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:

Accessible, cytoscape.view.CyWindow, EventListener, ImageObserver, MenuContainer, PropertyChangeListener, RootPaneContainer, Serializable, WindowConstants

public class CytoscapeDesktop

extends JFrame

implements PropertyChangeListener, cytoscape.view.CyWindow

The CytoscapeDesktop is the central Window for working with Cytoscape

See Also:

Serialized Form

Field Summary

static int	EXTERNAL_VIEW Displays all network views in JFrames, so each Network has its own window.
static int	INTERNAL_VIEW Displays all network views in JInternalFrames, using the mock desktop interface.
static String	NETWORK_VIEW_CREATED
static String	NETWORK_VIEW_DESTROYED
static String	NETWORK_VIEW_FOCUS
static String	NETWORK_VIEW_FOCUSED
static int	TABBED_VIEW Displays all network views in TabbedPanes ( like Mozilla )
static UndoManager	undo Cytoscape UndoManager
static String	VISUAL_STYLE
static String	VIZMAP_ENABLED

Fields inherited from class javax.swing.JFrame

EXIT_ON_CLOSE

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	applyLayout(GraphView lview) Deprecated.
void	applySelLayout() Deprecated.
void	applyVizmapSettings() Deprecated.
void	clearStatusBar() Clears the Status Bar Message.
CyMenus	getCyMenus() Returns the object that holds references to the menu bars and several of the major submenus.
CytoPanel	getCytoPanel(int compassDirection) Gets a cytoPanel given a Compass direction.
cytoscape.view.GraphViewController	getGraphViewController() TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
javax.help.HelpBroker	getHelpBroker()
javax.help.HelpSet	getHelpSet()
JFrame	getMainFrame() Deprecated.
CyNetwork	getNetwork() Deprecated.
cytoscape.view.NetworkPanel	getNetworkPanel()
cytoscape.view.NetworkViewManager	getNetworkViewManager() Gets the NetworkView Manager.
SwingPropertyChangeSupport	getSwingPropertyChangeSupport()
GraphView	getView() Deprecated.
VisualMappingManager	getVizMapManager() Returns the visual mapping manager that controls the appearance of nodes and edges in this display.
cytoscape.visual.ui.VizMapUI	getVizMapUI() returns the top-level UI object for the visual mapper.
String	getWindowTitle() Deprecated.
void	propertyChange(PropertyChangeEvent e)
void	redrawGraph() Deprecated.
void	redrawGraph(boolean doLayout) Deprecated.
void	redrawGraph(boolean doLayout, boolean applyAppearances) Deprecated.
void	setFocus(String network_id)
void	setInteractivity(boolean newState) Deprecated.
void	setNewNetwork(CyNetwork newNetwork)
void	setStatusBarMsg(String msg) Sets the Status Bar Message.
void	setVisualMapperEnabled(boolean newState) Deprecated.
VisualStyle	setVisualStyle(VisualStyle style)
void	setWindowTitle(String newTitle) Deprecated.
void	showWindow() Deprecated.
void	showWindow(int width, int height) Deprecated.
void	switchToEditMode() Deprecated.
void	switchToReadOnlyMode() Deprecated.
void	toggleVisualMapperEnabled() Deprecated.

Methods inherited from class javax.swing.JFrame

getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, update

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setIconImage, 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, isFocusableWindow, isFocusCycleRoot, isFocused, isShowing, pack, postEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setCursor, setFocusableWindowState, setFocusCycleRoot, 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, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, 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, 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, isOpaque, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

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 )

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

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 cytoscape.view.NetworkPanel getNetworkPanel()

getHelpBroker

public javax.help.HelpBroker getHelpBroker()

getHelpSet

public javax.help.HelpSet getHelpSet()

addEdit

public void addEdit(UndoableEdit edit)

getNetwork

public CyNetwork getNetwork()

Deprecated.

This will return the network currently under focus. however use this: Cytoscape.getCurrentNetwork()

Specified by:

getNetwork in interface cytoscape.view.CyWindow

getView

public GraphView getView()

Deprecated.

Returns the UI component that renders the displayed graph. Cytoscape.getCurrentNetworkView()

Specified by:

getView in interface cytoscape.view.CyWindow

getMainFrame

public JFrame getMainFrame()

Deprecated.

This will actually return an instance of this class.. Cytoscape.getDesktop()

Specified by:

getMainFrame in interface cytoscape.view.CyWindow

getCyMenus

public CyMenus getCyMenus()

Description copied from interface: cytoscape.view.CyWindow

Returns the object that holds references to the menu bars and several of the major submenus.

Specified by:

getCyMenus in interface cytoscape.view.CyWindow

setNewNetwork

public void setNewNetwork(CyNetwork newNetwork)

Specified by:

setNewNetwork in interface cytoscape.view.CyWindow

Parameters:

newNetwork - the new network to display

getWindowTitle

public String getWindowTitle()

Deprecated.

This doesn't apply anymore as the title will never change.

Specified by:

getWindowTitle in interface cytoscape.view.CyWindow

setWindowTitle

public void setWindowTitle(String newTitle)

Deprecated.

CyNetworkView.setTitle( String )

Specified by:

setWindowTitle in interface cytoscape.view.CyWindow

setInteractivity

public void setInteractivity(boolean newState)

Deprecated.

no longer used

Specified by:

setInteractivity in interface cytoscape.view.CyWindow

redrawGraph

public void redrawGraph()

Deprecated.

CyNetworkView.redrawGraph( boolean, boolean ) Redraws the graph - equivalent to redrawGraph(false, true). That is, no new layout will be performed, but the visual appearances will be reapplied.

Specified by:

redrawGraph in interface cytoscape.view.CyWindow

redrawGraph

public void redrawGraph(boolean doLayout)

Deprecated.

CyNetworkView.redrawGraph( boolean, boolean ) Redraws the graph - equivalent to redrawGraph(doLayout, true). That is, the visual appearances will be reapplied, and layout will be done iff the argument is true.

Specified by:

redrawGraph in interface cytoscape.view.CyWindow

redrawGraph

public void redrawGraph(boolean doLayout,
                        boolean applyAppearances)

Deprecated.

CyNetworkView.redrawGraph( boolean, boolean ) Redraws the graph. A new layout will be performed if the first argument is true, and the visual appearances will be recalculated and reapplied by the visual mapper if the second argument is true and the visual mapper is not disabled.

Specified by:

redrawGraph in interface cytoscape.view.CyWindow

showWindow

public void showWindow(int width,
                       int height)

Deprecated.

not used

Specified by:

showWindow in interface cytoscape.view.CyWindow

showWindow

public void showWindow()

Deprecated.

not used

Specified by:

showWindow in interface cytoscape.view.CyWindow

applyLayout

public void applyLayout(GraphView lview)

Deprecated.

not used

Specified by:

applyLayout in interface cytoscape.view.CyWindow

applySelLayout

public void applySelLayout()

Deprecated.

not used

Specified by:

applySelLayout in interface cytoscape.view.CyWindow

applyVizmapSettings

public void applyVizmapSettings()

Deprecated.

not used

setVisualMapperEnabled

public void setVisualMapperEnabled(boolean newState)

Deprecated.

not used

Specified by:

setVisualMapperEnabled in interface cytoscape.view.CyWindow

toggleVisualMapperEnabled

public void toggleVisualMapperEnabled()

Deprecated.

not used

Specified by:

toggleVisualMapperEnabled in interface cytoscape.view.CyWindow

switchToReadOnlyMode

public void switchToReadOnlyMode()

Deprecated.

not used

Specified by:

switchToReadOnlyMode in interface cytoscape.view.CyWindow

switchToEditMode

public void switchToEditMode()

Deprecated.

not used

Specified by:

switchToEditMode in interface cytoscape.view.CyWindow

getVizMapManager

public VisualMappingManager getVizMapManager()

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

Specified by:

getVizMapManager in interface cytoscape.view.CyWindow

getVizMapUI

public cytoscape.visual.ui.VizMapUI getVizMapUI()

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

Specified by:

getVizMapUI in interface cytoscape.view.CyWindow

setVisualStyle

public VisualStyle setVisualStyle(VisualStyle style)

Parameters:

style - the NEW VisualStyle

Returns:

the OLD VisualStyle

setFocus

public void setFocus(String network_id)

getGraphViewController

public cytoscape.view.GraphViewController getGraphViewController()

TO keep things clearer there is one GraphView Controller per CytoscapeDesktop

Specified by:

getGraphViewController in interface cytoscape.view.CyWindow

Returns:

a cytoscape.view.GraphViewController

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.

getNetworkViewManager

public cytoscape.view.NetworkViewManager getNetworkViewManager()

Gets the NetworkView Manager.

Returns:

NetworkViewManager Object.