ControlPanel

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

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

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.systemsbiology.gaggle.geese.cy.tileViewer.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
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 GeneFinder`	`geneFinder`
`protected UndoableGraphHider`	`graphHider`
`protected java.awt.GridBagLayout`	`gridbagLayout`
`protected javax.swing.JTextField`	`nodeInClusterSelectionTextField`
`protected javax.swing.JTextField`	`nodeSelectionTextField`
`protected javax.swing.JToolBar`	`tileNavigationToolbar`

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
`protected void`	`clearNetworkSelections()` *********************************************** protected void broadcastClusterMatrix () { // System.out.println ("broadcastClusterMatrix"); NodeCursor nc = cw.getGraph().selectedNodes (); ArrayList clusterNodes = new ArrayList (); while (nc.ok ()) { String name = cw.getNodeAttributes().getCanonicalName (nc.node ()); String type = cw.getNodeAttributes().getStringValue ("type", name); if (type != null && type.equals ("cluster")) clusterNodes.add (name); nc.next (); } if (clusterNodes.size () != 1) { JOptionPane.showMessageDialog (null, "Please choose exactly one cluster to broadcast.", "TileViewer Control Panel Error", JOptionPane.ERROR_MESSAGE); return; } String clusterName = (String) clusterNodes.get (0); String [] clusteredGenes = cw.getNodeAttributes().getStringArrayValues ("clusterGenes", clusterName); for (int i=0; i < clusteredGenes.length; i++) clusteredGenes [i] = clusteredGenes [i].toUpperCase (); String [] conditionNames = cw.getNodeAttributes().getStringArrayValues ("clusterConditions", clusterName); String [] fixedConditionNames = new String [conditionNames.length]; for (int i=0; i < conditionNames.length; i++) { String name = conditionNames [i]; // if (conditionNameFixer.containsKey (name)) // name = (String) conditionNameFixer.get (name); // else // System.err.println ("found no map for old condition name '" + name + "'"); fixedConditionNames [i] = name; } // for i //System.out.println (clusteredGenes.length + " genes in " + // fixedConditionNames.length + " conditions."); //for (int i=0; i < clusteredGenes.length; i++) // System.out.println (clusteredGenes [i]); //for (int i=0; i < fixedConditionNames.length; i++) // System.out.println (fixedConditionNames [i]); try { System.out.println ("ICP broadcast cluster: " + clusteredGenes.length + " genes " + fixedConditionNames.length + " clusters"); gaggleBoss.broadcast (myGaggleName, species, clusteredGenes, fixedConditionNames); } catch (RemoteException rex0) { System.err.println ("ControlPanel.broadcastClusterMatrix: " + rex0.getMessage ()); } } // broadcastClusterMatrix **************************************
`void`	`clearSelections()`
`void`	`connectToGaggle()`
`protected int`	`countRegulatoryEdges(Node logicGateNode)`
`protected javax.swing.JToolBar`	`createGaggleToolBar()`
`protected javax.swing.JToolBar`	`createTileNavigationToolBar()`
`void`	`doBroadcastList()`
`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()`
`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`	`hideEdgesByWeight(double min)`
`void`	`hideNodesByThreshold(java.lang.String nodeAttributeName, double threshold, int aboveOrBelow)`
`protected void`	`hideOrphans()` 'orphan' is defined broadly here to include, not only all unconnected nodes, but also all nodes not connected, directly or indirectly, to a bicluster.
`void`	`selectAllRegulatedClusters()`
`void`	`selectAllRegulatorsOfSelectedClusters()`
`protected void`	`selectClustersRegulatedByThisGene(Node regulatorNode)` select all clusters, all co-regulating genes, and all logicGate nodes within one or two steps from the specified regulator.
`protected void`	`selectNodes()`
`protected void`	`selectRegulatorsOfOneCluster(Node clusterNode)`
`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`	`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 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.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.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

connectButton

protected javax.swing.JButton connectButton

disconnectButton

protected javax.swing.JButton disconnectButton

tileNavigationToolbar

protected javax.swing.JToolBar tileNavigationToolbar

gridbagLayout

protected java.awt.GridBagLayout gridbagLayout

nodeSelectionTextField

protected javax.swing.JTextField nodeSelectionTextField

nodeInClusterSelectionTextField

protected javax.swing.JTextField nodeInClusterSelectionTextField

cw

protected CytoscapeWindow cw

dataServer

protected BioDataServer dataServer

graphHider

protected UndoableGraphHider graphHider

geneFinder

protected GeneFinder geneFinder

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()

createTileNavigationToolBar

protected javax.swing.JToolBar createTileNavigationToolBar()

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()

hideOrphans

protected void hideOrphans()

'orphan' is defined broadly here to include, not only all unconnected nodes, but also all nodes not connected, directly or indirectly, to a bicluster. a simple trick makes it easy to figure out where the second rule applies:

find all the logicGate nodes
for each, count the number of regulatory edges (type = 'activates' or 'represses')
when that count is zero, remove ALL edges on the logicGate node

after these edges are removed, the final step is simply to hide all nodes with no edges

countRegulatoryEdges

protected int countRegulatoryEdges(Node logicGateNode)

clearNetworkSelections

protected void clearNetworkSelections()

************************************************* protected void broadcastClusterMatrix () { // System.out.println ("broadcastClusterMatrix");

NodeCursor nc = cw.getGraph().selectedNodes ();

ArrayList clusterNodes = new ArrayList (); while (nc.ok ()) { String name = cw.getNodeAttributes().getCanonicalName (nc.node ()); String type = cw.getNodeAttributes().getStringValue ("type", name); if (type != null && type.equals ("cluster")) clusterNodes.add (name); nc.next (); }

if (clusterNodes.size () != 1) { JOptionPane.showMessageDialog (null, "Please choose exactly one cluster to broadcast.", "TileViewer Control Panel Error", JOptionPane.ERROR_MESSAGE); return; }

String clusterName = (String) clusterNodes.get (0); String [] clusteredGenes = cw.getNodeAttributes().getStringArrayValues ("clusterGenes", clusterName); for (int i=0; i < clusteredGenes.length; i++) clusteredGenes [i] = clusteredGenes [i].toUpperCase ();

String [] conditionNames = cw.getNodeAttributes().getStringArrayValues ("clusterConditions", clusterName);

String [] fixedConditionNames = new String [conditionNames.length]; for (int i=0; i < conditionNames.length; i++) { String name = conditionNames [i]; // if (conditionNameFixer.containsKey (name)) // name = (String) conditionNameFixer.get (name); // else // System.err.println ("found no map for old condition name '" + name + "'"); fixedConditionNames [i] = name; } // for i

//System.out.println (clusteredGenes.length + " genes in " + // fixedConditionNames.length + " conditions.");

//for (int i=0; i < clusteredGenes.length; i++) // System.out.println (clusteredGenes [i]);

//for (int i=0; i < fixedConditionNames.length; i++) // System.out.println (fixedConditionNames [i]);

try { System.out.println ("ICP broadcast cluster: " + clusteredGenes.length + " genes " + fixedConditionNames.length + " clusters"); gaggleBoss.broadcast (myGaggleName, species, clusteredGenes, fixedConditionNames); } catch (RemoteException rex0) { System.err.println ("ControlPanel.broadcastClusterMatrix: " + rex0.getMessage ()); }

} // broadcastClusterMatrix ****************************************

hideEdgesByWeight

public void hideEdgesByWeight(double min)

hideNodesByThreshold

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

selectAllRegulatorsOfSelectedClusters

public void selectAllRegulatorsOfSelectedClusters()

selectRegulatorsOfOneCluster

protected void selectRegulatorsOfOneCluster(Node clusterNode)

selectAllRegulatedClusters

public void selectAllRegulatedClusters()

selectClustersRegulatedByThisGene

protected void selectClustersRegulatedByThisGene(Node regulatorNode)

select all clusters, all co-regulating genes, and all logicGate nodes within one or two steps from the specified regulator. the success of the current algorithm depends upon there being either zero or one logic gates between regulators and the clusters they regulate.

getDoubleEdgeAttributes

public double[] getDoubleEdgeAttributes(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

doExit

public void doExit()

Description copied from interface: Goose

Tells the goose to exit (terminate).

Specified by:: doExit in interface Goose

getCommands

public java.lang.String[] getCommands()

createGaggleToolBar

protected javax.swing.JToolBar createGaggleToolBar()

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);

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

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

activeGooseNames

connectButton

disconnectButton

tileNavigationToolbar

gridbagLayout

nodeSelectionTextField

nodeInClusterSelectionTextField

cw

dataServer

graphHider

geneFinder

defaultCursor

busyCursor

ControlPanel

connectToGaggle

createTileNavigationToolBar

selectTilesAboveCurrentRatioThreshold

selectTilesAboveCurrentLambdaThreshold

zoomInOnNextSelectedNode

zoomInOnPreviousSelectedNode

getCommonNamesInHash

selectNodes

getCanonicalNamesOfNodesInGraph

getGeneClusters

hideOrphans

countRegulatoryEdges

clearNetworkSelections

hideEdgesByWeight

hideNodesByThreshold

selectAllRegulatorsOfSelectedClusters

selectRegulatorsOfOneCluster

selectAllRegulatedClusters

selectClustersRegulatedByThisGene

getDoubleEdgeAttributes

getDoubleNodeAttributes

getEdgeWeights

handleNameList

handleMatrix

handleTuple

handleCluster

handleNetwork

getName

setName

getSelectionCount

doHide

doShow

clearSelections

setGeometry

doBroadcastList

doExit

getCommands

createGaggleToolBar

update

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