Serialized Form

Package ur_rna.GUITester
- Class ur_rna.GUITester.RuntimeTools.ActionArgumentException extends RuntimeTools.ActionException implements Serializable
- Class ur_rna.GUITester.RuntimeTools.ActionException extends ScriptRuntimeException implements Serializable
- Class ur_rna.GUITester.RuntimeTools.UnsupportedActionException extends RuntimeTools.ActionException implements Serializable
- Class ur_rna.GUITester.ScriptRuntimeException extends ExtensibleException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - _node
```
ScriptNode _node
```
Package ur_rna.GUITester.GuiTools
- Class ur_rna.GUITester.GuiTools.GuiItemNotFoundException extends ExtensibleException implements Serializable
  
  serialVersionUID:
  
  1L
Package ur_rna.GUITester.ScriptParser
- Class ur_rna.GUITester.ScriptParser.ParseException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentToken
```
Token currentToken
```
      This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.
    - expectedTokenSequences
```
int[][] expectedTokenSequences
```
      Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.
    - tokenImage
```
java.lang.String[] tokenImage
```
      This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.
- Class ur_rna.GUITester.ScriptParser.ParseFormatException extends ParseException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ur_rna.GUITester.ScriptParser.Token extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - kind
```
int kind
```
      An integer that describes the kind of this token. This numbering system is determined by JavaCCParser, and a table of these numbers is stored in the file ...Constants.java.
    - beginLine
```
int beginLine
```
      The line number of the first character of this Token.
    - beginColumn
```
int beginColumn
```
      The column number of the first character of this Token.
    - endLine
```
int endLine
```
      The line number of the last character of this Token.
    - endColumn
```
int endColumn
```
      The column number of the last character of this Token.
    - image
```
java.lang.String image
```
      The string image of the token.
    - next
```
Token next
```
      A reference to the next regular (non-special) token from the input stream. If this is the last token from the input stream, or if the token manager has not read tokens beyond this one, this field is set to null. This is true only if this token is also a regular token. Otherwise, see below for a description of the contents of this field.
    - specialToken
```
Token specialToken
```
      This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token. If there are no such special tokens, this field is set to null. When there are more than one such special token, this field refers to the last of these special tokens, which in turn refers to the next previous special token through its specialToken field, and so on until the first special token (whose specialToken field is null). The next fields of special tokens refer to other special tokens that immediately follow it (without an intervening regular token). If there is no such token, this field is null.
- Class ur_rna.GUITester.ScriptParser.TokenMgrError extends java.lang.Error implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorCode
```
int errorCode
```
      Indicates the reason why the exception is thrown. It will have one of the above 4 values.
Package ur_rna.RNAstructure
- Class ur_rna.RNAstructure.RnaBackendException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - file
```
java.lang.String file
```
    - errorCode
```
int errorCode
```
Package ur_rna.RNAstructureUI
- Class ur_rna.RNAstructureUI.AppMainFrame extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  20160128L
  - Serialized Fields
    - log
```
AppLog log
```
    - menuBar
```
javax.swing.JMenuBar menuBar
```
    - toolBar
```
javax.swing.JToolBar toolBar
```
    - statusBar
```
javax.swing.JPanel statusBar
```
    - infoLabel
```
javax.swing.JLabel infoLabel
```
    - desktop
```
javax.swing.JDesktopPane desktop
```
    - mainMenus
```
MenuList mainMenus
```
    - menuMerger
```
MergeManager menuMerger
```
    - InfoLabelConsumer
```
java.util.function.Consumer<T> InfoLabelConsumer
```
    - keepToolBarItems
```
java.awt.Component[] keepToolBarItems
```
    - frameListener
```
javax.swing.event.InternalFrameListener frameListener
```
- Class ur_rna.RNAstructureUI.RNAstructure extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
Package ur_rna.RNAstructureUI.drawing.dialogs
- Class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog extends javax.swing.JInternalFrame implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - customMenus
```
MenuList customMenus
```
    - error
```
java.lang.String error
```
      The error message generated while building this panel, if any.
    - file
```
java.lang.String file
```
      The file that is drawn in some way on this panel.
    - label
```
javax.swing.JLabel label
```
      The main label that describes the panel.
    - legendGrid
```
javax.swing.JPanel legendGrid
```
      The panel that contains the legend grid.
    - mainPanel
```
javax.swing.JPanel mainPanel
```
      The main panel that the drawing resides on.
    - imgSizeX
```
double imgSizeX
```
      The maximum X bound of the image.
    - imgSizeY
```
double imgSizeY
```
      The maximum Y bound of the image.
    - job
```
java.awt.print.PrinterJob job
```
      The job that prints out this panel
    - preferredDialogWidth
```
int preferredDialogWidth
```
      The preferred dialog width.
    - scale
```
double scale
```
      The scale at which the image is seen.
- Class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog extends ImageDialog implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - backend
```
DotPlotBackend backend
```
      The back end object that reads data for dot plots.
    - strand
```
int strand
```
      The strand being drawn.
    - plotLength
```
int plotLength
```
      The length of the plot.
- Class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog extends ImageDialog implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - drawOptions
```
int drawOptions
```
    - backend
```
StructureBackend backend
```
      The back end object that reads data for structures.
    - data
```
java.lang.String[] data
```
      The array of data for a particular structure.
    - hasPairs
```
boolean hasPairs
```
      Whether the current structure has pairs.
    - number
```
int number
```
      The structure number viewed on this panel.
    - regex
```
java.lang.String[] regex
```
      The array of regexes used to pull data about a structure.
Package ur_rna.RNAstructureUI.drawing.menus
- Class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - dialog
```
StructureDialog dialog
```
      The structure panel connected to this menu.
- Class ur_rna.RNAstructureUI.drawing.menus.DotsMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120615L
  - Serialized Fields
    - dialog
```
PlotDialog dialog
```
      The structure dialog connected to this menu.
- Class ur_rna.RNAstructureUI.drawing.menus.PlotMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120615L
  - Serialized Fields
    - dialog
```
PlotDialog dialog
```
      The plot dialog connected to this menu.
- Class ur_rna.RNAstructureUI.drawing.menus.StructureMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - dialog
```
StructureDialog dialog
```
      The structure dialog connected to this menu.
    - circular
```
CheckMergeItem circular
```
    - flat
```
CheckMergeItem flat
```
    - flipped
```
CheckMergeItem flipped
```
    - circled
```
CheckMergeItem circled
```
Package ur_rna.RNAstructureUI.drawing.runners
- Class ur_rna.RNAstructureUI.drawing.runners.PlotRunner extends RunnerTemplate implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.drawing.runners.StructureRunner extends RunnerTemplate implements Serializable
  
  serialVersionUID:
  
  20120802L
Package ur_rna.RNAstructureUI.menus
- Class ur_rna.RNAstructureUI.menus.ConstraintsMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - backend
```
RNAstructureBackendCalculator backend
```
      The back end calculator that's linked to this menu.
    - str
```
int str
```
      The strand this constraints menu deals with.
- Class ur_rna.RNAstructureUI.menus.ConstraintsMenu.NucOrHelixDialog extends ValueSelectionDialog implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.menus.FileMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - drawOptionMenu
```
MergeMenu drawOptionMenu
```
- Class ur_rna.RNAstructureUI.menus.HelpMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - guiInfoListener
```
java.awt.event.MouseAdapter guiInfoListener
```
- Class ur_rna.RNAstructureUI.menus.MainMenu extends MergeMenu implements Serializable
  
  serialVersionUID:
  
  20160315L
  - Serialized Fields
    - mainFrame
```
AppMainFrame mainFrame
```
    - menuListener
```
java.awt.event.ActionListener menuListener
```
      The ActionLister that will be used to delegate ActionEvents produced by the menu items. The default is null, which indicates that menu events are handled internally (i.e. in a sub-class)
- Class ur_rna.RNAstructureUI.menus.MenuList extends java.util.ArrayList<MergeMenu> implements Serializable
  - Serialized Fields
    - subItemMergePos
```
int subItemMergePos
```
- Class ur_rna.RNAstructureUI.menus.MenuRolloverAdapter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - rollovers
```
java.util.HashMap<K,V> rollovers
```
    - rolloverHandler
```
java.util.function.Consumer<T> rolloverHandler
```
- Class ur_rna.RNAstructureUI.menus.NucleicAcidMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - acidName
```
java.lang.String acidName
```
- Class ur_rna.RNAstructureUI.menus.PredictMenu extends MainMenu implements Serializable
  
  serialVersionUID:
  
  20160121L
- Class ur_rna.RNAstructureUI.menus.RolloverListener extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20160316L
  - Serialized Fields
    - handler
```
java.util.function.Consumer<T> handler
```
    - text
```
java.lang.String text
```
Package ur_rna.RNAstructureUI.ui
- Class ur_rna.RNAstructureUI.ui.BorderBuilder extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.BorderedButtonPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.Dialogs extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.FieldPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - specifiedPanelWidth
```
int specifiedPanelWidth
```
      The specified width of the panel.
    - textFields
```
java.util.ArrayList<E> textFields
```
      The array of text fields.
- Class ur_rna.RNAstructureUI.ui.FieldPanel.FilePanel extends FieldPanel implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - buttonListener
```
java.awt.event.ActionListener buttonListener
```
- Class ur_rna.RNAstructureUI.ui.FileField extends javax.swing.JTextField implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - isOutputFile
```
boolean isOutputFile
```
    - isInputFile
```
boolean isInputFile
```
    - filters
```
java.lang.String filters
```
- Class ur_rna.RNAstructureUI.ui.HTMLCheckBox extends javax.swing.JCheckBox implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.NumberField extends javax.swing.JTextField implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - initial
```
java.lang.Number initial
```
      The initial default value of the field.
    - maximum
```
java.lang.Number maximum
```
      The maximum value of the field.
    - minimum
```
java.lang.Number minimum
```
      The minimum value of the field.
- Class ur_rna.RNAstructureUI.ui.NumberField.DoubleField extends NumberField implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.NumberField.FloatField extends NumberField implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.NumberField.IntegerField extends NumberField implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.ProgressPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - progressBar
```
javax.swing.JProgressBar progressBar
```
    - label
```
javax.swing.JLabel label
```
    - button
```
javax.swing.JButton button
```
    - timer
```
javax.swing.Timer timer
```
    - started
```
boolean started
```
- Class ur_rna.RNAstructureUI.ui.RadioButtonPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - group
```
javax.swing.ButtonGroup group
```
      The button group connected to this panel.
    - group2
```
java.util.ArrayList<E> group2
```
      The button group, as a list, for ease of access to each.
    - names
```
java.lang.String[] names
```
      The names of the buttons in the group.
- Class ur_rna.RNAstructureUI.ui.RecentFileButton extends javax.swing.JButton implements Serializable
  - Serialized Fields
    - filters
```
java.lang.String filters
```
    - onFileSelected
```
java.util.function.Consumer<T> onFileSelected
```
- Class ur_rna.RNAstructureUI.ui.ScrollerPane extends javax.swing.JScrollPane implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.ui.StandardFileChooser extends javax.swing.JFileChooser implements Serializable
  - Serialized Fields
    - fileShouldExist
```
boolean fileShouldExist
```
    - isCurDirSet
```
boolean isCurDirSet
```
    - context
```
java.lang.String context
```
    - modifyDir
```
boolean modifyDir
```
- Class ur_rna.RNAstructureUI.ui.ValueSelectionDialog extends javax.swing.JDialog implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - fields
```
NumberField[] fields
```
      The array of number fields this dialog holds.
Package ur_rna.RNAstructureUI.utilities
- Class ur_rna.RNAstructureUI.utilities.CalcParams extends java.util.HashMap<java.lang.String,java.lang.Object> implements Serializable
  - Serialized Fields
    - verifyType
```
boolean verifyType
```
- Class ur_rna.RNAstructureUI.utilities.FileSelectedEvent extends java.awt.event.ActionEvent implements Serializable
  - Serialized Fields
    - file
```
java.io.File file
```
- Class ur_rna.RNAstructureUI.utilities.ImageGrabber extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
Package ur_rna.RNAstructureUI.windows
- Class ur_rna.RNAstructureUI.windows.AboutWindow extends javax.swing.JInternalFrame implements Serializable
  - Serialized Fields
    - btnExtract
```
javax.swing.JButton btnExtract
```
    - mainPanel
```
javax.swing.JPanel mainPanel
```
    - btnClose
```
javax.swing.JButton btnClose
```
    - lblWebsite
```
javax.swing.JLabel lblWebsite
```
    - lblHelp
```
javax.swing.JLabel lblHelp
```
    - lblLogo
```
javax.swing.JLabel lblLogo
```
- Class ur_rna.RNAstructureUI.windows.AccessFoldWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20160714L
- Class ur_rna.RNAstructureUI.windows.ChildWindow extends javax.swing.JInternalFrame implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - disableClose
```
boolean disableClose
```
    - mainFrame
```
AppMainFrame mainFrame
```
    - customMenus
```
MenuList customMenus
```
    - log
```
AppLog log
```
    - warnings
```
java.util.HashSet<E> warnings
```
    - commandListener
```
java.awt.event.ActionListener commandListener
```
    - frameListener
```
javax.swing.event.InternalFrameListener frameListener
```
    - changeListener
```
java.beans.VetoableChangeListener changeListener
```
- Class ur_rna.RNAstructureUI.windows.DesignWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20160524L
  - Serialized Fields
    - maxdefect
```
NumberField.DoubleField maxdefect
```
    - maxdepth
```
NumberField.IntegerField maxdepth
```
    - maxmutate
```
NumberField.IntegerField maxmutate
```
    - maxleaf
```
NumberField.IntegerField maxleaf
```
    - maxredesign
```
NumberField.IntegerField maxredesign
```
- Class ur_rna.RNAstructureUI.windows.DrawingWindow extends InternalWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - dialog
```
ImageDialog dialog
```
      The image dialog connected to this window.
    - error
```
boolean error
```
      True if an error occurred building this window, false if not.
    - strand
```
int strand
```
      The strand being drawn.
- Class ur_rna.RNAstructureUI.windows.DuplexFoldWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20160714L
- Class ur_rna.RNAstructureUI.windows.DynalignFoldWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.DynalignRefoldWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.Efn2Window extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.FoldDoubleWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.FoldSingleWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.FoldSuboptimalWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.InternalWindow extends javax.swing.JInternalFrame implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - mainFrame
```
AppMainFrame mainFrame
```
    - desktop
```
javax.swing.JDesktopPane desktop
```
    - disableClose
```
boolean disableClose
```
    - log
```
AppLog log
```
    - backend
```
RNAstructureBackendCalculator backend
```
      The back end calculator that's linked to this window.
    - customMenus
```
MenuList customMenus
```
      Any custom menus that are associated to this window are added to the customMenus MenuList.
    - warnings
```
java.util.HashSet<E> warnings
```
    - frameListener
```
javax.swing.event.InternalFrameListener frameListener
```
    - changeListener
```
java.beans.VetoableChangeListener changeListener
```
- Class ur_rna.RNAstructureUI.windows.MaxExpectWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.ModuleWindow extends InternalWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - self
```
ModuleWindow self
```
    - constraints
```
java.awt.GridBagConstraints constraints
```
      The GridBagConstraints for this window.
    - layout
```
java.awt.GridBagLayout layout
```
      The layout for this window.
    - isRNA
```
boolean isRNA
```
      A boolean, true if the calculation handles RNA, false if not.
    - progressIndicator
```
java.awt.Component progressIndicator
```
      The progress bar dialog for this window.
    - mainCalcThread
```
java.lang.Thread mainCalcThread
```
    - startButton
```
javax.swing.JButton startButton
```
    - calcCancelListener
```
java.awt.event.ActionListener calcCancelListener
```
    - calcCompleted
```
long calcCompleted
```
    - calcProgressListener
```
java.awt.event.ActionListener calcProgressListener
```
    - lastUpdate
```
long lastUpdate
```
    - calcCanceled
```
boolean calcCanceled
```
    - enabledState
```
java.util.HashMap<K,V> enabledState
```
- Class ur_rna.RNAstructureUI.windows.MultilignWindow extends MultiWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.MultiWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - columnWidth
```
int columnWidth
```
      The width of each column of the window (input controls in column 1, sequence set in column 2).
    - imageDialogs
```
java.util.ArrayList<E> imageDialogs
```
      The list of drawing windows shown after the calculation is done.
    - options
```
javax.swing.Box options
```
      The box that holds a particular window's unique options.
    - scroll
```
ScrollerPane scroll
```
      The scroll pane holding the sequence set.
- Class ur_rna.RNAstructureUI.windows.OligoScreenWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.OligoWalkWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - isInputWindow
```
boolean isInputWindow
```
      A boolean that tells whether this window is an input window or not.
    - panelInput
```
javax.swing.JPanel panelInput
```
    - panelResults
```
javax.swing.JPanel panelResults
```
      The box that holds the results.
- Class ur_rna.RNAstructureUI.windows.OligoWalkWindow.OligoSelectionDialog extends ValueSelectionDialog implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.OligoWalkWindow.SpinnerPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - spinner
```
javax.swing.JSpinner spinner
```
      The spinner in this panel.
- Class ur_rna.RNAstructureUI.windows.OligoWalkWindow.StringComboBox extends javax.swing.JComboBox implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.PartitionDoubleWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.PartitionSingleWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.PredictBimolStructureWindow extends PredictWindowBase implements Serializable
  
  serialVersionUID:
  
  20160122L
  - Serialized Fields
    - contentPanel
```
javax.swing.JPanel contentPanel
```
    - txtSeqFile1
```
javax.swing.JTextField txtSeqFile1
```
    - tabControls
```
javax.swing.JTabbedPane tabControls
```
    - spnMaxEnergyDiff
```
javax.swing.JSpinner spnMaxEnergyDiff
```
    - spnWindowSize
```
javax.swing.JSpinner spnWindowSize
```
    - spnMaxStructs
```
javax.swing.JSpinner spnMaxStructs
```
    - txtConFile1
```
javax.swing.JTextField txtConFile1
```
    - btnStartCalc
```
javax.swing.JButton btnStartCalc
```
    - txtOutputFile1
```
javax.swing.JTextField txtOutputFile1
```
    - txtOutputFile2
```
javax.swing.JTextField txtOutputFile2
```
    - btnResetOptions
```
javax.swing.JButton btnResetOptions
```
    - lblOptionWarning
```
javax.swing.JLabel lblOptionWarning
```
    - btnCancelTask
```
javax.swing.JButton btnCancelTask
```
    - prgTaskProgress
```
javax.swing.JProgressBar prgTaskProgress
```
    - lblTaskStatus
```
javax.swing.JLabel lblTaskStatus
```
    - pnlTaskStatus
```
javax.swing.JPanel pnlTaskStatus
```
    - chkShowDescription
```
javax.swing.JCheckBox chkShowDescription
```
    - lblToolDescription
```
javax.swing.JLabel lblToolDescription
```
    - txtSeqFile2
```
javax.swing.JTextField txtSeqFile2
```
    - txtConFile2
```
javax.swing.JTextField txtConFile2
```
    - pnlOutput
```
javax.swing.JPanel pnlOutput
```
    - pnlSequences
```
javax.swing.JPanel pnlSequences
```
    - pnlOptions
```
javax.swing.JPanel pnlOptions
```
    - pnlConstraints
```
javax.swing.JPanel pnlConstraints
```
    - btnResetAll
```
javax.swing.JButton btnResetAll
```
    - lblProgressPercent
```
javax.swing.JLabel lblProgressPercent
```
    - optRNA
```
javax.swing.JRadioButton optRNA
```
    - optDNA
```
javax.swing.JRadioButton optDNA
```
    - spnMaxLoopSize
```
javax.swing.JSpinner spnMaxLoopSize
```
    - spnTemperature
```
javax.swing.JSpinner spnTemperature
```
    - defaultOptionValues
```
java.util.HashMap<K,V> defaultOptionValues
```
    - optionsControls
```
java.util.ArrayList<E> optionsControls
```
    - settingsControls
```
java.util.ArrayList<E> settingsControls
```
    - settingsNodeName
```
java.lang.String settingsNodeName
```
    - lastSeqFile1
```
java.lang.String lastSeqFile1
```
    - lastOutFile1
```
java.lang.String lastOutFile1
```
    - lastSeqFile2
```
java.lang.String lastSeqFile2
```
    - lastOutFile2
```
java.lang.String lastOutFile2
```
- Class ur_rna.RNAstructureUI.windows.PredictionResultsWindow extends InternalWindow implements Serializable
  - Serialized Fields
    - pnlFiles
```
javax.swing.JPanel pnlFiles
```
    - lblResults
```
javax.swing.JLabel lblResults
```
    - btnClose
```
javax.swing.JButton btnClose
```
    - pnlDrawings
```
javax.swing.JPanel pnlDrawings
```
    - pnlContent
```
javax.swing.JPanel pnlContent
```
    - lblFile
```
javax.swing.JLabel lblFile
```
    - btnShowAbbreviations
```
javax.swing.JButton btnShowAbbreviations
```
    - pnlClient
```
javax.swing.JPanel pnlClient
```
    - plotResults
```
java.util.HashMap<K,V> plotResults
```
    - fileCount
```
int fileCount
```
    - plotRow
```
int plotRow
```
    - plotCol
```
int plotCol
```
    - headerFont
```
java.awt.Font headerFont
```
- Class ur_rna.RNAstructureUI.windows.PredictMultiStructureWindow extends PredictWindowBase implements Serializable
  
  serialVersionUID:
  
  20160122L
  - Serialized Fields
    - contentPanel
```
javax.swing.JPanel contentPanel
```
    - tabControls
```
javax.swing.JTabbedPane tabControls
```
    - spnTemperature
```
javax.swing.JSpinner spnTemperature
```
    - btnStartCalc
```
javax.swing.JButton btnStartCalc
```
    - txtOutputFile
```
javax.swing.JTextField txtOutputFile
```
    - btnResetOptions
```
javax.swing.JButton btnResetOptions
```
    - lblOptionWarning
```
javax.swing.JLabel lblOptionWarning
```
    - btnCancelTask
```
javax.swing.JButton btnCancelTask
```
    - prgTaskProgress
```
javax.swing.JProgressBar prgTaskProgress
```
    - lblTaskStatus
```
javax.swing.JLabel lblTaskStatus
```
    - pnlTaskStatus
```
javax.swing.JPanel pnlTaskStatus
```
    - chkShowDescription
```
javax.swing.JCheckBox chkShowDescription
```
    - lblToolDescription
```
javax.swing.JLabel lblToolDescription
```
    - cmbTurboMode
```
javax.swing.JComboBox<E> cmbTurboMode
```
    - pnlOutput
```
javax.swing.JPanel pnlOutput
```
    - pnlSequences
```
javax.swing.JPanel pnlSequences
```
    - pnlOptions
```
javax.swing.JPanel pnlOptions
```
    - pnlTurboOptions
```
javax.swing.JPanel pnlTurboOptions
```
    - btnResetAll
```
javax.swing.JButton btnResetAll
```
    - btnResetTurboOptions
```
javax.swing.JButton btnResetTurboOptions
```
    - lstSeqs
```
javax.swing.JList<E> lstSeqs
```
    - spnTurboGamma
```
javax.swing.JSpinner spnTurboGamma
```
    - spnTurboIterations
```
javax.swing.JSpinner spnTurboIterations
```
    - spnTurboMaxEnergyDiff
```
javax.swing.JSpinner spnTurboMaxEnergyDiff
```
    - spnTurboWindowSize
```
javax.swing.JSpinner spnTurboWindowSize
```
    - spnTurboMEAGamma
```
javax.swing.JSpinner spnTurboMEAGamma
```
    - spnTurboThreshold
```
javax.swing.JSpinner spnTurboThreshold
```
    - spnTurboMinHelix
```
javax.swing.JSpinner spnTurboMinHelix
```
    - spnTurboPKIterations
```
javax.swing.JSpinner spnTurboPKIterations
```
    - spnMultiIterations
```
javax.swing.JSpinner spnMultiIterations
```
    - spnMultiDsvChange
```
javax.swing.JSpinner spnMultiDsvChange
```
    - spnMultiGapPenalty
```
javax.swing.JSpinner spnMultiGapPenalty
```
    - spnMultiAlnSize
```
javax.swing.JSpinner spnMultiAlnSize
```
    - spnMultiWindowSize
```
javax.swing.JSpinner spnMultiWindowSize
```
    - spnMultiMaxStructures
```
javax.swing.JSpinner spnMultiMaxStructures
```
    - spnMultiMaxEnergyDiff
```
javax.swing.JSpinner spnMultiMaxEnergyDiff
```
    - chkAllowBaseInserts
```
javax.swing.JCheckBox chkAllowBaseInserts
```
    - pnlMultiOptions
```
javax.swing.JPanel pnlMultiOptions
```
    - btnMoveUp
```
javax.swing.JButton btnMoveUp
```
    - btnMoveDn
```
javax.swing.JButton btnMoveDn
```
    - btnRemove
```
javax.swing.JButton btnRemove
```
    - btnClearList
```
javax.swing.JButton btnClearList
```
    - spnTurboMaxStructures
```
javax.swing.JSpinner spnTurboMaxStructures
```
    - lblBaseInserts
```
javax.swing.JLabel lblBaseInserts
```
    - btnResetMultiOptions
```
javax.swing.JButton btnResetMultiOptions
```
    - pnlSeqInfo
```
javax.swing.JPanel pnlSeqInfo
```
    - spnMultiMaxPairs
```
javax.swing.JSpinner spnMultiMaxPairs
```
    - lblProgressPercent
```
javax.swing.JLabel lblProgressPercent
```
    - txtSeqFile
```
javax.swing.JTextField txtSeqFile
```
    - txtMSeqFile
```
javax.swing.JTextField txtMSeqFile
```
    - defaultOptionValues
```
java.util.HashMap<K,V> defaultOptionValues
```
    - optionsControls
```
java.util.ArrayList<E> optionsControls
```
    - settingsControls
```
java.util.ArrayList<E> settingsControls
```
    - settingsNodeName
```
java.lang.String settingsNodeName
```
    - _seqInfoUpdating
```
boolean _seqInfoUpdating
```
    - seqList
```
java.util.ArrayList<E> seqList
```
- Class ur_rna.RNAstructureUI.windows.PredictSingleStructureWindow extends PredictWindowBase implements Serializable
  
  serialVersionUID:
  
  20160122L
  - Serialized Fields
    - contentPanel
```
javax.swing.JPanel contentPanel
```
    - txtSeqFile
```
javax.swing.JTextField txtSeqFile
```
    - optSeqFile
```
javax.swing.JRadioButton optSeqFile
```
    - btnBrowseSeq
```
javax.swing.JButton btnBrowseSeq
```
    - txtSequence
```
javax.swing.JTextArea txtSequence
```
    - txtSeqTitle
```
javax.swing.JTextField txtSeqTitle
```
    - optRNA
```
javax.swing.JRadioButton optRNA
```
    - spnTemperature
```
javax.swing.JSpinner spnTemperature
```
    - tabControls
```
javax.swing.JTabbedPane tabControls
```
    - spnMaxLoopSize
```
javax.swing.JSpinner spnMaxLoopSize
```
    - spnMaxEnergyDiff
```
javax.swing.JSpinner spnMaxEnergyDiff
```
    - spnMinHelixLen
```
javax.swing.JSpinner spnMinHelixLen
```
    - spnIterations
```
javax.swing.JSpinner spnIterations
```
    - spnGamma
```
javax.swing.JSpinner spnGamma
```
    - spnWindowSize
```
javax.swing.JSpinner spnWindowSize
```
    - spnMaxStructs
```
javax.swing.JSpinner spnMaxStructs
```
    - optDNA
```
javax.swing.JRadioButton optDNA
```
    - optEnterSeq
```
javax.swing.JRadioButton optEnterSeq
```
    - txtConFile
```
javax.swing.JTextField txtConFile
```
    - btnBrowseCon
```
javax.swing.JButton btnBrowseCon
```
    - txtShapeFile
```
javax.swing.JTextField txtShapeFile
```
    - btnBrowseShape
```
javax.swing.JButton btnBrowseShape
```
    - spnShapeIntercept
```
javax.swing.JSpinner spnShapeIntercept
```
    - spnShapeSlope
```
javax.swing.JSpinner spnShapeSlope
```
    - btnStartCalc
```
javax.swing.JButton btnStartCalc
```
    - txtOutputFile
```
javax.swing.JTextField txtOutputFile
```
    - btnBrowseOutput
```
javax.swing.JButton btnBrowseOutput
```
    - btnRecentSeq
```
javax.swing.JButton btnRecentSeq
```
    - btnRecentOutput
```
javax.swing.JButton btnRecentOutput
```
    - btnRecentCon
```
javax.swing.JButton btnRecentCon
```
    - btnRecentShape
```
javax.swing.JButton btnRecentShape
```
    - btnResetOptions
```
javax.swing.JButton btnResetOptions
```
    - lblOptionWarning
```
javax.swing.JLabel lblOptionWarning
```
    - scrlSequence
```
javax.swing.JScrollPane scrlSequence
```
    - btnCancelTask
```
javax.swing.JButton btnCancelTask
```
    - prgTaskProgress
```
javax.swing.JProgressBar prgTaskProgress
```
    - lblTaskStatus
```
javax.swing.JLabel lblTaskStatus
```
    - pnlTaskStatus
```
javax.swing.JPanel pnlTaskStatus
```
    - chkShowDescription
```
javax.swing.JCheckBox chkShowDescription
```
    - lblToolDescription
```
javax.swing.JLabel lblToolDescription
```
    - pnlOutput
```
javax.swing.JPanel pnlOutput
```
    - lblProgressPercent
```
javax.swing.JLabel lblProgressPercent
```
    - defaultOptionValues
```
java.util.HashMap<K,V> defaultOptionValues
```
    - optionsControls
```
java.util.ArrayList<E> optionsControls
```
    - settingsControls
```
java.util.ArrayList<E> settingsControls
```
    - settingsNodeName
```
java.lang.String settingsNodeName
```
    - lastSeqFile
```
java.lang.String lastSeqFile
```
    - lastOutFile
```
java.lang.String lastOutFile
```
- Class ur_rna.RNAstructureUI.windows.PredictTwoStructureWindow extends PredictWindowBase implements Serializable
  
  serialVersionUID:
  
  20160122L
  - Serialized Fields
    - contentPanel
```
javax.swing.JPanel contentPanel
```
    - txtSeqFile1
```
javax.swing.JTextField txtSeqFile1
```
    - tabControls
```
javax.swing.JTabbedPane tabControls
```
    - spnMaxEnergyDiff
```
javax.swing.JSpinner spnMaxEnergyDiff
```
    - spnWindowSize
```
javax.swing.JSpinner spnWindowSize
```
    - spnMaxStructs
```
javax.swing.JSpinner spnMaxStructs
```
    - txtConFile1
```
javax.swing.JTextField txtConFile1
```
    - btnStartCalc
```
javax.swing.JButton btnStartCalc
```
    - txtOutputFile1
```
javax.swing.JTextField txtOutputFile1
```
    - txtOutputFile2
```
javax.swing.JTextField txtOutputFile2
```
    - btnResetOptions
```
javax.swing.JButton btnResetOptions
```
    - lblOptionWarning
```
javax.swing.JLabel lblOptionWarning
```
    - btnCancelTask
```
javax.swing.JButton btnCancelTask
```
    - prgTaskProgress
```
javax.swing.JProgressBar prgTaskProgress
```
    - lblTaskStatus
```
javax.swing.JLabel lblTaskStatus
```
    - pnlTaskStatus
```
javax.swing.JPanel pnlTaskStatus
```
    - chkShowDescription
```
javax.swing.JCheckBox chkShowDescription
```
    - lblToolDescription
```
javax.swing.JLabel lblToolDescription
```
    - txtSeqFile2
```
javax.swing.JTextField txtSeqFile2
```
    - spnAlnWindowSize
```
javax.swing.JSpinner spnAlnWindowSize
```
    - spnGapPenalty
```
javax.swing.JSpinner spnGapPenalty
```
    - chkBaseInserts
```
javax.swing.JCheckBox chkBaseInserts
```
    - cmbPartsMode
```
javax.swing.JComboBox<E> cmbPartsMode
```
    - lblBaseInserts
```
javax.swing.JLabel lblBaseInserts
```
    - spnStochasticSamples
```
javax.swing.JSpinner spnStochasticSamples
```
    - txtConFile2
```
javax.swing.JTextField txtConFile2
```
    - pnlOutput
```
javax.swing.JPanel pnlOutput
```
    - pnlSequences
```
javax.swing.JPanel pnlSequences
```
    - pnlOptions
```
javax.swing.JPanel pnlOptions
```
    - pnlPartsOptions
```
javax.swing.JPanel pnlPartsOptions
```
    - pnlConstraints
```
javax.swing.JPanel pnlConstraints
```
    - btnResetAll
```
javax.swing.JButton btnResetAll
```
    - btnResetPartsOptions
```
javax.swing.JButton btnResetPartsOptions
```
    - lblProgressPercent
```
javax.swing.JLabel lblProgressPercent
```
    - defaultOptionValues
```
java.util.HashMap<K,V> defaultOptionValues
```
    - optionsControls
```
java.util.ArrayList<E> optionsControls
```
    - settingsControls
```
java.util.ArrayList<E> settingsControls
```
    - settingsNodeName
```
java.lang.String settingsNodeName
```
    - lastSeqFile1
```
java.lang.String lastSeqFile1
```
    - lastOutFile1
```
java.lang.String lastOutFile1
```
    - lastSeqFile2
```
java.lang.String lastSeqFile2
```
    - lastOutFile2
```
java.lang.String lastOutFile2
```
- Class ur_rna.RNAstructureUI.windows.PredictWindowBase extends InternalWindow implements Serializable
  - Serialized Fields
    - uiUpdateTimer
```
javax.swing.Timer uiUpdateTimer
```
    - pnlClient
```
javax.swing.JPanel pnlClient
```
    - pnlContent
```
javax.swing.JPanel pnlContent
```
    - fileFields
```
java.util.HashMap<K,V> fileFields
```
    - fields
```
java.util.HashMap<K,V> fields
```
    - runningTask
```
PredictWindowBase.BackgroundTask runningTask
```
    - numberFormatter
```
java.text.DecimalFormat numberFormatter
```
- Class ur_rna.RNAstructureUI.windows.ProbKnotWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.PseudoknotWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.RefoldWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.SequenceDisplayWindow extends InternalWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - defaultFont
```
java.awt.Font defaultFont
```
    - titleBox
```
javax.swing.JTextArea titleBox
```
      The array of text areas in this window.
    - commentBox
```
javax.swing.JTextArea commentBox
```
    - sequenceBox
```
javax.swing.JTextPane sequenceBox
```
    - sequenceDoc
```
javax.swing.text.StyledDocument sequenceDoc
```
    - edited
```
boolean edited
```
      A boolean, true if the sequence has been edited, false if not.
    - userAcceptedInvalidSequence
```
boolean userAcceptedInvalidSequence
```
    - speakPosition
```
int speakPosition
```
      The position at which speaking is occurring.
    - speakButton
```
javax.swing.JButton speakButton
```
      The button which can be clicked to start or stop speaking.
    - speakWhileTyping
```
boolean speakWhileTyping
```
      A boolean, true if speaking while typing is active, false if not.
    - speakingFullSequence
```
boolean speakingFullSequence
```
    - speakTimer
```
javax.swing.Timer speakTimer
```
      The timer that aids in speaking nucleotides in rhythm.
    - styleTimer
```
javax.swing.Timer styleTimer
```
      The timer that updates syntax highlighting
    - styleStandardBase
```
javax.swing.text.Style styleStandardBase
```
    - styleInvalidChar
```
javax.swing.text.Style styleInvalidChar
```
    - styleUnpairedBase
```
javax.swing.text.Style styleUnpairedBase
```
    - styleUnspecifiedBase
```
javax.swing.text.Style styleUnspecifiedBase
```
    - styleIgnoredChar
```
javax.swing.text.Style styleIgnoredChar
```
    - _speakPlayer
```
SequenceDisplayWindow.SoundPlayer _speakPlayer
```
    - _speakStreams
```
java.util.HashMap<K,V> _speakStreams
```
    - invalidSoundClip
```
java.io.InputStream invalidSoundClip
```
    - speakMenu
```
SequenceDisplayWindow.SpeakMenu speakMenu
```
- Class ur_rna.RNAstructureUI.windows.StochasticWindow extends ModuleWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.RNAstructureUI.windows.TurboFoldWindow extends MultiWindow implements Serializable
  
  serialVersionUID:
  
  20120802L
  - Serialized Fields
    - cards
```
java.awt.CardLayout cards
```
      The layout that holds the dynamic options applicable to a mode.
    - specificPanel
```
javax.swing.JPanel specificPanel
```
      The panel that holds the dynamic options applicable to a mode.

Package ur_rna.StructureEditor

Class ur_rna.StructureEditor.MainFrame extends MdiParentFrame implements Serializable

Serialized Fields

log
```
AppLog log
```
menuBar
```
javax.swing.JMenuBar menuBar
```
toolBar
```
javax.swing.JToolBar toolBar
```
statusBar
```
javax.swing.JPanel statusBar
```
infoLabel
```
javax.swing.JLabel infoLabel
```
desktop
```
javax.swing.JDesktopPane desktop
```
program
```
Program program
```
recentFiles
```
RecentFileList recentFiles
```
recentFilesMenu
```
RecentFileMenuManager recentFilesMenu
```
dashboard
```
DashboardFrame dashboard
```
menuMerger
```
MergeManager menuMerger
```
testIconsTimer
```
javax.swing.Timer testIconsTimer
```
originalToolbar
```
java.awt.Component[] originalToolbar
```

Package ur_rna.StructureEditor.menus
- Class ur_rna.StructureEditor.menus.DrawingEditMenu extends MergeMenu implements Serializable
  - Serialized Fields
    - owner
```
DrawWindow owner
```
- Class ur_rna.StructureEditor.menus.DrawingFileMenu extends MergeMenu implements Serializable
  - Serialized Fields
    - owner
```
DrawWindow owner
```
- Class ur_rna.StructureEditor.menus.DrawingFormatMenu extends MergeMenu implements Serializable
  - Serialized Fields
    - owner
```
DrawWindow owner
```
- Class ur_rna.StructureEditor.menus.DrawingViewMenu extends MergeMenu implements Serializable
  - Serialized Fields
    - owner
```
DrawWindow owner
```
- Class ur_rna.StructureEditor.menus.FileMenu extends MainMenu implements Serializable
  - Serialized Fields
    - recent
```
MergeMenu recent
```
- Class ur_rna.StructureEditor.menus.MainMenu extends MergeMenu implements Serializable
  
  serialVersionUID:
  
  20160315L
- Class ur_rna.StructureEditor.menus.SettingsMenu extends MainMenu implements Serializable
  - Serialized Fields
    - settings
```
Settings settings
```
    - updatingSettings
```
boolean updatingSettings
```
- Class ur_rna.StructureEditor.menus.WindowsMenu extends MainMenu implements Serializable
  - Serialized Fields
    - nextWindow
```
UiAction nextWindow
```
    - prevWindow
```
UiAction prevWindow
```
    - desktop
```
javax.swing.JDesktopPane desktop
```
    - popup
```
javax.swing.JPopupMenu popup
```
    - windowFilter
```
java.util.function.Predicate<T> windowFilter
```
    - noWindowsItem
```
javax.swing.JMenuItem noWindowsItem
```
Package ur_rna.StructureEditor.models
- Class ur_rna.StructureEditor.models.RnaSceneGroup extends java.util.ArrayList<RnaScene> implements Serializable
  - Serialized Fields
    - filePath
```
java.lang.String filePath
```
    - originalType
```
FileType originalType
```
    - title
```
java.lang.String title
```
    - settings
```
DrawSettings settings
```
Package ur_rna.StructureEditor.ui
- Class ur_rna.StructureEditor.ui.DrawPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - scale
```
float scale
```
    - offset
```
java.awt.geom.Point2D.Float offset
```
    - tr
```
java.awt.geom.AffineTransform tr
```
    - MARGIN
```
int MARGIN
```
    - view
```
View2D view
```
    - drawnView
```
View2D drawnView
```
    - renderer
```
SceneRenderer renderer
```
    - viewChanged
```
EventSource.NoArg viewChanged
```
    - scrollTargetModel
```
java.awt.geom.Point2D scrollTargetModel
```
    - scrollTargetView
```
java.awt.Point scrollTargetView
```
    - prevBounds
```
java.awt.Rectangle prevBounds
```
    - IDENTITY_VIEW
```
View2D IDENTITY_VIEW
```
- Class ur_rna.StructureEditor.ui.SliderToolWindow extends ToolWindow implements Serializable
  - Serialized Fields
    - slider
```
javax.swing.JSlider slider
```
    - lblValue
```
javax.swing.JLabel lblValue
```
    - btnCancel
```
javax.swing.JButton btnCancel
```
    - btnAccept
```
javax.swing.JButton btnAccept
```
    - txtValue
```
javax.swing.JTextField txtValue
```
    - lblPrompt
```
javax.swing.JLabel lblPrompt
```
- Class ur_rna.StructureEditor.ui.ToolWindow extends javax.swing.JInternalFrame implements Serializable

Package ur_rna.StructureEditor.windows

Class ur_rna.StructureEditor.windows.AboutWindow extends ChildFrame implements Serializable

Serialized Fields

mainPanel
```
javax.swing.JPanel mainPanel
```
btnClose
```
javax.swing.JButton btnClose
```
lblWebsite
```
javax.swing.JLabel lblWebsite
```
lblHelp
```
javax.swing.JLabel lblHelp
```
lblLogo
```
javax.swing.JLabel lblLogo
```
pnlLogo
```
javax.swing.JPanel pnlLogo
```
lblVersion
```
javax.swing.JLabel lblVersion
```
lblCopyright
```
javax.swing.JLabel lblCopyright
```
lblProgramTitle
```
javax.swing.JLabel lblProgramTitle
```
lblFeedback
```
javax.swing.JLabel lblFeedback
```

Class ur_rna.StructureEditor.windows.ChildFrame extends MdiChildFrame implements Serializable

Class ur_rna.StructureEditor.windows.ColorizeDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

pnlMain
```
javax.swing.JPanel pnlMain
```
btnClose
```
javax.swing.JButton btnClose
```
btnApplyText
```
javax.swing.JButton btnApplyText
```

optStructuresAll

javax.swing.JRadioButton optStructuresAll

tabs
```
javax.swing.JTabbedPane tabs
```
txtBase
```
javax.swing.JTextArea txtBase
```
chkUse
```
javax.swing.JCheckBox chkUse
```

optBasesSelected

javax.swing.JRadioButton optBasesSelected

btnChooseColor
```
javax.swing.JButton btnChooseColor
```
txtColor
```
javax.swing.JTextArea txtColor
```
btnAddSymbolRule
```
javax.swing.JButton btnAddSymbolRule
```
pnlSymbolColors
```
javax.swing.JPanel pnlSymbolColors
```
lblColor
```
javax.swing.JLabel lblColor
```

optStructuresCurrent

javax.swing.JRadioButton optStructuresCurrent

optBasesAll
```
javax.swing.JRadioButton optBasesAll
```
btnResetSymbolRules
```
javax.swing.JButton btnResetSymbolRules
```
txtSingleColor
```
javax.swing.JTextField txtSingleColor
```
lblSingleColor
```
javax.swing.JLabel lblSingleColor
```
btnSingleColor
```
javax.swing.JButton btnSingleColor
```
chkIgnoreCase
```
javax.swing.JCheckBox chkIgnoreCase
```
txtModData
```
javax.swing.JTextArea txtModData
```
btnLoadModFile
```
javax.swing.JButton btnLoadModFile
```
btnHelpMod
```
javax.swing.JButton btnHelpMod
```
txtValueLimit
```
javax.swing.JTextField txtValueLimit
```
txtValueColor
```
javax.swing.JTextField txtValueColor
```
lblValueColor
```
javax.swing.JLabel lblValueColor
```
btnResetValueRules
```
javax.swing.JButton btnResetValueRules
```
btnValueChooseColor
```
javax.swing.JButton btnValueChooseColor
```
pnlValueColors
```
javax.swing.JPanel pnlValueColors
```
btnAddValueRule
```
javax.swing.JButton btnAddValueRule
```
btnRemValueRule
```
javax.swing.JButton btnRemValueRule
```
btnClearValueText
```
javax.swing.JButton btnClearValueText
```

cmbValueComparison

javax.swing.JComboBox<E> cmbValueComparison

lblValueColorHeader
```
javax.swing.JLabel lblValueColorHeader
```
txtProbData
```
javax.swing.JTextArea txtProbData
```
lblProbColorHeader
```
javax.swing.JLabel lblProbColorHeader
```
pnlProbColors
```
javax.swing.JPanel pnlProbColors
```
btnAddProbRule
```
javax.swing.JButton btnAddProbRule
```
btnRemProbRule
```
javax.swing.JButton btnRemProbRule
```
btnResetProbRules
```
javax.swing.JButton btnResetProbRules
```
btnLoadProbFile
```
javax.swing.JButton btnLoadProbFile
```
btnClearProbText
```
javax.swing.JButton btnClearProbText
```
btnHelpProb
```
javax.swing.JButton btnHelpProb
```
btnRemSymbolRule
```
javax.swing.JButton btnRemSymbolRule
```

cmbProbComparison

javax.swing.JComboBox<E> cmbProbComparison

btnApplyFill
```
javax.swing.JButton btnApplyFill
```
btnApplyOutline
```
javax.swing.JButton btnApplyOutline
```
btnApplyBond
```
javax.swing.JButton btnApplyBond
```
btnResetText
```
javax.swing.JButton btnResetText
```
btnResetFill
```
javax.swing.JButton btnResetFill
```
btnResetOutline
```
javax.swing.JButton btnResetOutline
```
btnResetBond
```
javax.swing.JButton btnResetBond
```
btnResetAll
```
javax.swing.JButton btnResetAll
```
updateTimer
```
javax.swing.Timer updateTimer
```
docListener
```
TextDocListener docListener
```
prefs
```
java.util.prefs.Preferences prefs
```

singleColor

ColorizeDialog.SimpleColorControl singleColor

lastValueDataPath
```
java.lang.String lastValueDataPath
```
lastProbDataPath
```
java.lang.String lastProbDataPath
```
buttonFont
```
java.awt.Font buttonFont
```
buttonFontBold
```
java.awt.Font buttonFontBold
```
symbolColorRules
```
java.util.ArrayList<E> symbolColorRules
```
valueColorRules
```
java.util.ArrayList<E> valueColorRules
```
probColorRules
```
java.util.ArrayList<E> probColorRules
```
_lastColorEffect
```
java.lang.String _lastColorEffect
```

Class ur_rna.StructureEditor.windows.DashboardFrame extends javax.swing.JInternalFrame implements Serializable

Serialized Fields

btnWebsite
```
javax.swing.JButton btnWebsite
```
btnHelp
```
javax.swing.JButton btnHelp
```
lstRecent
```
javax.swing.JList<E> lstRecent
```
pnlMain
```
javax.swing.JPanel pnlMain
```
lstExamples
```
javax.swing.JList<E> lstExamples
```
btnCleanupRecent
```
javax.swing.JButton btnCleanupRecent
```
btnClearRecent
```
javax.swing.JButton btnClearRecent
```

chkDisableDashboard

javax.swing.JCheckBox chkDisableDashboard

btnOpenFile
```
javax.swing.JButton btnOpenFile
```
btnFeedback
```
javax.swing.JButton btnFeedback
```
updatingSettings
```
boolean updatingSettings
```

ancestorResizeListener

java.awt.event.HierarchyBoundsAdapter ancestorResizeListener

Class ur_rna.StructureEditor.windows.DrawWindow extends ChildFrame implements Serializable

Serialized Fields

scrollPane
```
javax.swing.JScrollPane scrollPane
```
panel
```
DrawPanel panel
```
controller
```
RnaDrawController controller
```
menus
```
java.util.List<E> menus
```
structureMenu
```
MergeMenu structureMenu
```
formatBondType
```
MergeMenu formatBondType
```
structureList
```
ButtonGroupList structureList
```
toolButtons
```
DrawWindow.ToolButtonList toolButtons
```
scenes
```
RnaSceneGroup scenes
```
currentScene
```
RnaScene currentScene
```
sceneInfo
```
DrawWindow.SceneInfo[] sceneInfo
```
layout
```
NucLayout layout
```

structureMenuToolbarButton

javax.swing.JButton structureMenuToolbarButton

btnSelModeNuc

javax.swing.AbstractButton btnSelModeNuc

btnSelModeHelix

javax.swing.AbstractButton btnSelModeHelix

btnSelModeBranch

javax.swing.AbstractButton btnSelModeBranch

drawSettings
```
DrawSettings drawSettings
```
asyncUpdateTimer
```
javax.swing.Timer asyncUpdateTimer
```
pnlTaskProgress
```
javax.swing.JPanel pnlTaskProgress
```
lblTaskStatus
```
javax.swing.JLabel lblTaskStatus
```

prgTaskProgress

javax.swing.JProgressBar prgTaskProgress

lblTaskProgress
```
javax.swing.JLabel lblTaskProgress
```
_asyncTask
```
RnaFileIO.AsyncTask<TResult> _asyncTask
```
selType
```
RnaDrawController.SelectionType selType
```
actionSave
```
UiAction actionSave
```
actionSaveAs
```
UiAction actionSaveAs
```
actionExport
```
UiAction actionExport
```
actionClose
```
UiAction actionClose
```
actionEditUndo
```
UiAction actionEditUndo
```
actionEditRedo
```
UiAction actionEditRedo
```
actionSelectAll
```
UiAction actionSelectAll
```
actionSelectExpand
```
UiAction actionSelectExpand
```
actionSelectNuc
```
UiAction actionSelectNuc
```
actionSelectHelix
```
UiAction actionSelectHelix
```
actionSelectBranch
```
UiAction actionSelectBranch
```
actionZoomAuto
```
UiAction actionZoomAuto
```
actionZoomIn
```
UiAction actionZoomIn
```
actionZoomOut
```
UiAction actionZoomOut
```
actionZoomReset
```
UiAction actionZoomReset
```
actionChooseStructure
```
UiAction actionChooseStructure
```
actionNextStructure
```
UiAction actionNextStructure
```
actionPrevStructure
```
UiAction actionPrevStructure
```
actionShowEnergy
```
UiAction actionShowEnergy
```
actionIdentifyPseudoKnots
```
UiAction actionIdentifyPseudoKnots
```
actionSetBondTypePseduo
```
UiAction actionSetBondTypePseduo
```
actionSetBondTypeNormal
```
UiAction actionSetBondTypeNormal
```
actionSetBondTypeForced
```
UiAction actionSetBondTypeForced
```
actionSetBondTypeBanned
```
UiAction actionSetBondTypeBanned
```
actionSetBondTypeSpecial
```
UiAction actionSetBondTypeSpecial
```
actionBreakBonds
```
UiAction actionBreakBonds
```
actionSplitStrand
```
UiAction actionSplitStrand
```
actionJoinStrands
```
UiAction actionJoinStrands
```
actionRemoveNucs
```
UiAction actionRemoveNucs
```
actionInsertNucs
```
UiAction actionInsertNucs
```
actionEditNucs
```
UiAction actionEditNucs
```
actionFold
```
UiAction actionFold
```
actionFormatColor
```
UiAction actionFormatColor
```
actionFormatRemoveColor
```
UiAction actionFormatRemoveColor
```
actionFormatRemoveAllColor
```
UiAction actionFormatRemoveAllColor
```
actionColorHelices
```
UiAction actionColorHelices
```
actionRedraw
```
UiAction actionRedraw
```
actionRedrawCirc
```
UiAction actionRedrawCirc
```
actionRedrawLinear
```
UiAction actionRedrawLinear
```
actionFlipScene
```
UiAction actionFlipScene
```
actionLocalRedraw
```
UiAction actionLocalRedraw
```
testAction
```
UiAction testAction
```

Class ur_rna.StructureEditor.windows.DrawWindow.ToolButtonList extends java.util.ArrayList<java.awt.Component> implements Serializable
- Serialized Fields
  - mergePos
```
int mergePos
```
Class ur_rna.StructureEditor.windows.InsertBasesDialog extends javax.swing.JPanel implements Serializable
- Serialized Fields
  - txtBases
```
javax.swing.JTextArea txtBases
```
  - cmbRelative
```
javax.swing.JComboBox<E> cmbRelative
```
  - pnlMain
```
javax.swing.JPanel pnlMain
```

Class ur_rna.StructureEditor.windows.NewFileWindow extends ChildFrame implements Serializable

Serialized Fields

txtSequence
```
javax.swing.JTextPane txtSequence
```
btnCancel
```
javax.swing.JButton btnCancel
```
btnOK
```
javax.swing.JButton btnOK
```
txtStructure
```
javax.swing.JTextPane txtStructure
```
txtTitle
```
javax.swing.JTextField txtTitle
```
pnlMain
```
javax.swing.JPanel pnlMain
```
chkWrapSequence
```
javax.swing.JCheckBox chkWrapSequence
```
chkWrapStructure
```
javax.swing.JCheckBox chkWrapStructure
```
btnStructureHelp
```
javax.swing.JButton btnStructureHelp
```
btnSequenceHelp
```
javax.swing.JButton btnSequenceHelp
```
txtDebug
```
javax.swing.JTextPane txtDebug
```
lblLocation
```
javax.swing.JLabel lblLocation
```
docSeq
```
javax.swing.text.StyledDocument docSeq
```
docStr
```
javax.swing.text.StyledDocument docStr
```
tmrUpdate
```
javax.swing.Timer tmrUpdate
```
defaultFont
```
java.awt.Font defaultFont
```
seqLookup
```
int[] seqLookup
```
revSeqLookup
```
int[] revSeqLookup
```
seqLen
```
int seqLen
```
structure
```
java.util.ArrayList<E> structure
```

selectedStructItem

NewFileWindow.StructItem selectedStructItem

selectedPair
```
int selectedPair
```
selectedBase
```
int selectedBase
```
selectedHelixLen
```
int selectedHelixLen
```
seqText
```
java.lang.String seqText
```
strText
```
java.lang.String strText
```
undoSeq
```
javax.swing.undo.UndoManager undoSeq
```
undoStr
```
javax.swing.undo.UndoManager undoStr
```
docUpdateListener
```
TextDocListener docUpdateListener
```
_lastActivePane
```
javax.swing.JTextPane _lastActivePane
```
styleSeqDefault
```
javax.swing.text.Style styleSeqDefault
```
styleStrDefault
```
javax.swing.text.Style styleStrDefault
```
styleStrInvalid
```
javax.swing.text.Style styleStrInvalid
```
styleSeqPaired
```
javax.swing.text.Style styleSeqPaired
```
styleStrSel
```
javax.swing.text.Style styleStrSel
```

Package ur_rna.Utilities
- Class ur_rna.Utilities.ExtensibleException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - updatedMessage
```
java.lang.String updatedMessage
```
    - data
```
java.util.HashMap<K,V> data
```
    - readOnlyData
```
java.util.Map<K,V> readOnlyData
```
- Class ur_rna.Utilities.FormatterException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class ur_rna.Utilities.JniLoader.NativeLibLoadError extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class ur_rna.Utilities.KeyAlreadyExistsException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - existingKey
```
java.lang.Object existingKey
```
    - existingValue
```
java.lang.Object existingValue
```
- Class ur_rna.Utilities.OSInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20120802L
- Class ur_rna.Utilities.SimpleDataSerializer.SSONList extends java.util.ArrayList<java.lang.Object> implements Serializable
- Class ur_rna.Utilities.SimpleDataSerializer.SSONMap extends java.util.LinkedHashMap<java.lang.String,java.lang.Object> implements Serializable
- Class ur_rna.Utilities.StringBuilderEx extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  42L
  - Serialized Fields
    - _sb
```
java.lang.StringBuilder _sb
```
- Class ur_rna.Utilities.SyntaxErrorException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - errorDescription
```
java.lang.String errorDescription
```
      A brief description or name of the error, e.g. "Invalid number format" or "Unterminated string constant".
    - offendingText
```
java.lang.String offendingText
```
      The part of the subject string most closely associated with the error.
    - location
```
java.lang.String location
```
      Information about the location of the offending segment in the subject, so the user can find it easily. If set to any value other than null, this overrides the default return value of SyntaxErrorException.getLocation().
    - lineOffset
```
int lineOffset
```
      The estimated line where the syntax error occurred.
    - columnOffset
```
int columnOffset
```
      The estimated column number or character offset of the start of the syntax error.
Package ur_rna.Utilities.geom
- Class ur_rna.Utilities.geom.Ellipses.Circle extends java.awt.geom.Ellipse2D.Float implements Serializable
  - Serialized Fields
    - _radius
```
float _radius
```
    - _center
```
java.awt.geom.Point2D.Float _center
```
- Class ur_rna.Utilities.geom.Matrix3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  20160913L
  - Serialized Fields
    - m00
```
double m00
```
      The matrix element in row 1, column 1.
    - m01
```
double m01
```
      The matrix element in row 1, column 2.
    - m02
```
double m02
```
      The matrix element in row 1, column 3.
    - m10
```
double m10
```
      The matrix element in row 2, column 1.
    - m11
```
double m11
```
      The matrix element in row 2, column 2.
    - m12
```
double m12
```
      The matrix element in row 2, column 3.
    - m20
```
double m20
```
      The matrix element in row 3, column 1.
    - m21
```
double m21
```
      The matrix element in row 3, column 2.
    - m22
```
double m22
```
      The matrix element in row 3, column 3.
- Class ur_rna.Utilities.geom.Vec2D extends java.awt.geom.Point2D.Double implements Serializable
Package ur_rna.Utilities.swing
- Class ur_rna.Utilities.swing.ButtonGroupList extends javax.swing.ButtonGroup implements Serializable
- Class ur_rna.Utilities.swing.CheckMergeItem extends javax.swing.JCheckBoxMenuItem implements Serializable
  - Serialized Fields
    - pos
```
int pos
```
    - tag
```
java.lang.Object tag
```
      allows storage of user-defined additional information
- Class ur_rna.Utilities.swing.FileDialog extends javax.swing.JFileChooser implements Serializable
  - Serialized Fields
    - fileShouldExist
```
boolean fileShouldExist
```
    - isCurDirSet
```
boolean isCurDirSet
```
    - context
```
java.lang.String context
```
    - modifyDir
```
boolean modifyDir
```
    - owner
```
java.awt.Component owner
```
- Class ur_rna.Utilities.swing.FormValidationException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  20170810L
  - Serialized Fields
    - control
```
javax.swing.JComponent control
```
- Class ur_rna.Utilities.swing.JActionLabel extends javax.swing.JLabel implements Serializable
  - Serialized Fields
    - link
```
java.lang.String link
```
    - linkURI
```
java.net.URI linkURI
```
    - action
```
javax.swing.Action action
```
    - actionCommand
```
java.lang.String actionCommand
```
    - listener
```
java.awt.event.ActionListener listener
```
    - listeners
```
java.util.List<E> listeners
```
- Class ur_rna.Utilities.swing.JFlatButton extends javax.swing.JButton implements Serializable
  - Serialized Fields
    - link
```
java.lang.String link
```
    - linkURI
```
java.net.URI linkURI
```
- Class ur_rna.Utilities.swing.MdiChildFrame extends javax.swing.JInternalFrame implements Serializable
  - Serialized Fields
    - parentFrame
```
MdiParentFrame parentFrame
```
- Class ur_rna.Utilities.swing.MdiParentFrame extends javax.swing.JFrame implements Serializable
- Class ur_rna.Utilities.swing.MergeButton extends javax.swing.JButton implements Serializable
  - Serialized Fields
    - mergePos
```
int mergePos
```
- Class ur_rna.Utilities.swing.MergeButton.Separator extends javax.swing.JToolBar.Separator implements Serializable
  - Serialized Fields
    - pos
```
int pos
```
- Class ur_rna.Utilities.swing.MergeItem extends javax.swing.JMenuItem implements Serializable
  - Serialized Fields
    - pos
```
int pos
```
    - tag
```
java.lang.Object tag
```
      allows storage of user-defined additional information
- Class ur_rna.Utilities.swing.MergeItem.Separator extends javax.swing.JPopupMenu.Separator implements Serializable
  - Serialized Fields
    - pos
```
int pos
```
- Class ur_rna.Utilities.swing.MergeMenu extends javax.swing.JMenu implements Serializable
  - Serialized Fields
    - subItemMergePos
```
int subItemMergePos
```
    - mergePos
```
int mergePos
```
- Class ur_rna.Utilities.swing.MergeToggleButton extends javax.swing.JToggleButton implements Serializable
  - Serialized Fields
    - mergePos
```
int mergePos
```
- Class ur_rna.Utilities.swing.UiAction extends javax.swing.AbstractAction implements Serializable
  - Serialized Fields
    - listener
```
java.awt.event.ActionListener listener
```
    - listeners
```
java.util.Set<E> listeners
```
- Class ur_rna.Utilities.swing.WaitDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - message
```
java.lang.String message
```
    - showProgress
```
boolean showProgress
```
    - showCancel
```
boolean showCancel
```
    - progressValue
```
float progressValue
```
    - progressTotal
```
float progressTotal
```
    - cancelListener
```
java.awt.event.ActionListener cancelListener
```
    - canceled
```
boolean canceled
```
    - lblMessage
```
javax.swing.JLabel lblMessage
```
    - prgProgress
```
javax.swing.JProgressBar prgProgress
```
    - btnCancel
```
javax.swing.JButton btnCancel
```
    - closeOnCancel
```
boolean closeOnCancel
```

Serialized Form

Package ur_rna.GUITester

Class ur_rna.GUITester.RuntimeTools.ActionArgumentException extends RuntimeTools.ActionException implements Serializable

Class ur_rna.GUITester.RuntimeTools.ActionException extends ScriptRuntimeException implements Serializable

Class ur_rna.GUITester.RuntimeTools.UnsupportedActionException extends RuntimeTools.ActionException implements Serializable

Class ur_rna.GUITester.ScriptRuntimeException extends ExtensibleException implements Serializable

Serialized Fields

_node

Package ur_rna.GUITester.GuiTools

Class ur_rna.GUITester.GuiTools.GuiItemNotFoundException extends ExtensibleException implements Serializable

Package ur_rna.GUITester.ScriptParser

Class ur_rna.GUITester.ScriptParser.ParseException extends java.lang.Exception implements Serializable

Serialized Fields

currentToken

expectedTokenSequences

tokenImage

Class ur_rna.GUITester.ScriptParser.ParseFormatException extends ParseException implements Serializable

Class ur_rna.GUITester.ScriptParser.Token extends java.lang.Object implements Serializable

Serialized Fields

kind

beginLine

beginColumn

endLine

endColumn

image

next

specialToken

Class ur_rna.GUITester.ScriptParser.TokenMgrError extends java.lang.Error implements Serializable

Serialized Fields

errorCode

Package ur_rna.RNAstructure

Class ur_rna.RNAstructure.RnaBackendException extends java.lang.Exception implements Serializable

Serialized Fields

file

errorCode

Package ur_rna.RNAstructureUI

Class ur_rna.RNAstructureUI.AppMainFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

log

menuBar

toolBar

statusBar

infoLabel

desktop

mainMenus

menuMerger

InfoLabelConsumer

keepToolBarItems

frameListener

Class ur_rna.RNAstructureUI.RNAstructure extends java.lang.Object implements Serializable

Package ur_rna.RNAstructureUI.drawing.dialogs

Class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog extends javax.swing.JInternalFrame implements Serializable

Serialized Fields

customMenus

error

file

label

legendGrid

mainPanel

imgSizeX

imgSizeY

job

preferredDialogWidth

scale

Class ur_rna.RNAstructureUI.drawing.dialogs.ImageDialog.PrintMenu extends MainMenu implements Serializable

Class ur_rna.RNAstructureUI.drawing.dialogs.PlotDialog extends ImageDialog implements Serializable

Serialized Fields

backend

strand

plotLength

Class ur_rna.RNAstructureUI.drawing.dialogs.StructureDialog extends ImageDialog implements Serializable

Serialized Fields

drawOptions

backend

data

hasPairs

number

regex

Package ur_rna.RNAstructureUI.drawing.menus

Class ur_rna.RNAstructureUI.drawing.menus.AnnotationMenu extends MainMenu implements Serializable