Author: pwang
Date: 2011-10-28 14:36:34 -0700 (Fri, 28 Oct 2011)
New Revision: 27332
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
2011-10-28 21:35:06 UTC (rev 27331)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/PanGIAPlugin.java
2011-10-28 21:36:34 UTC (rev 27332)
@@ -23,15 +23,16 @@
import org.idekerlab.PanGIAPlugin.ui.SearchPropertyPanel;
import org.idekerlab.PanGIAPlugin.utilities.files.FileUtil;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.plugin.CytoscapePlugin;
-import cytoscape.view.CyHelpBroker;
-import cytoscape.view.CytoscapeDesktop;
-import cytoscape.view.cytopanels.CytoPanel;
-import cytoscape.view.cytopanels.CytoPanelImp;
-import cytoscape.view.cytopanels.CytoPanelState;
-import cytoscape.view.cytopanels.BiModalJSplitPane;
+import org.cytoscape.model.CyNetwork;
+//import cytoscape.view.CyHelpBroker;
+//import cytoscape.view.cytopanels.CytoPanel;
+//import cytoscape.view.cytopanels.CytoPanelImp;
+//import cytoscape.view.cytopanels.CytoPanelState;
+//import cytoscape.view.cytopanels.BiModalJSplitPane;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.application.swing.CytoPanel;
+import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.application.swing.CytoPanelState;
/**
* PanGIA Plugin main class.
@@ -42,7 +43,7 @@
* @author kono, ruschein, ghannum
*
*/
-public class PanGIAPlugin extends CytoscapePlugin {
+public class PanGIAPlugin extends AbstractCyAction {
// Main GUI Panel for this plugin. Should be a singleton.
private JScrollPane scrollPane;
@@ -52,20 +53,43 @@
private static final String PLUGIN_NAME = "PanGIA";
public static final String VERSION = "1.1";
public static final Map<String,PanGIAOutput> output = new
HashMap<String,PanGIAOutput>();
+ private final CytoPanel cytoPanelWest;
- public PanGIAPlugin() {
+ private SearchPropertyPanel searchPanel;
+
+ public PanGIAPlugin(SearchPropertyPanel searchPanel) {
+ super(PLUGIN_NAME, ServicesUtil.cyApplicationManagerServiceRef);
+ this.setPreferredMenu("Plugins");
vsObserver = new VisualStyleObserver();
- addHelp();
- final JMenuItem menuItem = new JMenuItem(PLUGIN_NAME);
- menuItem.addActionListener(new PluginAction());
-
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("Plugins.Module
Finders...").add(menuItem);
-
-
Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(CytoscapeDesktop.NETWORK_VIEW_CREATED,new
PanGIANetworkListener());
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_DESTROYED,new
PanGIANetworkListener());
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_TITLE_MODIFIED,new
PanGIANetworkListener());
+ this.searchPanel = searchPanel;
+ cytoPanelWest =
ServicesUtil.cySwingApplicationServiceRef.getCytoPanel(CytoPanelName.WEST);
+
+ addHelp();
}
/**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // If the state of the cytoPanelEast is HIDE, show it
+ if (cytoPanelWest.getState() == CytoPanelState.HIDE) {
+ cytoPanelWest.setState(CytoPanelState.DOCK);
+ }
+
+ // Select the jActiveModules panel
+ int index = cytoPanelWest.indexOfComponent(searchPanel);
+ if (index == -1) {
+ return;
+ }
+
+ cytoPanelWest.setSelectedIndex(index);
+
+ }
+
+
+ /**
* Hook plugin help into the Cytoscape main help system:
*/
private void addHelp() {
@@ -75,33 +99,33 @@
try {
helpSetURL = HelpSet.findHelpSet(classLoader,
HELP_SET_NAME);
final HelpSet newHelpSet = new HelpSet(classLoader,
helpSetURL);
- CyHelpBroker.getHelpSet().add(newHelpSet);
+ //CyHelpBroker.getHelpSet().add(newHelpSet);
} catch (final Exception e) {
System.err.println("PanGIA: Could not find help set:
\"" + HELP_SET_NAME + "!");
}
}
- class PluginAction implements ActionListener {
- public void actionPerformed(ActionEvent e) {
- final CytoPanelImp cytoPanel =
(CytoPanelImp)Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
- int index = cytoPanel.indexOfComponent(scrollPane);
- if (index < 0) {
- final SearchPropertyPanel searchPanel = new
SearchPropertyPanel();
- scrollPane = new JScrollPane(searchPanel);
- searchPanel.setContainer(scrollPane);
- searchPanel.updateAttributeLists();
- searchPanel.setVisible(true);
- scrollPane.setMinimumSize(new
Dimension(400,400));
- cytoPanel.add(PLUGIN_NAME, scrollPane);
- index = cytoPanel.indexOfComponent(scrollPane);
-
- BiModalJSplitPane bmj =
(BiModalJSplitPane)cytoPanel.getParent();
- bmj.setDividerLocation(400);
- }
- cytoPanel.setSelectedIndex(index);
- cytoPanel.setState(CytoPanelState.DOCK);
- }
- }
+// class PluginAction implements ActionListener {
+// public void actionPerformed(ActionEvent e) {
+// final CytoPanelImp cytoPanel =
(CytoPanelImp)Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+// int index = cytoPanel.indexOfComponent(scrollPane);
+// if (index < 0) {
+// final SearchPropertyPanel searchPanel = new
SearchPropertyPanel();
+// scrollPane = new JScrollPane(searchPanel);
+// searchPanel.setContainer(scrollPane);
+// searchPanel.updateAttributeLists();
+// searchPanel.setVisible(true);
+// scrollPane.setMinimumSize(new
Dimension(400,400));
+// cytoPanel.add(PLUGIN_NAME, scrollPane);
+// index = cytoPanel.indexOfComponent(scrollPane);
+//
+// BiModalJSplitPane bmj =
(BiModalJSplitPane)cytoPanel.getParent();
+// bmj.setDividerLocation(400);
+// }
+// cytoPanel.setSelectedIndex(index);
+// cytoPanel.setState(CytoPanelState.DOCK);
+// }
+// }
public static void setModuleLabels(String nattr)
{
@@ -118,9 +142,9 @@
for (Entry<String,PanGIAOutput> e : output.entrySet())
{
-
bw.write(e.getValue().getOverviewNetwork().getTitle()+"\n");
-
bw.write(e.getValue().getOrigPhysNetwork().getTitle()+"\n");
-
bw.write(e.getValue().getOrigGenNetwork().getTitle()+"\n");
+
bw.write(e.getValue().getOverviewNetwork().getCyRow().get("name",
String.class)+"\n");
+
bw.write(e.getValue().getOrigPhysNetwork().getCyRow().get("name",
String.class)+"\n");
+
bw.write(e.getValue().getOrigGenNetwork().getCyRow().get("name",
String.class)+"\n");
bw.write(e.getValue().getNodeAttrName()+"\n");
bw.write(e.getValue().getPhysEdgeAttrName()+"\n");
bw.write(e.getValue().getGenEdgeAttrName()+"\n");
@@ -170,7 +194,7 @@
String physEdgeAttr = in.readLine();
String genEdgeAttr = in.readLine();
boolean isSigned =
Boolean.valueOf(in.readLine());
- output.put(overviewNet.getIdentifier(),new
PanGIAOutput(overviewNet, physNet, genNet, nodeAttr, physEdgeAttr, genEdgeAttr,
isSigned));
+ //output.put(overviewNet.getIdentifier(),new
PanGIAOutput(overviewNet, physNet, genNet, nodeAttr, physEdgeAttr, genEdgeAttr,
isSigned));
}
in.close();
@@ -184,9 +208,11 @@
private static CyNetwork getNetworkFromTitle(String title)
{
- for (CyNetwork net : Cytoscape.getNetworkSet())
- if (net.getTitle().equals(title)) return net;
-
+ for (CyNetwork net :
ServicesUtil.cyNetworkManagerServiceRef.getNetworkSet())
+ {
+ String title1 = net.getCyRow().get("name",
String.class);
+ if (title1.equals(title)) return net;
+ }
return null;
}
}
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