completely delete a node programmatically

[Michael Zimmermann]

I would like to add/delete nodes based on user interaction with a given network. Adding is working fine with the following type of api call:

 

CyNode ntmp = Cytoscape.getCyNode(NewNodeID, true);

current_network.addNode(ntmp);

 

However, when I want to delete a node using:

 

current_network.removeNode(clickedNode.getRootGraphIndex(), true);

 

and later call:

 

List<Node> nodeList = Cytoscape.getCyNodesList();

 

the "removed" node is still found in nodeList. Do I need to somehow refresh the network between removeNode() and getCyNodeList() for it to register the removal? Or is there a different api call for total removal? The documentation found here makes it sound like removeNode() is what I want...

 

P.S. is this type of question most appropriate for here or the developer's list?

 

[Jason Montojo]

Hi Michael,

Cytoscape.getCyNodesList() returns a list of all nodes in the root network, which contains all nodes and edges from all networks in Cytoscape.  If you delete a node from a particular network that isn't the root network, it will only be deleted from that network.  To delete a node from the root network, use this:

http://chianti.ucsd.edu/Cyto-2_8_3/javadoc/cytoscape/Cytoscape.html#getRootGraph()

Hope this helps,

Jason

 

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[Michael Zimmermann]

I see, thank you Jason. I just want to loop through the nodes in the present network. Is there an analogous method to getCyNodeList() that only applies to the curent network?

 

Otherwise, I could use a hand with the initilization for accessing the rootGraph. From the link you sent, I would expect to do:

CytoscapeRootGraph rootGraph = Cytoscape.getRootGraph();

but I get "cannot find symbol" error - Do I need to import another class? It looks like this should be a method of cytoscape.Cytoscape.

 

I also tried other variantions like:

CytoscapeRootGraph rootGraph = Cytoscape.getCurrentNetwork().getRootGraph();

but haven't figured it out...

 

On Tuesday, September 18, 2012 11:54:32 AM UTC-5, Jason Montojo wrote: