Serialized Form

Package com.biomatters.geneious.publicapi.components

Class com.biomatters.geneious.publicapi.components.AlertPanel

class AlertPanel extends GPanel implements Serializable

Serialized Fields

cardLayout

CardLayout cardLayout

cardLayoutPanel

GPanel cardLayoutPanel

defaultMoreDetailsActionListener

ActionListener defaultMoreDetailsActionListener

moreDetailsButton

JButton moreDetailsButton

moreDetailsComponent

JComponent moreDetailsComponent

moreDetailsMessage

String moreDetailsMessage

moreDetailsOveridden

boolean moreDetailsOveridden

summaryLine

JLabel summaryLine

Class com.biomatters.geneious.publicapi.components.AlertPanel.RoundedAlertBorder

class RoundedAlertBorder extends AbstractBorder implements Serializable

Serialized Fields

borderColour

Color borderColour

Class com.biomatters.geneious.publicapi.components.BorderlessScrollPane

class BorderlessScrollPane extends JScrollPane implements Serializable

Class com.biomatters.geneious.publicapi.components.DialogButtonPanel

class DialogButtonPanel extends GPanel implements Serializable

Serialized Fields

allButtons

List<GButton> allButtons

cancelButton

GButton cancelButton

okButton

GButton okButton

Class com.biomatters.geneious.publicapi.components.GButton

class GButton extends JButton implements Serializable

Serialized Fields

ancestorListener

AncestorListener ancestorListener

isSmall

boolean isSmall

originalFont

Font originalFont

showBorderListener

MouseListener showBorderListener

Class com.biomatters.geneious.publicapi.components.GCheckBox

class GCheckBox extends JCheckBox implements Serializable

Serialized Fields

originalFont

Font originalFont

Class com.biomatters.geneious.publicapi.components.GComboBox

class GComboBox extends JComboBox<E> implements Serializable

Serialized Fields

fastRoughCalculationOfDropdownWidth

boolean fastRoughCalculationOfDropdownWidth

list

JList<E> list

originalFont

Font originalFont

Class com.biomatters.geneious.publicapi.components.GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged

class DefaultModelWhereSetSelectedItemDoesntFireContentsChanged extends DefaultComboBoxModel<E> implements Serializable

Serialized Fields

isEditableComboBox

boolean isEditableComboBox

selectedObjectField

Field selectedObjectField

Class com.biomatters.geneious.publicapi.components.GDefaultTreeCellRenderer

class GDefaultTreeCellRenderer extends DefaultTreeCellRenderer implements Serializable

Serialized Fields

dropTargetNode

TreeNode dropTargetNode

Class com.biomatters.geneious.publicapi.components.GDialog

class GDialog extends JeblDialog implements Serializable

Serialized Fields

maxDimensions

Dimension maxDimensions

Class com.biomatters.geneious.publicapi.components.GEditorPane

class GEditorPane extends JEditorPane implements Serializable

Class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar

class GeneiousActionToolbar extends GPanel implements Serializable

Serialized Fields

allComponents

Map<GeneiousAction,JComponent> allComponents

autoHideLabels

boolean autoHideLabels

buttonFocusListener

ActionListener buttonFocusListener

defaultLabels

boolean defaultLabels

defaultLarge

boolean defaultLarge

displayLargeLabelsHorizontal

boolean displayLargeLabelsHorizontal

dividerCount

int dividerCount

dividerIds

Map<String,String> dividerIds

focusComponent

JComponent focusComponent

groupedActions

Map<String,List<GeneiousAction>> groupedActions

groupedComponents

Map<String,List<JComponent>> groupedComponents

groupedLabels

Map<String,GLabel> groupedLabels

groupedPanels

Map<String,GPanel> groupedPanels

hiddenActions

List<GeneiousAction> hiddenActions

Actions that have been hidden by the user unchecking it in the popup.

iconSizeEnabled

boolean iconSizeEnabled

iconSizeItem

JCheckBoxMenuItem iconSizeItem

mainToolBar

JToolBar mainToolBar

originalActions

Map<String,GeneiousAction> originalActions

overridePosition

boolean overridePosition

popupAction

GeneiousAction.SubMenu popupAction

popupActions

List<GeneiousAction> popupActions

Actions that can't fit in the toolbar so they have been put under a popup menu

popupButton

AbstractButton popupButton

popupComponents

List<JComponent> popupComponents

Components that can't fit in the toolbar so they have been put under a popup menu

popupEnabled

boolean popupEnabled

popupMouseListener

MouseListener popupMouseListener

popupToolBar

JToolBar popupToolBar

preferencesAbsolutePath

String preferencesAbsolutePath

rightToolBar

JToolBar rightToolBar

rightToolBarActions

List<GeneiousAction> rightToolBarActions

rightToolBarComponents

List<JComponent> rightToolBarComponents

showLabelsItem

JCheckBoxMenuItem showLabelsItem

toolBarActions

List<GeneiousAction> toolBarActions

Actions in toolbar (as apposed to the popup) in the order they are in the toolbar

toolBarComponents

List<JComponent> toolBarComponents

Components in the main toolbar (as apposed to the popup) in the order they are in the toolbar

toolbars

Set<JToolBar> toolbars

widthListener

ComponentAdapter widthListener

Class com.biomatters.geneious.publicapi.components.GLabel

class GLabel extends JLabel implements Serializable

Serialized Fields

originalFont

Font originalFont

Class com.biomatters.geneious.publicapi.components.GMenuItem

class GMenuItem extends JMenuItem implements Serializable

Class com.biomatters.geneious.publicapi.components.GPanel

class GPanel extends JPanel implements Serializable

Class com.biomatters.geneious.publicapi.components.GPopupMenu

class GPopupMenu extends JPopupMenu implements Serializable

Serialized Fields

menuChangeListeners

Map<JMenu,ChangeListener> menuChangeListeners

parentFrame

JFrame parentFrame

windowListener

WindowAdapter windowListener

Class com.biomatters.geneious.publicapi.components.GScrollPane

class GScrollPane extends JScrollPane implements Serializable

Class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel

class GSpinnerNumberModel extends SpinnerNumberModel implements Serializable

Class com.biomatters.geneious.publicapi.components.GTable

class GTable extends JTable implements Serializable

Serialized Fields

hoveredRow

int hoveredRow

Class com.biomatters.geneious.publicapi.components.GTextArea

class GTextArea extends JTextArea implements Serializable

Class com.biomatters.geneious.publicapi.components.GTextField

class GTextField extends JTextField implements Serializable

Class com.biomatters.geneious.publicapi.components.GTextPane

class GTextPane extends JTextPane implements Serializable

Class com.biomatters.geneious.publicapi.components.HyperlinkButton

class HyperlinkButton extends GButton implements Serializable

Serialized Fields

caption

String caption

colorWhenMouseNotOver

Color colorWhenMouseNotOver

isProOnly

boolean isProOnly

Class com.biomatters.geneious.publicapi.components.MoreOptionsButton

class MoreOptionsButton extends GButton implements Serializable

Serialized Fields

changeListeners

SimpleListenerManager changeListeners

isMore

boolean isMore

lessText

String lessText

moreText

String moreText

Class com.biomatters.geneious.publicapi.components.OptionsPanel

class OptionsPanel extends JPanel implements Serializable

Serialized Fields

componentAnchor

int componentAnchor

componentVisibilityCopiers

List<com.biomatters.geneious.publicapi.components.OptionsPanel.ComponentVisibilityCopier> componentVisibilityCopiers

constraints

GridBagConstraints constraints

defaultWeightY

double defaultWeightY

horizontallyCompact

boolean horizontallyCompact

labelAnchor

int labelAnchor

leftAlignEverything

boolean leftAlignEverything

panel

JPanel panel

rightSpacingWeight

double rightSpacingWeight

subPanel

OptionsPanel subPanel

verticalSpacingAbove

int verticalSpacingAbove

verticalSpacingBelow

int verticalSpacingBelow

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button

class Button extends GButton implements Serializable

Serialized Fields

enabled

boolean enabled

proMode

boolean proMode

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox

class CheckBox extends GCheckBox implements Serializable

Serialized Fields

enabled

boolean enabled

name

String name

showProOnlyText

ProOnlyComponents.CheckBox.ProOnlySuffix showProOnlyText

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem

class CheckBoxMenuItem extends JCheckBoxMenuItem implements Serializable

Serialized Fields

enabled

boolean enabled

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox

class ComboBox extends GComboBox implements Serializable

Serialized Fields

enabled

boolean enabled

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Label

class Label extends GLabel implements Serializable

Serialized Fields

enabled

boolean enabled

name

String name

showProOnlyText

boolean showProOnlyText

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Menu

class Menu extends JMenu implements Serializable

Serialized Fields

enabled

boolean enabled

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem

class MenuItem extends GMenuItem implements Serializable

Serialized Fields

enabled

boolean enabled

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Panel

class Panel extends JPanel implements Serializable

Serialized Fields

component

JComponent component

proOnlyLabel

JLabel proOnlyLabel

Class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton

class ToggleButton extends JToggleButton implements Serializable

Serialized Fields

enabled

boolean enabled

proMode

boolean proMode

Class com.biomatters.geneious.publicapi.components.ScrollPaneLayoutThatCorrectlyAccountsForVerticalScrollbarWidth

class ScrollPaneLayoutThatCorrectlyAccountsForVerticalScrollbarWidth extends ScrollPaneLayout implements Serializable

Class com.biomatters.geneious.publicapi.components.ZoomChangeEvent

class ZoomChangeEvent extends ChangeEvent implements Serializable

Serialized Fields

fitToScreen

boolean fitToScreen

zoomLevel

double zoomLevel

Class com.biomatters.geneious.publicapi.components.ZoomPanel

class ZoomPanel extends JPanel implements Serializable

Serialized Fields

bigZoomFactor

double bigZoomFactor

fitToScreen

JButton fitToScreen

fitToScreenZoomLevel

double fitToScreenZoomLevel

forceFitToScreenButtonEnabled

boolean forceFitToScreenButtonEnabled

listeners

Vector<ChangeListener> listeners

maxZoomLevel

double maxZoomLevel

minZoomLevel

double minZoomLevel

settingSpinner

boolean settingSpinner

slider

JSlider slider

targetZoomLevel

double targetZoomLevel

zoomFactor

double zoomFactor

zoomIn

JButton zoomIn

zoomLevel

double zoomLevel

zoomOut

JButton zoomOut

zoomSpinnerModel

SpinnerNumberModel zoomSpinnerModel

zoomTo100Percent

JButton zoomTo100Percent

zoomToSelection

JButton zoomToSelection

Package com.biomatters.geneious.publicapi.databaseservice

Exception Class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException

class DatabaseServiceException extends Exception implements Serializable

Serialized Fields

isNetworkConnectionError

boolean isNetworkConnectionError

isTransientConnectionError

boolean isTransientConnectionError

userMessage

String userMessage

Exception Class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException.Canceled

class Canceled extends DatabaseServiceException implements Serializable

Exception Class com.biomatters.geneious.publicapi.databaseservice.SearchIndexCorruptOrMissingException

class SearchIndexCorruptOrMissingException extends DatabaseServiceException implements Serializable

Package com.biomatters.geneious.publicapi.documents

Exception Class com.biomatters.geneious.publicapi.documents.MalformedURNException

class MalformedURNException extends Exception implements Serializable

Exception Class com.biomatters.geneious.publicapi.documents.XMLSerializationException

class XMLSerializationException extends Exception implements Serializable

Package com.biomatters.geneious.publicapi.implementations

Class com.biomatters.geneious.publicapi.implementations.EValue

class EValue extends Number implements Serializable

Serialized Fields

decimalPlacesDisplayed

Integer decimalPlacesDisplayed

value

Double value

Class com.biomatters.geneious.publicapi.implementations.Percentage

class Percentage extends Number implements Serializable

Serialized Fields

decimalPlacesDisplayed

int decimalPlacesDisplayed

value

double value

Package com.biomatters.geneious.publicapi.laf

Class com.biomatters.geneious.publicapi.laf.UI.ThemeInvertedColor

class ThemeInvertedColor extends Color implements Serializable

Package com.biomatters.geneious.publicapi.plugin

Exception Class com.biomatters.geneious.publicapi.plugin.DocumentImportException

class DocumentImportException extends Exception implements Serializable

Exception Class com.biomatters.geneious.publicapi.plugin.DocumentImportException.Canceled

class Canceled extends DocumentImportException implements Serializable

Exception Class com.biomatters.geneious.publicapi.plugin.DocumentOperationException

class DocumentOperationException extends Exception implements Serializable

Exception Class com.biomatters.geneious.publicapi.plugin.DocumentOperationException.Canceled

class Canceled extends com.biomatters.geneious.publicapi.plugin.DocumentOperationException implements Serializable

Class com.biomatters.geneious.publicapi.plugin.GeneiousAction

class GeneiousAction extends AbstractAction implements Serializable

Serialized Fields

actionOptions

GeneiousActionOptions actionOptions

buttonPropertyListeners

List<com.biomatters.geneious.publicapi.plugin.GeneiousAction.ButtonPropertyListener> buttonPropertyListeners

freeUpMemoryNow

Runnable freeUpMemoryNow

internalAction

GeneiousAction internalAction

Class com.biomatters.geneious.publicapi.plugin.GeneiousAction.Divider

class Divider extends GeneiousAction implements Serializable

Class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu

class SubMenu extends GeneiousAction implements Serializable

Serialized Fields

actionsChangedListeners

SimpleListenerManager actionsChangedListeners

lastPopupCanceled

long lastPopupCanceled

popupIcons

Icons popupIcons

subActions

List<GeneiousAction> subActions

Class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction

class ToggleAction extends GeneiousAction implements Serializable

Serialized Fields

isSelected

boolean isSelected

Exception Class com.biomatters.geneious.publicapi.plugin.RuntimeDocumentOperationException

class RuntimeDocumentOperationException extends RuntimeException implements Serializable

Exception Class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException

class SelectionWrongForDocumentsException extends SequenceSelectionWithDocuments.SelectedDocumentsModifiedException implements Serializable

Serialized Fields

documents

List<AnnotatedPluginDocument> documents

Deprecated.

Exception Class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.DocumentsInvalidException

class DocumentsInvalidException extends com.biomatters.geneious.publicapi.plugin.DocumentOperationException implements Serializable

Exception Class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.SelectedDocumentsModifiedException

class SelectedDocumentsModifiedException extends IllegalStateException implements Serializable

Class com.biomatters.geneious.publicapi.plugin.WritableDatabaseServiceTree

class WritableDatabaseServiceTree extends JTree implements Serializable

Serialized Fields

disabledServices

Set<GeneiousService> disabledServices

Package com.biomatters.geneious.publicapi.utilities

Exception Class com.biomatters.geneious.publicapi.utilities.InvalidZipEntryException

class InvalidZipEntryException extends IOException implements Serializable

Serialized Fields

entry

String entry

Exception Class com.biomatters.geneious.publicapi.utilities.ProgressInputStream.ProgressInterruptedIOException

class ProgressInterruptedIOException extends InterruptedIOException implements Serializable