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.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

protected String	currentNetworkID Current network and view.
protected String	currentNetworkViewID
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	cytoPanelSouthWest
protected CytoPanelImp	cytoPanelWest
protected VisualStyle	defaultVisualStyle
protected GraphViewController	graphViewController The GraphViewController for all NetworkViews that we know about
protected long	lastPluginRegistryUpdate
protected JPanel	main_panel
static String	NETWORK_VIEW_CREATED
static String	NETWORK_VIEW_DESTROYED
static String	NETWORK_VIEW_FOCUS
static String	NETWORK_VIEW_FOCUSED
static String	NETWORK_VIEWS_SELECTED
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 int	returnVal
protected JLabel	statusBar
protected int	styleBoxIndex
static String	VISUAL_STYLE
static String	VIZMAP_ENABLED
protected VizMapperMainPanel	vizmapperUI New VizMapper UI
protected VisualMappingManager	vmm Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

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()
Creates a new CytoscapeDesktop object.

Method Summary

void	clearStatusBar() Clears the Status Bar Message.
protected void	createBottomLeft()
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.
cytoscape.view.BirdsEyeViewHandler	getBirdsEyeViewHandler() DOCUMENT ME!
CyMenus	getCyMenus() DOCUMENT ME!
CytoPanel	getCytoPanel(int compassDirection) Gets a cytoPanel given a Compass direction.
GraphViewController	getGraphViewController() TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
NetworkPanel	getNetworkPanel() DOCUMENT ME!
NetworkViewManager	getNetworkViewManager() Gets the NetworkView Manager.
SwingPropertyChangeSupport	getSwingPropertyChangeSupport() DOCUMENT ME!
VizMapperMainPanel	getVizMapperUI() Returns new vizmapper GUI.
static int	parseViewType(String vt) Deprecated. View types are no longer support so stop using this. Will be removed August 2008.
void	propertyChange(PropertyChangeEvent e) DOCUMENT ME!
void	setFocus(String network_id) TODO: We should remove one of this event!
void	setNewNetwork(CyNetwork newNetwork) DOCUMENT ME!
void	setStatusBarMsg(String msg) Sets the Status Bar Message.
VisualStyle	setVisualStyle(VisualStyle style) Deprecated. use VisualMappingManager.setVisualStyle(VisualStyle style) instead.
protected void	updateFocus(String network_id)

Methods inherited from class javax.swing.JFrame

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

Methods inherited from class java.awt.Frame

addNotify, 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, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setVisible, 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, 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, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, 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, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

lastPluginRegistryUpdate

protected long lastPluginRegistryUpdate

returnVal

protected int returnVal

NETWORK_VIEWS_SELECTED

public static final String NETWORK_VIEWS_SELECTED

See Also:

Constant Field Values

NETWORK_VIEW_FOCUSED

public static final String NETWORK_VIEW_FOCUSED

See Also:

Constant Field Values

NETWORK_VIEW_FOCUS

public static final String NETWORK_VIEW_FOCUS

See Also:

Constant Field Values

NETWORK_VIEW_CREATED

public static final String NETWORK_VIEW_CREATED

See Also:

Constant Field Values

NETWORK_VIEW_DESTROYED

public static final String NETWORK_VIEW_DESTROYED

See Also:

Constant Field Values

VISUAL_STYLE

public static final String VISUAL_STYLE

See Also:

Constant Field Values

VIZMAP_ENABLED

public static final String VIZMAP_ENABLED

See Also:

Constant Field Values

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

pcs

protected final SwingPropertyChangeSupport pcs

provides support for property change events

graphViewController

protected GraphViewController graphViewController

The GraphViewController for all NetworkViews that we know about

vmm

protected VisualMappingManager vmm

Provides Operations for Mapping Data Attributes of CyNetworks to CyNetworkViews

vizmapperUI

protected VizMapperMainPanel vizmapperUI

New VizMapper UI

currentNetworkID

protected String currentNetworkID

Current network and view.

currentNetworkViewID

protected String currentNetworkViewID

cytoPanelWest

protected CytoPanelImp cytoPanelWest

cytoPanelEast

protected CytoPanelImp cytoPanelEast

cytoPanelSouth

protected CytoPanelImp cytoPanelSouth

cytoPanelSouthWest

protected CytoPanelImp cytoPanelSouthWest

statusBar

protected JLabel statusBar

main_panel

protected final JPanel main_panel

styleBoxIndex

protected int styleBoxIndex

Constructor Detail

CytoscapeDesktop

public CytoscapeDesktop()

Creates a new CytoscapeDesktop object.

Method Detail

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()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getCyMenus

public CyMenus getCyMenus()

DOCUMENT ME!

Returns:

DOCUMENT ME!

setNewNetwork

public void setNewNetwork(CyNetwork newNetwork)

DOCUMENT ME!

Parameters:

newNetwork - DOCUMENT ME!

getVizMapperUI

public VizMapperMainPanel getVizMapperUI()

Returns new vizmapper GUI.

Returns:

DOCUMENT ME!

setVisualStyle

@Deprecated
public VisualStyle setVisualStyle(VisualStyle style)

Deprecated. use VisualMappingManager.setVisualStyle(VisualStyle style) instead.

Parameters:

style - the NEW VisualStyle

Returns:

the OLD VisualStyle

updateFocus

protected void updateFocus(String network_id)

setFocus

public void setFocus(String network_id)

TODO: We should remove one of this event!

Parameters:

network_id - DOCUMENT ME!

getGraphViewController

public GraphViewController getGraphViewController()

TO keep things clearer there is one GraphView Controller per CytoscapeDesktop

getSwingPropertyChangeSupport

public SwingPropertyChangeSupport getSwingPropertyChangeSupport()

DOCUMENT ME!

Returns:

DOCUMENT ME!

propertyChange

public void propertyChange(PropertyChangeEvent e)

DOCUMENT ME!

Specified by:

propertyChange in interface PropertyChangeListener

Parameters:

e - DOCUMENT ME!

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.

createBottomLeft

protected void createBottomLeft()

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.

getBirdsEyeViewHandler

public cytoscape.view.BirdsEyeViewHandler getBirdsEyeViewHandler()

DOCUMENT ME!

Returns:

DOCUMENT ME!

parseViewType

public static int parseViewType(String vt)

Deprecated. View types are no longer support so stop using this. Will be removed August 2008.

DOCUMENT ME!

Parameters:

vt - DOCUMENT ME!

Returns:

DOCUMENT ME!