org.systemsbiology.gaggle.geese.cy.jdrf
Class ControlPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.systemsbiology.gaggle.geese.cy.jdrf.ControlPanel

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.rmi.Remote, javax.accessibility.Accessible, Goose

public class ControlPanel
extends javax.swing.JPanel
implements Goose, java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JPanel.AccessibleJPanel

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected CytoscapeWindow	cw
protected BioDataServer	dataServer
protected UndoableGraphHider	graphHider
protected javax.swing.JTextField	movieConditionReadout
protected javax.swing.JTextField	nodeSelectionTextField

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

ControlPanel(CytoscapeWindow cw)

Method Summary

double[]	absoluteValue(double[] array)
protected void	clearNetworkSelections()
void	clearSelections()
void	connectToGaggle()
protected javax.swing.JPanel	createCyControlPanel()
protected javax.swing.JToolBar	createGaggleToolBar()
protected javax.swing.JPanel	createMovieReadoutPanel()
void	doBroadcastList()
void	doBroadcastNetwork()
void	doExit() Tells the goose to exit (terminate).
void	doHide() Tells the goose to hide itself
void	doShow() Tells the goose to show itself
protected java.lang.String[]	getCanonicalNamesOfNodesInGraph()
java.lang.String[]	getCommands()
protected java.util.HashMap	getCommonNamesInHash(java.lang.String[] canonicalNames)
protected java.lang.String[]	getCurrentNodeNames(Graph2D graph)
protected java.util.HashMap	getCurrentNodes(Graph2D graph)
double[]	getDoubleEdgeAttributes(java.lang.String attributeName)
double[]	getDoubleNodeAttributes(java.lang.String attributeName)
protected java.util.HashMap	getGeneClusters()
java.lang.String	getName() Returns the name of the goose.
int	getSelectionCount()
void	handleCluster(java.lang.String source, Cluster cluster) Called when the goose receives a Cluster object
void	handleMatrix(java.lang.String source, DataMatrix matrix) Called when the goose receives a DataMatrix object
void	handleNameList(java.lang.String source, Namelist nameList) Called when the goose receives a NameList object
void	handleNetwork(java.lang.String source, Network network) Called when the goose receives a Network object
void	handleTuple(java.lang.String source, GaggleTuple gaggleTuple) Called when the goose receives a GaggleTuple object
void	hideEdgesByCorrelation(double min)
protected void	selectNodes()
protected void	selectNodesByName(java.lang.String[] candidates)
void	setGeometry(int x, int y, int width, int height)
void	setName(java.lang.String newValue) Sets the name of (renames) the goose.
void	update(java.lang.String[] gooseNames) Provides the goose with an updated list of the names of active geese.

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

nodeSelectionTextField

protected javax.swing.JTextField nodeSelectionTextField

movieConditionReadout

protected javax.swing.JTextField movieConditionReadout

cw

protected CytoscapeWindow cw

dataServer

protected BioDataServer dataServer

graphHider

protected UndoableGraphHider graphHider

Constructor Detail

ControlPanel

public ControlPanel(CytoscapeWindow cw)

Method Detail

connectToGaggle

public void connectToGaggle()

createGaggleToolBar

protected javax.swing.JToolBar createGaggleToolBar()

createCyControlPanel

protected javax.swing.JPanel createCyControlPanel()

createMovieReadoutPanel

protected javax.swing.JPanel createMovieReadoutPanel()

getCommonNamesInHash

protected java.util.HashMap getCommonNamesInHash(java.lang.String[] canonicalNames)

selectNodes

protected void selectNodes()

selectNodesByName

protected void selectNodesByName(java.lang.String[] candidates)

getCanonicalNamesOfNodesInGraph

protected java.lang.String[] getCanonicalNamesOfNodesInGraph()

getGeneClusters

protected java.util.HashMap getGeneClusters()

clearNetworkSelections

protected void clearNetworkSelections()

hideEdgesByCorrelation

public void hideEdgesByCorrelation(double min)

absoluteValue

public double[] absoluteValue(double[] array)

getDoubleEdgeAttributes

public double[] getDoubleEdgeAttributes(java.lang.String attributeName)

getDoubleNodeAttributes

public double[] getDoubleNodeAttributes(java.lang.String attributeName)

handleNameList

public void handleNameList(java.lang.String source,
                           Namelist nameList)
                    throws java.rmi.RemoteException

Description copied from interface: Goose

Called when the goose receives a NameList object

Specified by:

handleNameList in interface Goose

Parameters:

source - Optional string indicating name of source goose

nameList - The NameList object

Throws:

java.rmi.RemoteException - if RMI communication fails

handleMatrix

public void handleMatrix(java.lang.String source,
                         DataMatrix matrix)

Description copied from interface: Goose

Called when the goose receives a DataMatrix object

Specified by:

handleMatrix in interface Goose

Parameters:

source - Optional string indicating name of source goose

matrix - The DataMatrix object

handleCluster

public void handleCluster(java.lang.String source,
                          Cluster cluster)

Description copied from interface: Goose

Called when the goose receives a Cluster object

Specified by:

handleCluster in interface Goose

Parameters:

source - Optional string indicating name of source goose

cluster - The Cluster object

handleNetwork

public void handleNetwork(java.lang.String source,
                          Network network)
                   throws java.rmi.RemoteException

Description copied from interface: Goose

Called when the goose receives a Network object

Specified by:

handleNetwork in interface Goose

Parameters:

source - Optional string indicating name of source goose

network - The Network object

Throws:

java.rmi.RemoteException - if RMI communication fails

getCurrentNodes

protected java.util.HashMap getCurrentNodes(Graph2D graph)

getCurrentNodeNames

protected java.lang.String[] getCurrentNodeNames(Graph2D graph)

handleTuple

public void handleTuple(java.lang.String source,
                        GaggleTuple gaggleTuple)

Description copied from interface: Goose

Called when the goose receives a GaggleTuple object

Specified by:

handleTuple in interface Goose

Parameters:

source - Optional string indicating name of source goose

gaggleTuple - The GaggleTuple object

getName

public java.lang.String getName()

Description copied from interface: Goose

Returns the name of the goose.

Specified by:

getName in interface Goose

Overrides:

getName in class java.awt.Component

Returns:

the name of the goose

setName

public void setName(java.lang.String newValue)

Description copied from interface: Goose

Sets the name of (renames) the goose.

Specified by:

setName in interface Goose

Overrides:

setName in class java.awt.Component

Parameters:

newValue - The new name of the goose

getSelectionCount

public int getSelectionCount()

doBroadcastNetwork

public void doBroadcastNetwork()

doHide

public void doHide()

Description copied from interface: Goose

Tells the goose to hide itself

Specified by:

doHide in interface Goose

doShow

public void doShow()

Description copied from interface: Goose

Tells the goose to show itself

Specified by:

doShow in interface Goose

clearSelections

public void clearSelections()

setGeometry

public void setGeometry(int x,
                        int y,
                        int width,
                        int height)

doBroadcastList

public void doBroadcastList()

Specified by:

doBroadcastList in interface Goose

doExit

public void doExit()

Description copied from interface: Goose

Tells the goose to exit (terminate).

Specified by:

doExit in interface Goose

update

public void update(java.lang.String[] gooseNames)

Description copied from interface: Goose

Provides the goose with an updated list of the names of active geese. This list includes the name of the goose receiving the list.

Specified by:

update in interface Goose

Parameters:

gooseNames - the names of the currently active geese

See Also:

MiscUtil.updateGooseChooser(javax.swing.JComboBox gooseChooser, String callingGoose, String[] allGeese);

getCommands

public java.lang.String[] getCommands()