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$$$getRootComponent$$$() - 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
 
$$$setupUI$$$() - 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 >>> IMPORTANT!! <<< 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 >>> IMPORTANT!! <<< 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 >>> IMPORTANT!! <<< 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 >>> IMPORTANT!! <<< 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 >>> IMPORTANT!! <<< DO NOT edit this method OR call it in your code!

A

AboutWindow - Class in ur_rna.RNAstructureUI.windows
Created by Richard on 4/6/2016.
AboutWindow() - Constructor for class ur_rna.RNAstructureUI.windows.AboutWindow
 
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
 
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
 
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
 
ActionHandler<T extends EventArgs> - Interface in ur_rna.Utilities
Created by Richard on 2/11/2016.
ActionHandlers - Class in ur_rna.Utilities
Created by Richard on 2/11/2016.
ActionHandlers() - Constructor for class ur_rna.Utilities.ActionHandlers
 
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
 
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
 
actionWhenSet - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
 
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
 
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(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(TSubscriber) - Method in class ur_rna.Utilities.EventSource
 
add(EventSource<T>, T) - Method in class ur_rna.Utilities.EventSource.Manager
 
add(T) - Method in class ur_rna.Utilities.TreeNode
 
addAcidMenuItem(String, String, String) - Method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
 
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
 
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
 
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
 
addComponentInfo(Component, StringBuilder) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
addField(JComponent, String, String) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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
 
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.
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
 
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.
addLibName(String) - Method in class ur_rna.Utilities.JniLoader
 
addList() - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONList
 
addMainMenu(MergeMenu, int) - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
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.
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
 
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
 
addRelative(GuiItemRef) - Method in exception ur_rna.GUITester.GuiTools.GuiItemNotFoundException
 
addSaveRestoreSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
Add a menu section that handles saving and restoring constraints.
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.
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.
addSlash(String) - Static method in class ur_rna.Utilities.PathTools
 
addTurboFoldTuple(String, String, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
addTurboFoldTuple(String, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
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.
allowBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.PredictTask
 
allowBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow.PredictTask
 
allowedChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
allowedNames - Variable in class ur_rna.Utilities.JniLoader
 
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
 
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
 
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
 
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.
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(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.
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
 
appendIfEmpty(String) - Method in class ur_rna.Utilities.StringBuilderEx
 
appendIfNotEmpty(String) - Method in class ur_rna.Utilities.StringBuilderEx
 
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.
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.AppInfoProvider - Interface in ur_rna.Utilities
 
AppLog - Class in ur_rna.Utilities
Created by Richard
AppLog() - Constructor for class ur_rna.Utilities.AppLog
 
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."
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.Utilities.AppInfo
 
AppOptions() - Constructor for class ur_rna.GUITester.Startup.AppOptions
 
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
 
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
 
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
 
AT_END - Static variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
 
AT_END - Static variable in class ur_rna.Utilities.Filter.FilterIterator
 
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

BACK_SLASH - Static variable in class ur_rna.Utilities.CharConstants
 
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.
backendValue() - Method in enum ur_rna.RNAstructureUI.utilities.FileType
 
BackgroundWorker - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 2/10/2016.
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.
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
 
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
 
BoolEventArgs(boolean) - Constructor for class ur_rna.Utilities.EventArgs.BoolEventArgs
 
boolValue() - Method in class ur_rna.Utilities.NamedArg
 
Bracket - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
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
 
Brown - Static variable in class ur_rna.Utilities.Colors
 
browse(String) - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
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
 
browseRecentFile(JComponent, PredictWindowBase.FileFieldInfo) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
browseWebsite() - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
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
 
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
 
btnClearList - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
btnClose - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
btnClose - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
btnExtract - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
btnMoveDn - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
btnMoveUp - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
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
 
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
 
btnResetPartsOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
 
btnResetTurboOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
btnShowAbbreviations - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
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
 
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.
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.
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
 
buildStochasticDataStructure(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
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
 

C

CadetBlue - Static variable in class ur_rna.Utilities.Colors
 
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
 
CalcParams - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 2/12/2016.
CalcParams() - Constructor for class ur_rna.RNAstructureUI.utilities.CalcParams
 
calcProgressListener - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
calcWasCanceled() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
canCancel - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
 
cancel() - Method in interface ur_rna.RNAstructureUI.windows.PredictWindowBase.BackgroundTask
 
cancel() - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
 
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
 
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.
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.
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
 
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
 
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
 
children - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
 
children - Variable in class ur_rna.Utilities.TreeNode
 
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
 
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
 
Chocolate - Static variable in class ur_rna.Utilities.Colors
 
ChooseStructureDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
Constructor.
circled - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
 
circular - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
 
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
 
clearAnnotation() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Clear annotation from this dialog.
clearDynalignAlignmentConstraints() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
clearFoldingConstraints(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
clearFound(boolean) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
 
clearNamed() - Method in class ur_rna.Utilities.StopWatch
Remove all named StopWatches
clearNodeScope(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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.Utilities.ConsoleTools.FixedStream
 
close() - Method in class ur_rna.Utilities.ExtendedBufferedReader
Closes the stream.
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
 
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
 
cmbTurboMode - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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.
COLON - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
ColorDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
Constructor.
Colors - Class in ur_rna.Utilities
List of common Colors and color utilities.
Colors() - Constructor for class ur_rna.Utilities.Colors
 
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
 
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.
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
 
compareBothItems() - Static method in class ur_rna.Utilities.Tuple.Pair
 
compareFirstItem() - Static method in class ur_rna.Utilities.Tuple.Pair
 
compareTo(Version) - Method in class ur_rna.Utilities.Version
 
ComponentMatcher(Component) - Constructor for class ur_rna.GUITester.GuiTools.GuiItemRef.ComponentMatcher
 
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
 
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(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
 
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
 
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).
controlPrefixes - Static variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
Convert - Class in ur_rna.Utilities
Created by Richard on 3/19/2015.
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
 
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
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
 
CR - Static variable in class ur_rna.Utilities.CharConstants
 
CR - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
 
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.windows.OligoWalkWindow.OligoSelectionDialog
 
createCheckItem(String, String) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
 
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
 
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.
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
 
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.
createLine(AudioFormat) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
createMenuItem(String, String, String, KeyStroke) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
 
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.
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.windows.OligoWalkWindow.OligoSelectionDialog
 
CreateStyledDocument() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
createToolbar(JToolBar) - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
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
 
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
 
curChar - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
curLexState - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
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.
currentToken - Variable in exception ur_rna.GUITester.ScriptParser.ParseException
This is the last token that has been consumed successfully.
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.
Cyan - Static variable in class ur_rna.Utilities.Colors
 

D

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
 
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
 
DateHelper - Class in ur_rna.Utilities
Created by Richard on 3/11/2015.
DateHelper() - Constructor for class ur_rna.Utilities.DateHelper
 
DBL_QUOT - Static variable in class ur_rna.Utilities.CharConstants
 
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
 
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 class ur_rna.Utilities.EventArgs
 
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_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_UPDATE_INTERVAL - Static variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
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.
defaultAllowRepeatFlags - Variable in class ur_rna.Utilities.CommandLineParser
 
defaultAppLog - Static variable in class ur_rna.Utilities.AppLog
 
DefaultBufferSize - Static variable in class ur_rna.Utilities.Strings
 
defaultColor - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
The default color forthis button.
defaultFont - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
defaultGuessLineLength - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
 
defaultLexState - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
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
 
defaultOutput - Static variable in class ur_rna.Utilities.StopWatch
 
defaultParamAffinity - Variable in class ur_rna.Utilities.CommandLineParser
 
DEL - Static variable in class ur_rna.Utilities.CharConstants
 
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_DotPlotBackend(long) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
 
delete_RNAstructureBackendCalculator(long) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
 
delete_StructureBackend(long) - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
 
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
 
deleteSequence(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
deleteTurboFoldTuple(long) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
desc - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FieldInfo
 
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
 
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.
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
 
determineOligoMaximum(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
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
 
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.
disableClose - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow
 
disableClose - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
 
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.
doAction(String, Object[]) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
DodgerBlue - Static variable in class ur_rna.Utilities.Colors
 
doInBackground() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
Done() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
Set buffers back to null when finished.
doRevalidate() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
Revalidate the drawing window.
DOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
DOT - Static variable in class ur_rna.Utilities.CharType
 
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 (")
doubleValue() - Method in class ur_rna.Utilities.NamedArg
 
doVerify(String, Object, Class<?>) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
DRAW_ALWAYS - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
DRAW_NEVER - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
DRAW_PROMPT - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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
 
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
 
DrawSection - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
 
drawStructures - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
drawStructures(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
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.
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

edited - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
A boolean, true if the sequence has been edited, false if not.
EditMenu() - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
Constructor.
EditMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
 
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.
EMPTY_ARRAY - Static variable in class ur_rna.Utilities.PathTools.FileName
 
EMPTY_BOOL_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
 
EMPTY_INT_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
 
EMPTY_OBJECT_ARRAY - Static variable in class ur_rna.Utilities.ObjTools
 
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
 
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
 
end() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
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.
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.
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.
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
 
EOF - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
End of File.
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
 
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.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(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
 
errorCode - Variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
Indicates the reason why the exception is thrown.
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
Created by Richard on 2/11/2016.
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
 
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.
exitScope() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
 
ExpandBuff(boolean) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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.
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
 
extPos - Variable in class ur_rna.Utilities.PathTools.FileName
 
ExtractExamples() - Static method in class ur_rna.RNAstructureUI.RNAstructure
 

F

FALSE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
 
FALSE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
fields - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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
 
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
 
fileExists(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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.
FileMenuSection - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
 
FileName(String) - Constructor for class ur_rna.Utilities.PathTools.FileName
 
FileName(String, boolean) - Constructor for class ur_rna.Utilities.PathTools.FileName
 
filePath - Variable in class ur_rna.GUITester.Script
 
FileSelectedEvent - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 4/8/2016.
FileSelectedEvent(Object, File, String) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
 
FileType - Enum in ur_rna.RNAstructureUI.utilities
 
FileType(int) - Constructor for enum ur_rna.RNAstructureUI.utilities.FileType
 
FillBuff() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
 
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.windows.PredictWindowBase.FileFieldInfo
 
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
 
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.
findLocalPath(String) - Static method in class ur_rna.Utilities.PathTools
 
findLocalPath(Class, String, String...) - Static method in class ur_rna.Utilities.PathTools
 
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(Iterable<T>) - Static method in class ur_rna.Utilities.ObjTools
 
first(Iterable<T>, T) - Static method in class ur_rna.Utilities.ObjTools
 
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
 
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
 
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
 
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.
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
 
fmt(String, Object...) - Static method in class ur_rna.Utilities.Strings
 
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.
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.
FoldingSav - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
foldOligo(String, int, boolean, boolean, String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
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
 
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
 
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
 
fromCallable(Callable) - Static method in class ur_rna.Utilities.ActionHandlers
 
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
 
fromEventListner(ActionListener) - Static method in class ur_rna.Utilities.ActionHandlers
 
fromFile() - Method in class ur_rna.GUITester.Script
 
fromImportance(int) - Static method in enum ur_rna.Utilities.Verbosity
 
fromRunnable(Runnable) - Static method in class ur_rna.Utilities.ActionHandlers
 
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

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
 
generateParseException() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
Generate ParseException.
get(int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
get(String) - Static method in class ur_rna.RNAstructureUI.utilities.Resources
 
get(Preferences, String, String) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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.
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
 
getAppLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
 
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 interface ur_rna.Utilities.AppInfo.AppInfoProvider
 
getAppTitle() - Static method in class ur_rna.Utilities.AppInfo
 
getAppVersion() - Method in interface ur_rna.Utilities.AppInfo.AppInfoProvider
 
getAppVersion() - Static method in class ur_rna.Utilities.AppInfo
 
getBaseDir() - Method in class ur_rna.Utilities.ResourceLoader
 
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.
getBeginColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
getBeginLine() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
 
getBounds() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
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()
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
 
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
 
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
 
getCloneMethod() - Static method in class ur_rna.Utilities.ObjTools
 
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
 
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
 
getComponent() - Method in class ur_rna.RNAstructureUI.menus.MenuList
 
getComponentInfo(Component) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
getControlDescription(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
getControlValue(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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
 
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
 
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
 
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.
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
 
getDebug() - Method in class ur_rna.Utilities.AppLog
 
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.
getDefaultMax() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
getDefaultMin() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
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
 
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
 
getDocumentsDirPath() - Static method in class ur_rna.Utilities.OSInfo
 
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
 
getDynalignAlignmentConstraints() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getDynalignAlignmentWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getDynalignStructureWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getEndColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
Get end column.
getEndLine() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
Get end line.
getEnvVar(String) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getError() - Method in class ur_rna.GUITester.ScriptRunner
 
GetErrorCode() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getErrorDescription() - Method in exception ur_rna.Utilities.SyntaxErrorException
 
getErrorInfo(Throwable) - Static method in class ur_rna.Utilities.AppLog
 
getErrorMessages() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
getErrors() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
getErrStream() - Method in class ur_rna.Utilities.AppLog
 
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 (.)
getFile() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Get the file drawn on this dialog.
getFile() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
 
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
 
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.
getFoldingConstraints(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getFoldWindowSize() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
GetFullErrorMessage() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getFullPath(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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
 
getHierarchy(Collection) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
getHomeDir() - Static method in class ur_rna.Utilities.PathTools
 
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.
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.
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
 
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.
getInt(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
getInt(String, int) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
getIntResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
 
getInvalidArgMessage(String, Object[], int, String) - Static method in class ur_rna.GUITester.RuntimeTools
 
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.Utilities.Pair
Returns the key corresponding to this entry.
getLastChar() - Method in class ur_rna.Utilities.ExtendedBufferedReader
Returns the last character that was read as an integer (0 to 65535).
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
 
getList() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
getList(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.SSONMap
 
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
 
getMainClass() - Static method in class ur_rna.Utilities.AppInfo
 
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
 
getMaxLoop() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getMaxPair() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getMenuItems() - Method in class ur_rna.RNAstructureUI.menus.MenuList
 
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
 
getMergeName() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
 
getMessage() - Method in error ur_rna.GUITester.ScriptParser.TokenMgrError
You can also modify the body of this method to customize your error messages.
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.
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
 
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
 
getMyLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
 
getName(Color) - Static method in class ur_rna.Utilities.Colors
 
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
 
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
 
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
 
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
getOriginalMessage() - Method in exception ur_rna.Utilities.ExtensibleException
This returns the original message passed in the constructor (to Throwable).
getOSType(String) - Static method in class ur_rna.Utilities.OSInfo
 
getOSType() - Static method in class ur_rna.Utilities.OSInfo
 
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
 
getParseError() - Method in class ur_rna.GUITester.ScriptRunner
 
getPlot() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
 
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
 
getPrefs() - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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
 
getProgressNumber() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getProvider() - Static method in class ur_rna.Utilities.AppInfo
 
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
 
getResourceLocation(String) - Method in class ur_rna.Utilities.ResourceLoader
Returns the full path to a resource if it is found, or null otherwise.
getResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
 
getRhs() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
getRootFrame() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
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
 
getScale() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Get the scale at which the image is zoomed.
getScript() - Method in class ur_rna.GUITester.ScriptRuntime
 
getSearchDirs() - Method in class ur_rna.Utilities.ResourceLoader
 
getSegmentInfo() - Method in class ur_rna.GUITester.Script
 
getSelectedItem() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
 
getSelectedSequence() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
getSequenceComment() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getSequenceData() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
getSettingsName(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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
 
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.
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
 
getStr(String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
getStr(String, String) - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
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.
getStrResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
 
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.RNAstructureUI.drawing.dialogs.StructureDialog
 
getStructureType() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getSuboptimalAbsoluteDiff() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getSuboptimalPercentDiff() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
GetSuffix(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
getTabSize() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
getTemperature() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
getToolBarItem(String) - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
getTrackLineColumn() - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
getTrStream() - Method in class ur_rna.Utilities.AppLog
 
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
 
getUnnamedValues() - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
Get the list of Unnamed Arguments (i.e.
getUsageMessage() - Method in class ur_rna.Utilities.CommandLineParser
 
getUseSimpleFileChooser() - Static method in class ur_rna.RNAstructureUI.AppMainFrame
 
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.windows.OligoWalkWindow.SpinnerPanel
Get the spinner value.
getValue() - Method in class ur_rna.Utilities.Pair
Returns the value corresponding to this entry.
getVar(String) - Method in class ur_rna.GUITester.ScriptRuntime
 
getVerbosity() - Method in class ur_rna.Utilities.AppLog
 
getVerify() - Method in class ur_rna.RNAstructureUI.utilities.CalcParams
 
getVersion() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getVisible() - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
 
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
 
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(int) - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
group(String) - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
GT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
Created by Richard
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.
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
 
hadErrors() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
handle(Object, T) - Method in interface ur_rna.Utilities.ActionHandler
 
handled - Variable in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
 
handleEvent(T) - Method in interface ur_rna.Utilities.Listener
 
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
 
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
 
has_run - Variable in class ur_rna.Utilities.RunOnce
 
hasAnyFlag(String...) - Method in class ur_rna.Utilities.CommandLineParser.ParseResults
Returns true if any of the listed flags were found.
hasChildren() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
hasChildren() - Method in class ur_rna.Utilities.TreeNode
 
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.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.
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
 
headerFont - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
Helix - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
HELP_URL - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
 
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
 
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
 
HoneyDew - Static variable in class ur_rna.Utilities.Colors
 
HOOK - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
HotPink - Static variable in class ur_rna.Utilities.Colors
 

I

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
 
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
 
ignoreChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
ignoreFlagCase - Variable in class ur_rna.Utilities.CommandLineParser
 
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
 
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.
importance - Variable in enum ur_rna.Utilities.Verbosity
 
inBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
INCR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
indent - Variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
 
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(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
 
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
 
InfoLabelConsumer - Variable in class ur_rna.RNAstructureUI.AppMainFrame
 
initDetails(Object, Object) - Method in exception ur_rna.Utilities.KeyAlreadyExistsException
 
initFocus() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
 
initItem(JMenuItem, String, String, String, KeyStroke) - Method in class ur_rna.RNAstructureUI.menus.MainMenu
Perform initial setup of the JMenuItem
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_stream - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
inputStream - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
 
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.
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.
IntEventArgs(int) - Constructor for class ur_rna.Utilities.EventArgs.IntEventArgs
 
intValue() - Method in class ur_rna.Utilities.NamedArg
 
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
 
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
 
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
 
isActiveFrame() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
 
isAnySet(int, int) - Static method in class ur_rna.Utilities.ObjTools
 
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
 
isClosed() - Method in class ur_rna.Utilities.ExtendedBufferedReader
 
isDebugEnabled() - Method in class ur_rna.Utilities.AppLog
 
isDir(String) - Static method in class ur_rna.Utilities.PathTools
 
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(Verbosity) - Method in class ur_rna.Utilities.AppLog
 
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.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
 
isFixed - Static variable in class ur_rna.Utilities.ConsoleTools
 
isHandled() - Method in class ur_rna.RNAstructureUI.windows.ChildWindow.CommandInfo
 
isIgnoredSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
isInputWindow - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
A boolean that tells whether this window is an input window or not.
isInvalidSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
isListOrMap(Object) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
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
 
isNix() - Static method in class ur_rna.Utilities.OSInfo
 
ISO8601 - Static variable in class ur_rna.Utilities.DateHelper
 
ISO8601Format - Static variable in class ur_rna.Utilities.DateHelper
 
isOutput - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
 
isPlaying() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
isProgressIndeterminate() - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
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
 
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
 
isTraceEnabled() - Method in class ur_rna.Utilities.AppLog
 
isUnpairedSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
isUnspecifiedSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
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 - 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

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.
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, 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
 
JSON - Static variable in class ur_rna.Utilities.SimpleDataSerializer.OutputFormatSettings
 

K

keepToolBarItems - Variable in class ur_rna.RNAstructureUI.AppMainFrame
 
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
 
keyClick(int) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
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

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.windows.PredictMultiStructureWindow.SequenceItem
 
last - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
last() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
 
LAST_ASCII - Static variable in class ur_rna.Utilities.CharConstants
 
lastFound - Variable in class ur_rna.GUITester.GuiTools.GuiItemRef
 
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
 
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
 
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.
layoutComponent(Component) - Static method in class ur_rna.GUITester.GuiTools.ScreenCapture
 
lblBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
lblBaseInserts - Variable in class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow
 
lblFile - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
lblHelp - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
lblLogo - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
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
 
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
 
lblResults - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
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
 
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
 
lblWebsite - Variable in class ur_rna.RNAstructureUI.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.
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.
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
 
length() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
length() - Method in class ur_rna.Utilities.StringBuilderEx
Returns the length (character count).
LETTER - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
line - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
Linen - Static variable in class ur_rna.Utilities.Colors
 
lineOffset - Variable in exception ur_rna.Utilities.SyntaxErrorException
The estimated line where the syntax error occurred.
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
 
Listener<T> - Interface in ur_rna.Utilities
Represents an event listener.
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
 
Literal() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
load(Preferences) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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
 
loadFromStorage() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
loadRecent(String, JComponent...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
loadSequenceInfo(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
LOCAL_HELP_PAGE - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
 
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.Startup
 
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(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
 
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.
logFmt(String, Verbosity, Object...) - Method in class ur_rna.Utilities.AppLog
 
logVerbosity - Variable in class ur_rna.GUITester.Startup.AppOptions
 
LookaheadSuccess() - Constructor for error ur_rna.GUITester.ScriptParser.GuiTestScriptParser.LookaheadSuccess
 
LOOP_DETECTED - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
Detected (and bailed out of) an infinite loop in the token manager.
LOWER_ALPHA - Static variable in class ur_rna.Utilities.CharType
a-z
LPAREN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
LSHIFTASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
lstSeqs - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
LT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.

M

m - Variable in class ur_rna.Utilities.SimpleDataSerializer.Token
 
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.
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.GUITester.Startup
 
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.
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
 
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
 
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
 
Major - Variable in class ur_rna.Utilities.Version
 
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
 
makeStartButton(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Create the "START" button.
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
 
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
 
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
 
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
 
MathUtil - Class in ur_rna.Utilities
Extended math functions.
MathUtil() - Constructor for class ur_rna.Utilities.MathUtil
 
max - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
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.
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
 
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.
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
 
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.
menuMerger - Variable in class ur_rna.RNAstructureUI.AppMainFrame
 
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
 
message - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.ErrorInfo
 
METHOD_PREFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
MidnightBlue - Static variable in class ur_rna.Utilities.Colors
 
minHelixLen - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
 
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.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
 
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.
modeNames - Static variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
An array that holds the names of the TurboFold modes.
ModifierKey(int) - Constructor for enum ur_rna.GUITester.GuiTools.GuiRobot.ModifierKey
 
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.
mouseClicked(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
 
mouseClicked(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
 
mouseEntered(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
 
mouseEntered(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
 
mouseExited(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
 
mouseExited(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
 
mousePressed(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
 
mousePressed(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
 
mouseReleased(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter
 
mouseReleased(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverListener
 
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
Created by Richard on 4/10/2016.
MRUFileStorage() - Constructor for class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
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.
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
 
MultiSequence - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
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
 

N

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
 
NamedArg - Class in ur_rna.Utilities
Created by Richard on 7/22/2016.
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
 
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.
new_DotPlotBackend() - Static method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackendProxyJNI
 
new_RNAstructureBackendCalculator() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
 
new_StructureBackend() - Static method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackendProxyJNI
 
NEWLINE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
NEWLINE - Static variable in class ur_rna.Utilities.CharType
CR and LF
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
 
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 - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
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
 
nextCharBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
nextCharInd - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
nextStep(String, boolean, int) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
 
nextStepWork - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
 
NO_ALIASES - Static variable in class ur_rna.Utilities.CommandLineParser.FlagDef
 
NoArg() - Constructor for class ur_rna.Utilities.EventSource.NoArg
 
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
 
nodes - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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 class ur_rna.Utilities.CharType
 
normalizeFlagName(String) - Method in class ur_rna.Utilities.CommandLineParser
 
NOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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.
NotNull - Annotation Type in ur_rna.Utilities.annotation
 
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
 
NucOrHelixDialog(String, String) - Constructor for class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
Constructor.
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
 
number - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
The structure number viewed on this panel.
numberFormatter - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 

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.
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
 
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
 
onFocusGained(FocusEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
 
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
 
onSequenceSelected(ListSelectionEvent) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
openNodeScope(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
OPERATION - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
 
operatorKind - Variable in class ur_rna.GUITester.ScriptParser.ASTAssignment
 
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.Startup
 
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
 
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
 
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
 
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
 
outMaxExpectCt - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow.PredictSingleStructureTask
 
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
 
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
 

P

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
 
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.
paintComponent(Graphics) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
 
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
 
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
 
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
 
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.Startup
 
parseArray(SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
parseCommandArgs(String[]) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
ParseContext(SimpleDataSerializer.Token[], int, int[]) - Constructor for class ur_rna.Utilities.SimpleDataSerializer.ParseContext
 
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(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.
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.
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.Startup.AppOptions
 
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 *
parseSONValue(SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
parseString(SimpleDataSerializer.Token, SimpleDataSerializer.ParseContext) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
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.
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
 
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() - 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.Utilities.ExtendedBufferedReader
Returns the next character in the current reader without consuming it.
peek() - Method in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
 
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
 
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
.
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
 
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
 
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
 
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
 
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
 
pnlTurboOptions - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
popNode() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
popNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
popTypedNode(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
pos - Variable in class ur_rna.Utilities.SimpleDataSerializer.ParseContext
 
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
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
 
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
 
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 - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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
 
prevCharIsCR - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
prevCharIsLF - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
prevValue - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
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
 
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.
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.
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.
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.
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
 
ProgressChange - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
progressChanged(int) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
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.
promptDraw() - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
promptDraw(String, String) - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
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
 
providerFailed - Static variable in class ur_rna.Utilities.AppInfo
 
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
 
pushLevel(boolean) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
 
pushNode(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
put(Preferences, String, String) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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
 

Q

Quad(T1, T2, T3, T4) - Constructor for class ur_rna.Utilities.Tuple.Quad
 
Quad() - Constructor for class ur_rna.Utilities.Tuple.Quad
 
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
 
range - Variable in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
The number panel that holds the range data.
RangeDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
Constructor.
RBRACE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
RBRACKET - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
read() - Method in class ur_rna.Utilities.ExtendedBufferedReader
 
read(char[], int, int) - Method in class ur_rna.Utilities.ExtendedBufferedReader
 
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.
readData(String, int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
readDynalignAlignmentConstraintsFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.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
 
readOnlyData - Variable in exception ur_rna.Utilities.ExtensibleException
 
readSequenceData(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
readStructureData(String) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
readSystemProperties() - Method in class ur_rna.Utilities.AppLog
 
rebuildMainMenu(MenuList) - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
rebuildToolBar() - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
Red - Static variable in class ur_rna.Utilities.Colors
 
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
 
reflectedClassLoaderField - Static variable in class ur_rna.Utilities.ClassLoaderInfo
 
RefoldSection - Static variable in class ur_rna.RNAstructureUI.menus.FileMenu
 
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.
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
 
rem(EventSource<T>, T) - Method in class ur_rna.Utilities.EventSource.Manager
 
REMASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
remove(String) - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
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
 
removeAnnotation() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
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
 
removeListener - Variable in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
 
removeMenuMnemonics(Component[]) - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
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.
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
 
REQUIRED_DLL_VERSION - Static variable in class ur_rna.RNAstructureUI.RNAstructure
 
reset() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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 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.
resetInfoLabel() - Method in class ur_rna.RNAstructureUI.AppMainFrame
Reset the info bar at the bottom of the main window to its default.
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.
resetOptionsInPanel(JComponent) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
restart() - Method in class ur_rna.Utilities.StopWatch
Reset elapsed time to 0 and start the timer.
result - Variable in class ur_rna.RNAstructureUI.utilities.RunFunc
 
result() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
reverse() - Method in class ur_rna.Utilities.StringBuilderEx
 
Revision - Variable in class ur_rna.Utilities.Version
 
RHS - Static variable in interface ur_rna.GUITester.ScriptParser.ScriptNodePropConstants
 
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.
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
 
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
 
rootNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
RosyBrown - Static variable in class ur_rna.Utilities.Colors
 
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.
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
Created by Richard on 4/12/2016.
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

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
 
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
 
saveRecent(String, JComponent...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
saveRecentFiles(JTextField...) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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.
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.
scope - Variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
 
scopeToString(int) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
 
ScreenCapture - Class in ur_rna.GUITester.GuiTools
 
ScreenCapture() - Constructor for class ur_rna.GUITester.GuiTools.ScreenCapture
 
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
Created by Richard on 4/11/2016.
ScriptActions(ScriptRuntime) - Constructor for class ur_rna.GUITester.ScriptActions
 
scriptList - Variable in class ur_rna.GUITester.Startup.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.Startup.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.
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
 
select() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
Select this button.
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
 
selectionColor - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
The selection color for this button.
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
 
SEMICOLON - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
sendKeyString(String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
sepPos - Variable in class ur_rna.Utilities.PathTools.FileName
 
seqList - Variable in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
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
 
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 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.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 exception ur_rna.Utilities.ExtensibleException
 
serialVersionUID - Static variable in exception ur_rna.Utilities.FormatterException
 
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.SyntaxErrorException
 
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.
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
 
setBarColor(Color) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
Set the default color that will be painted on this button.
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 (/).
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
 
setCleavedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
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
 
setControlValue(JComponent, Object) - Method in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
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.RNAstructureUI.RNAstructure
 
setDebug(boolean) - Method in class ur_rna.Utilities.AppLog
 
setDebugStream(PrintStream) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
Set debug output.
setDefault(AppLog) - Static method in class ur_rna.Utilities.AppLog
 
setDefaultFileOpenDir() - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
setDoubleStrandedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setDynalignAlignmentConstraint(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
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.
setFlipped(boolean) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
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.
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.
setInsets(int, int, int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Set the external padding of the constraints.
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
setLoader(ClassLoader) - Method in class ur_rna.Utilities.ResourceLoader
 
setMainClass(Class<?>) - Static method in class ur_rna.Utilities.AppInfo
 
setMaxLoop(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setMaxPair(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setMessage(String) - Method in exception ur_rna.Utilities.ExtensibleException
Allows the calling code to update the message stored in this exception.
setModifiedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
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
 
setPad(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Set the internal padding of the constraints.
setPref(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
setProgressIndeterminate(boolean) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
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
 
setRelative(GuiItemRef, GuiRelative) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
 
setRhs(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
setSaveFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setScale(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Set the image scale.
setSelectedSequence(PredictMultiStructureWindow.SequenceItem) - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
setSequenceText(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
setSequenceTitle(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setSHAPEFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
setSingleStrandedNucleotide(int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
setStatus(String) - Method in class ur_rna.RNAstructureUI.utilities.BackgroundWorker
 
setStructureNumber(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Set the structure number.
setSubItemMergePos(int) - Method in class ur_rna.RNAstructureUI.menus.MenuList
 
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.RNAstructureUI.RNAstructureBackendCalculator
 
setText(Component, String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
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
 
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
 
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
 
setUseSimpleFileChooser(boolean) - Static method in class ur_rna.RNAstructureUI.AppMainFrame
 
setValue(Object) - Method in class ur_rna.GUITester.ScriptParser.ASTLiteral
 
setValue(Object) - Method in class ur_rna.Utilities.Pair
Replaces the value corresponding to this entry with the specified value (optional operation).
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
 
setVisible(boolean) - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
 
SHAPE - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
Select a SHAPE file.
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
 
shouldTrace() - Method in class ur_rna.GUITester.ScriptRuntime
 
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
 
ShowAppHelp() - Static method in class ur_rna.GUITester.Startup
 
showDeletionConfirmation() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
Show a dialog that asks whether constraints should be deleted.
showDrawProgress() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
showDrawProgress(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
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
 
showPlotWindow(InternalWindow) - Method in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow
 
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
 
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
 
showWarning(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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.
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
 
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
 
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
 
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
 
SingleGuiItem() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
Singlet(T1) - Constructor for class ur_rna.Utilities.Tuple.Singlet
 
Singlet() - Constructor for class ur_rna.Utilities.Tuple.Singlet
 
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
 
SNG_QUOT - Static variable in class ur_rna.Utilities.CharConstants
 
Snow - Static variable in class ur_rna.Utilities.Colors
 
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.
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 - 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.
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.
spinner - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
The spinner in this panel.
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.
splitFlagValue(String) - Method in class ur_rna.Utilities.CommandLineParser
 
splitScriptSuite(Reader, String, String) - Static method in class ur_rna.GUITester.Startup
 
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
 
standardBases - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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.Utilities.SimpleDataSerializer.Token
 
start() - Method in class ur_rna.Utilities.StopWatch
Start the timer.
startButton - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
startLine - Variable in class ur_rna.GUITester.Script
 
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
 
Startup - Class in ur_rna.GUITester
The main entry-point for the test application.
Startup() - Constructor for class ur_rna.GUITester.Startup
 
Startup.AppOptions - Class in ur_rna.GUITester
 
Startup.ScriptSource - Enum in ur_rna.GUITester
 
state - Variable in class ur_rna.RNAstructureUI.utilities.BackgroundWorker.StateChangeEventArgs
 
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
 
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
 
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
 
stepProgress - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.PredictTaskBase
 
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.Utilities.StopWatch
Stop the timer, but store the elapsed time so that when StopWatch.start() is called, the elapsed time will continue to increase.
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
 
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.
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
 
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
 
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.
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.ChooseStructureDialog - Class in ur_rna.RNAstructureUI.drawing.menus
An inner class which creates a dialog that moves to a structure.
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.
styleIgnoredChar - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
styleInvalidChar - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
styleStandardBase - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
subItemMergePos - Variable in class ur_rna.RNAstructureUI.menus.MenuList
 
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.
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.
SVG - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
Select an SVG file.
swap() - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
 
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.RNAstructureUI.drawing.proxy.DotPlotBackend
 
swigCPtr - Variable in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
swigCPtr - Variable in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
SYMBOLS - Static variable in class ur_rna.Utilities.CharType
All Lower-ASCII symbols.
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
 

T

TAB - Static variable in class ur_rna.Utilities.CharConstants
 
TAB - Static variable in class ur_rna.Utilities.CharType
The tab character (#9)
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
 
tabSize - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
Tan - Static variable in class ur_rna.Utilities.Colors
 
target - Variable in class ur_rna.Utilities.ConsoleTools.FixedStream
 
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
 
testTopNodeType(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
text - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
text - Variable in class ur_rna.RNAstructureUI.menus.RolloverListener
 
text() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
textArea - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
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
 
title - Variable in class ur_rna.GUITester.Script
 
titleBox - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
The array of text areas in this window.
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
 
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(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
 
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
 
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
 
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 class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow.SequenceItem
 
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.SimpleDataSerializer.Token
 
toString(Object, SimpleDataSerializer.OutputFormatSettings) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
toString() - Method in class ur_rna.Utilities.StringBuilderEx
 
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
 
toType(Object, Class) - Static method in class ur_rna.Utilities.Convert
 
toType(Object, T) - Static method in class ur_rna.Utilities.Convert
 
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
 
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
 
TRUE - Static variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase
 
TRUE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
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
 
txt - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase.FileFieldInfo
 
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
 
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
 
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
 
txtShapeFile - Variable in class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow
 
type() - Method in class ur_rna.Utilities.SimpleDataSerializer.Token
 
types - Static variable in class ur_rna.GUITester.GuiTools.ScreenCapture
 

U

uiUpdateTimer - Variable in class ur_rna.RNAstructureUI.windows.PredictWindowBase
 
UNDERSCORE - Static variable in class ur_rna.Utilities.CharType
 
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.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
 
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
 
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
 
updateActiveFrameInfo() - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
updateCalcProgress(ProgressPanel) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
updateDisplay() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
updatedMessage - Variable in exception ur_rna.Utilities.ExtensibleException
 
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.
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
 
updateNavUI() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
updateSequenceInfoFromUI() - Method in class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow
 
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
 
UPPER_ALPHA - Static variable in class ur_rna.Utilities.CharType
A-Z
UPPER_ASCII - Static variable in class ur_rna.Utilities.CharConstants
 
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.RNAstructureUI - package ur_rna.RNAstructureUI
 
ur_rna.RNAstructureUI.drawing.dialogs - package ur_rna.RNAstructureUI.drawing.dialogs
 
ur_rna.RNAstructureUI.drawing.menus - package ur_rna.RNAstructureUI.drawing.menus
 
ur_rna.RNAstructureUI.drawing.proxy - package ur_rna.RNAstructureUI.drawing.proxy
 
ur_rna.RNAstructureUI.drawing.runners - package ur_rna.RNAstructureUI.drawing.runners
 
ur_rna.RNAstructureUI.menus - package ur_rna.RNAstructureUI.menus
 
ur_rna.RNAstructureUI.utilities - package ur_rna.RNAstructureUI.utilities
 
ur_rna.RNAstructureUI.windows - package ur_rna.RNAstructureUI.windows
 
ur_rna.Utilities - package ur_rna.Utilities
 
ur_rna.Utilities.annotation - package ur_rna.Utilities.annotation
 
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
 
userAcceptedInvalidSequence - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
UserOptions - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 4/10/2016.
UserOptions() - Constructor for class ur_rna.RNAstructureUI.utilities.UserOptions
 
useSimpleFileChooser - Static variable in class ur_rna.RNAstructureUI.AppMainFrame
 

V

val - Variable in class ur_rna.GUITester.ScriptParser.ASTNamedArgument
 
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
 
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.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
 
valueChanged() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
valueField - Variable in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.ChooseStructureDialog
 
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.GUITester.Startup.ScriptSource
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.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.Verbosity
Returns the enum constant of this type with the specified name.
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.GUITester.Startup.ScriptSource
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.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.Verbosity
Returns an array containing the constants of this enum type, in the order they are declared.
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
 
verb - Variable in class ur_rna.GUITester.ScriptParser.ASTAction
 
Verbosity - Enum in ur_rna.Utilities
Created by Richard on 9/20/2015.
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.
verifyDataPath() - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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
 
verifySequence() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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 class ur_rna.RNAstructureUI.RNAstructure
 
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
 
versionCheck - Variable in class ur_rna.Utilities.JniLoader
 
versionCompare(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
Compares two version strings.
viewDialog() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
View the dialog.
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

warn(String) - Method in class ur_rna.Utilities.AppLog
 
warn(String, Object...) - Method in class ur_rna.Utilities.AppLog
 
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
 
Wheat - Static variable in class ur_rna.Utilities.Colors
 
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
window - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
window - Variable in class ur_rna.RNAstructureUI.windows.PredictionResultsWindow.PlotResult
 
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
 
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
 
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
 
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
 
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
 
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
 
writeMap(Map<?, ?>, Writer, SimpleDataSerializer.OutputFormatSettings, Queue<String>) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
writeNumber(Number, SimpleDataSerializer.OutputFormatSettings) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
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
 
writeSequenceFile(String) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
writeString(String, boolean) - Method in class ur_rna.Utilities.SimpleDataSerializer
 
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
 
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
 
writeTo(OutputStream) - Method in class ur_rna.Utilities.NullPrintStream.NullByteArrayOutputStream
 

X

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.

Y

YEAR - Static variable in class ur_rna.RNAstructureUI.RNAstructure
 
Yellow - Static variable in class ur_rna.Utilities.Colors
 
YellowGreen - Static variable in class ur_rna.Utilities.Colors
 

Z

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.

_

_a - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
_actions - Variable in class ur_rna.GUITester.ScriptRuntime
 
_b - Variable in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
_classes - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
 
_cls - Variable in class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.SingleClassMatcher
 
_currentClip - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
_debug - Variable in class ur_rna.Utilities.AppLog
 
_disableTrace - Variable in class ur_rna.GUITester.ScriptRuntime
 
_doParsingOnly - Variable in class ur_rna.GUITester.ScriptRuntime
 
_find - Variable in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
 
_finder - Variable in class ur_rna.GUITester.GuiTools.GuiAppManager
 
_gui - Variable in class ur_rna.GUITester.ScriptActions
 
_gui - Variable in class ur_rna.GUITester.ScriptRuntime
 
_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
 
_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
 
_queue - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
_requiredVerbosity - Variable in class ur_rna.Utilities.AppLog
 
_res - Static variable in class ur_rna.RNAstructureUI.utilities.Resources
 
_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
 
_subjectApp - Variable in class ur_rna.GUITester.ScriptRunner
 
_vars - Variable in class ur_rna.GUITester.ScriptRuntime
 
_vis - Variable in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
 
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