org.systemsbiology.gaggle.geese.cy.mastermap
Class MasterMapPlugin

java.lang.Object
  AbstractPlugin
      org.systemsbiology.gaggle.geese.cy.mastermap.MasterMapPlugin

All Implemented Interfaces:

java.io.Serializable, java.rmi.Remote, Goose

public class MasterMapPlugin
extends AbstractPlugin
implements Goose, java.io.Serializable

Field Summary

protected UndoableGraphHider	graphHider
protected javax.swing.JTextField	mapNameReadout
protected javax.swing.JTextField	nodeSelectionTextField
protected javax.swing.JTextField	scoreReadout

Constructor Summary

MasterMapPlugin(CytoscapeWindow cytoscapeWindow)

Method Summary

protected void	broadcastGenes() find all the genes in each selected node, make a list, broadcast them
void	clearSelections()
void	connectToGaggle()
protected javax.swing.JPanel	createCytoscapeControls()
protected javax.swing.JToolBar	createGaggleToolBar()
protected javax.swing.JPanel	createGui()
protected javax.swing.JPanel	createMapNameReadout()
protected java.lang.String	discoverGooseName(java.lang.String[] commandLineArgs)
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()
protected java.util.HashSet	getCurrentEdgeNames(Graph2D graph)
protected java.lang.String[]	getCurrentNodeNames(Graph2D graph)
protected java.util.HashMap	getCurrentNodes(Graph2D graph)
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	hideNodesByThreshold(java.lang.String nodeAttributeName, double threshold, int aboveOrBelow)
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 java.lang.Object

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

Field Detail

graphHider

protected UndoableGraphHider graphHider

nodeSelectionTextField

protected javax.swing.JTextField nodeSelectionTextField

scoreReadout

protected javax.swing.JTextField scoreReadout

mapNameReadout

protected javax.swing.JTextField mapNameReadout

Constructor Detail

MasterMapPlugin

public MasterMapPlugin(CytoscapeWindow cytoscapeWindow)

Method Detail

createGui

protected javax.swing.JPanel createGui()

createMapNameReadout

protected javax.swing.JPanel createMapNameReadout()

createGaggleToolBar

protected javax.swing.JToolBar createGaggleToolBar()

createCytoscapeControls

protected javax.swing.JPanel createCytoscapeControls()

hideNodesByThreshold

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

discoverGooseName

protected java.lang.String discoverGooseName(java.lang.String[] commandLineArgs)

doBroadcastList

public void doBroadcastList()

Specified by:

doBroadcastList in interface Goose

doBroadcastNetwork

public void doBroadcastNetwork()

broadcastGenes

protected void broadcastGenes()

find all the genes in each selected node, make a list, broadcast them

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

getCanonicalNamesOfNodesInGraph

protected java.lang.String[] getCanonicalNamesOfNodesInGraph()

selectNodesByName

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

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

selectNodes

protected void selectNodes()

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)
                   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)

getCurrentEdgeNames

protected java.util.HashSet getCurrentEdgeNames(Graph2D graph)

getName

public java.lang.String getName()

Description copied from interface: Goose

Returns the name of the goose.

Specified by:

getName in interface Goose

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

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)

doExit

public void doExit()

Description copied from interface: Goose

Tells the goose to exit (terminate).

Specified by:

doExit in interface Goose

connectToGaggle

public void connectToGaggle()

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);