$ 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

$ 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 _