Date: 2014-08-08

# Serialized Form

- ## Package melting.exceptions

  - ### Class melting.exceptions.FileException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      -8477108314961282300L

  - ### Class melting.exceptions.MethodNotApplicableException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      7901928613998187436L

  - ### Class melting.exceptions.NoExistingMethodException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      4480352056557369137L

  - ### Class melting.exceptions.NoExistingOutputFileException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      8580334876179097236L

  - ### Class melting.exceptions.NucleicAcidNotKnownException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      8913295672203816812L

  - ### Class melting.exceptions.OptionSyntaxError extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      -68893338772781425L

  - ### Class melting.exceptions.SequenceException extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      -7494134302550466479L

  - ### Class melting.exceptions.ThermodynamicParameterError extends java.lang.RuntimeException implements Serializable

    serialVersionUID:
      -8458644289304464405L

- ## Package meltinggui

  - ### Class meltinggui.MeltingGui extends javax.swing.JFrame implements Serializable

    - ### Serialized Fields

      - #### outerFrame

            OuterFrame outerFrame

        Frame holding all the other components.

      - #### commandLineText

            java.lang.String commandLineText

        The text that would be entered into the command line were the user using the command line.

      - #### mandatoryCommandLineText

            java.lang.String mandatoryCommandLineText

        The mandatory part of the command line text.

      - #### generalCommandLineText

            java.lang.String generalCommandLineText

        The optional part of the command line text.

  - ### Class meltinggui.MeltingLayout extends java.lang.Object implements Serializable

    - ### Serialized Fields

      - #### parent

            java.awt.Container parent

        The parent `Container`.

      - #### hgap

            int hgap

        The horizontal gap between components.

      - #### vgap

            int vgap

        The vertical gap between components.

      - #### isValid

            boolean isValid

        Whether or not the layout is valid.

      - #### componentGroupTypes

            java.util.Map<K,V> componentGroupTypes

        Maps from components to the group they are in (label group or input group).

      - #### componentLines

            java.util.LinkedList<E> componentLines

        List of component lines: each line is made up of a label group and a input group.

- ## Package meltinggui.dialogs

  - ### Class meltinggui.dialogs.ComboBoxDialog extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### commandLineTag

            java.lang.String commandLineTag

        The command line tag corresponding to the dialog.

      - #### comboBoxLabel

            javax.swing.JLabel comboBoxLabel

        Label telling the user what the combo box is.

      - #### comboBox

            MeltingComboBox comboBox

        The combo box where the user can select options.

  - ### Class meltinggui.dialogs.HybridizationDialog extends InputField<HybridizationWidget> implements Serializable

  - ### Class meltinggui.dialogs.IonConcentrationDialog extends javax.swing.JComboBox implements Serializable

    - ### Serialized Fields

      - #### ionNames

            java.lang.String[] ionNames

        The different ions available.

      - #### comboBoxOptions

            java.lang.String[] comboBoxOptions

        The options dispayed on the combo box.

      - #### currentIonIndex

            int currentIonIndex

        The index of the currently selected ion.

      - #### editor

            meltinggui.dialogs.IonConcentrationDialog.IonDialogEditor editor

        The editor used in the combo box.

  - ### Class meltinggui.dialogs.OligomerConcentrationDialog extends InputField<MeltingTextField> implements Serializable

    - ### Serialized Fields

      - #### unitsLabel

            javax.swing.JLabel unitsLabel

        A label showing the units (mol/L).

  - ### Class meltinggui.dialogs.ResultsPanel extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### enthalpyOutputField

            OutputField enthalpyOutputField

      - #### enthalpyUnitsLabel

            javax.swing.JLabel enthalpyUnitsLabel

      - #### entropyOutputField

            OutputField entropyOutputField

      - #### entropyUnitsLabel

            javax.swing.JLabel entropyUnitsLabel

      - #### tmOutputField

            OutputField tmOutputField

      - #### tmUnitsLabel

            javax.swing.JLabel tmUnitsLabel

  - ### Class meltinggui.dialogs.SequenceDialog extends InputFieldArray<MeltingTextArea> implements Serializable

- ## Package meltinggui.frames

  - ### Class meltinggui.frames.ErrorFrame extends javax.swing.JInternalFrame implements Serializable

    - ### Serialized Fields

      - #### centerBox

            javax.swing.Box centerBox

        Panel for holding all the widgets.

      - #### titleLabel

            javax.swing.JLabel titleLabel

        Label with the title - 'An error has occurred.' on it.

      - #### exceptionLogTextArea

            javax.swing.JTextArea exceptionLogTextArea

        Text area for displaying error messages.

      - #### exceptionLogScrollPane

            javax.swing.JScrollPane exceptionLogScrollPane

        Scroll pane for holding the text area.

  - ### Class meltinggui.frames.FrameScreenPosition extends java.lang.Object implements Serializable

    - ### Serialized Fields

      - #### frameBounds

            java.awt.Rectangle frameBounds

        The bounds of the frame.

      - #### maximized

            boolean maximized

        Whether the frame is maximized.

      - #### iconified

            boolean iconified

        Whether the frame is iconified.

      - #### visible

            boolean visible

        Whether the frame is visible.

  - ### Class meltinggui.frames.GuiScreenPositions extends java.lang.Object implements Serializable

    - ### Serialized Fields

      - #### outerFrameScreenPosition

            FrameScreenPosition outerFrameScreenPosition

        The screen position of the outer frame.

      - #### meltingFrameScreenPosition

            FrameScreenPosition meltingFrameScreenPosition

        The screen position of the MELTING frame.

      - #### errorFrameScreenPosition

            FrameScreenPosition errorFrameScreenPosition

        The screen position of the error frame.

  - ### Class meltinggui.frames.MeltingFrame extends javax.swing.JInternalFrame implements Serializable

    - ### Serialized Fields

      - #### observable

            MeltingObservable observable

        Observable used to send messages back to all observers.

      - #### commandLineText

            java.lang.String commandLineText

        The text that would be entered into the command line were the user using the command line. Only mandatory options (-C -S -E -P -H) are included.

      - #### mainPanel

            javax.swing.JPanel mainPanel

      - #### sequencesPanel

            javax.swing.JPanel sequencesPanel

      - #### sequenceDialog

            SequenceDialog sequenceDialog

      - #### hybridizationPanel

            javax.swing.JPanel hybridizationPanel

      - #### hybridizationDialog

            HybridizationDialog hybridizationDialog

      - #### oligomerConcentrationPanel

            javax.swing.JPanel oligomerConcentrationPanel

      - #### oligomerConcentrationDialog

            OligomerConcentrationDialog oligomerConcentrationDialog

      - #### ionConcentrationsPanel

            javax.swing.JPanel ionConcentrationsPanel

      - #### ionConcentrationDialog

            IonConcentrationDialog ionConcentrationDialog

      - #### buttonsPanel

            javax.swing.JPanel buttonsPanel

      - #### getThermodynamicsButton

            javax.swing.JButton getThermodynamicsButton

      - #### moreOptionsButton

            javax.swing.JToggleButton moreOptionsButton

      - #### commandLinePanel

            javax.swing.JPanel commandLinePanel

      - #### commandLineTextArea

            javax.swing.JTextArea commandLineTextArea

      - #### resultsPanelPanel

            javax.swing.JPanel resultsPanelPanel

      - #### resultsPanel

            ResultsPanel resultsPanel

  - ### Class meltinggui.frames.OuterFrame extends javax.swing.JFrame implements Serializable

    - ### Serialized Fields

      - #### desktopPane

            javax.swing.JDesktopPane desktopPane

        Desktop for putting the different frames on.

      - #### meltingFrame

            MeltingFrame meltingFrame

        Instance of the principle MELTING frame.

      - #### errorFrame

            ErrorFrame errorFrame

        Error frame for displaying errors.

      - #### screenPositionsPath

            java.lang.String screenPositionsPath

        The full path to the screen positions file.

- ## Package meltinggui.widgets

  - ### Class meltinggui.widgets.HybridizationWidget extends MeltingComboBox implements Serializable

  - ### Class meltinggui.widgets.InputField extends InputFieldArray<W extends java.awt.Component & InputWidgetInterface> implements Serializable

  - ### Class meltinggui.widgets.InputFieldArray extends javax.swing.JPanel implements Serializable

    - ### Serialized Fields

      - #### labels

            java.util.List<E> labels

        The labels in the array.

      - #### widgets

            java.util.List<E> widgets

        The widgets on the array.

      - #### numberOfWidgets

            int numberOfWidgets

        Number of widgets to create.

  - ### Class meltinggui.widgets.MeltingComboBox extends javax.swing.JComboBox implements Serializable

    - ### Serialized Fields

      - #### comboBoxOptions

            ComboBoxOption[] comboBoxOptions

        Array of combo box options for the combo box.

  - ### Class meltinggui.widgets.MeltingTextArea extends javax.swing.JTextArea implements Serializable

  - ### Class meltinggui.widgets.MeltingTextField extends javax.swing.JTextField implements Serializable

  - ### Class meltinggui.widgets.OutputField extends InputField<MeltingTextField> implements Serializable