fr.systemsbiology.cyni
Class AbstractCyniTask

java.lang.Object
  org.cytoscape.work.AbstractTask
      fr.systemsbiology.cyni.AbstractCyniTask

All Implemented Interfaces:

org.cytoscape.work.ObservableTask, org.cytoscape.work.Task

public abstract class AbstractCyniTask
extends org.cytoscape.work.AbstractTask
implements org.cytoscape.work.ObservableTask

This is a basic implementation of a CyniAlgorithm Task that does some bookkeeping, but primarily delegates to the doCyniTask() method.

Field Summary

protected org.cytoscape.model.CyNetworkFactory	netFactory
protected org.cytoscape.model.CyNetworkManager	netMgr
protected org.cytoscape.model.CyNetworkTableManager	netTableMgr
protected org.cytoscape.model.CyNetwork	newNetwork This variable holds the new network that will be created if an inference algorithm is executed.
protected int	nThreads Indicates the maximum number of threads that this task can use
protected String	outputMessage This variable holds the message that will be shown after task is done
protected org.cytoscape.model.subnetwork.CyRootNetworkManager	rootNetMgr
protected boolean	selectedOnly Indicates whether to apply the algorithm to all rows or only the selected rows.
protected org.cytoscape.view.model.CyNetworkViewFactory	viewFactory
protected org.cytoscape.view.model.CyNetworkViewManager	viewMgr
protected org.cytoscape.view.vizmap.VisualMappingManager	vmMgr

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

AbstractCyniTask(String name, CyniAlgorithmContext context)
This Constructor can be used for Cyni tasks that don't need to create a new network such as Discretization or Imputation algorithms

AbstractCyniTask(String name, CyniAlgorithmContext context, org.cytoscape.model.CyNetworkFactory networkFactory, org.cytoscape.view.model.CyNetworkViewFactory networkViewFactory, org.cytoscape.model.CyNetworkManager networkManager, org.cytoscape.view.model.CyNetworkViewManager networkViewManager, org.cytoscape.model.CyNetworkTableManager netTableMgr, org.cytoscape.model.subnetwork.CyRootNetworkManager rootNetMgr, org.cytoscape.view.vizmap.VisualMappingManager visualMapperManager)
Constructor.

Method Summary

protected abstract void	doCyniTask(org.cytoscape.work.TaskMonitor taskMonitor) This method is designed to actually encapsulate the cyni algorithm.
Object	getResults(Class requestedType)
void	run(org.cytoscape.work.TaskMonitor taskMonitor)

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

Methods inherited from interface org.cytoscape.work.Task

cancel

Field Detail

netTableMgr

protected final org.cytoscape.model.CyNetworkTableManager netTableMgr

rootNetMgr

protected final org.cytoscape.model.subnetwork.CyRootNetworkManager rootNetMgr

netFactory

protected org.cytoscape.model.CyNetworkFactory netFactory

viewFactory

protected org.cytoscape.view.model.CyNetworkViewFactory viewFactory

netMgr

protected org.cytoscape.model.CyNetworkManager netMgr

viewMgr

protected org.cytoscape.view.model.CyNetworkViewManager viewMgr

vmMgr

protected org.cytoscape.view.vizmap.VisualMappingManager vmMgr

selectedOnly

protected final boolean selectedOnly

Indicates whether to apply the algorithm to all rows or only the selected rows.

nThreads

protected int nThreads

Indicates the maximum number of threads that this task can use

newNetwork

protected org.cytoscape.model.CyNetwork newNetwork

This variable holds the new network that will be created if an inference algorithm is executed.

outputMessage

protected String outputMessage

This variable holds the message that will be shown after task is done

Constructor Detail

AbstractCyniTask

public AbstractCyniTask(String name,
                        CyniAlgorithmContext context,
                        org.cytoscape.model.CyNetworkFactory networkFactory,
                        org.cytoscape.view.model.CyNetworkViewFactory networkViewFactory,
                        org.cytoscape.model.CyNetworkManager networkManager,
                        org.cytoscape.view.model.CyNetworkViewManager networkViewManager,
                        org.cytoscape.model.CyNetworkTableManager netTableMgr,
                        org.cytoscape.model.subnetwork.CyRootNetworkManager rootNetMgr,
                        org.cytoscape.view.vizmap.VisualMappingManager visualMapperManager)

Constructor.

Parameters:

name - The name of the algorithm.

context - The context with the parameters to apply the algorithm

networkFactory - The network factory to create a new network

networkViewFactory - The network view factory to create a new network view

networkManager - The network manager

networkViewManager - The network view manager

netTableMgr - The network table manager to generate a new network and its table

rootNetMgr - The root network manager to generate a new root network

vmMgr - The Visual mapping manager that allows changing the visual style of a network

AbstractCyniTask

public AbstractCyniTask(String name,
                        CyniAlgorithmContext context)

This Constructor can be used for Cyni tasks that don't need to create a new network such as Discretization or Imputation algorithms

Parameters:

name - The name of the algorithm.

context - The context with the parameters to apply the algorithm

Method Detail

run

public final void run(org.cytoscape.work.TaskMonitor taskMonitor)

Specified by:

run in interface org.cytoscape.work.Task

Specified by:

run in class org.cytoscape.work.AbstractTask

getResults

public Object getResults(Class requestedType)

Specified by:

getResults in interface org.cytoscape.work.ObservableTask

doCyniTask

protected abstract void doCyniTask(org.cytoscape.work.TaskMonitor taskMonitor)

This method is designed to actually encapsulate the cyni algorithm. It will be called from within the run() method of the task.

Parameters:

taskMonitor - Provided to allow updates to the task status.