cytoscape.view
Class CytoscapeDesktop

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      cytoscape.view.CytoscapeDesktop

All Implemented Interfaces:

ImageObserver, MenuContainer, PropertyChangeListener, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants

public class CytoscapeDesktop
extends JFrame
implements PropertyChangeListener

The CytoscapeDesktop is the central Window for working with Cytoscape

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

protected String	currentNetworkID
protected String	currentNetworkViewID
protected CyHelpBroker	cyHelpBroker The HelpBroker provides access to JavaHelp
protected CyMenus	cyMenus The CyMenus object provides access to the all of the menus and toolbars that will be needed.
protected CytoPanelImp	cytoPanelEast
protected CytoPanelImp	cytoPanelSouth
protected CytoPanelImp	cytoPanelWest
protected VisualStyle	defaultVisualStyle
static int	EXTERNAL_VIEW Displays all network views in JFrames, so each Network has its own window.
protected GraphViewController	graphViewController The GraphViewController for all NetworkViews that we know about
static int	INTERNAL_VIEW Displays all network views in JInternalFrames, using the mock desktop interface.
protected long	lastPluginRegistryUpdate
static String	NETWORK_VIEW_CREATED
static String	NETWORK_VIEW_DESTROYED
static String	NETWORK_VIEW_FOCUS
static String	NETWORK_VIEW_FOCUSED
protected NetworkPanel	networkPanel The network panel that sends out events when a network is selected from the Tree that it contains.
protected NetworkViewManager	networkViewManager The NetworkViewManager can support three types of interfaces.
protected SwingPropertyChangeSupport	pcs provides support for property change events
protected JLabel	statusBar
static int	TABBED_VIEW Displays all network views in TabbedPanes ( like Mozilla )
static UndoManager	undo Cytoscape UndoManager
protected int	VIEW_TYPE The type of view, should be considered final
static String	VISUAL_STYLE
static String	VIZMAP_ENABLED
protected VisualMappingManager	vizMapper Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews
protected VizMapUI	vizMapUI user interface to the VisualMappingManager vizMapper.
protected HashMap	vsAssociationMap

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

CytoscapeDesktop()
The Default constructor uses a TabbedView

CytoscapeDesktop(int view_type)
Create a CytoscapeDesktop that conforms the given view type.

Method Summary

void	addEdit(UndoableEdit edit)
void	clearStatusBar() Clears the Status Bar Message.
protected BiModalJSplitPane	createMasterPane(NetworkPanel networkPanel, BiModalJSplitPane rightPane) Creates the Master Split Pane.
protected BiModalJSplitPane	createRightPane(BiModalJSplitPane topRightPane) Creates the Right Panel.
protected BiModalJSplitPane	createTopRightPane(NetworkViewManager networkViewManager) Creates the TopRight Pane.
CyMenus	getCyMenus()
CytoPanel	getCytoPanel(int compassDirection) Gets a cytoPanel given a Compass direction.
GraphViewController	getGraphViewController() TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
javax.help.HelpBroker	getHelpBroker()
javax.help.HelpSet	getHelpSet()
NetworkPanel	getNetworkPanel()
NetworkViewManager	getNetworkViewManager() Gets the NetworkView Manager.
SwingPropertyChangeSupport	getSwingPropertyChangeSupport()
int	getViewType() Return the view type for this CytoscapeDesktop
VisualMappingManager	getVizMapManager() Deprecated. Use Cytoscape.getVisualMappingManager() instead. This will be removed at 03/2007 (possibly sooner).
VizMapUI	getVizMapUI() returns the top-level UI object for the visual mapper.
protected void	initialize()
static int	parseViewType(String vt)
void	propertyChange(PropertyChangeEvent e)
void	setFocus(String network_id)
void	setNewNetwork(CyNetwork newNetwork)
void	setStatusBarMsg(String msg) Sets the Status Bar Message.
protected BiModalJSplitPane	setupCytoPanels(NetworkPanel networkPanel, NetworkViewManager networkViewManager) Create the CytoPanels UI.
protected void	setupVizMapper(JPanel panel) Create the VizMapper and the UI for it.
VisualStyle	setVisualStyle(VisualStyle style)
protected void	updateFocus(String network_id)

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

lastPluginRegistryUpdate

protected long lastPluginRegistryUpdate

NETWORK_VIEW_FOCUSED

public static String NETWORK_VIEW_FOCUSED

NETWORK_VIEW_FOCUS

public static String NETWORK_VIEW_FOCUS

NETWORK_VIEW_CREATED

public static String NETWORK_VIEW_CREATED

NETWORK_VIEW_DESTROYED

public static String NETWORK_VIEW_DESTROYED

VISUAL_STYLE

public static String VISUAL_STYLE

VIZMAP_ENABLED

public static String VIZMAP_ENABLED

undo

public static UndoManager undo

Cytoscape UndoManager

TABBED_VIEW

public static int TABBED_VIEW

Displays all network views in TabbedPanes ( like Mozilla )

INTERNAL_VIEW

public static int INTERNAL_VIEW

Displays all network views in JInternalFrames, using the mock desktop interface. ( like MS Office )

EXTERNAL_VIEW

public static int EXTERNAL_VIEW

Displays all network views in JFrames, so each Network has its own window. ( like the GIMP )

VIEW_TYPE

protected int VIEW_TYPE

The type of view, should be considered final

defaultVisualStyle

protected VisualStyle defaultVisualStyle

networkPanel

protected NetworkPanel networkPanel

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

cyMenus

protected CyMenus cyMenus

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

networkViewManager

protected NetworkViewManager networkViewManager

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

cyHelpBroker

protected CyHelpBroker cyHelpBroker

The HelpBroker provides access to JavaHelp

pcs

protected SwingPropertyChangeSupport pcs

provides support for property change events

graphViewController

protected GraphViewController graphViewController

The GraphViewController for all NetworkViews that we know about

vizMapper

protected VisualMappingManager vizMapper

Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

vizMapUI

protected VizMapUI vizMapUI

user interface to the VisualMappingManager vizMapper.

currentNetworkID

protected String currentNetworkID

currentNetworkViewID

protected String currentNetworkViewID

cytoPanelWest

protected CytoPanelImp cytoPanelWest

cytoPanelEast

protected CytoPanelImp cytoPanelEast

cytoPanelSouth

protected CytoPanelImp cytoPanelSouth

statusBar

protected JLabel statusBar

vsAssociationMap

protected HashMap vsAssociationMap

Constructor Detail

CytoscapeDesktop

public CytoscapeDesktop()

The Default constructor uses a TabbedView

CytoscapeDesktop

public CytoscapeDesktop(int view_type)

Create a CytoscapeDesktop that conforms the given view type.

Parameters:

view_type - one of the ViewTypes

Method Detail

initialize

protected void initialize()

setStatusBarMsg

public void setStatusBarMsg(String msg)

Sets the Status Bar Message.

Parameters:

msg - Status Bar Message.

clearStatusBar

public void clearStatusBar()

Clears the Status Bar Message.

getNetworkPanel

public NetworkPanel getNetworkPanel()

getHelpBroker

public javax.help.HelpBroker getHelpBroker()

getHelpSet

public javax.help.HelpSet getHelpSet()

addEdit

public void addEdit(UndoableEdit edit)

getViewType

public int getViewType()

Return the view type for this CytoscapeDesktop

getCyMenus

public CyMenus getCyMenus()

setNewNetwork

public void setNewNetwork(CyNetwork newNetwork)

getVizMapManager

public VisualMappingManager getVizMapManager()

Deprecated. Use Cytoscape.getVisualMappingManager() instead. This will be removed at 03/2007 (possibly sooner).

Returns the visual mapping manager that controls the appearance of nodes and edges in this display.

getVizMapUI

public VizMapUI getVizMapUI()

returns the top-level UI object for the visual mapper.

setupVizMapper

protected void setupVizMapper(JPanel panel)

Create the VizMapper and the UI for it.

setVisualStyle

public VisualStyle setVisualStyle(VisualStyle style)

Parameters:

style - the NEW VisualStyle

Returns:

the OLD VisualStyle

updateFocus

protected void updateFocus(String network_id)

setFocus

public void setFocus(String network_id)

getGraphViewController

public GraphViewController getGraphViewController()

TO keep things clearer there is one GraphView Controller per CytoscapeDesktop

getSwingPropertyChangeSupport

public SwingPropertyChangeSupport getSwingPropertyChangeSupport()

propertyChange

public void propertyChange(PropertyChangeEvent e)

Specified by:

propertyChange in interface PropertyChangeListener

getCytoPanel

public CytoPanel getCytoPanel(int compassDirection)

Gets a cytoPanel given a Compass direction.

Parameters:

compassDirection - Compass Direction (SwingConstants.{SOUTH,EAST,WEST}).

Returns:

CytoPanel The CytoPanel that lives in the region specified by compass direction.

setupCytoPanels

protected BiModalJSplitPane setupCytoPanels(NetworkPanel networkPanel,
                                            NetworkViewManager networkViewManager)

Create the CytoPanels UI.

Parameters:

networkPanel - to load on left side of right bimodal.

networkViewManager - to load on left side (CytoPanel West).

Returns:

BiModalJSplitPane Object.

createTopRightPane

protected BiModalJSplitPane createTopRightPane(NetworkViewManager networkViewManager)

Creates the TopRight Pane.

Parameters:

networkViewManager - to load on left side of top right bimodal.

Returns:

BiModalJSplitPane Object.

createRightPane

protected BiModalJSplitPane createRightPane(BiModalJSplitPane topRightPane)

Creates the Right Panel.

Parameters:

topRightPane - TopRightPane Object.

Returns:

BiModalJSplitPane Object

createMasterPane

protected BiModalJSplitPane createMasterPane(NetworkPanel networkPanel,
                                             BiModalJSplitPane rightPane)

Creates the Master Split Pane.

Parameters:

networkPanel - to load on left side of CytoPanel (cytoPanelWest).

rightPane - BiModalJSplitPane Object.

Returns:

BiModalJSplitPane Object.

getNetworkViewManager

public NetworkViewManager getNetworkViewManager()

Gets the NetworkView Manager.

Returns:

NetworkViewManager Object.

parseViewType

public static int parseViewType(String vt)