- 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
-
- 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
-
- 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.
- 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.
- 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
-
- 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(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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-