# Serialized Form

## Package RNAstructure_java_drawing.source.dialogs

### Class RNAstructure_java_drawing.source.dialogs.ImageDialog extends JDialog implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### error

    String error

The error message generated while building this panel, if any.

#### file

    String file

The file that is drawn in some way on this panel.

#### label

    JLabel label

The main label that describes the panel.

#### legendGrid

    JPanel legendGrid

The panel that contains the legend grid.

#### mainPanel

    JPanel mainPanel

The main panel that the drawing resides on.

#### maxBoundX

    double maxBoundX

The maximum X bound of the image.

#### maxBoundY

    double maxBoundY

The maximum Y bound of the image.

#### job

    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 RNAstructure_java_drawing.source.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 RNAstructure_java_drawing.source.dialogs.StructureDialog extends ImageDialog implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### backend

    StructureBackend backend

The back end object that reads data for structures.

#### data

    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

    String[] regex

The array of regexes used to pull data about a structure.

## Package RNAstructure_java_drawing.source.menus

### Class RNAstructure_java_drawing.source.menus.AnnotationMenu extends RNAstructureMenu implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### dialog

    StructureDialog dialog

The structure panel connected to this menu.

### Class RNAstructure_java_drawing.source.menus.DotsMenu extends RNAstructureMenu implements Serializable

serialVersionUID:
  20120615L

### Serialized Fields

#### dialog

    PlotDialog dialog

The structure dialog connected to this menu.

### Class RNAstructure_java_drawing.source.menus.PlotMenu extends RNAstructureMenu implements Serializable

serialVersionUID:
  20120615L

### Serialized Fields

#### dialog

    PlotDialog dialog

The plot dialog connected to this menu.

### Class RNAstructure_java_drawing.source.menus.StructureMenu extends RNAstructureMenu implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### dialog

    StructureDialog dialog

The structure dialog connected to this menu.

## Package RNAstructure_java_drawing.source.runners

### Class RNAstructure_java_drawing.source.runners.PlotRunner extends RunnerTemplate implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_drawing.source.runners.StructureRunner extends RunnerTemplate implements Serializable

serialVersionUID:
  20120802L

## Package RNAstructure_java_interface.source.menus

### Class RNAstructure_java_interface.source.menus.ConstraintsMenu extends RolloverMenu 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 RNAstructure_java_interface.source.menus.ConstraintsMenu.NucOrHelixDialog extends ValueSelectionDialog implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.DynamicMenuBar extends JMenuBar implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.FileMenu extends RolloverMenu implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.HelpMenu extends RolloverMenu implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.NucleicAcidMenu extends RolloverMenu implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.RolloverMenu extends RNAstructureMenu implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.menus.RolloverMenu.RolloverListener extends Object implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### rollover

    String rollover

The rollover text for this listener.

## Package RNAstructure_java_interface.source.startup

### Class RNAstructure_java_interface.source.startup.ApplicationRootFrame extends JFrame implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### bar

    JToolBar bar

The main RNAstructure toolbar.

### Class RNAstructure_java_interface.source.startup.RNAstructure extends Object implements Serializable

serialVersionUID:
  20120802L

## Package RNAstructure_java_interface.source.windows

### Class RNAstructure_java_interface.source.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 RNAstructure_java_interface.source.windows.DynalignFoldWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.DynalignRefoldWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.Efn2Window extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.FoldDoubleWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.FoldSingleWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.FoldSuboptimalWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.InternalWindow extends JInternalFrame implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### backend

    RNAstructureBackendCalculator backend

The back end calculator that's linked to this window.

#### dialogHandler

    SimpleDialogHandler dialogHandler

A dialog handler to show any simple dialog messages that pop up from this window.

#### menuBar

    DynamicMenuBar menuBar

The menu bar that's attached to this window.

### Class RNAstructure_java_interface.source.windows.MaxExpectWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.ModuleWindow extends InternalWindow implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### constraints

    GridBagConstraints constraints

The GridBagConstraints for this window.

#### layout

    GridBagLayout layout

The layout for this window.

#### isRNA

    boolean isRNA

A boolean, true if the calculation handles RNA, false if not.

#### progressBar

    JDialog progressBar

The progress bar dialog for this window.

### Class RNAstructure_java_interface.source.windows.MultilignWindow extends MultiWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.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

    ArrayList<E> imageDialogs

The list of drawing windows shown after the calculation is done.

#### options

    Box options

The box that holds a particular window's unique options.

#### scroll

    ScrollerPane scroll

The scroll pane holding the sequence set.

### Class RNAstructure_java_interface.source.windows.OligoScreenWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.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

    JPanel panelInput

#### panelResults

    JPanel panelResults

The box that holds the results.

### Class RNAstructure_java_interface.source.windows.OligoWalkWindow.OligoSelectionDialog extends ValueSelectionDialog implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.OligoWalkWindow.SpinnerPanel extends JPanel implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### spinner

    JSpinner spinner

The spinner in this panel.

### Class RNAstructure_java_interface.source.windows.OligoWalkWindow.StringComboBox extends JComboBox implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.PartitionDoubleWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.PartitionSingleWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.ProbKnotWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.PseudoknotWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.RefoldWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.SequenceDisplayWindow extends InternalWindow implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### areas

    ArrayList<E> areas

The array of text areas in this window.

#### edited

    boolean edited

A boolean, true if the sequence has been edited, false if not.

#### position

    int position

The position at which reading is occurring.

#### readButton

    JButton readButton

The button which can be clicked to start or stop reading.

#### reading

    boolean reading

A boolean, true if reading while typing is active, false if not.

#### timer

    Timer timer

The timer that aids in reading nucleotides in rhythm.

### Class RNAstructure_java_interface.source.windows.StochasticWindow extends ModuleWindow implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_interface.source.windows.TurboFoldWindow extends MultiWindow implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### cards

    CardLayout cards

The layout that holds the dynamic options applicable to a mode.

#### specificPanel

    JPanel specificPanel

The panel that holds the dynamic options applicable to a mode.

## Package RNAstructure_java_utilities

### Class RNAstructure_java_utilities.BorderBuilder extends Object implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.BorderedButtonPanel extends JPanel implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.FieldPanel extends JPanel implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### components

    JComponent[] components

The components on this panel (buttons or labels).

#### specifiedPanelWidth

    int specifiedPanelWidth

The specified width of the panel.

#### textFields

    JTextField[] textFields

The array of text fields.

### Class RNAstructure_java_utilities.FieldPanel.FilePanel extends FieldPanel implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.FieldPanel.NumberPanel extends FieldPanel implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.FileChooser extends Object implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### defaultFile

    String defaultFile

The default file name for this file chooser, if necessary.

#### selectorType

    FileChooser.Types selectorType

The type of file type selector.

### Class RNAstructure_java_utilities.FileField extends JTextField implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.HTMLCheckBox extends JCheckBox implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.ImageGrabber extends Object implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.MacChecker extends Object implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.NumberField extends JTextField implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### initial

    Number initial

The initial default value of the field.

#### maximum

    Number maximum

The maximum value of the field.

#### minimum

    Number minimum

The minimum value of the field.

### Class RNAstructure_java_utilities.NumberField.DoubleField extends NumberField implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.NumberField.FloatField extends NumberField implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.NumberField.IntegerField extends NumberField implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.RadioButtonPanel extends JPanel implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### group

    ButtonGroup group

The button group connected to this panel.

#### group2

    ArrayList<E> group2

The button group, as a list, for ease of access to each.

#### names

    String[] names

The names of the buttons in the group.

### Class RNAstructure_java_utilities.RNAstructureMenu extends JMenu implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.ScrollerPane extends JScrollPane implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.SimpleDialogHandler extends Object implements Serializable

serialVersionUID:
  20120802L

### Class RNAstructure_java_utilities.ValueSelectionDialog extends JDialog implements Serializable

serialVersionUID:
  20120802L

### Serialized Fields

#### fields

    NumberField[] fields

The array of number fields this dialog holds.