Serialized Form

Class cytoscape.view.cytopanels.BiModalJSplitPane extends JSplitPane implements Serializable

Serialized Fields

frame

JFrame frame

Reference application frame.

currentMode

int currentMode

The current mode.

defaultDividerSize

int defaultDividerSize

The default divider size.

dividerLocation

int dividerLocation

The saved divider location.

Class cytoscape.data.servers.BioDataServerRmi extends UnicastRemoteObject implements Serializable

Serialized Fields

annotations

HashMap annotations

thesauri

HashMap thesauri

startTime

Date startTime

lastAccessTime

Date lastAccessTime

Class cytoscape.view.cytopanels.CytoPanelImp extends JPanel implements Serializable

Serialized Fields

tabbedPane

JTabbedPane tabbedPane

The JTabbedPane we hide.

cytoPanelState

CytoPanelState cytoPanelState

Our state.

compassDirection

int compassDirection

Our compass direction.

cytoPanelListenerList

ArrayList cytoPanelListenerList

An array of CytoPanelListeners

NOTIFICATION_STATE_CHANGE

int NOTIFICATION_STATE_CHANGE

Notification state change.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_SELECTED

int NOTIFICATION_COMPONENT_SELECTED

Notification component selected.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_ADDED

int NOTIFICATION_COMPONENT_ADDED

Notification component added.

See Also:

Constant Field Values

NOTIFICATION_COMPONENT_REMOVED

int NOTIFICATION_COMPONENT_REMOVED

Notification component removed.

See Also:

Constant Field Values

cytoPanelContainer

CytoPanelContainer cytoPanelContainer

Reference to CytoPanelContainer we live in.

externalFrame

JFrame externalFrame

External window used to hold the floating CytoPanel.

floatIcon

ImageIcon floatIcon

The float icon.

dockIcon

ImageIcon dockIcon

The dock icon.

floatLabel

JLabel floatLabel

The label which contains the tab title - not sure if its needed.

floatButton

JButton floatButton

The float/dock button.

FLOAT_PANEL_SCALE_FACTOR

int FLOAT_PANEL_SCALE_FACTOR

The float/dock button.

See Also:

Constant Field Values

FLOAT_PANEL_COLOR

Color FLOAT_PANEL_COLOR

Color of the dock/float button panel.

Class cytoscape.util.CytoscapeAction extends AbstractAction implements Serializable

Serialized Fields

preferredMenu

String preferredMenu

preferredButtonGroup

String preferredButtonGroup

menuIndex

Integer menuIndex

acceleratorSet

boolean acceleratorSet

keyModifiers

int keyModifiers

keyCode

int keyCode

consoleName

String consoleName

Class cytoscape.view.CytoscapeDesktop extends JFrame implements Serializable

Serialized Fields

lastPluginRegistryUpdate

long lastPluginRegistryUpdate

returnVal

int returnVal

VIEW_TYPE

int VIEW_TYPE

The type of view, should be considered final

defaultVisualStyle

VisualStyle defaultVisualStyle

networkPanel

cytoscape.view.NetworkPanel networkPanel

The network panel that sends out events when a network is selected from the Tree that it contains.

cyMenus

CyMenus cyMenus

The CyMenus object provides access to the all of the menus and toolbars that will be needed.

networkViewManager

cytoscape.view.NetworkViewManager networkViewManager

The NetworkViewManager can support three types of interfaces. Tabbed/InternalFrame/ExternalFrame

cyHelpBroker

cytoscape.view.CyHelpBroker cyHelpBroker

The HelpBroker provides access to JavaHelp

pcs

SwingPropertyChangeSupport pcs

provides support for property change events

graphViewController

cytoscape.view.GraphViewController graphViewController

The GraphViewController for all NetworkViews that we know about

vizMapper

VisualMappingManager vizMapper

Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

vizMapUI

cytoscape.visual.ui.VizMapUI vizMapUI

user interface to the VisualMappingManager vizMapper.

currentNetworkID

String currentNetworkID

currentNetworkViewID

String currentNetworkViewID

cytoPanelWest

CytoPanelImp cytoPanelWest

cytoPanelEast

CytoPanelImp cytoPanelEast

cytoPanelSouth

CytoPanelImp cytoPanelSouth

statusBar

JLabel statusBar

vsAssociationMap

HashMap vsAssociationMap

main_panel

JPanel main_panel

currentStyleBox

JComboBox currentStyleBox

styleBoxIndex

int styleBoxIndex

Class cytoscape.util.CytoscapeMenuBar extends JMenuBar implements Serializable

Serialized Fields

defaultMenuSpecifier

String defaultMenuSpecifier

actionMembersSet

Set actionMembersSet

actionMenuItemMap

Map actionMenuItemMap

menuMap

Map menuMap

menuEffectiveLastIndexMap

Map menuEffectiveLastIndexMap

identifier

String identifier

Class cytoscape.util.CytoscapeProgressMonitor extends JFrame implements Serializable

Serialized Fields

pMonitor

ProgressMonitor pMonitor

timer

Timer timer

parentComponent

Component parentComponent

monitoredTask

MonitoredTask monitoredTask

Class cytoscape.util.CytoscapeToolBar extends JToolBar implements Serializable

Serialized Fields

actionButtonMap

Map actionButtonMap

actionMembersSet

Set actionMembersSet

Class cytoscape.data.ExpressionData extends Object implements Serializable

Serialized Fields

taskMonitor

cytoscape.task.TaskMonitor taskMonitor

significanceType

int significanceType

keyAttributeName

String keyAttributeName

mappingByAttribute

boolean mappingByAttribute

filename

String filename

numGenes

int numGenes

numConds

int numConds

extraTokens

int extraTokens

haveSigValues

boolean haveSigValues

geneNames

Vector geneNames

geneDescripts

Vector geneDescripts

condNames

Vector condNames

geneNameToIndex

Hashtable geneNameToIndex

condNameToIndex

Hashtable condNameToIndex

minExp

double minExp

maxExp

double maxExp

minSig

double minSig

maxSig

double maxSig

allMeasurements

Vector allMeasurements

Class cytoscape.util.IndeterminateProgressBar extends JDialog implements Serializable

Serialized Fields

mainPanel

JPanel mainPanel

labelPanel

JPanel labelPanel

barPanel

JPanel barPanel

label

JLabel label

labelText

String labelText

pBar

JProgressBar pBar

Class cytoscape.util.swing.JTreeTable extends JTable implements Serializable

Serialized Fields

tree

JTreeTable.TreeTableCellRenderer tree

A subclass of JTree.

Class cytoscape.util.swing.JTreeTable.TreeTableCellRenderer extends JTree implements Serializable

Serialized Fields

visibleRow

int visibleRow

Last table/tree row asked to renderer.

Class cytoscape.plugin.NotAPluginException extends Exception implements Serializable

Class cytoscape.util.swing.TreeTableModelAdapter extends AbstractTableModel implements Serializable

Serialized Fields

tree

JTree tree

treeTableModel

TreeTableModel treeTableModel