cytoscape.layout
Class AbstractLayout

java.lang.Object
  cytoscape.layout.AbstractLayout

All Implemented Interfaces:

CyLayoutAlgorithm

Direct Known Subclasses:

GridNodeLayout

public abstract class AbstractLayout
extends Object
implements CyLayoutAlgorithm

The AbstractLayout provides nice starting point for Layouts written for Cytoscape.

Field Summary

protected boolean	canceled
protected Dimension	currentSize
protected String	edgeAttribute
protected CyNetwork	network
protected CyNetworkView	networkView
protected String	nodeAttribute
protected static TaskMonitor	nullTaskMonitor
protected HashMap	propertyMap
protected String	propertyPrefix
protected HashMap	savedPropertyMap
protected boolean	selectedOnly
protected Set<NodeView>	staticNodes
protected TaskMonitor	taskMonitor

Constructor Summary

AbstractLayout()
The Constructor is null

Method Summary

abstract void	construct() These abstract methods must be overridden.
void	doLayout() doLayout on current network view.
void	doLayout(CyNetworkView nview) doLayout on specified network view.
void	doLayout(CyNetworkView nview, TaskMonitor monitor) doLayout on specified network view with specified monitor.
List<String>	getInitialAttributeList() This returns the list of "attributes" that are provided by an algorithm for internal purposes.
abstract String	getName() getName is used to construct property strings for this layout.
LayoutProperties	getSettings() Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.
JPanel	getSettingsPanel() Returns a JPanel to be used as part of the Settings dialog for this layout algorithm.
void	halt() Halt the algorithm.
protected void	initialize_local() Initializes all local information, and is called immediately within the initialize() process.
void	initialize() Initializer, calls intialize_local to start construction process.
protected boolean	isLocked(NodeView v)
void	lockNode(NodeView v) Lock this node (i.e.
void	lockNodes(NodeView[] nodes) Lock these nodes (i.e.
protected void	resetLabelPositions() Deletes labelPosition attribute of selected nodes (if selectedOnly) or all nodes This has the effect of moving labels back to their parent nodes position
void	revertSettings() Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.
void	setLayoutAttribute(String attributeName) Set the name of the attribute to use for attribute dependent layout algorithms.
void	setSelectedOnly(boolean selectedOnly) Set the flag that indicates that this algorithm should only operate on the currently selected nodes.
byte[]	supportsEdgeAttributes() Returns the types of edge attributes supported by this algorithm.
byte[]	supportsNodeAttributes() Returns the types of node attributes supported by this algorithm.
boolean	supportsSelectedOnly() These methods should be overridden
abstract String	toString() toString is used to get the user-visible name of the layout
void	unlockAllNodes() Unlock all nodes
void	unlockNode(NodeView v) Unlock this node
void	updateSettings() Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.

Methods inherited from class java.lang.Object

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

Field Detail

staticNodes

protected Set<NodeView> staticNodes

networkView

protected CyNetworkView networkView

network

protected CyNetwork network

selectedOnly

protected boolean selectedOnly

edgeAttribute

protected String edgeAttribute

nodeAttribute

protected String nodeAttribute

canceled

protected boolean canceled

currentSize

protected Dimension currentSize

propertyMap

protected HashMap propertyMap

savedPropertyMap

protected HashMap savedPropertyMap

taskMonitor

protected TaskMonitor taskMonitor

nullTaskMonitor

protected static TaskMonitor nullTaskMonitor

propertyPrefix

protected String propertyPrefix

Constructor Detail

AbstractLayout

public AbstractLayout()

The Constructor is null

Method Detail

construct

public abstract void construct()

These abstract methods must be overridden.

getName

public abstract String getName()

getName is used to construct property strings for this layout.

Specified by:

getName in interface CyLayoutAlgorithm

Returns:

String representing the name of the layout.

toString

public abstract String toString()

toString is used to get the user-visible name of the layout

Overrides:

toString in class Object

supportsSelectedOnly

public boolean supportsSelectedOnly()

These methods should be overridden

Specified by:

supportsSelectedOnly in interface CyLayoutAlgorithm

Returns:

true if layout supports layouts on a subset of the nodes

setSelectedOnly

public void setSelectedOnly(boolean selectedOnly)

Set the flag that indicates that this algorithm should only operate on the currently selected nodes.

Specified by:

setSelectedOnly in interface CyLayoutAlgorithm

Parameters:

selectedOnly - set to "true" if the algorithm should only apply to selected nodes only

supportsNodeAttributes

public byte[] supportsNodeAttributes()

Returns the types of node attributes supported by this algorithm. This should be overloaded by the specific algorithm

Specified by:

supportsNodeAttributes in interface CyLayoutAlgorithm

Returns:

the list of supported attribute types, or null if node attributes are not supported

supportsEdgeAttributes

public byte[] supportsEdgeAttributes()

Returns the types of edge attributes supported by this algorithm. This should be overloaded by the specific algorithm

Specified by:

supportsEdgeAttributes in interface CyLayoutAlgorithm

Returns:

the list of supported attribute types, or null if edge attributes are not supported

setLayoutAttribute

public void setLayoutAttribute(String attributeName)

Set the name of the attribute to use for attribute dependent layout algorithms.

Specified by:

setLayoutAttribute in interface CyLayoutAlgorithm

Parameters:

attributeName - The name of the attribute

getInitialAttributeList

public List<String> getInitialAttributeList()

This returns the list of "attributes" that are provided by an algorithm for internal purposes. For example, an edge-weighted algorithmn might seed the list of attributes with "unweighted". This should be overloaded by algorithms that intend to return custom attributes.

Specified by:

getInitialAttributeList in interface CyLayoutAlgorithm

Returns:

A (possibly empty) list of attributes

getSettingsPanel

public JPanel getSettingsPanel()

Returns a JPanel to be used as part of the Settings dialog for this layout algorithm.

Specified by:

getSettingsPanel in interface CyLayoutAlgorithm

Returns:

JPanel that will be used in the LayoutSettingsDialog. If this algorithm does not support a UI for settings, it should return null

revertSettings

public void revertSettings()

Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.

Specified by:

revertSettings in interface CyLayoutAlgorithm

updateSettings

public void updateSettings()

Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.

Specified by:

updateSettings in interface CyLayoutAlgorithm

getSettings

public LayoutProperties getSettings()

Property handling -- these must be overridden by any algorithms that want to use properties or have a settings UI.

Specified by:

getSettings in interface CyLayoutAlgorithm

Returns:

the layout properties for this algorithm

doLayout

public void doLayout()

doLayout on current network view.

Specified by:

doLayout in interface CyLayoutAlgorithm

doLayout

public void doLayout(CyNetworkView nview)

doLayout on specified network view.

Specified by:

doLayout in interface CyLayoutAlgorithm

Parameters:

nview - the CyNetworkView on which to perform the layout

doLayout

public void doLayout(CyNetworkView nview,
                     TaskMonitor monitor)

doLayout on specified network view with specified monitor.

Specified by:

doLayout in interface CyLayoutAlgorithm

Parameters:

nview - the CyNetworkView on which to perform the layout

monitor - the task monitor to use

initialize

public void initialize()

Initializer, calls intialize_local to start construction process.

initialize_local

protected void initialize_local()

Initializes all local information, and is called immediately within the initialize() process. The user is responsible for overriding this method to do any construction that may be necessary: for example, to initialize local per-edge or graph-wide data.

lockNodes

public void lockNodes(NodeView[] nodes)

Lock these nodes (i.e. prevent them from moving).

Specified by:

lockNodes in interface CyLayoutAlgorithm

Parameters:

nodes - An array of NodeView's to lock

lockNode

public void lockNode(NodeView v)

Lock this node (i.e. prevent it from moving).

Specified by:

lockNode in interface CyLayoutAlgorithm

Parameters:

v - A NodeView to lock

unlockNode

public void unlockNode(NodeView v)

Unlock this node

Specified by:

unlockNode in interface CyLayoutAlgorithm

Parameters:

v - A NodeView to unlock

isLocked

protected boolean isLocked(NodeView v)

unlockAllNodes

public void unlockAllNodes()

Unlock all nodes

Specified by:

unlockAllNodes in interface CyLayoutAlgorithm

halt

public void halt()

Halt the algorithm.

Specified by:

halt in interface CyLayoutAlgorithm

resetLabelPositions

protected void resetLabelPositions()

Deletes labelPosition attribute of selected nodes (if selectedOnly) or all nodes This has the effect of moving labels back to their parent nodes position