# 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