org.cytoscape.cyni
Class CyniNetworkUtils

java.lang.Object
  org.cytoscape.cyni.CyniNetworkUtils

public class CyniNetworkUtils
extends Object

This is a class that contains several methods to help while creating a new network

Field Summary

protected org.cytoscape.model.CyNetworkManager	netMgr
protected org.cytoscape.view.model.CyNetworkViewFactory	viewFactory
protected org.cytoscape.view.model.CyNetworkViewManager	viewMgr
protected org.cytoscape.view.vizmap.VisualMappingManager	vmMgr

Constructor Summary

CyniNetworkUtils(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

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 columns that belong to a table associated to a network to a new table associated to a new network.
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
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
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
void	removeNodesWithoutEdges(org.cytoscape.model.CyNetwork network) Remove nodes that do not have any edge

Methods inherited from class java.lang.Object

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

Field Detail

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

Constructor Detail

CyniNetworkUtils

public CyniNetworkUtils(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:

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

Method Detail

addColumns

public 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 columns that belong to a table associated to a network to a new table associated to a new network. Basically, allows copying all columns from one table to another one

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

cloneRow

public 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

public 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

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

Remove nodes that do not have any edge

Parameters:

network - The network to remove nodes

displayNewNetwork

public 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