Author: pwang
Date: 2011-10-14 12:53:21 -0700 (Fri, 14 Oct 2011)
New Revision: 27188
Added:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
Log:
Copy from jActiveModules3
Added:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
(rev 0)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
2011-10-14 19:53:21 UTC (rev 27188)
@@ -0,0 +1,237 @@
+package csplugins.jActiveModules;
+
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URL;
+
+import javax.help.HelpSet;
+import javax.swing.AbstractAction;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+
+import csplugins.jActiveModules.data.ActivePathFinderParameters;
+import csplugins.jActiveModules.dialogs.ActivePathsParameterPanel;
+
+import cytoscape.CyNetwork;
+import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.data.attr.MultiHashMapDefinitionListener;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.view.cytopanels.CytoPanel;
+import cytoscape.view.cytopanels.CytoPanelState;
+import cytoscape.view.CyHelpBroker;
+
+
+/**
+ * UI for Active Modules. Manages the various menu items
+ */
+public class ActiveModulesUI extends CytoscapePlugin {
+ protected ActivePaths activePaths;
+ protected ActivePathFinderParameters apfParams;
+ protected ThreadExceptionHandler xHandler;
+
+ private ActivePathsParameterPanel mainPanel;
+
+ public static String JACTIVEMODULES_TOP_N_MODULE =
"jactivemodules_top_n_modules";
+ public static String JACTIVEMODULES_TOP_N_MODULE_DEFAULT = "5";
+
+ public ActiveModulesUI() {
+ final JMenuItem menuItem = new JMenuItem("jActiveModules...");
+ menuItem.addActionListener(new SetParametersAction());
+
+ Cytoscape.getDesktop().getCyMenus().getMenuBar().
+ getMenu("Plugins.Module Finders...").add(menuItem);
+
+ /* initialize variables */
+ apfParams = new ActivePathFinderParameters(CytoscapeInit
+ .getProperties());
+ apfParams.reloadExpressionAttributes();
+ AttrChangeListener acl = new AttrChangeListener();
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
+ Cytoscape.ATTRIBUTES_CHANGED, acl);
+ Cytoscape.getNodeAttributes().getMultiHashMapDefinition()
+ .addDataDefinitionListener(acl);
+ xHandler = new ThreadExceptionHandler();
+
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ addHelp();
+ }
+
+ /**
+ * Hook plugin help into the Cytoscape main help system:
+ */
+ private void addHelp() {
+ final String HELP_SET_NAME = "/help/jhelpset";
+ final ClassLoader classLoader =
ActiveModulesUI.class.getClassLoader();
+ URL helpSetURL;
+ final CyLogger logger =
CyLogger.getLogger(ActiveModulesUI.class);
+ try {
+ helpSetURL = HelpSet.findHelpSet(classLoader,
HELP_SET_NAME);
+ final HelpSet newHelpSet = new HelpSet(classLoader,
helpSetURL);
+ CyHelpBroker.getHelpSet().add(newHelpSet);
+ } catch (final Exception e) {
+ logger.warn("Could not find help set: \"" +
HELP_SET_NAME + "!");
+ }
+ }
+
+ public void propertyChange(PropertyChangeEvent evt) {
+ if (evt.getPropertyName() == Cytoscape.CYTOSCAPE_INITIALIZED
+ && apfParams.getRun()) {
+ if (apfParams.getRandomizeExpression()) {
+
startRandomizeAndRun(mainPanel.getTargetNetwork());
+ } else {
+ activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
+ apfParams, this);
+ Thread t = new Thread(activePaths);
+ t.start();
+ }
+ }
+ }
+
+ /**
+ * Action to allow the user to change the current options for running
+ * jActiveModules, wiht a gui interface
+ */
+ protected class SetParametersAction extends AbstractAction {
+ private static final long serialVersionUID =
-7836213413255212288L;
+
+ public SetParametersAction() {
+ super("jActiveModules");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if (apfParams.getPossibleExpressionAttributes().size()
== 0) {
+ JOptionPane
+ .showMessageDialog(
+
Cytoscape.getDesktop(),
+ "JActiveModules
cannot start because it cannot find\n"
+
+ "any p-value attributes! JActiveModules requires at\n"
+
+ "least one node attribute with values ranging between\n"
+
+ "0 and 1 of type 'float' (i.e. decimal or real number).\n"
+
+ "Please load an appropriate attribute and try again.",
+
"jActiveModules", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
+ SwingConstants.WEST);
+ if (mainPanel == null) {
+ mainPanel = new
ActivePathsParameterPanel(apfParams,
+ ActiveModulesUI.this);
+ }
+ int index = cytoPanel.indexOfComponent(mainPanel);
+ if (index < 0) {
+ cytoPanel.add("jActiveModules", mainPanel);
+ index = cytoPanel.indexOfComponent(mainPanel);
+ }
+ cytoPanel.setSelectedIndex(index);
+ cytoPanel.setState(CytoPanelState.DOCK);
+ }
+ }
+
+ public void startFindActivePaths(CyNetwork network) {
+ try {
+ activePaths = new ActivePaths(network, apfParams, this);
+ } catch (final Exception e) {
+ e.printStackTrace(System.err);
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Error running jActiveModules (1)! " +
e.getMessage(),
+ "Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ Thread t = new Thread(activePaths);
+ t.setUncaughtExceptionHandler(xHandler);
+ t.start();
+ }
+
+ /**
+ * This action will run activePaths with the current parameters
+ */
+ protected class FindActivePathsAction extends AbstractAction {
+
+ FindActivePathsAction() {
+ super("Active Modules: Find Modules");
+ }
+
+ public void actionPerformed(ActionEvent ae) {
+ startFindActivePaths(mainPanel.getTargetNetwork());
+ }
+ }
+
+ protected class ThreadExceptionHandler implements
+ Thread.UncaughtExceptionHandler {
+ public void uncaughtException(Thread t, Throwable e) {
+ e.printStackTrace(System.err);
+ CyLogger logger =
CyLogger.getLogger(ActiveModulesUI.class);
+ logger.warn("Non-fatal exception in Thread " +
t.getName(), e);
+ logger.warn("The previous exception was non-fatal -
Don't panic!");
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+ "Error running jActiveModules (2)! " +
e.getMessage(),
+ "Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ /**
+ * This action will generate a score for the currently selected nodes
in the
+ * view
+ */
+ protected class ScoreSubComponentAction extends AbstractAction {
+
+ ScoreSubComponentAction() {
+ super("Active Modules: Score Selected Nodes");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
+ apfParams, ActiveModulesUI.this);
+ activePaths.scoreActivePath();
+ }
+ }
+
+ public void startRandomizeAndRun(CyNetwork network) {
+ activePaths = new ActivePaths(network, apfParams,
ActiveModulesUI.this);
+ Thread t = new ScoreDistributionThread(network, activePaths,
apfParams);
+ t.setUncaughtExceptionHandler(xHandler);
+ t.start();
+ }
+
+ public class RandomizeAndRunAction extends AbstractAction {
+
+ public RandomizeAndRunAction() {
+ super("Active Modules: Score Distribution");
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ startRandomizeAndRun(mainPanel.getTargetNetwork());
+ }
+ }
+
+ /**
+ * This is used to update the expression attributes in the params
object so
+ * that they match those that exist in CyAttributes.
+ */
+ protected class AttrChangeListener implements PropertyChangeListener,
+ MultiHashMapDefinitionListener {
+
+ public void propertyChange(PropertyChangeEvent e) {
+ if
(e.getPropertyName().equals(Cytoscape.ATTRIBUTES_CHANGED))
+ apfParams.reloadExpressionAttributes();
+ }
+
+ /**
+ * There is no point in listening to attributeDefined events
because
+ * this only defines the attr and when this is fired, no attr
values
+ * actually exist.
+ */
+ public void attributeDefined(String attributeName) {
+ }
+
+ public void attributeUndefined(String attributeName) {
+ apfParams.reloadExpressionAttributes();
+ }
+ }
+}
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