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

public class CytoscapeDesktop

extends JFrame

implements PropertyChangeListener

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. ( like the GIMP )
static int	INTERNAL_VIEW Displays all network views in JInternalFrames, using the mock desktop interface. ( like MS Office )
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	clearStatusBar() Clears the Status Bar Message.
CyMenus	getCyMenus()
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()
cytoscape.view.NetworkPanel	getNetworkPanel()
cytoscape.view.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).
cytoscape.visual.ui.VizMapUI	getVizMapUI() returns the top-level UI object for the visual mapper.
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.
void	setupVizMapper() Create the VizMapper and the UI for it.
VisualStyle	setVisualStyle(VisualStyle style)

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 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

undo

public static UndoManager undo

Cytoscape UndoManager

TABBED_VIEW

public static final int TABBED_VIEW

Displays all network views in TabbedPanes ( like Mozilla )

See Also:

Constant Field Values

INTERNAL_VIEW

public static final int INTERNAL_VIEW

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

See Also:

Constant Field Values

EXTERNAL_VIEW

public static final int EXTERNAL_VIEW

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

See Also:

Constant Field Values

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)

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 cytoscape.visual.ui.VizMapUI getVizMapUI()

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

setupVizMapper

public void setupVizMapper()

Create the VizMapper and the UI for it.

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

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.

parseViewType

public static int parseViewType(String vt)