUtils.TestMethod, Class) - Static method in class ur_rna.Utilities.testing.TestUtils
assertError(TestUtils.TestMethod, Class, boolean) - Static method in class ur_rna.Utilities.testing.TestUtils
assertInstanceOf(Class, Object) - Static method in class ur_rna.Utilities.testing.TestUtils
assertInstanceOf(Class, Class) - Static method in class ur_rna.Utilities.testing.TestUtils
ASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
ASSIGN_REF - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Assignment() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
AssignmentOperator() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
ASTAction - Class in ur_rna.GUITester.ScriptParser
ASTAction(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTAction
ASTAction(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTAction
ASTAssignment - Class in ur_rna.GUITester.ScriptParser
ASTAssignment(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTAssignment
ASTAssignment(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTAssignment
ASTGuiReference - Class in ur_rna.GUITester.ScriptParser
ASTGuiReference(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTGuiReference
ASTGuiReference(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTGuiReference
ASTGuiSearchCriteria - Class in ur_rna.GUITester.ScriptParser
ASTGuiSearchCriteria(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTGuiSearchCriteria
ASTGuiSearchCriteria(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTGuiSearchCriteria
ASTLiteral - Class in ur_rna.GUITester.ScriptParser
ASTLiteral(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTLiteral
ASTLiteral(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTLiteral
ASTNamedArgument - Class in ur_rna.GUITester.ScriptParser
ASTNamedArgument(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTNamedArgument
ASTNamedArgument(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTNamedArgument
ASTRoot - Class in ur_rna.GUITester.ScriptParser
ASTRoot(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTRoot
ASTRoot(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTRoot
ASTVarRef - Class in ur_rna.GUITester.ScriptParser
ASTVarRef(int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTVarRef
ASTVarRef(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ASTVarRef
asyncTimer_elapsed() - Method in class ur_rna.StructureEditor.windows.DrawWindow
asyncUpdateTimer - Variable in class ur_rna.StructureEditor.windows.DrawWindow
at(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
AT_END - Static variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
AT_END - Static variable in class ur_rna.Utilities.Filter.FilterIterator
atBool() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
atEndOfLine() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
atEOF() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
atNumber() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
autoFlush() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
autoScale(Dimension) - Method in class ur_rna.StructureEditor.ui.DrawPanel
autoScale() - Method in class ur_rna.StructureEditor.windows.DrawWindow
autoSetFieldNames() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Automatically set the names of controls (JComponents) that are direct Fields of this class.
available - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
AWAITING_CONSUMER - Static variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
AWAITING_CONSUMER - Static variable in class ur_rna.Utilities.Filter.FilterIterator
Azure - Static variable in class ur_rna.Utilities.Colors

## B

b3 - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
b5 - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
BACK_SLASH - Static variable in class ur_rna.Utilities.CharConstants
backboneColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
backboneStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
backboneWidth - Variable in class ur_rna.StructureEditor.models.DrawSettings
backend - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  The back end object that reads data for dot plots.
backend - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  The back end object that reads data for structures.
backend - Variable in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  The back end calculator that's linked to this menu.
backend - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
  The back end calculator that's linked to this window.
BackendCalc() - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
backendPairIndex(Nuc) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
backendProgress - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
backendRedrawRadial(RnaScene, RNA, int) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
backendValue() - Method in enum ur_rna.RNAstructureUI.utilities.FileType
background - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Current background color.
BackgroundOp(Color) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
BackgroundWork() - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
BackgroundWorker - Class in ur_rna.RNAstructureUI.utilities
BackgroundWorker() - Constructor for class ur_rna.RNAstructureUI.utilities.BackgroundWorker
BackgroundWorker.ErrorInfo - Class in ur_rna.RNAstructureUI.utilities
BackgroundWorker.StateChangeEventArgs - Class in ur_rna.RNAstructureUI.utilities
BACKSLASH - Static variable in class ur_rna.Utilities.CharType
backup(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Retreat.
BarButton() - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  Constructor.
base - Variable in class ur_rna.StructureEditor.models.Motif.Branch
base - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
baseDir - Variable in class ur_rna.Utilities.ResourceLoader
baseName() - Method in class ur_rna.Utilities.PathTools.FileName
baseOutputName - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
baseOutputName1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
baseOutputName2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
baseOutputNameShared - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
bc - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
beginColumn - Variable in class ur_rna.GUITester.ScriptParser.Token
  The column number of the first character of this Token.
beginLine - Variable in class ur_rna.GUITester.ScriptParser.Token
  The line number of the first character of this Token.
BeginToken() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
behaviorMode - Variable in class ur_rna.StructureEditor.services.RnaDrawController
BehaviorMode() - Constructor for enum ur_rna.StructureEditor.services.RnaDrawController.BehaviorMode
Beige - Static variable in class ur_rna.Utilities.Colors
BinaryMatcher(Matcher, Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
Bisque - Static variable in class ur_rna.Utilities.Colors
BIT_AND - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
BIT_NOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
BIT_OR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
BKSP - Static variable in class ur_rna.Utilities.CharConstants
Black - Static variable in class ur_rna.Utilities.Colors
BlanchedAlmond - Static variable in class ur_rna.Utilities.Colors
Blue - Static variable in class ur_rna.Utilities.Colors
BlueViolet - Static variable in class ur_rna.Utilities.Colors
bold() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
  Do something to emphasize this hint.
bold() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawShape
bold() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
Bond - Class in ur_rna.StructureEditor.models
  Represents a bond between two nucleotides.
Bond(Nuc, Nuc) - Constructor for class ur_rna.StructureEditor.models.Bond
Bond(Nuc, Nuc, BondType) - Constructor for class ur_rna.StructureEditor.models.Bond
Bond - Static variable in interface ur_rna.StructureEditor.services.SceneColorizer.ColorMode
Bond.BondInfo - Class in ur_rna.StructureEditor.models
  A class for storing the indices of bonded nucleotides instead of direct references.
Bond.MultiLoopRole - Enum in ur_rna.StructureEditor.models
BOND_COLOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
BOND_NUCS - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
BOND_TYPE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
BOND_TYPE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
bondColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
bondColor - Variable in class ur_rna.StructureEditor.models.NucStyle
bondColorPseudo - Variable in class ur_rna.StructureEditor.models.DrawSettings
BondInfo(int, int, BondType) - Constructor for class ur_rna.StructureEditor.models.Bond.BondInfo
bondIsNextInHelix(Bond, Bond, ObjTools.RefInt) - Static method in class ur_rna.StructureEditor.models.Motif.Helix
  Determines whether the "current" bond is immediately after the "prev" bond in a helix.
bondLength - Variable in class ur_rna.StructureEditor.models.DrawSettings
bonds - Variable in class ur_rna.StructureEditor.models.RnaSceneState
Bonds - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
BONDS - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
bondStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
bondStrokePseudo - Variable in class ur_rna.StructureEditor.models.DrawSettings
BondType - Enum in ur_rna.StructureEditor.models
  These Bond types reflect additional user-input that could not be garnered directly from the bases on either side of the bonds.
BondType(String, String) - Constructor for enum ur_rna.StructureEditor.models.BondType
BondType - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
bondWidth - Variable in class ur_rna.StructureEditor.models.DrawSettings
BOOL - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
BoolEventArgs(boolean) - Constructor for class ur_rna.Utilities.EventArgs.BoolEventArgs
boolValue() - Method in class ur_rna.Utilities.NamedArg
BorderBuilder - Class in ur_rna.RNAstructureUI.ui
  A class that places a border type on a specified component type.
BorderBuilder() - Constructor for class ur_rna.RNAstructureUI.ui.BorderBuilder
BorderedButtonPanel - Class in ur_rna.RNAstructureUI.ui
  A class that produces a panel which contains a button with a border around it.
BorderedButtonPanel(ActionListener, String) - Constructor for class ur_rna.RNAstructureUI.ui.BorderedButtonPanel
  Text Constructor.
BorderedButtonPanel(ActionListener, String, int) - Constructor for class ur_rna.RNAstructureUI.ui.BorderedButtonPanel
  Border Constructor.
BOTTOM_POS - Static variable in class ur_rna.StructureEditor.menus.FileMenu
bounded(int, int, int) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
bounds - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
box - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
boxSize - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
BP - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Bracket - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
bracketChars - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
Branch() - Constructor for class ur_rna.StructureEditor.models.Motif.Branch
Branch(Nuc) - Constructor for class ur_rna.StructureEditor.models.Motif.Branch
  Creates a unimolecular branch that extends from the specified nucleotide to its pair.
Branch(Motif.Helix, boolean) - Constructor for class ur_rna.StructureEditor.models.Motif.Branch
branch_end_line - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
branch_indent - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
branch_mid_line - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
branchBonds - Variable in class ur_rna.StructureEditor.models.Motif.MultiLoop
branchNucs - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
BranchSlider - Class in ur_rna.StructureEditor.services.drawing
  A DrawHandle that allows a user to "slide" an RNA branch (i.e.
BranchSlider(SceneController) - Constructor for class ur_rna.StructureEditor.services.drawing.BranchSlider
Break - Static variable in class ur_rna.RNAstructure.Nucleobase
  Represents and intermolecular break between separate strands ("I")
breakBackendPseudoknots(RnaScene, RNA, int) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
breakBond(Bond) - Method in class ur_rna.StructureEditor.models.RnaScene
breakBonds(int...) - Method in class ur_rna.StructureEditor.models.RnaScene
BreakPseudoknot(boolean, int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
BreakPseudoknot(boolean, int) - Method in class ur_rna.RNAstructure.backend.RNA
BreakPseudoknot(boolean) - Method in class ur_rna.RNAstructure.backend.RNA
BreakPseudoknot() - Method in class ur_rna.RNAstructure.backend.RNA
BreakPseudoknots(int) - Method in class ur_rna.RNAstructure.backend.structure
breakSelectedBonds() - Method in class ur_rna.StructureEditor.services.RnaDrawController
Brown - Static variable in class ur_rna.Utilities.Colors
browse(String) - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
browse(String) - Static method in class ur_rna.StructureEditor.AppActions
browseFile(ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
browseFile(PredictWindowBase.FileFieldInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
browseFile(JTextComponent, String, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
browseHelp() - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
browseLoadProbData() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
browseLoadValueData() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
browseLocalHelp() - Static method in class ur_rna.StructureEditor.AppActions
browseRecentFile(JComponent, PredictWindowBase.FileFieldInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
browseWebsite() - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
btnAccept - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
btnAddProbRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnAddSymbolRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnAddValueRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnApplyBond - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnApplyFill - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnApplyOutline - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnApplyText - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnBrowseCon - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnBrowseOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnBrowseSeq - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnBrowseShape - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnCancel - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
btnCancel - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
btnCancel - Variable in class ur_rna.Utilities.swing.WaitDialog
btnCancelTask - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
btnCancelTask - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnCancelTask - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnCancelTask - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
btnChoose - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
btnChoose - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
btnChooseColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnCleanupRecent - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
btnClearList - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnClearProbText - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnClearRecent - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
btnClearValueText - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnClose - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
btnClose - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
btnClose - Variable in class ur_rna.StructureEditor.windows.AboutWindow
btnClose - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnExtract - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
btnFeedback - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
btnHelp - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
btnHelpMod - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnHelpProb - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnLoadModFile - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnLoadProbFile - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnMoveDn - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnMoveUp - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnOK - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
btnOpenFile - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
btnRecentCon - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnRecentOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnRecentSeq - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnRecentShape - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnRemove - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnRemProbRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnRemSymbolRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnRemValueRule - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetAll - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
btnResetAll - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnResetAll - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
btnResetAll - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetBond - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetFill - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetMultiOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnResetOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
btnResetOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnResetOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnResetOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
btnResetOutline - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetPartsOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
btnResetProbRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetSymbolRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetText - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnResetTurboOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnResetValueRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnSelModeBranch - Variable in class ur_rna.StructureEditor.windows.DrawWindow
btnSelModeHelix - Variable in class ur_rna.StructureEditor.windows.DrawWindow
btnSelModeNuc - Variable in class ur_rna.StructureEditor.windows.DrawWindow
btnSequenceHelp - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
btnShowAbbreviations - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
btnSingleColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnStartCalc - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
btnStartCalc - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
btnStartCalc - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
btnStartCalc - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
btnStructureHelp - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
btnValueChooseColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
btnWebsite - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
bufcolumn - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
buffer - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
bufline - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
bufpos - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Position in buffer.
bufsize - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
Build - Variable in class ur_rna.Utilities.Version
buildAccessFoldDataStructure(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildAllSubDataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildArgListString(ScriptNode) - Method in class ur_rna.GUITester.ScriptRuntime
buildBifoldDataStructure(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildBipartitionDataStructure(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildButtonPanel() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Make the button panel at the bottom of the window.
buildColors() - Static method in class ur_rna.Utilities.Colors
buildDesktop() - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Create the gray back panel that fills the main frame.
buildDesktop() - Method in class ur_rna.StructureEditor.MainFrame
  Create the gray back panel that fills the main frame.
buildDialog(String, NumberField...) - Method in class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
  Build the value selection dialog.
buildDuplexFoldDataStructure(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildDynalignAlignmentMenu() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Build a complete menu that handles Dynalign alignment constraints.
buildDynalignDataStructure(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildEfn2DataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildFoldDataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildInfoLabel(JComponent) - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Create the label at the bottom of the main frame.
buildInfoLabel() - Method in class ur_rna.StructureEditor.MainFrame
  Create the label at the bottom of the main frame.
buildLegend(String...) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Build the legend grid for this panel.
buildLocationInfo(StringBuilderEx, int, int, String) - Static method in exception ur_rna.Utilities.SyntaxErrorException
buildMainMenu() - Method in class ur_rna.RNAstructureUI.AppMainFrame
buildMatcher(ASTGuiSearchCriteria) - Method in class ur_rna.GUITester.ScriptRuntime
buildMaxExpectDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildMaxLoopMenu() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Build a complete menu that handles maximum loop size.
buildMenuBar() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Create the image dialog's menu bar.
buildMessage(Token, int[][], String[]) - Static method in exception ur_rna.GUITester.ScriptParser.ParseException
  It uses "currentToken" and "expectedTokenSequences" to generate a parse error message and returns it.
buildMessage(boolean, int, int, int, String, char) - Static method in error ur_rna.GUITester.ScriptParser.TokenMgrError
  Returns a detailed message for the error when it is thrown by the token manager to indicate a lexical error.
buildMessage(String, String, int, int, String) - Static method in exception ur_rna.Utilities.SyntaxErrorException
buildOligoScreenDataStructure() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildOligoWalkDataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildPartitionDataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildProbKnotDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildRefoldDynalignDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildRefoldSingleDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildRemovePseudoknotsDataStructure(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildResultsWindow(String, int, int, int) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Build the results window for this OligoWalk calculation.
buildSourceIndex(CharSequence) - Method in class ur_rna.Utilities.SimpleDataSerializer
buildSpecificOptionsPanel() - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
buildSpecificOptionsPanel() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Build an input options box specific to this window.
buildSpecificOptionsPanel() - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
buildStatusBar() - Method in class ur_rna.RNAstructureUI.AppMainFrame
buildStatusBar(JLabel) - Method in class ur_rna.StructureEditor.MainFrame
buildStochasticDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
buildStrandIndex(int, int) - Method in class ur_rna.StructureEditor.models.RnaScene
  Creates a lookup-index where element[I] is the starting nuclotide index of the nucleotide belonging to strand[I].
buildStructureMenu() - Method in class ur_rna.StructureEditor.windows.DrawWindow
buildTemperatureMenu() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Build a complete menu that handles temperature.
buildTextBoxPanel(int, String, JTextComponent, String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Build a text input region for this window.
buildToolBar() - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Build the main RNAstructure toolbar.
buildToolBar() - Method in class ur_rna.StructureEditor.MainFrame
  Build the main RNAstructure toolbar.
buildUI() - Method in class ur_rna.Utilities.swing.WaitDialog
buildUnimolecularMenu() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Build a complete menu that handles if unimolecular pairs are allowed.
BurlyWood - Static variable in class ur_rna.Utilities.Colors
button - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
button - Variable in class ur_rna.RNAstructureUI.ui.ProgressPanel
buttonFont - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
buttonFontBold - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
ButtonGroupList - Class in ur_rna.Utilities.swing
  Extends `ButtonGroup` to allow selecting items by index.
ButtonGroupList() - Constructor for class ur_rna.Utilities.swing.ButtonGroupList
buttonListener - Variable in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
ButtonListener(int) - Constructor for class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel.ButtonListener

## C

C - Static variable in class ur_rna.RNAstructure.Nucleobase
C_YEAR - Static variable in class ur_rna.StructureEditor.Program
cachedBounds - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
cachedProps - Variable in class ur_rna.Utilities.prefs.FilePreferences.RootNode
CadetBlue - Static variable in class ur_rna.Utilities.Colors
calcArcExtent(double, double, boolean) - Static method in class ur_rna.Utilities.geom.Ellipses
calcBondLength() - Method in class ur_rna.StructureEditor.models.DrawSettings
calcBounds(Graphics2D, View2D, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
calcBounds(Graphics2D, View2D, boolean) - Method in interface ur_rna.StructureEditor.services.SceneRenderer
calcBoxPos(Point2D, Point2D, double, DrawSettings, AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Calculates the position of the DrawHandle's box based on a starting point and the suggested direction to move away from that point.
calcCanceled - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
calcCancelListener - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
calcComplete(PredictBimolStructureWindow.PredictTask) - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
calcComplete(PredictMultiStructureWindow.PredictTask) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
calcComplete(PredictSingleStructureWindow.PredictSingleStructureTask) - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
calcComplete(PredictTwoStructureWindow.PredictTask) - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
calcCompleted - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
calcFromPoints(Point2D, Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.Ellipses.Circle
  Calculate the center and radius of a circle from from 3 points on the circle.
calcHandleOffset() - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
calcLeastSquaresFit(Point2D...) - Static method in class ur_rna.Utilities.geom.Ellipses.Circle
calcLocation(Point2D.Float) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
calcLocation(Point2D.Float, SelectionRotater.RotationCenter) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
calcLoopBestFitCircle(Motif.Loop) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
calcLoopType(Motif.Loop) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
calcMaxNucCount(RnaSceneGroup) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
calcMultiLoopBestFitCircle(Motif.MultiLoop) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
calcNormalToNuc(Nuc) - Method in class ur_rna.StructureEditor.services.RnaDrawController
calcNormalToNuc(Nuc) - Method in interface ur_rna.StructureEditor.services.SceneController
calcNucGroupCenter(Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
calcOptimalLoopDistance(Nuc, Nuc, int) - Method in class ur_rna.StructureEditor.models.DrawSettings
  Calculate the optimal circumference for a circle containing nucs in the given region.
calcOptimalLoopDistance(int, int) - Method in class ur_rna.StructureEditor.models.DrawSettings
  Calculate the optimal circumference for a circle containing the given number of nucleotides.
calcOptimalMultiLoopRadius(Motif.MultiLoop) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
calcOptimalNuc2NucDistance(Nuc, Nuc) - Method in class ur_rna.StructureEditor.models.DrawSettings
  Calculate the optimal distance between nuc midpoints.
calcOptimalNuc2NucDistance(int) - Method in class ur_rna.StructureEditor.models.DrawSettings
calcOptimalOuterDistance(Nuc, Nuc, int) - Method in class ur_rna.StructureEditor.models.DrawSettings
  Calculate the optimal distance from the outside of one nuc to the outside of another.
calcOptimalOuterDistance(int, int) - Method in class ur_rna.StructureEditor.models.DrawSettings
CalcParams - Class in ur_rna.RNAstructureUI.utilities
CalcParams() - Constructor for class ur_rna.RNAstructureUI.utilities.CalcParams
calcProgressListener - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
calcPureRender() - Method in class ur_rna.StructureEditor.ui.DrawPanel
  Renders the scene with no applied transform and no output to the device (because it is clipped).
calcResult() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
calcTextBox(Graphics2D, String, double, double) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
calcTextBox(Graphics2D, String, double, double, boolean) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
calcTextBox(Graphics2D, String, double, double, boolean, ObjTools.RefInt) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
calculateEnergy(RnaScene) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
  Calculates the free energy of the structure in kcal/mol
CalculateFreeEnergy(int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
CalculateFreeEnergy(int) - Method in class ur_rna.RNAstructure.backend.RNA
CalculateFreeEnergy() - Method in class ur_rna.RNAstructure.backend.RNA
calculateOffset() - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
calcWasCanceled() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
canCancel - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
canCancel() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
canCancel() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
cancel() - Method in class ur_rna.RNAstructure.backend.PartialProgress
cancel() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
cancel() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
cancel() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
cancel() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
cancel() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
cancel() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
cancel() - Method in class ur_rna.Utilities.swing.WaitDialog
CancelButton - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
canceled() - Method in class ur_rna.RNAstructure.backend.PartialProgress
canceled() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
canceled - Variable in class ur_rna.Utilities.swing.WaitDialog
canceled(ActionEvent) - Method in class ur_rna.Utilities.swing.WaitDialog
cancelListener - Variable in class ur_rna.Utilities.swing.WaitDialog
cancelMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
cancelOperation() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
cancelRunningTask() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Cancel the active background task (if there is one) if it is cancelable.
canFoldOligoOligo(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
canFoldOligoSelf(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
canRedo() - Method in class ur_rna.StructureEditor.services.History
canRedo() - Method in class ur_rna.StructureEditor.services.RnaDrawController
canRedo() - Method in interface ur_rna.StructureEditor.services.SceneController
canUndo() - Method in class ur_rna.StructureEditor.services.History
canUndo() - Method in class ur_rna.StructureEditor.services.RnaDrawController
canUndo() - Method in interface ur_rna.StructureEditor.services.SceneController
canvas - Variable in class ur_rna.StructureEditor.services.RnaDrawController
canvasComponent - Variable in class ur_rna.StructureEditor.services.RnaDrawController
capacity() - Method in class ur_rna.RNAstructure.backend.CDblVector
capacity() - Method in class ur_rna.RNAstructure.backend.CIntVector
capacity() - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the current capacity.
caption - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
captureDesktopImage() - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
  Convenience method to create a BufferedImage of the desktop
captureDesktopImage(Rectangle) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
  Create a BufferedImage from a rectangular region on the screen.
captureImage(JComponent) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
captureImage(JComponent, Rectangle) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
captureImage(Component) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
cards - Variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
  The layout that holds the dynamic options applicable to a mode.
category - Variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
CDblVector - Class in ur_rna.RNAstructure.backend
CDblVector(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.CDblVector
CDblVector() - Constructor for class ur_rna.RNAstructure.backend.CDblVector
CDblVector(long) - Constructor for class ur_rna.RNAstructure.backend.CDblVector
CDblVector_add(long, CDblVector, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_capacity(long, CDblVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_clear(long, CDblVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_get(long, CDblVector, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_isEmpty(long, CDblVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_reserve(long, CDblVector, long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_set(long, CDblVector, int, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CDblVector_size(long, CDblVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
center - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater
center - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
center() - Method in class ur_rna.Utilities.geom.Ellipses.Circle
center(Point2D) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
center(double, double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
CenterPoint(SceneController, SelectionRotater) - Constructor for class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
changed - Variable in class ur_rna.Utilities.swing.TextDocListener
changedUpdate(DocumentEvent) - Method in interface ur_rna.Utilities.swing.SimpleDocumentListener
changedUpdate(DocumentEvent) - Method in class ur_rna.Utilities.swing.TextDocListener
changeExt(String) - Method in class ur_rna.Utilities.PathTools.FileName
changeExtension(String, String) - Static method in class ur_rna.Utilities.PathTools
changeListener - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
changeListener - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
charAt(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the `char` value in this sequence at the specified index.
CharConstants - Class in ur_rna.Utilities
CharConstants() - Constructor for class ur_rna.Utilities.CharConstants
chars() - Method in class ur_rna.Utilities.StringBuilderEx
  Returns a stream of `int` zero-extending the `char` values from this sequence.
CHARSET_UTF8 - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
Chartreuse - Static variable in class ur_rna.Utilities.Colors
CharType - Class in ur_rna.Utilities
CharType() - Constructor for class ur_rna.Utilities.CharType
charValue() - Method in class ur_rna.Utilities.NamedArg
check - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
checkAll(Container, boolean) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
checkBox1 - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
checkError(String...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
checkError(RNAstructureBackendCalculator...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
checkError(RNA...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
checkError(int...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
checkError(TwoRNA...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
checkErrors(RNA, String) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
checkErrors() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
checkForErrors(RNA) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
CheckMergeItem - Class in ur_rna.Utilities.swing
  A container for a merge-able menu item.
CheckMergeItem() - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(int) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(Action) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(Action, int) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(Action, String, int) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(String) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(String, int) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(String, ActionListener, String) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
CheckMergeItem(String, ActionListener, String, int, KeyStroke) - Constructor for class ur_rna.Utilities.swing.CheckMergeItem
checkMergePos(int) - Method in class ur_rna.Utilities.swing.MergeMenu
checkSettingChanged(ActionEvent) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
checkValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField
  Check the value of a field to make sure it's valid.
checkValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
checkValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.FloatField
checkValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
CHILD - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
child(int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
childCount() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
ChildFrame - Class in ur_rna.StructureEditor.windows
ChildFrame() - Constructor for class ur_rna.StructureEditor.windows.ChildFrame
ChildFrame(String) - Constructor for class ur_rna.StructureEditor.windows.ChildFrame
ChildFrame(String, boolean) - Constructor for class ur_rna.StructureEditor.windows.ChildFrame
childNames - Variable in class ur_rna.Utilities.prefs.FilePreferences
children - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
children - Variable in class ur_rna.Utilities.TreeNode
childrenNamesSpi() - Method in class ur_rna.Utilities.prefs.FilePreferences
childSpi(String) - Method in class ur_rna.Utilities.prefs.FilePreferences
ChildWindow - Class in ur_rna.RNAstructureUI.windows
  The base class for all RNAstructure GUI dialogs and windows.
ChildWindow() - Constructor for class ur_rna.RNAstructureUI.windows.ChildWindow
  Constructor.
ChildWindow.CommandInfo - Class in ur_rna.RNAstructureUI.windows
chkAllowBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
chkBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
chkDisableDashboard - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
chkEnable - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
chkIgnoreCase - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
chkShowDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
chkShowDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
chkShowDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
chkShowDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
chkUse - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
chkWrapSequence - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
chkWrapStructure - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
Chocolate - Static variable in class ur_rna.Utilities.Colors
ChooseStructureDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
  Constructor.
CIntVector - Class in ur_rna.RNAstructure.backend
CIntVector(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.CIntVector
CIntVector() - Constructor for class ur_rna.RNAstructure.backend.CIntVector
CIntVector(long) - Constructor for class ur_rna.RNAstructure.backend.CIntVector
CIntVector_add(long, CIntVector, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_capacity(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_clear(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_get(long, CIntVector, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_isEmpty(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_reserve(long, CIntVector, long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_set(long, CIntVector, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
CIntVector_size(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Circle(Point2D, double) - Constructor for class ur_rna.Utilities.geom.Ellipses.Circle
Circle(double) - Constructor for class ur_rna.Utilities.geom.Ellipses.Circle
Circle(double, double, double) - Constructor for class ur_rna.Utilities.geom.Ellipses.Circle
circled - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
circular - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
circularStartAngle - Variable in class ur_rna.StructureEditor.models.DrawSettings
ClassLoaderInfo - Class in ur_rna.Utilities
  Gets information about native libraries that have been loaded by a `ClassLoader`.
ClassLoaderInfo() - Constructor for class ur_rna.Utilities.ClassLoaderInfo
ClassMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
ClassMatcher() - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
ClassMatcher.MultiClassMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
ClassMatcher.SingleClassMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
cleanRecent(boolean) - Method in class ur_rna.StructureEditor.MainFrame
CleanStructure(int) - Method in class ur_rna.RNAstructure.backend.structure
CLEANUP_RECENT_FILES - Static variable in class ur_rna.StructureEditor.AppActions
clear() - Method in class ur_rna.RNAstructure.backend.CDblVector
clear() - Method in class ur_rna.RNAstructure.backend.CIntVector
clear() - Method in class ur_rna.StructureEditor.models.Strand
clear() - Method in class ur_rna.StructureEditor.services.History
clear() - Method in class ur_rna.StructureEditor.services.RecentFileList
CLEAR_RECENT_FILES - Static variable in class ur_rna.StructureEditor.AppActions
clearAnnotation() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Clear annotation from this dialog.
clearBonds() - Method in class ur_rna.StructureEditor.models.RnaScene
clearCache(Container) - Method in class ur_rna.Utilities.swing.MergeManager
clearDynalignAlignmentConstraints() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
ClearEnergies() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
ClearEnthalpies() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
clearFilters() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Clear any existing filters.
clearFilters() - Method in class ur_rna.Utilities.swing.FileDialog
  Clear any existing filters.
clearFoldingConstraints(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
clearFound(boolean) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
ClearHintsOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearHintsOp
clearNamed() - Method in class ur_rna.Utilities.StopWatch
  Remove all named StopWatches
clearNodeScope(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
ClearOp(Rectangle) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearOp
clearRect(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
clearRedo() - Method in class ur_rna.StructureEditor.services.History
  Clear all entries in front of the current position.
clearSelection() - Method in class ur_rna.StructureEditor.services.RnaDrawController
clearUndo() - Method in class ur_rna.StructureEditor.services.RnaDrawController
clearUndo() - Method in interface ur_rna.StructureEditor.services.SceneController
clip(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
clip - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
clip - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Shape used for clipping.
ClipOp(Shape, boolean) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
clippingPathElements - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
clipRect(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
clone() - Method in class ur_rna.StructureEditor.models.Bond
clone() - Method in class ur_rna.StructureEditor.models.Nuc
clone() - Method in class ur_rna.StructureEditor.models.NucStyle
clone() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
clone() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
clone() - Method in class ur_rna.Utilities.geom.Matrix3D
  Creates a new object of the same class as this object.
clone(Shape) - Static method in class ur_rna.Utilities.geom.ShapeUtil
clone() - Method in class ur_rna.Utilities.geom.Vec2D
clone() - Method in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
clone() - Method in class ur_rna.Utilities.Tuple.Pair
clone() - Method in class ur_rna.Utilities.Tuple.Quad
clone() - Method in class ur_rna.Utilities.Tuple.Triplet
cloneMethod - Static variable in class ur_rna.Utilities.ObjTools
close() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
  Close the GUI application including all existing Windows.
close() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
close() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
close() - Method in class ur_rna.StructureEditor.windows.ChildFrame
close() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
close() - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
close() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Closes the stream.
close() - Method in class ur_rna.Utilities.swing.MdiParentFrame
close() - Method in class ur_rna.Utilities.swing.WaitDialog
CLOSE_FILE_POS - Static variable in class ur_rna.StructureEditor.menus.FileMenu
closed - Variable in class ur_rna.Utilities.ExtendedBufferedReader
  Whether or not this reader has been closed.
closeNodeScope(Node, int) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
closeNodeScope(Node, boolean) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
closeOnCancel - Variable in class ur_rna.Utilities.swing.WaitDialog
closeProgress() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
closeProgress(boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
cmbPartsMode - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
cmbProbComparison - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
cmbRelative - Variable in class ur_rna.StructureEditor.windows.InsertBasesDialog
cmbTurboMode - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
cmbValueComparison - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
cmp - Variable in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
code - Variable in enum ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
codePointAt(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the character (Unicode code point) at the specified index.
codePointBefore(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the character (Unicode code point) before the specified index.
codePointCount(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the number of Unicode code points in the specified text range of this sequence.
codePoints() - Method in class ur_rna.Utilities.StringBuilderEx
  Returns a stream of code point values from this sequence.
cold - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
colNumber() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
COLON - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
color(Color) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
color(Color, Color) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
color(Color, int) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
color - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
color - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
color - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp
color - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Current stroke color.
color(Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.SceneColorizer
  Return true if any nucs were affected.
color(Nuc) - Method in class ur_rna.StructureEditor.services.SceneColorizer
COLOR_EMPTY - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
ColorByDataValue(double[], SceneColorizer.NumberRangeList, int) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
ColorByProbability(SceneColorizer.PairProbabilityData, SceneColorizer.NumberRangeList, int) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
ColorBySymbol(Map<String, Color>, int) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
ColorDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
  Constructor.
colorFill - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint
colorize(SceneColorizer) - Method in class ur_rna.StructureEditor.models.RnaScene
colorize(SceneColorizer, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
ColorizeDialog - Class in ur_rna.StructureEditor.windows
  Allows the user to choose how to color nucleobases.
ColorizeDialog(DrawWindow, Preferences, boolean) - Constructor for class ur_rna.StructureEditor.windows.ColorizeDialog
ColorizeDialog.ColorEditControl - Interface in ur_rna.StructureEditor.windows
ColorizeDialog.SimpleColorControl - Class in ur_rna.StructureEditor.windows
ColorizeDialog.SymbolColorRule - Class in ur_rna.StructureEditor.windows
ColorizeDialog.ValueColorRule - Class in ur_rna.StructureEditor.windows
colorizeScenes(SceneColorizer, boolean, boolean) - Method in class ur_rna.StructureEditor.windows.DrawWindow
colorLine - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint
colorMode - Variable in class ur_rna.StructureEditor.services.SceneColorizer
ColorOp(Color) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
ColorRemover(int) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
Colors() - Constructor for class ur_rna.StructureEditor.services.RnaDrawController.Colors
colors - Variable in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
Colors - Class in ur_rna.Utilities
  List of common Colors and color utilities.
Colors() - Constructor for class ur_rna.Utilities.Colors
colorsEqual(Color, Color) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
column - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
columnOffset - Variable in exception ur_rna.Utilities.SyntaxErrorException
  The estimated column number or character offset of the start of the syntax error.
columnWidth - Variable in class ur_rna.RNAstructureUI.windows.MultiWindow
  The width of each column of the window (input controls in column 1, sequence set in column 2).
combineFileNames(String, String, String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Combine two file names into a new file name.
combo - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
comboBox1 - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
COMMA - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
COMMA - Static variable in class ur_rna.Utilities.CharType
command - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
command - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
  The name or title of the command.
command() - Method in class ur_rna.Utilities.swing.UiAction
COMMAND_MODIFIER_MASK - Static variable in class ur_rna.Utilities.swing.ActionHelper
CommandInfo(String, int, Object) - Constructor for class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
CommandInfo(String, Object) - Constructor for class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
CommandInfo(String) - Constructor for class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
CommandInfo(String) - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
CommandInfo(ActionEvent) - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
CommandInfo(String, Object) - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
CommandInfo(String, Object, ActionEvent) - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
CommandLineParser - Class in ur_rna.Utilities
CommandLineParser() - Constructor for class ur_rna.Utilities.CommandLineParser
CommandLineParser(boolean) - Constructor for class ur_rna.Utilities.CommandLineParser
CommandLineParser(boolean, CommandLineParser.ParamAffinity, boolean) - Constructor for class ur_rna.Utilities.CommandLineParser
CommandLineParser.Argument - Class in ur_rna.Utilities
  Arguments are the results of parsing a commandline.
CommandLineParser.FlagArg - Class in ur_rna.Utilities
  Flags arguments are indicated by a preceding hyphen (-) or slash (/).
CommandLineParser.FlagDef - Class in ur_rna.Utilities
  Contains information about flags expected on the command-line.
CommandLineParser.ParamAffinity - Enum in ur_rna.Utilities
  Describes whether a parameter value is required, optional (allowed), or forbidden (invalid) for a given flag.
CommandLineParser.ParseResults - Class in ur_rna.Utilities
CommandLineParser.UnnamedArg - Class in ur_rna.Utilities
  Unnamed Arguments are those that stand alone on the command line.
CommandLineSplitter - Class in ur_rna.Utilities
  Split a string into an array in a manner similar to how a console command line is split.
CommandLineSplitter() - Constructor for class ur_rna.Utilities.CommandLineSplitter
commandListener - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
commasInLists - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
commasInMaps - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
commentBox - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
compare(Bond, Bond) - Static method in class ur_rna.StructureEditor.models.Bond
compare(Nuc, Nuc) - Static method in class ur_rna.StructureEditor.models.Nuc
  Compares based on index in scene.
compare(double, double) - Method in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
compare(double, double) - Method in interface ur_rna.StructureEditor.services.SceneColorizer.DoubleComparer
compare(Font, Font) - Method in class ur_rna.Utilities.swing.FontUtil.FontExpressivenessComparator
compareBothItems() - Static method in class ur_rna.Utilities.Tuple.Pair
compareByMergePos(Component, Component) - Static method in interface ur_rna.Utilities.swing.IMergeItem
compareByMergePos(IMergeItem, IMergeItem) - Static method in interface ur_rna.Utilities.swing.IMergeItem
compareFirstItem() - Static method in class ur_rna.Utilities.Tuple.Pair
comparer - Variable in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
compareTo(Bond) - Method in class ur_rna.StructureEditor.models.Bond
compareTo(Nuc) - Method in class ur_rna.StructureEditor.models.Nuc
  Compares based on index in scene.
compareTo(Version) - Method in class ur_rna.Utilities.Version
Comparison(String, SceneColorizer.DoubleComparer) - Constructor for enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
comparison - Variable in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
completeAction(int) - Method in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
component - Variable in class ur_rna.Utilities.swing.IMergeItem.Proxy
ComponentMatcher(Component) - Constructor for class ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher
Components - Class in ur_rna.Utilities.swing
  Utility to help with Swing Components
Components() - Constructor for class ur_rna.Utilities.swing.Components
composable(Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
ComposableBase - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase() - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
ComposableBase.BinaryMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase.BinaryMatcher.And - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase.BinaryMatcher.Or - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase.BinaryMatcher.Xor - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase.Identity - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableBase.Inverse - Class in ur_rna.GUITester.GuiTools.Matchers
ComposableMatcher - Interface in ur_rna.GUITester.GuiTools.Matchers
composite - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
composite - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Method used for mixing colors.
CompositeOp(Composite) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
COMPOUNDMESSAGELENGTH - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
COMPOUNDMESSAGELENGTH_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
compute_2X2(double, double, double, double[], double[], double[], double[], double[], int) - Static method in class ur_rna.Utilities.geom.Matrix3D
compute_qr(double[], double[], double[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
compute_rot(double, double, double[], double[], int, int) - Static method in class ur_rna.Utilities.geom.Matrix3D
compute_shift(double, double, double) - Static method in class ur_rna.Utilities.geom.Matrix3D
compute_svd(double[], double[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
conFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
conFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
conFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
conFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
conFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
ConsoleTools - Class in ur_rna.Utilities
ConsoleTools() - Constructor for class ur_rna.Utilities.ConsoleTools
ConsoleTools.FixedStream - Class in ur_rna.Utilities
Constants - Class in ur_rna.Utilities
Constants() - Constructor for class ur_rna.Utilities.Constants
Constraints - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
constraints - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
  The GridBagConstraints for this window.
ConstraintsMenu - Class in ur_rna.RNAstructureUI.menus
  A class that creates a folding constraints menu.
ConstraintsMenu(RNAstructureBackendCalculator) - Constructor for class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  General Constructor.
ConstraintsMenu.NucOrHelixDialog - Class in ur_rna.RNAstructureUI.menus
  An inner class which creates a dialog that sets constraints on single nucleotides or helices.
contains(Nuc) - Method in class ur_rna.StructureEditor.models.Bond
contains(Object) - Method in class ur_rna.StructureEditor.models.StrandList
contains(String) - Method in class ur_rna.StructureEditor.services.RecentFileList
contains(T[], T) - Static method in class ur_rna.Utilities.ObjTools
contains(T[], Predicate<T>) - Static method in class ur_rna.Utilities.ObjTools
containsAnyKey(String...) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
containsBase(int) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  Returns true if this helix element the nucleobase as the given index.
ContainsPseudoknot(int) - Method in class ur_rna.RNAstructure.backend.RNA
contentPanel - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
contentPanel - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
contentPanel - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
contentPanel - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
context - Variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
context - Variable in class ur_rna.Utilities.swing.FileDialog
CONTROL - Static variable in class ur_rna.Utilities.CharType
  ASCII Control codes (#0 to #31 and #127, but NOT including the white space charcters TAB=#9, LF=#10, and CR=#13).
control - Variable in exception ur_rna.Utilities.swing.FormValidationException
controller - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
controller - Variable in class ur_rna.StructureEditor.windows.DrawWindow
controllerHistoryUpdate(HistoryUpdateEvent) - Method in class ur_rna.StructureEditor.ui.DrawPanel
ControlOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ControlOp
controlPrefixes - Static variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
Controls - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
controlsUpdated() - Method in class ur_rna.StructureEditor.services.RnaDrawController
controlsUpdated() - Method in interface ur_rna.StructureEditor.services.SceneController
Convert - Class in ur_rna.Utilities
Convert() - Constructor for class ur_rna.Utilities.Convert
convert(T) - Method in class ur_rna.Utilities.ConverterFilter
convert(Object) - Method in class ur_rna.Utilities.ConverterFilter.SimpleCast
ConverterFilter<T,C> - Class in ur_rna.Utilities
ConverterFilter() - Constructor for class ur_rna.Utilities.ConverterFilter
ConverterFilter.FilterIterator - Class in ur_rna.Utilities
ConverterFilter.SimpleCast - Class in ur_rna.Utilities
convertGuiSearchRelationship(int) - Static method in class ur_rna.GUITester.ScriptRuntime
convertTooltipsToRollovers(JMenuItem) - Method in class ur_rna.RNAstructureUI.AppMainFrame
cool - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
coords - Variable in class ur_rna.StructureEditor.services.RnaDrawController
copy() - Method in class ur_rna.StructureEditor.models.DrawSettings
copyAction(String, AbstractButton) - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Copy the ActionCommand and ActionListener from an existing menu item.
copyAction(AbstractButton, AbstractButton) - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Copy the ActionCommand and ActionListener from the source to the destination AbstractButton
copyAction(AbstractButton, AbstractButton) - Method in class ur_rna.StructureEditor.MainFrame
  Copy the ActionCommand and ActionListener from the source to the destination AbstractButton
copyArea(int, int, int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
copyBonds(RnaScene) - Method in class ur_rna.StructureEditor.models.RnaScene
copyFrom(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
copyProps() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
CopyThermo(Thermodynamics) - Method in class ur_rna.RNAstructure.backend.RNA
copyTo(NucStyle) - Method in class ur_rna.StructureEditor.models.NucStyle
copyTo(List<? extends T>, T[]) - Static method in class ur_rna.Utilities.ObjTools
  Copies from the list to the array
copyTo(List<? extends T>, T[], int) - Static method in class ur_rna.Utilities.ObjTools
  Copies from the list to the array.
copyTo(List<? extends T>, T[], int, int) - Static method in class ur_rna.Utilities.ObjTools
  Copies the specified number of elements from the list to the array.
copyTo(Collection<? extends T>, T[]) - Static method in class ur_rna.Utilities.ObjTools
  Copies from the collection to the array
copyTo(Collection<? extends T>, T[], int) - Static method in class ur_rna.Utilities.ObjTools
  Copies from the collection to the array.
copyTo(Collection<? extends T>, T[], int, int) - Static method in class ur_rna.Utilities.ObjTools
  Copies the specified number of elements from the collection to the array.
Coral - Static variable in class ur_rna.Utilities.Colors
CornflowerBlue - Static variable in class ur_rna.Utilities.Colors
Cornsilk - Static variable in class ur_rna.Utilities.Colors
correctPreferredHeight(JComponent...) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
count - Variable in class ur_rna.Utilities.swing.TextDocListener
countLinkers(char[]) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
countLoops() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
CR - Static variable in class ur_rna.Utilities.CharConstants
CR - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
create() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
create(String) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
create(String, boolean) - Static method in class ur_rna.Utilities.StopWatch
  Create a new named StopWatch and optionally start it if `started` is true.
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
  Create any additional controls that need to show up on this dialog.
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
  Create any additional controls that need to show up on this dialog.
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
createCheckItem(String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
createCompatibleImage(int, int, boolean) - Static method in class ur_rna.Utilities.swing.ImageUtil
  Returns a `BufferedImage` that supports the specified transparency and has a data layout and color model compatible with this `GraphicsConfiguration`.
createConvertException(Object, Class) - Static method in class ur_rna.Utilities.Convert
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.AccessFoldWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  Override to create one or more custom menus that should be added to the main frame whenever this internal frame is active.
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
createCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
createDefaultScene() - Method in class ur_rna.StructureEditor.services.RnaDrawController
createDirectionalIcons(BufferedImage) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
createDisabled(String) - Static method in class ur_rna.RNAstructureUI.ui.FileField
  Create a disabled file input field.
createDNA() - Static method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
  Create a DNA menu.
createDocsFolder() - Static method in class ur_rna.RNAstructureUI.RNAstructure
  This is called from within AppMainFrame during startup when the program is being run for the first time.
createDrawing() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
createDrawnImage(Graphics2D) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Create the image drawn on this panel.
createDrawnImage(Graphics2D) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
createDrawnImage(Graphics2D) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
createDrawStructuresMenu() - Method in class ur_rna.RNAstructureUI.menus.FileMenu
createEditorWindow(RnaSceneGroup) - Static method in class ur_rna.StructureEditor.AppActions
createEmptyBox(String) - Static method in class ur_rna.RNAstructureUI.ui.HTMLCheckBox
  Create an empty check box.
createEnabled(String) - Static method in class ur_rna.RNAstructureUI.ui.FileField
  Create an enabled file input field.
createExampleFilesClicked - Static variable in class ur_rna.RNAstructureUI.ui.RecentFileButton
createFileItem(File, Consumer<File>, boolean) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
createGuiReference(ASTGuiReference) - Method in class ur_rna.GUITester.ScriptRuntime
createInputPanel() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Create the panel which holds input controls.
createLayout() - Static method in class ur_rna.StructureEditor.AppActions
createLine(AudioFormat) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
createMainMenus() - Method in class ur_rna.StructureEditor.MainFrame
createMainToolButtons() - Method in class ur_rna.StructureEditor.MainFrame
createMenuItem(String, String, String, KeyStroke) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
createMenuItem(String, ActionListener) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
createMenuItem(String, ActionListener, Font) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
createMenus() - Method in class ur_rna.StructureEditor.windows.DrawWindow
createNewFile() - Static method in class ur_rna.StructureEditor.AppActions
createNotFoundException(String) - Static method in class ur_rna.Utilities.ResourceLoader
createResultsPanel() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Create the panel which holds results data.
createRNA() - Static method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
  Create a RNA menu.
createRNAfromScene(RnaScene, boolean, boolean, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
createRoot() - Static method in class ur_rna.Utilities.prefs.FilePreferences
createRoot(String) - Static method in class ur_rna.Utilities.prefs.FilePreferences
createSceneFromRNA(RNA, int, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
  Create new RnaScene from an RNA structure.
createSelectedBox(String) - Static method in class ur_rna.RNAstructureUI.ui.HTMLCheckBox
  Create a selected check box.
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.ZoomDialog
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
createSelectionAction() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
createSelectionAction() - Method in class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
  Create the action that occurs once values are selected.
createSelectionAction() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
createStyleContext() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
CreateStyledDocument() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
createTextPanel(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
createTextPanel(String, Font) - Static method in class ur_rna.Utilities.swing.Dialogs
createToolbar(JToolBar) - Method in class ur_rna.RNAstructureUI.AppMainFrame
createToolButtons() - Method in class ur_rna.StructureEditor.windows.DrawWindow
createUI() - Method in class ur_rna.StructureEditor.windows.DrawWindow
createUIComponents() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
createUIComponents() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
createUIComponents() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
createUIComponents() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
createUIComponents() - Method in class ur_rna.StructureEditor.ui.SliderToolWindow
createUIComponents() - Method in class ur_rna.StructureEditor.windows.AboutWindow
createUIComponents() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
createUIComponents() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
createUIComponents() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
createWindowItem(JInternalFrame) - Method in class ur_rna.StructureEditor.menus.WindowsMenu
Crimson - Static variable in class ur_rna.Utilities.Colors
CRLF - Static variable in class ur_rna.Utilities.CharConstants
CT - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
CTEWriter(Writer) - Constructor for class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTEWriter
ctout(String) - Method in class ur_rna.RNAstructure.backend.structure
ctx - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
curChar - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
curLexState - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
curPos - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
current() - Method in class ur_rna.StructureEditor.services.History
currentColor - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  The current color painted on this button.
currentLine - Variable in class ur_rna.Utilities.ExtendedBufferedReader
  The current line index.
currentScene - Variable in class ur_rna.StructureEditor.windows.DrawWindow
currentStyle - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
currentToken - Variable in exception ur_rna.GUITester.ScriptParser.ParseException
  This is the last token that has been consumed successfully.
customCursor - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
customHelix - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
customMenus - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
customMenus - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
customMenus - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
  Any custom menus that are associated to this window are added to the customMenus MenuList.
customNuc - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
Cyan - Static variable in class ur_rna.Utilities.Colors

## D

d_sign(double, double) - Static method in class ur_rna.Utilities.geom.Matrix3D
DarkBlue - Static variable in class ur_rna.Utilities.Colors
DarkCyan - Static variable in class ur_rna.Utilities.Colors
DarkGoldenRod - Static variable in class ur_rna.Utilities.Colors
DarkGray - Static variable in class ur_rna.Utilities.Colors
DarkGreen - Static variable in class ur_rna.Utilities.Colors
DarkKhaki - Static variable in class ur_rna.Utilities.Colors
DarkMagenta - Static variable in class ur_rna.Utilities.Colors
DarkOliveGreen - Static variable in class ur_rna.Utilities.Colors
DarkOrange - Static variable in class ur_rna.Utilities.Colors
DarkOrchid - Static variable in class ur_rna.Utilities.Colors
DarkRed - Static variable in class ur_rna.Utilities.Colors
DarkSalmon - Static variable in class ur_rna.Utilities.Colors
DarkSeaGreen - Static variable in class ur_rna.Utilities.Colors
DarkSlateBlue - Static variable in class ur_rna.Utilities.Colors
DarkSlateGray - Static variable in class ur_rna.Utilities.Colors
DarkTurquoise - Static variable in class ur_rna.Utilities.Colors
DarkViolet - Static variable in class ur_rna.Utilities.Colors
dashboard - Variable in class ur_rna.StructureEditor.MainFrame
DashboardFrame - Class in ur_rna.StructureEditor.windows
  This screen is shown on startup and whenever there are no files loaded.
DashboardFrame() - Constructor for class ur_rna.StructureEditor.windows.DashboardFrame
DashboardFrame.ListItem - Class in ur_rna.StructureEditor.windows
dashed() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
data - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  The array of data for a particular structure.
data - Variable in exception ur_rna.Utilities.ExtensibleException
DATA_PATH - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
datatable - Class in ur_rna.RNAstructure.backend
datatable(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.datatable
datatable() - Constructor for class ur_rna.RNAstructure.backend.datatable
DateHelper - Class in ur_rna.Utilities
DateHelper() - Constructor for class ur_rna.Utilities.DateHelper
DBL_QUOT - Static variable in class ur_rna.Utilities.CharConstants
DBN_BIT_MULTI_SEQ - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DBN_BIT_MULTI_SEQ_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_BIT_MULTI_TITLE - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DBN_BIT_MULTI_TITLE_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_BIT_SEQ_LABEL - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DBN_BIT_SEQ_LABEL_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_BIT_SIDE_TITLES - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DBN_BIT_SIDE_TITLES_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_FMT_MULTI_TITLE_AND_SEQ_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_FMT_MULTI_TITLE_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_FMT_SIDE_TITLES_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DBN_FMT_SINGLE_TITLE_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
debug(String) - Method in class ur_rna.Utilities.AppLog
debug(String, Object...) - Method in class ur_rna.Utilities.AppLog
DEBUG_GUI_MATCHER - Variable in class ur_rna.GUITester.ScriptRuntime
debugStream - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  debug output.
DECIMAL_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
DECIMAL_NUMBER - Static variable in class ur_rna.Utilities.CharType
decodeColor(Object, Color) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
decodeFont(Object, Font) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
decodeHexRGB(String) - Static method in class ur_rna.Utilities.Colors
  This is the same as `Color.decode(String)` except that it does NOT throw a `NumberFormatException`, but instead returns null if decoding fails.
DECR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
DeepPink - Static variable in class ur_rna.Utilities.Colors
DeepSkyBlue - Static variable in class ur_rna.Utilities.Colors
DEFAULT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  Lexical state.
Default - Static variable in enum ur_rna.StructureEditor.models.BondType
Default - Static variable in class ur_rna.Utilities.EventArgs
DEFAULT_BACKGROUND - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_CLIP - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_COLOR - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_COMPOSITE - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_CONTEXT - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
DEFAULT_CONTEXT - Static variable in class ur_rna.Utilities.swing.FileDialog
DEFAULT_FONT - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_MARGIN - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
DEFAULT_MERGE_POS - Static variable in class ur_rna.Utilities.swing.MergeManager
DEFAULT_MESSAGE - Static variable in class ur_rna.Utilities.swing.WaitDialog
DEFAULT_PAINT - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_POLL_TIME - Static variable in class ur_rna.GUITester.GuiTools.GuiRobot
  Number of milliseconds to sleep between attempts to poll for a component.
DEFAULT_SHAPE_INTERCEPT - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DEFAULT_SHAPE_INTERCEPT_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DEFAULT_SHAPE_SLOPE - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
DEFAULT_SHAPE_SLOPE_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DEFAULT_STROKE - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_TEST_WAIT_TIME - Static variable in class ur_rna.GUITester.GuiTools.GuiRobot
  Total number of milliseconds to wait for a GUI component, when simply testing for its existence.
DEFAULT_TITLE - Static variable in class ur_rna.Utilities.swing.WaitDialog
DEFAULT_TRANSFORM - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
DEFAULT_UPDATE_INTERVAL - Static variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
DEFAULT_USER - Static variable in class ur_rna.StructureEditor.services.UserPrefs
DEFAULT_WAIT_TIME - Static variable in class ur_rna.GUITester.GuiTools.GuiRobot
  Total number of milliseconds to wait for a GUI component to be created, before returning an error.
DEFAULT_XOR_MODE - Static variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
defaultAllowRepeatFlags - Variable in class ur_rna.Utilities.CommandLineParser
defaultAppLog - Static variable in class ur_rna.Utilities.AppLog
defaultBgColor - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
defaultBoxSize - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
DefaultBufferSize - Static variable in class ur_rna.Utilities.Strings
defaultColor - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  The default color forthis button.
defaultColor - Variable in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
defaultFont - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
defaultFont - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
defaultFont - Static variable in class ur_rna.Utilities.swing.Dialogs
defaultFont - Static variable in class ur_rna.Utilities.swing.FontUtil
defaultGuessLineLength - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
defaultLexState - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
defaultLineColor - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
defaultLocalSearchSubDirs - Static variable in class ur_rna.Utilities.PathTools
DefaultLogImportance - Static variable in class ur_rna.Utilities.AppLog
defaultMessage - Static variable in exception ur_rna.Utilities.KeyAlreadyExistsException
defaultOptionValues - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
defaultOptionValues - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
defaultOptionValues - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
defaultOptionValues - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
defaultOutline - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
defaultOutput - Static variable in class ur_rna.Utilities.StopWatch
defaultParamAffinity - Variable in class ur_rna.Utilities.CommandLineParser
defaultStyle - Variable in class ur_rna.StructureEditor.models.DrawSettings
defaultWindowSize(RNA) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
defs - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
DEL - Static variable in class ur_rna.Utilities.CharConstants
delayBetweenSteps - Variable in class ur_rna.GUITester.ScriptRuntime
delegateToParent(MouseWheelEvent) - Method in class ur_rna.StructureEditor.ui.DrawPanel
  bubble the mouse wheel event up to the parent JScrollPane
delete() - Method in class ur_rna.RNAstructure.backend.CDblVector
delete() - Method in class ur_rna.RNAstructure.backend.CIntVector
delete() - Method in class ur_rna.RNAstructure.backend.datatable
delete() - Method in class ur_rna.RNAstructure.backend.Dynalign_object
delete() - Method in class ur_rna.RNAstructure.backend.HybridRNA
delete() - Method in class ur_rna.RNAstructure.backend.PartialProgress
delete() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
delete() - Method in class ur_rna.RNAstructure.backend.RNA
delete() - Method in class ur_rna.RNAstructure.backend.SimpleProgressHandler
delete() - Method in class ur_rna.RNAstructure.backend.singlestructure
delete() - Method in class ur_rna.RNAstructure.backend.structure
delete() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
delete() - Method in class ur_rna.RNAstructure.backend.TProgressDialog
delete() - Method in class ur_rna.RNAstructure.backend.TwoRNA
delete() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
delete() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
delete() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
delete(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
delete_CDblVector(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_CIntVector(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_datatable(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_DotPlotBackend(long) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
delete_Dynalign_object(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_HybridRNA(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_PartialProgress(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_ProgressHandler(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_RNA(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_RNAstructureBackendCalculator(long) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
delete_SimpleProgressHandler(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_singlestructure(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_structure(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_StructureBackend(long) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
delete_Thermodynamics(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_TProgressDialog(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
delete_TwoRNA(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
deleteBackendTuple(int) - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
deleteBackendTuple(int) - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Delete a tuple from the calculation back end.
deleteBackendTuple(int) - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
deleteCharAt(int) - Method in class ur_rna.Utilities.StringBuilderEx
deleteMultilignTuple(long) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
deleteSelectedBases() - Method in class ur_rna.StructureEditor.services.RnaDrawController
deleteSequence(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
DeleteSHAPE() - Method in class ur_rna.RNAstructure.backend.structure
deleteTurboFoldTuple(long) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
desc - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
desc - Variable in class ur_rna.StructureEditor.windows.DashboardFrame.ListItem
desc() - Method in class ur_rna.Utilities.swing.UiAction
DESCENDANT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
descendant_line - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
describeSource(Object) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
description - Variable in enum ur_rna.StructureEditor.FileType
description - Variable in enum ur_rna.StructureEditor.models.BondType
description - Variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
description - Variable in class ur_rna.StructureEditor.services.SceneUpdateEvent
DescriptionMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
DescriptionMatcher(String) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
DescriptionMatcher(String, int) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
deselect() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  Deselect this button.
DESELECT_ONLY - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
deselectNuc - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
DesignWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the Design module, which attempts to find a sequence that is expected to fold into the structure given in a CT file.
DesignWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.DesignWindow
  Constructor.
desktop - Variable in class ur_rna.RNAstructureUI.AppMainFrame
desktop - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
desktop - Variable in class ur_rna.StructureEditor.MainFrame
desktop - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
determinant() - Method in class ur_rna.Utilities.geom.Matrix3D
  Computes the determinant of this matrix.
DetermineDrawingCoordinates(int, int, int) - Method in class ur_rna.RNAstructure.backend.RNA
DetermineDrawingCoordinates(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
determineOligoMaximum(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
deviceConfig - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Device configuration settings.
dialog - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
dialog - Variable in class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
  The structure panel connected to this menu.
dialog - Variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu
  The structure dialog connected to this menu.
dialog - Variable in class ur_rna.RNAstructureUI.drawing.menus.PlotMenu
  The plot dialog connected to this menu.
dialog - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
  The structure dialog connected to this menu.
dialog - Variable in class ur_rna.RNAstructureUI.windows.DrawingWindow
  The image dialog connected to this window.
Dialogs - Class in ur_rna.RNAstructureUI.ui
  A class that handles simple dialogs used in the RNAstructure GUI.
Dialogs() - Constructor for class ur_rna.RNAstructureUI.ui.Dialogs
Dialogs - Class in ur_rna.Utilities.swing
  Common "MessageBox" dialogs.
Dialogs() - Constructor for class ur_rna.Utilities.swing.Dialogs
diff(Point2D, Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to p1 - p2.
diff(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
DIGIT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
DIGITS - Static variable in class ur_rna.Utilities.CharType
  '0'-'9'
DimGray - Static variable in class ur_rna.Utilities.Colors
dir() - Method in class ur_rna.Utilities.PathTools.FileName
  Returns the directory portion of the path, INCLUDING the final slash (!!) (The final slash may be necessary to distinguish eg.
dir(boolean) - Method in class ur_rna.Utilities.PathTools.FileName
directionalIcons - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
DIRECTIVE_PREFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
disable_tracing() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Disable tracing.
DisableBranchSlide - Variable in class ur_rna.StructureEditor.Settings
disableClose - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
disableClose - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
disableHints - Variable in class ur_rna.StructureEditor.services.SceneController.DragOpts
DisableLoopResize - Variable in class ur_rna.StructureEditor.Settings
disableOptionClick(ActionEvent) - Method in class ur_rna.StructureEditor.windows.DashboardFrame
DisableRotation - Variable in class ur_rna.StructureEditor.Settings
display - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
Displayable - Interface in ur_rna.Utilities
displayCalcError(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Handle finishing of a module.
dispose() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
disposed - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Flag that tells whether this graphics object has been disposed.
dist(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
distance(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.Vec2D
  Returns the distance between two points.
DistanceLimited() - Method in class ur_rna.RNAstructure.backend.structure
distanceSq(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.Vec2D
  Returns the square of the distance between two points, i.e.
distSqr(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
divideStrand(Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
divideStrand(Strand, int) - Method in class ur_rna.StructureEditor.models.StrandList
  Divides one strand into two separate strands.
divideStrand(int, int) - Method in class ur_rna.StructureEditor.models.StrandList
  Divides one strand into two separate strands.
dnaSymbols - Static variable in class ur_rna.RNAstructure.Nucleobase
dnaSymbolsLc - Static variable in class ur_rna.RNAstructure.Nucleobase
doAction(String, Object[]) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.ui.NumberField
  Do any additional necessary checks on a key character to make sure it's valid to be output.
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.ui.NumberField.FloatField
doc - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
docChanged() - Method in class ur_rna.StructureEditor.ui.SliderToolWindow
docListener - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
docSeq - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
docStr - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
documentsDirs - Static variable in class ur_rna.Utilities.PathTools
docUpdateListener - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
DodgerBlue - Static variable in class ur_rna.Utilities.Colors
doInBackground() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
doInitialStartup() - Method in class ur_rna.StructureEditor.Program
Domain() - Constructor for class ur_rna.StructureEditor.models.Motif.Domain
Domain(Nuc) - Constructor for class ur_rna.StructureEditor.models.Motif.Domain
Domain(Bond) - Constructor for class ur_rna.StructureEditor.models.Motif.Domain
Done() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Set buffers back to null when finished.
doRedo(ActionEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
doRevalidate() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
  Revalidate the drawing window.
doStepDelay() - Method in class ur_rna.GUITester.ScriptRuntime
DOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
DOT - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Dot(int, int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
DOT - Static variable in class ur_rna.Utilities.CharType
dot(Vec2D) - Method in class ur_rna.Utilities.geom.Vec2D
dot(Point2D, Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
DotBracketFormat - Enum in ur_rna.RNAstructure.backend
DotBracketFormat() - Constructor for enum ur_rna.RNAstructure.backend.DotBracketFormat
DotBracketFormat(int) - Constructor for enum ur_rna.RNAstructure.backend.DotBracketFormat
DotBracketFormat(DotBracketFormat) - Constructor for enum ur_rna.RNAstructure.backend.DotBracketFormat
DotBracketFormat.SwigNext - Class in ur_rna.RNAstructure.backend
DotPlot - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
DotPlotBackend - Class in ur_rna.RNAstructureUI.drawing.proxy
DotPlotBackend(long, boolean) - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
DotPlotBackend() - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
DotPlotBackend_getBounds(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getColors(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getCurrentMax(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getCurrentMin(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDefaultMax(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDefaultMin(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDotData(long, DotPlotBackend, int, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getDotDataByLocation(long, DotPlotBackend, int, int, double) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getGridLine(long, DotPlotBackend, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getLegendData(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_getLength(long, DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_readData(long, DotPlotBackend, String, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_setColors(long, DotPlotBackend, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_setRange(long, DotPlotBackend, double, double) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writePostscriptFile(long, DotPlotBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeStructuresFile(long, DotPlotBackend, String, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeSVGFile(long, DotPlotBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackend_writeTextFile(long, DotPlotBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotPlotBackendProxyJNI - Class in ur_rna.RNAstructureUI.drawing.proxy
DotPlotBackendProxyJNI() - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
DotsMenu - Class in ur_rna.RNAstructureUI.drawing.menus
  A class that handles a menu which can manipulate a drawn dot plot.
DotsMenu(PlotDialog) - Constructor for class ur_rna.RNAstructureUI.drawing.menus.DotsMenu
  Constructor.
DotsMenu.ColorDialog - Class in ur_rna.RNAstructureUI.drawing.menus
  An inner class which creates a dialog that sets the number of colors in a dot plot.
DotsMenu.RangeDialog - Class in ur_rna.RNAstructureUI.drawing.menus
  An inner class which creates a dialog that sets the range of values in a dot plot.
DOUBLE_QUOTES - Static variable in class ur_rna.Utilities.CharType
  Double quotes (")
DoubleField(String, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
  Unbounded Constructor.
DoubleField(String, Number, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
  Minimum Bounds Constructor.
DoubleField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
  Minimum and Maximum Bounds Constructor.
DoubleStrand(int, int) - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
doubleValue() - Method in class ur_rna.Utilities.NamedArg
doUndo(ActionEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
doVerify(String, Object, Class<?>) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
DPI - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
drag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Called when this handle has been dragged by the user.
DRAG_EXPANDED_MOTIF_MASK - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
DRAG_SPECIAL_MASK - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
dragComplete(boolean) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Called when the user has completed dragging (e.g.
dragComplete(boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
dragComplete(boolean) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
DRAGGING - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
dragIsValid - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
dragNucs(Nuc, Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.RnaDrawController
dragObject - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
DragOpts() - Constructor for class ur_rna.StructureEditor.services.SceneController.DragOpts
DragOpts(boolean, boolean, boolean) - Constructor for class ur_rna.StructureEditor.services.SceneController.DragOpts
dragStarted(Point) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
draw(Graphics2D, View2D, DrawSettings, boolean) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
draw(Graphics2D, View2D, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
draw(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
draw(Shape, boolean) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  The the outline of the specified Shape.
draw(Graphics2D, View2D, DrawSettings, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
DRAW_ALWAYS - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
DRAW_FLIP - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
DRAW_MODE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
DRAW_NEVER - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
DRAW_PROMPT - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
drawArc(int, int, int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawBackboneCurved - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawBackboneInHelix - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawBackboneInLoops - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawBonds(Graphics2D, View2D, List<IScreenObject>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
drawBondsInHelix - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawBox(Graphics2D, View2D, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
DrawClockwise - Variable in class ur_rna.StructureEditor.Settings
drawCurvedBackbones(Graphics2D, boolean[], float) - Method in class ur_rna.StructureEditor.services.RnaDrawController
drawFlipped - Variable in class ur_rna.StructureEditor.models.RnaScene
  Whether this nucleotides were drawn flipped (Clockwise) or normal (Counter-Clockwise)
drawGlyphVector(GlyphVector, float, float) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
DrawHandle - Class in ur_rna.StructureEditor.services.drawing
  Represents a handle that the user can click, drag or interact with on the screen to cause an effect in the scene.
DrawHandle(SceneController) - Constructor for class ur_rna.StructureEditor.services.drawing.DrawHandle
drawHandles - Variable in class ur_rna.StructureEditor.services.RnaDrawController
DrawHint - Class in ur_rna.StructureEditor.services.drawing
  Provides a way to specify the drawing of shapes and text outside of the actual rendering process.
DrawHint() - Constructor for class ur_rna.StructureEditor.services.drawing.DrawHint
drawHint(Graphics2D, View2D, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
drawHint(Graphics2D, View2D, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawShape
drawHint(Graphics2D, View2D, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
DrawHint.DrawShape - Class in ur_rna.StructureEditor.services.drawing
DrawHint.DrawText - Class in ur_rna.StructureEditor.services.drawing
drawHints - Variable in class ur_rna.StructureEditor.services.RnaDrawController
drawImage(Image, AffineTransform, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(BufferedImage, BufferedImageOp, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, Color, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, int, int, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
DrawImageOp(Image, int, int, int, int, int, int) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
DrawingEditMenu - Class in ur_rna.StructureEditor.menus
DrawingEditMenu(DrawWindow) - Constructor for class ur_rna.StructureEditor.menus.DrawingEditMenu
DrawingFileExtension - Static variable in class ur_rna.StructureEditor.Program
DrawingFileIO - Class in ur_rna.StructureEditor.services.fileIO
  There are two types of native drawing file formats.
DrawingFileIO() - Constructor for class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
DrawingFileIO.CTE - Interface in ur_rna.StructureEditor.services.fileIO
  Constants for CTE File IO
DrawingFileIO.CTEWriter - Class in ur_rna.StructureEditor.services.fileIO
DrawingFileIO.NSD - Interface in ur_rna.StructureEditor.services.fileIO
  Constants for Nucleotide Structure Drawing (NSD) File IO
DrawingFileIO.SimpleScanner - Class in ur_rna.StructureEditor.services.fileIO
  This replacement for Scanner automatically skips whitespace, but does NOT skip over newlines unless `DrawingFileIO.SimpleScanner.nextLine()` is called.
DrawingFileIO.TextWriter - Class in ur_rna.StructureEditor.services.fileIO
  Simplifies writing tabular text data in which the table formatting is achieved by padding values with spaces.
DrawingFileMenu - Class in ur_rna.StructureEditor.menus
DrawingFileMenu(DrawWindow) - Constructor for class ur_rna.StructureEditor.menus.DrawingFileMenu
DrawingFormatMenu - Class in ur_rna.StructureEditor.menus
DrawingFormatMenu(DrawWindow) - Constructor for class ur_rna.StructureEditor.menus.DrawingFormatMenu
DrawingViewMenu - Class in ur_rna.StructureEditor.menus
DrawingViewMenu(DrawWindow) - Constructor for class ur_rna.StructureEditor.menus.DrawingViewMenu
DrawingWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for displaying a drawing window.
DrawingWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.DrawingWindow
  File Constructor.
DrawingWindow(String, int) - Constructor for class ur_rna.RNAstructureUI.windows.DrawingWindow
  Strand Constructor.
DrawingWindow(String, int, FileType) - Constructor for class ur_rna.RNAstructureUI.windows.DrawingWindow
drawLine(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawMode - Variable in class ur_rna.StructureEditor.models.RnaScene
drawNucNumber(Graphics2D, View2D, Nuc, int) - Method in class ur_rna.StructureEditor.services.RnaDrawController
drawNucOutline(Graphics2D, Nuc, Color) - Method in class ur_rna.StructureEditor.services.RnaDrawController
drawNumbers - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawNumbersAtHelix - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawNumbersInterval - Variable in class ur_rna.StructureEditor.models.DrawSettings
drawnView - Variable in class ur_rna.StructureEditor.ui.DrawPanel
drawOptionMenu - Variable in class ur_rna.RNAstructureUI.menus.FileMenu
drawOptions - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
DrawOptions() - Constructor for enum ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog.DrawOptions
drawOval(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
DrawPanel - Class in ur_rna.StructureEditor.ui
  A double-buffered canvas on which the RNA scene can be drawn, implemented on top of a JPanel
DrawPanel() - Constructor for class ur_rna.StructureEditor.ui.DrawPanel
drawPolygon(Polygon) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawPolygon(int[], int[], int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawPolyline(int[], int[], int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawRect(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawRenderableImage(RenderableImage, AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawRenderedImage(RenderedImage, AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawRoundRect(int, int, int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
DrawSection - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
DrawSettings - Class in ur_rna.StructureEditor.models
  Container for settings related to drawing RNA scenes.
DrawSettings() - Constructor for class ur_rna.StructureEditor.models.DrawSettings
drawSettings - Variable in class ur_rna.StructureEditor.services.drawing.NucLayout
drawSettings - Variable in class ur_rna.StructureEditor.Settings
drawSettings - Variable in class ur_rna.StructureEditor.windows.DrawWindow
DrawShape(Shape) - Constructor for class ur_rna.StructureEditor.services.drawing.DrawHint.DrawShape
DrawShapeOp(Shape, boolean) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
drawSimpleBackbones(Graphics2D, boolean[], float) - Method in class ur_rna.StructureEditor.services.RnaDrawController
drawString(String, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawString(String, float, float) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawString(AttributedCharacterIterator, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
drawString(AttributedCharacterIterator, float, float) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
DrawStringOp(String, float, float) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
drawStructures - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
drawStructures(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
DrawText(String, Point2D) - Constructor for class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
drawTextCentered(Graphics2D, String, Rectangle2D) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
drawTextCentered(Graphics2D, String, Point2D) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
drawTextCentered(Graphics2D, String, double, double) - Static method in class ur_rna.Utilities.geom.GraphicsUtil
DrawWindow - Class in ur_rna.StructureEditor.windows
  Basic child window for drawing.
DrawWindow() - Constructor for class ur_rna.StructureEditor.windows.DrawWindow
DrawWindow.SceneInfo - Class in ur_rna.StructureEditor.windows
DrawWindow.ToolButtonList - Class in ur_rna.StructureEditor.windows
dump(String) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
dump(String, PrintStream) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
dump(ScriptNode.DumpState) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
dump(ScriptNode.DumpState, int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
dump(String) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
dumpHierarchy(StringBuilder, Container, String) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
DumpState(PrintStream, String) - Constructor for class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
DuplexFoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the DuplexFold module, which folds two strands of nucleic acids into their likely hybrid structure.
DuplexFoldWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
  Constructor.
Dynalign(short, short, short, short, short, float, boolean, String, boolean, short, boolean, short, int) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean, String, boolean, short, boolean, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean, String, boolean, short, boolean) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean, String, boolean, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean, String, boolean) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean, String) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float, boolean) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short, float) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short, short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign(short) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign() - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object - Class in ur_rna.RNAstructure.backend
Dynalign_object(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object() - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, String, boolean) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, String) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, int, String, int, boolean) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, int, String, int) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, int, String, int, Thermodynamics) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object(String, short, short, short, short) - Constructor for class ur_rna.RNAstructure.backend.Dynalign_object
Dynalign_object_Dynalign__SWIG_0(long, Dynalign_object, short, short, short, short, short, float, boolean, String, boolean, short, boolean, short, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_1(long, Dynalign_object, short, short, short, short, short, float, boolean, String, boolean, short, boolean, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_10(long, Dynalign_object, short, short, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_11(long, Dynalign_object, short, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_12(long, Dynalign_object, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_13(long, Dynalign_object) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_2(long, Dynalign_object, short, short, short, short, short, float, boolean, String, boolean, short, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_3(long, Dynalign_object, short, short, short, short, short, float, boolean, String, boolean, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_4(long, Dynalign_object, short, short, short, short, short, float, boolean, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_5(long, Dynalign_object, short, short, short, short, short, float, boolean, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_6(long, Dynalign_object, short, short, short, short, short, float, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_7(long, Dynalign_object, short, short, short, short, short, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_8(long, Dynalign_object, short, short, short, short, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Dynalign__SWIG_9(long, Dynalign_object, short, short, short, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_ForceAlignment(long, Dynalign_object, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_GetBestPairEnergy(long, Dynalign_object, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_GetErrorMessage(long, Dynalign_object, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_GetForcedAlignment(long, Dynalign_object, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_GetLowestEnergy(long, Dynalign_object) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_ReadAlignmentConstraints(long, Dynalign_object, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_SetProgress(long, Dynalign_object, long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_StopProgress(long, Dynalign_object) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Templatefromct(long, Dynalign_object, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_Templatefromdsv(long, Dynalign_object, String, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Dynalign_object_WriteAlignment(long, Dynalign_object, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
DynalignFoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the Dynalign module, which calculates common structures for two strands of nucleic acids.
DynalignFoldWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
  Constructor.
DynalignRefoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the Dynalign refold module, which refolds a previous Dynalign calculation from a save file.
DynalignRefoldWindow() - Constructor for class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
  Constructor.
DynalignSav - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters

## E

earth - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
EDIT_CLICK_MASK - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
editBond - Variable in class ur_rna.StructureEditor.services.RnaDrawController
editBondStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
edited - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  A boolean, true if the sequence has been edited, false if not.
EditHistory - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
EDITING - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
EditMenu() - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
  Constructor.
EditMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
EditMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
editSelectedBases() - Method in class ur_rna.StructureEditor.windows.DrawWindow
Efn2Window - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the efn2 (Energy Function 2) module, which calculates the folding free energy of structures.
Efn2Window(String) - Constructor for class ur_rna.RNAstructureUI.windows.Efn2Window
  Constructor.
elapsed(String) - Static method in class ur_rna.Utilities.StopWatch
  Get the elapsed time of the named StopWatch.
elapsed() - Method in class ur_rna.Utilities.StopWatch
  The total elapsed time in milliseconds.
elements - Variable in class ur_rna.StructureEditor.models.Motif.MultiLoop
Ellipses - Class in ur_rna.Utilities.geom
Ellipses() - Constructor for class ur_rna.Utilities.geom.Ellipses
Ellipses.Circle - Class in ur_rna.Utilities.geom
EMPTY_ARRAY - Static variable in class ur_rna.Utilities.PathTools.FileName
EMPTY_BOOL_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
EMPTY_COMPONENT_ARRAY - Static variable in class ur_rna.Utilities.swing.Components
EMPTY_COMPONENT_ARRAY - Static variable in class ur_rna.Utilities.swing.MergeManager
EMPTY_COMPONENT_LIST - Static variable in class ur_rna.Utilities.swing.Components
EMPTY_INT_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
EMPTY_LISTENERS - Static variable in class ur_rna.Utilities.swing.UiAction
EMPTY_NAME_ARRAY - Static variable in class ur_rna.Utilities.prefs.FilePreferences
EMPTY_OBJECT_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
EMPTY_SELECTION - Variable in class ur_rna.StructureEditor.services.RnaDrawController
EMPTY_STRING_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
emptyChildArray - Static variable in class ur_rna.GUITester.ScriptParser.ScriptNode
EN_US - Static variable in class ur_rna.Utilities.DateHelper
EN_US_Format - Static variable in class ur_rna.Utilities.DateHelper
enable_tracing() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Enable tracing.
enableControls(Container, boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
enabled - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
enableDescendants(Container, boolean, Component...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
enabledState - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
enableMenus() - Method in class ur_rna.RNAstructureUI.menus.MenuList
enableTabNext(JComponent) - Static method in class ur_rna.StructureEditor.menus.WindowsMenu
encode(Font) - Static method in class ur_rna.Utilities.swing.FontUtil
encodeImage(BufferedImage, String) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
end - Variable in class ur_rna.StructureEditor.models.Motif.Segment
  The end of the segment (the 3' side)
end() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
END_TOKEN - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
END_TOKEN - Static variable in class ur_rna.Utilities.SimpleDataSerializer
endColumn - Variable in class ur_rna.GUITester.ScriptParser.Token
  The column number of the last character of this Token.
endGroup() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
endLine - Variable in class ur_rna.GUITester.Script
endLine - Variable in class ur_rna.GUITester.ScriptParser.Token
  The line number of the last character of this Token.
EndOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.EndOp
endsWith(String) - Method in class ur_rna.Utilities.StringBuilderEx
endsWith(String, boolean) - Method in class ur_rna.Utilities.StringBuilderEx
ensureCapacity(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Ensures that the capacity is at least equal to the specified minimum.
EnsureStructureCapcacity(int) - Method in class ur_rna.RNAstructure.backend.RNA
enter(String) - Static method in class ur_rna.Utilities.StopWatch
  Gets the named StopWatch and starts it.
enterScope() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
entries() - Method in class ur_rna.StructureEditor.services.History
EOF - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  End of File.
eof - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
EOF - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
EOL - Static variable in exception ur_rna.GUITester.ScriptParser.ParseException
  The end of line string for this machine.
EOS() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
EPSILON - Static variable in class ur_rna.Utilities.geom.Matrix3D
epsilonEquals(Matrix3D, double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.
EQ - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
equals(int) - Method in enum ur_rna.RNAstructureUI.utilities.FileType
equals(Object) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
equals(GraphicsStyle) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
equals(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Returns true if all of the data members of Matrix3D m1 are equal to the corresponding data members in this Matrix3D.
equals(Object) - Method in class ur_rna.Utilities.geom.Matrix3D
  Returns true if the Object t1 is of type Matrix3D and all of the data members of t1 are equal to the corresponding data members in this Matrix3D.
equals(Shape, Shape) - Static method in class ur_rna.Utilities.geom.ShapeUtil
equals(Object) - Method in class ur_rna.Utilities.Pair
equals(Map.Entry) - Method in class ur_rna.Utilities.Pair
equals(Object) - Method in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
equals(Object) - Method in class ur_rna.Utilities.Version
equalsClass(Class, Class) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
error - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The error message generated while building this panel, if any.
error - Variable in class ur_rna.RNAstructureUI.windows.DrawingWindow
  True if an error occurred building this window, false if not.
ERROR - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Error(int, int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Error(int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
error(String) - Method in class ur_rna.Utilities.AppLog
error(String, Object...) - Method in class ur_rna.Utilities.AppLog
error(String, Throwable) - Method in class ur_rna.Utilities.AppLog
ERROR - Static variable in class ur_rna.Utilities.swing.Dialogs
errorCode - Variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  Indicates the reason why the exception is thrown.
errorCode - Variable in exception ur_rna.RNAstructure.RnaBackendException
errorDescription - Variable in exception ur_rna.Utilities.SyntaxErrorException
  A brief description or name of the error, e.g.
ErrorInfo() - Constructor for class ur_rna.RNAstructureUI.utilities.BackgroundWorker.ErrorInfo
errorMessage - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
errors - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
ESC - Static variable in class ur_rna.Utilities.CharConstants
ESC_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
ESCAPED_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
escapeHTML(String) - Static method in class ur_rna.Utilities.Strings
escapeStringLiteral(String) - Static method in class ur_rna.Utilities.Strings
  Used to convert raw characters to their escaped version when these raw version cannot be used as part of a Java string literal.
escapeStringLiteral(String, int) - Static method in class ur_rna.Utilities.Strings
  Used to convert raw characters to their escaped version when these raw version cannot be used as part of a Java string literal.
evalGuiRef(Object) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
evalGuiRef(Object, boolean) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
evalGuiRef(Object, boolean, boolean, int) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
EvalLiteral(String, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
EvalLiteralToken(Token, String) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
evaluateScriptArgList(ScriptNode, boolean) - Method in class ur_rna.GUITester.ScriptRuntime
evaluateScriptNode(ScriptNode) - Method in class ur_rna.GUITester.ScriptRuntime
event - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
event - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
  A reference to the original ActionEvent that invoked this command, if any.
event - Variable in class ur_rna.Utilities.EventArgs.ActionEventArgs
event - Variable in class ur_rna.Utilities.EventArgs.EventObjectArgs
event - Variable in class ur_rna.Utilities.EventSource.Manager.Subscriber
EventArgs - Class in ur_rna.Utilities
EventArgs() - Constructor for class ur_rna.Utilities.EventArgs
EventArgs.ActionEventArgs - Class in ur_rna.Utilities
EventArgs.BoolEventArgs - Class in ur_rna.Utilities
EventArgs.EventObjectArgs - Class in ur_rna.Utilities
EventArgs.InfoBagEventArgs - Class in ur_rna.Utilities
EventArgs.IntEventArgs - Class in ur_rna.Utilities
EventArgs.ObjEventArgs<T> - Class in ur_rna.Utilities
EventArgs.StringEventArgs - Class in ur_rna.Utilities
EventObjectArgs(EventObject) - Constructor for class ur_rna.Utilities.EventArgs.EventObjectArgs
EventSource<TSubscriber> - Class in ur_rna.Utilities
EventSource() - Constructor for class ur_rna.Utilities.EventSource
EventSource(EventSource.Manager) - Constructor for class ur_rna.Utilities.EventSource
EventSource.Manager - Class in ur_rna.Utilities
EventSource.Manager.Subscriber - Class in ur_rna.Utilities
EventSource.NoArg - Class in ur_rna.Utilities
EventSource.OneArg<TArg> - Class in ur_rna.Utilities
EventSource.TwoArgs<TArg1,TArg2> - Class in ur_rna.Utilities
ex - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.ErrorInfo
EXAMPLE_INDICATOR - Static variable in class ur_rna.StructureEditor.windows.DashboardFrame
examplesDir - Static variable in class ur_rna.RNAstructureUI.RNAstructure
ExceptionHelper - Class in ur_rna.Utilities
  Tools for helping with exceptions.
ExceptionHelper() - Constructor for class ur_rna.Utilities.ExceptionHelper
exec(ScriptNode) - Method in class ur_rna.GUITester.ScriptRunner
exec(ScriptNode) - Method in class ur_rna.GUITester.ScriptRuntime
executeScriptAction(ASTAction) - Method in class ur_rna.GUITester.ScriptRuntime
executeScriptAssignment(ASTAssignment) - Method in class ur_rna.GUITester.ScriptRuntime
existingKey - Variable in exception ur_rna.Utilities.KeyAlreadyExistsException
existingValue - Variable in exception ur_rna.Utilities.KeyAlreadyExistsException
exists(String) - Static method in class ur_rna.Utilities.PathTools
exit(String) - Static method in class ur_rna.Utilities.StopWatch
  Gets the named StopWatch and stops it.
EXIT_PROGRAM - Static variable in class ur_rna.StructureEditor.AppActions
exitApp() - Static method in class ur_rna.StructureEditor.AppActions
exitGroup() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
exitScope() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
ExpandBuff(boolean) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
expandMotif - Variable in class ur_rna.StructureEditor.services.SceneController.DragOpts
ExpandMotif - Variable in class ur_rna.StructureEditor.Settings
expandMultiLoop(SceneController, Motif.MultiLoop, Point2D.Float, Point2D.Float, Ellipses.Circle, SceneController.DragOpts) - Static method in class ur_rna.StructureEditor.services.drawing.LoopResizer
expandPointAboutCenter(Vec2D, Point2D, Point2D, Point2D, double) - Static method in class ur_rna.StructureEditor.services.drawing.LoopResizer
expandSelection() - Method in class ur_rna.StructureEditor.services.RnaDrawController
  If a nucleotide is selected, this expands to the helix or loop.
expectArgs(String, Object[], int, int) - Static method in class ur_rna.GUITester.RuntimeTools
expectArgType(String, Object[], int, String, boolean, Class...) - Static method in class ur_rna.GUITester.RuntimeTools
expectedTokenSequences - Variable in exception ur_rna.GUITester.ScriptParser.ParseException
  Each entry in this array is an array of integers.
expectList(Object, String) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
expectMap(Object, String) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
EXPONENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Expression() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
ext() - Method in class ur_rna.Utilities.PathTools.FileName
ext(boolean) - Method in class ur_rna.Utilities.PathTools.FileName
EXT_ASCII - Static variable in class ur_rna.Utilities.CharType
  Extended ASCII characters (129-255)
ExtendedBufferedReader - Class in ur_rna.Utilities
  A special buffered reader which tracks the current character position and line index.
ExtendedBufferedReader(Reader) - Constructor for class ur_rna.Utilities.ExtendedBufferedReader
  Created extended buffered reader using default buffer-size
ExtensibleException - Exception in ur_rna.Utilities
  Exception that allows additional details to be added.
ExtensibleException() - Constructor for exception ur_rna.Utilities.ExtensibleException
ExtensibleException(String) - Constructor for exception ur_rna.Utilities.ExtensibleException
ExtensibleException(Throwable) - Constructor for exception ur_rna.Utilities.ExtensibleException
ExtensibleException(String, Throwable) - Constructor for exception ur_rna.Utilities.ExtensibleException
ExtensionFileFilter(boolean, String...) - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
ExtensionFileFilter(String...) - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
ExtensionFileFilter() - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
extensions - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
extensions - Variable in enum ur_rna.StructureEditor.FileType
extMap - Static variable in enum ur_rna.StructureEditor.FileType
extPos - Variable in class ur_rna.Utilities.PathTools.FileName
extractExample(String) - Static method in class ur_rna.StructureEditor.windows.DashboardFrame
ExtractExamples() - Static method in class ur_rna.RNAstructureUI.RNAstructure

## F

Factory() - Constructor for class ur_rna.Utilities.prefs.FilePreferences.Factory
FALSE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
FALSE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
FEEDBACK_SECRET - Static variable in class ur_rna.StructureEditor.AppActions
FEEDBACK_URL - Static variable in class ur_rna.StructureEditor.AppActions
FF - Static variable in class ur_rna.Utilities.CharConstants
field - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
field - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
FieldInfo(JComponent, String, String) - Constructor for class ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
FieldPanel - Class in ur_rna.RNAstructureUI.ui
  A class that creates a panel which holds aligned input fields.
FieldPanel() - Constructor for class ur_rna.RNAstructureUI.ui.FieldPanel
FieldPanel(JTextField...) - Constructor for class ur_rna.RNAstructureUI.ui.FieldPanel
  Constructor.
FieldPanel.FilePanel - Class in ur_rna.RNAstructureUI.ui
  An inner class that handles a panel which contains file fields.
FieldPanel.FilePanel.ButtonListener - Class in ur_rna.RNAstructureUI.ui
fields - Variable in class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
  The array of number fields this dialog holds.
fields - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
fields - Static variable in class ur_rna.StructureEditor.Settings
file - Variable in exception ur_rna.RNAstructure.RnaBackendException
file - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The file that is drawn in some way on this panel.
file - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
file - Variable in class ur_rna.StructureEditor.windows.DashboardFrame.ListItem
file - Variable in class ur_rna.Utilities.prefs.FilePreferences.RootNode
FILE_CT - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
FILE_CT_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
FILE_DBN - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
FILE_DBN_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
FILE_PFS - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
FILE_PFS_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
FILE_SAV - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
FILE_SAV_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
FILE_SEQ - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
FILE_SEQ_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
fileCount - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
FileDate - Static variable in class ur_rna.Utilities.DateHelper
FileDateFormat - Static variable in class ur_rna.Utilities.DateHelper
FileDateTime - Static variable in class ur_rna.Utilities.DateHelper
FileDateTimeFormat - Static variable in class ur_rna.Utilities.DateHelper
FileDialog - Class in ur_rna.Utilities.swing
  A file-open and -save dialog.
FileDialog() - Constructor for class ur_rna.Utilities.swing.FileDialog
FileDialog(boolean, String, String) - Constructor for class ur_rna.Utilities.swing.FileDialog
FileDialog(int, String, String) - Constructor for class ur_rna.Utilities.swing.FileDialog
fileExists(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
FileField - Class in ur_rna.RNAstructureUI.ui
  A class that creates a text field which holds a file name.
FileField(String, boolean) - Constructor for class ur_rna.RNAstructureUI.ui.FileField
  Constructor.
FileFieldInfo(JTextComponent, String, boolean, String) - Constructor for class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
fileFields - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
FileFilters - Class in ur_rna.RNAstructureUI.utilities
  A list of constants for common file extensions.
FileFilters() - Constructor for class ur_rna.RNAstructureUI.utilities.FileFilters
fileFromPath(String) - Static method in class ur_rna.Utilities.PathTools
fileFromPath(String, boolean) - Static method in class ur_rna.Utilities.PathTools
FileMenu - Class in ur_rna.RNAstructureUI.menus
  A class that creates a "File" menu.
FileMenu() - Constructor for class ur_rna.RNAstructureUI.menus.FileMenu
  Constructor.
FileMenu - Class in ur_rna.StructureEditor.menus
FileMenu() - Constructor for class ur_rna.StructureEditor.menus.FileMenu
FileMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
FileMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
FileName(String) - Constructor for class ur_rna.Utilities.PathTools.FileName
FileName(String, boolean) - Constructor for class ur_rna.Utilities.PathTools.FileName
FilePanel(ActionListener, FileField...) - Constructor for class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
  Constructor.
filePath - Variable in class ur_rna.GUITester.Script
filePath - Variable in class ur_rna.StructureEditor.models.RnaSceneGroup
FilePreferences - Class in ur_rna.Utilities.prefs
  Preferences implementation that stores to a user-defined file.
FilePreferences(AbstractPreferences, String) - Constructor for class ur_rna.Utilities.prefs.FilePreferences
FilePreferences.Factory - Class in ur_rna.Utilities.prefs
  PreferencesFactory implementation that stores the preferences in an XML file.
FilePreferences.RootNode - Class in ur_rna.Utilities.prefs
files - Variable in class ur_rna.StructureEditor.Program.StartupArgs
FileSelectedEvent - Class in ur_rna.RNAstructureUI.utilities
FileSelectedEvent(Object, File, String) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
fileShouldExist - Variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
fileShouldExist - Variable in class ur_rna.Utilities.swing.FileDialog
FileType - Enum in ur_rna.RNAstructureUI.utilities
FileType(int) - Constructor for enum ur_rna.RNAstructureUI.utilities.FileType
FileType - Enum in ur_rna.StructureEditor
FileType(String, FileType...) - Constructor for enum ur_rna.StructureEditor.FileType
FileType(String, String) - Constructor for enum ur_rna.StructureEditor.FileType
FileType(String, String, Set<FileType>) - Constructor for enum ur_rna.StructureEditor.FileType
fill(Color) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
fill(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fill(Shape, boolean) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Fill the specified Shape.
fill - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
Fill - Static variable in interface ur_rna.StructureEditor.services.SceneColorizer.ColorMode
FILL_COLOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
fillAlpha(int) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
fillArc(int, int, int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
FillBuff() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
fillColor - Variable in class ur_rna.StructureEditor.models.NucStyle
fillOval(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fillPolygon(Polygon) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fillPolygon(int[], int[], int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fillRect(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fillRoundRect(int, int, int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
fillStyle(Nuc, NucStyle) - Method in class ur_rna.StructureEditor.models.DrawSettings
filter(Iterator<T>) - Method in class ur_rna.Utilities.ConverterFilter
filter(Iterable<T>) - Method in class ur_rna.Utilities.ConverterFilter
Filter<T> - Class in ur_rna.Utilities
Filter() - Constructor for class ur_rna.Utilities.Filter
filter(Iterator<T>) - Method in class ur_rna.Utilities.Filter
filter(Iterable<T>) - Method in class ur_rna.Utilities.Filter
Filter.FilterIterator - Class in ur_rna.Utilities
filterAcceptAll - Static variable in class ur_rna.RNAstructureUI.ui.RecentFileButton
filterChanged(PropertyChangeEvent) - Method in class ur_rna.Utilities.swing.FileDialog
filterFiles(List<File>, FileFilter) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
FilterIterator(Iterator<T>) - Constructor for class ur_rna.Utilities.ConverterFilter.FilterIterator
FilterIterator(Iterator<T>) - Constructor for class ur_rna.Utilities.Filter.FilterIterator
filters - Variable in class ur_rna.RNAstructureUI.ui.FileField
filters - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton
filters - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
finalize() - Method in class ur_rna.RNAstructure.backend.CDblVector
finalize() - Method in class ur_rna.RNAstructure.backend.CIntVector
finalize() - Method in class ur_rna.RNAstructure.backend.datatable
finalize() - Method in class ur_rna.RNAstructure.backend.Dynalign_object
finalize() - Method in class ur_rna.RNAstructure.backend.HybridRNA
finalize() - Method in class ur_rna.RNAstructure.backend.PartialProgress
finalize() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
finalize() - Method in class ur_rna.RNAstructure.backend.RNA
finalize() - Method in class ur_rna.RNAstructure.backend.SimpleProgressHandler
finalize() - Method in class ur_rna.RNAstructure.backend.singlestructure
finalize() - Method in class ur_rna.RNAstructure.backend.structure
finalize() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
finalize() - Method in class ur_rna.RNAstructure.backend.TProgressDialog
finalize() - Method in class ur_rna.RNAstructure.backend.TwoRNA
finalize() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
finalize() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
finalize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
finalShutdown() - Static method in class ur_rna.GUITester.GuiTools.GuiRobot
  A final shutdown that cleans up some resources the Abbot Robot leaves around.
find(Matcher) - Method in class ur_rna.GUITester.GuiTools.GuiFinder
  Find a component.
find(String, GuiRelative, Component) - Method in class ur_rna.GUITester.GuiTools.GuiFinder
  Find a component using a `DescriptionMatcher`.
find(Matcher, GuiRelative, Component) - Method in class ur_rna.GUITester.GuiTools.GuiFinder
  Find a component with the built-in BasicFinder.
find(Container, Matcher) - Method in class ur_rna.GUITester.GuiTools.GuiFinder
find(GuiItemRef, boolean) - Method in class ur_rna.GUITester.GuiTools.GuiFinder
findAll(RnaScene) - Static method in class ur_rna.StructureEditor.models.Motif.Helix
  Find all distinct helices in specified list of strands.
findAll(RnaScene) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
  Find all distinct single-stranded regions in specified list of strands.
findAll(RnaScene, int, boolean) - Static method in class ur_rna.StructureEditor.models.Motif.MultiLoop
findAll(List<Motif.MultiLoop>, Bond, int) - Static method in class ur_rna.StructureEditor.models.Motif.MultiLoop
findBaseHelix(Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
findBaseHelix(Collection<Nuc>) - Method in interface ur_rna.StructureEditor.services.SceneController
findByAction(Action) - Method in interface ur_rna.Utilities.swing.IMenuItem
findByAction(Component, Action) - Static method in class ur_rna.Utilities.swing.Menus
findByAction(IMenuItem, Action) - Static method in class ur_rna.Utilities.swing.Menus
findByName(String) - Method in interface ur_rna.Utilities.swing.IMenuItem
findByName(Component, String) - Static method in class ur_rna.Utilities.swing.Menus
findByName(IMenuItem, String) - Static method in class ur_rna.Utilities.swing.Menus
findByTreePath(String) - Method in interface ur_rna.Utilities.swing.IMenuItem
findByTreePath(Component, String) - Static method in class ur_rna.Utilities.swing.Menus
findByTreePath(IMenuItem, String) - Static method in class ur_rna.Utilities.swing.Menus
findClass(String) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
FindClassMatcher(Matcher) - Method in class ur_rna.GUITester.ScriptRuntime
findDataPath() - Static method in class ur_rna.RNAstructureUI.RNAstructure
findFlagDef(String) - Method in class ur_rna.Utilities.CommandLineParser
  Finds the FlagDef associated with the given name.
findFlagDef(String, boolean) - Method in class ur_rna.Utilities.CommandLineParser
  /** Finds the FlagDef associated with the given name.
findHelices() - Method in class ur_rna.StructureEditor.windows.DrawWindow
findLocalPath(String) - Static method in class ur_rna.Utilities.PathTools
findLocalPath(Class, String, String...) - Static method in class ur_rna.Utilities.PathTools
findMatchingFilter(File) - Method in class ur_rna.Utilities.swing.FileDialog
findNonCrossingBonds(RnaScene) - Static method in class ur_rna.StructureEditor.models.Motif
findNonCrossingBonds(Collection<Bond>) - Static method in class ur_rna.StructureEditor.models.Motif
findNonCrossingBonds(Collection<Bond>, Collection<Bond>) - Static method in class ur_rna.StructureEditor.models.Motif
findPseudoknots(CIntVector, CIntVector, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackend
findPseudoknots(CIntVector, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackend
findPseudoknots(CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackend
FindPseudoknots(int, CIntVector, CIntVector) - Method in class ur_rna.RNAstructure.backend.structure
FindPseudoknots(int, CIntVector) - Method in class ur_rna.RNAstructure.backend.structure
FindPseudoknots(int) - Method in class ur_rna.RNAstructure.backend.structure
findPseudoKnots(RnaScene) - Static method in class ur_rna.StructureEditor.models.Motif
findPseudoKnots() - Method in class ur_rna.StructureEditor.windows.DrawWindow
findPseudoknots__SWIG_0(long, CIntVector, long, CIntVector, long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
findPseudoknots__SWIG_1(long, CIntVector, long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
findPseudoknots__SWIG_2(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
findPseudoKnotsBackend() - Method in class ur_rna.StructureEditor.windows.DrawWindow
fireActionPerformed(ActionEvent) - Method in class ur_rna.Utilities.swing.JActionLabel
fireActionPerformed(ActionEvent) - Method in class ur_rna.Utilities.swing.JFlatButton
FireBrick - Static variable in class ur_rna.Utilities.Colors
first - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
first - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
first() - Method in class ur_rna.StructureEditor.models.Motif.Helix
first() - Method in class ur_rna.StructureEditor.models.Strand
first() - Method in class ur_rna.StructureEditor.models.StrandList
first(Iterable<T>) - Static method in class ur_rna.Utilities.ObjTools
first(Iterable<T>, T) - Static method in class ur_rna.Utilities.ObjTools
firstExtension() - Method in enum ur_rna.StructureEditor.FileType
firstNonEmpty(String...) - Static method in class ur_rna.Utilities.Strings
  Returns the first string in the list of parameters that is not null or empty ("") Returns empty ("") if all strings are either null or empty.
firstOfType(Object[], Class<T>) - Static method in class ur_rna.Utilities.ObjTools
firstStrand() - Method in class ur_rna.StructureEditor.models.RnaScene
fixConsole() - Static method in class ur_rna.Utilities.ConsoleTools
  Inserts a 200ms delay into the System.err or System.out OutputStreams every time the output switches from one to the other.
FixedStream(OutputStream) - Constructor for class ur_rna.Utilities.ConsoleTools.FixedStream
fixInvalid(int) - Static method in interface ur_rna.Utilities.swing.IMergeItem
flag - Variable in class ur_rna.Utilities.CommandLineParser.FlagArg
  The Flag associated with this Argument, which specifies the name (and aliases) of the flag as well as the rules used to parse it.
FlagArg(String, int, CommandLineParser.FlagDef, String, String, Object) - Constructor for class ur_rna.Utilities.CommandLineParser.FlagArg
FlagDef(String, CommandLineParser.ParamAffinity, boolean) - Constructor for class ur_rna.Utilities.CommandLineParser.FlagDef
FlagDef(String, CommandLineParser.ParamAffinity, boolean, String...) - Constructor for class ur_rna.Utilities.CommandLineParser.FlagDef
flagDefMap - Variable in class ur_rna.Utilities.CommandLineParser
flags - Variable in class ur_rna.Utilities.CommandLineParser.ParseResults
flagText - Variable in class ur_rna.Utilities.CommandLineParser.FlagArg
  Gets the actual flag name from the command-line, without any parameter value or separator that might have been present.
flat - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
flip() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
Flip - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
flip(boolean, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
flipped - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
FLOAT_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
FLOAT_SUFFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
FloatField(String, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.FloatField
  Unbounded Constructor.
FloatField(String, Number, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.FloatField
  Minimum Bounds Constructor.
FloatField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.FloatField
  Minimum and Maximum Bounds Constructor.
floatValue() - Method in class ur_rna.Utilities.NamedArg
FloralWhite - Static variable in class ur_rna.Utilities.Colors
flush() - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
flush() - Method in class ur_rna.Utilities.prefs.FilePreferences
flushSpi() - Method in class ur_rna.Utilities.prefs.FilePreferences
fmt(Rectangle2D) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
fmt(Point2D) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
fmt(Dimension2D) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
fmt(String, Object...) - Static method in class ur_rna.Utilities.Strings
fmtMsg(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
fmtNumber(double) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
fmtNumber(double) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
fmtObj(Object) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
fmtTransform(AffineTransform) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
focused - Variable in class ur_rna.StructureEditor.services.RnaDrawController
focusField(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Attempts to show the field and set focus to it, possibly by activating the tab on which the control is placed.
focusGained(FocusEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  Invoked when a component gains the keyboard focus.
focusLost(FocusEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  Invoked when a component loses the keyboard focus.
FoldBimolecular(float, int, int, String, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldBimolecular(float, int, int, String) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldBimolecular(float, int, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldBimolecular(float, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldBimolecular(float) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldBimolecular() - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldDoubleWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the bifold module, which folds two strands of nucleic acids into their likely hybrid structure.
FoldDoubleWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
  Constructor.
FoldDuplex(float, int, int, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldDuplex(float, int, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldDuplex(float, int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldDuplex(float) - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldDuplex() - Method in class ur_rna.RNAstructure.backend.HybridRNA
FoldingSav - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
foldOligo(String, int, boolean, boolean, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
foldSeq(String, int) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
foldSequence() - Method in class ur_rna.StructureEditor.windows.DrawWindow
FoldSingleStrand(float, int, int, String, int, boolean, boolean, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int, int, String, int, boolean, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int, int, String, int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int, int, String, int) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int, int, String) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int, int) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float, int) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand(float) - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleStrand() - Method in class ur_rna.RNAstructure.backend.RNA
FoldSingleWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the Fold module, which folds a strand of nucleic acids into their likely lowest free energy structure.
FoldSingleWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.FoldSingleWindow
  Constructor.
FoldSuboptimalWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the AllSub module, which calculates the free energy of a varied group of suboptimal structures.
FoldSuboptimalWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
  Constructor.
font - Variable in class ur_rna.StructureEditor.models.NucStyle
font - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
font - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Current font.
FONT - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
FONT_EXPRESSIVENESS_COMPARATOR - Static variable in class ur_rna.Utilities.swing.FontUtil
FONT_RENDER_CONTEXT - Static variable in class ur_rna.Utilities.swing.FontUtil
FONT_TEST_STRING - Static variable in class ur_rna.Utilities.swing.FontUtil
FontExpressivenessComparator() - Constructor for class ur_rna.Utilities.swing.FontUtil.FontExpressivenessComparator
FontOp(Font) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
fontRenderContext - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Context settings used to render fonts.
FontUtil - Class in ur_rna.Utilities.swing
FontUtil() - Constructor for class ur_rna.Utilities.swing.FontUtil
FontUtil.FontExpressivenessComparator - Class in ur_rna.Utilities.swing
ForceAlignment(int, int) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
ForceDoubleStranded(int) - Method in class ur_rna.RNAstructure.backend.RNA
forceEnabled - Variable in class ur_rna.Utilities.AppLog
ForceFMNCleavage(int) - Method in class ur_rna.RNAstructure.backend.RNA
ForceMaximumPairingDistance(int) - Method in class ur_rna.RNAstructure.backend.RNA
ForceModification(int) - Method in class ur_rna.RNAstructure.backend.RNA
ForcePair(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
ForceProhibitPair(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
ForceSingleStranded(int) - Method in class ur_rna.RNAstructure.backend.RNA
forEach(Consumer<? super RecentFileList.RecentFile>) - Method in class ur_rna.StructureEditor.services.RecentFileList
ForestGreen - Static variable in class ur_rna.Utilities.Colors
format(Date, int) - Static method in class ur_rna.Utilities.DateHelper
format(Date, String) - Static method in class ur_rna.Utilities.DateHelper
FormatBases - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
formatBondType - Variable in class ur_rna.StructureEditor.windows.DrawWindow
formatFileError(String, FileType, String, Exception) - Static method in class ur_rna.StructureEditor.AppActions
FormatMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
formatSequence(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Format the sequence in the text area.
formatSequenceBox() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
FormatterException - Exception in ur_rna.Utilities
  Represents an error converting an Object or Value to a String.
FormatterException() - Constructor for exception ur_rna.Utilities.FormatterException
FormatterException(String) - Constructor for exception ur_rna.Utilities.FormatterException
FormatterException(Throwable) - Constructor for exception ur_rna.Utilities.FormatterException
FormatterException(String, Throwable) - Constructor for exception ur_rna.Utilities.FormatterException
formatTrace(Queue<String>) - Method in class ur_rna.Utilities.SimpleDataSerializer
formatValue(Object) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
FormValidationException - Exception in ur_rna.Utilities.swing
FormValidationException() - Constructor for exception ur_rna.Utilities.swing.FormValidationException
FormValidationException(String) - Constructor for exception ur_rna.Utilities.swing.FormValidationException
FormValidationException(String, JComponent) - Constructor for exception ur_rna.Utilities.swing.FormValidationException
FormValidationException(String, JComponent, Throwable) - Constructor for exception ur_rna.Utilities.swing.FormValidationException
foundAllFlags(String...) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
foundItem - Variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
foundItem - Variable in class ur_rna.Utilities.Filter.FilterIterator
frameActivated(boolean, InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
frameActivated(boolean, InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
frameClosed(InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
frameClosed(InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
frameClosing(InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  Indicates that the InternalFrame is closing.
frameClosing(InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  Indicates that the InternalFrame is closing.
frameClosing(InternalFrameEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
frameListener - Variable in class ur_rna.RNAstructureUI.AppMainFrame
frameListener - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
frameListener - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
from(RnaScene...) - Static method in class ur_rna.StructureEditor.models.RnaSceneGroup
from(Component) - Static method in interface ur_rna.Utilities.swing.IMenuItem
fromAbbrev(String) - Static method in enum ur_rna.StructureEditor.models.BondType
  Gets the BondType corresponding to an abbreviation.
fromAbbrev(String, BondType) - Static method in enum ur_rna.StructureEditor.models.BondType
  Gets the BondType corresponding to an abbreviation.
fromAngle(double) - Static method in class ur_rna.Utilities.geom.Vec2D
fromAny(String, String, String, String, FileType) - Static method in enum ur_rna.StructureEditor.FileType
fromCallable(Callable) - Static method in class ur_rna.Utilities.ActionHandlers
fromCenter(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(Vec2D, double, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(double, double, double, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(Point2D, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(Vec2D, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(double, double, double) - Static method in class ur_rna.Utilities.geom.Ellipses
fromCenter(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.Rectangles
fromCenter(Vec2D, double, double) - Static method in class ur_rna.Utilities.geom.Rectangles
fromCenter(Point, int, int) - Static method in class ur_rna.Utilities.geom.Rectangles
fromCenter(Point2D, double) - Static method in class ur_rna.Utilities.geom.Rectangles
fromCenter(Vec2D, double) - Static method in class ur_rna.Utilities.geom.Rectangles
fromCenter(Point, int) - Static method in class ur_rna.Utilities.geom.Rectangles
fromChar(char, int) - Static method in class ur_rna.Utilities.Strings
  Creates a string of the specified length, composed by repeating the specified character.
fromConsumer(Consumer<EventArgs>) - Static method in class ur_rna.Utilities.ActionHandlers
fromConsumerT(Consumer<T>) - Static method in class ur_rna.Utilities.ActionHandlers
fromDesc(String) - Static method in enum ur_rna.StructureEditor.FileType
fromEventListner(ActionListener) - Static method in class ur_rna.Utilities.ActionHandlers
fromExt(String) - Static method in enum ur_rna.StructureEditor.FileType
fromFile() - Method in class ur_rna.GUITester.Script
fromFilter(FileFilter) - Static method in enum ur_rna.StructureEditor.FileType
fromImportance(int) - Static method in enum ur_rna.Utilities.Verbosity
fromModel() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
fromName(String) - Static method in enum ur_rna.StructureEditor.FileType
fromPoints(Point, Point) - Static method in class ur_rna.Utilities.geom.Rectangles
fromPoints(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.Rectangles
fromPoints(Vec2D, Vec2D) - Static method in class ur_rna.Utilities.geom.Rectangles
fromRect(Rectangle2D) - Static method in class ur_rna.Utilities.geom.Ellipses
fromRunnable(Runnable) - Static method in class ur_rna.Utilities.ActionHandlers
fromSymbol(String) - Static method in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
fromToolTips(Consumer<String>, JComponent) - Static method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
Fuchsia - Static variable in class ur_rna.Utilities.Colors
fullPath - Variable in class ur_rna.Utilities.PathTools.FileName
fullText - Variable in class ur_rna.Utilities.CommandLineParser.Argument
  The full original text of this Argument in the command line.

## G

G - Static variable in class ur_rna.RNAstructure.Nucleobase
Gainsboro - Static variable in class ur_rna.Utilities.Colors
gamma - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
gapPenalty - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
GE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
gen - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
GenerateAllSuboptimalStructures(float, double) - Method in class ur_rna.RNAstructure.backend.RNA
GenerateAllSuboptimalStructures(float) - Method in class ur_rna.RNAstructure.backend.RNA
GenerateAllSuboptimalStructures() - Method in class ur_rna.RNAstructure.backend.RNA
generateParseException() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Generate ParseException.
get(int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
get(int) - Method in class ur_rna.RNAstructure.backend.CDblVector
get(int) - Method in class ur_rna.RNAstructure.backend.CIntVector
get(String) - Static method in class ur_rna.RNAstructureUI.utilities.Resources
get(Preferences, String, String) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
get(String, T) - Method in class ur_rna.StructureEditor.models.HistoryState
get(String) - Method in class ur_rna.StructureEditor.models.HistoryState
get(int) - Method in class ur_rna.StructureEditor.models.Strand
get(int) - Method in class ur_rna.StructureEditor.models.StrandList
get(int) - Method in class ur_rna.StructureEditor.services.History
get(String) - Method in class ur_rna.StructureEditor.services.UserPrefs
get(String, String) - Method in class ur_rna.StructureEditor.services.UserPrefs
get(String) - Method in class ur_rna.StructureEditor.Settings
get(Field) - Method in class ur_rna.StructureEditor.Settings
get(EventSource<T>) - Method in class ur_rna.Utilities.EventSource.Manager
get(String, int) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
get(String, double) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
get(String, String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
get(String, float) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
get(String, boolean) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
get(String, boolean) - Static method in class ur_rna.Utilities.StopWatch
  Get named StopWatch if it exists.
get(String) - Static method in class ur_rna.Utilities.StopWatch
  Get named StopWatch if it exists.
getAbbrev() - Method in enum ur_rna.StructureEditor.models.BondType
getAction() - Method in class ur_rna.Utilities.swing.JActionLabel
getActionCommand() - Method in class ur_rna.Utilities.swing.JActionLabel
getActionListeners() - Method in class ur_rna.Utilities.swing.JActionLabel
getActiveChild() - Method in class ur_rna.StructureEditor.MainFrame
getActiveChild() - Method in class ur_rna.Utilities.swing.MdiParentFrame
getActiveDrawing() - Method in class ur_rna.StructureEditor.MainFrame
getActiveDrawing(boolean) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
getActiveUndoManager() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
getAdded(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
getAllLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
getAllOligoData(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getAllowedLibNames() - Method in class ur_rna.Utilities.JniLoader
getAllSearchDirs() - Method in class ur_rna.Utilities.ResourceLoader
GetAlphabetName() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
getAlphaImage(BufferedImage) - Static method in class ur_rna.Utilities.swing.ImageUtil
getAltKeyName() - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getAltKeyName(boolean) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getAngle() - Method in class ur_rna.Utilities.geom.Vec2D
getAppInfo() - Method in class ur_rna.StructureEditor.Program
getAppLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
getAppName() - Method in class ur_rna.StructureEditor.Program
getAppName() - Method in class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
getAppName() - Method in interface ur_rna.Utilities.AppInfo.AppInfoProvider
getAppName() - Static method in class ur_rna.Utilities.AppInfo
getAppPath(Class) - Static method in class ur_rna.Utilities.PathTools
  Gets the absolute path to the directory containing the class file for referenceClass.
getAppRoot() - Static method in class ur_rna.RNAstructureUI.AppMainFrame
  Get the top frame of the application.
getAppTitle() - Method in class ur_rna.StructureEditor.Program
getAppTitle() - Method in class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
getAppTitle() - Method in interface ur_rna.Utilities.AppInfo.AppInfoProvider
getAppTitle() - Static method in class ur_rna.Utilities.AppInfo
getAppVersion() - Method in class ur_rna.StructureEditor.Program
getAppVersion() - Method in class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
getAppVersion() - Method in interface ur_rna.Utilities.AppInfo.AppInfoProvider
getAppVersion() - Static method in class ur_rna.Utilities.AppInfo
GetBackboneType() - Method in class ur_rna.RNAstructure.backend.RNA
getBackendIndex(Nuc) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
getBackendIndex(Nuc) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
getBackendIndex(Nuc) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.MultiStrand
getBackground() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getBackground() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Background color only affects the clear operation; It is NOT the fill color of shapes.
GetBase(int) - Method in class ur_rna.RNAstructure.backend.structure
getBase(int) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  Returns the sequence-index of the 5'-base at the 0-based position in this helix
getBaseDir() - Method in class ur_rna.Utilities.ResourceLoader
getBaseHelix() - Method in class ur_rna.StructureEditor.models.Motif.Branch
getBaseName(String) - Static method in class ur_rna.Utilities.PathTools
  Gets the base name of the file -- i.e.
getBaseName(String, boolean) - Static method in class ur_rna.Utilities.PathTools
  Gets the base name of the file -- i.e.
getBasePair(int) - Method in class ur_rna.RNAstructure.backend.singlestructure
getBases() - Method in interface ur_rna.StructureEditor.models.INucGroup
  Get a set of all nucleotides included in the group.
getBases() - Method in class ur_rna.StructureEditor.models.Motif.Branch
  Get a set of all nucleotides included in the group.
getBases() - Method in class ur_rna.StructureEditor.models.Motif.Helix
getBases() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
getBases() - Method in class ur_rna.StructureEditor.models.Motif.Segment
  Get a set of all nucleotides included in the group.
getBases() - Method in class ur_rna.StructureEditor.models.Nuc
  Implementation of `INucGroup.getBases()`
getBases() - Method in class ur_rna.StructureEditor.models.Strand
  Implements `INucGroup.getBases()`
getBases() - Method in class ur_rna.StructureEditor.services.RnaDrawController.NucGroup
getBeginColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getBeginLine() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getBehaviorMode() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getBestOrientation(double[], double[], double[], double) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
GetBestPairEnergy(int, int, int) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
getBondColor(Bond) - Method in class ur_rna.StructureEditor.services.RnaDrawController
getBonds() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
getBonds() - Method in class ur_rna.StructureEditor.models.RnaScene
getBonds(boolean) - Method in class ur_rna.StructureEditor.models.RnaScene
getBonds(Iterable<Nuc>, boolean) - Method in class ur_rna.StructureEditor.models.RnaScene
  Get all bonds associated with nucleotides in the specified region, which can be a Strand or a Motif etc.
getBool(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getBool(String, boolean) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getBoolResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
getBoolSetting(String) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
getBounds() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getBounds() - Method in interface ur_rna.StructureEditor.models.IScreenObject
getBounds() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
getBounds() - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
getBounds() - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
getBounds(Iterable<IScreenObject>) - Method in class ur_rna.StructureEditor.ui.DrawPanel
getBoxSize() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Get the size of the default DrawHandle box that the user can click.
getBranch(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Branch
  Return the smallest branch that contains nuc or null if nuc is not contained in any branch (e.g.
getBranch() - Method in class ur_rna.StructureEditor.models.Nuc
getBranch(Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
getButtons() - Method in class ur_rna.Utilities.swing.ButtonGroupList
getCancelListener() - Method in class ur_rna.Utilities.swing.WaitDialog
getCancelListeners() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
getCanonicalPath(String) - Static method in class ur_rna.Utilities.PathTools
  Get the canonical form of a file-system path by: Converting it to unix format (if Windows) Replacing `//` with `/` Replacing `/./` with `/` Replacing `dirname/../` with `/`
getCanonicalPath(String, boolean, boolean, boolean, boolean) - Static method in class ur_rna.Utilities.PathTools
  Get the canonical form of a file-system path by: Converting it to unix format (if Windows) Removing starting slashes (if `removeStartSlash` is true) Adding an ending slash (if `addEndSlash` is true} Removing an ending slash (if `removeEndSlash` is true Replacing `//` with `/` Replacing `/./` with `/` Replacing `dirname/../` with `/` Removing `./` at the start of a path (if `removeDotSlashAtStart` is true)
getCanonicalPath(File) - Static method in class ur_rna.Utilities.PathTools
  Unlike the other getCanonicalPath overloads, this one simply uses `File.getCanonicalPath()`
getCanvas() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getCanvas() - Method in interface ur_rna.StructureEditor.services.SceneController
getCenterPoint() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
getChars(int, int, char[], int) - Method in class ur_rna.Utilities.StringBuilderEx
  Characters are copied from this sequence into the destination character array `dst`.
getCharStyle(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
getChidren() - Method in class ur_rna.Utilities.TreeNode
getChildFrames() - Method in class ur_rna.StructureEditor.MainFrame
getChildFrames(Class) - Method in class ur_rna.Utilities.swing.MdiParentFrame
getChildMatchers() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
getChildMatchers() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
getChildMatchers() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
getChildMatchers() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
getChildMatchers() - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
  Return an array of all Matchers that are immediate descendants of this one, or an empty array if there are none.
getChildren() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
getChordHeight(double, double, double) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
getCircleX(double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
  get the x-coordinate of the circle at the specified angle.
getCircleY(double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
  get the y-coordinate of the circle at the specified angle.
getCircularBond(Bond) - Static method in class ur_rna.StructureEditor.services.drawing.NucLayout
getClassMatcher(String) - Method in class ur_rna.GUITester.ScriptRuntime
getClassNames() - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
getClassNames() - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
getClassNames() - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
getClip() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getClip() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
getClip() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getClipBounds() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getClipElement(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getCloneMethod() - Static method in class ur_rna.Utilities.ObjTools
getColor() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getColor() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
getColor() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
getColor() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp
getColor() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getColor() - Method in interface ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
getColor() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
getColor(String) - Static method in class ur_rna.Utilities.Colors
getColor(String, Color) - Static method in class ur_rna.Utilities.Colors
getColor(String, boolean) - Static method in class ur_rna.Utilities.Colors
getColors() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Get the range of colors allowed in this dialog.
getColors() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getColorText() - Method in interface ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
getColorText() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
getColumn(int, double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Copies the matrix values in the specified column into the array parameter.
getColumn() - Method in exception ur_rna.Utilities.SyntaxErrorException
getCommand() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
getCommand() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
getCommand(Action) - Static method in class ur_rna.Utilities.swing.UiAction
GetCommentString(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetCommentString() - Method in class ur_rna.RNAstructure.backend.RNA
getComparer() - Method in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
getCompletionEvent() - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
getCompletionEvent() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
getCompletionEvent() - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
getCompletionEvent() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
getCompletionEvent() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
getComponent() - Method in class ur_rna.RNAstructureUI.menus.MenuList
getComponent() - Method in interface ur_rna.StructureEditor.services.drawing.ICanvas
getComponent() - Method in class ur_rna.StructureEditor.services.RecentFileMenuManager
getComponent() - Method in class ur_rna.StructureEditor.ui.DrawPanel
getComponent(int) - Method in interface ur_rna.Utilities.swing.IContainer
getComponent(Object, int) - Static method in interface ur_rna.Utilities.swing.IContainer
getComponent() - Method in interface ur_rna.Utilities.swing.IMenuItem
getComponent() - Method in interface ur_rna.Utilities.swing.IMergeItem
getComponent() - Method in class ur_rna.Utilities.swing.IMergeItem.Proxy
getComponent() - Method in class ur_rna.Utilities.swing.MergeButton
getComponent() - Method in class ur_rna.Utilities.swing.MergeButton.Separator
getComponent() - Method in class ur_rna.Utilities.swing.MergeItem.Separator
getComponent() - Method in class ur_rna.Utilities.swing.MergeToggleButton
getComponentCount() - Method in interface ur_rna.Utilities.swing.IContainer
getComponentCount(Object) - Static method in interface ur_rna.Utilities.swing.IContainer
getComponentInfo(Component) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
getComponentInfo(Component) - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
getComponents() - Method in interface ur_rna.Utilities.swing.IContainer
getComponents(Object) - Static method in interface ur_rna.Utilities.swing.IContainer
getComposite() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getComposite() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
getComposite() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getCompoundmessage() - Method in class ur_rna.RNAstructure.backend.TwoRNA
getContainer() - Method in interface ur_rna.Utilities.swing.IMenuItem
  Gets the container that holds JMenuItem and JMenu children.
getContext() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getContext() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getContext() - Method in class ur_rna.Utilities.swing.FileDialog
getControl() - Method in exception ur_rna.Utilities.swing.FormValidationException
getControlDescription(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getControlValue(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getCPtr(CDblVector) - Static method in class ur_rna.RNAstructure.backend.CDblVector
getCPtr(CIntVector) - Static method in class ur_rna.RNAstructure.backend.CIntVector
getCPtr(datatable) - Static method in class ur_rna.RNAstructure.backend.datatable
getCPtr(Dynalign_object) - Static method in class ur_rna.RNAstructure.backend.Dynalign_object
getCPtr(HybridRNA) - Static method in class ur_rna.RNAstructure.backend.HybridRNA
getCPtr(PartialProgress) - Static method in class ur_rna.RNAstructure.backend.PartialProgress
getCPtr(ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.ProgressHandler
getCPtr(RNA) - Static method in class ur_rna.RNAstructure.backend.RNA
getCPtr(SimpleProgressHandler) - Static method in class ur_rna.RNAstructure.backend.SimpleProgressHandler
getCPtr(singlestructure) - Static method in class ur_rna.RNAstructure.backend.singlestructure
getCPtr(structure) - Static method in class ur_rna.RNAstructure.backend.structure
getCPtr(Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.Thermodynamics
getCPtr(TProgressDialog) - Static method in class ur_rna.RNAstructure.backend.TProgressDialog
getCPtr(TwoRNA) - Static method in class ur_rna.RNAstructure.backend.TwoRNA
getCPtr(DotPlotBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getCPtr(StructureBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
getCPtr(RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getCtlabel() - Method in class ur_rna.RNAstructure.backend.singlestructure
GetCtLabel(int) - Method in class ur_rna.RNAstructure.backend.structure
getCurrent(int) - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
getCurrent() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
getCurrentBounds() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Get the current bounds allowed in this dialog.
getCurrentLineNumber() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Returns the current line number
getCurrentMax() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getCurrentMin() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getCurrentNodePrefix(boolean) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
getCurrentScene() - Method in class ur_rna.StructureEditor.windows.DrawWindow
getCurrentSceneIndex() - Method in class ur_rna.StructureEditor.windows.DrawWindow
getCustomMenus() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
getCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
getCustomMenus() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
getCustomStream(String) - Method in class ur_rna.Utilities.AppLog
getDashboard() - Method in class ur_rna.StructureEditor.MainFrame
getData() - Method in exception ur_rna.Utilities.ExtensibleException
getData(String) - Method in exception ur_rna.Utilities.ExtensibleException
  Returns the value stored in the data table for the specified key if it exists, or null otherwise.
getData(String, Serializable) - Method in exception ur_rna.Utilities.ExtensibleException
  Returns the value stored in the data table for the specified key if it exists, or defaultValue otherwise.
getDataPath(String) - Static method in class ur_rna.RNAstructure.backend.RNABackend
getDataPath() - Static method in class ur_rna.RNAstructure.backend.RNABackend
getDataPath() - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getDataPath__SWIG_0(String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
getDataPath__SWIG_1() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
GetDatatable() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
getDate() - Static method in class ur_rna.Utilities.DateHelper
getDbgStream() - Method in class ur_rna.Utilities.AppLog
getDbl(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getDbl(String, double) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getDefault() - Static method in class ur_rna.Utilities.AppLog
getDefaultBounds() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Get the default bounds allowed in this dialog.
getDefaultDir() - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getDefaultDir() - Static method in class ur_rna.Utilities.swing.FileDialog
getDefaultExtension() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getDefaultExtension() - Method in class ur_rna.Utilities.swing.FileDialog
getDefaultFont() - Static method in class ur_rna.Utilities.swing.Dialogs
getDefaultMax() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getDefaultMin() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getDefaultPreferenceStorage() - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getDefaultPreferenceStorage() - Static method in class ur_rna.Utilities.swing.FileDialog
getDesc(Action) - Static method in class ur_rna.Utilities.swing.UiAction
getDescription() - Method in enum ur_rna.StructureEditor.FileType
getDescription() - Method in enum ur_rna.StructureEditor.models.BondType
getDescriptions(Component, Map<String, String>) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
  Get a list of all text descriptions associated with this Component.
getDesktop() - Method in class ur_rna.StructureEditor.MainFrame
getDesktop() - Method in class ur_rna.Utilities.swing.MdiParentFrame
getDeviceConfiguration() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getDialogContent() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
  Get the data from a dialog to put in this window.
getDir(String) - Static method in class ur_rna.Utilities.PathTools
  Get the full parent directory path, including the final slash.
getDir(String, boolean) - Static method in class ur_rna.Utilities.PathTools
getDirectionalIcon(double) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
getDirFromPackage(Class<?>, String) - Static method in class ur_rna.Utilities.ResourceLoader
getDirFromPackage(Package, String) - Static method in class ur_rna.Utilities.ResourceLoader
getDisplayedOligo(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getDocumentsDir() - Static method in class ur_rna.Utilities.OSInfo
getDocumentsDir() - Static method in class ur_rna.Utilities.PathTools
getDocumentsDirPath() - Static method in class ur_rna.Utilities.OSInfo
getDomain(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Domain
  Gets the domain that starts at the specified nucleotide (and ends with its paired nucleotide) or null if the nucleotide is unpaired or is paired with a nucleotide on a different strand.
getDomain() - Method in class ur_rna.StructureEditor.models.Nuc
getDomain(Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
getDotData(int, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getDotDataByLocation(int, int, double) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
GetDouble(int) - Method in class ur_rna.RNAstructure.backend.structure
getDrawColor(Color, DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
getDrawSettings() - Method in class ur_rna.StructureEditor.Settings
getDrawStyle(boolean) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getDynalignAlignmentConstraints() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getDynalignAlignmentWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getDynalignStructureWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getElement(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getElement(String, double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getElement(Image, double, double, double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getElement(int, int) - Method in class ur_rna.Utilities.geom.Matrix3D
  Retrieves the value at the specified row and column of the specified matrix.
getEnd() - Method in class ur_rna.StructureEditor.models.Strand
  Get the scene index of the last nucleotide in this strand plus one.
getEndColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Get end column.
getEndLine() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Get end line.
getEnergy() - Method in class ur_rna.RNAstructure.backend.singlestructure
GetEnergy(int) - Method in class ur_rna.RNAstructure.backend.structure
GetEnergyRead() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
GetEnsembleDefect(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetEnsembleDefect() - Method in class ur_rna.RNAstructure.backend.RNA
GetEnsembleEnergy() - Method in class ur_rna.RNAstructure.backend.RNA
GetEnthalpyTable(String) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
GetEnthalpyTable() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
getEnvVar(String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getError() - Method in class ur_rna.GUITester.ScriptRunner
getError() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
getError() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
GetErrorCode() - Method in class ur_rna.RNAstructure.backend.HybridRNA
GetErrorCode() - Method in class ur_rna.RNAstructure.backend.RNA
GetErrorCode() - Method in class ur_rna.RNAstructure.backend.TwoRNA
getErrorCode() - Method in exception ur_rna.RNAstructure.RnaBackendException
GetErrorCode() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getErrorDescription() - Method in exception ur_rna.Utilities.SyntaxErrorException
GetErrorDetails() - Method in class ur_rna.RNAstructure.backend.RNA
GetErrorDetails() - Method in class ur_rna.RNAstructure.backend.structure
GetErrorDetails() - Method in class ur_rna.RNAstructure.backend.TwoRNA
getErrorInfo(Throwable) - Static method in class ur_rna.Utilities.AppLog
GetErrorMessage(int) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
GetErrorMessage(int) - Static method in class ur_rna.RNAstructure.backend.RNA
GetErrorMessage(int) - Method in class ur_rna.RNAstructure.backend.TwoRNA
getErrorMessages() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
GetErrorMessageString(int) - Method in class ur_rna.RNAstructure.backend.TwoRNA
getErrors() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
getErrStream() - Method in class ur_rna.Utilities.AppLog
getExamples() - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
getExamplesDir() - Static method in class ur_rna.RNAstructureUI.RNAstructure
getExistingKey() - Method in exception ur_rna.Utilities.KeyAlreadyExistsException
getExistingValue() - Method in exception ur_rna.Utilities.KeyAlreadyExistsException
getExt(String) - Static method in class ur_rna.Utilities.PathTools
  Gets the extension of the file including the preceding dot (.) If the file name contains multiple dot (.) characters, the extension is defined as the segment starting with the final dot.
getExt(String, boolean, boolean) - Static method in class ur_rna.Utilities.PathTools
  Gets the extension of the file including the preceding dot (.)
getExtensions() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
getExtensions() - Method in enum ur_rna.StructureEditor.FileType
getField(int) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
  Get a particular input field.
getField(String) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
getFile() - Method in exception ur_rna.RNAstructure.RnaBackendException
getFile() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Get the file drawn on this dialog.
getFile(int) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
  Get a file name from a particular input field.
getFile() - Method in class ur_rna.RNAstructureUI.ui.FileField
  Get the file name in the field.
getFile() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
getFile() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
getFileField(String, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getFileField(JTextComponent, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getFileInfo(boolean) - Method in class ur_rna.GUITester.Script
getFileName(boolean, Component, String, String, String, String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getFileName(boolean, Component, String, String, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getFileName(boolean, Component, String, String, String, String) - Static method in class ur_rna.Utilities.swing.FileDialog
getFileName(boolean, Component, String, String, String, String, boolean, String) - Static method in class ur_rna.Utilities.swing.FileDialog
getFilePath() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
getFiles() - Method in class ur_rna.StructureEditor.services.RecentFileList
getFileShouldExist() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getFileShouldExist() - Method in class ur_rna.Utilities.swing.FileDialog
getFileType() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
getFilters() - Method in class ur_rna.RNAstructureUI.ui.FileField
  Gets the file filters associated with this field.
getFilterString() - Method in enum ur_rna.StructureEditor.FileType
getFilterString(boolean) - Method in enum ur_rna.StructureEditor.FileType
getFirstExisting(File, boolean, boolean, String...) - Static method in class ur_rna.Utilities.PathTools
getFlag(String) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
getFlagDefinitions() - Method in class ur_rna.Utilities.CommandLineParser
getFlagValue(String) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
  Returns the value of the flag that matches the given name or alias.
getFocused() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getFoldingConstraints(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getFoldWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getFont() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getFont() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
getFont() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getFontMetrics(Font) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getFontRenderContext() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getFontStyle(Font) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getFor(Nuc, int, boolean) - Static method in class ur_rna.StructureEditor.models.Motif.MultiLoop
GetForbiddenPair3(int) - Method in class ur_rna.RNAstructure.backend.structure
GetForbiddenPair5(int) - Method in class ur_rna.RNAstructure.backend.structure
GetForbidIntramolecular() - Method in class ur_rna.RNAstructure.backend.HybridRNA
GetForcedAlignment(int, int) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
GetForcedDoubleStranded(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetForcedFMNCleavage(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetForcedModification(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetForcedPair(int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
GetForcedProhibitedPair(int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
GetForcedSingleStranded(int) - Method in class ur_rna.RNAstructure.backend.RNA
getFormattedDate(String) - Static method in class ur_rna.Utilities.DateHelper
getFormattedDate(int) - Static method in class ur_rna.Utilities.DateHelper
getFrame() - Static method in class ur_rna.RNAstructureUI.AppMainFrame
GetFreeEnergy(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetFullErrorMessage() - Method in class ur_rna.RNAstructure.backend.RNA
GetFullErrorMessage() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getFullPath(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
getGraphicsOps() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Returns a `CommandSequence` representing all calls that were issued to this `VectorGraphics2D` object.
getGraphRegionBegin() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getGraphRegionEnd() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getGridLine(int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getGui() - Method in class ur_rna.GUITester.ScriptRuntime
getGuiInfo(Object) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
getGuiTree(Component) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
GetGUpair(int) - Method in class ur_rna.RNAstructure.backend.structure
getHeight() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getHeight() - Method in class ur_rna.StructureEditor.services.drawing.export.PageSize
getHelices() - Method in class ur_rna.StructureEditor.models.RnaScene
  Returns the list of helices in the RNA scene
getHelix() - Method in class ur_rna.StructureEditor.models.Bond
getHelix(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Helix
  Return the helix that contains the given nuc or null if nuc is not in a helix (ie.
getHelix() - Method in class ur_rna.StructureEditor.models.Nuc
getHelix(Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
getHierarchy(Collection) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
getHints() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getHomeDir() - Static method in class ur_rna.Utilities.PathTools
getIcon(String) - Static method in class ur_rna.StructureEditor.Program
getIcon(Action) - Static method in class ur_rna.Utilities.swing.UiAction
getId() - Method in interface ur_rna.GUITester.ScriptParser.Node
getId() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
getId() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
getId() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
GetImage() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getImage(String) - Static method in class ur_rna.RNAstructureUI.utilities.ImageGrabber
  Create an image.
getImage(String) - Static method in class ur_rna.StructureEditor.Program
getImage() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getImageIcon(String) - Static method in class ur_rna.RNAstructureUI.utilities.ImageGrabber
  Create an image icon.
getImageLabel(String) - Static method in class ur_rna.RNAstructureUI.utilities.ImageGrabber
  Create an image label.
getImageOutput(Image, boolean) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getImageResources() - Static method in class ur_rna.StructureEditor.Program
getIndex() - Method in class ur_rna.StructureEditor.models.Strand
  Get the index of this strand in the list of RnaScene strands.
getInfoFromToken(Token) - Static method in exception ur_rna.GUITester.ScriptParser.ParseFormatException
  Uses "currentToken" to generate additional information to help the user locate the source of the error.
getInput() - Method in class ur_rna.GUITester.Script
getInput(String, String, Object) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show an input dialog that gets a string.
getInput(NumberField.DoubleField) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show an input dialog that gets a double within a certain range.
getInput(NumberField.IntegerField) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show an input dialog that gets an integer within a certain range.
getInputControl(int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Get a particular input control from the content pane.
getInputControl(Container, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Get a particular input control from a given container.
getInstance() - Static method in class ur_rna.StructureEditor.Program
getInt(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getInt(String, int) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getIntAt(int) - Method in class ur_rna.RNAstructure.backend.RNA
getInterStrandLinker() - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getIntResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
getInts(int[], int) - Method in class ur_rna.RNAstructure.backend.RNA
getInvalidArgMessage(String, Object[], int, String) - Static method in class ur_rna.GUITester.RuntimeTools
getIsrna() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
getItemName() - Method in interface ur_rna.Utilities.swing.IMenuItem
getJvmBits(String, String) - Static method in class ur_rna.Utilities.JniLoader
  Detect the architecture of the Java platform (32 or 64 bits -- this is NOT necessarily the architecture of the OS!!)
getJvmBits() - Static method in class ur_rna.Utilities.JniLoader
getKey() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
getKey() - Method in class ur_rna.Utilities.Pair
  Returns the key corresponding to this entry.
getKey(char) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getKey(String) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getKeyStroke() - Method in class ur_rna.Utilities.swing.CheckMergeItem
getKeyStroke() - Method in class ur_rna.Utilities.swing.MergeItem
getKeyStroke(Action) - Static method in class ur_rna.Utilities.swing.UiAction
getKT() - Static method in class ur_rna.RNAstructure.backend.structure
GetLabelXCoordinate(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetLabelYCoordinate(int) - Method in class ur_rna.RNAstructure.backend.RNA
getLandscape() - Method in class ur_rna.StructureEditor.services.drawing.export.PageSize
getLastChar() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Returns the last character that was read as an integer (0 to 65535).
getLastChosenFilter() - Static method in class ur_rna.Utilities.swing.FileDialog
getLastFound() - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
getLegendData() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getLength() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
getLhs() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
getLibNames() - Method in class ur_rna.Utilities.JniLoader
getLine() - Method in exception ur_rna.Utilities.SyntaxErrorException
getLinearBond(Bond) - Static method in class ur_rna.StructureEditor.services.drawing.NucLayout
getLink() - Method in class ur_rna.Utilities.swing.JActionLabel
getLink() - Method in class ur_rna.Utilities.swing.JFlatButton
getLinkUri() - Method in class ur_rna.Utilities.swing.JActionLabel
getLinkUri() - Method in class ur_rna.Utilities.swing.JFlatButton
getList() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
getList(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
getListener() - Method in class ur_rna.Utilities.swing.UiAction
  Get the main listener (which is usually specified in the constructor).
getListeners() - Method in class ur_rna.Utilities.swing.UiAction
  Get a list of all listeners of this action, including the main listener (which is usually specified in the constructor).
getLoadedLib() - Method in class ur_rna.Utilities.JniLoader
getLoadedLibraries(ClassLoader) - Static method in class ur_rna.Utilities.ClassLoaderInfo
getLoadedLibraries(ClassLoader[]) - Static method in class ur_rna.Utilities.ClassLoaderInfo
getLocation() - Method in exception ur_rna.Utilities.SyntaxErrorException
getLocationDescription() - Method in exception ur_rna.Utilities.SyntaxErrorException
getLog() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
getLog() - Method in class ur_rna.GUITester.ScriptRuntime
getLoop(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
  Return the single-stranded region (loop) that contains the given nuc or null if nuc is not in a loop (i.e.
getLoop() - Method in class ur_rna.StructureEditor.models.Nuc
getLoop(Nuc) - Method in class ur_rna.StructureEditor.models.RnaScene
getLoops() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
getLoops() - Method in class ur_rna.StructureEditor.models.RnaScene
GetLowestEnergy() - Method in class ur_rna.RNAstructure.backend.Dynalign_object
getM00() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the first matrix element in the first row.
getM01() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the second matrix element in the first row.
getM02() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the third matrix element in the first row.
getM10() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get first matrix element in the second row.
getM11() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get second matrix element in the second row.
getM12() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the third matrix element in the second row.
getM20() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the first matrix element in the third row.
getM21() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the second matrix element in the third row.
getM22() - Method in class ur_rna.Utilities.geom.Matrix3D
  Get the third matrix element in the third row .
getMainClass() - Static method in class ur_rna.Utilities.AppInfo
getMainFrame() - Method in class ur_rna.StructureEditor.Program
getMainMenu() - Method in class ur_rna.RNAstructureUI.AppMainFrame
getMainWindow() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
getManager() - Method in class ur_rna.Utilities.EventSource
getMap(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
getMaxConstraintIndex(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
GetMaximumPairingDistance() - Method in class ur_rna.RNAstructure.backend.RNA
getMaxItemCount() - Method in class ur_rna.StructureEditor.services.RecentFileList
getMaxLoop() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMaxPair() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMdiChildFrames(Class) - Method in class ur_rna.Utilities.swing.MdiParentFrame
getMenu() - Method in class ur_rna.StructureEditor.services.RecentFileMenuManager
getMenuItem() - Method in class ur_rna.Utilities.swing.CheckMergeItem
getMenuItem() - Method in interface ur_rna.Utilities.swing.IMenuItem
getMenuItem() - Method in class ur_rna.Utilities.swing.MergeItem
getMenuItems() - Method in class ur_rna.RNAstructureUI.menus.MenuList
getMenuItems() - Method in interface ur_rna.Utilities.swing.IMenuItem
getMenuItems(Component) - Static method in class ur_rna.Utilities.swing.Menus
getMenuPath(JMenuItem) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
getMenus() - Method in class ur_rna.RNAstructureUI.AppMainFrame
getMenus() - Method in class ur_rna.RNAstructureUI.menus.MenuList
getMenus() - Method in class ur_rna.StructureEditor.windows.ChildFrame
getMenus() - Method in class ur_rna.StructureEditor.windows.DrawWindow
getMenus() - Method in interface ur_rna.Utilities.swing.IMenuItem
getMenus(Component) - Static method in class ur_rna.Utilities.swing.Menus
getMenuText(RecentFileList.RecentFile) - Method in class ur_rna.StructureEditor.services.RecentFileMenuManager
getMergeName() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
getMergeName() - Method in interface ur_rna.Utilities.swing.IMergeItem
getMergeName(Component) - Static method in interface ur_rna.Utilities.swing.IMergeItem
getMergeName(Object) - Method in class ur_rna.Utilities.swing.MergeManager
getMergePos() - Method in class ur_rna.Utilities.swing.CheckMergeItem
getMergePos() - Method in interface ur_rna.Utilities.swing.IMergeItem
getMergePos(Component) - Static method in interface ur_rna.Utilities.swing.IMergeItem
getMergePos() - Method in class ur_rna.Utilities.swing.IMergeItem.Proxy
getMergePos() - Method in class ur_rna.Utilities.swing.MergeButton
getMergePos() - Method in class ur_rna.Utilities.swing.MergeButton.Separator
getMergePos() - Method in class ur_rna.Utilities.swing.MergeItem
getMergePos() - Method in class ur_rna.Utilities.swing.MergeItem.Separator
getMergePos() - Method in class ur_rna.Utilities.swing.MergeMenu
getMergePos() - Method in class ur_rna.Utilities.swing.MergeToggleButton
getMessage() - Method in error ur_rna.GUITester.ScriptParser.TokenMgrError
  You can also modify the body of this method to customize your error messages.
getMessage() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
getMessage(Throwable) - Static method in class ur_rna.Utilities.ExceptionHelper
  Java exceptions often contain no message or a few details *without* describing the actual error.
getMessage() - Method in exception ur_rna.Utilities.ExtensibleException
  If a new message has been stored (using `setMessage`) this will return the new message.
getMessage() - Method in class ur_rna.Utilities.swing.WaitDialog
getMetaKeyName() - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getMetaKeyName(boolean) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getMidpoint(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
getMidpoint(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.Vec2D
getMnemonic(String) - Static method in class ur_rna.Utilities.swing.KeyMnemonic
getMnemonic(Action) - Static method in class ur_rna.Utilities.swing.UiAction
getMnemonicIndex(String) - Static method in class ur_rna.Utilities.swing.KeyMnemonic
  Returns the index in the string at which the mnemonic character is found.
getModel() - Method in interface ur_rna.StructureEditor.models.IScreenObject
getModel() - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
getModel() - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
getModelSpaceDeltaTransform(Point, Point) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
GetModified(int) - Method in class ur_rna.RNAstructure.backend.structure
getModifierKeyName(int) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getModifierKeyName(int, boolean) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getMonospaceFont() - Static method in class ur_rna.Utilities.swing.Dialogs
getMostRecentFrame() - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Get the most recent internal frame in the application.
getMostStableOligo() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMotif(Nuc, RnaDrawController.SelectionType, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
getMultiBranchBasePairs(Nuc, boolean, Bond.MultiLoopRole) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
  Retrieve a list of all bonds that are part of a multi-branch loop.
getMultiBranchBasePairs(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
getMultiBranchBasePairs(Nuc, boolean) - Static method in class ur_rna.StructureEditor.models.Motif.Loop
getMultilignCT(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMultilignMaxPairs() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMultilignSequenceSetData() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getMultiLoop(int, boolean) - Method in class ur_rna.StructureEditor.models.Nuc
getMultiLoopRole(Nuc) - Method in class ur_rna.StructureEditor.models.Bond
  Determine whether this bond is the "entrance" ("Trunk") to a Multi-Branch Loop by passing in another reference nucleotide that is in the same loop.
getMultiLoops(int, boolean) - Method in class ur_rna.StructureEditor.models.RnaScene
getMultiplied(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
GetMyErrorMessage(int) - Method in class ur_rna.RNAstructure.backend.HybridRNA
getMyLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
getN3() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
  Get the "ending" base -- i.e.
getN5() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
  Get the "starting" base -- i.e.
getName(Color) - Static method in class ur_rna.Utilities.Colors
getName(Action) - Static method in class ur_rna.Utilities.swing.UiAction
getNameOrText(Component) - Static method in class ur_rna.Utilities.swing.Components
  Return the first non-null non-empty String of the following: the item's name, text, or actionCommand.
getNegated() - Method in class ur_rna.Utilities.geom.Vec2D
getNext() - Method in class ur_rna.StructureEditor.models.Nuc
getNext(int) - Method in class ur_rna.StructureEditor.models.Nuc
getNext(Nuc) - Method in class ur_rna.StructureEditor.models.Strand
getNext(Nuc, int) - Method in class ur_rna.StructureEditor.models.Strand
getNextInScene(Nuc, int, boolean) - Method in class ur_rna.StructureEditor.models.Strand
  Returns the next nucleotide after the specified one, regardless of whether it is in this strand or another one.
getNextToken() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Get the next Token.
getNextToken() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Get the next Token.
getNode() - Method in exception ur_rna.GUITester.ScriptRuntimeException
  Get the current script node at the time of the error.
getNodeName() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
getNodeName(int) - Static method in class ur_rna.GUITester.ScriptParser.ScriptNode
getNormalized() - Method in class ur_rna.Utilities.geom.Vec2D
getNormalizedExtensions() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
getNuc(int) - Method in class ur_rna.StructureEditor.models.RnaScene
getNuc3() - Method in class ur_rna.StructureEditor.models.Bond
getNuc3() - Method in class ur_rna.StructureEditor.models.Motif.Segment
getNuc5() - Method in class ur_rna.StructureEditor.models.Bond
getNuc5() - Method in class ur_rna.StructureEditor.models.Motif.Segment
getNucAt(int) - Method in class ur_rna.StructureEditor.models.Motif.Segment
getNucCount() - Method in class ur_rna.StructureEditor.models.RnaScene
GetNucleotide(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetNucleotideXCoordinate(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetNucleotideYCoordinate(int) - Method in class ur_rna.RNAstructure.backend.RNA
getNucShape(Nuc) - Method in class ur_rna.StructureEditor.services.RnaDrawController
GetNumberofDoubles() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberofForbiddenPairs() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberOfForcedDoubleStranded() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberOfForcedFMNCleavages() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberOfForcedModifications() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberOfForcedPairs() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberOfForcedProhibitedPairs() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberOfForcedSingleStranded() - Method in class ur_rna.RNAstructure.backend.RNA
GetNumberofGU() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberofModified() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberofPairs() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberofSingles() - Method in class ur_rna.RNAstructure.backend.structure
GetNumberofStructures() - Method in class ur_rna.RNAstructure.backend.structure
getNumMultilignSequences() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getNumSequences() - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
getNumSequences() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Get the number of sequences this window handles.
getNumSequences() - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
getNumTurboFoldSequences() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getOffendingText() - Method in exception ur_rna.Utilities.SyntaxErrorException
getOffset() - Method in class ur_rna.StructureEditor.ui.DrawPanel
getOligoLabelData(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getOligoTargetLength() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getOligoTargetSequence() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getOpenName(String, String, String, String, Component) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getOpenName(String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getOpenName(String, String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getOpenName(String, String, String, String, Component) - Static method in class ur_rna.Utilities.swing.FileDialog
getOpenName(String) - Static method in class ur_rna.Utilities.swing.FileDialog
getOpenName(String, String) - Static method in class ur_rna.Utilities.swing.FileDialog
getOperandName() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
getOption(StructureDialog.DrawOptions) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Determine whether the specified option is set
getOriginalHeight() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getOriginalMessage() - Method in exception ur_rna.Utilities.ExtensibleException
  This returns the original message passed in the constructor (to Throwable).
getOriginalWidth() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getOSType(String) - Static method in class ur_rna.Utilities.OSInfo
getOSType() - Static method in class ur_rna.Utilities.OSInfo
getOther(Nuc) - Method in class ur_rna.StructureEditor.models.Bond
  Given a nucleotide on one side of the bond, this returns the nucleotide on the other side.
getOutput(Color) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getOutput(Shape) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
getOutputFile(String, String) - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Replace the extension on a file name.
getOutputFile(String) - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
getOwner() - Method in class ur_rna.Utilities.swing.FileDialog
getPaint() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getPaint() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
getPaint() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
GetPair(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
GetPair(int) - Method in class ur_rna.RNAstructure.backend.RNA
GetPair(int, int) - Method in class ur_rna.RNAstructure.backend.structure
GetPair(int) - Method in class ur_rna.RNAstructure.backend.structure
getPair(int) - Method in class ur_rna.StructureEditor.models.Motif.Helix
getPair(int, int) - Method in class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
  Get the probability of pairing between Nucs I and J.
getPair(int) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  Returns -1 if the given index does not belong to this structure element or if it is not paired.
GetPair3(int) - Method in class ur_rna.RNAstructure.backend.structure
GetPair5(int) - Method in class ur_rna.RNAstructure.backend.structure
getPairBond() - Method in class ur_rna.StructureEditor.models.Nuc
getPaired() - Method in class ur_rna.StructureEditor.models.Nuc
getPaired(boolean) - Method in class ur_rna.StructureEditor.models.Nuc
GetPairEnergy(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
GetPairingDistanceLimit() - Method in class ur_rna.RNAstructure.backend.structure
GetPairProbabilities(double[], int) - Method in class ur_rna.RNAstructure.backend.RNA
GetPairProbability(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
getPanel() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
getParentFrame() - Method in class ur_rna.Utilities.swing.MdiChildFrame
getParseError() - Method in class ur_rna.GUITester.ScriptRunner
getPhysicalFont(Font, String) - Static method in class ur_rna.Utilities.swing.FontUtil
  Try to guess physical font from the properties of a logical font, like "Dialog", "Serif", "Monospaced" etc.
getPhysicalFont(Font) - Static method in class ur_rna.Utilities.swing.FontUtil
getPlot() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
getPoint(double, Point2D) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
getPoint(double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
getPointAlong(Point2D, double) - Method in class ur_rna.Utilities.geom.Vec2D
  Returns the location of result to be the point that would be reached by starting at startPoint and traveling along the direction of this vector the distance specified by lengthAlongVector.
getPointAlongScaled(Point2D, double) - Method in class ur_rna.Utilities.geom.Vec2D
  Sets the location of result to be the point that would be reached by starting at startPoint and traveling along the direction of this vector the specified multiple of this vector's length.
getPointBetween(Point2D, Point2D, double) - Static method in class ur_rna.Utilities.geom.Vec2D
getPortrait() - Method in class ur_rna.StructureEditor.services.drawing.export.PageSize
getPosition() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Gets the character position in the reader.
getPositionFromEnd() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
getPref(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
getPref(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
getPreferencesFile() - Static method in class ur_rna.Utilities.prefs.FilePreferences.Factory
getPreferencesFile() - Method in class ur_rna.Utilities.prefs.FilePreferences
getPrefs() - Static method in class ur_rna.RNAstructureUI.RNAstructure
getPrev() - Method in class ur_rna.StructureEditor.models.Nuc
getPrev(Nuc) - Method in class ur_rna.StructureEditor.models.Strand
getProbComparisonSymbol() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
GetProgress() - Method in class ur_rna.RNAstructure.backend.RNA
getProgress() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
getProgress() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
getProgress() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
getProgress() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
getProgress() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
getProgress() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
getProgress() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
getProgressNumber() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getProgressTotal() - Method in class ur_rna.Utilities.swing.WaitDialog
getProgressValue() - Method in class ur_rna.Utilities.swing.WaitDialog
getProps() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
getProvider() - Static method in class ur_rna.Utilities.AppInfo
  Attempts to get the AppInfoProvider that has been registered for this application.
GetPseudoknotRanks(CIntVector, int) - Method in class ur_rna.RNAstructure.backend.structure
GetPseudoknotRanks(CIntVector) - Method in class ur_rna.RNAstructure.backend.structure
getRadiusFromArcAndChord(double, double) - Static method in class ur_rna.Utilities.geom.Ellipses.Circle
  This calculates the circumference of a circle based on an arc that is cut by a chord.
getRecent() - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
getRecentDir(String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getRecentDir(String, boolean) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getRecentDir(String, boolean, File) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getRecentDir(String) - Static method in class ur_rna.Utilities.swing.FileDialog
getRecentDir(String, boolean) - Static method in class ur_rna.Utilities.swing.FileDialog
getRecentDir(String, boolean, File) - Static method in class ur_rna.Utilities.swing.FileDialog
getRecentDirOrDefault(String, boolean) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getRecentDirOrDefault(String, boolean) - Static method in class ur_rna.Utilities.swing.FileDialog
getRecentFilesNode() - Method in class ur_rna.StructureEditor.MainFrame
getRect() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearOp
getReference() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
getReference() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
getRefoldWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getRelationship() - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
getRelative() - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
getRenderer() - Method in class ur_rna.StructureEditor.ui.DrawPanel
getRenderingHint(RenderingHints.Key) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getRenderingHints() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getResource(String) - Static method in class ur_rna.StructureEditor.Program
getResourceFile(String) - Static method in class ur_rna.StructureEditor.Program
getResourceLocation(String) - Method in class ur_rna.Utilities.ResourceLoader
  Returns the full path to a resource if it is found, or null otherwise.
getResourceStream(String) - Static method in class ur_rna.StructureEditor.Program
getResourceText(String) - Static method in class ur_rna.StructureEditor.Program
getResourceText(String, String) - Static method in class ur_rna.StructureEditor.Program
getResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
getResult() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
getResult() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
getRhs() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
GetRNA1() - Method in class ur_rna.RNAstructure.backend.HybridRNA
GetRNA1() - Method in class ur_rna.RNAstructure.backend.TwoRNA
GetRNA2() - Method in class ur_rna.RNAstructure.backend.HybridRNA
GetRNA2() - Method in class ur_rna.RNAstructure.backend.TwoRNA
getRNASequence(RnaScene) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getRNAstructureGroup(RNA) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getRNAType(FileType) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getRoot() - Method in class ur_rna.Utilities.prefs.FilePreferences
getRootFrame() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
getRotated(double) - Method in class ur_rna.Utilities.geom.Vec2D
  Get a copy of this vector rotated counter-clockwise by the specified angle (in radians)
getRotated90() - Method in class ur_rna.Utilities.geom.Vec2D
  Get a copy of this vector rotated counter-clockwise by 90 degrees
getRow(int, double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Copies the matrix values in the specified row into the array parameter.
getRunningTask() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getRunTimeError() - Method in class ur_rna.GUITester.ScriptRunner
getSaveFile() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getSaveName(String, String, String, String, Component) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getSaveName(String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getSaveName(String, String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
getSaveName(String, String, String, String, Component) - Static method in class ur_rna.Utilities.swing.FileDialog
getSaveName(String, String, String, String, Component, String) - Static method in class ur_rna.Utilities.swing.FileDialog
getSaveName(String) - Static method in class ur_rna.Utilities.swing.FileDialog
getSaveName(String, String) - Static method in class ur_rna.Utilities.swing.FileDialog
getScale() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Get the scale at which the image is zoomed.
getScale() - Method in class ur_rna.StructureEditor.ui.DrawPanel
getScale() - Method in class ur_rna.Utilities.geom.Matrix3D
  Performs an SVD normalization of this matrix to calculate and return the uniform scale factor.
getScaled(double) - Method in class ur_rna.Utilities.geom.Vec2D
getScaled(double, double) - Method in class ur_rna.Utilities.geom.Vec2D
getScaleRotate(double[], double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  perform SVD (if necessary to get rotational component
getScene() - Method in class ur_rna.StructureEditor.models.Bond
getScene() - Method in class ur_rna.StructureEditor.models.Motif.Helix
getScene() - Method in class ur_rna.StructureEditor.models.Nuc
getScene() - Method in class ur_rna.StructureEditor.models.Strand
getScene() - Method in class ur_rna.StructureEditor.models.StrandList
getScene() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getSceneBounds(boolean) - Method in class ur_rna.StructureEditor.windows.DrawWindow
getSceneEnd() - Method in class ur_rna.StructureEditor.models.Strand
  Get the index (relative to all nucleotides in the scene) immediately AFTER last nucleotide in this Strand
getSceneNuc(RnaScene, int) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
getSceneNuc(RnaScene, int) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
getSceneNuc(RnaScene, int) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.MultiStrand
getScenes() - Method in class ur_rna.StructureEditor.windows.DrawWindow
getSceneStart() - Method in class ur_rna.StructureEditor.models.Strand
  Get the index (relative to all nucleotides in the scene) of the first nucleotide in this Strand
getScreenObject(Nuc, View2D, int) - Method in class ur_rna.StructureEditor.services.RnaDrawController
getScreenWorkingArea(Window) - Static method in class ur_rna.Utilities.swing.Dialogs
  getScreenWorkingArea, This returns the working area of the screen.
getScript() - Method in class ur_rna.GUITester.ScriptRuntime
getSearchDirs() - Method in class ur_rna.Utilities.ResourceLoader
getSegmentInfo() - Method in class ur_rna.GUITester.Script
getSelected() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getSelectedFile() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Returns the selected file.
getSelectedFile() - Method in class ur_rna.Utilities.swing.FileDialog
  Returns the selected file.
getSelectedIndex() - Method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Get the index of the selected button from this panel.
getSelectedItem() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
getSelectedName() - Method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Get the command of the selected button from this panel.
getSelectedSequence() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
getSelectionHashCode(Iterable<Nuc>) - Static method in class ur_rna.StructureEditor.services.drawing.DrawHandle
getSelectionState() - Method in class ur_rna.StructureEditor.services.RnaDrawController
GetSequence() - Method in class ur_rna.RNAstructure.backend.RNA
GetSequence() - Method in class ur_rna.RNAstructure.backend.structure
getSequence() - Method in class ur_rna.StructureEditor.windows.InsertBasesDialog
getSequenceComment() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getSequenceData() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
GetSequenceLabel() - Method in class ur_rna.RNAstructure.backend.structure
GetSequenceLength() - Method in class ur_rna.RNAstructure.backend.RNA
getSequenceLength() - Method in class ur_rna.RNAstructure.backend.singlestructure
GetSequenceLength() - Method in class ur_rna.RNAstructure.backend.structure
getSequenceSetAsString() - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
getSequenceSetAsString() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Get a representation of the sequence set as a string.
getSequenceSetAsString() - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
getSequenceTitle() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getSettings() - Method in class ur_rna.StructureEditor.services.RnaDrawController
getSettings() - Method in interface ur_rna.StructureEditor.services.SceneController
getSettings() - Method in interface ur_rna.StructureEditor.services.SceneRenderer
getSettingsField(String) - Method in class ur_rna.StructureEditor.Settings
getSettingsName(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getShape() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
getSHAPEFileRead() - Method in class ur_rna.RNAstructure.backend.structure
getShortcutModifierKeyName() - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getShortcutModifierKeyName(boolean) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
getShowWarnings() - Static method in class ur_rna.RNAstructure.backend.structure
GetSingle(int) - Method in class ur_rna.RNAstructure.backend.structure
getSingle(int) - Method in class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
  Get the probability that Nuc I is single-stranded.
getSource() - Method in class ur_rna.GUITester.ScriptRunner
getSource() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
getSource() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
getSpecialKey(String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
getSpecialValue(String) - Method in class ur_rna.GUITester.ScriptRuntime
getSpi(String) - Method in class ur_rna.Utilities.prefs.FilePreferences
getSpin(JSpinner) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getSpinDbl(JSpinner) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getSpinInt(JSpinner) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
getSpinner() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
  Get the spinner.
getStackTrace(Throwable) - Static method in class ur_rna.Utilities.ExceptionHelper
  Gets the stack trace as a String (i.e.
getState() - Method in class ur_rna.StructureEditor.models.RnaScene
getStatus() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
getStatus() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
getStatus() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
getStatus() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
getStatus() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
getStr(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getStr(String, String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getStrand() - Method in class ur_rna.StructureEditor.models.Nuc
getStrand(int) - Method in class ur_rna.StructureEditor.models.RnaScene
getStrand(int, boolean) - Method in class ur_rna.StructureEditor.models.RnaScene
getStrandIndex() - Method in class ur_rna.StructureEditor.models.Nuc
getStream(Verbosity) - Method in class ur_rna.Utilities.AppLog
getStream(String) - Method in class ur_rna.Utilities.ResourceLoader
  Searches for the specified resource in all search directories and returns an an InputStream representing the resource.
getStream(String, boolean) - Method in class ur_rna.Utilities.ResourceLoader
getStringBuilder() - Method in class ur_rna.Utilities.StringBuilderEx
  Get the internal StringBuilder.
getStroke() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getStroke() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
getStroke() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getStrResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
GetStructure() - Method in class ur_rna.RNAstructure.backend.RNA
getStructure() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
getStructureCount() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
getStructureCount() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
getStructureData(int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
GetStructureNumber() - Method in class ur_rna.RNAstructure.backend.RNA
getStructureNumber() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
getStructureTitle(RNA, int) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
getStructureType() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getStyle(Nuc) - Method in class ur_rna.StructureEditor.models.DrawSettings
getSubItemContainer(Component) - Static method in class ur_rna.Utilities.swing.Menus
getSubItemMergePos() - Method in class ur_rna.Utilities.swing.MergeMenu
  Gets the current mergePos at which sub-items will be added by default.
getSuboptimalAbsoluteDiff() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getSuboptimalPercentDiff() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getSubtr(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
GetSuffix(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getSumShapeRepeats() - Static method in class ur_rna.RNAstructure.backend.structure
getSymbol(int, boolean, boolean) - Static method in class ur_rna.RNAstructure.Nucleobase
getSymbol(int, boolean) - Static method in class ur_rna.RNAstructure.Nucleobase
getSymbol(int) - Static method in class ur_rna.RNAstructure.Nucleobase
getSymbol() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
getSysProp(String...) - Static method in class ur_rna.Utilities.AppLog
  Checks for the existence of a system property in multiple places.
getSysProp(String) - Static method in class ur_rna.Utilities.AppLog
getTab() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
getTabSize() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getTag() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
getTag() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
GetTemperature() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
GetTemperature() - Method in class ur_rna.RNAstructure.backend.TwoRNA
getTemperature() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getText() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
getTextRegion(int[]) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  A client calls with with an already-created array of integers.
GetThermodynamicDataTable() - Method in class ur_rna.RNAstructure.backend.structure
getTitle() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
getToken(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Get the specific Token.
getTokenKind() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
getTokenName() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
getTokenName(int) - Static method in class ur_rna.GUITester.ScriptParser.ScriptNode
getToolBar() - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Get the toolbar.
getToolBar() - Method in class ur_rna.StructureEditor.MainFrame
  Get the toolbar.
getToolbarButtons() - Method in class ur_rna.StructureEditor.windows.ChildFrame
getToolbarButtons() - Method in class ur_rna.StructureEditor.windows.DrawWindow
getToolBarItem(String) - Method in class ur_rna.RNAstructureUI.AppMainFrame
getToolBarItem(String) - Method in class ur_rna.StructureEditor.MainFrame
getTrackLineColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
getTransform() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
getTransform() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
getTransform() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
getTransformed(AffineTransform) - Method in class ur_rna.Utilities.geom.Vec2D
getTransformedImage(Image, AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Returns a transformed version of an image.
getTrStream() - Method in class ur_rna.Utilities.AppLog
getTrunk() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
getTurboFoldCT(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getTurboFoldSaveFile(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getTurboFoldSequenceSetData() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getType() - Method in class ur_rna.StructureEditor.models.Bond
getType() - Method in class ur_rna.StructureEditor.models.Motif.Loop
getUnnamedValues() - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
  Get the list of Unnamed Arguments (i.e.
getUpdateListeners() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
getUsageMessage() - Method in class ur_rna.Utilities.CommandLineParser
getUser() - Method in class ur_rna.StructureEditor.services.UserPrefs
getUseSimpleFileChooser() - Static method in class ur_rna.RNAstructureUI.AppMainFrame
getValidMergePos(Component) - Static method in interface ur_rna.Utilities.swing.IMergeItem
getValue() - Method in class ur_rna.GUITester.ScriptParser.ASTLiteral
getValue() - Method in class ur_rna.GUITester.ScriptParser.Token
  An optional attribute value of the Token.
getValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
getValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.FloatField
getValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField
  Get the text field's numeric value.
getValue() - Method in class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
getValue() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
  Get the spinner value.
getValue() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
getValue() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
getValue() - Method in class ur_rna.Utilities.Pair
  Returns the value corresponding to this entry.
getValueComparisonSymbol() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
getVar(String) - Method in class ur_rna.GUITester.ScriptRuntime
getVerbosity() - Method in class ur_rna.Utilities.AppLog
  Returns the log-level (aka importance or verbosity) required for log entries to be processed.
getVerifiedSymbol(String) - Static method in class ur_rna.RNAstructure.Nucleobase
getVerifiedSymbol(String, char) - Static method in class ur_rna.RNAstructure.Nucleobase
getVerify() - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
getVersion() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
getVersion() - Static method in class ur_rna.StructureEditor.Program
getView() - Method in interface ur_rna.StructureEditor.services.drawing.ICanvas
getView() - Method in class ur_rna.StructureEditor.ui.DrawPanel
getVisible() - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
getVKCode(char) - Static method in class ur_rna.Utilities.swing.KeyMnemonic
getWidth() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getWidth() - Method in class ur_rna.StructureEditor.services.drawing.export.PageSize
getWorkInNextStep() - Method in class ur_rna.RNAstructure.backend.PartialProgress
getWrap() - Method in class ur_rna.StructureEditor.windows.NewFileWindow.JWrapTextPane
getX() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getX() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
getXORMode() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
  Returns the current XOR background color.
getXorMode() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Returns the current XOR background color if XOR Mode is in effect.
getY() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
getY() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
getZoomScroll(Dimension, Dimension) - Method in class ur_rna.StructureEditor.ui.DrawPanel
getZOrder() - Method in interface ur_rna.StructureEditor.models.IScreenObject
getZOrder() - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
getZOrder() - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
GhostWhite - Static variable in class ur_rna.Utilities.Colors
globToRegex(String) - Static method in class ur_rna.Utilities.Convert
  Converts a standard POSIX Shell globbing pattern into a regular expression pattern.
Gold - Static variable in class ur_rna.Utilities.Colors
GoldenRod - Static variable in class ur_rna.Utilities.Colors
GotoHistory - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
gotoNext(int) - Method in class ur_rna.StructureEditor.menus.WindowsMenu
Graphics2DRecorder - Class in ur_rna.StructureEditor.services.drawing.export
  A class that can be substituted for a Graphics2D object, but instead of performing any actual drawing, it simply records the drawing instructions.
Graphics2DRecorder() - Constructor for class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
GraphicsOp - Interface in ur_rna.StructureEditor.services.drawing.export
  Represents a graphics operation that can be applied to a Graphics2D object.
GraphicsOp.ActionOp - Class in ur_rna.StructureEditor.services.drawing.export
  Represents an operation that does not change the state of the graphics context.
GraphicsOp.BackgroundOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.ClearHintsOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.ClearOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.ClipOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.ColorOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.CompositeOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.ControlOp - Class in ur_rna.StructureEditor.services.drawing.export
  Represents an operation that is for control purposes only.
GraphicsOp.DrawImageOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.DrawShapeOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.DrawStringOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.EndOp - Class in ur_rna.StructureEditor.services.drawing.export
  Indicates the end of a graphics record.
GraphicsOp.FontOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.GroupEndOp - Class in ur_rna.StructureEditor.services.drawing.export
  Indicates the end of group of graphics objects (e.g.
GraphicsOp.GroupStartOp - Class in ur_rna.StructureEditor.services.drawing.export
  Indicates the start of a new group of graphics objects (e.g.
GraphicsOp.HintOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.InitOp - Class in ur_rna.StructureEditor.services.drawing.export
  Signifies the start of a new graphics record.
GraphicsOp.PaintOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.StateOp - Class in ur_rna.StructureEditor.services.drawing.export
  Represents an operation that changes the state of the graphics context, but does not perform any drawing on its own.
GraphicsOp.StrokeOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.TransformOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsOp.XorModeOp - Class in ur_rna.StructureEditor.services.drawing.export
GraphicsStyle - Class in ur_rna.StructureEditor.services.drawing.export
  Tracks the state of various Graphics properties.
GraphicsStyle() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
graphicsStyles - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
GraphicsUtil - Class in ur_rna.Utilities.geom
  Utilities to help with `Graphics2D` drawing and graphics.
GraphicsUtil() - Constructor for class ur_rna.Utilities.geom.GraphicsUtil
grass - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
Gray - Static variable in class ur_rna.Utilities.Colors
Green - Static variable in class ur_rna.Utilities.Colors
GreenYellow - Static variable in class ur_rna.Utilities.Colors
group - Variable in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  The button group connected to this panel.
group - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
group(int) - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
group(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
group2 - Variable in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  The button group, as a list, for ease of access to each.
GroupEndOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.GroupEndOp
GroupStartOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.GroupStartOp
groupStyle - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
groupStyles - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
grow(Rectangle2D, double) - Static method in class ur_rna.Utilities.geom.Rectangles
grow(Rectangle2D, double, double) - Static method in class ur_rna.Utilities.geom.Rectangles
GT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
guessTitle() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
guessTypeFromFilePath(String) - Static method in enum ur_rna.RNAstructureUI.utilities.FileType
GuiAppManager - Class in ur_rna.GUITester.GuiTools
GuiAppManager(AppLog) - Constructor for class ur_rna.GUITester.GuiTools.GuiAppManager
guiFinder() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
GuiFinder - Class in ur_rna.GUITester.GuiTools
GuiFinder(GuiAppManager) - Constructor for class ur_rna.GUITester.GuiTools.GuiFinder
guiInfoListener - Variable in class ur_rna.RNAstructureUI.menus.HelpMenu
guiItem - Variable in class ur_rna.GUITester.ScriptParser.ASTGuiReference
GuiItemNotFoundException - Exception in ur_rna.GUITester.GuiTools
GuiItemNotFoundException() - Constructor for exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
GuiItemNotFoundException(String) - Constructor for exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
GuiItemNotFoundException(GuiItemRef) - Constructor for exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
GuiItemNotFoundException(Throwable) - Constructor for exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
GuiItemNotFoundException(String, Throwable) - Constructor for exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
GuiItemRef - Class in ur_rna.GUITester.GuiTools
GuiItemRef(Matcher) - Constructor for class ur_rna.GUITester.GuiTools.GuiItemRef
GuiItemRef(Component) - Constructor for class ur_rna.GUITester.GuiTools.GuiItemRef
  Returns a GuiItemRef that always matches a single known component.
GuiItemRef.ComponentMatcher - Class in ur_rna.GUITester.GuiTools
  Returns a Matcher that always matches a single known component.
GuiReference() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
GuiRelation() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
GuiRelative - Enum in ur_rna.GUITester.GuiTools
  Describes the relationship between two GUI Components.
GuiRelative() - Constructor for enum ur_rna.GUITester.GuiTools.GuiRelative
guiRobot() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
GuiRobot - Class in ur_rna.GUITester.GuiTools
GuiRobot(GuiAppManager) - Constructor for class ur_rna.GUITester.GuiTools.GuiRobot
GuiRobot.ModifierKey - Enum in ur_rna.GUITester.GuiTools
  These constants correspond to numbers used in abbot.Robot to set and test for modifier keys.
GUITesterStartup - Class in ur_rna.GUITester
  The main entry-point for the test application.
GUITesterStartup() - Constructor for class ur_rna.GUITester.GUITesterStartup
GUITesterStartup.AppOptions - Class in ur_rna.GUITester
GUITesterStartup.ScriptSource - Enum in ur_rna.GUITester
GuiTestScriptParser - Class in ur_rna.GUITester.ScriptParser
  Script Parser for GUI Test Framework
GuiTestScriptParser(InputStream) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Constructor with InputStream.
GuiTestScriptParser(InputStream, String) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Constructor with InputStream and supplied encoding
GuiTestScriptParser(Reader) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Constructor.
GuiTestScriptParser(GuiTestScriptParserTokenManager) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Constructor with generated Token Manager.
GuiTestScriptParser.JJCalls - Class in ur_rna.GUITester.ScriptParser
GuiTestScriptParser.LookaheadSuccess - Error in ur_rna.GUITester.ScriptParser
GuiTestScriptParserConstants - Interface in ur_rna.GUITester.ScriptParser
  Token literal values and constants.
GuiTestScriptParserTokenManager - Class in ur_rna.GUITester.ScriptParser
  Token Manager.
GuiTestScriptParserTokenManager(JavaCharStream) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Constructor.
GuiTestScriptParserTokenManager(JavaCharStream, int) - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Constructor.
GuiTestScriptParserTreeConstants - Interface in ur_rna.GUITester.ScriptParser
GuiWaitTime - Variable in class ur_rna.GUITester.GuiTools.GuiRobot

## H

hadError() - Method in class ur_rna.GUITester.ScriptRunner
hadError - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
hadError() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
hadErrors() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
handle(Object, T) - Method in interface ur_rna.Utilities.ActionHandler
handleBranchSlide - Variable in class ur_rna.StructureEditor.services.RnaDrawController
handled - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
handleEvent(T) - Method in interface ur_rna.Utilities.Listener
handleLoopResize - Variable in class ur_rna.StructureEditor.services.RnaDrawController
handleOffset - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
handleOffsetDir - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
handler - Variable in class ur_rna.RNAstructureUI.menus.RolloverListener
handler - Variable in class ur_rna.Utilities.EventSource.Manager.Subscriber
handleRecentControlValues(boolean, String, Iterable<JComponent>) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
handleRotate - Variable in class ur_rna.StructureEditor.services.RnaDrawController
handleSelectionChange() - Method in class ur_rna.StructureEditor.services.RnaDrawController
handleSettings(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
handleSettings(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
handleSettings(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
handleSettings(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
handleSettings(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
handleTextSelection(JTextPane) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
handleView(RnaScene, boolean) - Method in class ur_rna.StructureEditor.windows.DrawWindow
has_run - Variable in class ur_rna.Utilities.RunOnce
hasAlpha(Image) - Static method in class ur_rna.Utilities.swing.ImageUtil
  This method returns `true` if the specified image has the possibility to store transparent pixels.
hasAnyFlag(String...) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
  Returns true if any of the listed flags were found.
hasBonds() - Method in class ur_rna.StructureEditor.models.RnaScene
hasChanged() - Method in class ur_rna.Utilities.swing.TextDocListener
hasChildren() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
hasChildren() - Method in class ur_rna.Utilities.TreeNode
hasClickAction() - Method in class ur_rna.Utilities.swing.JActionLabel
  Returns true if some action is performed on click.
hasDir() - Method in class ur_rna.Utilities.PathTools.FileName
hasExt() - Method in class ur_rna.Utilities.PathTools.FileName
hasFlag(String) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
  Returns true if the specified flag was found.
hashCode() - Method in class ur_rna.StructureEditor.services.drawing.View2D
hashCode() - Method in class ur_rna.Utilities.geom.Matrix3D
  Returns a hash code value based on the data values in this object.
hashCode() - Method in class ur_rna.Utilities.Pair
hashCode() - Method in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
hashCode() - Method in class ur_rna.Utilities.Version
hasLocationInfo() - Method in exception ur_rna.Utilities.SyntaxErrorException
hasName() - Method in class ur_rna.Utilities.NamedArg
hasNext() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
hasNext() - Method in class ur_rna.Utilities.Filter.FilterIterator
hasNext() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
hasPairs - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Whether the current structure has pairs.
hasPseudoknots(CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackend
hasPseudoknots(long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HasPseudoknots(int) - Method in class ur_rna.RNAstructure.backend.structure
HasPseudoknots() - Method in class ur_rna.RNAstructure.backend.structure
hasPseudoKnots(RnaScene, boolean) - Static method in class ur_rna.StructureEditor.models.Motif
hasResource(String) - Method in class ur_rna.Utilities.ResourceLoader
  Determine whether the specified resource exists.
hasRun() - Method in interface ur_rna.Utilities.RunnableOnce
  Indicates whether `Runnable.run()` has been called.
hasRun() - Method in class ur_rna.Utilities.RunOnce
  Indicates whether `RunOnce.run()` has been called.
hasSubItems() - Method in class ur_rna.RNAstructureUI.menus.MenuList
hasSubItems() - Method in interface ur_rna.Utilities.swing.IMenuItem
hasSubItems(Component) - Static method in class ur_rna.Utilities.swing.Menus
headerFont - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
height - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
height - Variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
  Height of the page in mm
Helix - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
Helix(Nuc, int) - Constructor for class ur_rna.StructureEditor.models.Motif.Helix
helix - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
HELIX - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Helix(int, int, int, int, int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
helixCount() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
helixH3 - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
helixInvalid - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
helixPair - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
helixParsePatterns - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
helixSep - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
HELP_URL - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
HELP_URL - Static variable in class ur_rna.StructureEditor.AppActions
HelpMenu - Class in ur_rna.RNAstructureUI.menus
  A class that creates a "Help" menu.
HelpMenu() - Constructor for class ur_rna.RNAstructureUI.menus.HelpMenu
  Constructor.
HelpMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
HelpMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
HEX_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
HEX_DIGIT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
HEX_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
HEX_RADIX - Static variable in class ur_rna.Utilities.CharConstants
HEX_RADIX - Static variable in class ur_rna.Utilities.Constants
hexval(char) - Static method in class ur_rna.GUITester.ScriptParser.JavaCharStream
hideDashboard() - Method in class ur_rna.StructureEditor.MainFrame
hint - Variable in class ur_rna.StructureEditor.models.DrawSettings
HintColorDefault - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHint
HintColorReference - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHint
hintEmphasis - Variable in class ur_rna.StructureEditor.models.DrawSettings
HintLineDefault - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHint
HintLineThick - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHint
HintOp(RenderingHints.Key, Object) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
hints - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Current Rendering hints.
history - Variable in class ur_rna.StructureEditor.models.RnaScene
History<T> - Class in ur_rna.StructureEditor.services
  Stores the history of an arbitrary model for undo/redo
History() - Constructor for class ur_rna.StructureEditor.services.History
historyEvent - Variable in class ur_rna.StructureEditor.services.RnaDrawController
HistoryState - Class in ur_rna.StructureEditor.models
HistoryState(RnaSceneState, SceneUpdateInfo) - Constructor for class ur_rna.StructureEditor.models.HistoryState
historyUpdated() - Method in class ur_rna.StructureEditor.services.RnaDrawController
historyUpdated() - Method in interface ur_rna.StructureEditor.services.SceneController
HistoryUpdateEvent - Class in ur_rna.StructureEditor.models
HistoryUpdateEvent(Object, boolean, HistoryState) - Constructor for class ur_rna.StructureEditor.models.HistoryUpdateEvent
hit(Rectangle, Shape, boolean) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
hitDistance - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
hitDistanceSq - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
hitTest(Point2D) - Method in interface ur_rna.StructureEditor.models.IScreenObject
  Determine if the object contains the given point (in screen coordinates)
hitTest(Rectangle) - Method in interface ur_rna.StructureEditor.models.IScreenObject
  Determine if the object intersects the given rectangle (in screen coordinates)
hitTest(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
  Determine if the object contains the given point (in screen coordinates)
hitTest(Rectangle) - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
  Determine if the object intersects the given rectangle (in screen coordinates)
hitTest(Iterable<IScreenObject>, Point2D, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
hitTest(Iterable<IScreenObject>, Rectangle, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
hitTest(Point2D) - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
hitTest(Rectangle) - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
HoneyDew - Static variable in class ur_rna.Utilities.Colors
HOOK - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
hot - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
HotPink - Static variable in class ur_rna.Utilities.Colors
hoverNuc - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
htmlCenter(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Converts a simple text message to an html-formatted message by prepending `<html><center>` and escaping all html special characters within the message.
HTMLCheckBox - Class in ur_rna.RNAstructureUI.ui
  A class that creates a check box whose text is HTML.
HTMLCheckBox(String, boolean) - Constructor for class ur_rna.RNAstructureUI.ui.HTMLCheckBox
  Constructor.
HybridRNA - Class in ur_rna.RNAstructure.backend
HybridRNA(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA(String, String, boolean) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA(String, String) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA(String, int, String, int, boolean) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA(String, int, String, int) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA(String, int, String, int, String) - Constructor for class ur_rna.RNAstructure.backend.HybridRNA
HybridRNA_AccessFold__SWIG_0(long, HybridRNA, double, float, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_AccessFold__SWIG_1(long, HybridRNA, double, float, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_AccessFold__SWIG_2(long, HybridRNA, double, float, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_AccessFold__SWIG_3(long, HybridRNA, double, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_AccessFold__SWIG_4(long, HybridRNA, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_AccessFold__SWIG_5(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_0(long, HybridRNA, float, int, int, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_1(long, HybridRNA, float, int, int, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_2(long, HybridRNA, float, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_3(long, HybridRNA, float, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_4(long, HybridRNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldBimolecular__SWIG_5(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldDuplex__SWIG_0(long, HybridRNA, float, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldDuplex__SWIG_1(long, HybridRNA, float, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldDuplex__SWIG_2(long, HybridRNA, float, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldDuplex__SWIG_3(long, HybridRNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_FoldDuplex__SWIG_4(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_GetErrorCode(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_GetForbidIntramolecular(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_GetMyErrorMessage(long, HybridRNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_GetRNA1(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_GetRNA2(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_PartitionFunctionBimolecular__SWIG_0(long, HybridRNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_PartitionFunctionBimolecular__SWIG_1(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_SetForbidIntramolecular(long, HybridRNA, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_SetProgress(long, HybridRNA, long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_StopProgress(long, HybridRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
HybridRNA_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI

## I

i - Variable in class ur_rna.StructureEditor.models.Motif.IntervalStack
  Current values
ICanvas - Interface in ur_rna.StructureEditor.services.drawing
  Represents a swing component (e.g.
iceil(double) - Static method in class ur_rna.StructureEditor.services.drawing.NucLayout
icon - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
icon() - Method in class ur_rna.Utilities.swing.UiAction
IContainer - Interface in ur_rna.Utilities.swing
id - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
id - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
IDENTIFIER - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
identifierMatcher - Static variable in class ur_rna.Utilities.SimpleDataSerializer
identifyPseudoknots() - Method in class ur_rna.StructureEditor.models.RnaScene
identifyPseudoKnotsBackend(RnaScene) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
identity - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher
identity(Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
Identity(Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
IDENTITY - Static variable in class ur_rna.StructureEditor.services.drawing.View2D
IDENTITY_VIEW - Variable in class ur_rna.StructureEditor.ui.DrawPanel
ignoreChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
ignoreFlagCase - Variable in class ur_rna.Utilities.CommandLineParser
IgnoreStylesUndoManager() - Constructor for class ur_rna.StructureEditor.windows.NewFileWindow.IgnoreStylesUndoManager
image - Variable in class ur_rna.GUITester.ScriptParser.Token
  The string image of the token.
ImageDialog - Class in ur_rna.RNAstructureUI.drawing.dialogs
  A printable and zoomable dialog that holds drawn images.
ImageDialog(String) - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Constructor.
ImageDialog.PrintMenu - Class in ur_rna.RNAstructureUI.drawing.dialogs
  An inner class which creates a print menu.
ImageDialog.ZoomDialog - Class in ur_rna.RNAstructureUI.drawing.dialogs
  An inner class which creates a dialog that zooms a structure.
imageDialogs - Variable in class ur_rna.RNAstructureUI.windows.MultiWindow
  The list of drawing windows shown after the calculation is done.
ImageGrabber - Class in ur_rna.RNAstructureUI.utilities
  A class that creates images in various contexts for the RNAstructure GUI.
ImageGrabber() - Constructor for class ur_rna.RNAstructureUI.utilities.ImageGrabber
ImageUtil - Class in ur_rna.Utilities.swing
  Image Utilities
ImageUtil() - Constructor for class ur_rna.Utilities.swing.ImageUtil
IMenuItem - Interface in ur_rna.Utilities.swing
  Utility class for dealing with JMenuItem
IMergeItem - Interface in ur_rna.Utilities.swing
  Provides an interface for a UI component that be included in a hierarchical list.
IMergeItem.Proxy - Class in ur_rna.Utilities.swing
img - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
imgSizeX - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The maximum X bound of the image.
imgSizeY - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The maximum Y bound of the image.
IMotif - Interface in ur_rna.StructureEditor.models
  Represents a structural element (motif) of an RNA structure -- e.g.
importance - Variable in enum ur_rna.Utilities.Verbosity
inBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
includeDirs - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
includeFolders() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
includes(FileType) - Method in enum ur_rna.StructureEditor.FileType
INCR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
indent - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
index - Variable in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel.ButtonListener
index - Variable in class ur_rna.StructureEditor.models.Strand
indexInScene - Variable in class ur_rna.StructureEditor.models.Nuc
  Stores the index of the nucleotide within the full scene.
indexInScene(int[]) - Method in class ur_rna.StructureEditor.models.Nuc
  Gets the overall index of this nucleotide, given the starting indices for each strand as specified in strandIndexes For example: strandIndexes = int[] { 1, 20, 100 } for a Nuc with index=0 in the first strand, indexInScene would return 1.
indexInScene() - Method in class ur_rna.StructureEditor.models.Nuc
  Gets the overall index of this nucleotide, including all nucleotides in previous strands.
indexInStrand() - Method in class ur_rna.StructureEditor.models.Nuc
indexOf(Object) - Method in class ur_rna.StructureEditor.models.StrandList
indexOf(String) - Method in class ur_rna.StructureEditor.services.RecentFileList
indexOf(T[], Predicate<T>) - Static method in class ur_rna.Utilities.ObjTools
indexOf(T[], T) - Static method in class ur_rna.Utilities.ObjTools
indexOf(String[], String) - Static method in class ur_rna.Utilities.ObjTools
indexOf(String[], String, boolean) - Static method in class ur_rna.Utilities.ObjTools
indexOf(String) - Method in class ur_rna.Utilities.StringBuilderEx
indexOf(String, int) - Method in class ur_rna.Utilities.StringBuilderEx
IndianRed - Static variable in class ur_rna.Utilities.Colors
Indigo - Static variable in class ur_rna.Utilities.Colors
info - Variable in class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
info(String) - Method in class ur_rna.Utilities.AppLog
info(String, Object...) - Method in class ur_rna.Utilities.AppLog
info - Variable in class ur_rna.Utilities.EventArgs.InfoBagEventArgs
INFO - Static variable in class ur_rna.Utilities.swing.Dialogs
InfoBagEventArgs() - Constructor for class ur_rna.Utilities.EventArgs.InfoBagEventArgs
InfoBagEventArgs(String, Object) - Constructor for class ur_rna.Utilities.EventArgs.InfoBagEventArgs
InfoBagEventArgs(String, Object, String, Object) - Constructor for class ur_rna.Utilities.EventArgs.InfoBagEventArgs
InfoBagEventArgs(String, Object, String, Object, String, Object) - Constructor for class ur_rna.Utilities.EventArgs.InfoBagEventArgs
InfoBagEventArgs(Object...) - Constructor for class ur_rna.Utilities.EventArgs.InfoBagEventArgs
infoLabel - Variable in class ur_rna.RNAstructureUI.AppMainFrame
infoLabel - Variable in class ur_rna.StructureEditor.MainFrame
InfoLabelConsumer - Variable in class ur_rna.RNAstructureUI.AppMainFrame
init(List<Bond>, boolean) - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
initDetails(Object, Object) - Method in exception ur_rna.Utilities.KeyAlreadyExistsException
initDocRoot() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
initErrorCode(int) - Method in exception ur_rna.RNAstructure.RnaBackendException
initFile(String) - Method in exception ur_rna.RNAstructure.RnaBackendException
initFocus() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
initGroup(Element) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
initial - Variable in class ur_rna.RNAstructureUI.ui.NumberField
  The initial default value of the field.
Initial - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
initInts() - Method in class ur_rna.RNAstructure.backend.RNA
initItem(JMenuItem, String, String, String, KeyStroke) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Perform initial setup of the JMenuItem
InitOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.InitOp
inlineLists - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
inlineMaps - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
inner - Variable in class ur_rna.Utilities.RunOnce
input - Variable in class ur_rna.GUITester.Script
input(String, String, String) - Static method in class ur_rna.Utilities.swing.Dialogs
input_stream - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
InputAdapter - Class in ur_rna.Utilities.swing
  Funnels 10 input events (from MouseListener, MouseMotionListener, and KeyListener) into two events -- one for key input and one for mouse input.
InputAdapter() - Constructor for class ur_rna.Utilities.swing.InputAdapter
InputAdapter.InputType - Enum in ur_rna.Utilities.swing
InputAdapter.Keyboard - Class in ur_rna.Utilities.swing
InputAdapter.Mouse - Class in ur_rna.Utilities.swing
inputFile(boolean) - Method in class ur_rna.RNAstructureUI.ui.FileField
  Indicate whether or not this field is used to accept an input file (as opposed to an output file)
inputFile() - Method in class ur_rna.RNAstructureUI.ui.FileField
inputFile(String) - Method in class ur_rna.RNAstructureUI.ui.FileField
inputStream - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
InputType() - Constructor for enum ur_rna.Utilities.swing.InputAdapter.InputType
inSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
insert(int, char[], int, int) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, Object) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, String) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, char[]) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, CharSequence) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, CharSequence, int, int) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, boolean) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, char) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, long) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, float) - Method in class ur_rna.Utilities.StringBuilderEx
insert(int, double) - Method in class ur_rna.Utilities.StringBuilderEx
insertBases(String, Nuc, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
  Insert new bases before or after the specified nucleotide.
insertBases() - Method in class ur_rna.StructureEditor.windows.DrawWindow
InsertBasesDialog - Class in ur_rna.StructureEditor.windows
  A dialog for the user to enter bases to insert into a drawing.
InsertBasesDialog() - Constructor for class ur_rna.StructureEditor.windows.InsertBasesDialog
insertMergeGap() - Method in class ur_rna.Utilities.swing.MergeMenu
  Increments by 10 the current mergePos at which sub-items will be added by default.
insertMergeGap(int) - Method in class ur_rna.Utilities.swing.MergeMenu
  Increments (by gap) the current mergePos at which sub-items will be added by default.
insertUpdate(DocumentEvent) - Method in interface ur_rna.Utilities.swing.SimpleDocumentListener
insertUpdate(DocumentEvent) - Method in class ur_rna.Utilities.swing.TextDocListener
instance - Static variable in class ur_rna.StructureEditor.Program
Instruction() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
INT_SUFFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
INTEGER_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
IntegerField(String, Integer) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
  Unbounded Constructor.
IntegerField(String, Integer, Integer) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
  Minimum Bounds Constructor.
IntegerField(String, Integer, Integer, Integer) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
  Minimum and Maximum Bounds Constructor.
InterMolecularBreakChar - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
InterMolecularBreakLength - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
InterMolecularBreakStr - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
internalFrameActivated(InternalFrameEvent) - Method in class ur_rna.StructureEditor.MainFrame
  Invoked when a child frame is activated.
internalFrameActivated(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame is activated.
internalFrameClosed(InternalFrameEvent) - Method in class ur_rna.StructureEditor.MainFrame
  Invoked when a child frame has been closed.
internalFrameClosed(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame has been closed.
internalFrameClosing(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame is in the process of being closed.
internalFrameDeactivated(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame is de-activated.
internalFrameDeiconified(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame is de-iconified.
internalFrameIconified(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when an internal frame is iconified.
internalFrameOpened(InternalFrameEvent) - Method in class ur_rna.Utilities.swing.MdiParentFrame
  Invoked when a internal frame has been opened.
InternalWindow - Class in ur_rna.RNAstructureUI.windows
  The base class for all RNAstructure GUI dialogs and windows.
InternalWindow() - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow
  Constructor.
InternalWindow.CommandInfo - Class in ur_rna.RNAstructureUI.windows
  An immutable object that represents a command invoked by some part of the program, e.g.
intersection(Shape, Shape) - Static method in class ur_rna.Utilities.geom.ShapeUtil
IntervalStack() - Constructor for class ur_rna.StructureEditor.models.Motif.IntervalStack
IntervalStack(int) - Constructor for class ur_rna.StructureEditor.models.Motif.IntervalStack
IntEventArgs(int) - Constructor for class ur_rna.Utilities.EventArgs.IntEventArgs
intValue() - Method in class ur_rna.Utilities.NamedArg
INucGroup - Interface in ur_rna.StructureEditor.models
  Represents any grouping (collection) of nucleotides.
INVALID_LEXICAL_STATE - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  Tried to change to an invalid lexical state.
invalidSoundClip - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
inverse(Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
inverse() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
Inverse(Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
inverse() - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
inverseTransform(Shape, AffineTransform) - Static method in class ur_rna.Utilities.geom.ShapeUtil
invert(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the matrix inverse of the passed matrix m1.
invert() - Method in class ur_rna.Utilities.geom.Matrix3D
  Inverts this matrix in place.
invertGeneral(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  General invert routine.
invoke(Consumer<TSubscriber>) - Method in class ur_rna.Utilities.EventSource
invoke() - Method in class ur_rna.Utilities.EventSource.NoArg
invoke(TArg) - Method in class ur_rna.Utilities.EventSource.OneArg
invoke(TArg1, TArg2) - Method in class ur_rna.Utilities.EventSource.TwoArgs
invoke(Object) - Method in class ur_rna.Utilities.swing.UiAction
invoke(Object, String) - Method in class ur_rna.Utilities.swing.UiAction
invokeCommand(String) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
invokeCommand(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
invokeCommand(String, Object) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
invokeScrollToComponent(Component) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
isActiveFrame() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
IsAlphabetLoaded() - Method in class ur_rna.RNAstructure.backend.structure
IsAlphabetRead() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
isAncestor(Component, Container) - Static method in class ur_rna.Utilities.swing.Components
  Returns true if the component c is equal to possibleAncestor or is a child or descendant of possibleAncestor.
isAnySet(int, int) - Static method in class ur_rna.Utilities.ObjTools
isAppend() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
isAppend() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
isBold - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
isCancelable() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
isCancelable() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
isCanceled - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
isCanceled() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
isCanceled() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
isCanceled() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
isCanceled() - Method in class ur_rna.Utilities.swing.WaitDialog
isCancelVisible() - Method in class ur_rna.Utilities.swing.WaitDialog
isClockwise() - Method in class ur_rna.StructureEditor.models.Motif.Helix
isClosed() - Method in class ur_rna.Utilities.ExtendedBufferedReader
isCloseOnCancel() - Method in class ur_rna.Utilities.swing.WaitDialog
IScreenObject - Interface in ur_rna.StructureEditor.models
  Represents a model-space object that can be
isCurDirSet - Variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
isCurDirSet - Variable in class ur_rna.Utilities.swing.FileDialog
isDebugEnabled() - Method in class ur_rna.Utilities.AppLog
  Returns true if Debug log messages are enabled, either via the current Verbosity setting or by force-enabling them specifically (e.g.
isDefault() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
isDir(String) - Static method in class ur_rna.Utilities.PathTools
isDisposed() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
isDone() - Method in interface ur_rna.StructureEditor.services.fileIO.RnaFileIO.AsyncTask
isDone() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
isDotBracket(String) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
isEmpty() - Method in class ur_rna.RNAstructure.backend.CDblVector
isEmpty() - Method in class ur_rna.RNAstructure.backend.CIntVector
isEmpty() - Method in class ur_rna.StructureEditor.models.NucStyle
isEmpty() - Method in class ur_rna.StructureEditor.models.StrandList
isEmpty(String) - Static method in class ur_rna.Utilities.Strings
  Returns true if the string is null or empty ("").
isEmpty() - Method in class ur_rna.Utilities.Version
isEnabled() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
isEnabled() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
isEnabled(Verbosity) - Method in class ur_rna.Utilities.AppLog
  Returns true if the specified log-level is enabled, either via the current Verbosity setting or by force-enabling the specific log-level (e.g.
isEnabled(int) - Method in class ur_rna.Utilities.AppLog
  Returns true if the specified log-level is enabled, either via the current Verbosity setting or by force-enabling the specific log-level (e.g.
isEnabledSpecial(Verbosity) - Method in class ur_rna.Utilities.AppLog
  Returns true if the specified log-level has been force-enabled (e.g.
isError() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Get whether this panel ran into an error while being built.
isError() - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
  Get whether any fields are empty; an empty field is an error.
isError() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
  Get whether this window encountered an error.
isExampleFile(File) - Static method in class ur_rna.RNAstructureUI.RNAstructure
isFile(String) - Static method in class ur_rna.Utilities.PathTools
isFill() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
isFirst() - Method in class ur_rna.StructureEditor.models.Bond
isFixed - Static variable in class ur_rna.Utilities.ConsoleTools
isFullMotifSelected() - Method in class ur_rna.StructureEditor.services.RnaDrawController
isHandled() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
isHelixBond(Bond) - Static method in class ur_rna.StructureEditor.models.Motif.Helix
isHybrid() - Method in class ur_rna.StructureEditor.models.Bond
  Whether this bond represents an inter-molecular bond (i.e.
isHybrid() - Method in class ur_rna.StructureEditor.models.Motif.Branch
isHybrid() - Method in class ur_rna.StructureEditor.models.Motif.Helix
  Whether or not the helix contains inter-molecular pairs (i.e.
isIgnoredSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
isIndeterminate() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
isInModelBounds(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
isInModelBounds(Shape) - Method in class ur_rna.StructureEditor.services.drawing.View2D
isInputFile - Variable in class ur_rna.RNAstructureUI.ui.FileField
isInputFile() - Method in class ur_rna.RNAstructureUI.ui.FileField
isInputWindow - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  A boolean that tells whether this window is an input window or not.
isInScreenBounds(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
isInScreenBounds(Shape) - Method in class ur_rna.StructureEditor.services.drawing.View2D
isInsertAfter() - Method in class ur_rna.StructureEditor.windows.InsertBasesDialog
isInterStrandLinker(char) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
isInvalidSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
isLast() - Method in class ur_rna.StructureEditor.models.Bond
isListOrMap(Object) - Method in class ur_rna.Utilities.SimpleDataSerializer
isLogicalFontFamily(String) - Static method in class ur_rna.Utilities.swing.FontUtil
isLowerBranch - Variable in class ur_rna.StructureEditor.models.Motif.Branch
isMac() - Static method in class ur_rna.Utilities.OSInfo
  Get whether the current OS is a Mac.
isMatch(String) - Method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
isModelCoords - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint
isModified() - Method in class ur_rna.Utilities.prefs.FilePreferences
isNix() - Static method in class ur_rna.Utilities.OSInfo
IsNuc(int, char) - Method in class ur_rna.RNAstructure.backend.structure
IsNuc(int, char, datatable) - Method in class ur_rna.RNAstructure.backend.structure
ISO8601 - Static variable in class ur_rna.Utilities.DateHelper
ISO8601Format - Static variable in class ur_rna.Utilities.DateHelper
isOrdered() - Method in class ur_rna.StructureEditor.models.Bond
  Returns true if the nucleotides are in canonical order.
isOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
isOutputFile - Variable in class ur_rna.RNAstructureUI.ui.FileField
isOutputFile() - Method in class ur_rna.RNAstructureUI.ui.FileField
isPaired() - Method in class ur_rna.StructureEditor.models.Nuc
isPaired(boolean) - Method in class ur_rna.StructureEditor.models.Nuc
isParallel() - Method in class ur_rna.StructureEditor.models.Motif.Branch
isParallel() - Method in class ur_rna.StructureEditor.models.Motif.Helix
isPerformingDrag - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
isPlaying() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
isProgressIndeterminate() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
isProgressVisible() - Method in class ur_rna.Utilities.swing.WaitDialog
isRNA - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
  A boolean, true if the calculation handles RNA, false if not.
isRNA - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
isSegment() - Method in class ur_rna.GUITester.Script
isSelected(int, int) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
  Returns true if the selection falls inside the element and NOT beyond it.
isSelected(int) - Method in class ur_rna.Utilities.swing.ButtonGroupList
isSelected(Action) - Static method in class ur_rna.Utilities.swing.UiAction
isSet(int, int) - Static method in class ur_rna.Utilities.ObjTools
isShowing() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
isStarted() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
isStarted() - Method in class ur_rna.Utilities.StopWatch
isStructureError(NewFileWindow.StructItem) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
isSubTypeOf(FileType...) - Method in enum ur_rna.StructureEditor.FileType
isTaskRunning() - Method in class ur_rna.StructureEditor.windows.DrawWindow
IsThermoDataLoaded() - Method in class ur_rna.RNAstructure.backend.structure
isTraceEnabled() - Method in class ur_rna.Utilities.AppLog
  Returns true if Trace log messages are enabled, either via the current Verbosity setting or by force-enabling them specifically (e.g.
isTruePair() - Method in class ur_rna.StructureEditor.models.Bond
  Returns true for any bond that is not a PseudoKnot bond or a Prohibited-Constraint Bond.
isUnpairedSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
isUnspecifiedSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
isUpdating() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Returns true when this DragHandle is performing updates in response to being dragged.
isUserActionInProgress() - Method in class ur_rna.StructureEditor.services.RnaDrawController
isValid() - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
isValid() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
isValid() - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
isValid() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
isValid() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
isVersionCompatible(Version, Version) - Static method in class ur_rna.Utilities.Version
isVersionCompatible(String, String) - Static method in class ur_rna.Utilities.Version
isWhiteSpace(String) - Static method in class ur_rna.Utilities.Strings
  Returns true if the string is null, empty or is composed entirely of whitespace (as determined by Character.is (e.g.
isWin() - Static method in class ur_rna.Utilities.OSInfo
item1 - Variable in class ur_rna.Utilities.Tuple.Pair
item1 - Variable in class ur_rna.Utilities.Tuple.Quad
item1 - Variable in class ur_rna.Utilities.Tuple.Singlet
item1 - Variable in class ur_rna.Utilities.Tuple.Triplet
item2 - Variable in class ur_rna.Utilities.Tuple.Pair
item2 - Variable in class ur_rna.Utilities.Tuple.Quad
item2 - Variable in class ur_rna.Utilities.Tuple.Triplet
item3 - Variable in class ur_rna.Utilities.Tuple.Quad
item3 - Variable in class ur_rna.Utilities.Tuple.Triplet
item4 - Variable in class ur_rna.Utilities.Tuple.Quad
itemSelected(ItemEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
itemsEqual(Tuple.Pair<T1, T2>) - Method in class ur_rna.Utilities.Tuple.Pair
itemsEqual(Tuple.Quad<T1, T2, T3, T4>) - Method in class ur_rna.Utilities.Tuple.Quad
itemsEqual(Tuple.Triplet<T1, T2, T3>) - Method in class ur_rna.Utilities.Tuple.Triplet
itemType - Variable in class ur_rna.GUITester.ScriptParser.ASTGuiSearchCriteria
ITERATING - Static variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
ITERATING - Static variable in class ur_rna.Utilities.Filter.FilterIterator
iterations - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
iterator() - Method in interface ur_rna.StructureEditor.models.INucGroup
  Returns an iterator over all Nucletotides in the group.
iterator() - Method in class ur_rna.StructureEditor.models.Strand
iterator() - Method in class ur_rna.StructureEditor.services.RecentFileList
iterator - Variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
iterator - Variable in class ur_rna.Utilities.Filter.FilterIterator
Ivory - Static variable in class ur_rna.Utilities.Colors

## J

j - Variable in class ur_rna.StructureEditor.models.Motif.IntervalStack
  Current values
JActionLabel - Class in ur_rna.Utilities.swing
  A label that reacts to clicks by calling `ActionListener.actionPerformed(ActionEvent)` or `ActionListener.actionPerformed(ActionEvent)` with a custom actionCommand.
JActionLabel(Icon) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel(String) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel(String, String) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel(Action) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel(String, Icon) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel(String, Icon, int) - Constructor for class ur_rna.Utilities.swing.JActionLabel
JActionLabel() - Constructor for class ur_rna.Utilities.swing.JActionLabel
JavaCharStream - Class in ur_rna.GUITester.ScriptParser
  An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (with java-like unicode escape processing).
JavaCharStream(Reader, int, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(Reader, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(Reader) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream, String, int, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream, int, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream, String, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream, int, int) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream, String) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JavaCharStream(InputStream) - Constructor for class ur_rna.GUITester.ScriptParser.JavaCharStream
  Constructor.
JFlatButton - Class in ur_rna.Utilities.swing
  A button that lacks the typical boarder and styling of a button.
JFlatButton(Icon) - Constructor for class ur_rna.Utilities.swing.JFlatButton
JFlatButton(String) - Constructor for class ur_rna.Utilities.swing.JFlatButton
JFlatButton(Action) - Constructor for class ur_rna.Utilities.swing.JFlatButton
JFlatButton(String, Icon) - Constructor for class ur_rna.Utilities.swing.JFlatButton
JFlatButton() - Constructor for class ur_rna.Utilities.swing.JFlatButton
jj_2_1(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_2_2(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_2_3(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_2_4(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_2_rtns - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3_1() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3_2() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3_3() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3_4() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3R_10() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3R_6() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3R_7() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3R_8() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_3R_9() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_add_error_token(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_consume_token(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_endpos - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_expentries - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_expentry - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_gc - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_gen - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_input_stream - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_kind - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1 - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_0 - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_1 - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_2 - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_init_0() - Static method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_init_1() - Static method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_la1_init_2() - Static method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_lastpos - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_lasttokens - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_ls - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_nt - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Next token.
jj_ntk - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_ntk_f() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_rescan - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_rescan_token() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_save(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_scan_token(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jj_scanpos - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
jjAddStates(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjbitVec0 - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjbitVec2 - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
JJCalls() - Constructor for class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
jjCanMove_0(int, int, int, long, long) - Static method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjCheckNAdd(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjCheckNAddStates(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjCheckNAddTwoStates(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjFillToken() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjmatchedKind - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjmatchedPos - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveNfa_0(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveStringLiteralDfa0_0() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveStringLiteralDfa1_0(long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveStringLiteralDfa2_0(long, long, long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveStringLiteralDfa3_0(long, long, long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjMoveStringLiteralDfa4_0(long, long, long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjnewStateCnt - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjnextStates - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjround - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjrounds - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjStartNfa_0(int, long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjStartNfaWithStates_0(int, int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjstateSet - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjStopAtPos(int, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjStopStringLiteralDfa_0(int, long, long) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjstrLiteralImages - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Token literal values.
JJTACTION - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
jjtAddChild(Node, int) - Method in interface ur_rna.GUITester.ScriptParser.Node
  This method tells the node to add its argument to the node's list of children.
jjtAddChild(Node, int) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
JJTASSIGNMENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
jjtClose() - Method in interface ur_rna.GUITester.ScriptParser.Node
  This method is called after all the child nodes have been added.
jjtClose() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtGetChild(int) - Method in interface ur_rna.GUITester.ScriptParser.Node
  This method returns a child node.
jjtGetChild(int) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtGetNumChildren() - Method in interface ur_rna.GUITester.ScriptParser.Node
  Return the number of children the node has.
jjtGetNumChildren() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtGetParent() - Method in interface ur_rna.GUITester.ScriptParser.Node
jjtGetParent() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtGetValue() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
JJTGUIREFERENCE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
JJTGUISEARCHCRITERIA - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
JJTGuiTestScriptParserState - Class in ur_rna.GUITester.ScriptParser
JJTGuiTestScriptParserState() - Constructor for class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
JJTLITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
JJTNAMEDARGUMENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
jjtNodeName - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
jjtOpen() - Method in interface ur_rna.GUITester.ScriptParser.Node
  This method is called after the node has been made the current node.
jjtOpen() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtoSkip - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjtoSpecial - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjtoToken - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
jjtree - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
JJTROOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
jjtSetParent(Node) - Method in interface ur_rna.GUITester.ScriptParser.Node
  This pair of methods are used to inform the node of its parent.
jjtSetParent(Node) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
jjtSetValue(Object) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
JJTVARREF - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
JJTVOID - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserTreeConstants
JniLoader - Class in ur_rna.Utilities
  Loads a Native library or returns helpful error information if unsuccessful.
JniLoader(String) - Constructor for class ur_rna.Utilities.JniLoader
JniLoader(String, String...) - Constructor for class ur_rna.Utilities.JniLoader
JniLoader(String, Supplier<String>, String, String...) - Constructor for class ur_rna.Utilities.JniLoader
JniLoader.NativeLibLoadError - Exception in ur_rna.Utilities
job - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The job that prints out this panel
join(String, double...) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
join(String, float...) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
join(String, Iterable<T>, Function<? super T, String>) - Static method in class ur_rna.Utilities.Strings
join(String, Iterable<T>) - Static method in class ur_rna.Utilities.Strings
join(String, T[]) - Static method in class ur_rna.Utilities.Strings
joinArgs(Object[], boolean) - Method in class ur_rna.GUITester.ScriptActions
joinSelectionStrands() - Method in class ur_rna.StructureEditor.services.RnaDrawController
joinStrands(Strand, Strand) - Method in class ur_rna.StructureEditor.models.RnaScene
joinStrands(Strand, Strand) - Method in class ur_rna.StructureEditor.models.StrandList
JSON - Static variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
JWrapTextPane() - Constructor for class ur_rna.StructureEditor.windows.NewFileWindow.JWrapTextPane

## K

keepToolBarItems - Variable in class ur_rna.RNAstructureUI.AppMainFrame
key - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
key - Variable in class ur_rna.Utilities.Pair
KeyAlreadyExistsException - Exception in ur_rna.Utilities
KeyAlreadyExistsException() - Constructor for exception ur_rna.Utilities.KeyAlreadyExistsException
KeyAlreadyExistsException(String) - Constructor for exception ur_rna.Utilities.KeyAlreadyExistsException
KeyAlreadyExistsException(Throwable) - Constructor for exception ur_rna.Utilities.KeyAlreadyExistsException
KeyAlreadyExistsException(String, Throwable) - Constructor for exception ur_rna.Utilities.KeyAlreadyExistsException
KeyBindFocus(int) - Constructor for enum ur_rna.Utilities.swing.ActionHelper.KeyBindFocus
Keyboard() - Constructor for class ur_rna.Utilities.swing.InputAdapter.Keyboard
keyClick(int) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
KeyMnemonic - Class in ur_rna.Utilities.swing
KeyMnemonic() - Constructor for class ur_rna.Utilities.swing.KeyMnemonic
keyPressed(KeyEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Keyboard
  Invoked when a key has been pressed.
keyReleased(KeyEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Keyboard
  Invoked when a key has been released.
keysSpi() - Method in class ur_rna.Utilities.prefs.FilePreferences
keyStroke() - Method in class ur_rna.Utilities.swing.UiAction
keyTyped(KeyEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Keyboard
  Invoked when a key has been typed.
Khaki - Static variable in class ur_rna.Utilities.Colors
kind - Variable in class ur_rna.GUITester.ScriptParser.Token
  An integer that describes the kind of this token.
knownDirs - Static variable in class ur_rna.RNAstructureUI.windows.ModuleWindow

## L

l3 - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
l5 - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
label - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
label - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The main label that describes the panel.
label - Variable in class ur_rna.RNAstructureUI.ui.ProgressPanel
label - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
last - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
last() - Method in class ur_rna.StructureEditor.models.Motif.Helix
last() - Method in class ur_rna.StructureEditor.models.Strand
last() - Method in class ur_rna.StructureEditor.models.StrandList
last() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
LAST_ASCII - Static variable in class ur_rna.Utilities.CharConstants
lastChosenFilter - Static variable in class ur_rna.Utilities.swing.FileDialog
lastFound - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef
lastIndexOf(Object) - Method in class ur_rna.StructureEditor.models.StrandList
lastIndexOf(String) - Method in class ur_rna.Utilities.StringBuilderEx
lastIndexOf(String, int) - Method in class ur_rna.Utilities.StringBuilderEx
lastKind() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the kind of the last consumed token.
lastKind(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the kind of the token consumed pos steps before last.
lastOutFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lastOutFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lastOutFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lastOutFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lastOutFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lastPair() - Method in class ur_rna.StructureEditor.models.Motif.Helix
lastProbDataPath - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lastReadChar - Variable in class ur_rna.Utilities.ExtendedBufferedReader
  The last char returned from read() (or an overload) Usage: If lastReadChar is CR and a LF is encountered next, the currentLine should NOT be incremented.
lastSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lastSeqFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lastSeqFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lastSeqFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lastSeqFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lastStream - Static variable in class ur_rna.Utilities.ConsoleTools
lastText() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the text (image) of the last consumed token.
lastText(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the text (image) of the token consumed pos steps before last.
lastToken() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the last consumed token.
lastToken(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Return the token consumed pos steps before last.
lastUpdate - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
lastValueDataPath - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
launchDrawing(String, FileType, String, FileType, int) - Static method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
launchSubjectApp(String[]) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
Lavender - Static variable in class ur_rna.Utilities.Colors
LavenderBlush - Static variable in class ur_rna.Utilities.Colors
LawnGreen - Static variable in class ur_rna.Utilities.Colors
layout - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
  The layout for this window.
Layout - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
layout - Variable in class ur_rna.StructureEditor.windows.DrawWindow
layoutComponent(Component) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
layoutUpdated() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Called when any nucleotides in the scene changed position.
layoutUpdated(SceneUpdateInfo) - Method in class ur_rna.StructureEditor.services.RnaDrawController
layoutUpdated(SceneUpdateInfo, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
layoutUpdated(SceneUpdateInfo) - Method in interface ur_rna.StructureEditor.services.SceneController
layoutUpdated(SceneUpdateInfo, boolean) - Method in interface ur_rna.StructureEditor.services.SceneController
lblBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
lblBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lblColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lblColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
lblColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
lblCopyright - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblFeedback - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblFile - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
lblHelp - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
lblHelp - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblLocation - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
lblLogo - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
lblLogo - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblMessage - Variable in class ur_rna.Utilities.swing.WaitDialog
lblOptionWarning - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lblOptionWarning - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
lblOptionWarning - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lblOptionWarning - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lblProbColorHeader - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lblProgramTitle - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblProgressPercent - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lblProgressPercent - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
lblProgressPercent - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lblProgressPercent - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lblPrompt - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
lblResults - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
lblSingleColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lblTaskProgress - Variable in class ur_rna.StructureEditor.windows.DrawWindow
lblTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lblTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
lblTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lblTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lblTaskStatus - Variable in class ur_rna.StructureEditor.windows.DrawWindow
lblToolDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
lblToolDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
lblToolDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
lblToolDescription - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
lblValue - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
lblValueColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lblValueColorHeader - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
lblVersion - Variable in class ur_rna.StructureEditor.windows.AboutWindow
lblWebsite - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
lblWebsite - Variable in class ur_rna.StructureEditor.windows.AboutWindow
LBRACE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
LBRACKET - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
LE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
LEDGER - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
left(Nuc) - Method in class ur_rna.StructureEditor.models.Bond
leftCodeQuote - Static variable in exception ur_rna.Utilities.SyntaxErrorException
  `SyntaxErrorException.leftCodeQuote` and `SyntaxErrorException.rightCodeQuote` are the quote characters used to distinguish the offending segment of code in the error message.
LEGAL - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
legendGrid - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The panel that contains the legend grid.
LemonChiffon - Static variable in class ur_rna.Utilities.Colors
len - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
length() - Method in class ur_rna.Utilities.geom.Vec2D
  The magnitude (aka Euclidean length) of the vector.
length() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
length() - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the length (character count).
lengthSqr() - Method in class ur_rna.Utilities.geom.Vec2D
LETTER - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
LETTER - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
level - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
LEXICAL_ERROR - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  Lexical error occurred.
lexStateNames - Static variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Lexer state names.
LF - Static variable in class ur_rna.Utilities.CharConstants
LF - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
LHS - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
libraryTitle - Variable in class ur_rna.Utilities.JniLoader
LightBlue - Static variable in class ur_rna.Utilities.Colors
LightCoral - Static variable in class ur_rna.Utilities.Colors
LightCyan - Static variable in class ur_rna.Utilities.Colors
LightGoldenRodYellow - Static variable in class ur_rna.Utilities.Colors
LightGray - Static variable in class ur_rna.Utilities.Colors
LightGreen - Static variable in class ur_rna.Utilities.Colors
LightPink - Static variable in class ur_rna.Utilities.Colors
LightSalmon - Static variable in class ur_rna.Utilities.Colors
LightSeaGreen - Static variable in class ur_rna.Utilities.Colors
LightSkyBlue - Static variable in class ur_rna.Utilities.Colors
LightSlateGray - Static variable in class ur_rna.Utilities.Colors
LightSteelBlue - Static variable in class ur_rna.Utilities.Colors
LightYellow - Static variable in class ur_rna.Utilities.Colors
Lime - Static variable in class ur_rna.Utilities.Colors
LimeGreen - Static variable in class ur_rna.Utilities.Colors
limits - Variable in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
line - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
line(float, float...) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
line(float) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
line(Stroke) - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
line - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
LINE_COLOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
Linen - Static variable in class ur_rna.Utilities.Colors
lineNum - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
lineNumber() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
lineOffset - Variable in exception ur_rna.Utilities.SyntaxErrorException
  The estimated line where the syntax error occurred.
lineStyle - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint
link - Variable in class ur_rna.Utilities.swing.JActionLabel
link - Variable in class ur_rna.Utilities.swing.JFlatButton
linkerEnd - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
linkers - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.MultiStrand
linkerStart - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.DoubleStrand
linkURI - Variable in class ur_rna.Utilities.swing.JActionLabel
linkURI - Variable in class ur_rna.Utilities.swing.JFlatButton
list - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
List - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
list - Variable in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
list - Variable in class ur_rna.StructureEditor.services.RecentFileList
list - Variable in class ur_rna.StructureEditor.services.RnaDrawController.NucGroup
listen(Component) - Method in class ur_rna.Utilities.swing.InputAdapter.Keyboard
listen(Component) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
listen(Component, boolean, boolean, boolean) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
listen(JTextComponent, SimpleDocumentListener) - Static method in interface ur_rna.Utilities.swing.SimpleDocumentListener
listen(JTextComponent) - Method in class ur_rna.Utilities.swing.TextDocListener
  Add this as a DocumentListener to a JTextComponent's Document.
Listener<T> - Interface in ur_rna.Utilities
  Represents an event listener.
listener - Variable in class ur_rna.Utilities.swing.JActionLabel
listener - Variable in class ur_rna.Utilities.swing.UiAction
listeners - Variable in class ur_rna.Utilities.swing.JActionLabel
listeners - Variable in class ur_rna.Utilities.swing.TextDocListener
listeners - Variable in class ur_rna.Utilities.swing.UiAction
listenForActions(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
listenForActions(JComponent, Class<? extends AbstractButton>, ActionListener) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
listenForActions(AbstractButton...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
listFiles(String, String) - Static method in class ur_rna.Utilities.PathTools
  Lists all files in a directory that match the specified filter, which should be a a glob expression such as "*.{java,class,jar}" Glob expressions are fairly uniform across platforms.
ListItem(RecentFileList.RecentFile, String) - Constructor for class ur_rna.StructureEditor.windows.DashboardFrame.ListItem
listItemSelected(ListSelectionEvent) - Method in class ur_rna.StructureEditor.windows.DashboardFrame
listIterator(int) - Method in class ur_rna.StructureEditor.models.Strand
Literal() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
load(Preferences) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
load(Preferences) - Method in class ur_rna.StructureEditor.services.RecentFileList
load(Preferences) - Method in class ur_rna.StructureEditor.Settings
load() - Method in class ur_rna.Utilities.JniLoader
loadClip(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
loadDoubleRNA(String, String, boolean, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
loadDoubleRNA(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
loader() - Static method in class ur_rna.RNAstructureUI.utilities.Resources
loader - Variable in class ur_rna.Utilities.ResourceLoader
loadExamples() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
loadFile(RnaSceneGroup) - Method in class ur_rna.StructureEditor.windows.DrawWindow
loadFromStorage() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
loadNativeLib() - Static method in class ur_rna.StructureEditor.Program
loadProps() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
loadRecent(String, JComponent...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
loadRecentFiles() - Method in class ur_rna.StructureEditor.MainFrame
loadRecentPaths() - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
loadRecentPaths(Preferences) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
loadRecentPaths() - Static method in class ur_rna.Utilities.swing.FileDialog
loadRecentPaths(Preferences) - Static method in class ur_rna.Utilities.swing.FileDialog
loadScene(RnaScene) - Method in class ur_rna.StructureEditor.windows.DrawWindow
loadSequenceInfo(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
loadSettings() - Method in class ur_rna.StructureEditor.menus.SettingsMenu
loadSettings(Component) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
loadSettings() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
loadSettings() - Method in class ur_rna.StructureEditor.windows.DrawWindow
loadSettingsDefaults() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
loadSettingsDefaults() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
loadSettingsDefaults() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
loadSettingsDefaults() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
loadSingleRNA(String, boolean, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
loadSingleRNA(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
loadSpeakClips() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
loadState(RnaSceneState) - Method in class ur_rna.StructureEditor.models.RnaScene
loadStructure(int) - Method in class ur_rna.StructureEditor.windows.DrawWindow
LOC_ZERO - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
LOCAL_HELP_PAGE - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
LOCAL_HELP_PAGE - Static variable in class ur_rna.StructureEditor.AppActions
LOCAL_HELP_URLS - Static variable in class ur_rna.StructureEditor.AppActions
location - Variable in class ur_rna.StructureEditor.models.Nuc
location - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
location - Variable in exception ur_rna.Utilities.SyntaxErrorException
  Information about the location of the offending segment in the subject, so the user can find it easily.
log - Static variable in class ur_rna.GUITester.GUITesterStartup
log - Variable in class ur_rna.RNAstructureUI.AppMainFrame
log - Static variable in class ur_rna.RNAstructureUI.RNAstructure
log - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
log - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
log - Static variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
log - Static variable in class ur_rna.StructureEditor.AppActions
log - Variable in class ur_rna.StructureEditor.MainFrame
log - Static variable in class ur_rna.StructureEditor.Program
log - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
log(String, Object...) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
log(boolean, String, Object...) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
log(String) - Method in class ur_rna.Utilities.AppLog
log(String, Object...) - Method in class ur_rna.Utilities.AppLog
log(String, Verbosity) - Method in class ur_rna.Utilities.AppLog
log - Static variable in class ur_rna.Utilities.prefs.FilePreferences.Factory
log - Static variable in class ur_rna.Utilities.prefs.FilePreferences
log2(double) - Static method in class ur_rna.Utilities.MathUtil
  Returns the base 2 logarithm of a number.
log2i(double) - Static method in class ur_rna.Utilities.MathUtil
  Returns the smallest integer x such that 2^x is greater than or equal to the specified value.
loge(String, Object...) - Static method in class ur_rna.StructureEditor.ui.DrawPanel
logError(String, Object...) - Method in class ur_rna.StructureEditor.Settings
logFmt(String, Verbosity, Object...) - Method in class ur_rna.Utilities.AppLog
logVerbosity - Variable in class ur_rna.GUITester.GUITesterStartup.AppOptions
LookaheadSuccess() - Constructor for error ur_rna.GUITester.ScriptParser.GuiTestScriptParser.LookaheadSuccess
lookup(double) - Method in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
Loop() - Constructor for class ur_rna.StructureEditor.models.Motif.Loop
Loop(Nuc, Nuc) - Constructor for class ur_rna.StructureEditor.models.Motif.Loop
Loop(Nuc, Nuc, Motif.Loop.LoopType) - Constructor for class ur_rna.StructureEditor.models.Motif.Loop
Loop - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
loop - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
LOOP_DETECTED - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  Detected (and bailed out of) an infinite loop in the token manager.
loopNucCount() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
loopNucs - Variable in class ur_rna.StructureEditor.models.Motif.MultiLoop
LoopResizer - Class in ur_rna.StructureEditor.services.drawing
  A DrawHandle that allows a user to resize an RNA Loop (a single stranded region) in a uniform way.
LoopResizer(SceneController) - Constructor for class ur_rna.StructureEditor.services.drawing.LoopResizer
loops - Variable in class ur_rna.StructureEditor.models.Motif.MultiLoop
loopSpacing - Variable in class ur_rna.StructureEditor.models.DrawSettings
  Spacing between nucs in a loop or hairpin.
LoopType() - Constructor for enum ur_rna.StructureEditor.models.Motif.Loop.LoopType
LOWER_ALPHA - Static variable in class ur_rna.Utilities.CharType
  a-z
lowestUpdateNucIndex - Variable in class ur_rna.StructureEditor.models.StrandList
LPAREN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
LSHIFTASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
lstExamples - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
lstRecent - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
lstSeqs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
LT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
luBacksubstitution(double[], int[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
  Solves a set of linear equations.
luDecomposition(double[], int[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
  Given a 3x3 array "matrix0", this function replaces it with the LU decomposition of a row-wise permutation of itself.

## M

m - Variable in class ur_rna.Utilities.SimpleDataSerializer.Token
m00 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 1, column 1.
m01 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 1, column 2.
m02 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 1, column 3.
m10 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 2, column 1.
m11 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 2, column 2.
m12 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 2, column 3.
m20 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 3, column 1.
m21 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 3, column 2.
m22 - Variable in class ur_rna.Utilities.geom.Matrix3D
  The matrix element in row 3, column 3.
Magenta - Static variable in class ur_rna.Utilities.Colors
MagicConstant - Annotation Type in ur_rna.Utilities.annotation
  Indicates that the decorated target represents an enumerated constant, rather than a pure primitive value (e.g.
magnitude(Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  Returns the absolute length of the vector pointing to p
main(String[]) - Static method in class ur_rna.GUITester.GUITesterStartup
main(String[]) - Static method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Main entry point, if used as a stand-alone program (e.g.
main(String[]) - Static method in class ur_rna.RNAstructureUI.drawing.runners.PlotRunner
  The main method.
main(String[]) - Static method in class ur_rna.RNAstructureUI.drawing.runners.StructureRunner
  The main method.
main(String[]) - Static method in class ur_rna.RNAstructureUI.RNAstructure
  The main method.
main(String[]) - Static method in class ur_rna.StructureEditor.Program
  The main program entry-point.
mainCalcThread - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
mainClass - Static variable in class ur_rna.Utilities.AppInfo
mainFrame - Variable in class ur_rna.RNAstructureUI.menus.MainMenu
mainFrame - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
mainFrame - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
MainFrame - Class in ur_rna.StructureEditor
  The application's main window, which hosts the menubar, toolbar, statusbar, and the contains the desktop on which child windows are shown.
MainFrame() - Constructor for class ur_rna.StructureEditor.MainFrame
  Constructor.
mainFrame - Variable in class ur_rna.StructureEditor.Program
MainMenu - Class in ur_rna.RNAstructureUI.menus
  A MainMenu is essentially an MergeMenu that is designed to be subclassed and to handle the actions of its child menu items by attaching itself as an ActionListener to all child menu items.
MainMenu(String) - Constructor for class ur_rna.RNAstructureUI.menus.MainMenu
MainMenu(String, int) - Constructor for class ur_rna.RNAstructureUI.menus.MainMenu
MainMenu(String, ActionListener) - Constructor for class ur_rna.RNAstructureUI.menus.MainMenu
MainMenu(String, int, ActionListener) - Constructor for class ur_rna.RNAstructureUI.menus.MainMenu
MainMenu - Class in ur_rna.StructureEditor.menus
  A MainMenu is essentially an MergeMenu that is designed to be subclassed and to handle the actions of its child menu items by attaching itself as an ActionListener to all child menu items.
MainMenu(String) - Constructor for class ur_rna.StructureEditor.menus.MainMenu
  The ActionLister that will be used to delegate ActionEvents produced by the menu items.
mainMenus - Variable in class ur_rna.RNAstructureUI.AppMainFrame
mainPanel - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The main panel that the drawing resides on.
mainPanel - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
mainPanel - Variable in class ur_rna.StructureEditor.windows.AboutWindow
Major - Variable in class ur_rna.Utilities.Version
makeBottomBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty bottom border on a component.
makeEmptyBorder(String, int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty border on a component.
makeEqualBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty equidistant border on a component.
makeFlat() - Method in class ur_rna.Utilities.swing.JFlatButton
makeHorizontal(String[]) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a horizontal layout.
makeHorizontal(String, String...) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a title and horizontal layout.
makeHorizontal(String, ActionListener, String...) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a title, horizontal layout, and an action listener associated with the buttons.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.AccessFoldWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
makeLeftBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty left border on a component.
makeOrdered() - Method in class ur_rna.StructureEditor.models.Bond
makePanel() - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
  Build the panel.
makeRightBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty right border on a component.
makeStartButton(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Create the "START" button.
makeTitledBorder(String, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create a padded titled border on a component.
makeTopBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.ui.BorderBuilder
  Create an empty top border on a component.
makeVertical(String[]) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a vertical layout.
makeVertical(String, String...) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a title and vertical layout.
makeVertical(String, ActionListener, String...) - Static method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Create a button panel with a title, vertical layout, and an action listener associated with the buttons.
manager - Variable in class ur_rna.Utilities.EventSource
Manager() - Constructor for class ur_rna.Utilities.EventSource.Manager
mapList(Collection<T>, Function<T, T2>) - Static method in class ur_rna.Utilities.ObjTools
mapList(Collection<T>, List<T2>, Function<? super T, ? extends T2>) - Static method in class ur_rna.Utilities.ObjTools
mapMap(Map<K, V>, Function<? super K, ? extends K2>, Function<? super V, ? extends V2>) - Static method in class ur_rna.Utilities.ObjTools
mapMap(Map<K, V>, Map<K2, V2>, Function<? super K, ? extends K2>, Function<? super V, ? extends V2>) - Static method in class ur_rna.Utilities.ObjTools
mapMapEntries(Map<K, V>, Function<? super Map.Entry<K, V>, ? extends K2>, Function<? super Map.Entry<K, V>, ? extends V2>) - Static method in class ur_rna.Utilities.ObjTools
mapMapEntries(Map<K, V>, Map<K2, V2>, Function<? super Map.Entry<K, V>, ? extends K2>, Function<? super Map.Entry<K, V>, ? extends V2>) - Static method in class ur_rna.Utilities.ObjTools
MARGIN - Variable in class ur_rna.StructureEditor.ui.DrawPanel
markChanged() - Method in class ur_rna.Utilities.swing.TextDocListener
markEdited(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
markHandled() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
marks - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
Maroon - Static variable in class ur_rna.Utilities.Colors
mat_mul(double[], double[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
match(CharSequence, int) - Method in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
match(CharSequence, int, int) - Method in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
matcher - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef
matcher - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
matches(Component) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.And
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Or
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Xor
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
matches(Component) - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
matchNext(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
MathUtil - Class in ur_rna.Utilities
  Extended math functions.
MathUtil() - Constructor for class ur_rna.Utilities.MathUtil
Matrix3D - Class in ur_rna.Utilities.geom
  A double precision 3x3 matrix.
Matrix3D(double, double, double, double, double, double, double, double, double) - Constructor for class ur_rna.Utilities.geom.Matrix3D
  Constructs a Matrix3D from the individual matrix components.
Matrix3D(double[]) - Constructor for class ur_rna.Utilities.geom.Matrix3D
  Constructs a Matrix3D from a nine-element array.
Matrix3D(Matrix3D) - Constructor for class ur_rna.Utilities.geom.Matrix3D
  Constructs a new matrix with the same values as the Matrix3D parameter.
Matrix3D() - Constructor for class ur_rna.Utilities.geom.Matrix3D
  Constructs a Matrix3D with all zeros.
max - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
max(double, double) - Static method in class ur_rna.Utilities.geom.Matrix3D
max(T[], ToIntFunction<T>) - Static method in class ur_rna.Utilities.ObjTools
max3(double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
MAX_SEQUENCE_LENGTH - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
maxdefect - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
maxdepth - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
maxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
maxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
maxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
MaxExpectWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the MaxExpect module, which generates a group of structures containing pairs with the maximum probability of being accurate.
MaxExpectWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.MaxExpectWindow
  Constructor.
MaximizeExpectedAccuracy(double, int, int, double) - Method in class ur_rna.RNAstructure.backend.RNA
MaximizeExpectedAccuracy(double, int, int) - Method in class ur_rna.RNAstructure.backend.RNA
MaximizeExpectedAccuracy(double, int) - Method in class ur_rna.RNAstructure.backend.RNA
MaximizeExpectedAccuracy(double) - Method in class ur_rna.RNAstructure.backend.RNA
MaximizeExpectedAccuracy() - Method in class ur_rna.RNAstructure.backend.RNA
maximum - Variable in class ur_rna.RNAstructureUI.ui.NumberField
  The maximum value of the field.
maxItemCount - Variable in class ur_rna.StructureEditor.services.RecentFileList
maxleaf - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
maxLoopSize - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
maxLoopSize - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
maxmutate - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
maxNextCharInd - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
maxOf(T[], ToIntFunction<T>) - Static method in class ur_rna.Utilities.ObjTools
maxredesign - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
maxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
maxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
maxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
md5(String) - Static method in class ur_rna.Utilities.Strings
  Returns a 32-character hexadecimal-formatted MD5 hash of the subject string.
MdiChildFrame - Class in ur_rna.Utilities.swing
MdiChildFrame() - Constructor for class ur_rna.Utilities.swing.MdiChildFrame
MdiChildFrame(String) - Constructor for class ur_rna.Utilities.swing.MdiChildFrame
MdiChildFrame(String, boolean) - Constructor for class ur_rna.Utilities.swing.MdiChildFrame
MdiParentFrame - Class in ur_rna.Utilities.swing
MdiParentFrame() - Constructor for class ur_rna.Utilities.swing.MdiParentFrame
MdiParentFrame(String) - Constructor for class ur_rna.Utilities.swing.MdiParentFrame
MdiParentFrame(String, GraphicsConfiguration) - Constructor for class ur_rna.Utilities.swing.MdiParentFrame
MediumAquaMarine - Static variable in class ur_rna.Utilities.Colors
MediumBlue - Static variable in class ur_rna.Utilities.Colors
MediumOrchid - Static variable in class ur_rna.Utilities.Colors
MediumPurple - Static variable in class ur_rna.Utilities.Colors
MediumSeaGreen - Static variable in class ur_rna.Utilities.Colors
MediumSlateBlue - Static variable in class ur_rna.Utilities.Colors
MediumSpringGreen - Static variable in class ur_rna.Utilities.Colors
MediumTurquoise - Static variable in class ur_rna.Utilities.Colors
MediumVioletRed - Static variable in class ur_rna.Utilities.Colors
menu - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
menuBar - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
menuBar - Variable in class ur_rna.RNAstructureUI.AppMainFrame
menuBar - Variable in class ur_rna.StructureEditor.MainFrame
menuClickListener(ActionEvent) - Method in class ur_rna.StructureEditor.services.RecentFileMenuManager
menuItem - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
MenuList - Class in ur_rna.RNAstructureUI.menus
  A list of MainMenu items that should be incorporated into the application MenuBar when a Window receives focus.
MenuList() - Constructor for class ur_rna.RNAstructureUI.menus.MenuList
menuListener - Variable in class ur_rna.RNAstructureUI.menus.MainMenu
  The ActionLister that will be used to delegate ActionEvents produced by the menu items.
menuMap - Variable in class ur_rna.StructureEditor.services.RecentFileMenuManager
menuMerger - Variable in class ur_rna.RNAstructureUI.AppMainFrame
menuMerger - Variable in class ur_rna.StructureEditor.MainFrame
MenuRolloverAdapter - Class in ur_rna.RNAstructureUI.menus
  An inner class that creates a rollover listener for menus in the RNAstructure GUI.
MenuRolloverAdapter(Consumer<String>) - Constructor for class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
menus - Variable in class ur_rna.StructureEditor.windows.DrawWindow
Menus - Class in ur_rna.Utilities.swing
  A utility class to help with JMenus and JMenuItems
Menus() - Constructor for class ur_rna.Utilities.swing.Menus
merge(Component, Component) - Method in class ur_rna.Utilities.swing.MergeManager
merge(Component, Component[]) - Method in class ur_rna.Utilities.swing.MergeManager
MergeButton - Class in ur_rna.Utilities.swing
MergeButton() - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button with no set text or icon.
MergeButton(String) - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button with text.
MergeButton(Action) - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button where properties are taken from the `Action` supplied.
MergeButton(String, Icon) - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button with initial text and an icon.
MergeButton(String, int) - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button with text.
MergeButton(Action, int) - Constructor for class ur_rna.Utilities.swing.MergeButton
  Creates a button where properties are taken from the `Action` supplied.
MergeButton.Separator - Class in ur_rna.Utilities.swing
mergeEnd() - Method in interface ur_rna.Utilities.swing.IMergeItem
MergeItem - Class in ur_rna.Utilities.swing
  A container for a merge-able menu item.
MergeItem() - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(int) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(Action) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(Action, int) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(Action, String, int) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(String) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(String, int) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem(String, ActionListener, String, int, KeyStroke) - Constructor for class ur_rna.Utilities.swing.MergeItem
MergeItem.Separator - Class in ur_rna.Utilities.swing
mergeItems(Component[], Component[], Component[]) - Method in class ur_rna.Utilities.swing.MergeManager
MergeManager - Class in ur_rna.Utilities.swing
MergeManager() - Constructor for class ur_rna.Utilities.swing.MergeManager
MergeMenu - Class in ur_rna.Utilities.swing
  A class that creates a menu.
MergeMenu(String) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(Action, int) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(Action, String, int) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(String, String) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(String, String, int) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(String, int) - Constructor for class ur_rna.Utilities.swing.MergeMenu
MergeMenu(JMenu) - Constructor for class ur_rna.Utilities.swing.MergeMenu
  MergeMenu Conversion Constructor.
mergePos - Variable in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
mergePos - Variable in class ur_rna.Utilities.swing.IMergeItem.Proxy
mergePos - Variable in class ur_rna.Utilities.swing.MergeButton
mergePos - Variable in class ur_rna.Utilities.swing.MergeMenu
mergePos - Variable in class ur_rna.Utilities.swing.MergeToggleButton
MergePosDefault - Static variable in interface ur_rna.Utilities.swing.IMergeItem
  The default merge position for NON-merging items or merge items that have never been positioned.
MergePosInitial - Static variable in interface ur_rna.Utilities.swing.IMergeItem
  The merge position for newly created items.
MergePosInvalid - Static variable in interface ur_rna.Utilities.swing.IMergeItem
  Indicates an invalid merge position.
mergePosMap - Variable in class ur_rna.Utilities.swing.MergeManager
MergePosMax - Static variable in interface ur_rna.Utilities.swing.IMergeItem
  The maximum allowed merge position.
MergePosMin - Static variable in interface ur_rna.Utilities.swing.IMergeItem
  The minimum allowed merge position.
mergeStart() - Method in interface ur_rna.Utilities.swing.IMergeItem
MergeToggleButton - Class in ur_rna.Utilities.swing
MergeToggleButton() - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button with no set text or icon.
MergeToggleButton(String) - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button with text.
MergeToggleButton(Action) - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button where properties are taken from the `Action` supplied.
MergeToggleButton(String, Icon) - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button with initial text and an icon.
MergeToggleButton(String, int) - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button with text.
MergeToggleButton(Action, int) - Constructor for class ur_rna.Utilities.swing.MergeToggleButton
  Creates a button where properties are taken from the `Action` supplied.
message - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.ErrorInfo
message - Variable in class ur_rna.Utilities.swing.WaitDialog
METHOD_PREFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
MidnightBlue - Static variable in class ur_rna.Utilities.Colors
midpoint(Point2D) - Method in class ur_rna.StructureEditor.models.Bond
  Returns the midpoint between the two nucleotides in the bond.
midpoint() - Method in class ur_rna.StructureEditor.models.Bond
midpoint(Point2D, Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  Returns the mid-point between two points.
midpoint(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
min(double, double) - Static method in class ur_rna.Utilities.geom.Matrix3D
min(T[], ToIntFunction<T>) - Static method in class ur_rna.Utilities.ObjTools
minBiasRange - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
minDragDistSq - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
minHelixLen - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
minimum - Variable in class ur_rna.RNAstructureUI.ui.NumberField
  The minimum value of the field.
minOf(T[], ToIntFunction<T>) - Static method in class ur_rna.Utilities.ObjTools
Minor - Variable in class ur_rna.Utilities.Version
MintCream - Static variable in class ur_rna.Utilities.Colors
MINUS - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
MINUSASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
minVersion - Variable in class ur_rna.Utilities.JniLoader
MISC_SYMBOLS - Static variable in class ur_rna.Utilities.CharType
  Lower-ASCII Symbols not accounted for by any other flag.
Missing - Static variable in class ur_rna.StructureEditor.Settings
MISSING - Static variable in class ur_rna.Utilities.ObjTools
  An object that can be used to represent a missing value.
MistyRose - Static variable in class ur_rna.Utilities.Colors
mk - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
MM_PER_INCH - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
mnemonic() - Method in class ur_rna.Utilities.swing.UiAction
Moccasin - Static variable in class ur_rna.Utilities.Colors
mockRun() - Method in class ur_rna.Utilities.RunOnce
  Fakes a call to run.
MOD - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
mod2PI(double) - Static method in class ur_rna.Utilities.geom.Vec2D
  Given any angle in radians, this returns an equivalent angle in the range [0, 2*PI ) Note that 2*PI is an exclusive upper limit (unlike wrapTo2PI).
model - Variable in class ur_rna.StructureEditor.services.drawing.ScreenShape
modelBounds - Variable in class ur_rna.StructureEditor.services.drawing.View2D
  Represents the bounds of the screen in model coordinates.
modelLocation - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
modeNames - Static variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
  An array that holds the names of the TurboFold modes.
modified - Variable in class ur_rna.Utilities.prefs.FilePreferences
ModifierKey(int) - Constructor for enum ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
modifyDir - Variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
modifyDir() - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Gets the property 'modifyDir', which affects whether the user's actions (i.e.
modifyDir - Variable in class ur_rna.Utilities.swing.FileDialog
modifyDir() - Method in class ur_rna.Utilities.swing.FileDialog
  Gets the property 'modifyDir', which affects whether the user's actions (i.e.
ModuleWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for creating and displaying a window that enables a user to input data for one of the RNAstructure modules.
ModuleWindow(String, String) - Constructor for class ur_rna.RNAstructureUI.windows.ModuleWindow
  Constructor.
monitorAsyncTask(RnaFileIO.AsyncTask) - Method in class ur_rna.StructureEditor.windows.DrawWindow
monospaceFont - Static variable in class ur_rna.Utilities.swing.Dialogs
Motif - Class in ur_rna.StructureEditor.models
  Represents a structural element (motif) of an RNA structure -- e.g.
Motif() - Constructor for class ur_rna.StructureEditor.models.Motif
Motif.Branch - Class in ur_rna.StructureEditor.models
  Represents a complete helix (the "base" of the Branch) along with all helix and loop regions on one side of it.
Motif.Domain - Class in ur_rna.StructureEditor.models
  Represents a segment of an RNA strand that extends from a nucleotide to its pair.
Motif.Helix - Class in ur_rna.StructureEditor.models
  A helix represents a series of adjacent nucleotides which are all paired to a another series of adjacent nucleotides on the same RNA strand or a different RNA strand.
Motif.IntervalStack - Class in ur_rna.StructureEditor.models
Motif.Loop - Class in ur_rna.StructureEditor.models
  A Loop represents a series of adjacent unpaired nucleotides.
Motif.Loop.LoopType - Enum in ur_rna.StructureEditor.models
Motif.MultiLoop - Class in ur_rna.StructureEditor.models
Motif.Segment - Class in ur_rna.StructureEditor.models
  Represents a contiguous section of an RNA strand.
Mouse() - Constructor for class ur_rna.Utilities.swing.InputAdapter.Mouse
mouseClicked(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
mouseClicked(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
mouseClicked(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when the mouse button has been clicked (pressed and released) on a component.
mouseDragged(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when a mouse button is pressed on a component and then dragged.
mouseEntered(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
mouseEntered(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
mouseEntered(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when the mouse enters a component.
mouseExited(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
mouseExited(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
mouseExited(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when the mouse exits a component.
mouseHandler - Variable in class ur_rna.StructureEditor.services.RnaDrawController
MouseHandler() - Constructor for class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
mouseMoved(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when the mouse cursor has been moved onto a component but no buttons have been pushed.
mousePressed(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
mousePressed(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
mousePressed(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when a mouse button has been pressed on a component.
mouseReleased(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
mouseReleased(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
mouseReleased(MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when a mouse button has been released on a component.
mouseWheelMoved(MouseWheelEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Invoked when the mouse wheel is rotated.
moveLocation(Point, Point) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
moveSequence(PredictMultiStructureWindow.SequenceItem, int) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
moveToNext() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
  Advances the underlying iterator and searches for the next passing item.
moveToNext() - Method in class ur_rna.Utilities.Filter.FilterIterator
  Advances the underlying iterator and searches for the next passing item.
MRUFiles - Static variable in class ur_rna.RNAstructureUI.RNAstructure
MRUFileStorage - Class in ur_rna.RNAstructureUI.utilities
MRUFileStorage() - Constructor for class ur_rna.RNAstructureUI.utilities.MRUFileStorage
mruPaths() - Method in class ur_rna.StructureEditor.Program
mul(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies each element of this matrix by a scalar.
mul(double, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies each element of matrix m1 by a scalar and places the result into this.
mul(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the result of multiplying itself with matrix m1.
mul(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the result of multiplying the two argument matrices together.
mulNormalize(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies this matrix by matrix m1, does an SVD normalization of the result, and places the result back into this matrix this = SVDnorm(this*m1).
mulNormalize(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies matrix m1 by matrix m2, does an SVD normalization of the result, and places the result into this matrix this = SVDnorm(m1*m2).
MULTI_LINE_COMMENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
multiAln - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiAlnSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
MultiClassMatcher(Class...) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
multiCTs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiDsvChange - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiGapPenalty - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
MultilignWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the Multilign module, which calculates common secondary structures of multiple sequences using multiple iterations of Dynalign.
MultilignWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.MultilignWindow
  Constructor.
MultiLoop() - Constructor for class ur_rna.StructureEditor.models.Motif.MultiLoop
MultiLoop(Nuc) - Constructor for class ur_rna.StructureEditor.models.Motif.MultiLoop
MultiLoop(List<Bond>, boolean) - Constructor for class ur_rna.StructureEditor.models.Motif.MultiLoop
multiLoop - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
MultiLoopRole() - Constructor for enum ur_rna.StructureEditor.models.Bond.MultiLoopRole
multiMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiMaxPairs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiMaxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiPFSs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
multiply(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
MultiSequence - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
MultiStrand(int[]) - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter.MultiStrand
MultiWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for creating and displaying an input window that takes multiple arbitrary sequences and CT files as input.
MultiWindow(String, String) - Constructor for class ur_rna.RNAstructureUI.windows.MultiWindow
  Constructor.
multiWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
mulTransposeBoth(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies the transpose of matrix m1 times the transpose of matrix m2, and places the result into this.
mulTransposeLeft(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies the transpose of matrix m1 times matrix m2, and places the result into this.
mulTransposeRight(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiplies matrix m1 times the transpose of matrix m2, and places the result into this.
mustExist - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
mustExist() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter

## N

N - Variable in class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
n1 - Variable in class ur_rna.StructureEditor.models.Bond.BondInfo
n2 - Variable in class ur_rna.StructureEditor.models.Bond.BondInfo
n3 - Variable in class ur_rna.StructureEditor.models.Bond
n5 - Variable in class ur_rna.StructureEditor.models.Bond
name - Variable in class ur_rna.GUITester.ScriptParser.ASTNamedArgument
name - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
name - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
name - Variable in class ur_rna.Utilities.NamedArg
name() - Method in class ur_rna.Utilities.PathTools.FileName
name() - Method in class ur_rna.Utilities.swing.UiAction
  Get the name of this Action.
NamedArg - Class in ur_rna.Utilities
NamedArg(String, Object) - Constructor for class ur_rna.Utilities.NamedArg
NamedArgument() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
NamedArgumentList() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
names - Variable in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  The names of the buttons in the group.
NativeLibLoadError() - Constructor for exception ur_rna.Utilities.JniLoader.NativeLibLoadError
NativeLibLoadError(String) - Constructor for exception ur_rna.Utilities.JniLoader.NativeLibLoadError
NativeLibLoadError(Throwable) - Constructor for exception ur_rna.Utilities.JniLoader.NativeLibLoadError
NativeLibLoadError(String, Throwable) - Constructor for exception ur_rna.Utilities.JniLoader.NativeLibLoadError
NavajoWhite - Static variable in class ur_rna.Utilities.Colors
Navy - Static variable in class ur_rna.Utilities.Colors
NE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
negate() - Method in class ur_rna.Utilities.geom.Matrix3D
  Negates the value of this matrix: this = -this.
negate(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix equal to the negation of of the Matrix3D parameter.
negate(Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to -p.
negate() - Method in class ur_rna.Utilities.geom.Vec2D
negative(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to -p.
negative(Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
NEVER - Static variable in class ur_rna.RNAstructureUI.ui.ScrollerPane
  A generic constant symbolizing that a scroll bar must never be used.
new_CDblVector__SWIG_0() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_CDblVector__SWIG_1(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_CIntVector__SWIG_0() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_CIntVector__SWIG_1(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_datatable() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_DotPlotBackend() - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
new_Dynalign_object__SWIG_0() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_1(String, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_2(String, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_3(String, int, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_4(String, int, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_5(String, int, String, int, long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_6(String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Dynalign_object__SWIG_7(String, short, short, short, short) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
NEW_FILE - Static variable in class ur_rna.StructureEditor.AppActions
new_HybridRNA__SWIG_0(String, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_HybridRNA__SWIG_1(String, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_HybridRNA__SWIG_2(String, int, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_HybridRNA__SWIG_3(String, int, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_HybridRNA__SWIG_4(String, int, String, int, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_PartialProgress(long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_0(String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_1(String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_2(String, int, String, boolean, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_3(String, int, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_4(String, int, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_5(String, int, long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_6(String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_7(String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_8(boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNA__SWIG_9() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_RNAstructureBackendCalculator() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
new_SimpleProgressHandler() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_singlestructure(int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_structure__SWIG_0(int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_structure__SWIG_1() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_StructureBackend() - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
new_Thermodynamics__SWIG_0(boolean, String, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Thermodynamics__SWIG_1(boolean, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Thermodynamics__SWIG_2(boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Thermodynamics__SWIG_3() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_Thermodynamics__SWIG_4(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TProgressDialog() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_0(String, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_1(String, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_2(String, int, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_3(String, int, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_4(String, int, String, int, long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
new_TwoRNA__SWIG_5() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
NewFileWindow - Class in ur_rna.StructureEditor.windows
  Displays a dialog that allows a user to enter a sequence and structure information for a new drawing.
NewFileWindow() - Constructor for class ur_rna.StructureEditor.windows.NewFileWindow
NewFileWindow.IgnoreStylesUndoManager - Class in ur_rna.StructureEditor.windows
NewFileWindow.JWrapTextPane - Class in ur_rna.StructureEditor.windows
NewFileWindow.StructItem - Class in ur_rna.StructureEditor.windows
newGroup() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
NEWLINE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
NEWLINE - Static variable in class ur_rna.Utilities.CharType
  CR and LF
newStrand(int) - Method in class ur_rna.StructureEditor.models.StrandList
newStrand(int, int, int) - Method in class ur_rna.StructureEditor.models.StrandList
newToken(int, String) - Static method in class ur_rna.GUITester.ScriptParser.Token
  Returns a new Token object, by default.
newToken(int) - Static method in class ur_rna.GUITester.ScriptParser.Token
newUTF8Writer(String, boolean) - Static method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  Simplified version of `Files.newBufferedWriter(Path, Charset, OpenOption...)` that uses `StandardCharsets.UTF_8` as the charset and accepts a boolean "append" instead of an `OpenOption` argument list.
newUTF8Writer(String, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
  Simplified version of `Files.newBufferedWriter(Path, Charset, OpenOption...)` that uses `StandardCharsets.UTF_8` as the charset and accepts a boolean "append" instead of an `OpenOption` argument list.
newValue - Variable in class ur_rna.GUITester.ScriptParser.ASTAssignment
next - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
next - Variable in class ur_rna.GUITester.ScriptParser.Token
  A reference to the next regular (non-special) token from the input stream.
next - Static variable in class ur_rna.RNAstructure.backend.DotBracketFormat.SwigNext
next - Static variable in class ur_rna.RNAstructure.backend.RestraintType.SwigNext
next - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
next() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
  Returns the text of the next token, regardless of type, and advance the read position.
next(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
next() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
next() - Method in class ur_rna.Utilities.Filter.FilterIterator
next() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
nextBool() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
nextCharBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
nextCharInd - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
nextDouble() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
nextFloat() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
nextInHelix() - Method in class ur_rna.StructureEditor.models.Bond
nextInHelix(int) - Method in class ur_rna.StructureEditor.models.Bond
nextInScene() - Method in class ur_rna.StructureEditor.models.Nuc
nextInScene(int, boolean) - Method in class ur_rna.StructureEditor.models.Nuc
nextInt() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
nextLine() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
  Returns the remaining content on the current line (i.e.
nextMatch(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
nextStep(String, boolean, int) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
nextStep(int) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
nextStep(int, String, boolean) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
nextStepWork - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
nextWindow - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
nl2br(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
NO_ALIASES - Static variable in class ur_rna.Utilities.CommandLineParser.FlagDef
NO_REINDEX - Static variable in class ur_rna.StructureEditor.models.StrandList
NoArg() - Constructor for class ur_rna.Utilities.EventSource.NoArg
noChangeError() - Method in class ur_rna.StructureEditor.models.StrandList
Node - Interface in ur_rna.GUITester.ScriptParser
node_created - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
nodeArity() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
nodeCreated() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
nodePrefix() - Method in class ur_rna.Utilities.prefs.FilePreferences
  Returns the absolute path and ensures that it ends with a slash (/) For child nodes this is the same as `absolutePath() + '/'` but for the root node it is just '/'.
nodePrefix() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
  Returns the absolute path and ensures that it ends with a slash (/) For child nodes this is the same as `absolutePath() + '/'` but for the root node it is just '/'.
nodes - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
noFill() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
nohtml(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
noLine() - Method in class ur_rna.StructureEditor.services.drawing.DrawHint
NON_PRINTABLE - Static variable in class ur_rna.Utilities.CharType
  Non-printable characters, including control characters, TAB, CR, and LF.
nonchild_indent - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
None - Static variable in interface ur_rna.StructureEditor.services.SceneColorizer.ColorMode
NONE - Static variable in class ur_rna.Utilities.CharType
normal(Vec2D) - Method in class ur_rna.StructureEditor.models.Bond
  Returns a Vec2D that represents the direction normal to the bond -- i.e.
normal() - Method in class ur_rna.StructureEditor.models.Bond
normalize() - Method in class ur_rna.Utilities.geom.Matrix3D
  Performs singular value decomposition normalization of this matrix.
normalize(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Perform singular value decomposition normalization of matrix m1 and place the normalized values into this.
normalize(Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  Assumes p represents a vector and mormalizes it to a unit vector -- i.e.
normalize() - Method in class ur_rna.Utilities.geom.Vec2D
normalize(double, double) - Method in class ur_rna.Utilities.geom.Vec2D
normalizeCP() - Method in class ur_rna.Utilities.geom.Matrix3D
  Perform cross product normalization of this matrix.
normalizeCP(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Perform cross product normalization of matrix m1 and place the normalized values into this.
normalized(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  Assumes p is a vector and sets result to the corresponding normalized unit vector (i.e.
normalized(Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
normalizedExt - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
normalizeFlagName(String) - Method in class ur_rna.Utilities.CommandLineParser
NOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
notifyChanged() - Method in class ur_rna.StructureEditor.Settings
notifyListeners(DocumentEvent) - Method in class ur_rna.Utilities.swing.TextDocListener
notifyUpdate() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
notifyUpdate(SceneUpdateInfo, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
notifyUpdate(SceneUpdateInfo) - Method in class ur_rna.StructureEditor.services.RnaDrawController
notifyUpdate(SceneUpdateInfo) - Method in interface ur_rna.StructureEditor.services.SceneController
notifyUpdate(SceneUpdateInfo, boolean) - Method in interface ur_rna.StructureEditor.services.SceneController
notifyUpdated() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  Call this if changes are made to the window that could require the JDesktopPane or the AppMainFrame to update.
notImpl() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
NotNull - Annotation Type in ur_rna.Utilities.annotation
noWindowsItem - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
nowrap - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.JWrapTextPane
Nuc - Class in ur_rna.StructureEditor.models
  Represents a single nucleotide.
Nuc() - Constructor for class ur_rna.StructureEditor.models.Nuc
Nuc(String) - Constructor for class ur_rna.StructureEditor.models.Nuc
Nuc(String, float, float) - Constructor for class ur_rna.StructureEditor.models.Nuc
nuc - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
nuc5 - Variable in class ur_rna.StructureEditor.models.Motif.Helix
  The 5'-most nucleotide in the helix.
NUC_ID - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
NUC_NUMBER - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
NUC_SYMBOL - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
nucAtSceneIndex(int) - Method in class ur_rna.StructureEditor.models.RnaScene
nucCount() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
nucDiameter() - Method in class ur_rna.StructureEditor.models.DrawSettings
nucFillColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucFitsCircle(int, Ellipses.Circle) - Method in class ur_rna.StructureEditor.services.RnaDrawController
nucFocusColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucFont - Variable in class ur_rna.StructureEditor.models.DrawSettings
NucGroup(Collection<Nuc>) - Constructor for class ur_rna.StructureEditor.services.RnaDrawController.NucGroup
NucGroup() - Constructor for class ur_rna.StructureEditor.services.RnaDrawController.NucGroup
nucHitColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
NucIndexConverter() - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
NucLayout - Class in ur_rna.StructureEditor.services.drawing
  Performs nucleotide layouts of various types.
NucLayout() - Constructor for class ur_rna.StructureEditor.services.drawing.NucLayout
NucLayout(DrawSettings) - Constructor for class ur_rna.StructureEditor.services.drawing.NucLayout
NucleicAcidMenu - Class in ur_rna.RNAstructureUI.menus
  A class that creates a menu which holds commands specific for a nucleic acid type.
NucleicAcidMenu(String) - Constructor for class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
  Constructor.
NucleicAcidMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
Nucleobase - Class in ur_rna.RNAstructure
  Nucleobase symbols and corresponding numeric values (as per the RNA backend)
Nucleobase() - Constructor for class ur_rna.RNAstructure.Nucleobase
nucleotideRadius(Nuc) - Method in class ur_rna.StructureEditor.models.DrawSettings
NucOrHelixDialog(String, String) - Constructor for class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
  Constructor.
nucOutlineColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucOutlineSelStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucOutlineStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucOutlineWidth - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucPositionsChanged() - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
nucPositionsChanged() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Called when any nucleotides in the scene changed position, EXCEPT when THIS DrawHandle is in the middle of a performDrag operation (because any nucleotide changes then are likely due to its own drag operation).
nucPositionsChanged() - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
nucPositionsChanged() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
nucPositionsChanged() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
nucRadius - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucs - Variable in class ur_rna.StructureEditor.models.RnaScene
nucs - Variable in class ur_rna.StructureEditor.models.StrandList
nucScreenShapes - Variable in class ur_rna.StructureEditor.services.RnaDrawController
nucSelColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
nucShapes - Variable in class ur_rna.StructureEditor.services.RnaDrawController
nucSpacing - Variable in class ur_rna.StructureEditor.models.DrawSettings
  Spacing between nucs in a helix.
NucState() - Constructor for class ur_rna.StructureEditor.models.RnaSceneState.NucState
NucStyle - Class in ur_rna.StructureEditor.models
  Contains formatting information, which affects how nucleotides are drawn.
NucStyle() - Constructor for class ur_rna.StructureEditor.models.NucStyle
NucStyle(Color, Color, Color, Color, Font) - Constructor for class ur_rna.StructureEditor.models.NucStyle
nucTextColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
NUL - Static variable in class ur_rna.Utilities.CharConstants
NULL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Nullable - Annotation Type in ur_rna.Utilities.annotation
NullByteArrayOutputStream() - Constructor for class ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream
NullPrintStream - Class in ur_rna.Utilities
NullPrintStream() - Constructor for class ur_rna.Utilities.NullPrintStream
NullPrintStream.NullByteArrayOutputStream - Class in ur_rna.Utilities
nullStream - Static variable in class ur_rna.Utilities.AppLog
nullValue - Static variable in class ur_rna.StructureEditor.Settings
NUM - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
number - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  The structure number viewed on this panel.
number - Variable in class ur_rna.StructureEditor.models.Nuc
number - Variable in class ur_rna.StructureEditor.models.RnaSceneState.NucState
numberDistance - Variable in class ur_rna.StructureEditor.models.DrawSettings
NumberField - Class in ur_rna.RNAstructureUI.ui
  A class that creates a text field whose contents may be bounded by a minimum or maximum value.
NumberField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.ui.NumberField
  Constructor.
NumberField.DoubleField - Class in ur_rna.RNAstructureUI.ui
  An inner class that handles a field which contains a double value.
NumberField.FloatField - Class in ur_rna.RNAstructureUI.ui
  An inner class that handles a field which contains a float value.
NumberField.IntegerField - Class in ur_rna.RNAstructureUI.ui
  An inner class that handles a field which contains an integer value.
numberFont - Variable in class ur_rna.StructureEditor.models.DrawSettings
numberFormatter - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
numberLineColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
numberLineMargin - Variable in class ur_rna.StructureEditor.models.DrawSettings
numberLineStroke - Variable in class ur_rna.StructureEditor.models.DrawSettings
numberLineWidth - Variable in class ur_rna.StructureEditor.models.DrawSettings
NumberRangeList() - Constructor for class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
NumberRangeList(double[], Color[], String, Color) - Constructor for class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
NumberRangeList(double[], Color[], SceneColorizer.Comparison, Color) - Constructor for class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList

## O

ObjEventArgs(T) - Constructor for class ur_rna.Utilities.EventArgs.ObjEventArgs
ObjTools - Class in ur_rna.Utilities
ObjTools() - Constructor for class ur_rna.Utilities.ObjTools
ObjTools.RefBool - Class in ur_rna.Utilities
  Use to make up for the lack of pass-by-reference in Java
ObjTools.RefInt - Class in ur_rna.Utilities
  Use to make up for the lack of pass-by-reference in Java
ObjTools.RefStr - Class in ur_rna.Utilities
  Use to make up for the lack of pass-by-reference in Java
OCTAL_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
OCTAL_RADIX - Static variable in class ur_rna.Utilities.Constants
of(Class) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
of(Class...) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
offendingText - Variable in exception ur_rna.Utilities.SyntaxErrorException
  The part of the subject string most closely associated with the error.
offset - Variable in class ur_rna.StructureEditor.models.Strand
offset - Variable in class ur_rna.StructureEditor.ui.DrawPanel
offset - Variable in class ur_rna.StructureEditor.windows.DrawWindow.SceneInfo
offsetByCodePoints(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns the index within this sequence that is offset from the given `index` by `codePointOffset` code points.
ofType(String) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
OKButton - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
old - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.StateChangeEventArgs
OldLace - Static variable in class ur_rna.Utilities.Colors
oligomerChemistry - Static variable in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
  The oligomer chemistry.
OligoScreenWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the OligoScreen module, which calculates thermodynamic properties for a list of oligonucleotides.
OligoScreenWindow() - Constructor for class ur_rna.RNAstructureUI.windows.OligoScreenWindow
  Constructor.
OligoSelectionDialog() - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
  Constructor.
OligoWalkResultsMenu() - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoWalkResultsMenu
  Constructor.
OligoWalkWindow - Class in ur_rna.RNAstructureUI.windows
  A class that handles creation of windows for the OligoWalk module.
OligoWalkWindow() - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Constructor.
OligoWalkWindow.BarButton - Class in ur_rna.RNAstructureUI.windows
  An inner class that encapsulates a bar button.
OligoWalkWindow.OligoSelectionDialog - Class in ur_rna.RNAstructureUI.windows
  An inner class which creates a dialog that selects a particular oligo to move to in the results window.
OligoWalkWindow.OligoWalkResultsMenu - Class in ur_rna.RNAstructureUI.windows
  An inner class that handles creation of the oligo graph menu for the OligoWalk results window.
OligoWalkWindow.SpinnerPanel - Class in ur_rna.RNAstructureUI.windows
  An class that creates a panel containing a single spinner with a label.
OligoWalkWindow.StringComboBox - Class in ur_rna.RNAstructureUI.windows
  An inner class that creates a combo box holding a string list.
Olive - Static variable in class ur_rna.Utilities.Colors
OliveDrab - Static variable in class ur_rna.Utilities.Colors
onComplete() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
  Show the results window.
OneArg() - Constructor for class ur_rna.Utilities.EventSource.OneArg
onFileSelected - Variable in class ur_rna.RNAstructureUI.ui.RecentFileButton
onFocusGained(FocusEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
onHistoryUpdate(HistoryUpdateEvent) - Method in class ur_rna.StructureEditor.windows.DrawWindow
onKeyInput(InputAdapter.InputType, KeyEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Keyboard
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.drawing.menus.PlotMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.FileMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
  Do any actions specific to this menu.
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.PredictMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoWalkResultsMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
onMenuAction(String, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
onMouseInput(InputAdapter.InputType, MouseEvent) - Method in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
  Respond to mouse input.
onMouseInput(InputAdapter.InputType, MouseEvent) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
  Override this to respond to mouse input.
onSceneUpdate(SceneUpdateEvent) - Method in class ur_rna.StructureEditor.services.RnaDrawController
onSceneUpdate(SceneUpdateEvent) - Method in class ur_rna.StructureEditor.windows.DrawWindow
onSequenceSelected(ListSelectionEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
onSettingsChanged() - Method in class ur_rna.StructureEditor.models.DrawSettings
  Call this to update dependent settings whenever settings have been changed.
onUpdate(Consumer<? super RnaFileIO.BackgroundWork<TResult>>) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
OPEN_FILE_POS - Static variable in class ur_rna.StructureEditor.menus.FileMenu
OPEN_WEBSITE - Static variable in class ur_rna.StructureEditor.AppActions
openct(String) - Method in class ur_rna.RNAstructure.backend.structure
opendbn(String) - Method in class ur_rna.RNAstructure.backend.structure
openFile(String, String) - Static method in class ur_rna.StructureEditor.AppActions
openFile(String, FileType) - Static method in class ur_rna.StructureEditor.AppActions
openNodeScope(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
openseq(String) - Method in class ur_rna.RNAstructure.backend.structure
openseqx(String) - Method in class ur_rna.RNAstructure.backend.structure
OPERATION - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
operatorKind - Variable in class ur_rna.GUITester.ScriptParser.ASTAssignment
ops - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
optBasesAll - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
optBasesSelected - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
optDNA - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
optDNA - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
optEnterSeq - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
options - Static variable in class ur_rna.GUITester.GUITesterStartup
options - Static variable in class ur_rna.RNAstructureUI.RNAstructure
options - Variable in class ur_rna.RNAstructureUI.windows.MultiWindow
  The box that holds a particular window's unique options.
optionsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
optionsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
optionsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
optionsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
optRNA - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
optRNA - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
optSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
optStructuresAll - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
optStructuresCurrent - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
or(Matcher, Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
Or(Matcher, Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Or
or(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
or(Matcher) - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
Orange - Static variable in class ur_rna.Utilities.Colors
OrangeRed - Static variable in class ur_rna.Utilities.Colors
ORASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Orchid - Static variable in class ur_rna.Utilities.Colors
orderNucs() - Method in class ur_rna.StructureEditor.models.Motif.Segment
originalComponents - Variable in class ur_rna.Utilities.swing.MergeManager
originalHeight - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
originalToolbar - Variable in class ur_rna.StructureEditor.MainFrame
originalType - Variable in class ur_rna.StructureEditor.models.RnaSceneGroup
originalWidth - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
OSInfo - Class in ur_rna.Utilities
  A class that handles checking whether an OS is a Mac, and setting general properties if that is the case.
OSInfo() - Constructor for class ur_rna.Utilities.OSInfo
OSInfo.OSType - Enum in ur_rna.Utilities
osType - Static variable in class ur_rna.Utilities.OSInfo
OSType() - Constructor for enum ur_rna.Utilities.OSInfo.OSType
others - Variable in class ur_rna.StructureEditor.models.StrandList
others() - Method in class ur_rna.StructureEditor.models.StrandList
OUT - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
out - Variable in class ur_rna.Utilities.StopWatch
outBase1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
outBase2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
outBiCt - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
outCtFile - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
outDsv - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outDupCt - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
outDynAln - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outDynCt1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outDynCt2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outFoldCt - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
Outline - Static variable in interface ur_rna.StructureEditor.services.SceneColorizer.ColorMode
OUTLINE_WIDTH - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
outlineColor - Variable in class ur_rna.StructureEditor.models.NucStyle
outMaxExpectCt - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
outOfBoundsMsg(int) - Method in class ur_rna.StructureEditor.models.Strand
outOfBoundsMsg(int) - Method in class ur_rna.StructureEditor.models.StrandList
outPartsCt1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outPartsCt2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
outPfs - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
outPkCt - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
outputFile(boolean) - Method in class ur_rna.RNAstructureUI.ui.FileField
outputFile() - Method in class ur_rna.RNAstructureUI.ui.FileField
outputFile(String) - Method in class ur_rna.RNAstructureUI.ui.FileField
OutputFormatSettings() - Constructor for class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
OutputFormatSettings(int, boolean) - Constructor for class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
OutputFormatSettings(int, boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
outputStream - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
outSav - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
outShared - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
override(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.UserOptions
overrides - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
owner - Variable in class ur_rna.StructureEditor.menus.DrawingEditMenu
owner - Variable in class ur_rna.StructureEditor.menus.DrawingFileMenu
owner - Variable in class ur_rna.StructureEditor.menus.DrawingFormatMenu
owner - Variable in class ur_rna.StructureEditor.menus.DrawingViewMenu
owner - Variable in class ur_rna.StructureEditor.models.Strand
owner - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
owner - Variable in class ur_rna.Utilities.swing.FileDialog
owningComponent - Static variable in class ur_rna.Utilities.swing.Dialogs

## P

p - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
p - Variable in class ur_rna.Utilities.SimpleDataSerializer.Token
p - Variable in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
pack() - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
pack() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
pad(int, String, char, int) - Static method in class ur_rna.Utilities.Strings
  Pad a string with the specified character.
pad(int, String) - Static method in class ur_rna.Utilities.Strings
pad0s(int, String) - Static method in class ur_rna.Utilities.Strings
PAD_COLOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
PAD_FONT - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
PAD_INDEX - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
PAD_LOC - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
PAD_SYMBOL - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
PAD_TOTAL - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
padl(int, String) - Static method in class ur_rna.Utilities.Strings
  Pad-Left.
padr(int, String) - Static method in class ur_rna.Utilities.Strings
  Pad-Right.
PageSize - Class in ur_rna.StructureEditor.services.drawing.export
  Represents the dimensions of a fixed-size page (e.g.
PageSize(double, double) - Constructor for class ur_rna.StructureEditor.services.drawing.export.PageSize
PageSize(Dimension2D) - Constructor for class ur_rna.StructureEditor.services.drawing.export.PageSize
pageSize - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
paint - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
paint - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Paint used to fill shapes.
paintComponent(Graphics) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
paintComponent(Graphics) - Method in class ur_rna.StructureEditor.ui.DrawPanel
PaintOp(Paint) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
pair - Variable in class ur_rna.StructureEditor.models.Nuc
Pair(int, int, int, int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
Pair<K,V> - Class in ur_rna.Utilities
  General purpose key-value pair.
Pair(K, V) - Constructor for class ur_rna.Utilities.Pair
Pair(T1, T2) - Constructor for class ur_rna.Utilities.Tuple.Pair
Pair() - Constructor for class ur_rna.Utilities.Tuple.Pair
pairCount - Variable in class ur_rna.StructureEditor.models.Motif.Helix
  The number of basepairs in the helix.
pairCount() - Method in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
PairProbabilityData(int) - Constructor for class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
PaleGoldenRod - Static variable in class ur_rna.Utilities.Colors
PaleGreen - Static variable in class ur_rna.Utilities.Colors
PaleTurquoise - Static variable in class ur_rna.Utilities.Colors
PaleVioletRed - Static variable in class ur_rna.Utilities.Colors
panel - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
panel - Variable in class ur_rna.StructureEditor.windows.DrawWindow
panelInput - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
panelResults - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  The box that holds the results.
PapayaWhip - Static variable in class ur_rna.Utilities.Colors
param - Variable in class ur_rna.RNAstructureUI.utilities.RunFunc
paramAffinity - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
ParamAffinity() - Constructor for enum ur_rna.Utilities.CommandLineParser.ParamAffinity
PARENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
parent - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
parent - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
parent - Variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
parent - Variable in class ur_rna.StructureEditor.services.RecentFileMenuManager
parentFrame - Variable in class ur_rna.Utilities.swing.MdiChildFrame
parse() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
parse(boolean) - Method in class ur_rna.GUITester.ScriptRunner
parse(String) - Method in class ur_rna.Utilities.CommandLineParser
parse(String[]) - Method in class ur_rna.Utilities.CommandLineParser
parse(String) - Static method in class ur_rna.Utilities.PathTools
parse(String, boolean) - Static method in class ur_rna.Utilities.PathTools
parse(CharSequence, int[]) - Method in class ur_rna.Utilities.SimpleDataSerializer
  Parses text into an SONMap characterSourceIndex is an array that provides information about the original line and column of a particular character index in the final input code.
parseArgs(String[]) - Static method in class ur_rna.GUITester.GUITesterStartup
parseArray(SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
parseCommandArgs(String[]) - Static method in class ur_rna.RNAstructureUI.RNAstructure
parseCommandArgs(String[]) - Static method in class ur_rna.StructureEditor.Program
ParseContext(SimpleDataSerializer.Token[], int, int[]) - Constructor for class ur_rna.Utilities.SimpleDataSerializer.ParseContext
parseDouble(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
parsedValue - Variable in class ur_rna.Utilities.CommandLineParser.FlagArg
  Gets the value of this flag once it has been converted to the type specified in the associated Flag
parseError(DrawingFileIO.SimpleScanner, String, Object...) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
parseError(int, int, String, Object...) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
parseError(String, int) - Static method in class ur_rna.Utilities.Strings
ParseException - Exception in ur_rna.GUITester.ScriptParser
  This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseException
  This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception ur_rna.GUITester.ScriptParser.ParseException
  The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseException
  Constructor with message.
ParseException(String, Throwable) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseException
  Constructor with message.
parseFileType(String, String) - Static method in class ur_rna.StructureEditor.services.RecentFileList
parseFilters(String) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
parseFlagDefs(String) - Method in class ur_rna.Utilities.CommandLineParser
parseFlagDefs(String, boolean) - Method in class ur_rna.Utilities.CommandLineParser
ParseFormatException - Exception in ur_rna.GUITester.ScriptParser
  This exception is thrown when high-level parse errors, such as evaluation of a literal are encountered.
ParseFormatException(String, Token, Throwable) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseFormatException
  This constructor is used by the method "generateParseException" in the generated parser.
ParseFormatException(String, Token) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseFormatException
ParseFormatException() - Constructor for exception ur_rna.GUITester.ScriptParser.ParseFormatException
ParseFormatException(String) - Constructor for exception ur_rna.GUITester.ScriptParser.ParseFormatException
  Constructor with message.
parseInt(String, int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
parseModData(String, int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
parseNumber(SimpleDataSerializer.Token, SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
parseObject(SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
parseOnly - Variable in class ur_rna.GUITester.GUITesterStartup.AppOptions
parseProbData(String, int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
parser - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
parser - Variable in class ur_rna.Utilities.CommandLineParser.ParseResults
ParseResults(CommandLineParser, List<CommandLineParser.Argument>) - Constructor for class ur_rna.Utilities.CommandLineParser.ParseResults
ParseScriptProgram() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  THE SCRIPT LANGUAGE GRAMMAR STARTS HERE *
parseSequence(String) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
parseSONValue(SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
parseString(SimpleDataSerializer.Token, SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
parseStructure(String) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
PartialProgress - Class in ur_rna.RNAstructure.backend
PartialProgress(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.PartialProgress
PartialProgress(ProgressHandler) - Constructor for class ur_rna.RNAstructure.backend.PartialProgress
PartialProgress_advanceToNextStep(long, PartialProgress, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_cancel(long, PartialProgress) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_canceled(long, PartialProgress) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_setClient(long, PartialProgress, long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_setNextStep(long, PartialProgress, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_setWorkComplete(long, PartialProgress, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_stepComplete(long, PartialProgress) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_update(long, PartialProgress, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_workInNextStep_get(long, PartialProgress) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartialProgress_workInNextStep_set(long, PartialProgress, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
PartitionDoubleWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the bipartition module, which calculates the partition function for two strands of nucleic acids.
PartitionDoubleWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
  Constructor.
PartitionFunction(String, double, boolean, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
PartitionFunction(String, double, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
PartitionFunction(String, double) - Method in class ur_rna.RNAstructure.backend.RNA
PartitionFunction(String) - Method in class ur_rna.RNAstructure.backend.RNA
PartitionFunction() - Method in class ur_rna.RNAstructure.backend.RNA
PartitionFunctionBimolecular(String) - Method in class ur_rna.RNAstructure.backend.HybridRNA
PartitionFunctionBimolecular() - Method in class ur_rna.RNAstructure.backend.HybridRNA
PartitionSav - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
PartitionSingleWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the partition module, which calculates the partition function for a single strand of nucleic acids.
PartitionSingleWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
  Constructor.
partsMode - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
passes(T) - Method in class ur_rna.Utilities.ConverterFilter
passes(T) - Method in class ur_rna.Utilities.Filter
passesFilter(File) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
passesFilter(File) - Method in class ur_rna.Utilities.swing.FileDialog
path - Variable in class ur_rna.StructureEditor.services.RecentFileList.RecentFile
pathSep - Static variable in class ur_rna.Utilities.ResourceLoader
PathTools - Class in ur_rna.Utilities
PathTools() - Constructor for class ur_rna.Utilities.PathTools
PathTools.FileName - Class in ur_rna.Utilities
pattern - Static variable in class ur_rna.StructureEditor.Program
pattern() - Method in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
pause(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
PeachPuff - Static variable in class ur_rna.Utilities.Colors
peek() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
  Returns the text of the next token, regardless of type, but does not advance the read position.
peek() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Returns the next character in the current reader without consuming it.
peek() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
peekMatch(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
  Returns a Matchresult if the pattern was matched, or null otherwise.
peekNode() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
peekNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
peekNodeId() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
performAction(String, Object[]) - Method in class ur_rna.GUITester.ScriptActions
performDrag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
  Called when this handle has been dragged by the user.
performDrag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Called when this handle has been dragged by the user.
performDrag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
  Called when this handle has been dragged by the user.
performDrag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
performDrag(Point, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
  Called when this handle has been dragged by the user.
performGuiAction(String, Object[]) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
  Peform a named action on a GuiRef.
Peru - Static variable in class ur_rna.Utilities.Colors
Pink - Static variable in class ur_rna.Utilities.Colors
placeComponent(int, int, JComponent) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  .
PLAIN - Static variable in class ur_rna.Utilities.swing.Dialogs
play(InputStream) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
playNext() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
plotButtonHandler(ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
plotCol - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
plotCreator - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
PlotDialog - Class in ur_rna.RNAstructureUI.drawing.dialogs
  A dialog that holds dot plot images.
PlotDialog(String) - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  File Constructor.
PlotDialog(String, int) - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Strand Constructor.
plotLength - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  The length of the plot.
PlotMenu - Class in ur_rna.RNAstructureUI.drawing.menus
  A class that handles a menu which can manipulate a drawn dot plot.
PlotMenu(PlotDialog) - Constructor for class ur_rna.RNAstructureUI.drawing.menus.PlotMenu
  Constructor.
PlotResult(String, Supplier<InternalWindow>) - Constructor for class ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
plotResults - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
plotRow - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
PlotRunner - Class in ur_rna.RNAstructureUI.drawing.runners
  A class that runs RNAstructure Java dot plot drawing independently of the main RNAstructure application.
PlotRunner() - Constructor for class ur_rna.RNAstructureUI.drawing.runners.PlotRunner
  Constructor.
Plum - Static variable in class ur_rna.Utilities.Colors
PLUS - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
PLUSASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
pnlClient - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
pnlClient - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
pnlColorPicker - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
pnlConstraints - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
pnlConstraints - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlContent - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
pnlContent - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
pnlDrawings - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
pnlFiles - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
pnlLogo - Variable in class ur_rna.StructureEditor.windows.AboutWindow
pnlMain - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
pnlMain - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
pnlMain - Variable in class ur_rna.StructureEditor.windows.InsertBasesDialog
pnlMain - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
pnlMultiOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
pnlOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
pnlOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
pnlOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlPartsOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlProbColors - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
pnlSelect - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
pnlSeqInfo - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlSequences - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
pnlSequences - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlSequences - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlSpinner - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
pnlSymbolColors - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
pnlTaskProgress - Variable in class ur_rna.StructureEditor.windows.DrawWindow
pnlTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
pnlTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
pnlTaskStatus - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
pnlText - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
pnlTurboOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
pnlValueColors - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
PointMath - Class in ur_rna.Utilities.geom
PointMath() - Constructor for class ur_rna.Utilities.geom.PointMath
pop() - Method in class ur_rna.StructureEditor.models.Motif.IntervalStack
popNode() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
popNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
popState() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  Pops the GraphicsStyle from the top of the stack and returns it.
popTypedNode(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
popup - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
pos - Variable in class ur_rna.StructureEditor.models.Motif.IntervalStack
pos - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
pos - Variable in class ur_rna.StructureEditor.services.History
pos - Variable in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
pos - Variable in class ur_rna.Utilities.swing.CheckMergeItem
pos - Variable in class ur_rna.Utilities.swing.MergeButton.Separator
pos - Variable in class ur_rna.Utilities.swing.MergeItem
pos - Variable in class ur_rna.Utilities.swing.MergeItem.Separator
pos1 - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
pos2 - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
position() - Method in class ur_rna.StructureEditor.services.History
position - Variable in class ur_rna.Utilities.CommandLineParser.Argument
  The position of this Argument in the parsed command line.
position - Variable in class ur_rna.Utilities.ExtendedBufferedReader
  The position, which is number of characters read so far
positionLinear(Nuc, Nuc, boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
positionLinear(Nuc, Nuc, Point2D, Point2D, boolean, boolean, boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
positionLoopBetweenHelices(Point2D.Float, Nuc, Nuc, boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
positionLoopNucs(Motif.Segment, Ellipses.Circle, boolean) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
positionNucs(Point2D.Float, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
positionNucs(Point2D.Float, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
positionNucsRotate(Point2D.Float, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
positionTerminalEndPoint(Point2D.Float, Nuc, Nuc, int, boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
positionTerminalLoop(Point2D.Float, Nuc, Nuc, boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
Postscript - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
POW - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
pow2(double) - Static method in class ur_rna.Utilities.MathUtil
  Returns the smallest power of 2 greater than or equal to the specified value.
pow2i(double) - Static method in class ur_rna.Utilities.MathUtil
  Returns the smallest power of 2 greater than or equal to the specified value.
pow2L(double) - Static method in class ur_rna.Utilities.MathUtil
  Returns the smallest power of 2 greater than or equal to the specified value.
PowderBlue - Static variable in class ur_rna.Utilities.Colors
PredictBimolStructureWindow - Class in ur_rna.RNAstructureUI.windows
PredictBimolStructureWindow() - Constructor for class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
  Constructor.
PredictBimolStructureWindow.PredictTask - Class in ur_rna.RNAstructureUI.windows
PredictionResultsWindow - Class in ur_rna.RNAstructureUI.windows
  Used by the Predict*StructureWindow classes to show prediction results to the user.
PredictionResultsWindow() - Constructor for class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
PredictionResultsWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
PredictionResultsWindow.PlotResult - Class in ur_rna.RNAstructureUI.windows
PredictMenu - Class in ur_rna.RNAstructureUI.menus
  A class that creates a "File" menu.
PredictMenu() - Constructor for class ur_rna.RNAstructureUI.menus.PredictMenu
  Constructor.
PredictMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
PredictMultiStructureWindow - Class in ur_rna.RNAstructureUI.windows
PredictMultiStructureWindow() - Constructor for class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
  Constructor.
PredictMultiStructureWindow.PredictTask - Class in ur_rna.RNAstructureUI.windows
PredictMultiStructureWindow.SequenceItem - Class in ur_rna.RNAstructureUI.windows
PredictProbablePairs(float) - Method in class ur_rna.RNAstructure.backend.RNA
PredictProbablePairs() - Method in class ur_rna.RNAstructure.backend.RNA
PredictSingleStructureTask() - Constructor for class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
PredictSingleStructureWindow - Class in ur_rna.RNAstructureUI.windows
PredictSingleStructureWindow() - Constructor for class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
  Constructor.
PredictSingleStructureWindow.PredictSingleStructureTask - Class in ur_rna.RNAstructureUI.windows
PredictTask() - Constructor for class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
PredictTask() - Constructor for class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
PredictTask() - Constructor for class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
PredictTaskBase() - Constructor for class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
PredictTwoStructureWindow - Class in ur_rna.RNAstructureUI.windows
PredictTwoStructureWindow() - Constructor for class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
  Constructor.
PredictTwoStructureWindow.PredictTask - Class in ur_rna.RNAstructureUI.windows
PredictWindowBase - Class in ur_rna.RNAstructureUI.windows
  A base class for the Structure Prediction Windows
PredictWindowBase() - Constructor for class ur_rna.RNAstructureUI.windows.PredictWindowBase
PredictWindowBase.BackgroundTask - Interface in ur_rna.RNAstructureUI.windows
PredictWindowBase.FieldInfo - Class in ur_rna.RNAstructureUI.windows
PredictWindowBase.FileFieldInfo - Class in ur_rna.RNAstructureUI.windows
PredictWindowBase.PredictTaskBase - Class in ur_rna.RNAstructureUI.windows
preemptFileName - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
preemptFiltersRequired - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
preemptNextFileNameRequest(String, String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Causes the next call to getFileName to return with the specified file WITHOUT showing the dialog.
preemptTimeout - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
preferencesFile - Static variable in class ur_rna.Utilities.prefs.FilePreferences.Factory
preferencesNode - Static variable in class ur_rna.RNAstructureUI.RNAstructure
preferredDialogWidth - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The preferred dialog width.
prefix - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
PREFS - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
prefs - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
prefs() - Method in class ur_rna.StructureEditor.Program
prefs - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
prefs - Variable in class ur_rna.Utilities.prefs.FilePreferences
PREFS - Static variable in class ur_rna.Utilities.swing.FileDialog
prepareAdd() - Method in class ur_rna.StructureEditor.services.RecentFileList
prepareDraw(boolean) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
prepareDraw(boolean) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
prepareDraw(boolean) - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
prepareDraw(boolean) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
prepareDraw(boolean) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
PrettyJSON - Static variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
PrettySSON - Static variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
prev - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
prevBias - Variable in class ur_rna.StructureEditor.services.RnaDrawController
prevBounds - Variable in class ur_rna.StructureEditor.ui.DrawPanel
prevCharIsCR - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
prevCharIsLF - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
prevInHelix() - Method in class ur_rna.StructureEditor.models.Bond
previousCenter - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
prevModifiers - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
prevPos - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
prevStart - Variable in class ur_rna.StructureEditor.services.RnaDrawController
prevTheta - Variable in class ur_rna.StructureEditor.services.RnaDrawController
prevValue - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
prevWindow - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
prgProgress - Variable in class ur_rna.Utilities.swing.WaitDialog
prgTaskProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
prgTaskProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
prgTaskProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
prgTaskProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
prgTaskProgress - Variable in class ur_rna.StructureEditor.windows.DrawWindow
primaryTypes - Static variable in enum ur_rna.StructureEditor.FileType
PRIMITIVE - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
print(String) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
print(Graphics, PageFormat, int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Render the panel for the print job.
print_det(double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
print_mat(double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
printAll() - Method in class ur_rna.Utilities.StopWatch
  Prints the elapsed time and current state of all named StopWatches.
printAll(long) - Method in class ur_rna.Utilities.StopWatch
  Prints the elapsed time and current state of all named StopWatches
printAll(String, long) - Method in class ur_rna.Utilities.StopWatch
  Prints the elapsed time and current state of all named StopWatches using the specified format.
PrintDPI - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
printf(String, String, Object...) - Static method in class ur_rna.Utilities.StopWatch
  Write a message to the named StopWatch.
printf(String, Object...) - Method in class ur_rna.Utilities.StopWatch
printHierarchyTrace() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
println(String) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
println(String, String, String) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
println(String, String) - Static method in class ur_rna.Utilities.StopWatch
  Write a message to the named StopWatch.
println(String) - Method in class ur_rna.Utilities.StopWatch
PrintMenu() - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu
  Constructor.
printPanel() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Print if the user decides to, then reset the printer job properties.
probColorRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
probComparisonChanged(ItemEvent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
ProbKnot(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnot(int) - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnot() - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnotFromSample(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnotFromSample(int) - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnotFromSample() - Method in class ur_rna.RNAstructure.backend.RNA
ProbKnotWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the ProbKnot module, which predicts pseudoknots in a strand of nucleic acids.
ProbKnotWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.ProbKnotWindow
  Constructor.
ProblemwithStructures() - Method in class ur_rna.RNAstructure.backend.structure
process(List<Void>) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
  Receives data chunks from the `publish` method asynchronously on the Event Dispatch Thread.
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.AccessFoldWindow
processCommand(String, ChildWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  Do any actions specific to this window.
processCommand(String) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
  Perform an action specific to this window.
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  Perform an action specific to this window.
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Perform an action specific to this window.
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Perform an action specific to this window.
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
processCommand(InternalWindow.CommandInfo) - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
processOutput(Object) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
program - Variable in class ur_rna.StructureEditor.MainFrame
Program - Class in ur_rna.StructureEditor
  Main class for running the structure editor as a standalone drawing program.
Program() - Constructor for class ur_rna.StructureEditor.Program
Program.StartupArgs - Class in ur_rna.StructureEditor
programSettings() - Method in interface ur_rna.StructureEditor.services.SceneController
programSettingsChanged(Settings) - Method in class ur_rna.StructureEditor.services.RnaDrawController
programSettingsUpdated() - Method in class ur_rna.StructureEditor.windows.ChildFrame
  Called when Program Settings have changed.
programSettingsUpdated() - Method in class ur_rna.StructureEditor.windows.DrawWindow
programTitle - Static variable in class ur_rna.Utilities.swing.Dialogs
progress() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
progressBar - Variable in class ur_rna.RNAstructureUI.ui.ProgressPanel
ProgressChange - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
progressChanged(int) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
ProgressHandler - Class in ur_rna.RNAstructure.backend
ProgressHandler(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.ProgressHandler
ProgressHandler_cancel(long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_canceled(long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_progress(long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_reset(long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_update__SWIG_0(long, ProgressHandler, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_update__SWIG_1(long, ProgressHandler, double, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
ProgressHandler_updateFraction(long, ProgressHandler, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
progressIndeterminate - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
progressIndicator - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
  The progress bar dialog for this window.
ProgressPanel - Class in ur_rna.RNAstructureUI.ui
ProgressPanel() - Constructor for class ur_rna.RNAstructureUI.ui.ProgressPanel
ProgressPanel(String, ActionListener, ActionListener) - Constructor for class ur_rna.RNAstructureUI.ui.ProgressPanel
progressTotal - Variable in class ur_rna.Utilities.swing.WaitDialog
progressValue - Variable in class ur_rna.Utilities.swing.WaitDialog
projectedOn(Vec2D) - Method in class ur_rna.Utilities.geom.Vec2D
  Calculates the projection of this vector onto the vector specified by direction.
prompt(String) - Static method in class ur_rna.Utilities.swing.Dialogs
prompt(String, String, int) - Static method in class ur_rna.Utilities.swing.Dialogs
prompt(String, String, Object[], Object) - Static method in class ur_rna.Utilities.swing.Dialogs
PROMPT_NONE - Static variable in class ur_rna.Utilities.swing.Dialogs
PROMPT_OK_CANCEL - Static variable in class ur_rna.Utilities.swing.Dialogs
PROMPT_YES_NO - Static variable in class ur_rna.Utilities.swing.Dialogs
PROMPT_YES_NO_CANCEL - Static variable in class ur_rna.Utilities.swing.Dialogs
promptDraw() - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
promptDraw(String, String) - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
PROP_SEPARATOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
propertyChange(PropertyChangeEvent) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
propertyChanged(String, PropertyChangeEvent) - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
propertyChanged(String, PropertyChangeEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
propsToString() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
protectedExamplesDir - Static variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
provider - Static variable in class ur_rna.Utilities.AppInfo
Proxy(Component) - Constructor for class ur_rna.Utilities.swing.IMergeItem.Proxy
Proxy(Component, int) - Constructor for class ur_rna.Utilities.swing.IMergeItem.Proxy
pseudoBondWidth - Variable in class ur_rna.StructureEditor.models.DrawSettings
PseudoknotWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the RemovePseudoknots module, which removes pseudoknots from a nucleic acid sequence.
PseudoknotWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.PseudoknotWindow
  Constructor.
PUNCTUATION - Static variable in class ur_rna.Utilities.CharType
Purple - Static variable in class ur_rna.Utilities.Colors
push(int, int) - Method in class ur_rna.StructureEditor.models.Motif.IntervalStack
pushLevel(boolean) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
pushNode(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
pushState() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  Pushes a new GraphicsStyle (cloned from the current one) to the top of the stack and returns it.
put(Preferences, String, String) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
put(String, Object) - Method in class ur_rna.StructureEditor.models.HistoryState
put(String, String) - Method in class ur_rna.StructureEditor.services.UserPrefs
putData(String, Serializable) - Method in exception ur_rna.Utilities.ExtensibleException
putData(String, Serializable, boolean) - Method in exception ur_rna.Utilities.ExtensibleException
putList(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
putMap(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
putSpi(String, String) - Method in class ur_rna.Utilities.prefs.FilePreferences
PX_PER_MM - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter

## Q

Quad(T1, T2, T3, T4) - Constructor for class ur_rna.Utilities.Tuple.Quad
Quad() - Constructor for class ur_rna.Utilities.Tuple.Quad
QUESTION - Static variable in class ur_rna.Utilities.swing.Dialogs
quoteAlways - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
quoteIfNeeded(String) - Static method in class ur_rna.Utilities.SimpleDataSerializer
quoteProps - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
QUOTES - Static variable in class ur_rna.Utilities.CharType
  Single (') and double (") quotes.

## R

radio - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
RadioButtonPanel - Class in ur_rna.RNAstructureUI.ui
  A class that creates a panel containing a group of radio buttons.
RadioButtonPanel(String, String, ActionListener, String...) - Constructor for class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Constructor.
radius() - Method in class ur_rna.Utilities.geom.Ellipses.Circle
radius(double) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
radToDeg - Static variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
range - Variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
  The number panel that holds the range data.
rangeCheck(int) - Method in class ur_rna.StructureEditor.models.Strand
rangeCheck(int) - Method in class ur_rna.StructureEditor.models.StrandList
rangeCheckForAdd(int) - Method in class ur_rna.StructureEditor.models.Strand
RangeDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
  Constructor.
rayToModel(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
rayToModel(Point2D, Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
rayToScreen(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
rayToScreen(Point2D, Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
RBRACE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
RBRACKET - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
rc - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearOp
read() - Method in class ur_rna.Utilities.ExtendedBufferedReader
read(char[], int, int) - Method in class ur_rna.Utilities.ExtendedBufferedReader
ReadAlignmentConstraints(String) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
readAll(InputStream, Charset) - Static method in class ur_rna.Utilities.Strings
readAll(InputStream, String, int) - Static method in class ur_rna.Utilities.Strings
readAll(InputStream, String) - Static method in class ur_rna.Utilities.Strings
readAll(InputStream) - Static method in class ur_rna.Utilities.Strings
readAll(InputStream, Charset, int) - Static method in class ur_rna.Utilities.Strings
ReadByte() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
readChar() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Read a character.
ReadConstraints(String) - Method in class ur_rna.RNAstructure.backend.RNA
readCteDrawingFile(String) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
readCteDrawingFile(Reader) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
readData(String, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
ReadDMS(String) - Method in class ur_rna.RNAstructure.backend.RNA
ReadDSO(String) - Method in class ur_rna.RNAstructure.backend.RNA
readDynalignAlignmentConstraintsFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
reader - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
ReadExperimentalPairBonus(String, double, double) - Method in class ur_rna.RNAstructure.backend.RNA
ReadExperimentalPairBonus(String, double, double) - Method in class ur_rna.RNAstructure.backend.structure
ReadExperimentalPairBonus(String, double) - Method in class ur_rna.RNAstructure.backend.structure
ReadExperimentalPairBonus(String) - Method in class ur_rna.RNAstructure.backend.structure
readFileAsScene(String, FileType) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
readFoldingConstraintsFile(String, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
readImageData() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Read image data from a particular file.
readImageData() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
readImageData() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
readLine() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
readLine() - Method in class ur_rna.Utilities.ExtendedBufferedReader
  Does not call `BufferedReader.readLine()` because that method drops the line terminator(s).
readLine(boolean) - Method in class ur_rna.Utilities.ExtendedBufferedReader
readLine(boolean, int) - Method in class ur_rna.Utilities.ExtendedBufferedReader
readLinkers(char[], int[]) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
readNsdDrawingFile(String) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
readNsdDrawingFile(Reader) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
readNsdDrawingFile(Object) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
readNumericRules(List<ColorizeDialog.ValueColorRule>, String, String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
ReadOffset(String, String) - Method in class ur_rna.RNAstructure.backend.structure
readOnlyData - Variable in exception ur_rna.Utilities.ExtensibleException
readOnlyNucs - Variable in class ur_rna.StructureEditor.models.StrandList
readProps() - Method in class ur_rna.Utilities.prefs.FilePreferences
readSceneFile(String, FileType) - Static method in class ur_rna.StructureEditor.AppActions
readSequenceData(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
ReadSHAPE(String, double, double, RestraintType, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
ReadSHAPE(String, double, double, RestraintType) - Method in class ur_rna.RNAstructure.backend.RNA
ReadSHAPE(String, double, double) - Method in class ur_rna.RNAstructure.backend.RNA
ReadSHAPE(String, double, double, double, double, RestraintType) - Method in class ur_rna.RNAstructure.backend.RNA
ReadSHAPE(String, double, double, double, double) - Method in class ur_rna.RNAstructure.backend.RNA
ReadSHAPE(String, float, float) - Method in class ur_rna.RNAstructure.backend.structure
ReadSHAPE(String, RestraintType, boolean) - Method in class ur_rna.RNAstructure.backend.structure
ReadSHAPE(String, RestraintType) - Method in class ur_rna.RNAstructure.backend.structure
ReadSHAPE(String) - Method in class ur_rna.RNAstructure.backend.structure
ReadSSO(String) - Method in class ur_rna.RNAstructure.backend.RNA
readStructureData(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
readSystemProperties() - Method in class ur_rna.Utilities.AppLog
readTempFile(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
ReadThermodynamic(String, String, double) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
ReadThermodynamic(String, String) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
ReadThermodynamic(String) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
ReadThermodynamic() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
rebuildMainMenu(MenuList) - Method in class ur_rna.RNAstructureUI.AppMainFrame
rebuildMainMenu(Collection<? extends Component>) - Method in class ur_rna.StructureEditor.MainFrame
rebuildToolBar() - Method in class ur_rna.RNAstructureUI.AppMainFrame
rebuildToolBar(Collection<? extends Component>) - Method in class ur_rna.StructureEditor.MainFrame
recent - Variable in class ur_rna.StructureEditor.menus.FileMenu
recentDirs - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
recentDirs - Static variable in class ur_rna.Utilities.swing.FileDialog
RecentFile(String) - Constructor for class ur_rna.StructureEditor.services.RecentFileList.RecentFile
RecentFile(String, FileType) - Constructor for class ur_rna.StructureEditor.services.RecentFileList.RecentFile
RecentFileButton - Class in ur_rna.RNAstructureUI.ui
RecentFileButton() - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton
RecentFileButton(String, String, ActionListener, String) - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton
RecentFileButton(String, String, Consumer<File>) - Constructor for class ur_rna.RNAstructureUI.ui.RecentFileButton
RecentFileButton.ExtensionFileFilter - Class in ur_rna.RNAstructureUI.ui
RecentFileList - Class in ur_rna.StructureEditor.services
  List of recent files that prevents duplicate paths.
RecentFileList() - Constructor for class ur_rna.StructureEditor.services.RecentFileList
RecentFileList.RecentFile - Class in ur_rna.StructureEditor.services
RecentFileMenuManager - Class in ur_rna.StructureEditor.services
  Handles recent file menu.
RecentFileMenuManager(MergeMenu) - Constructor for class ur_rna.StructureEditor.services.RecentFileMenuManager
recentFiles - Static variable in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
recentFiles - Variable in class ur_rna.StructureEditor.MainFrame
recentFilesMenu - Variable in class ur_rna.StructureEditor.MainFrame
recentFilesMenu() - Method in class ur_rna.StructureEditor.menus.FileMenu
recentPathPreferences - Static variable in class ur_rna.RNAstructureUI.ui.StandardFileChooser
recentPathPreferences - Static variable in class ur_rna.Utilities.swing.FileDialog
Rectangles - Class in ur_rna.Utilities.geom
Rectangles() - Constructor for class ur_rna.Utilities.geom.Rectangles
Red - Static variable in class ur_rna.Utilities.Colors
redo() - Method in class ur_rna.StructureEditor.services.History
redo() - Method in class ur_rna.StructureEditor.services.RnaDrawController
redo() - Method in interface ur_rna.StructureEditor.services.SceneController
redraw() - Method in class ur_rna.StructureEditor.services.RnaDrawController
redrawCircular(RnaScene) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawCircular() - Method in class ur_rna.StructureEditor.windows.DrawWindow
redrawHelix(Motif.Helix) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawLinear(RnaScene) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawLinear() - Method in class ur_rna.StructureEditor.windows.DrawWindow
redrawLoop(Motif.Loop) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawMultiLoop(Motif.MultiLoop, SceneController) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawRadial(RnaScene) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawRadial(RnaSceneGroup) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
redrawScene() - Method in class ur_rna.StructureEditor.windows.DrawWindow
redrawSelection() - Method in class ur_rna.StructureEditor.services.RnaDrawController
redrawStructure() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
RefBool() - Constructor for class ur_rna.Utilities.ObjTools.RefBool
RefBool(boolean) - Constructor for class ur_rna.Utilities.ObjTools.RefBool
RefInt() - Constructor for class ur_rna.Utilities.ObjTools.RefInt
RefInt(int) - Constructor for class ur_rna.Utilities.ObjTools.RefInt
reflect(Point2D, Vec2D, Point2D) - Static method in class ur_rna.Utilities.geom.Vec2D
reflectedClassLoaderField - Static variable in class ur_rna.Utilities.ClassLoaderInfo
RefoldSection - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
ReFoldSingleStrand(float, int, int) - Method in class ur_rna.RNAstructure.backend.RNA
ReFoldSingleStrand(float, int) - Method in class ur_rna.RNAstructure.backend.RNA
ReFoldSingleStrand(float) - Method in class ur_rna.RNAstructure.backend.RNA
ReFoldSingleStrand() - Method in class ur_rna.RNAstructure.backend.RNA
RefoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the refold module, which refolds a previous folding calculation from a save file.
RefoldWindow() - Constructor for class ur_rna.RNAstructureUI.windows.RefoldWindow
  Constructor.
refresh() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Refresh this dialog.
refreshSeqList(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
refreshSeqList(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
refreshSeqList() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
RefStr() - Constructor for class ur_rna.Utilities.ObjTools.RefStr
RefStr(String) - Constructor for class ur_rna.Utilities.ObjTools.RefStr
regex - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  The array of regexes used to pull data about a structure.
register() - Static method in class ur_rna.StructureEditor.services.UserPrefs
register() - Static method in class ur_rna.Utilities.prefs.FilePreferences.Factory
  Sets the system property `java.util.prefs.PreferencesFactory` to the `FilePreferences.Factory` class so that the `Preferences` class will use it for the global singleton PreferencesFactory.
register(File) - Static method in class ur_rna.Utilities.prefs.FilePreferences.Factory
reIndexNucs(int) - Method in class ur_rna.StructureEditor.models.StrandList
ReInit(InputStream) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Reinitialise.
ReInit(InputStream, String) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Reinitialise.
ReInit(Reader) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Reinitialise.
ReInit(GuiTestScriptParserTokenManager) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Reinitialise.
ReInit(JavaCharStream) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Reinitialise parser.
ReInit(JavaCharStream, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Reinitialise parser.
ReInit(Reader, int, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(Reader, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(Reader) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream, int, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream, String, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream, int, int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream, String) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInit(InputStream) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Reinitialise.
ReInitRounds() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
REL_LABEL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
relationship - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef
relationshipKind - Variable in class ur_rna.GUITester.ScriptParser.ASTGuiReference
relative - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef
relative - Variable in class ur_rna.GUITester.ScriptParser.ASTGuiReference
relativeToString(boolean) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
RELEASE_DATE - Static variable in interface ur_rna.RNAstructure.RNAstructureVersion
RELEASE_DATE - Static variable in class ur_rna.RNAstructureUI.RNAstructure
ReloadDataTables(double) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
ReloadDataTables() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
rem(EventSource<T>, T) - Method in class ur_rna.Utilities.EventSource.Manager
REMASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
RemBonds - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
remove(String) - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
remove(int) - Method in class ur_rna.StructureEditor.models.Strand
remove(RecentFileList.RecentFile) - Method in class ur_rna.StructureEditor.services.RecentFileList
remove(String) - Method in class ur_rna.StructureEditor.services.RecentFileList
remove() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
remove() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
remove() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
remove() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
remove(TSubscriber) - Method in class ur_rna.Utilities.EventSource
remove() - Method in class ur_rna.Utilities.Filter.FilterIterator
remove(Component) - Method in class ur_rna.Utilities.swing.InputAdapter.Mouse
removeActionListener(ActionListener) - Method in class ur_rna.Utilities.swing.JActionLabel
removeAll(Collection<?>) - Method in class ur_rna.StructureEditor.models.Strand
removeAll() - Method in class ur_rna.Utilities.swing.ButtonGroupList
RemoveAllStructures() - Method in class ur_rna.RNAstructure.backend.structure
removeAllTabTraversalKeys(Component...) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
  Disable the default behavior of TAB, Shift+TAB, Ctrl+TAB, Ctrl+Shift+TAB etc, which is to move to the next/previous component respectively.
removeAnnotation() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
RemoveBasePair(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
RemoveBasePair(int) - Method in class ur_rna.RNAstructure.backend.RNA
removeCancelListener(ActionListener) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
removeChangeHandler(Runnable) - Method in class ur_rna.StructureEditor.Settings
removeColors(boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
RemoveConstraints() - Method in class ur_rna.RNAstructure.backend.RNA
RemoveConstraints() - Method in class ur_rna.RNAstructure.backend.structure
removeDirect(int) - Method in class ur_rna.StructureEditor.models.StrandList
RemoveEnergyLabels(String) - Method in class ur_rna.RNAstructure.backend.structure
RemoveEnergyLabels() - Method in class ur_rna.RNAstructure.backend.structure
removeExt() - Method in class ur_rna.Utilities.PathTools.FileName
  Returns the original path, including the directory, but without any extension.
removeFlagPrefix(String) - Method in class ur_rna.Utilities.CommandLineParser
removeHistoryListener(Consumer<HistoryUpdateEvent>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
removeHistoryListener(Consumer<HistoryUpdateEvent>) - Method in interface ur_rna.StructureEditor.services.SceneController
removeLastRule(List<? extends ColorizeDialog.SimpleColorControl>) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
RemoveLastStructure() - Method in class ur_rna.RNAstructure.backend.structure
removeListener - Variable in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
removeListener(Object) - Method in class ur_rna.Utilities.swing.TextDocListener
removeListener(ActionListener) - Method in class ur_rna.Utilities.swing.UiAction
  Remove an ActionListener that should no longer be notified when this Action is invoked.
removeMenuMnemonics(Component[]) - Method in class ur_rna.RNAstructureUI.AppMainFrame
removeMenuMnemonics(Component[]) - Method in class ur_rna.StructureEditor.MainFrame
removeMnemonics(Collection<? extends Component>) - Method in class ur_rna.StructureEditor.MainFrame
removeNodeSpi() - Method in class ur_rna.Utilities.prefs.FilePreferences
removeNonHeaders(JComponent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
removeNucs(Nuc[]) - Method in class ur_rna.StructureEditor.models.RnaScene
RemovePair(int, int) - Method in class ur_rna.RNAstructure.backend.structure
RemovePair(int) - Method in class ur_rna.RNAstructure.backend.structure
RemovePairs(int, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
RemovePairs(int) - Method in class ur_rna.RNAstructure.backend.RNA
RemovePairs() - Method in class ur_rna.RNAstructure.backend.RNA
removeProps(String, boolean) - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
removeSceneUpdateListener(Consumer<SceneUpdateEvent>) - Method in class ur_rna.StructureEditor.services.RnaDrawController
removeSceneUpdateListener(Consumer<SceneUpdateEvent>) - Method in interface ur_rna.StructureEditor.services.SceneController
removeSpi(String) - Method in class ur_rna.Utilities.prefs.FilePreferences
RemoveStructure(int) - Method in class ur_rna.RNAstructure.backend.structure
removeTabTraversalKeys(Component, AWTKeyStroke...) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
  Disable the default behavior of TAB, Shift+TAB, Ctrl+TAB, Ctrl+Shift+TAB etc, which is to move to the next/previous component respectively.
removeUpdate(DocumentEvent) - Method in interface ur_rna.Utilities.swing.SimpleDocumentListener
removeUpdate(DocumentEvent) - Method in class ur_rna.Utilities.swing.TextDocListener
removeUpdateListener(ActionListener) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
removeWindowItems() - Method in class ur_rna.StructureEditor.menus.WindowsMenu
render(Graphics2D, View2D, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
render(Graphics2D, View2D, boolean) - Method in interface ur_rna.StructureEditor.services.SceneRenderer
renderer - Variable in class ur_rna.StructureEditor.ui.DrawPanel
renderFullSceneToImage(Graphics2D, boolean) - Method in class ur_rna.StructureEditor.windows.DrawWindow
repaintRequired() - Method in interface ur_rna.StructureEditor.services.drawing.ICanvas
repaintRequired() - Method in class ur_rna.StructureEditor.ui.DrawPanel
replace(int, int, String) - Method in class ur_rna.Utilities.StringBuilderEx
replaceNonPrintable(String, char, char) - Static method in class ur_rna.Utilities.Strings
replaceNonPrintableU(String, char, char) - Static method in class ur_rna.Utilities.Strings
  Same as `Strings.replaceNonPrintable(java.lang.String, char, char)` but includes support for unicode characters, including Surrogate pairs.
replaceResUrls(String) - Static method in class ur_rna.StructureEditor.Program
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ActionOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.BackgroundOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearHintsOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClearOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ClipOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ColorOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.CompositeOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.ControlOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.FontOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.PaintOp
replay(Graphics2D) - Method in interface ur_rna.StructureEditor.services.drawing.export.GraphicsOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
replay(Graphics2D) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp
Report - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
RequestFocusListener - Class in ur_rna.RNAstructureUI.utilities
  Convenience class to request focus on a component.
RequestFocusListener() - Constructor for class ur_rna.RNAstructureUI.utilities.RequestFocusListener
RequestFocusListener(boolean) - Constructor for class ur_rna.RNAstructureUI.utilities.RequestFocusListener
require(Pattern) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
REQUIRED_DLL_VERSION - Static variable in class ur_rna.RNAstructureUI.RNAstructure
reserve(long) - Method in class ur_rna.RNAstructure.backend.CDblVector
reserve(long) - Method in class ur_rna.RNAstructure.backend.CIntVector
reset() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
reset() - Method in class ur_rna.RNAstructure.backend.ProgressHandler
reset() - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
  Reset the main frame message bar text to its default.
reset() - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
  Reset the main frame message bar text to its default.
reset() - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Reset all properties to their default values.
reset() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
reset() - Method in interface ur_rna.Utilities.RunnableOnce
  Resets the internal state of the RunnableOnce instance, so `Runnable.run()` can be called again, even if it has already been called once.
reset() - Method in class ur_rna.Utilities.RunOnce
  Resets the internal state of the RunnableOnce instance, so `RunOnce.run()` can be called again, even if it has already been called once.
reset() - Method in class ur_rna.Utilities.StopWatch
  Reset elapsed time to 0 and stop the timer.
reset() - Method in class ur_rna.Utilities.swing.MergeManager
reset() - Method in class ur_rna.Utilities.swing.TextDocListener
ResetError() - Method in class ur_rna.RNAstructure.backend.RNA
ResetError() - Method in class ur_rna.RNAstructure.backend.TwoRNA
resetExistingBaseColors(int) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
resetField(Number) - Method in class ur_rna.RNAstructureUI.ui.NumberField
  Reset a field value, if it's within bounds.
resetField(Number, Number, Number) - Method in class ur_rna.RNAstructureUI.ui.NumberField
  Reset a field value and bounds.
resetIfChanged() - Method in class ur_rna.Utilities.swing.TextDocListener
  Sets the `TextDocListener.hasChanged()` state to false and returns the previous value before the reset.
resetInfoLabel() - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Reset the info bar at the bottom of the main window to its default.
resetInfoLabel() - Method in class ur_rna.StructureEditor.MainFrame
  Reset the info bar at the bottom of the main window to its default.
resetLocation() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
resetMessage() - Method in exception ur_rna.Utilities.ExtensibleException
  If a new message has been stored (using `setMessage`) this will revert the message back to the original (passed in the constructor.)
resetModel(int, int, int) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
  Reset the model for the spinner.
resetOffset() - Method in class ur_rna.StructureEditor.ui.DrawPanel
resetOptionsInPanel(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
resetProbColorRules() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
resetRnaCoords() - Method in class ur_rna.StructureEditor.services.RnaDrawController
resetStructure() - Method in class ur_rna.StructureEditor.services.RnaDrawController
resetSymbolColorRules() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
resetTabTraversalKeys(Component...) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
  Some Components (e.g.
resetValueColorRules() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
ResizeLoop - Static variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
resizeMultiLoopIcon - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
resizeSegmentIcon - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
reSlash - Static variable in class ur_rna.Utilities.PathTools.FileName
ResourceLoader - Class in ur_rna.Utilities
ResourceLoader() - Constructor for class ur_rna.Utilities.ResourceLoader
ResourceLoader(String) - Constructor for class ur_rna.Utilities.ResourceLoader
ResourceLoader(String, ClassLoader) - Constructor for class ur_rna.Utilities.ResourceLoader
ResourceLoader(Class, String) - Constructor for class ur_rna.Utilities.ResourceLoader
  Create a new ResourceLoader and set its resource directory based on the package name of the specified class by converting each dot (.) in the package name to a slash (/).
Resources - Class in ur_rna.RNAstructureUI.utilities
Resources() - Constructor for class ur_rna.RNAstructureUI.utilities.Resources
RESOURCES - Static variable in class ur_rna.StructureEditor.Program
restart() - Method in class ur_rna.Utilities.StopWatch
  Reset elapsed time to 0 and start the timer.
RestraintType - Enum in ur_rna.RNAstructure.backend
RestraintType() - Constructor for enum ur_rna.RNAstructure.backend.RestraintType
RestraintType(int) - Constructor for enum ur_rna.RNAstructure.backend.RestraintType
RestraintType(RestraintType) - Constructor for enum ur_rna.RNAstructure.backend.RestraintType
RestraintType.SwigNext - Class in ur_rna.RNAstructure.backend
restyleSequence() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
restyleStructure() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
result - Variable in class ur_rna.RNAstructureUI.utilities.RunFunc
result() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
resumeChangeNotification() - Method in class ur_rna.StructureEditor.Settings
resumeRecording() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
resumeRedraw(boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
resumeUpdate() - Method in class ur_rna.StructureEditor.models.StrandList
resumeUpdate(boolean) - Method in class ur_rna.StructureEditor.models.StrandList
resumeUpdates() - Method in class ur_rna.StructureEditor.services.RnaDrawController
resumeUpdates() - Method in class ur_rna.Utilities.swing.TextDocListener
retainAll(Collection<?>) - Method in class ur_rna.StructureEditor.models.Strand
reverse() - Method in class ur_rna.Utilities.StringBuilderEx
Revision - Variable in class ur_rna.Utilities.Version
revSeqLookup - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
RHS - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
right(Nuc) - Method in class ur_rna.StructureEditor.models.Bond
  Assume we are traveling around a multi-branch loop from 5' to 3'.
rightCodeQuote - Static variable in exception ur_rna.Utilities.SyntaxErrorException
  `SyntaxErrorException.leftCodeQuote` and `SyntaxErrorException.rightCodeQuote` are the quote characters used to distinguish the offending segment of code in the error message.
RNA - Class in ur_rna.RNAstructure.backend
RNA(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int, String, boolean, boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int, String, boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int, String) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int, Thermodynamics) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int, boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(String, int) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA(boolean) - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA() - Constructor for class ur_rna.RNAstructure.backend.RNA
RNA_AddComment__SWIG_0(long, RNA, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_AddComment__SWIG_1(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_BreakPseudoknot__SWIG_0(long, RNA, boolean, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_BreakPseudoknot__SWIG_1(long, RNA, boolean, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_BreakPseudoknot__SWIG_2(long, RNA, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_BreakPseudoknot__SWIG_3(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_CalculateFreeEnergy__SWIG_0(long, RNA, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_CalculateFreeEnergy__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_CalculateFreeEnergy__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ContainsPseudoknot(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_CopyThermo(long, RNA, long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_DetermineDrawingCoordinates__SWIG_0(long, RNA, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_DetermineDrawingCoordinates__SWIG_1(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_EnsureStructureCapcacity(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_0(long, RNA, float, int, int, String, int, boolean, boolean, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_1(long, RNA, float, int, int, String, int, boolean, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_2(long, RNA, float, int, int, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_3(long, RNA, float, int, int, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_4(long, RNA, float, int, int, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_5(long, RNA, float, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_6(long, RNA, float, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_7(long, RNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_FoldSingleStrand__SWIG_8(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceDoubleStranded(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceFMNCleavage(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceMaximumPairingDistance(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceModification(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForcePair(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceProhibitPair(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ForceSingleStranded(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GenerateAllSuboptimalStructures__SWIG_0(long, RNA, float, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GenerateAllSuboptimalStructures__SWIG_1(long, RNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GenerateAllSuboptimalStructures__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetBackboneType(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetCommentString__SWIG_0(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetCommentString__SWIG_1(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetEnsembleDefect__SWIG_0(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetEnsembleDefect__SWIG_1(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetEnsembleEnergy(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetErrorCode(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetErrorDetails(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetErrorMessage(int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedDoubleStranded(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedFMNCleavage(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedModification(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedPair(long, RNA, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedProhibitedPair(long, RNA, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetForcedSingleStranded(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetFreeEnergy(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetFullErrorMessage(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_getIntAt(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_getInts(long, RNA, int[], int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetLabelXCoordinate(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetLabelYCoordinate(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetMaximumPairingDistance(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNucleotide(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNucleotideXCoordinate(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNucleotideYCoordinate(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedDoubleStranded(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedFMNCleavages(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedModifications(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedPairs(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedProhibitedPairs(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetNumberOfForcedSingleStranded(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetPair__SWIG_0(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetPair__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetPairEnergy(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetPairProbabilities(long, RNA, double[], int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetPairProbability(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetProgress(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetSequence(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetSequenceLength(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetStructure(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_GetStructureNumber(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_initInts(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_MaximizeExpectedAccuracy__SWIG_0(long, RNA, double, int, int, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_MaximizeExpectedAccuracy__SWIG_1(long, RNA, double, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_MaximizeExpectedAccuracy__SWIG_2(long, RNA, double, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_MaximizeExpectedAccuracy__SWIG_3(long, RNA, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_MaximizeExpectedAccuracy__SWIG_4(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PartitionFunction__SWIG_0(long, RNA, String, double, boolean, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PartitionFunction__SWIG_1(long, RNA, String, double, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PartitionFunction__SWIG_2(long, RNA, String, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PartitionFunction__SWIG_3(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PartitionFunction__SWIG_4(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PredictProbablePairs__SWIG_0(long, RNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_PredictProbablePairs__SWIG_1(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnot__SWIG_0(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnot__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnot__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnotFromSample__SWIG_0(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnotFromSample__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ProbKnotFromSample__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadConstraints(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadDMS(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadDSO(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadExperimentalPairBonus(long, RNA, String, double, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSHAPE__SWIG_0(long, RNA, String, double, double, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSHAPE__SWIG_1(long, RNA, String, double, double, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSHAPE__SWIG_2(long, RNA, String, double, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSHAPE__SWIG_3(long, RNA, String, double, double, double, double, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSHAPE__SWIG_4(long, RNA, String, double, double, double, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReadSSO(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReFoldSingleStrand__SWIG_0(long, RNA, float, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReFoldSingleStrand__SWIG_1(long, RNA, float, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReFoldSingleStrand__SWIG_2(long, RNA, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ReFoldSingleStrand__SWIG_3(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemoveBasePair__SWIG_0(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemoveBasePair__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemoveConstraints(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemovePairs__SWIG_0(long, RNA, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemovePairs__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_RemovePairs__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_ResetError(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SetErrorDetails(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SetExtrinsic(long, RNA, int, int, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SetProgress(long, RNA, long, ProgressHandler) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SpecifyPair__SWIG_0(long, RNA, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SpecifyPair__SWIG_1(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_Stochastic__SWIG_0(long, RNA, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_Stochastic__SWIG_1(long, RNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_Stochastic__SWIG_2(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_StopProgress(long, RNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteConstraints(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteCt(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteDotBracket__SWIG_0(long, RNA, String, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteDotBracket__SWIG_1(long, RNA, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteDotBracket__SWIG_2(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteThermodynamicDetails__SWIG_0(long, RNA, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNA_WriteThermodynamicDetails__SWIG_1(long, RNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
RNABackend - Class in ur_rna.RNAstructure.backend
RNABackend() - Constructor for class ur_rna.RNAstructure.backend.RNABackend
RNABackendConstants - Interface in ur_rna.RNAstructure.backend
RnaBackendException - Exception in ur_rna.RNAstructure
  Encapsulates errors raised in RNABackendJNI functions, e.g.
RnaBackendException() - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(String) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(Throwable) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(String, Throwable) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(String, int) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(String, int, String) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RnaBackendException(String, int, String, Throwable) - Constructor for exception ur_rna.RNAstructure.RnaBackendException
RNABackendJNI - Class in ur_rna.RNAstructure.backend
RNABackendJNI() - Constructor for class ur_rna.RNAstructure.backend.RNABackendJNI
RnaDrawController - Class in ur_rna.StructureEditor.services
  The controller that interprets input from the screens, modifies the RNAscene, keeps a history of changes, and reports updates to subscribed listeners.
RnaDrawController() - Constructor for class ur_rna.StructureEditor.services.RnaDrawController
RnaDrawController.BehaviorMode - Enum in ur_rna.StructureEditor.services
  BehaviorMode defines two separate "behavior modes" that combine selection behavior along with draw-handle and dragging behaviors.
RnaDrawController.Colors - Class in ur_rna.StructureEditor.services
RnaDrawController.MouseHandler - Class in ur_rna.StructureEditor.services
RnaDrawController.NucGroup - Class in ur_rna.StructureEditor.services
RnaDrawController.ScreenNuc - Class in ur_rna.StructureEditor.services
RnaDrawController.SelectionType - Enum in ur_rna.StructureEditor.services
RnaFileIO - Class in ur_rna.StructureEditor.services.fileIO
  RnaFileIO is used to load and save RNA files (CT, SEQ etc)
RnaFileIO() - Constructor for class ur_rna.StructureEditor.services.fileIO.RnaFileIO
RnaFileIO.AsyncTask<TResult> - Interface in ur_rna.StructureEditor.services.fileIO
RnaFileIO.BackendCalc<TResult> - Class in ur_rna.StructureEditor.services.fileIO
  A task that is run in the RNAstructure Backend (JNI).
RnaFileIO.BackgroundWork<TResult> - Class in ur_rna.StructureEditor.services.fileIO
RnaFileIO.NucIndexConverter - Class in ur_rna.StructureEditor.services.fileIO
  The backend uses "III" (or some other character in extended nucleobase alphabets) to indicate an inter-molecular linker.
RnaFileIO.NucIndexConverter.DoubleStrand - Class in ur_rna.StructureEditor.services.fileIO
RnaFileIO.NucIndexConverter.MultiStrand - Class in ur_rna.StructureEditor.services.fileIO
RnaScene - Class in ur_rna.StructureEditor.models
  Encompases all the information needed to an RNA "scene" which can include one or more strands of RNA in a specific 2D layout.
RnaScene() - Constructor for class ur_rna.StructureEditor.models.RnaScene
RnaSceneGroup - Class in ur_rna.StructureEditor.models
  A group of related RnaScene objects.
RnaSceneGroup() - Constructor for class ur_rna.StructureEditor.models.RnaSceneGroup
RnaSceneState - Class in ur_rna.StructureEditor.models
  Represents a compressed version of an RnaScene that can be stored quickly and restored to form an identical RnaScene that is completely separate, in terms of mutable Object references from the original.
RnaSceneState() - Constructor for class ur_rna.StructureEditor.models.RnaSceneState
RnaSceneState.NucState - Class in ur_rna.StructureEditor.models
RNAstructure - Class in ur_rna.RNAstructureUI
  A class that starts the RNAstructure interface.
RNAstructure() - Constructor for class ur_rna.RNAstructureUI.RNAstructure
RNAstructureBackendCalculator - Class in ur_rna.RNAstructureUI
RNAstructureBackendCalculator(long, boolean) - Constructor for class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RNAstructureBackendCalculator() - Constructor for class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RNAstructureBackendCalculator_activateMultilign(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_activateTurboFold(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_addMultilignTuple(long, RNAstructureBackendCalculator, String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_0(long, RNAstructureBackendCalculator, String, String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_addTurboFoldTuple__SWIG_1(long, RNAstructureBackendCalculator, String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildAccessFoldDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildAllSubDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildBifoldDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildBipartitionDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildDuplexFoldDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildDynalignDataStructure(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildEfn2DataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildFoldDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildMaxExpectDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildOligoScreenDataStructure(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildOligoWalkDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildPartitionDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildProbKnotDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRefoldDynalignDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRefoldSingleDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildRemovePseudoknotsDataStructure(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_buildStochasticDataStructure(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_cancelOperation(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_canFoldOligoOligo(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_canFoldOligoSelf(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_clearDynalignAlignmentConstraints(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_clearFoldingConstraints(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_deleteMultilignTuple(long, RNAstructureBackendCalculator, long) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_deleteTurboFoldTuple(long, RNAstructureBackendCalculator, long) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_determineOligoMaximum(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_foldOligo(long, RNAstructureBackendCalculator, String, int, boolean, boolean, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getAllOligoData(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDisplayedOligo(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignAlignmentConstraints(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignAlignmentWindowSize(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getDynalignStructureWindowSize(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getEnvVar(String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_GetErrorCode(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getFoldingConstraints(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getFoldWindowSize(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_GetFullErrorMessage(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getGraphRegionBegin(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getGraphRegionEnd(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxConstraintIndex(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxLoop(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMaxPair(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMostStableOligo(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignCT(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignMaxPairs(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getMultilignSequenceSetData(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getNumMultilignSequences(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getNumTurboFoldSequences(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoLabelData(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoTargetLength(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getOligoTargetSequence(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getProgressNumber(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getRefoldWindowSize(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSaveFile(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceComment(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceData(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSequenceTitle(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getStructureType(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSuboptimalAbsoluteDiff(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getSuboptimalPercentDiff(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTemperature(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldCT(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldSaveFile(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getTurboFoldSequenceSetData(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_getVersion() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_loadDoubleRNA__SWIG_0(long, RNAstructureBackendCalculator, String, String, boolean, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_loadDoubleRNA__SWIG_1(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_loadSingleRNA__SWIG_0(long, RNAstructureBackendCalculator, String, boolean, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_loadSingleRNA__SWIG_1(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readDynalignAlignmentConstraintsFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readFoldingConstraintsFile(long, RNAstructureBackendCalculator, String, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_readSequenceData(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runAccessFold(long, RNAstructureBackendCalculator, String, float, int, double, int, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runAllSub(long, RNAstructureBackendCalculator, String, float, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runBifold(long, RNAstructureBackendCalculator, String, float, int, int, boolean, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runBipartition(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runDuplexFold(long, RNAstructureBackendCalculator, String, float, int, int, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runDynalign(long, RNAstructureBackendCalculator, String, String, String, String, double, int, int, int, float, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runDynalignRefold(long, RNAstructureBackendCalculator, String, String, String, int, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runEfn2(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runFold(long, RNAstructureBackendCalculator, String, int, int, int, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runMaxExpect(long, RNAstructureBackendCalculator, String, double, int, int, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runMultilign(long, RNAstructureBackendCalculator, int, int, int, int, double, boolean, double, int, int, String, boolean, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runOligoScreen(long, RNAstructureBackendCalculator, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runOligoWalk(long, RNAstructureBackendCalculator, String, int, String, boolean, int, int, String, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPartition(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPseudoknotPrediction(long, RNAstructureBackendCalculator, String, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runPseudoknotRemoval(long, RNAstructureBackendCalculator, String, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runRefold(long, RNAstructureBackendCalculator, String, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runStochastic(long, RNAstructureBackendCalculator, String, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_0(long, RNAstructureBackendCalculator, double, int, double, int, int, double, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldMaximumExpectedAccuracy__SWIG_1(long, RNAstructureBackendCalculator, double, int, double, int, int, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_0(long, RNAstructureBackendCalculator, double, int, int, int, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldPseudoknot__SWIG_1(long, RNAstructureBackendCalculator, double, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_0(long, RNAstructureBackendCalculator, double, int, double, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_runTurboFoldThreshold__SWIG_1(long, RNAstructureBackendCalculator, double, int, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setCleavedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setDoubleStrandedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setDynalignAlignmentConstraint(long, RNAstructureBackendCalculator, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setEnvVar(String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setForcedHelix(long, RNAstructureBackendCalculator, int, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setMaxLoop(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setMaxPair(long, RNAstructureBackendCalculator, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setModifiedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setProhibitedHelix(long, RNAstructureBackendCalculator, int, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSaveFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceComment(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceData(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSequenceTitle(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEParam1(long, RNAstructureBackendCalculator, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEParam2(long, RNAstructureBackendCalculator, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSHAPEType(long, RNAstructureBackendCalculator, boolean) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setSingleStrandedNucleotide(long, RNAstructureBackendCalculator, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_setTemperature(long, RNAstructureBackendCalculator, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_wasCanceled(long, RNAstructureBackendCalculator) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeDynalignAlignmentConstraintsFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeFastaFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeFoldingConstraintsFile(long, RNAstructureBackendCalculator, String, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculator_writeSequenceFile(long, RNAstructureBackendCalculator, String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureBackendCalculatorProxyJNI - Class in ur_rna.RNAstructureUI
RNAstructureBackendCalculatorProxyJNI() - Constructor for class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
RNAstructureVersion - Interface in ur_rna.RNAstructure
  Interface that contains constants related to the current RNAstructure Release information.
rnaSymbols - Static variable in class ur_rna.RNAstructure.Nucleobase
rnaSymbolsLc - Static variable in class ur_rna.RNAstructure.Nucleobase
rolloverHandler - Variable in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
RolloverListener - Class in ur_rna.RNAstructureUI.menus
  A class that creates a rollover listener for menus in the RNAstructure GUI.
RolloverListener(Consumer<String>, String) - Constructor for class ur_rna.RNAstructureUI.menus.RolloverListener
rollovers - Variable in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
root - Variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
root - Variable in class ur_rna.StructureEditor.services.UserPrefs
root - Variable in class ur_rna.Utilities.prefs.FilePreferences
rootNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
rootNode() - Method in class ur_rna.Utilities.prefs.FilePreferences
RootNode(File) - Constructor for class ur_rna.Utilities.prefs.FilePreferences.RootNode
rootPreferences - Variable in class ur_rna.Utilities.prefs.FilePreferences.Factory
RosyBrown - Static variable in class ur_rna.Utilities.Colors
Rotate - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
rotate(double) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
rotate(double, double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
rotate(double) - Method in class ur_rna.Utilities.geom.Vec2D
rotate90() - Method in class ur_rna.Utilities.geom.Vec2D
  Rotates this vector 90 degrees counter-clockwise.
rotateNucs(Collection<Nuc>, Point2D, Point, Point, SceneController.DragOpts) - Method in class ur_rna.StructureEditor.services.RnaDrawController
rotateNucs(Collection<Nuc>, Point2D, Point, Point, SceneController.DragOpts, Motif.Helix, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
rotateNucs(Collection<Nuc>, Point2D, double) - Method in class ur_rna.StructureEditor.services.RnaDrawController
rotateNucs(Collection<Nuc>, Point2D, Point, Point, SceneController.DragOpts) - Method in interface ur_rna.StructureEditor.services.SceneController
rotateNucs(Collection<Nuc>, Point2D, Point, Point, SceneController.DragOpts, Motif.Helix, boolean) - Method in interface ur_rna.StructureEditor.services.SceneController
rotateNucs(Collection<Nuc>, Point2D, double) - Method in interface ur_rna.StructureEditor.services.SceneController
RotationCenter() - Constructor for enum ur_rna.StructureEditor.services.drawing.SelectionRotater.RotationCenter
rotX(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to a counter clockwise rotation about the x axis.
rotY(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to a counter clockwise rotation about the y axis.
rotZ(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to a counter clockwise rotation about the z axis.
roundLoc(float) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
  round locations to the nearest 0.1
RoyalBlue - Static variable in class ur_rna.Utilities.Colors
RPAREN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
RSIGNEDSHIFTASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
run() - Method in class ur_rna.GUITester.ScriptRunner
run() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
run(Object) - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
run() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
run() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
run() - Method in class ur_rna.Utilities.RunOnce
  When an object implementing interface `Runnable` is used to create a thread, starting the thread causes the object's `run` method to be called in that separately executing thread.
run() - Method in interface ur_rna.Utilities.testing.TestUtils.TestMethod
runAccessFold(String, float, int, double, int, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runAllSub(String, float, double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runBifold(String, float, int, int, boolean, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runBipartition(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
runCalc() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
runDuplexFold(String, float, int, int, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runDynalign(String, String, String, String, double, int, int, int, float, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runDynalignRefold(String, String, String, int, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runEfn2(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runFold(String, int, int, int, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RunFunc - Class in ur_rna.RNAstructureUI.utilities
RunFunc(Object) - Constructor for class ur_rna.RNAstructureUI.utilities.RunFunc
RunFunc() - Constructor for class ur_rna.RNAstructureUI.utilities.RunFunc
runInBackground(TTask, Consumer<TTask>) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.AccessFoldWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Run the module calculation in the back end.
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
runMainCalculationMultipleSequences() - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
runMainCalculationMultipleSequences() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Run the multiple sequence dependent module calculation in the back end.
runMainCalculationMultipleSequences() - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
runMaxExpect(String, double, int, int, double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runMultilign(int, int, int, int, double, boolean, double, int, int, String, boolean, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RunnableOnce - Interface in ur_rna.Utilities
  Indicates that a call to `Runnable.run()` will be effective at most once.
RunnerTemplate - Class in ur_rna.RNAstructureUI.drawing.runners
  A class that templates the way in which the RNAstructure Java drawing framework is run independently.
RunnerTemplate(String) - Constructor for class ur_rna.RNAstructureUI.drawing.runners.RunnerTemplate
  Constructor.
runningTask - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
runOligoScreen(String, String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runOligoWalk(String, int, String, boolean, int, int, String, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RunOnce - Class in ur_rna.Utilities
  This class operates as a proxy for a `Runnable`.
RunOnce() - Constructor for class ur_rna.Utilities.RunOnce
RunOnce(Runnable) - Constructor for class ur_rna.Utilities.RunOnce
runOnUiThread(Runnable) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
runPartition(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runPseudoknotPrediction(String, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runPseudoknotRemoval(String, boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runRefold(String, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RUNSIGNEDSHIFTASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
runStochastic(String, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
RuntimeTools - Class in ur_rna.GUITester
RuntimeTools() - Constructor for class ur_rna.GUITester.RuntimeTools
RuntimeTools.ActionArgumentException - Exception in ur_rna.GUITester
  Thrown if the number or type of arguments is invalid for the given action.
RuntimeTools.ActionException - Exception in ur_rna.GUITester
  Base class for exceptions thrown from `doAction`
RuntimeTools.UnsupportedActionException - Exception in ur_rna.GUITester
  Thrown if the action is unknown or not implemented.
runTurboFoldMaximumExpectedAccuracy(double, int, double, int, int, double, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runTurboFoldMaximumExpectedAccuracy(double, int, double, int, int, double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runTurboFoldPseudoknot(double, int, int, int, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runTurboFoldPseudoknot(double, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runTurboFoldThreshold(double, int, double, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
runTurboFoldThreshold(double, int, double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator

## S

s1 - Variable in class ur_rna.StructureEditor.models.StrandList
s2 - Variable in class ur_rna.StructureEditor.models.StrandList
SaddleBrown - Static variable in class ur_rna.Utilities.Colors
safeClone(ArrayList<T>) - Static method in class ur_rna.Utilities.ObjTools
safeClone(T) - Static method in class ur_rna.Utilities.ObjTools
safeEvaluateScriptNode(ScriptNode) - Method in class ur_rna.GUITester.ScriptRuntime
SafeParseInt(String, Integer) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Salmon - Static variable in class ur_rna.Utilities.Colors
sand - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
SandyBrown - Static variable in class ur_rna.Utilities.Colors
save(Preferences) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
save() - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
save(Preferences) - Method in class ur_rna.StructureEditor.services.RecentFileList
save() - Method in class ur_rna.StructureEditor.services.UserPrefs
  Save user preferences to file.
save(Preferences) - Method in class ur_rna.StructureEditor.Settings
save(FileType, boolean, boolean) - Method in class ur_rna.StructureEditor.windows.DrawWindow
SAVE_FILE_POS - Static variable in class ur_rna.StructureEditor.menus.FileMenu
saveRecent() - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
saveRecent(String, JComponent...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
saveRecentFiles(JTextField...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
saveRecentPaths() - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
saveRecentPaths(Preferences) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
saveRecentPaths() - Static method in class ur_rna.Utilities.swing.FileDialog
saveRecentPaths(Preferences) - Static method in class ur_rna.Utilities.swing.FileDialog
saveRelativeLocation() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
saveSceneAsRastorImage(String, FileType) - Method in class ur_rna.StructureEditor.windows.DrawWindow
saveSceneAsVectorImage(String, FileType) - Method in class ur_rna.StructureEditor.windows.DrawWindow
saveSequence() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Save a sequence.
saveSequence(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Save a sequence.
saveSettings() - Method in class ur_rna.StructureEditor.menus.SettingsMenu
saveSettings(Component) - Method in class ur_rna.StructureEditor.menus.SettingsMenu
saveSettings() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
saveToStorage() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
sb - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
SC_AND - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
SC_OR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
scale - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  The scale at which the image is seen.
scale(double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
scale - Variable in class ur_rna.StructureEditor.ui.DrawPanel
scale - Variable in class ur_rna.StructureEditor.windows.DrawWindow.SceneInfo
scale(Point2D, double) - Static method in class ur_rna.Utilities.geom.PointMath
  scales p by the given factor.
scale(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.PointMath
scale(double) - Method in class ur_rna.Utilities.geom.Vec2D
scale(double, double) - Method in class ur_rna.Utilities.geom.Vec2D
scaled(Point2D, double, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to scale * p.
scaled(Point2D, double) - Static method in class ur_rna.Utilities.geom.PointMath
scaled(Point2D, double, double, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
scaled(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.PointMath
scene - Variable in class ur_rna.StructureEditor.models.Strand
scene - Variable in class ur_rna.StructureEditor.models.StrandList
scene - Variable in class ur_rna.StructureEditor.services.RnaDrawController
scene - Variable in class ur_rna.StructureEditor.services.SceneUpdateEvent
sceneBgColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
SceneColorizer - Class in ur_rna.StructureEditor.services
  Applies color to nucleobases in a scene.
SceneColorizer(int) - Constructor for class ur_rna.StructureEditor.services.SceneColorizer
SceneColorizer.ColorMode - Interface in ur_rna.StructureEditor.services
SceneColorizer.Comparison - Enum in ur_rna.StructureEditor.services
SceneColorizer.DoubleComparer - Interface in ur_rna.StructureEditor.services
SceneColorizer.NumberRangeList - Class in ur_rna.StructureEditor.services
SceneColorizer.PairProbabilityData - Class in ur_rna.StructureEditor.services
SceneController - Interface in ur_rna.StructureEditor.services
  Abstract some things away from RnaDrawController
SceneController.DragOpts - Class in ur_rna.StructureEditor.services
  flags passed to DrawHandle and dragNuc methods to indicate that the user is modifying the default behavior.
SceneDrawMode - Enum in ur_rna.StructureEditor.services
  Represents different modes of drawing a Scene
SceneDrawMode() - Constructor for enum ur_rna.StructureEditor.services.SceneDrawMode
sceneInfo - Variable in class ur_rna.StructureEditor.windows.DrawWindow
SceneInfo() - Constructor for class ur_rna.StructureEditor.windows.DrawWindow.SceneInfo
SceneRenderer - Interface in ur_rna.StructureEditor.services
scenes - Variable in class ur_rna.StructureEditor.windows.DrawWindow
sceneToStrandIndex(int) - Method in class ur_rna.StructureEditor.models.Strand
SceneUpdateCategory - Enum in ur_rna.StructureEditor.services
  Various types of changes that can occur to a Scene as a result of user interaction.
SceneUpdateCategory() - Constructor for enum ur_rna.StructureEditor.services.SceneUpdateCategory
sceneUpdated - Variable in class ur_rna.StructureEditor.services.RnaDrawController
SceneUpdateEvent - Class in ur_rna.StructureEditor.services
  Event that indicates an update has occurred in the specified RnaScene.
SceneUpdateEvent(Object, SceneUpdateInfo, RnaScene) - Constructor for class ur_rna.StructureEditor.services.SceneUpdateEvent
SceneUpdateInfo - Class in ur_rna.StructureEditor.models
  Represents the type of update that was applied to the RnaScene (e.g.
SceneUpdateInfo(SceneUpdateCategory, String) - Constructor for class ur_rna.StructureEditor.models.SceneUpdateInfo
SceneUpdateInfo(SceneUpdateCategory, String, SceneUpdateInfo) - Constructor for class ur_rna.StructureEditor.models.SceneUpdateInfo
scope - Variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
scopeToString(int) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
screenBounds - Variable in class ur_rna.StructureEditor.services.drawing.View2D
  Represents the bounds of the screen (in screen) coordinates, so the location is always (0,0).
ScreenCapture - Class in ur_rna.GUITester.GuiTools
ScreenCapture() - Constructor for class ur_rna.GUITester.GuiTools.ScreenCapture
ScreenDPI - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
screenMargin - Variable in class ur_rna.StructureEditor.services.drawing.View2D
ScreenNuc(Nuc, DrawSettings) - Constructor for class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
screenObjects - Variable in class ur_rna.StructureEditor.services.RnaDrawController
screenPos - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
screenRadius - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
ScreenShape - Class in ur_rna.StructureEditor.services.drawing
  Represents an object drawn onscreen that is meant to be interacted with by the user.
ScreenShape(Object, Shape, int) - Constructor for class ur_rna.StructureEditor.services.drawing.ScreenShape
Script - Class in ur_rna.GUITester
Script(String, String) - Constructor for class ur_rna.GUITester.Script
Script(String, Reader) - Constructor for class ur_rna.GUITester.Script
Script(String, Reader, long, long) - Constructor for class ur_rna.GUITester.Script
ScriptActions - Class in ur_rna.GUITester
ScriptActions(ScriptRuntime) - Constructor for class ur_rna.GUITester.ScriptActions
scriptList - Variable in class ur_rna.GUITester.GUITesterStartup.AppOptions
ScriptNode - Class in ur_rna.GUITester.ScriptParser
ScriptNode(int) - Constructor for class ur_rna.GUITester.ScriptParser.ScriptNode
ScriptNode(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.ScriptNode
ScriptNode.DumpState - Class in ur_rna.GUITester.ScriptParser
ScriptNodePropConstants - Interface in ur_rna.GUITester.ScriptParser
ScriptRunner - Class in ur_rna.GUITester
ScriptRunner(Script, GuiAppManager, AppLog) - Constructor for class ur_rna.GUITester.ScriptRunner
ScriptRuntime - Class in ur_rna.GUITester
ScriptRuntime(Script, GuiAppManager, AppLog) - Constructor for class ur_rna.GUITester.ScriptRuntime
ScriptRuntimeException - Exception in ur_rna.GUITester
ScriptRuntimeException() - Constructor for exception ur_rna.GUITester.ScriptRuntimeException
  Default constructor.
ScriptRuntimeException(String) - Constructor for exception ur_rna.GUITester.ScriptRuntimeException
ScriptRuntimeException(Throwable) - Constructor for exception ur_rna.GUITester.ScriptRuntimeException
ScriptRuntimeException(String, Throwable) - Constructor for exception ur_rna.GUITester.ScriptRuntimeException
ScriptRuntimeException(String, Throwable, ScriptNode) - Constructor for exception ur_rna.GUITester.ScriptRuntimeException
ScriptSource() - Constructor for enum ur_rna.GUITester.GUITesterStartup.ScriptSource
scrlSequence - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
scroll - Variable in class ur_rna.RNAstructureUI.windows.MultiWindow
  The scroll pane holding the sequence set.
ScrollerPane - Class in ur_rna.RNAstructureUI.ui
  A class that creates a scroll pane that can be controlled via the keyboard.
ScrollerPane(Component, int, int) - Constructor for class ur_rna.RNAstructureUI.ui.ScrollerPane
  Constructor.
scrollPane - Variable in class ur_rna.StructureEditor.windows.DrawWindow
scrollPos - Variable in class ur_rna.StructureEditor.windows.DrawWindow.SceneInfo
scrollTargetModel - Variable in class ur_rna.StructureEditor.ui.DrawPanel
scrollTargetView - Variable in class ur_rna.StructureEditor.ui.DrawPanel
scrollToPoint(Point) - Method in class ur_rna.StructureEditor.ui.DrawPanel
SeaGreen - Static variable in class ur_rna.Utilities.Colors
SEARCH_ACCESSIBLE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_ACCESSIBLE_DESC - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_ACCESSIBLE_NAME - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_ACCESSIBLE_TEXT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_ALL - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_CAPTION - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_COMMENT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_INPUT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_NAME - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_NONE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_SELECTION - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TEXT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TOOLTIP - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TRUE_CAPTION - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TRUE_INPUT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TRUE_NAME - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
SEARCH_TRUE_TEXT - Static variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
searchDirs - Variable in class ur_rna.Utilities.ResourceLoader
searchForResources(ResourceLoader) - Static method in class ur_rna.RNAstructureUI.utilities.Resources
SeaShell - Static variable in class ur_rna.Utilities.Colors
second() - Method in class ur_rna.StructureEditor.models.StrandList
secondStrand() - Method in class ur_rna.StructureEditor.models.RnaScene
Segment() - Constructor for class ur_rna.StructureEditor.models.Motif.Segment
Segment(Strand, int, int) - Constructor for class ur_rna.StructureEditor.models.Motif.Segment
Segment(Nuc, Nuc) - Constructor for class ur_rna.StructureEditor.models.Motif.Segment
Segment(Nuc, int) - Constructor for class ur_rna.StructureEditor.models.Motif.Segment
selBandFillColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
selBandLineColor - Variable in class ur_rna.StructureEditor.models.DrawSettings
selBandOutline - Variable in class ur_rna.StructureEditor.models.DrawSettings
select() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  Select this button.
select(int) - Method in class ur_rna.Utilities.swing.ButtonGroupList
SELECT_ONLY - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
selectAll() - Method in class ur_rna.StructureEditor.services.RnaDrawController
selectedBase - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
selectedHelixLen - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
selectedPair - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
selectedStructItem - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
selectFile() - Method in class ur_rna.RNAstructureUI.drawing.runners.PlotRunner
selectFile() - Method in class ur_rna.RNAstructureUI.drawing.runners.RunnerTemplate
  Select an image file.
selectFile() - Method in class ur_rna.RNAstructureUI.drawing.runners.StructureRunner
SELECTING - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
Selection - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
selection - Variable in class ur_rna.StructureEditor.services.RnaDrawController
SELECTION_ADD_MASK - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
selectionBand - Variable in class ur_rna.StructureEditor.services.RnaDrawController
selectionBorder - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
selectionChanged() - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
selectionChanged() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
selectionChanged() - Method in class ur_rna.StructureEditor.services.drawing.LoopResizer
selectionChanged() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
selectionChanged() - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
selectionColor - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  The selection color for this button.
selectionHash - Variable in class ur_rna.StructureEditor.services.drawing.SelectionRotater.CenterPoint
SelectionRotater - Class in ur_rna.StructureEditor.services.drawing
  A Drawhandle that allows the user to rotate a group of selected Nucleotides.
SelectionRotater(SceneController) - Constructor for class ur_rna.StructureEditor.services.drawing.SelectionRotater
SelectionRotater.CenterPoint - Class in ur_rna.StructureEditor.services.drawing
SelectionRotater.RotationCenter - Enum in ur_rna.StructureEditor.services.drawing
SelectionType() - Constructor for enum ur_rna.StructureEditor.services.RnaDrawController.SelectionType
selectionUpdated() - Method in class ur_rna.StructureEditor.services.RnaDrawController
selectionUpdated() - Method in interface ur_rna.StructureEditor.services.SceneController
selectMotif(Nuc, boolean, RnaDrawController.SelectionType) - Method in class ur_rna.StructureEditor.services.RnaDrawController
selectNucs(Iterable<Nuc>, boolean) - Method in class ur_rna.StructureEditor.services.RnaDrawController
selectSpecial(RnaDrawController.SelectionType) - Method in class ur_rna.StructureEditor.services.RnaDrawController
self() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
self() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
self() - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
self - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
selType - Variable in class ur_rna.StructureEditor.services.RnaDrawController
selType - Variable in class ur_rna.StructureEditor.windows.DrawWindow
SEMICOLON - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
SEND_FEEDBACK - Static variable in class ur_rna.StructureEditor.AppActions
sendFeedbackFromBrowser() - Static method in class ur_rna.StructureEditor.AppActions
sendKeyString(String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
Separator() - Constructor for class ur_rna.Utilities.swing.MergeButton.Separator
Separator(int) - Constructor for class ur_rna.Utilities.swing.MergeButton.Separator
Separator() - Constructor for class ur_rna.Utilities.swing.MergeItem.Separator
Separator(int) - Constructor for class ur_rna.Utilities.swing.MergeItem.Separator
sepPos - Variable in class ur_rna.Utilities.PathTools.FileName
seq1 - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
seq2 - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
seqLen - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
seqList - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
seqLookup - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
seqText - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
seqType - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
seqType1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
seqType1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
seqType2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
seqType2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
Sequence - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
sequence - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
sequence1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
sequence1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
sequence2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
sequence2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
SEQUENCE_FMT_FASTA - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
SEQUENCE_FMT_SEQ - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
SEQUENCE_FMT_TEXT - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
SEQUENCE_STRING - Static variable in interface ur_rna.RNAstructure.backend.RNABackendConstants
SEQUENCE_STRING_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
sequenceBox - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
SequenceDisplayWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for displaying a window that allows a user to examine raw sequence data.
SequenceDisplayWindow() - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Default Constructor.
SequenceDisplayWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  File Constructor.
SequenceDisplayWindow.EditMenu - Class in ur_rna.RNAstructureUI.windows
  An inner class that creates a sequence editing menu.
SequenceDisplayWindow.SoundPlayer - Class in ur_rna.RNAstructureUI.windows
SequenceDisplayWindow.SpeakMenu - Class in ur_rna.RNAstructureUI.windows
  An inner class that creates a sequence speaking menu.
sequenceDoc - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
SequenceExtended - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
  Select a sequence file in its extended context, with more than its usual possible file types.
SequenceItem(String, String, String) - Constructor for class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
SequenceSection - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
SequenceSize - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
SequenceText - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
sequenceTitle - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
serialVersionUID - Static variable in exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
serialVersionUID - Static variable in exception ur_rna.GUITester.ScriptParser.ParseException
  The version identifier for this Serializable class.
serialVersionUID - Static variable in exception ur_rna.GUITester.ScriptParser.ParseFormatException
  The version identifier for this Serializable class.
serialVersionUID - Static variable in class ur_rna.GUITester.ScriptParser.Token
  The version identifier for this Serializable class.
serialVersionUID - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  The version identifier for this Serializable class.
serialVersionUID - Static variable in exception ur_rna.GUITester.ScriptRuntimeException
serialVersionUID - Static variable in exception ur_rna.RNAstructure.RnaBackendException
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.ZoomDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.PlotMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.runners.PlotRunner
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.drawing.runners.StructureRunner
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.MainMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.PredictMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.RolloverListener
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.RNAstructure
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.BorderBuilder
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.BorderedButtonPanel
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.Dialogs
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.FieldPanel
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.FileField
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.HTMLCheckBox
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.NumberField.DoubleField
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.NumberField.FloatField
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.NumberField
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.ScrollerPane
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.ImageGrabber
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.AccessFoldWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.ChildWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.DesignWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.DrawingWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.DuplexFoldWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.Efn2Window
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.InternalWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.MultilignWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.MultiWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoWalkResultsMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.RefoldWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.StochasticWindow
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
serialVersionUID - Static variable in class ur_rna.StructureEditor.menus.MainMenu
serialVersionUID - Static variable in exception ur_rna.Utilities.ExtensibleException
serialVersionUID - Static variable in exception ur_rna.Utilities.FormatterException
serialVersionUID - Static variable in class ur_rna.Utilities.geom.Matrix3D
serialVersionUID - Static variable in exception ur_rna.Utilities.JniLoader.NativeLibLoadError
serialVersionUID - Static variable in exception ur_rna.Utilities.KeyAlreadyExistsException
serialVersionUID - Static variable in class ur_rna.Utilities.OSInfo
serialVersionUID - Static variable in class ur_rna.Utilities.StringBuilderEx
serialVersionUID - Static variable in exception ur_rna.Utilities.swing.FormValidationException
serialVersionUID - Static variable in exception ur_rna.Utilities.SyntaxErrorException
set(int, double) - Method in class ur_rna.RNAstructure.backend.CDblVector
set(int, int) - Method in class ur_rna.RNAstructure.backend.CIntVector
set(Object) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
  Set the main frame message bar text to this listener's specific rollover text.
set(String) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
  Set the main frame message bar text to this listener's specific rollover text.
set(int, Nuc) - Method in class ur_rna.StructureEditor.models.Strand
set(String, Object) - Method in class ur_rna.StructureEditor.Settings
set(Field, Object) - Method in class ur_rna.StructureEditor.Settings
set(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the value of the Matrix3D argument.
set(double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the values in this Matrix3D equal to the row-major array parameter (ie, the first three elements of the array will be copied into the first row of this matrix, etc.).
set(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to a scale matrix with the passed scale amount.
setAcceptAll(boolean) - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
setAction(Action) - Method in class ur_rna.Utilities.swing.JActionLabel
setActionCommand(String) - Method in class ur_rna.Utilities.swing.JActionLabel
setAllowCancel(boolean) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
setAlpha(Color, int) - Static method in class ur_rna.Utilities.Colors
setAlpha(Color, float) - Static method in class ur_rna.Utilities.Colors
setAnchorCenter() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the anchoring area for the GridBagConstraints to CENTER.
setAnchorNorth() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the anchoring area for the GridBagConstraints to NORTH.
setAnnotation(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Set the annotation for this structure drawing.
setAnnotation(String, FileType) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
setAppName(String) - Static method in class ur_rna.Utilities.AppInfo
setAppTitle(String) - Static method in class ur_rna.Utilities.AppInfo
setBackboneStyle(int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
setBackground(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setBackground(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Background color only affects the clear operation; It is NOT the fill color of shapes.
setBarColor(Color) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
  Set the default color that will be painted on this button.
setBarPolicies(int, int) - Method in class ur_rna.RNAstructureUI.ui.ScrollerPane
  Set the scroll bar policies for this scroll pane.
setBaseDir(String) - Method in class ur_rna.Utilities.ResourceLoader
setBaseDir(Class<?>, String) - Method in class ur_rna.Utilities.ResourceLoader
  Set the resource directory based on the package name of the specified class by converting each dot (.) in the package name to a slash (/).
setBasePair(int, int) - Method in class ur_rna.RNAstructure.backend.singlestructure
setBehaviorMode(RnaDrawController.BehaviorMode) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setBoxSize(int) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
  Set the size of the default DrawHandle box that the user can click.
setButtonText(String) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Set the text that appears on the accept (OK) button.
setButtonText(String) - Method in class ur_rna.Utilities.swing.FileDialog
  Set the text that appears on the accept (OK) button.
setCancelListener(ActionListener) - Method in class ur_rna.Utilities.swing.WaitDialog
setCancelVisible(boolean) - Method in class ur_rna.Utilities.swing.WaitDialog
setCanvas(ICanvas) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setCanvasComponent(Component) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setCaption(String) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  Set the caption text on this window (which is also shown on the main RNAstructure window caption bar).
setCharAt(int, char) - Method in class ur_rna.Utilities.StringBuilderEx
  The character at the specified index is set to `ch`.
setCharStyle(int, Style) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
setCharStyle(StyledDocument, int, int, Style) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
setCircle(Point2D, float) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
setCleavedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setClient(ProgressHandler) - Method in class ur_rna.RNAstructure.backend.PartialProgress
setClip(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setClip(int, int, int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setClip(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setCloseOnCancel(boolean) - Method in class ur_rna.Utilities.swing.WaitDialog
setColor(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setColor(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setColor(Nuc, Color) - Method in class ur_rna.StructureEditor.services.SceneColorizer
setColor(Nuc, Color, int) - Method in class ur_rna.StructureEditor.services.SceneColorizer
setColor(Color) - Method in interface ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
setColor(Color) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
setColorFromText() - Method in interface ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
setColors(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Set the number of colors in the plot on this dialog.
setColors(int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
setColorText(String) - Method in interface ur_rna.StructureEditor.windows.ColorizeDialog.ColorEditControl
setColorText(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
setColumn(int, double, double, double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the specified column of this matrix3d to the three values provided.
setColumn(int, double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the specified column of this matrix3d to the three values provided.
setCommand(String) - Method in class ur_rna.Utilities.swing.UiAction
setComponents(Container, Component[]) - Method in class ur_rna.Utilities.swing.MergeManager
setComposite(Composite) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setComposite(Composite) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setCompoundmessage(String) - Method in class ur_rna.RNAstructure.backend.TwoRNA
setConstraint(String) - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
  Set a constraint using this dialog.
setContent(JPanel) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setContext(String) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Set the context for default startup folder.
setContext(String) - Method in class ur_rna.Utilities.swing.FileDialog
  Set the context for default startup folder.
setControlValue(JComponent, Object) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setCtlabel(String) - Method in class ur_rna.RNAstructure.backend.singlestructure
SetCtLabel(String, int) - Method in class ur_rna.RNAstructure.backend.structure
setCurrent(int) - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
setCustomMenus(MenuList) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
setDataAutomatically(String) - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
  Set the window's data automatically.
setDataPath(String) - Static method in class ur_rna.RNAstructure.backend.RNABackend
setDataPath(String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
setDataPath(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
setDebugStream(PrintStream) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Set debug output.
setDefault(AppLog) - Static method in class ur_rna.Utilities.AppLog
setDefaultDir(File) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setDefaultDir(File) - Static method in class ur_rna.Utilities.swing.FileDialog
setDefaultFile(String) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setDefaultFile(File) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setDefaultFile(String) - Method in class ur_rna.Utilities.swing.FileDialog
setDefaultFile(File) - Method in class ur_rna.Utilities.swing.FileDialog
setDefaultFileOpenDir() - Static method in class ur_rna.RNAstructureUI.RNAstructure
setDesc(String) - Method in class ur_rna.Utilities.swing.UiAction
setDoubleStrandedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setDrawSettings(DrawSettings) - Method in class ur_rna.StructureEditor.services.drawing.NucLayout
setDynalignAlignmentConstraint(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setElement(int, int, double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the specified element of this matrix3f to the value provided.
setEnabled(boolean) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
setEnabled(boolean) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
setEnabled(IMenuItem, boolean) - Static method in class ur_rna.Utilities.swing.Menus
setEnabledSpecial(Verbosity, boolean) - Method in class ur_rna.Utilities.AppLog
setEnd(int) - Method in class ur_rna.StructureEditor.models.Strand
setEnergy(int) - Method in class ur_rna.RNAstructure.backend.singlestructure
SetEnergy(int, int) - Method in class ur_rna.RNAstructure.backend.structure
setEnvVar(String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setError(Exception) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
setError(String) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
setError(String, Exception) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
setError(String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
setError(String) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
setError(Exception) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
SetErrorDetails(String) - Method in class ur_rna.RNAstructure.backend.RNA
SetErrorDetails(String) - Method in class ur_rna.RNAstructure.backend.TwoRNA
setExtensions(String[]) - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
SetExtrinsic(int, int, double) - Method in class ur_rna.RNAstructure.backend.RNA
setFile(int, String) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel
  Set a file name in a particular input field.
setFile(File) - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
setFileShouldExist(boolean) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setFileShouldExist(boolean) - Method in class ur_rna.Utilities.swing.FileDialog
setFillCenter() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the fill for the GridBagConstraints as CENTER.
setFillHorizontal() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the fill for the GridBagConstraints as HORIZONTAL.
setFilterFromExt(String) - Method in class ur_rna.Utilities.swing.FileDialog
setFilterFromFile(File) - Method in class ur_rna.Utilities.swing.FileDialog
setFilterIndex(int) - Method in class ur_rna.Utilities.swing.FileDialog
setFilters(String) - Method in class ur_rna.RNAstructureUI.ui.FileField
  Sets the file filters associated with this field.
setFlipped(boolean) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
setFont(Font) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setFont(Font) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
SetForbidIntramolecular(boolean) - Method in class ur_rna.RNAstructure.backend.HybridRNA
setForcedHelix(int, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setGrid(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the amount of space a component takes up in the grid.
setIcon(BufferedImage) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
setIcon(Icon) - Method in class ur_rna.Utilities.swing.UiAction
setIcon(Image) - Method in class ur_rna.Utilities.swing.UiAction
setIdentity() - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets this Matrix3D to identity.
setIncludeFolders(boolean) - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
setIndeterminate(boolean) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
setInfoLabel(String) - Method in class ur_rna.RNAstructureUI.AppMainFrame
  Set the info bar at the bottom of the main window to contain the specified text.
setInfoLabel(String) - Method in class ur_rna.StructureEditor.MainFrame
  Set the info bar at the bottom of the main window to contain the specified text.
setInitialMergePos(IMergeItem, int) - Static method in interface ur_rna.Utilities.swing.IMergeItem
setInsets(int, int, int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the external padding of the constraints.
setIsrna(boolean) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
setKeyStroke(char) - Method in class ur_rna.Utilities.swing.CheckMergeItem
setKeyStroke(String) - Method in class ur_rna.Utilities.swing.CheckMergeItem
setKeyStroke(KeyStroke) - Method in class ur_rna.Utilities.swing.CheckMergeItem
setKeyStroke(char) - Method in class ur_rna.Utilities.swing.MergeItem
setKeyStroke(String) - Method in class ur_rna.Utilities.swing.MergeItem
setKeyStroke(KeyStroke) - Method in class ur_rna.Utilities.swing.MergeItem
setKeyStroke(KeyStroke) - Method in class ur_rna.Utilities.swing.UiAction
setKeyStroke(String) - Method in class ur_rna.Utilities.swing.UiAction
setKeyStroke(char) - Method in class ur_rna.Utilities.swing.UiAction
setLength(double) - Method in class ur_rna.Utilities.geom.Vec2D
  Sets the length (magnitude) of this vector.
setLength(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Sets the length of the character sequence.
setLhs(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
setLibPath(String) - Method in class ur_rna.Utilities.JniLoader
  Set the java.library.path System property and ensure that it will be re-evaluated by ClassLoaders
setLink(String) - Method in class ur_rna.Utilities.swing.JActionLabel
setLink(String) - Method in class ur_rna.Utilities.swing.JFlatButton
setLinkUri(URI) - Method in class ur_rna.Utilities.swing.JActionLabel
setLinkUri(URI) - Method in class ur_rna.Utilities.swing.JFlatButton
setLoader(ClassLoader) - Method in class ur_rna.Utilities.ResourceLoader
setLongDesc(String) - Method in class ur_rna.Utilities.swing.UiAction
setM00(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the first matrix element in the first row.
setM01(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the second matrix element in the first row.
setM02(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the third matrix element in the first row.
setM10(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set first matrix element in the second row.
setM11(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the second matrix element in the second row.
setM12(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the third matrix element in the second row.
setM20(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the first matrix element in the third row.
setM21(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the second matrix element in the third row.
setM22(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Set the third matrix element in the third row.
setMainClass(Class<?>) - Static method in class ur_rna.Utilities.AppInfo
setMaxItemCount(int) - Method in class ur_rna.StructureEditor.services.RecentFileList
setMaxLoop(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setMaxPair(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setMergePos(int) - Method in class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
setMergePos(int) - Method in class ur_rna.Utilities.swing.CheckMergeItem
setMergePos(int) - Method in class ur_rna.Utilities.swing.IMergeItem.Proxy
setMergePos(int) - Method in interface ur_rna.Utilities.swing.IMergeItem
setMergePos(IMergeItem, int) - Static method in interface ur_rna.Utilities.swing.IMergeItem
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeButton.Separator
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeButton
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeItem.Separator
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeItem
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeMenu
setMergePos(int) - Method in class ur_rna.Utilities.swing.MergeToggleButton
setMessage(String) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
setMessage(String) - Method in exception ur_rna.Utilities.ExtensibleException
  Allows the calling code to update the message stored in this exception.
setMessage(String) - Method in class ur_rna.Utilities.swing.WaitDialog
setMnemonic(int) - Method in class ur_rna.Utilities.swing.UiAction
setModifiedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setModifyDir(boolean) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Sets the property 'modifyDir', which affects whether the user's actions (i.e.
setModifyDir(boolean) - Method in class ur_rna.Utilities.swing.FileDialog
  Sets the property 'modifyDir', which affects whether the user's actions (i.e.
setMustExist(boolean) - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton.ExtensionFileFilter
setName(String) - Method in class ur_rna.Utilities.swing.UiAction
setNextStep(int) - Method in class ur_rna.RNAstructure.backend.PartialProgress
setNode(ScriptNode) - Method in exception ur_rna.GUITester.ScriptRuntimeException
setNode(ScriptNode, boolean) - Method in exception ur_rna.GUITester.ScriptRuntimeException
setNucleotidesCircled(boolean) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
setOffset(float, float) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setOffset(Point2D) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setOligoData(int) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
  Set the data for a particular oligo.
setOption(StructureDialog.DrawOptions) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
setOption(StructureDialog.DrawOptions, boolean) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
setOwner(Component) - Method in class ur_rna.Utilities.swing.FileDialog
setPad(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Set the internal padding of the constraints.
setPaint(Paint) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setPaint(Paint) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setPaintMode() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
SetPair(int, int, int) - Method in class ur_rna.RNAstructure.backend.structure
SetPair(int, int) - Method in class ur_rna.RNAstructure.backend.structure
setPair(int, int, double) - Method in class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
  Set the probability of pairing between Nucs I and J.
SetPairingDistance(int) - Method in class ur_rna.RNAstructure.backend.structure
setPanelWidth(int) - Method in class ur_rna.RNAstructureUI.ui.FieldPanel
  Set the width of the panel.
setParentFrame(MdiParentFrame) - Method in class ur_rna.Utilities.swing.MdiChildFrame
setParentFrame_Internal(MdiParentFrame) - Method in class ur_rna.Utilities.swing.MdiChildFrame
  For use only from within MdiParentFrame
setPref(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
setPreferencesFile(String) - Static method in class ur_rna.Utilities.prefs.FilePreferences.Factory
setPreferencesFile(File) - Static method in class ur_rna.Utilities.prefs.FilePreferences.Factory
setPreferencesFile(File) - Method in class ur_rna.Utilities.prefs.FilePreferences
setProbComparison(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
SetProgress(ProgressHandler) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
SetProgress(ProgressHandler) - Method in class ur_rna.RNAstructure.backend.HybridRNA
SetProgress(ProgressHandler) - Method in class ur_rna.RNAstructure.backend.RNA
setProgress(int) - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
setProgressIndeterminate(boolean) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
setProgressTotal(float) - Method in class ur_rna.Utilities.swing.WaitDialog
setProgressValue(float) - Method in class ur_rna.Utilities.swing.WaitDialog
setProgressVisible(boolean) - Method in class ur_rna.Utilities.swing.WaitDialog
setProhibitedHelix(int, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setProvider(AppInfo.AppInfoProvider) - Static method in class ur_rna.Utilities.AppInfo
setRange(double, double) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Set the range of the plot on this dialog.
setRange(double, double) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
setRecent(RecentFileList) - Method in class ur_rna.StructureEditor.services.RecentFileMenuManager
setRecent(RecentFileList) - Method in class ur_rna.StructureEditor.windows.DashboardFrame
setRecentDir(String, String) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setRecentDir(String, File) - Static method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setRecentDir(String, String) - Static method in class ur_rna.Utilities.swing.FileDialog
setRecentDir(String, File) - Static method in class ur_rna.Utilities.swing.FileDialog
setRelative(GuiItemRef, GuiRelative) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
setRenderer(SceneRenderer) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setRenderingHint(RenderingHints.Key, Object) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setRenderingHints(Map<?, ?>) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setRhs(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
setRow(int, double, double, double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the specified row of this matrix3d to the 4 values provided.
setRow(int, double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the specified row of this matrix3d to the three values provided.
setSaveFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setScale(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Set the image scale.
setScale(float) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setScale(double) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the scale component of the current matrix by factoring out the current scale (by doing an SVD) and multiplying by the new scale.
setScene(RnaScene) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setSelected(int, boolean) - Method in class ur_rna.Utilities.swing.ButtonGroupList
setSelected(Action, boolean) - Static method in class ur_rna.Utilities.swing.UiAction
setSelectedBondType(BondType) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setSelectedBondType(BondType) - Method in class ur_rna.StructureEditor.windows.DrawWindow
setSelectedButton(String) - Method in class ur_rna.RNAstructureUI.ui.RadioButtonPanel
  Set a particular button in this group to be selected.
setSelectedSequence(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
setSelection(Nuc, Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.drawing.BranchSlider
setSelection(Nuc, Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
setSelection(Nuc, Collection<Nuc>) - Method in class ur_rna.StructureEditor.services.drawing.SelectionRotater
setSelectionState(int[]) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setSelMode(RnaDrawController.SelectionType) - Method in class ur_rna.StructureEditor.windows.DrawWindow
setSelType(RnaDrawController.SelectionType) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setSelType(RnaDrawController.SelectionType) - Method in class ur_rna.StructureEditor.windows.DrawWindow
SetSequence(String) - Method in class ur_rna.RNAstructure.backend.structure
setSequenceComment(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSequenceData(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSequenceFile(String) - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
setSequenceFile(String) - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
SetSequenceLabel(String) - Method in class ur_rna.RNAstructure.backend.structure
setSequenceLength(int) - Method in class ur_rna.RNAstructure.backend.singlestructure
setSequenceText(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
setSequenceTitle(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSettings(DrawSettings) - Method in class ur_rna.StructureEditor.services.RnaDrawController
setSHAPEFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSHAPEFileRead(boolean) - Method in class ur_rna.RNAstructure.backend.structure
setSHAPEParam1(double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSHAPEParam2(double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSHAPEType(boolean) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setShowWarnings(int) - Static method in class ur_rna.RNAstructure.backend.structure
setSingleStrandedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setSize(double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.PageSize
setSizes(int, int) - Method in class ur_rna.RNAstructureUI.ui.ScrollerPane
  Set the size of the scroller pane by setting preferred, minimum, and maximum sizes all at once.
setSource(String, FileType) - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
setSpeakWhileTyping(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Set whether or not the window should be speaking while typing.
setSpin(JSpinner, double, double, double, double) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Initialize a spinner with a SpinnerNumberModel.
setSpin(JSpinner, int, int, int, int) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setSpin(JSpinner, double, double, double) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setSpin(JSpinner, int, int, int) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setSpin(JSpinner, double) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setSpin(JSpinner, int) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
setStartDir(String) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setStartDir(File) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
setStartDir(String) - Method in class ur_rna.Utilities.swing.FileDialog
setStartDir(File) - Method in class ur_rna.Utilities.swing.FileDialog
setStatus(String) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
setStream(Verbosity, PrintStream) - Method in class ur_rna.Utilities.AppLog
setStroke(Stroke) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setStroke(Stroke) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setStructureNumber(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Set the structure number.
setStructureTitle(RNA, int, String) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
setSubItemMergePos(int) - Method in class ur_rna.RNAstructureUI.menus.MenuList
setSubItemMergePos(int) - Method in class ur_rna.Utilities.swing.MergeMenu
  Sets the current mergePos at which sub-items will be added by default.
setSubItemsEnabled(boolean) - Method in class ur_rna.Utilities.swing.MergeMenu
  Enable or Disable the menus in this list.
setSubItemsVisible(boolean) - Method in class ur_rna.Utilities.swing.MergeMenu
  Set visibility for all sub-items
setSumShapeRepeats(boolean) - Static method in class ur_rna.RNAstructure.backend.structure
setSymbol(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
setTab(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
setTabSize(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
setTaskStatus(int, String) - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
setTaskStatus(int, String) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
setTaskStatus(int, String) - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
setTaskStatus(int, String) - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
SetTemperature(double) - Method in class ur_rna.RNAstructure.backend.Thermodynamics
SetTemperature(double) - Method in class ur_rna.RNAstructure.backend.TwoRNA
setTemperature(double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
setText(Component, String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
setText(String) - Method in class ur_rna.Utilities.swing.CheckMergeItem
setText(String) - Method in class ur_rna.Utilities.swing.MergeItem
setText(String) - Method in class ur_rna.Utilities.swing.MergeMenu
setTextWithMnemonic(AbstractButton, String, Consumer<String>) - Static method in class ur_rna.Utilities.swing.Menus
SetThermodynamicDataTable(datatable) - Method in class ur_rna.RNAstructure.backend.structure
settings - Variable in class ur_rna.StructureEditor.menus.SettingsMenu
settings - Variable in class ur_rna.StructureEditor.models.RnaSceneGroup
settings - Variable in class ur_rna.StructureEditor.Program
settings() - Method in class ur_rna.StructureEditor.Program
settings - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
settings - Variable in class ur_rna.StructureEditor.services.RnaDrawController
Settings - Class in ur_rna.StructureEditor
  Holds program options and settings.
Settings() - Constructor for class ur_rna.StructureEditor.Settings
settingsChanged() - Method in class ur_rna.StructureEditor.MainFrame
settingsChanged() - Method in class ur_rna.StructureEditor.menus.SettingsMenu
settingsChanged() - Method in class ur_rna.StructureEditor.services.drawing.DrawHandle
settingsChanged() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
settingsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
settingsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
settingsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
settingsControls - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
SettingsMenu - Class in ur_rna.StructureEditor.menus
SettingsMenu() - Constructor for class ur_rna.StructureEditor.menus.SettingsMenu
SettingsMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
settingsNodeName - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
settingsNodeName - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
settingsNodeName - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
settingsNodeName - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
settingsWereChanged - Variable in class ur_rna.StructureEditor.Settings
SettingsWindow - Class in ur_rna.StructureEditor.windows
SettingsWindow() - Constructor for class ur_rna.StructureEditor.windows.SettingsWindow
setTitle(String) - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
setTo(double, double) - Method in class ur_rna.Utilities.geom.Vec2D
  Alias of `Point2D.Double.setLocation(double, double)`
setTo(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
  Alias of `Point2D.setLocation(Point2D)`
setTo(Vec2D) - Method in class ur_rna.Utilities.geom.Vec2D
setTokenKind(int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
setTopCaption(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Set the text on the info label.
setTrackLineColumn(boolean) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
setTransform(AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setTransform(AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setUser(String) - Method in class ur_rna.StructureEditor.services.UserPrefs
setUseSimpleFileChooser(boolean) - Static method in class ur_rna.RNAstructureUI.AppMainFrame
setValue(Component, Object) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
setValue(Object) - Method in class ur_rna.GUITester.ScriptParser.ASTLiteral
setValue(int) - Method in class ur_rna.RNAstructureUI.ui.NumberField.IntegerField
setValue(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
setValue(Object) - Method in class ur_rna.Utilities.Pair
  Replaces the value corresponding to this entry with the specified value (optional operation).
setValueComparison(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
setVar(String, Object) - Method in class ur_rna.GUITester.ScriptRuntime
setVerbosity(int) - Method in class ur_rna.Utilities.AppLog
setVerbosity(Verbosity) - Method in class ur_rna.Utilities.AppLog
setVerify(boolean) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
setView(View2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
setView(AffineTransform, Rectangle) - Method in class ur_rna.StructureEditor.services.drawing.View2D
setView(float, Point2D) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setView(float, float, float) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setVisible(boolean) - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
setWorkComplete(int) - Method in class ur_rna.RNAstructure.backend.PartialProgress
setWorkInNextStep(int) - Method in class ur_rna.RNAstructure.backend.PartialProgress
setWrap(boolean) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.JWrapTextPane
setXORMode(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
setXorMode(Color) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
setZero() - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets this matrix to all zeros.
setZoomScroll(Point) - Method in class ur_rna.StructureEditor.ui.DrawPanel
setZorder(int) - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
SHAPE - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
  Select a SHAPE file.
shape - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawShape
shape(Shape) - Static method in class ur_rna.StructureEditor.services.drawing.DrawHint
shape - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawShapeOp
shape - Variable in class ur_rna.StructureEditor.services.drawing.ScreenShape
shapeFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
shapeFile - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
shapeIntercept - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
shapeSlope - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
ShapeUtil - Class in ur_rna.Utilities.geom
  Shape Utilities.
ShapeUtil() - Constructor for class ur_rna.Utilities.geom.ShapeUtil
shear(double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
shouldTrace() - Method in class ur_rna.GUITester.ScriptRuntime
show(ChildFrame) - Method in class ur_rna.StructureEditor.MainFrame
show(ChildFrame, Point) - Method in class ur_rna.StructureEditor.MainFrame
show(Frame, String) - Static method in class ur_rna.Utilities.swing.WaitDialog
SHOW_ABOUT_WINDOW - Static variable in class ur_rna.StructureEditor.AppActions
SHOW_DASHBOARD - Static variable in class ur_rna.StructureEditor.AppActions
SHOW_LOCAL_HELP - Static variable in class ur_rna.StructureEditor.AppActions
SHOW_ONLINE_HELP - Static variable in class ur_rna.StructureEditor.AppActions
SHOW_OPEN_FILE - Static variable in class ur_rna.StructureEditor.AppActions
showAbbreviations(boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
showAbbreviations() - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
showAboutWindow() - Method in class ur_rna.RNAstructureUI.AppMainFrame
showAboutWindow() - Static method in class ur_rna.StructureEditor.AppActions
ShowAppHelp() - Static method in class ur_rna.GUITester.GUITesterStartup
showCalcEnergy() - Method in class ur_rna.StructureEditor.windows.DrawWindow
showCancel - Variable in class ur_rna.Utilities.swing.WaitDialog
showCentered(ChildFrame) - Method in class ur_rna.StructureEditor.MainFrame
showColorChooser(ColorizeDialog.ColorEditControl) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
showColorizeDialog() - Method in class ur_rna.StructureEditor.windows.DrawWindow
showConfirm(Object) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a dialog that gives the user one of two choices to make.
showConfirm(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a dialog that gives the user one of two choices to make.
showDashboard(boolean) - Method in class ur_rna.StructureEditor.MainFrame
ShowDashboard - Variable in class ur_rna.StructureEditor.Settings
showDebug() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
showDeletionConfirmation() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  Show a dialog that asks whether constraints should be deleted.
showDialog() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
showDialog(Component, String) - Method in class ur_rna.StructureEditor.windows.InsertBasesDialog
showDrawProgress() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
showDrawProgress(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
showError(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show an error dialog.
showError(String, String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
showFileDialog(Component) - Method in class ur_rna.RNAstructureUI.ui.StandardFileChooser
  Show the File Chooser and return the selected file path, if successful, or null if the user cancels.
showFileDialog(Component) - Method in class ur_rna.Utilities.swing.FileDialog
  Show the File Chooser and return the selected file path, if successful, or null if the user cancels.
showFileSelectMenu() - Method in class ur_rna.RNAstructureUI.ui.RecentFileButton
showFileTypePrompt() - Static method in class ur_rna.StructureEditor.AppActions
showHelp(String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
ShowHints - Variable in class ur_rna.StructureEditor.Settings
showImageDialogs() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
  Show the image dialogs, if possible.
showInfo(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
showInfo(String) - Static method in class ur_rna.Utilities.swing.Dialogs
showInfo(String, String) - Static method in class ur_rna.Utilities.swing.Dialogs
showMessage(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a message dialog using String.format to create the message.
showMessage(String, Object...) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a message dialog using String.format to create the message.
showMessage(String, String, int) - Static method in class ur_rna.Utilities.swing.Dialogs
showMessage(String, String, int, boolean) - Static method in class ur_rna.Utilities.swing.Dialogs
showMessage(String, String, int, Font) - Static method in class ur_rna.Utilities.swing.Dialogs
showNextStructure() - Method in class ur_rna.StructureEditor.windows.DrawWindow
showOpenFile() - Static method in class ur_rna.StructureEditor.AppActions
showPlotWindow(InternalWindow) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
showPrevStructure() - Method in class ur_rna.StructureEditor.windows.DrawWindow
showProgress() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Create a determinate progress bar.
showProgress(boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Create a progress bar.
showProgress(boolean, boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
showProgress(boolean, boolean, String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
showProgress - Variable in class ur_rna.Utilities.swing.WaitDialog
showRecentFileMenu(JComponent, String, Consumer<File>) - Static method in class ur_rna.RNAstructureUI.ui.RecentFileButton
showResults() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
  Show the results window.
showResults() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
  Show the results window.
showResults() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
  Show the results window.
showResults() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
  Show the results window.
showResults() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
showStartupInfo() - Method in class ur_rna.RNAstructureUI.AppMainFrame
showStructureMenu() - Method in class ur_rna.StructureEditor.windows.DrawWindow
showWarning(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
showWarning(Component) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a warning dialog.
showWarning(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a warning dialog.
showWarning(String, boolean) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a warning dialog.
showWarning(String) - Static method in class ur_rna.Utilities.swing.Dialogs
showWarning(String, String) - Static method in class ur_rna.Utilities.swing.Dialogs
showWindow() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  View the window.
showWindow() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
  View the window.
showWindow() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
showWindow() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
showWindow() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
showWindow() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
showWindow() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
showWindow() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  View the window.
showYesNoCancel(Object) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a dialog that gives the user one of three choices to make.
showYesNoCancel(String) - Static method in class ur_rna.RNAstructureUI.ui.Dialogs
  Show a dialog that gives the user one of three choices to make.
shutdown() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
SIBLING - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Sienna - Static variable in class ur_rna.Utilities.Colors
SignedNumber() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Usually numbers of the format (+|-)NUMBER (e.g.
silentMode() - Static method in class ur_rna.RNAstructureUI.RNAstructure
Silver - Static variable in class ur_rna.Utilities.Colors
SimpleCast() - Constructor for class ur_rna.Utilities.ConverterFilter.SimpleCast
SimpleColorControl(JTextComponent, JComponent) - Constructor for class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
SimpleDataSerializer - Class in ur_rna.Utilities
  SimpleDataSerializer Serializes Lists, Maps and primitive types (Strings, Numbers, Booleans) to a simple text format.
SimpleDataSerializer() - Constructor for class ur_rna.Utilities.SimpleDataSerializer
SimpleDataSerializer.OutputFormatSettings - Class in ur_rna.Utilities
SimpleDataSerializer.ParseContext - Class in ur_rna.Utilities
SimpleDataSerializer.SSONList - Class in ur_rna.Utilities
SimpleDataSerializer.SSONMap - Class in ur_rna.Utilities
SimpleDataSerializer.Token - Class in ur_rna.Utilities
SimpleDataSerializer.TokenPattern - Enum in ur_rna.Utilities
SimpleDocumentListener - Interface in ur_rna.Utilities.swing
  Similar to TextDocListener, but this is lighter weight and allows for lambda syntax.
SimpleNode - Class in ur_rna.GUITester.ScriptParser
SimpleNode(int) - Constructor for class ur_rna.GUITester.ScriptParser.SimpleNode
SimpleNode(GuiTestScriptParser, int) - Constructor for class ur_rna.GUITester.ScriptParser.SimpleNode
SimpleProgressHandler - Class in ur_rna.RNAstructure.backend
SimpleProgressHandler(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.SimpleProgressHandler
SimpleProgressHandler() - Constructor for class ur_rna.RNAstructure.backend.SimpleProgressHandler
SimpleProgressHandler_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
SimpleScanner(String) - Constructor for class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
SimpleScanner(Reader) - Constructor for class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.And
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Or
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Xor
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
simplify(Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
simplify() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
simplify() - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
SINGLE_LINE_COMMENT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
SINGLE_QUOTE - Static variable in class ur_rna.Utilities.CharType
  Single quotes (')
SingleClassMatcher(Class) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
SingleColor(Color, int) - Static method in class ur_rna.StructureEditor.services.SceneColorizer
singleColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
SingleGuiItem() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
SingleStrand - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.NucIndexConverter
singlestructure - Class in ur_rna.RNAstructure.backend
singlestructure(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.singlestructure
singlestructure(int) - Constructor for class ur_rna.RNAstructure.backend.singlestructure
singlestructure_ctlabel_get(long, singlestructure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_ctlabel_set(long, singlestructure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_energy_get(long, singlestructure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_energy_set(long, singlestructure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_getBasePair(long, singlestructure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_getSequenceLength(long, singlestructure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_setBasePair(long, singlestructure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
singlestructure_setSequenceLength(long, singlestructure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Singlet(T1) - Constructor for class ur_rna.Utilities.Tuple.Singlet
Singlet() - Constructor for class ur_rna.Utilities.Tuple.Singlet
size() - Method in class ur_rna.RNAstructure.backend.CDblVector
size() - Method in class ur_rna.RNAstructure.backend.CIntVector
size() - Method in class ur_rna.StructureEditor.models.Motif.Helix
  Get the number of base-pairs in the helix (which is half the number of nucleotides).
size() - Method in class ur_rna.StructureEditor.models.Motif.Segment
  Get the number of nucleotides in the loop.
size - Variable in class ur_rna.StructureEditor.models.Strand
size() - Method in class ur_rna.StructureEditor.models.Strand
size - Variable in class ur_rna.StructureEditor.models.StrandList
size() - Method in class ur_rna.StructureEditor.models.StrandList
size() - Method in class ur_rna.StructureEditor.services.History
size() - Method in class ur_rna.StructureEditor.services.RecentFileList
SkyBlue - Static variable in class ur_rna.Utilities.Colors
SLASH - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
SLASH - Static variable in class ur_rna.Utilities.CharConstants
SLASH - Static variable in class ur_rna.Utilities.CharType
SLASHASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
SlateBlue - Static variable in class ur_rna.Utilities.Colors
SlateGray - Static variable in class ur_rna.Utilities.Colors
SlideBranch - Static variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
slider - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
SliderToolWindow - Class in ur_rna.StructureEditor.ui
SliderToolWindow() - Constructor for class ur_rna.StructureEditor.ui.SliderToolWindow
SNAP_DISTANCE - Static variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
SnapGuides - Variable in class ur_rna.StructureEditor.Settings
SNG_QUOT - Static variable in class ur_rna.Utilities.CharConstants
Snow - Static variable in class ur_rna.Utilities.Colors
sort() - Method in class ur_rna.RNAstructure.backend.structure
sort(Component) - Method in class ur_rna.Utilities.swing.MergeManager
sortForComparison() - Method in class ur_rna.StructureEditor.services.SceneColorizer.NumberRangeList
SoundPlayer() - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
source - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
source - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow.CommandInfo
  The source of the command -- e.g.
source - Variable in class ur_rna.StructureEditor.models.HistoryUpdateEvent
source - Variable in class ur_rna.StructureEditor.models.Strand
source - Variable in class ur_rna.StructureEditor.services.SceneUpdateEvent
sourceIndex - Variable in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
sp - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
SP - Static variable in class ur_rna.Utilities.CharConstants
space() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTEWriter
SPACE - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.SimpleScanner
space() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
  Write a single space character.
space(int) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
  Write the specified number of space characters.
SPACE - Static variable in class ur_rna.Utilities.CharType
  The space character (#32)
spaceAfterProp - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
speakButton - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  The button which can be clicked to start or stop speaking.
speakFullSequence(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
speakingFullSequence - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
speakMenu - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
SpeakMenu(SequenceDisplayWindow) - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
  Constructor.
speakPosition - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  The position at which speaking is occurring.
speakSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  Play a sound clip, depending on the nucleotide.
speakSequence - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
speakTimer - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  The timer that aids in speaking nucleotides in rhythm.
speakWhileTyping - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
speakWhileTyping - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  A boolean, true if speaking while typing is active, false if not.
special - Variable in class ur_rna.StructureEditor.services.SceneController.DragOpts
specialToken - Variable in class ur_rna.GUITester.ScriptParser.Token
  This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
specificPanel - Variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
  The panel that holds the dynamic options applicable to a mode.
specifiedPanelWidth - Variable in class ur_rna.RNAstructureUI.ui.FieldPanel
  The specified width of the panel.
SpecifyPair(int, int, int) - Method in class ur_rna.RNAstructure.backend.RNA
SpecifyPair(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
spinner - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
spinner - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
  The spinner in this panel.
spinner1 - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
SpinnerPanel(String, int, int, int) - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
  Constructor.
split(String) - Static method in class ur_rna.Utilities.CommandLineSplitter
splitDirs() - Method in class ur_rna.Utilities.PathTools.FileName
  Return an array of all ancestor directories of the file.
spliterator() - Method in class ur_rna.StructureEditor.services.RecentFileList
splitFlagValue(String) - Method in class ur_rna.Utilities.CommandLineParser
splitScriptSuite(Reader, String, String) - Static method in class ur_rna.GUITester.GUITesterStartup
splitStrandsAtLinkers(RnaScene) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
splitStrandsAtSelection() - Method in class ur_rna.StructureEditor.services.RnaDrawController
spnAlnWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
spnGamma - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnGapPenalty - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
spnIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
spnMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
spnMaxLoopSize - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
spnMaxLoopSize - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnMaxStructs - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
spnMaxStructs - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnMaxStructs - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
spnMinHelixLen - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnMultiAlnSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiDsvChange - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiGapPenalty - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiMaxPairs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiMaxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnMultiWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnShapeIntercept - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnShapeSlope - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnStochasticSamples - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
spnTemperature - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
spnTemperature - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTemperature - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnTurboGamma - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboMaxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboMEAGamma - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboMinHelix - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboPKIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboThreshold - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnTurboWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
spnWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
spnWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
spnWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
SpringGreen - Static variable in class ur_rna.Utilities.Colors
SSON - Static variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
SSONList() - Constructor for class ur_rna.Utilities.SimpleDataSerializer.SSONList
SSONMap() - Constructor for class ur_rna.Utilities.SimpleDataSerializer.SSONMap
stack - Variable in class ur_rna.StructureEditor.models.Motif.IntervalStack
stack - Variable in class ur_rna.StructureEditor.services.History
standardBases - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
StandardFileChooser - Class in ur_rna.RNAstructureUI.ui
StandardFileChooser() - Constructor for class ur_rna.RNAstructureUI.ui.StandardFileChooser
StandardFileChooser(boolean, String, String) - Constructor for class ur_rna.RNAstructureUI.ui.StandardFileChooser
StandardFileChooser(int, String, String) - Constructor for class ur_rna.RNAstructureUI.ui.StandardFileChooser
STAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
STARASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
start(String) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
  Start the GUI application.
start(String[]) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
start() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
start - Variable in class ur_rna.StructureEditor.models.Motif.Segment
  The start of the segment (the 5' side)
start() - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
start() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
start() - Method in class ur_rna.Utilities.StopWatch
  Start the timer.
startButton - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
started - Variable in class ur_rna.RNAstructureUI.ui.ProgressPanel
startGroup() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
startLine - Variable in class ur_rna.GUITester.Script
startLocation - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
startPos - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
startsWith(String) - Method in class ur_rna.Utilities.StringBuilderEx
startsWith(String, boolean) - Method in class ur_rna.Utilities.StringBuilderEx
startUiTimer() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
StartupArgs() - Constructor for class ur_rna.StructureEditor.Program.StartupArgs
state - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.StateChangeEventArgs
state - Variable in class ur_rna.StructureEditor.models.HistoryState
state - Variable in class ur_rna.StructureEditor.models.HistoryUpdateEvent
state - Variable in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
state - Variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
state - Variable in class ur_rna.Utilities.Filter.FilterIterator
StateChange - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
stateChanged(SwingWorker.StateValue, SwingWorker.StateValue) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
StateChangeEventArgs(SwingWorker.StateValue, SwingWorker.StateValue) - Constructor for class ur_rna.RNAstructureUI.utilities.BackgroundWorker.StateChangeEventArgs
stateInfo - Variable in class ur_rna.StructureEditor.models.HistoryState
StateOp() - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StateOp
STATIC_LEXER_ERROR - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
  An attempt was made to create a second instance of a static token manager.
staticFlag - Static variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
  Whether parser is static.
status - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
status - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
statusBar - Variable in class ur_rna.RNAstructureUI.AppMainFrame
statusBar - Variable in class ur_rna.StructureEditor.MainFrame
StatusChange - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
statusChanged(String) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
SteelBlue - Static variable in class ur_rna.Utilities.Colors
stepComplete() - Method in class ur_rna.RNAstructure.backend.PartialProgress
stepProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
stickyRotationAngles - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
stickyRotationEpsilon - Static variable in class ur_rna.StructureEditor.services.RnaDrawController
Stochastic(int, int) - Method in class ur_rna.RNAstructure.backend.RNA
Stochastic(int) - Method in class ur_rna.RNAstructure.backend.RNA
Stochastic() - Method in class ur_rna.RNAstructure.backend.RNA
stochasticSamples - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
StochasticWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the stochastic module, which generates a stochastic sample of structures.
StochasticWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.StochasticWindow
  Constructor.
stop() - Method in class ur_rna.RNAstructureUI.ui.ProgressPanel
stop() - Method in class ur_rna.Utilities.StopWatch
  Stop the timer, but store the elapsed time so that when `StopWatch.start()` is called, the elapsed time will continue to increase.
StopProgress() - Method in class ur_rna.RNAstructure.backend.Dynalign_object
StopProgress() - Method in class ur_rna.RNAstructure.backend.HybridRNA
StopProgress() - Method in class ur_rna.RNAstructure.backend.RNA
stopUiTimer() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
StopWatch - Class in ur_rna.Utilities
  Class used for debugging and diagnostics to display the ellapsed time for sections of code at runtime.
StopWatch() - Constructor for class ur_rna.Utilities.StopWatch
StopWatch(boolean) - Constructor for class ur_rna.Utilities.StopWatch
StopWatch(boolean, PrintWriter) - Constructor for class ur_rna.Utilities.StopWatch
StopWatch(boolean, PrintStream) - Constructor for class ur_rna.Utilities.StopWatch
store(T) - Method in class ur_rna.StructureEditor.services.History
  Store the current state of the model.
storeComponents(Container, Component[]) - Method in class ur_rna.Utilities.swing.MergeManager
storeMouse(MouseEvent) - Method in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
storeProps() - Method in class ur_rna.Utilities.prefs.FilePreferences.RootNode
storeRnaCoords() - Method in class ur_rna.StructureEditor.services.RnaDrawController
storing - Variable in class ur_rna.StructureEditor.models.HistoryUpdateEvent
str - Variable in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
  The strand this constraints menu deals with.
strand - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  The strand being drawn.
strand - Variable in class ur_rna.RNAstructureUI.windows.DrawingWindow
  The strand being drawn.
strand - Variable in class ur_rna.StructureEditor.models.Nuc
Strand - Class in ur_rna.StructureEditor.models
  A Strand represents a single RNA strand.
Strand(RnaScene, StrandList, int, List<Nuc>, int, int) - Constructor for class ur_rna.StructureEditor.models.Strand
STRAND_NUCS - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
StrandDivisions - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
StrandList - Class in ur_rna.StructureEditor.models
  A list of `Strand` that coordinates strand divisions etc to ensure the segmentation of nucleotides is consistent.
StrandList(RnaScene, List<Nuc>) - Constructor for class ur_rna.StructureEditor.models.StrandList
strands - Variable in class ur_rna.StructureEditor.models.RnaScene
strands - Variable in class ur_rna.StructureEditor.models.RnaSceneState
STRANDS - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
strandToSceneIndex(int) - Method in class ur_rna.StructureEditor.models.Strand
streams - Variable in class ur_rna.Utilities.AppLog
STRING_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
STRING_ESCAPE_OPTIONS - Static variable in class ur_rna.Utilities.SimpleDataSerializer
STRING_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
StringBuilderEx - Class in ur_rna.Utilities
  Delegates most functionality to the `StringBuilder` class, while adding a few additional methods.
StringBuilderEx(StringBuilder) - Constructor for class ur_rna.Utilities.StringBuilderEx
  Use the given StringBuilder as the internal builder.
StringBuilderEx() - Constructor for class ur_rna.Utilities.StringBuilderEx
StringBuilderEx(int) - Constructor for class ur_rna.Utilities.StringBuilderEx
StringBuilderEx(String) - Constructor for class ur_rna.Utilities.StringBuilderEx
StringBuilderEx(CharSequence) - Constructor for class ur_rna.Utilities.StringBuilderEx
StringComboBox(String...) - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
  Constructor.
StringEventArgs(String) - Constructor for class ur_rna.Utilities.EventArgs.StringEventArgs
Strings - Class in ur_rna.Utilities
  A collection of String utilities.
Strings() - Constructor for class ur_rna.Utilities.Strings
stringsMatch(String, String) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
  Performs a fuzzy string match that can be altered with various prefix symbols, called modifiers.
stringValue() - Method in class ur_rna.Utilities.NamedArg
stripControlPrefix(String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
stripEnergyTitle(String) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
stripEnergyTitleRegex - Static variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
stripMnemonics(String) - Static method in class ur_rna.Utilities.swing.KeyMnemonic
stroke - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
stroke - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Stroke used for drawing shapes.
STROKE_ENDCAPS - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  Mapping of stroke endcap values from Java to SVG.
STROKE_LINEJOIN - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
  Mapping of line join values for path drawing from Java to SVG.
StrokeOp(Stroke) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.StrokeOp
strOrDefault(String, String) - Method in class ur_rna.StructureEditor.windows.DrawWindow
strText - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
StructItem(int, int, int) - Constructor for class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
structure - Class in ur_rna.RNAstructure.backend
structure(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.structure
structure(int) - Constructor for class ur_rna.RNAstructure.backend.structure
structure() - Constructor for class ur_rna.RNAstructure.backend.structure
structure - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
structure_AddDouble(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddForbiddenPair(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddGUPair(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddModified(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddPair(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddSingle(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AddStructure(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_allocateconstant(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_AllocateSHAPE(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_allocatetem(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_BreakPseudoknots(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_CleanStructure(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ctout(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_DeleteSHAPE(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_DistanceLimited(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_FindPseudoknots__SWIG_0(long, structure, int, long, CIntVector, long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_FindPseudoknots__SWIG_1(long, structure, int, long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_FindPseudoknots__SWIG_2(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetBase(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetCtLabel(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetDouble(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetEnergy(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetErrorDetails(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetForbiddenPair3(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetForbiddenPair5(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetGUpair(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetModified(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofDoubles(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofForbiddenPairs(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofGU(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofModified(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofPairs(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofSingles(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetNumberofStructures(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPair3(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPair5(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPair__SWIG_0(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPair__SWIG_1(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPairingDistanceLimit(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPseudoknotRanks__SWIG_0(long, structure, long, CIntVector, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetPseudoknotRanks__SWIG_1(long, structure, long, CIntVector) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetSequence(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetSequenceLabel(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetSequenceLength(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetSingle(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_GetThermodynamicDataTable(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_HasPseudoknots__SWIG_0(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_HasPseudoknots__SWIG_1(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_IsAlphabetLoaded(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_IsNuc__SWIG_0(long, structure, int, char) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_IsNuc__SWIG_1(long, structure, int, char, long, datatable) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_IsThermoDataLoaded(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_kT_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_openct(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_opendbn(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_openseq(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_openseqx(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ProblemwithStructures(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadExperimentalPairBonus__SWIG_0(long, structure, String, double, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadExperimentalPairBonus__SWIG_1(long, structure, String, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadExperimentalPairBonus__SWIG_2(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadOffset(long, structure, String, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadSHAPE__SWIG_0(long, structure, String, float, float) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadSHAPE__SWIG_1(long, structure, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadSHAPE__SWIG_2(long, structure, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ReadSHAPE__SWIG_3(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveAllStructures(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveConstraints(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveEnergyLabels__SWIG_0(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveEnergyLabels__SWIG_1(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveLastStructure(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemovePair__SWIG_0(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemovePair__SWIG_1(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_RemoveStructure(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetCtLabel(long, structure, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetEnergy(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetPair__SWIG_0(long, structure, int, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetPair__SWIG_1(long, structure, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetPairingDistance(long, structure, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetSequence(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetSequenceLabel(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SetThermodynamicDataTable(long, structure, long, datatable) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SHAPEFileRead_get(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SHAPEFileRead_set(long, structure, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ShowWarnings_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_ShowWarnings_set(int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_sort(long, structure) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SumShapeRepeats_get() - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_SumShapeRepeats_set(boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writedotbracket__SWIG_0(long, structure, String, int, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writedotbracket__SWIG_1(long, structure, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writedotbracket__SWIG_2(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writeseq__SWIG_0(long, structure, String, int, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writeseq__SWIG_1(long, structure, String, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_writeseq__SWIG_2(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_WriteSHAPE__SWIG_0(long, structure, String, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
structure_WriteSHAPE__SWIG_1(long, structure, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
StructureBackend - Class in ur_rna.RNAstructureUI.drawing.proxy
StructureBackend(long, boolean) - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
StructureBackend() - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
StructureBackend_addAnnotationProbability(long, StructureBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_addAnnotationSHAPE(long, StructureBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_flip(long, StructureBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_getStructureCount(long, StructureBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_getStructureData(long, StructureBackend, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_readStructureData(long, StructureBackend, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_removeAnnotation(long, StructureBackend) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_setBackboneStyle(long, StructureBackend, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_setFlipped(long, StructureBackend, boolean) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_setNucleotidesCircled(long, StructureBackend, boolean) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_writeDotBracketFile(long, StructureBackend, String, String) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_writeHelixFile(long, StructureBackend, String, String, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_writePostscriptFile(long, StructureBackend, String, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackend_writeSVGFile(long, StructureBackend, String, int) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
StructureBackendProxyJNI - Class in ur_rna.RNAstructureUI.drawing.proxy
StructureBackendProxyJNI() - Constructor for class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
structureCount() - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
StructureDialog - Class in ur_rna.RNAstructureUI.drawing.dialogs
  A dialog that holds structure images.
StructureDialog(String) - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Constructor.
StructureDialog.DrawOptions - Enum in ur_rna.RNAstructureUI.drawing.dialogs
  Enum that provides choices for backbone rendering style: Normal (Radial) flat (linear) or circular.
structureList - Variable in class ur_rna.StructureEditor.windows.DrawWindow
StructureMenu - Class in ur_rna.RNAstructureUI.drawing.menus
  A class that handles a menu which can manipulate a drawn structure.
StructureMenu(StructureDialog) - Constructor for class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
  Constructor.
structureMenu - Variable in class ur_rna.StructureEditor.windows.DrawWindow
StructureMenu.ChooseStructureDialog - Class in ur_rna.RNAstructureUI.drawing.menus
  An inner class which creates a dialog that moves to a structure.
structureMenuToolbarButton - Variable in class ur_rna.StructureEditor.windows.DrawWindow
StructureRunner - Class in ur_rna.RNAstructureUI.drawing.runners
  A class that runs RNAstructure Java structure drawing independently of the main RNAstructure application.
StructureRunner() - Constructor for class ur_rna.RNAstructureUI.drawing.runners.StructureRunner
  Constructor.
structureUpdated(SceneUpdateInfo) - Method in class ur_rna.StructureEditor.services.RnaDrawController
structureUpdated(SceneUpdateInfo) - Method in interface ur_rna.StructureEditor.services.SceneController
style - Variable in class ur_rna.StructureEditor.models.Nuc
style() - Method in class ur_rna.StructureEditor.models.Nuc
  Returns the style for this nucleotide, creating a new one if necessary.
style - Variable in class ur_rna.StructureEditor.models.RnaSceneState.NucState
STYLE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLE_BOND - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLE_FILL - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLE_FONT - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLE_LINE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLE_TEXT - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
styleIgnoredChar - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
styleInvalidChar - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
STYLES - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
STYLES - Static variable in class ur_rna.Utilities.swing.FontUtil.FontExpressivenessComparator
styleSeqDefault - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
styleSeqPaired - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
styleStandardBase - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
styleStrDefault - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
styleStrInvalid - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
styleStrSel - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
styleTimer - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  The timer that updates syntax highlighting
styleUnpairedBase - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
styleUnspecifiedBase - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
styleUpdated(SceneUpdateInfo) - Method in class ur_rna.StructureEditor.services.RnaDrawController
styleUpdated(SceneUpdateInfo) - Method in interface ur_rna.StructureEditor.services.SceneController
sub(Matrix3D, Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the matrix difference of matrices m1 and m2.
sub(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).
subItemMergePos - Variable in class ur_rna.RNAstructureUI.menus.MenuList
subItemMergePos - Variable in class ur_rna.Utilities.swing.MergeMenu
subject - Variable in class ur_rna.GUITester.ScriptParser.ASTAssignment
Subscriber(EventSource<T>, T) - Constructor for class ur_rna.Utilities.EventSource.Manager.Subscriber
subscribers - Variable in class ur_rna.Utilities.EventSource.Manager
subSequence(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns a new character sequence that is a subsequence of this sequence.
subset(RnaScene...) - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
subset(int...) - Method in class ur_rna.StructureEditor.models.RnaSceneGroup
substring(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns a new `String` that contains a subsequence of characters currently contained in this character sequence.
substring(int, int) - Method in class ur_rna.Utilities.StringBuilderEx
  Returns a new `String` that contains a subsequence of characters currently contained in this sequence.
subtr(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
subType(String) - Method in class ur_rna.StructureEditor.models.SceneUpdateInfo
subTypes - Variable in enum ur_rna.StructureEditor.FileType
subTypes() - Method in enum ur_rna.StructureEditor.FileType
sum(Point2D, Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to p1 + p2.
sum(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
sum(Point2D, double, double, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  sets result to (p.x + dx, p.y + dy) If result is null, a new Point2D (cloned from p1) will be returned.
sum(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.PointMath
suppressUpdateCounter - Variable in class ur_rna.StructureEditor.models.StrandList
suspendChangeNotification() - Method in class ur_rna.StructureEditor.Settings
suspendChanges - Variable in class ur_rna.StructureEditor.Settings
suspendCount - Variable in class ur_rna.Utilities.swing.TextDocListener
suspendRecording() - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
suspendRecordingCounter - Variable in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
suspendRedraw() - Method in class ur_rna.StructureEditor.services.RnaDrawController
suspendUpdate() - Method in class ur_rna.StructureEditor.models.StrandList
suspendUpdates() - Method in class ur_rna.StructureEditor.services.RnaDrawController
suspendUpdates() - Method in class ur_rna.Utilities.swing.TextDocListener
svdReorder(double[], double[], double[], double[], double[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
SVG - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
  Select an SVG file.
SVG_DOCTYPE_NAME - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
SVG_DOCTYPE_PUBLIC_ID - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
SVG_DOCTYPE_SYSTEM_ID - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
SVG_NAMESPACE_URI - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
SvgGraphicsExporter - Class in ur_rna.StructureEditor.services.drawing.export
  Saves Graphics operations (recorded by a Graphics2DRecorder) to SVG format.
SvgGraphicsExporter(PageSize, double) - Constructor for class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
swap() - Method in class ur_rna.StructureEditor.models.Bond
  Swap the order of the nucleotides.
swap() - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
swapNucs() - Method in class ur_rna.StructureEditor.models.Motif.Segment
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.CDblVector
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.CIntVector
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.datatable
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.ProgressHandler
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.singlestructure
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.structure
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.Thermodynamics
swigCMemOwn - Variable in class ur_rna.RNAstructure.backend.TwoRNA
swigCMemOwn - Variable in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
swigCMemOwn - Variable in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
swigCMemOwn - Variable in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
swigCPtr - Variable in class ur_rna.RNAstructure.backend.CDblVector
swigCPtr - Variable in class ur_rna.RNAstructure.backend.CIntVector
swigCPtr - Variable in class ur_rna.RNAstructure.backend.datatable
swigCPtr - Variable in class ur_rna.RNAstructure.backend.Dynalign_object
swigCPtr - Variable in class ur_rna.RNAstructure.backend.HybridRNA
swigCPtr - Variable in class ur_rna.RNAstructure.backend.PartialProgress
swigCPtr - Variable in class ur_rna.RNAstructure.backend.ProgressHandler
swigCPtr - Variable in class ur_rna.RNAstructure.backend.RNA
swigCPtr - Variable in class ur_rna.RNAstructure.backend.SimpleProgressHandler
swigCPtr - Variable in class ur_rna.RNAstructure.backend.singlestructure
swigCPtr - Variable in class ur_rna.RNAstructure.backend.structure
swigCPtr - Variable in class ur_rna.RNAstructure.backend.Thermodynamics
swigCPtr - Variable in class ur_rna.RNAstructure.backend.TProgressDialog
swigCPtr - Variable in class ur_rna.RNAstructure.backend.TwoRNA
swigCPtr - Variable in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
swigCPtr - Variable in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
swigCPtr - Variable in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
SwigNext() - Constructor for class ur_rna.RNAstructure.backend.DotBracketFormat.SwigNext
SwigNext() - Constructor for class ur_rna.RNAstructure.backend.RestraintType.SwigNext
swigToEnum(int) - Static method in enum ur_rna.RNAstructure.backend.DotBracketFormat
swigToEnum(int) - Static method in enum ur_rna.RNAstructure.backend.RestraintType
swigValue - Variable in enum ur_rna.RNAstructure.backend.DotBracketFormat
swigValue() - Method in enum ur_rna.RNAstructure.backend.DotBracketFormat
swigValue - Variable in enum ur_rna.RNAstructure.backend.RestraintType
swigValue() - Method in enum ur_rna.RNAstructure.backend.RestraintType
SwingClassMatchers - Class in ur_rna.GUITester.GuiTools.Matchers
SwingClassMatchers() - Constructor for class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
SwitchTo(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
  Switch to specified lex state.
symbol - Variable in class ur_rna.StructureEditor.models.Nuc
symbol - Variable in class ur_rna.StructureEditor.models.RnaSceneState.NucState
symbol - Variable in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
SymbolColorRule(ColorizeDialog) - Constructor for class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
symbolColorRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
SYMBOLS - Static variable in class ur_rna.Utilities.CharType
  All Lower-ASCII symbols.
sync() - Method in class ur_rna.Utilities.prefs.FilePreferences
syncSpi() - Method in class ur_rna.Utilities.prefs.FilePreferences
syntaxErr(String, int, int[], String) - Method in class ur_rna.Utilities.SimpleDataSerializer
SyntaxErrorException - Exception in ur_rna.Utilities
  Indicates that there is a format or syntax error in the string argument passed to the method.
SyntaxErrorException() - Constructor for exception ur_rna.Utilities.SyntaxErrorException
  Default constructor.
SyntaxErrorException(String) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
  Basic exception constructor, delegated to super class.
SyntaxErrorException(Throwable) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
SyntaxErrorException(String, Throwable) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
  Basic exception constructor, delegated to super class.
SyntaxErrorException(String, String, String, String, int, int, Throwable) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
SyntaxErrorException(String, String, int, int) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
SyntaxErrorException(String, String, String) - Constructor for exception ur_rna.Utilities.SyntaxErrorException
SystemMenuKeyModifier - Static variable in class ur_rna.Utilities.swing.AcceleratorKey
  The integer key code that represents the standard modifier key for menu shortcuts.
systemRoot() - Method in class ur_rna.Utilities.prefs.FilePreferences.Factory

## T

T - Static variable in class ur_rna.RNAstructure.Nucleobase
TAB - Static variable in class ur_rna.Utilities.CharConstants
TAB - Static variable in class ur_rna.Utilities.CharType
  The tab character (#9)
tabbedPane1 - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
tabControls - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
tabControls - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
tabControls - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
tabControls - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
TABLOID - Static variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
tabs - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
tabSize - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
tag - Variable in class ur_rna.Utilities.swing.CheckMergeItem
  allows storage of user-defined additional information
tag - Variable in class ur_rna.Utilities.swing.MergeItem
  allows storage of user-defined additional information
Tan - Static variable in class ur_rna.Utilities.Colors
target - Variable in class ur_rna.Utilities.ConsoleTools.FixedStream
targetNuc - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
Teal - Static variable in class ur_rna.Utilities.Colors
TEMP_37C - Static variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
temperature - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
temperature - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
temperature - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
Templatefromct(String) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
Templatefromdsv(String, float) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
test() - Method in class ur_rna.StructureEditor.MainFrame
test() - Method in class ur_rna.StructureEditor.windows.DrawWindow
testAction - Variable in class ur_rna.StructureEditor.windows.DrawWindow
testIcons() - Method in class ur_rna.StructureEditor.MainFrame
testIconsTimer - Variable in class ur_rna.StructureEditor.MainFrame
testTopNodeType(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
TestUtils - Class in ur_rna.Utilities.testing
  Utilites to aid in unit tests.
TestUtils() - Constructor for class ur_rna.Utilities.testing.TestUtils
TestUtils.TestMethod - Interface in ur_rna.Utilities.testing
text - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
text - Variable in class ur_rna.RNAstructureUI.menus.RolloverListener
text - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
text(String, Point2D) - Static method in class ur_rna.StructureEditor.services.drawing.DrawHint
text - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
Text - Static variable in interface ur_rna.StructureEditor.services.SceneColorizer.ColorMode
text() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
TEXT_COLOR - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
TEXT_KEY - Static variable in class ur_rna.Utilities.swing.UiAction
textArea - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
textCaretEvent(CaretEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
textColor - Variable in class ur_rna.StructureEditor.models.NucStyle
TextDocListener - Class in ur_rna.Utilities.swing
  Simplifies management of JTextComponent text-change event handling.
TextDocListener() - Constructor for class ur_rna.Utilities.swing.TextDocListener
TextDocListener(Runnable) - Constructor for class ur_rna.Utilities.swing.TextDocListener
TextDocListener(Consumer<DocumentEvent>) - Constructor for class ur_rna.Utilities.swing.TextDocListener
textField1 - Variable in class ur_rna.StructureEditor.windows.SettingsWindow
textFields - Variable in class ur_rna.RNAstructureUI.ui.FieldPanel
  The array of text fields.
textPos - Variable in class ur_rna.StructureEditor.services.drawing.DrawHint.DrawText
TextWriter(Writer) - Constructor for class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
Thermodynamics - Class in ur_rna.RNAstructure.backend
Thermodynamics(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics(boolean, String, double) - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics(boolean, String) - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics(boolean) - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics() - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics(Thermodynamics) - Constructor for class ur_rna.RNAstructure.backend.Thermodynamics
Thermodynamics_ClearEnergies(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ClearEnthalpies(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetAlphabetName(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetDatatable(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetEnergyRead(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetEnthalpyTable__SWIG_0(long, Thermodynamics, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetEnthalpyTable__SWIG_1(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_GetTemperature(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_IsAlphabetRead(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_isrna_get(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_isrna_set(long, Thermodynamics, boolean) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReadThermodynamic__SWIG_0(long, Thermodynamics, String, String, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReadThermodynamic__SWIG_1(long, Thermodynamics, String, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReadThermodynamic__SWIG_2(long, Thermodynamics, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReadThermodynamic__SWIG_3(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReloadDataTables__SWIG_0(long, Thermodynamics, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_ReloadDataTables__SWIG_1(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_SetTemperature(long, Thermodynamics, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thermodynamics_VerifyThermodynamic(long, Thermodynamics) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
Thistle - Static variable in class ur_rna.Utilities.Colors
time - Variable in class ur_rna.Utilities.StopWatch
time() - Static method in class ur_rna.Utilities.StopWatch
timer - Variable in class ur_rna.RNAstructureUI.ui.ProgressPanel
title - Variable in class ur_rna.GUITester.Script
title - Variable in class ur_rna.StructureEditor.models.RnaScene
title - Variable in class ur_rna.StructureEditor.models.RnaSceneGroup
title - Variable in class ur_rna.StructureEditor.models.RnaSceneState
TITLE - Static variable in class ur_rna.StructureEditor.Program
TITLE - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
titleBox - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
  The array of text areas in this window.
tmpNucShape - Variable in class ur_rna.StructureEditor.services.RnaDrawController
tmpPt1 - Variable in class ur_rna.StructureEditor.services.drawing.View2D
tmpPt2 - Variable in class ur_rna.StructureEditor.services.drawing.View2D
tmrUpdate - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
toArray() - Method in class ur_rna.StructureEditor.models.StrandList
toBool(Object, boolean) - Static method in class ur_rna.Utilities.Convert
toBool(Object) - Static method in class ur_rna.Utilities.Convert
toBool(String) - Static method in class ur_rna.Utilities.Convert
toBufferedImage(Image, boolean) - Static method in class ur_rna.Utilities.swing.ImageUtil
  This method returns a buffered image with the contents of an image.
toBufferedImage(Image) - Static method in class ur_rna.Utilities.swing.ImageUtil
  This method returns a buffered image with the contents of an image.
toBufferedImage(RenderedImage) - Static method in class ur_rna.Utilities.swing.ImageUtil
  Converts an arbitrary image to a `BufferedImage`.
toChar(Object) - Static method in class ur_rna.Utilities.Convert
toChar(Object, char) - Static method in class ur_rna.Utilities.Convert
toChar(Object, char, boolean) - Static method in class ur_rna.Utilities.Convert
toColor(Object) - Static method in class ur_rna.Utilities.Convert
toColor(Object, Color) - Static method in class ur_rna.Utilities.Convert
toColor(Object, Color, boolean) - Static method in class ur_rna.Utilities.Convert
toDisplayString() - Method in interface ur_rna.Utilities.Displayable
  Returns an informative representation of the object, which should indicate its type if it is not obvious.
toDisplayString(Object) - Static method in class ur_rna.Utilities.ObjTools
toDouble(Object) - Static method in class ur_rna.Utilities.Convert
toDouble(Object, double) - Static method in class ur_rna.Utilities.Convert
toDouble(Object, double, boolean) - Static method in class ur_rna.Utilities.Convert
toFloat(Object) - Static method in class ur_rna.Utilities.Convert
toFloat(Object, float) - Static method in class ur_rna.Utilities.Convert
toFloat(Object, float, boolean) - Static method in class ur_rna.Utilities.Convert
toFont(Object) - Static method in class ur_rna.Utilities.Convert
toFont(Object, Font) - Static method in class ur_rna.Utilities.Convert
toFont(Object, Font, boolean) - Static method in class ur_rna.Utilities.Convert
toFriendlyName(String) - Static method in class ur_rna.Utilities.Strings
  Converts a camel-case name into space separated words.
ToFriendlyString - Annotation Type in ur_rna.Utilities.annotation
toggle - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
toggleOption(StructureDialog.DrawOptions) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
toHex(Color) - Static method in class ur_rna.Utilities.Colors
toHex(Color, String) - Static method in class ur_rna.Utilities.Colors
toInt(String) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow
toInt(String, int) - Static method in class ur_rna.StructureEditor.windows.NewFileWindow
toInt(Object) - Static method in class ur_rna.Utilities.Convert
toInt(Object, int) - Static method in class ur_rna.Utilities.Convert
toInt(Object, int, boolean) - Static method in class ur_rna.Utilities.Convert
token - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Current token.
Token - Class in ur_rna.GUITester.ScriptParser
  Describes the input token stream.
Token() - Constructor for class ur_rna.GUITester.ScriptParser.Token
  No-argument constructor
Token(int) - Constructor for class ur_rna.GUITester.ScriptParser.Token
  Constructs a new token for the specified Image.
Token(int, String) - Constructor for class ur_rna.GUITester.ScriptParser.Token
  Constructs a new token for the specified Image and Kind.
Token(Matcher, SimpleDataSerializer.TokenPattern) - Constructor for class ur_rna.Utilities.SimpleDataSerializer.Token
token_source - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
  Generated Token Manager.
tokenBegin - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
tokenImage - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  Literal token values.
tokenImage - Variable in exception ur_rna.GUITester.ScriptParser.ParseException
  This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
tokenize(CharSequence, int[], boolean, boolean) - Method in class ur_rna.Utilities.SimpleDataSerializer
tokenKind - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode
TokenMgrError - Error in ur_rna.GUITester.ScriptParser
  Token Manager error.
TokenMgrError() - Constructor for error ur_rna.GUITester.ScriptParser.TokenMgrError
  No arg constructor.
TokenMgrError(String, int) - Constructor for error ur_rna.GUITester.ScriptParser.TokenMgrError
  Constructor with message and reason.
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error ur_rna.GUITester.ScriptParser.TokenMgrError
  Full Constructor.
TokenPattern(Pattern) - Constructor for enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
tokens - Variable in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
toLine() - Method in class ur_rna.Utilities.geom.Vec2D
  Returns a line starting at (0,0) and ending at the tip of the vector -- (x, y).
toLine(Point2D) - Method in class ur_rna.Utilities.geom.Vec2D
  Returns a line starting at the given point and ending at the starting point + the vector -- i.e.
toLine(Point2D, double) - Method in class ur_rna.Utilities.geom.Vec2D
  Returns a line starting at the given point, in the direction of the vector, and with the specified distance.
toList(double[]) - Static method in class ur_rna.Utilities.ObjTools
toList(float[]) - Static method in class ur_rna.Utilities.ObjTools
toList(int[]) - Static method in class ur_rna.Utilities.ObjTools
toMap(NamedArg[], boolean) - Static method in class ur_rna.Utilities.NamedArg
toMap(NamedArg[], boolean, String) - Static method in class ur_rna.Utilities.NamedArg
toMap(K[], V[]) - Static method in class ur_rna.Utilities.ObjTools
Tomato - Static variable in class ur_rna.Utilities.Colors
toModel(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toModel(Point2D, Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toModel(Rectangle2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toModel(Rectangle2D, Rectangle2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toObjArr(double[]) - Static method in class ur_rna.Utilities.ObjTools
toObjArr(float[]) - Static method in class ur_rna.Utilities.ObjTools
toObjArr(int[]) - Static method in class ur_rna.Utilities.ObjTools
toolBar - Variable in class ur_rna.RNAstructureUI.AppMainFrame
toolBar - Variable in class ur_rna.StructureEditor.MainFrame
ToolButtonList() - Constructor for class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList
toolButtons - Variable in class ur_rna.StructureEditor.windows.DrawWindow
ToolWindow - Class in ur_rna.StructureEditor.ui
ToolWindow() - Constructor for class ur_rna.StructureEditor.ui.ToolWindow
toPoint() - Method in class ur_rna.Utilities.geom.Vec2D
toPointF() - Method in class ur_rna.Utilities.geom.Vec2D
toScreen(Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toScreen(Point2D, Point2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toScreen(Rectangle2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toScreen(Rectangle2D, Rectangle2D) - Method in class ur_rna.StructureEditor.services.drawing.View2D
toScreenDegrees - Static variable in class ur_rna.Utilities.geom.Ellipses
toStr(Object) - Static method in class ur_rna.Utilities.ObjTools
toStr(Object, String) - Static method in class ur_rna.Utilities.ObjTools
toString() - Method in class ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher
toString() - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
toString(boolean) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
toString() - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
toString() - Method in class ur_rna.GUITester.Script
toString() - Method in class ur_rna.GUITester.ScriptParser.ASTAssignment
toString() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
toString() - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
toString(String) - Method in class ur_rna.GUITester.ScriptParser.SimpleNode
toString() - Method in class ur_rna.GUITester.ScriptParser.Token
  Returns the image.
toString() - Method in exception ur_rna.RNAstructure.RnaBackendException
toString() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
toString() - Method in enum ur_rna.StructureEditor.FileType
toString() - Method in class ur_rna.StructureEditor.models.Bond
toString() - Method in class ur_rna.StructureEditor.models.Motif.Loop
toString() - Method in class ur_rna.StructureEditor.models.Motif.MultiLoop
toString() - Method in class ur_rna.StructureEditor.models.Nuc
  Returns a string representation of the object.
toString(String) - Method in class ur_rna.StructureEditor.models.Nuc
toString() - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
toString() - Method in class ur_rna.StructureEditor.windows.DashboardFrame.ListItem
toString(Object) - Static method in class ur_rna.Utilities.Convert
toString(Object, String) - Static method in class ur_rna.Utilities.Convert
toString() - Method in class ur_rna.Utilities.geom.Matrix3D
  Returns a string that contains the values of this Matrix3D.
toString() - Method in class ur_rna.Utilities.geom.Vec2D
toString() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
toString(Object, SimpleDataSerializer.OutputFormatSettings) - Method in class ur_rna.Utilities.SimpleDataSerializer
toString() - Method in class ur_rna.Utilities.StringBuilderEx
toString(KeyStroke) - Static method in class ur_rna.Utilities.swing.AcceleratorKey
  Return a nice string representation of the given keystroke (the toString method of KeyStroke isn't nice.)
toString() - Method in class ur_rna.Utilities.swing.CheckMergeItem
toString() - Method in class ur_rna.Utilities.swing.MergeItem
toString() - Method in class ur_rna.Utilities.Tuple.Pair
toString() - Method in class ur_rna.Utilities.Tuple.Quad
toString() - Method in class ur_rna.Utilities.Tuple.Triplet
toString() - Method in class ur_rna.Utilities.Version
toStringRoundFactor - Static variable in class ur_rna.Utilities.geom.Vec2D
toType(Object, Class) - Static method in class ur_rna.Utilities.Convert
toType(Object, T) - Static method in class ur_rna.Utilities.Convert
TProgressDialog - Class in ur_rna.RNAstructure.backend
TProgressDialog(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.TProgressDialog
TProgressDialog() - Constructor for class ur_rna.RNAstructure.backend.TProgressDialog
TProgressDialog_SWIGUpcast(long) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TProgressDialog_update(long, TProgressDialog, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
tr - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
tr - Variable in class ur_rna.StructureEditor.ui.DrawPanel
trace(String, Object...) - Method in class ur_rna.GUITester.ScriptRuntime
trace(String) - Method in class ur_rna.GUITester.ScriptRuntime
trace(String) - Method in class ur_rna.Utilities.AppLog
trace(String, Object...) - Method in class ur_rna.Utilities.AppLog
trace_call(String) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trace_enabled - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trace_indent - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
TRACE_PARSE_TREE - Static variable in class ur_rna.GUITester.ScriptRunner
trace_return(String) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trace_scan(Token, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trace_token(Token, String) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trackLineColumn - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
transform(AffineTransform) - Method in class ur_rna.StructureEditor.models.Nuc
transform(AffineTransform) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
transform - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  Current transformation matrix.
transform(double[]) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiply this matrix by the 3D vector represented by the xyz array and place the result back into the same array.
transform(double[], int, int) - Method in class ur_rna.Utilities.geom.Matrix3D
  Multiply this matrix by the 3D vector represented by the xyz array and place the result back into the same array.
transform(Shape, AffineTransform) - Static method in class ur_rna.Utilities.geom.ShapeUtil
transform(AffineTransform) - Method in class ur_rna.Utilities.geom.Vec2D
transformAll(AffineTransform) - Method in interface ur_rna.StructureEditor.models.INucGroup
transformAll(AffineTransform) - Method in class ur_rna.StructureEditor.models.Nuc
  Implementation of `INucGroup.transformAll(AffineTransform)`
transformNucs(Collection<Nuc>, AffineTransform) - Method in class ur_rna.StructureEditor.services.RnaDrawController
TransformOp(AffineTransform, boolean) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.TransformOp
transformShape(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
translate(float, float) - Method in class ur_rna.StructureEditor.models.Nuc
translate(int, int) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
translate(double, double) - Method in class ur_rna.StructureEditor.services.drawing.export.Graphics2DRecorder
translate(float, float) - Method in class ur_rna.Utilities.geom.Ellipses.Circle
translate(Point2D, Point2D) - Static method in class ur_rna.Utilities.geom.PointMath
  translates p by (p.x, p.y).
translate(Point2D, double, double) - Static method in class ur_rna.Utilities.geom.PointMath
  ranslates p by (dx, dy).
translateScreenNucs(Collection<Nuc>, Point, Point) - Method in class ur_rna.StructureEditor.services.RnaDrawController
  Translates all selected nucleotides by the x and y coordinates of the delta point, which is assumed to be in screen coordinates.
translateScreenNucs(Collection<Nuc>, Point2D) - Method in class ur_rna.StructureEditor.services.RnaDrawController
  Translates all selected nucleotides by the x and y coordinates of the delta point, which is assumed to be in screen coordinates.
transpose() - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to its transpose.
transpose(Matrix3D) - Method in class ur_rna.Utilities.geom.Matrix3D
  Sets the value of this matrix to the transpose of the argument matrix.
transpose_mat(double[], double[]) - Static method in class ur_rna.Utilities.geom.Matrix3D
TreeNode<T extends TreeNode> - Class in ur_rna.Utilities
  Represents an abstract Tree data structure.
TreeNode() - Constructor for class ur_rna.Utilities.TreeNode
trimEnd(char) - Method in class ur_rna.Utilities.StringBuilderEx
  Remove one or more instances of the specified character from the end of the StringBuilder.
trimEnd(char, int) - Method in class ur_rna.Utilities.StringBuilderEx
  Remove one or more instances of the specified character from the end of the StringBuilder.
trimEnd(char...) - Method in class ur_rna.Utilities.StringBuilderEx
  Remove one or more instances of any of the specified characters from the end of the StringBuilder.
trimEnd(char[], int) - Method in class ur_rna.Utilities.StringBuilderEx
  Remove one or more instances of any of the specified characters from the end of the StringBuilder.
trimRight(String, int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
trimToSize() - Method in class ur_rna.Utilities.StringBuilderEx
  Attempts to reduce storage used for the character sequence.
Triplet(T1, T2, T3) - Constructor for class ur_rna.Utilities.Tuple.Triplet
Triplet() - Constructor for class ur_rna.Utilities.Tuple.Triplet
trToModel - Variable in class ur_rna.StructureEditor.services.drawing.View2D
  Converts screen coordinates to model coordinates.
trToScreen - Variable in class ur_rna.StructureEditor.services.drawing.View2D
  Converts model coordinates to screen coordinates.
TRUE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
TRUE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
TrueScreenDPI - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
truncate(int) - Method in class ur_rna.Utilities.StringBuilderEx
  Remove the specified number of characters from the end of the string.
tryGet(String) - Static method in class ur_rna.RNAstructureUI.utilities.Resources
tryGetClass(String) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher
tryGetImage(String) - Static method in class ur_rna.RNAstructureUI.utilities.ImageGrabber
  Create an image.
tryGetImageIcon(String) - Static method in class ur_rna.RNAstructureUI.utilities.ImageGrabber
  Create an image icon.
tryGetStream(String) - Method in class ur_rna.Utilities.ResourceLoader
  Searches for the specified resource in all search directories and returns either an InputStream (if the resource is found) or null (if it cannot be found).
tryGetVar(String) - Method in class ur_rna.GUITester.ScriptRuntime
tryLoadLibrary(String[], Throwable[]) - Method in class ur_rna.Utilities.JniLoader
tryParse(String) - Static method in class ur_rna.Utilities.Version
  Returns a Version object if the passed-in String argument represents a valid version string.
tryPopTypedNode(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
Tuple - Class in ur_rna.Utilities
  Implementation of Tuples that have mutable items.
Tuple() - Constructor for class ur_rna.Utilities.Tuple
Tuple.Pair<T1,T2> - Class in ur_rna.Utilities
Tuple.Quad<T1,T2,T3,T4> - Class in ur_rna.Utilities
Tuple.Singlet<T1> - Class in ur_rna.Utilities
Tuple.Triplet<T1,T2,T3> - Class in ur_rna.Utilities
turboAln - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboCTs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
TurboFoldWindow - Class in ur_rna.RNAstructureUI.windows
  A class responsible for initializing and running the TurboFold module, which calculates common secondary structures of multiple sequences using the partition function and probabalistic alignments.
TurboFoldWindow() - Constructor for class ur_rna.RNAstructureUI.windows.TurboFoldWindow
  Constructor.
turboGamma - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboMaxEnergyDiff - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboMaxStructures - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboMEAGamma - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboMinHelix - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboMode - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboPFSs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboPKIterations - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboThreshold - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
turboWindowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
Turquoise - Static variable in class ur_rna.Utilities.Colors
TwoArgs() - Constructor for class ur_rna.Utilities.EventSource.TwoArgs
TwoPI - Static variable in class ur_rna.Utilities.geom.Vec2D
TwoRNA - Class in ur_rna.RNAstructure.backend
TwoRNA(long, boolean) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA(String, String, boolean) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA(String, String) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA(String, int, String, int, boolean) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA(String, int, String, int) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA(String, int, String, int, Thermodynamics) - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA() - Constructor for class ur_rna.RNAstructure.backend.TwoRNA
TwoRNA_compoundmessage_get(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_compoundmessage_set(long, TwoRNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetErrorCode(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetErrorDetails(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetErrorMessage(long, TwoRNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetErrorMessageString(long, TwoRNA, int) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetRNA1(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetRNA2(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_GetTemperature(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_ResetError(long, TwoRNA) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_SetErrorDetails(long, TwoRNA, String) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
TwoRNA_SetTemperature(long, TwoRNA, double) - Static method in class ur_rna.RNAstructure.backend.RNABackendJNI
txt - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
txt - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SimpleColorControl
txtBase - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtBases - Variable in class ur_rna.StructureEditor.windows.InsertBasesDialog
txtColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
txtColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
txtConFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtConFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtConFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtConFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtConFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtDebug - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
txtModData - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtMSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
txtOutputFile - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
txtOutputFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtOutputFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtOutputFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtOutputFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtOutputFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtProbData - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
txtSeqFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtSeqFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtSeqFile1 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtSeqFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
txtSeqFile2 - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
txtSeqTitle - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtSequence - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtSequence - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
txtShapeFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
txtSingleColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtStructure - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
txtSymbol - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
txtTitle - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
txtValue - Variable in class ur_rna.StructureEditor.ui.SliderToolWindow
txtValue - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
txtValueColor - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
txtValueLimit - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
type - Variable in class ur_rna.StructureEditor.models.Bond.BondInfo
type - Variable in class ur_rna.StructureEditor.models.Bond
  S1 and S2 represent the strand indices, N1 and N2 represent the nucleotide indices within each respective strand.
type - Variable in class ur_rna.StructureEditor.models.Motif.Loop
type - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
type - Variable in class ur_rna.StructureEditor.services.RecentFileList.RecentFile
type - Variable in class ur_rna.StructureEditor.services.SceneUpdateEvent
type - Variable in class ur_rna.StructureEditor.windows.NewFileWindow.StructItem
type() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
types - Static variable in class ur_rna.GUITester.GuiTools.ScreenCapture

## U

UiAction - Class in ur_rna.Utilities.swing
  Extension of the swing `AbstractAction` class that accepts various methods of handling the action.
UiAction(String, Runnable) - Constructor for class ur_rna.Utilities.swing.UiAction
UiAction(String, Runnable, Icon) - Constructor for class ur_rna.Utilities.swing.UiAction
UiAction(String, ActionListener) - Constructor for class ur_rna.Utilities.swing.UiAction
UiAction(String, ActionListener, Icon) - Constructor for class ur_rna.Utilities.swing.UiAction
uiUpdateTimer - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
UNDERSCORE - Static variable in class ur_rna.Utilities.CharType
undo() - Method in class ur_rna.StructureEditor.services.History
undo() - Method in class ur_rna.StructureEditor.services.RnaDrawController
undo() - Method in interface ur_rna.StructureEditor.services.SceneController
undoableEditHappened(UndoableEditEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow.IgnoreStylesUndoManager
undoSeq - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
undoStr - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
unescapeStringLiteral(String) - Static method in class ur_rna.Utilities.Strings
  UN-escapes a string by replacing backslash-escaped sequences with the character literals they represent.
UNICODE_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
Unknown - Static variable in class ur_rna.RNAstructure.Nucleobase
UNKNOWN - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
unnamed - Variable in class ur_rna.Utilities.CommandLineParser.ParseResults
UnnamedArg(String, int) - Constructor for class ur_rna.Utilities.CommandLineParser.UnnamedArg
unnamedValues - Variable in class ur_rna.Utilities.CommandLineParser.ParseResults
unpair() - Method in class ur_rna.StructureEditor.models.Bond
unpairedBases - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
unsetSubItemMergePos() - Method in class ur_rna.RNAstructureUI.menus.MenuList
unspecifiedBases - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
UNSTYLED - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
unsupported() - Method in class ur_rna.StructureEditor.models.Strand
UnsupportedActionException() - Constructor for exception ur_rna.GUITester.RuntimeTools.UnsupportedActionException
UnsupportedActionException(String) - Constructor for exception ur_rna.GUITester.RuntimeTools.UnsupportedActionException
UnsupportedActionException(Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.UnsupportedActionException
UnsupportedActionException(String, Throwable) - Constructor for exception ur_rna.GUITester.RuntimeTools.UnsupportedActionException
untransformShape(Shape) - Method in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
update(int) - Method in class ur_rna.RNAstructure.backend.PartialProgress
update(int) - Method in class ur_rna.RNAstructure.backend.ProgressHandler
update(double, double) - Method in class ur_rna.RNAstructure.backend.ProgressHandler
update(int) - Method in class ur_rna.RNAstructure.backend.TProgressDialog
update - Variable in class ur_rna.StructureEditor.models.HistoryState
update(int, String) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
update(int) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
update(DocumentEvent) - Method in interface ur_rna.Utilities.swing.SimpleDocumentListener
update(DocumentEvent) - Method in class ur_rna.Utilities.swing.TextDocListener
updateActiveFrameInfo() - Method in class ur_rna.RNAstructureUI.AppMainFrame
updateActiveFrameInfo() - Method in class ur_rna.StructureEditor.MainFrame
updateBackendBonds(RnaScene, RNA, int) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
  Clear the RNA structure's bonds and re-read them from the RnaScene.
updateCalcProgress(ProgressPanel) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
updateContentSize(Rectangle) - Method in class ur_rna.StructureEditor.ui.DrawPanel
updateCursor() - Method in class ur_rna.Utilities.swing.JActionLabel
updateDisplay() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
updatedMessage - Variable in exception ur_rna.Utilities.ExtensibleException
updateEnabledUI(ItemEvent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog.SymbolColorRule
updateFileUI() - Method in class ur_rna.StructureEditor.windows.DrawWindow
updateFormUI() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
updateFormUI() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
updateFormUI() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
updateFormUI() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
updateFormUI() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Called periodically by a timer to update the user interface.
updateFraction(double) - Method in class ur_rna.RNAstructure.backend.ProgressHandler
updateLayout() - Method in class ur_rna.StructureEditor.windows.DashboardFrame
UpdateLineColumn(char) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
updateMainFrame() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow
  Call this if changes are made to the window that could require the JDesktopPane or the AppMainFrame to update.
updateMenuUI() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
updateMousePos(MouseEvent) - Method in class ur_rna.StructureEditor.services.RnaDrawController.MouseHandler
updateNavUI() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
updateRecentFilesUI() - Method in class ur_rna.StructureEditor.MainFrame
updateSceneBonds(RnaScene, RNA, int) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
  Clear the RnaScene's bonds and re-write them from the RNA structure.
updateSelection(boolean, Nuc, int) - Method in class ur_rna.StructureEditor.services.RnaDrawController
  Updates the set of selected Nucs based on the current selection and the user's intention.
updateSelection(boolean, Rectangle) - Method in class ur_rna.StructureEditor.services.RnaDrawController
updateSelectionUI() - Method in class ur_rna.StructureEditor.windows.DrawWindow
updateSequenceInfoFromUI() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
updateStrands(int) - Method in class ur_rna.StructureEditor.models.StrandList
updateStructure() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
UpdateSyntaxStyles() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
UpdateSyntaxStyles(int, int) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
updateTextUI() - Method in class ur_rna.StructureEditor.windows.NewFileWindow
updateTimer - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
updateTimerElapsed(ActionEvent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
updateTimerElapsed(ActionEvent) - Method in class ur_rna.StructureEditor.windows.NewFileWindow
updateTransform() - Method in class ur_rna.StructureEditor.ui.DrawPanel
updateUI() - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
updateUI() - Method in class ur_rna.Utilities.swing.WaitDialog
updateView(View2D) - Method in interface ur_rna.StructureEditor.models.IScreenObject
  Called before any other methods to notify the screen object of the current screen coordinates.
updateView(View2D) - Method in class ur_rna.StructureEditor.services.drawing.ScreenShape
  Called before any other methods to notify the screen object of the current screen coordinates.
updateView(View2D) - Method in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
updateView() - Method in class ur_rna.StructureEditor.ui.DrawPanel
updateWindowList() - Method in class ur_rna.StructureEditor.menus.WindowsMenu
updatingSettings - Variable in class ur_rna.StructureEditor.menus.SettingsMenu
updatingSettings - Variable in class ur_rna.StructureEditor.windows.DashboardFrame
UPPER_ALPHA - Static variable in class ur_rna.Utilities.CharType
  A-Z
UPPER_ASCII - Static variable in class ur_rna.Utilities.CharConstants
ur_rna - package ur_rna
ur_rna.GUITester - package ur_rna.GUITester
ur_rna.GUITester.GuiTools - package ur_rna.GUITester.GuiTools
ur_rna.GUITester.GuiTools.Matchers - package ur_rna.GUITester.GuiTools.Matchers
ur_rna.GUITester.ScriptParser - package ur_rna.GUITester.ScriptParser
ur_rna.RNAstructure - package ur_rna.RNAstructure
ur_rna.RNAstructure.backend - package ur_rna.RNAstructure.backend
ur_rna.RNAstructureUI - package ur_rna.RNAstructureUI
  A package that encapsulates all the Java classes that comprise the RNAstructure Java interface.
ur_rna.RNAstructureUI.drawing - package ur_rna.RNAstructureUI.drawing
  A package that encapsulates all the Java classes that handle structure and dot plot drawing.
ur_rna.RNAstructureUI.drawing.dialogs - package ur_rna.RNAstructureUI.drawing.dialogs
  A package that holds all Java drawing dialogs.
ur_rna.RNAstructureUI.drawing.menus - package ur_rna.RNAstructureUI.drawing.menus
  A package that holds all menus used in the drawing framework.
ur_rna.RNAstructureUI.drawing.proxy - package ur_rna.RNAstructureUI.drawing.proxy
  A package that holds all Java drawing classes generated by SWIG that connect the C++ back end to the Java front end.
ur_rna.RNAstructureUI.drawing.runners - package ur_rna.RNAstructureUI.drawing.runners
  A package that holds the run templates that are used when the Java drawing framework is wrapped into self-contained executables.
ur_rna.RNAstructureUI.menus - package ur_rna.RNAstructureUI.menus
  A package that holds all menus used in the Java RNAstructure interface.
ur_rna.RNAstructureUI.ui - package ur_rna.RNAstructureUI.ui
ur_rna.RNAstructureUI.utilities - package ur_rna.RNAstructureUI.utilities
  A package that holds a variety of utilities classes.
ur_rna.RNAstructureUI.windows - package ur_rna.RNAstructureUI.windows
  A package that holds all internal windows used in the drawing framework.
ur_rna.StructureEditor - package ur_rna.StructureEditor
ur_rna.StructureEditor.menus - package ur_rna.StructureEditor.menus
ur_rna.StructureEditor.models - package ur_rna.StructureEditor.models
ur_rna.StructureEditor.services - package ur_rna.StructureEditor.services
ur_rna.StructureEditor.services.drawing - package ur_rna.StructureEditor.services.drawing
ur_rna.StructureEditor.services.drawing.export - package ur_rna.StructureEditor.services.drawing.export
ur_rna.StructureEditor.services.fileIO - package ur_rna.StructureEditor.services.fileIO
ur_rna.StructureEditor.ui - package ur_rna.StructureEditor.ui
ur_rna.StructureEditor.windows - package ur_rna.StructureEditor.windows
ur_rna.Utilities - package ur_rna.Utilities
ur_rna.Utilities.annotation - package ur_rna.Utilities.annotation
ur_rna.Utilities.geom - package ur_rna.Utilities.geom
ur_rna.Utilities.prefs - package ur_rna.Utilities.prefs
ur_rna.Utilities.swing - package ur_rna.Utilities.swing
ur_rna.Utilities.testing - package ur_rna.Utilities.testing
urlenc(String) - Static method in class ur_rna.StructureEditor.AppActions
useNativeLAF - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
useNativeMenus - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
useNativeMenus() - Static method in class ur_rna.Utilities.OSInfo
user() - Method in class ur_rna.StructureEditor.services.UserPrefs
  Store user-specific settings here.
userAcceptedInvalidSequence - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
useRecorder - Variable in class ur_rna.StructureEditor.services.RnaDrawController
userNode - Variable in class ur_rna.StructureEditor.services.UserPrefs
UserOptions - Class in ur_rna.RNAstructureUI.utilities
UserOptions() - Constructor for class ur_rna.RNAstructureUI.utilities.UserOptions
userPrefs - Variable in class ur_rna.StructureEditor.Program
UserPrefs - Class in ur_rna.StructureEditor.services
  Assists with storing User Preferences to file.
UserPrefs(String) - Constructor for class ur_rna.StructureEditor.services.UserPrefs
UserPrefs(File) - Constructor for class ur_rna.StructureEditor.services.UserPrefs
userRoot() - Method in class ur_rna.Utilities.prefs.FilePreferences.Factory
usesAlpha(Image) - Static method in class ur_rna.Utilities.swing.ImageUtil
  This method returns `true` if the specified image has at least one pixel that is not fully opaque.
useSimpleFileChooser - Static variable in class ur_rna.RNAstructureUI.AppMainFrame

## V

val - Variable in class ur_rna.GUITester.ScriptParser.ASTNamedArgument
validate() - Method in class ur_rna.StructureEditor.models.Motif.Branch
validateFailed(JComponent, String, Object...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
validateFileField(JTextComponent, boolean, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
  Verifies the existence of a file in a JTextComponent that has been added as a named file-field.
validateFileField(JTextComponent, boolean) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
validatePair(Nuc) - Static method in class ur_rna.StructureEditor.models.Motif.Domain
validateRequiredField(JTextComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
value - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
value - Variable in enum ur_rna.RNAstructureUI.utilities.FileType
value - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.HintOp
value - Variable in class ur_rna.Utilities.EventArgs.BoolEventArgs
value - Variable in class ur_rna.Utilities.EventArgs.IntEventArgs
value - Variable in class ur_rna.Utilities.EventArgs.ObjEventArgs
value - Variable in class ur_rna.Utilities.EventArgs.StringEventArgs
value - Variable in class ur_rna.Utilities.NamedArg
value - Variable in class ur_rna.Utilities.ObjTools.RefBool
value - Variable in class ur_rna.Utilities.ObjTools.RefInt
value - Variable in class ur_rna.Utilities.ObjTools.RefStr
value - Variable in class ur_rna.Utilities.Pair
value - Variable in enum ur_rna.Utilities.swing.ActionHelper.KeyBindFocus
valueChanged() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
ValueColorRule(ColorizeDialog) - Constructor for class ur_rna.StructureEditor.windows.ColorizeDialog.ValueColorRule
valueColorRules - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
valueComparisonChanged(ItemEvent) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
valueComparisonSymbols - Static variable in class ur_rna.StructureEditor.windows.ColorizeDialog
valueField - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
valueOf(String) - Static method in enum ur_rna.GUITester.GUITesterStartup.ScriptSource
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.GUITester.GuiTools.GuiRelative
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.RNAstructure.backend.DotBracketFormat
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.RNAstructure.backend.RestraintType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog.DrawOptions
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.RNAstructureUI.utilities.FileType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.FileType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.models.Bond.MultiLoopRole
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.models.BondType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.models.Motif.Loop.LoopType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.drawing.SelectionRotater.RotationCenter
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.RnaDrawController.BehaviorMode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.RnaDrawController.SelectionType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.SceneDrawMode
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.StructureEditor.services.SceneUpdateCategory
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.CommandLineParser.ParamAffinity
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.OSInfo.OSType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.swing.ActionHelper.KeyBindFocus
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.swing.InputAdapter.InputType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ur_rna.Utilities.Verbosity
  Returns the enum constant of this type with the specified name.
values() - Static method in enum ur_rna.GUITester.GUITesterStartup.ScriptSource
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.GUITester.GuiTools.GuiRelative
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.RNAstructure.backend.DotBracketFormat
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.RNAstructure.backend.RestraintType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog.DrawOptions
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.RNAstructureUI.utilities.FileType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.FileType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.models.Bond.MultiLoopRole
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.models.BondType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.models.Motif.Loop.LoopType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.services.drawing.SelectionRotater.RotationCenter
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.services.RnaDrawController.BehaviorMode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.services.RnaDrawController.SelectionType
  Returns an array containing the constants of this enum type, in the order they are declared.
values - Static variable in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
values() - Static method in enum ur_rna.StructureEditor.services.SceneColorizer.Comparison
  Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ur_rna.StructureEditor.services.SceneColorizer.PairProbabilityData
values() - Static method in enum ur_rna.StructureEditor.services.SceneDrawMode
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.StructureEditor.services.SceneUpdateCategory
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.CommandLineParser.ParamAffinity
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.OSInfo.OSType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.SimpleDataSerializer.TokenPattern
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.swing.ActionHelper.KeyBindFocus
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.swing.InputAdapter.InputType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ur_rna.Utilities.Verbosity
  Returns an array containing the constants of this enum type, in the order they are declared.
ValueSelectionDialog - Class in ur_rna.RNAstructureUI.ui
  A class which creates a dialog that selects values from labeled text fields.
ValueSelectionDialog(String) - Constructor for class ur_rna.RNAstructureUI.ui.ValueSelectionDialog
  Constructor.
valueText - Variable in class ur_rna.Utilities.CommandLineParser.FlagArg
  Gets the value of this flag, if one was specified, or null otherwise.
varName - Variable in class ur_rna.GUITester.ScriptParser.ASTVarRef
VarRef() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
Vec2D - Class in ur_rna.Utilities.geom
Vec2D(double, double) - Constructor for class ur_rna.Utilities.geom.Vec2D
Vec2D() - Constructor for class ur_rna.Utilities.geom.Vec2D
Vec2D(Point2D) - Constructor for class ur_rna.Utilities.geom.Vec2D
Vec2D(Point2D, Point2D) - Constructor for class ur_rna.Utilities.geom.Vec2D
ver - Variable in class ur_rna.Utilities.AppInfo.AnnotationAppInfoProvider
verb - Variable in class ur_rna.GUITester.ScriptParser.ASTAction
Verbosity - Enum in ur_rna.Utilities
Verbosity(int) - Constructor for enum ur_rna.Utilities.Verbosity
verify() - Static method in class ur_rna.RNAstructureUI.utilities.Resources
verifyBackendResult(String, String, Object...) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
  Check to see if the module was initialized correctly.
verifyDataFiles(String) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
verifyDataPath() - Static method in class ur_rna.RNAstructureUI.RNAstructure
verifyDataPath() - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
verifyInput() - Method in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow
verifyInput() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
verifyInput() - Method in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
verifyInput() - Method in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
verifyMenuMnemonics(Component[]) - Method in class ur_rna.RNAstructureUI.AppMainFrame
verifyMenuMnemonics(Component[]) - Method in class ur_rna.StructureEditor.MainFrame
verifySequence() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
VerifyThermodynamic() - Method in class ur_rna.RNAstructure.backend.Thermodynamics
verifyType - Variable in class ur_rna.RNAstructureUI.utilities.CalcParams
verifyWritable(File) - Static method in class ur_rna.Utilities.PathTools
  Verify that a directory is writeable by writing a new file (and then deleting it).
VERSION - Static variable in interface ur_rna.RNAstructure.RNAstructureVersion
VERSION - Static variable in class ur_rna.RNAstructureUI.RNAstructure
VERSION - Static variable in class ur_rna.StructureEditor.Program
VERSION - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
Version - Class in ur_rna.Utilities
  Implements semantic versioning for Java.
Version(int, int, int, int) - Constructor for class ur_rna.Utilities.Version
Version(int, int, int) - Constructor for class ur_rna.Utilities.Version
Version(int, int) - Constructor for class ur_rna.Utilities.Version
Version(String) - Constructor for class ur_rna.Utilities.Version
VERSION_MAJOR - Static variable in class ur_rna.StructureEditor.Program
VERSION_MINOR - Static variable in class ur_rna.StructureEditor.Program
versionCheck - Variable in class ur_rna.Utilities.JniLoader
versionCompare(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
  Compares two version strings.
View - Static variable in class ur_rna.StructureEditor.models.SceneUpdateInfo
view - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
view - Variable in class ur_rna.StructureEditor.ui.DrawPanel
View2D - Class in ur_rna.StructureEditor.services.drawing
  Encapsulates the AffineTransform that converts from model coordinates to screen coordinates along with its inverse transform and allows conversion of points between the two.
View2D() - Constructor for class ur_rna.StructureEditor.services.drawing.View2D
View2D(AffineTransform, Rectangle) - Constructor for class ur_rna.StructureEditor.services.drawing.View2D
viewChanged - Variable in class ur_rna.StructureEditor.ui.DrawPanel
viewDialog() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  View the dialog.
ViewMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
viewUpdated() - Method in class ur_rna.StructureEditor.services.RnaDrawController
viewUpdated() - Method in interface ur_rna.StructureEditor.services.SceneController
viewZoomDialog() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  View a zooming dialog.
Violet - Static variable in class ur_rna.Utilities.Colors
VisibilityMatcher - Class in ur_rna.GUITester.GuiTools.Matchers
  Tests the visibility of the GUI component (whether it is showing or not)
VisibilityMatcher() - Constructor for class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
VisibilityMatcher(boolean) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher

## W

WaitDialog - Class in ur_rna.Utilities.swing
  A simple wait dialog
WaitDialog() - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(Frame) - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(String) - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(Frame, String) - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(Frame, String, String) - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(Frame, String, String, boolean, ActionListener) - Constructor for class ur_rna.Utilities.swing.WaitDialog
WaitDialog(Frame, String, String, boolean, boolean) - Constructor for class ur_rna.Utilities.swing.WaitDialog
warm - Static variable in class ur_rna.StructureEditor.services.RnaDrawController.Colors
warn(String) - Method in class ur_rna.Utilities.AppLog
warn(String, Object...) - Method in class ur_rna.Utilities.AppLog
WARNING - Static variable in class ur_rna.Utilities.swing.Dialogs
warnings - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
warnings - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
wasCanceled() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
watches - Static variable in class ur_rna.Utilities.StopWatch
WEB_URL - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
WEB_URL - Static variable in class ur_rna.StructureEditor.AppActions
Wheat - Static variable in class ur_rna.Utilities.Colors
whenDone(Consumer<? super RnaFileIO.BackgroundWork<TResult>>) - Method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
White - Static variable in class ur_rna.Utilities.Colors
WhiteSmoke - Static variable in class ur_rna.Utilities.Colors
WHITESPACE - Static variable in class ur_rna.Utilities.CharType
  Whitespace characters: TAB, CR, LF, and SPACE
width - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
width - Variable in class ur_rna.StructureEditor.services.drawing.export.PageSize
  Width of the page in mm
window - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
window - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
window() - Static method in class ur_rna.StructureEditor.AppActions
window - Variable in class ur_rna.StructureEditor.menus.WindowsMenu.WindowItem
windowFilter - Variable in class ur_rna.StructureEditor.menus.WindowsMenu
WindowItem(JInternalFrame) - Constructor for class ur_rna.StructureEditor.menus.WindowsMenu.WindowItem
windowItem_click(ActionEvent) - Method in class ur_rna.StructureEditor.menus.WindowsMenu
windowMenuFilter(JInternalFrame) - Method in class ur_rna.StructureEditor.MainFrame
  Determines which windows should be listed in the "Windows" menu
windowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow.PredictTask
windowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
windowSize - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
WindowsMenu - Class in ur_rna.StructureEditor.menus
WindowsMenu(JDesktopPane, Predicate<JInternalFrame>) - Constructor for class ur_rna.StructureEditor.menus.WindowsMenu
WindowsMenu.WindowItem - Class in ur_rna.StructureEditor.menus
WindowsMenuSection - Static variable in class ur_rna.StructureEditor.MainFrame
withText(String) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
withText(String, int) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
withText(String, boolean, boolean, boolean) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
WORD_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
WORD_CHARS - Static variable in class ur_rna.Utilities.CharType
WORD_START_CHAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
work() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
WorkDone - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
workDone - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
wrapTo2PI(double) - Static method in class ur_rna.Utilities.geom.Vec2D
  Given any angle in radians, this returns an equivalent angle in the range [0, 2*PI] In general, multiples of 2*PI map to 0 if they are negative and to 2*PI if they are positive.
wrapToPI(double) - Static method in class ur_rna.Utilities.geom.Vec2D
  Given any angle in radians, this returns an equivalent angle in the range [-PI, PI] In general, odd multiples of PI map to -PI if they are negative and to PI if they are positive.
write(List<GraphicsOp>, String) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
write(List<GraphicsOp>, Writer) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
write(String) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(char) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(int) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(Number) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(int, String) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
  Write a value padded with spaces on the left (if padding is positive) or right (if padding is negative).
write(int, char) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(int, int) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(int, Number) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
write(int) - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
write(byte[]) - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
write(byte[], int, int) - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
write(int) - Method in class ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream
write(byte[], int, int) - Method in class ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream
write(Object, Writer, SimpleDataSerializer.OutputFormatSettings) - Method in class ur_rna.Utilities.SimpleDataSerializer
write(Object, Writer, SimpleDataSerializer.OutputFormatSettings, Queue<String>) - Method in class ur_rna.Utilities.SimpleDataSerializer
WriteAlignment(String) - Method in class ur_rna.RNAstructure.backend.Dynalign_object
writeAll(String, OutputStream, Charset) - Static method in class ur_rna.Utilities.Strings
writeAll(String, OutputStream, String, int) - Static method in class ur_rna.Utilities.Strings
writeAll(String, OutputStream, String) - Static method in class ur_rna.Utilities.Strings
writeAll(String, OutputStream) - Static method in class ur_rna.Utilities.Strings
writeAll(String, OutputStream, Charset, int) - Static method in class ur_rna.Utilities.Strings
WriteConstraints(String) - Method in class ur_rna.RNAstructure.backend.RNA
WriteCt(String) - Method in class ur_rna.RNAstructure.backend.RNA
writeCteDrawingFile(RnaSceneGroup, String, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
  Write an Extended CT (CTE) Drawing files.
writeCteDrawingFile(RnaSceneGroup, Writer, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
  Write an Extended CT (CTE) Drawing files.
writeCtFile(RnaSceneGroup, String, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
WriteDotBracket(String, int, DotBracketFormat) - Method in class ur_rna.RNAstructure.backend.RNA
WriteDotBracket(String, int) - Method in class ur_rna.RNAstructure.backend.RNA
WriteDotBracket(String) - Method in class ur_rna.RNAstructure.backend.RNA
writedotbracket(String, int, DotBracketFormat) - Method in class ur_rna.RNAstructure.backend.structure
writedotbracket(String, int) - Method in class ur_rna.RNAstructure.backend.structure
writedotbracket(String) - Method in class ur_rna.RNAstructure.backend.structure
writeDotBracketFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Write a dot bracket file of all structures on this dialog.
writeDotBracketFile(String, String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
writeDrawPref(MergeMenu, String) - Method in class ur_rna.RNAstructureUI.menus.FileMenu
writeDynalignAlignmentConstraintsFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
writeFastaFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
writeFile(RnaSceneGroup, String, FileType, boolean, boolean) - Static method in class ur_rna.StructureEditor.AppActions
writeFoldingConstraintsFile(String, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
writeHelixFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Write a helix file from the current structure on this dialog.
writeHelixFile(String, String, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
writeImage(BufferedImage, String) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
  Write a BufferedImage to a File.
writeIndent(Writer, SimpleDataSerializer.OutputFormatSettings, int) - Method in class ur_rna.Utilities.SimpleDataSerializer
writeList(List<?>, Writer, SimpleDataSerializer.OutputFormatSettings, Queue<String>) - Method in class ur_rna.Utilities.SimpleDataSerializer
writeln() - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
  Write a system-specific line separator
writeMap(Map<?, ?>, Writer, SimpleDataSerializer.OutputFormatSettings, Queue<String>) - Method in class ur_rna.Utilities.SimpleDataSerializer
writeNsdDrawingFile(RnaSceneGroup, String, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
writeNsdDrawingFile(RnaSceneGroup, String, boolean, int, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
writeNsdDrawingFile(RnaSceneGroup, Writer, int, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
writeNumber(Number, SimpleDataSerializer.OutputFormatSettings) - Method in class ur_rna.Utilities.SimpleDataSerializer
writep(String, int, String) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTEWriter
  Write a property value
writep(String, int, int) - Method in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTEWriter
writePostscriptFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Write a Postscript file from the plot on this dialog.
writePostscriptFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Write a Postscript file from the current structure on this dialog.
writePostscriptFile(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
writePostscriptFile(String, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
writeProps(StringBuilder) - Method in class ur_rna.GUITester.ScriptParser.ASTAction
writeProps(StringBuilder) - Method in class ur_rna.GUITester.ScriptParser.ASTLiteral
writeProps(StringBuilder) - Method in class ur_rna.GUITester.ScriptParser.ASTVarRef
writeProps(StringBuilder) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
writer - Variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO.TextWriter
writeRNAstructureGroup(RnaSceneGroup, boolean, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
writeseq(String, int, boolean) - Method in class ur_rna.RNAstructure.backend.structure
writeseq(String, int) - Method in class ur_rna.RNAstructure.backend.structure
writeseq(String) - Method in class ur_rna.RNAstructure.backend.structure
writeSequenceFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
writeSequenceFile(RnaScene, String, FileType, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
WriteSHAPE(String, boolean) - Method in class ur_rna.RNAstructure.backend.structure
WriteSHAPE(String) - Method in class ur_rna.RNAstructure.backend.structure
writeString(String, boolean) - Method in class ur_rna.Utilities.SimpleDataSerializer
writeStructureFile(RnaSceneGroup, String, FileType, boolean) - Static method in class ur_rna.StructureEditor.services.fileIO.RnaFileIO
writeStructuresFile(String, boolean) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Write a probable structures file from the plot on this dialog.
writeStructuresFile(String, String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
writeSVGFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Write an SVG file from the plot on this dialog.
writeSVGFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
  Write an SVG file from the current structure on this dialog.
writeSVGFile(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
writeSVGFile(String, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
writeTempFile(String, String) - Method in class ur_rna.StructureEditor.windows.ColorizeDialog
writeTextFile(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog
  Write a text file from the plot on this dialog.
writeTextFile(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
WriteThermodynamicDetails(String, boolean) - Method in class ur_rna.RNAstructure.backend.RNA
WriteThermodynamicDetails(String) - Method in class ur_rna.RNAstructure.backend.RNA
writeTo(StreamResult) - Method in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
writeTo(OutputStream) - Method in class ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream

## X

X - Variable in class ur_rna.StructureEditor.models.RnaSceneState.NucState
x - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
x - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
X - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
X - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
XLINK_NAMESPACE - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
XLINK_NAMESPACE_URI - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
xor(Matcher, Matcher) - Static method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
Xor(Matcher, Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher.Xor
xor(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
xor(Matcher) - Method in interface ur_rna.GUITester.GuiTools.Matchers.ComposableMatcher
XOR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
XORASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
  RegularExpression Id.
xorMode - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsStyle
  XOR mode used for rendering.
XorModeOp(Color) - Constructor for class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.XorModeOp

## Y

Y - Variable in class ur_rna.StructureEditor.models.RnaSceneState.NucState
y - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawImageOp
y - Variable in class ur_rna.StructureEditor.services.drawing.export.GraphicsOp.DrawStringOp
Y - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.CTE
Y - Static variable in interface ur_rna.StructureEditor.services.fileIO.DrawingFileIO.NSD
Yellow - Static variable in class ur_rna.Utilities.Colors
YellowGreen - Static variable in class ur_rna.Utilities.Colors

## Z

zoom(int) - Method in class ur_rna.StructureEditor.ui.DrawPanel
ZOOM_MASK - Static variable in class ur_rna.StructureEditor.ui.DrawPanel
ZoomDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.ZoomDialog
  Constructor.
zoomImage() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
  Zoom the image on the panel.
zorder - Variable in class ur_rna.StructureEditor.services.drawing.ScreenShape
zorder - Variable in class ur_rna.StructureEditor.services.RnaDrawController.ScreenNuc
ZORDER_MAX - Static variable in interface ur_rna.StructureEditor.models.IScreenObject
ZORDER_MIN - Static variable in interface ur_rna.StructureEditor.models.IScreenObject

## _

_a - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
_actions - Variable in class ur_rna.GUITester.ScriptRuntime
_app - Static variable in class ur_rna.StructureEditor.AppActions
_asyncTask - Variable in class ur_rna.StructureEditor.windows.DrawWindow
_b - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
_backboneDir - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_backboneEnd - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_backboneLine - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_backboneStart - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_canCancel - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_center - Variable in class ur_rna.Utilities.geom.Ellipses.Circle
_changeEvent - Variable in class ur_rna.StructureEditor.Settings
_classes - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
_cls - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
_complete - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_currentClip - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
_customStreams - Variable in class ur_rna.Utilities.AppLog
_dblFormat - Static variable in class ur_rna.StructureEditor.services.fileIO.DrawingFileIO
_disableTrace - Variable in class ur_rna.GUITester.ScriptRuntime
_doParsingOnly - Variable in class ur_rna.GUITester.ScriptRuntime
_dummyGraphics - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_err - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_find - Variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
_finder - Variable in class ur_rna.GUITester.GuiTools.GuiAppManager
_fmtSimpleDouble - Static variable in class ur_rna.StructureEditor.services.drawing.export.SvgGraphicsExporter
_fontSizeFormatter - Static variable in class ur_rna.Utilities.swing.FontUtil
_gui - Variable in class ur_rna.GUITester.ScriptActions
_gui - Variable in class ur_rna.GUITester.ScriptRuntime
_isCanceled - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_isDone - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_lastActivePane - Variable in class ur_rna.StructureEditor.windows.NewFileWindow
_lastColorEffect - Variable in class ur_rna.StructureEditor.windows.ColorizeDialog
_len - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
_line - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
_log - Variable in class ur_rna.GUITester.GuiTools.GuiAppManager
_log - Variable in class ur_rna.GUITester.GuiTools.GuiFinder
_log - Variable in class ur_rna.GUITester.GuiTools.GuiRobot
_log - Variable in class ur_rna.GUITester.ScriptActions
_log - Variable in class ur_rna.GUITester.ScriptRunner
_log - Variable in class ur_rna.GUITester.ScriptRuntime
_lookup - Static variable in enum ur_rna.StructureEditor.models.BondType
_m - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Identity
_m - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.Inverse
_nameToColor - Static variable in class ur_rna.Utilities.Colors
_node - Variable in exception ur_rna.GUITester.ScriptRuntimeException
_owner - Variable in class ur_rna.GUITester.GuiTools.GuiFinder
_owner - Variable in class ur_rna.GUITester.GuiTools.GuiRobot
_parseError - Variable in class ur_rna.GUITester.ScriptRunner
_paused - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
_playing - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
_progress - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_ptModel - Variable in class ur_rna.StructureEditor.services.drawing.BranchSlider
_ptModel - Variable in class ur_rna.StructureEditor.services.drawing.LoopResizer
_queue - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
_radius - Variable in class ur_rna.Utilities.geom.Ellipses.Circle
_requiredVerbosity - Variable in class ur_rna.Utilities.AppLog
_res - Static variable in class ur_rna.RNAstructureUI.utilities.Resources
_result - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_robot - Variable in class ur_rna.GUITester.GuiTools.GuiAppManager
_rootFrame - Variable in class ur_rna.GUITester.GuiTools.GuiAppManager
_rt - Variable in class ur_rna.GUITester.ScriptActions
_runError - Variable in class ur_rna.GUITester.ScriptRunner
_sb - Variable in class ur_rna.Utilities.StringBuilderEx
_script - Variable in class ur_rna.GUITester.ScriptRuntime
_seqInfoUpdating - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
_speakPlayer - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
_speakStreams - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
_src - Variable in class ur_rna.GUITester.ScriptRunner
_status - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_stepWork - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc
_subjectApp - Variable in class ur_rna.GUITester.ScriptRunner
_suspendRedraw - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_suspendUpdatesCounter - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_tag - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_textRegions - Static variable in class ur_rna.StructureEditor.windows.NewFileWindow
_tmpPt - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
_tmpPt - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_tmpTr - Variable in class ur_rna.StructureEditor.services.drawing.DrawHandle
_tmpTr - Variable in class ur_rna.StructureEditor.services.RnaDrawController
_update - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackgroundWork
_vars - Variable in class ur_rna.GUITester.ScriptRuntime
_vis - Variable in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
_window - Static variable in class ur_rna.StructureEditor.AppActions
_workComplete - Variable in class ur_rna.StructureEditor.services.fileIO.RnaFileIO.BackendCalc

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