Author: ghuck
Date: 2011-06-15 13:10:19 -0700 (Wed, 15 Jun 2011)
New Revision: 25764
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
Log:
Added support for passing only selected nodes to Igraph
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-15 20:03:15 UTC (rev 25763)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphPlugin.java
2011-06-15 20:10:19 UTC (rev 25764)
@@ -67,8 +67,11 @@
NodeCount nodeCountAction = new NodeCount(this);
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
nodeCountAction);
- IsConnected isConnectedAction = new IsConnected(this);
-
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction);
+ IsConnected isConnectedAction1 = new IsConnected(this, "All
nodes",false);
+
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction1);
+
+ IsConnected isConnectedAction2 = new IsConnected(this, "Selected
Nodes", true);
+
Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction)
isConnectedAction2);
}
private boolean isOldVersion(){
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
2011-06-15 20:03:15 UTC (rev 25763)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IsConnected.java
2011-06-15 20:10:19 UTC (rev 25764)
@@ -1,3 +1,22 @@
+/**************************************************************************************
+Copyright (C) Gerardo Huck, 2011
+
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+**************************************************************************************/
+
package cytoscape.plugins.igraph;
import java.awt.event.ActionEvent;
@@ -9,10 +28,7 @@
import cytoscape.data.*;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.util.CytoscapeAction;
-import cytoscape.task.Task;
-import cytoscape.task.TaskMonitor;
-
import giny.model.*;
import com.sun.jna.Library;
@@ -21,103 +37,107 @@
public class IsConnected extends CytoscapeAction {
+ Boolean selectedOnly;
- private IgraphTaskThread t; //This thread is actually where the action is
- private Thread currentThread;
-
-
- public IsConnected(IgraphPlugin myPlugin) {
- super("IsConnected");
- setPreferredMenu("Plugins.Igraph");
+ public IsConnected(IgraphPlugin myPlugin, String name, boolean
selectedOnly) {
+ super(name);
+ setPreferredMenu("Plugins.Igraph.IsConnected");
+ this.selectedOnly = new Boolean(selectedOnly);
}
public void actionPerformed(ActionEvent e) {
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is Connected?: "
+ isConnected());
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Is Connected?: "
+ isConnected(this.selectedOnly));
}
- public boolean isConnected() {
-
- loadGraph_optimized();
- return IgraphInterface.isConnected(); //Only call this function if the
graph has been loaded
-
-
-// boolean res = false;
-// try {
-// ArrayList<Integer> nodes = loadGraph_optimized();
-// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Graph
loaded...Number of nodes: " + nodes.size());
-// res = IgraphInterface.isConnected();
-// }
-// catch (Exception e) {
-// e.printStackTrace();
-// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Igraph
Plugin error:\n" + e.getMessage());
-// res = false;
-// }
-// finally{
-// return res;
-// }
-
-
-// t = new IgraphTaskThread();
-// t.setAlgorithm(1);
-
-// //This marks the current thread
-// currentThread = Thread.currentThread();
-
-// t.start();
-// try{
-// t.join(); //Join the background thread running the algorithm
with the current thread showing the progressbar
-// }
-// catch(InterruptedException e){
-// //System.out.println("Algorithm terminated");
-// //The failed C algorithm may cause issues here
-// e.printStackTrace();
-// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Igraph
Plugin error:\n" + e.getMessage());
-// }
-
-// return t.getResult();
+ public boolean isConnected(boolean selectedOnly) {
+ loadGraph_optimized(selectedOnly);
+ return IgraphInterface.isConnected();
}
//This will load the graph into c
- public static ArrayList<Integer> loadGraph_optimized(){
+ public static HashMap<Integer,Integer> loadGraph_optimized(boolean
selectedOnly){
// Nodes are ordered according to node array.
CyNetwork network = Cytoscape.getCurrentNetwork();
- ArrayList<Integer> selectedNodeIndices = new ArrayList<Integer>();
+ // ArrayList<Integer> selectedNodeIndices = new
ArrayList<Integer>();
- int[] edgeIndicesArray = network.getEdgeIndicesArray();
- int[] nodeArray = network.getNodeIndicesArray();
+ // int[] edgeIndicesArray = network.getEdgeIndicesArray();
+ // int[] nodeArray = network.getNodeIndicesArray();
+ // Set<Node> selectedNodes = network.geSelectedNodes();
// Create a reverse mapping
- HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeArray.length);
- for(int i=0; i<nodeArray.length; i++){
- nodeIdMapping.put(nodeArray[i], i);
+ int nodeCount;
+ if(selectedOnly) {
+ nodeCount = network.getSelectedNodes().size();
+ } else {
+ nodeCount = network.getNodeCount();
+ }
+ HashMap<Integer, Integer> nodeIdMapping = new HashMap<Integer,
Integer>(nodeCount);
+ int j = 0;
+ Iterator<Node> nodeIt;
+ if(selectedOnly) {
+ nodeIt = network.getSelectedNodes().iterator();
+ } else {
+ nodeIt = network.nodesIterator();
+ }
+
+ while(nodeIt.hasNext()){
+ Node node = nodeIt.next();
+ nodeIdMapping.put(node.getRootGraphIndex(), j);
+ j++;
}
+
+// for(int i=0; i<nodeArray.length; i++){
+// nodeIdMapping.put(nodeArray[i],i);
+// }
+
// Get the selectedNodes
// Return the selected node array list
- Iterator<Node> nodeIt = network.getSelectedNodes().iterator();
- while(nodeIt.hasNext()){
+// Iterator<Node> nodeIt = network.getSelectedNodes().iterator();
+// while(nodeIt.hasNext()){
- Node node = nodeIt.next();
- ////System.out.println("This is gd:" +
nodeIdMapping.get(node.getRootGraphIndex()));
-
selectedNodeIndices.add(nodeIdMapping.get(node.getRootGraphIndex()));
- }
+// Node node = nodeIt.next();
+// ////System.out.println("This is gd:" +
nodeIdMapping.get(node.getRootGraphIndex()));
+//
selectedNodeIndices.add(nodeIdMapping.get(node.getRootGraphIndex()));
+// }
//If this works then it will be a lot faster
- int[] edgeArray = new int[edgeIndicesArray.length * 2];
- //Get all edges, then simplify in igraph
- for(int i = 0; i < edgeIndicesArray.length; i++){
- edgeArray[i*2] =
nodeIdMapping.get(network.getEdgeSourceIndex(edgeIndicesArray[i]));
- edgeArray[i*2 + 1] =
nodeIdMapping.get(network.getEdgeTargetIndex(edgeIndicesArray[i]));
- }
+ int[] edgeArray = new int[network.getEdgeCount() * 2];
+ int i = 0;
- IgraphInterface.createGraph(edgeArray, edgeArray.length);
- IgraphInterface.simplify();
+ Iterator<Edge> it = network.edgesIterator();
- return selectedNodeIndices;
+ while (it.hasNext()) {
+ Edge e = (CyEdge) it.next();
+
+ Node source = e.getSource();
+ Node target = e.getTarget();
+
+ if(!selectedOnly || (network.isSelected(source) &&
network.isSelected(target)) ){
+ edgeArray[i] =
nodeIdMapping.get(source.getRootGraphIndex());
+ edgeArray[i + 1] =
nodeIdMapping.get(target.getRootGraphIndex());
+ i += 2;
+ }
+ }
+
+
+// for(int i = 0; i < edgeIndicesArray.length; i++){
+
+// if(!selectedOnly ||
+// (network.isSelected() && network.isSelected()) ){
+// edgeArray[i * 2] =
nodeIdMapping.get(network.getEdgeTargetIndex(edgeIndicesArray[i]));
+// edgeArray[i * 2 + 1] =
nodeIdMapping.get(network.getEdgeSourceIndex(edgeIndicesArray[i]));
+// }
+// }
+
+ IgraphInterface.createGraph(edgeArray, i);
+ // IgraphInterface.simplify();
+
+ return nodeIdMapping;
}
}
\ No newline at end of file
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