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$$$getRootComponent$$$() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
 
$$$setupUI$$$() - 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!

A

AboutWindow - Class in ur_rna.RNAstructureUI.windows
Created by Richard on 4/6/2016.
AboutWindow() - Constructor for class ur_rna.RNAstructureUI.windows.AboutWindow
 
accept(File) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
Tests whether or not the specified pathname should be included in a pathname list.
acceptAll - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
AcceptAll(boolean) - Static method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
acceptAll() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
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
 
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
 
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel.ButtonListener
 
actionPerformed(ActionEvent) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
 
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
 
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
 
add(Node) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
add(String) - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
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
 
addCancelListener(ActionListener) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
addCheckBoxMenuItem(String, String) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Add a check box menu item with rollover text.
addCheckBoxMenuItem(String, String, boolean) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
 
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.
addComponentInfo(Component, StringBuilder) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
addField(JTextField) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
addField(JTextField, String) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
addField(JTextField, String, String) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
addField(JTextField, String, String, ActionListener) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
addFieldCore(JTextField, String, String, ActionListener, GridBagConstraints) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
addFieldCore(JTextField, String, String, ActionListener, GridBagConstraints) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
 
addFilters(String) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Adds a set of filter-specs to the list of file filters for the FileChooser.
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.
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
 
addMaxPairingDistanceSection() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
Add a menu section that handles maximum pairing distance.
addMenuItem(String, String) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Add a plain text menu item with rollover text.
addMenuItem(String, String, char) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Add a plain text menu item with rollover text and a key stroke which can activate it.
addMenuItem(String, String, String) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Add a plain text menu item with rollover text and a key stroke which can activate it.
addMenus(RolloverMenu...) - Method in class ur_rna.RNAstructureUI.menus.DynamicMenuBar
 
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
 
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.
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) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
addUpdateListener(ActionListener) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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
 
aliases - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
 
Alignment - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
ALL - Static variable in class ur_rna.Utilities.CharType
All character types.
allowCancel() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
allowedSequenceChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
ALPHA - Static variable in class ur_rna.Utilities.CharType
 
ALPHA_NUM - Static variable in class ur_rna.Utilities.CharType
 
ALWAYS - Static variable in class ur_rna.RNAstructureUI.utilities.ScrollerPane
A generic constant symbolizing that a scroll bar must always be used.
ANCESTOR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
ancestorAdded(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
 
ancestorMoved(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
 
ancestorRemoved(AncestorEvent) - Method in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
 
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.
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
 
AppLog - Class in ur_rna.Utilities
Created by Richard
AppLog() - Constructor for class ur_rna.Utilities.AppLog
 
applyNativeLookAndFeel() - Static method in class ur_rna.RNAstructureUI.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.
AppOptions() - Constructor for class ur_rna.GUITester.Startup.AppOptions
 
approveSelection() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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.ObjTools
Attempts to convert a string representing a conceptual "true/false" into a boolean.
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
 
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
 

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.
BACKSLASH - Static variable in class ur_rna.Utilities.CharType
 
backup(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
Retreat.
bar - Variable in class ur_rna.RNAstructureUI.AppMainFrame
The main RNAstructure toolbar.
BarButton() - Constructor for class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
Constructor.
baseDir - Variable in class ur_rna.Utilities.ResourceLoader
 
baseName - Variable in class ur_rna.Utilities.PathTools.PathParts
 
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
 
BinaryMatcher(Matcher, Matcher) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
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
 
BorderBuilder - Class in ur_rna.RNAstructureUI.utilities
A class that places a border type on a specified component type.
BorderBuilder() - Constructor for class ur_rna.RNAstructureUI.utilities.BorderBuilder
 
BorderedButtonPanel - Class in ur_rna.RNAstructureUI.utilities
A class that produces a panel which contains a button with a border around it.
BorderedButtonPanel(ActionListener, String) - Constructor for class ur_rna.RNAstructureUI.utilities.BorderedButtonPanel
Text Constructor.
BorderedButtonPanel(ActionListener, String, int) - Constructor for class ur_rna.RNAstructureUI.utilities.BorderedButtonPanel
Border Constructor.
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
 
browse(String) - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
browseHelp() - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
browseWebsite() - Static method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
btnClose - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
btnExtract - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
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
 
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.
buildDesktop() - Method in class ur_rna.RNAstructureUI.AppMainFrame
Create the gray back panel that fills the main frame.
buildDialog(String, NumberField...) - Method in class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
Build the value selection dialog.
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() - 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
 
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.
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.
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
 
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.
button - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
button - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
buttonListener - Variable in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
 
ButtonListener(int) - Constructor for class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel.ButtonListener
 

C

calcCanceled - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
calcCancelListener - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
calcCompleted - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
calcProgressListener - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
calcWasCanceled() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
cancelMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
cancelOperation() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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.
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.
changeExtension(String, String) - Static method in class ur_rna.Utilities.PathTools
 
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.
CharType - Class in ur_rna.Utilities
 
CharType() - Constructor for class ur_rna.Utilities.CharType
 
check - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
checkValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField
Check the value of a field to make sure it's valid.
checkValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
 
checkValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
 
checkValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
 
CHILD - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
child(int) - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
childCount() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
children - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
 
CIRCLED_NUCS - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Boolean that tells whether a structure's nucleotides are circled.
ClassLoaderInfo - Class in ur_rna.Utilities
 
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
 
clearFilters() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Clear any existing filters.
clearFoldingConstraints(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
clearFound(boolean) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
 
clearNodeScope(Node) - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
CLOCKWISE_STRUCTURE - Static variable in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Boolean that tells whether a structure is rendered clockwise.
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
 
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.
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.utilities.FileSelectButton
 
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.
commentBox - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
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.
context - Variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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).
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
 
convertToolTips() - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu
Convert tooltips to rollover text.
copyTo(List<T>, T[]) - Static method in class ur_rna.Utilities.ObjTools
 
copyTo(List<T>, T[], int) - Static method in class ur_rna.Utilities.ObjTools
 
copyTo(List<T>, T[], int, int) - Static method in class ur_rna.Utilities.ObjTools
 
CR - Static variable in class ur_rna.Utilities.CharConstants
 
CR - Static variable in class ur_rna.Utilities.ExtendedBufferedReader
 
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
 
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
Create any additional controls that need to show up on this dialog.
createAdditionalControls() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
 
createDefaultMenuBar(RNAstructureMenu...) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Create the image dialog's default menu bar.
createDisabled(String) - Static method in class ur_rna.RNAstructureUI.utilities.FileField
Create a disabled file input field.
createDNA() - Static method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
Create a DNA menu.
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
 
createEmptyBox(String) - Static method in class ur_rna.RNAstructureUI.utilities.HTMLCheckBox
Create an empty check box.
createEnabled(String) - Static method in class ur_rna.RNAstructureUI.utilities.FileField
Create an enabled file input field.
createExampleFilesClicked - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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
 
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.
createSelectedBox(String) - Static method in class ur_rna.RNAstructureUI.utilities.HTMLCheckBox
Create a selected check box.
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.ZoomDialog
 
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.ColorDialog
 
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu.RangeDialog
 
createSelectionAction() - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.MoveDialog
 
createSelectionAction() - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog
 
createSelectionAction() - Method in class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
Create the action that occurs once values are selected.
createSelectionAction() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog
 
CreateStyledDocument() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
createTextPanel(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
 
createUIComponents() - Method in class ur_rna.RNAstructureUI.windows.AboutWindow
 
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.

D

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
 
DECR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
DEFAULT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
Lexical state.
DEFAULT_CONTEXT - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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_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
 
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
 
defaultKeyStrokeModifier - Variable in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
 
defaultLexState - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
DefaultLogImportance - Static variable in class ur_rna.Utilities.AppLog
 
defaultMessage - Static variable in exception ur_rna.Utilities.KeyAlreadyExistsException
 
defaultParamAffinity - Variable in class ur_rna.Utilities.CommandLineParser
 
defaultStyle - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
deleteTurboFoldTuple(long) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
DESCENDANT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
descendant_line - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
 
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.
Dialogs - Class in ur_rna.RNAstructureUI.utilities
A class that handles simple dialogs used in the RNAstructure GUI.
Dialogs() - Constructor for class ur_rna.RNAstructureUI.utilities.Dialogs
 
DIGIT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
DIGITS - Static variable in class ur_rna.Utilities.CharType
'0'-'9'
DIRECTIVE_PREFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
dirs - Variable in class ur_rna.Utilities.PathTools.PathParts
 
disable_tracing() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
Disable tracing.
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
 
doActions(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
Do any actions specific to this window.
doActions(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
Do any actions specific to this window.
doActions(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
doActions(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.utilities.NumberField
Do any additional necessary checks on a key character to make sure it's valid to be output.
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
 
doAdditionalCheck(char) - Method in class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.drawing.menus.DotsMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.drawing.menus.PlotMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.drawing.menus.StructureMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.menus.ConstraintsMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.menus.FileMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.menus.HelpMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.menus.NucleicAcidMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Do any actions specific to this menu.
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoWalkResultsMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.EditMenu
 
doMenuActions(String) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SpeakMenu
 
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 (")
DoubleField(String, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
Unbounded Constructor.
DoubleField(String, Number, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
Minimum Bounds Constructor.
DoubleField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
Minimum and Maximum Bounds Constructor.
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.
drawOptionMenu - 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
 
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
 
DynamicMenuBar - Class in ur_rna.RNAstructureUI.menus
A class that creates a menu bar.
DynamicMenuBar(InternalWindow, RolloverMenu...) - Constructor for class ur_rna.RNAstructureUI.menus.DynamicMenuBar
Constructor.

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.
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() - Method in class ur_rna.Utilities.StopWatch
The total elapsed time in milliseconds.
EMPTY_ARRAY - Static variable in class ur_rna.Utilities.PathTools.PathParts
 
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
 
enabledState - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
enableMenus() - Method in class ur_rna.RNAstructureUI.menus.DynamicMenuBar
Enable the menus on this menu bar.
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.
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(Object) - Method in class ur_rna.Utilities.Pair
Indicates whether some other object is "equal to" this one.
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.
errorStyle - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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.ObjTools
 
escapeStringLiteral(String) - Static method in class ur_rna.Utilities.ObjTools
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.ObjTools
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
 
examplesDir - Static variable in class ur_rna.RNAstructureUI.RNAstructure
 
exec(ScriptNode) - Method in class ur_rna.GUITester.ScriptRunner
 
exec(ScriptNode) - Method in class ur_rna.GUITester.ScriptRuntime
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
 
executeModuleAction(String, Object) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Execute an action within a particular module.
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.MultilignWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
 
executeModuleAction(String, Component, ActionEvent) - Method in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
 
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
 
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 - Variable in class ur_rna.Utilities.PathTools.PathParts
 
EXT_ASCII - Static variable in class ur_rna.Utilities.CharType
Extended ASCII characters (129-255)
ExtendedBufferedReader - Class in ur_rna.Utilities
A special buffered reader which tracks the current character position and line index.
ExtendedBufferedReader(Reader) - Constructor for class ur_rna.Utilities.ExtendedBufferedReader
Created extended buffered reader using default buffer-size
ExtensibleException - Exception in ur_rna.Utilities
Exception that allows additional details to be added.
ExtensibleException() - Constructor for exception ur_rna.Utilities.ExtensibleException
 
ExtensibleException(String) - Constructor for exception ur_rna.Utilities.ExtensibleException
 
ExtensibleException(Throwable) - Constructor for exception ur_rna.Utilities.ExtensibleException
 
ExtensibleException(String, Throwable) - Constructor for exception ur_rna.Utilities.ExtensibleException
 
ExtensionFileFilter(boolean, String...) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
ExtensionFileFilter(String...) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
ExtensionFileFilter() - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
extensions - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
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
 
FieldPanel - Class in ur_rna.RNAstructureUI.utilities
A class that creates a panel which holds aligned input fields.
FieldPanel() - Constructor for class ur_rna.RNAstructureUI.utilities.FieldPanel
 
FieldPanel(JTextField...) - Constructor for class ur_rna.RNAstructureUI.utilities.FieldPanel
Constructor.
FieldPanel.FilePanel - Class in ur_rna.RNAstructureUI.utilities
An inner class that handles a panel which contains file fields.
FieldPanel.FilePanel.ButtonListener - Class in ur_rna.RNAstructureUI.utilities
 
fields - Variable in class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
The array of number fields this dialog holds.
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.FileSelectButton.FileMenuItem
 
file - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
 
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
 
FileField - Class in ur_rna.RNAstructureUI.utilities
A class that creates a text field which holds a file name.
FileField(String, boolean) - Constructor for class ur_rna.RNAstructureUI.utilities.FileField
Constructor.
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(InternalWindow) - Constructor for class ur_rna.RNAstructureUI.menus.FileMenu
Constructor.
FileMenuItem(File) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton.FileMenuItem
 
FileMenuItem(File, String, ActionListener) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton.FileMenuItem
 
FilePanel(ActionListener, FileField...) - Constructor for class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
Constructor.
filePath - Variable in class ur_rna.GUITester.Script
 
FileSelectButton - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 4/8/2016.
FileSelectButton() - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
FileSelectButton(String, String, String, ActionListener) - Constructor for class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
FileSelectButton.ExtensionFileFilter - Class in ur_rna.RNAstructureUI.utilities
 
FileSelectButton.FileMenuItem - Class in ur_rna.RNAstructureUI.utilities
 
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
 
fileShouldExist - Variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
filterAcceptAll - Static variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
filterFiles(List<File>, FileFilter) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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.utilities.FileField
 
filters - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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.SwingClassMatchers
 
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
 
first - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser.JJCalls
 
firstNonEmpty(String...) - Static method in class ur_rna.Utilities.ObjTools
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.
flip() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Flip the structure image horizontally.
flip() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
FLOAT_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
FLOAT_SUFFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
FloatField(String, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
Unbounded Constructor.
FloatField(String, Number, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
Minimum Bounds Constructor.
FloatField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
Minimum and Maximum Bounds Constructor.
flush() - Method in class ur_rna.Utilities.ConsoleTools.FixedStream
 
fmt(String, Object...) - Static method in class ur_rna.Utilities.ObjTools
 
fmtMsg(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
 
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.
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
 
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
 
fromFile() - Method in class ur_rna.GUITester.Script
 
fromImportance(int) - Static method in enum ur_rna.Utilities.Verbosity
 
fullText - Variable in class ur_rna.Utilities.CommandLineParser.Argument
The full original text of this Argument in the command line.

G

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
 
getAllLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
 
getAllOligoData(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getAllSearchDirs() - Method in class ur_rna.Utilities.ResourceLoader
 
getAppLoadedLibraries() - Static method in class ur_rna.Utilities.ClassLoaderInfo
 
getAppPath(Class) - Static method in class ur_rna.Utilities.PathTools
Gets the absolute path to the directory containing the class file for referenceClass.
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
 
getBoolResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
 
getBounds() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
getCancelListeners() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
getCanonicalPath(String) - Static method in class ur_rna.Utilities.PathTools
Get the canonical form of a file-system path by: Converting it to unix format (if Windows) Replacing // with / Replacing /./ with / Replacing dirname/../ with /
getCanonicalPath(String, boolean, boolean, boolean, boolean) - Static method in class ur_rna.Utilities.PathTools
Get the canonical form of a file-system path by: Converting it to unix format (if Windows) Removing starting slashes (if removeStartSlash is true) Adding an ending slash (if addEndSlash is true} Removing an ending slash (if removeEndSlash is true Replacing // with / Replacing /./ with / Replacing dirname/../ with / Removing ./ at the start of a path (if removeDotSlashAtStart is true)
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
 
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
 
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
 
getComponentInfo(Component) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
getContext() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
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
 
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
 
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.
getDefaultDir() - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getDefaultExtension() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getDefaultMax() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
getDefaultMin() - Method in class ur_rna.RNAstructureUI.drawing.proxy.DotPlotBackend
 
getDefaultPreferenceStorage() - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getDialogContent() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
Get the data from a dialog to put in this window.
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
 
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
 
getErrorDescription() - Method in exception ur_rna.Utilities.SyntaxErrorException
 
getErrorInfo(Throwable) - Static method in class ur_rna.Utilities.AppLog
 
getErrStream() - Method in class ur_rna.Utilities.AppLog
 
getExamples() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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) - Static method in class ur_rna.Utilities.PathTools
Gets the extension of the file including the preceding dot (.)
getExtensions() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
getField(int) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
Get a particular input field.
getField(String) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
getFile() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Get the file drawn on this dialog.
getFile(int) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
Get a file name from a particular input field.
getFile() - Method in class ur_rna.RNAstructureUI.utilities.FileField
Get the file name in the field.
getFile() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectedEvent
 
getFileInfo(boolean) - Method in class ur_rna.GUITester.Script
 
getFileName(boolean, Component, String, String, String, String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getFileName(boolean, Component, String, String, String, String, boolean) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getFileShouldExist() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getFilters() - Method in class ur_rna.RNAstructureUI.utilities.FileField
Gets the file filters associated with this field.
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
Get the top frame of the application.
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
 
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
 
getInput(String, String, Object) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show an input dialog that gets a string.
getInput(NumberField.DoubleField) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show an input dialog that gets a double within a certain range.
getInput(NumberField.IntegerField) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show an input dialog that gets an integer within a certain range.
getInputControl(int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Get a particular input control from the content pane.
getInputControl(Container, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Get a particular input control from a given container.
getIntResult() - Method in class ur_rna.RNAstructureUI.utilities.RunFunc
 
getInvalidArgMessage(String, Object[], int, String) - Static method in class ur_rna.GUITester.RuntimeTools
 
getKey(String) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
 
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
 
getLine() - Method in exception ur_rna.Utilities.SyntaxErrorException
 
getList() - Method in class ur_rna.RNAstructureUI.utilities.MRUFileStorage
 
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
 
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
 
getMenuPath(JMenuItem) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
 
getMessage() - Method in error ur_rna.GUITester.ScriptParser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMessage() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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
 
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
 
getNormalizedExtensions() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
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
 
getOpenName(String, String, String, String, Component) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getOpenName(String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getOpenName(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getOperandName() - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
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.RNAstructureUI.utilities.OSInfo
 
getOSType() - Static method in class ur_rna.RNAstructureUI.utilities.OSInfo
 
getOutputFile(String, String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Replace the extension on a file name.
getOutputFile(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
getParseError() - Method in class ur_rna.GUITester.ScriptRunner
 
getParts(String) - Static method in class ur_rna.Utilities.PathTools
 
getParts(String, boolean) - Static method in class ur_rna.Utilities.PathTools
 
getParts(String, boolean, boolean) - Static method in class ur_rna.Utilities.PathTools
 
getPath(String) - Static method in class ur_rna.Utilities.PathTools
Get the full parent directory path, including the final slash.
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.ModuleWindow.ProgressPanel
 
getProgressNumber() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getRecent() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
getRecentDir(String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getRecentDir(String, boolean) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getRecentDir(String, boolean, File) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getRecentDirOrDefault(String, boolean) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
getRunTimeError() - Method in class ur_rna.GUITester.ScriptRunner
 
getSaveName(String, String, String, String, Component) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getSaveName(String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
getSaveName(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
getSelectedFile() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Returns the selected file.
getSelectedIndex() - Method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Get the index of the selected button from this panel.
getSelectedItem() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox
 
getSelectedName() - Method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Get the command of the selected button from this panel.
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
 
getSource() - Method in class ur_rna.GUITester.ScriptRunner
 
getSpecialKey(String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
getSpecialValue(String) - Method in class ur_rna.GUITester.ScriptRuntime
 
getSpinner() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel
Get the spinner.
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
 
getStructureData(int) - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
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
 
getTime() - Static method in class ur_rna.Utilities.StopWatch
 
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.
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.
getUpdateListeners() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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.utilities.NumberField.DoubleField
 
getValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
 
getValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField
Get the text field's numeric value.
getValue() - Method in class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
 
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
 
getVersion() - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
getVisible() - Method in class ur_rna.GUITester.GuiTools.Matchers.VisibilityMatcher
 
globToRegex(String) - Static method in class ur_rna.Utilities.Convert
Converts a standard POSIX Shell globbing pattern into a regular expression pattern.
group - Variable in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
The button group connected to this panel.
group2 - Variable in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
The button group, as a list, for ease of access to each.
GT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
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
 
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
Returns a hash code value for the object.
hasLocationInfo() - Method in exception ur_rna.Utilities.SyntaxErrorException
 
hasNext() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
 
hasNext() - Method in class ur_rna.Utilities.Filter.FilterIterator
 
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.
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.
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
 
HOOK - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
htmlCenter(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Converts a simple text message to an html-formatted message by prepending <html><center> and escaping all html special characters within the message.
HTMLCheckBox - Class in ur_rna.RNAstructureUI.utilities
A class that creates a check box whose text is HTML.
HTMLCheckBox(String, boolean) - Constructor for class ur_rna.RNAstructureUI.utilities.HTMLCheckBox
Constructor.

I

id - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
 
IDENTIFIER - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
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
 
importance - Variable in enum ur_rna.Utilities.Verbosity
 
inBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
includeDirs - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
includeFolders() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
INCR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
index - Variable in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel.ButtonListener
 
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
 
info(String) - Method in class ur_rna.Utilities.AppLog
 
info(String, Object...) - Method in class ur_rna.Utilities.AppLog
 
infoLabel - 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
 
initial - Variable in class ur_rna.RNAstructureUI.utilities.NumberField
The initial default value of the field.
input - Variable in class ur_rna.GUITester.Script
 
input_stream - Variable in class ur_rna.GUITester.ScriptParser.GuiTestScriptParserTokenManager
 
inputFile(boolean) - Method in class ur_rna.RNAstructureUI.utilities.FileField
Indicate whether or not this field is used to accept an input file (as opposed to an output file)
inputFile() - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
inputFile(String) - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
inputStream - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
 
insertMenuItem(String, String, ActionListener, int) - Method in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Insert a plain text menu item with rollover text.
Instruction() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
INT_SUFFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
INTEGER_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
IntegerField(String, Integer) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
Unbounded Constructor.
IntegerField(String, Integer, Integer) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
Minimum Bounds Constructor.
IntegerField(String, Integer, Integer, Integer) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
Minimum and Maximum Bounds Constructor.
InternalWindow - Class in ur_rna.RNAstructureUI.windows
A class that holds internal frames for the RNAstructure GUI.
InternalWindow() - Constructor for class ur_rna.RNAstructureUI.windows.InternalWindow
Constructor.
INVALID_LEXICAL_STATE - Static variable in error ur_rna.GUITester.ScriptParser.TokenMgrError
Tried to change to an invalid lexical state.
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
 
isAnySet(int, int) - Static method in class ur_rna.Utilities.ObjTools
 
isClosed() - Method in class ur_rna.Utilities.ExtendedBufferedReader
 
isCurDirSet - Variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
isDebugEnabled() - Method in class ur_rna.Utilities.AppLog
 
isEmpty(String) - Static method in class ur_rna.Utilities.ObjTools
Returns true if the string is null or empty ("").
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.utilities.FieldPanel.FilePanel
Get whether any fields are empty; an empty field is an error.
isError() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
Get whether this window encountered an error.
isExampleFile(File) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
isFixed - Static variable in class ur_rna.Utilities.ConsoleTools
 
isIndeterminate() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
isInputFile - Variable in class ur_rna.RNAstructureUI.utilities.FileField
 
isInputFile() - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
isInputWindow - Variable in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
A boolean that tells whether this window is an input window or not.
isMac() - Static method in class ur_rna.RNAstructureUI.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.RNAstructureUI.utilities.OSInfo
 
ISO8601 - Static variable in class ur_rna.Utilities.DateHelper
 
ISO8601Format - Static variable in class ur_rna.Utilities.DateHelper
 
isOutputFile - Variable in class ur_rna.RNAstructureUI.utilities.FileField
 
isOutputFile() - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
isPlaying() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
isRNA - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
A boolean, true if the calculation handles RNA, false if not.
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
 
isSpecialSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
isValidSeqChar(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
isVersionCompatible(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
isWin() - Static method in class ur_rna.RNAstructureUI.utilities.OSInfo
 
item(JComponent, int) - Method in class ur_rna.RNAstructureUI.menus.FileMenu
 
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
 
iterator - Variable in class ur_rna.Utilities.ConverterFilter.FilterIterator
 
iterator - Variable in class ur_rna.Utilities.Filter.FilterIterator
 

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
 
job - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
The job that prints out this panel

K

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
 
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.ModuleWindow.ProgressPanel
 
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.
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.
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
 
launchSubjectApp(String[]) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
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
 
lblHelp - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
lblLogo - Variable in class ur_rna.RNAstructureUI.windows.AboutWindow
 
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.
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
 
line - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
 
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
 
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
 
loadNativeLib() - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
loadRecentPaths() - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
loadRecentPaths(Preferences) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
LOCAL_HELP_PAGE - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
 
localFolderPaths - Static variable in class ur_rna.Utilities.PathTools
 
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 - 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
 
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.
LT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.

M

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
 
mainFrame - Variable in class ur_rna.RNAstructureUI.windows.InternalWindow
 
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
 
makeBottomBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty bottom border on a component.
makeEmptyBorder(String, int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty border on a component.
makeEqualBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty equidistant border on a component.
makeHorizontal(String[]) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a horizontal layout.
makeHorizontal(String, String...) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a title and horizontal layout.
makeHorizontal(String, ActionListener, String...) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a title, horizontal layout, and an action listener associated with the buttons.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
Make any input controls necessary to get data from this window for a calculation.
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
 
makeInputControls() - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
 
makeLeftBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty left border on a component.
makePanel() - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
Build the panel.
makeRightBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty right border on a component.
makeStartButton(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Create the "START" button.
makeTitledBorder(String, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create a padded titled border on a component.
makeTopBorder(int, JComponent) - Method in class ur_rna.RNAstructureUI.utilities.BorderBuilder
Create an empty top border on a component.
makeVertical(String[]) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a vertical layout.
makeVertical(String, String...) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a title and vertical layout.
makeVertical(String, ActionListener, String...) - Static method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Create a button panel with a title, vertical layout, and an action listener associated with the buttons.
markEdited(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
marks - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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
 
maxBoundX - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
The maximum X bound of the image.
maxBoundY - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
The maximum Y bound of the image.
maxdefect - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
 
maxdepth - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
 
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.
maximum - Variable in class ur_rna.RNAstructureUI.utilities.NumberField
The maximum value of the field.
maxleaf - Variable in class ur_rna.RNAstructureUI.windows.DesignWindow
 
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
 
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.windows.InternalWindow
The menu bar that's attached to this window.
menuItem - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
menuItemClicked - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
METHOD_PREFIX - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
minimum - Variable in class ur_rna.RNAstructureUI.utilities.NumberField
The minimum value of the field.
MINUS - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
MINUSASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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.
mk - Variable in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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
 
modifyDir - Variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
modifyDir() - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Gets the property 'modifyDir', which affects whether the user's actions (i.e.
ModuleWindow - Class in ur_rna.RNAstructureUI.windows
A class responsible for creating and displaying a window that enables a user to input data for one of the RNAstructure modules.
ModuleWindow(String, String) - Constructor for class ur_rna.RNAstructureUI.windows.ModuleWindow
Constructor.
ModuleWindow.ProgressPanel - Class in ur_rna.RNAstructureUI.windows
 
mouseClicked(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
mouseEntered(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
mouseExited(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
mousePressed(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
mouseReleased(MouseEvent) - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
MoveDialog() - Constructor for class ur_rna.RNAstructureUI.drawing.menus.StructureMenu.MoveDialog
Constructor.
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.
MultiClassMatcher(Class...) - Constructor for class ur_rna.GUITester.GuiTools.Matchers.ClassMatcher.MultiClassMatcher
 
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.
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.
mustExist - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
mustExist() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 

N

name - Variable in class ur_rna.GUITester.ScriptParser.ASTNamedArgument
 
name - Variable in class ur_rna.Utilities.CommandLineParser.FlagDef
 
name - Variable in class ur_rna.Utilities.PathTools.PathParts
 
NamedArgument() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
NamedArgumentList() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
names - Variable in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
The names of the buttons in the group.
NE - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
NEVER - Static variable in class ur_rna.RNAstructureUI.utilities.ScrollerPane
A generic constant symbolizing that a scroll bar must never be used.
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() - Method in class ur_rna.Utilities.ConverterFilter.FilterIterator
 
next() - Method in class ur_rna.Utilities.Filter.FilterIterator
 
nextCharBuf - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
nextCharInd - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
nl2br(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
 
NO_ALIASES - Static variable in class ur_rna.Utilities.CommandLineParser.FlagDef
 
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
 
nohtml(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
 
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
 
normalizedExt - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
normalizeFlagName(String) - Method in class ur_rna.Utilities.CommandLineParser
 
NOT - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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.
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.
NumberField - Class in ur_rna.RNAstructureUI.utilities
A class that creates a text field whose contents may be bounded by a minimum or maximum value.
NumberField(String, Number, Number, Number) - Constructor for class ur_rna.RNAstructureUI.utilities.NumberField
Constructor.
NumberField.DoubleField - Class in ur_rna.RNAstructureUI.utilities
An inner class that handles a field which contains a double value.
NumberField.FloatField - Class in ur_rna.RNAstructureUI.utilities
An inner class that handles a field which contains a float value.
NumberField.IntegerField - Class in ur_rna.RNAstructureUI.utilities
An inner class that handles a field which contains an integer value.

O

ObjTools - Class in ur_rna.Utilities
 
ObjTools() - Constructor for class ur_rna.Utilities.ObjTools
 
OCTAL_LITERAL - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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.SwingClassMatchers
 
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.
onFileSelected - Variable in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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
 
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.
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
 
ORASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
OSInfo - Class in ur_rna.RNAstructureUI.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.RNAstructureUI.utilities.OSInfo
 
OSInfo.OSType - Enum in ur_rna.RNAstructureUI.utilities
 
osType - Static variable in class ur_rna.RNAstructureUI.utilities.OSInfo
 
OSType() - Constructor for enum ur_rna.RNAstructureUI.utilities.OSInfo.OSType
 
OUT - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
outputFile(boolean) - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
outputFile() - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
outputFile(String) - Method in class ur_rna.RNAstructureUI.utilities.FileField
 
outputStream - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
 
override(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
overrides - Static variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 

P

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
 
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.
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
 
parseArgs(String[]) - Static method in class ur_rna.GUITester.Startup
 
parseCommandArgs(String[]) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
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
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.
parseFilters(String) - Static method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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.
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 *
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.
passes(T) - Method in class ur_rna.Utilities.ConverterFilter
 
passes(T) - Method in class ur_rna.Utilities.Filter
 
passesFilter(File) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
path - Variable in class ur_rna.Utilities.PathTools.PathParts
 
PathParts(String) - Constructor for class ur_rna.Utilities.PathTools.PathParts
 
PathParts(String, boolean) - Constructor for class ur_rna.Utilities.PathTools.PathParts
 
PathParts(String, boolean, boolean) - Constructor for class ur_rna.Utilities.PathTools.PathParts
 
pathSep - Static variable in class ur_rna.Utilities.ResourceLoader
 
PathTools - Class in ur_rna.Utilities
 
PathTools() - Constructor for class ur_rna.Utilities.PathTools
 
PathTools.PathParts - Class in ur_rna.Utilities
 
pause(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
peek() - Method in class ur_rna.Utilities.ExtendedBufferedReader
Returns the next character in the current reader without consuming it.
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.
placeComponent(int, int, JComponent) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
.
play(InputStream) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
playClip(char) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
Play a sound clip, depending on the nucleotide.
playNext() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
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.
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.
PLUS - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
PLUSASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
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.
preemptFileName - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
preemptFiltersRequired - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
preemptNextFileNameRequest(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Causes the next call to getFileName to return with the specified file WITHOUT showing the dialog.
preemptTimeout - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
preferencesNode - Static variable in class ur_rna.RNAstructureUI.RNAstructure
 
preferredDialogWidth - Variable in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
The preferred dialog width.
prefix - Variable in class ur_rna.GUITester.ScriptParser.ScriptNode.DumpState
 
PREFS - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
prefs - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
prevCharIsCR - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
prevCharIsLF - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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.
printElapsed(String) - 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
 
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.
progressBar - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
progressIndicator - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
The progress bar dialog for this window.
ProgressPanel() - Constructor for class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
ProgressPanel(String, ActionListener, ActionListener) - Constructor for class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
promptDraw() - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
promptDraw(String, String) - Static method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
propsToString() - Method in class ur_rna.GUITester.ScriptParser.ScriptNode
 
protectedExamplesDir - Static variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
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
 
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
 

Q

QUOTES - Static variable in class ur_rna.Utilities.CharType
Single (') and double (") quotes.

R

radio - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
RadioButtonPanel - Class in ur_rna.RNAstructureUI.utilities
A class that creates a panel containing a group of radio buttons.
RadioButtonPanel(String, String, ActionListener, String...) - Constructor for class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Constructor.
raiseFileSelectedEvent(File) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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
 
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
 
recentDirs - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
recentFiles - Static variable in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
 
recentPathPreferences - Static variable in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
reflectedClassLoaderField - Static variable in class ur_rna.Utilities.ClassLoaderInfo
 
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.
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
 
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() - Method in class ur_rna.Utilities.Filter.FilterIterator
 
removeAnnotation() - Method in class ur_rna.RNAstructureUI.drawing.proxy.StructureBackend
 
removeCancelListener(ActionListener) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
removeFlagPrefix(String) - Method in class ur_rna.Utilities.CommandLineParser
 
removeListener - Variable in class ur_rna.RNAstructureUI.utilities.RequestFocusListener
 
removeUpdateListener(ActionListener) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
replace(int, int, String) - Method in class ur_rna.Utilities.StringBuilderEx
 
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.RolloverMenu.RolloverListener
Reset the main frame message bar text to its default.
reset() - Method in class ur_rna.Utilities.StopWatch
Reset elapsed time to 0 and stop the timer.
resetField(Number) - Method in class ur_rna.RNAstructureUI.utilities.NumberField
Reset a field value, if it's within bounds.
resetField(Number, Number, Number) - Method in class ur_rna.RNAstructureUI.utilities.NumberField
Reset a field value and bounds.
resetFrame() - Method in class ur_rna.RNAstructureUI.AppMainFrame
Reset the frame to its original state before any windows were opened.
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.
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
 
reverse() - Method in class ur_rna.Utilities.StringBuilderEx
 
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(long, RNAstructureBackendCalculator, String, String) - 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_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_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_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_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_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_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_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(long, RNAstructureBackendCalculator, double, int, double, int, int, double) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
 
RNAstructureBackendCalculator_runTurboFoldPseudoknot(long, RNAstructureBackendCalculator, double, int, int, int) - Static method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculatorProxyJNI
 
RNAstructureBackendCalculator_runTurboFoldThreshold(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_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
 
RNAstructureMenu - Class in ur_rna.RNAstructureUI.utilities
A class that creates a menu.
RNAstructureMenu(String) - Constructor for class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
Constructor.
rollover - Variable in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
The rollover text for this listener.
RolloverListener(String) - Constructor for class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
Constructor.
RolloverMenu - Class in ur_rna.RNAstructureUI.menus
A class that creates a menu for the RNAstructure GUI.
RolloverMenu(RNAstructureMenu) - Constructor for class ur_rna.RNAstructureUI.menus.RolloverMenu
RNAstructureMenu Conversion Constructor.
RolloverMenu(String) - Constructor for class ur_rna.RNAstructureUI.menus.RolloverMenu
Title Constructor.
RolloverMenu.RolloverListener - Class in ur_rna.RNAstructureUI.menus
An inner class that creates a rollover listener for menus in the RNAstructure GUI.
rootNode() - Method in class ur_rna.GUITester.ScriptParser.JJTGuiTestScriptParserState
 
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
 
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
 
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
 
runMainCalculation() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
 
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
 
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.
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
 
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) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
runTurboFoldPseudoknot(double, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
runTurboFoldThreshold(double, int, double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 

S

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
 
save(Preferences) - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
save() - Method in class ur_rna.RNAstructureUI.utilities.UserOptions
 
saveRecent() - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
 
saveRecentPaths() - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
saveRecentPaths(Preferences) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
scroll - Variable in class ur_rna.RNAstructureUI.windows.MultiWindow
The scroll pane holding the sequence set.
ScrollerPane - Class in ur_rna.RNAstructureUI.utilities
A class that creates a scroll pane that can be controlled via the keyboard.
ScrollerPane(Component, int, int) - Constructor for class ur_rna.RNAstructureUI.utilities.ScrollerPane
Constructor.
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
 
select(JComponent, int, boolean) - Method in class ur_rna.RNAstructureUI.menus.FileMenu
 
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
 
Sequence - Static variable in class ur_rna.RNAstructureUI.utilities.FileFilters
 
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.
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.MoveDialog
 
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.DynamicMenuBar
 
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.NucleicAcidMenu
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.menus.RolloverMenu
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.RNAstructure
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.BorderBuilder
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.BorderedButtonPanel
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.Dialogs
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.FieldPanel
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.FileField
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.HTMLCheckBox
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.ImageGrabber
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.NumberField.DoubleField
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.NumberField.FloatField
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.NumberField.IntegerField
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.NumberField
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.OSInfo
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.RNAstructureMenu
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.ScrollerPane
 
serialVersionUID - Static variable in class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
 
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.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.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.KeyAlreadyExistsException
 
serialVersionUID - Static variable in class ur_rna.Utilities.StringBuilderEx
 
serialVersionUID - Static variable in exception ur_rna.Utilities.SyntaxErrorException
 
set() - Method in class ur_rna.RNAstructureUI.menus.RolloverMenu.RolloverListener
Set the main frame message bar text to this listener's specific rollover text.
setAcceptAll(boolean) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
setAllowCancel(boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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.
setBarColor(Color) - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow.BarButton
Set the default color that will be painted on this button.
setBarPolicies(int, int) - Method in class ur_rna.RNAstructureUI.utilities.ScrollerPane
Set the scroll bar policies for this scroll pane.
setBaseDir(String) - Method in class ur_rna.Utilities.ResourceLoader
 
setBaseDir(Class<?>, String) - Method in class ur_rna.Utilities.ResourceLoader
Set the resource directory based on the package name of the specified class by converting each dot (.) in the package name to a slash (/).
setButtonText(String) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Set the text that appears on the accept (OK) button.
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.
setContext(String) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Set the context for default startup folder.
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
 
setDefaultDir(File) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setDefaultFile(String) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setDefaultFile(File) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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
 
setExtensions(String[]) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
setFile(int, String) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel.FilePanel
Set a file name in a particular input field.
setFileShouldExist(boolean) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
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.
setFilters(String) - Method in class ur_rna.RNAstructureUI.utilities.FileField
Sets the file filters associated with this field.
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.
setIncludeFolders(boolean) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
setIndeterminate(boolean) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
setInfoLabel(String) - Method in class ur_rna.RNAstructureUI.AppMainFrame
Set the info bar at the bottom of the main window to contain the specified text.
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) - Static method in class ur_rna.RNAstructureUI.RNAstructure
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
 
setMaxLoop(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setMaxPair(int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.DesignWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.DrawingWindow
Create the array of variable menus used by this window.
setMenus() - Method in class ur_rna.RNAstructureUI.windows.DynalignFoldWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.Efn2Window
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldDoubleWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldSingleWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
Create the array of variable menus used by this window.
setMenus() - Method in class ur_rna.RNAstructureUI.windows.MaxExpectWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.MultiWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.OligoScreenWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.OligoWalkWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.PartitionSingleWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.ProbKnotWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.PseudoknotWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.RefoldWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
setMenus() - Method in class ur_rna.RNAstructureUI.windows.StochasticWindow
 
setMessage(String) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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
 
setModifyDir(boolean) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Sets the property 'modifyDir', which affects whether the user's actions (i.e.
setMustExist(boolean) - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.ExtensionFileFilter
 
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.
setPad(int, int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
Set the internal padding of the constraints.
setPanelWidth(int) - Method in class ur_rna.RNAstructureUI.utilities.FieldPanel
Set the width of the panel.
setPref(String, String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
setProgress(int) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
setProhibitedHelix(int, int, int, int) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
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
 
setRecentDir(String, String) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setRecentDir(String, File) - Static method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setRelative(GuiItemRef, GuiRelative) - Method in class ur_rna.GUITester.GuiTools.GuiItemRef
 
setRhs(Matcher) - Method in class ur_rna.GUITester.GuiTools.Matchers.ComposableBase.BinaryMatcher
 
setScale(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
Set the image scale.
setSelectedButton(String) - Method in class ur_rna.RNAstructureUI.utilities.RadioButtonPanel
Set a particular button in this group to be selected.
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
 
setSizes(int, int) - Method in class ur_rna.RNAstructureUI.utilities.ScrollerPane
Set the size of the scroller pane by setting preferred, minimum, and maximum sizes all at once.
setSpeakWhileTyping(boolean) - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
Set whether or not the window should be speaking while typing.
setStartDir(String) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setStartDir(File) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
setStructureNumber(int) - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Set the structure number.
setTabSize(int) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
setTemperature(double) - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
setText(Component, String) - Method in class ur_rna.GUITester.GuiTools.GuiRobot
 
setTitles(String) - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
Set the title of both this window and the main window.
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
 
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.
shouldTrace() - Method in class ur_rna.GUITester.ScriptRuntime
 
showAboutWindow() - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
ShowAppHelp() - Static method in class ur_rna.GUITester.Startup
 
showConfirm(Object) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a dialog that gives the user one of two choices to make.
showConfirm(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a dialog that gives the user one of two choices to make.
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
 
showError(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show an error dialog.
showFileDialog(Component) - Method in class ur_rna.RNAstructureUI.utilities.StandardFileChooser
Show the File Chooser and return the selected file path, if successful, or null if the user cancels.
showFileSelectMenu() - Method in class ur_rna.RNAstructureUI.utilities.FileSelectButton
 
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
 
showMessage(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a message dialog using String.format to create the message.
showMessage(String, Object...) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a message dialog using String.format to create the message.
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
 
showStartupInfo() - Method in class ur_rna.RNAstructureUI.AppMainFrame
 
showWarning(String) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
showWarning(Component) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a warning dialog.
showWarning(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a warning dialog.
showWarning(String, boolean) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a warning dialog.
showYesNoCancel(Object) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a dialog that gives the user one of three choices to make.
showYesNoCancel(String) - Static method in class ur_rna.RNAstructureUI.utilities.Dialogs
Show a dialog that gives the user one of three choices to make.
shutdown() - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
SIBLING - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
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
 
SimpleCast() - Constructor for class ur_rna.Utilities.ConverterFilter.SimpleCast
 
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_EMPTY_ITEM_ARRAY - Static variable in class ur_rna.Utilities.PathTools.PathParts
 
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
 
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.
SNG_QUOT - Static variable in class ur_rna.Utilities.CharConstants
 
SoundPlayer() - Constructor for class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow.SoundPlayer
 
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)
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.
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.
specialSequenceChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
specialStyle - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
specialToken - Variable in class ur_rna.GUITester.ScriptParser.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
specificPanel - Variable in class ur_rna.RNAstructureUI.windows.TurboFoldWindow
The panel that holds the dynamic options applicable to a mode.
specifiedPanelWidth - Variable in class ur_rna.RNAstructureUI.utilities.FieldPanel
The specified width of the panel.
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.
splitFlagValue(String) - Method in class ur_rna.Utilities.CommandLineParser
 
splitScriptSuite(Reader, String, String) - Static method in class ur_rna.GUITester.Startup
 
StandardFileChooser - Class in ur_rna.RNAstructureUI.utilities
Created by Richard on 10/23/2015.
StandardFileChooser() - Constructor for class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
StandardFileChooser(boolean, String, String) - Constructor for class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
StandardFileChooser(int, String, String) - Constructor for class ur_rna.RNAstructureUI.utilities.StandardFileChooser
 
STAR - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
STARASSIGN - Static variable in interface ur_rna.GUITester.ScriptParser.GuiTestScriptParserConstants
RegularExpression Id.
start(String) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
Start the GUI application.
start(String[]) - Method in class ur_rna.GUITester.GuiTools.GuiAppManager
 
start() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
start() - Method in class ur_rna.Utilities.StopWatch
Start the timer.
startButton - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
started - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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
 
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.Utilities.ConverterFilter.FilterIterator
 
state - Variable in class ur_rna.Utilities.Filter.FilterIterator
 
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.
StochasticWindow - Class in ur_rna.RNAstructureUI.windows
A class responsible for initializing and running the stochastic module, which generates a stochastic sample of structures.
StochasticWindow(String) - Constructor for class ur_rna.RNAstructureUI.windows.StochasticWindow
Constructor.
stop() - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
stop() - Method in class ur_rna.Utilities.StopWatch
Stop the timer, but store the elapsed time so that when StopWatch.start() is called, the elapsed time will continue to increase.
StopWatch - Class in ur_rna.Utilities
Created by Richard on 4/12/2016.
StopWatch() - 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_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.
stringsMatch(String, String) - Static method in class ur_rna.GUITester.GuiTools.Matchers.DescriptionMatcher
Match with a regexp if the pattern contains a ".*" or is bounded by slashes (/regexp/).
stripExt(String) - Static method in class ur_rna.RNAstructureUI.utilities.FileSelectButton.FileMenuItem
 
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_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_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.
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.MoveDialog - 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.
styleTimer - Variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
The timer that updates syntax highlighting
subject - Variable in class ur_rna.GUITester.ScriptParser.ASTAssignment
 
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
 
switchCircled() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog
Switch circled nucleotides on or off.
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.
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)
tabSize - Variable in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
target - Variable in class ur_rna.Utilities.ConsoleTools.FixedStream
 
testTopNodeType(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
text - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
textArea - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
textFields - Variable in class ur_rna.RNAstructureUI.utilities.FieldPanel
The array of text fields.
time - Variable in class ur_rna.Utilities.StopWatch
 
timer - Variable in class ur_rna.RNAstructureUI.windows.ModuleWindow.ProgressPanel
 
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) - Static method in class ur_rna.Utilities.Convert
 
ToBool(String) - 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(String, double) - Static method in class ur_rna.Utilities.Convert
 
ToFriendlyString - Annotation Type in ur_rna.Utilities.annotation
 
toggle - Static variable in class ur_rna.GUITester.GuiTools.Matchers.SwingClassMatchers
 
ToInt(String, int) - 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_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.
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.
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.Utilities.StringBuilderEx
 
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
 
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.
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.SwingClassMatchers
 
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[]) - Static method in class ur_rna.RNAstructureUI.RNAstructure
 
tryPopTypedNode(int) - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
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.
types - Static variable in class ur_rna.GUITester.GuiTools.ScreenCapture
 

U

UNDERSCORE - Static variable in class ur_rna.Utilities.CharType
 
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
 
unpairedSequenceChars - Static variable in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
unpairedStyle - 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
 
updateCalcProgress(ModuleWindow.ProgressPanel) - Method in class ur_rna.RNAstructureUI.windows.ModuleWindow
 
updatedMessage - Variable in exception ur_rna.Utilities.ExtensibleException
 
UpdateLineColumn(char) - Method in class ur_rna.GUITester.ScriptParser.JavaCharStream
 
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
A package that holds all Java RNAstructure interface classes that are directly called at the Java interface startup.
ur_rna.RNAstructureUI.drawing.dialogs - package ur_rna.RNAstructureUI.drawing.dialogs
A package that holds all Java drawing dialogs.
ur_rna.RNAstructureUI.drawing.menus - package ur_rna.RNAstructureUI.drawing.menus
A package that holds all menus used in the drawing framework.
ur_rna.RNAstructureUI.drawing.proxy - package ur_rna.RNAstructureUI.drawing.proxy
A package that holds all Java drawing classes generated by SWIG that connect the C++ back end to the Java front end.
ur_rna.RNAstructureUI.drawing.runners - package ur_rna.RNAstructureUI.drawing.runners
A package that holds the run templates that are used when the Java drawing framework is wrapped into self-contained executables.
ur_rna.RNAstructureUI.menus - package ur_rna.RNAstructureUI.menus
A package that holds all menus used in the Java RNAstructure interface.
ur_rna.RNAstructureUI.utilities - package ur_rna.RNAstructureUI.utilities
A package that holds a variety of utilities classes.
ur_rna.RNAstructureUI.windows - package ur_rna.RNAstructureUI.windows
A package that holds all internal windows used in the drawing framework.
ur_rna.Utilities - package ur_rna.Utilities
 
ur_rna.Utilities.annotation - package ur_rna.Utilities.annotation
 
useNativeLAF - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
useNativeMenus() - Static method in class ur_rna.RNAstructureUI.utilities.OSInfo
 
useNativeMenus - Variable in class ur_rna.RNAstructureUI.utilities.UserOptions
 
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
 
value - Variable in class ur_rna.GUITester.ScriptParser.SimpleNode
 
value - Variable in class ur_rna.Utilities.Pair
 
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.utilities.OSInfo.OSType
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.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.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.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.Verbosity
Returns an array containing the constants of this enum type, in the order they are declared.
ValueSelectionDialog - Class in ur_rna.RNAstructureUI.utilities
A class which creates a dialog that selects values from labeled text fields.
ValueSelectionDialog(String) - Constructor for class ur_rna.RNAstructureUI.utilities.ValueSelectionDialog
Constructor.
valueText - Variable in class ur_rna.Utilities.CommandLineParser.FlagArg
Gets the value of this flag, if one was specified, or null otherwise.
varName - Variable in class ur_rna.GUITester.ScriptParser.ASTVarRef
 
VarRef() - Method in class ur_rna.GUITester.ScriptParser.GuiTestScriptParser
 
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
 
verifySequence() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
 
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
 
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.
viewWindow() - Method in class ur_rna.RNAstructureUI.windows.InternalWindow
View the window.
viewWindow() - Method in class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow
View the window.
viewZoomDialog() - Method in class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog
View a zooming dialog.
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
 
wasCanceled() - Method in class ur_rna.RNAstructureUI.RNAstructureBackendCalculator
 
WEB_URL - Static variable in class ur_rna.RNAstructureUI.menus.HelpMenu
 
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
 
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.
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
 
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(JComponent, 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.
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
 
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
 

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
 
_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
 
_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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