Cytoscape WikiThis guide is intended to provide code examples for using CytoscapeData to access all of your information. Any questions should be directed to cytoscape-discuss@googlegroups.com
1. Acessing Cytoscape Data
All attributes in Cytoscape are shared acrosss all CyNetworks. So there is only one global CytoscapeData instance for nodes and edges. These are available from the cytoscape.Cytoscape class.
1 import cytoscape.Cytoscape;
2 import cytoscape.data.CytoscapeData;
3
4 public class MyDataClass {
5
6 MyDataClass () {
7
8 // get the node CytoscapeData Instance
9 CytoscapeData node_data = Cytoscape.getNodeNetworkData();
10
11 // get the edge CytoscapeData Instance
12 CytoscapeData edge_data = Cytoscape.getEdgeNetworkData();
13 }
14
(We will assume that these import statements are being used for all subsequent examples.)
As discussed on the CytoscapeData description page, there are 3 ways of adding data. All are compatible, but based on how your data is structured, one might present itself as being more suitable.
2. Single Value Access
If you only have a single value for an attribute, i.e. the name of a node, the single access methods will work fine.
1 // add a value to a node
2
3 GraphObject object; // this can be a Node or Edge.
4 String attribute_name = "test_attribute"; // an attribute name
5 Object value = new Double( 5 ); // a Double of value "5"
6
7 // get the node CytoscapeData Instance
8 CytoscapeData data = Cytoscape.getNodeNetworkData();
9
10 // add the value
11 data.setAttributeValue( object.getIdentifier(), attribute_name, value );
12