attachment:NeighborNodeSelection.java of Neighbor_Node_Selection_Cytoscape_Plugin

   1 import java.util.*;
   2 import java.awt.event.ActionEvent;
   3 import javax.swing.JOptionPane;
   4 
   5 import giny.model.Node;
   6 import giny.view.NodeView;
   7 
   8 import cytoscape.plugin.CytoscapePlugin;
   9 import cytoscape.util.CytoscapeAction;
  10 import cytoscape.Cytoscape;
  11 import cytoscape.CyNetwork;
  12 import cytoscape.CyNode;
  13 import cytoscape.CyEdge;
  14 import cytoscape.view.CyNetworkView;
  15 import cytoscape.data.Semantics;
  16 
  17 /**
  18  * This is a sample Cytoscape plugin using core graph and data structures. 
  19  * For each currently selected node in the graph view, the action method 
  20  * of this plugin additionally selects the neighbors of that node.
  21  *
  22  * Note that selection is a property of the view of the graph, while neighbors
  23  * are a property of the graph itself. Thus this plugin must access both the
  24  * graph and its view.
  25  */
  26 public class NeighborNodeSelection extends CytoscapePlugin {
  27     
  28     /**
  29      * This constructor creates an action and adds it to the Plugins menu.
  30      */
  31     public NeighborNodeSelection() {
  32         //create a new action to respond to menu activation
  33         NeighborNodeSelectionAction action = new NeighborNodeSelectionAction();
  34         //set the preferred menu
  35         action.setPreferredMenu("Plugins");
  36         //and add it to the menus
  37         Cytoscape.getDesktop().getCyMenus().addAction(action);
  38     }
  39     
  40     /**
  41      * Gives a description of this plugin.
  42      */
  43     public String describe() {
  44         StringBuffer sb = new StringBuffer();
  45         sb.append("For every currently selected node in the graph view, this ");
  46         sb.append("plugin additionally selects each neighbor of that node if ");
  47         sb.append("the canonical names of the two nodes have the same last letter.");
  48         return sb.toString();
  49     }
  50         
  51     /**
  52      * This class gets attached to the menu item.
  53      */
  54     public class NeighborNodeSelectionAction extends CytoscapeAction {
  55         
  56         /**
  57          * The constructor sets the text that should appear on the menu item.
  58          */
  59         public NeighborNodeSelectionAction() {super("NeighborNodeSelection");}
  60         
  61         /**
  62          * This method is called when the user selects the menu item.
  63          */
  64         public void actionPerformed(ActionEvent ae) {
  65             //get the network object; this contains the graph
  66             CyNetwork network = Cytoscape.getCurrentNetwork();
  67             //get the network view object
  68             CyNetworkView view = Cytoscape.getCurrentNetworkView();
  69             //can't continue if either of these is null
  70             if (network == null || view == null) {return;}
  71             //put up a dialog if there are no selected nodes
  72             if (view.getSelectedNodes().size() == 0) {
  73                 JOptionPane.showMessageDialog(view.getComponent(),
  74                         "Please select one or more nodes.");
  75             }
  76             
  77             //a container to hold the objects we're going to select
  78             Set nodeViewsToSelect = new HashSet();
  79             //iterate over every node view
  80             for (Iterator i = view.getSelectedNodes().iterator(); i.hasNext(); ) {
  81                 NodeView nView = (NodeView)i.next();
  82                 //first get the corresponding node in the network
  83                 CyNode node = (CyNode)nView.getNode();
  84                 // get the neighbors of that node
  85                 List neighbors = network.neighborsList(node);
  86                 // and iterate over the neighbors
  87                 for (Iterator ni = neighbors.iterator(); ni.hasNext(); ) {
  88                     CyNode neighbor = (CyNode)ni.next();
  89 		    // get the view on this neighbor
  90 		    NodeView neighborView = view.getNodeView(neighbor);
  91 		    //and add that view to our container of objects to select
  92 		    nodeViewsToSelect.add(neighborView);
  93                 }
  94             }
  95             //now go through our container and select each view
  96             for (Iterator i = nodeViewsToSelect.iterator(); i.hasNext(); ) {
  97                 NodeView nView = (NodeView)i.next();
  98                 nView.setSelected(true);
  99             }
 100             //tell the view to redraw since we've changed the selection
 101             view.redrawGraph(false, true);
 102         }
 103         
 104         /**
 105          * Gets the canonical name of the given node from the network object
 106          * and returns a String holding just the last letter of that name.
 107          *
 108          * Returns null if a valid name cannot be obtained.
 109          */
 110         private String getLastLetter(CyNetwork network, CyNode node) {
 111             String canonicalName = (String)network.getNodeAttributeValue(node, Semantics.CANONICAL_NAME);
 112             //return nothing if we can't get a valid name
 113             if (canonicalName == null || canonicalName.length() == 0) {return null;}
 114             //extract the last letter
 115             int length = canonicalName.length();
 116             String lastLetter = canonicalName.substring(length-1);
 117             return lastLetter;
 118         }
 119     }
 120 }
 121