org.cytoscape.view.layout

Class AbstractPartitionLayoutTask

java.lang.Object

org.cytoscape.work.AbstractTask

org.cytoscape.view.layout.AbstractLayoutTask

org.cytoscape.view.layout.AbstractPartitionLayoutTask

All Implemented Interfaces:

Task

Direct Known Subclasses:

AbstractParallelPartitionLayoutTask

public abstract class AbstractPartitionLayoutTask
extends AbstractLayoutTask

This is a more helpful implementation of a LayoutAlgorithm Task that extends AbstractBasicLayoutTask and does the work of partitioning the CyNetworkView so that partitions may be laid out individually. Extensions of this class are meant to implement the layoutPartition() method and operate on the LayoutParition object that is passed to that method as an argument.

Cytoscape Backwards Compatibility (Abstract Class): This class is abstract and meant to be extended by users. This means that we may add methods for minor version updates. Methods will only be removed for major version updates.

Module: layout-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>layout-api</artifactId>
</dependency>

Field Summary

Fields

Modifier and Type	Field and Description
protected double	current_size Partition size used for taskMonitor.
protected double	current_start Starting node number used for taskMonitor.
protected EdgeWeighter	edgeWeighter The EdgeWeighter used for edge weight calculations.
protected double	incr The value used for spacing nodes.
protected List<LayoutPartition>	partitionList The list of LayoutPartition objects that get laid out.
protected TaskMonitor	taskMonitor The TaskMonitor initially set in the run method of the task.
protected double	total_nodes Total number of nodes used for taskMonitor.

Fields inherited from class org.cytoscape.view.layout.AbstractLayoutTask

LAYOUT_ALGORITHM, layoutAttribute, networkView, nodesToLayOut, recenter, undo

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor and Description
AbstractPartitionLayoutTask(String displayName, boolean singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut, String layoutAttribute, UndoSupport undo) Creates a new AbstractPartitionLayoutTask object.

Method Summary

Modifier and Type	Method and Description
void	doLayout(TaskMonitor taskMonitor) AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.
abstract void	layoutPartition(LayoutPartition partition) Override this method and layout the LayoutPartion just like you would a NetworkView.
protected void	setTaskStatus(int percent) Used for

Methods inherited from class org.cytoscape.view.layout.AbstractLayoutTask

run

Methods inherited from class org.cytoscape.work.AbstractTask

cancel, insertTasksAfterCurrentTask, insertTasksAfterCurrentTask, setTaskIterator

Methods inherited from class java.lang.Object

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

Field Detail

taskMonitor

protected TaskMonitor taskMonitor

The TaskMonitor initially set in the run method of the task. Used to track the layout progress.

incr

protected double incr

The value used for spacing nodes. Defaults to 100.

partitionList

protected List<LayoutPartition> partitionList

The list of LayoutPartition objects that get laid out.

edgeWeighter

protected EdgeWeighter edgeWeighter

The EdgeWeighter used for edge weight calculations.

current_start

protected double current_start

Starting node number used for taskMonitor.

current_size

protected double current_size

Partition size used for taskMonitor.

total_nodes

protected double total_nodes

Total number of nodes used for taskMonitor.

Constructor Detail

AbstractPartitionLayoutTask

public AbstractPartitionLayoutTask(String displayName,
                                   boolean singlePartition,
                                   CyNetworkView networkView,
                                   Set<View<CyNode>> nodesToLayOut,
                                   String layoutAttribute,
                                   UndoSupport undo)

Creates a new AbstractPartitionLayoutTask object.

Parameters:

name - The name of the layout algorithm.

singlePartition - Whether this layout algorithm should execute on a single partition instead of multiple partitions.

networkView - the CyNetworkView being partitioned.

nodesToLayOut - the set of nodes to layout.

layoutAttribute - the name of the attribute to use for this layout. Allowed to be empty or null.

Method Detail

layoutPartition

public abstract void layoutPartition(LayoutPartition partition)

Override this method and layout the LayoutPartion just like you would a NetworkView.

Parameters:

partition - The LayoutPartition to be laid out.

setTaskStatus

protected void setTaskStatus(int percent)

Used for

Parameters:

percent - The percentage of completion for this partition. Value must be between 0 and 100.

doLayout

public void doLayout(TaskMonitor taskMonitor)

AbstractGraphPartitionLayout implements the doLayout method of AbstractBasicLayout in which it calls the layoutParition method on each LayoutPartition object created for the network.

Specified by:

doLayout in class AbstractLayoutTask

Parameters:

taskMonitor - the TaskMonitor provided by the run() method of the Task.