Author: pwang
Date: 2011-10-29 11:16:58 -0700 (Sat, 29 Oct 2011)
New Revision: 27338
Added:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTask.java
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTaskFactory.java
Log:
Original creation
Added:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTask.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTask.java
2011-10-29 18:16:58 UTC (rev 27338)
@@ -0,0 +1,160 @@
+package org.idekerlab.PanGIAPlugin;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JFileChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+
+public class PanGIANodeViewTask extends AbstractTask {
+
+ private View<CyNode> nodeView;
+ private CyNetworkView networkView;
+
+ public PanGIANodeViewTask(CyNetworkView networkview, View<CyNode>
nodeView) {
+ this.nodeView = nodeView;
+ this.networkView = networkView;
+ }
+
+ @Override
+ public void run(TaskMonitor tm) {
+// CyNode node = nodeView.getModel();
+// String identifier = node.getCyRow().get("name", String.class);
+//
+//
+// boolean selectedHasNested = false;
+//
+// if (node.getNetwork()!=null)
+// {
+// selectedHasNested = true;
+// break;
+// }
+//
+// boolean isOverviewNetwork =
PanGIAPlugin.output.containsKey(aview.getNetwork().getIdentifier());
+//
+// //ITEM1
+// if (selectedHasNested && isOverviewNetwork)
+// {
+// JMenuItem item = new JMenuItem();
+// item.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e) {
+// DetailedNetworkCreator.createDetailedView(aview);
+// }
+// });
+// item.setText("Create Detailed View");
+//
+// pangiaMenu.add(item);
+// }
+//
+// //ITEM2
+// if (isOverviewNetwork)
+// {
+// JMenuItem item2 = new JMenuItem();
+// item2.setText("Export Modules to Tab-Delimited File");
+// item2.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e) {
+// saveModules(aview,
PanGIAPlugin.output.get(aview.getNetwork().getIdentifier()).getNodeAttrName());
+// }
+// });
+// pangiaMenu.add(item2);
+// }
+//
+// //ITEM3
+// if (isOverviewNetwork)
+// {
+// JMenuItem item3 = new JMenuItem();
+// item3.setText("Export Module Map to Tab-Delimited File");
+// item3.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e) {
+// saveOverviewNetwork(aview);
+// }
+// });
+// pangiaMenu.add(item3);
+// }
+//
+// //ITEM4
+// if (isOverviewNetwork)
+// {
+// JMenu item1 = new JMenu();
+// item1.setText("Save Selected Nodes to Matrix File");
+//
+// final PanGIAOutput output =
PanGIAPlugin.output.get(aview.getNetwork().getIdentifier());
+//
+// //String[] ean = edgeAttr.getAttributeNames();
+//
+// String[] ean = new
String[]{output.getPhysEdgeAttrName(),output.getGenEdgeAttrName()};
+//
+// List<String> eaNames = new ArrayList<String>(ean.length);
+// for (String s : ean) eaNames.add(s);
+//
+//
eaNames.removeAll(NestedNetworkCreator.getEdgeAttributeNames());
+//
eaNames.remove(NestedNetworkCreator.REFERENCE_NETWORK_NAME_ATTRIB);
+//
+// for (final String ea : eaNames)
+// {
+// JMenuItem eaItem = new JMenuItem();
+// eaItem.setText(ea);
+//
+// eaItem.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e) {
+// JFileChooser jfc = new JFileChooser();
+// jfc.setCurrentDirectory(new File("."));
+// int returnVal =
jfc.showSaveDialog(aview.getComponent());
+//
+// if (returnVal==JFileChooser.APPROVE_OPTION)
+// saveNodesToMatrix(aview,
jfc.getSelectedFile(),output.getNodeAttrName(),ea);
+// }
+// });
+// item1.add(eaItem);
+// }
+// pangiaMenu.add(item1);
+// }
+//
+// /*
+// //Copy network with new node IDs
+// JMenuItem item1 = new JMenuItem();
+// item1.setText("Copy Network");
+//
+//
+// for (final String aname :
Cytoscape.getNodeAttributes().getAttributeNames())
+// {
+// if (!edgeAttr.getType(aname).equals("String")) continue;
+//
+// JMenuItem eaItem = new JMenuItem();
+// eaItem.setText(aname);
+// eaItem.addActionListener(new ActionListener()
+// {
+// public void actionPerformed(ActionEvent e) {
+// copyNetworkWithNewIDs(aview.getNetwork(), aname);
+// }
+// });
+// item1.add(eaItem);
+// }
+//
+// pangiaMenu.add(item1);
+// */
+//
+// //MENU
+// if (pangiaMenu.getItemCount()>0) menu.add(pangiaMenu);
+// }
+
+ }
+
+ @Override
+ public void cancel() {
+ }
+}
Added:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTaskFactory.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTaskFactory.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIANodeViewTaskFactory.java
2011-10-29 18:16:58 UTC (rev 27338)
@@ -0,0 +1,13 @@
+package org.idekerlab.PanGIAPlugin;
+
+import org.cytoscape.task.AbstractNodeViewTaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+public class PanGIANodeViewTaskFactory extends AbstractNodeViewTaskFactory {
+ public PanGIANodeViewTaskFactory() {
+ super();
+ }
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new PanGIANodeViewTask(this.netView,
this.nodeView));
+ }
+}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
