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

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.systemsbiology.gaggle.geese.cy.ip.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 java.lang.String[]	activeGooseNames
protected java.awt.Cursor	busyCursor
protected javax.swing.JButton	connectButton
protected CytoscapeWindow	cw
protected BioDataServer	dataServer
protected java.awt.Cursor	defaultCursor
protected javax.swing.JButton	disconnectButton
protected UndoableGraphHider	graphHider
protected java.awt.GridBagLayout	gridbagLayout
protected javax.swing.JTextField	nodeSelectionTextField
protected int	peptideMaxCountThreshold
protected javax.swing.JTextField	peptideMaxCountThresholdReadout
protected int	peptideMinCountThreshold
protected javax.swing.JTextField	peptideMinCountThresholdReadout
protected double	probabilityThreshold
protected javax.swing.JTextField	probabilityThresholdReadout
protected javax.swing.JToolBar	toolbar

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

void	clearSelections()
void	connectToGaggle()
protected javax.swing.JToolBar	createGaggleToolBar()
protected javax.swing.JToolBar	createLocalToolBar()
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) ********************** public String [] getSelectedNodeNames () { Graph2D graph = cw.getGraph (); ArrayList list = new ArrayList (); for (NodeCursor nc = graph.selectedNodes(); nc.ok(); nc.next()) { Node node = nc.node (); String canonicalName = cw.getCanonicalNodeName (node); String organism = cw.getNodeAttributes().getStringValue ("species", canonicalName); list.add (canonicalName); } // for nc return (String []) list.toArray (new String [0]); } // getSelectedNodeNames ***********************
double[]	getDoubleEdgeAttributes(java.lang.String attributeName)
double[]	getDoubleNodeAttributes(java.lang.String attributeName)
double[]	getEdgeWeights()
protected java.util.HashMap	getGeneClusters()
int[]	getIntegerEdgeAttributes(java.lang.String attributeName)
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	hideEdgesByAttribute(java.lang.String attributeName, double threshold, java.lang.String minOrMax)
void	hideEdgesByAttribute(java.lang.String attributeName, int threshold, java.lang.String minOrMax)
void	hideNodesByThreshold(java.lang.String nodeAttributeName, double threshold, int aboveOrBelow)
protected void	hideOrphans()
protected void	hideProteinAPrey() lots of things stick to Protein A.
protected void	selectNodes()
void	selectTilesAboveCurrentLambdaThreshold()
void	selectTilesAboveCurrentRatioThreshold()
void	setGeometry(int x, int y, int width, int height)
void	setName(java.lang.String newValue) Sets the name of (renames) the goose.
void	showAll()
void	update(java.lang.String[] gooseNames) Provides the goose with an updated list of the names of active geese.
void	zoomInOnNextSelectedNode()
void	zoomInOnPreviousSelectedNode()

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

activeGooseNames

protected java.lang.String[] activeGooseNames

toolbar

protected javax.swing.JToolBar toolbar

connectButton

protected javax.swing.JButton connectButton

disconnectButton

protected javax.swing.JButton disconnectButton

gridbagLayout

protected java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

protected javax.swing.JTextField nodeSelectionTextField

probabilityThresholdReadout

protected javax.swing.JTextField probabilityThresholdReadout

probabilityThreshold

protected double probabilityThreshold

peptideMinCountThresholdReadout

protected javax.swing.JTextField peptideMinCountThresholdReadout

peptideMinCountThreshold

protected int peptideMinCountThreshold

peptideMaxCountThresholdReadout

protected javax.swing.JTextField peptideMaxCountThresholdReadout

peptideMaxCountThreshold

protected int peptideMaxCountThreshold

cw

protected CytoscapeWindow cw

dataServer

protected BioDataServer dataServer

graphHider

protected UndoableGraphHider graphHider

defaultCursor

protected java.awt.Cursor defaultCursor

busyCursor

protected java.awt.Cursor busyCursor

Constructor Detail

ControlPanel

public ControlPanel(CytoscapeWindow cw)

Method Detail

connectToGaggle

public void connectToGaggle()

createGaggleToolBar

protected javax.swing.JToolBar createGaggleToolBar()

createLocalToolBar

protected javax.swing.JToolBar createLocalToolBar()

selectTilesAboveCurrentRatioThreshold

public void selectTilesAboveCurrentRatioThreshold()

selectTilesAboveCurrentLambdaThreshold

public void selectTilesAboveCurrentLambdaThreshold()

zoomInOnNextSelectedNode

public void zoomInOnNextSelectedNode()

zoomInOnPreviousSelectedNode

public void zoomInOnPreviousSelectedNode()

getCommonNamesInHash

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

********************** public String [] getSelectedNodeNames () { Graph2D graph = cw.getGraph (); ArrayList list = new ArrayList (); for (NodeCursor nc = graph.selectedNodes(); nc.ok(); nc.next()) { Node node = nc.node (); String canonicalName = cw.getCanonicalNodeName (node); String organism = cw.getNodeAttributes().getStringValue ("species", canonicalName); list.add (canonicalName); } // for nc

return (String []) list.toArray (new String [0]);

} // getSelectedNodeNames ***********************

selectNodes

protected void selectNodes()

getCanonicalNamesOfNodesInGraph

protected java.lang.String[] getCanonicalNamesOfNodesInGraph()

getGeneClusters

protected java.util.HashMap getGeneClusters()

showAll

public void showAll()

hideOrphans

protected void hideOrphans()

hideProteinAPrey

protected void hideProteinAPrey()

lots of things stick to Protein A. hide them all unless they, too, happen to have been bait, in their own right

hideEdgesByAttribute

public void hideEdgesByAttribute(java.lang.String attributeName,
                                 double threshold,
                                 java.lang.String minOrMax)

hideEdgesByAttribute

public void hideEdgesByAttribute(java.lang.String attributeName,
                                 int threshold,
                                 java.lang.String minOrMax)

hideNodesByThreshold

public void hideNodesByThreshold(java.lang.String nodeAttributeName,
                                 double threshold,
                                 int aboveOrBelow)

getDoubleEdgeAttributes

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

getIntegerEdgeAttributes

public int[] getIntegerEdgeAttributes(java.lang.String attributeName)

getDoubleNodeAttributes

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

getEdgeWeights

public double[] getEdgeWeights()

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)
                  throws java.rmi.RemoteException

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

Throws:

java.rmi.RemoteException - if RMI communication fails

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

handleCluster

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

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

Throws:

java.rmi.RemoteException - if RMI communication fails

handleNetwork

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

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

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()

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

doBroadcastNetwork

public void doBroadcastNetwork()

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()