This plugin works with multiple networks. When active, it links all Cytoscape networks so that any node or edge that is flagged in one network is flagged in all networks. In Cytoscape, the flagged state of an object in a network is synchronized with the selection state of the corresponding object in any view of that network. A graph object can also be flagged in a network that has no view (useful for marking objects as interesting to other plugins). Thus, this plugin allows the user or a plugin to flag or select nodes in one network or view and have them automatically flagged in all networks and selected in all views that also have those graph objects.

This plugin illustrates three different types of Cytoscape event handling. It captures events fired by any network's flagger to update the flagged state in all networks. It catches graph change events to handle nodes or edges that are hidden. Finally, it catches network creation events to synchronize the new network with the flag/selection state of all the other networks.

To see the plugin in action, run Cytoscape with the plugin and a network loaded. Create a subnetwork of the first network by selecting some nodes and using the Select->To New Window->Selected Nodes, All Edges menu option. You might need to create a view on this new network with the Edit->Create View menu option if the network is large. You should see that objects selected in one view are also selected in the other view if they exist in both views.

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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