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

Field Summary

static int	EXTERNAL_VIEW Deprecated. View types are no longer support so stop using this. Will be removed August 2008.
static int	INTERNAL_VIEW Deprecated. View types are no longer support so stop using this. Will be removed August 2008.
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
static int	TABBED_VIEW Deprecated. View types are no longer support so stop using this. Will be removed August 2008.
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()
Creates a new CytoscapeDesktop object.

CytoscapeDesktop(int view_type)
Deprecated. view_type is no longer used. Use the other CytoscapeDesktop() instead. Will be gone August 1008.

Method Summary

void	addEdit(UndoableEdit edit) Deprecated. Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008.
void	clearStatusBar() Clears the Status Bar Message.
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
javax.help.HelpBroker	getHelpBroker() Deprecated. Will be removed April 2008. Use CyHelpBroker.getHelpBroker() instead.
javax.help.HelpSet	getHelpSet() Deprecated. Will be removed April 2008. Use CyHelpBroker.getHelpSet() instead.
NetworkPanel	getNetworkPanel() DOCUMENT ME!
NetworkViewManager	getNetworkViewManager() Gets the NetworkView Manager.
SwingPropertyChangeSupport	getSwingPropertyChangeSupport() DOCUMENT ME!
int	getViewType() Deprecated. View type is no longer used, so just don't use this method. Will be gone August 2008.
VizMapperMainPanel	getVizMapperUI() Returns new vizmapper GUI.
VizMapUI	getVizMapUI() Deprecated. use getVizMapperUI() isntead.
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.
void	setupVizMapper() Deprecated. use VizMapperMainPanel instead.
VisualStyle	setVisualStyle(VisualStyle style)

Methods inherited from class javax.swing.JFrame

getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, 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, 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, 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, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, 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, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, 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

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

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

TABBED_VIEW

public static final int TABBED_VIEW

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

Displays all network views in TabbedPanes ( like Mozilla )

See Also:

Constant Field Values

INTERNAL_VIEW

public static final int INTERNAL_VIEW

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

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

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

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(int view_type)

Deprecated. view_type is no longer used. Use the other CytoscapeDesktop() instead. Will be gone August 1008.

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!

getHelpBroker

public javax.help.HelpBroker getHelpBroker()

Deprecated. Will be removed April 2008. Use CyHelpBroker.getHelpBroker() instead.

getHelpSet

public javax.help.HelpSet getHelpSet()

Deprecated. Will be removed April 2008. Use CyHelpBroker.getHelpSet() instead.

addEdit

public void addEdit(UndoableEdit edit)

Deprecated. Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008.

Don't use this!

Parameters:

edit - An undoable edit.

getViewType

public int getViewType()

Deprecated. View type is no longer used, so just don't use this method. Will be gone August 2008.

Return the view type for this CytoscapeDesktop

getCyMenus

public CyMenus getCyMenus()

DOCUMENT ME!

Returns:

DOCUMENT ME!

setNewNetwork

public void setNewNetwork(CyNetwork newNetwork)

DOCUMENT ME!

Parameters:

newNetwork - DOCUMENT ME!

getVizMapUI

@Deprecated
public VizMapUI getVizMapUI()

Deprecated. use getVizMapperUI() isntead.

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

getVizMapperUI

public VizMapperMainPanel getVizMapperUI()

Returns new vizmapper GUI.

Returns:

DOCUMENT ME!

setupVizMapper

@Deprecated
public void setupVizMapper()

Deprecated. use VizMapperMainPanel instead.

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)

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.

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!