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 Map<Integer,ArrayList<Integer>>	nodeParents This variable maps an integer representing a node/row with a list of integers that represents a list of parents for that node/row In oder to use it correctly, this variable needs to be initialized and a previous map between a node and its corresponding integer is also required
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, AbstractCyniAlgorithmContext 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 void	addColumns(org.cytoscape.model.CyNetwork origNet, org.cytoscape.model.CyNetwork newNet, org.cytoscape.model.CyTable origTable, Class<? extends org.cytoscape.model.CyIdentifiable> tableType, String namespace) Add a column that belongs to a table associated to a network to a new table associated to a new network
protected void	addVirtualColumn(org.cytoscape.model.CyColumn col, org.cytoscape.model.CyTable subTable) Add a virtual column to a table
protected void	cloneRow(org.cytoscape.model.CyNetwork newNet, Class<? extends org.cytoscape.model.CyIdentifiable> tableType, org.cytoscape.model.CyRow from, org.cytoscape.model.CyRow to) Clone a row to be added to a new network
protected void	copyColumn(org.cytoscape.model.CyColumn col, org.cytoscape.model.CyTable subTable) Copy a column to a table
protected org.cytoscape.view.model.CyNetworkView	displayNewNetwork(org.cytoscape.model.CyNetwork newNetwork, org.cytoscape.model.CyNetwork oldNetwork, boolean directed) This method displays the new network and return a network view that might be used to modify the display features such as the layout
protected abstract void	doCyniTask(org.cytoscape.work.TaskMonitor taskMonitor) This method is designed to actually encapsulate the cyni algorithm.
protected org.cytoscape.model.CyNetwork	getNetworkAssociatedToTable(org.cytoscape.model.CyTable table) Checks if the table is associated to a network, if so it return the associated network otherwise it returns null
boolean	isGraphCyclic(int nodeToCheck) This method allows checking if there is a cycle in a graph starting from a defined node.
protected void	removeNodesWithoutEdges(org.cytoscape.model.CyNetwork network) Remove nodes that does not have any edge
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

Field Detail

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

nodeParents

protected Map<Integer,ArrayList<Integer>> nodeParents

This variable maps an integer representing a node/row with a list of integers that represents a list of parents for that node/row In oder to use it correctly, this variable needs to be initialized and a previous map between a node and its corresponding integer is also required

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

Constructor Detail

AbstractCyniTask

public AbstractCyniTask(String name,
                        AbstractCyniAlgorithmContext 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

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

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

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

addColumns

protected void addColumns(org.cytoscape.model.CyNetwork origNet,
                          org.cytoscape.model.CyNetwork newNet,
                          org.cytoscape.model.CyTable origTable,
                          Class<? extends org.cytoscape.model.CyIdentifiable> tableType,
                          String namespace)

Add a column that belongs to a table associated to a network to a new table associated to a new network

Parameters:

origNet - The original network

newNet - The new network

origTable - The original table

tableType - The type of the table

namespace - The namespace of the table

addVirtualColumn

protected void addVirtualColumn(org.cytoscape.model.CyColumn col,
                                org.cytoscape.model.CyTable subTable)

Add a virtual column to a table

Parameters:

col - The column to add.

subTable - The CyTable to add the column.

copyColumn

protected void copyColumn(org.cytoscape.model.CyColumn col,
                          org.cytoscape.model.CyTable subTable)

Copy a column to a table

Parameters:

col - The column to copy

subTable - The CyTable to add the column.

cloneRow

protected void cloneRow(org.cytoscape.model.CyNetwork newNet,
                        Class<? extends org.cytoscape.model.CyIdentifiable> tableType,
                        org.cytoscape.model.CyRow from,
                        org.cytoscape.model.CyRow to)

Clone a row to be added to a new network

Parameters:

newNet - The new network.

tableType - The type of the table.

from - The source row

to - The target row

getNetworkAssociatedToTable

protected org.cytoscape.model.CyNetwork getNetworkAssociatedToTable(org.cytoscape.model.CyTable table)

Checks if the table is associated to a network, if so it return the associated network otherwise it returns null

Parameters:

table - The table to check

Returns:

null if no network is associated to the table or the network associated

removeNodesWithoutEdges

protected void removeNodesWithoutEdges(org.cytoscape.model.CyNetwork network)

Remove nodes that does not have any edge

Parameters:

network - The network to remove nodes

displayNewNetwork

protected org.cytoscape.view.model.CyNetworkView displayNewNetwork(org.cytoscape.model.CyNetwork newNetwork,
                                                                   org.cytoscape.model.CyNetwork oldNetwork,
                                                                   boolean directed)

This method displays the new network and return a network view that might be used to modify the display features such as the layout

Parameters:

newNetwork - The new network

oldNetwork - The old network in case we are using a table associated to a network otherwise it is a null

directed - Tells whether the new network is a directed graph or not

Returns:

the new network view

isGraphCyclic

public boolean isGraphCyclic(int nodeToCheck)

This method allows checking if there is a cycle in a graph starting from a defined node. It also uses the nodeParents variable so to make a good use of this function, the nodeParents variable needs to be previously initialized

Parameters:

nodeToCheck - The index corresponding to the starting node from where we want to check if there is a cycle in the graph

Returns:

True if the graph is cyclic or false if not or the nodeParents has not been initialized

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.