org.cytoscape.cyni
Class AbstractCyniTask
java.lang.Object
org.cytoscape.work.AbstractTask
org.cytoscape.cyni.AbstractCyniTask
- All Implemented Interfaces:
- org.cytoscape.work.Task
public abstract class AbstractCyniTask
- extends org.cytoscape.work.AbstractTask
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 int |
nThreads
Indicates the maximum number of threads that this task can use |
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,
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. |
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 |
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
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 algorithmnetworkFactory
- The network factory to create a new networknetworkViewFactory
- The network view factory to create a new network viewnetworkManager
- The network managernetworkViewManager
- The network view managernetTableMgr
- The network table manager to generate a new network and its tablerootNetMgr
- The root network manager to generate a new root networkvmMgr
- The Visual mapping manager that allows changing the visual style of a network
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
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.
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